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libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/uiobolistwidget.ui | 166 libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.cpp | 136 libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.h | 85 libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/uiobotermform.ui | 166 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp | 977 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h | 31 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.cpp | 257 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.h | 108 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp | 2240 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.h | 134 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp | 127 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h | 4 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp | 117 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.h | 26 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp | 4 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.cpp | 82 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.h | 43 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp | 141 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h | 15 libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp | 4 libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp | 2 libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.h | 2 libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp | 73 libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h | 63 libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.cpp | 4 libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.h | 2 libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.cpp | 6 libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.h | 2 libpappsomspp-0.8.58/src/pappsomspp/xic/xic.cpp | 4 libpappsomspp-0.8.58/src/pappsomspp/xic/xic.h | 1 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp | 70 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.h | 68 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp | 154 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.h | 118 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunslice.cpp | 4 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp | 87 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.h | 56 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp | 52 libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h | 15 libpappsomspp-0.8.58/src/resources/PSI-MOD.obo | 8808 + libpappsomspp-0.8.58/src/resources/icons/switch_off.svg | 86 libpappsomspp-0.8.58/src/resources/icons/switch_on.svg | 86 libpappsomspp-0.8.58/tests/CMakeLists.txt | 85 libpappsomspp-0.8.58/tests/common.cpp | 81 libpappsomspp-0.8.58/tests/common.h | 91 libpappsomspp-0.8.58/tests/config.h.cmake | 1 libpappsomspp-0.8.58/tests/data/alignment/result_delta_rt.tsv | 4251 libpappsomspp-0.8.58/tests/data/alignment/result_rt_align.tsv | 4652 + libpappsomspp-0.8.58/tests/data/asr1_digested_peptides.txt | 28 libpappsomspp-0.8.58/tests/data/fuzzy.fasta | 9 libpappsomspp-0.8.58/tests/data/peaklist_15046.mgf | 405 libpappsomspp-0.8.58/tests/data/peaklist_15046_simple_xt.mgf | 102 libpappsomspp-0.8.58/tests/data/scan_15968.mgf | 310 libpappsomspp-0.8.58/tests/data/scan_2016.mgf | 93 libpappsomspp-0.8.58/tests/data/scan_PXD001468.mgf | 133 libpappsomspp-0.8.58/tests/data/tandem/database.xml | 7 libpappsomspp-0.8.58/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml | 81 libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf.xml | 87 libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf_wrong.xml | 87 libpappsomspp-0.8.58/tests/data/tandem/tandem_result_file.xml |44302 ++++++++++ libpappsomspp-0.8.58/tests/data/tandem/tandem_run_params.xml | 12 libpappsomspp-0.8.58/tests/data/tandem/wrapper/wrapped_tandem_input.xml | 11 libpappsomspp-0.8.58/tests/data/xic/PXD014777_xic.tsv |12029 ++ libpappsomspp-0.8.58/tests/memory/test_tandemwrapperrun.cpp | 67 libpappsomspp-0.8.58/tests/memory/test_timsdata_reader_memory.cpp | 259 libpappsomspp-0.8.58/tests/test_aa.cpp | 50 libpappsomspp-0.8.58/tests/test_big_hyperscore.cpp | 6 libpappsomspp-0.8.58/tests/test_fasta_reader.cpp | 30 libpappsomspp-0.8.58/tests/test_fragmentationcid.cpp | 39 libpappsomspp-0.8.58/tests/test_hyperscore.cpp | 22 libpappsomspp-0.8.58/tests/test_isotope_with_spectrum.cpp | 12 libpappsomspp-0.8.58/tests/test_massrange.cpp | 95 libpappsomspp-0.8.58/tests/test_massspectrumcombiner.cpp | 15 libpappsomspp-0.8.58/tests/test_msrunalignment.cpp | 236 libpappsomspp-0.8.58/tests/test_msrunoutput.cpp | 8 libpappsomspp-0.8.58/tests/test_mzintegrationparams.cpp | 129 libpappsomspp-0.8.58/tests/test_natural_isotope_average.cpp | 50 libpappsomspp-0.8.58/tests/test_peptide.cpp | 328 libpappsomspp-0.8.58/tests/test_peptidefragment.cpp | 16 libpappsomspp-0.8.58/tests/test_peptidenaturalisotopelist.cpp | 102 libpappsomspp-0.8.58/tests/test_protein.cpp | 700 libpappsomspp-0.8.58/tests/test_psm.cpp | 246 libpappsomspp-0.8.58/tests/test_rawmasslist.cpp | 2 libpappsomspp-0.8.58/tests/test_scan_15968.cpp | 14 libpappsomspp-0.8.58/tests/test_tandem_run_wrapper.cpp | 164 libpappsomspp-0.8.58/tests/test_tims_data_xic_chromatogram.cpp | 136 libpappsomspp-0.8.58/tests/test_timsframe.cpp | 316 libpappsomspp-0.8.58/tests/test_timsxicextractor.cpp | 178 libpappsomspp-0.8.58/tests/test_timsxicextractor_based_masspec.cpp | 199 libpappsomspp-0.8.58/tests/test_trace.cpp | 10 libpappsomspp-0.8.58/tests/test_trace_filters.cpp | 130 libpappsomspp-0.8.58/tests/test_uimonitor.cpp | 72 libpappsomspp-0.8.58/tests/test_xic.cpp | 173 libpappsomspp-0.8.58/tests/test_xicextractor.cpp | 83 libpappsomspp-0.8.58/tests/test_xtandem_spectrum.cpp | 6 libpappsomspp-0.8.58/tests/widget/CMakeLists.txt | 39 libpappsomspp-0.8.58/tests/widget/main.cpp | 70 libpappsomspp-0.8.58/tests/widget/testwidgetgui.cpp | 48 libpappsomspp-0.8.58/tests/widget/testwidgetgui.h | 55 libpappsomspp-0.8.58/tests/widget/uitestwidgetgui.ui | 52 328 files changed, 95824 insertions(+), 10439 deletions(-) diff -Nru libpappsomspp-0.8.15/.gitattributes libpappsomspp-0.8.58/.gitattributes --- libpappsomspp-0.8.15/.gitattributes 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/.gitattributes 2022-10-27 09:16:15.000000000 +0000 @@ -2,7 +2,7 @@ *.swp export-ignore #debian export-ignore devdoc/html export-ignore -tests/data/* export-ignore +#tests/data/* export-ignore maintainer-scripts/__pycache__/ export-ignore *~ export-ignore Session.vim export-ignore diff -Nru libpappsomspp-0.8.15/.gitignore libpappsomspp-0.8.58/.gitignore --- libpappsomspp-0.8.15/.gitignore 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/.gitignore 2022-10-27 09:16:15.000000000 +0000 @@ -1,7 +1,11 @@ -*~ -Session.vim -maintainer-scripts/__pycache__/ -compile_commands.json +*-swp *.swp .ycm_extra_conf.py +compile_commands.json +Session.vim + +.cache +.kdev4 +development.kdev4 +CMakeStuff/local-config.cmake diff -Nru libpappsomspp-0.8.15/AUTHORS libpappsomspp-0.8.58/AUTHORS --- libpappsomspp-0.8.15/AUTHORS 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/AUTHORS 2022-10-27 09:16:15.000000000 +0000 @@ -1,3 +1,3 @@ -Olivier Langella -Filippo Rusconi +Olivier Langella +Filippo Rusconi diff -Nru libpappsomspp-0.8.15/CMakeLists.txt libpappsomspp-0.8.58/CMakeLists.txt --- libpappsomspp-0.8.15/CMakeLists.txt 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/CMakeLists.txt 2022-10-27 09:16:15.000000000 +0000 @@ -13,10 +13,10 @@ set(PAPPSOMSPP_VERSION_MAJOR "0") set(PAPPSOMSPP_VERSION_MINOR "8") -set(PAPPSOMSPP_VERSION_PATCH "15") +set(PAPPSOMSPP_VERSION_PATCH "58") set(PAPPSOMSPP_VERSION "${PAPPSOMSPP_VERSION_MAJOR}.${PAPPSOMSPP_VERSION_MINOR}.${PAPPSOMSPP_VERSION_PATCH}") # This *NUMERICAL* VERSION is parseable by the makeOrigTarball script. -set(VERSION 0.8.15) +set(VERSION 0.8.58) # Command to enable debug and tests # cmake -DCMAKE_BUILD_TYPE=Debug -DMAKE_TESTS=1 -DUSEPAPPSOTREE=0 .. @@ -41,7 +41,6 @@ set(CMAKE_MODULE_PATH ${CMAKE_UTILS_PATH}/modules) #message("CMAKE_MODULE_PATH:" ${CMAKE_MODULE_PATH}) - # This include must come before all the others # It must include the config-generated config.h file # before the others. @@ -70,7 +69,6 @@ ) endif() - # We want C++17 set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD_REQUIRED ON) @@ -100,8 +98,8 @@ if(MXE) # Run the following cmake command line: # x86_64-w64-mingw32.shared-cmake -DCMAKE_BUILD_TYPE=Release -DMXE=1 ../development - include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain.cmake) - #include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain-olivier.cmake) + #include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain.cmake) + include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain-olivier.cmake) # Set the name to the systemUname variable because in this situation that name # is not found, it it passed as a flag in the command line. @@ -312,7 +310,7 @@ #dch -Dstretch "message" #cmake .. #make deb -# scp libpappsomspp* proteus.moulon.inra.fr:/var/www/apt/incoming +# scp libpappsomspp* proteus.ideev.universite-paris-saclay.fr:/var/www/apt/incoming # reprepro -Vb /var/www/apt processincoming default # apt-get remove libpappsomspp* # diff -Nru libpappsomspp-0.8.15/CMakeStuff/toolchains/mxe-toolchain-olivier.cmake libpappsomspp-0.8.58/CMakeStuff/toolchains/mxe-toolchain-olivier.cmake --- libpappsomspp-0.8.15/CMakeStuff/toolchains/mxe-toolchain-olivier.cmake 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/CMakeStuff/toolchains/mxe-toolchain-olivier.cmake 2022-10-27 09:16:15.000000000 +0000 @@ -6,7 +6,7 @@ message("Please run the configuration like this:") message("x86_64-w64-mingw32.shared-cmake -DMXE= 1 -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Release ../../development") - +set(HOME_DEVEL_DIR /win64) set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/include) set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/include) @@ -30,7 +30,7 @@ set(QCustomPlot_FOUND 1) set(QCustomPlot_INCLUDE_DIR "/win64/qcustomplot-2.0.1+dfsg1") -set(QCustomPlot_LIBRARIES "/win64/qcustomplot-2.0.1+dfsg1/build/libqcustomplot.dll") +set(QCustomPlot_LIBRARIES "/win64/qcustomplot-2.0.1+dfsg1/wbuild/libqcustomplot.dll") if(NOT TARGET QCustomPlot::QCustomPlot) add_library(QCustomPlot::QCustomPlot UNKNOWN IMPORTED) set_target_properties(QCustomPlot::QCustomPlot PROPERTIES @@ -68,8 +68,8 @@ set(Alglib_FOUND 1) -set(Alglib_INCLUDE_DIR "/home/langella/developpement/git/alglib/src") -set(Alglib_LIBRARY "/home/langella/developpement/git/alglib/wbuild/libalglib.dll") +set(Alglib_INCLUDE_DIR "/win64/alglib/src") +set(Alglib_LIBRARY "/win64/alglib/wbuild/libalglib.dll") if(NOT TARGET Alglib::Alglib) add_library(Alglib::Alglib UNKNOWN IMPORTED) set_target_properties(Alglib::Alglib PROPERTIES @@ -81,11 +81,11 @@ # All this belly dance does not seem necessary. Just perform like for the other # libraries... # Look for the necessary header -set(Zstd_INCLUDE_DIR /mxe/usr/x86_64-w64-mingw32.shared/include) +set(Zstd_INCLUDE_DIR ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/include) mark_as_advanced(Zstd_INCLUDE_DIR) set(Zstd_INCLUDE_DIRS ${Zstd_INCLUDE_DIR}) # Look for the necessary library -set(Zstd_LIBRARY /mxe/usr/x86_64-w64-mingw32.shared/bin/libzstd.dll) +set(Zstd_LIBRARY ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/bin/libzstd.dll) mark_as_advanced(Zstd_LIBRARY) # Mark the lib as found set(Zstd_FOUND 1) @@ -99,6 +99,18 @@ +set(QCustomPlot_FOUND 1) +set(QCustomPlot_INCLUDE_DIR "/win64/qcustomplot-2.0.1+dfsg1") +set(QCustomPlot_LIBRARIES "/win64/qcustomplot-2.0.1+dfsg1/wbuild/libqcustomplot.dll") +if(NOT TARGET QCustomPlot::QCustomPlot) + add_library(QCustomPlot::QCustomPlot UNKNOWN IMPORTED) + set_target_properties(QCustomPlot::QCustomPlot PROPERTIES + IMPORTED_LOCATION "${QCustomPlot_LIBRARIES}" + INTERFACE_INCLUDE_DIRECTORIES "${QCustomPlot_INCLUDE_DIR}" + INTERFACE_COMPILE_DEFINITIONS QCUSTOMPLOT_USE_LIBRARY) +endif() + + set(PwizLite_FOUND 1) set(PwizLite_INCLUDE_DIRS "/home/langella/developpement/git/libpwizlite/src") @@ -111,3 +123,20 @@ ) endif() + +# langella@themis:/win64/liblzf-3.6$ x86_64-w64-mingw32.shared-gcc -c lzf_c.c lzfP.h +# langella@themis:/win64/liblzf-3.6$ x86_64-w64-mingw32.shared-gcc -c lzf_d.c lzfP.h +# langella@themis:/win64/liblzf-3.6$ x86_64-w64-mingw32.shared-gcc -shared -o liblzf.dll lzf_c.o lzf_d.o +set(liblzf_FOUND 1) +set(liblzf_INCLUDE_DIR "/win64/liblzf-3.6") +set(liblzf_INCLUDE_DIRS "/win64/liblzf-3.6/") + +set(liblzf_LIBRARIES "/win64/liblzf-3.6/liblzf.dll") +if(NOT TARGET liblzf::liblzf) + add_library(liblzf::liblzf UNKNOWN IMPORTED) + set_target_properties(liblzf::liblzf PROPERTIES + IMPORTED_LOCATION "${liblzf_LIBRARIES}" + INTERFACE_INCLUDE_DIRECTORIES "${liblzf_INCLUDE_DIRS}" + INTERFACE_COMPILE_DEFINITIONS LIBLZF_USE_LIBRARY) +endif() + diff -Nru libpappsomspp-0.8.15/CMakeStuff/toolchains/mxe-toolchain.cmake libpappsomspp-0.8.58/CMakeStuff/toolchains/mxe-toolchain.cmake --- libpappsomspp-0.8.15/CMakeStuff/toolchains/mxe-toolchain.cmake 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/CMakeStuff/toolchains/mxe-toolchain.cmake 2022-10-27 09:16:15.000000000 +0000 @@ -1,11 +1,8 @@ -# File:///home/langella/developpement/git/pappsomspp/CMakeStuff/toolchains/mxe-toolchain.cmake# -# This file should be included if the command line reads like this: -# x86_64-w64-mingw32.shared-cmake -DCMAKE_BUILD_TYPE=Release -DMXE=1 .. - message("MXE (M cross environment) https://mxe.cc/") message("Please run the configuration like this:") -message("x86_64-w64-mingw32.shared-cmake -DMXE= 1 -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Release ../../development") +message("x86_64-w64-mingw32.shared-cmake -DMXE=1 -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Release ../../development") +set(HOME_DEVEL_DIR "/home/rusconi/devel") set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/include) set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES ${HOME_DEVEL_DIR}/mxe/usr/x86_64-w64-mingw32.shared/include) @@ -24,10 +21,6 @@ find_package(SQLite3 REQUIRED) -#install MXE qtsvg package -#langella@piccolo:/media/langella/pappso/mxe$ make qtsvg - - set(QCustomPlot_FOUND 1) set(QCustomPlot_INCLUDE_DIR "${HOME_DEVEL_DIR}/qcustomplot/development") set(QCustomPlot_LIBRARIES "${HOME_DEVEL_DIR}/qcustomplot/build-area/mxe/libqcustomplot.dll") @@ -56,8 +49,8 @@ set(OdsStream_QT5_FOUND 1) -set(OdsStream_INCLUDE_DIR "c:/msys64/home/mydar/devel/odsstream/src") -set(OdsStream_QT5_LIBRARY "c:/msys64/home/mydar/devel/odsstream/build-area/mxe/src/libodsstream-qt5.dll") +set(OdsStream_INCLUDE_DIR "${HOME_DEVEL_DIR}/odsstream/src") +set(OdsStream_QT5_LIBRARY "${HOME_DEVEL_DIR}/odsstream/build-area/mxe/src/libodsstream-qt5.dll") if(NOT TARGET OdsStream::Core) add_library(OdsStream::Core UNKNOWN IMPORTED) set_target_properties(OdsStream::Core PROPERTIES @@ -98,3 +91,28 @@ endif() +set(PwizLite_FOUND 1) +set(PwizLite_INCLUDE_DIRS "${HOME_DEVEL_DIR}/pwizlite/development/src") +set(PwizLite_LIBRARIES "${HOME_DEVEL_DIR}/pwizlite/build-area/mxe/src/libpwizlite.dll") +if(NOT TARGET PwizLite::PwizLite) + add_library(PwizLite::PwizLite UNKNOWN IMPORTED) + set_target_properties(PwizLite::PwizLite PROPERTIES + IMPORTED_LOCATION "${PwizLite_LIBRARIES}" + INTERFACE_INCLUDE_DIRECTORIES "${PwizLite_INCLUDE_DIRS}" + ) +endif() + + +set(liblzf_FOUND 1) +set(liblzf_INCLUDE_DIRS "${HOME_DEVEL_DIR}/lzf/development") + +set(liblzf_LIBRARIES "${HOME_DEVEL_DIR}/lzf/build-area/mxe/liblzf.dll") +if(NOT TARGET liblzf::liblzf) + add_library(liblzf::liblzf UNKNOWN IMPORTED) + set_target_properties(liblzf::liblzf PROPERTIES + IMPORTED_LOCATION "${liblzf_LIBRARIES}" + INTERFACE_INCLUDE_DIRECTORIES "${liblzf_INCLUDE_DIRS}" + INTERFACE_COMPILE_DEFINITIONS LIBLZF_USE_LIBRARY) +endif() + + diff -Nru libpappsomspp-0.8.15/CMakeStuff/toolchains/unix-toolchain.cmake libpappsomspp-0.8.58/CMakeStuff/toolchains/unix-toolchain.cmake --- libpappsomspp-0.8.15/CMakeStuff/toolchains/unix-toolchain.cmake 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/CMakeStuff/toolchains/unix-toolchain.cmake 2022-10-27 09:16:15.000000000 +0000 @@ -13,7 +13,10 @@ find_package(Zstd REQUIRED) -if(MAKE_TEST) +find_package(liblzf REQUIRED) + + +if(BUILD_TESTING) find_package(QuaZip QUIET) if(NOT QUAZIP_FOUND) @@ -22,7 +25,7 @@ find_package(QuaZip REQUIRED) endif() -endif() +endif(BUILD_TESTING) find_package(QCustomPlot REQUIRED) diff -Nru libpappsomspp-0.8.15/CMakeStuff/toolchains/win10-mingw64-toolchain.cmake libpappsomspp-0.8.58/CMakeStuff/toolchains/win10-mingw64-toolchain.cmake --- libpappsomspp-0.8.15/CMakeStuff/toolchains/win10-mingw64-toolchain.cmake 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/CMakeStuff/toolchains/win10-mingw64-toolchain.cmake 2022-10-27 09:16:15.000000000 +0000 @@ -6,7 +6,7 @@ set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES "c:/msys64/mingw64/include") set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES "c:/msys64/mingw64/bin") -set(HOME_DEVEL_DIR "c:/msys64/home/mydar/devel") +set(HOME_DEVEL_DIR "$ENV{HOME}/devel") # We do not build the tests under Win10. @@ -17,6 +17,9 @@ message(STATUS "Building with WIN32 defined.") endif() +# see https://cmake.org/pipermail/cmake/2015-December/062166.html +set(CMAKE_NO_SYSTEM_FROM_IMPORTED 1) + message(STATUS "${BoldGreen}Setting definition -DPMSPP_LIBRARY for symbol DLL export.${ColourReset}") add_definitions(-DPMSPP_LIBRARY) @@ -28,8 +31,8 @@ if(MAKE_TEST) set(Quazip5_FOUND 1) - set(Quazip5_INCLUDE_DIRS "${HOME_DEVEL_DIR}/quazip5/development") - set(Quazip5_LIBRARY "${HOME_DEVEL_DIR}/quazip5/build-area/mingw64/libquazip5.dll") + set(Quazip5_INCLUDE_DIRS /c/msys64/mingw64/include/QuaZip-Qt5-1.3) + set(Quazip5_LIBRARY /c/msys64/mingw64/bin/libquazip1-qt5.dll) if(NOT TARGET Quazip5::Quazip5) add_library(Quazip5::Quazip5 UNKNOWN IMPORTED) set_target_properties(Quazip5::Quazip5 PROPERTIES @@ -40,6 +43,18 @@ endif() +set(liblzf_FOUND 1) +set(liblzf_INCLUDE_DIRS "${HOME_DEVEL_DIR}/lzf/development") +set(liblzf_LIBRARIES "${HOME_DEVEL_DIR}/lzf/build-area/mingw64/liblzf.dll") +if(NOT TARGET liblzf::liblzf) + add_library(liblzf::liblzf UNKNOWN IMPORTED) + set_target_properties(liblzf::liblzf PROPERTIES + IMPORTED_LOCATION "${liblzf_LIBRARIES}" + INTERFACE_INCLUDE_DIRECTORIES "${liblzf_INCLUDE_DIRS}" + ) +endif() + + set(PwizLite_FOUND 1) set(PwizLite_INCLUDE_DIRS "${HOME_DEVEL_DIR}/pwizlite/development/src") set(PwizLite_LIBRARIES "${HOME_DEVEL_DIR}/pwizlite/build-area/mingw64/src/libpwizlite.dll") diff -Nru libpappsomspp-0.8.15/debian/changelog libpappsomspp-0.8.58/debian/changelog --- libpappsomspp-0.8.15/debian/changelog 2020-12-21 17:05:07.000000000 +0000 +++ libpappsomspp-0.8.58/debian/changelog 2022-10-27 08:38:00.000000000 +0000 @@ -1,3 +1,395 @@ +libpappsomspp (0.8.58-1) bullseye; urgency=low + + * New upstream version (see 0.8.57-1~bullseye+1). + + * Standards-Version: 4.6.1. + + * d/rules: Fix by Adrian Bunk to work around the excess precision of the x87 + FPU that causes + https://buildd.debian.org/status/logs.php?pkg=libpappsomspp&arch=i386. + + -- Filippo Rusconi Thu, 27 Oct 2022 10:38:00 +0200 + +libpappsomspp (0.8.57-1~bullseye+1) bullseye; urgency=medium + + [ Olivier Langella ] + * avoid nullptr calls in custom plot widgets + * new tims frame widget color map + * better tdf handler + * new tests for protein , enzyme, psm, psmfeaures + * new psm feature API + [ Filippo Rusconi ] + * refactoring work to compile using Qt6 + + -- Olivier Langella Tue, 04 Oct 2022 17:02:43 +0200 + +libpappsomspp (0.8.56-1) unstable; urgency=low + + * New version that implements features in the dt|rt,m/z color map realms. + + -- Filippo Rusconi Tue, 30 Aug 2022 14:54:53 +0200 + +libpappsomspp (0.8.55-1) unstable; urgency=low + + * New version to fix the destination distribution. + + -- Filippo Rusconi Mon, 11 Jul 2022 13:06:19 +0200 + +libpappsomspp (0.8.54-1) bullseye; urgency=low + + * New upstream release fixing bug in color map plot panning when any axis is + locked (Filippo Rusconi). + + * d/control: bump-up dependency for odsstream to 0.8.1. + + -- Filippo Rusconi Fri, 08 Jul 2022 15:52:47 +0200 + +libpappsomspp (0.8.53-1~bullseye+1) bullseye; urgency=medium + + * fix for issue #17 in MassChroQ + + -- Olivier Langella Thu, 30 Jun 2022 13:40:16 +0200 + +libpappsomspp (0.8.52-1) unstable; urgency=low + + * New upstream version fixing one critical bug in the calculation of the + decimals in a value (infinite loop). + + -- Filippo Rusconi Wed, 29 Jun 2022 20:12:33 +0200 + +libpappsomspp (0.8.51-1~bullseye+2) bullseye; urgency=medium + + * fix for issue #11 + + -- Olivier Langella Thu, 23 Jun 2022 13:19:23 +0200 + +libpappsomspp (0.8.51-1~bullseye+1) bullseye; urgency=medium + + * tdf reader enhancements + + -- Olivier Langella Wed, 22 Jun 2022 09:42:32 +0200 + +libpappsomspp (0.8.50-1) unstable; urgency=low + + * New upstream version. + + -- Filippo Rusconi Fri, 17 Jun 2022 10:23:51 +0200 + +libpappsomspp (0.8.49-1) unstable; urgency=medium + + * New upstream release. + + -- Filippo Rusconi Tue, 15 Mar 2022 16:42:27 +0100 + +libpappsomspp (0.8.49-1~bullseye+1) bullseye; urgency=medium + + * mzdata conversion time displayed in tandemwrapper + * new package using libpwizlite 3.0.4 + + -- Olivier Langella Sun, 13 Mar 2022 17:52:32 +0100 + +libpappsomspp (0.8.48-1) unstable; urgency=low + + * New upstream version with new features from Olivier Langella (see stanzas + below) and Filippo Rusconi (mainly a new low intensity threshold removal + filter). + + -- Filippo Rusconi Mon, 31 Jan 2022 16:00:07 +0100 + +libpappsomspp (0.8.47-1~bullseye+1) bullseye; urgency=medium + + * new msrun alignment API + + -- Olivier Langella Wed, 26 Jan 2022 09:20:02 +0100 + +libpappsomspp (0.8.46-1~bullseye+1) bullseye; urgency=medium + + * XML stream reader also reads from a QString + + -- Olivier Langella Mon, 24 Jan 2022 14:47:52 +0100 + +libpappsomspp (0.8.45-1~bullseye+1) bullseye; urgency=medium + + * fix xml stream reader emty string problem + * fix tdf filename and sample name + * better filter suite string and iterators + * more efficient multithreaded xic extraction + * mzformat is written into tandem result file + + -- Olivier Langella Sun, 02 Jan 2022 17:10:58 +0100 + +libpappsomspp (0.8.44-1~bullseye+1) bullseye; urgency=medium + + * fix quantile on trace size equal 0 + + -- Olivier Langella Tue, 21 Dec 2021 13:03:26 +0100 + +libpappsomspp (0.8.43-1~bullseye+1) bullseye; urgency=medium + + * fix fragment ion name API design + * new filter to remove intensity using a quantile function : implementation and tests + + -- Olivier Langella Tue, 21 Dec 2021 08:44:14 +0100 + +libpappsomspp (0.8.42-1~bullseye+1) bullseye; urgency=medium + + * better peptide fragment ion names for phopho acid loss + * rework of alignment API + + -- Olivier Langella Thu, 16 Dec 2021 12:05:31 +0100 + +libpappsomspp (0.8.41-1~bullseye+1) bullseye; urgency=medium + + [ Olivier Langella ] + * remove pseudo centroid filter and remaining pwiz files + * fix C12 abundance + * parallelized xic extractor + * better XML error handler + * better ion names in mass spectrum widget + * fix tandem wrapper and new tests + [ Filippo Rusconi ] + * improvements to the documentation and comments + * convenient function to insert/update datapoints in traces + * new tests (xic chromatogram and xic extractor to mass spectrum) + + -- Olivier Langella Sat, 11 Dec 2021 11:13:39 +0100 + +libpappsomspp (0.8.40-1~bullseye+1) bullseye; urgency=medium + + * new bullseye package + + -- Olivier Langella Tue, 23 Nov 2021 08:52:11 +0100 + +libpappsomspp (0.8.39-1~bullseye+2) bullseye; urgency=medium + + * new bullseye package + + -- Olivier Langella Mon, 22 Nov 2021 14:56:09 +0100 + +libpappsomspp (0.8.39-1) unstable; urgency=low + + * New upstream version (see below). + + * Fixes to the build by adding #include where required (build with + g++ v 11.2.0). + + Many thanks to Adrian Bunk for the patch (although not + applied as-is). Closes: #984199. + + * Bump-up Standards to 4.6.0 + + * Add watch file that points to the forgemia GitLab repos instance. + + -- Filippo Rusconi Wed, 10 Nov 2021 16:32:10 +0100 + +libpappsomspp (0.8.38-1~buster+1) buster; urgency=medium + + * essential function to allow compression type 1 XIC extraction + + -- Olivier Langella Sun, 07 Nov 2021 09:01:21 +0100 + +libpappsomspp (0.8.37-1~buster+1) buster; urgency=medium + + [ Olivier Langella ] + * more exceptions concerning timsTOF data reader for better reliability + * support for the timsTOF compression type 1 (legacy data files) and tests + * better tandemrunwrapper + [ Filippo Rusconi ] + * improvements to the filters + * better mz integration tests + + -- Olivier Langella Fri, 05 Nov 2021 16:11:09 +0100 + +libpappsomspp (0.8.36-1~buster+1) buster; urgency=medium + + * fix a new peak detection crash on small XICs, tests added + + -- Olivier Langella Thu, 30 Sep 2021 09:14:00 +0200 + +libpappsomspp (0.8.35-1~buster+1) buster; urgency=medium + + [ Olivier Langella ] + * fix peak detection crash on small XICs, tests added + [ Filippo Rusconi ] + * better plot widget color map + * new function in filter name interface to get the name of the filter + + -- Olivier Langella Tue, 28 Sep 2021 09:27:45 +0200 + +libpappsomspp (0.8.34-1~buster+1) buster; urgency=medium + + * new text user interface monitor to display progress using percent + * new function to add filters from QStrings in a filter suite + + -- Olivier Langella Mon, 27 Sep 2021 09:29:36 +0200 + +libpappsomspp (0.8.33-1~buster+1) buster; urgency=medium + + * fix out of range possible access when extracting XIC on tims data + * new trace peak vector and convenient API to choose matched peaks + + -- Olivier Langella Mon, 20 Sep 2021 15:40:38 +0200 + +libpappsomspp (0.8.32-1~buster+1) buster; urgency=medium + + * msrun reader collection handler refactoring + * better reader performance on timstof data + * special API for MassChroQ + + -- Olivier Langella Wed, 15 Sep 2021 11:30:24 +0200 + +libpappsomspp (0.8.31-1~buster+1) buster; urgency=medium + + * new widget to handle a switch button, Thomas Renne + + -- Olivier Langella Tue, 24 Aug 2021 15:59:55 +0200 + +libpappsomspp (0.8.30-1~buster+1) buster; urgency=medium + + * fix QProcess mecanism to execute tandem + + -- Olivier Langella Wed, 23 Jun 2021 10:35:48 +0200 + +libpappsomspp (0.8.29-1~buster+1) buster; urgency=medium + + * issue #9 fixed : conversion problem between uint and ulong + * better memory management in TIMS frame decoder + + -- Olivier Langella Thu, 03 Jun 2021 07:54:59 +0200 + +libpappsomspp (0.8.28-1~buster+1) buster; urgency=medium + + * new TandemRunWrapper, runs on any mz data file + * generic UiMonitorInterface to manage long process + * X!Tandem error management + + -- Olivier Langella Thu, 20 May 2021 10:14:29 +0200 + +libpappsomspp (0.8.27-1~buster+1) buster; urgency=medium + + * binary package for PAPPSO repository + + -- Olivier Langella Wed, 12 May 2021 18:14:27 +0200 + +libpappsomspp (0.8.26-2) buster; urgency=medium + + * new tandem run wrapper API + + -- Olivier Langella Wed, 12 May 2021 17:14:27 +0200 + +libpappsomspp (0.8.26-1) buster; urgency=medium + + * new XIC extraction API, enabling ion mobility + + -- Olivier Langella Thu, 06 May 2021 14:34:14 +0200 + +libpappsomspp (0.8.25-2) unstable; urgency=low + + * New upload with orig.tar.gz. The buster version by Olivier made dpkg think + this was not a version needing orig.tar.gz. + + -- Filippo Rusconi Wed, 21 Apr 2021 22:21:44 +0200 + +libpappsomspp (0.8.25-1) unstable; urgency=low + + * New upstream version with new noise reduction + features for the color maps. + + -- Filippo Rusconi Wed, 21 Apr 2021 15:59:49 +0200 + +libpappsomsp (0.8.25-1~buster+1) buster; urgency=medium + + * widgets to handle OBO terms + + -- Olivier Langella Wed, 21 Apr 2021 14:40:23 +0200 + +libpappsomspp (0.8.24-1) unstable; urgency=low + + * New upstream version. + + -- Filippo Rusconi Thu, 08 Apr 2021 09:54:26 +0200 + +libpappsomspp (0.8.23-1~buster+1) buster; urgency=medium + + * mass spectrum widget API modified to highlight precursor + + -- Olivier Langella Thu, 01 Apr 2021 14:24:04 +0200 + +libpappsomspp (0.8.23-1) unstable; urgency=low + + * The tests that failed in i386 could not be fixed for some reason. However, + the software is working fine as tested in a VirtualBox environment of + i386. The failing tests are conditionally dropped for i386. + + -- Filippo Rusconi Wed, 31 Mar 2021 14:28:43 +0200 + +libpappsomspp (0.8.22-1) unstable; urgency=low + + * Rewrite the Trace::containsX() function so that it passes the i386-based + tests. All tests pass on an i386 VirtualBox-based testing Debian box. + + -- Filippo Rusconi Tue, 30 Mar 2021 10:18:36 +0200 + +libpappsomspp (0.8.21-1) unstable; urgency=low + + * Try to fix the build failures on i386 platforms due to double precision + varying on 32 bits vs 64 bits platforms. + + -- Filippo Rusconi Mon, 29 Mar 2021 14:14:24 +0200 + +libpappsomspp (0.8.20-1) unstable; urgency=low + + * New upstream version with all the integration region selection reworked to + cope with the specific case of integration skewed selection rectangle. + + * Add d/not-installed to list uninstalled files (those that are shipped as + symbolic links). + + * Build-Depends: debhelper-compat (= 13). + + -- Filippo Rusconi Tue, 23 Mar 2021 17:01:09 +0100 + +libpappsomspp (0.8.19-1~buster+1) buster; urgency=medium + + * new test to control memory usage + * no cache in mzcalibration timstof model + * XIC shared pointer initialization in timstof reader + + -- Olivier Langella Wed, 03 Mar 2021 16:30:53 +0100 + +libpappsomspp (0.8.18-1) unstable; urgency=low + + * New upstream version (see below). + + * Fixed a bunch of QT DEPRECATED warnings. + + * Standards-Version: 4.5.1 (no changes needed). + + -- Filippo Rusconi Thu, 25 Feb 2021 06:21:37 +0100 + +libpappsomspp (0.8.17-1~buster+1) buster; urgency=medium + + * tandemrunwrapper memory leak problem fixed + * first working version of a TimsTofPRO XIC extractor + * new test for tandemrunwrapper, TimsTofPROT xic extraction + + -- Olivier Langella Tue, 23 Feb 2021 09:26:43 +0100 + +libpappsomspp (0.8.16-1~buster+2) buster; urgency=medium + + * TimsData reader performance enhancements + * changing isotope natural abundance to use the massXpert definitions + * DeepProt enumerations for controlled vocabulary across PAPPSO software + * enabling test execution in debian package process + + -- Olivier Langella Thu, 28 Jan 2021 11:46:15 +0100 + +libpappsomspp (0.8.16-1~buster+1) buster; urgency=medium + + * development package + + -- Olivier Langella Fri, 22 Jan 2021 13:22:56 +0100 + libpappsomspp (0.8.15-1) unstable; urgency=low * New upstream version depending on libodsstream 0.7.11. diff -Nru libpappsomspp-0.8.15/debian/control libpappsomspp-0.8.58/debian/control --- libpappsomspp-0.8.15/debian/control 2020-12-21 17:05:07.000000000 +0000 +++ libpappsomspp-0.8.58/debian/control 2022-10-27 08:38:00.000000000 +0000 @@ -10,13 +10,13 @@ d-shlibs (>= 0.48~), qtbase5-dev, libqt5svg5-dev (>= 5.7.0), - qhelpgenerator-qt5 (>= 5.15.2), - libpwizlite-dev (>= 3.0.2), + libpwizlite-dev (>= 3.0.4), libqcustomplot-dev (>= 2.0.1), - libodsstream-dev (>= 0.7.11), + libodsstream-dev (>= 0.8.4), libalglib-dev, libsqlite3-dev, libzstd-dev (>= 1.3.3), + liblzf-dev, libboost-dev, libboost-iostreams-dev, libboost-thread-dev, @@ -24,8 +24,10 @@ libboost-filesystem-dev, libboost-chrono-dev, doxygen, - catch2 -Standards-Version: 4.5.0 + catch2, + zlib1g-dev, + libquazip5-dev +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/libpappsomspp Vcs-Git: https://salsa.debian.org/debichem-team/libpappsomspp.git Homepage: http://pappso.inrae.fr/bioinfo @@ -55,7 +57,6 @@ Multi-Arch: same Replaces: libpappsomspp-dev (<< ${binary:Version}) Depends: libpappsomspp0 (= ${binary:Version}), - ${shlibs:Depends}, ${misc:Depends} Recommends: libpappsomspp-doc Description: C++ library to handle mass spectrometry data (development files) @@ -96,7 +97,6 @@ Replaces: libpappsomspp-widget-dev (<< ${binary:Version}) Depends: libpappsomspp-widget0 (= ${binary:Version}), libpappsomspp-dev, - ${shlibs:Depends}, ${misc:Depends} Recommends: libpappsomspp-doc Description: C++ library to handle mass spectrometry data (GUI development files) diff -Nru libpappsomspp-0.8.15/debian/copyright libpappsomspp-0.8.58/debian/copyright --- libpappsomspp-0.8.15/debian/copyright 2020-12-21 17:05:07.000000000 +0000 +++ libpappsomspp-0.8.58/debian/copyright 2022-10-27 08:38:00.000000000 +0000 @@ -15,26 +15,3 @@ LICENSE at /usr/share/common-licenses/GPL-3. -Files: src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp - src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp - src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp -Copyright: ETH Zurich - 2020 Olivier Langella -License: Apache-2.0 - Apache License Version 2.0 - . - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - . - http://www.apache.org/licenses/LICENSE-2.0 - . - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. - . - On Debian systems you can read the full text of the Apache 2.0 - LICENSE at /usr/share/common-licenses/Apache-2.0.License: Apache-2.0 - diff -Nru libpappsomspp-0.8.15/debian/not-installed libpappsomspp-0.8.58/debian/not-installed --- libpappsomspp-0.8.15/debian/not-installed 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/debian/not-installed 2022-10-27 08:38:00.000000000 +0000 @@ -0,0 +1,12 @@ +#! /usr/bin/dh-exec + +# Filippo Rusconi 20200611 - This is the cleanest solution: +# https://wiki.debian.org/Multiarch/Implementation#Dynamic_debian.2F.2A_files + +# Make sure this file is executable !!! + +debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}/libpappsomspp.so +debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}/libpappsomspp.so.0 + +debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}/libpappsomspp-widget.so +debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}/libpappsomspp-widget.so.0 diff -Nru libpappsomspp-0.8.15/debian/rules libpappsomspp-0.8.58/debian/rules --- libpappsomspp-0.8.15/debian/rules 2020-12-21 17:05:07.000000000 +0000 +++ libpappsomspp-0.8.58/debian/rules 2022-10-27 08:38:00.000000000 +0000 @@ -11,6 +11,11 @@ DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk +ifneq (,$(filter $(DEB_HOST_ARCH_CPU), i386)) + export DEB_CXXFLAGS_MAINT_APPEND += -ffloat-store +endif + + %: dh $@ --buildsystem=cmake @@ -22,13 +27,14 @@ dh_auto_configure -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release \ - -DMAKE_TESTS=0 \ + -DMAKE_TESTS=1 \ -DCMAKE_SKIP_RPATH=1 \ -DUSEPAPPSOTREE=0 override_dh_auto_build: - dh_auto_build --no-parallel + dh_auto_build dh_auto_build -- doc + dh_auto_test # Required because it would not run automatically # make test diff -Nru libpappsomspp-0.8.15/debian/watch libpappsomspp-0.8.58/debian/watch --- libpappsomspp-0.8.15/debian/watch 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/debian/watch 2022-10-27 08:38:00.000000000 +0000 @@ -0,0 +1,12 @@ +version=4 + +# The following page lists the releases +# https://forgemia.inra.fr/pappso/pappsomspp/-/tags +# And the actual href in the page is +# href="/pappso/pappsomspp/-/archive/0.8.38/pappsomspp-0.8.38.tar.gz" + +#https://forgemia.inra.fr/pappso/pappsomspp/-/tags \ + #.*/@PACKAGE@-@ANY_VERSION@@ARCHIVE_EXT@ + +https://forgemia.inra.fr/pappso/pappsomspp/-/tags \ + .*/pappsomspp-(\d\S+)@ARCHIVE_EXT@ diff -Nru libpappsomspp-0.8.15/maintainer-scripts/sync-header-files-to-system.sh libpappsomspp-0.8.58/maintainer-scripts/sync-header-files-to-system.sh --- libpappsomspp-0.8.15/maintainer-scripts/sync-header-files-to-system.sh 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/maintainer-scripts/sync-header-files-to-system.sh 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,20 @@ +#!/bin/sh + + +if [ ! -d "pappsomspp" ] +then + echo "Please, this works only if you are located in the src directory that" + echo "should contain the pappsomspp directory" + + exit 1 +fi + +for file in $(find -name "*.h") +do + if [ ! -d /usr/include/$(dirname ${file}) ] + then + mkdir -p /usr/include/$(dirname ${file}) + fi + + cp -v ${file} /usr/include/$(dirname ${file})/$(basename ${file}) +done diff -Nru libpappsomspp-0.8.15/src/CMakeLists.txt libpappsomspp-0.8.58/src/CMakeLists.txt --- libpappsomspp-0.8.15/src/CMakeLists.txt 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/CMakeLists.txt 2022-10-27 09:16:15.000000000 +0000 @@ -19,18 +19,33 @@ pappsomspp/mzrange.cpp pappsomspp/precision.cpp + pappsomspp/massspectrum/massspectrumid.cpp + pappsomspp/massspectrum/massspectrum.cpp + pappsomspp/massspectrum/qualifiedmassspectrum.cpp + pappsomspp/processing/combiners/mzintegrationparams.cpp + pappsomspp/processing/combiners/selectionpolygon.cpp pappsomspp/processing/combiners/tracecombiner.cpp pappsomspp/processing/combiners/traceminuscombiner.cpp pappsomspp/processing/combiners/tracepluscombiner.cpp + pappsomspp/processing/combiners/massdatacombinerinterface.cpp + pappsomspp/processing/combiners/massspectrumcombiner.cpp + pappsomspp/processing/combiners/massspectrumpluscombiner.cpp + pappsomspp/processing/combiners/massspectrumminuscombiner.cpp + + + pappsomspp/processing/detection/tracedetectionzivy.cpp + pappsomspp/processing/detection/tracedetectionmoulon.cpp + pappsomspp/processing/detection/tracepeak.cpp + pappsomspp/processing/detection/tracepeaklist.cpp pappsomspp/processing/filters/filterchargedeconvolution.cpp pappsomspp/processing/filters/filtercomplementionenhancer.cpp + pappsomspp/processing/filters/filterexclusionmz.cpp pappsomspp/processing/filters/filterlocalmaximum.cpp pappsomspp/processing/filters/filtermorpho.cpp pappsomspp/processing/filters/filternameinterface.cpp pappsomspp/processing/filters/filterpass.cpp - pappsomspp/processing/filters/filterpseudocentroid.cpp pappsomspp/processing/filters/filterremovec13.cpp pappsomspp/processing/filters/filterresample.cpp pappsomspp/processing/filters/filtersuite.cpp @@ -38,24 +53,19 @@ pappsomspp/processing/filters/filtertandemremovec13.cpp pappsomspp/processing/filters/filtertriangle.cpp pappsomspp/processing/filters/savgolfilter.cpp - - pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp - pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp - pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp + pappsomspp/processing/filters/filterflooramplitudepercentage.cpp + pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp + pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp - pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp - pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp - pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp - - pappsomspp/massspectrum/massspectrumid.cpp - pappsomspp/massspectrum/massspectrum.cpp - pappsomspp/massspectrum/qualifiedmassspectrum.cpp - - pappsomspp/processing/combiners/massdatacombinerinterface.cpp - pappsomspp/processing/combiners/massspectrumcombiner.cpp - pappsomspp/processing/combiners/massspectrumpluscombiner.cpp - pappsomspp/processing/combiners/massspectrumminuscombiner.cpp + pappsomspp/processing/tandemwrapper/wraptandeminput.cpp + pappsomspp/processing/tandemwrapper/wraptandemresults.cpp + pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp + + pappsomspp/processing/uimonitor/uimonitortext.cpp + pappsomspp/processing/uimonitor/uimonitortextpercent.cpp + + pappsomspp/processing/xml/xmlstreamreaderinterface.cpp pappsomspp/amino_acid/aabase.cpp pappsomspp/amino_acid/aa.cpp @@ -78,6 +88,7 @@ pappsomspp/msfile/msfileaccessor.cpp pappsomspp/msfile/msfilereader.cpp + pappsomspp/msfile/mzformatenumstr.cpp pappsomspp/msfile/pwizmsfilereader.cpp pappsomspp/msfile/timsmsfilereader.cpp pappsomspp/msfile/xymsfilereader.cpp @@ -94,9 +105,12 @@ pappsomspp/msrun/private/timsmsrunreader.cpp pappsomspp/msrun/private/timsmsrunreaderms2.cpp pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp + pappsomspp/msrun/xiccoord/xiccoord.cpp + pappsomspp/msrun/xiccoord/xiccoordtims.cpp pappsomspp/msrun/xymsrunreader.cpp pappsomspp/obo/obopsimod.cpp + pappsomspp/obo/obopsimodterm.cpp pappsomspp/obo/filterobopsimodsink.cpp pappsomspp/obo/filterobopsimodtermaccession.cpp pappsomspp/obo/filterobopsimodtermlabel.cpp @@ -128,7 +142,9 @@ pappsomspp/protein/peptidemodificatorpipeline.cpp pappsomspp/protein/peptidesemienzyme.cpp + pappsomspp/psm/deepprot/deepprotenum.cpp pappsomspp/psm/experimental/ionisotoperatioscore.cpp + pappsomspp/psm/features/psmfeatures.cpp pappsomspp/psm/morpheus/morpheusscore.cpp pappsomspp/psm/peakionmatch.cpp pappsomspp/psm/peakionisotopematch.cpp @@ -151,7 +167,9 @@ pappsomspp/vendors/tims/timsbindec.cpp pappsomspp/vendors/tims/timsdata.cpp pappsomspp/vendors/tims/timsframe.cpp + pappsomspp/vendors/tims/timsframerawdatachunck.cpp pappsomspp/vendors/tims/timsframebase.cpp + pappsomspp/vendors/tims/timsframetype1.cpp pappsomspp/vendors/tims/timsms2centroidfilter.cpp pappsomspp/xic/xic.cpp @@ -160,9 +178,6 @@ pappsomspp/xic/xicpeptidefragmention.cpp pappsomspp/xic/xicpeptidefragmentionnaturalisotope.cpp - pappsomspp/processing/detection/tracedetectionzivy.cpp - pappsomspp/processing/detection/tracedetectionmoulon.cpp - pappsomspp/processing/detection/tracepeak.cpp pappsomspp/xicextractor/private/msrunslice.cpp pappsomspp/xicextractor/private/msrunxicextractor.cpp @@ -198,6 +213,7 @@ target_include_directories(pappsomspp-static PUBLIC ${PwizLite_INCLUDE_DIRS} + ${liblzf_INCLUDE_DIRS} ) target_link_libraries(pappsomspp-static @@ -243,6 +259,7 @@ target_include_directories(pappsomspp-shared PUBLIC ${PwizLite_INCLUDE_DIRS} + ${liblzf_INCLUDE_DIRS} ) target_link_libraries(pappsomspp-shared @@ -262,6 +279,7 @@ Boost::chrono ZLIB::ZLIB PwizLite::PwizLite + liblzf::liblzf ) diff -Nru libpappsomspp-0.8.15/src/Makefile libpappsomspp-0.8.58/src/Makefile --- libpappsomspp-0.8.15/src/Makefile 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/Makefile 2022-10-27 09:16:15.000000000 +0000 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apidoc-stable" + @echo "... deb" + @echo "... doc" + @echo "... lintian" + @echo "... pappsomspp-shared_autogen" + @echo "... pappsomspp-static_autogen" + @echo "... pappsomspp-widget-shared_autogen" + @echo "... pappsomspp-widget-static_autogen" + @echo "... targz" + @echo "... pappsomspp-shared" + @echo "... pappsomspp-static" + @echo "... pappsomspp-widget-shared" + @echo "... pappsomspp-widget-static" +.PHONY : help + + + +#============================================================================= +# Special targets to cleanup operation of make. + +# Special rule to run CMake to check the build system integrity. +# No rule that depends on this can have commands that come from listfiles +# because they might be regenerated. +cmake_check_build_system: + $(CMAKE_COMMAND) -S$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0 +.PHONY : cmake_check_build_system + diff -Nru libpappsomspp-0.8.15/src/libpappsomsppresources.qrc libpappsomspp-0.8.58/src/libpappsomsppresources.qrc --- libpappsomspp-0.8.15/src/libpappsomsppresources.qrc 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/libpappsomsppresources.qrc 2022-10-27 09:16:15.000000000 +0000 @@ -3,4 +3,8 @@ resources/PSI-MOD.obo + + resources/icons/switch_off.svg + resources/icons/switch_on.svg + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/Makefile libpappsomspp-0.8.58/src/pappsomspp/Makefile --- libpappsomspp-0.8.15/src/pappsomspp/Makefile 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/Makefile 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,11 @@ +mkfile_path := $(abspath $(lastword $(MAKEFILE_LIST))) +current_dir := $(notdir $(patsubst %/,%,$(dir $(mkfile_path)))) + +all: + cd ../../../build-area/unix && make + +.PHONY: clean +clean: + cd ../../../build-area/unix && make clean + + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aa.cpp libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aa.cpp --- libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aa.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aa.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -143,7 +143,7 @@ m_listMod.erase(it); } - qDebug() << m_listMod << endl; + qDebug() << m_listMod << Qt::endl; } void diff -Nru libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aamodification.cpp libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aamodification.cpp --- libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aamodification.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aamodification.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -28,7 +28,7 @@ *implementation ******************************************************************************/ -#include +#include #include #include @@ -54,7 +54,7 @@ QMutex AaModification::m_mutex; AaModification::AaModification(const QString &accession, pappso_double mass) - : m_mass(mass), m_accession(accession) + : m_accession(accession), m_mass(mass) { m_atomCount = {{AtomIsotopeSurvey::C, 0}, {AtomIsotopeSurvey::H, 0}, @@ -74,10 +74,11 @@ AaModification::AaModification(AaModification &&toCopy) // move constructor - : m_mass(toCopy.m_mass), + : m_accession(toCopy.m_accession), + m_name(toCopy.m_name), + m_mass(toCopy.m_mass), m_atomCount(std::move(toCopy.m_atomCount)), - m_mapIsotope(toCopy.m_mapIsotope), - m_accession(toCopy.m_accession) + m_mapIsotope(toCopy.m_mapIsotope) { m_origin = toCopy.m_origin; } @@ -90,7 +91,7 @@ AaModification::getAccession() const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); return m_accession; } const QString & @@ -141,16 +142,14 @@ } if(accession.startsWith("MUTATION:")) { - QRegExp regexp_mutation("^MUTATION:([A-Z])=>([A-Z])$"); - if(regexp_mutation.exactMatch(accession)) + QRegularExpression regexp_mutation("^MUTATION:([A-Z])=>([A-Z])$"); + QRegularExpressionMatch match = regexp_mutation.match(accession); + if(match.hasMatch()) { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - << regexp_mutation.capturedTexts()[1].at(0) << " " - << regexp_mutation.capturedTexts()[2].at(0); - - Aa aa_from( - regexp_mutation.capturedTexts()[1].toStdString().c_str()[0]); - Aa aa_to(regexp_mutation.capturedTexts()[2].toStdString().c_str()[0]); + qDebug() << match.captured(1).at(0) << " " << match.captured(2).at(0); + + Aa aa_from(match.captured(1).toStdString().c_str()[0]); + Aa aa_to(match.captured(2).toStdString().c_str()[0]); AaModificationP instance_mutation = createInstanceMutation(aa_from, aa_to); return instance_mutation; @@ -185,96 +184,99 @@ void AaModification::setDiffFormula(const QString &diff_formula) { - QRegExp rx("(^|\\s)([C,H,O,N,H,S])\\s([-]{0,1}\\d+)"); - int pos = 0; + QRegularExpression rx("(^|\\s)([C,H,O,N,H,S])\\s([-]{0,1}\\d+)"); + + QRegularExpressionMatchIterator match_it = rx.globalMatch(diff_formula); - while((pos = rx.indexIn(diff_formula, pos)) != -1) + while(match_it.hasNext()) { - qDebug() << rx.cap(2) << " " << rx.cap(3); - if(rx.cap(2) == "C") + QRegularExpressionMatch match_rx = match_it.next(); + qDebug() << match_rx.captured(2) << " " << match_rx.captured(3); + if(match_rx.captured(2) == "C") { - m_atomCount[AtomIsotopeSurvey::C] = rx.cap(3).toInt(); + m_atomCount[AtomIsotopeSurvey::C] = match_rx.captured(3).toInt(); } - else if(rx.cap(2) == "H") + else if(match_rx.captured(2) == "H") { - m_atomCount[AtomIsotopeSurvey::H] = rx.cap(3).toInt(); + m_atomCount[AtomIsotopeSurvey::H] = match_rx.captured(3).toInt(); } - else if(rx.cap(2) == "N") + else if(match_rx.captured(2) == "N") { - m_atomCount[AtomIsotopeSurvey::N] = rx.cap(3).toInt(); + m_atomCount[AtomIsotopeSurvey::N] = match_rx.captured(3).toInt(); } - else if(rx.cap(2) == "O") + else if(match_rx.captured(2) == "O") { - m_atomCount[AtomIsotopeSurvey::O] = rx.cap(3).toInt(); + m_atomCount[AtomIsotopeSurvey::O] = match_rx.captured(3).toInt(); } - else if(rx.cap(2) == "S") + else if(match_rx.captured(2) == "S") { - m_atomCount[AtomIsotopeSurvey::S] = rx.cap(3).toInt(); + m_atomCount[AtomIsotopeSurvey::S] = match_rx.captured(3).toInt(); } - pos += rx.matchedLength(); } // look for isotopes : rx.setPattern("\\(([-]{0,1}\\d+)\\)([C,H,O,N,H,S])\\s([-]{0,1}\\d+)"); - pos = 0; - while((pos = rx.indexIn(diff_formula, pos)) != -1) + match_it = rx.globalMatch(diff_formula); + + while(match_it.hasNext()) { - qDebug() << rx.cap(1) << " " << rx.cap(2) << " " << rx.cap(3); - int number_of_isotopes = rx.cap(3).toInt(); - if(rx.cap(2) == "C") + QRegularExpressionMatch match_rx = match_it.next(); + qDebug() << match_rx.captured(1) << " " << match_rx.captured(2) << " " + << match_rx.captured(3); + int number_of_isotopes = match_rx.captured(3).toInt(); + if(match_rx.captured(2) == "C") { - if(rx.cap(1) == "13") + if(match_rx.captured(1) == "13") { m_mapIsotope.at(Isotope::C13) = number_of_isotopes; } m_atomCount[AtomIsotopeSurvey::C] += number_of_isotopes; } - else if(rx.cap(2) == "H") + else if(match_rx.captured(2) == "H") { - if(rx.cap(1) == "2") + if(match_rx.captured(1) == "2") { m_mapIsotope.at(Isotope::H2) = number_of_isotopes; } m_atomCount[AtomIsotopeSurvey::H] += number_of_isotopes; } - else if(rx.cap(2) == "N") + else if(match_rx.captured(2) == "N") { - if(rx.cap(1) == "15") + if(match_rx.captured(1) == "15") { m_mapIsotope.at(Isotope::N15) = number_of_isotopes; } m_atomCount[AtomIsotopeSurvey::N] += number_of_isotopes; } - else if(rx.cap(2) == "O") + else if(match_rx.captured(2) == "O") { - if(rx.cap(1) == "17") + if(match_rx.captured(1) == "17") { m_mapIsotope.at(Isotope::O17) = number_of_isotopes; } - else if(rx.cap(1) == "18") + else if(match_rx.captured(1) == "18") { m_mapIsotope.at(Isotope::O18) = number_of_isotopes; } m_atomCount[AtomIsotopeSurvey::O] += number_of_isotopes; } - else if(rx.cap(2) == "S") + else if(match_rx.captured(2) == "S") { - if(rx.cap(1) == "33") + if(match_rx.captured(1) == "33") { m_mapIsotope.at(Isotope::S33) = number_of_isotopes; } - else if(rx.cap(1) == "34") + else if(match_rx.captured(1) == "34") { m_mapIsotope.at(Isotope::S34) = number_of_isotopes; } - else if(rx.cap(1) == "36") + else if(match_rx.captured(1) == "36") { m_mapIsotope.at(Isotope::S36) = number_of_isotopes; } m_atomCount[AtomIsotopeSurvey::S] += number_of_isotopes; } - pos += rx.matchedLength(); } @@ -331,8 +333,7 @@ if(diff < 0.001) { m_mass = theoreticalm_mass; - qDebug() << "AaModification::calculateMassFromChemicalComponents " - << diff; + qDebug() << diff; } else { @@ -347,7 +348,7 @@ AaModification::getInstanceCustomizedMod(pappso_double modificationMass) { QString accession = QString("%1").arg(modificationMass); - qDebug() << "AaModification::getInstanceCustomizedMod " << accession; + qDebug() << accession; QMutexLocker locker(&m_mutex); if(m_mapAccessionModifications.find(accession) == m_mapAccessionModifications.end()) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aamodification.h libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aamodification.h --- libpappsomspp-0.8.15/src/pappsomspp/amino_acid/aamodification.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/amino_acid/aamodification.h 2022-10-27 09:16:15.000000000 +0000 @@ -55,35 +55,6 @@ class PMSPP_LIB_DECL AaModification : public AtomNumberInterface { - private: - pappso_double m_mass; - QString m_origin; - std::map m_atomCount; - std::map m_mapIsotope; - - AaModification(const QString &accession, pappso_double mass); - static AaModificationP createInstance(const QString &saccession); - static AaModificationP createInstance(const OboPsiModTerm &term); - static AaModificationP createInstanceMutation(const Aa &aa_from, - const Aa &aa_to); - void calculateMassFromChemicalComponents(); - - using MapAccessionModifications = std::map; - static MapAccessionModifications m_mapAccessionModifications; - - static QMutex m_mutex; - - protected: - const QString m_accession; - QString m_name; - void setDiffFormula(const QString &diff_formula); - /** @brief set list of amino acid on which this modification takes place - * - * @arg origin string of the form "S T" for Serine or Threonine, "X" for any - * amino acid (see OBO PSI format) - * */ - void setXrefOrigin(const QString &origin); - public: AaModification(AaModification &&toCopy); // move constructor @@ -114,6 +85,43 @@ int getNumberOfAtom(AtomIsotopeSurvey atom) const override final; int getNumberOfIsotope(Isotope isotope) const override final; bool isInternal() const; + + + protected: + const QString m_accession; + QString m_name; + + protected: + void setDiffFormula(const QString &diff_formula); + /** @brief set list of amino acid on which this modification takes place + * + * @arg origin string of the form "S T" for Serine or Threonine, "X" for any + * amino acid (see OBO PSI format) + * */ + void setXrefOrigin(const QString &origin); + + + private: + AaModification(const QString &accession, pappso_double mass); + static AaModificationP createInstance(const QString &saccession); + static AaModificationP createInstance(const OboPsiModTerm &term); + static AaModificationP createInstanceMutation(const Aa &aa_from, + const Aa &aa_to); + void calculateMassFromChemicalComponents(); + + using MapAccessionModifications = std::map; + + + private: + pappso_double m_mass; + QString m_origin; + std::map m_atomCount; + std::map m_mapIsotope; + + + static MapAccessionModifications m_mapAccessionModifications; + + static QMutex m_mutex; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/exception/exceptioninterrupted.h libpappsomspp-0.8.58/src/pappsomspp/exception/exceptioninterrupted.h --- libpappsomspp-0.8.15/src/pappsomspp/exception/exceptioninterrupted.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/exception/exceptioninterrupted.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,49 @@ +/** + * \file pappsomspp/exception/exceptioninterrupted.h + * \date 14/5/2021 + * \author Olivier Langella + * \brief process interrupted exception + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "../pappsoexception.h" + +namespace pappso +{ +class ExceptionInterrupted : public PappsoException +{ + public: + ExceptionInterrupted(const QString &message) throw() + : PappsoException(message) + { + } + + virtual QException * + clone() const override + { + return new ExceptionInterrupted(*this); + } +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/fasta/fastaoutputstream.cpp libpappsomspp-0.8.58/src/pappsomspp/fasta/fastaoutputstream.cpp --- libpappsomspp-0.8.15/src/pappsomspp/fasta/fastaoutputstream.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/fasta/fastaoutputstream.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -39,8 +39,8 @@ { m_ofastastream << ">" << protein.getAccession() << " " - << protein.getDescription() << endl; - m_ofastastream << protein.getSequence() << endl; + << protein.getDescription() << Qt::endl; + m_ofastastream << protein.getSequence() << Qt::endl; } } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/massspectrum/massspectrumid.cpp libpappsomspp-0.8.58/src/pappsomspp/massspectrum/massspectrumid.cpp --- libpappsomspp-0.8.15/src/pappsomspp/massspectrum/massspectrumid.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/massspectrum/massspectrumid.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -22,6 +22,9 @@ ******************************************************************************/ +#include + + #include "massspectrumid.h" namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/massspectrum/massspectrumid.h libpappsomspp-0.8.58/src/pappsomspp/massspectrum/massspectrumid.h --- libpappsomspp-0.8.15/src/pappsomspp/massspectrum/massspectrumid.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/massspectrum/massspectrumid.h 2022-10-27 09:16:15.000000000 +0000 @@ -24,6 +24,8 @@ #pragma once +#include + #include #include "../exportinmportconfig.h" diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/msfileaccessor.cpp libpappsomspp-0.8.58/src/pappsomspp/msfile/msfileaccessor.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msfile/msfileaccessor.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/msfileaccessor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -93,6 +93,7 @@ { tims_dir = QFileInfo(m_fileName).absolutePath(); } + TimsMsFileReader tims_file_reader(tims_dir); ms_run_ids = tims_file_reader.getMsRunIds(m_xmlPrefix); @@ -222,6 +223,13 @@ MsRunReaderSPtr MsFileAccessor::buildMsRunReaderSPtr(MsRunIdCstSPtr ms_run_id) { + return buildMsRunReaderSPtr(ms_run_id, pappso::FileReaderType::tims); +} + +MsRunReaderSPtr +MsFileAccessor::buildMsRunReaderSPtr( + MsRunIdCstSPtr ms_run_id, pappso::FileReaderType prefered_file_reader_type) +{ QFile file(ms_run_id.get()->getFileName()); if(!file.exists()) @@ -245,6 +253,16 @@ } else if(file_format == MzFormat::brukerTims) { + if(prefered_file_reader_type == pappso::FileReaderType::tims) + { + return std::make_shared(ms_run_id); + } + else if(prefered_file_reader_type == pappso::FileReaderType::tims_ms2) + { + qDebug(); + return std::make_shared(ms_run_id); + } + qDebug() << "by default, build a TimsMsRunReader."; return std::make_shared(ms_run_id); } @@ -307,4 +325,9 @@ } } +FileReaderType +MsFileAccessor::getFileReaderType() const +{ + return m_fileReaderType; +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/msfileaccessor.h libpappsomspp-0.8.58/src/pappsomspp/msfile/msfileaccessor.h --- libpappsomspp-0.8.15/src/pappsomspp/msfile/msfileaccessor.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/msfileaccessor.h 2022-10-27 09:16:15.000000000 +0000 @@ -44,6 +44,10 @@ */ MzFormat getFileFormat() const; + /** @brief get the file reader type + */ + FileReaderType getFileReaderType() const; + /** @brief given an mz format, explicitly set the prefered reader */ void setPreferedFileReaderType(MzFormat format, FileReaderType reader_type); @@ -65,9 +69,26 @@ * * no need to check the file format or filename : all is already part of the * msrunid + * + * @param ms_run_id msrun identifier + * @return msrun reader shared pointer */ static MsRunReaderSPtr buildMsRunReaderSPtr(MsRunIdCstSPtr ms_run_id); + /** @brief get an MsRunReader directly from a valid MsRun ID + * + * no need to check the file format or filename : all is already part of the + * msrunid + * + * @param ms_run_id msrun identifier + * @param prefered_file_reader_type the prefered file reader type to use + * (depending on the mz format) + * @return msrun reader shared pointer + */ + static MsRunReaderSPtr + buildMsRunReaderSPtr(MsRunIdCstSPtr ms_run_id, + pappso::FileReaderType prefered_file_reader_type); + /** @brief if possible, builds directly a dedicated Tims TOF tdf file reader */ TimsMsRunReaderMs2SPtr buildTimsMsRunReaderMs2SPtr(); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/mzformatenumstr.cpp libpappsomspp-0.8.58/src/pappsomspp/msfile/mzformatenumstr.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msfile/mzformatenumstr.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/mzformatenumstr.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,95 @@ +/** + * \file pappsomspp/msfile/mzformatenumstr.cpp + * \date 12/2/2021 + * \author Olivier Langella + * \brief convert mzformat enumerations to strings + * + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "mzformatenumstr.h" +#include "../pappsoexception.h" + +using namespace pappso; + +const QString +pappso::MzFormatEnumStr::toString(pappso::MzFormat mz_format_enum) +{ + + QString mz_format_str; + switch(mz_format_enum) + { + case MzFormat::abSciexT2D: + mz_format_str = "abSciexT2D"; + break; + case MzFormat::abSciexWiff: + mz_format_str = "abSciexWiff"; + break; + case MzFormat::agilentMassHunter: + mz_format_str = "agilentMassHunter"; + break; + case MzFormat::brukerBaf: + mz_format_str = "brukerBaf"; + break; + case MzFormat::brukerFid: + mz_format_str = "brukerFid"; + break; + case MzFormat::brukerTims: + mz_format_str = "brukerTims"; + break; + case MzFormat::brukerYep: + mz_format_str = "brukerYep"; + break; + case MzFormat::MGF: + mz_format_str = "MGF"; + break; + case MzFormat::msn: + mz_format_str = "msn"; + break; + case MzFormat::mz5: + mz_format_str = "mz5"; + break; + case MzFormat::mzML: + mz_format_str = "mzML"; + break; + case MzFormat::mzXML: + mz_format_str = "mzXML"; + break; + case MzFormat::SQLite3: + mz_format_str = "SQLite3"; + break; + case MzFormat::thermoRaw: + mz_format_str = "thermoRaw"; + break; + case MzFormat::watersRaw: + mz_format_str = "watersRaw"; + break; + case MzFormat::xy: + mz_format_str = "xy"; + break; + default: + throw pappso::PappsoException(QObject::tr("MzFormat unknown :\n%1") + .arg((std::uint8_t)mz_format_enum)); + } + return mz_format_str; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/mzformatenumstr.h libpappsomspp-0.8.58/src/pappsomspp/msfile/mzformatenumstr.h --- libpappsomspp-0.8.15/src/pappsomspp/msfile/mzformatenumstr.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/mzformatenumstr.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,48 @@ +/** + * \file pappsomspp/msfile/mzformatenumstr.h + * \date 12/2/2021 + * \author Olivier Langella + * \brief convert mzformat enumerations to strings + * + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once +#include "../exportinmportconfig.h" +#include +#include "../types.h" + +namespace pappso +{ + +/** @brief static functions to convert mz file formats + */ +class PMSPP_LIB_DECL MzFormatEnumStr +{ + public: + /** @brief convert mz format enumeration to human readable string + */ + static const QString toString(MzFormat mz_format_enum); +}; + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/pwizmsfilereader.cpp libpappsomspp-0.8.58/src/pappsomspp/msfile/pwizmsfilereader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msfile/pwizmsfilereader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/pwizmsfilereader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -51,9 +51,12 @@ throw PappsoException( QObject::tr( - "libpwiz ERROR reading MS data file %1 (std::runtime_error):\n%2") + "libpwiz ERROR reading MS data file %1 " + "(std::runtime_error):\n%2\nsource file:%3 - source line:%4") .arg(m_fileName) - .arg(error.what())); + .arg(error.what()) + .arg(__FILE__) + .arg(__LINE__)); } catch(std::exception &error) { @@ -61,12 +64,14 @@ throw PappsoException( QObject::tr( - "libpwiz ERROR reading MS data file %1 (std::exception):\n%2") + "libpwiz ERROR reading MS data file %1 " + "(std::runtime_error):\n%2\nsource file:%3 - source line:%4") .arg(m_fileName) - .arg(error.what())); + .arg(error.what()) + .arg(__FILE__) + .arg(__LINE__)); } - if(readerName.empty()) { qDebug() << "Failed to identify the file."; @@ -124,9 +129,12 @@ throw PappsoException( QObject::tr( - "libpwiz ERROR reading MS data file %1 (std::runtime_error):\n%2") + "libpwiz ERROR reading MS data file %1 " + "(std::runtime_error):\n%2\nsource file:%3 - source line:%4") .arg(m_fileName) - .arg(error.what())); + .arg(error.what()) + .arg(__FILE__) + .arg(__LINE__)); } catch(std::exception &error) { @@ -134,10 +142,14 @@ throw PappsoException( QObject::tr( - "libpwiz ERROR reading MS data file %1 (std::exception):\n%2") + "libpwiz ERROR reading MS data file %1 " + "(std::runtime_error):\n%2\nsource file:%3 - source line:%4") .arg(m_fileName) - .arg(error.what())); + .arg(error.what()) + .arg(__FILE__) + .arg(__LINE__)); } + qDebug() << "The number of runs is:" << m_msDataPtrVector.size() << "The reader type is:" << QString::fromStdString(readerName) << "The number of spectra in first run is:" diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/timsmsfilereader.cpp libpappsomspp-0.8.58/src/pappsomspp/msfile/timsmsfilereader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msfile/timsmsfilereader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/timsmsfilereader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -28,6 +28,7 @@ #include "timsmsfilereader.h" #include "../vendors/tims/timsdata.h" #include "../pappsoexception.h" +#include "../exception/exceptionnotimplemented.h" #include #include @@ -58,6 +59,14 @@ TimsData tims_data(m_fileName); m_fileFormat = MzFormat::brukerTims; } + catch(ExceptionNotImplemented &error) + { + m_fileFormat = MzFormat::brukerTims; + throw pappso::ExceptionNotImplemented( + QObject::tr("Error reading Bruker tims data in %1 :\n%2") + .arg(m_fileName) + .arg(error.qwhat())); + } catch(PappsoException &error) { return 0; @@ -95,8 +104,7 @@ ms_run_id.setSampleName(QFileInfo(m_fileName).baseName()); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()" - << "Current ms_run_id:" << ms_run_id.toString(); + qDebug() << "Current ms_run_id:" << ms_run_id.toString(); // Finally make a shared pointer out of it and append it to the vector. ms_run_ids.push_back(std::make_shared(ms_run_id)); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msfile/timsmsfilereader.h libpappsomspp-0.8.58/src/pappsomspp/msfile/timsmsfilereader.h --- libpappsomspp-0.8.15/src/pappsomspp/msfile/timsmsfilereader.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msfile/timsmsfilereader.h 2022-10-27 09:16:15.000000000 +0000 @@ -39,9 +39,6 @@ */ class TimsMsFileReader : MsFileReader { - private: - virtual std::size_t initialize(); - public: TimsMsFileReader(const QString &file_name); virtual ~TimsMsFileReader(); @@ -52,5 +49,8 @@ getMsRunIds(const QString &run_prefix) override; MsRunReader *selectMsRunReader(const QString &file_name) const; + + private: + virtual std::size_t initialize(); }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/alignment/msrunretentiontime.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/alignment/msrunretentiontime.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/alignment/msrunretentiontime.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/alignment/msrunretentiontime.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,68 +31,18 @@ using namespace pappso; -/* -void -writeTrace(const QString &filename, const pappso::Trace &trace) -{ - QFile file(filename); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " - << QFileInfo(filename).absoluteFilePath(); - // file.open(QIODevice::WriteOnly); - OdsDocWriter writer(&file); - - for(auto &data_point : trace) - { - writer.writeCell(data_point.x); - writer.writeCell(data_point.y); - writer.writeLine(); - } - writer.close(); -} -*/ - -class RetentionTimeReader : public SpectrumCollectionHandlerInterface -{ - - public: - RetentionTimeReader(std::vector &rt_points) - : m_rtPoints(rt_points){}; - virtual ~RetentionTimeReader(){}; - virtual void - setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override - { - if(spectrum.getMsLevel() == 1) - { - m_rtPoints.push_back({spectrum.getRtInSeconds(), - spectrum.getMassSpectrumId().getSpectrumIndex()}); - } - }; - virtual bool - needPeakList() const override - { - return false; - }; - - private: - std::vector &m_rtPoints; -}; - - template MsRunRetentionTime::MsRunRetentionTime(MsRunReaderSPtr msrun_reader_sp) : m_ms2MedianFilter(10), m_ms2MeanFilter(15), m_ms1MeanFilter(1) { - msp_msrunReader = msrun_reader_sp; - mcsp_msrunId = msp_msrunReader.get()->getMsRunId(); - RetentionTimeReader handler(m_ms1RetentionTimeVector); - msrun_reader_sp.get()->readSpectrumCollection(handler); + msp_msrunReader = msrun_reader_sp; + mcsp_msrunId = msp_msrunReader.get()->getMsRunId(); + m_ms1RetentionTimeVector = msp_msrunReader.get()->getRetentionTimeLine(); std::sort(m_ms1RetentionTimeVector.begin(), m_ms1RetentionTimeVector.end(), - [](const RtPoint &a, const RtPoint &b) { - return (a.retentionTime < b.retentionTime); - }); + [](const double &a, const double &b) { return (a < b); }); } template @@ -120,6 +70,20 @@ } template +const MsRunId & +MsRunRetentionTime::getMsRunId() const +{ + return *(mcsp_msrunId.get()); +} + +template +const pappso::FilterMorphoMedian & +pappso::MsRunRetentionTime::getMs2MedianFilter() const +{ + return m_ms2MedianFilter; +} + +template void MsRunRetentionTime::setMs2MedianFilter( const FilterMorphoMedian &ms2MedianFilter) @@ -127,6 +91,14 @@ m_ms2MedianFilter = ms2MedianFilter; } +template +const pappso::FilterMorphoMean & +pappso::MsRunRetentionTime::getMs2MeanFilter() const +{ + return m_ms2MeanFilter; +} + + template void MsRunRetentionTime::setMs2MeanFilter(const FilterMorphoMean &ms2MeanFilter) @@ -134,6 +106,13 @@ m_ms2MeanFilter = ms2MeanFilter; } +template +const pappso::FilterMorphoMean & +pappso::MsRunRetentionTime::getMs1MeanFilter() const +{ + return m_ms1MeanFilter; +} + template void MsRunRetentionTime::setMs1MeanFilter(const FilterMorphoMean &ms1MeanFilter) @@ -163,7 +142,7 @@ return m_valuesCorrected; } template -const std::vector & +const std::vector & MsRunRetentionTime::getMs1RetentionTimeVector() const { return m_ms1RetentionTimeVector; @@ -203,14 +182,28 @@ template void -MsRunRetentionTime::computePeptideRetentionTimes() +MsRunRetentionTime::addPeptideAsSeamark(const T &peptide_id, + double retentionTime, + double precursorIntensity) +{ + PeptideMs2Point ms2point; + ms2point.entityHash = peptide_id; + ms2point.precursorIntensity = precursorIntensity; + ms2point.retentionTime = retentionTime; + m_allMs2Points.push_back(ms2point); +} + + +template +void +MsRunRetentionTime::computeSeamarks() { qDebug(); - if(msp_msrunReader == nullptr) + if(m_allMs2Points.size() == 0) { - throw ExceptionNotPossible( - QObject::tr("ERROR : msp_msrunReader == nullptr")); + // already computed + return; } m_seamarks.clear(); if(m_retentionTimeReferenceMethod == @@ -243,7 +236,6 @@ it++; } } - msp_msrunReader = nullptr; m_allMs2Points.clear(); std::sort(m_seamarks.begin(), @@ -320,7 +312,7 @@ { return m_alignedRetentionTimeVector.front(); } - return m_ms1RetentionTimeVector.front().retentionTime; + return m_ms1RetentionTimeVector.front(); } template double @@ -330,7 +322,7 @@ { return m_alignedRetentionTimeVector.back(); } - return m_ms1RetentionTimeVector.back().retentionTime; + return m_ms1RetentionTimeVector.back(); } @@ -357,8 +349,8 @@ auto it_plus = std::find_if(m_ms1RetentionTimeVector.begin(), m_ms1RetentionTimeVector.end(), - [original_retention_time](const RtPoint &rt_point) { - return original_retention_time < rt_point.retentionTime; + [original_retention_time](const double &rt_point) { + return original_retention_time < rt_point; }); double rt1_a, rt2_a, rt1_b, rt2_b; if(it_plus == m_ms1RetentionTimeVector.end()) @@ -371,8 +363,8 @@ } auto it_minus = it_plus - 1; - rt1_a = it_minus->retentionTime; - rt2_a = it_plus->retentionTime; + rt1_a = *it_minus; + rt2_a = *it_plus; double ratio = (original_retention_time - rt1_a) / (rt2_a - rt1_a); @@ -387,6 +379,57 @@ } template +double +MsRunRetentionTime::translateAligned2OriginalRetentionTime( + double aligned_retention_time) const +{ + if(m_alignedRetentionTimeVector.size() < 3) + { + throw ExceptionNotPossible( + QObject::tr("ERROR : too few aligned points to compute aligned " + "retention time (%1)") + .arg(m_ms1RetentionTimeVector.size())); + } + if(m_alignedRetentionTimeVector.size() != m_ms1RetentionTimeVector.size()) + { + throw ExceptionNotPossible( + QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 " + "m_ms1RetentionTimeVector.size()") + .arg(m_alignedRetentionTimeVector.size()) + .arg(m_ms1RetentionTimeVector.size())); + } + auto it_plus = std::find_if(m_alignedRetentionTimeVector.begin(), + m_alignedRetentionTimeVector.end(), + [aligned_retention_time](const double &rt_point) { + return aligned_retention_time < rt_point; + }); + double rt1_a, rt2_a, rt1_b, rt2_b; + if(it_plus == m_alignedRetentionTimeVector.end()) + { + it_plus--; + } + if(it_plus == m_alignedRetentionTimeVector.begin()) + { + it_plus++; + } + auto it_minus = it_plus - 1; + + rt1_a = *it_minus; + rt2_a = *it_plus; + + double ratio = (aligned_retention_time - rt1_a) / (rt2_a - rt1_a); + + auto itref = m_ms1RetentionTimeVector.begin() + + std::distance(m_alignedRetentionTimeVector.begin(), it_minus); + + rt1_b = *itref; + itref++; + rt2_b = *itref; + + return (((rt2_b - rt1_b) * ratio) + rt1_b); +} + +template const std::vector> MsRunRetentionTime::getSeamarksReferences() const { @@ -411,6 +454,7 @@ MsRunRetentionTime::align( const MsRunRetentionTime &msrun_retention_time_reference) { + computeSeamarks(); std::vector> other_seamarks; if(msrun_retention_time_reference.isAligned()) { @@ -452,20 +496,20 @@ // add a first point to ensure coherence: DataPoint first_point; - first_point.x = m_ms1RetentionTimeVector.front().retentionTime - (double)1; + first_point.x = m_ms1RetentionTimeVector.front() - (double)1; if(first_point.x < 0) { first_point.x = 0; } first_point.y = - m_ms1RetentionTimeVector.front().retentionTime - + m_ms1RetentionTimeVector.front() - msrun_retention_time_reference.getFrontRetentionTimeReference(); common_points.push_back(first_point); // add a last point to ensure coherence: DataPoint last_point; - last_point.x = m_ms1RetentionTimeVector.back().retentionTime + 1; - last_point.y = m_ms1RetentionTimeVector.back().retentionTime - + last_point.x = m_ms1RetentionTimeVector.back() + 1; + last_point.y = m_ms1RetentionTimeVector.back() - msrun_retention_time_reference.getBackRetentionTimeReference(); common_points.push_back(last_point); common_points.sortX(); @@ -497,8 +541,7 @@ // Here, the correction parameter is the slope of old rt points curve // (divided by 4 to get a finer correction). double correction_parameter = - (m_ms1RetentionTimeVector.back().retentionTime - - m_ms1RetentionTimeVector.front().retentionTime) / + (m_ms1RetentionTimeVector.back() - m_ms1RetentionTimeVector.front()) / (ms1_aligned_points.size()); // set_correction_parameter(correction_parameter / 4); correction_parameter = correction_parameter / (double)4; @@ -532,10 +575,10 @@ } qDebug() << "() itms2->x=" << itms2->x << " itms2->y=" << itms2->y; - for(RtPoint &original_rt_point : m_ms1RetentionTimeVector) + for(double &original_rt_point : m_ms1RetentionTimeVector) { DataPoint ms1_point; - ms1_point.x = original_rt_point.retentionTime; + ms1_point.x = original_rt_point; while(ms1_point.x > itms2next->x) { @@ -585,9 +628,76 @@ } -template +template pappso::MsRunReaderSPtr pappso::MsRunRetentionTime::getMsRunReaderSPtr() const { return msp_msrunReader; } + +template +void +pappso::MsRunRetentionTime::setAlignedRetentionTimeVector( + const std::vector &aligned_times) +{ + + if(aligned_times.size() == m_ms1RetentionTimeVector.size()) + { + m_alignedRetentionTimeVector = aligned_times; + } + else + { + if(aligned_times.size() == m_ms1RetentionTimeVector.size() * 2) + { + m_alignedRetentionTimeVector = m_ms1RetentionTimeVector; + for(std::size_t i = 0; i < m_ms1RetentionTimeVector.size(); i++) + { + if(aligned_times[2 * i] != m_ms1RetentionTimeVector[i]) + { + throw pappso::PappsoException( + QObject::tr( + "ERROR : aligned_times (size=%1) vector does not have " + "required size (size=%2)") + .arg(aligned_times.size()) + .arg(m_ms1RetentionTimeVector.size())); + } + m_alignedRetentionTimeVector[i] = aligned_times[(2 * i) + 1]; + } + } + else + { + throw ExceptionNotPossible( + QObject::tr("ERROR : aligned_times (size=%1) vector does not have " + "required size (size=%2)") + .arg(aligned_times.size()) + .arg(m_ms1RetentionTimeVector.size())); + } + } +} + + +template +Trace +MsRunRetentionTime::getCommonSeamarksDeltaRt( + const MsRunRetentionTime &msrun_retention_time_reference) const +{ + // computeSeamarks(); + std::vector> other_seamarks; + if(msrun_retention_time_reference.isAligned()) + { + other_seamarks = msrun_retention_time_reference.getSeamarksReferences(); + } + else + { + other_seamarks = msrun_retention_time_reference.getSeamarks(); + } + qDebug(); + + qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime + << " " << other_seamarks[0].entityHash + << other_seamarks[0].retentionTime << " "; + // both seamarks has to be ordered + Trace common_points; + getCommonDeltaRt(common_points, other_seamarks); + return common_points; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/alignment/msrunretentiontime.h libpappsomspp-0.8.58/src/pappsomspp/msrun/alignment/msrunretentiontime.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/alignment/msrunretentiontime.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/alignment/msrunretentiontime.h 2022-10-27 09:16:15.000000000 +0000 @@ -29,13 +29,6 @@ namespace pappso { -struct RtPoint -{ - double retentionTime; - std::size_t spectrumIndex; -}; - - template struct MsRunRetentionTimeSeamarkPoint { @@ -69,39 +62,87 @@ ~MsRunRetentionTime(); pappso::MsRunReaderSPtr getMsRunReaderSPtr() const; + const MsRunId &getMsRunId() const; void setMs2MedianFilter(const FilterMorphoMedian &ms2MedianFilter); void setMs2MeanFilter(const FilterMorphoMean &ms2MeanFilter); void setMs1MeanFilter(const FilterMorphoMean &ms1MeanFilter); + const FilterMorphoMedian &getMs2MedianFilter() const; + const FilterMorphoMean &getMs2MeanFilter() const; + const FilterMorphoMean &getMs1MeanFilter() const; + Trace getCommonDeltaRt( const std::vector> &other_seamarks) const; /** @brief collects all peptide evidences of a given MSrun * seamarks has to be converted to peptide retention time using * computePeptideRetentionTimes + * + * @param peptide_id unique identifier (whichever type) of a peptide + * @param ms2_spectrum_index associated MS2 spectrum index ot this peptide */ - void addPeptideAsSeamark(const T &peptide_str, - std::size_t ms2_spectrum_index); + void addPeptideAsSeamark(const T &peptide_id, std::size_t ms2_spectrum_index); - /** @brief convert Peptide seamarks into PeptideMs2Point - * this is required before computing alignment + + /** @brief collects all peptide evidences of a given MSrun + * seamarks has to be converted to peptide retention time using + * computePeptideRetentionTimes + * + * @param peptide_id unique identifier (whichever type) of a peptide + * @param retentionTime retention time of this peptide observation + * @param precursorIntensity MS2 precursorIntensity of this peptide */ - void computePeptideRetentionTimes(); + void addPeptideAsSeamark(const T &peptide_id, + double retentionTime, + double precursorIntensity); + std::size_t getNumberOfCorrectedValues() const; + /** @brief align the current msrunretentiontime object using the given + * reference + * @param msrun_retention_time_reference the reference + * @return a trace containing aligned MS1 retention times + */ Trace align(const MsRunRetentionTime &msrun_retention_time_reference); + /** @brief get common seamarks between msrunretentiontime objects and their + * deltart + * @param msrun_retention_time_reference the reference + * @return a trace containing MS2 common points and their deltart + */ + Trace getCommonSeamarksDeltaRt( + const MsRunRetentionTime &msrun_retention_time_reference) const; + const std::vector> &getSeamarks() const; + + /** @brief get aligned retention time vector + * @return vector of seconds (as double) + */ const std::vector &getAlignedRetentionTimeVector() const; - const std::vector &getMs1RetentionTimeVector() const; + + void setAlignedRetentionTimeVector(const std::vector &aligned_times); + + /** @brief get orginal retention time vector (not aligned) + * @return vector of seconds (as double) + */ + const std::vector &getMs1RetentionTimeVector() const; bool isAligned() const; double translateOriginal2AlignedRetentionTime(double original_retention_time) const; + + double + translateAligned2OriginalRetentionTime(double aligned_retention_time) const; + + /** @brief convert PeptideMs2Point into Peptide seamarks + * this is required before computing alignment + */ + void computeSeamarks(); + protected: double getFrontRetentionTimeReference() const; double getBackRetentionTimeReference() const; @@ -109,6 +150,12 @@ getSeamarksReferences() const; private: + /** @brief get a trace of common MS2 retention times (x values) by their + * deltart (y values) + * @param delta_rt the trace result (common MS2 retention times vs counter + * part deltart) + * @param other_seamarks seamarks of the counter part (reference) + */ void getCommonDeltaRt( Trace &delta_rt, const std::vector> &other_seamarks) const; @@ -124,7 +171,7 @@ FilterMorphoMean m_ms1MeanFilter; pappso::MsRunReaderSPtr msp_msrunReader; pappso::MsRunIdCstSPtr mcsp_msrunId; - std::vector m_ms1RetentionTimeVector; + std::vector m_ms1RetentionTimeVector; std::vector m_alignedRetentionTimeVector; std::vector> m_seamarks; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/msrundatasettree.h libpappsomspp-0.8.58/src/pappsomspp/msrun/msrundatasettree.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/msrundatasettree.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/msrundatasettree.h 2022-10-27 09:16:15.000000000 +0000 @@ -9,14 +9,12 @@ /////////////////////// Qt includes -/////////////////////// pappsomspp includes - - /////////////////////// Local includes #include "msrundatasettreevisitor.h" #include "msrundatasettreenode.h" #include "msrunid.h" #include "../exportinmportconfig.h" +#include "../processing/combiners/selectionpolygon.h" namespace pappso @@ -93,6 +91,10 @@ NodeVector &nodes, DataKind data_kind) const; + std::size_t addDataSetTreeNodesInsideDtRtPolygon(const SelectionPolygon &selectionPolygon, + NodeVector &nodes, + DataKind data_kind) const; + std::size_t removeDataSetTreeNodesOutsideDtRtRange(double start, double end, NodeVector &nodes, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunid.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunid.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunid.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunid.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -23,6 +23,7 @@ #include "msrunid.h" #include +#include int msRunIdMetaTypeId = qRegisterMetaType("pappso::MsRunId"); @@ -43,7 +44,12 @@ MsRunId::MsRunId(const QString &file_name) : m_fileName(file_name) { // by default, the sample name is given by the file name - m_sampleName = QFileInfo(file_name).baseName(); + QFileInfo fileinfo(m_fileName); + if(fileinfo.fileName() == "analysis.tdf") + { + m_fileName = fileinfo.absoluteDir().absolutePath(); + } + m_sampleName = QFileInfo(m_fileName).baseName(); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunreader.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunreader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunreader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunreader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -23,9 +23,6 @@ * You should have received a copy of the GNU General Public License * along with PAPPSOms++. If not, see . * - * Contributors: - * Olivier Langella - initial API and - *implementation ******************************************************************************/ #include @@ -52,8 +49,8 @@ { } void -SpectrumCollectionHandlerInterface::spectrumListHasSize([ - [maybe_unused]] std::size_t size) +SpectrumCollectionHandlerInterface::spectrumListHasSize( + [[maybe_unused]] std::size_t size) { } void @@ -115,6 +112,11 @@ MsRunSimpleStatistics::setQualifiedMassSpectrum( const QualifiedMassSpectrum &qspectrum) { + // The vector[0] contains the number of spectra at MS + // The vector[1] contains the number of spectra at MS^2 + // The vector[2] contains the number of spectra at MS^3 + // ... + unsigned int ms_level = qspectrum.getMsLevel(); if(ms_level == 0) return; @@ -217,6 +219,41 @@ } +MsRunReaderRetentionTimeLine::MsRunReaderRetentionTimeLine() +{ + // qDebug(); +} + + +MsRunReaderRetentionTimeLine::~MsRunReaderRetentionTimeLine() +{ + // qDebug(); +} + + +bool +MsRunReaderRetentionTimeLine::needPeakList() const +{ + return false; +} + + +void +MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum( + const QualifiedMassSpectrum &qspectrum) +{ + qDebug() << " " << qspectrum.getMassSpectrumId().getNativeId(); + + m_retention_time_list.push_back(qspectrum.getRtInSeconds()); +} + +const std::vector & +MsRunReaderRetentionTimeLine::getRetentionTimeLine() const +{ + return m_retention_time_list; +} + + MsRunReader::MsRunReader(MsRunIdCstSPtr &ms_run_id) : mcsp_msRunId(ms_run_id) { } @@ -225,6 +262,7 @@ : mcsp_msRunId(other.mcsp_msRunId) { mpa_multiMapScanNumber = nullptr; + m_isMonoThread = other.m_isMonoThread; } @@ -241,6 +279,18 @@ delete mpa_multiMapScanNumber; } +void +MsRunReader::setMonoThread(bool is_mono_thread) +{ + m_isMonoThread = is_mono_thread; +} + +bool +MsRunReader::isMonoThread() const +{ + return m_isMonoThread; +} + std::size_t MsRunReader::scanNumber2SpectrumIndex(std::size_t scan_number) @@ -279,4 +329,123 @@ return false; } +std::vector +MsRunReader::getRetentionTimeLine() +{ + qDebug(); + + try + { + + MsRunReaderRetentionTimeLine reader_timeline; + + readSpectrumCollectionByMsLevel(reader_timeline, 1); + + return reader_timeline.getRetentionTimeLine(); + } + + catch(ExceptionNotFound &error) + { + throw ExceptionNotFound(QObject::tr("error reading file %1 : %2") + .arg(mcsp_msRunId.get()->getFileName()) + .arg(error.qwhat())); + } + catch(PappsoException &error) + { + throw PappsoException(QObject::tr("error reading file %1 : %2") + .arg(mcsp_msRunId.get()->getFileName()) + .arg(error.qwhat())); + } +} + + +Trace +MsRunReader::getTicChromatogram() +{ + qDebug(); + + try + { + MsRunReaderTicChromatogram ms_run_reader; + + readSpectrumCollection(ms_run_reader); + + return ms_run_reader.getTicChromatogram(); + } + + catch(ExceptionNotFound &error) + { + throw ExceptionNotFound(QObject::tr("error reading file %1 : %2") + .arg(mcsp_msRunId.get()->getFileName()) + .arg(error.qwhat())); + } + catch(PappsoException &error) + { + throw PappsoException(QObject::tr("error reading file %1 : %2") + .arg(mcsp_msRunId.get()->getFileName()) + .arg(error.qwhat())); + } +} + + +MsRunReaderTicChromatogram::MsRunReaderTicChromatogram() +{ +} + + +MsRunReaderTicChromatogram::~MsRunReaderTicChromatogram() +{ +} + + +bool +MsRunReaderTicChromatogram::needPeakList() const +{ + return true; +} + + +void +MsRunReaderTicChromatogram::setQualifiedMassSpectrum( + const QualifiedMassSpectrum &qualified_mass_spectrum) +{ + // In this specialized reader we want to compute the total ion current + // chromatogram that plot the sum of all the ion intensities in the spectra as + // a function of the retention time. + + uint spectrum_ms_level = qualified_mass_spectrum.getMsLevel(); + + if(spectrum_ms_level != 1) + return; + + double sumY = qualified_mass_spectrum.getMassSpectrumSPtr()->sumY(); + + if(!sumY) + return; + + double rt = qualified_mass_spectrum.getRtInMinutes(); + + using Pair = std::pair; + using Map = std::map; + using Iterator = Map::iterator; + + std::pair res = m_ticChromMapTrace.insert(Pair(rt, sumY)); + + if(!res.second) + { + // One other same rt value was seen already (like in ion mobility mass + // spectrometry, for example). Only increment the y value. + + res.first->second += sumY; + } +} + + +Trace +MsRunReaderTicChromatogram::getTicChromatogram() const +{ + return m_ticChromMapTrace.toTrace(); +} + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunreader.h libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunreader.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/msrunreader.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/msrunreader.h 2022-10-27 09:16:15.000000000 +0000 @@ -23,9 +23,6 @@ * You should have received a copy of the GNU General Public License * along with PAPPSOms++. If not, see . * - * Contributors: - * Olivier Langella - initial API and - *implementation ******************************************************************************/ #pragma once @@ -41,14 +38,14 @@ /////////////////////// pappsomspp includes - +#include "../trace/maptrace.h" /////////////////////// Local includes #include "msrunid.h" #include "../massspectrum/qualifiedmassspectrum.h" #include "../msfile/msfilereader.h" #include "../exportinmportconfig.h" - +#include "xiccoord/xiccoord.h" namespace pappso { @@ -147,6 +144,42 @@ }; +/** @brief collect retention times along MS run */ +class PMSPP_LIB_DECL MsRunReaderRetentionTimeLine + : public SpectrumCollectionHandlerInterface +{ + private: + std::vector m_retention_time_list; + + public: + MsRunReaderRetentionTimeLine(); + virtual ~MsRunReaderRetentionTimeLine(); + virtual void + setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override; + virtual bool needPeakList() const override; + + const std::vector &getRetentionTimeLine() const; +}; + + +/** @brief calculate a TIC chromatogram */ +class PMSPP_LIB_DECL MsRunReaderTicChromatogram + : public SpectrumCollectionHandlerInterface +{ + public: + MsRunReaderTicChromatogram(); + virtual ~MsRunReaderTicChromatogram(); + virtual void setQualifiedMassSpectrum( + const QualifiedMassSpectrum &qualified_mass_spectrum) override; + virtual bool needPeakList() const override; + + Trace getTicChromatogram() const; + + private: + MapTrace m_ticChromMapTrace; +}; + + class PMSPP_LIB_DECL MsRunReader; typedef std::shared_ptr MsRunReaderSPtr; typedef std::shared_ptr MsRunReaderCstSPtr; @@ -178,6 +211,19 @@ qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data = true) const = 0; + + /** @brief get a xic coordinate object from a given spectrum index + */ + virtual XicCoordSPtr + newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, + PrecisionPtr precision) const = 0; + + /** @brief get a xic coordinate object from a given spectrum + */ + virtual XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum( + const QualifiedMassSpectrum &mass_spectrum, + PrecisionPtr precision) const = 0; + /** @brief get the totat number of spectrum conained in the MSrun data file */ virtual std::size_t spectrumListSize() const = 0; @@ -188,6 +234,15 @@ virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) = 0; + + /** @brief function to visit an MsRunReader and get each Spectrum in a + * spectrum collection handler by Ms Levels + */ + virtual void + readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) = 0; + + /** @brief if possible, converts a scan number into a spectrum index * This is a convenient function to help transition from the old scan number * (not implemented by all vendors) to more secure spectrum index (not vendor @@ -215,6 +270,22 @@ */ virtual bool acquireDevice() = 0; + /** @brief retention timeline + * get retention times along the MSrun in seconds + * @return vector of retention times (seconds) + */ + virtual std::vector getRetentionTimeLine(); + + virtual Trace getTicChromatogram(); + + + /** @brief set only one is_mono_thread to true + * + * this avoid to use qtconcurrent + */ + void setMonoThread(bool is_mono_thread); + + bool isMonoThread() const; protected: MsRunIdCstSPtr mcsp_msRunId; @@ -227,6 +298,9 @@ * format */ virtual bool accept(const QString &file_name) const = 0; + + private: + bool m_isMonoThread = false; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mgfoutput.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mgfoutput.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mgfoutput.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mgfoutput.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -25,7 +25,7 @@ 89.06031799 258758.140625 90.06361389 12425.6162109375 */ - *mpa_outputStream << "BEGIN IONS" << endl; + *mpa_outputStream << "BEGIN IONS" << Qt::endl; *mpa_outputStream << "TITLE=" << mass_spectrum.getMassSpectrumId() .getMsRunIdCstSPtr() @@ -33,28 +33,28 @@ ->getSampleName() << "." << mass_spectrum.getMassSpectrumId().getSpectrumIndex() - << endl; + << Qt::endl; *mpa_outputStream << "RTINSECONDS=" << QString::number(mass_spectrum.getRtInSeconds(), 'f', 2) - << endl; + << Qt::endl; *mpa_outputStream << "PEPMASS=" << QString::number(mass_spectrum.getPrecursorMz(), 'g', 15) << " " << QString::number( mass_spectrum.getPrecursorIntensity(), 'f', 5) - << endl; + << Qt::endl; *mpa_outputStream << "CHARGE=" << mass_spectrum.getPrecursorCharge() << "+" - << endl; + << Qt::endl; if(mass_spectrum.getMassSpectrumCstSPtr() != nullptr) { for(auto &&peak : *(mass_spectrum.getMassSpectrumCstSPtr().get())) { *mpa_outputStream << QString::number(peak.x, 'g', 15) << " " - << QString::number(peak.y, 'g', 15) << endl; + << QString::number(peak.y, 'g', 15) << Qt::endl; } } - *mpa_outputStream << "END IONS" << endl; + *mpa_outputStream << "END IONS" << Qt::endl; } void diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mzxmloutput.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mzxmloutput.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mzxmloutput.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mzxmloutput.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -61,6 +61,7 @@ const QualifiedMassSpectrum &spectrum) { qDebug(); + mp_output->m_monitor.count(); mp_output->writeQualifiedMassSpectrum(spectrum); qDebug(); } @@ -71,7 +72,9 @@ } -MzxmlOutput::MzxmlOutput(QIODevice *p_output_device) +MzxmlOutput::MzxmlOutput(UiMonitorInterface &monitor, + QIODevice *p_output_device) + : m_monitor(monitor) { mpa_outputStream = new QXmlStreamWriter(p_output_device); @@ -95,6 +98,7 @@ MzxmlOutput::write(MsRunReader *p_msrunreader) { qDebug(); + m_monitor.setTotalSteps(p_msrunreader->spectrumListSize()); writeHeader(p_msrunreader); Translater translater(this); @@ -105,6 +109,8 @@ // translater.setNeedMsLevelPeakList(1, false); // translater.setNeedMsLevelPeakList(2, false); p_msrunreader->readSpectrumCollection(translater); + + m_monitor.setTotalSteps(0); qDebug(); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mzxmloutput.h libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mzxmloutput.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/output/mzxmloutput.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/output/mzxmloutput.h 2022-10-27 09:16:15.000000000 +0000 @@ -32,6 +32,7 @@ #include "../msrunreader.h" #include +#include "../../processing/uimonitor/uimonitorinterface.h" namespace pappso { @@ -45,7 +46,7 @@ /** * Default constructor */ - MzxmlOutput(QIODevice *p_output_device); + MzxmlOutput(UiMonitorInterface &monitor, QIODevice *p_output_device); /** * Destructor @@ -86,6 +87,7 @@ private: + UiMonitorInterface &m_monitor; QXmlStreamWriter *mpa_outputStream; bool m_isReadAhead = false; bool m_ms1IsMasked = false; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/pwizmsrunreader.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/private/pwizmsrunreader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/pwizmsrunreader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/pwizmsrunreader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -787,6 +787,14 @@ PwizMsRunReader::readSpectrumCollection( SpectrumCollectionHandlerInterface &handler) { + readSpectrumCollectionByMsLevel(handler, 0); +} + + +void +PwizMsRunReader::readSpectrumCollectionByMsLevel( + SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) +{ acquireDevice(); // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; @@ -896,7 +904,17 @@ // The handler will receive the index of the mass spectrum in the // current run via the mass spectrum id member datum. - handler.setQualifiedMassSpectrum(qualified_mass_spectrum); + if(ms_level == 0) + { + handler.setQualifiedMassSpectrum(qualified_mass_spectrum); + } + else + { + if(qualified_mass_spectrum.getMsLevel() == ms_level) + { + handler.setQualifiedMassSpectrum(qualified_mass_spectrum); + } + } } setlocale(LC_ALL, env.c_str()); @@ -911,7 +929,6 @@ handler.loadingEnded(); } - std::size_t PwizMsRunReader::spectrumListSize() const { @@ -941,4 +958,30 @@ return true; } + +XicCoordSPtr +PwizMsRunReader::newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const +{ + + QualifiedMassSpectrum mass_spectrum = + qualifiedMassSpectrum(spectrum_index, false); + + return newXicCoordSPtrFromQualifiedMassSpectrum(mass_spectrum, precision); +} + +XicCoordSPtr +PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const +{ + XicCoordSPtr xic_coord = std::make_shared(); + + xic_coord.get()->rtTarget = mass_spectrum.getRtInSeconds(); + + xic_coord.get()->mzRange = MzRange(mass_spectrum.getPrecursorMz(), precision); + + return xic_coord; +} + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/pwizmsrunreader.h libpappsomspp-0.8.58/src/pappsomspp/msrun/private/pwizmsrunreader.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/pwizmsrunreader.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/pwizmsrunreader.h 2022-10-27 09:16:15.000000000 +0000 @@ -62,6 +62,19 @@ virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override; + virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const override; + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const override; + + + virtual void + readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) override; + + virtual std::size_t spectrumListSize() const override; virtual bool hasScanNumbers() const override; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreader.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -39,24 +39,26 @@ TimsMsRunReader::~TimsMsRunReader() { - if(mpa_timsData != nullptr) - { - delete mpa_timsData; - } + msp_timsData = nullptr; } void -pappso::TimsMsRunReader::initialize() +TimsMsRunReader::initialize() { - mpa_timsData = new TimsData(mcsp_msRunId.get()->getFileName()); + msp_timsData = std::make_shared(mcsp_msRunId.get()->getFileName()); + if(msp_timsData == nullptr) + { + throw PappsoException(QObject::tr("ERROR in TimsMsRunReader::initialize " + "msp_timsData is null for MsRunId %1") + .arg(mcsp_msRunId.get()->toString())); + } } bool TimsMsRunReader::accept(const QString &file_name) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - << file_name; + qDebug() << file_name; return true; } @@ -73,7 +75,7 @@ pappso::MassSpectrumCstSPtr TimsMsRunReader::massSpectrumCstSPtr(std::size_t spectrum_index) { - return mpa_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index); + return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index); } @@ -82,18 +84,10 @@ bool want_binary_data) const { - QualifiedMassSpectrum mass_spectrum = - mpa_timsData->getQualifiedMassSpectrumByRawIndex(spectrum_index, - want_binary_data); - - MassSpectrumId spectrum_id(mass_spectrum.getMassSpectrumId()); - spectrum_id.setMsRunId(getMsRunId()); - mass_spectrum.setMassSpectrumId(spectrum_id); - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - //<< mass_spectrum.toString(); + QualifiedMassSpectrum mass_spectrum; - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - //<< mass_spectrum.getMassSpectrumSPtr().get()->toString(); + msp_timsData->getQualifiedMassSpectrumByRawIndex( + getMsRunId(), mass_spectrum, spectrum_index, want_binary_data); return mass_spectrum; } @@ -102,50 +96,20 @@ TimsMsRunReader::readSpectrumCollection( SpectrumCollectionHandlerInterface &handler) { - qDebug(); - - const bool want_binary_data = handler.needPeakList(); - - // We'll need it to perform the looping in the spectrum list. - std::size_t spectrum_list_size = spectrumListSize(); + readSpectrumCollectionByMsLevel(handler, 0); +} - qDebug() << "The spectrum list has size:" << spectrum_list_size; - // Inform the handler of the spectrum list so that it can handle feedback to - // the user. - handler.spectrumListHasSize(spectrum_list_size); +void +TimsMsRunReader::readSpectrumCollectionByMsLevel( + SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) +{ - // Iterate in the full list of spectra. - // mpa_timsData->iterateOnAllScans(mcsp_msRunId, handler); + qDebug(); - for(std::size_t iter = 0; iter < spectrum_list_size; iter++) - { - // If the user of this reader instance wants to stop reading the spectra, - // then break this loop. - if(handler.shouldStop()) - { - qDebug() << "The operation was cancelled. Breaking the loop."; - break; - } - - - bool get_data = want_binary_data; - if(get_data) - { - get_data = handler.needMsLevelPeakList( - mpa_timsData->getMsLevelBySpectrumIndex(iter)); - } - qDebug(); - - QualifiedMassSpectrum qualified_mass_spectrum = - qualifiedMassSpectrum(iter, get_data); - qDebug(); - handler.setQualifiedMassSpectrum(qualified_mass_spectrum); - qDebug(); - } - // End of - // for(std::size_t iter = 0; iter < spectrum_list_size; iter++) + msp_timsData.get()->rawReaderSpectrumCollectionByMsLevel( + getMsRunId(), handler, ms_level); // Now let the loading handler know that the loading of the data has ended. // The handler might need this "signal" to perform additional tasks or to @@ -159,7 +123,7 @@ std::size_t TimsMsRunReader::spectrumListSize() const { - return mpa_timsData->getTotalNumberOfScans(); + return msp_timsData->getTotalNumberOfScans(); } @@ -173,17 +137,60 @@ bool TimsMsRunReader::releaseDevice() { - delete mpa_timsData; - mpa_timsData = nullptr; + msp_timsData = nullptr; return true; } bool TimsMsRunReader::acquireDevice() { - if(mpa_timsData == nullptr) + if(msp_timsData == nullptr) { initialize(); } return true; } + + +XicCoordSPtr +TimsMsRunReader::newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index + [[maybe_unused]], + pappso::PrecisionPtr precision + [[maybe_unused]]) const +{ + throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__)); +} + +XicCoordSPtr +TimsMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum [[maybe_unused]], + pappso::PrecisionPtr precision [[maybe_unused]]) const +{ + throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__)); +} + +TimsDataSp +TimsMsRunReader::getTimsDataSPtr() +{ + acquireDevice(); + return msp_timsData; +} + + +Trace +TimsMsRunReader::getTicChromatogram() +{ + // Use the Sqlite database to fetch the total ion current chromatogram (TIC + // chromatogram). + + acquireDevice(); + + return msp_timsData->getTicChromatogram(); +} + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreader.h libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreader.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreader.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreader.h 2022-10-27 09:16:15.000000000 +0000 @@ -57,6 +57,19 @@ virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override; + virtual void + readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) override; + + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const override; + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const override; + + virtual std::size_t spectrumListSize() const override; virtual bool hasScanNumbers() const override; @@ -64,6 +77,13 @@ virtual bool releaseDevice() override; virtual bool acquireDevice() override; + + + /** @brief give an access to the underlying raw data pointer + */ + virtual TimsDataSp getTimsDataSPtr(); + + virtual Trace getTicChromatogram() override; protected: @@ -71,7 +91,7 @@ virtual bool accept(const QString &file_name) const override; private: - TimsData *mpa_timsData = nullptr; + TimsDataSp msp_timsData = nullptr; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,8 +29,9 @@ #include "timsmsrunreaderms2.h" #include "../../exception/exceptionnotimplemented.h" +#include "../../exception/exceptionnotfound.h" +#include "../../msrun/xiccoord/xiccoordtims.h" #include -#include using namespace pappso; @@ -52,6 +53,13 @@ pappso::TimsMsRunReaderMs2::initialize() { msp_timsData = std::make_shared(mcsp_msRunId.get()->getFileName()); + if(msp_timsData == nullptr) + { + throw PappsoException( + QObject::tr("ERROR in TimsMsRunReaderMs2::initialize " + "msp_timsData is null for MsRunId %1") + .arg(mcsp_msRunId.get()->toString())); + } } void @@ -134,17 +142,28 @@ { std::size_t precursor_index = (spectrum_index / 2) + 1; + TimsData::SpectrumDescr spectrum_descr; + try + { + spectrum_descr = + msp_timsData.get()->getSpectrumDescrWithPrecursorId(precursor_index); + } + catch(ExceptionNotFound &error) + { + throw ExceptionNotFound( + QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3") + .arg(spectrum_index) + .arg(getMsRunId().get()->getFileName()) + .arg(error.qwhat())); + } if(spectrum_index % 2 == 0) { - qDebug(); + qDebug() << "MS1 spectrum precursor_index=" << precursor_index; // this is an MS1 spectrum - QualifiedMassSpectrum mass_spectrum_ms1 = - msp_timsData->getQualifiedMs1MassSpectrumByPrecursorId( - spectrum_index, precursor_index, want_binary_data); - MassSpectrumId spectrum_id(mass_spectrum_ms1.getMassSpectrumId()); - spectrum_id.setMsRunId(getMsRunId()); - mass_spectrum_ms1.setMassSpectrumId(spectrum_id); + QualifiedMassSpectrum mass_spectrum_ms1; + msp_timsData->getQualifiedMs1MassSpectrumByPrecursorId( + getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data); qDebug(); // << mass_spectrum_ms1.toString(); // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString(); @@ -152,13 +171,23 @@ } else { - qDebug(); + qDebug() << "MS2 spectrum precursor_index=" << precursor_index; QualifiedMassSpectrum mass_spectrum_ms2; + if(spectrum_descr.ms2_index != spectrum_index) + { + qDebug(); + throw PappsoException( + QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != " + "spectrum_index(%5)") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__) + .arg(spectrum_descr.ms2_index) + .arg(spectrum_index)); + } + msp_timsData->getQualifiedMs2MassSpectrumByPrecursorId( - mass_spectrum_ms2, spectrum_index, precursor_index, want_binary_data); - MassSpectrumId spectrum_id(mass_spectrum_ms2.getMassSpectrumId()); - spectrum_id.setMsRunId(getMsRunId()); - mass_spectrum_ms2.setMassSpectrumId(spectrum_id); + getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data); qDebug(); // << mass_spectrum_ms2.toString(); // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString(); @@ -171,9 +200,14 @@ TimsMsRunReaderMs2::readSpectrumCollection( SpectrumCollectionHandlerInterface &handler) { - const bool want_binary_data = handler.needPeakList(); - // const bool want_binary_data = false; + readSpectrumCollectionByMsLevel(handler, 0); +} +void +TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel( + SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) +{ + qDebug() << " ms_level=" << ms_level; // We'll need it to perform the looping in the spectrum list. std::size_t spectrum_list_size = spectrumListSize(); @@ -183,103 +217,11 @@ // the user. handler.spectrumListHasSize(spectrum_list_size); - // Iterate in the full list of spectra. - bool readAhead = handler.isReadAhead(); - - if(readAhead) - { - - std::size_t process_list_size = 300; - - struct tmp_item - { - QualifiedMassSpectrum qualified_mass_spectrum; - std::size_t iter; - bool want_binary_data; - }; - for(std::size_t i = 0; i < spectrum_list_size; i += process_list_size) - { - qDebug(); - // If the user of this reader instance wants to stop reading the - // spectra, then break this loop. - if(handler.shouldStop()) - { - qDebug() << "The operation was cancelled. Breaking the loop."; - break; - } - std::vector item_list; - for(std::size_t iter = 0; - (iter < process_list_size) && ((iter + i) < spectrum_list_size); - iter++) - { - - bool get_data = want_binary_data; - if((iter + i) % 2 == 0) - { // MS1 - get_data = handler.needMsLevelPeakList(1); - } - else - { - get_data = handler.needMsLevelPeakList(2); - } - - item_list.push_back( - {QualifiedMassSpectrum(), iter + i, get_data}); - } - qDebug() << item_list.size(); - // Use QtConcurrentBlocking::mapped to apply the scale function to all - // the images in the list. - QtConcurrent::blockingMap( - item_list.begin(), item_list.end(), [this](tmp_item &one_item) { - qDebug() << one_item.iter; - one_item.qualified_mass_spectrum = - qualifiedMassSpectrum(one_item.iter, one_item.want_binary_data); - - // qDebug() << one_item.qualified_mass_spectrum.size() << " " << - // one_item.qualified_mass_spectrum.getMassSpectrumSPtr().get()->toString(); - }); - - qDebug() << item_list.size(); - for(auto &item : item_list) - { - // qDebug() << item.qualified_mass_spectrum.getMassSpectrumSPtr() - // .get() - // ->toString(); - handler.setQualifiedMassSpectrum(item.qualified_mass_spectrum); - qDebug(); - } - } - } - else - { - for(std::size_t iter = 0; iter < spectrum_list_size; iter++) - { - qDebug(); - // If the user of this reader instance wants to stop reading the - // spectra, then break this loop. - if(handler.shouldStop()) - { - qDebug() << "The operation was cancelled. Breaking the loop."; - break; - } - bool get_data = want_binary_data; - if(iter % 2 == 0) - { // MS1 - if(!handler.needMsLevelPeakList(1)) - { - get_data = false; - } - } - QualifiedMassSpectrum qualified_mass_spectrum = - qualifiedMassSpectrum(iter, get_data); - handler.setQualifiedMassSpectrum(qualified_mass_spectrum); - qDebug(); - } - } - // End of - // for(std::size_t iter = 0; iter < spectrum_list_size; iter++) + msp_timsData.get()->setMonoThread(isMonoThread()); + msp_timsData.get()->ms2ReaderSpectrumCollectionByMsLevel( + getMsRunId(), handler, ms_level); // Now let the loading handler know that the loading of the data has ended. // The handler might need this "signal" to perform additional tasks or to // cleanup cruft. @@ -338,3 +280,48 @@ acquireDevice(); return msp_timsData; } + + +XicCoordSPtr +TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const +{ + XicCoordTimsSPtr xic_coord = std::make_shared(); + std::size_t precursor_index = (spectrum_index / 2) + 1; + auto xic = this->msp_timsData.get()->getXicCoordTimsFromPrecursorId( + precursor_index, precision); + + xic_coord.get()->mzRange = xic.mzRange; + xic_coord.get()->rtTarget = xic.rtTarget; + xic_coord.get()->scanNumBegin = xic.scanNumBegin; + xic_coord.get()->scanNumEnd = xic.scanNumEnd; + + + return xic_coord; +} + +pappso::XicCoordSPtr +TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const +{ + return newXicCoordSPtrFromSpectrumIndex( + mass_spectrum.getMassSpectrumId().getSpectrumIndex(), precision); +} + +std::vector +pappso::TimsMsRunReaderMs2::getRetentionTimeLine() +{ + return msp_timsData.get()->getRetentionTimeLine(); +} + +Trace +TimsMsRunReaderMs2::getTicChromatogram() +{ + // Use the Sqlite database to fetch the total ion current chromatogram (TIC + // chromatogram). + + acquireDevice(); + + return msp_timsData->getTicChromatogram(); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2.h libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2.h 2022-10-27 09:16:15.000000000 +0000 @@ -59,6 +59,19 @@ virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override; + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const override; + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const override; + + + virtual void + readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) override; + virtual std::size_t spectrumListSize() const override; virtual bool hasScanNumbers() const override; @@ -85,6 +98,15 @@ */ virtual TimsDataSp getTimsDataSPtr(); + + /** @brief retention timeline + * get retention times along the MSrun in seconds + * @return vector of retention times (seconds) + */ + virtual std::vector getRetentionTimeLine() override; + + virtual Trace getTicChromatogram() override; + protected: virtual void initialize() override; virtual bool accept(const QString &file_name) const override; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -120,16 +120,16 @@ std::size_t precursor_index = (spectrum_index / 2) + 1; + TimsData::SpectrumDescr spectrum_descr = + mpa_timsData->getSpectrumDescrWithPrecursorId(precursor_index); + if(spectrum_index % 2 == 0) { qDebug(); // this is an MS1 spectrum - QualifiedMassSpectrum mass_spectrum_ms1 = - mpa_timsData->getQualifiedMs1MassSpectrumByPrecursorId( - spectrum_index, precursor_index, want_binary_data); - MassSpectrumId spectrum_id(mass_spectrum_ms1.getMassSpectrumId()); - spectrum_id.setMsRunId(getMsRunId()); - mass_spectrum_ms1.setMassSpectrumId(spectrum_id); + QualifiedMassSpectrum mass_spectrum_ms1; + mpa_timsData->getQualifiedMs1MassSpectrumByPrecursorId( + getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data); qDebug(); // << mass_spectrum_ms1.toString(); // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString(); @@ -139,11 +139,18 @@ { qDebug(); QualifiedMassSpectrum mass_spectrum_ms2; + if(spectrum_descr.ms2_index != spectrum_index) + { + qDebug(); + throw PappsoException( + QObject::tr( + "ERROR in %1 %2 %3 spectrum_descr.ms2_index != spectrum_index") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__)); + } mpa_timsData->getQualifiedMs2MassSpectrumByPrecursorId( - mass_spectrum_ms2, spectrum_index, precursor_index, want_binary_data); - MassSpectrumId spectrum_id(mass_spectrum_ms2.getMassSpectrumId()); - spectrum_id.setMsRunId(getMsRunId()); - mass_spectrum_ms2.setMassSpectrumId(spectrum_id); + getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data); qDebug(); // << mass_spectrum_ms2.toString(); // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString(); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoord.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoord.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoord.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoord.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,118 @@ +/** + * \file pappsomspp/msrun/xiccoord/xiccoord.cpp + * \date 22/04/2021 + * \author Olivier Langella + * \brief XIC coordinate in MSrun + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +#include "xiccoord.h" + +using namespace pappso; + +pappso::XicCoord::XicCoord() + : mzRange(pappso_double(1), PrecisionFactory::getPpmInstance(10.0)), + rtTarget(0) +{ +} + + +XicCoord::XicCoord(const XicCoord &other) + : mzRange(other.mzRange), rtTarget(other.rtTarget) +{ + xicSptr = other.xicSptr; +} + +XicCoord::~XicCoord() +{ +} + +pappso::XicCoordSPtr +pappso::XicCoord::initializeAndClone() const +{ + XicCoordSPtr xic_coord_sp = std::make_shared(*this); + + xic_coord_sp.get()->xicSptr = std::make_shared(); + + return xic_coord_sp; +} + + +pappso::XicCoordSPtr +pappso::XicCoord::addition(XicCoordSPtr &to_add) const +{ + XicCoordSPtr xic_coord_sp = std::make_shared(*this); + + // xic_coord_sp.get()->xicSptr = nullptr; + + xic_coord_sp.get()->rtTarget += to_add.get()->rtTarget; + + xic_coord_sp.get()->mzRange += to_add.get()->mzRange; + + return xic_coord_sp; +} + +XicCoordSPtr +XicCoord::multiplyBy(double number) const +{ + XicCoordSPtr xic_coord_sp = std::make_shared(*this); + + // xic_coord_sp.get()->xicSptr = nullptr; + + xic_coord_sp.get()->rtTarget *= number; + xic_coord_sp.get()->mzRange *= number; + + return xic_coord_sp; +} + +pappso::XicCoordSPtr +pappso::XicCoord::divideBy(double number) const +{ + XicCoordSPtr xic_coord_sp = std::make_shared(*this); + + // xic_coord_sp.get()->xicSptr = nullptr; + + xic_coord_sp.get()->rtTarget /= number; + xic_coord_sp.get()->mzRange *= (double)((double)1 / number); + + return xic_coord_sp; +} + + +void +pappso::XicCoord::reset() +{ + + xicSptr = nullptr; + + rtTarget = 0; + mzRange = MzRange(0.0, 0.0); +} + +QString +pappso::XicCoord::toString() const +{ + return QString("mz=%1 rt=%2").arg(mzRange.toString()).arg(rtTarget); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoord.h libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoord.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoord.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoord.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,115 @@ +/** + * \file pappsomspp/msrun/xiccoord/xiccoord.h + * \date 22/04/2021 + * \author Olivier Langella + * \brief XIC coordinate in MSrun + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "../../exportinmportconfig.h" +#include "../../mzrange.h" +#include "../../xic/xic.h" +#include + +namespace pappso +{ + + +struct XicCoord; + +typedef std::shared_ptr XicCoordSPtr; + +/** @brief coordinates of the XIC to extract and the resulting XIC after + * extraction + * + * to extract a XIC, we need basically the mass to extract it + * this structure is meant to extact a XIC quickly and not to maintain + * information about it : no peptide, no scan number, no retention time... + * + */ +struct PMSPP_LIB_DECL XicCoord +{ + /** + * Default constructor + */ + XicCoord(); + + /** + * Copy constructor + * + * @param other TODO + */ + XicCoord(const XicCoord &other); + + /** + * Destructor + */ + virtual ~XicCoord(); + + + /** @brief intialize the XIC and make a deep copy of object + */ + virtual XicCoordSPtr initializeAndClone() const; + + /** @brief compute a new XIC coord as the sum of the given one + */ + virtual XicCoordSPtr addition(XicCoordSPtr &to_add) const; + + + /** @brief compute a new xic coord as a product by + */ + virtual XicCoordSPtr multiplyBy(double number) const; + + + /** @brief compute a new xic coord as a division by + */ + virtual XicCoordSPtr divideBy(double number) const; + + + /** @brief reset to zero + */ + virtual void reset(); + + /** @brief get a description of the XIC coordinate in a string + */ + virtual QString toString() const; + + + /** @brief the mass to extract + * */ + MzRange mzRange; + + /** @brief the targeted retention time to extract around + * intended in seconds, and related to one msrun. This is not a reference, + * just to save memory and cpu usage when extracting xic + */ + double rtTarget = 0; + + /** @brief extracted xic + */ + XicSPtr xicSptr = nullptr; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoordtims.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoordtims.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoordtims.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoordtims.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,150 @@ +/** + * \file pappsomspp/msrun/xiccoord/xiccoordtims.cpp + * \date 22/04/2021 + * \author Olivier Langella + * \brief XIC coordinate in a Tims MSrun + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +#include "xiccoordtims.h" +#include "../../exception/exceptionnotpossible.h" + + +namespace pappso +{ + +XicCoordTims::XicCoordTims(const XicCoordTims &other) : XicCoord(other) +{ + scanNumBegin = other.scanNumBegin; + scanNumEnd = other.scanNumEnd; +} + + +XicCoordTims::~XicCoordTims() +{ +} + + +XicCoordSPtr +XicCoordTims::initializeAndClone() const +{ + + XicCoordTimsSPtr xic_coord_sp = std::make_shared(*this); + + xic_coord_sp.get()->xicSptr = std::make_shared(); + + return xic_coord_sp; +} + + +XicCoordSPtr +XicCoordTims::addition(XicCoordSPtr &to_add) const +{ + XicCoordTimsSPtr xic_coord_sp = std::make_shared(*this); + + XicCoordTims *toadd = dynamic_cast(to_add.get()); + + if(toadd == nullptr) + { + throw ExceptionNotPossible( + QObject::tr("XicCoord to add is of a different type")); + } + + // xic_coord_sp.get()->xicSptr = xic_coord_sp.get()->xicSptr; + + xic_coord_sp.get()->mzRange += to_add.get()->mzRange; + xic_coord_sp.get()->rtTarget += to_add.get()->rtTarget; + xic_coord_sp.get()->scanNumBegin += toadd->scanNumBegin; + xic_coord_sp.get()->scanNumEnd += toadd->scanNumEnd; + + qDebug() << "xic_coord_sp.get()->scanNumBegin=" + << xic_coord_sp.get()->scanNumBegin; + qDebug() << "xic_coord_sp.get()->scanNumEnd=" + << xic_coord_sp.get()->scanNumEnd; + return xic_coord_sp; +} + + +XicCoordSPtr +XicCoordTims::multiplyBy(double number) const +{ + XicCoordTimsSPtr xic_coord_sp = std::make_shared(*this); + + // xic_coord_sp.get()->xicSptr = nullptr; + + xic_coord_sp.get()->rtTarget *= number; + xic_coord_sp.get()->mzRange *= number; + + xic_coord_sp.get()->scanNumBegin *= number; + xic_coord_sp.get()->scanNumEnd *= number; + + return xic_coord_sp; +} + +XicCoordSPtr +XicCoordTims::divideBy(double number) const +{ + + XicCoordTimsSPtr xic_coord_sp = std::make_shared(*this); + + // xic_coord_sp.get()->xicSptr = nullptr; + + xic_coord_sp.get()->rtTarget /= number; + xic_coord_sp.get()->mzRange *= (double)((double)1 / number); + + xic_coord_sp.get()->scanNumBegin /= number; + xic_coord_sp.get()->scanNumEnd /= number; + + qDebug() << "xic_coord_sp.get()->scanNumBegin=" + << xic_coord_sp.get()->scanNumBegin; + qDebug() << "xic_coord_sp.get()->scanNumEnd=" + << xic_coord_sp.get()->scanNumEnd; + return xic_coord_sp; +} + + +void +XicCoordTims::reset() +{ + + xicSptr = nullptr; + + rtTarget = 0; + mzRange = MzRange(0.0, 0.0); + scanNumBegin = 0; + scanNumEnd = 0; +} + +QString +XicCoordTims::toString() const +{ + return QString("%1 begin=%2 end=%3") + .arg(XicCoord::toString()) + .arg(scanNumBegin) + .arg(scanNumEnd); +} + +} // namespace pappso + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoordtims.h libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoordtims.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xiccoord/xiccoordtims.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xiccoord/xiccoordtims.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,94 @@ +/** + * \file pappsomspp/msrun/xiccoord/xiccoordtims.h + * \date 22/04/2021 + * \author Olivier Langella + * \brief XIC coordinate in a Tims MSrun + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "xiccoord.h" + +namespace pappso +{ + + +struct XicCoordTims; + +typedef std::shared_ptr XicCoordTimsSPtr; + +/** @brief coordinates of the XIC to extract and the resulting XIC after + * extraction + * + * to extract a XIC, we need basically the mass to extract it + * this structure is meant to extact a XIC quickly and not to maintain + * information about it : no peptide, no scan number, no retention time... + * + */ +struct PMSPP_LIB_DECL XicCoordTims : XicCoord +{ + /** + * Default constructor + */ + XicCoordTims() : XicCoord(){}; + + /** + * Copy constructor + * + * @param other TODO + */ + XicCoordTims(const XicCoordTims &other); + + /** + * Destructor + */ + virtual ~XicCoordTims(); + + + /** @brief intialize the XIC and make a deep copy of object + */ + virtual XicCoordSPtr initializeAndClone() const override; + + + virtual XicCoordSPtr addition(XicCoordSPtr &to_add) const override; + + virtual XicCoordSPtr multiplyBy(double number) const override; + virtual XicCoordSPtr divideBy(double number) const override; + + virtual void reset() override; + + virtual QString toString() const override; + + + /** @brief mobility index begin + */ + std::size_t scanNumBegin; + + /** @brief mobility index end + */ + std::size_t scanNumEnd; +}; + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xymsrunreader.cpp libpappsomspp-0.8.58/src/pappsomspp/msrun/xymsrunreader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xymsrunreader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xymsrunreader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -17,6 +17,7 @@ #include "../pappsoexception.h" #include "../exception/exceptionnotfound.h" #include "../exception/exceptionnotpossible.h" +#include "../exception/exceptionnotimplemented.h" namespace pappso @@ -263,6 +264,34 @@ } +void +XyMsRunReader::readSpectrumCollectionByMsLevel( + SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) +{ + // qDebug(); + + // In reality there is only one mass spectrum in the file. + + MassSpectrumId massSpectrumId(mcsp_msRunId, 0 /* spectrum index*/); + + QualifiedMassSpectrum qualified_mass_spectrum = + qualifiedMassSpectrumFromXyMSDataFile(massSpectrumId); + + // qDebug() << "qualified mass spectrum has size:" + //<< qualified_mass_spectrum.getMassSpectrumSPtr()->size(); + + // The handler will receive the index of the mass spectrum in the + // current run via the mass spectrum id member datum. + + if(qualified_mass_spectrum.getMsLevel() == ms_level) + { + handler.setQualifiedMassSpectrum(qualified_mass_spectrum); + } + + // qDebug() << "Loading ended"; + handler.loadingEnded(); +} + std::size_t XyMsRunReader::spectrumListSize() const { @@ -281,5 +310,27 @@ return true; } +XicCoordSPtr +XyMsRunReader::newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index + [[maybe_unused]], + pappso::PrecisionPtr precision + [[maybe_unused]]) const +{ + throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__)); +} + +XicCoordSPtr +XyMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum [[maybe_unused]], + pappso::PrecisionPtr precision [[maybe_unused]]) const +{ + throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(__LINE__)); +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/msrun/xymsrunreader.h libpappsomspp-0.8.58/src/pappsomspp/msrun/xymsrunreader.h --- libpappsomspp-0.8.15/src/pappsomspp/msrun/xymsrunreader.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/msrun/xymsrunreader.h 2022-10-27 09:16:15.000000000 +0000 @@ -27,6 +27,18 @@ virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override; + virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex( + std::size_t spectrum_index, pappso::PrecisionPtr precision) const override; + + virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum( + const pappso::QualifiedMassSpectrum &mass_spectrum, + pappso::PrecisionPtr precision) const override; + + virtual void + readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) override; + + virtual std::size_t spectrumListSize() const override; virtual bool releaseDevice() override; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/mzrange.cpp libpappsomspp-0.8.58/src/pappsomspp/mzrange.cpp --- libpappsomspp-0.8.15/src/pappsomspp/mzrange.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/mzrange.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -73,7 +73,7 @@ MzRange::MzRange(const MzRange &other) : m_mz(other.m_mz), m_delta(other.m_delta) { - // std::cout << "MzRange::MzRange (const MzRange & other)" << endl; + // std::cout << "MzRange::MzRange (const MzRange & other)" << std::endl; } @@ -92,6 +92,24 @@ } +MzRange & +MzRange::operator+=(const MzRange &other) +{ + m_mz += other.m_mz; + m_delta += other.m_delta; + + return *this; +} + +MzRange & +MzRange::operator*=(double number) +{ + m_mz *= number; + m_delta *= number; + + return *this; +} + pappso_double MzRange::getMz() const { diff -Nru libpappsomspp-0.8.15/src/pappsomspp/mzrange.h libpappsomspp-0.8.58/src/pappsomspp/mzrange.h --- libpappsomspp-0.8.15/src/pappsomspp/mzrange.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/mzrange.h 2022-10-27 09:16:15.000000000 +0000 @@ -44,9 +44,6 @@ class PMSPP_LIB_DECL MzRange { - private: - pappso_double m_mz; - pappso_double m_delta; public: MzRange(pappso_double mz, PrecisionPtr precision); @@ -62,6 +59,8 @@ virtual ~MzRange(); MzRange &operator=(const MzRange &other); + MzRange &operator+=(const MzRange &other); + MzRange &operator*=(double number); pappso_double getMz() const; @@ -79,6 +78,11 @@ { return (m_mz + m_delta); }; + + + private: + pappso_double m_mz; + pappso_double m_delta; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodsink.h libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodsink.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodsink.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodsink.h 2022-10-27 09:16:15.000000000 +0000 @@ -26,12 +26,12 @@ #include + #include "obopsimod.h" namespace pappso { - class PMSPP_LIB_DECL FilterOboPsiModSink : public OboPsiModHandlerInterface { private: diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermaccession.h libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermaccession.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermaccession.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermaccession.h 2022-10-27 09:16:15.000000000 +0000 @@ -23,7 +23,10 @@ #pragma once -#include "obopsimod.h" + + +#include "obopsimodhandlerinterface.h" +#include "obopsimodterm.h" namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermdiffmono.h libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermdiffmono.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermdiffmono.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermdiffmono.h 2022-10-27 09:16:15.000000000 +0000 @@ -25,7 +25,10 @@ #pragma once -#include "obopsimod.h" + +#include "obopsimodhandlerinterface.h" +#include "obopsimodterm.h" + #include "../mzrange.h" namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermlabel.cpp libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermlabel.cpp --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermlabel.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermlabel.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -33,7 +33,7 @@ : m_sink(sink) { m_labelMatch.setPattern(QString(label_search).replace("*", "(.*)")); - m_labelMatch.setCaseSensitivity(Qt::CaseInsensitive); + m_labelMatch.setPatternOptions(QRegularExpression::CaseInsensitiveOption); } FilterOboPsiModTermLabel::~FilterOboPsiModTermLabel() @@ -50,11 +50,11 @@ FilterOboPsiModTermLabel::setOboPsiModTerm(const OboPsiModTerm &term) { // qDebug() << term._psi_mod_label << " " << term._psi_ms_label; - if(m_labelMatch.exactMatch(term.m_psiModLabel)) + if(m_labelMatch.match(term.m_psiModLabel).hasMatch()) { m_sink.setOboPsiModTerm(term); } - else if(m_labelMatch.exactMatch(term.m_psiMsLabel)) + else if(m_labelMatch.match(term.m_psiMsLabel).hasMatch()) { m_sink.setOboPsiModTerm(term); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermlabel.h libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermlabel.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermlabel.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermlabel.h 2022-10-27 09:16:15.000000000 +0000 @@ -32,7 +32,7 @@ class PMSPP_LIB_DECL FilterOboPsiModTermLabel : public OboPsiModHandlerInterface { private: - QRegExp m_labelMatch; + QRegularExpression m_labelMatch; OboPsiModHandlerInterface &m_sink; public: diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermname.cpp libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermname.cpp --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermname.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermname.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -30,7 +30,7 @@ : m_sink(sink) { m_nameMatch.setPattern(QString(name_search).replace("*", "(.*)")); - m_nameMatch.setCaseSensitivity(Qt::CaseInsensitive); + m_nameMatch.setPatternOptions(QRegularExpression::CaseInsensitiveOption); } FilterOboPsiModTermName::~FilterOboPsiModTermName() @@ -42,7 +42,7 @@ FilterOboPsiModTermName::setOboPsiModTerm(const OboPsiModTerm &term) { // qDebug() << term._psi_mod_label << " " << term._psi_ms_label; - if(m_nameMatch.indexIn(term.m_name) >= 0) + if(m_nameMatch.match(term.m_name).hasMatch()) { m_sink.setOboPsiModTerm(term); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermname.h libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermname.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/filterobopsimodtermname.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/filterobopsimodtermname.h 2022-10-27 09:16:15.000000000 +0000 @@ -24,13 +24,15 @@ #pragma once -#include "obopsimod.h" +#include "obopsimodhandlerinterface.h" +#include "obopsimodterm.h" + namespace pappso { class PMSPP_LIB_DECL FilterOboPsiModTermName : public OboPsiModHandlerInterface { private: - QRegExp m_nameMatch; + QRegularExpression m_nameMatch; OboPsiModHandlerInterface &m_sink; public: diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimod.cpp libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimod.cpp --- libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimod.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimod.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -38,97 +38,9 @@ namespace pappso { - -QRegExp OboPsiModTerm::m_firstParse("^([a-z,A-Z]+):\\s(.*)$"); -QRegExp OboPsiModTerm::m_findExactPsiModLabel( - "^(.*)\\sEXACT\\sPSI-MOD-label\\s\\[\\]$"); - -// synonym: "Carbamidomethyl" RELATED PSI-MS-label [] -QRegExp OboPsiModTerm::m_findRelatedPsiMsLabel( - "^(.*)\\sRELATED\\sPSI-MS-label\\s\\[\\]$"); - -void -OboPsiModTerm::parseLine(const QString &line) -{ - // qDebug() << "OboPsiModTerm::parseLine begin " << line; - // id: MOD:00007 - if(m_firstParse.exactMatch(line)) - { - QStringList pline = m_firstParse.capturedTexts(); - // qDebug() << "OboPsiModTerm::parseLine match " << pline[0] << pline[1]; - if(pline[1] == "id") - { - m_accession = pline[2].trimmed(); - // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession; - } - else if(pline[1] == "name") - { - m_name = pline[2].trimmed(); - // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession; - } - else if(pline[1] == "xref") - { - // xref: DiffMono: "1.007276" - if(m_firstParse.exactMatch(pline[2])) - { - QStringList psecond = m_firstParse.capturedTexts(); - if(psecond[1] == "DiffMono") - { - m_diffMono = psecond[2].replace("\"", "").toDouble(); - // qDebug() << "OboPsiModTerm::parseLine m_diffMono = " << - // m_diffMono; - } - else if(psecond[1] == "DiffFormula") - { - m_diffFormula = psecond[2].trimmed().replace("\"", ""); - // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" << - // m_diffFormula<<"|"; - } - else if(psecond[1] == "Origin") - { - m_origin = - psecond[2].trimmed().replace("\"", "").replace(",", ""); - // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" << - // m_diffFormula<<"|"; - } - } - } - else if(pline[1] == "synonym") - { - // synonym: "Se(S)Res" EXACT PSI-MOD-label [] - if(m_findExactPsiModLabel.exactMatch(pline[2])) - { - m_psiModLabel = - m_findExactPsiModLabel.capturedTexts()[1].trimmed().replace( - "\"", ""); - // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" << - // m_psiModLabel<<"|"; - } - else if(m_findRelatedPsiMsLabel.exactMatch(pline[2])) - { - m_psiMsLabel = - m_findRelatedPsiMsLabel.capturedTexts()[1].trimmed().replace( - "\"", ""); - // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" << - // m_psiModLabel<<"|"; - } - } - } -} -void -OboPsiModTerm::clearTerm() -{ - m_accession = ""; - m_name = ""; - m_psiModLabel = ""; - m_diffFormula = ""; - m_diffMono = 0; - m_origin = ""; -} - OboPsiMod::OboPsiMod(OboPsiModHandlerInterface &handler) : m_handler(handler) { - qDebug() << "OboPsiMod::OboPsiMod"; + qDebug(); initMyResource(); parse(); } @@ -141,7 +53,7 @@ void OboPsiMod::parse() { - // std::cout << "OboPsiMod::parse Begin parsing OBO file" << endl; + // std::cout << "OboPsiMod::parse Begin parsing OBO file" << std::endl; qDebug() << "OboPsiMod::parse Begin parsing OBO file"; QFile obofile(":/resources/PSI-MOD.obo"); if(!obofile.exists()) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimod.h libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimod.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimod.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimod.h 2022-10-27 09:16:15.000000000 +0000 @@ -23,60 +23,27 @@ #pragma once -#include +#include #include "../types.h" #include "../exportinmportconfig.h" +#include "obopsimodterm.h" +#include "obopsimodhandlerinterface.h" namespace pappso { - -class OboPsiMod; - -class PMSPP_LIB_DECL OboPsiModTerm -{ - friend OboPsiMod; - - private: - void parseLine(const QString &line); - void clearTerm(); - - static QRegExp m_firstParse; - static QRegExp m_findExactPsiModLabel; - static QRegExp m_findRelatedPsiMsLabel; - - public: - QString m_accession; - QString m_name; - QString m_psiModLabel; - QString m_psiMsLabel; - QString m_diffFormula; - QString m_origin; - - pappso_double m_diffMono; - - bool - isValid() const - { - return (!m_accession.isEmpty()); - }; -}; - -class OboPsiModHandlerInterface +class PMSPP_LIB_DECL OboPsiMod { public: - virtual void setOboPsiModTerm(const OboPsiModTerm &term) = 0; -}; + OboPsiMod(OboPsiModHandlerInterface &handler); + ~OboPsiMod(); -class PMSPP_LIB_DECL OboPsiMod -{ private: OboPsiModTerm m_term; OboPsiModHandlerInterface &m_handler; + /** @brief starts reading obo file and reports each term with the callback + * function + */ void parse(); - - public: - OboPsiMod(OboPsiModHandlerInterface &handler); - ~OboPsiMod(); }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodhandlerinterface.h libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodhandlerinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodhandlerinterface.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodhandlerinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,38 @@ +/******************************************************************************* + * Copyright (c) 2015 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + * Contributors: + * Olivier Langella - initial API and + *implementation + ******************************************************************************/ + +#pragma once +#include "obopsimodterm.h" + +namespace pappso +{ + +class OboPsiModHandlerInterface +{ + public: + /** @brief triggered function on each obo term when parsing obo file + */ + virtual void setOboPsiModTerm(const OboPsiModTerm &term) = 0; +}; + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodterm.cpp libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodterm.cpp --- libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodterm.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodterm.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,149 @@ + +/******************************************************************************* + * Copyright (c) 2015 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + * Contributors: + * Olivier Langella - initial API and + *implementation + ******************************************************************************/ + +#include +#include "obopsimodterm.h" +#include "../pappsoexception.h" + +int oboPsiModTermMetaTypeId = + qRegisterMetaType("pappso::OboPsiModTerm"); + +inline void +initMyResource() +{ + Q_INIT_RESOURCE(libpappsomsppresources); +} + + +namespace pappso +{ + +QRegularExpression OboPsiModTerm::m_firstParse("^([a-z,A-Z]+):\\s(.*)$"); +QRegularExpression OboPsiModTerm::m_findExactPsiModLabel( + "^(.*)\\sEXACT\\sPSI-MOD-label\\s\\[\\]$"); + +// synonym: "Carbamidomethyl" RELATED PSI-MS-label [] +QRegularExpression OboPsiModTerm::m_findRelatedPsiMsLabel( + "^(.*)\\sRELATED\\sPSI-MS-label\\s\\[\\]$"); + +bool +OboPsiModTerm::isValid() const +{ + return (!m_accession.isEmpty()); +} + +void +OboPsiModTerm::parseLine(const QString &line) +{ + // qDebug() << "OboPsiModTerm::parseLine begin " << line; + // id: MOD:00007 + QRegularExpressionMatch match_line = m_firstParse.match(line); + if(match_line.hasMatch()) + { + QStringList pline = match_line.capturedTexts(); + // qDebug() << "OboPsiModTerm::parseLine match " << pline[0] << pline[1]; + if(pline[1] == "id") + { + m_accession = pline[2].trimmed(); + // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession; + } + else if(pline[1] == "name") + { + m_name = pline[2].trimmed(); + // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession; + } + else if(pline[1] == "xref") + { + // xref: DiffMono: "1.007276" + QRegularExpressionMatch match_subline = m_firstParse.match(pline[2]); + if(match_subline.hasMatch()) + { + QStringList psecond = match_subline.capturedTexts(); + if(psecond[1] == "DiffMono") + { + m_diffMono = psecond[2].replace("\"", "").toDouble(); + // qDebug() << "OboPsiModTerm::parseLine m_diffMono = " << + // m_diffMono; + } + else if(psecond[1] == "DiffFormula") + { + m_diffFormula = psecond[2].trimmed().replace("\"", ""); + // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" << + // m_diffFormula<<"|"; + } + else if(psecond[1] == "Origin") + { + m_origin = + psecond[2].trimmed().replace("\"", "").replace(",", ""); + // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" << + // m_diffFormula<<"|"; + } + } + } + else if(pline[1] == "synonym") + { + // synonym: "Se(S)Res" EXACT PSI-MOD-label [] + QRegularExpressionMatch match_exact_psimod = + m_findExactPsiModLabel.match(pline[2]); + if(match_exact_psimod.hasMatch()) + { + m_psiModLabel = + match_exact_psimod.captured(1).trimmed().replace("\"", ""); + // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" << + // m_psiModLabel<<"|"; + } + else + { + QRegularExpressionMatch match_related_psims = + m_findRelatedPsiMsLabel.match(pline[2]); + if(match_related_psims.hasMatch()) + { + m_psiMsLabel = + match_related_psims.captured(1).trimmed().replace("\"", ""); + // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" << + // m_psiModLabel<<"|"; + } + } + } + else if(pline[1] == "def") + { + // def: "A protein modification that modifies an L-asparagine + // residue." [PubMed:18688235] + m_definition = pline[2]; + } + } +} +void +OboPsiModTerm::clearTerm() +{ + m_accession = ""; + m_name = ""; + m_definition = ""; + m_psiModLabel = ""; + m_diffFormula = ""; + m_diffMono = 0; + m_origin = ""; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodterm.h libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodterm.h --- libpappsomspp-0.8.15/src/pappsomspp/obo/obopsimodterm.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/obo/obopsimodterm.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,67 @@ +/******************************************************************************* + * Copyright (c) 2015 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include "../exportinmportconfig.h" + +namespace pappso +{ + +class OboPsiMod; + +class PMSPP_LIB_DECL OboPsiModTerm +{ + friend OboPsiMod; + + public: + OboPsiModTerm() = default; + ~OboPsiModTerm() = default; + OboPsiModTerm(const OboPsiModTerm &) = default; + OboPsiModTerm &operator=(const OboPsiModTerm &) = default; + + bool isValid() const; + + public: + QString m_accession; + QString m_name; + QString m_definition; + QString m_psiModLabel; + QString m_psiMsLabel; + QString m_diffFormula; + QString m_origin; + + double m_diffMono; + + private: + void parseLine(const QString &line); + void clearTerm(); + + static QRegularExpression m_firstParse; + static QRegularExpression m_findExactPsiModLabel; + static QRegularExpression m_findRelatedPsiMsLabel; +}; + +} // namespace pappso + + + +extern int oboPsiModTermMetaTypeId; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptide.cpp libpappsomspp-0.8.58/src/pappsomspp/peptide/peptide.cpp --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptide.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptide.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -39,6 +39,22 @@ namespace pappso { +bool +peptideIonTypeIsComplement(PeptideIon ion_type_ref, PeptideIon ion_type) +{ + if(peptideIonIsNter(ion_type)) + std::swap(ion_type_ref, ion_type); + if(peptideIonIsNter(ion_type)) + return false; + if((ion_type_ref == PeptideIon::b) && (ion_type == PeptideIon::y)) + return true; + if((ion_type_ref == PeptideIon::ao) && (ion_type == PeptideIon::yo)) + return true; + if((ion_type_ref == PeptideIon::bstar) && (ion_type == PeptideIon::ystar)) + return true; + + return false; +} bool peptideIonIsNter(PeptideIon ion_type) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptide.h libpappsomspp-0.8.58/src/pappsomspp/peptide/peptide.h --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptide.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptide.h 2022-10-27 09:16:15.000000000 +0000 @@ -52,14 +52,21 @@ /** \brief tells if an ion is Nter * \param ion_type the ion to test */ -bool peptideIonIsNter(PeptideIon ion_type); +PMSPP_LIB_DECL bool peptideIonIsNter(PeptideIon ion_type); + +/** \brief tells if an ion type is the complement ion of the other + * \param ion_type_ref the ion type reference + * \param ion_type the ion to test + */ +PMSPP_LIB_DECL bool peptideIonTypeIsComplement(PeptideIon ion_type_ref, + PeptideIon ion_type); /** \brief get the direction of a peptide ion * \param ion_type the ion to test * \return the peptide direction */ -PeptideDirection getPeptideIonDirection(PeptideIon ion_type); +PMSPP_LIB_DECL PeptideDirection getPeptideIonDirection(PeptideIon ion_type); enum class PeptideIonNter { diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidefragmention.cpp libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidefragmention.cpp --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidefragmention.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidefragmention.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -105,12 +105,43 @@ return pappso::getPeptideIonDirection(ion_type); } + +const QString +PeptideFragmentIon::getCompletePeptideIonName(unsigned int charge) const +{ + + std::size_t size = msp_fragment.get()->size(); + QString plusstr = "+"; + plusstr = plusstr.repeated(charge); + if(m_ionType == PeptideIon::yp) + { + return QString("y%1(-P%2)%3") + .arg(size) + .arg(m_neutralPhosphoLossNumber) + .arg(plusstr); + } + else if(m_ionType == PeptideIon::bp) + { + return QString("b%1(-P%2)%3") + .arg(size) + .arg(m_neutralPhosphoLossNumber) + .arg(plusstr); + } + + return QString("%1%2%3") + .arg(getPeptideIonName(m_ionType)) + .arg(size) + .arg(plusstr); +} + const QString PeptideFragmentIon::getPeptideIonName() const { if((m_ionType == PeptideIon::yp) || (m_ionType == PeptideIon::bp)) { - return getPeptideIonName(m_ionType) + m_neutralPhosphoLossNumber; + return QString("%1(%2)") + .arg(getPeptideIonName(m_ionType)) + .arg(m_neutralPhosphoLossNumber); } return getPeptideIonName(m_ionType); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidefragmention.h libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidefragmention.h --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidefragmention.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidefragmention.h 2022-10-27 09:16:15.000000000 +0000 @@ -73,8 +73,14 @@ const QString getPeptideIonName() const; + /** @brief get a complete ion name string + * @param charge + * */ + const QString getCompletePeptideIonName(unsigned int charge) const; + static PeptideDirection getPeptideIonDirection(PeptideIon ion_type); static const QString getPeptideIonName(PeptideIon ion_type); + static const QColor getPeptideIonColor(PeptideIon ion_type); PeptideIon getPeptideIonType() const; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotope.h libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotope.h --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotope.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotope.h 2022-10-27 09:16:15.000000000 +0000 @@ -48,7 +48,7 @@ PeptideNaturalIsotope(const PeptideInterfaceSp &peptide, const std::map &map_isotope); PeptideNaturalIsotope(const PeptideNaturalIsotope &other); - ~PeptideNaturalIsotope(); + virtual ~PeptideNaturalIsotope(); virtual unsigned int size() const override; virtual const QString getSequence() const override; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,6 +29,28 @@ namespace pappso { + + +PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage( + const PeptideInterfaceSp &peptide, + unsigned int isotopeNumber, + unsigned int charge, + PrecisionPtr precision) + : mcsp_peptideSp(peptide), + m_isotopeLevel(isotopeNumber), + m_isotopeRank(1), + m_z(charge), + mp_precision(precision) +{ + + m_peptideNaturalIsotopeSpList.clear(); + + double diffC13 = ((double)isotopeNumber * DIFFC12C13) / (double)charge; + + m_averageMz = peptide.get()->getMz(charge) + diffC13; + m_abundanceRatio = 0; +} + PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage( const PeptideInterfaceSp &peptide, unsigned int askedIsotopeRank, @@ -161,6 +183,7 @@ : mcsp_peptideSp(other.mcsp_peptideSp), mp_precision(other.mp_precision) { + qDebug(); m_peptideNaturalIsotopeSpList = other.m_peptideNaturalIsotopeSpList; m_averageMz = other.m_averageMz; @@ -168,6 +191,7 @@ m_isotopeLevel = other.m_isotopeLevel; m_isotopeRank = other.m_isotopeRank; m_z = other.m_z; + qDebug(); } PeptideNaturalIsotopeAverage::~PeptideNaturalIsotopeAverage() @@ -237,4 +261,14 @@ return (m_peptideNaturalIsotopeSpList.size() == 0); } +QString +PeptideNaturalIsotopeAverage::toString() const +{ + return QString("%1 l%2 mz%3 z%4 N%5") + .arg(getPeptideInterfaceSp().get()->getSequence()) + .arg(getPeptideInterfaceSp().get()->size()) + .arg(getMz()) + .arg(getCharge()) + .arg(getIsotopeNumber()); +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h 2022-10-27 09:16:15.000000000 +0000 @@ -42,6 +42,14 @@ class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage { public: + /** @brief fast constructor + * simple isotope build, not computing isotope ratio + */ + PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide, + unsigned int isotopeNumber, + unsigned int charge, + PrecisionPtr precision); + PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide, unsigned int askedIsotopeRank, unsigned int isotopeLevel, @@ -54,7 +62,7 @@ PrecisionPtr precision); PeptideNaturalIsotopeAverage(const PeptideNaturalIsotopeAverage &other); - ~PeptideNaturalIsotopeAverage(); + virtual ~PeptideNaturalIsotopeAverage(); PeptideNaturalIsotopeAverageSp makePeptideNaturalIsotopeAverageSp() const; pappso_double getMz() const; @@ -67,6 +75,7 @@ PrecisionPtr getPrecision() const; virtual bool matchPeak(pappso_double peak_mz) const final; bool isEmpty() const; + virtual QString toString() const; private: void recursiveDepletion(std::vector &v_isotope_list, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidestrparser.cpp libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidestrparser.cpp --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidestrparser.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidestrparser.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -1,4 +1,3 @@ - /******************************************************************************* * Copyright (c) 2015 Olivier Langella . * @@ -31,9 +30,9 @@ { -QRegExp PeptideStrParser::_mod_parser("\\([^)]*\\)"); -QRegExp PeptideStrParser::_rx_psimod("MOD:[0-9]+"); -QRegExp PeptideStrParser::_rx_modmass("[-+]?[0-9]*\\.?[0-9]*"); +QRegularExpression PeptideStrParser::_mod_parser("\\([^)]*\\)"); +QRegularExpression PeptideStrParser::_rx_psimod("MOD:[0-9]+"); +QRegularExpression PeptideStrParser::_rx_modmass("[-+]?[0-9]+\\.?[0-9]*"); void PeptideStrParser::parseStringToPeptide(const QString &pepstr, Peptide &peptide) @@ -41,25 +40,31 @@ // Peptide // peptide2("C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK"); // CCAADDKEACFAVEGPK - QRegExp mod_parser(_mod_parser); - QRegExp rx_psimod(_rx_psimod); - QRegExp rx_modmass(_rx_modmass); /* */ - int pos = 0; int matched_length_cumul = 0; - while((pos = mod_parser.indexIn(pepstr, pos)) != -1) + int pos = 0; + + QRegularExpressionMatch match_mod = _mod_parser.match(pepstr, pos); + + while(match_mod.hasMatch()) { - QStringList mod_list = pepstr.mid(pos + 1, mod_parser.matchedLength() - 2) - .split(QRegExp("[+,\\,]")); + pos = match_mod.capturedStart(0); + QString captured = match_mod.captured(0); + qDebug() << " captured=" << captured << " pos=" << pos + << " match_mod.lastCapturedIndex()=" + << match_mod.lastCapturedIndex(); + QStringList mod_list = captured.mid(1, captured.size() - 2) + .split(QRegularExpression("[+,\\,]")); for(QString &mod : mod_list) { qDebug() << "PeptideStrParser::parseString mod " << mod; - if(rx_psimod.exactMatch(mod)) + QRegularExpressionMatch match_psimod = _rx_psimod.match(mod); + if(match_psimod.hasMatch()) { qDebug() << "PeptideStrParser::parseString pos-1 " << (pos - 1 - matched_length_cumul); @@ -76,41 +81,53 @@ peptide.setInternalCterModification( AaModification::getInstance(mod)); } - else if(rx_modmass.exactMatch(mod)) + else { - // number - if(!mod.contains(".")) + qDebug() << "mod=" << mod; + QRegularExpressionMatch match_modmass = _rx_modmass.match(mod); + if(match_modmass.hasMatch()) { - // integer - mod = "MOD:0000" + mod; - while(mod.size() > 9) + // number + qDebug() << "number mod=" << mod + << " cap=" << match_modmass.captured(0); + if(!mod.contains(".")) + { + // integer + qDebug() << "integer mod=" << mod; + mod = "MOD:0000" + mod; + while(mod.size() > 9) + { + mod = mod.replace(4, 1, ""); + } + peptide.addAaModification( + AaModification::getInstance(mod), + pos - 1 - matched_length_cumul); + } + else { - mod = mod.replace(4, 1, ""); + qDebug() << "double mod=" << mod; + peptide.addAaModification( + AaModification::getInstanceCustomizedMod( + mod.toDouble()), + pos - 1 - matched_length_cumul); } - peptide.addAaModification(AaModification::getInstance(mod), - pos - 1 - matched_length_cumul); } else { + qDebug() << "not a number mod=" << mod; + FilterOboPsiModSink term_list; + FilterOboPsiModTermLabel filter_label(term_list, mod); + + OboPsiMod psimod(filter_label); + peptide.addAaModification( - AaModification::getInstanceCustomizedMod(mod.toDouble()), + AaModification::getInstance(term_list.getFirst()), pos - 1 - matched_length_cumul); } } - else - { - FilterOboPsiModSink term_list; - FilterOboPsiModTermLabel filter_label(term_list, mod); - - OboPsiMod psimod(filter_label); - - peptide.addAaModification( - AaModification::getInstance(term_list.getFirst()), - pos - 1 - matched_length_cumul); - } } - matched_length_cumul += mod_parser.matchedLength(); - pos += mod_parser.matchedLength(); + matched_length_cumul += captured.size(); + match_mod = _mod_parser.match(pepstr, pos + 1); } } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidestrparser.h libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidestrparser.h --- libpappsomspp-0.8.15/src/pappsomspp/peptide/peptidestrparser.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/peptide/peptidestrparser.h 2022-10-27 09:16:15.000000000 +0000 @@ -25,6 +25,7 @@ #pragma once #include "peptide.h" +#include namespace pappso { @@ -38,9 +39,9 @@ static void parseStringToPeptide(const QString &pepstr, Peptide &peptide); private: - static QRegExp _mod_parser; - static QRegExp _rx_psimod; - static QRegExp _rx_modmass; + static QRegularExpression _mod_parser; + static QRegularExpression _rx_psimod; + static QRegularExpression _rx_modmass; // static QMutex _mutex; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/precision.cpp libpappsomspp-0.8.58/src/pappsomspp/precision.cpp --- libpappsomspp-0.8.15/src/pappsomspp/precision.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/precision.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -34,6 +34,7 @@ #include #include #include +#include namespace pappso { @@ -77,7 +78,7 @@ // If there only once component, that is, is omitted and charge is // not provided, then "dalton" is considered. - QStringList list = str.split(QRegExp("\\s+"), QString::SkipEmptyParts); + QStringList list = str.split(QRegularExpression("\\s+"), Qt::SkipEmptyParts); if(list.size() > 0) { diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massdatacombinerinterface.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massdatacombinerinterface.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massdatacombinerinterface.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massdatacombinerinterface.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,6 +26,7 @@ { } + void MassDataCombinerInterface::setDecimalPlaces(int value) { @@ -40,15 +41,6 @@ } -void -MassDataCombinerInterface::setFilterResampleKeepXRange( - const FilterResampleKeepXRange &range) -{ - m_filterXRange = range; - m_isApplyXRangeFilter = true; -} - - MapTrace & MassDataCombinerInterface::combine(MapTrace &map_trace, Iterator begin, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massdatacombinerinterface.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massdatacombinerinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massdatacombinerinterface.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massdatacombinerinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -11,7 +11,10 @@ /////////////////////// Local includes +#include "../../types.h" +#include "selectionpolygon.h" #include "../../trace/maptrace.h" +#include "../../massspectrum/qualifiedmassspectrum.h" #include "../filters/filterresample.h" #include "../../exportinmportconfig.h" @@ -19,7 +22,6 @@ namespace pappso { - class PMSPP_LIB_DECL MassDataCombinerInterface { @@ -30,22 +32,16 @@ void setDecimalPlaces(int value); int getDecimalPlaces() const; - void setFilterResampleKeepXRange(const FilterResampleKeepXRange &range); + using Iterator = std::vector::const_iterator; + virtual MapTrace &combine(MapTrace &map_trace, Iterator begin, Iterator end); virtual MapTrace &combine(MapTrace &map_trace, const Trace &trace) const = 0; virtual MapTrace &combine(MapTrace &map_trace_out, const MapTrace &map_trace_in) const = 0; - using Iterator = std::vector::const_iterator; - virtual MapTrace &combine(MapTrace &map_trace, Iterator begin, Iterator end); - protected: //! Number of decimals to use for the keys (x values) int m_decimalPlaces = -1; - - bool m_isApplyXRangeFilter = false; - - FilterResampleKeepXRange m_filterXRange; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -30,33 +30,43 @@ } -MassSpectrumCombiner::MassSpectrumCombiner(std::vector bins, - int decimalPlaces) - : MassDataCombinerInterface(decimalPlaces), m_bins(bins) +MassSpectrumCombiner::MassSpectrumCombiner(int decimal_places) + : MassDataCombinerInterface(decimal_places) { } -MassSpectrumCombiner::MassSpectrumCombiner(int decimal_places) - : MassDataCombinerInterface(decimal_places) +MassSpectrumCombiner::MassSpectrumCombiner(std::vector bins, + int decimalPlaces) + : MassDataCombinerInterface(decimalPlaces) { + m_bins.assign(bins.begin(), bins.end()); } MassSpectrumCombiner::MassSpectrumCombiner(const MassSpectrumCombiner &other) : MassDataCombinerInterface(other.m_decimalPlaces) { - // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; - m_bins.assign(other.m_bins.begin(), other.m_bins.end()); + + //QString debug_string = QString( + //"Number of bins: %1\n" + //"First bins: %2 %3 %4 -- Last bins: %5 %6 %7\n") + //.arg(m_bins.size()) + //.arg(m_bins[0], 0, 'f', 6) + //.arg(m_bins[1], 0, 'f', 6) + //.arg(m_bins[2], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 3], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 2], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 1], 0, 'f', 6); + + //qDebug().noquote() << debug_string; } MassSpectrumCombiner::MassSpectrumCombiner(MassSpectrumCombinerCstSPtr other) : MassDataCombinerInterface(other->m_decimalPlaces) { - // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; - m_bins.assign(other->m_bins.begin(), other->m_bins.end()); } @@ -64,7 +74,6 @@ //! Destruct the instance. MassSpectrumCombiner::~MassSpectrumCombiner() { - // Calls the destructor for each DataPoint object in the vector. m_bins.clear(); } @@ -74,9 +83,18 @@ { m_bins.assign(bins.begin(), bins.end()); - // qDebug() << "After bins assignment, local bins are of this size:" - //<< m_bins.size() << "Starting at:" << m_bins.front() - //<< "and ending at:" << m_bins.back(); + //QString debug_string = QString( + //"Number of bins: %1\n" + //"First bins: %2 %3 %4 -- Last bins: %5 %6 %7\n") + //.arg(m_bins.size()) + //.arg(m_bins[0], 0, 'f', 6) + //.arg(m_bins[1], 0, 'f', 6) + //.arg(m_bins[2], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 3], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 2], 0, 'f', 6) + //.arg(m_bins[m_bins.size() - 1], 0, 'f', 6); + + //qDebug().noquote() << debug_string; } @@ -87,34 +105,6 @@ } -std::vector::iterator -MassSpectrumCombiner::begin() -{ - return m_bins.begin(); -} - - -std::vector::iterator -MassSpectrumCombiner::end() -{ - return m_bins.end(); -} - - -std::vector::const_iterator -MassSpectrumCombiner::begin() const -{ - return m_bins.begin(); -} - - -std::vector::const_iterator -MassSpectrumCombiner::end() const -{ - return m_bins.end(); -} - - std::size_t MassSpectrumCombiner::binCount() const { @@ -123,7 +113,6 @@ //! Find the bin that will contain \p mz. - std::vector::iterator MassSpectrumCombiner::findBin(pappso_double mz) { @@ -133,68 +122,17 @@ } -MapTrace & -MassSpectrumCombiner::combine(MapTrace &map_trace, const Trace &trace) const +QString +MassSpectrumCombiner::binsAsString() const { + QString text; - // qDebug() << "Thread:" << QThread::currentThreadId() - //<< "Going to combine a trace this size:" << trace.size(); - - if(!trace.size()) - { - // qDebug() << "Thread:" << QThread::currentThreadId() - //<< "Returning right away because trace is empty."; - return map_trace; - } - - - // Let's check if we need to apply a filter to the input data. - - if(m_isApplyXRangeFilter) - { - Trace filtered_trace(trace); - - m_filterXRange.filter(filtered_trace); - - if(!filtered_trace.size()) - return map_trace; + for(auto &bin : m_bins) + text += QString("%1\n").arg(bin, 0, 'f', 6); - return combineNoFilteringStep(map_trace, filtered_trace); - } + text += "\n"; - return combineNoFilteringStep(map_trace, trace); + return text; } - -MapTrace & -MassSpectrumCombiner::combine(MapTrace &map_trace_out, - const MapTrace &map_trace_in) const -{ - - // qDebug() << "Thread:" << QThread::currentThreadId() - //<< "Going to combine a map_trace_in this size:" << map_trace_in.size(); - - if(!map_trace_in.size()) - { - // qDebug() << "Thread:" << QThread::currentThreadId() - //<< "Returning right away because map_trace_in is empty."; - return map_trace_out; - } - - // Let's check if we need to apply a filter to the input data. - - Trace filtered_trace_in(map_trace_in); - - if(m_isApplyXRangeFilter) - { - m_filterXRange.filter(filtered_trace_in); - - if(!filtered_trace_in.size()) - return map_trace_out; - } - - return combineNoFilteringStep(map_trace_out, filtered_trace_in); -} - - } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -19,7 +19,6 @@ namespace pappso { - class MassSpectrumCombiner; typedef std::shared_ptr MassSpectrumCombinerCstSPtr; @@ -29,44 +28,26 @@ class PMSPP_LIB_DECL MassSpectrumCombiner : public MassDataCombinerInterface { - public: MassSpectrumCombiner(); - MassSpectrumCombiner(std::vector bins, int decimalPlaces = -1); MassSpectrumCombiner(int decimal_places); + MassSpectrumCombiner(std::vector bins, int decimalPlaces = -1); MassSpectrumCombiner(MassSpectrumCombinerCstSPtr other); MassSpectrumCombiner(const MassSpectrumCombiner &other); MassSpectrumCombiner(const MassSpectrumCombiner &&other); virtual ~MassSpectrumCombiner(); - std::vector::const_iterator begin() const; - std::vector::const_iterator end() const; - std::vector::iterator begin(); - std::vector::iterator end(); - void setBins(std::vector bins); const std::vector &getBins() const; std::size_t binCount() const; - virtual MapTrace &combine(MapTrace &map_trace, const Trace &trace) const; - - virtual MapTrace &combine(MapTrace &map_trace_out, - const MapTrace &map_trace_in) const; + QString binsAsString() const; protected: std::vector m_bins; std::vector::iterator findBin(pappso_double mz); - - private: - // This function combines trace into map_trace but does not handle the - // situation where any filtering step was asked for. This function is called - // by public combine function after filtering work has occurred already. This - // function is the functional lowest common denominator for all the public - // combine functions. - virtual MapTrace &combineNoFilteringStep(MapTrace &map_trace, - const Trace &trace) const = 0; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,397 +0,0 @@ -/** - * \file pappsomspp/mass_range.cpp - * \date 4/3/2015 - * \author Olivier Langella - * \brief object to handle a mass range (an mz value + or - some delta) - */ - -/******************************************************************************* - * Copyright (c) 2015 Olivier Langella . - * - * This file is part of the PAPPSOms++ library. - * - * PAPPSOms++ is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms++ is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms++. If not, see . - * - * Contributors: - * Olivier Langella - initial API and - *implementation - ******************************************************************************/ - -#include "precision.h" -#include "mzrange.h" -#include "exception/exceptionnotpossible.h" -#include -#include -#include - -namespace pappso -{ - - -PrecisionFactory::MapDaltonPrecision PrecisionFactory::m_mapDalton = [] { - MapDaltonPrecision ret; - - return ret; -}(); - - -PrecisionFactory::MapPpmPrecision PrecisionFactory::m_mapPpm = [] { - MapPpmPrecision ret; - - return ret; -}(); - - -PrecisionFactory::MapResPrecision PrecisionFactory::m_mapRes = [] { - MapResPrecision ret; - - return ret; -}(); - - -PrecisionFactory::MapMzPrecision PrecisionFactory::m_mapMz = [] { - MapMzPrecision ret; - - return ret; -}(); - - -pappso_double -PrecisionBase::getNominal() const -{ - return m_nominal; -} - - -PrecisionPtr -PrecisionFactory::fromString(const QString &str) -{ - - // The format of the string is with string either - // "ppm" or "dalton" or "res" or "mz". - // - // If there only once component, that is, is omitted and charge is - // not provided, then "dalton" is considered. - - QStringList list = str.split(QRegExp("\\s+"), QString::SkipEmptyParts); - - if(list.size() > 0) - { - bool ok; - pappso_double value = list[0].toDouble(&ok); - if(!ok) - { - throw ExceptionNotPossible( - QObject::tr("ERROR getting precision from string :\nunable to " - "convert %1 to number in %2") - .arg(value) - .arg(str)); - } - if(list.size() == 1) - { - return PrecisionFactory::getDaltonInstance(value); - } - else - { - if(list.size() == 2) - { - if(list[1].toLower() == "dalton") - { - return PrecisionFactory::getDaltonInstance(value); - } - - if(list[1].toLower() == "ppm") - { - return PrecisionFactory::getPpmInstance(value); - } - - if(list[1].toLower() == "res") - { - return PrecisionFactory::getResInstance(value); - } - - throw ExceptionNotPossible( - QObject::tr("ERROR getting precision from string :\nprecision " - "unit %1 to not known in %2") - .arg(list[1]) - .arg(str)); - } - else if(list.size() == 3) - { - // We are handling a mz precision instance. - // Thus, first item is the value, the second item has to be - // charge. - - bool ok; - int charge = list[1].toInt(&ok); - - if(!ok || list[2] != "mz") - { - throw ExceptionNotPossible( - QObject::tr("ERROR getting charge from string :\nunable to " - "convert %1 to int in %2, or string is not mz") - .arg(charge) - .arg(str)); - } - - return PrecisionFactory::getMzInstance(value, charge); - } - } - } - - throw ExceptionNotPossible(QObject::tr("ERROR getting precision from string " - ":\nunable to convert %1 to precision") - .arg(str)); -} - -PrecisionPtr -PrecisionFactory::getDaltonInstance(pappso_double value) -{ - MapDaltonPrecision::iterator it = m_mapDalton.find(value); - if(it == m_mapDalton.end()) - { - // not found - std::pair insert_res = - m_mapDalton.insert(std::pair( - value, new DaltonPrecision(value))); - it = insert_res.first; - } - else - { - // found - } - return it->second; -} - - -PrecisionPtr -PrecisionFactory::getPpmInstance(pappso_double value) -{ - if(!value) - throw ExceptionNotPossible( - QObject::tr("Fatal error at %1@%2 in %3 -- %4(). ") - .arg(__FILE__) - .arg(__LINE__) - .arg(__FUNCTION__) - .arg("ERROR trying to set a Resolution precision value of 0." - "Program aborted.")); - - MapPpmPrecision::iterator it = m_mapPpm.find(value); - - if(it == m_mapPpm.end()) - { - // Not found. - std::pair insert_res = - m_mapPpm.insert(std::pair( - value, new PpmPrecision(value))); - it = insert_res.first; - } - else - { - // found - } - return it->second; -} - - -PrecisionPtr -PrecisionFactory::getResInstance(pappso_double value) -{ - if(!value) - throw ExceptionNotPossible( - QObject::tr("Fatal error at %1@%2 in %3 -- %4(). ") - .arg(__FILE__) - .arg(__LINE__) - .arg(__FUNCTION__) - .arg("ERROR trying to set a Resolution precision value of 0." - "Program aborted.")); - - MapResPrecision::iterator it = m_mapRes.find(value); - - if(it == m_mapRes.end()) - { - // not found - std::pair insert_res = - m_mapRes.insert(std::pair( - value, new ResPrecision(value))); - it = insert_res.first; - } - else - { - // found - } - return it->second; -} - - -PrecisionPtr -PrecisionFactory::getMzInstance(pappso_double value, int charge) -{ - // Special find_if search because we need to confirm the presence of the - // value, charge pair, not only the value. - - MapMzPrecision::iterator it = std::find_if( - std::begin(m_mapMz), - std::end(m_mapMz), - [value, charge](const std::pair &pair) { - return ((pair.first == value) && (pair.second->charge() == charge)); - }); - - if(it == m_mapMz.end()) - { - // Not found. - std::pair insert_res = - m_mapMz.insert(std::pair( - value, new MzPrecision(value, charge))); - - it = insert_res.first; - } - else - { - // Found. - } - - return it->second; -} - - -DaltonPrecision::DaltonPrecision(pappso_double x) : PrecisionBase(x) -{ -} - -DaltonPrecision::~DaltonPrecision() -{ -} - -PrecisionUnit -DaltonPrecision::unit() const -{ - return PrecisionUnit::dalton; -} - -pappso_double -DaltonPrecision::delta(pappso_double value) const -{ - return m_nominal; -} - -QString -DaltonPrecision::toString() const -{ - return (QString("%1 dalton").arg(m_nominal)); -} - - -PpmPrecision::PpmPrecision(pappso_double x) : PrecisionBase(x) -{ -} - - -PpmPrecision::~PpmPrecision() -{ -} - -PrecisionUnit -PpmPrecision::unit() const -{ - return PrecisionUnit::ppm; -} - - -pappso_double -PpmPrecision::delta(pappso_double value) const -{ - return ((value / ONEMILLION) * m_nominal); -} - - -QString -PpmPrecision::toString() const -{ - return (QString("%1 ppm").arg(m_nominal)); -} - - -ResPrecision::ResPrecision(pappso_double x) : PrecisionBase(x) -{ -} - - -ResPrecision::~ResPrecision() -{ -} - -PrecisionUnit -ResPrecision::unit() const -{ - return PrecisionUnit::res; -} - - -pappso_double -ResPrecision::delta(pappso_double value) const -{ - return (value / m_nominal); -} - - -QString -ResPrecision::toString() const -{ - return (QString("%1 res").arg(m_nominal)); -} - - -MzPrecision::MzPrecision(pappso_double value, int charge) - : PrecisionBase(value), m_charge(charge) -{ -} - - -MzPrecision::~MzPrecision() -{ -} - - -PrecisionUnit -MzPrecision::unit() const -{ - return PrecisionUnit::mz; -} - - -pappso_double -MzPrecision::delta(pappso_double value) const -{ - if(!m_charge) - return m_nominal; - else - return m_nominal / m_charge; -} - - -int -MzPrecision::charge() const -{ - return m_charge; -}; - - -QString -MzPrecision::toString() const -{ - return (QString("%1 %2 mz").arg(m_nominal).arg(m_charge)); -}; - -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,167 +0,0 @@ -// Filippo Rusconi 2019 - -#pragma once - -#include - -#include "types.h" - -namespace pappso -{ - - -class MassSpectrumCombinerFactory -{ - - using MapDaltonPrecision = std::map; - using MapPpmPrecision = std::map; - using MapResPrecision = std::map; - using MapMzPrecision = std::map; - - private: - static MapDaltonPrecision m_mapDalton; - static MapPpmPrecision m_mapPpm; - static MapResPrecision m_mapRes; - static MapMzPrecision m_mapMz; - - public: - MassDataCombiner getPlusCombiner(MzIntegrationParams &integration_params); - getPlusCombiner(MzIntegrationParams &integration_params); - - static PrecisionPtr fromString(const QString &str); - static PrecisionPtr getDaltonInstance(pappso_double value); - static PrecisionPtr getPpmInstance(pappso_double value); - static PrecisionPtr getResInstance(pappso_double value); - static PrecisionPtr getMzInstance(pappso_double value, int charge); -}; - - -class PrecisionBase -{ - protected: - const pappso_double m_nominal; - - PrecisionBase(pappso_double nominal) : m_nominal(nominal) - { - } - - public: - virtual PrecisionUnit unit() const = 0; - virtual pappso_double getNominal() const final; - virtual pappso_double delta(pappso_double value) const = 0; - virtual QString toString() const = 0; -}; - - -/** \def specific type for a dalton precision - * - */ -class DaltonPrecision : public PrecisionBase -{ - friend class PrecisionFactory; - - protected: - DaltonPrecision(pappso_double x); - - public: - virtual ~DaltonPrecision(); - - virtual PrecisionUnit unit() const override; - - virtual pappso_double delta(pappso_double value) const override; - - virtual QString toString() const override; -}; - -/** \def specific type for a ppm precision - * - */ -class PpmPrecision : public PrecisionBase -{ - friend class PrecisionFactory; - - protected: - PpmPrecision(pappso_double x); - - public: - virtual ~PpmPrecision(); - - virtual PrecisionUnit unit() const override; - - virtual pappso_double delta(pappso_double value) const override; - - virtual QString toString() const override; -}; - - -/** \def specific type for a res precision - * - */ -class ResPrecision : public PrecisionBase -{ - friend class PrecisionFactory; - - protected: - ResPrecision(pappso_double x); - - public: - virtual ~ResPrecision(); - - virtual PrecisionUnit unit() const override; - - virtual pappso_double delta(pappso_double value) const override; - - virtual QString toString() const override; -}; - - -/** \def specific type for a m/z precision - * - */ -class MzPrecision : public PrecisionBase -{ - friend class PrecisionFactory; - - protected: - const int m_charge = 1; - MzPrecision(pappso_double value, int charge); - - public: - virtual ~MzPrecision(); - - virtual PrecisionUnit unit() const override; - - virtual pappso_double delta(pappso_double value) const override; - - int charge() const; - - virtual QString toString() const override; -}; - - -typedef const PrecisionBase *PrecisionPtr; - - -// was class Precision -class PrecisionFactory -{ - using MapDaltonPrecision = std::map; - using MapPpmPrecision = std::map; - using MapResPrecision = std::map; - using MapMzPrecision = std::map; - - private: - static MapDaltonPrecision m_mapDalton; - static MapPpmPrecision m_mapPpm; - static MapResPrecision m_mapRes; - static MapMzPrecision m_mapMz; - - public: - static PrecisionPtr fromString(const QString &str); - static PrecisionPtr getDaltonInstance(pappso_double value); - static PrecisionPtr getPpmInstance(pappso_double value); - static PrecisionPtr getResInstance(pappso_double value); - static PrecisionPtr getMzInstance(pappso_double value, int charge); -}; - -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumminuscombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumminuscombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumminuscombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumminuscombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -48,7 +48,6 @@ : MassSpectrumCombiner(other) { - // qDebug() << __FILE__ << " @ " << __LINE__ << __FUNCTION__ << "()"; } @@ -57,7 +56,6 @@ : MassSpectrumCombiner(other) { - // qDebug() << __FILE__ << " @ " << __LINE__ << __FUNCTION__ << "()"; } @@ -67,11 +65,25 @@ } +MassSpectrumMinusCombiner & +MassSpectrumMinusCombiner::operator=(const MassSpectrumMinusCombiner &other) +{ + if(this == &other) + return *this; + + m_decimalPlaces = other.m_decimalPlaces; + + m_bins.assign(other.m_bins.begin(), other.m_bins.end()); + + return *this; +} + + MapTrace & -MassSpectrumMinusCombiner::combineNoFilteringStep(MapTrace &map_trace, - const Trace &trace) const +MassSpectrumMinusCombiner::combine(MapTrace &map_trace, + const Trace &trace) const { - //qDebug(); + // qDebug(); if(!trace.size()) { @@ -140,10 +152,10 @@ { current_bin_mz_value = *bin_iter; - //qDebug() << "Iterating in new bin:" - //<< QString("%1").arg(current_bin_mz_value, 0, 'f', 15) - //<< "at a distance from the first bin of:" - //<< std::distance(m_bins.begin(), bin_iter); + // qDebug() << "Iterating in new bin:" + //<< QString("%1").arg(current_bin_mz_value, 0, 'f', 15) + //<< "at a distance from the first bin of:" + //<< std::distance(m_bins.begin(), bin_iter); // For the current bin, we start by instantiating a new DataPoint. By // essence, each bin will have at most one corresponding DataPoint. @@ -156,8 +168,8 @@ bin_data_point.x = current_bin_mz_value; - //qDebug() << "Seed bin_data_point.x with current_bin_mz_value value:" - //<< QString("%1").arg(bin_data_point.x, 0, 'f', 15); + // qDebug() << "Seed bin_data_point.x with current_bin_mz_value value:" + //<< QString("%1").arg(bin_data_point.x, 0, 'f', 15); // Now perform a loop over the data points in the mass spectrum. @@ -172,13 +184,13 @@ // qDebug() << "Thread:" << QThread::currentThreadId(); - //qDebug() << "Iterating in new trace datapoint:" - //<< trace_iter->toString(15) << "at distance:" - //<< std::distance(trace_iter_begin, trace_iter); + // qDebug() << "Iterating in new trace datapoint:" + //<< trace_iter->toString(15) << "at distance:" + //<< std::distance(trace_iter_begin, trace_iter); if(trace_iter->y) { - //qDebug() << "The y value of trace iterated value is not 0."; + // qDebug() << "The y value of trace iterated value is not 0."; // trace_x is the m/z value that we need to combine, @@ -191,13 +203,13 @@ if(trace_x <= current_bin_mz_value) { - //qDebug() - //<< "trace_x <= current_bin_mz_value: the match happened."; + // qDebug() + //<< "trace_x <= current_bin_mz_value: the match happened."; - //qDebug() << "Going to compute" << bin_data_point.y << "-" - //<< trace_y << "with current_bin_mz_value:" - //<< QString("%1").arg( - //current_bin_mz_value, 0, 'f', 15); + // qDebug() << "Going to compute" << bin_data_point.y << "-" + //<< trace_y << "with current_bin_mz_value:" + //<< QString("%1").arg( + // current_bin_mz_value, 0, 'f', 15); // This is where the bin_data_point actually gets decremented // by the y value of the currently iterated trace data point. @@ -206,7 +218,8 @@ // bin_data_point.y; code line elsewhere in this function. bin_data_point.y -= trace_y; - //qDebug() << "New bin_data_point.y value:" << bin_data_point.y; + // qDebug() << "New bin_data_point.y value:" << + // bin_data_point.y; // Let's record that we matched. trace_matched = true; @@ -214,9 +227,9 @@ // Because we matched, we can step-up with the // iterator. - //qDebug() << "The values matched, increment the trace " - //"itereator but not the bin iterator, as maybe " - //"the next trace datapoint also matches the bin."; + // qDebug() << "The values matched, increment the trace " + //"itereator but not the bin iterator, as maybe " + //"the next trace datapoint also matches the bin."; ++trace_iter; } @@ -236,9 +249,9 @@ // below code think that we have matched the point and iterate one // step up. - //qDebug() << "The y value of the currently iterated trace data " - //"point is almost equal to 0, increment the " - //"trace iter but do nothing else."; + // qDebug() << "The y value of the currently iterated trace data " + //"point is almost equal to 0, increment the " + //"trace iter but do nothing else."; trace_matched = true; ++trace_iter; @@ -250,8 +263,8 @@ if(!trace_matched) { - //qDebug() << "The currently iterated trace datapoint did not " - //"match the current bin."; + // qDebug() << "The currently iterated trace datapoint did not " + //"match the current bin."; // The trace data point did not match the currently iterated bin. // All we have to do is go to the next bin. We break and the bin @@ -264,9 +277,9 @@ if(bin_data_point.isValid()) { - //qDebug() << "But we had a valid bin data point cooking, so " - //"we have to take that into account:" - //<< bin_data_point.toString(15); + // qDebug() << "But we had a valid bin data point cooking, so + // " "we have to take that into account:" + //<< bin_data_point.toString(15); // We need to check if that bin value is present already in // the map_trace object passed as parameter. @@ -279,15 +292,15 @@ if(!result.second) { - //qDebug() - //<< "The x value (mz) was already present in the " - //"map trace, simply update its y value (intensity)."; + // qDebug() + //<< "The x value (mz) was already present in the " + //"map trace, simply update its y value (intensity)."; // The key already existed! The item was not inserted. We // need to update the y value. - //qDebug() << "Going to compute" << result.first->second - //<< "+" << bin_data_point.y; + // qDebug() << "Going to compute" << result.first->second + //<< "+" << bin_data_point.y; // This might be counterintuitive: one would expect the // use of the '-=' operator because we are @@ -297,18 +310,19 @@ // the same as +value). result.first->second += bin_data_point.y; - //qDebug() << "New y value for the item in the map trace " - //"(result.first->second value):" - //<< result.first->second; + // qDebug() << "New y value for the item in the map trace + // " + //"(result.first->second value):" + //<< result.first->second; } - //else - //{ - //qDebug() - //<< "The data point has a mz value that was not present " - //"in the map trace." - //<< " Inserted a new data point into the map trace:" - //<< bin_data_point.x << "," << bin_data_point.y; - //} + // else + //{ + // qDebug() + //<< "The data point has a mz value that was not present " + //"in the map trace." + //<< " Inserted a new data point into the map trace:" + //<< bin_data_point.x << "," << bin_data_point.y; + //} } // We need to break this loop! That will increment the @@ -340,15 +354,16 @@ if(!result.second) { - //qDebug() - //<< "The x value (mz) was already present in the " - //"map trace, simply update its y value (intensity)."; + // qDebug() + //<< "The x value (mz) was already present in the " + //"map trace, simply update its y value (intensity)."; // The key already existed! The item was not inserted. We // need to update the y value. - //qDebug() << "Going to compute" << result.first->second << "+" - //<< bin_data_point.y; + // qDebug() << "Going to compute" << result.first->second << + // "+" + //<< bin_data_point.y; // This might be counterintuitive: one would expect the @@ -359,18 +374,18 @@ // the same as +value). result.first->second += bin_data_point.y; - //qDebug() << "New y value for the item in the map trace " - //"(result.first->second value):" - //<< result.first->second; + // qDebug() << "New y value for the item in the map trace " + //"(result.first->second value):" + //<< result.first->second; } - //else - //{ - //qDebug() - //<< "The data point has a mz value that was not present " - //"in the map trace." - //<< " Inserted a new data point into the map trace:" - //<< bin_data_point.x << "," << bin_data_point.y; - //} + // else + //{ + // qDebug() + //<< "The data point has a mz value that was not present " + //"in the map trace." + //<< " Inserted a new data point into the map trace:" + //<< bin_data_point.x << "," << bin_data_point.y; + //} } // Now truly exit the loops... @@ -390,4 +405,22 @@ } +MapTrace & +MassSpectrumMinusCombiner::combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const +{ + // qDebug(); + + if(!map_trace_in.size()) + { + // qDebug() << "Thread:" << QThread::currentThreadId() + //<< "Returning right away because map_trace_in is empty."; + return map_trace_out; + } + + Trace trace(map_trace_in); + + return combine(map_trace_out, trace); +} + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumminuscombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumminuscombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumminuscombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumminuscombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -30,14 +30,15 @@ MassSpectrumMinusCombiner(int decimal_places); MassSpectrumMinusCombiner(MassSpectrumMinusCombinerCstSPtr other); MassSpectrumMinusCombiner(const MassSpectrumMinusCombiner &other); - MassSpectrumMinusCombiner(const MassSpectrumCombiner &&other); virtual ~MassSpectrumMinusCombiner(); - protected: - private: - virtual MapTrace &combineNoFilteringStep(MapTrace &map_trace, - const Trace &trace) const; + MassSpectrumMinusCombiner &operator=(const MassSpectrumMinusCombiner &other); + + virtual MapTrace &combine(MapTrace &map_trace, + const Trace &trace) const override; + virtual MapTrace &combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const override; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumpluscombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumpluscombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumpluscombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumpluscombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -48,7 +48,6 @@ : MassSpectrumCombiner(other) { - // qDebug() << __FILE__ << " @ " << __LINE__ << __FUNCTION__ << "()"; } @@ -57,7 +56,6 @@ : MassSpectrumCombiner(other) { - // qDebug() << __FILE__ << " @ " << __LINE__ << __FUNCTION__ << "()"; } @@ -67,12 +65,34 @@ } +MassSpectrumPlusCombiner & +MassSpectrumPlusCombiner::operator=(const MassSpectrumPlusCombiner &other) +{ + if(this == &other) + return *this; + + m_decimalPlaces = other.m_decimalPlaces; + + m_bins.assign(other.m_bins.begin(), other.m_bins.end()); + + return *this; +} + + +// We get a trace as parameter that this combiner needs to combine to the +// map_trace we also get as parameter. This combiner is for a mass spectrum, and +// thus it needs to have been configured to hold a vector of m/z values that are +// bins into which DataPoints from trace are combined into map_trace. It is the +// bins that drive the the traversal of trace. For each bin, check if there is +// (or are, if bins are big) data points in the trace that fit in it. + MapTrace & -MassSpectrumPlusCombiner::combineNoFilteringStep(MapTrace &map_trace, - const Trace &trace) const +MassSpectrumPlusCombiner::combine(MapTrace &map_trace, const Trace &trace) const { - //qDebug(); + // qDebug(); + // If there is no single point in the trace we need to combine into the + // map_trace, then there is nothing to do. if(!trace.size()) { // qDebug() << "Thread:" << QThread::currentThreadId() @@ -109,7 +129,7 @@ // Iterate in the vector of bins and for each bin check if there are matching // data points in the trace. - pappso_double current_bin = 0; + pappso_double current_bin_mz = 0; pappso_double trace_x = 0; pappso_double trace_y = 0; @@ -130,10 +150,13 @@ while(bin_iter != bin_end_iter) { - current_bin = *bin_iter; + current_bin_mz = *bin_iter; + + // std::cout << std::setprecision(10) << "current bin: " << current_bin_mz + //<< std::endl; - // qDebug() << "Current bin:" << QString("%1").arg(current_bin, 0, 'f', - // 15) + // qDebug() << "Current bin:" + //<< QString("%1").arg(current_bin_mz, 0, 'f', 15) //<< "at a distance of:" //<< std::distance(m_bins.begin(), bin_iter); @@ -145,16 +168,21 @@ // Do not set the y value to 0 so that we can actually test if the // data point is valid later on (try not to push back y=0 data // points). - new_data_point.x = current_bin; + new_data_point.x = current_bin_mz; // Now perform a loop over the data points in the mass spectrum. - // qDebug() << "trace_iter:" << trace_iter->toString() + // qDebug() << "Start looping in the trace to check if its DataPoint.x " + //"value matches that of the current bin." + //<< "trace_iter:" << trace_iter->toString() //<< "data point distance:" //<< std::distance(trace_iter_begin, trace_iter); while(trace_iter != trace_iter_end) { + // std::cout << std::setprecision(10) + //<< "trace data point being iterated into: " << trace_iter->x + //<< " - " << trace_iter->y << std::endl; bool trace_matched = false; @@ -169,10 +197,25 @@ //<< std::distance(trace_iter_begin, trace_iter); // if(!Utils::almostEqual(trace_iter->y, 0.0, 10)) - if(trace_iter->y) + + trace_x = trace_iter->x; + trace_y = trace_iter->y; + + if(trace_y) { - trace_x = trace_iter->x; - trace_y = trace_iter->y; + + // FIXME: unbelievable behaviour: when building in release mode + // this code, under i386 (but not x86_64), this code fails if the + // following cout statement is missing. There are a variety of + // variants that work, the common denominator being that trace_x + // has to be output along with a string. + + // std::cout << std::setprecision(10) + //<< "iterated trace point: " << trace_x << " - " + //<< trace_y << std::endl; + + // For this reason I had to deactivate the related tests + // for i386 in tests/test_massspectrumcombiner.cpp // trace_x is the m/z value that we need to combine, // so make sure we check if there is a mz shift to apply. @@ -184,12 +227,21 @@ if(m_decimalPlaces != -1) trace_x = Utils::roundToDecimals(trace_x, m_decimalPlaces); - if(trace_x <= current_bin) + if(trace_x <= current_bin_mz) { - // qDebug() << "Matched, increment trace_iter"; + // std::cout + //<< std::setprecision(10) + //<< "Matched, because trace point.x is <= the current " + //"bin; increment trace_iter" + //<< std::endl; + new_data_point.y += trace_y; + // std::cout << std::setprecision(10) + //<< "After incrementation of the intensity: " + //<< new_data_point.y << std::endl; + // Let's record that we matched. trace_matched = true; @@ -207,6 +259,11 @@ // if(trace_iter->y) else { + // std::cout << std::setprecision(10) + //<< "itered trace point intensity is 0: " << trace_x + //<< " - " << trace_y << std::endl; + + // We iterated into a y=0 data point, so just skip it. Let // the below code think that we have matched the point and // iterate one step up. @@ -249,8 +306,8 @@ result.first->second += new_data_point.y; - // qDebug() << "Incremented the data point in the map - // trace."; + // qDebug() + //<< "Incremented the data point in the map trace."; } // else //{ @@ -266,7 +323,7 @@ } } // End of - // while(1) + // while(trace_iter != trace_iter_end) // Each time we get here, that means that we have consumed all // the mass spectra data points that matched the current bin. @@ -309,5 +366,24 @@ } +MapTrace & +MassSpectrumPlusCombiner::combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const +{ + // qDebug(); + + if(!map_trace_in.size()) + { + // qDebug() << "Thread:" << QThread::currentThreadId() + //<< "Returning right away because map_trace_in is empty."; + return map_trace_out; + } + + Trace trace(map_trace_in); + + return combine(map_trace_out, trace); +} + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumpluscombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumpluscombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/massspectrumpluscombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/massspectrumpluscombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -32,10 +32,12 @@ virtual ~MassSpectrumPlusCombiner(); - protected: - private: - virtual MapTrace &combineNoFilteringStep(MapTrace &map_trace, - const Trace &trace) const; + MassSpectrumPlusCombiner &operator=(const MassSpectrumPlusCombiner &other); + + virtual MapTrace &combine(MapTrace &map_trace, + const Trace &trace) const override; + virtual MapTrace &combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const override; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/mzintegrationparams.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/mzintegrationparams.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/mzintegrationparams.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/mzintegrationparams.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -100,22 +100,10 @@ mp_precision(other.mp_precision), m_applyMzShift(other.m_applyMzShift), m_mzShift(other.m_mzShift), - m_removeZeroValDataPoints(other.m_removeZeroValDataPoints), - m_applySavGolFilter(other.m_applySavGolFilter) + m_removeZeroValDataPoints(other.m_removeZeroValDataPoints) { if(mp_precision == nullptr) mp_precision = pappso::PrecisionFactory::getPpmInstance(20); - - m_savGolParams.initialize(other.m_savGolParams); -} - - -MzIntegrationParams::MzIntegrationParams( - const pappso::SavGolParams &savGolParams) -{ - m_binningType = BinningType::NONE; - mp_precision = pappso::PrecisionFactory::getPpmInstance(20); - setSavGolParams(savGolParams); } @@ -144,10 +132,6 @@ m_mzShift = other.m_mzShift; m_removeZeroValDataPoints = other.m_removeZeroValDataPoints; - setSavGolParams(other.m_savGolParams); - - m_applySavGolFilter = other.m_applySavGolFilter; - return *this; } @@ -276,50 +260,6 @@ } -void -MzIntegrationParams::setApplySavGolFilter(bool applySavGolFilter) -{ - m_applySavGolFilter = applySavGolFilter; -} - - -bool -MzIntegrationParams::isApplySavGolFilter() const -{ - return m_applySavGolFilter; -} - - -void -MzIntegrationParams::setSavGolParams( - int nL, int nR, int m, int lD, bool convolveWithNr) -{ - m_savGolParams.nL = nL; - m_savGolParams.nR = nR; - m_savGolParams.m = m; - m_savGolParams.lD = lD; - m_savGolParams.convolveWithNr = convolveWithNr; -} - - -void -MzIntegrationParams::setSavGolParams(const pappso::SavGolParams ¶ms) -{ - m_savGolParams.nL = params.nL; - m_savGolParams.nR = params.nR; - m_savGolParams.m = params.m; - m_savGolParams.lD = params.lD; - m_savGolParams.convolveWithNr = params.convolveWithNr; -} - - -pappso::SavGolParams -MzIntegrationParams::getSavGolParams() const -{ - return m_savGolParams; -} - - //! Reset the instance to default values. void MzIntegrationParams::reset() @@ -334,14 +274,6 @@ m_applyMzShift = false; m_mzShift = 0; m_removeZeroValDataPoints = false; - - m_savGolParams.nL = 15; - m_savGolParams.nR = 15; - m_savGolParams.m = 4; - m_savGolParams.lD = 0; - m_savGolParams.convolveWithNr = false; - - m_applySavGolFilter = false; } @@ -451,27 +383,28 @@ MzIntegrationParams::createArbitraryBins() { - // qDebug(); + //qDebug(); // Now starts the tricky stuff. Depending on how the binning has been // configured, we need to take diverse actions. - // qDebug() << "Bin size:" << mp_precision->toString(); + //qDebug() << "Bin specification:" << mp_precision->toString(); pappso::pappso_double min_mz = m_smallestMz; pappso::pappso_double max_mz = m_greatestMz; - // qDebug() << QString::asprintf("min_mz: %.6f\n", min_mz) - //<< QString::asprintf("max_mz: %.6f\n", max_mz); + //qDebug() << QString::asprintf("min_mz: %.6f\n", min_mz) + //<< QString::asprintf("max_mz: %.6f\n", max_mz); pappso::pappso_double binSize = mp_precision->delta(min_mz); - // qDebug() << QString::asprintf( - //"binSize is the precision delta for min_mz: %.6f\n", binSize); + //qDebug() << QString::asprintf( + //"binSize is the precision delta for min_mz: %.6f\n", binSize); // Only compute the decimal places if they were not configured already. if(m_decimalPlaces == -1) { + // qDebug() << "Now checking how many decimal places are needed."; // We want as many decimal places as there are 0s between the integral // part of the double and the first non-0 cipher. For example, if @@ -480,8 +413,8 @@ m_decimalPlaces = pappso::Utils::zeroDecimalsInValue(binSize) + 1; - // qDebug() << "With the binSize m_decimalPlaces was computed to be:" - //<< m_decimalPlaces; + // qDebug() << "With binSize" << binSize + //<< " m_decimalPlaces was computed to be:" << m_decimalPlaces; } // Now that we have defined the value of m_decimalPlaces, let's use that @@ -524,11 +457,15 @@ while(previous_mz_bin <= last_mz) { + // qDebug() << "Now starting the bin creation loop."; + // Calculate dynamically the precision delta according to the current mz // value. - double current_mz = - previous_mz_bin + mp_precision->delta(previous_mz_bin); + //double precision_delta = mp_precision->delta(previous_mz_bin); + // qDebug() << "precision_delta: " << precision_delta; + + double current_mz = previous_mz_bin + mp_precision->delta(previous_mz_bin); // qDebug() << QString::asprintf( //"previous_mzBin: %.6f and current_mz: %.6f\n", @@ -560,9 +497,9 @@ ceil((current_mz * pow(10, m_decimalPlaces)) - 0.49) / pow(10, m_decimalPlaces); - qDebug().noquote() - << "Had to increment decimal places by one while creating the bins " - "in BinningType::ARBITRARY mode.."; + // qDebug().noquote() + //<< "Had to increment decimal places by one while creating the bins " + //"in BinningType::ARBITRARY mode.."; } bins.push_back(current_rounded_mz); @@ -790,25 +727,6 @@ text += QString("Remove 0-val data points: %1\n") .arg(m_removeZeroValDataPoints ? "true" : "false"); - // Finally the Savitzy-Golay parameters (if requested) - - if(m_applySavGolFilter) - { - text += lead; - text += spacer; - text.append("Savitzky-Golay parameters\n"); - text += lead; - text += spacer; - text += spacer; - text += - QString("nL = %1 ; nR = %2 ; m = %3 ; lD = %4 ; convolveWithNr = %5\n") - .arg(m_savGolParams.nL) - .arg(m_savGolParams.nR) - .arg(m_savGolParams.m) - .arg(m_savGolParams.lD) - .arg(m_savGolParams.convolveWithNr ? "true" : "false"); - } - return text; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/mzintegrationparams.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/mzintegrationparams.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/mzintegrationparams.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/mzintegrationparams.h 2022-10-27 09:16:15.000000000 +0000 @@ -37,7 +37,6 @@ #include #include "../../precision.h" -#include "../filters/savgolfilter.h" #include "../../massspectrum/massspectrum.h" namespace pappso @@ -97,7 +96,6 @@ bool removeZeroValDataPoints); MzIntegrationParams(const MzIntegrationParams &other); - MzIntegrationParams(const pappso::SavGolParams &savGolParams); virtual ~MzIntegrationParams(); @@ -129,17 +127,6 @@ void setRemoveZeroValDataPoints(bool removeOrNot = true); bool isRemoveZeroValDataPoints() const; - void setApplySavGolFilter(bool applySavGolFilter); - bool isApplySavGolFilter() const; - - void setSavGolParams(int nL = 15, - int nR = 15, - int m = 4, - int lD = 0, - bool convolveWithNr = false); - void setSavGolParams(const pappso::SavGolParams ¶ms); - pappso::SavGolParams getSavGolParams() const; - void reset(); bool isValid() const; @@ -173,9 +160,6 @@ pappso::pappso_double m_mzShift = 0; bool m_removeZeroValDataPoints = true; - bool m_applySavGolFilter = false; - pappso::SavGolParams m_savGolParams; - std::vector createArbitraryBins(); std::vector createDataBasedBins(pappso::MassSpectrumCstSPtr massSpectrum); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/selectionpolygon.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/selectionpolygon.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/selectionpolygon.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/selectionpolygon.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,1141 @@ +// Copyright 2021 Filippo Rusconi +// GPLv3+ + + +/////////////////////// StdLib includes +#include +#include + + +/////////////////////// Qt includes +#include + + +/////////////////////// Local includes +#include "selectionpolygon.h" + + +namespace pappso +{ + +SelectionPolygon::SelectionPolygon() +{ + // When we create a polygon, we create it as immense as possible, so that any + // other polygon will fill inside it and *this polygon by necessity will + // contain another one based on experimental data. See the header file for the + // creation of the four points. +} + + +SelectionPolygon::SelectionPolygon(QPointF top_left_point, + QPointF top_right_point) +{ + // First clear the default values points because we want to push_back + // new points and we want to only ever have 4 points. + m_points.clear(); + + // We get only two points that provide the horizontal range of the polygon. + // These two points show the x range of the polygon. We need to craft a + // polygon that has: + // + // that specified x range and + // + // the widest y range possible. + + // top left point + m_points.push_back( + QPointF(top_left_point.x(), std::numeric_limits::max())); + + // top right point + m_points.push_back( + QPointF(top_right_point.x(), std::numeric_limits::max())); + + // bottom right point + m_points.push_back( + QPointF(top_right_point.x(), std::numeric_limits::min())); + + // bottom left point + m_points.push_back( + QPointF(top_left_point.x(), std::numeric_limits::min())); + + // Compute the min|max x|y coordinates of the polygon that will be used to + // quickly check if a point is outside. + computeMinMaxCoordinates(); +} + + +SelectionPolygon::SelectionPolygon(QPointF top_left_point, + QPointF top_right_point, + QPointF bottom_right_point, + QPointF bottom_left_point) +{ + // First clear the default values points. + m_points.clear(); + + // Attention, we need to push back the points starting top left and clockwise. + + m_points.push_back(top_left_point); + m_points.push_back(top_right_point); + m_points.push_back(bottom_right_point); + m_points.push_back(bottom_left_point); + + // Compute the min|max x|y coordinates of the polygon that will be used to + // quickly check if a point is outside. + computeMinMaxCoordinates(); +} + + +SelectionPolygon::SelectionPolygon(const SelectionPolygon &other) +{ + if(other.m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal( + "The template selection polygon must have four points, no less, no more"); + + // First clear the default values points. + m_points.clear(); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + m_points.push_back(other.m_points[iter]); + } + + m_minX = other.m_minX; + m_minY = other.m_minY; + + m_maxX = other.m_maxX; + m_maxY = other.m_maxY; +} + + +SelectionPolygon::~SelectionPolygon() +{ +} + + +void +SelectionPolygon::setPoint(PointSpecs point_spec, double x, double y) +{ + m_points[static_cast(point_spec)].setX(x); + m_points[static_cast(point_spec)].setY(y); + + computeMinMaxCoordinates(); +} + + +void +SelectionPolygon::setPoint(PointSpecs point_spec, QPointF point) +{ + setPoint(point_spec, point.x(), point.y()); + + computeMinMaxCoordinates(); +} + + +void +SelectionPolygon::copyPoint(PointSpecs point_spec_src, + PointSpecs point_spec_dest) +{ + QPointF src_point = getPoint(point_spec_src); + setPoint(point_spec_dest, src_point); + + computeMinMaxCoordinates(); +} + + +void +SelectionPolygon::set1D(double x_range_start, double x_range_end) +{ + // We get only two points that provide the horizontal range of the polygon. + // These two points show the x range of the polygon. We need to craft a + // polygon that has: + // + // that specified x range and + // + // the widest y range possible. + + resetPoints(); + + // top left point + setPoint(PointSpecs::TOP_LEFT_POINT, + QPointF(x_range_start, std::numeric_limits::max())); + + // top right point + setPoint(PointSpecs::TOP_RIGHT_POINT, + QPointF(x_range_end, std::numeric_limits::max())); + + // bottom right point + setPoint(PointSpecs::BOTTOM_RIGHT_POINT, + QPointF(x_range_end, std::numeric_limits::min())); + + // bottom left point + setPoint(PointSpecs::BOTTOM_LEFT_POINT, + QPointF(x_range_start, std::numeric_limits::min())); + + // Compute the min|max x|y coordinates of the polygon that will be used to + // quickly check if a point is outside. + computeMinMaxCoordinates(); +} + + +void +SelectionPolygon::set2D(QPointF top_left, + QPointF top_right, + QPointF bottom_right, + QPointF bottom_left) +{ + resetPoints(); + + // top left point + setPoint(PointSpecs::TOP_LEFT_POINT, top_left); + // qDebug() << "PointSpecs::TOP_LEFT_POINT:" << top_left; + + // top right point + setPoint(PointSpecs::TOP_RIGHT_POINT, top_right); + // qDebug() << "PointSpecs::TOP_RIGHT_POINT:" << top_right; + + // bottom right point + setPoint(PointSpecs::BOTTOM_RIGHT_POINT, bottom_right); + // qDebug() << "PointSpecs::BOTTOM_RIGHT_POINT:" << bottom_right; + + // bottom left point + setPoint(PointSpecs::BOTTOM_LEFT_POINT, bottom_left); + // qDebug() << "PointSpecs::BOTTOM_LEFT_POINT:" << bottom_left; + + // Compute the min|max x|y coordinates of the polygon that will be used to + // quickly check if a point is outside. + computeMinMaxCoordinates(); + + // qDebug() << toString(); +} + + +void +SelectionPolygon::convertTo1D() +{ + // When a 2D polygon is converted to a 1D polygon, the x axis range is + // unchanged, but the height is set to its maximum possible with the bottom + // line at y = min and the top line at y = max. + + computeMinMaxCoordinates(); + + set1D(m_minX, m_maxX); +} + + +QPointF +SelectionPolygon::getLeftMostPoint() const +{ + // When we say leftmost, that means that we are implicitely interesed in + // x-axis coordinate of the points. + + QPointF temp_point(std::numeric_limits::max(), 0); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + if(m_points[iter].x() < temp_point.x()) + { + temp_point = m_points[iter]; + } + } + + return temp_point; +} + + +QPointF +SelectionPolygon::getRightMostPoint() const +{ + // When we say rightmost, that means that we are implicitely interesed in + // x-axis coordinate of the points. + + QPointF temp_point(std::numeric_limits::min(), 0); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + if(m_points[iter].x() > temp_point.x()) + { + temp_point = m_points[iter]; + } + } + + return temp_point; +} + + +QPointF +SelectionPolygon::getTopMostPoint() const +{ + // When we say topmost or bottommost , that means that we are implicitely + // interesed in y-axis coordinate of the points. + + QPointF temp_point(0, std::numeric_limits::min()); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + if(m_points[iter].y() > temp_point.y()) + { + temp_point = m_points[iter]; + } + } + + return temp_point; +} + + +QPointF +SelectionPolygon::getBottomMostPoint() const +{ + // When we say topmost or bottommost , that means that we are implicitely + // interesed in y-axis coordinate of the points. + + QPointF temp_point(0, std::numeric_limits::max()); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + if(m_points[iter].y() < temp_point.y()) + { + temp_point = m_points[iter]; + } + } + + return temp_point; +} + + +const std::vector & +SelectionPolygon::getPoints() const +{ + return m_points; +} + + +QPointF +SelectionPolygon::getPoint(PointSpecs point_spec) const +{ + return m_points[static_cast(point_spec)]; +} + + +bool +SelectionPolygon::computeMinMaxCoordinates() +{ + // Set the variable to starting values that allow easy value comparisons with + // std::min() and std::max() for checking the x|y values below. + + m_minX = std::numeric_limits::max(); + m_minY = std::numeric_limits::max(); + m_maxX = std::numeric_limits::min(); + m_maxY = std::numeric_limits::min(); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + m_minX = std::min(m_points.at(iter).x(), m_minX); + m_maxX = std::max(m_points.at(iter).x(), m_maxX); + + m_minY = std::min(m_points.at(iter).y(), m_minY); + m_maxY = std::max(m_points.at(iter).y(), m_maxY); + } + + return true; +} + + +bool +SelectionPolygon::computeMinMaxCoordinates(double &min_x, + double &max_x, + double &min_y, + double &max_y) const +{ + // Set the variable to starting values that allow easy value comparisons with + // std::min() and std::max() for checking the x|y values below. + + min_x = std::numeric_limits::max(); + min_y = std::numeric_limits::max(); + max_x = std::numeric_limits::min(); + max_y = std::numeric_limits::min(); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + min_x = std::min(m_points.at(iter).x(), min_x); + max_x = std::max(m_points.at(iter).x(), max_x); + + min_y = std::min(m_points.at(iter).y(), min_y); + max_y = std::max(m_points.at(iter).y(), max_y); + } + + // qDebug() << "min_x:" << min_x << "max_x:" << max_x << "min_y:" << min_y + //<< "max_y:" << max_y; + + return true; +} + + +double +SelectionPolygon::width(bool &ok) const +{ + double min_x; + double min_y; + double max_x; + double max_y; + + computeMinMaxCoordinates(min_x, max_x, min_y, max_y); + + ok = true; + return max_x - min_x; +} + + +double +SelectionPolygon::height(bool &ok) const +{ + double min_x; + double min_y; + double max_x; + double max_y; + + computeMinMaxCoordinates(min_x, max_x, min_y, max_y); + + ok = true; + return max_y - min_y; +} + + +bool +SelectionPolygon::rangeX(double &range_start, double &range_end) const +{ + double min_y = std::numeric_limits::max(); + double max_y = std::numeric_limits::min(); + + return computeMinMaxCoordinates(range_start, range_end, min_y, max_y); +} + + +bool +SelectionPolygon::rangeY(double &range_start, double &range_end) const +{ + double min_x = std::numeric_limits::max(); + double max_x = std::numeric_limits::min(); + + return computeMinMaxCoordinates(min_x, max_x, range_start, range_end); +} + + +bool +SelectionPolygon::range(Axis axis, double &range_start, double &range_end) const +{ + if(axis == Axis::x) + return rangeX(range_start, range_end); + else if(axis == Axis::y) + return rangeY(range_start, range_end); + + return false; +} + + +// All this is valid only if the polygon has four sides. +// +// Transposing means that we take each point and permute x with y. +// During transposition, the TOP_RIGHT_POINT BOTTOM_LEFT_POINT are invariant. +// +// Transposition is like rotating the polygon arount the +// BOTTOM_LEFT_POINT--TOP_RIGHT_POINT axis, which make them invariant and +// permutates TOP_LEFT_POINT with BOTTOM_RIGHT_POINT. +// +// If iteration in the points is clockwise before, iteration below +// counter-clockwise after transposition, that is: +// TOP_LEFT_POINT becomes BOTTOM_RIGHT_POINT +// +SelectionPolygon +SelectionPolygon::transpose() const +{ + SelectionPolygon selection_polygon; + + // Make sure we do this for a polygon with four sides. + + if(m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal("The polygon must have four points, no less, no more"); + + // The two invariant points, that is, the two points that do no change + // position in the polygon corners. Of course, x becomes y. + selection_polygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + QPointF(getPoint(PointSpecs::TOP_RIGHT_POINT).y(), + getPoint(PointSpecs::TOP_RIGHT_POINT).x())); + + selection_polygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + QPointF(getPoint(PointSpecs::BOTTOM_LEFT_POINT).y(), + getPoint(PointSpecs::BOTTOM_LEFT_POINT).x())); + + // The two other points. + + selection_polygon.setPoint(PointSpecs::BOTTOM_RIGHT_POINT, + QPointF(getPoint(PointSpecs::TOP_LEFT_POINT).y(), + getPoint(PointSpecs::TOP_LEFT_POINT).x())); + + selection_polygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + QPointF(getPoint(PointSpecs::BOTTOM_RIGHT_POINT).y(), + getPoint(PointSpecs::BOTTOM_RIGHT_POINT).x())); + + return selection_polygon; +} + + +bool +SelectionPolygon::contains(const QPointF &tested_point) const +{ + // Easy check: if the point lies outside of most external limits of the + // polygon, return false. + + if(tested_point.x() < m_minX || tested_point.x() > m_maxX || + tested_point.y() < m_minY || tested_point.y() > m_maxY) + { + //qDebug() << "Testing point:" << tested_point + //<< "aginst polygon:" << toString() + //<< "is out of x and y ranges."; + return false; + } + + // There are two situations: + // + // 1. The selection polygon is a rectangle, we can check the tested_point very + // easily. + // + // 2. The selection polygon is a skewed rectangle, that is, it is a + // parallelogram, we need to really use the point-in-polygon algorithm. + + if(isRectangle()) + { + //qDebug() << "Selection polygon *is* rectangle."; + + double x = tested_point.x(); + double y = tested_point.y(); + + // return (x >= getPoint(PointSpecs::TOP_LEFT_POINT).x() && + // x <= getPoint(PointSpecs::TOP_RIGHT_POINT).x() && + // y >= getPoint(PointSpecs::BOTTOM_LEFT_POINT).y() && + // y <= getPoint(PointSpecs::TOP_LEFT_POINT).y()); + + bool res = x >= m_minX && x <= m_maxX && y >= m_minY && y <= m_maxY; + + //qDebug() << qSetRealNumberPrecision(10) << "Returning: " << res + //<< "for point:" << tested_point + //<< "and selection polygon:" << toString(); + + return res; + } + + //qDebug() << "Testing point:" << tested_point + //<< "aginst polygon:" << toString() + //<< "is tested against a skewed selection polygon rectangle."; + + // At this point, we know the selection polygon is not rectangle, we have to + // make the real check using the point-in-polygon algorithm. + + // This code is inspired by the work described here: + // https://wrf.ecse.rpi.edu/Research/Short_Notes/pnpoly.html + + // int pnpoly(int vertex_count, float *vertx, float *verty, float testx, + // float testy) + + int i = 0; + int j = 0; + bool is_inside = false; + + int vertex_count = m_points.size(); + + for(i = 0, j = vertex_count - 1; i < vertex_count; j = i++) + { + if(((m_points.at(i).y() > tested_point.y()) != + (m_points.at(j).y() > tested_point.y())) && + (tested_point.x() < (m_points.at(j).x() - m_points.at(i).x()) * + (tested_point.y() - m_points.at(i).y()) / + (m_points.at(j).y() - m_points.at(i).y()) + + m_points.at(i).x())) + is_inside = !is_inside; + } + + //if(is_inside) + //qDebug() << "Testing point:" << tested_point + //<< "aginst polygon:" << toString() << "turns out be in."; + //else + //qDebug() << "Testing point:" << tested_point + //<< "aginst polygon:" << toString() << "turns out be out."; + + return is_inside; +} + + +bool +SelectionPolygon::contains(const SelectionPolygon &selection_polygon) const +{ + // A polygon is inside another polygon if all its points are inside the + // polygon. + + bool is_inside = true; + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + if(!contains(selection_polygon.getPoint(static_cast(iter)))) + is_inside = false; + } + + return is_inside; +} + + +SelectionPolygon & +SelectionPolygon::operator=(const SelectionPolygon &other) +{ + if(this == &other) + return *this; + + if(other.m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal("Programming error."); + + if(m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal("Programming error."); + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + m_points[iter] = other.m_points[iter]; + + m_minX = other.m_minX; + m_minY = other.m_minY; + + m_maxX = other.m_maxX; + m_maxY = other.m_maxY; + + return *this; +} + + +void +SelectionPolygon::resetPoints() +{ + // Reset the points exactly as they were set upon construction of an empty + // polygon. + + m_points[0] = QPointF(std::numeric_limits::min(), + std::numeric_limits::max()); + m_points[0] = QPointF(std::numeric_limits::max(), + std::numeric_limits::max()); + m_points[0] = QPointF(std::numeric_limits::max(), + std::numeric_limits::min()); + m_points[0] = QPointF(std::numeric_limits::min(), + std::numeric_limits::max()); +} + + +bool +SelectionPolygon::is1D() const +{ + // qDebug() << "Selection polygon:" << toString(); + + bool ok = false; + + double width_value = width(ok); + if(!ok) + return false; + + double height_value = height(ok); + if(!ok) + return false; + + // qDebug() << "Width and height computations succeeded:" + //<< "width:" << width_value << "height:" << height_value; + + // A polygon is mono-dimensional if it has both non-0 width and no (max-min) + // width AND if the height is 0 or (max-min). + return ( + (width_value > 0 && width_value < std::numeric_limits::max() - + std::numeric_limits::min()) && + (height_value == 0 || + height_value == std::numeric_limits::max() - + std::numeric_limits::min())); +} + + +bool +SelectionPolygon::is2D() const +{ + // A selection polygon can behave like a line segment if the bottom side + // confounds with the top side. + + bool ok = false; + + double width_value = width(ok); + if(!ok) + return false; + + double height_value = height(ok); + if(!ok) + return false; + + // A polygon is two-dimensional if it has both non-0 width and no (max-min) + // width AND same for height. + return ( + (width_value > 0 && width_value < std::numeric_limits::max() - + std::numeric_limits::min()) && + (height_value > 0 && height_value < std::numeric_limits::max() - + std::numeric_limits::min())); +} + + +bool +SelectionPolygon::isRectangle() const +{ + // A skewed rectangle polygon has the following conditions verified: + // + // 1. If its left|right sides are vertical, then its top|bottom lines are + // *not* horizontal. + // + // 2 If its top|bottom lines are horizontal, then its left|right sides are + // *not* vertical. + // + // 3. Then, if a selection polygon is rectangle, its top|bottom lines are + // horizontal and its left|right lines are vertical. + + // A line is vertical if its two defining points have the same X. + // A line is horizontal if its two defining points have the same Y. + + // Try the horiontal top|bottom lines. + + if(getPoint(PointSpecs::TOP_LEFT_POINT).y() == + getPoint(PointSpecs::TOP_RIGHT_POINT).y() && + getPoint(PointSpecs::BOTTOM_LEFT_POINT).y() == + getPoint(PointSpecs::BOTTOM_RIGHT_POINT).y()) + { + // We have horizontal top|bottom lines + + // Try the vertical lines + + if(getPoint(PointSpecs::TOP_LEFT_POINT).x() == + getPoint(PointSpecs::BOTTOM_LEFT_POINT).x() && + getPoint(PointSpecs::TOP_RIGHT_POINT).x() == + getPoint(PointSpecs::BOTTOM_RIGHT_POINT).x()) + { + // The top|bottom lines are vertical + + return true; + } + } + + return false; +} + + +QString +SelectionPolygon::toString() const +{ + // By essence, a selection polygon is designed to always have 4 points. + + if(m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal("Programming error."); + + // qDebug() << "size:" << m_points.size(); + + QString text = "Selection polygon points, from top left, clockwise\n"; + + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + QPointF iter_point = m_points[iter]; + + QString x_string = "NOT_SET"; + + if(iter_point.x() != std::numeric_limits::min() && + iter_point.x() != std::numeric_limits::max()) + x_string = QString("%1").arg(iter_point.x(), 0, 'f', 10); + + QString y_string = "NOT_SET"; + + if(iter_point.y() != std::numeric_limits::min() && + iter_point.y() != std::numeric_limits::max()) + y_string = QString("%1").arg(iter_point.y(), 0, 'f', 10); + + text += QString("(%1,%2)\n").arg(x_string).arg(y_string); + } + + if(m_minX != std::numeric_limits::min() && m_minX != std::numeric_limits::max()) + text += QString("minX: %1 - ").arg(m_minX, 0, 'f', 10); + else + text += QString("minX: NOT_SET - "); + + if(m_maxX != std::numeric_limits::min() && m_maxX != std::numeric_limits::max()) + text += QString("maxX: %1 - ").arg(m_maxX, 0, 'f', 10); + else + text += QString("maxX: NOT_SET - "); + + if(m_minY != std::numeric_limits::min() && m_minY != std::numeric_limits::max()) + text += QString("minY: %1 - ").arg(m_minY, 0, 'f', 10); + else + text += QString("minY: NOT_SET - "); + + if(m_maxY != std::numeric_limits::min() && m_maxY != std::numeric_limits::max()) + text += QString("maxY: %1 - ").arg(m_maxY, 0, 'f', 10); + else + text += QString("maxY: NOT_SET - "); + + return text; +} + + +QString +SelectionPolygon::toShort4PointsString() const +{ + // By essence, a selection polygon is designed to always have 4 points. + + if(m_points.size() != static_cast(PointSpecs::ENUM_LAST)) + qFatal("Programming error."); + + // qDebug() << "size:" << m_points.size(); + + QString text = "["; + + QString x_string = "NOT_SET"; + QString y_string = "NOT_SET"; + + // There are two situations: + // + // 1. The selection polygon is 1D, we only need to provide two points + // + // 2. The selection polygon is 2D, we need to provide four points. + + if(is1D()) + { + text += QString("(%1,%2)").arg(getLeftMostPoint().x()).arg("NOT_SET"); + text += QString("(%1,%2)").arg(getRightMostPoint().x()).arg("NOT_SET"); + } + else + { + for(int iter = 0; iter < static_cast(PointSpecs::ENUM_LAST); ++iter) + { + QPointF iter_point = m_points[iter]; + + + if(iter_point.x() != std::numeric_limits::min() && + iter_point.x() != std::numeric_limits::max()) + x_string = QString("%1").arg(iter_point.x(), 0, 'f', 3); + + if(iter_point.y() != std::numeric_limits::min() && + iter_point.y() != std::numeric_limits::max()) + y_string = QString("%1").arg(iter_point.y(), 0, 'f', 3); + + text += QString("(%1,%2)").arg(x_string).arg(y_string); + } + } + + text += "]"; + + return text; +} + + +void +SelectionPolygon::debugAlgorithm(const SelectionPolygon &selection_polygon, + const QPointF &tested_point) +{ + bool is_point_inside = false; + + QString debug_string; + + is_point_inside = selection_polygon.contains(tested_point); + debug_string = QString("(%1,%2) is inside: %3") + .arg(tested_point.x(), 0, 'f', 10) + .arg(tested_point.y(), 0, 'f', 10) + .arg(is_point_inside ? "true" : "false"); + qDebug().noquote() << debug_string; +} +} // namespace pappso + +#if 0 + +// This is to test the algo that check if a point is left of a line or right of +// it or onto it. In this implementation, two lines define the vertical sides of +// a polygon (square to ease analysis) and if the point is on the left line, then it +// is considered ok, that is, that it is on the right side of the line and if it +// is on the right line, then it is considered ok, that is that it is on the +// left side of the line. If both conditions are ok, then the point is inside +// the vertical lines of the polygon. + + qDebug(); + + pappso::SelectionPolygon selection_polygon(QPointF(22.4, 473), + QPointF(28.9, 473), + QPointF(28.9, 250), + QPointF(22.4, 250)); + qDebug() << "The test selection polygon:" << selection_polygon.toString(); + + std::vector test_points; + + test_points.push_back(QPointF(25, 250)); + test_points.push_back(QPointF(22.3, 362)); + test_points.push_back(QPointF(22.4, 473)); + test_points.push_back(QPointF(22.4, 473.5)); + test_points.push_back(QPointF(25, 250)); + test_points.push_back(QPointF(25, 250.5)); + test_points.push_back(QPointF(25, 360)); + test_points.push_back(QPointF(28.9, 250)); + test_points.push_back(QPointF(29, 250)); + test_points.push_back(QPointF(29, 360)); + test_points.push_back(QPointF(28.9, 473)); + test_points.push_back(QPointF(28.9, 473.5)); + test_points.push_back(QPointF(20, 200)); + test_points.push_back(QPointF(20, 600)); + test_points.push_back(QPointF(35, 200)); + test_points.push_back(QPointF(35, 600)); + + // double res = sideofline(XX;YY;xA;yA;xB;yB) = + // (xB-xA) * (YY-yA) - (yB-yA) * (XX-xA) + + // If res == 0, the point is on the line + // If rest < 0, the point is on the right of the line + // If rest > 0, the point is on the left of the line + + for(auto &&data_point : test_points) + { + // Left vertical line of the polygon + + // Bottom point + double xA_left = + selection_polygon.getPoint(pappso::PointSpecs::BOTTOM_LEFT_POINT).x(); + double yA_left = + selection_polygon.getPoint(pappso::PointSpecs::BOTTOM_LEFT_POINT).y(); + + // Top point + double xB_left = + selection_polygon.getPoint(pappso::PointSpecs::TOP_LEFT_POINT).x(); + double yB_left = + selection_polygon.getPoint(pappso::PointSpecs::TOP_LEFT_POINT).y(); + + if((xB_left - xA_left) * (data_point.y() - yA_left) - + (yB_left - yA_left) * (data_point.x() - xA_left) > + 0) + { + // The point is left of the left line. We can remove the point + // from the mass spectrum. + + qDebug() << qSetRealNumberPrecision(10) + << "Filtered out point (left of left line):" + << data_point.x() << "-" << data_point.y(); + continue; + } + else + { + qDebug() << qSetRealNumberPrecision(10) + << "Kept point (right of left line):" << data_point.x() + << "-" << data_point.y(); + } + + // Right vertical line of the polygon + + // Bottom point + double xA_right = + selection_polygon.getPoint(pappso::PointSpecs::BOTTOM_RIGHT_POINT).x(); + double yA_right = + selection_polygon.getPoint(pappso::PointSpecs::BOTTOM_RIGHT_POINT).y(); + + // Top point + double xB_right = + selection_polygon.getPoint(pappso::PointSpecs::TOP_RIGHT_POINT).x(); + double yB_right = + selection_polygon.getPoint(pappso::PointSpecs::TOP_RIGHT_POINT).y(); + + if((xB_right - xA_right) * (data_point.y() - yA_right) - + (yB_right - yA_right) * (data_point.x() - xA_right) < + 0) + { + qDebug() << qSetRealNumberPrecision(10) + << "Filtered out point (right of right line):" + << data_point.x() << "-" << data_point.y(); + } + else + { + qDebug() << qSetRealNumberPrecision(10) + << "Definitively kept point (left of right line):" + << data_point.x() << "-" << data_point.y(); + } + } +#endif + + +#if 0 + // This is code to test the algorithm we have to establish if a given + // point is inside a selection polygon. + + // First polygon that is square. + SelectionPolygon first_polygon( + QPointF(3, 8), QPointF(12, 8), QPointF(12, 3), QPointF(3, 3)); + + qDebug() << "square rectangle polygon: " << first_polygon.toString(); + + qDebug() << "outside"; + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(2,1)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(2.999999,5)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(2.999999,8.000001)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(2,5)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(2,9)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,1)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,8.0000001)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(12,1)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(12.0000001,3)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(14,3)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(14,5)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(14,8)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(14,9)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,9)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,2.9999999)); + + qDebug() << "on the lines"; + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(3,4)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,3)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(12,3)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(12,7)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(12,8)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,8)); + + qDebug() << "inside"; + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(4,4)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(3.00001, 3.00001)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,4)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,3.1)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(11,5)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(11.99999,5)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF(7,7.9)); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + SelectionPolygon::debugAlgorithm(first_polygon, QPointF()); + + + // Second polygon that is skewed. + SelectionPolygon second_polygon( + QPointF(9, 8), QPointF(12, 8), QPointF(6, 2), QPointF(3, 2)); + + qDebug() << "skewed rectangle polygon: " << second_polygon.toString(); + + qDebug() << "outside"; + + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2,1)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2.999999,1.999999)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2.999999,3)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2.999999,8.000001)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2,5)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(2,9)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(6,5.0000001)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(7,1)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(7,2.999999)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(9,4.999999)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(9,8.0000001)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(12.00000001,8)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(12,7.999999)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(14,3)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(14,5)); + + qDebug() << "on the lines"; + + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(3,2)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(6,5)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(12,8)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(9,8)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(9,5)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(11,7)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(7,6)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(4,3)); + + qDebug() << "inside"; + + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(3.00001,2.000001)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(4,2.000001)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(6.000001,2.00003)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(7,4)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(8.99999,5)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(10,7.99999)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(5,3)); + SelectionPolygon::debugAlgorithm(second_polygon, QPointF(5,3.99999)); +#endif + + +#if 0 + +void +SelectionPolygon::reorderPoints() +{ + // We want to make sure that we actually have the right QPointF instances at + // the right corners. + + computeMinMaxCoordinates(); + + // Start by finding a point almost centered in the polygon. Not exactly + // centered because our polygon can be squared and we'll look at angles + // between the center-point->polygon-point_n and + // center-point->polygon-point_n'. + + double PI = 3.14159265358979323846; + QPointF center_point(0, 0); + + for(auto &point : m_points) + { + center_point.setX(center_point.x() + point.x()); + center_point.setY(center_point.y() + point.y()); + } + + center_point.setX(center_point.x() / m_points.size()); + center_point.setY(center_point.y() / m_points.size()); + + // For a rectangle polygon, that would be the exact center and the angles + // between the line segments would be similar two-by-two. So we need to move + // the center_point a bit. + + double distance_x = center_point.x() - m_minX; + double distance_y = center_point.y() - m_minY; + + center_point.setX(center_point.x() - (distance_x / 20)); + center_point.setY(center_point.y() - (distance_y / 20)); + + std::sort(m_points.begin(), + m_points.end(), + [center_point, PI](const QPointF &a, const QPointF &b) -> bool { + double a1 = std::fmod( + std::atan2(a.x() - center_point.x(), a.y() - center_point.y()) * + 180.0 / PI + + 360, + (double)360); + + double a2 = std::fmod( + std::atan2(b.x() - center_point.x(), b.y() - center_point.y()) * + 180.0 / PI + + 360, + (double)360); + + // Original version that had problems because arguments to '%' + // were double and int. fmod() is % for double. + //(std::atan2(b.x() - center_point.x(), b.y() - center_point.y()) + //* 180.0 / PI + 360) % 360; + + return (int)(a1 - a2); + }); +} + +#endif + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/selectionpolygon.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/selectionpolygon.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/selectionpolygon.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/selectionpolygon.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,216 @@ +// Copyright 2021 Filippo Rusconi +// GPLv3+ + +#pragma once + +/////////////////////// StdLib includes +#include +#include + +/////////////////////// Qt includes +#include +#include + + +/////////////////////// Local includes +#include "../../exportinmportconfig.h" +#include "../../types.h" + +namespace pappso +{ + + +enum class PointSpecs +{ + // Starting top left and then clockwise + TOP_LEFT_POINT = 0, + TOP_RIGHT_POINT = 1, + BOTTOM_RIGHT_POINT = 2, + BOTTOM_LEFT_POINT = 3, + ENUM_LAST = 4, +}; + + +enum class DataDimension +{ + NOT_SET = 0, + HORIZONTAL, + VERTICAL +}; + + +enum class PolygonType +{ + NOT_SET = 0x0000, + + TOP_LINE = 1 << 0, + BOTTOM_LINE = 1 << 1, + + HORIZONTAL_LINES = (TOP_LINE | BOTTOM_LINE), + + RIGHT_LINE = 1 << 2, + LEFT_LINE = 1 << 3, + + VERTICAL_LINES = (RIGHT_LINE | LEFT_LINE), + + FULL_POLYGON = (HORIZONTAL_LINES | VERTICAL_LINES) +}; + + +class PMSPP_LIB_DECL SelectionPolygon +{ + public: + // Constructor with no arguments + SelectionPolygon(); + + SelectionPolygon(QPointF top_left_point, QPointF top_right_point); + + SelectionPolygon(QPointF top_left_point, + QPointF top_right_point, + QPointF bottom_right_point, + QPointF bottom_left_point); + + SelectionPolygon(const SelectionPolygon &other); + + virtual ~SelectionPolygon(); + + + void setPoint(PointSpecs point_spec, double x, double y); + void setPoint(PointSpecs point_spec, QPointF point); + void copyPoint(PointSpecs point_spec_src, PointSpecs point_spec_dest); + + void set1D(double x_range_start, double x_range_end); + void set2D(QPointF top_left, + QPointF top_right, + QPointF bottom_right, + QPointF bottom_left); + void convertTo1D(); + + const std::vector &getPoints() const; + + QPointF getLeftMostPoint() const; + QPointF getRightMostPoint() const; + QPointF getTopMostPoint() const; + QPointF getBottomMostPoint() const; + + QPointF getPoint(PointSpecs point_spec) const; + + bool computeMinMaxCoordinates(); + bool computeMinMaxCoordinates(double &min_x, + double &max_x, + double &min_y, + double &max_y) const; + + double width(bool &ok) const; + double height(bool &ok) const; + + bool rangeX(double &range_start, double &range_end) const; + bool rangeY(double &range_start, double &range_end) const; + bool range(Axis axis, double &range_start, double &range_end) const; + + SelectionPolygon transpose() const; + + bool contains(const QPointF &tested_point) const; + bool contains(const SelectionPolygon &selection_polygon) const; + + SelectionPolygon &operator=(const SelectionPolygon &other); + + void resetPoints(); + + bool is1D() const; + bool is2D() const; + bool isRectangle() const; + + QString toShort4PointsString() const; + QString toString() const; + + + static void debugAlgorithm(const SelectionPolygon &selection_polygon, + const QPointF &tested_point); + + protected: + // The PointSpecs enum and the setPoint function ensure that there are no more + // than four points in the vector. + + // We want to create a largest polygon possible, by settting the first point, + // top_left on the lowest_x and highest_y, the top_right on the highest_x and + // highest_y, the bottom_right on the highest_x and lowest_y, the bottom_left + // at the lowest_x and lowest_y. + std::vector m_points = {QPointF(std::numeric_limits::min(), + std::numeric_limits::max()), + QPointF(std::numeric_limits::max(), + std::numeric_limits::max()), + QPointF(std::numeric_limits::max(), + std::numeric_limits::min()), + QPointF(std::numeric_limits::min(), + std::numeric_limits::min())}; + + double m_minX = std::numeric_limits::min(); + double m_minY = std::numeric_limits::min(); + + double m_maxX = std::numeric_limits::max(); + double m_maxY = std::numeric_limits::max(); +}; + + +struct PMSPP_LIB_DECL SelectionPolygonSpec +{ + + SelectionPolygon selectionPolygon; + DataKind dataKind = DataKind::unset; + + // NO specification of the axis because it is implicit that MZ is Y and the + // checked value is either DT or RT depending on dataKind. + + SelectionPolygonSpec(); + + SelectionPolygonSpec(const SelectionPolygon &selection_polygon, + DataKind data_kind) + : selectionPolygon(selection_polygon), + dataKind(data_kind) + { + } + + SelectionPolygonSpec(const SelectionPolygonSpec &other) + : selectionPolygon(other.selectionPolygon), + dataKind(other.dataKind) + { + } + + SelectionPolygonSpec & + operator=(const SelectionPolygonSpec &other) + { + if(this == &other) + return *this; + + selectionPolygon = other.selectionPolygon; + dataKind = other.dataKind; + + return *this; + } + + + QString + toString() const + { + QString text = "Selection polygon spec:"; + text += selectionPolygon.toString(); + + text += " - data kind: "; + + if(dataKind == DataKind::dt) + text += "dt."; + else if(dataKind == DataKind::mz) + text += "m/z."; + else if(dataKind == DataKind::rt) + text += "rt."; + else + text += "unset."; + + return text; + } +}; + + +} // namespace pappso + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracecombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracecombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracecombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracecombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -46,4 +46,5 @@ } + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracecombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracecombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracecombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracecombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -32,9 +32,8 @@ TraceCombiner(int decimal_places); TraceCombiner(const TraceCombiner &other); TraceCombiner(TraceCombinerCstSPtr other); - virtual ~TraceCombiner(); - protected: + virtual ~TraceCombiner(); }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/traceminuscombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/traceminuscombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/traceminuscombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/traceminuscombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,13 +31,13 @@ TraceMinusCombiner::TraceMinusCombiner(const TraceMinusCombiner &other) - : TraceCombiner(other.m_decimalPlaces) + : TraceCombiner(other) { } TraceMinusCombiner::TraceMinusCombiner(TraceMinusCombinerCstSPtr other) - : TraceCombiner(other->m_decimalPlaces) + : TraceCombiner(other) { } @@ -116,40 +116,7 @@ if(!map_trace_in.size()) return map_trace_out; - for(auto &map_pair : map_trace_in) - { - - // If the data point is 0-intensity, then do nothing! - if(!map_pair.second) - continue; - - double x = Utils::roundToDecimals(map_pair.first, m_decimalPlaces); - - std::map::iterator map_iterator; - - std::pair::iterator, bool> result; - - result = map_trace_out.insert( - std::pair(x, -map_pair.second)); - - if(result.second) - { - // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()"; - // The new element was inserted, we have nothing to do. - } - else - { - // The key already existed! The item was not inserted. We need to - // update the value. - - result.first->second -= map_pair.second; - } - } - - // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()" - //<< "Prior to returning map_trace_out, its size is:" << map_trace_out.size(); - - return map_trace_out; + return combine(map_trace_out, map_trace_in.toTrace()); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/traceminuscombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/traceminuscombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/traceminuscombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/traceminuscombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -34,13 +34,14 @@ TraceMinusCombiner(int decimal_places); TraceMinusCombiner(const TraceMinusCombiner &other); TraceMinusCombiner(TraceMinusCombinerCstSPtr other); + virtual ~TraceMinusCombiner(); virtual MapTrace &combine(MapTrace &map_trace, - const Trace &trace) const override; + const Trace &trace) const override; - virtual MapTrace &combine(MapTrace &map_trace_out, - const MapTrace &map_trace_in) const override; + MapTrace &combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const override; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracepluscombiner.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracepluscombiner.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracepluscombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracepluscombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -20,7 +20,7 @@ { -TracePlusCombiner::TracePlusCombiner() +TracePlusCombiner::TracePlusCombiner() : TraceCombiner() { } @@ -32,14 +32,15 @@ TracePlusCombiner::TracePlusCombiner(const TracePlusCombiner &other) - : TraceCombiner(other.m_decimalPlaces) + : TraceCombiner(other) { } TracePlusCombiner::TracePlusCombiner(TracePlusCombinerCstSPtr other) - : TraceCombiner(other->m_decimalPlaces) + : TraceCombiner(other) { + qDebug(); } @@ -49,26 +50,15 @@ MapTrace & -TracePlusCombiner::combine(MapTrace &map_trace, const Trace &trace) const +TracePlusCombiner::combine(MapTrace &map_trace, + const Trace &trace) const { - // qDebug(); + //qDebug(); if(!trace.size()) return map_trace; - // Let's check if we need to apply a filter to the input data. - - Trace filtered_trace(trace); - - if(m_isApplyXRangeFilter) - { - m_filterXRange.filter(filtered_trace); - - if(!filtered_trace.size()) - return map_trace; - } - - for(auto ¤t_data_point : filtered_trace) + for(auto ¤t_data_point : trace) { // If the data point is 0-intensity, then do nothing! @@ -107,7 +97,7 @@ MapTrace & TracePlusCombiner::combine(MapTrace &map_trace_out, - const MapTrace &map_trace_in) const + const MapTrace &map_trace_in) const { // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()" //<< "map trace size:" << map_trace_out.size() @@ -116,8 +106,6 @@ if(!map_trace_in.size()) return map_trace_out; - // The call below will ensure that if there are filtering steps to apply, they - // are actually applied. return combine(map_trace_out, map_trace_in.toTrace()); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracepluscombiner.h libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracepluscombiner.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/combiners/tracepluscombiner.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/combiners/tracepluscombiner.h 2022-10-27 09:16:15.000000000 +0000 @@ -28,18 +28,19 @@ friend class MassSpectrumPlusCombiner; - protected: public: TracePlusCombiner(); TracePlusCombiner(int decimal_places); TracePlusCombiner(const TracePlusCombiner &other); TracePlusCombiner(TracePlusCombinerCstSPtr other); + virtual ~TracePlusCombiner(); virtual MapTrace &combine(MapTrace &map_trace, - const Trace &trace) const override; - virtual MapTrace &combine(MapTrace &map_trace_out, - const MapTrace &map_trace_in) const override; + const Trace &trace) const override; + + MapTrace &combine(MapTrace &map_trace_out, + const MapTrace &map_trace_in) const override; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracedetectionzivy.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracedetectionzivy.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracedetectionzivy.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracedetectionzivy.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -111,30 +111,49 @@ // strictly greater than the two surrounding values. In case of // equality (very rare, can happen with some old old spectrometers) we // take the last equal point to be the peak - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); + std::size_t size = xic.size(); + if(size < 4) + { + qDebug() << QObject::tr( + "The original XIC is too small to detect peaks (%1)") + .arg(xic.size()); + return; + } + if(size <= m_maxMin.getMaxMinHalfEdgeWindows()) + return; + if(size <= m_minMax.getMinMaxHalfEdgeWindows()) + return; + Trace xic_minmax(xic); //"close" courbe du haut if(m_smooth.getMeanHalfEdgeWindows() != 0) { + qDebug() << "f"; m_smooth.filter(xic_minmax); } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); Trace xic_maxmin(xic_minmax); //"open" courbe du bas - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); + try { + qDebug() << "f1"; m_minMax.filter(xic_minmax); + qDebug() << "f2"; m_maxMin.filter(xic_maxmin); } catch(const ExceptionOutOfRange &e) { - throw ExceptionNotPossible( - QObject::tr("The original XIC is too small to detect peaks (%1) :\n%2") - .arg(xic.size()) - .arg(e.qwhat())); + qDebug() << QObject::tr( + "The original XIC is too small to detect peaks (%1) :\n%2") + .arg(xic.size()) + .arg(e.qwhat()); + return; } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug() << "a"; + std::vector::const_iterator previous_rt = xic_minmax.begin(); std::vector::const_iterator current_rt = (previous_rt + 1); std::vector::const_iterator last_rt = (xic_minmax.end() - 1); @@ -143,7 +162,7 @@ (xic_maxmin.begin() + 1); std::vector::const_iterator xic_position = xic.begin(); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug() << "b"; while(current_rt != last_rt) // for (unsigned int i = 1, count = 0; i < xic_minmax.size() - 1; ) { @@ -220,6 +239,6 @@ current_rt_on_maxmin++; } } // end loop for peaks - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); } } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracedetectionzivy.h libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracedetectionzivy.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracedetectionzivy.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracedetectionzivy.h 2022-10-27 09:16:15.000000000 +0000 @@ -35,12 +35,6 @@ class PMSPP_LIB_DECL TraceDetectionZivy : public TraceDetectionInterface { - private: - FilterMorphoMean m_smooth; - FilterMorphoMinMax m_minMax; - FilterMorphoMaxMin m_maxMin; - pappso_double m_detectionThresholdOnMinMax; - pappso_double m_detectionThresholdOnMaxMin; public: TraceDetectionZivy(unsigned int smoothing_half_window_length, @@ -66,6 +60,14 @@ void detect(const Trace &xic, TraceDetectionSinkInterface &sink) const override; + + + private: + FilterMorphoMean m_smooth; + FilterMorphoMinMax m_minMax; + FilterMorphoMaxMin m_maxMin; + pappso_double m_detectionThresholdOnMinMax; + pappso_double m_detectionThresholdOnMaxMin; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeak.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeak.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeak.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeak.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,6 +31,7 @@ TracePeak::TracePeak() { } + TracePeak::TracePeak(std::vector::const_iterator it_begin, std::vector::const_iterator it_end) { @@ -41,6 +42,24 @@ m_area = areaTrace(it_begin, it_end); } +TracePeak::TracePeak(std::vector::const_iterator it_begin, + std::vector::const_iterator it_end, + bool remove_base) +{ + + m_left = *it_begin; + m_right = *(it_end - 1); + m_max = *maxYDataPoint(it_begin, it_end); + m_area = areaTrace(it_begin, it_end); + if(remove_base) + { + // remove the base of this peak + m_area -= std::min(m_left.y, m_right.y) * (m_right.x - m_left.x); + if(m_area < 0) + m_area = 0; + } +} + TracePeak::TracePeak(const TracePeak &other) { m_area = other.m_area; @@ -117,4 +136,38 @@ return (false); } + +const DataPoint & +TracePeak::getMaxXicElement() const +{ + return m_max; +} + +const DataPoint & +TracePeak::getLeftBoundary() const +{ + return m_left; +} + + +bool +TracePeak::operator==(const TracePeak &other) const +{ + return ((m_area == other.m_area) && (m_max == other.m_max) && + (m_left == other.m_left) && (m_right == other.m_right)); +} + +TracePeak & +TracePeak::operator=(const TracePeak &other) +{ + if(this == &other) + return *this; + + m_area = other.m_area; + m_max = other.m_max; + m_left = other.m_left; + m_right = other.m_right; + + return *this; +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeak.h libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeak.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeak.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeak.h 2022-10-27 09:16:15.000000000 +0000 @@ -38,18 +38,22 @@ * */ class PMSPP_LIB_DECL TracePeak { - protected: - pappso_double m_area = 0; - DataPoint m_max; - DataPoint m_left; - DataPoint m_right; - public: TracePeak(); /** @brief construct a peak given a trace, begin and end x coordinate */ TracePeak(std::vector::const_iterator it_begin, std::vector::const_iterator it_end); + + /** @brief construct a peak given a trace, begin and end x coordinate + * + * @param it_begin begining of trace + * @param it_end end of trace + * @param remove_base if true, remove the base peak signal + */ + TracePeak(std::vector::const_iterator it_begin, + std::vector::const_iterator it_end, + bool remove_base); TracePeak(const TracePeak &other); ~TracePeak(); @@ -57,36 +61,34 @@ TracePeakCstSPtr makeTracePeakCstSPtr() const; DataPoint &getMaxXicElement(); - const DataPoint & - getMaxXicElement() const - { - return m_max; - }; + const DataPoint &getMaxXicElement() const; void setMaxXicElement(const DataPoint &max); DataPoint &getLeftBoundary(); - const DataPoint & - getLeftBoundary() const - { - return m_left; - }; + const DataPoint &getLeftBoundary() const; void setLeftBoundary(const DataPoint &left); DataPoint &getRightBoundary(); const DataPoint &getRightBoundary() const; void setRightBoundary(const DataPoint &right); pappso_double getArea() const; + + void setArea(pappso_double area); bool containsRt(pappso::pappso_double rt) const; - bool - operator==(const TracePeak &other) const - { - return ((m_area == other.m_area) && (m_max == other.m_max) && - (m_left == other.m_left) && (m_right == other.m_right)); - }; + bool operator==(const TracePeak &other) const; + + TracePeak &operator=(const TracePeak &other); + + + protected: + pappso_double m_area = 0; + DataPoint m_max; + DataPoint m_left; + DataPoint m_right; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeaklist.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeaklist.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeaklist.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeaklist.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,87 @@ +/** + * \file pappsomspp/processing/detection/tracepeaklist.cpp + * \date 15/09/2021 + * \author Olivier Langella + * \brief trace peak list + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +#include "tracepeaklist.h" + +using namespace pappso; + +TracePeakList::TracePeakList() +{ +} + +TracePeakList::TracePeakList(const TracePeakList &other) + : std::vector(other) +{ +} + +TracePeakList::~TracePeakList() +{ +} + +void +pappso::TracePeakList::setTracePeak(pappso::TracePeak &xic_peak) +{ + push_back(xic_peak); +} + + +std::vector::iterator +pappso::findBestTracePeakGivenRtList(std::vector::iterator begin, + std::vector::iterator end, + const std::vector &rt_list, + std::size_t &nb_peaks) +{ + // get peak containing rt ahead : + auto itend = std::partition(begin, end, [rt_list](const TracePeak &a) { + for(double rt : rt_list) + { + if(a.containsRt(rt)) + { + return true; + }; + } + return false; + }); + nb_peaks = std::distance(begin, itend); + if(nb_peaks == 0) + return end; + return std::max_element( + begin, itend, [](const TracePeak &a, const TracePeak &b) { + return a.getArea() < b.getArea(); + }); +} + +std::vector::iterator +pappso::findTracePeakGivenRt(std::vector::iterator begin, + std::vector::iterator end, + double rt) +{ + return find_if( + begin, end, [rt](const TracePeak &a) { return a.containsRt(rt); }); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeaklist.h libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeaklist.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/detection/tracepeaklist.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/detection/tracepeaklist.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,97 @@ +/** + * \file pappsomspp/processing/detection/tracepeaklist.h + * \date 15/09/2021 + * \author Olivier Langella + * \brief trace peak list + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +#pragma once + +#include "tracepeak.h" +#include "tracedetectioninterface.h" + + +namespace pappso +{ +/** + * @todo write docs + */ +class PMSPP_LIB_DECL TracePeakList : public std::vector, + public TraceDetectionSinkInterface +{ + public: + /** + * Default constructor + */ + TracePeakList(); + + /** + * Copy constructor + * + * @param other TODO + */ + TracePeakList(const TracePeakList &other); + + /** + * Destructor + */ + virtual ~TracePeakList(); + + virtual void setTracePeak(TracePeak &xic_peak) override; +}; + + +/** @brief find the best peak matching a list of retention times + * + * @param begin begin iterator + * @param end end iterator + * @param rt_list retention time list in seconds + * @param nb_peaks retrieve the number of detected peaks concerned by the + * retention times + * @return iterator on the best peak (bigger area) concerned by the retention + * times + * + * */ +PMSPP_LIB_DECL std::vector::iterator +findBestTracePeakGivenRtList(std::vector::iterator begin, + std::vector::iterator end, + const std::vector &rt_list, + std::size_t &nb_peaks); + + +/** @brief find the peak matching a retention time + * + * @param begin begin iterator + * @param end end iterator + * @param rt retention time in seconds + * @return iterator on the peak concerned by the retention time + * */ +PMSPP_LIB_DECL std::vector::iterator +findTracePeakGivenRt(std::vector::iterator begin, + std::vector::iterator end, + double rt); + + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,164 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#include + + +#include +#include + +#include "../../exception/exceptionnotrecognized.h" + +#include "filterceilingamplitudepercentage.h" + + +namespace pappso +{ + + +FilterCeilingAmplitudePercentage::FilterCeilingAmplitudePercentage( + double percentage) +{ + m_percentage = percentage; +} + + +FilterCeilingAmplitudePercentage::FilterCeilingAmplitudePercentage( + const FilterCeilingAmplitudePercentage &other) +{ + m_percentage = other.m_percentage; +} + + +FilterCeilingAmplitudePercentage::~FilterCeilingAmplitudePercentage() +{ +} + +FilterCeilingAmplitudePercentage & +FilterCeilingAmplitudePercentage::operator=( + const FilterCeilingAmplitudePercentage &other) +{ + if(&other == this) + return *this; + + m_percentage = other.m_percentage; + + return *this; +} + + +FilterCeilingAmplitudePercentage::FilterCeilingAmplitudePercentage( + const QString ¶meters) +{ + buildFilterFromString(parameters); +} + + +void +FilterCeilingAmplitudePercentage::buildFilterFromString(const QString ¶meters) +{ + // Typical string: "CeilingAmplitudePercentage|15" + if(parameters.startsWith(QString("%1|").arg(name()))) + { + QStringList params = parameters.split("|").back().split(";"); + + m_percentage = params.at(0).toDouble(); + } + else + { + throw pappso::ExceptionNotRecognized( + QString( + "Building of FilterCeilingAmplitudePercentage from string %1 failed") + .arg(parameters)); + } +} + + +Trace & +FilterCeilingAmplitudePercentage::filter(Trace &data_points) const +{ + + auto it_min = minYDataPoint(data_points.begin(), data_points.end()); + auto it_max = maxYDataPoint(data_points.begin(), data_points.end()); + + if(it_min == data_points.end() || it_max == data_points.end()) + return data_points; + + double min = it_min->y; + double max = it_max->y; + + double amplitude = max - min; + + double amplitude_ratio = amplitude * m_percentage / 100; + + double threshold = min + amplitude_ratio; + + // Since we never remove points, we only change their y value, we can do the + // filtering inplace. + + for(auto &&data_point : data_points) + { + // Change the value to be threshold (re-ceiling in action). + if(data_point.y > threshold) + { + data_point.y = threshold; + } + } + + return data_points; +} + + +double +FilterCeilingAmplitudePercentage::getPercentage() const +{ + return m_percentage; +} + + +//! Return a string with the textual representation of the configuration data. +QString +FilterCeilingAmplitudePercentage::toString() const +{ + return QString("%1|%2").arg(name()).arg( + QString::number(m_percentage, 'f', 2)); +} + + +QString +FilterCeilingAmplitudePercentage::name() const +{ + return "CeilingAmplitudePercentage"; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterceilingamplitudepercentage.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,93 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#pragma once + + +#include + +#include "../../trace/trace.h" +#include "../../exportinmportconfig.h" +#include "filternameinterface.h" + + +namespace pappso +{ + + +class FilterCeilingAmplitudePercentage; + +typedef std::shared_ptr FilterCeilingAmplitudePercentageSPtr; +typedef std::shared_ptr FilterCeilingAmplitudePercentageCstSPtr; + + +/** + * @brief Redefines the ceiling intensity of the Trace + * + * The amplitude of the trace is computed (maxValue - minValue) + * Its fraction is calculated = amplitude * (percentage / 100) + * The threshold value is computed as (minValue + fraction) + * + * When the values to be filtered are above that threshold they acquire that + * threshold value. + * + * When the values to be filtered are below that threshold they remain + * unchanged. + * + * This effectively re-ceilings the values to threshold. + */ +class PMSPP_LIB_DECL FilterCeilingAmplitudePercentage : public FilterNameInterface +{ + public: + FilterCeilingAmplitudePercentage(double percentage); + FilterCeilingAmplitudePercentage(const QString ¶meters); + FilterCeilingAmplitudePercentage(const FilterCeilingAmplitudePercentage &other); + + virtual ~FilterCeilingAmplitudePercentage(); + + FilterCeilingAmplitudePercentage &operator=(const FilterCeilingAmplitudePercentage &other); + + Trace &filter(Trace &data_points) const override; + + double getPercentage() const; + QString name() const override; + + QString toString() const override; + + protected: + void buildFilterFromString(const QString &strBuildParams) override; + + private: + double m_percentage; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -34,6 +34,7 @@ const QString &strBuildParams) { buildFilterFromString(strBuildParams); + // qInfo() << "ChargeDeconvolution created"; } @@ -48,7 +49,7 @@ // pappso::PrecisionFactory::getPrecisionDividedBy(m_precisionPtrZ1, 2): - qInfo() << m_precisionPtrZ2->getNominal(); + // qInfo() << m_precisionPtrZ2->getNominal(); } FilterChargeDeconvolution::FilterChargeDeconvolution( @@ -62,6 +63,7 @@ FilterChargeDeconvolution::~FilterChargeDeconvolution() { + qDebug() << "ChargeDeconvolution destroyed"; } @@ -74,14 +76,13 @@ if(strBuildParams.startsWith("chargeDeconvolution|")) { QStringList params = - strBuildParams.split("|").back().split(";", QString::SkipEmptyParts); + strBuildParams.split("|").back().split(";", Qt::SkipEmptyParts); QString precision = params.at(0); m_precisionPtrZ1 = PrecisionFactory::fromString(precision.replace("dalton", " dalton") .replace("ppm", " ppm") .replace("res", " res")); - qDebug(); m_precisionPtrZ2 = pappso::PrecisionFactory::getPrecisionPtrFractionInstance( @@ -102,10 +103,18 @@ QString +pappso::FilterChargeDeconvolution::name() const +{ + return "chargeDeconvolution"; +} + + +QString pappso::FilterChargeDeconvolution::toString() const { QString strCode = - QString("chargeDeconvolution|%1").arg(m_precisionPtrZ1->toString()); + QString("%1|%2").arg(name()).arg(m_precisionPtrZ1->toString()); + strCode.replace(" ", ""); return strCode; @@ -117,7 +126,7 @@ qDebug(); std::vector data_points_info; data_points.sortY(); - + qDebug() << data_points.size(); Trace new_trace; for(auto &data_point : data_points) @@ -126,19 +135,19 @@ } computeBestChargeOfDataPoint(data_points_info); - qDebug() << data_points_info.size(); + // qDebug() << data_points_info.size(); computeIsotopeDeconvolution(data_points_info); - qDebug() << data_points_info.size(); + // qDebug() << data_points_info.size(); transformToMonoChargedForAllDataPoint(data_points_info); for(DataPointInfoSp &dpi : data_points_info) { - qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge; + // qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge; new_trace.push_back(dpi->new_mono_charge_data_point); } new_trace.sortX(); data_points = std::move(new_trace); - + qDebug() << data_points.size(); qDebug(); return data_points; } @@ -178,11 +187,11 @@ // add the datapoint to the list and add the parent pointer i_z1->get()->z1_vect.push_back(new_dpi); new_dpi->parent = *i_z1; - DataPointInfoSp parent_z1 = i_z1->get()->parent; + DataPointInfoSp parent_z1 = i_z1->get()->parent.lock(); while(parent_z1 != nullptr) { parent_z1.get()->z1_vect.push_back(new_dpi); - parent_z1 = parent_z1->parent; + parent_z1 = parent_z1->parent.lock(); } i_z1++; } @@ -202,11 +211,11 @@ // add the datapoint to the list and add the parent pointer i_z2->get()->z2_vect.push_back(new_dpi); new_dpi->parent = *i_z2; - DataPointInfoSp parent_z2 = i_z2->get()->parent; + DataPointInfoSp parent_z2 = i_z2->get()->parent.lock(); while(parent_z2 != nullptr) { parent_z2.get()->z2_vect.push_back(new_dpi); - parent_z2 = parent_z2->parent; + parent_z2 = parent_z2->parent.lock(); } i_z2++; } @@ -223,27 +232,30 @@ if(data_point_info.get()->z1_vect.size() >= 1 && data_point_info.get()->z2_vect.size() == 0) { - for(DataPointInfoSp other : data_point_info.get()->z1_vect) + for(std::weak_ptr other : + data_point_info.get()->z1_vect) { - other->z_charge = 1; + other.lock()->z_charge = 1; } data_point_info.get()->z_charge = 1; } else if(data_point_info.get()->z1_vect.size() == 0 && data_point_info.get()->z2_vect.size() >= 1) { - for(DataPointInfoSp other : data_point_info.get()->z2_vect) + for(std::weak_ptr other : + data_point_info.get()->z2_vect) { - other->z_charge = 2; + other.lock()->z_charge = 2; } data_point_info.get()->z_charge = 2; } else if(data_point_info.get()->z1_vect.size() >= 1 && data_point_info.get()->z2_vect.size() >= 1) { - for(DataPointInfoSp other : data_point_info.get()->z2_vect) + for(std::weak_ptr other : + data_point_info.get()->z2_vect) { - other->z_charge = 2; + other.lock()->z_charge = 2; } data_point_info.get()->z_charge = 2; } @@ -267,7 +279,7 @@ for(DataPointInfoSp &data_point_info : data_points_info) { - if(data_point_info->parent == nullptr) + if(data_point_info->parent.lock() == nullptr) { DataPointInfoSp deconvoluted_point(std::make_shared()); @@ -278,18 +290,18 @@ if(data_point_info->z_charge == 1) { - for(DataPointInfoSp data : data_point_info->z1_vect) + for(std::weak_ptr data : data_point_info->z1_vect) { deconvoluted_point->new_mono_charge_data_point.y += - data->data_point.y; + data.lock()->data_point.y; } } else if(data_point_info->z_charge == 2) { - for(DataPointInfoSp data : data_point_info->z2_vect) + for(std::weak_ptr data : data_point_info->z2_vect) { deconvoluted_point->new_mono_charge_data_point.y += - data->data_point.y; + data.lock()->data_point.y; } } else // if z.charge == 0 diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterchargedeconvolution.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterchargedeconvolution.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterchargedeconvolution.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterchargedeconvolution.h 2022-10-27 09:16:15.000000000 +0000 @@ -57,11 +57,11 @@ // range of mass possible for z2 peak (~0.5mz) std::pair z2_range; // datapointInfo where the mass is in the range - FilterChargeDeconvolution::DataPointInfoSp parent = nullptr; + std::weak_ptr parent; // list of datapointinfo with 1mz diff multiple - std::vector z1_vect; + std::vector> z1_vect; // list of datapointinfo with 2mz diff multiple - std::vector z2_vect; + std::vector> z2_vect; }; public: @@ -97,6 +97,7 @@ Trace &filter(Trace &data_points) const override; + virtual QString name() const override; QString toString() const override; protected: @@ -112,7 +113,7 @@ std::vector &points, DataPoint &data_point) const; /** - * @brief For eache datapointInfo add the datapoint to the lists by their + * @brief For each datapointInfo add the datapoint to the lists by their * exclusion range * @return the vecotr of datapointInfo with their lists of isotopics peaks */ diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtercomplementionenhancer.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtercomplementionenhancer.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtercomplementionenhancer.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtercomplementionenhancer.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -85,10 +85,19 @@ } } + +QString +pappso::FilterComplementIonEnhancer::name() const +{ + return "complementIonEnhancer"; +} + + QString pappso::FilterComplementIonEnhancer::toString() const { - QString strCode = QString("complementIonEnhancer|%1;%2") + QString strCode = QString("%1|%2;%3") + .arg(name()) .arg(QString::number(m_targetMzSum, 'g', 15)) .arg(m_precisionPtr->toString()); strCode.replace(" ", ""); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtercomplementionenhancer.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtercomplementionenhancer.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtercomplementionenhancer.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtercomplementionenhancer.h 2022-10-27 09:16:15.000000000 +0000 @@ -83,6 +83,7 @@ void buildFilterFromString(const QString &strBuildParams) override; + QString name() const override; QString toString() const override; private: diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterexclusionmz.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterexclusionmz.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterexclusionmz.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterexclusionmz.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,135 @@ +/** + * \file pappsomspp/processing/filters/filterexclusionmz.cpp + * \date 09/02/2021 + * \author Thomas Renne + * \brief Delete small peaks in the exclusion range + */ + +/******************************************************************************* + * Copyright (c) 2021 Thomas Renne . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "filterexclusionmz.h" +#include +#include "../../exception/exceptionnotrecognized.h" + +using namespace pappso; + +FilterMzExclusion::FilterMzExclusion(const QString &strBuildParams) +{ + buildFilterFromString(strBuildParams); +} + +FilterMzExclusion::FilterMzExclusion(pappso::PrecisionPtr precision_ptr) + : m_exclusionPrecision(precision_ptr) +{ +} + +FilterMzExclusion::FilterMzExclusion(const pappso::FilterMzExclusion &other) + : m_exclusionPrecision(other.m_exclusionPrecision) +{ +} + +FilterMzExclusion::~FilterMzExclusion() +{ +} + +void +pappso::FilterMzExclusion::buildFilterFromString(const QString &strBuildParams) +{ + qDebug(); + if(strBuildParams.startsWith("mzExclusion|")) + { + QStringList params = + strBuildParams.split("|").back().split(";", Qt::SkipEmptyParts); + + QString precision = params.at(0); + m_exclusionPrecision = + PrecisionFactory::fromString(precision.replace("dalton", " dalton") + .replace("ppm", " ppm") + .replace("res", " res")); + } + else + { + throw pappso::ExceptionNotRecognized( + QString("building mzExclusion from string %1 is not possible") + .arg(strBuildParams)); + } + qDebug(); +} + +pappso::Trace & +pappso::FilterMzExclusion::filter(pappso::Trace &data_points) const +{ + qDebug(); + qDebug() << "before" << data_points.size(); + data_points.sortY(); + + Trace new_trace = removeTraceInExclusionMargin(data_points); + new_trace.sortX(); + data_points = std::move(new_trace); + qDebug() << "after" << data_points.size(); + qDebug(); + return data_points; +} + +QString +pappso::FilterMzExclusion::name() const +{ + return "mzExclusion"; +} + + +QString +pappso::FilterMzExclusion::toString() const +{ + QString strCode = + QString("%1|%2").arg(name()).arg(m_exclusionPrecision->toString()); + + strCode.replace(" ", ""); + + return strCode; +} + +pappso::Trace +pappso::FilterMzExclusion::removeTraceInExclusionMargin( + pappso::Trace &points) const +{ + Trace new_trace; + std::vector excluded_ranges; + + for(auto &data_point : points) + { + auto exclude_index = excluded_ranges.begin(), end = excluded_ranges.end(); + + exclude_index = + std::find_if(exclude_index, end, [&data_point](MzRange range) { + return (data_point.x >= range.lower() && + data_point.x <= range.upper()); + }); + if(exclude_index == end) + { + new_trace.push_back(data_point); + MzRange new_range(data_point.x, m_exclusionPrecision); + excluded_ranges.push_back(new_range); + } + } + + return new_trace; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterexclusionmz.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterexclusionmz.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterexclusionmz.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterexclusionmz.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,81 @@ +/** + * \file pappsomspp/processing/filters/filterexclusionmz.h + * \date 09/02/2021 + * \author Thomas Renne + * \brief Delete small peaks in the exclusion range + */ + +/******************************************************************************* + * Copyright (c) 2021 Thomas Renne . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "filternameinterface.h" +#include "../../trace/trace.h" + +namespace pappso +{ + +class PMSPP_LIB_DECL FilterMzExclusion : public FilterNameInterface +{ + public: + /** + * Default constructor + */ + FilterMzExclusion(PrecisionPtr precision_ptr); + + + /** + * @param strBuildParams string to build the filter + * "mzExclusion|0.02dalton" + */ + FilterMzExclusion(const QString &strBuildParams); + + /** + * Copy constructor + * + * @param other TODO + */ + FilterMzExclusion(const FilterMzExclusion &other); + + /** + * Destructor + */ + virtual ~FilterMzExclusion(); + + QString name() const override; + QString toString() const override; + + /** + * @brief get all the datapoints and remove different isotope and add their + * intensity and change to charge = 1 when the charge is known + * @return a list of datapoint + */ + Trace &filter(Trace &data_points) const override; + + private: + void buildFilterFromString(const QString &strBuildParams) override; + Trace removeTraceInExclusionMargin(Trace &points) const; + + + private: + PrecisionPtr m_exclusionPrecision; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterflooramplitudepercentage.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterflooramplitudepercentage.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterflooramplitudepercentage.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterflooramplitudepercentage.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,164 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#include + + +#include +#include + +#include "../../exception/exceptionnotrecognized.h" + +#include "filterflooramplitudepercentage.h" + + +namespace pappso +{ + + +FilterFloorAmplitudePercentage::FilterFloorAmplitudePercentage( + double percentage) +{ + m_percentage = percentage; +} + + +FilterFloorAmplitudePercentage::FilterFloorAmplitudePercentage( + const FilterFloorAmplitudePercentage &other) +{ + m_percentage = other.m_percentage; +} + + +FilterFloorAmplitudePercentage::~FilterFloorAmplitudePercentage() +{ +} + +FilterFloorAmplitudePercentage & +FilterFloorAmplitudePercentage::operator=( + const FilterFloorAmplitudePercentage &other) +{ + if(&other == this) + return *this; + + m_percentage = other.m_percentage; + + return *this; +} + + +FilterFloorAmplitudePercentage::FilterFloorAmplitudePercentage( + const QString ¶meters) +{ + buildFilterFromString(parameters); +} + + +void +FilterFloorAmplitudePercentage::buildFilterFromString(const QString ¶meters) +{ + // Typical string: "FloorAmplitudePercentage|15" + if(parameters.startsWith(QString("%1|").arg(name()))) + { + QStringList params = parameters.split("|").back().split(";"); + + m_percentage = params.at(0).toDouble(); + } + else + { + throw pappso::ExceptionNotRecognized( + QString( + "Building of FilterFloorAmplitudePercentage from string %1 failed") + .arg(parameters)); + } +} + + +Trace & +FilterFloorAmplitudePercentage::filter(Trace &data_points) const +{ + + auto it_min = minYDataPoint(data_points.begin(), data_points.end()); + auto it_max = maxYDataPoint(data_points.begin(), data_points.end()); + + if(it_min == data_points.end() || it_max == data_points.end()) + return data_points; + + double min = it_min->y; + double max = it_max->y; + + double amplitude = max - min; + + double amplitude_ratio = amplitude * m_percentage / 100; + + double threshold = min + amplitude_ratio; + + // Since we never remove points, we only change their y value, we can do the + // filtering inplace. + + for(auto &&data_point : data_points) + { + // Change the value to be threshold (re-flooring in action). + if(data_point.y < threshold) + { + data_point.y = threshold; + } + } + + return data_points; +} + + +double +FilterFloorAmplitudePercentage::getPercentage() const +{ + return m_percentage; +} + + +//! Return a string with the textual representation of the configuration data. +QString +FilterFloorAmplitudePercentage::toString() const +{ + return QString("%1|%2").arg(name()).arg( + QString::number(m_percentage, 'f', 2)); +} + + +QString +FilterFloorAmplitudePercentage::name() const +{ + return "FloorAmplitudePercentage"; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterflooramplitudepercentage.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterflooramplitudepercentage.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterflooramplitudepercentage.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterflooramplitudepercentage.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,96 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#pragma once + + +#include + +#include "../../trace/trace.h" +#include "../../exportinmportconfig.h" +#include "filternameinterface.h" + + +namespace pappso +{ + + +class FilterFloorAmplitudePercentage; + +typedef std::shared_ptr + FilterFloorAmplitudePercentageSPtr; +typedef std::shared_ptr + FilterFloorAmplitudePercentageCstSPtr; + + +/** + * @brief Redefines the floor intensity of the Trace + * + * The amplitude of the trace is computed (maxValue - minValue) + * Its fraction is calculated = amplitude * (percentage / 100) + * The threshold value is computed as (minValue + fraction) + * + * When the values to be filtered are below that threshold they acquire that + * threshold value. + * + * When the values to be filtered are above that threshold they remain + * unchanged. + * + * This effectively re-floors the values to threshold. + */ +class PMSPP_LIB_DECL FilterFloorAmplitudePercentage : public FilterNameInterface +{ + public: + FilterFloorAmplitudePercentage(double percentage); + FilterFloorAmplitudePercentage(const QString ¶meters); + FilterFloorAmplitudePercentage(const FilterFloorAmplitudePercentage &other); + + virtual ~FilterFloorAmplitudePercentage(); + + FilterFloorAmplitudePercentage & + operator=(const FilterFloorAmplitudePercentage &other); + + Trace &filter(Trace &data_points) const override; + + double getPercentage() const; + QString name() const override; + + QString toString() const override; + + protected: + void buildFilterFromString(const QString &strBuildParams) override; + + private: + double m_percentage; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterinterface.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterinterface.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -57,7 +57,8 @@ public: virtual MassSpectrum &filter(MassSpectrum &spectrum) const = 0; - virtual ~MassSpectrumFilterInterface(){}; }; + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,661 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#include + +#include +#include + +#include +#include + +#include "../../exception/exceptionnotrecognized.h" + +#include "filterlowintensitysignalremoval.h" +#include "../../trace/maptrace.h" + + +namespace pappso +{ + + +FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval( + double mean, double std_dev, double threshold) +{ + m_noiseMean = mean; + m_noiseStdDev = std_dev; + m_threshold = threshold; +} + + +FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval( + const QString ¶meters) +{ + buildFilterFromString(parameters); +} + + +FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval( + const FilterLowIntensitySignalRemoval &other) +{ + m_noiseMean = other.m_noiseMean; + m_noiseStdDev = other.m_noiseStdDev; + m_threshold = other.m_threshold; +} + + +FilterLowIntensitySignalRemoval::~FilterLowIntensitySignalRemoval() +{ +} + + +FilterLowIntensitySignalRemoval & +FilterLowIntensitySignalRemoval:: +operator=(const FilterLowIntensitySignalRemoval &other) +{ + if(&other == this) + return *this; + + m_noiseMean = other.m_noiseMean; + m_noiseStdDev = other.m_noiseStdDev; + m_threshold = other.m_threshold; + + return *this; +} + + +void +FilterLowIntensitySignalRemoval::buildFilterFromString( + const QString ¶meters) +{ + // Typical string: "FloorAmplitudePercentage|15" + if(parameters.startsWith(QString("%1|").arg(name()))) + { + QStringList params = parameters.split("|").back().split(";"); + + m_noiseMean = params.at(0).toDouble(); + m_noiseStdDev = params.at(1).toDouble(); + m_threshold = params.at(2).toDouble(); + } + else + { + throw pappso::ExceptionNotRecognized( + QString( + "Building of FilterLowIntensitySignalRemoval from string %1 failed") + .arg(parameters)); + } +} + + +std::size_t +FilterLowIntensitySignalRemoval::detectClusterApices(const Trace &trace) +{ + // We want to iterate in the trace and check if we can get the apicess + // isolated one by one. An apex is nothing more than the top cusp of a + // triangle. We only store apices that have a value > m_threshold. + + m_clusters.clear(); + + std::size_t trace_size = trace.size(); + if(trace_size <= 2) + { + //qDebug() << "The original trace has less than 3 points. Returning it " + //"without modification."; + return m_clusters.size(); + } + //else + //qDebug() << "The original trace has" << trace_size << "data points"; + + // Seed the system with the first point of the trace. + m_curIter = trace.cbegin(); + m_prevIter = trace.cbegin(); + + //qDebug() << "First trace point: " + //<< "(" << m_prevIter->x << "," << m_prevIter->y << ");"; + + // We still have not found any apex! + m_prevApex = trace.cend(); + + // We will need to know if we were ascending to an apex. + bool was_ascending_to_apex = false; + + // Prepare a first apex cluster. + ApicesSPtr cluster_apices = std::make_shared(); + + // Now that we have seeded the system with the first point of the original + // trace, go to the next one. + ++m_curIter; + + // And now iterate in the original trace and make sure we detect all the + // apicess. + + while(m_curIter != trace.cend()) + { + //qDebug() << "Current trace point: " + //<< "(" << m_curIter->x << "," << m_curIter->y << ");"; + + // We monitor if we are going up or down a peak. + + if(m_curIter->y > m_prevIter->y) + // We are ascending a peak. We do not know if we are at the apex. + { + //qDebug().noquote() << "We are ascending to an apex.\n"; + was_ascending_to_apex = true; + } + else + // We are descending a peak. + { + //qDebug().noquote() << "Descending a peak. "; + + // There are two situations: + // + // 1. Either we were ascending to an apex, and m_prev is that apex, + // + // 2. Or we were not ascending to an apex and in fact all we are doing + // is going down an apex that occurred more than one trace point ago. + + if(!was_ascending_to_apex) + // We were not ascending to an apex. + { + // Do nothing here. + + //qDebug().noquote() + //<< "But, we were not ascending to an apex, so do nothing.\n"; + } + else + // We are effectively descending a peak right after the apex was + // reached at the previous iteration. + { + m_curApex = m_prevIter; + + //qDebug().noquote() + //<< "And, we were ascending to an apex, so " + //"m_curApex has become m_prevIter: (" + //<< m_curApex->x << "," << m_curApex->y << ")\n"; + + // We might have two situations: + + // 1. We had already encountered an apex. + // 2. We had not yet encountered an apex. + + if(m_prevApex != trace.cend()) + // We had already encountered an apex. + { + // Was that apex far on the left of the current apex ? + + if(m_curApex->x - m_prevApex->x > + INTRA_CLUSTER_INTER_PEAK_DISTANCE) + // The distance is not compatible with both apices to belong + // to the same apices cluster. + { + // We are creating a new isotopic apices. + + // But, since another apex had been encountered already, + // that means that an isotopic apices was cooking + // already. We must store it. + + if(!cluster_apices->size()) + qFatal("Cannot be that the apices has no apex."); + + // Store the crafted apices cluster. + m_clusters.push_back(cluster_apices); + + //qDebug().noquote() + //<< "There was a previous apex already, BUT " + //"outside of apices range. " + //"Pushing the cooking apices that has size:" + //<< cluster_apices->size(); + + // Now create a brand new apices for later work. + cluster_apices = std::make_shared(); + + //qDebug() << "Created a brand new apices."; + + // We only start the new apices with the current apex if + // that apex is above the threshold. + + if(m_curApex->y > m_threshold) + { + // And start it with the current apex. + cluster_apices->push_back(m_curApex); + + //qDebug() + //<< "Since the current apex is above the threshold, " + //"we PUSH it to the newly created apices: (" + //<< m_curApex->x << "," << m_curApex->y << ")"; + + m_prevApex = m_curApex; + + //qDebug() << "Set prev apex to be cur apex."; + } + else + { + //qDebug() + //<< "Since the current apex is below the threshold, " + //"we DO NOT push it to the newly created " + //"apices: (" + //<< m_curApex->x << "," << m_curApex->y << ")"; + + // Since previous apex went to the closed apices, we + // need to reset it. + + m_prevApex = trace.cend(); + + //qDebug() << "Since the previous apex went to the " + //"closed apices, and cur apex has too " + //"small an intensity, we reset prev apex " + //"to trace.cend()."; + } + } + else + // The distance is compatible with both apices to belong to + // the same isotopic apices. + { + + // But we only push back the current apex to the apices + // if its intensity is above the threshold. + + if(m_curApex->y > m_threshold) + // The current apex was above the threshold + { + cluster_apices->push_back(m_curApex); + + //qDebug().noquote() + //<< "There was an apex already inside of apices " + //"range. " + //"AND, since the current apex was above the " + //"threshold, we indeed push it to apices.\n"; + + //qDebug().noquote() + //<< "Current apex PUSHED: " << m_curApex->x << ", " + //<< m_curApex->y; + + m_prevApex = m_curApex; + + //qDebug() << "We set prev apex to be cur apex."; + } + else + { + //qDebug().noquote() + //<< "There was an apex already inside of apices " + //"range. " + //"BUT, since the current apex was below the " + //"threshold, we do not push it to apices.\n"; + + //qDebug().noquote() + //<< "Current apex NOT pushed: " << m_curApex->x + //<< ", " << m_curApex->y; + } + } + } + else + // No apex was previously found. We are fillin-up a new isotopic + // apices. + { + if(m_curApex->y > m_threshold) + // We can actually add that apex to a new isotopic apices. + { + if(cluster_apices->size()) + qCritical( + "At this point, the apices should be new and " + "empty."); + + cluster_apices->push_back(m_curApex); + + //qDebug().noquote() + //<< "No previous apex was found. Since current apex' " + //"intensity is above threshold, we push it back to " + //"the " + //"apices.\n"; + + // Store current apex as previous apex for next rounds. + m_prevApex = m_curApex; + + //qDebug().noquote() << "And thus we store the current " + //"apex as previous apex.\n"; + } + else + { + //qDebug().noquote() + //<< "No previous apex was found. Since current apex' " + //"intensity is below threshold, we do nothing.\n"; + } + } + } + // End of + // ! if(!was_ascending_to_apex) + // That is, we were ascending to an apex. + + // Tell what it is: we were not ascending to an apex. + was_ascending_to_apex = false; + } + // End of + // ! if(m_curIter->y > m_prevIter->y) + // That is, we are descending a peak. + + // At this point, prepare next round. + + //qDebug().noquote() + //<< "Preparing next round, with m_prevIter = m_curIter and ++index.\n"; + + m_prevIter = m_curIter; + + ++m_curIter; + } + // End of + // while(index < trace_size) + + // At this point, if a apices had been cooking, add it. + + if(cluster_apices->size()) + m_clusters.push_back(cluster_apices); + + return m_clusters.size(); +} + + +Trace::const_iterator +FilterLowIntensitySignalRemoval::backwardFindApex(const Trace &trace, + Trace::const_iterator iter, + double distance_threshold) +{ + // We receive an iterator that points to an apex. We want iterate back in the + // trace working copy and look if there are apices that are distant less than + // 1.1~Th. + + Trace::const_iterator init_iter = iter; + + if(iter == trace.cbegin()) + return iter; + + // Seed the previous iter to iter, because we'll move from there right away. + Trace::const_iterator prev_iter = init_iter; + + Trace::const_iterator last_apex_iter = init_iter; + + // We will need to know if we were ascending to an apex. + bool was_ascending_to_apex = false; + + // Now that we have seeded the system, we can move iter one data point: + --iter; + + while(iter != trace.cbegin()) + { + // If we are already outside of distance_threshold, return the last apex + // that was found (or initial iter if none was encountered) + + if(abs(init_iter->x - iter->x) >= distance_threshold) + return last_apex_iter; + + if(iter->y > prev_iter->y) + { + // New data point has greater intensity. Just record that fact. + was_ascending_to_apex = true; + } + else + { + // New data point has smaller intensity. We are descending a peak. + + if(was_ascending_to_apex) + { + // We had an apex at previous iter. We are inside the distance + // threshold. That is good. But we still could find another apex + // while moving along the trace that is in the distance threshold. + // This is why we keep going, but we store the previous iter as + // the last encountered apex. + + last_apex_iter = prev_iter; + } + } + + prev_iter = iter; + + // Move. + --iter; + } + + //qDebug() << "Init m/z: " << init_iter->x + //<< "Returning m/z: " << last_apex_iter->x + //<< "at distance:" << std::distance(last_apex_iter, init_iter); + + // At this point last_apex_iter is the same as the initial iter. + return last_apex_iter; +} + + +Trace::const_iterator +FilterLowIntensitySignalRemoval::forwardFindApex(const Trace &trace, + Trace::const_iterator iter, + double distance_threshold) +{ + // We receive an iterator that points to an apex. We want iterate back in the + // trace working copy and look if there are apices that are distant less than + // 1.1~Th. + + Trace::const_iterator init_iter = iter; + + if(iter == trace.cend()) + return iter; + + // Seed the previous iter to iter, because we'll move from there right away. + Trace::const_iterator prev_iter = init_iter; + + Trace::const_iterator last_apex_iter = init_iter; + + // We will need to know if we were ascending to an apex. + bool was_ascending_to_apex = false; + + // Now that we have seeded the system, we can move iter one data point: + ++iter; + + while(iter != trace.cend()) + { + // If we are already outside of distance_threshold, return the last apex + // that was found (or initial iter if none was encountered) + + // FIXME: maybe we should compare prev_iter->x with iter->x so that we + // continue moving if all the succcessive apices found are each one in the + // distance_threshold from the previous one ? + + if(abs(init_iter->x - iter->x) >= distance_threshold) + return last_apex_iter; + + if(iter->y > prev_iter->y) + { + // New data point has greater intensity. Just record that fact. + was_ascending_to_apex = true; + } + else + { + // New data point has smaller intensity. We are descending a peak. + + if(was_ascending_to_apex) + { + // We had an apex at previous iter. We are inside the distance + // threshold. That is good. But we still could find another apex + // while moving along the trace that is in the distance threshold. + // This is why we keep going, but we store the previous iter as + // the last encountered apex. + + last_apex_iter = prev_iter; + } + } + + prev_iter = iter; + + // Move. + ++iter; + } + + // At this point last_apex_iter is the same as the initial iter. + return last_apex_iter; +} + + +Trace +FilterLowIntensitySignalRemoval::reconstructTrace(const Trace &trace) +{ + // We start from the vector of apices and try to remake a high resolution + // trace out of these apices. + + MapTrace map_trace; + + // The general idea is that apices were detected, and only apices having + // their intensity above the threshold were stored. That means that we need to + // add points to the trace to reconstruct a meaningful trace. Indeed, imagine + // a heavy peptide isotopic cluster: the first peak's apex is below threshold + // and was not stored. The second peak is also below. But the third isotopic + // cluster peak is above and was stored. + // + // How do we reconstruct the trace to have all these points that were + // preceding the first isotopic cluster apex that was detected. + // + // The same applies to the last peaks of the cluster that are below the + // threshold whil the preceeding ones were above! + + // The general idea is to iterate in the vector of apices and for each apex + // that is encountered, ask if there were apices + + // m_clusters is a vector that contains vectors of Trace::const_iter. + // Each vector in m_clusters should represent all the apices of a cluster. + + //qDebug() << "Reconstructing trace with " << m_clusters.size() << "clusters."; + + Trace::const_iterator left_begin_iter = trace.cend(); + Trace::const_iterator right_end_iter = trace.cend(); + + for(auto &&cluster_apices : m_clusters) + { + // cluster_apices is a vector of Trace::const_iterator. If we want to + // reconstruct the Trace, we need to iterate through all the DataPoint + // objects in between cluster_apices.begin() and cluster_apices.end(). + + Trace::const_iterator begin_iter = *(cluster_apices->begin()); + Trace::const_iterator end_iter = *(std::prev(cluster_apices->end())); + + //qDebug() << "Iterating in a new cluster apices with boundaries:" + //<< begin_iter->x << "-" << end_iter->x; + + left_begin_iter = + backwardFindApex(trace, begin_iter, INTRA_CLUSTER_INTER_PEAK_DISTANCE); + + //qDebug() << "After backwardFindApex, left_begin_iter points to:" + //<< left_begin_iter->toString() << "with distance:" + //<< std::distance(left_begin_iter, begin_iter); + + right_end_iter = forwardFindApex( + trace, end_iter, 1.5 * INTRA_CLUSTER_INTER_PEAK_DISTANCE); + + for(Trace::const_iterator iter = left_begin_iter; iter != right_end_iter; + ++iter) + { + map_trace[iter->x] = iter->y; + } + + // Now reset the left and right iters to intensity 0 to avoid having + // disgraceful oblique lines connnecting trace segments. + + map_trace[left_begin_iter->x] = 0; + map_trace[std::prev(right_end_iter)->x] = 0; + + } + + return map_trace.toTrace(); +} + + +Trace & +FilterLowIntensitySignalRemoval::filter(Trace &trace) const +{ + //qDebug(); + + // Horrible hack to have a non const filtering process. + return const_cast(this)->nonConstFilter( + trace); +} + + +Trace & +FilterLowIntensitySignalRemoval::nonConstFilter(Trace &trace) +{ + //qDebug(); + + if(trace.size() <= 2) + { + //qDebug() << "The original trace has less than 3 points. Returning it " + //"without modification."; + return trace; + } + //else + //qDebug() << "The original trace had" << trace.size() << "data points"; + + std::size_t cluster_count = detectClusterApices(trace); + + //qDebug() << "Number of detected cluster apices: " << cluster_count; + + if(!cluster_count) + return trace; + + // At this point we want to work on the apices and reconstruct a full + // trace. + + Trace reconstructed_trace = reconstructTrace(trace); + + trace = std::move(reconstructed_trace); + + return trace; +} + + +double +FilterLowIntensitySignalRemoval::getThreshold() const +{ + return m_threshold; +} + + +//! Return a string with the textual representation of the configuration data. +QString +FilterLowIntensitySignalRemoval::toString() const +{ + return QString("%1|%2").arg(name()).arg(QString::number(m_threshold, 'f', 2)); +} + + +QString +FilterLowIntensitySignalRemoval::name() const +{ + return "FilterLowIntensitySignalRemoval"; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterlowintensitysignalremoval.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,143 @@ +/* BEGIN software license + * + * msXpertSuite - mass spectrometry software suite + * ----------------------------------------------- + * Copyright(C) 2009,...,2021 Filippo Rusconi + * + * http://www.msxpertsuite.org + * + * This file is part of the msXpertSuite project. + * + * The msXpertSuite project is the successor of the massXpert project. This + * project now includes various independent modules: + * + * - massXpert, model polymer chemistries and simulate mass spectrometric data; + * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * + * END software license + */ + + +#pragma once + + +#include + +#include "../../trace/trace.h" +#include "../../exportinmportconfig.h" +#include "filternameinterface.h" + + +namespace pappso +{ + + +class FilterLowIntensitySignalRemoval; + +typedef std::shared_ptr + FilterLowIntensitySignalRemovalSPtr; +typedef std::shared_ptr + FilterLowIntensitySignalRemovalCstSPtr; + + +/** + * @brief Redefines the floor intensity of the Trace + * + * The amplitude of the trace is computed (maxValue - minValue) + * Its fraction is calculated = amplitude * (percentage / 100) + * The threshold value is computed as (minValue + fraction) + * + * When the values to be filtered are below that threshold they acquire that + * threshold value. + * + * When the values to be filtered are above that threshold they remain + * unchanged. + * + * This effectively re-floors the values to threshold. + */ +class PMSPP_LIB_DECL FilterLowIntensitySignalRemoval + : public FilterNameInterface +{ + public: + FilterLowIntensitySignalRemoval(double mean, + double std_dev, + double threshold); + FilterLowIntensitySignalRemoval(const QString ¶meters); + FilterLowIntensitySignalRemoval(const FilterLowIntensitySignalRemoval &other); + + virtual ~FilterLowIntensitySignalRemoval(); + + FilterLowIntensitySignalRemoval & + operator=(const FilterLowIntensitySignalRemoval &other); + + Trace &filter(Trace &data_points) const override; + + double getThreshold() const; + QString name() const override; + + QString toString() const override; + + protected: + void buildFilterFromString(const QString &strBuildParams) override; + + Trace &nonConstFilter(Trace &data_points); + + std::size_t detectClusterApices(const Trace &trace); + + Trace::const_iterator backwardFindApex(const Trace &trace, + Trace::const_iterator iter, + double distance_threshold); + + Trace::const_iterator forwardFindApex(const Trace &trace, + Trace::const_iterator iter, + double distance_threshold); + Trace reconstructTrace(const Trace &trace); + + private: + static constexpr double nan = std::numeric_limits::quiet_NaN(); + + double m_threshold; + double m_noiseMean; + double m_noiseStdDev; + + constexpr static double INTRA_CLUSTER_INTER_PEAK_DISTANCE = 1.1; + + const std::size_t m_minIntPointCount = 5; + const std::size_t m_minIntStdDevFactor = 2; + + double m_min; + double m_max; + double m_minMean; + double m_minStdDev; + double m_noiseLevel; + + bool m_seen_upward_phase = false; + + using TraceCIter = Trace::const_iterator; + + // Beware HYPER-ROUGH inialization of the iterator ! + TraceCIter m_prevApex = static_cast(0); + TraceCIter m_curApex = static_cast(0); + TraceCIter m_curIter = static_cast(0); + TraceCIter m_prevIter = static_cast(0); + + using ClusterApices = std::vector; + using ApicesSPtr = std::shared_ptr; + + // All the cluster apices + std::vector m_clusters; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtermorpho.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtermorpho.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtermorpho.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtermorpho.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,6 +29,7 @@ #include "../../trace/trace.h" #include #include "../../exception/exceptionoutofrange.h" +#include "../../exception/exceptionnotrecognized.h" using namespace pappso; @@ -60,10 +61,12 @@ FilterMorphoWindowBase::filter(Trace &data_points) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - << m_halfWindowSize << " data_points.size()" << data_points.size(); + qDebug() << " " << m_halfWindowSize << " data_points.size()" + << data_points.size(); if(m_halfWindowSize == 0) return data_points; + if(data_points.size() <= m_halfWindowSize) + return data_points; Trace old_trace(data_points); auto it = old_trace.begin(); auto itend = old_trace.end() - m_halfWindowSize - 1; @@ -107,7 +110,7 @@ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; // problem with move or swap : this lead to segmentation faults in some cases // data_points = std::move(new_trace); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); return data_points; } @@ -134,7 +137,7 @@ std::vector::const_iterator end) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); return sumYTrace(begin, end, 0); } @@ -223,10 +226,10 @@ Trace & FilterMorphoMinMax::filter(Trace &data_points) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); m_filterMax.filter(data_points); m_filterMin.filter(data_points); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); return data_points; } std::size_t @@ -257,10 +260,10 @@ Trace & FilterMorphoMaxMin::filter(Trace &data_points) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); m_filterMin.filter(data_points); m_filterMax.filter(data_points); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); return data_points; } std::size_t @@ -273,11 +276,52 @@ : m_halfWindowSize(half_window_size) { } + FilterMorphoAntiSpike::FilterMorphoAntiSpike(const FilterMorphoAntiSpike &other) : m_halfWindowSize(other.m_halfWindowSize) { } +pappso::FilterMorphoAntiSpike::FilterMorphoAntiSpike( + const QString &strBuildParams) +{ + buildFilterFromString(strBuildParams); +} + +void +pappso::FilterMorphoAntiSpike::buildFilterFromString( + const QString &strBuildParams) +{ + //"antiSpike|2" + if(strBuildParams.startsWith("antiSpike|")) + { + QStringList params = strBuildParams.split("|").back().split(";"); + + m_halfWindowSize = params.at(0).toUInt(); + } + else + { + throw pappso::ExceptionNotRecognized( + QString("building FilterMorphoAntiSpike from string %1 is not possible") + .arg(strBuildParams)); + } +} + +QString +pappso::FilterMorphoAntiSpike::toString() const +{ + QString strCode = QString("antiSpike|%1").arg(m_halfWindowSize); + + return strCode; +} + +QString +pappso::FilterMorphoAntiSpike::name() const +{ + return "antiSpike"; +} + + FilterMorphoAntiSpike & FilterMorphoAntiSpike::operator=(const FilterMorphoAntiSpike &other) { @@ -294,8 +338,11 @@ Trace & FilterMorphoAntiSpike::filter(Trace &data_points) const { + // qDebug(); if(m_halfWindowSize == 0) return data_points; + if(data_points.size() < m_halfWindowSize) + return data_points; Trace old_trace(data_points); auto it = old_trace.begin(); auto it_target = data_points.begin(); @@ -304,6 +351,7 @@ auto itend = old_trace.end() - m_halfWindowSize - 1; // new_trace.reserve(data_points.size()); + // qDebug(); while((it != old_trace.end()) && (std::distance(old_trace.begin(), it) < (int)m_halfWindowSize)) { @@ -311,19 +359,24 @@ it++; it_target++; } - while(it != itend) + // qDebug(); + while((it != itend) && (it != old_trace.end())) { + // qDebug(); auto itwend = it + m_halfWindowSize + 1; itw = findDifferentYvalue(it - m_halfWindowSize, it + 1, 0); if(itw == it) { + // qDebug(); itw = findDifferentYvalue(it + 1, itwend, 0); if(itw == itwend) { it_target->y = 0; } + // qDebug(); } + // qDebug(); it++; it_target++; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtermorpho.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtermorpho.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtermorpho.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtermorpho.h 2022-10-27 09:16:15.000000000 +0000 @@ -154,13 +154,19 @@ /** @brief anti spike filter * set to zero alone values inside the window */ -class PMSPP_LIB_DECL FilterMorphoAntiSpike : public FilterInterface +class PMSPP_LIB_DECL FilterMorphoAntiSpike : public FilterNameInterface { private: std::size_t m_halfWindowSize = 0; public: FilterMorphoAntiSpike(std::size_t half_window_size); + /** + * @param strBuildParams string to build the filter + * "antiSpike|2" + */ + FilterMorphoAntiSpike(const QString &strBuildParams); + FilterMorphoAntiSpike(const FilterMorphoAntiSpike &other); virtual ~FilterMorphoAntiSpike(){}; @@ -168,6 +174,13 @@ Trace &filter(Trace &data_points) const override; std::size_t getHalfWindowSize() const; + + + void buildFilterFromString(const QString &strBuildParams) override; + + QString toString() const override; + + QString name() const override; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filternameinterface.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filternameinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filternameinterface.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filternameinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -41,12 +41,13 @@ class PMSPP_LIB_DECL FilterNameInterface : public FilterInterface { public: + virtual QString name() const = 0; virtual QString toString() const = 0; virtual ~FilterNameInterface(){}; protected: - /** @brief build this filer using a string + /** @brief build this filter using a string * @param strBuildParams a string coding the filter and its parameters * "filterName|param1;param2;param3" * diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpass.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpass.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpass.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpass.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,6 +31,7 @@ #include #include "../../massspectrum/massspectrum.h" #include "../../exception/exceptionoutofrange.h" +#include "../../exception/exceptionnotrecognized.h" using namespace pappso; @@ -459,3 +460,129 @@ { return m_factor; } + +FilterRemoveY::FilterRemoveY(double valueToRemove) + : m_valueToRemove(valueToRemove) +{ +} + +FilterRemoveY::FilterRemoveY(const FilterRemoveY &other) + : m_valueToRemove(other.m_valueToRemove) +{ +} + +FilterRemoveY & +FilterRemoveY::operator=(const FilterRemoveY &other) +{ + m_valueToRemove = other.m_valueToRemove; + return *this; +} + +double +FilterRemoveY::getValue() const +{ + return m_valueToRemove; +} + +Trace & +FilterRemoveY::filter(Trace &data_points) const +{ + for(auto &&dataPoint : data_points) + { + if(dataPoint.y < m_valueToRemove) + dataPoint.y = 0; + else + dataPoint.y = dataPoint.y - m_valueToRemove; + } + return data_points; +} + + +FilterQuantileBasedRemoveY::FilterQuantileBasedRemoveY(double quantile) + : m_quantile(quantile) +{ +} + +FilterQuantileBasedRemoveY::FilterQuantileBasedRemoveY( + const FilterQuantileBasedRemoveY &other) + : m_quantile(other.m_quantile) +{ +} + +FilterQuantileBasedRemoveY & +FilterQuantileBasedRemoveY::operator=(const FilterQuantileBasedRemoveY &other) +{ + m_quantile = other.m_quantile; + return *this; +} + +double +FilterQuantileBasedRemoveY::getQuantileThreshold() const +{ + return m_quantile; +} + +Trace & +pappso::FilterQuantileBasedRemoveY::filter(pappso::Trace &data_points) const +{ + + if(data_points.size() == 0) + return data_points; + double value_to_temove = + quantileYTrace(data_points.begin(), data_points.end(), m_quantile); + for(auto &&dataPoint : data_points) + { + if(dataPoint.y < value_to_temove) + dataPoint.y = 0; + else + dataPoint.y = dataPoint.y - value_to_temove; + } + return data_points; +} + +pappso::FilterQuantileBasedRemoveY::FilterQuantileBasedRemoveY( + const QString &strBuildParams) +{ + buildFilterFromString(strBuildParams); +} + + +void +pappso::FilterQuantileBasedRemoveY::buildFilterFromString( + const QString &strBuildParams) +{ + //"passQuantileBasedRemoveY|0.6" + qDebug(); + if(strBuildParams.startsWith("passQuantileBasedRemoveY|")) + { + QStringList params = + strBuildParams.split("|").back().split(";", Qt::SkipEmptyParts); + + QString value = params.at(0); + m_quantile = value.toDouble(); + } + else + { + throw pappso::ExceptionNotRecognized( + QString( + "building passQuantileBasedRemoveY from string %1 is not possible") + .arg(strBuildParams)); + } + qDebug(); +} + + +QString +pappso::FilterQuantileBasedRemoveY::name() const +{ + return "passQuantileBasedRemoveY"; +} + + +QString +pappso::FilterQuantileBasedRemoveY::toString() const +{ + QString strCode = QString("%1|%2").arg(name()).arg(m_quantile); + + return strCode; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpass.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpass.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpass.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpass.h 2022-10-27 09:16:15.000000000 +0000 @@ -27,7 +27,7 @@ #pragma once -#include "filterinterface.h" +#include "filternameinterface.h" #include #include "../../exportinmportconfig.h" @@ -228,4 +228,61 @@ double getScaleFactorY() const; }; + +/** @brief removes a value to all Y values + */ +class PMSPP_LIB_DECL FilterRemoveY : public FilterInterface +{ + private: + double m_valueToRemove = 0; + + public: + FilterRemoveY(double valueToRemove); + FilterRemoveY(const FilterRemoveY &other); + virtual ~FilterRemoveY(){}; + + FilterRemoveY &operator=(const FilterRemoveY &other); + + Trace &filter(Trace &data_points) const override; + + double getValue() const; +}; + + +/** @brief removes a value found by quantile to all Y values + * + * sort all values by Y intensity and take the iest value located at the defined + * quantile the use it to remove this value to all Y intensities + */ +class PMSPP_LIB_DECL FilterQuantileBasedRemoveY : public FilterNameInterface +{ + public: + FilterQuantileBasedRemoveY(double quantile_threshold); + + /** + * @param strBuildParams string to build the filter + * "passQuantileBasedRemoveY|0.6" + */ + FilterQuantileBasedRemoveY(const QString &strBuildParams); + + FilterQuantileBasedRemoveY(const FilterQuantileBasedRemoveY &other); + virtual ~FilterQuantileBasedRemoveY(){}; + + FilterQuantileBasedRemoveY & + operator=(const FilterQuantileBasedRemoveY &other); + + Trace &filter(Trace &data_points) const override; + + double getQuantileThreshold() const; + + virtual QString name() const override; + QString toString() const override; + + protected: + void buildFilterFromString(const QString &strBuildParams) override; + + private: + double m_quantile = 0; +}; + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpseudocentroid.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpseudocentroid.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpseudocentroid.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpseudocentroid.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,118 +0,0 @@ -/** - * \file pappsomspp/filers/filterpseudocentroid.cpp - * \date 7/12/2019 - * \author Olivier Langella - * \brief apply a pseudo centroid algorithm on a tims tof spectrum - */ - -/******************************************************************************* - * Copyright (c) 2019 Olivier Langella . - * - * This file is part of the PAPPSOms++ library. - * - * PAPPSOms++ is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms++ is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms++. If not, see . - * - ******************************************************************************/ - -#include -#include "filterpseudocentroid.h" -#include "pwiz/ms/peakpickerqtof.hpp" - -using namespace pappso; - -FilterPseudoCentroid::FilterPseudoCentroid(double resolution, - double smoothwidth, - double integrationWidth, - double intensityThreshold, - bool area, - uint32_t maxnumberofpeaks) -{ - - m_resolution = resolution; //!< instrument resolution - m_smoothwidth = smoothwidth; //!< smoothwidth - m_integrationWidth = integrationWidth; //! integration width - m_intensityThreshold = intensityThreshold; - m_area = area; //!< do you want to store are or intensity - m_maxnumberofpeaks = - maxnumberofpeaks; //!< max number of peaks returned by picker -} - -FilterPseudoCentroid::FilterPseudoCentroid(const FilterPseudoCentroid &other) -{ - m_resolution = other.m_resolution; //!< instrument resolution - m_smoothwidth = other.m_smoothwidth; //!< smoothwidth - m_integrationWidth = other.m_integrationWidth; //! integration width - m_intensityThreshold = other.m_intensityThreshold; - m_area = other.m_area; //!< do you want to store are or intensity - m_maxnumberofpeaks = - other.m_maxnumberofpeaks; //!< max number of peaks returned by picker -} - -FilterPseudoCentroid::~FilterPseudoCentroid() -{ -} - -Trace & -FilterPseudoCentroid::filter(Trace &data_points) const -{ - /* -QTOFPeakPickerFilter( - const pwiz::msdata::SpectrumListPtr & inner, //!< spectrum list - double resolution, //!< instrument resolution - double smoothwidth = 2., //!< smoothwidth - double integrationWidth = 4, //! integration width - double intensityThreshold = 10., - bool area = true, //!< do you want to store are or intensity -uint32_t maxnumberofpeaks = 0 //!< max number of peaks returned by picker - ) - */ - qDebug(); - - std::pair range = - std::make_pair(data_points.front().x, data_points.back().x); - // construct peak picker - qDebug() << "===========================================\n" << m_resolution << range << m_smoothwidth << m_integrationWidth << m_intensityThreshold << m_area << m_maxnumberofpeaks << "\n================================================"; - ralab::base::ms::PeakPicker pp( - m_resolution, - range, - m_smoothwidth, - m_integrationWidth, - m_intensityThreshold, - m_area, - m_maxnumberofpeaks); - - std::vector mzs = data_points.xValues(); - std::vector intensities = data_points.yValues(); - qDebug() << data_points.xValues().size(); - qDebug() << data_points.yValues().size(); - qDebug() << data_points.xValues(); - qDebug() << data_points.yValues(); - pp(mzs.begin(), mzs.end(), intensities.begin()); - qDebug(); - data_points.clear(); - qDebug(); - auto itmz = pp.getPeakMass().begin(); - auto itint = pp.getPeakArea().begin(); - - qDebug() << pp.getPeakMass().size(); - while(itmz != pp.getPeakMass().end()) - { - data_points.push_back({*itmz, *itint}); - itmz++; - itint++; - } - - qDebug(); - return data_points; -} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpseudocentroid.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpseudocentroid.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterpseudocentroid.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterpseudocentroid.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,79 +0,0 @@ -/** - * \file pappsomspp/filers/filterpseudocentroid.h - * \date 7/12/2019 - * \author Olivier Langella - * \brief apply a pseudo centroid algorithm on a tims tof spectrum - * actually this class is a wrapper for proteowizard ralab::base::ms::PeakPicker - * class - */ - -/******************************************************************************* - * Copyright (c) 2019 Olivier Langella . - * - * This file is part of the PAPPSOms++ library. - * - * PAPPSOms++ is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms++ is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms++. If not, see . - * - ******************************************************************************/ - -#pragma once - -#include "filterinterface.h" -#include "../../trace/trace.h" - -namespace pappso -{ -/** - * @todo write docs - */ -class PMSPP_LIB_DECL FilterPseudoCentroid : public FilterInterface -{ - public: - /** - * Default constructor - */ - FilterPseudoCentroid( - double resolution, //!< instrument resolution - double smoothwidth = 2., //!< smoothwidth - double integrationWidth = 4, //! integration width - double intensityThreshold = 10., - bool area = true, //!< do you want to store are or intensity - uint32_t maxnumberofpeaks = 0 //!< max number of peaks returned by picker - - ); - - /** - * Copy constructor - * - * @param other TODO - */ - FilterPseudoCentroid(const FilterPseudoCentroid &other); - - /** - * Destructor - */ - ~FilterPseudoCentroid(); - - Trace &filter(Trace &data_points) const override; - - private: - double m_resolution; //!< instrument resolution - double m_smoothwidth = 2.; //!< smoothwidth - double m_integrationWidth = 4; //! integration width - double m_intensityThreshold = 10.; - bool m_area = true; //!< do you want to store are or intensity - uint32_t m_maxnumberofpeaks = 0; //!< max number of peaks returned by picker -}; - -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterresample.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterresample.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterresample.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterresample.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,7 +29,9 @@ #include "../../massspectrum/massspectrum.h" #include -using namespace pappso; +namespace pappso +{ + FilterResampleKeepSmaller::FilterResampleKeepSmaller(double x_value) : m_value(x_value) @@ -81,12 +83,13 @@ Trace & FilterResampleKeepGreater::filter(Trace &spectrum) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " spectrum.size()=" << spectrum.size(); + // qDebug() << " spectrum.size()=" << spectrum.size(); + auto last_it = findFirstGreaterX(spectrum.begin(), spectrum.end(), m_value); spectrum.erase(spectrum.begin(), last_it); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " spectrum.size()=" << spectrum.size(); + + // qDebug() << " spectrum.size()=" << spectrum.size(); + return spectrum; } @@ -143,7 +146,7 @@ FilterResampleKeepXRange::FilterResampleKeepXRange( const FilterResampleKeepXRange &other) - : FilterResampleKeepXRange(other.m_minX, other.m_maxX) + : m_minX(other.m_minX), m_maxX(other.m_maxX) { } @@ -151,6 +154,9 @@ FilterResampleKeepXRange & FilterResampleKeepXRange::operator=(const FilterResampleKeepXRange &other) { + if(&other == this) + return *this; + m_minX = other.m_minX; m_maxX = other.m_maxX; @@ -161,18 +167,33 @@ Trace & FilterResampleKeepXRange::filter(Trace &spectrum) const { + // qDebug() << "The range to keep:" << m_minX << "-" << m_maxX; + auto begin_it = findFirstEqualOrGreaterX(spectrum.begin(), spectrum.end(), m_minX); - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - //<< " begin_it->x=" << begin_it->x; + + // qDebug() << "Found begin iterator (for m_minX) having:" << begin_it->x + //<< "x (m/z) value"; + auto end_it = findFirstGreaterX(begin_it, spectrum.end(), m_maxX); - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - //<< " end_it->x=" << end_it->x; + + if(end_it == spectrum.end()) + { + // qDebug() << "The end iterator (for m_maxX) is the end(). The prev " + //"iterator has" + //<< std::prev(end_it)->x << " x(m / z) value."; + } + else + { + // qDebug() << "Found end iterator (for m_maxX) having:" << end_it->x + //<< "x (m/z) value"; + } + + // qDebug() << "Only keeping range" << begin_it->x << "-" + //<< std::prev(end_it)->x; spectrum.erase(end_it, spectrum.end()); spectrum.erase(spectrum.begin(), begin_it); - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - //<< " spectrum.size()=" << spectrum.size(); return spectrum; } @@ -194,9 +215,8 @@ MassSpectrum & MassSpectrumFilterResampleRemoveMzRange::filter(MassSpectrum &spectrum) const { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + // qDebug() << m_filterRange.filter(spectrum); m_filterRange.filter(spectrum); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; return spectrum; } @@ -219,3 +239,312 @@ m_filterRange.filter(spectrum); return spectrum; } + + +FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon() +{ +} + + +FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon( + const SelectionPolygon &selection_polygon, DataKind data_kind) +{ + // It is assumed that the selection polygon always has x:MZ and y:DT|RT + // depending on the spec data kind. + + m_selectionPolygonSpecs.push_back( + SelectionPolygonSpec(selection_polygon, data_kind)); + + m_lowestMz = + m_selectionPolygonSpecs.front().selectionPolygon.getBottomMostPoint().y(); + m_greatestMz = + m_selectionPolygonSpecs.front().selectionPolygon.getTopMostPoint().y(); +} + + +FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon( + const SelectionPolygonSpecVector &selection_polygon_specs) +{ + // qDebug(); + + m_selectionPolygonSpecs.assign(selection_polygon_specs.begin(), + selection_polygon_specs.end()); + + for(auto &&item : m_selectionPolygonSpecs) + { + m_lowestMz = + std::min(m_lowestMz, item.selectionPolygon.getBottomMostPoint().y()); + + m_greatestMz = + std::max(m_greatestMz, item.selectionPolygon.getTopMostPoint().y()); + } +} + + +FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon( + const FilterResampleKeepPointInPolygon &other) +{ + // qDebug(); + + m_selectionPolygonSpecs.assign(other.m_selectionPolygonSpecs.begin(), + other.m_selectionPolygonSpecs.end()); + + for(auto &&item : m_selectionPolygonSpecs) + { + m_lowestMz = + std::min(m_lowestMz, item.selectionPolygon.getBottomMostPoint().y()); + + m_greatestMz = + std::max(m_greatestMz, item.selectionPolygon.getTopMostPoint().y()); + } +} + + +void +FilterResampleKeepPointInPolygon::newSelectionPolygonSpec( + const SelectionPolygonSpec &selection_polygon_spec) +{ + // It is assumed that the selection polygon always has x:MZ and y:DT|RT + // depending on the spec data kind. + + m_selectionPolygonSpecs.push_back(selection_polygon_spec); + + m_lowestMz = std::min( + m_lowestMz, + m_selectionPolygonSpecs.back().selectionPolygon.getBottomMostPoint().y()); + + m_greatestMz = std::max( + m_greatestMz, + m_selectionPolygonSpecs.back().selectionPolygon.getTopMostPoint().y()); +} + + +FilterResampleKeepPointInPolygon & +FilterResampleKeepPointInPolygon:: +operator=(const FilterResampleKeepPointInPolygon &other) +{ + if(this == &other) + return *this; + + m_selectionPolygonSpecs.assign(other.m_selectionPolygonSpecs.begin(), + other.m_selectionPolygonSpecs.end()); + + m_lowestMz = other.m_lowestMz; + m_greatestMz = other.m_greatestMz; + + return *this; +} + + +Trace & +FilterResampleKeepPointInPolygon::filter([[maybe_unused]] Trace &trace) const +{ + qFatal("Programming error."); + return trace; +} + + +Trace & +FilterResampleKeepPointInPolygon::filter(Trace &trace, + double dt_value, + double rt_value) const +{ + // Each time a new selection polygon spec is added, the lowest and greatest + // m/z values are computed. We use these values to remove from the spectrum + // all the points that are outside of that lowest-gratest range. + + // Find the iterator to the most front of the DataPoint vector (mass + // spectrum). + + // Note that the m_lowestMz and m_greatestMz are set during construction of + // this FilterResampleKeepPointInPolygon filter using the + // selection polygon specs. + + // qDebug() << "The lowest and greatest m/z values:" << m_lowestMz << "and" + //<< m_greatestMz; + + // Start by filtering away all the data points outside of the + // [m_lowestMz--m_greatestMz] range. + + FilterResampleKeepXRange the_filter(m_lowestMz, m_greatestMz); + + trace = the_filter.filter(trace); + + // Now iterate in all the data points remaining in the trace and for each + // point craft a "virtual" point using the dt|rt value and the m/z value of + // the data point (data_point.x). + + auto begin_it = trace.begin(); + auto end_it = trace.end(); + + // qDebug() << "Iterating in the m/z range:" << begin_it->x << "-" + //<< std::prev(end_it)->x; + + // Start at the end of the range. The iter is outside of the requested range, + // in fact, as shown using iter-- below. + auto iter = end_it; + + while(iter > begin_it) + { + // Immediately go to the last data point of the desired iteration range of + // the trace that we need to filter. Remember that end() is not pointing + // to any vector item, but past the last one. + iter--; + + // qDebug() << "Iterating in trace data point with m/z value:" << iter->x; + + // Now that we have the m/z value, we can check it, in combination with + // the value in the selection polygon spec (to make a point) against the + // various selection polygon specs in our member vector. + + double checked_value; + + for(auto &&spec : m_selectionPolygonSpecs) + { + // qDebug() << "Iterating in selection polygon spec:" << + // spec.toString(); + + if(spec.dataKind == DataKind::dt) + { + if(dt_value == -1) + qFatal("Programming error."); + + checked_value = dt_value; + + // qDebug() << "The data kind: dt."; + } + else if(spec.dataKind == DataKind::rt) + { + checked_value = rt_value; + + // qDebug() << "The data kind: rt."; + } + else + qFatal("Programming error."); + + // First version doing the whole computation on the basis of the + // selection polygon's all faces. + // + if(!spec.selectionPolygon.contains(QPointF(checked_value, iter->x))) + iter = trace.erase(iter); + +#if 0 + + //This code does not work because depending on the orientation of the + //skewed selection polygon (left bottom to right top or left top to + //right bottom or or Or depending on the axes of the + //bi-dimensional colormap, requiring transposition or not), the + //notion of "left line" and of "right line" changes. + + // Second version checking that point is right of left vertical line + // of polygon and left of right vertical line. + + // double res = sideofline(XX;YY;xA;yA;xB;yB) = + // (xB-xA) * (YY-yA) - (yB-yA) * (XX-xA) + + // If res == 0, the point is on the line + // If rest < 0, the point is on the right of the line + // If rest > 0, the point is on the left of the line + + // Left vertical line of the polygon + + // Bottom point + double xA_left = + spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT).x(); + double yA_left = + spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT).y(); + + // Top point + double xB_left = + spec.selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT).x(); + double yB_left = + spec.selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT).y(); + + qDebug() << "The left line goes: (" << xA_left << "," << yA_left + << ")->(" << xB_left << "," << yB_left << ")"; + + if((xB_left - xA_left) * (iter->x - yA_left) - + (yB_left - yA_left) * (checked_value - xA_left) > + 0) + { + // The point is left of the left line. We can remove the point + // from the mass spectrum. + + qDebug() << qSetRealNumberPrecision(10) + << "Filtered out point (left of left line):" + << checked_value << "-" << iter->x; + + iter = trace.erase(iter); + + // No need to go on with the analysis, just go to the next (that + // is, previous, since we iterate backwards) data point. + + continue; + } + else + { + qDebug() << qSetRealNumberPrecision(10) + << "Kept point (right of left line):" << checked_value + << "-" << iter->x; + } + + // Right vertical line of the polygon + + // Bottom point + double xA_right = + spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT).x(); + double yA_right = + spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT).y(); + + // Top point + double xB_right = + spec.selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT).x(); + double yB_right = + spec.selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT).y(); + + qDebug() << "The right line goes: (" << xA_right << "," << yA_right + << ")->(" << xB_right << "," << yB_right << ")"; + + if((xB_right - xA_right) * (iter->x - yA_right) - + (yB_right - yA_right) * (checked_value - xA_right) < + 0) + { + qDebug() << qSetRealNumberPrecision(10) + << "Filtered out point (right of right line):" + << checked_value << "-" << iter->x; + + // The point is right of the right line. We can remove the point + // from the mass spectrum. + iter = trace.erase(iter); + + // Here, continue is implicit. + // No need to go on with the analysis, just go to the next (that + // is, previous, since we iterate backwards) data point. + // continue; + } + else + { + if(iter->x >= 449 && iter->x <= 450 && checked_value > 19.5 && + checked_value < 20) + qDebug() + << qSetRealNumberPrecision(10) + << "SHOULD NOT Definitively kept point (left of right line):" + << checked_value << "-" << iter->x; + else + qDebug() + << qSetRealNumberPrecision(10) + << "MIGHT Definitively kept point (left of right line):" + << checked_value << "-" << iter->x; + } +#endif + } + // End of + // for(auto &&spec : m_selectionPolygonSpecs) + } + // End of + // while(iter > begin_it) + + return trace; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterresample.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterresample.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filterresample.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filterresample.h 2022-10-27 09:16:15.000000000 +0000 @@ -31,6 +31,7 @@ #include #include "../../mzrange.h" #include "../../exportinmportconfig.h" +#include "../combiners/selectionpolygon.h" namespace pappso { @@ -47,6 +48,7 @@ Trace &filter(Trace &trace) const override; }; + class PMSPP_LIB_DECL FilterResampleKeepGreater : public FilterInterface { private: @@ -63,6 +65,7 @@ double getThresholdX() const; }; + class PMSPP_LIB_DECL FilterResampleRemoveXRange : public FilterInterface { private: @@ -79,6 +82,7 @@ Trace &filter(Trace &trace) const override; }; + class PMSPP_LIB_DECL FilterResampleKeepXRange : public FilterInterface { private: @@ -95,6 +99,43 @@ Trace &filter(Trace &trace) const override; }; + +using SelectionPolygonSpecVector = std::vector; + +class PMSPP_LIB_DECL FilterResampleKeepPointInPolygon : public FilterInterface +{ + public: + FilterResampleKeepPointInPolygon(); + + FilterResampleKeepPointInPolygon(const SelectionPolygon &selection_polygon, + DataKind data_kind); + + FilterResampleKeepPointInPolygon( + const SelectionPolygonSpecVector &selection_polygon_specs); + + FilterResampleKeepPointInPolygon( + const FilterResampleKeepPointInPolygon &other); + + virtual ~FilterResampleKeepPointInPolygon(){}; + + void + newSelectionPolygonSpec(const SelectionPolygonSpec &selection_polygon_spec); + + FilterResampleKeepPointInPolygon & + operator=(const FilterResampleKeepPointInPolygon &other); + + using FilterInterface::filter; + + Trace &filter(Trace &trace) const override; + Trace &filter(Trace &trace, double dt_value, double rt_value) const; + + private: + std::vector m_selectionPolygonSpecs; + double m_lowestMz = std::numeric_limits::max(); + double m_greatestMz = std::numeric_limits::min(); +}; + + class PMSPP_LIB_DECL MassSpectrumFilterResampleRemoveMzRange : public MassSpectrumFilterInterface { @@ -123,4 +164,6 @@ virtual ~MassSpectrumFilterResampleKeepMzRange(){}; MassSpectrum &filter(MassSpectrum &spectrum) const override; }; + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtersuitestring.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtersuitestring.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtersuitestring.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtersuitestring.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,9 +29,14 @@ #include "filtersuitestring.h" #include "filterchargedeconvolution.h" #include "filtercomplementionenhancer.h" +#include "filterpass.h" +#include "filtermorpho.h" #include #include #include "../../exception/exceptionnotrecognized.h" +#include "filterexclusionmz.h" + + namespace pappso { FilterSuiteString::FilterSuiteString(const QString &strBuildParams) @@ -60,6 +65,16 @@ qDebug(); return data_points; } + + +QString +pappso::FilterSuiteString::name() const +{ + // FIXME: check if this makes sense + return "Suite of filters"; +} + + QString FilterSuiteString::toString() const { @@ -72,35 +87,66 @@ return filter_str_list.join(" "); } + void FilterSuiteString::buildFilterFromString(const QString &strBuildParams) { - qDebug() << strBuildParams; - QStringList filters = strBuildParams.split(" ", QString::SkipEmptyParts); + // qInfo() << strBuildParams; + QStringList filters = strBuildParams.split(" ", Qt::SkipEmptyParts); for(QString filter_str : filters) { - qDebug() << filter_str; if(filter_str.startsWith("complementIonEnhancer|")) { m_filterVector.push_back( std::make_shared(filter_str)); } + else if(filter_str.startsWith("chargeDeconvolution|")) + { + m_filterVector.push_back( + std::make_shared(filter_str)); + } + else if(filter_str.startsWith("mzExclusion|")) + { + m_filterVector.push_back( + std::make_shared(filter_str)); + } + else if(filter_str.startsWith("passQuantileBasedRemoveY|")) + { + m_filterVector.push_back( + std::make_shared(filter_str)); + } + + else if(filter_str.startsWith("antiSpike|")) + { + m_filterVector.push_back( + std::make_shared(filter_str)); + } else { - if(filter_str.startsWith("chargeDeconvolution|")) - { - m_filterVector.push_back( - std::make_shared(filter_str)); - } - else - { - throw pappso::ExceptionNotRecognized( - QString("building Filter from string %1 is " - "not possible") - .arg(filter_str)); - } + throw pappso::ExceptionNotRecognized( + QString("building Filter from string %1 is " + "not possible") + .arg(filter_str)); } } } +void +FilterSuiteString::addFilterFromString(const QString &strBuildParams) +{ + buildFilterFromString(strBuildParams); +} + + +FilterSuiteString::FilterNameType::const_iterator +FilterSuiteString::begin() +{ + return m_filterVector.begin(); +}; +FilterSuiteString::FilterNameType::const_iterator +FilterSuiteString::end() +{ + return m_filterVector.end(); +}; + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtersuitestring.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtersuitestring.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/filtersuitestring.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/filtersuitestring.h 2022-10-27 09:16:15.000000000 +0000 @@ -49,16 +49,30 @@ /** * Destructor */ - ~FilterSuiteString(); + virtual ~FilterSuiteString(); pappso::Trace &filter(pappso::Trace &data_points) const override; + virtual QString name() const override; QString toString() const override; + /** @brief takes a string that describes filters to add + * @param strBuildParams string to build the filter + * "chargeDeconvolution|0.02dalton anotherFilter|param1;param2" + */ + void addFilterFromString(const QString &strBuildParams); + + using FilterNameType = std::vector; + + FilterNameType::const_iterator begin(); + FilterNameType::const_iterator end(); + protected: void buildFilterFromString(const QString &strBuildParams) override; private: std::vector m_filterVector; }; + +typedef std::shared_ptr FilterSuiteStringSPtr; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,293 +0,0 @@ -// -// $Id$ -// -// -// Original author: Witold Wolski -// -// Copyright : ETH Zurich -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -# pragma once - -//#include -#include "QDebug" -#include "../resample/convert2dense.hpp" -#include "pwiz/utility/findmf/base/filter/filter.hpp" -#include "simplepicker.hpp" -#include "pwiz/utility/findmf/base/filter/gaussfilter.hpp" -#include "pwiz/utility/findmf/base/base/interpolate.hpp" -#include "pwiz/utility/findmf/base/resample/determinebinwidth.hpp" -#include "pwiz/utility/findmf/base/base/copyif.hpp" - -namespace ralab { -namespace base { -namespace ms { - - -/// resamples spectrum, apply smoothing, -/// determines zero crossings, -/// integrates peaks. - -template -struct SimplePeakArea { - TReal integwith_; - - SimplePeakArea(TReal integwith):integwith_(integwith) {} - - /// intagrates the peak intesnities - template - void operator()( Tzerocross beginZ, - Tzerocross endZ, - [[maybe_unused]] Tintensity intensity, - Tintensity resmpled, - Tout area)const - { - typedef typename std::iterator_traits::value_type AreaType; - for( ; beginZ != endZ ; ++beginZ, ++area ) - { - size_t idx = static_cast( *beginZ ); - size_t start = static_cast( std::round( idx - integwith_ ) ); - size_t end = static_cast( std::round( idx + integwith_ + 2.) ); - AreaType aread = 0.; - for( ; start != end ; ++start ) - { - aread += *(resmpled + start); - } - *area = aread; - } - } -}; - -/// extends peak to the left and to the right to the next local minimum or a predefined threshol -/// or a maximum allowed extension. -template -struct LocalMinPeakArea { - typedef TReal value_type; - TReal integwith_; - TReal threshold_; - - LocalMinPeakArea(TReal integwith,//! - void operator()( Tzerocross beginZ, - Tzerocross endZ, - Tintensity intensity, - Tintensity resampled, - Tout area) const - { - typedef typename std::iterator_traits::value_type AreaType; - for( ; beginZ != endZ ; ++beginZ, ++area ) - { - size_t idx = static_cast( *beginZ ); - size_t start = static_cast( std::round( idx - integwith_ ) ); - size_t end = static_cast( std::round( idx + integwith_ + 2) ); - - Tintensity st = intensity + start; - Tintensity en = intensity + end; - Tintensity center = intensity + idx; - std::ptrdiff_t x1 = std::distance(st, center); - std::ptrdiff_t y1 = std::distance(center,en); - mextend(st, en, center); - std::ptrdiff_t x2 = std::distance(intensity,st); - std::ptrdiff_t y2 = std::distance(intensity,en); - std::ptrdiff_t pp = std::distance(st,en); - AreaType areav = std::accumulate(resampled+x2,resampled+y2,0.); - *area = areav; - } - } - -private: - ///exend peak to left and rigth - template - void mextend( TInt &start, TInt &end, TInt idx) const - { - typedef typename std::iterator_traits::value_type Intensitytype; - // - for(TInt intens = idx ; intens >= start; --intens) { - Intensitytype val1 = *intens; - Intensitytype val2 = *(intens-1); - if(val1 > threshold_) { - if(val1 < val2 ) { - start = intens; - break; - } - } - else { - start = intens; - break; - } - } - - for(TInt intens = idx ; intens <= end; ++intens) { - Intensitytype val1 = *intens; - Intensitytype val2 = *(intens+1); - if(val1 > threshold_) { - if(val1 < val2 ) { - end = intens; - break; - } - } - else { - end = intens; - break; - } - } - } -}; - -/// resamples spectrum, apply smoothing, -/// determines zero crossings, -/// integrates peaks. -template class TIntegrator > -struct PeakPicker { - typedef TReal value_type; - typedef TIntegrator PeakIntegrator; - - TReal resolution_; - ralab::base::resample::Convert2Dense c2d_; // resamples spectrum - std::vector resampledmz_, resampledintensity_; // keeps result of convert to dense - std::vector filter_, zerocross_, smoothedintensity_; // working variables - std::vector peakmass_, peakarea_; //results - TReal smoothwith_; - TReal integrationWidth_; - ralab::base::ms::SimplePicker simplepicker_; - ralab::base::resample::SamplingWith sw_; - PeakIntegrator integrator_; - TReal intensitythreshold_; - bool area_; - uint32_t maxnumbersofpeaks_; - - PeakPicker(TReal resolution, //!< instrument resolution - std::pair & massrange, //!< mass range of spectrum - TReal width = 2., //!< smooth width - TReal intwidth = 2., //!< integration width used for area compuation - TReal intensitythreshold = 10., // intensity threshold - bool area = true,//!< compute area or height? default - height. - uint32_t maxnumberofpeaks = 0, //!< maximum of peaks returned by picker - double c2d = 1e-5 //!< instrument resampling with small default dissables automatic determination - ): resolution_(resolution),c2d_( c2d ),smoothwith_(width), - integrationWidth_(intwidth),sw_(),integrator_(integrationWidth_), - intensitythreshold_(intensitythreshold),area_(area),maxnumbersofpeaks_(maxnumberofpeaks) - { - c2d_.defBreak(massrange,ralab::base::resample::resolution2ppm(resolution)); - c2d_.getMids(resampledmz_); - ralab::base::filter::getGaussianFilterQuantile(filter_,width); - } - - - template - void operator()(Tmass begmz, Tmass endmz, Tintensity begint ) - { - // get the first position of the peak begining (intensity > 0.1) - typename std::iterator_traits::value_type minint = *std::upper_bound(begint,begint+std::distance(begmz,endmz),0.1); - - //determine sampling with - double a = sw_(begmz,endmz); - - //resmpale the spectrum - c2d_.am_ = a; - c2d_.convert2dense(begmz,endmz, begint, resampledintensity_); - - //smooth the resampled spectrum - ralab::base::filter::filter(resampledintensity_, filter_, smoothedintensity_, true); - //determine zero crossings - zerocross_.resize( smoothedintensity_.size()/2 ); - size_t nrzerocross = simplepicker_( smoothedintensity_.begin( ), smoothedintensity_.end(), zerocross_.begin(), zerocross_.size()); - - peakmass_.resize(nrzerocross); - //determine mass of zerocrossing - ralab::base::base::interpolate_linear( resampledmz_.begin(), resampledmz_.end(), - zerocross_.begin(), zerocross_.begin()+nrzerocross, - peakmass_.begin()); - - //determine peak area - if(area_) { - peakarea_.resize(nrzerocross); - integrator_( zerocross_.begin(), zerocross_.begin() + nrzerocross, - smoothedintensity_.begin(),resampledintensity_.begin(), peakarea_.begin() ); - } else { - //determine intensity - peakarea_.resize(nrzerocross); - ralab::base::base::interpolate_cubic( smoothedintensity_.begin(), smoothedintensity_.end(), - zerocross_.begin(), zerocross_.begin()+nrzerocross, - peakarea_.begin()); - } - - TReal threshold = static_cast(minint) * intensitythreshold_; - - if(maxnumbersofpeaks_ > 0) { - double threshmax = getNToppeaks(); - if(threshmax > threshold) - threshold = threshmax; - } - - - if(threshold > 0.01) { - filter(threshold); - } - } - - /// get min instensity of peak to qualify for max-intensity; - TReal getNToppeaks() { - TReal intthres = 0.; - if(maxnumbersofpeaks_ < peakarea_.size()) - { - std::vector tmparea( peakarea_.begin(), peakarea_.end() ); - std::nth_element(tmparea.begin(),tmparea.end() - maxnumbersofpeaks_, tmparea.end()); - intthres = *(tmparea.end() - maxnumbersofpeaks_); - } - return intthres; - } - - - /// clean the masses using the threshold - void filter(TReal threshold) { - typename std::vector::iterator a = ralab::base::utils::copy_if(peakarea_.begin(),peakarea_.end(),peakmass_.begin(), - peakmass_.begin(),boost::bind(std::greater(),_1,threshold)); - peakmass_.resize(std::distance(peakmass_.begin(),a)); - typename std::vector::iterator b = ralab::base::utils::copy_if(peakarea_.begin(),peakarea_.end(), - peakarea_.begin(),boost::bind(std::greater(),_1,threshold)); - peakarea_.resize(std::distance(peakarea_.begin(),b)); - //int x = 1; - } - - const std::vector & getPeakMass() { - return peakmass_; - } - - const std::vector & getPeakArea() { - return peakarea_; - } - - const std::vector & getResampledMZ() { - return resampledmz_; - } - - const std::vector & getResampledIntensity() { - return resampledintensity_; - } - - const std::vector & getSmoothedIntensity() { - return smoothedintensity_; - } -}; -}//ms -}//base -}//ralab diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,123 +0,0 @@ -// -// $Id$ -// -// -// Original author: Witold Wolski -// -// Copyright : ETH Zurich -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#ifndef SIMPLEPICKER_H -#define SIMPLEPICKER_H - -#include -#include -#include -//#include - -namespace ralab -{ - namespace base - { - namespace ms - { - /*! computes first derivative of a sequence, looks for zero crossings - */ - template - struct SimplePicker{ - std::vector worker_; - double epsilon_; - bool problem_; //indicates if not the whole signal was picked. - - SimplePicker(TReal epsilon = 1e-3):epsilon_(epsilon),problem_(false){} - /*! - *returns number of zero crossings found - */ - template - size_t operator()(Tit beg, Tit end , - Outit zerocrossings, //! picked peaks - size_t nzercross, - std::ptrdiff_t lag = 2 //must be even (leave odd out) - ) - { - if((lag % 2 ) == 1){ - return -1; - } - worker_.resize(std::distance(beg,end) - lag); - TReal * pworkerBeg = &worker_[0]; - TReal * pworkerEnd = &worker_[0] + worker_.size(); - - Tit tbegin = beg; - Tit tbeginm1 = tbegin + ( lag); - for(;tbeginm1 != end ; ++tbeginm1, ++tbegin, ++pworkerBeg ) - { - *pworkerBeg = (*tbeginm1 - *tbegin); - } - - //reset worker - pworkerBeg = &worker_[0]; - std::size_t crosscount = 0; - for( int i = 0 ; (pworkerBeg != pworkerEnd-1) ; ++pworkerBeg , ++i ) - { - if(crosscount >= nzercross){ - problem_ = true; - return crosscount; // protect against memmory violations - std::string x = "nzerocross:"; - x+=boost::lexical_cast(nzercross); - x+=" crosscount:"; - x+=boost::lexical_cast(crosscount); - x+=" i: "; - x+= boost::lexical_cast(i); - x+=" worker size "; - x+= boost::lexical_cast( worker_.size() ); - x+=" : "; - x+=boost::lexical_cast(__LINE__); - x+=" : "; - x+= __FILE__; - throw std::length_error(x.c_str()); - } - TReal v1 = (*pworkerBeg); - TReal v2 = *(pworkerBeg + 1); - //peak detected ... detect a zero crossing - if((v1 > 0 && v2 < 0) && ((v1 - v2) > epsilon_)) - { - //determine zero crossing.... - double frac = v1 / ( v1 - v2 ); - double idx = static_cast(i + lag/2) + frac; - *zerocrossings = ( idx ); - ++zerocrossings; - ++crosscount; - }else if( v1 > 0 && v2 == 0 ){ - TReal v3 = *(pworkerBeg + 2); - if((v3 < 0) && ((v1 - v3) > epsilon_)){ - *zerocrossings = (i + lag/2 + 1.); - } - }else{ - //just continue, nothing to handle... - } - } - return crosscount; - } - - bool getProblem() const{ - return problem_; - } - - }; - }//ms - }//base -}//ralab - -#endif // SIMPLEPICKER_H diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -// -// $Id$ -// -// -// Original author: Witold Wolski -// -// Copyright : ETH Zurich -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#ifndef CONVERT2DENSE_H -#define CONVERT2DENSE_H - -#include -#include -#include -//#include -//#include -#include "pwiz/utility/findmf/base/resample/masscomparefunctors.hpp" -#include "pwiz/utility/findmf/base/resample/breakspec.hpp" -#include "pwiz/utility/findmf/base/resample/bin1d.hpp" -#include -#include "../../../../exception/exceptionoutofrange.h" - - -namespace ralab -{ -namespace base -{ -namespace resample -{ -//typedef boost::int32_t int32_t; -struct Convert2Dense -{ - ralab::base::resample::Bin1D bin_; - std::vector idx_; // small workder vecs - std::vector weight_; - double am_; // parameter describing the sampling width - Convert2Dense(double am [[maybe_unused]] = 0.1) : bin_(), idx_(), weight_(), am_() - { - } - - /// computes split points of an map. - std::size_t - defBreak(std::pair &mzrange, double ppm) - { - ralab::base::resample::PPMCompFunctor ppmf(ppm); - qDebug() << ppm << ppmf.ppm_ << ppmf.window_; - ralab::base::resample::breaks( - mzrange.first - 1., mzrange.second + 1., ppmf, bin_.breaks_); - bin_.reset(); - return bin_.breaks_.size(); - } - - /// Converts a sparse spec to a dense spec - template - void - convert2dense(Tmass beginMass, Tmass endMass, Tintens intens, Tout ass) - { - for(; beginMass != (endMass - 1); ++beginMass, ++intens) - { - double mass1 = *beginMass; - double mass2 = *(beginMass + 1); - double predmass2 = mass1 + (am_ * sqrt(mass1)) * 1.01; - - if(mass2 > predmass2) - { - mass2 = predmass2; - } - - double deltamass = mass2 - mass1; - double deltamasshalf; - if(true) - { - deltamasshalf = deltamass / 2.; - } - else - { - deltamasshalf = deltamass; - } - - bin_(mass1 - deltamasshalf, mass2 - deltamasshalf, idx_, weight_); - - double intensd = static_cast(*intens); - double sum = std::accumulate(weight_.begin(), weight_.end(), 0.); - - if(fabs(deltamass - sum) > 1e-11) - { - // BOOST_ASSERT(fabs(deltamass- sum) < 1e-11); - throw pappso::ExceptionOutOfRange( - QObject::tr("ERROR pwiz convert2dense :\n " - "BOOST_ASSERT(fabs(deltamass- sum) < 1e-11)")); - } - - double check = 0.; - for(std::size_t i = 0; i < idx_.size(); ++i) - { - if((idx_[i] >= 0) & - (idx_[i] < static_cast(bin_.breaks_.size() - 1))) - { - double bb = intensd * weight_[i] / deltamass; - *(ass + idx_[i]) += bb; - check += bb; - } - } - // BOOST_ASSERT( fabs(check - intensd) < 1e-3 ); - } - } // convert2dense - - void - getMids(std::vector &mids) - { - ralab::base::resample::getMids(bin_.breaks_, mids); - } - - /// Converts a sparse spec to a dense spec - template - void - convert2dense( - Tmass beginMass, - Tmass endMass, - Tintens intens, - std::vector::value_type> &gg) - { - gg.resize(bin_.breaks_.size() - 1); - convert2dense(beginMass, endMass, intens, gg.begin()); - } -}; - - -} // namespace resample -} // namespace base -} // namespace ralab -#endif // CONVERT2DENSE_H diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/savgolfilter.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/filters/savgolfilter.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/savgolfilter.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/savgolfilter.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -37,6 +37,7 @@ #include #include +#include "../../exception/exceptionnotrecognized.h" #include "savgolfilter.h" @@ -54,11 +55,21 @@ FilterSavitzkyGolay::FilterSavitzkyGolay( int nL, int nR, int m, int lD, bool convolveWithNr) { - m_nL = nL; - m_nR = nR; - m_m = m; - m_lD = lD; - m_convolveWithNr = convolveWithNr; + m_params.nL = nL; + m_params.nR = nR; + m_params.m = m; + m_params.lD = lD; + m_params.convolveWithNr = convolveWithNr; +} + + +FilterSavitzkyGolay::FilterSavitzkyGolay(const SavGolParams sav_gol_params) +{ + m_params.nL = sav_gol_params.nL; + m_params.nR = sav_gol_params.nR; + m_params.m = sav_gol_params.m; + m_params.lD = sav_gol_params.lD; + m_params.convolveWithNr = sav_gol_params.convolveWithNr; } @@ -66,11 +77,11 @@ { // This function only copies the parameters, not the data. - m_nL = other.m_nL; - m_nR = other.m_nR; - m_m = other.m_m; - m_lD = other.m_lD; - m_convolveWithNr = other.m_convolveWithNr; + m_params.nL = other.m_params.nL; + m_params.nR = other.m_params.nR; + m_params.m = other.m_params.m; + m_params.lD = other.m_params.lD; + m_params.convolveWithNr = other.m_params.convolveWithNr; } @@ -86,16 +97,45 @@ // This function only copies the parameters, not the data. - m_nL = other.m_nL; - m_nR = other.m_nR; - m_m = other.m_m; - m_lD = other.m_lD; - m_convolveWithNr = other.m_convolveWithNr; + m_params.nL = other.m_params.nL; + m_params.nR = other.m_params.nR; + m_params.m = other.m_params.m; + m_params.lD = other.m_params.lD; + m_params.convolveWithNr = other.m_params.convolveWithNr; return *this; } +FilterSavitzkyGolay::FilterSavitzkyGolay(const QString ¶meters) +{ + buildFilterFromString(parameters); +} + + +void +FilterSavitzkyGolay::buildFilterFromString(const QString ¶meters) +{ + // Typical string: "Savitzky-Golay|15;15;4;0;false" + if(parameters.startsWith(QString("%1|").arg(name()))) + { + QStringList params = parameters.split("|").back().split(";"); + + m_params.nL = params.at(0).toInt(); + m_params.nR = params.at(1).toInt(); + m_params.m = params.at(2).toInt(); + m_params.lD = params.at(3).toInt(); + m_params.convolveWithNr = (params.at(4) == "true" ? true : false); + } + else + { + throw pappso::ExceptionNotRecognized( + QString("Building of FilterSavitzkyGolay from string %1 failed") + .arg(parameters)); + } +} + + Trace & FilterSavitzkyGolay::filter(Trace &data_points) const { @@ -109,7 +149,7 @@ pappso_double *y_initial_data_p = dvector(1, data_point_count); pappso_double *y_filtered_data_p = nullptr; - if(m_convolveWithNr) + if(m_params.convolveWithNr) y_filtered_data_p = dvector(1, 2 * data_point_count); else y_filtered_data_p = dvector(1, data_point_count); @@ -139,7 +179,8 @@ SavGolParams FilterSavitzkyGolay::getParameters() const { - return SavGolParams(m_nL, m_nR, m_m, m_lD, m_convolveWithNr); + return SavGolParams( + m_params.nL, m_params.nR, m_params.m, m_params.lD, m_params.convolveWithNr); } @@ -147,14 +188,14 @@ QString FilterSavitzkyGolay::toString() const { - return QString::asprintf( - "Savitzy-Golay filter parameters:\n" - "nL: %d ; nR: %d ; m: %d ; lD: %d ; convolveWithNr : %s", - m_nL, - m_nR, - m_m, - m_lD, - (m_convolveWithNr ? "true" : "false")); + return QString("%1|%2").arg(name()).arg(m_params.toString()); +} + + +QString +FilterSavitzkyGolay::name() const +{ + return "Savitzky-Golay"; } @@ -589,14 +630,15 @@ //! Perform the Savitzky-Golay filtering process. /* - The results are in the \c y_filtered_data_p C array of pappso_double values. + The results are in the \c y_filtered_data_p C array of pappso_double + values. */ char FilterSavitzkyGolay::runFilter(double *y_data_p, double *y_filtered_data_p, int data_point_count) const { - int np = m_nL + 1 + m_nR; + int np = m_params.nL + 1 + m_params.nR; pappso_double *c; char retval; @@ -609,46 +651,52 @@ #else int j; long int k; - c = dvector(1, m_nL + m_nR + 1); - retval = sgcoeff(c, np, m_nL, m_nR, m_lD, m_m); + c = dvector(1, m_params.nL + m_params.nR + 1); + retval = sgcoeff(c, np, m_params.nL, m_params.nR, m_params.lD, m_params.m); if(retval == 0) { qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" << "retval is 0"; - for(k = 1; k <= m_nL; k++) + for(k = 1; k <= m_params.nL; k++) { - for(y_filtered_data_p[k] = 0.0, j = -m_nL; j <= m_nR; j++) + for(y_filtered_data_p[k] = 0.0, j = -m_params.nL; j <= m_params.nR; + j++) { if(k + j >= 1) { y_filtered_data_p[k] += - c[(j >= 0 ? j + 1 : m_nR + m_nL + 2 + j)] * y_data_p[k + j]; + c[(j >= 0 ? j + 1 : m_params.nR + m_params.nL + 2 + j)] * + y_data_p[k + j]; } } } - for(k = m_nL + 1; k <= data_point_count - m_nR; k++) + for(k = m_params.nL + 1; k <= data_point_count - m_params.nR; k++) { - for(y_filtered_data_p[k] = 0.0, j = -m_nL; j <= m_nR; j++) + for(y_filtered_data_p[k] = 0.0, j = -m_params.nL; j <= m_params.nR; + j++) { y_filtered_data_p[k] += - c[(j >= 0 ? j + 1 : m_nR + m_nL + 2 + j)] * y_data_p[k + j]; + c[(j >= 0 ? j + 1 : m_params.nR + m_params.nL + 2 + j)] * + y_data_p[k + j]; } } - for(k = data_point_count - m_nR + 1; k <= data_point_count; k++) + for(k = data_point_count - m_params.nR + 1; k <= data_point_count; k++) { - for(y_filtered_data_p[k] = 0.0, j = -m_nL; j <= m_nR; j++) + for(y_filtered_data_p[k] = 0.0, j = -m_params.nL; j <= m_params.nR; + j++) { if(k + j <= data_point_count) { y_filtered_data_p[k] += - c[(j >= 0 ? j + 1 : m_nR + m_nL + 2 + j)] * y_data_p[k + j]; + c[(j >= 0 ? j + 1 : m_params.nR + m_params.nL + 2 + j)] * + y_data_p[k + j]; } } } } - free_dvector(c, 1, m_nR + m_nL + 1); + free_dvector(c, 1, m_params.nR + m_params.nL + 1); #endif return (retval); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/filters/savgolfilter.h libpappsomspp-0.8.58/src/pappsomspp/processing/filters/savgolfilter.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/filters/savgolfilter.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/filters/savgolfilter.h 2022-10-27 09:16:15.000000000 +0000 @@ -38,6 +38,7 @@ #include "../../trace/trace.h" #include "../../exportinmportconfig.h" +#include "filternameinterface.h" namespace pappso @@ -101,13 +102,30 @@ lD = other.lD; convolveWithNr = other.convolveWithNr; } + + QString + toString() const + { + return QString("%1;%2;%3;%4;%5") + .arg(QString::number(nL)) + .arg(QString::number(nR)) + .arg(QString::number(m)) + .arg(QString::number(lD)) + .arg(convolveWithNr ? "true" : "false"); + } }; +class FilterSavitzkyGolay; + +typedef std::shared_ptr FilterSavitzkyGolaySPtr; +typedef std::shared_ptr FilterSavitzkyGolayCstSPtr; + + /** * @brief uses Savitsky-Golay filter on trace */ -class PMSPP_LIB_DECL FilterSavitzkyGolay : public FilterInterface +class PMSPP_LIB_DECL FilterSavitzkyGolay : public FilterNameInterface { public: /** Construct a FilterSavitzkyGolay instance using the Savitzky-Golay @@ -120,6 +138,10 @@ FilterSavitzkyGolay( int nL, int nR, int m, int lD, bool convolveWithNr = false); + FilterSavitzkyGolay(const SavGolParams sav_gol_params); + + FilterSavitzkyGolay(const QString ¶meters); + /** * Copy constructor * @@ -144,21 +166,19 @@ void filteredData(std::vector &data); + QString name() const override; + + // Utility function + + QString toString() const override; + + protected: + void buildFilterFromString(const QString &strBuildParams) override; + private: ///// Parameters to configure the Savitzky-Golay filter algorithm - int m_nL = 15; - //!< number of data points on the left of the filtered point - int m_nR = 15; - //!< number of data points on the right of the filtered point - int m_m = 4; - //!< order of the polynomial to use in the regression analysis leading to the - //! Savitzky-Golay coefficients (typically between 2 and 6) - int m_lD = 0; - //!< specifies the order of the derivative to extract from the Savitzky-Golay - //! smoothing algorithm (for regular smoothing, use 0) - bool m_convolveWithNr = false; - //!< set to false for best results + SavGolParams m_params; ///// Data used for running the algorithm. @@ -196,9 +216,5 @@ int isign, pappso_double ans[]); char sgcoeff(pappso_double c[], int np, int nl, int nr, int ld, int m) const; - - // Utility function - - QString toString() const; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,19 +31,21 @@ #include #include #include -#include "../../pappsoexception.h" +#include +#include "../../exception/exceptioninterrupted.h" #include "../../msfile/msfileaccessor.h" #include "../../msrun/private/timsmsrunreaderms2.h" -#include "../../processing/filters/filterpseudocentroid.h" #include "../../processing/filters/filtertriangle.h" #include "../../processing/filters/filterchargedeconvolution.h" #include "../../msrun/output/mzxmloutput.h" -#include "xtandeminputsaxhandler.h" -#include "xtandemoutputsaxhandler.h" -#include "xtandempresetsaxhandler.h" +#include "wraptandemresults.h" +#include "xtandempresetreader.h" +#include "wraptandeminput.h" namespace pappso { + + TandemWrapperRun::TandemWrapperRun(const QString &tandem_binary, const QString &tmp_dir) { @@ -74,6 +76,11 @@ { delete mpa_temporaryDirectory; } + + if(m_xtProcess != nullptr) + { + m_xtProcess->deleteLater(); + } } void @@ -162,16 +169,18 @@ // X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) - QRegExp parse_version("(.*) TANDEM ([A-Z,a-z, ]+) \\(([^ ,^\\)]*)(.*)"); + QRegularExpression parse_version( + "(.*) TANDEM ([A-Z,a-z, ]+) \\(([^ ,^\\)]*)(.*)"); qDebug() << parse_version; // Pattern patt = Pattern.compile("X! TANDEM [A-Z]+ \\((.*)\\)", // Pattern.CASE_INSENSITIVE); - - if(parse_version.exactMatch(result.constData())) + QRegularExpressionMatch match_parse_version = + parse_version.match(result.constData()); + if(match_parse_version.hasMatch()) { version_return = QString("X!Tandem %1 %2") - .arg(parse_version.capturedTexts()[2]) - .arg(parse_version.capturedTexts()[3]); //.join(" "); + .arg(match_parse_version.captured(2)) + .arg(match_parse_version.captured(3)); //.join(" "); } else { @@ -195,26 +204,39 @@ return version_return; } - -bool -TandemWrapperRun::shouldIstop() -{ - return false; -} - - void TandemWrapperRun::readyReadStandardOutput() { - *mp_outputStream << m_xtProcess->readAllStandardOutput(); - mp_outputStream->flush(); + QString message(m_xtProcess->readAllStandardOutput()); + mp_monitor->appendText(message); + + if(message.toLower().contains("error")) + { + throw pappso::XtandemError(message); + } + + if(mp_monitor->shouldIstop()) + { + m_xtProcess->kill(); + delete m_xtProcess; + m_xtProcess = nullptr; + throw pappso::ExceptionInterrupted( + QObject::tr("X!Tandem stopped by the user")); + } } void TandemWrapperRun::readyReadStandardError() { - *mp_errorStream << m_xtProcess->readAllStandardError(); - mp_errorStream->flush(); + mp_monitor->appendText(m_xtProcess->readAllStandardError()); + if(mp_monitor->shouldIstop()) + { + m_xtProcess->kill(); + delete m_xtProcess; + m_xtProcess = nullptr; + throw pappso::ExceptionInterrupted( + QObject::tr("X!Tandem stopped by the user")); + } } void @@ -223,20 +245,31 @@ const QString &final_tandem_output, const QString &original_msdata_file_name) { + mp_monitor->setStatus(QObject::tr("Rewriting X!Tandem XML result file")); - XtandemOutputSaxHandler wrap_output(final_tandem_output, - original_msdata_file_name); + WrapTandemResults wrap_output(final_tandem_output, original_msdata_file_name); wrap_output.setInputParameters("spectrum, timstof MS2 filters", getMs2FilterSuiteString()); + wrap_output.setInputParameters("spectrum, mzFormat", + QString("%1").arg((int)m_mzFormat)); - QFile qfile(tmp_tandem_output); - QXmlInputSource xmlInputSource(&qfile); - QXmlSimpleReader simplereader; - simplereader.setContentHandler(&wrap_output); - simplereader.setErrorHandler(&wrap_output); + if(m_convertMzDataUsingSpectrumIndex) + { + wrap_output.setInputParameters("output, spectrum index", "true"); + } + else + { + } - if(simplereader.parse(xmlInputSource)) + if(m_conversionTime != 0) + { + wrap_output.setInputParameters( + "timing, tandemwrapper conversion time (sec)", + QString("%1").arg(m_conversionTime / 1000)); + } + + if(wrap_output.readFile(tmp_tandem_output)) { } else @@ -253,15 +286,10 @@ { // get number of threads and centroid parameters from tandem preset - XtandemPresetSaxHandler preset_handler; + XtandemPresetReader preset_handler; - QFile qfile(tandem_preset_file); - QXmlInputSource xmlInputSource(&qfile); - QXmlSimpleReader simplereader; - simplereader.setContentHandler(&preset_handler); - simplereader.setErrorHandler(&preset_handler); - if(simplereader.parse(xmlInputSource)) + if(preset_handler.readFile(tandem_preset_file)) { int ideal_number_of_thread = QThread::idealThreadCount(); @@ -284,8 +312,17 @@ } QString ms2_filters_str = preset_handler.getMs2FiltersOptions(); - msp_ms2FilterSuiteString = - std::make_shared(ms2_filters_str); + if(!ms2_filters_str.isEmpty()) + { + msp_ms2FilterSuiteString = + std::make_shared(ms2_filters_str); + } + else + { + msp_ms2FilterSuiteString = + std::make_shared( + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"); + } } else { @@ -304,16 +341,42 @@ // store original ms data file name // create new mzXML data file in temporary directory // create new tandem input file based on new mzXML file + + QString mzxml_data_file_name = mpa_temporaryDirectory->filePath("msdata.mzxml"); QString wrapped_tandem_input = mpa_temporaryDirectory->filePath("input_tandem.xml"); QString wrapped_tandem_output = mpa_temporaryDirectory->filePath("output_tandem.xml"); - XtandemInputSaxHandler wrap_input( + + WrapTandemInput wrap_tandem_input( mzxml_data_file_name, wrapped_tandem_input, wrapped_tandem_output); + + if(wrap_tandem_input.readFile(tandem_input_file)) + { + } + else + { + throw pappso::PappsoException( + QObject::tr("Error reading %1 X!Tandem input file :\n %2") + .arg(tandem_input_file) + .arg(wrap_tandem_input.errorString())); + } + + + /* + * + XtandemInputSaxHandler wrap_input( + mzxml_data_file_name, wrapped_tandem_input, wrapped_tandem_output); QFile qfile(tandem_input_file); + if(!qfile.exists()) + { + throw pappso::PappsoException( + QObject::tr("Tandem input file %1 does not exists") + .arg(QFileInfo(tandem_input_file).absoluteFilePath())); + } QXmlInputSource xmlInputSource(&qfile); QXmlSimpleReader simplereader; simplereader.setContentHandler(&wrap_input); @@ -329,96 +392,141 @@ .arg(tandem_input_file) .arg(wrap_input.errorString())); } - +*/ // get number of threads and centroid parameters from tandem preset - readTandemPresetFile(wrap_input.getOriginalTandemPresetFileName()); + readTandemPresetFile(wrap_tandem_input.getOriginalTandemPresetFileName()); // convert to mzXML - QString original_msdata_file_name = wrap_input.getOriginalMsDataFileName(); - convertOrginalMsData2mzXmlData(original_msdata_file_name, - mzxml_data_file_name); + QString original_msdata_file_name = + wrap_tandem_input.getOriginalMsDataFileName(); + if(convertOrginalMsData2mzXmlData(original_msdata_file_name, + mzxml_data_file_name)) + { + + // launch tandem + runTandem(wrapped_tandem_input); - // launch tandem - runTandem(wrapped_tandem_input); - - // rewrite tandem result file - writeFinalTandemOutput(wrapped_tandem_output, - wrap_input.getOriginalTandemOutputFileName(), - original_msdata_file_name); + // rewrite tandem result file + writeFinalTandemOutput( + wrapped_tandem_output, + wrap_tandem_input.getOriginalTandemOutputFileName(), + original_msdata_file_name); + } + else + { + // launch tandem on original file + runTandem(tandem_input_file); + } } -void +bool TandemWrapperRun::convertOrginalMsData2mzXmlData(const QString &origin, - const QString &target) const + const QString &target) { qDebug(); pappso::MsFileAccessor origin_access(origin, "runa1"); origin_access.setPreferedFileReaderType(pappso::MzFormat::brukerTims, pappso::FileReaderType::tims_ms2); origin_access.getMsRunIds(); + m_mzFormat = origin_access.getFileFormat(); + if(m_mzFormat == pappso::MzFormat::unknown) + { + throw pappso::PappsoException( + QObject::tr("%1 file format not known").arg(origin)); + } - pappso::MsRunReaderSPtr p_reader; - p_reader = origin_access.msRunReaderSp(origin_access.getMsRunIds().front()); + if(origin_access.getFileFormat() == pappso::MzFormat::brukerTims) + { + m_convertMzDataUsingSpectrumIndex = true; + } - pappso::TimsMsRunReaderMs2 *tims2_reader = - dynamic_cast(p_reader.get()); - if(tims2_reader != nullptr) + if((origin_access.getFileFormat() == pappso::MzFormat::mzML) || + (origin_access.getFileFormat() == pappso::MzFormat::brukerTims)) { - qDebug(); - tims2_reader->setMs2BuiltinCentroid(true); + mp_monitor->setStatus( + QObject::tr("Converting %1 to mzXML %2").arg(origin).arg(target)); + pappso::MsRunReaderSPtr p_reader; + p_reader = + origin_access.msRunReaderSp(origin_access.getMsRunIds().front()); - if(msp_ms2FilterSuiteString != nullptr) + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_reader.get()); + if(tims2_reader != nullptr) { - tims2_reader->setMs2FilterCstSPtr(msp_ms2FilterSuiteString); + qDebug(); + tims2_reader->setMs2BuiltinCentroid(true); + + if(msp_ms2FilterSuiteString != nullptr) + { + tims2_reader->setMs2FilterCstSPtr(msp_ms2FilterSuiteString); + } + qDebug(); } - qDebug(); - } - pappso::MzxmlOutput *p_mzxml_output; - QFile output_file(target); - // qDebug() << " TsvDirectoryWriter::writeSheet " << - // QFileInfo(*_p_ofile).absoluteFilePath(); - if(output_file.open(QIODevice::WriteOnly)) - { - p_mzxml_output = - new pappso::MzxmlOutput(QTextStream(&output_file).device()); + pappso::MzxmlOutput *p_mzxml_output; + QFile output_file(target); + // qDebug() << " TsvDirectoryWriter::writeSheet " << + // QFileInfo(*_p_ofile).absoluteFilePath(); + if(output_file.open(QIODevice::WriteOnly)) + { + QElapsedTimer timer; + m_conversionTime = 0; + timer.start(); + p_mzxml_output = new pappso::MzxmlOutput( + *mp_monitor, QTextStream(&output_file).device()); + + p_mzxml_output->maskMs1(true); + + p_mzxml_output->setReadAhead(true); - p_mzxml_output->maskMs1(true); + p_mzxml_output->write(p_reader.get()); - p_mzxml_output->setReadAhead(true); + p_mzxml_output->close(); - p_mzxml_output->write(p_reader.get()); + delete p_mzxml_output; + m_conversionTime = timer.elapsed(); + + mp_monitor->setStatus(QObject::tr("Conversion finished in %1 seconds") + .arg(m_conversionTime / 1000)); + } + else + { + throw pappso::PappsoException( + QObject::tr("unable to write into %1 mzXML output file") + .arg(target)); + } - p_mzxml_output->close(); + qDebug(); + return true; } else - { - throw pappso::PappsoException( - tr("unable to write into %1 mzXML output file").arg(target)); + { // other mz data formats + return false; } - - qDebug(); + return true; } void -TandemWrapperRun::run(const QString &tandem_input_file, - QTextStream &output_stream, - QTextStream &error_stream) +TandemWrapperRun::run(UiMonitorInterface &monitor, + const QString &tandem_input_file) { - mp_outputStream = &output_stream; - mp_errorStream = &error_stream; + mp_monitor = &monitor; wrapTandemInputFile(tandem_input_file); - mp_outputStream = nullptr; - mp_errorStream = nullptr; + mp_monitor = nullptr; } void TandemWrapperRun::runTandem(const QString &tandem_input_file) { - + if(mp_monitor->shouldIstop()) + { + throw pappso::ExceptionInterrupted( + QObject::tr("X!Tandem stopped by the user processing on file %1") + .arg(tandem_input_file)); + } m_xtProcess = new QProcess(); QStringList arguments; @@ -442,6 +550,8 @@ qDebug() << m_tandemBinary << " " << m_xtProcess->arguments(); + mp_monitor->setStatus(QObject::tr("Running X!Tandem")); + if(!m_xtProcess->waitForStarted()) { throw pappso::PappsoException( @@ -449,16 +559,16 @@ } qDebug() << m_tandemBinary << " " << m_xtProcess->arguments(); - - while(m_xtProcess->waitForFinished(m_maxTandemRunTimeMs)) + while(m_xtProcess->waitForFinished(m_maxTandemRunTimeMs) == false) { //_p_monitor->appendText(xt_process->readAll().data()); // data.append(xt_process->readAll()); - if(shouldIstop()) + if(mp_monitor->shouldIstop()) { m_xtProcess->kill(); delete m_xtProcess; - throw pappso::PappsoException( + m_xtProcess = nullptr; + throw pappso::ExceptionInterrupted( QObject::tr("X!Tandem stopped by the user processing on file %1") .arg(tandem_input_file)); } @@ -467,7 +577,7 @@ QProcess::ExitStatus Status = m_xtProcess->exitStatus(); delete m_xtProcess; - if(Status != 0) + if(Status != QProcess::ExitStatus::NormalExit) { // != QProcess::NormalExit throw pappso::PappsoException( diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h 2022-10-27 09:16:15.000000000 +0000 @@ -31,15 +31,33 @@ #include #include #include +#include #include "../../exportinmportconfig.h" #include "../../processing/filters/filtersuitestring.h" +#include "../uimonitor/uimonitorinterface.h" +#include "../../pappsoexception.h" +#include "../../types.h" /** * @todo write docs */ namespace pappso { +class XtandemError : public PappsoException +{ + public: + XtandemError(const QString &message) throw() : PappsoException(message) + { + } + + virtual QException * + clone() const override + { + return new XtandemError(*this); + } +}; + class PMSPP_LIB_DECL TandemWrapperRun : public QObject { Q_OBJECT @@ -60,13 +78,10 @@ * A default value of "chargeDeconvolution|0.02dalton" is recommended for this * additional tandem input parameter * + * @param monitor user interface monitor * @param tandem_input_file tandem xml input file - * @param output_stream standard output where to write tandem stdout - * @param error_stream standard error where to write tandem stderr */ - void run(const QString &tandem_input_file, - QTextStream &output_stream, - QTextStream &error_stream); + void run(UiMonitorInterface &monitor, const QString &tandem_input_file); void readTandemPresetFile(const QString &tandem_preset_file); @@ -81,14 +96,17 @@ */ ~TandemWrapperRun(); + signals: + void tandemProgressMessage(QString message); + + private: void setTandemBinaryPath(const QString &tandem_binary_path); - bool shouldIstop(); const QString checkXtandemVersion(const QString &tandem_bin_path); void wrapTandemInputFile(const QString &tandem_input_file); - void convertOrginalMsData2mzXmlData(const QString &origin, - const QString &target) const; + bool convertOrginalMsData2mzXmlData(const QString &origin, + const QString &target); /** @brief run a tandem job @@ -113,19 +131,22 @@ void readyReadStandardError(); private: + UiMonitorInterface *mp_monitor; QString m_tandemBinary; QString m_tandemVersion; QString m_tmpDir; - int m_maxTandemRunTimeMs = (60000 * 60 * 24); // 1 day - QProcess *m_xtProcess = nullptr; - - std::shared_ptr msp_ms2FilterSuiteString = - std::make_shared( - "chargeDeconvolution|0.02dalton"); + int m_maxTandemRunTimeMs = + 1000; // If msecs is -1, this function will not time out. + QProcess *m_xtProcess = nullptr; - QTextStream *mp_outputStream = nullptr; - QTextStream *mp_errorStream = nullptr; + std::shared_ptr msp_ms2FilterSuiteString = nullptr; QTemporaryDir *mpa_temporaryDirectory = nullptr; + + bool m_convertMzDataUsingSpectrumIndex = false; + + pappso::MzFormat m_mzFormat = pappso::MzFormat::unknown; + + qint64 m_conversionTime=0; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandeminput.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandeminput.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandeminput.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandeminput.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,159 @@ +/** + * \file pappsomspp/processing/tandemwrapper/wraptandeminput.cpp + * \date 13/11/2021 + * \author Olivier Langella + * \brief rewrites tandem xml input file with temporary files + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + + +#include "wraptandeminput.h" +#include +#include "../../pappsoexception.h" + + +namespace pappso +{ +WrapTandemInput::WrapTandemInput(const QString &destinationMzXmlFile, + const QString &destinationTandemInputFile, + const QString &destinationTandemOutputFile) + : m_destinationTandemInputFile(destinationTandemInputFile) +{ + m_destinationMzXmlFileName = destinationMzXmlFile; + m_destinationTandemOutputFileName = destinationTandemOutputFile; + m_destinationTandemInputFileName = + QFileInfo(destinationTandemInputFile).absoluteFilePath(); + + if(destinationTandemInputFile.isEmpty()) + { + throw pappso::PappsoException( + QObject::tr("ERROR: X!Tandem input file path is empty")); + } + + if(!m_destinationTandemInputFile.open(QIODevice::WriteOnly)) + { + throw pappso::PappsoException( + QObject::tr("ERROR: unable to open %1 tandem output file for write") + .arg(destinationTandemInputFile)); + } + + m_writerXmlTandemInput.setDevice(&m_destinationTandemInputFile); + m_writerXmlTandemInput.setAutoFormatting(true); + m_writerXmlTandemInput.writeStartDocument("1.0"); +} + +WrapTandemInput::~WrapTandemInput() +{ + m_destinationTandemInputFile.close(); +} + + +void +WrapTandemInput::readStream() +{ + qDebug(); + if(m_qxmlStreamReader.readNextStartElement()) + { + if(m_qxmlStreamReader.name() == "bioml") + { + cloneStartElement(m_writerXmlTandemInput); + qDebug(); + while(m_qxmlStreamReader.readNextStartElement()) + { + // qDebug() << m_qxmlStreamReader.name(); + // read_note(); + cloneStartElement(m_writerXmlTandemInput); + + QString type = + m_qxmlStreamReader.attributes().value("type").toString(); + QString label = + m_qxmlStreamReader.attributes().value("label").toString(); + + if((type == "input") && (label == "spectrum, path")) + { + // + + m_originMzDataFileName = m_qxmlStreamReader.readElementText(); + m_writerXmlTandemInput.writeCharacters( + m_destinationMzXmlFileName); + // m_qxmlStreamReader.skipCurrentElement(); + } + else if((type == "input") && (label == "output, path")) + { + // + m_originTandemOutpuFileName = + m_qxmlStreamReader.readElementText(); + m_writerXmlTandemInput.writeCharacters( + m_destinationTandemOutputFileName); + // m_qxmlStreamReader.skipCurrentElement(); + } + // list path, default parameters + else if((type == "input") && + (label == "list path, default parameters")) + { + ///gorgone/pappso/tmp/xtpcpp.AjyZGg/Lumos_trypsin_rev_camC_oxM_10ppm_HCDOT_12102017CH.xml + + m_originTandemPresetFileName = + m_qxmlStreamReader.readElementText(); + m_writerXmlTandemInput.writeCharacters( + m_originTandemPresetFileName); + } + else + { + m_writerXmlTandemInput.writeCharacters( + m_qxmlStreamReader.readElementText()); + } + m_writerXmlTandemInput.writeEndElement(); + } + } + else + { + m_qxmlStreamReader.raiseError( + QObject::tr("Not an X!Tandem input file")); + m_qxmlStreamReader.skipCurrentElement(); + } + } + m_writerXmlTandemInput.writeEndDocument(); + m_destinationTandemInputFile.close(); + qDebug(); +} + + +const QString & +WrapTandemInput::getOriginalMsDataFileName() const +{ + return m_originMzDataFileName; +} + +const QString & +WrapTandemInput::getOriginalTandemOutputFileName() const +{ + return m_originTandemOutpuFileName; +} + +const QString & +WrapTandemInput::getOriginalTandemPresetFileName() const +{ + return m_originTandemPresetFileName; +} +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandeminput.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandeminput.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandeminput.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandeminput.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,77 @@ +/** + * \file pappsomspp/processing/tandemwrapper/wraptandeminput.h + * \date 13/11/2021 + * \author Olivier Langella + * \brief rewrites tandem xml input file with temporary files + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include +#include "../xml/xmlstreamreaderinterface.h" +/** + * @todo write docs + */ +namespace pappso +{ + +/** + * @todo write docs + */ +class WrapTandemInput : public XmlStreamReaderInterface +{ + public: + /** + * Default constructor + */ + WrapTandemInput(const QString &destinationMzXmlFile, + const QString &destinationTandemInputFile, + const QString &destinationTandemOutputFile); + + /** + * Destructor + */ + virtual ~WrapTandemInput(); + + + const QString &getOriginalMsDataFileName() const; + const QString &getOriginalTandemOutputFileName() const; + + const QString &getOriginalTandemPresetFileName() const; + + + protected: + virtual void readStream() override; + + private: + QString m_destinationMzXmlFileName; + QString m_originMzDataFileName; + QString m_destinationTandemInputFileName; + QString m_originTandemPresetFileName; + QString m_originTandemOutpuFileName; + QString m_destinationTandemOutputFileName; + QFile m_destinationTandemInputFile; + QXmlStreamWriter m_writerXmlTandemInput; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandemresults.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandemresults.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandemresults.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandemresults.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,202 @@ +/** + * \file pappsomspp/processing/tandemwrapper/wraptandemresults.cpp + * \date 13/11/2021 + * \author Olivier Langella + * \brief rewrites tandem xml output file with temporary files + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#include "wraptandemresults.h" +#include +#include "../../pappsoexception.h" + + +namespace pappso +{ + +WrapTandemResults::WrapTandemResults(const QString &final_tandem_output, + const QString &original_msdata_file_name) + : m_destinationTandemOutputFile(final_tandem_output) +{ + qDebug() << final_tandem_output; + m_originalMsDataFileName = + QFileInfo(original_msdata_file_name).absoluteFilePath(); + if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly)) + { + throw pappso::PappsoException( + QObject::tr("ERROR: unable to open %1 to write XML output") + .arg(final_tandem_output)); + } + m_writerXmlTandemOutput.setDevice(&m_destinationTandemOutputFile); + m_writerXmlTandemOutput.writeStartDocument("1.0"); + m_writerXmlTandemOutput.setAutoFormatting(true); +} + +WrapTandemResults::~WrapTandemResults() +{ +} + +void +WrapTandemResults::setInputParameters(const QString &label_name_attribute, + const QString &input_value) +{ + m_mapTandemInputParameters.insert( + std::pair(label_name_attribute, input_value)); +} + +void +WrapTandemResults::process_group_note() +{ + cloneStartElement(m_writerXmlTandemOutput); + while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement()) + { + if(m_qxmlStreamReader.isStartElement()) + { + QString type = + m_qxmlStreamReader.attributes().value("type").toString(); + QString label = + m_qxmlStreamReader.attributes().value("label").toString(); + qDebug() << "type=" << type << " label=" << label; + // qDebug() << "XtandemParamSaxHandler::endElement_note begin " << + // /tmp/tandemwrapper-IehrEL/msdata.mzxml + + if(label == "spectrum, path") + { + ///gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML + // m_originMzDataFileName = m_currentText; + // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName); + + m_writerXmlTandemOutput.writeStartElement("note"); + m_writerXmlTandemOutput.writeAttributes( + m_qxmlStreamReader.attributes()); + m_writerXmlTandemOutput.writeCharacters(m_originalMsDataFileName); + m_writerXmlTandemOutput.writeEndElement(); + + + for(auto pair_input : m_mapTandemInputParameters) + { + m_writerXmlTandemOutput.writeStartElement("note"); + m_writerXmlTandemOutput.writeAttribute("type", "input"); + m_writerXmlTandemOutput.writeAttribute("label", + pair_input.first); + m_writerXmlTandemOutput.writeCharacters(pair_input.second); + + m_writerXmlTandemOutput.writeEndElement(); + } + m_qxmlStreamReader.skipCurrentElement(); + } + else if(label == "output, path") + { + + ///tmp/tandemwrapper-sSGxtE/output_tandem.xml + + m_writerXmlTandemOutput.writeStartElement("note"); + m_writerXmlTandemOutput.writeAttributes( + m_qxmlStreamReader.attributes()); + m_writerXmlTandemOutput.writeCharacters( + QFileInfo(m_destinationTandemOutputFile).absoluteFilePath()); + m_writerXmlTandemOutput.writeEndElement(); + m_qxmlStreamReader.skipCurrentElement(); + } + else + { + cloneElement(m_writerXmlTandemOutput); + } + } + } + m_writerXmlTandemOutput.writeEndElement(); +} + +void +WrapTandemResults::readStream() +{ + qDebug(); + if(m_qxmlStreamReader.readNextStartElement()) + { + if(m_qxmlStreamReader.name() == "bioml") + { + cloneStartElement(m_writerXmlTandemOutput); + qDebug(); + while(m_qxmlStreamReader.readNextStartElement()) + { + if(m_qxmlStreamReader.name() == "group") + { + QString type = + m_qxmlStreamReader.attributes().value("type").toString(); + if(type == "model") + { + cloneElement(m_writerXmlTandemOutput); + } + else if(type == "parameters") + { + QString label = m_qxmlStreamReader.attributes() + .value("label") + .toString(); + if(label == "performance parameters") + { + cloneElement(m_writerXmlTandemOutput); + } + else if(label == "input parameters") + { + process_group_note(); + // cloneElement(m_writerXmlTandemOutput); + } + else if(label == "unused input parameters") + { + cloneElement(m_writerXmlTandemOutput); + } + else + { + m_qxmlStreamReader.skipCurrentElement(); + } + } + } + else + { + qDebug() << m_qxmlStreamReader.name(); + // read_note(); + cloneStartElement(m_writerXmlTandemOutput); + + + m_writerXmlTandemOutput.writeCharacters( + m_qxmlStreamReader.readElementText()); + + m_writerXmlTandemOutput.writeEndElement(); + } + } + } + else + { + m_qxmlStreamReader.raiseError( + QObject::tr("Not an X!Tandem result file")); + m_qxmlStreamReader.skipCurrentElement(); + } + } + m_writerXmlTandemOutput.writeEndDocument(); + m_destinationTandemOutputFile.close(); + qDebug(); +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandemresults.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandemresults.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/wraptandemresults.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/wraptandemresults.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,73 @@ +/** + * \file pappsomspp/processing/tandemwrapper/wraptandemresults.h + * \date 13/11/2021 + * \author Olivier Langella + * \brief rewrites tandem xml output file with temporary files + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include +#include "../xml/xmlstreamreaderinterface.h" + + +namespace pappso +{ + + +/** + * @todo write docs + */ +class WrapTandemResults : public XmlStreamReaderInterface +{ + public: + /** + * Default constructor + */ + WrapTandemResults(const QString &final_tandem_output, + const QString &original_msdata_file_name); + + /** + * Destructor + */ + virtual ~WrapTandemResults(); + + void setInputParameters(const QString &label_name_attribute, + const QString &input_value); + + protected: + virtual void readStream() override; + + private: + void process_group_note(); + + + private: + QFile m_destinationTandemOutputFile; + QXmlStreamWriter m_writerXmlTandemOutput; + QString m_originalMsDataFileName; + + std::map m_mapTandemInputParameters; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,341 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp - * \date 25/01/2020 - * \author Olivier Langella - * \brief rewrites tandem xml input file with temporary files - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - - -#include "xtandeminputsaxhandler.h" -#include "../../pappsoexception.h" -#include -namespace pappso -{ -XtandemInputSaxHandler::XtandemInputSaxHandler( - const QString &destinationMzXmlFile, - const QString &destinationTandemInputFile, - const QString &destinationTandemOutputFile) - : m_destinationTandemInputFile(destinationTandemInputFile) -{ - m_destinationMzXmlFileName = destinationMzXmlFile; - m_destinationTandemOutputFileName = destinationTandemOutputFile; - m_destinationTandemInputFileName = - QFileInfo(destinationTandemInputFile).absoluteFilePath(); - - if(destinationTandemInputFile.isEmpty()) - { - throw pappso::PappsoException( - QObject::tr("ERROR: X!Tandem input file path is empty")); - } - - if(!m_destinationTandemInputFile.open(QIODevice::WriteOnly)) - { - throw pappso::PappsoException( - QObject::tr("ERROR: unable to open %1 tandem output file for write") - .arg(destinationTandemInputFile)); - } - - p_writeXmlTandemInput = new QXmlStreamWriter(); - p_writeXmlTandemInput->setDevice(&m_destinationTandemInputFile); -} - -XtandemInputSaxHandler::~XtandemInputSaxHandler() -{ - if(p_writeXmlTandemInput != nullptr) - { - m_destinationTandemInputFile.close(); - delete p_writeXmlTandemInput; - } -} - -void -XtandemInputSaxHandler::writeOpenTag(const QString &qName, - const QXmlAttributes &attributes) -{ - p_writeXmlTandemInput->writeStartElement(qName); - for(int i = 0; i < attributes.length(); i++) - { - p_writeXmlTandemInput->writeAttribute(attributes.qName(i), - attributes.value(i)); - } -} - -bool -XtandemInputSaxHandler::startElement( - [[maybe_unused]] const QString &namespaceURI, - [[maybe_unused]] const QString &localName, - const QString &qName, - const QXmlAttributes &attributes) -{ - /* - - -Paths -/gorgone/pappso/jouy/presets/metapappso/Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml -/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/params/xtandem_database_third_step_test_condor_22janv.database -/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML -Protein general -usedefined -Output -/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml - -*/ - m_tagStack.push_back(qName); - bool is_ok = true; - - try - { - m_currentText.clear(); - // - if(m_tagStack.size() == 1) - { - if(qName != "bioml") - { - m_errorString = QObject::tr( - "ERROR in XtandemInputSaxHandler::startElement " - "root tag %1 is not ") - .arg(qName); - m_isTandemParameter = false; - return false; - } - else - { - - m_isTandemParameter = true; - // label="20191222_18_EF1_test_condor_22janv_third_step.xml" - m_labelName = attributes.value("label"); - - writeOpenTag(qName, attributes); - } - } - // startElement_group - - if(qName == "note") - { - is_ok = startElement_note(attributes); - } - } - catch(pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemInputSaxHandler::startElement " - "tag %1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemInputSaxHandler::startElement " - "tag %1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - return is_ok; -} - -bool -XtandemInputSaxHandler::endElement([[maybe_unused]] const QString &namespaceURI, - [[maybe_unused]] const QString &localName, - const QString &qName) -{ - - bool is_ok = true; - // endElement_peptide_list - try - { - - if(qName == "note") - { - is_ok = endElement_note(); - } - else - { - p_writeXmlTandemInput->writeCharacters(m_currentText); - p_writeXmlTandemInput->writeEndElement(); - } - } - catch(pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemInputSaxHandler::endElement tag " - "%1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemInputSaxHandler::endElement tag " - "%1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - - m_currentText.clear(); - m_tagStack.pop_back(); - - return is_ok; -} - -bool -XtandemInputSaxHandler::startDocument() -{ - - p_writeXmlTandemInput->setAutoFormatting(true); - p_writeXmlTandemInput->writeStartDocument("1.0"); - return true; -} - -bool -XtandemInputSaxHandler::endDocument() -{ - p_writeXmlTandemInput->writeEndDocument(); - - m_destinationTandemInputFile.close(); - delete p_writeXmlTandemInput; - p_writeXmlTandemInput = nullptr; - return true; -} - -bool -XtandemInputSaxHandler::characters(const QString &str) -{ - m_currentText += str; - return true; -} - - -bool -XtandemInputSaxHandler::error(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - - -bool -XtandemInputSaxHandler::fatalError(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - -QString -XtandemInputSaxHandler::errorString() const -{ - return m_errorString; -} - - -bool -XtandemInputSaxHandler::startElement_note(QXmlAttributes attributes) -{ - // qDebug() << "XtandemParamSaxHandler::startElement_note begin " << - // /gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml - - writeOpenTag("note", attributes); - m_currentLabel = ""; - - if(attributes.value("type") == "input") - { - m_currentLabel = attributes.value("label"); - } - - // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " << - // _current_label; - return true; -} - -bool -XtandemInputSaxHandler::endElement_note() -{ - // qDebug() << "XtandemParamSaxHandler::endElement_note begin " << - // _current_label << " " << _current_text.simplified(); - if(m_currentLabel == "output, path") - { - m_originTandemOutpuFileName = m_currentText; - p_writeXmlTandemInput->writeCharacters(m_destinationTandemOutputFileName); - } - else if(m_currentLabel == "list path, default parameters") - { - // - p_writeXmlTandemInput->writeCharacters(m_currentText); - m_originTandemPresetFileName = - QFileInfo(m_currentText).absoluteFilePath(); - } - else if(m_currentLabel == "spectrum, path") - { - ///gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML - m_originMzDataFileName = m_currentText; - p_writeXmlTandemInput->writeCharacters(m_destinationMzXmlFileName); - } - else - { - p_writeXmlTandemInput->writeCharacters(m_currentText); - } - p_writeXmlTandemInput->writeEndElement(); - return true; -} - - -const QString & -XtandemInputSaxHandler::getOriginalMsDataFileName() const -{ - return m_originMzDataFileName; -} - -const QString & -XtandemInputSaxHandler::getOriginalTandemOutputFileName() const -{ - return m_originTandemOutpuFileName; -} - -const QString & -XtandemInputSaxHandler::getOriginalTandemPresetFileName() const -{ - return m_originTandemPresetFileName; -} -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,101 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h - * \date 25/01/2020 - * \author Olivier Langella - * \brief rewrites tandem xml input file with temporary files - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - -#pragma once - -#include -#include -#include -/** - * @todo write docs - */ -namespace pappso -{ -class XtandemInputSaxHandler : public QXmlDefaultHandler -{ - public: - /** - * Default constructor - */ - XtandemInputSaxHandler(const QString &destinationMzXmlFile, - const QString &destinationTandemInputFile, - const QString &destinationTandemOutputFile); - - /** - * Destructor - */ - ~XtandemInputSaxHandler(); - - - bool startElement(const QString &namespaceURI, - const QString &localName, - const QString &qName, - const QXmlAttributes &attributes) override; - - bool endElement(const QString &namespaceURI, - const QString &localName, - const QString &qName) override; - - bool startDocument() override; - - bool endDocument() override; - - bool characters(const QString &str) override; - - bool fatalError(const QXmlParseException &exception) override; - bool error(const QXmlParseException &exception) override; - - QString errorString() const; - - const QString &getOriginalMsDataFileName() const; - const QString &getOriginalTandemOutputFileName() const; - - const QString &getOriginalTandemPresetFileName() const; - - private: - bool startElement_note(QXmlAttributes attributes); - bool endElement_note(); - void writeOpenTag(const QString &qName, const QXmlAttributes &attributes); - - - private: - QString m_destinationMzXmlFileName; - QString m_originMzDataFileName; - QString m_destinationTandemInputFileName; - QString m_originTandemPresetFileName; - QString m_originTandemOutpuFileName; - QString m_destinationTandemOutputFileName; - QFile m_destinationTandemInputFile; - QXmlStreamWriter *p_writeXmlTandemInput; - std::vector m_tagStack; - bool m_isTandemParameter = false; - QString m_errorString; - QString m_currentText; - QString m_currentLabel; - QString m_labelName; -}; -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,329 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp - * \date 01/02/2020 - * \author Olivier Langella - * \brief rewrites tandem xml input file with temporary files - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - - -#include "xtandemoutputsaxhandler.h" -#include "../../../pappsomspp/pappsoexception.h" -#include - -namespace pappso -{ -XtandemOutputSaxHandler::XtandemOutputSaxHandler( - const QString &final_tandem_output, const QString &original_msdata_file_name) - : m_destinationTandemOutputFile(final_tandem_output) -{ - qDebug() << final_tandem_output; - m_originalMsDataFileName = - QFileInfo(original_msdata_file_name).absoluteFilePath(); - if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly)) - { - throw pappso::PappsoException( - QObject::tr("ERROR: unable to open %1 to write XML output") - .arg(final_tandem_output)); - } - p_writeXmlTandemOutput = new QXmlStreamWriter(); - p_writeXmlTandemOutput->setAutoFormatting(true); - p_writeXmlTandemOutput->setDevice(&m_destinationTandemOutputFile); -} - -XtandemOutputSaxHandler::~XtandemOutputSaxHandler() -{ - if(p_writeXmlTandemOutput != nullptr) - { - m_destinationTandemOutputFile.close(); - delete p_writeXmlTandemOutput; - } -} - -void -XtandemOutputSaxHandler::writeOpenTag(const QString &qName, - const QXmlAttributes &attributes) -{ - p_writeXmlTandemOutput->writeStartElement(qName); - for(int i = 0; i < attributes.length(); i++) - { - p_writeXmlTandemOutput->writeAttribute(attributes.qName(i), - attributes.value(i)); - } -} - -bool -XtandemOutputSaxHandler::startElement( - [[maybe_unused]] const QString &namespaceURI, - [[maybe_unused]] const QString &localName, - const QString &qName, - const QXmlAttributes &attributes) -{ - m_tagStack.push_back(qName); - bool is_ok = true; - - try - { - m_currentText.clear(); - // - if(m_tagStack.size() == 1) - { - if(qName != "bioml") - { - m_errorString = - QObject::tr( - "ERROR in XtandemOutputSaxHandler::startElement " - "root tag %1 is not ") - .arg(qName); - m_isTandemParameter = false; - return false; - } - else - { - - m_isTandemParameter = true; - - // - p_writeXmlTandemOutput->writeStartElement("bioml"); - p_writeXmlTandemOutput->writeAttribute( - "xmlns:GAML", attributes.value("xmlns:GAML")); - p_writeXmlTandemOutput->writeAttribute( - "label", - QString("models from '%1'").arg(m_originalMsDataFileName)); - return true; - } - } - // startElement_group - - if(qName == "note") - { - is_ok = startElement_note(attributes); - } - else - { - writeOpenTag(qName, attributes); - } - } - catch(const pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemOutputSaxHandler::startElement " - "tag %1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(const std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemOutputSaxHandler::startElement " - "tag %1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - return is_ok; -} - -bool -XtandemOutputSaxHandler::endElement( - [[maybe_unused]] const QString &namespaceURI, - [[maybe_unused]] const QString &localName, - const QString &qName) -{ - - bool is_ok = true; - // endElement_peptide_list - try - { - - if(qName == "note") - { - is_ok = endElement_note(); - } - else - { - p_writeXmlTandemOutput->writeEndElement(); - } - } - catch(const pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemOutputSaxHandler::endElement tag " - "%1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(const std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemOutputSaxHandler::endElement tag " - "%1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - - m_currentText.clear(); - m_tagStack.pop_back(); - - return is_ok; -} - -bool -XtandemOutputSaxHandler::startDocument() -{ - - p_writeXmlTandemOutput->setAutoFormatting(true); - p_writeXmlTandemOutput->writeStartDocument("1.0"); - return true; -} - -bool -XtandemOutputSaxHandler::endDocument() -{ - p_writeXmlTandemOutput->writeEndDocument(); - - m_destinationTandemOutputFile.close(); - delete p_writeXmlTandemOutput; - p_writeXmlTandemOutput = nullptr; - return true; -} - -bool -XtandemOutputSaxHandler::characters(const QString &str) -{ - m_currentText += str; - if(m_tagStack.back() != "note") - { - p_writeXmlTandemOutput->writeCharacters(str); - } - return true; -} - - -bool -XtandemOutputSaxHandler::error(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - - -bool -XtandemOutputSaxHandler::fatalError(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - -QString -XtandemOutputSaxHandler::errorString() const -{ - return m_errorString; -} - - -bool -XtandemOutputSaxHandler::startElement_note(QXmlAttributes attributes) -{ - // qDebug() << "XtandemParamSaxHandler::startElement_note begin " << - // /gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml - - writeOpenTag("note", attributes); - m_currentLabel = ""; - - if(attributes.value("type") == "input") - { - m_currentLabel = attributes.value("label"); - } - - // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " << - // _current_label; - return true; -} - -bool -XtandemOutputSaxHandler::endElement_note() -{ - // qDebug() << "XtandemParamSaxHandler::endElement_note begin " << - // /tmp/tandemwrapper-IehrEL/msdata.mzxml - - if(m_currentLabel == "spectrum, path") - { - ///gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML - // m_originMzDataFileName = m_currentText; - // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName); - p_writeXmlTandemOutput->writeCharacters(m_originalMsDataFileName); - p_writeXmlTandemOutput->writeEndElement(); - - - for(auto pair_input : m_mapTandemInputParameters) - { - p_writeXmlTandemOutput->writeStartElement("note"); - p_writeXmlTandemOutput->writeAttribute("type", "input"); - p_writeXmlTandemOutput->writeAttribute("label", pair_input.first); - p_writeXmlTandemOutput->writeCharacters(pair_input.second); - p_writeXmlTandemOutput->writeEndElement(); - } - } - else if(m_currentLabel == "output, path") - { - ///tmp/tandemwrapper-sSGxtE/output_tandem.xml - p_writeXmlTandemOutput->writeCharacters( - QFileInfo(m_destinationTandemOutputFile).absoluteFilePath()); - p_writeXmlTandemOutput->writeEndElement(); - } - else - { - p_writeXmlTandemOutput->writeCharacters(m_currentText); - p_writeXmlTandemOutput->writeEndElement(); - } - return true; -} - -void -XtandemOutputSaxHandler::setInputParameters(const QString &label_name_attribute, - const QString &input_value) -{ - m_mapTandemInputParameters.insert( - std::pair(label_name_attribute, input_value)); -} -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,92 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h - * \date 01/02/2020 - * \author Olivier Langella - * \brief rewrites tandem xml output file with temporary files - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - -#pragma once - -#include -#include -#include -/** - * @todo write docs - */ -namespace pappso -{ -class XtandemOutputSaxHandler : public QXmlDefaultHandler -{ - public: - /** - * Default constructor - */ - XtandemOutputSaxHandler(const QString &final_tandem_output, - const QString &original_msdata_file_name); - - /** - * Destructor - */ - ~XtandemOutputSaxHandler(); - - - bool startElement(const QString &namespaceURI, - const QString &localName, - const QString &qName, - const QXmlAttributes &attributes) override; - - bool endElement(const QString &namespaceURI, - const QString &localName, - const QString &qName) override; - - bool startDocument() override; - - bool endDocument() override; - - bool characters(const QString &str) override; - - bool fatalError(const QXmlParseException &exception) override; - bool error(const QXmlParseException &exception) override; - - QString errorString() const; - - void setInputParameters(const QString &label_name_attribute, - const QString &input_value); - - private: - bool startElement_note(QXmlAttributes attributes); - bool endElement_note(); - void writeOpenTag(const QString &qName, const QXmlAttributes &attributes); - - private: - std::map m_mapTandemInputParameters; - std::vector m_tagStack; - QFile m_destinationTandemOutputFile; - QXmlStreamWriter *p_writeXmlTandemOutput; - QString m_errorString; - QString m_currentText; - bool m_isTandemParameter = false; - QString m_currentLabel; - QString m_originalMsDataFileName; -}; -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,167 @@ +/** + * \file pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp + * \date 06/02/2020 + * \author Olivier Langella + * \brief read tandem preset file to get centroid parameters and number of + * threads + */ + +/******************************************************************************* + * Copyright (c) 2020 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#include "xtandempresetreader.h" +#include "../../pappsoexception.h" +#include "../../precision.h" + +namespace pappso +{ +XtandemPresetReader::XtandemPresetReader() +{ +} + +XtandemPresetReader::~XtandemPresetReader() +{ +} + + +void +XtandemPresetReader::read_note() +{ + // /gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml + if(m_qxmlStreamReader.name() != "note") + { + m_qxmlStreamReader.skipCurrentElement(); + return; + } + Q_ASSERT(m_qxmlStreamReader.name() == "note"); + QString label; + + + m_countNote++; + if((m_qxmlStreamReader.attributes().hasAttribute("type")) && + (m_qxmlStreamReader.attributes().value("type").toString() == "input")) + { + if(m_qxmlStreamReader.attributes().hasAttribute("label")) + { + label = m_qxmlStreamReader.attributes().value("label").toString(); + } + } + if(label.isEmpty()) + { + } + else + { + if(label == "spectrum, timstof MS2 filters") + { + } + else if(label == "spectrum, threads") + { + m_threads = m_qxmlStreamReader.readElementText().toInt(); + return; + } + else if(label == "spectrum, fragment monoisotopic mass error units") + { + + m_ms2precisionUnit = PrecisionUnit::dalton; + if(m_qxmlStreamReader.readElementText().trimmed().toLower() == "ppm") + { + m_ms2precisionUnit = PrecisionUnit::ppm; + } + return; + } + else if(label == "spectrum, fragment monoisotopic mass error") + { + m_ms2precisionValue = m_qxmlStreamReader.readElementText().toDouble(); + return; + } + } + m_qxmlStreamReader.skipCurrentElement(); + // qDebug() << "end "; + // +} + + +int +XtandemPresetReader::getNumberOfThreads() const +{ + return m_threads; +} + + +const QString +XtandemPresetReader::getMs2FiltersOptions() const +{ + QString filter_suite; + PrecisionPtr precision = PrecisionFactory::getPrecisionPtrInstance( + m_ms2precisionUnit, m_ms2precisionValue); + QString charge_decon_filter = QString("chargeDeconvolution|%1") + .arg(precision->toString().replace(" ", "")); + + PrecisionPtr precision_exclu = PrecisionFactory::getPrecisionPtrInstance( + m_ms2precisionUnit, m_ms2precisionValue / 2); + QString mz_exclusion_filter = + QString("mzExclusion|%1").arg(precision_exclu->toString().replace(" ", "")); + filter_suite = charge_decon_filter + " " + mz_exclusion_filter; + return filter_suite; +} + + +void +XtandemPresetReader::readStream() +{ + qDebug(); + m_countNote = 0; + m_threads = -1; + m_ms2precisionUnit = PrecisionUnit::dalton; + m_ms2precisionValue = -1; + if(m_qxmlStreamReader.readNextStartElement()) + { + if(m_qxmlStreamReader.name() == "bioml") + { + qDebug(); + while(m_qxmlStreamReader.readNextStartElement()) + { + // qDebug() << m_qxmlStreamReader.name(); + read_note(); + } + } + else + { + m_qxmlStreamReader.raiseError( + QObject::tr("Not an X!Tandem preset file")); + m_qxmlStreamReader.skipCurrentElement(); + } + } + if(m_threads == -1) + { + qDebug(); + m_qxmlStreamReader.raiseError(QObject::tr("Not an X!Tandem preset file")); + } + qDebug(); +} + +int +XtandemPresetReader::getCountNote() const +{ + return m_countNote; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetreader.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,69 @@ +/** + * \file pappsomspp/processing/tandemwrapper/xtandempresetreader.h + * \date 06/02/2020 + * \author Olivier Langella + * \brief read tandem preset file to get centroid parameters and number of + * threads + */ + +/******************************************************************************* + * Copyright (c) 2020 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include "../../types.h" +#include "../xml/xmlstreamreaderinterface.h" +/** + * @todo write docs + */ +namespace pappso +{ +class XtandemPresetReader : public XmlStreamReaderInterface +{ + public: + /** + * Default constructor + */ + XtandemPresetReader(); + + /** + * Destructor + */ + virtual ~XtandemPresetReader(); + + int getNumberOfThreads() const; + const QString getMs2FiltersOptions() const; + int getCountNote() const; + + protected: + virtual void readStream() override; + + private: + void read_note(); + + private: + int m_countNote = -1; + int m_threads = -1; + + PrecisionUnit m_ms2precisionUnit = PrecisionUnit::dalton; + double m_ms2precisionValue = 0; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,269 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp - * \date 06/02/2020 - * \author Olivier Langella - * \brief read tandem preset file to get centroid parameters and number of - * threads - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - -#include "xtandempresetsaxhandler.h" -#include "../../pappsoexception.h" -#include "../../precision.h" - -namespace pappso -{ -XtandemPresetSaxHandler::XtandemPresetSaxHandler() -{ -} - -XtandemPresetSaxHandler::~XtandemPresetSaxHandler() -{ -} - - -bool -XtandemPresetSaxHandler::startElement(const QString &namespaceURI - [[maybe_unused]], - const QString &localName [[maybe_unused]], - const QString &qName, - const QXmlAttributes &attributes) -{ - m_tagStack.push_back(qName); - bool is_ok = true; - - try - { - m_currentText.clear(); - // - if(m_tagStack.size() == 1) - { - if(qName != "bioml") - { - m_errorString = - QObject::tr( - "ERROR in XtandemPresetSaxHandler::startElement " - "root tag %1 is not ") - .arg(qName); - m_isTandemParameter = false; - return false; - } - else - { - - m_isTandemParameter = true; - } - } - // startElement_group - - if(qName == "note") - { - is_ok = startElement_note(attributes); - } - } - catch(const pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemPresetSaxHandler::startElement " - "tag %1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(const std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemPresetSaxHandler::startElement " - "tag %1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - return is_ok; -} - -bool -XtandemPresetSaxHandler::endElement(const QString &namespaceURI - [[maybe_unused]], - const QString &localName [[maybe_unused]], - const QString &qName) -{ - - bool is_ok = true; - // endElement_peptide_list - try - { - - if(qName == "note") - { - is_ok = endElement_note(); - } - else - { - } - } - catch(const pappso::PappsoException &exception_pappso) - { - m_errorString = QObject::tr( - "ERROR in XtandemPresetSaxHandler::endElement tag " - "%1, PAPPSO exception:\n%2") - .arg(qName) - .arg(exception_pappso.qwhat()); - return false; - } - catch(const std::exception &exception_std) - { - m_errorString = QObject::tr( - "ERROR in XtandemPresetSaxHandler::endElement tag " - "%1, std exception:\n%2") - .arg(qName) - .arg(exception_std.what()); - return false; - } - - m_currentText.clear(); - m_tagStack.pop_back(); - - return is_ok; -} - -bool -XtandemPresetSaxHandler::startDocument() -{ - return true; -} - -bool -XtandemPresetSaxHandler::endDocument() -{ - return true; -} - -bool -XtandemPresetSaxHandler::characters(const QString &str) -{ - m_currentText += str; - return true; -} - - -bool -XtandemPresetSaxHandler::error(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - - -bool -XtandemPresetSaxHandler::fatalError(const QXmlParseException &exception) -{ - m_errorString = QObject::tr( - "Parse error at line %1, column %2 :\n" - "%3") - .arg(exception.lineNumber()) - .arg(exception.columnNumber()) - .arg(exception.message()); - qDebug() << m_errorString; - return false; -} - -QString -XtandemPresetSaxHandler::errorString() const -{ - return m_errorString; -} - - -bool -XtandemPresetSaxHandler::startElement_note(QXmlAttributes attributes) -{ - // qDebug() << "XtandemParamSaxHandler::startElement_note begin " << - // /gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml - - m_currentLabel = ""; - - if(attributes.value("type") == "input") - { - m_currentLabel = attributes.value("label"); - } - - // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " << - // _current_label; - return true; -} - -bool -XtandemPresetSaxHandler::endElement_note() -{ - // qDebug() << "XtandemParamSaxHandler::endElement_note begin " << - // _current_label << " " << _current_text.simplified(); - if(m_currentLabel == "spectrum, timstof MS2 filters") - { - // m_ms2filtersOptions = m_currentText; - } - else if(m_currentLabel == "spectrum, threads") - { - m_threads = m_currentText.toInt(); - } - else if(m_currentLabel == "spectrum, fragment monoisotopic mass error units") - { - m_ms2precisionUnit = PrecisionUnit::dalton; - if(m_currentText.trimmed().toLower() == "ppm") - { - m_ms2precisionUnit = PrecisionUnit::ppm; - } - } - else if(m_currentLabel == "spectrum, fragment monoisotopic mass error") - { - m_ms2precisionValue = m_currentText.toDouble(); - } - else - { - } - return true; -} - - -int -XtandemPresetSaxHandler::getNumberOfThreads() const -{ - return m_threads; -} - - -const QString -XtandemPresetSaxHandler::getMs2FiltersOptions() const -{ - PrecisionPtr precision = PrecisionFactory::getPrecisionPtrInstance( - m_ms2precisionUnit, m_ms2precisionValue); - return QString("chargeDeconvolution|%1") - .arg(precision->toString().replace(" ", "")); -} -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,91 +0,0 @@ -/** - * \file pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h - * \date 06/02/2020 - * \author Olivier Langella - * \brief read tandem preset file to get centroid parameters and number of - * threads - */ - -/******************************************************************************* - * Copyright (c) 2020 Olivier Langella . - * - * This file is part of PAPPSOms-tools. - * - * PAPPSOms-tools is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * PAPPSOms-tools is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with PAPPSOms-tools. If not, see . - * - ******************************************************************************/ - -#pragma once - -#include -#include -#include -#include "../../types.h" -/** - * @todo write docs - */ -namespace pappso -{ -class XtandemPresetSaxHandler : public QXmlDefaultHandler -{ - public: - /** - * Default constructor - */ - XtandemPresetSaxHandler(); - - /** - * Destructor - */ - ~XtandemPresetSaxHandler(); - - bool startElement(const QString &namespaceURI, - const QString &localName, - const QString &qName, - const QXmlAttributes &attributes) override; - - bool endElement(const QString &namespaceURI, - const QString &localName, - const QString &qName) override; - - bool startDocument() override; - - bool endDocument() override; - - bool characters(const QString &str) override; - - bool fatalError(const QXmlParseException &exception) override; - bool error(const QXmlParseException &exception) override; - - QString errorString() const; - - int getNumberOfThreads() const; - const QString getMs2FiltersOptions() const; - - private: - bool startElement_note(QXmlAttributes attributes); - bool endElement_note(); - - private: - QString m_errorString; - std::vector m_tagStack; - QString m_currentText; - bool m_isTandemParameter = false; - QString m_currentLabel; - int m_threads = -1; - - PrecisionUnit m_ms2precisionUnit = PrecisionUnit::dalton; - double m_ms2precisionValue = 0; -}; -} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitorinterface.h libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitorinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitorinterface.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitorinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,94 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitorinterface.h + * \date 14/5/2021 + * \author Olivier Langella + * \brief generic interface to monitor any long process + * A long process needs to be interrupted by the user and to report progress + *while running. This interface is used by long process in this library. + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include +#include "../../exportinmportconfig.h" + +namespace pappso +{ + +/** + * @todo pure virtual user interface class to monitor any long process + * it contains : + * - title, status, progress messages + * - callback functions to interrupt long process + * it does not contains any error messages functions : use + * pappso::ExceptionInterrupted to handle this + * + */ +class PMSPP_LIB_DECL UiMonitorInterface +{ + public: + /** @brief should the procces be stopped ? + * If true, then cancel process + * Use this function at strategic point of your process in order to interrupt + * it cleanly + * Implementation **must** take care of thread resistance if implemented + */ + virtual bool shouldIstop() = 0; + + /** @brief use it if the number of steps is known in an algorithm + * the total number of steps is usefull to report to the user a progress + * message in percents or with a progress bar + * @param total_number_of_steps the total number of steps + */ + virtual void + setTotalSteps(std::size_t total_number_of_steps) + { + m_totalSteps = total_number_of_steps; + }; + + /** @brief count steps + * report when a step is computed in an algorithm + */ + virtual void count() = 0; + + /** @brief current kind of process running + * @param title process title + */ + virtual void setTitle(const QString &title) = 0; + + /** @brief current status of the process + * @param status status message + */ + virtual void setStatus(const QString &status) = 0; + + /** @brief append a text to a long report + * @param text string to append in a long report + */ + virtual void appendText(const QString &text) = 0; + + protected: + std::size_t m_totalSteps = 0; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortext.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortext.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortext.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortext.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,91 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitortext.cpp + * \date 14/5/2021 + * \author Olivier Langella + * \brief simle text monitor implementation of the User Interface Monitor + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "uimonitortext.h" + +using namespace pappso; + +UiMonitorText::UiMonitorText(QTextStream &output_stream) + : m_outputStream(output_stream) +{ +} + +UiMonitorText::~UiMonitorText() +{ +} + +bool +pappso::UiMonitorText::shouldIstop() +{ + // by defaut not interruptible + return false; +} + +void +pappso::UiMonitorText::setTitle(const QString &title) +{ + m_outputStream << title << Qt::endl; + m_outputStream.flush(); +} + +void +pappso::UiMonitorText::setStatus(const QString &status) +{ + m_outputStream << status << Qt::endl; + m_outputStream.flush(); +} + +void +pappso::UiMonitorText::count() +{ + m_count++; + if(m_count <= m_totalSteps) + { + m_outputStream << m_count << " "; + } + else + { + m_outputStream << QObject::tr("%1 on %2").arg(m_count).arg(m_totalSteps) + << " "; + } + m_outputStream.flush(); +} + +void +pappso::UiMonitorText::appendText(const QString &text) +{ + m_outputStream << text; + m_outputStream.flush(); +} + +void +pappso::UiMonitorText::setTotalSteps(std::size_t total_number_of_steps) +{ + UiMonitorInterface::setTotalSteps(total_number_of_steps); + m_count = 0; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortext.h libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortext.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortext.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortext.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,83 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitortext.h + * \date 14/5/2021 + * \author Olivier Langella + * \brief simle text monitor implementation of the User Interface Monitor + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "uimonitorinterface.h" +#include + +namespace pappso +{ + + +/** + * @todo simple text monitor using text stream + */ +class PMSPP_LIB_DECL UiMonitorText : public UiMonitorInterface +{ + public: + /** + * Default constructor + */ + UiMonitorText(QTextStream &output_stream); + + /** + * Destructor + */ + ~UiMonitorText(); + + virtual bool shouldIstop() override; + + /** @brief count steps + * report when a step is computed in an algorithm + */ + virtual void count() override; + + /** @brief current kind of process running + * @param title process title + */ + virtual void setTitle(const QString &title) override; + + /** @brief current status of the process + * @param status status message + */ + virtual void setStatus(const QString &status) override; + + /** @brief append a text to a long report + * @param text string to append in a long report + */ + virtual void appendText(const QString &text) override; + + virtual void setTotalSteps(std::size_t total_number_of_steps); + + + protected: + QTextStream &m_outputStream; + std::size_t m_count = 0; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortextpercent.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortextpercent.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortextpercent.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortextpercent.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,79 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitortextpercent.cpp + * \date 25/9/2021 + * \author Olivier Langella + * \brief simle text monitor implementation of the User Interface Monitor + *displaying percent progression + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "uimonitortextpercent.h" +#include + +using namespace pappso; + +UiMonitorTextPercent::UiMonitorTextPercent(QTextStream &output_stream) + : UiMonitorText(output_stream) +{ + m_unit = -1; + m_totalSteps = 1; +} + +UiMonitorTextPercent::~UiMonitorTextPercent() +{ +} + + +void +pappso::UiMonitorTextPercent::setTotalSteps(std::size_t total_number_of_steps) +{ + if(m_count > 0) + { + + m_outputStream << Qt::endl; + m_outputStream.flush(); + } + UiMonitorText::setTotalSteps(total_number_of_steps); + m_unit = -1; + if(m_totalSteps == 0) + { + m_totalSteps = -1; + } +} + +void +pappso::UiMonitorTextPercent::count() +{ + m_count++; + if(m_count <= m_totalSteps) + { + int unit = (int)(((float)m_count / (float)m_totalSteps) * 10); + // qDebug() << unit; + if(unit > m_unit) + { + m_outputStream << (unit * 10) << "% "; + m_outputStream.flush(); + m_unit = unit; + } + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortextpercent.h libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortextpercent.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitortextpercent.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitortextpercent.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,69 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitortextpercent.h + * \date 25/9/2021 + * \author Olivier Langella + * \brief simle text monitor implementation of the User Interface Monitor + *displaying percent progression + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "uimonitorinterface.h" +#include "uimonitortext.h" +#include + +namespace pappso +{ + + +/** + * @todo write docs + */ +class PMSPP_LIB_DECL UiMonitorTextPercent : public UiMonitorText +{ + public: + /** + * Default constructor + */ + UiMonitorTextPercent(QTextStream &output_stream); + + /** + * Destructor + */ + virtual ~UiMonitorTextPercent(); + + + /** @brief count steps + * report when a step is computed in an algorithm + */ + virtual void count() override; + + + virtual void setTotalSteps(std::size_t total_number_of_steps); + + + protected: + int m_unit; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitorvoid.h libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitorvoid.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/uimonitor/uimonitorvoid.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/uimonitor/uimonitorvoid.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,57 @@ +/** + * \file pappsomspp/processing/uimonitor/uimonitorvoid.h + * \date 14/5/2021 + * \author Olivier Langella + * \brief simle monitor that does nothing + **/ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "uimonitorinterface.h" +#include + +namespace pappso +{ + + +/** + * @todo nothing monitor to save CPU and memory if needed + */ +class PMSPP_LIB_DECL UiMonitorVoid : public UiMonitorInterface +{ + public: + virtual bool + shouldIstop() override + { + return false; + }; + + virtual void setTotalSteps(std::size_t total_number_of_steps + [[maybe_unused]]) override{}; + virtual void count() override{}; + virtual void setTitle(const QString &title [[maybe_unused]]) override{}; + virtual void setStatus(const QString &status [[maybe_unused]]) override{}; + virtual void appendText(const QString &text [[maybe_unused]]) override{}; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/xml/xmlstreamreaderinterface.cpp libpappsomspp-0.8.58/src/pappsomspp/processing/xml/xmlstreamreaderinterface.cpp --- libpappsomspp-0.8.15/src/pappsomspp/processing/xml/xmlstreamreaderinterface.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/xml/xmlstreamreaderinterface.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,177 @@ +/** + * \file pappsomspp/processing/xml/xmlstreamreaderinterface.cpp + * \date 12/11/2021 + * \author Olivier Langella + * \brief common interface to read all XML streams containing convenient + * functions + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + + +#include "xmlstreamreaderinterface.h" +#include +#include +#include + +using namespace pappso; + +XmlStreamReaderInterface::XmlStreamReaderInterface() +{ +} + +XmlStreamReaderInterface::~XmlStreamReaderInterface() +{ +} + +QString +pappso::XmlStreamReaderInterface::errorString() const +{ + if(m_qxmlStreamReader.errorString().isEmpty()) + return ""; + else + { + QString error = QObject::tr("ERROR at line %1 column %2\n%3") + .arg(m_qxmlStreamReader.lineNumber()) + .arg(m_qxmlStreamReader.columnNumber()) + .arg(m_qxmlStreamReader.errorString()); + return error; + } +} + +bool +pappso::XmlStreamReaderInterface::readFile(const QString &fileName) +{ + QFile file(fileName); + if(!file.open(QFile::ReadOnly | QFile::Text)) + { + m_qxmlStreamReader.raiseError( + QObject::tr("Cannot read file %1 : %2") + .arg(QFileInfo(fileName).absoluteFilePath()) + .arg(m_qxmlStreamReader.errorString())); + return false; + } + + if(read(&file)) + { + file.close(); + return true; + } + else + { + file.close(); + m_qxmlStreamReader.raiseError( + QObject::tr("Error reading file %1 : %2") + .arg(QFileInfo(fileName).absoluteFilePath()) + .arg(m_qxmlStreamReader.errorString())); + return false; + } +} +bool +pappso::XmlStreamReaderInterface::read(QIODevice *device) +{ + + m_qxmlStreamReader.setDevice(device); + m_qxmlStreamReader.setNamespaceProcessing(true); + readStream(); + + return !m_qxmlStreamReader.error(); +} + +bool +pappso::XmlStreamReaderInterface::read(const QString &xml_content) +{ + m_qxmlStreamReader.clear(); + m_qxmlStreamReader.addData(xml_content); + m_qxmlStreamReader.setNamespaceProcessing(true); + readStream(); + + return !m_qxmlStreamReader.error(); +} +void +pappso::XmlStreamReaderInterface::cloneStartElement( + QXmlStreamWriter &output) const +{ + output.writeStartElement(m_qxmlStreamReader.name().toString()); + + for(auto declaration : m_qxmlStreamReader.namespaceDeclarations()) + { + output.writeNamespace(declaration.namespaceUri().toString(), + declaration.prefix().toString()); + } + output.writeAttributes(m_qxmlStreamReader.attributes()); +} + +void +pappso::XmlStreamReaderInterface::cloneElement(QXmlStreamWriter &output) +{ + qDebug() << " name=" << m_qxmlStreamReader.name(); + output.writeStartElement(m_qxmlStreamReader.namespaceUri().toString(), + m_qxmlStreamReader.name().toString()); + output.writeAttributes(m_qxmlStreamReader.attributes()); + + qDebug() << m_qxmlStreamReader.name(); + while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement()) + { + cloneNode(output); + if(output.hasError()) + { + qDebug(); + m_qxmlStreamReader.raiseError(QObject::tr("Error in output stream")); + } + } + qDebug(); + output.writeEndElement(); +} + +void +pappso::XmlStreamReaderInterface::cloneNode(QXmlStreamWriter &output) +{ + qDebug(); + if(m_qxmlStreamReader.isCharacters()) + { + qDebug() << "isCharacters " << m_qxmlStreamReader.text(); + if((m_qxmlStreamReader.text() == "\n") || + (m_qxmlStreamReader.text() == "\n\t")) + { + // xml cleaner + } + else + { + output.writeCharacters( + m_qxmlStreamReader.text().toString().trimmed()); + } + } + else if(m_qxmlStreamReader.isEndElement()) + { + qDebug() << "isEndElement"; + output.writeEndElement(); + } + else if(m_qxmlStreamReader.isStartElement()) + { + qDebug() << "isStartElement"; + cloneElement(output); + } + else + { + } + qDebug(); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/processing/xml/xmlstreamreaderinterface.h libpappsomspp-0.8.58/src/pappsomspp/processing/xml/xmlstreamreaderinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/processing/xml/xmlstreamreaderinterface.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/processing/xml/xmlstreamreaderinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,73 @@ +/** + * \file pappsomspp/processing/xml/xmlstreamreaderinterface.h + * \date 12/11/2021 + * \author Olivier Langella + * \brief common interface to read all XML streams containing convenient + * functions + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ +#pragma once + +#include +#include +#include +#include "../../exportinmportconfig.h" + +namespace pappso +{ +/** + * @brief convenient xml reader helper + */ +class PMSPP_LIB_DECL XmlStreamReaderInterface +{ + public: + /** + * Default constructor + */ + XmlStreamReaderInterface(); + + /** + * Destructor + */ + virtual ~XmlStreamReaderInterface(); + + + virtual bool readFile(const QString &fileName); + + bool read(QIODevice *device); + bool read(const QString &xml_content); + + + QString errorString() const; + + protected: + virtual void readStream() = 0; + + void cloneStartElement(QXmlStreamWriter &output) const; + + void cloneElement(QXmlStreamWriter &output); + void cloneNode(QXmlStreamWriter &output); + + protected: + QXmlStreamReader m_qxmlStreamReader; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/enzyme.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/enzyme.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/enzyme.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/enzyme.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -109,9 +109,13 @@ int pos = 0; int peptide_start = 0; int peptide_size = sequence.size(); - while((pos = m_recognitionSite.indexIn(sequence, pos)) != -1) - { - peptide_size = pos + m_recognitionSite.cap(1).length() - peptide_start; + QRegularExpressionMatch match_recognition_site = + m_recognitionSite.match(sequence, pos); + while(match_recognition_site.hasMatch()) + { + pos = match_recognition_site.capturedStart(0); + peptide_size = + pos + match_recognition_site.captured(1).length() - peptide_start; // qDebug() << "pos=" << pos << " peptide_start=" << peptide_start << " // peptide_size=" << peptide_size << " " << // sequence.mid(peptide_start,peptide_size); @@ -121,6 +125,7 @@ } peptide_start += peptide_size; pos = peptide_start; // all peptides MUST be consecutive + match_recognition_site = m_recognitionSite.match(sequence, pos); } peptide_size = sequence.size() - peptide_start; if(peptide_size > 0) @@ -344,7 +349,7 @@ } } -const QRegExp & +const QRegularExpression & Enzyme::getQRegExpRecognitionSite() const { return m_recognitionSite; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/enzyme.h libpappsomspp-0.8.58/src/pappsomspp/protein/enzyme.h --- libpappsomspp-0.8.15/src/pappsomspp/protein/enzyme.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/enzyme.h 2022-10-27 09:16:15.000000000 +0000 @@ -24,7 +24,7 @@ #pragma once #include "enzymeproductinterface.h" -#include +#include namespace pappso { @@ -81,12 +81,12 @@ void setMaxPeptideVariantListSize(std::size_t max_peptide_variant_list_size); - const QRegExp &getQRegExpRecognitionSite() const; + const QRegularExpression &getQRegExpRecognitionSite() const; private: /** \brief example with a kinase == [K,R] */ - QRegExp m_recognitionSite; + QRegularExpression m_recognitionSite; unsigned int m_miscleavage = 0; bool m_takeOnlyFirstWildcard = false; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorbase.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorbase.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorbase.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorbase.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -51,10 +51,13 @@ std::vector &position_list, const QString &peptide_str) { - int pos = 0; - while((pos = m_pattern.indexIn(peptide_str, pos)) != -1) + int pos = 0; + QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos); + + while(match_pattern.hasMatch()) { - if(m_pattern.pos(1) == -1) + pos = match_pattern.capturedStart(0); + if(match_pattern.lastCapturedIndex() == 0) { // no motif, just push position position_list.push_back(pos); @@ -63,18 +66,19 @@ else { // there is a motif : target this position - pos = m_pattern.pos(1); + pos = match_pattern.capturedStart(1); if((position_list.size() > 0) && (position_list.back() == (unsigned int)pos)) { - pos = m_pattern.pos(0) + 1; + pos = match_pattern.capturedStart(0) + 1; } else { position_list.push_back(pos); - pos = m_pattern.pos(0) + 1; + pos = match_pattern.capturedStart(0) + 1; } } + match_pattern = m_pattern.match(peptide_str, pos); } } @@ -86,11 +90,14 @@ unsigned int modification_counter) { - int pos = 0; - const QString peptide_str = p_peptide->getSequence(); - while((pos = m_pattern.indexIn(peptide_str, pos)) != -1) + int pos = 0; + const QString peptide_str = p_peptide->getSequence(); + QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos); + + while(match_pattern.hasMatch()) { - if(m_pattern.pos(1) == -1) + pos = match_pattern.capturedStart(0); + if(match_pattern.lastCapturedIndex() == 0) { // no motif, just push position if(p_peptide->getConstAa(pos).getNumberOfModification(mod) == @@ -103,11 +110,11 @@ else { // there is a motif : target this position - pos = m_pattern.pos(1); + pos = match_pattern.capturedStart(1); if((position_list.size() > 0) && (position_list.back() == (unsigned int)pos)) { - pos = m_pattern.pos(0) + 1; + pos = match_pattern.capturedStart(0) + 1; } else { @@ -116,9 +123,10 @@ { position_list.push_back(pos); } - pos = m_pattern.pos(0) + 1; + pos = match_pattern.capturedStart(0) + 1; } } + match_pattern = m_pattern.match(peptide_str, pos); } } } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorbase.h libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorbase.h --- libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorbase.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorbase.h 2022-10-27 09:16:15.000000000 +0000 @@ -63,7 +63,7 @@ protected: - QRegExp m_pattern; + QRegularExpression m_pattern; virtual void getModificationPositionList(std::vector &position_list, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorpipeline.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorpipeline.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/peptidemodificatorpipeline.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/peptidemodificatorpipeline.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -30,8 +30,6 @@ using namespace pappso; -// QRegExp PeptideModificatorPipeline::_rx_modmass("[-+]?[0-9]*\\.?[0-9]*"); - PeptideModificatorPipeline::PeptideModificatorPipeline() { } @@ -123,7 +121,7 @@ "addLabeledModificationString function")); } QStringList mod_list_str = - mod_str.simplified().replace(" ", "").split(",", QString::SkipEmptyParts); + mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts); for(auto i = 0; i < mod_list_str.size(); ++i) { parseFixedModification(mod_list_str[i], Nter, Cter, else_prot); @@ -138,7 +136,8 @@ bool else_prot) { - QStringList str_split = mod_str.split("@", QString::SkipEmptyParts); + QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts); + pappso::AaModificationP aa_mod = AaModification::getInstance(str_split[0]); PeptideFixedModificationBuilder *mod = @@ -196,7 +195,7 @@ } QStringList mod_list_str = - mod_str.simplified().replace(" ", "").split(",", QString::SkipEmptyParts); + mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts); for(auto i = 0; i < mod_list_str.size(); ++i) { parsePotentialModification(mod_list_str[i], Nter, Cter, else_prot); @@ -211,10 +210,10 @@ bool else_prot) { - QStringList str_split = mod_str.split("@", QString::SkipEmptyParts); + QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts); QString mod_acc_str = str_split[0]; - QStringList str_acc_split = mod_acc_str.split("(", QString::SkipEmptyParts); + QStringList str_acc_split = mod_acc_str.split("(", Qt::SkipEmptyParts); pappso::AaModificationP aa_mod = AaModification::getInstance(str_acc_split[0]); @@ -225,7 +224,7 @@ if(str_acc_split.length() == 2) { QStringList max_num_str_list = - str_acc_split[1].replace(")", "").split("-", QString::SkipEmptyParts); + str_acc_split[1].replace(")", "").split("-", Qt::SkipEmptyParts); if(max_num_str_list.length() == 1) { mod->setModificationCounter(max_num_str_list[0].toUInt()); @@ -284,7 +283,7 @@ QStringList mod_list_str = - mod_str.simplified().replace(" ", "").split(",", QString::SkipEmptyParts); + mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts); for(auto i = 0; i < mod_list_str.size(); ++i) { parseLabeledModification(mod_list_str[i], true, true, true); @@ -310,7 +309,7 @@ bool else_prot) { - QStringList str_split = mod_str.split("@", QString::SkipEmptyParts); + QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts); pappso::AaModificationP aa_mod = AaModification::getInstance(str_split[0]); PeptideFixedModificationBuilder *mod = @@ -339,14 +338,28 @@ unsigned int missed_cleavage_number, bool semi_enzyme) { - mp_firstModificator->setPeptideSp(sequence_database_id, - protein_sp, - is_decoy, - peptide_sp_original, - start, - is_nter, - missed_cleavage_number, - semi_enzyme); + if(mp_firstModificator == nullptr) + { + m_sink->setPeptideSp(sequence_database_id, + protein_sp, + is_decoy, + peptide_sp_original, + start, + is_nter, + missed_cleavage_number, + semi_enzyme); + } + else + { + mp_firstModificator->setPeptideSp(sequence_database_id, + protein_sp, + is_decoy, + peptide_sp_original, + start, + is_nter, + missed_cleavage_number, + semi_enzyme); + } } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -100,7 +100,6 @@ bool semi_enzyme) { // QString s = "Banana"; - // s.replace(QRegExp("a[mn]"), "ox"); bool modify_this_peptide = true; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/peptidevariablemodificationreplacement.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/peptidevariablemodificationreplacement.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/peptidevariablemodificationreplacement.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/peptidevariablemodificationreplacement.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -76,7 +76,6 @@ bool semi_enzyme) { // QString s = "Banana"; - // s.replace(QRegExp("a[mn]"), "ox"); bool modify_this_peptide = true; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/protein.cpp libpappsomspp-0.8.58/src/pappsomspp/protein/protein.cpp --- libpappsomspp-0.8.15/src/pappsomspp/protein/protein.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/protein.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -37,7 +37,7 @@ namespace pappso { -QRegExp Protein::m_removeTranslationStopRegExp("\\*$"); +QRegularExpression Protein::m_removeTranslationStopRegExp("\\*$"); /* * http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml @@ -156,8 +156,9 @@ // replace amino acid wildcard by E, just to give an random mass (assumed // it is not perfect) QString sequence(m_sequence); - sequence.replace(QRegExp("[^WGASPVTLINDKQEMHFRCYUBZX]"), ""); - pappso::Peptide peptide(sequence.replace(QRegExp("[BZX]"), "E")); + sequence.replace(QRegularExpression("[^WGASPVTLINDKQEMHFRCYUBZX]"), ""); + pappso::Peptide peptide( + sequence.replace(QRegularExpression("[BZX]"), "E")); return peptide.getMass(); } catch(pappso::PappsoException &error) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/protein/protein.h libpappsomspp-0.8.58/src/pappsomspp/protein/protein.h --- libpappsomspp-0.8.15/src/pappsomspp/protein/protein.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/protein/protein.h 2022-10-27 09:16:15.000000000 +0000 @@ -59,7 +59,7 @@ /** \brief number of amino acid */ unsigned int m_length = 0; - static QRegExp m_removeTranslationStopRegExp; + static QRegularExpression m_removeTranslationStopRegExp; public: Protein(); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/deepprot/deepprotenum.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/deepprot/deepprotenum.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/deepprot/deepprotenum.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/deepprot/deepprotenum.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,179 @@ +/** + * \file pappsomspp/psm/deepprot/deepprotenum.cpp + * \date 22/1/2021 + * \author Olivier Langella + * \brief base type definition to use in DeepProt + * + * DeepProt is the C++ implementation of the SpecOMS algorithm + * + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "deepprotenum.h" +#include "../../pappsoexception.h" + +pappso::DeepProtMatchType +pappso::DeepProtEnumStr::DeepProtMatchTypeFromString(const QString &name) +{ + DeepProtMatchType match_type = DeepProtMatchType::uncategorized; + if(name == "delta_position") + { + match_type = DeepProtMatchType::DeltaPosition; + } + else if(name == "no_delta_position") + { + match_type = DeepProtMatchType::NoDeltaPosition; + } + else if(name == "uncategorized") + { + match_type = DeepProtMatchType::uncategorized; + } + else if(name == "zero_mass_delta") + { + match_type = DeepProtMatchType::ZeroMassDelta; + } + else if(name == "zero_mass_delta_mc") + { + match_type = DeepProtMatchType::ZeroMassDeltaMissedCleavage; + } + else if(name == "zero_mass_delta_st") + { + match_type = DeepProtMatchType::ZeroMassDeltaSemiTryptic; + } + else + { + throw pappso::PappsoException( + QObject::tr("DeepProtMatchType unknown :\n%1").arg(name)); + } + return match_type; +} + + +pappso::DeepProtPeptideCandidateStatus +pappso::DeepProtEnumStr::DeepProtPeptideCandidateStatusFromString( + const QString &name) +{ + + DeepProtPeptideCandidateStatus status = + DeepProtPeptideCandidateStatus::unmodified; + if(name == "cter_removal") + { + status = DeepProtPeptideCandidateStatus::CterRemoval; + } + else if(name == "delta_position") + { + status = DeepProtPeptideCandidateStatus::DeltaPosition; + } + else if(name == "missed_cleavage") + { + status = DeepProtPeptideCandidateStatus::MissedCleavage; + } + else if(name == "no_delta_position") + { + status = DeepProtPeptideCandidateStatus::NoDeltaPosition; + } + else if(name == "nter_removal") + { + status = DeepProtPeptideCandidateStatus::NterRemoval; + } + else if(name == "zero_mass_delta") + { + status = DeepProtPeptideCandidateStatus::ZeroMassDelta; + } + + else + { + throw pappso::PappsoException( + QObject::tr("DeepProtPeptideCandidateStatus unknown :\n%1").arg(name)); + } + return status; +} + +const QString +pappso::DeepProtEnumStr::toString(pappso::DeepProtMatchType match_type) +{ + + QString match_type_str; + switch(match_type) + { + case DeepProtMatchType::DeltaPosition: + match_type_str = "delta_position"; + break; + case DeepProtMatchType::NoDeltaPosition: + match_type_str = "no_delta_position"; + break; + case DeepProtMatchType::uncategorized: + match_type_str = "uncategorized"; + break; + case DeepProtMatchType::ZeroMassDelta: + match_type_str = "zero_mass_delta"; + break; + case DeepProtMatchType::ZeroMassDeltaMissedCleavage: + match_type_str = "zero_mass_delta_mc"; + break; + case DeepProtMatchType::ZeroMassDeltaSemiTryptic: + match_type_str = "zero_mass_delta_st"; + break; + + default: + throw pappso::PappsoException( + QObject::tr("DeepProtMatchType unknown :\n%1") + .arg((std::uint8_t)match_type)); + } + return match_type_str; +} + +const QString +pappso::DeepProtEnumStr::toString(pappso::DeepProtPeptideCandidateStatus status) +{ + + QString status_str; + switch(status) + { + case DeepProtPeptideCandidateStatus::CterRemoval: + status_str = "cter_removal"; + break; + case DeepProtPeptideCandidateStatus::DeltaPosition: + status_str = "delta_position"; + break; + case DeepProtPeptideCandidateStatus::MissedCleavage: + status_str = "missed_cleavage"; + break; + case DeepProtPeptideCandidateStatus::NoDeltaPosition: + status_str = "no_delta_position"; + break; + case DeepProtPeptideCandidateStatus::NterRemoval: + status_str = "nter_removal"; + break; + case DeepProtPeptideCandidateStatus::ZeroMassDelta: + status_str = "zero_mass_delta"; + break; + + default: + throw pappso::PappsoException( + QObject::tr("DeepProtPeptideCandidateStatus unknown :\n%1") + .arg((std::uint8_t)status)); + } + + return status_str; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/deepprot/deepprotenum.h libpappsomspp-0.8.58/src/pappsomspp/psm/deepprot/deepprotenum.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/deepprot/deepprotenum.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/deepprot/deepprotenum.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,85 @@ +/** + * \file pappsomspp/psm/deepprot/deepprotenum.h + * \date 22/1/2021 + * \author Olivier Langella + * \brief base type definition to use in DeepProt + * + * DeepProt is the C++ implementation of the SpecOMS algorithm + * + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once +#include "../../exportinmportconfig.h" +#include + +namespace pappso +{ + +/** @brief definition of different class of PSMs used by DeepProt + */ +enum class DeepProtMatchType : std::uint8_t +{ + uncategorized = 0, ///< precursor mass was not compared + ZeroMassDelta = 1, ///< peptide candidate is in precursor mz range + ZeroMassDeltaMissedCleavage = + 2, ///< peptide candidate with missed cleavage is in precursor mz range + ZeroMassDeltaSemiTryptic = + 3, ///< semi tryptic peptide candidate is in precursor mz range + DeltaPosition = 4, ///< spectrum shifter on peptide candidate has detected a + ///< position for the mass delta + NoDeltaPosition = 5, ///< spectrum shifter on peptide candidate has not + ///< detected a position for the mass delta + last = 6 +}; + + +/** @brief definition of different status for potential peptide candidates on + * the same spectrum + */ +enum class DeepProtPeptideCandidateStatus : std::uint8_t +{ + unmodified = 0, ///< precursor mass was not compared + ZeroMassDelta = 1, + CterRemoval = 2, + NterRemoval = 3, + MissedCleavage = 4, + DeltaPosition = 5, + NoDeltaPosition = 6, + last = 7 +}; + +class PMSPP_LIB_DECL DeepProtEnumStr +{ + public: + static const QString toString(DeepProtMatchType match_type); + static const QString toString(DeepProtPeptideCandidateStatus status); + + static DeepProtPeptideCandidateStatus + DeepProtPeptideCandidateStatusFromString(const QString &name); + static DeepProtMatchType DeepProtMatchTypeFromString(const QString &name); +}; + +} // namespace pappso + + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/features/psmfeatures.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/features/psmfeatures.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/features/psmfeatures.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/features/psmfeatures.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,386 @@ +/** + * \file pappsomspp/psm/features/psmfeatures.cpp + * \date 19/07/2022 + * \author Olivier Langella + * \brief comutes various PSM (Peptide Spectrum Match) features + */ + +/******************************************************************************* + * Copyright (c) 2022 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + + +#include "psmfeatures.h" +#include +#include + +using namespace pappso; + +PsmFeatures::PsmFeatures(PrecisionPtr ms2precision, double minimumMz) +{ + + m_ms2precision = ms2precision; + + m_ionList.push_back(PeptideIon::y); + m_ionList.push_back(PeptideIon::b); + + + msp_filterKeepGreater = + std::make_shared(minimumMz); + + msp_filterChargeDeconvolution = + std::make_shared(m_ms2precision); + msp_filterMzExclusion = std::make_shared( + PrecisionFactory::getPrecisionPtrFractionInstance(m_ms2precision, 0.5)); +} + +PsmFeatures::~PsmFeatures() +{ +} + +void +PsmFeatures::setPeptideSpectrumCharge(const pappso::PeptideSp peptideSp, + const MassSpectrum *p_spectrum, + unsigned int parent_charge) +{ + m_peakIonPairs.clear(); + msp_peptide = peptideSp; + MassSpectrum spectrum(*p_spectrum); + msp_filterKeepGreater.get()->filter(spectrum); + // msp_filterChargeDeconvolution.get()->filter(spectrum); + // msp_filterMzExclusion.get()->filter(spectrum); + + msp_peptideSpectrumMatch = + std::make_shared(spectrum, + peptideSp, + parent_charge, + m_ms2precision, + m_ionList, + (unsigned int)1, + 0); + + msp_peptideSpectrumMatch.get()->dropPeaksLackingMonoisotope(); + m_spectrumSumIntensity = spectrum.sumY(); + + + qDebug() << " accumulate"; + std::vector delta_list; + + + // TODO compute number of matched complementary peaks having m/z compatible + // with the precursor + + m_precursorTheoreticalMz = peptideSp.get()->getMz(parent_charge); + m_precursorTheoreticalMass = peptideSp.get()->getMass(); + m_parentCharge = parent_charge; + + + findComplementIonPairs(peptideSp); + + + for(const pappso::PeakIonIsotopeMatch &peak_ion : + msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList()) + { + delta_list.push_back( + peak_ion.getPeptideFragmentIonSp().get()->getMz(peak_ion.getCharge()) - + peak_ion.getPeak().x); + } + pappso::pappso_double sum = + std::accumulate(delta_list.begin(), delta_list.end(), 0); + + qDebug() << " delta_list.size()=" << delta_list.size(); + m_matchedMzDiffMean = 0; + m_matchedMzDiffMedian = 0; + m_matchedMzDiffSd = 0; + if(delta_list.size() > 0) + { + m_matchedMzDiffMean = sum / ((pappso::pappso_double)delta_list.size()); + + std::sort(delta_list.begin(), delta_list.end()); + m_matchedMzDiffMedian = delta_list[(delta_list.size() / 2)]; + + + qDebug() << " sd"; + m_matchedMzDiffSd = 0; + for(pappso::pappso_double val : delta_list) + { + // sd = sd + ((val - mean) * (val - mean)); + m_matchedMzDiffSd += std::pow((val - m_matchedMzDiffMean), 2); + } + m_matchedMzDiffSd = m_matchedMzDiffSd / delta_list.size(); + m_matchedMzDiffSd = std::sqrt(m_matchedMzDiffSd); + } + else + { + } +} + + +double +PsmFeatures::getIntensityOfMatchedIon(PeptideIon ion_type) +{ + double sum = 0; + for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get()) + { + if(peak_ion_match.getPeptideIonType() == ion_type) + { + sum += peak_ion_match.getPeak().y; + } + } + return sum; +} +double +PsmFeatures::getTotalIntensityOfMatchedIons() const +{ + double sum = 0; + for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get()) + { + sum += peak_ion_match.getPeak().y; + } + return sum; +} + +double +PsmFeatures::getTotalIntensity() const +{ + return m_spectrumSumIntensity; +} + +std::size_t +pappso::PsmFeatures::countMatchedIonComplementPairs() const +{ + return m_peakIonPairs.size(); +} + +const std::vector< + std::pair> & +pappso::PsmFeatures::getPeakIonPairs() const +{ + return m_peakIonPairs; +} + +double +pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs() const +{ + + double sum = 0; + for(auto &peak_pairs : m_peakIonPairs) + { + sum += peak_pairs.first.getPeak().y; + sum += peak_pairs.second.getPeak().y; + } + return sum; +} + +double +pappso::PsmFeatures::getMatchedMzDiffSd() const +{ + return m_matchedMzDiffSd; +} + +double +pappso::PsmFeatures::getMatchedMzDiffMean() const +{ + return m_matchedMzDiffMean; +} + + +std::size_t +pappso::PsmFeatures::getNumberOfMatchedIons() const +{ + return msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().size(); +} + +std::size_t +pappso::PsmFeatures::getMaxConsecutiveIon(pappso::PeptideIon ion_type) +{ + std::size_t max = 0; + auto peak_ion_match_list = + msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList(); + + peak_ion_match_list.erase( + std::remove_if( + peak_ion_match_list.begin(), + peak_ion_match_list.end(), + [ion_type](const PeakIonIsotopeMatch &a) { + if(a.getPeptideIonType() != ion_type) + return true; + if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() > 0) + return true; + return false; + }), + peak_ion_match_list.end()); + + peak_ion_match_list.sort( + [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { + if(a.getCharge() < b.getCharge()) + return true; + if(a.getPeptideIonType() < b.getPeptideIonType()) + return true; + if(a.getPeptideFragmentIonSp().get()->size() < + b.getPeptideFragmentIonSp().get()->size()) + return true; + return false; + }); + + unsigned int charge = 0; + std::size_t size = 0; + std::size_t count = 0; + for(std::list::iterator it = peak_ion_match_list.begin(); + it != peak_ion_match_list.end(); + it++) + { + qDebug() + << it->toString() << max << " " << it->getPeak().x << " " + << it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber(); + count++; + if((charge != it->getCharge()) || + (size != (it->getPeptideFragmentIonSp().get()->size() - 1))) + { + count = 1; + charge = it->getCharge(); + } + if(max < count) + max = count; + + size = it->getPeptideFragmentIonSp().get()->size(); + } + + return max; +} + +std::size_t +pappso::PsmFeatures::getAaSequenceCoverage(pappso::PeptideIon ion_type) +{ + std::vector covered; + covered.resize(msp_peptide.get()->size(), false); + + for(auto &peak : msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList()) + { + if(peak.getPeptideIonType() == ion_type) + { + covered[peak.getPeptideFragmentIonSp().get()->size() - 1] = true; + } + } + return std::count(covered.begin(), covered.end(), true); +} + +std::size_t +pappso::PsmFeatures::getComplementPairsAaSequenceCoverage() +{ + + std::vector covered; + covered.resize(msp_peptide.get()->size(), false); + + for(auto &peak_pair : m_peakIonPairs) + { + std::size_t pos = + peak_pair.first.getPeptideFragmentIonSp().get()->size() - 1; + covered[pos] = true; + covered[pos + 1] = true; + } + return std::count(covered.begin(), covered.end(), true); +} + + +double +pappso::PsmFeatures::getMaxIntensityPeakIonMatch( + pappso::PeptideIon ion_type) const +{ + std::list peak_ion_type = + msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList(); + + peak_ion_type.remove_if([ion_type](const PeakIonIsotopeMatch &a) { + return (a.getPeptideIonType() != ion_type); + }); + auto peak_it = std::max_element( + peak_ion_type.begin(), + peak_ion_type.end(), + [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { + return (a.getPeak().y < b.getPeak().y); + }); + + if(peak_it == peak_ion_type.end()) + return 0; + return peak_it->getPeak().y; +} + +double +pappso::PsmFeatures::getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() + const +{ + auto peak_it = std::max_element( + m_peakIonPairs.begin(), + m_peakIonPairs.end(), + [](const std::pair + &a, + const std::pair + &b) { + return ((a.first.getPeak().y + a.second.getPeak().y) < + (b.first.getPeak().y + b.second.getPeak().y)); + }); + + if(peak_it == m_peakIonPairs.end()) + return 0; + + return getIonPairPrecursorMassDelta(*peak_it); +} + +double +pappso::PsmFeatures::getIonPairPrecursorMassDelta( + const std::pair + &ion_pair) const +{ + qDebug() << m_precursorTheoreticalMz << " " << ion_pair.first.getPeak().x + << " " << ion_pair.second.getPeak().x << " " + << ion_pair.second.getCharge() << " " << ion_pair.first.getCharge() + << " " << m_parentCharge; + double diff = + (m_precursorTheoreticalMass + (MHPLUS * ion_pair.first.getCharge())) / + ion_pair.first.getCharge(); + + + return (diff - (ion_pair.first.getPeak().x + ion_pair.second.getPeak().x - + ((MHPLUS * ion_pair.first.getCharge())) / + ion_pair.first.getCharge())); +} + + +void +pappso::PsmFeatures::findComplementIonPairs(const pappso::PeptideSp &peptideSp) +{ + std::size_t peptide_size = peptideSp.get()->size(); + std::vector ion_isotope_list( + msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(), + msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end()); + for(const pappso::PeakIonIsotopeMatch &peak_ion_ext : ion_isotope_list) + { + if(peptideIonIsNter(peak_ion_ext.getPeptideIonType())) + { + auto it = findComplementIonType(ion_isotope_list.begin(), + ion_isotope_list.end(), + peak_ion_ext, + peptide_size); + if(it != ion_isotope_list.end()) + { // contains the complementary ion + m_peakIonPairs.push_back({peak_ion_ext, *it}); + } + } + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/features/psmfeatures.h libpappsomspp-0.8.58/src/pappsomspp/psm/features/psmfeatures.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/features/psmfeatures.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/features/psmfeatures.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,161 @@ +/** + * \file pappsomspp/psm/features/psmfeatures.h + * \date 19/07/2022 + * \author Olivier Langella + * \brief comutes various PSM (Peptide Spectrum Match) features + */ + +/******************************************************************************* + * Copyright (c) 2022 Olivier Langella . + * + * This file is part of PAPPSOms-tools. + * + * PAPPSOms-tools is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms-tools is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms-tools. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "../../massspectrum/massspectrum.h" +#include "../../mzrange.h" +#include "../../peptide/peptidefragmention.h" +#include "../../processing/filters/filterchargedeconvolution.h" +#include "../../processing/filters/filterexclusionmz.h" +#include "../../processing/filters/filterresample.h" +#include "../peptideisotopespectrummatch.h" + +namespace pappso +{ +/** + * @todo write docs + */ +class PMSPP_LIB_DECL PsmFeatures +{ + public: + /** @brief compute psm features + * @param ms2precision precision of mass measurements for MS2 fragments + * @param minimumMz ignore mz values under this threshold + */ + PsmFeatures(PrecisionPtr ms2precision, double minimumMz); + + /** + * Destructor + */ + ~PsmFeatures(); + + void setPeptideSpectrumCharge(const pappso::PeptideSp peptideSp, + const MassSpectrum *p_spectrum, + unsigned int parent_charge); + + /** @brief get the sum of intensity of a specific ion + * @param ion_type ion species (y, b, ...) + */ + double getIntensityOfMatchedIon(PeptideIon ion_type); + + /** @brief sum of all peak intensities (matched or not) + */ + double getTotalIntensity() const; + + + /** @brief sum of matched peak intensities + */ + double getTotalIntensityOfMatchedIons() const; + + /** @brief number of matched ions (peaks) + */ + std::size_t getNumberOfMatchedIons() const; + + /** @brief count the number of matched ion complement + * + * matched ion complement are ions with a sum compatible to the precursor mass + * + */ + std::size_t countMatchedIonComplementPairs() const; + + /** @brief intensity of matched ion complement + */ + double getTotalIntensityOfMatchedIonComplementPairs() const; + + const std::vector< + std::pair> & + getPeakIonPairs() const; + + + /** @brief get mean deviation of matched peak mass delta + */ + double getMatchedMzDiffMean() const; + + + /** @brief get standard deviation of matched peak mass delta + */ + double getMatchedMzDiffSd() const; + + + /** @brief get the precursor mass delta of the maximum intensity pair of + * complement ions + */ + double getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() const; + + + /** @brief get the maximum consecutive fragments of one ion type + * @param ion_type ion species (y, b, ...) + */ + std::size_t getMaxConsecutiveIon(PeptideIon ion_type); + + /** @brief number of amino acid covered by matched ions + */ + std::size_t getAaSequenceCoverage(PeptideIon ion_type); + + + /** @brief number of amino acid covered by matched complement pairs of ions + */ + std::size_t getComplementPairsAaSequenceCoverage(); + + double getMaxIntensityPeakIonMatch(PeptideIon ion_type) const; + + + double getIonPairPrecursorMassDelta( + const std::pair + &ion_pair) const; + + + private: + void findComplementIonPairs(const pappso::PeptideSp &peptideSp); + + private: + std::shared_ptr msp_filterChargeDeconvolution; + std::shared_ptr msp_filterMzExclusion; + std::shared_ptr msp_filterKeepGreater; + + std::shared_ptr msp_peptideSpectrumMatch; + pappso::PeptideSp msp_peptide; + + PrecisionPtr m_ms2precision; + std::list m_ionList; + + double m_spectrumSumIntensity; + + double m_precursorTheoreticalMz; + double m_precursorTheoreticalMass; + unsigned int m_parentCharge = 1; + + std::vector< + std::pair> + m_peakIonPairs; + + double m_matchedMzDiffMean = 0; + double m_matchedMzDiffMedian = 0; + double m_matchedMzDiffSd = 0; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peakionisotopematch.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/peakionisotopematch.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/peakionisotopematch.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peakionisotopematch.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,6 +26,42 @@ namespace pappso { +std::vector::iterator +findComplementIonType(std::vector::iterator begin, + std::vector::iterator end, + const PeakIonIsotopeMatch &peak_ion, + std::size_t peptide_size) +{ + + return std::find_if( + begin, + end, + [peak_ion, peptide_size](const PeakIonIsotopeMatch &to_compare) { + if(to_compare.getCharge() == peak_ion.getCharge()) + { + if((to_compare.getPeptideFragmentIonSp().get()->size() + + peak_ion.getPeptideFragmentIonSp().get()->size()) == peptide_size) + { + if(peptideIonTypeIsComplement(to_compare.getPeptideIonType(), + peak_ion.getPeptideIonType())) + { + if(to_compare.getPeptideNaturalIsotopeAverageSp() + .get() + ->getIsotopeNumber() == + peak_ion.getPeptideNaturalIsotopeAverageSp() + .get() + ->getIsotopeNumber()) + { + return true; + } + } + } + } + + return false; + }); +} + PeakIonIsotopeMatch::PeakIonIsotopeMatch( const DataPoint &peak, @@ -34,12 +70,20 @@ : PeakIonMatch(peak, ion_sp, naturalIsotopeAverageSp.get()->getCharge()), _naturalIsotopeAverageSp(naturalIsotopeAverageSp) { + qDebug(); } PeakIonIsotopeMatch::PeakIonIsotopeMatch(const PeakIonIsotopeMatch &other) - : PeakIonMatch(other), - _naturalIsotopeAverageSp(other._naturalIsotopeAverageSp) + : PeakIonMatch(other) { + _naturalIsotopeAverageSp = other._naturalIsotopeAverageSp; +} + + +PeakIonIsotopeMatch::PeakIonIsotopeMatch(PeakIonIsotopeMatch &&other) + : PeakIonMatch(std::move(other)) +{ + _naturalIsotopeAverageSp = other._naturalIsotopeAverageSp; } PeakIonIsotopeMatch::~PeakIonIsotopeMatch() @@ -55,11 +99,21 @@ PeakIonIsotopeMatch & PeakIonIsotopeMatch::operator=(const PeakIonIsotopeMatch &other) { - + PeakIonMatch::operator =(other); _naturalIsotopeAverageSp = other._naturalIsotopeAverageSp; return *this; } +QString +PeakIonIsotopeMatch::toString() const +{ + return QString("%1isotope%2r%3mz%4") + .arg(PeakIonMatch::toString()) + .arg(_naturalIsotopeAverageSp.get()->getIsotopeNumber()) + .arg(_naturalIsotopeAverageSp.get()->getIsotopeRank()) + .arg(getPeak().x); +} + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peakionisotopematch.h libpappsomspp-0.8.58/src/pappsomspp/psm/peakionisotopematch.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/peakionisotopematch.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peakionisotopematch.h 2022-10-27 09:16:15.000000000 +0000 @@ -33,6 +33,16 @@ class PeakIonIsotopeMatch; typedef std::shared_ptr PeakIonIsotopeMatchCstSPtr; + +/** @brief find the first element containing the complementary ion + * complementary ion of y1 is b(n-1) for instance + * */ +PMSPP_LIB_DECL std::vector::iterator +findComplementIonType(std::vector::iterator begin, + std::vector::iterator end, + const PeakIonIsotopeMatch &peak_ion, + std::size_t peptide_size); + class PMSPP_LIB_DECL PeakIonIsotopeMatch : public PeakIonMatch { public: @@ -41,6 +51,7 @@ const PeptideNaturalIsotopeAverageSp &naturalIsotopeAverageSp, const PeptideFragmentIonSp &ion_sp); PeakIonIsotopeMatch(const PeakIonIsotopeMatch &other); + PeakIonIsotopeMatch(PeakIonIsotopeMatch &&other); virtual ~PeakIonIsotopeMatch(); virtual const PeptideNaturalIsotopeAverageSp & @@ -48,6 +59,7 @@ PeakIonIsotopeMatch &operator=(const PeakIonIsotopeMatch &other); + virtual QString toString() const; private: PeptideNaturalIsotopeAverageSp _naturalIsotopeAverageSp; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peakionmatch.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/peakionmatch.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/peakionmatch.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peakionmatch.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -44,9 +44,63 @@ { } +PeakIonMatch::PeakIonMatch(PeakIonMatch &&other) + : _peak(std::move(other._peak)), + _ion_sp(other._ion_sp), + _charge(std::move(other._charge)) +{ +} + PeakIonMatch::~PeakIonMatch() { } +PeakIonMatch & +PeakIonMatch::operator=(const PeakIonMatch &other) +{ + _peak = other._peak; + _ion_sp = other._ion_sp; + _charge = other._charge; + + return *this; +} + +const PeptideFragmentIonSp & +PeakIonMatch::getPeptideFragmentIonSp() const +{ + return _ion_sp; +} + +const DataPoint & +PeakIonMatch::getPeak() const +{ + return _peak; +} + +unsigned int +PeakIonMatch::getCharge() const +{ + return _charge; +} + +PeptideIon +PeakIonMatch::getPeptideIonType() const +{ + return _ion_sp.get()->getPeptideIonType(); +} + +PeptideDirection +PeakIonMatch::getPeptideIonDirection() const +{ + return _ion_sp.get()->getPeptideFragmentSp().get()->getPeptideIonDirection(); +} + +QString +PeakIonMatch::toString() const +{ + return QString("%1").arg( + _ion_sp.get()->getCompletePeptideIonName(getCharge())); +} + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peakionmatch.h libpappsomspp-0.8.58/src/pappsomspp/psm/peakionmatch.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/peakionmatch.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peakionmatch.h 2022-10-27 09:16:15.000000000 +0000 @@ -43,39 +43,22 @@ const PeptideFragmentIonSp &ion_sp, unsigned int charge); PeakIonMatch(const PeakIonMatch &other); + PeakIonMatch(PeakIonMatch &&other); virtual ~PeakIonMatch(); - virtual const PeptideFragmentIonSp & - getPeptideFragmentIonSp() const - { - return _ion_sp; - }; - - const DataPoint & - getPeak() const - { - return _peak; - }; - - unsigned int - getCharge() const - { - return _charge; - }; - - PeptideIon - getPeptideIonType() const - { - return _ion_sp.get()->getPeptideIonType(); - }; - PeptideDirection - getPeptideIonDirection() const - { - return _ion_sp.get() - ->getPeptideFragmentSp() - .get() - ->getPeptideIonDirection(); - }; + PeakIonMatch &operator=(const PeakIonMatch &other); + + virtual const PeptideFragmentIonSp &getPeptideFragmentIonSp() const; + + const DataPoint &getPeak() const; + + unsigned int getCharge() const; + + PeptideIon getPeptideIonType() const; + PeptideDirection getPeptideIonDirection() const; + + virtual QString toString() const; + private: DataPoint _peak; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peptideisotopespectrummatch.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/peptideisotopespectrummatch.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/peptideisotopespectrummatch.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peptideisotopespectrummatch.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -32,7 +32,7 @@ const PeptideSp &peptideSp, unsigned int parent_charge, PrecisionPtr precision, - std::list ion_type_list, + const std::list &ion_type_list, unsigned int max_isotope_number, [[maybe_unused]] unsigned int max_isotope_rank) : _precision(precision) @@ -40,6 +40,7 @@ try { + _peak_ion_match_list.clear(); qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch " "begin max_isotope_number=" << max_isotope_number; @@ -47,15 +48,10 @@ qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch " "peak_list spectrum.size=" << spectrum.size(); - std::list peak_list(spectrum.begin(), spectrum.end()); - - qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch " - "ion_type_list"; + std::vector peak_list(spectrum.begin(), spectrum.end()); for(auto ion_type : ion_type_list) { auto ion_list = fragmentIonList.getPeptideFragmentIonSp(ion_type); - qDebug() << "PeptideIsotopeSpectrumMatch::" - "PeptideIsotopeSpectrumMatch fragmentIonList"; for(unsigned int charge = 1; charge <= parent_charge; charge++) { @@ -66,13 +62,13 @@ isotope_number <= max_isotope_number; isotope_number++) { - PeptideNaturalIsotopeAverage isotopeIon(ion, - askedIsotopeRank, - isotope_number, - charge, - precision); + PeptideNaturalIsotopeAverage isotopeIon( + ion, isotope_number, charge, precision); + + qDebug() + << isotope_number << " " << isotopeIon.toString(); - std::list::iterator it_peak = + std::vector::iterator it_peak = getBestPeakIterator(peak_list, isotopeIon); if(it_peak != peak_list.end()) { @@ -81,13 +77,14 @@ isotopeIon.makePeptideNaturalIsotopeAverageSp(), ion)); peak_list.erase(it_peak); + + qDebug() << isotope_number << " " + << _peak_ion_match_list.back().toString(); } } } } } - qDebug() - << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch end"; } catch(PappsoException &exception_pappso) { @@ -120,7 +117,7 @@ PrecisionPtr precision) : _precision(precision) { - qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch begin"; + qDebug() << " begin"; if(v_peptideIsotopeList.size() != v_peptideIonList.size()) { throw PappsoException( @@ -132,11 +129,11 @@ auto isotopeIt = v_peptideIsotopeList.begin(); auto ionIt = v_peptideIonList.begin(); - std::list peak_list(spectrum.begin(), spectrum.end()); + std::vector peak_list(spectrum.begin(), spectrum.end()); while(isotopeIt != v_peptideIsotopeList.end()) { - std::list::iterator it_peak = + std::vector::iterator it_peak = getBestPeakIterator(peak_list, *(isotopeIt->get())); if(it_peak != peak_list.end()) { @@ -147,7 +144,7 @@ isotopeIt++; ionIt++; } - qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch end"; + qDebug() << " end"; } @@ -156,6 +153,7 @@ : _precision(other._precision), _peak_ion_match_list(other._peak_ion_match_list) { + qDebug(); } PeptideIsotopeSpectrumMatch::~PeptideIsotopeSpectrumMatch() @@ -163,15 +161,15 @@ } -std::list::iterator +std::vector::iterator PeptideIsotopeSpectrumMatch::getBestPeakIterator( - std::list &peak_list, + std::vector &peak_list, const PeptideNaturalIsotopeAverage &ion) const { // qDebug(); - std::list::iterator itpeak = peak_list.begin(); - std::list::iterator itend = peak_list.end(); - std::list::iterator itselect = peak_list.end(); + std::vector::iterator itpeak = peak_list.begin(); + std::vector::iterator itend = peak_list.end(); + std::vector::iterator itselect = peak_list.end(); pappso_double best_intensity = 0; @@ -197,5 +195,68 @@ return _peak_ion_match_list; } - +std::size_t +PeptideIsotopeSpectrumMatch::size() const +{ + return _peak_ion_match_list.size(); +} +PeptideIsotopeSpectrumMatch::const_iterator +PeptideIsotopeSpectrumMatch::begin() const +{ + return _peak_ion_match_list.begin(); +} +PeptideIsotopeSpectrumMatch::const_iterator +PeptideIsotopeSpectrumMatch::end() const +{ + return _peak_ion_match_list.end(); +} + +void +PeptideIsotopeSpectrumMatch::dropPeaksLackingMonoisotope() +{ + qDebug(); + _peak_ion_match_list.sort( + [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { + if(a.getPeptideIonType() < b.getPeptideIonType()) + return true; + if(a.getPeptideFragmentIonSp().get()->size() < + b.getPeptideFragmentIonSp().get()->size()) + return true; + if(a.getCharge() < b.getCharge()) + return true; + if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() < + b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber()) + return true; + return false; + }); + PeptideIon ion_type = PeptideIon::b; + std::size_t nserie = 0; + std::size_t isotopeserie = 0; + unsigned int charge = 0; + for(std::list::iterator it = + _peak_ion_match_list.begin(); + it != _peak_ion_match_list.end(); + it++) + { + if((nserie != it->getPeptideFragmentIonSp().get()->size()) || + (ion_type != it->getPeptideIonType()) || (charge != it->getCharge())) + { + ion_type = it->getPeptideIonType(); + isotopeserie = 0; + nserie = it->getPeptideFragmentIonSp().get()->size(); + charge = it->getCharge(); + } + if(isotopeserie <= + it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber()) + { + isotopeserie = + it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber(); + } + else + { + it = _peak_ion_match_list.erase(it); + } + } + qDebug(); +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peptideisotopespectrummatch.h libpappsomspp-0.8.58/src/pappsomspp/psm/peptideisotopespectrummatch.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/peptideisotopespectrummatch.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peptideisotopespectrummatch.h 2022-10-27 09:16:15.000000000 +0000 @@ -53,7 +53,7 @@ const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, - std::list ion_list, + const std::list &ion_type_list, unsigned int max_isotope_number, unsigned int max_isotope_rank); PeptideIsotopeSpectrumMatch( @@ -63,32 +63,22 @@ PrecisionPtr precision); PeptideIsotopeSpectrumMatch(const PeptideIsotopeSpectrumMatch &other); - ~PeptideIsotopeSpectrumMatch(); + virtual ~PeptideIsotopeSpectrumMatch(); const std::list &getPeakIonIsotopeMatchList() const; typedef std::list::const_iterator const_iterator; - unsigned int - size() const - { - return _peak_ion_match_list.size(); - } - const_iterator - begin() const - { - return _peak_ion_match_list.begin(); - } - const_iterator - end() const - { - return _peak_ion_match_list.end(); - } + std::size_t size() const; + const_iterator begin() const; + const_iterator end() const; + + void dropPeaksLackingMonoisotope(); private: - virtual std::list::iterator - getBestPeakIterator(std::list &peak_list, + virtual std::vector::iterator + getBestPeakIterator(std::vector &peak_list, const PeptideNaturalIsotopeAverage &ion) const; PrecisionPtr _precision; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/peptidespectrummatch.h libpappsomspp-0.8.58/src/pappsomspp/psm/peptidespectrummatch.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/peptidespectrummatch.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/peptidespectrummatch.h 2022-10-27 09:16:15.000000000 +0000 @@ -61,7 +61,7 @@ PrecisionPtr precision); PeptideSpectrumMatch(const PeptideSpectrumMatch &other); - ~PeptideSpectrumMatch(); + virtual ~PeptideSpectrumMatch(); bool contains(const PeptideFragmentIon *peptideFragmentIonSp, unsigned int z) const; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp libpappsomspp-0.8.58/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp --- libpappsomspp-0.8.15/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -150,6 +150,13 @@ } } +XtandemHyperscore::XtandemHyperscore(const XtandemHyperscore &other) +{ + _ion_count = other._ion_count; + _proto_hyperscore = other._proto_hyperscore; + _refine_spectrum_synthesis = other._refine_spectrum_synthesis; +} + unsigned int XtandemHyperscore::getMatchedIons(PeptideIon ion_type) const { @@ -255,9 +262,11 @@ { try { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " _proto_hyperscore=" << _proto_hyperscore; - return (log10(_proto_hyperscore) * 4); + qDebug() << " _proto_hyperscore=" << _proto_hyperscore; + double hyperscore = (log10(_proto_hyperscore) * 4); + if(hyperscore < 0) + return 0; + return hyperscore; } catch(PappsoException &exception_pappso) { diff -Nru libpappsomspp-0.8.15/src/pappsomspp/psm/xtandem/xtandemhyperscore.h libpappsomspp-0.8.58/src/pappsomspp/psm/xtandem/xtandemhyperscore.h --- libpappsomspp-0.8.15/src/pappsomspp/psm/xtandem/xtandemhyperscore.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/psm/xtandem/xtandemhyperscore.h 2022-10-27 09:16:15.000000000 +0000 @@ -49,6 +49,7 @@ PrecisionPtr precision, std::list ion_list, bool refine_spectrum_synthesis); + XtandemHyperscore(const XtandemHyperscore &other); ~XtandemHyperscore(); pappso_double getHyperscore() const; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/trace/maptrace.cpp libpappsomspp-0.8.58/src/pappsomspp/trace/maptrace.cpp --- libpappsomspp-0.8.15/src/pappsomspp/trace/maptrace.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/trace/maptrace.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -187,6 +187,33 @@ } +void +MapTrace::insertOrUpdate(const DataPoint &data_point) +{ + + // Try to insert the data point into the map. Check if that was done or + // not. + std::pair::iterator, bool> res = + insert(std::pair(data_point.x, data_point.y)); + + if(!res.second) + { + // One other same (x,y) value pair was seen already. Only increment the y + // value. + + res.first->second += data_point.y; + } +} + + +void +MapTrace::insertOrUpdate(const Trace &trace) +{ + for(const DataPoint &data_point : trace) + insertOrUpdate(data_point); +} + + Trace MapTrace::toTrace() const { diff -Nru libpappsomspp-0.8.15/src/pappsomspp/trace/maptrace.h libpappsomspp-0.8.58/src/pappsomspp/trace/maptrace.h --- libpappsomspp-0.8.15/src/pappsomspp/trace/maptrace.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/trace/maptrace.h 2022-10-27 09:16:15.000000000 +0000 @@ -54,6 +54,9 @@ std::vector xValues(); std::vector yValues(); + void insertOrUpdate(const DataPoint &data_point); + void insertOrUpdate(const Trace &trace); + Trace toTrace() const; QString toString() const; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/trace/trace.cpp libpappsomspp-0.8.58/src/pappsomspp/trace/trace.cpp --- libpappsomspp-0.8.15/src/pappsomspp/trace/trace.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/trace/trace.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -5,6 +5,7 @@ #include #include #include +#include #include @@ -93,6 +94,7 @@ { return true; } + return false; }); } @@ -107,6 +109,7 @@ { return true; } + return false; }); } @@ -218,11 +221,38 @@ return (sumYTrace(begin, end, 0) / nb_element); } + +double +quantileYTrace(std::vector::const_iterator begin, + std::vector::const_iterator end, + double quantile) +{ + std::size_t nb_element = distance(begin, end); + if(nb_element == 0) + throw ExceptionOutOfRange( + QObject::tr("unable to compute quantile on a trace of size 0")); + + + std::size_t ieth_element = std::round((double)nb_element * quantile); + if(ieth_element > nb_element) + throw ExceptionOutOfRange( + QObject::tr("quantile value must be lower than 1")); + + + std::vector data(begin, end); + std::nth_element( + data.begin(), + data.begin() + ieth_element, + data.end(), + [](const DataPoint &a, const DataPoint &b) { return a.y < b.y; }); + return data[ieth_element].y; +} + double medianYTrace(std::vector::const_iterator begin, std::vector::const_iterator end) { - pappso_double nb_element = distance(begin, end); + std::size_t nb_element = distance(begin, end); if(nb_element == 0) throw ExceptionOutOfRange( QObject::tr("unable to compute median on a trace of size 0")); @@ -256,6 +286,35 @@ } +double +areaTraceMinusBase(std::vector::const_iterator begin, + std::vector::const_iterator end) +{ + + if(begin == end) + return 0; + auto previous = begin; + auto next = begin + 1; + auto last = next; + double area = 0; + while(next != end) + { + last = next; + area += ((next->x - previous->x) * (previous->y + next->y)) / (double)2; + previous++; + next++; + } + if(area > 0) + { + // remove base peak area + area -= (((last->y + begin->y) * (last->x - begin->x)) / 2); + if(area < 0) + return 0; + } + return area; +} + + Trace flooredLocalMaxima(std::vector::const_iterator begin, std::vector::const_iterator end, @@ -655,22 +714,108 @@ DataPoint Trace::containsX(pappso_double value, PrecisionPtr precision_p) const { - auto iterator = std::find_if( - begin(), end(), [value, precision_p](const DataPoint &data_point) { - if(precision_p) - { - pappso_double delta = precision_p->delta(value); + // std::cout << std::setprecision(10) << "getting value: " << value + //<< " and precision: " << precision_p->getNominal() << std::endl; - if(data_point.x >= (value - delta) && data_point.x <= (value + delta)) - return true; - else - return false; - } - else - { - return (data_point.x == value); - } - }); + pappso_double delta = precision_p->delta(value); + + double left_most = value - delta; + double right_most = value + delta; + + // std::cout << std::setprecision(10) << "delta: " << delta + //<< " left_most: " << left_most << " right_most: " << right_most + //<< std::endl; + + auto iterator = + std::find_if(begin(), + end(), + [value, precision_p, delta, left_most, right_most]( + const DataPoint &data_point) { + if(precision_p) + { + + // FIXME: unbelievable behaviour: when building in + // release mode this code, under i386 (but not x86_64), + // this code fails if the following cout statement is + // missing. + + // std::cout << std::setprecision(10) + //<< "Testing data_point.x: " << data_point.x + //<< std::endl; + + // For this reason I had to deactivate the related tests + // for i386 in tests/test_trace.cpp + + double diff_to_left_most = data_point.x - left_most; + double diff_to_right_most = data_point.x - right_most; + + // std::cout << std::setprecision(10) + //<< "diff_to_left_most: " << diff_to_left_most + //<< " diff_to_right_most: " << diff_to_right_most << + // std::endl; + + // if(diff_to_left_most > 0) + //{ + // std::cout << std::setprecision(10) + //<< " point is right of left_most: " << + // diff_to_left_most + //<< std::endl; + //} + // if(diff_to_left_most < 0) + //{ + // std::cout << std::setprecision(10) + //<< "point is left of left_most: " << diff_to_left_most + //<< std::endl; + //} + // if(!diff_to_left_most) + //{ + // std::cout << std::setprecision(10) + //<< "point is spot on left_most: " << diff_to_left_most + //<< std::endl; + //} + + // if(diff_to_right_most > 0) + //{ + // std::cout << std::setprecision(10) + //<< "point is right of right_most: " << + // diff_to_right_most + //<< std::endl; + //} + // if(diff_to_right_most < 0) + //{ + // std::cout << std::setprecision(10) + //<< "point is left or of right_most: " + //<< diff_to_right_most << std::endl; + //} + // if(!diff_to_right_most) + //{ + // std::cout << std::setprecision(10) + //<< "point is spot on right_most: " << + // diff_to_right_most + //<< std::endl; + //} + + if(diff_to_left_most >= 0 && diff_to_right_most <= 0) + { + // std::cout << "The point is inside the range, + // should return true." + //<< std::endl; + return true; + } + else + { + // std::cout + //<< "The point is outside the range, should return + // false." + //<< std::endl; + return false; + } + } + else + { + return (data_point.x == value); + } + }); if(iterator != end()) { @@ -763,10 +908,9 @@ Trace::sumY(double mzStart, double mzEnd) const { auto begin_it = findFirstEqualOrGreaterX(this->begin(), this->end(), mzStart); - auto end_it = findFirstGreaterX(begin_it, this->end(), mzEnd) ; + auto end_it = findFirstGreaterX(begin_it, this->end(), mzEnd); - return sumYTrace( - begin_it, end_it, 0); + return sumYTrace(begin_it, end_it, 0); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/trace/trace.h libpappsomspp-0.8.58/src/pappsomspp/trace/trace.h --- libpappsomspp-0.8.15/src/pappsomspp/trace/trace.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/trace/trace.h 2022-10-27 09:16:15.000000000 +0000 @@ -17,8 +17,10 @@ class Trace; -QDataStream &operator<<(QDataStream &out, const Trace &trace); -QDataStream &operator>>(QDataStream &out, Trace &trace); +// @TODO function is not implemented : +PMSPP_LIB_DECL QDataStream &operator<<(QDataStream &out, const Trace &trace); +// @TODO function is not implemented : +PMSPP_LIB_DECL QDataStream &operator>>(QDataStream &out, Trace &trace); /** @brief find the first element in which X is equal or greater than the value * searched important : it implies that Trace is sorted by X @@ -106,6 +108,19 @@ PMSPP_LIB_DECL double medianYTrace(std::vector::const_iterator begin, std::vector::const_iterator end); + +/** @brief calculate the quantile of y value of a trace + * @param begin begin iterator + * @param end end iterator + * @param quantile the quantile value between 0 and 1 + * @return Y value at the quantile + * */ +PMSPP_LIB_DECL double +quantileYTrace(std::vector::const_iterator begin, + std::vector::const_iterator end, + double quantile); + + /** @brief calculate the area of a trace * */ PMSPP_LIB_DECL double areaTrace(std::vector::const_iterator begin, @@ -194,14 +209,17 @@ virtual Trace &filter(const FilterInterface &filter) final; QString toString() const; + /** @brief find datapoint with exactly x value + */ + std::vector::const_iterator + dataPointCstIteratorWithX(pappso_double value) const; + protected: //! Return a reference to the DataPoint instance that has its y member equal //! to \p value. // const DataPoint &dataPointWithX(pappso_double value) const; std::size_t dataPointIndexWithX(pappso_double value) const; std::vector::iterator dataPointIteratorWithX(pappso_double value); - std::vector::const_iterator - dataPointCstIteratorWithX(pappso_double value) const; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/types.h libpappsomspp-0.8.58/src/pappsomspp/types.h --- libpappsomspp-0.8.15/src/pappsomspp/types.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/types.h 2022-10-27 09:16:15.000000000 +0000 @@ -178,17 +178,17 @@ enum class Axis : std::int8_t { - unset = 0, - x = 1, - y = 2, - z = 3, + unset = 0x000, + x = 1 << 0, + y = 1 << 1, + z = 1 << 2, }; enum class AxisScale : std::int8_t { unset = 0, - orig = 1, + orig = 1, log10 = 2, }; @@ -229,6 +229,30 @@ const pappso_double ONEMILLION(1000000); +/** @file + * https://forgemia.inra.fr/pappso/massxpert/-/blob/be60e53480f68d36afa95c809cffd68d4fb46c79/data/polChemDefs/protein-1-letter-libisospec-atomic-data/protein-1-letter-libisospec-atomic-data.xml + * abundance of sulfur extracted from 'massXpert' polymer definitions + */ +// Sulfur +// S +// +// 31.9720711741 +// 94.985001199904004920426814351230859756469726562500000000000000 +// +// +// 32.9714589101 +// 0.751939844812414937003097747947322204709053039550781250000000 +// +// +// 33.9678670300 +// 4.252059835213182203972337447339668869972229003906250000000000 +// +// +// 35.9670812000 +// 0.010999120070394368536836893213148869108408689498901367187500 +// + + const pappso_double MASSOXYGEN(15.99491461956); const pappso_double MASSCARBON(12); const pappso_double MASSH2O((MPROTIUM * 2) + MASSOXYGEN); @@ -236,7 +260,7 @@ const pappso_double MASSNH3((MPROTIUM * 3) + MASSNITROGEN); const pappso_double MASSCO(MASSCARBON + MASSOXYGEN); const pappso_double MASSPHOSPHORUS(30.973761998); -const pappso_double MASSSULFUR(31.97207100); +const pappso_double MASSSULFUR(31.9720711741); // id: MOD:00696 name: phosphorylated residue H 1 O 3 P 1 const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM + (MASSOXYGEN * 3) + @@ -258,19 +282,19 @@ (32.97145876u) stable isotope of sulfur https://en.wikipedia.org/wiki/Isotopes_of_sulfur */ -const pappso_double DIFFS32S33(32.97145876 - MASSSULFUR); +const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR); /** \def DIFFS32S34 1.9957959 \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S34 (33.96786690u) stable isotope of sulfur */ -const pappso_double DIFFS32S34(33.96786690 - MASSSULFUR); +const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR); /** \def DIFFS32S36 3.99500976 \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S36 (35.96708076u) stable isotope of sulfur */ -const pappso_double DIFFS32S36(35.96708076 - MASSSULFUR); +const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR); /** \def DIFFH1H2 @@ -302,47 +326,57 @@ /** \def ABUNDANCEH2 0.0156% \brief H2 isotope abundance */ -const pappso_double ABUNDANCEH2(0.00015574); +const pappso_double + ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250); /** \def ABUNDANCEN15 0.00364 \brief N15 isotope abundance */ -const pappso_double ABUNDANCEN15(0.003663); +const pappso_double ABUNDANCEN15( + 0.00364198543205827118818262988497735932469367980957031250000000); /** \def ABUNDANCEO17 \brief O17 isotope abundance */ -const pappso_double ABUNDANCEO17(0.000372); +const pappso_double ABUNDANCEO17( + 0.00038099847600609595965615028489992255344986915588378906250000); /** \def ABUNDANCEO18 0.2% \brief O18 isotope abundance */ -const pappso_double ABUNDANCEO18(0.0020004); +const pappso_double ABUNDANCEO18( + 0.00205139179443282221315669744399201590567827224731445312500000); /** \def ABUNDANCEC13 1.109% \brief C13 isotope abundance */ -const pappso_double ABUNDANCEC13(0.011078); +const pappso_double ABUNDANCEC13( + 0.01078805814953308406245469086570665240287780761718750000000000); /** \def ABUNDANCEC12 98.89% \brief C12 abundance */ -const pappso_double ABUNDANCEC12(0.988922); +const pappso_double ABUNDANCEC12( + 0.98921194185046687152862432412803173065185546875000000000000000); + /** \def ABUNDANCES33 0.00750 \brief S33 abundance */ -const pappso_double ABUNDANCES33(0.00750); +const pappso_double ABUNDANCES33( + 0.00751939844812414937003097747947322204709053039550781250000000); /** \def ABUNDANCES34 0.0429 \brief S34 abundance */ -const pappso_double ABUNDANCES34(0.04215); +const pappso_double ABUNDANCES34( + 0.04252059835213182203972337447339668869972229003906250000000000); /** \def ABUNDANCES36 0.00020 \brief S36 abundance */ -const pappso_double ABUNDANCES36(0.00020); +const pappso_double ABUNDANCES36( + 0.00010999120070394368536836893213148869108408689498901367187500); /** \brief PeptideIon enum defines all types of ions (Nter or Cter) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/utils.cpp libpappsomspp-0.8.58/src/pappsomspp/utils.cpp --- libpappsomspp-0.8.15/src/pappsomspp/utils.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/utils.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -80,22 +80,37 @@ int Utils::zeroDecimalsInValue(pappso_double value) { + //qDebug() << qSetRealNumberPrecision(10) << "Double value: " << value; + int intPart = static_cast(value); + //qDebug() << "int part:" << intPart; + double decimalPart = value - intPart; - int count = -1; + //qDebug() << qSetRealNumberPrecision(10) << "decimal part: " << decimalPart; + + int count = 0; - while(1) + while(decimalPart > 0) { ++count; decimalPart *= 10; - if(decimalPart > 1) - return count; + //qDebug() << "Iteration " << count << "decimal part:" << decimalPart; + + if(decimalPart >= 1) + { + //qDebug() << "Because decimal part " << decimalPart + //<< "is >= 1, breaking loop while count is " << count << "."; + + break; + } } + //qDebug() << "Returning count:" << count; + return count; } @@ -111,6 +126,18 @@ } +long long int +Utils::roundToDecimal32bitsAsLongLongInt(pappso::pappso_double input) +{ + pappso::pappso_double test_decimal = 100000000000; + if(sizeof(int *) == 4) + { // 32bits + test_decimal = 100000000; + } + return (floor(input * test_decimal)); +} + + std::string Utils::toUtf8StandardString(const QString &text) { @@ -275,6 +302,13 @@ } +double +Utils::nearestGreater(double value) +{ + return std::nextafter(value, value + 1); +} + + QString Utils::chronoTimePointDebugString( const QString &msg, std::chrono::system_clock::time_point chrono_time) @@ -325,7 +359,7 @@ { QStringList string_list = - text.split(QRegularExpression("[\\s]+"), QString::SkipEmptyParts); + text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts); // qDebug() << "string list:" << string_list; @@ -359,7 +393,7 @@ // qDebug() << "Parsing text:" << text; QStringList string_list = - text.split(QRegularExpression("[\\s]+"), QString::SkipEmptyParts); + text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts); // qDebug() << "string list size:" << string_list.size() //<< "values:" << string_list; @@ -385,6 +419,12 @@ return sizet_vector; } - +QString +Utils::booleanToString(bool value) +{ + if(value) + return "TRUE"; + return "FALSE"; +} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/utils.h libpappsomspp-0.8.58/src/pappsomspp/utils.h --- libpappsomspp-0.8.15/src/pappsomspp/utils.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/utils.h 2022-10-27 09:16:15.000000000 +0000 @@ -66,6 +66,8 @@ static int zeroDecimalsInValue(pappso_double value); static pappso_double roundToDecimals(pappso_double value, int decimal_places); + static long long int + roundToDecimal32bitsAsLongLongInt(pappso::pappso_double input); static std::string toUtf8StandardString(const QString &text); @@ -78,6 +80,8 @@ static bool almostEqual(double value1, double value2, int decimalPlaces = 10); + static double nearestGreater(double value); + static QString chronoTimePointDebugString(const QString &msg, std::chrono::system_clock::time_point chrono_time = @@ -96,6 +100,12 @@ static std::vector splitSizetStringToSizetVectorWithSpaces(const QString &text, std::size_t &error_count); + + /** @brief convenient function to transform a boolean to QString "TRUE" or + * "FALSE" QString returned is readable by R + * @return QString "TRUE" or "FALSE" + */ + static QString booleanToString(bool value); }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -127,17 +127,19 @@ if(m_mzCalibrationArr[3] != 0) { X.push_back(m_mzCalibrationArr[3]); - qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3]; + // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3]; } else { - qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3]; + // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3]; } - qDebug() << "polynom_array :"; + // qDebug() << "polynom_array :"; + /* for(double arg : X) { qDebug() << arg; } + */ alglib::real_1d_array polynom_array; try { @@ -177,7 +179,8 @@ // PolynomialSolve: A[N]=0 throw pappso::PappsoException( - QObject::tr("ERROR in alglib::polynomialsolve :\n%1") + QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex, " + "alglib::polynomialsolve :\n%1") .arg(error.msg.c_str())); } @@ -186,19 +189,21 @@ if(m.length() == 0) { - throw pappso::PappsoException( - QObject::tr("ERROR in TimsFrame::getMzFromTof m.size() == 0")); + throw pappso::PappsoException(QObject::tr( + "ERROR in MzCalibrationModel1::getMzFromTofIndex m.size() == 0")); } // qDebug(); if(m[0].y != 0) { throw pappso::PappsoException( - QObject::tr("ERROR in TimsFrame::getMzFromTof m[0].y!= 0")); + QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex m[0].y!= " + "0 for tof index=%1") + .arg(tof_index)); } - qDebug() << "m.length()=" << m.length(); - qDebug() << "m1=" << pow(m[0].x, 2); - qDebug() << "m2=" << pow(m[1].x, 2); + // qDebug() << "m.length()=" << m.length(); + // qDebug() << "m1=" << pow(m[0].x, 2); + // qDebug() << "m2=" << pow(m[1].x, 2); return (pow(m[0].x, 2) - m_mzCalibrationArr[4]); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -47,7 +47,7 @@ double T2_frame, const QSqlRecord &mz_calibration_record) { - qDebug(); + //qDebug(); MzCalibrationInterfaceSPtr msp_mzCalibration = nullptr; QString mz_calibration_key = @@ -61,14 +61,14 @@ auto itmap = m_mapMzCalibrationSPtr.find(mz_calibration_key); if(itmap != m_mapMzCalibrationSPtr.end()) { - qDebug() << mz_calibration_key << " calibration object found"; + //qDebug() << mz_calibration_key << " calibration object found"; msp_mzCalibration = itmap->second; } else { if(mz_calibration_record.value("ModelType").toInt() == 1) { - msp_mzCalibration = std::make_shared( + msp_mzCalibration = std::make_shared( T1_frame, T2_frame, mz_calibration_record.value("DigitizerTimebase") @@ -87,7 +87,7 @@ } else { - qDebug(); + //qDebug(); throw PappsoException( QObject::tr( "ERROR in MzCalibrationStore::getInstance : MzCalibration " @@ -102,12 +102,12 @@ if(msp_mzCalibration == nullptr) { - qDebug(); + //qDebug(); throw PappsoException(QObject::tr( "ERROR in MzCalibrationStore::getInstance MzCalibration is NULL")); } - qDebug(); + //qDebug(); return (msp_mzCalibration); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsbindec.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsbindec.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsbindec.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsbindec.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -27,18 +27,23 @@ #include "timsbindec.h" #include "../../../pappsomspp/pappsoexception.h" +#include "../../../pappsomspp/exception/exceptionnotimplemented.h" +#include "timsframetype1.h" #include +#include #include +#include "timsframerawdatachunck.h" +#include "timsdata.h" using namespace pappso; TimsBinDec::TimsBinDec(const QFileInfo &timsBinFile, int timsCompressionType) : m_timsBinFile(timsBinFile.absoluteFilePath()) { - - if(timsCompressionType != 2) + m_timsCompressionType = timsCompressionType; + if((timsCompressionType != 1) && (timsCompressionType != 2)) { - throw pappso::PappsoException( + throw pappso::ExceptionNotImplemented( QObject::tr("compression type %1 not handled by this library") .arg(timsCompressionType)); } @@ -64,210 +69,286 @@ TimsBinDec::~TimsBinDec() { -} + if(mpa_decompressMemoryBuffer != nullptr) + { + delete[] mpa_decompressMemoryBuffer; + } + + if(mp_fileLinear != nullptr) + { + mp_fileLinear->close(); + delete mp_fileLinear; + } + if(mp_fileRandom != nullptr) + { + mp_fileRandom->close(); + delete mp_fileRandom; + } +} + void -TimsBinDec::indexingFile() +pappso::TimsBinDec::closeLinearRead() +{ + qDebug(); + if(mp_fileLinear != nullptr) + { + mp_fileLinear->close(); + delete mp_fileLinear; + } + mp_fileLinear = nullptr; + m_firstFrameId = 0; + m_lastFrameId = 0; + m_linearAccessRawDataChunckList.resize(0); + qDebug(); +} + + +QFile * +TimsBinDec::getQfileLinear( + std::size_t frameId, + const std::vector &frame_record_list) { + if(mp_fileLinear == nullptr) + { + mp_fileLinear = new QFile(m_timsBinFile); + if(!mp_fileLinear->open(QIODevice::ReadOnly)) + { + throw PappsoException( + QObject::tr("ERROR opening TIMS binary file %1 for read") + .arg(m_timsBinFile)); + } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; - QFile file(m_timsBinFile); - QDataStream bin_in(&file); - bin_in.setByteOrder(QDataStream::ByteOrder::LittleEndian); - // m_indexArray.push_back(0); - - // QChar first_char; - // txt_in >> first_char; - quint32 number_in; - qint64 position(0); - qint8 trash; - while(!bin_in.atEnd()) - { - while((!bin_in.atEnd()) && (position % 4 != 0)) - { - bin_in >> trash; - position += 1; - if(trash != 0) - { /* - throw PappsoException( - QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " - "trash%3 != 0") - .arg(m_indexArray.size()) - .arg(m_timsBinFile.fileName()) - .arg(trash));*/ - } - } - quint32 frame_len(0); - while((!bin_in.atEnd()) && (frame_len == 0)) - { - bin_in >> frame_len; - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " i=" << i; - position += 4; - } - - // m_indexArray.push_back(position - 4); - /* - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " frame_len=" << frame_len - << " frameid=" << m_indexArray.size() - 1 - << " back=" << m_indexArray.back() << " position=" << - position; - - - quint64 next_frame = m_indexArray.back() + frame_len; - */ - - bin_in >> number_in; - position += 4; - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " number_in(nb scans)=" << number_in - << " position=" << position; - ; - /* - - while((!bin_in.atEnd()) && (position < next_frame)) - { - bin_in >> trash; - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << - __LINE__ - // << " i=" << i; - position += 1; - }*/ + startLinearRead( + frameId, m_linearAccessRawDataChunckDequeSize, frame_record_list); + } + + return mp_fileLinear; +} + +QFile * +pappso::TimsBinDec::getQfileRandom() +{ + if(mp_fileRandom == nullptr) + { + mp_fileRandom = new QFile(m_timsBinFile); + if(!mp_fileRandom->open(QIODevice::ReadOnly)) + { + throw PappsoException( + QObject::tr("ERROR opening TIMS binary file %1 for read") + .arg(m_timsBinFile)); + } } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + return mp_fileRandom; } TimsFrameSPtr -TimsBinDec::getTimsFrameSPtrByOffset(std::size_t timsId, - std::size_t timsOffset) const +TimsBinDec::getTimsFrameSPtrByOffset( + std::size_t frameId, + const std::vector &frame_record_list) { - qDebug() << "timsId:" << timsId << "timsOffset:" << timsOffset; + + qDebug() << "frameId:" << frameId; // QMutexLocker locker(&m_mutex); - QFile file(m_timsBinFile); - if(!file.open(QIODevice::ReadOnly)) + QFile *p_file = getQfileLinear(frameId, frame_record_list); + + if(mp_fileLinear->pos() < + (qint64)frame_record_list[m_firstFrameId].tims_offset) { - throw PappsoException( - QObject::tr("ERROR opening TIMS binary file %1 for read") - .arg(m_timsBinFile)); } + else + { + if(frameId > m_lastFrameId) + { + if(frameId - m_lastFrameId < m_linearForwardThreshold) + { + // move forward + moveLinearReadForward(frame_record_list); + } + } + } + + auto it = std::find_if(m_linearAccessRawDataChunckList.begin(), + m_linearAccessRawDataChunckList.end(), + [frameId](const TimsFrameRawDataChunck &chunck) { + if(chunck.getFrameId() == frameId) + return true; + return false; + }); + if(it != m_linearAccessRawDataChunckList.end()) + { + try + { + return getTimsFrameFromRawDataChunck(*it); + } + catch(PappsoException &error) + { - bool seekpos_ok = file.seek(timsOffset); + throw PappsoException( + QObject::tr("ERROR reading TIMS binary file %1 with linear QFile: " + "%2") + .arg(m_timsBinFile) + .arg(error.qwhat())); + } + } + + // random access file + qDebug(); + p_file = getQfileRandom(); + bool seekpos_ok = p_file->seek(frame_record_list[frameId].tims_offset); if(!seekpos_ok) { throw PappsoException( QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " "m_timsBinFile.seek(%3) failed") - .arg(timsId) + .arg(frameId) .arg(m_timsBinFile) - .arg(timsOffset)); + .arg(frame_record_list[frameId].tims_offset)); } - quint32 frame_length; - file.read((char *)&frame_length, 4); - // frame_length = qToBigEndian(frame_length); - - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " frame_length=" << frame_length; - - quint32 scan_number; - file.read((char *)&scan_number, 4); - // scan_number = qToBigEndian(scan_number); - frame_length -= 8; - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " pos=" << m_timsBinFile.pos(); + try + { + m_randemAccessFrameRawDataChunck.readTimsFrame( + p_file, frameId, frame_record_list); + } + catch(PappsoException &error) + { - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " scan_number=" << scan_number; - // m_timsBinFile.seek(m_indexArray.at(timsId) + 8); + throw PappsoException( + QObject::tr("ERROR reading TIMS binary file %1 with random QFile: " + "%2") + .arg(m_timsBinFile) + .arg(error.qwhat())); + } + return getTimsFrameFromRawDataChunck(m_randemAccessFrameRawDataChunck); +} +void +pappso::TimsBinDec::moveLinearReadForward( + const std::vector &frame_record_list) +{ qDebug(); - - QByteArray frame_byte_array = file.read((qint64)frame_length + 2); - - file.close(); - - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " +frame_length-1=" - // << (quint8) * (frame_byte_array.constData() + frame_length - 1); - // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - // << " +frame_length=" - // << (quint8) * (frame_byte_array.constData() + frame_length); - // m_timsBinFile.seek(m_indexArray.at(timsId) + 8); - - if(frame_byte_array.size() - 2 != (qint64)frame_length) + for(std::size_t i = 0; i < m_linearForwardThreshold; i++) { - throw PappsoException( - QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " - "frame_byte_array.size()%3 != %4frame_length") - .arg(timsId) - .arg(m_timsBinFile) - .arg(frame_byte_array.size()) - .arg(frame_length)); + auto it = std::min_element( + m_linearAccessRawDataChunckList.begin(), + m_linearAccessRawDataChunckList.end(), + [](const TimsFrameRawDataChunck &a, const TimsFrameRawDataChunck &b) { + return a.getFrameId() < b.getFrameId(); + }); + m_lastFrameId++; + m_firstFrameId++; + if(m_lastFrameId >= frame_record_list.size()) + break; + it->readTimsFrame(mp_fileLinear, m_lastFrameId, frame_record_list); } + qDebug(); +} + + +TimsFrameSPtr +TimsBinDec::getTimsFrameFromRawDataChunck( + const TimsFrameRawDataChunck &raw_data_chunck) +{ + qDebug(); TimsFrameSPtr frame_sptr; - if(frame_length > 0) + if(raw_data_chunck.getCompressedSize() > 0) { - auto decompressed_size2 = - ZSTD_getFrameContentSize(frame_byte_array.constData(), frame_length); - - if(decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN) + qDebug(); + if(m_timsCompressionType == 2) { - throw PappsoException( - QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " - " decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN, " - "frame_length=%3") - .arg(timsId) - .arg(m_timsBinFile) - .arg(frame_length)); - } + auto decompressed_size2 = + ZSTD_getFrameContentSize(raw_data_chunck.getMemoryBuffer(), + raw_data_chunck.getCompressedSize()); + qDebug(); + if(decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN) + { + throw PappsoException( + QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck " + "reading TIMS frame %1 TIMS binary file %2: " + " decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN, " + "frame_length=%3") + .arg(raw_data_chunck.getFrameId()) + .arg(m_timsBinFile) + .arg(raw_data_chunck.getFrameLength())); + } + qDebug(); + if(decompressed_size2 == ZSTD_CONTENTSIZE_ERROR) + { + qDebug(); + throw PappsoException( + QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck " + "reading TIMS frame %1 TIMS binary file %2: " + " decompressed_size2 == ZSTD_CONTENTSIZE_ERROR, " + "frame_length=%3") + .arg(raw_data_chunck.getFrameId()) + .arg(m_timsBinFile) + .arg(raw_data_chunck.getFrameLength())); + } + qDebug() << " decompressed_size2=" << decompressed_size2; - if(decompressed_size2 == ZSTD_CONTENTSIZE_ERROR) - { - throw PappsoException( - QObject::tr( - "ERROR reading TIMS frame %1 TIMS binary file %2: " - " decompressed_size2 == ZSTD_CONTENTSIZE_ERROR, frame_length=%3") - .arg(timsId) - .arg(m_timsBinFile) - .arg(frame_length)); - } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " decompressed_size2=" << decompressed_size2; + if(m_decompressMemoryBufferSize < (decompressed_size2 + 10)) + { + if(mpa_decompressMemoryBuffer != nullptr) + { + delete[] mpa_decompressMemoryBuffer; + } + m_decompressMemoryBufferSize = decompressed_size2 + 10; + mpa_decompressMemoryBuffer = + new char[m_decompressMemoryBufferSize]; + } + std::size_t decompressed_size = + ZSTD_decompress(mpa_decompressMemoryBuffer, + m_decompressMemoryBufferSize, + raw_data_chunck.getMemoryBuffer(), + raw_data_chunck.getCompressedSize()); + qDebug(); + + if(decompressed_size != decompressed_size2) + { + throw PappsoException( + QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck " + "reading TIMS frame %1 TIMS binary file %2: " + "decompressed_size != decompressed_size2") + .arg(raw_data_chunck.getFrameId()) + .arg(m_timsBinFile) + .arg(decompressed_size) + .arg(decompressed_size2)); + } - char *uncompress = new char[decompressed_size2 + 10]; - std::size_t decompressed_size = - ZSTD_decompress(uncompress, - decompressed_size2 + 10, - frame_byte_array.constData(), - frame_length); - qDebug(); + qDebug(); - if(decompressed_size != decompressed_size2) - { - throw PappsoException( - QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " - "decompressed_size != decompressed_size2") - .arg(timsId) - .arg(m_timsBinFile) - .arg(decompressed_size) - .arg(decompressed_size2)); + frame_sptr = + std::make_shared(raw_data_chunck.getFrameId(), + raw_data_chunck.getFrameNumberOfScans(), + mpa_decompressMemoryBuffer, + decompressed_size); } + else + { - qDebug(); - - frame_sptr = std::make_shared( - timsId, scan_number, uncompress, decompressed_size); - - delete[] uncompress; + if(m_timsCompressionType == 1) + { + frame_sptr = std::make_shared( + raw_data_chunck.getFrameId(), + raw_data_chunck.getFrameNumberOfScans(), + raw_data_chunck.getMemoryBuffer(), + raw_data_chunck.getCompressedSize()); + } + } + // delete[] mpa_decompressMemoryBuffer; } else { - frame_sptr = std::make_shared(timsId, scan_number, nullptr, 0); + frame_sptr = + std::make_shared(raw_data_chunck.getFrameId(), + raw_data_chunck.getFrameNumberOfScans(), + nullptr, + 0); } return frame_sptr; } @@ -278,3 +359,59 @@ return getTimsFrameCstSPtrByOffset(timsId, m_indexArray[timsId]); } */ + +void +pappso::TimsBinDec::startLinearRead( + std::size_t start_frame_id, + std::size_t chunk_deque_size, + const std::vector &frame_record_list) +{ + qDebug(); + m_linearAccessRawDataChunckList.resize(chunk_deque_size); + m_firstFrameId = start_frame_id; + m_lastFrameId = start_frame_id; + + QFile *p_file = mp_fileLinear; + if(p_file == nullptr) + { + throw PappsoException(QObject::tr("ERROR mp_fileLinear == nullptr")); + } + + bool seekpos_ok = p_file->seek(frame_record_list[start_frame_id].tims_offset); + if(!seekpos_ok) + { + throw PappsoException( + QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: " + "m_timsBinFile.seek(%3) failed") + .arg(start_frame_id) + .arg(m_timsBinFile) + .arg(frame_record_list[start_frame_id].tims_offset)); + } + + try + { + for(TimsFrameRawDataChunck &chunck : m_linearAccessRawDataChunckList) + { + + chunck.readTimsFrame(p_file, start_frame_id, frame_record_list); + m_lastFrameId = start_frame_id; + start_frame_id++; + } + } + catch(PappsoException &error) + { + + throw PappsoException( + QObject::tr( + "ERROR in TimsBinDec::startLinearRead reading TIMS binary file %1:\n " + " start_frame_id=%2 m_firstFrameId=%3 m_lastFrameId=%4 " + "%5") + .arg(m_timsBinFile) + .arg(start_frame_id) + .arg(m_firstFrameId) + .arg(m_lastFrameId) + .arg(error.qwhat())); + } + + qDebug(); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsbindec.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsbindec.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsbindec.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsbindec.h 2022-10-27 09:16:15.000000000 +0000 @@ -29,7 +29,11 @@ #include #include +#include "timsframerecord.h" #include "timsframe.h" +#include "timsframerawdatachunck.h" +#include + namespace pappso { @@ -55,19 +59,60 @@ /** * Destructor */ - ~TimsBinDec(); + virtual ~TimsBinDec(); // TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId); - TimsFrameSPtr getTimsFrameSPtrByOffset(std::size_t timsId, - std::size_t timsOffset) const; + TimsFrameSPtr getTimsFrameSPtrByOffset( + std::size_t frameId, + const std::vector &frame_record_list); + + /** @brief close file access and flush cache + */ + void closeLinearRead(); + private: - void indexingFile(); + /** @brief open one QFile handler for linear read + */ + QFile * + getQfileLinear(std::size_t frameId, + const std::vector &frame_record_list); + /** @brief open one QFile handler for random read + */ + QFile *getQfileRandom(); + /** @brief populate a fifo buffer with TimsFrameRawDataChunck + * accelerates inputs from file + */ + void startLinearRead( + std::size_t start_frame_id, + std::size_t chunk_deque_size, + const std::vector &frame_record_list); + + + TimsFrameSPtr + getTimsFrameFromRawDataChunck(const TimsFrameRawDataChunck &raw_data_chunck); + + void moveLinearReadForward( + const std::vector &frame_record_list); private: + int m_timsCompressionType; QString m_timsBinFile; + QFile *mp_fileLinear = nullptr; + QFile *mp_fileRandom = nullptr; // QMutex m_mutex; // std::vector m_indexArray; + char *mpa_decompressMemoryBuffer = nullptr; + std::size_t m_decompressMemoryBufferSize = 0; + + TimsFrameRawDataChunck m_randemAccessFrameRawDataChunck; + + + std::vector m_linearAccessRawDataChunckList; + std::size_t m_firstFrameId = 0; + std::size_t m_lastFrameId = 0; + std::size_t m_linearAccessRawDataChunckDequeSize = 100; + std::size_t m_linearForwardThreshold = 30; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsdata.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsdata.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsdata.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsdata.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -27,10 +27,11 @@ #include "timsdata.h" #include "../../exception/exceptionnotfound.h" +#include "../../exception/exceptioninterrupted.h" #include "../../processing/combiners/tracepluscombiner.h" #include "../../processing/filters/filtertriangle.h" -#include "../../processing/filters/filterpseudocentroid.h" #include "../../processing/filters/filterpass.h" +#include "../../processing/filters/filtersuitestring.h" #include "./xicextractor/timsdirectxicextractor.h" #include #include @@ -40,14 +41,16 @@ #include #include #include +#include -using namespace pappso; +namespace pappso +{ TimsData::TimsData(QDir timsDataDirectory) : m_timsDataDirectory(timsDataDirectory) { - qDebug(); + qDebug() << "Start of construction of TimsData"; mpa_mzCalibrationStore = new MzCalibrationStore(); if(!m_timsDataDirectory.exists()) { @@ -95,10 +98,29 @@ QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf_bin")), compression_type); + qDebug(); // get number of precursors + m_totalNumberOfPrecursors = 0; if(!q.exec("SELECT COUNT( DISTINCT Id) FROM Precursors;")) { + m_hasPrecursorTable = false; + } + else + { + m_hasPrecursorTable = true; + if(q.next()) + { + m_totalNumberOfPrecursors = q.value(0).toLongLong(); + } + } + + + fillFrameIdDescrList(); + + // get number of scans + if(!q.exec("SELECT SUM(NumScans),COUNT(Id) FROM Frames")) + { qDebug(); throw PappsoException( QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " @@ -111,12 +133,33 @@ } if(q.next()) { - m_totalNumberOfPrecursors = q.value(0).toLongLong(); + m_totalNumberOfScans = q.value(0).toLongLong(); + m_totalNumberOfFrames = q.value(1).toLongLong(); } + if(!q.exec("select * from MzCalibration;")) + { + qDebug(); + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(q.lastQuery()) + .arg(q.lastError().databaseText()) + .arg(q.lastError().driverText()) + .arg(q.lastError().nativeErrorCode())); + } - // get number of scans - if(!q.exec("SELECT SUM(NumScans) FROM Frames")) + while(q.next()) + { + QSqlRecord record = q.record(); + m_mapMzCalibrationRecord.insert( + std::pair(record.value(0).toInt(), record)); + } + + // m_mapTimsCalibrationRecord + + if(!q.exec("select * from TimsCalibration;")) { qDebug(); throw PappsoException( @@ -124,16 +167,25 @@ "command %2:\n%3\n%4\n%5") .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); + .arg(q.lastError().databaseText()) + .arg(q.lastError().driverText()) + .arg(q.lastError().nativeErrorCode())); } - if(q.next()) + while(q.next()) { - m_totalNumberOfScans = q.value(0).toLongLong(); + QSqlRecord record = q.record(); + m_mapTimsCalibrationRecord.insert( + std::pair(record.value(0).toInt(), record)); } - if(!q.exec("select * from MzCalibration;")) + + // store frames + if(!q.exec("select Frames.TimsId, Frames.AccumulationTime, " // 1 + "Frames.MzCalibration, " // 2 + "Frames.T1, Frames.T2, " // 4 + "Frames.Time, Frames.MsMsType, Frames.TimsCalibration, " // 7 + "Frames.Id " // 8 + " FROM Frames;")) { qDebug(); throw PappsoException( @@ -146,22 +198,38 @@ .arg(q.lastError().nativeErrorCode())); } + m_mapFramesRecord.resize(m_totalNumberOfFrames + 1); while(q.next()) { QSqlRecord record = q.record(); - m_mapMzCalibrationRecord.insert( - std::pair(record.value(0).toInt(), record)); + TimsFrameRecord &frame_record = + m_mapFramesRecord[record.value(8).toULongLong()]; + + frame_record.tims_offset = record.value(0).toULongLong(); + frame_record.accumulation_time = record.value(1).toDouble(); + frame_record.mz_calibration_id = record.value(2).toULongLong(); + frame_record.frame_t1 = record.value(3).toDouble(); + frame_record.frame_t2 = record.value(4).toDouble(); + frame_record.frame_time = record.value(5).toDouble(); + frame_record.msms_type = record.value(6).toInt(); + frame_record.tims_calibration_id = record.value(7).toULongLong(); } - std::shared_ptr ms2filter = - std::make_shared(35000, 5, 0.5, 0.1); - mcsp_ms2Filter = ms2filter; + mcsp_ms2Filter = std::make_shared( + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"); std::shared_ptr ms1filter = std::make_shared(); ms1filter.get()->setTriangleSlope(50, 0.01); mcsp_ms1Filter = ms1filter; + qDebug(); +} + +void +TimsData::setMonoThread(bool is_mono_thread) +{ + m_isMonoThread = is_mono_thread; } QSqlDatabase @@ -207,6 +275,10 @@ { delete mpa_timsBinDec; } + if(mpa_mzCalibrationStore != nullptr) + { + delete mpa_mzCalibrationStore; + } } void @@ -221,10 +293,10 @@ return m_builtinMs2Centroid; } -std::pair -TimsData::getScanCoordinateFromRawIndex(std::size_t raw_index) const +void +TimsData::fillFrameIdDescrList() { - + qDebug(); QSqlDatabase qdb = openDatabaseConnection(); QSqlQuery q = @@ -242,23 +314,59 @@ .arg(qdb.lastError().driverText()) .arg(qdb.lastError().nativeErrorCode())); } - pappso::TimsFrameSPtr tims_frame; + TimsFrameSPtr tims_frame; bool index_found = false; std::size_t timsId; + /** @brief number of scans in mobility dimension (number of TOF scans) + */ std::size_t numberScans; - std::size_t offset = 0; + std::size_t cumulScans = 0; while(q.next() && (!index_found)) { - timsId = q.value(0).toUInt(); - numberScans = q.value(1).toUInt(); + timsId = q.value(0).toULongLong(); + numberScans = q.value(1).toULongLong(); + + // qDebug() << timsId; + + m_thousandIndexToFrameIdDescrListIndex.insert( + std::pair((cumulScans / 1000), + m_frameIdDescrList.size())); + + m_frameIdDescrList.push_back({timsId, numberScans, cumulScans}); + cumulScans += numberScans; + } + qDebug(); +} + +std::pair +TimsData::getScanCoordinateFromRawIndex(std::size_t raw_index) const +{ + + std::size_t fast_access = raw_index / 1000; + qDebug() << " fast_access=" << fast_access; + auto map_it = m_thousandIndexToFrameIdDescrListIndex.find(fast_access); + if(map_it == m_thousandIndexToFrameIdDescrListIndex.end()) + { + throw ExceptionNotFound( + QObject::tr("ERROR raw index %1 not found (fast_access)") + .arg(raw_index)); + } + std::size_t start_point_index = map_it->second; + while((start_point_index > 0) && + (m_frameIdDescrList[start_point_index].m_cumulSize > raw_index)) + { + start_point_index--; + } + for(std::size_t i = start_point_index; i < m_frameIdDescrList.size(); i++) + { - if(raw_index < (offset + numberScans)) + if(raw_index < + (m_frameIdDescrList[i].m_cumulSize + m_frameIdDescrList[i].m_size)) { - return std::pair(timsId, - raw_index - offset); + return std::pair( + m_frameIdDescrList[i].m_frameId, + raw_index - m_frameIdDescrList[i].m_cumulSize); } - - offset += numberScans; } throw ExceptionNotFound( @@ -271,38 +379,12 @@ std::size_t scan_num) const { - - QSqlDatabase qdb = openDatabaseConnection(); - QSqlQuery q = - qdb.exec(QString("SELECT Id, NumScans FROM " - "Frames ORDER BY Id")); - if(q.lastError().isValid()) - { - - throw PappsoException( - QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " - "command %2:\n%3\n%4\n%5") - .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) - .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); - } - bool index_found = false; - std::size_t timsId; - std::size_t numberScans; - std::size_t offset = 0; - while(q.next() && (!index_found)) + for(auto frameDescr : m_frameIdDescrList) { - timsId = q.value(0).toUInt(); - numberScans = q.value(1).toUInt(); - - if(timsId == frame_id) + if(frameDescr.m_frameId == frame_id) { - return offset + scan_num; + return frameDescr.m_cumulSize + scan_num; } - - offset += numberScans; } throw ExceptionNotFound( @@ -319,93 +401,93 @@ TimsData::getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index) { - auto coordinate = getScanCoordinateFromRawIndex(raw_index); - return getMassSpectrumCstSPtr(coordinate.first, coordinate.second); + qDebug() << " raw_index=" << raw_index; + try + { + auto coordinate = getScanCoordinateFromRawIndex(raw_index); + return getMassSpectrumCstSPtr(coordinate.first, coordinate.second); + } + catch(PappsoException &error) + { + throw PappsoException( + QObject::tr("Error TimsData::getMassSpectrumCstSPtrByRawIndex " + "raw_index=%1 :\n%2") + .arg(raw_index) + .arg(error.qwhat())); + } } TimsFrameBaseCstSPtr -TimsData::getTimsFrameBaseCstSPtr(std::size_t timsId) const +TimsData::getTimsFrameBaseCstSPtr(std::size_t timsId) { qDebug() << " timsId=" << timsId; - QSqlDatabase qdb = openDatabaseConnection(); - QSqlQuery q = qdb.exec( - QString("SELECT Frames.TimsId, Frames.AccumulationTime, " // 1 - "Frames.MzCalibration, " // 2 - "Frames.T1, Frames.T2, " // 4 - "Frames.Time, Frames.MsMsType, TimsCalibration.ModelType, " // 7 - "TimsCalibration.C0, TimsCalibration.C1, TimsCalibration.C2, " // 10 - "TimsCalibration.C3, TimsCalibration.C4, TimsCalibration.C5, " // 13 - "TimsCalibration.C6, TimsCalibration.C7, TimsCalibration.C8, " // 16 - "TimsCalibration.C9 FROM Frames" // 17 - " INNER JOIN TimsCalibration " - "ON Frames.TimsCalibration=TimsCalibration.Id where " - "Frames.Id=%1;") - .arg(timsId)); - if(q.lastError().isValid()) + const TimsFrameRecord &frame_record = m_mapFramesRecord[timsId]; + if(timsId > m_totalNumberOfScans) { - - throw PappsoException( - QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, " - "executing SQL " - "command %3:\n%4\n%5\n%6") - .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) - .arg(qdb.databaseName()) - .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); + throw ExceptionNotFound( + QObject::tr("ERROR Frames database id %1 not found").arg(timsId)); } - pappso::TimsFrameBaseSPtr tims_frame; - if(q.next()) - { + TimsFrameBaseSPtr tims_frame; - tims_frame = std::make_shared( - TimsFrameBase(timsId, q.value(0).toUInt())); + tims_frame = std::make_shared( + TimsFrameBase(timsId, frame_record.tims_offset)); - auto it_map_record = m_mapMzCalibrationRecord.find(q.value(2).toInt()); - if(it_map_record != m_mapMzCalibrationRecord.end()) - { - - double T1_frame = q.value(3).toDouble(); // Frames.T1 - double T2_frame = q.value(4).toDouble(); // Frames.T2 - - - tims_frame.get()->setMzCalibrationInterfaceSPtr( - mpa_mzCalibrationStore->getInstance( - T1_frame, T2_frame, it_map_record->second)); - } - else - { - throw ExceptionNotFound( - QObject::tr("ERROR MzCalibration database id %1 not found") - .arg(q.value(2).toInt())); - } + auto it_map_record = + m_mapMzCalibrationRecord.find(frame_record.mz_calibration_id); + if(it_map_record != m_mapMzCalibrationRecord.end()) + { - tims_frame.get()->setAccumulationTime(q.value(1).toDouble()); + double T1_frame = frame_record.frame_t1; // Frames.T1 + double T2_frame = frame_record.frame_t2; // Frames.T2 - tims_frame.get()->setTime(q.value(5).toDouble()); - tims_frame.get()->setMsMsType(q.value(6).toUInt()); - tims_frame.get()->setTimsCalibration(q.value(7).toInt(), - q.value(8).toDouble(), - q.value(9).toDouble(), - q.value(10).toDouble(), - q.value(11).toDouble(), - q.value(12).toDouble(), - q.value(13).toDouble(), - q.value(14).toDouble(), - q.value(15).toDouble(), - q.value(16).toDouble(), - q.value(17).toDouble()); - return tims_frame; + tims_frame.get()->setMzCalibrationInterfaceSPtr( + mpa_mzCalibrationStore->getInstance( + T1_frame, T2_frame, it_map_record->second)); + } + else + { + throw ExceptionNotFound( + QObject::tr("ERROR MzCalibration database id %1 not found") + .arg(frame_record.mz_calibration_id)); + } + + tims_frame.get()->setAccumulationTime(frame_record.accumulation_time); + + tims_frame.get()->setTime(frame_record.frame_time); + tims_frame.get()->setMsMsType(frame_record.msms_type); + + + auto it_map_record_tims_calibration = + m_mapTimsCalibrationRecord.find(frame_record.tims_calibration_id); + if(it_map_record_tims_calibration != m_mapTimsCalibrationRecord.end()) + { + + tims_frame.get()->setTimsCalibration( + it_map_record_tims_calibration->second.value(1).toInt(), + it_map_record_tims_calibration->second.value(2).toDouble(), + it_map_record_tims_calibration->second.value(3).toDouble(), + it_map_record_tims_calibration->second.value(4).toDouble(), + it_map_record_tims_calibration->second.value(5).toDouble(), + it_map_record_tims_calibration->second.value(6).toDouble(), + it_map_record_tims_calibration->second.value(7).toDouble(), + it_map_record_tims_calibration->second.value(8).toDouble(), + it_map_record_tims_calibration->second.value(9).toDouble(), + it_map_record_tims_calibration->second.value(10).toDouble(), + it_map_record_tims_calibration->second.value(11).toDouble()); + } + else + { + throw ExceptionNotFound( + QObject::tr("ERROR TimsCalibration database id %1 not found") + .arg(frame_record.tims_calibration_id)); } - throw ExceptionNotFound(QObject::tr("ERROR timsId %1 not found").arg(timsId)); - // return TimsFrameCstSPtr; + return tims_frame; } std::vector @@ -413,11 +495,13 @@ { qDebug() << " rt_begin=" << rt_begin << " rt_end=" << rt_end; + if(rt_begin < 0) + rt_begin = 0; std::vector tims_frameid_list; QSqlDatabase qdb = openDatabaseConnection(); - QSqlQuery q = qdb.exec(QString("SELECT Frames.TimsId FROM Frames WHERE " - "Frames.MsMsType=0 AND (Frames.Time=>%1) AND " - "(Frames.Time<=%2) SORT BY Frames.Time;") + QSqlQuery q = qdb.exec(QString("SELECT Frames.Id FROM Frames WHERE " + "Frames.MsMsType=0 AND (Frames.Time>=%1) AND " + "(Frames.Time<=%2) ORDER BY Frames.Time;") .arg(rt_begin) .arg(rt_end)); if(q.lastError().isValid()) @@ -437,100 +521,101 @@ while(q.next()) { - tims_frameid_list.push_back(q.value(0).toUInt()); + tims_frameid_list.push_back(q.value(0).toULongLong()); } return tims_frameid_list; } TimsFrameCstSPtr -TimsData::getTimsFrameCstSPtr(std::size_t timsId) const +TimsData::getTimsFrameCstSPtr(std::size_t timsId) { - qDebug() << " timsId=" << timsId; + qDebug() << " timsId=" << timsId + << " m_mapFramesRecord.size()=" << m_mapFramesRecord.size(); - QSqlDatabase qdb = openDatabaseConnection(); - QSqlQuery q = qdb.exec( - QString("SELECT Frames.TimsId, Frames.AccumulationTime, " // 1 - "Frames.MzCalibration, " // 2 - "Frames.T1, Frames.T2, " // 4 - "Frames.Time, Frames.MsMsType, TimsCalibration.ModelType, " // 7 - "TimsCalibration.C0, TimsCalibration.C1, TimsCalibration.C2, " // 10 - "TimsCalibration.C3, TimsCalibration.C4, TimsCalibration.C5, " // 13 - "TimsCalibration.C6, TimsCalibration.C7, TimsCalibration.C8, " // 16 - "TimsCalibration.C9 FROM Frames" // 17 - " INNER JOIN TimsCalibration " - "ON Frames.TimsCalibration=TimsCalibration.Id where " - "Frames.Id=%1;") - .arg(timsId)); - if(q.lastError().isValid()) - { + /* + for(auto pair_i : m_mapFramesRecord) + { - throw PappsoException( - QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, " - "executing SQL " - "command %3:\n%4\n%5\n%6") - .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) - .arg(qdb.databaseName()) - .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); - } - pappso::TimsFrameSPtr tims_frame; - if(q.next()) + qDebug() << " pair_i=" << pair_i.first; + } + */ + + const TimsFrameRecord &frame_record = m_mapFramesRecord[timsId]; + if(timsId > m_totalNumberOfScans) { + throw ExceptionNotFound( + QObject::tr("ERROR Frames database id %1 not found").arg(timsId)); + } + TimsFrameSPtr tims_frame; - tims_frame = - mpa_timsBinDec->getTimsFrameSPtrByOffset(timsId, q.value(0).toUInt()); + // QMutexLocker lock(&m_mutex); + tims_frame = + mpa_timsBinDec->getTimsFrameSPtrByOffset(timsId, m_mapFramesRecord); + // lock.unlock(); - auto it_map_record = m_mapMzCalibrationRecord.find(q.value(2).toInt()); - if(it_map_record != m_mapMzCalibrationRecord.end()) - { + qDebug(); + auto it_map_record = + m_mapMzCalibrationRecord.find(frame_record.mz_calibration_id); + if(it_map_record != m_mapMzCalibrationRecord.end()) + { - double T1_frame = q.value(3).toDouble(); // Frames.T1 - double T2_frame = q.value(4).toDouble(); // Frames.T2 + double T1_frame = frame_record.frame_t1; // Frames.T1 + double T2_frame = frame_record.frame_t2; // Frames.T2 - tims_frame.get()->setMzCalibrationInterfaceSPtr( - mpa_mzCalibrationStore->getInstance( - T1_frame, T2_frame, it_map_record->second)); - } - else - { - throw ExceptionNotFound( - QObject::tr("ERROR MzCalibration database id %1 not found") - .arg(q.value(2).toInt())); - } + tims_frame.get()->setMzCalibrationInterfaceSPtr( + mpa_mzCalibrationStore->getInstance( + T1_frame, T2_frame, it_map_record->second)); + } + else + { + throw ExceptionNotFound( + QObject::tr("ERROR MzCalibration database id %1 not found") + .arg(frame_record.mz_calibration_id)); + } - tims_frame.get()->setAccumulationTime(q.value(1).toDouble()); + tims_frame.get()->setAccumulationTime(frame_record.accumulation_time); - tims_frame.get()->setTime(q.value(5).toDouble()); - tims_frame.get()->setMsMsType(q.value(6).toUInt()); + tims_frame.get()->setTime(frame_record.frame_time); + tims_frame.get()->setMsMsType(frame_record.msms_type); - tims_frame.get()->setTimsCalibration(q.value(7).toInt(), - q.value(8).toDouble(), - q.value(9).toDouble(), - q.value(10).toDouble(), - q.value(11).toDouble(), - q.value(12).toDouble(), - q.value(13).toDouble(), - q.value(14).toDouble(), - q.value(15).toDouble(), - q.value(16).toDouble(), - q.value(17).toDouble()); - return tims_frame; + qDebug(); + auto it_map_record_tims_calibration = + m_mapTimsCalibrationRecord.find(frame_record.tims_calibration_id); + if(it_map_record_tims_calibration != m_mapTimsCalibrationRecord.end()) + { + + tims_frame.get()->setTimsCalibration( + it_map_record_tims_calibration->second.value(1).toInt(), + it_map_record_tims_calibration->second.value(2).toDouble(), + it_map_record_tims_calibration->second.value(3).toDouble(), + it_map_record_tims_calibration->second.value(4).toDouble(), + it_map_record_tims_calibration->second.value(5).toDouble(), + it_map_record_tims_calibration->second.value(6).toDouble(), + it_map_record_tims_calibration->second.value(7).toDouble(), + it_map_record_tims_calibration->second.value(8).toDouble(), + it_map_record_tims_calibration->second.value(9).toDouble(), + it_map_record_tims_calibration->second.value(10).toDouble(), + it_map_record_tims_calibration->second.value(11).toDouble()); } - - throw ExceptionNotFound(QObject::tr("ERROR timsId %1 not found").arg(timsId)); - // return TimsFrameCstSPtr; + else + { + throw ExceptionNotFound( + QObject::tr("ERROR TimsCalibration database id %1 not found") + .arg(frame_record.tims_calibration_id)); + } + qDebug(); + return tims_frame; } pappso::MassSpectrumCstSPtr TimsData::getMassSpectrumCstSPtr(std::size_t timsId, std::size_t scanNum) { + qDebug() << " timsId=" << timsId << " scanNum=" << scanNum; pappso::TimsFrameCstSPtr frame = getTimsFrameCstSPtrCached(timsId); return frame->getMassSpectrumCstSPtr(scanNum); @@ -561,7 +646,7 @@ QSqlDatabase qdb = openDatabaseConnection(); QSqlQuery q = qdb.exec( QString( - "SELECT Frames.time, Precursors.MonoisotopicMz, Precursors.Charge, " + "SELECT Frames.Time, Precursors.MonoisotopicMz, Precursors.Charge, " "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, " "PasefFrameMsMsInfo.scanNumEnd " "FROM Frames " @@ -570,7 +655,7 @@ "WHERE Precursors.Charge == %1 " "AND Precursors.MonoisotopicMz > %2 -0.01 " "AND Precursors.MonoisotopicMz < %2 +0.01 " - "AND Frames.Time >= %3 " + "AND Frames.Time >= %3 -1 " "AND Frames.Time < %3 +1; ") .arg(charge) .arg(mz_val) @@ -591,8 +676,8 @@ } while(q.next()) { - qInfo() << q.value(0).toDouble() << q.value(1).toDouble() - << q.value(2).toDouble() << q.value(3).toDouble(); + // qInfo() << q.value(0).toDouble() << q.value(1).toDouble() + // << q.value(2).toDouble() << q.value(3).toDouble(); std::vector sql_values; sql_values.push_back(q.value(4).toDouble()); // frame id @@ -643,7 +728,7 @@ double bko = tims_frame.get()->getOneOverK0Transformation(index[2]); double eko = tims_frame.get()->getOneOverK0Transformation(index[3]); - qInfo() << "diff" << (bko + eko) / 2; + // qInfo() << "diff" << (bko + eko) / 2; double mean_ko = (bko + eko) / 2; if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1) @@ -687,278 +772,500 @@ } -QualifiedMassSpectrum -TimsData::getQualifiedMassSpectrumByRawIndex(std::size_t spectrum_index, - bool want_binary_data) +void +TimsData::getQualifiedMassSpectrumByRawIndex( + const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + std::size_t spectrum_index, + bool want_binary_data) { - auto coordinate = getScanCoordinateFromRawIndex(spectrum_index); - TimsFrameBaseCstSPtr tims_frame; - if(want_binary_data) - { - tims_frame = getTimsFrameCstSPtrCached(coordinate.first); - } - else + try { - tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first); - } - QualifiedMassSpectrum mass_spectrum; - MassSpectrumId spectrum_id; + auto coordinate = getScanCoordinateFromRawIndex(spectrum_index); + TimsFrameBaseCstSPtr tims_frame; + if(want_binary_data) + { + tims_frame = getTimsFrameCstSPtrCached(coordinate.first); + } + else + { + tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first); + } + MassSpectrumId spectrum_id; - spectrum_id.setSpectrumIndex(spectrum_index); - spectrum_id.setNativeId(QString("frame=%1 scan=%2 index=%3") - .arg(coordinate.first) - .arg(coordinate.second) - .arg(spectrum_index)); - - mass_spectrum.setMassSpectrumId(spectrum_id); - - mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel()); - mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); - - mass_spectrum.setDtInMilliSeconds( - tims_frame.get()->getDriftTime(coordinate.second)); - // 1/K0 - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::OneOverK0, - tims_frame.get()->getOneOverK0Transformation(coordinate.second)); - - mass_spectrum.setEmptyMassSpectrum(true); - if(want_binary_data) - { - mass_spectrum.setMassSpectrumSPtr( - tims_frame.get()->getMassSpectrumSPtr(coordinate.second)); - if(mass_spectrum.size() > 0) + spectrum_id.setSpectrumIndex(spectrum_index); + spectrum_id.setMsRunId(msrun_id); + spectrum_id.setNativeId(QString("frame=%1 scan=%2 index=%3") + .arg(coordinate.first) + .arg(coordinate.second) + .arg(spectrum_index)); + + mass_spectrum.setMassSpectrumId(spectrum_id); + + mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel()); + mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); + + mass_spectrum.setDtInMilliSeconds( + tims_frame.get()->getDriftTime(coordinate.second)); + // 1/K0 + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0, + tims_frame.get()->getOneOverK0Transformation(coordinate.second)); + + mass_spectrum.setEmptyMassSpectrum(true); + if(want_binary_data) { + mass_spectrum.setMassSpectrumSPtr( + tims_frame.get()->getMassSpectrumSPtr(coordinate.second)); + if(mass_spectrum.size() > 0) + { + mass_spectrum.setEmptyMassSpectrum(false); + } + } + else + { + // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0) + //{ mass_spectrum.setEmptyMassSpectrum(false); + // } + } + if(tims_frame.get()->getMsLevel() > 1) + { + + auto spectrum_descr = getSpectrumDescrWithScanCoordinate(coordinate); + if(spectrum_descr.precursor_id > 0) + { + + mass_spectrum.appendPrecursorIonData( + spectrum_descr.precursor_ion_data); + + + MassSpectrumId spectrum_id; + std::size_t prec_spectrum_index = getRawIndexFromCoordinate( + spectrum_descr.parent_frame, coordinate.second); + + mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index); + mass_spectrum.setPrecursorNativeId( + QString("frame=%1 scan=%2 index=%3") + .arg(spectrum_descr.parent_frame) + .arg(coordinate.second) + .arg(prec_spectrum_index)); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationMz, + spectrum_descr.isolationMz); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationWidth, + spectrum_descr.isolationWidth); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::CollisionEnergy, + spectrum_descr.collisionEnergy); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::BrukerPrecursorIndex, + (quint64)spectrum_descr.precursor_id); + } } } - else + catch(PappsoException &error) { - // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0) - //{ - mass_spectrum.setEmptyMassSpectrum(false); - // } + throw pappso::PappsoException( + QObject::tr("Error TimsData::getQualifiedMassSpectrumByRawIndex " + "spectrum_index=%1 :\n%2") + .arg(spectrum_index) + .arg(error.qwhat())); } - if(tims_frame.get()->getMsLevel() > 1) +} + + +Trace +TimsData::getTicChromatogram() +{ + // In the Frames table, each frame has a record describing the + // SummedIntensities for all the mobility spectra. + + + MapTrace rt_tic_map_trace; + + using Pair = std::pair; + using Map = std::map; + using Iterator = Map::iterator; + + + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery q = + qdb.exec(QString("SELECT Time, SummedIntensities " + "FROM Frames WHERE MsMsType = 0 " + "ORDER BY Time;")); + + if(q.lastError().isValid()) { - QSqlDatabase qdb = openDatabaseConnection(); - QSqlQuery q = qdb.exec( - QString( - "SELECT PasefFrameMsMsInfo.*, Precursors.* FROM " - "PasefFrameMsMsInfo INNER JOIN Precursors ON " - "PasefFrameMsMsInfo.Precursor=Precursors.Id where " - "PasefFrameMsMsInfo.Frame=%1 and (PasefFrameMsMsInfo.ScanNumBegin " - "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);") - .arg(coordinate.first) - .arg(coordinate.second)); - if(q.lastError().isValid()) + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, " + "executing SQL " + "command %3:\n%4\n%5\n%6") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(qdb.databaseName()) + .arg(q.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); + } + + while(q.next()) + { + + bool ok = false; + + int cumulated_results = 2; + + double rt = q.value(0).toDouble(&ok); + cumulated_results -= ok; + + double sumY = q.value(1).toDouble(&ok); + cumulated_results -= ok; + + if(cumulated_results) { throw PappsoException( - QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " - "command %2:\n%3\n%4\n%5") + QObject::tr( + "ERROR in TIMS sqlite database file: could not read either the " + "retention time or the summed intensities (%1, database name " + "%2, " + "executing SQL " + "command %3:\n%4\n%5\n%6") .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(qdb.databaseName()) .arg(q.lastQuery()) .arg(qdb.lastError().databaseText()) .arg(qdb.lastError().driverText()) .arg(qdb.lastError().nativeErrorCode())); } - if(q.next()) - { - // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); - // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); - // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); - // mass_spectrum.setPrecursorSpectrumIndex(); - - mass_spectrum.appendPrecursorIonData( - PrecursorIonData(q.value(10).toDouble(), - q.value(11).toInt(), - q.value(13).toDouble())); + // Try to insert value sumY at key rt. + std::pair res = rt_tic_map_trace.insert(Pair(rt, sumY)); - MassSpectrumId spectrum_id; - std::size_t prec_spectrum_index = getRawIndexFromCoordinate( - q.value(14).toDouble(), coordinate.second); - - mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index); - mass_spectrum.setPrecursorNativeId( - QString("frame=%1 scan=%2 index=%3") - .arg(q.value(14).toDouble()) - .arg(coordinate.second) - .arg(prec_spectrum_index)); - - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::IsolationMz, q.value(3).toDouble()); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::IsolationWidth, - q.value(4).toDouble()); + if(!res.second) + { + // One other same rt value was seen already (like in ion mobility + // mass spectrometry, for example). Only increment the y value. - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::CollisionEnergy, - q.value(5).toFloat()); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::BrukerPrecursorIndex, - q.value(6).toInt()); + res.first->second += sumY; } } - return mass_spectrum; + // qDebug().noquote() << "The TIC chromatogram:\n" + //<< rt_tic_map_trace.toTrace().toString(); + + return rt_tic_map_trace.toTrace(); } -QualifiedMassSpectrum -TimsData::getQualifiedMs1MassSpectrumByPrecursorId(std::size_t ms2_index, - std::size_t precursor_index, - bool want_binary_data) +void +TimsData::getQualifiedMs1MassSpectrumByPrecursorId( + const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + SpectrumDescr &spectrum_descr, + bool want_binary_data) { - QualifiedMassSpectrum mass_spectrum; + + qDebug() << " ms2_index=" << spectrum_descr.ms2_index + << " precursor_index=" << spectrum_descr.precursor_id; + + TracePlusCombiner combiner; + MapTrace combiner_result; try { - QSqlDatabase qdb = openDatabaseConnection(); mass_spectrum.setMsLevel(1); mass_spectrum.setPrecursorSpectrumIndex(0); mass_spectrum.setEmptyMassSpectrum(true); - QSqlQuery q = - qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM " - "PasefFrameMsMsInfo INNER JOIN Precursors ON " - "PasefFrameMsMsInfo.Precursor=Precursors.Id where " - "Precursors.Id=%1;") - .arg(precursor_index)); - if(q.lastError().isValid()) - { - throw PappsoException( - QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " - "command %2:\n%3\n%4\n%5") - .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) - .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); - } - if(q.size() == 0) - { + MassSpectrumId spectrum_id; + spectrum_id.setSpectrumIndex(spectrum_descr.ms1_index); + spectrum_id.setNativeId( + QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms1=%5") + .arg(spectrum_descr.parent_frame) + .arg(spectrum_descr.scan_mobility_start) + .arg(spectrum_descr.scan_mobility_end) + .arg(spectrum_descr.precursor_id) + .arg(spectrum_descr.ms1_index)); - throw ExceptionNotFound( - QObject::tr( - "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor " - "id=%1 not found") - .arg(precursor_index)); + spectrum_id.setMsRunId(msrun_id); + + mass_spectrum.setMassSpectrumId(spectrum_id); + + + TimsFrameBaseCstSPtr tims_frame; + if(want_binary_data) + { + qDebug() << "bindec"; + tims_frame = getTimsFrameCstSPtrCached(spectrum_descr.parent_frame); } else { - TracePlusCombiner combiner; - MapTrace combiner_result; + tims_frame = + getTimsFrameBaseCstSPtrCached(spectrum_descr.parent_frame); + } + mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0begin, + tims_frame.get()->getOneOverK0Transformation( + spectrum_descr.scan_mobility_start)); - bool first = true; - std::size_t scan_mobility_start = 0; - std::size_t scan_mobility_end = 0; - std::set tims_frame_list; - while(q.next()) + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0end, + tims_frame.get()->getOneOverK0Transformation( + spectrum_descr.scan_mobility_end)); + + + if(want_binary_data) + { + combiner.combine(combiner_result, + tims_frame.get()->cumulateScanToTrace( + spectrum_descr.scan_mobility_start, + spectrum_descr.scan_mobility_end)); + + pappso::Trace trace(combiner_result); + qDebug(); + + if(trace.size() > 0) { - // get MS1 frame - tims_frame_list.insert(q.value(14).toLongLong()); - if(first) + if(mcsp_ms1Filter != nullptr) { + mcsp_ms1Filter->filter(trace); + } + qDebug(); + mass_spectrum.setMassSpectrumSPtr( + MassSpectrum(trace).makeMassSpectrumSPtr()); + mass_spectrum.setEmptyMassSpectrum(false); + } + else + { + mass_spectrum.setMassSpectrumSPtr(nullptr); + mass_spectrum.setEmptyMassSpectrum(true); + } + } + qDebug(); + } - MassSpectrumId spectrum_id; + catch(PappsoException &error) + { + throw error; + } + catch(std::exception &error) + { + qDebug() << QString("Failure %1 ").arg(error.what()); + } +} - spectrum_id.setSpectrumIndex(precursor_index); - spectrum_id.setNativeId( - QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5") - .arg(q.value(0).toLongLong()) - .arg(q.value(1).toLongLong()) - .arg(q.value(2).toLongLong()) - .arg(precursor_index) - .arg(ms2_index)); +TimsFrameBaseCstSPtr +TimsData::getTimsFrameBaseCstSPtrCached(std::size_t timsId) +{ + QMutexLocker locker(&m_mutex); + for(auto &tims_frame : m_timsFrameBaseCache) + { + if(tims_frame.get()->getId() == timsId) + { + m_timsFrameBaseCache.push_back(tims_frame); + if(m_timsFrameBaseCache.size() > m_cacheSize) + m_timsFrameBaseCache.pop_front(); + return tims_frame; + } + } - mass_spectrum.setMassSpectrumId(spectrum_id); + m_timsFrameBaseCache.push_back(getTimsFrameBaseCstSPtr(timsId)); + if(m_timsFrameBaseCache.size() > m_cacheSize) + m_timsFrameBaseCache.pop_front(); + return m_timsFrameBaseCache.back(); +} +TimsFrameCstSPtr +TimsData::getTimsFrameCstSPtrCached(std::size_t timsId) +{ + qDebug(); + QMutexLocker locker(&m_mutex); + for(auto &tims_frame : m_timsFrameCache) + { + if(tims_frame.get()->getId() == timsId) + { + m_timsFrameCache.push_back(tims_frame); + if(m_timsFrameCache.size() > m_cacheSize) + m_timsFrameCache.pop_front(); + return tims_frame; + } + } + pappso::TimsFrameCstSPtr frame_sptr = getTimsFrameCstSPtr(timsId); - scan_mobility_start = q.value(1).toLongLong(); - scan_mobility_end = q.value(2).toLongLong(); + // locker.relock(); + qDebug(); - first = false; - } - } + m_timsFrameCache.push_back(frame_sptr); + if(m_timsFrameCache.size() > m_cacheSize) + m_timsFrameCache.pop_front(); + qDebug(); + return m_timsFrameCache.back(); - first = true; - for(std::size_t tims_id : tims_frame_list) - { - TimsFrameBaseCstSPtr tims_frame = - getTimsFrameCstSPtrCached(tims_id); - if(first) - { - mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::OneOverK0begin, - tims_frame.get()->getOneOverK0Transformation( - scan_mobility_start)); - - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::OneOverK0end, - tims_frame.get()->getOneOverK0Transformation( - scan_mobility_end)); + /* +// the frame is not in the cache +if(std::find(m_someoneIsLoadingFrameId.begin(), + m_someoneIsLoadingFrameId.end(), + timsId) == m_someoneIsLoadingFrameId.end()) + { + // not found, we are alone on this frame + m_someoneIsLoadingFrameId.push_back(timsId); + qDebug(); + //locker.unlock(); + pappso::TimsFrameCstSPtr frame_sptr = getTimsFrameCstSPtr(timsId); + + // locker.relock(); + qDebug(); + m_someoneIsLoadingFrameId.erase( + std::find(m_someoneIsLoadingFrameId.begin(), + m_someoneIsLoadingFrameId.end(), + timsId)); + + m_timsFrameCache.push_back(frame_sptr); + if(m_timsFrameCache.size() > m_cacheSize) + m_timsFrameCache.pop_front(); + qDebug(); + return m_timsFrameCache.back(); + } +else + { + // this frame is loading by someone else, we have to wait + qDebug(); + // locker.unlock(); + // std::size_t another_frame_id = timsId; + while(true) + { + QThread::usleep(1); + // locker.relock(); - first = false; - } + for(auto &tims_frame : m_timsFrameCache) + { + if(tims_frame.get()->getId() == timsId) + { + m_timsFrameCache.push_back(tims_frame); + return tims_frame; + } + } + // locker.unlock(); +} +} // namespace pappso +*/ +} + +void +TimsData::setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter) +{ + mcsp_ms2Filter = filter; +} +void +TimsData::setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter) +{ + mcsp_ms1Filter = filter; +} +pappso::XicCoordTims +pappso::TimsData::getXicCoordTimsFromPrecursorId(std::size_t precursor_id, + PrecisionPtr precision_ptr) +{ - if(want_binary_data) - { - combiner.combine(combiner_result, - tims_frame.get()->cumulateScanToTrace( - scan_mobility_start, scan_mobility_end)); - } - else - { - break; - } - } + qDebug(); + XicCoordTims xic_coord_tims_struct; + try + { + if(m_mapXicCoordRecord.size() == 0) + { + QMutexLocker lock(&m_mutex); + // Go get records! - if(first == true) + // We proceed in this way: + + // 1. For each Precursor reference to the Precursors table's ID + // found in the PasefFrameMsMsInfo table, store the precursor ID for + // step 2. + + // 2. From the Precursors table's ID from step 1, get the + // MonoisotopicMz. + + // 3. From the PasefFrameMsMsInfo table, for the Precursors table's + // ID reference, get a reference to the Frames table's ID. Thanks to + // the Frames ID, look for the Time value (acquisition retention + // time) for the MS/MS spectrum. The Time value in the Frames tables + // always corresponds to a Frame of MsMsType 8 (that is, MS/MS), + // which is expected since we are looking into MS/MS data. + + // 4. From the PasefFrameMsMsInfo table, associate the values + // ScanNumBegin and ScanNumEnd, the mobility bins in which the + // precursor was found. + + + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery q = qdb.exec( + QString("SELECT Precursors.id, " + "min(Frames.Time), " + "min(PasefFrameMsMsInfo.ScanNumBegin), " + "max(PasefFrameMsMsInfo.ScanNumEnd), " + "Precursors.MonoisotopicMz " + "FROM " + "PasefFrameMsMsInfo INNER JOIN Precursors ON " + "PasefFrameMsMsInfo.Precursor=Precursors.Id INNER JOIN " + "Frames ON PasefFrameMsMsInfo.Frame=Frames.Id " + "GROUP BY Precursors.id;")); + if(q.lastError().isValid()) { - throw ExceptionNotFound( + qDebug(); + throw PappsoException( QObject::tr( - "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor " - "id=%1 not found") - .arg(precursor_index)); + "ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(q.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); } - - if(want_binary_data) + q.last(); // strange bug : get the last sql record and get back, + // otherwise it will not retrieve all records. + q.first(); + // std::size_t i = 0; + do { + QSqlRecord record = q.record(); + m_mapXicCoordRecord.insert(std::pair( + (std::size_t)record.value(0).toULongLong(), record)); + } + while(q.next()); + } - pappso::Trace trace(combiner_result); - qDebug(); - if(trace.size() > 0) - { - if(mcsp_ms1Filter != nullptr) - { - mcsp_ms1Filter->filter(trace); - } + auto it_map_xiccoord = m_mapXicCoordRecord.find(precursor_id); + if(it_map_xiccoord == m_mapXicCoordRecord.end()) + { - qDebug(); - mass_spectrum.setMassSpectrumSPtr( - MassSpectrum(trace).makeMassSpectrumSPtr()); - mass_spectrum.setEmptyMassSpectrum(false); - } - else - { - mass_spectrum.setMassSpectrumSPtr(nullptr); - mass_spectrum.setEmptyMassSpectrum(true); - } - } + throw ExceptionNotFound( + QObject::tr("ERROR Precursors database id %1 not found") + .arg(precursor_id)); } + + auto &q = it_map_xiccoord->second; + xic_coord_tims_struct.mzRange = + MzRange(q.value(4).toDouble(), precision_ptr); + xic_coord_tims_struct.scanNumBegin = q.value(2).toUInt(); + xic_coord_tims_struct.scanNumEnd = q.value(3).toUInt(); + xic_coord_tims_struct.rtTarget = q.value(1).toDouble(); + // xic_structure.charge = q.value(5).toUInt(); + xic_coord_tims_struct.xicSptr = std::make_shared(); } - catch(PappsoException &error) { throw error; @@ -967,46 +1274,20 @@ { qDebug() << QString("Failure %1 ").arg(error.what()); } - return mass_spectrum; + return xic_coord_tims_struct; } -void -TimsData::getQualifiedMs2MassSpectrumByPrecursorId( - QualifiedMassSpectrum &mass_spectrum, - std::size_t ms2_index, - std::size_t precursor_index, - bool want_binary_data) +std::map +TimsData::getRawMs2ByPrecursorId(std::size_t precursor_index) { qDebug(); + std::map raw_spectrum; try { QSqlDatabase qdb = openDatabaseConnection(); - MassSpectrumId spectrum_id; - - spectrum_id.setSpectrumIndex(precursor_index); - spectrum_id.setNativeId( - QString("precursor=%1 idxms2=%2").arg(precursor_index).arg(ms2_index)); - - mass_spectrum.setMassSpectrumId(spectrum_id); - - mass_spectrum.setMsLevel(2); - mass_spectrum.setPrecursorSpectrumIndex(ms2_index - 1); - - mass_spectrum.setEmptyMassSpectrum(true); qdb = openDatabaseConnection(); - // m_mutex.lock(); - // if(m_query != nullptr) - // { - // *m_query = - // qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* - // FROM " - // "PasefFrameMsMsInfo INNER JOIN Precursors ON " - // "PasefFrameMsMsInfo.Precursor=Precursors.Id - // where " "Precursors.Id=%1;") - // .arg(precursor_index)); - // } QSqlQuery q = qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM " "PasefFrameMsMsInfo INNER JOIN Precursors ON " @@ -1050,41 +1331,10 @@ tims_frame_list.push_back(q.value(0).toLongLong()); if(first) { - // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); - // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); - // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); - - mass_spectrum.appendPrecursorIonData( - PrecursorIonData(q.value(10).toDouble(), - q.value(11).toInt(), - q.value(13).toDouble())); - - mass_spectrum.setPrecursorNativeId( - QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5") - .arg(q.value(14).toLongLong()) - .arg(q.value(1).toLongLong()) - .arg(q.value(2).toLongLong()) - .arg(precursor_index) - .arg(ms2_index - 1)); - // mass_spectrum.setPrecursorSpectrumIndex(); scan_mobility_start = q.value(1).toLongLong(); scan_mobility_end = q.value(2).toLongLong(); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::IsolationMz, - q.value(3).toDouble()); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::IsolationWidth, - q.value(4).toDouble()); - - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::CollisionEnergy, - q.value(5).toFloat()); - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::BrukerPrecursorIndex, - q.value(6).toInt()); - first = false; } } @@ -1093,58 +1343,35 @@ pappso::TimsFrameCstSPtr tims_frame, previous_frame; // TracePlusCombiner combiner; // MapTrace combiner_result; - std::map raw_spectrum; - first = true; for(std::size_t tims_id : tims_frame_list) { - tims_frame = getTimsFrameCstSPtrCached(tims_id); - if(first) - { - mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); - - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::OneOverK0begin, - tims_frame.get()->getOneOverK0Transformation( - scan_mobility_start)); - - mass_spectrum.setParameterValue( - QualifiedMassSpectrumParameter::OneOverK0end, - tims_frame.get()->getOneOverK0Transformation( - scan_mobility_end)); - - first = false; - } - - - if(want_binary_data) + qDebug(); + /*combiner.combine(combiner_result, + tims_frame.get()->cumulateScanToTrace( + scan_mobility_start, scan_mobility_end));*/ + if(previous_frame.get() != nullptr) { - qDebug(); - /*combiner.combine(combiner_result, - tims_frame.get()->cumulateScanToTrace( - scan_mobility_start, scan_mobility_end));*/ - if(previous_frame.get() != nullptr) + if(previous_frame.get()->hasSameCalibrationData( + *tims_frame.get())) { - if(previous_frame.get()->hasSameCalibrationData( - *tims_frame.get())) - { - } - else - { - throw ExceptionNotFound( - QObject::tr( - "ERROR in %1 %2, different calibration data " - "between frame id %3 and frame id %4") - .arg(__FILE__) - .arg(__FUNCTION__) - .arg(previous_frame.get()->getId()) - .arg(tims_frame.get()->getId())); - } } - tims_frame.get()->cumulateScansInRawMap( - raw_spectrum, scan_mobility_start, scan_mobility_end); - qDebug(); + else + { + throw ExceptionNotFound( + QObject::tr( + "ERROR in %1 %2, different calibration data " + "between frame id %3 and frame id %4") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(previous_frame.get()->getId()) + .arg(tims_frame.get()->getId())); + } } + tims_frame.get()->cumulateScansInRawMap( + raw_spectrum, scan_mobility_start, scan_mobility_end); + qDebug(); + previous_frame = tims_frame; } qDebug() << " precursor_index=" << precursor_index @@ -1159,62 +1386,230 @@ "id=%1 not found") .arg(precursor_index)); } + qDebug(); + } + } + + catch(PappsoException &error) + { + throw PappsoException(QObject::tr("ERROR in %1 (precursor_index=%2):\n%3") + .arg(__FUNCTION__) + .arg(precursor_index) + .arg(error.qwhat())); + } + catch(std::exception &error) + { + qDebug() << QString("Failure %1 ").arg(error.what()); + } + return raw_spectrum; + qDebug(); +} + + +void +TimsData::getQualifiedMs2MassSpectrumByPrecursorId( + const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + SpectrumDescr &spectrum_descr, + bool want_binary_data) +{ + try + { + qDebug(); + MassSpectrumId spectrum_id; + + spectrum_id.setSpectrumIndex(spectrum_descr.ms2_index); + spectrum_id.setNativeId(QString("precursor=%1 idxms2=%2") + .arg(spectrum_descr.precursor_id) + .arg(spectrum_descr.ms2_index)); + spectrum_id.setMsRunId(msrun_id); + + mass_spectrum.setMassSpectrumId(spectrum_id); + + mass_spectrum.setMsLevel(2); + qDebug() << "spectrum_descr.precursor_id=" << spectrum_descr.precursor_id + << " spectrum_descr.ms1_index=" << spectrum_descr.ms1_index + << " spectrum_descr.ms2_index=" << spectrum_descr.ms2_index; + mass_spectrum.setPrecursorSpectrumIndex(spectrum_descr.ms1_index); + + mass_spectrum.setEmptyMassSpectrum(true); + + qDebug(); + + + mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data); + + mass_spectrum.setPrecursorNativeId( + QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms1=%5") + .arg(spectrum_descr.parent_frame) + .arg(spectrum_descr.scan_mobility_start) + .arg(spectrum_descr.scan_mobility_end) + .arg(spectrum_descr.precursor_id) + .arg(spectrum_descr.ms1_index)); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationMz, + spectrum_descr.isolationMz); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationWidth, + spectrum_descr.isolationWidth); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::CollisionEnergy, + spectrum_descr.collisionEnergy); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::BrukerPrecursorIndex, + (quint64)spectrum_descr.precursor_id); + + // QMutexLocker locker(&m_mutex_spectrum); + qDebug(); + pappso::TimsFrameBaseCstSPtr tims_frame, previous_frame; + // TracePlusCombiner combiner; + // MapTrace combiner_result; + std::map raw_spectrum; + bool first = true; + for(std::size_t tims_id : spectrum_descr.tims_frame_list) + { + qDebug() << " precursor_index=" << spectrum_descr.precursor_id + << " tims_id=" << tims_id + << (std::size_t)QThread::currentThreadId(); + ; + if(want_binary_data) + { + qDebug() << "bindec"; + tims_frame = getTimsFrameCstSPtrCached(tims_id); + } + else + { + tims_frame = getTimsFrameBaseCstSPtrCached(tims_id); + } + qDebug() << (std::size_t)QThread::currentThreadId(); + ; + if(first) + { + mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0begin, + tims_frame.get()->getOneOverK0Transformation( + spectrum_descr.scan_mobility_start)); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0end, + tims_frame.get()->getOneOverK0Transformation( + spectrum_descr.scan_mobility_end)); + + first = false; + } + + if(want_binary_data) { qDebug(); - // peak_pick.filter(trace); - pappso::Trace trace; - if(m_builtinMs2Centroid) + /*combiner.combine(combiner_result, + tims_frame.get()->cumulateScanToTrace( + scan_mobility_start, scan_mobility_end));*/ + if(previous_frame.get() != nullptr) { - trace = - tims_frame.get()->getTraceFromCumulatedScansBuiltinCentroid( - raw_spectrum); - } - else - { - // no builtin centroid: - - trace = - tims_frame.get()->getTraceFromCumulatedScans(raw_spectrum); + if(previous_frame.get()->hasSameCalibrationData( + *tims_frame.get())) + { + } + else + { + throw ExceptionNotFound( + QObject::tr( + "ERROR in %1 %2, different calibration data " + "between frame id %3 and frame id %4") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(previous_frame.get()->getId()) + .arg(tims_frame.get()->getId())); + } } + qDebug() << (std::size_t)QThread::currentThreadId(); + ; + tims_frame.get()->cumulateScansInRawMap( + raw_spectrum, + spectrum_descr.scan_mobility_start, + spectrum_descr.scan_mobility_end); + qDebug() << (std::size_t)QThread::currentThreadId(); + ; + } + previous_frame = tims_frame; + } + qDebug() << " precursor_index=" << spectrum_descr.precursor_id + << " num_rows=" << spectrum_descr.tims_frame_list.size() + << (std::size_t)QThread::currentThreadId(); + if(first == true) + { + throw ExceptionNotFound( + QObject::tr( + "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor " + "id=%1 not found") + .arg(spectrum_descr.precursor_id)); + } + if(want_binary_data) + { + qDebug() << " precursor_index=" << spectrum_descr.precursor_id; + // peak_pick.filter(trace); + pappso::Trace trace; + if(m_builtinMs2Centroid) + { + trace = + tims_frame.get()->getTraceFromCumulatedScansBuiltinCentroid( + raw_spectrum); + } + else + { + // no builtin centroid: - if(trace.size() > 0) - { - qDebug() << trace.size() << " " - << (std::size_t)QThread::currentThreadId(); + trace = + tims_frame.get()->getTraceFromCumulatedScans(raw_spectrum); + } - if(mcsp_ms2Filter != nullptr) - { - // FilterTriangle filter; - // filter.setTriangleSlope(50, 0.02); - // filter.filter(trace); - // trace.filter(pappso::FilterHighPass(10)); - mcsp_ms2Filter->filter(trace); - } + if(trace.size() > 0) + { + qDebug() << " precursor_index=" << spectrum_descr.precursor_id + << " " << trace.size() << " " + << (std::size_t)QThread::currentThreadId(); - // FilterScaleFactorY filter_scale((double)1 / - // (double)tims_frame_list.size()); - // filter_scale.filter(trace); - qDebug(); - mass_spectrum.setMassSpectrumSPtr( - MassSpectrum(trace).makeMassSpectrumSPtr()); - mass_spectrum.setEmptyMassSpectrum(false); - } - else + if(mcsp_ms2Filter != nullptr) { - mass_spectrum.setMassSpectrumSPtr(nullptr); - mass_spectrum.setEmptyMassSpectrum(true); + // FilterTriangle filter; + // filter.setTriangleSlope(50, 0.02); + // filter.filter(trace); + // trace.filter(pappso::FilterHighPass(10)); + mcsp_ms2Filter->filter(trace); } - qDebug(); + // FilterScaleFactorY filter_scale((double)1 / + // (double)tims_frame_list.size()); + // filter_scale.filter(trace); + qDebug() << " precursor_index=" << spectrum_descr.precursor_id; + mass_spectrum.setMassSpectrumSPtr( + MassSpectrum(trace).makeMassSpectrumSPtr()); + mass_spectrum.setEmptyMassSpectrum(false); } + else + { + mass_spectrum.setMassSpectrumSPtr(nullptr); + mass_spectrum.setEmptyMassSpectrum(true); + } + qDebug(); } + qDebug(); } catch(PappsoException &error) { - throw error; + throw PappsoException( + QObject::tr("ERROR in %1 (ms2_index=%2 precursor_index=%3):\n%4") + .arg(__FUNCTION__) + .arg(spectrum_descr.ms2_index) + .arg(spectrum_descr.precursor_id) + .arg(error.qwhat())); } catch(std::exception &error) { @@ -1223,131 +1618,726 @@ qDebug(); } - -TimsFrameBaseCstSPtr -TimsData::getTimsFrameBaseCstSPtrCached(std::size_t timsId) +void +pappso::TimsData::ms2ReaderSpectrumCollectionByMsLevel( + const MsRunIdCstSPtr &msrun_id, + pappso::SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) { - QMutexLocker locker(&m_mutex); - for(auto &tims_frame : m_timsFrameBaseCache) + qDebug() << " ms_level=" << ms_level; + if(!m_hasPrecursorTable) { - if(tims_frame.get()->getId() == timsId) + throw PappsoException( + QObject::tr("unable to read spectrum list : this data file does not " + "contain MS2 data, no precursor found.")); + } + + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery qprecursor_list = qdb.exec(QString( + "SELECT PasefFrameMsMsInfo.Frame, " // 0 + "PasefFrameMsMsInfo.ScanNumBegin, " // 1 + "PasefFrameMsMsInfo.ScanNumEnd, " // 2 + "PasefFrameMsMsInfo.IsolationMz, " // 3 + "PasefFrameMsMsInfo.IsolationWidth, " // 4 + "PasefFrameMsMsInfo.CollisionEnergy, " // 5 + "PasefFrameMsMsInfo.Precursor, " // 6 + "Precursors.Id, " // 7 + "Precursors.LargestPeakMz, " // 8 + "Precursors.AverageMz, " // 9 + "Precursors.MonoisotopicMz, " // 10 + "Precursors.Charge, " // 11 + "Precursors.ScanNumber, " // 12 + "Precursors.Intensity, " // 13 + "Precursors.Parent " // 14 + "FROM PasefFrameMsMsInfo " + "INNER JOIN Precursors ON " + "PasefFrameMsMsInfo.Precursor=Precursors.Id " + "ORDER BY PasefFrameMsMsInfo.Precursor, PasefFrameMsMsInfo.Frame ;")); + if(qprecursor_list.lastError().isValid()) + { + + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(qprecursor_list.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); + } + + + qDebug() << "qprecursor_list.size()=" << qprecursor_list.size(); + qDebug() << QObject::tr( + "TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(qprecursor_list.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode()); + + qDebug() << "qprecursor_list.isActive()=" << qprecursor_list.isActive(); + qDebug() << "qprecursor_list.isSelect()=" << qprecursor_list.isSelect(); + bool first = true; + SpectrumDescr spectrum_descr; + std::size_t i = 0; /* + while(qprecursor_list.next()) + { + qDebug() << "i=" << i; + i++; + }*/ + qprecursor_list.last(); // strange bug : get the last sql record and get + // back, unless it will not retrieve all records. + + qDebug() << "qprecursor_list.at()=" << qprecursor_list.at(); + qprecursor_list.first(); + std::vector spectrum_description_list; + spectrum_descr.precursor_id = 0; + // std::size_t i = 0; + + do + { + + if(spectrum_descr.precursor_id != + (std::size_t)qprecursor_list.value(6).toLongLong()) { - m_timsFrameBaseCache.push_back(tims_frame); - return tims_frame; + // new precursor + if(spectrum_descr.precursor_id > 0) + { + spectrum_description_list.push_back(spectrum_descr); + } + + spectrum_descr.tims_frame_list.clear(); + first = true; } + qDebug() << " qprecursor_list.value(6).toLongLong() =" + << qprecursor_list.value(6).toLongLong(); + spectrum_descr.precursor_id = + (std::size_t)qprecursor_list.value(6).toLongLong(); + qDebug() << " spectrum_descr.precursor_id =" + << spectrum_descr.precursor_id; + qDebug() << " cumul tims frame:" << qprecursor_list.value(0).toLongLong(); + spectrum_descr.tims_frame_list.push_back( + qprecursor_list.value(0).toLongLong()); + qDebug() << " first =" << first; + if(first) + { + qDebug(); + // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); + // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); + // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); + spectrum_descr.precursor_ion_data = + PrecursorIonData(qprecursor_list.value(10).toDouble(), + qprecursor_list.value(11).toInt(), + qprecursor_list.value(13).toDouble()); + + // spectrum_descr.precursor_id = q.value(6).toLongLong(); + spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1; + spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2; + + spectrum_descr.scan_mobility_start = + qprecursor_list.value(1).toLongLong(); + spectrum_descr.scan_mobility_end = + qprecursor_list.value(2).toLongLong(); + + spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble(); + spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble(); + spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat(); + spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong(); + + + first = false; + } + // qDebug() << "qprecursor_list.executedQuery()=" + // << qprecursor_list.executedQuery(); + // qDebug() << "qprecursor_list.last()=" << qprecursor_list.last(); + i++; } + while(qprecursor_list.next()); - m_timsFrameBaseCache.push_back(getTimsFrameBaseCstSPtr(timsId)); - if(m_timsFrameBaseCache.size() > m_cacheSize) - m_timsFrameBaseCache.pop_front(); - return m_timsFrameBaseCache.back(); + // last One + + // new precursor + if(spectrum_descr.precursor_id > 0) + { + spectrum_description_list.push_back(spectrum_descr); + } + + + QString local_filepath = m_timsDataDirectory.absoluteFilePath("analysis.tdf"); + + if(m_isMonoThread) + { + for(SpectrumDescr &spectrum_descr : spectrum_description_list) + { + + std::vector mass_spectrum_list; + ms2ReaderGenerateMS1MS2Spectrum( + msrun_id, mass_spectrum_list, handler, spectrum_descr, ms_level); + + for(auto &qualified_spectrum : mass_spectrum_list) + { + handler.setQualifiedMassSpectrum(qualified_spectrum); + } + + if(handler.shouldStop()) + { + qDebug() << "The operation was cancelled. Breaking the loop."; + throw ExceptionInterrupted( + QObject::tr("reading TimsTOF job cancelled by the user :\n%1") + .arg(local_filepath)); + } + } + } + else + { + + + TimsData *itself = this; + pappso::SpectrumCollectionHandlerInterface *pointer_handler = &handler; + + + std::function( + pappso::TimsData::SpectrumDescr &)> + generate_spectrum = [itself, msrun_id, pointer_handler, ms_level]( + pappso::TimsData::SpectrumDescr &spectrum_descr) + -> std::vector { + std::vector mass_spectrum_list; + itself->ms2ReaderGenerateMS1MS2Spectrum(msrun_id, + mass_spectrum_list, + *pointer_handler, + spectrum_descr, + ms_level); + + + return mass_spectrum_list; + }; + + QFuture res; + res = QtConcurrent::mappedReduced( + spectrum_description_list.begin(), + spectrum_description_list.end(), + generate_spectrum, + [pointer_handler, res, local_filepath]( + std::size_t &result, + std::vector qualified_spectrum_list) { + for(auto &qualified_spectrum : qualified_spectrum_list) + { + pointer_handler->setQualifiedMassSpectrum(qualified_spectrum); + } + + if(pointer_handler->shouldStop()) + { + qDebug() << "The operation was cancelled. Breaking the loop."; + throw ExceptionInterrupted( + QObject::tr("reading TimsTOF job cancelled by the user :\n%1") + .arg(local_filepath)); + } + result++; + }, + QtConcurrent::OrderedReduce); + res.waitForFinished(); + } + handler.loadingEnded(); + mpa_timsBinDec->closeLinearRead(); } -TimsFrameCstSPtr -TimsData::getTimsFrameCstSPtrCached(std::size_t timsId) + +void +pappso::TimsData::ms2ReaderGenerateMS1MS2Spectrum( + const MsRunIdCstSPtr &msrun_id, + std::vector &qualified_mass_spectrum_list, + pappso::SpectrumCollectionHandlerInterface &handler, + pappso::TimsData::SpectrumDescr &spectrum_descr, + unsigned int ms_level) +{ + + qDebug() << " ms_level=" << ms_level; + // The handler will receive the index of the mass spectrum in the + // current run via the mass spectrum id member datum. + if((ms_level == 0) || (ms_level == 1)) + { + qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum()); + getQualifiedMs1MassSpectrumByPrecursorId( + msrun_id, + qualified_mass_spectrum_list.back(), + spectrum_descr, + handler.needMsLevelPeakList(1)); + } + if((ms_level == 0) || (ms_level == 2)) + { + qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum()); + getQualifiedMs2MassSpectrumByPrecursorId( + msrun_id, + qualified_mass_spectrum_list.back(), + spectrum_descr, + handler.needMsLevelPeakList(2)); + } + qDebug(); +} + + +pappso::TimsData::SpectrumDescr +pappso::TimsData::getSpectrumDescrWithPrecursorId(std::size_t precursor_id) { - QMutexLocker locker(&m_mutex); - for(auto &tims_frame : m_timsFrameCache) + + SpectrumDescr spectrum_descr; + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery q = qdb.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0 + "PasefFrameMsMsInfo.ScanNumBegin, " // 1 + "PasefFrameMsMsInfo.ScanNumEnd, " // 2 + "PasefFrameMsMsInfo.IsolationMz, " // 3 + "PasefFrameMsMsInfo.IsolationWidth, " // 4 + "PasefFrameMsMsInfo.CollisionEnergy, " // 5 + "PasefFrameMsMsInfo.Precursor, " // 6 + "Precursors.Id, " // 7 + "Precursors.LargestPeakMz, " // 8 + "Precursors.AverageMz, " // 9 + "Precursors.MonoisotopicMz, " // 10 + "Precursors.Charge, " // 11 + "Precursors.ScanNumber, " // 12 + "Precursors.Intensity, " // 13 + "Precursors.Parent " // 14 + "FROM PasefFrameMsMsInfo " + "INNER JOIN Precursors ON " + "PasefFrameMsMsInfo.Precursor=Precursors.Id " + "WHERE Precursors.Id=%1;") + .arg(precursor_id)); + if(q.lastError().isValid()) { - if(tims_frame.get()->getId() == timsId) + + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(q.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); + } + + + bool first = true; + while(q.next()) + { + + qDebug() << " cumul tims frame:" << q.value(0).toLongLong(); + spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong()); + if(first) { - m_timsFrameCache.push_back(tims_frame); - return tims_frame; + // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); + // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); + // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); + spectrum_descr.precursor_ion_data = + PrecursorIonData(q.value(10).toDouble(), + q.value(11).toInt(), + q.value(13).toDouble()); + + spectrum_descr.precursor_id = q.value(6).toLongLong(); + spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1; + spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2; + + spectrum_descr.scan_mobility_start = q.value(1).toLongLong(); + spectrum_descr.scan_mobility_end = q.value(2).toLongLong(); + + spectrum_descr.isolationMz = q.value(3).toDouble(); + spectrum_descr.isolationWidth = q.value(4).toDouble(); + spectrum_descr.collisionEnergy = q.value(5).toFloat(); + spectrum_descr.parent_frame = q.value(14).toLongLong(); + + + first = false; } } + if(spectrum_descr.precursor_id == 0) + { + throw ExceptionNotFound( + QObject::tr("ERROR in %1 %2 : precursor id (%3) NOT FOUND ") + .arg(__FILE__) + .arg(__FUNCTION__) + .arg(precursor_id)); + } + return spectrum_descr; +} - m_timsFrameCache.push_back(getTimsFrameCstSPtr(timsId)); - if(m_timsFrameCache.size() > m_cacheSize) - m_timsFrameCache.pop_front(); - return m_timsFrameCache.back(); +std::vector +pappso::TimsData::getRetentionTimeLine() const +{ + std::vector timeline; + timeline.reserve(m_mapFramesRecord.size()); + for(const TimsFrameRecord &frame_record : m_mapFramesRecord) + { + if(frame_record.mz_calibration_id != 0) + { + timeline.push_back(frame_record.frame_time); + } + } + return timeline; } -void -TimsData::setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter) +pappso::TimsData::SpectrumDescr +pappso::TimsData::getSpectrumDescrWithScanCoordinate( + const std::pair &scan_coordinate) { - mcsp_ms2Filter = filter; + + SpectrumDescr spectrum_descr; + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery q = + qdb.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0 + "PasefFrameMsMsInfo.ScanNumBegin, " // 1 + "PasefFrameMsMsInfo.ScanNumEnd, " // 2 + "PasefFrameMsMsInfo.IsolationMz, " // 3 + "PasefFrameMsMsInfo.IsolationWidth, " // 4 + "PasefFrameMsMsInfo.CollisionEnergy, " // 5 + "PasefFrameMsMsInfo.Precursor, " // 6 + "Precursors.Id, " // 7 + "Precursors.LargestPeakMz, " // 8 + "Precursors.AverageMz, " // 9 + "Precursors.MonoisotopicMz, " // 10 + "Precursors.Charge, " // 11 + "Precursors.ScanNumber, " // 12 + "Precursors.Intensity, " // 13 + "Precursors.Parent " // 14 + "FROM PasefFrameMsMsInfo " + "INNER JOIN Precursors ON " + "PasefFrameMsMsInfo.Precursor=Precursors.Id " + "WHERE " + "PasefFrameMsMsInfo.Frame=%1 and " + "(PasefFrameMsMsInfo.ScanNumBegin " + "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);") + .arg(scan_coordinate.first) + .arg(scan_coordinate.second)); + if(q.lastError().isValid()) + { + + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(q.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); + } + + if(q.next()) + { + + qDebug() << " cumul tims frame:" << q.value(0).toLongLong(); + spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong()); + // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); + // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); + // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); + spectrum_descr.precursor_ion_data = PrecursorIonData( + q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble()); + + spectrum_descr.precursor_id = q.value(6).toLongLong(); + spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1; + spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2; + + spectrum_descr.scan_mobility_start = q.value(1).toLongLong(); + spectrum_descr.scan_mobility_end = q.value(2).toLongLong(); + + spectrum_descr.isolationMz = q.value(3).toDouble(); + spectrum_descr.isolationWidth = q.value(4).toDouble(); + spectrum_descr.collisionEnergy = q.value(5).toFloat(); + spectrum_descr.parent_frame = q.value(14).toLongLong(); + } + return spectrum_descr; } + + void -TimsData::setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter) +pappso::TimsData::fillSpectrumDescriptionWithSqlRecord( + pappso::TimsData::SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list) { - mcsp_ms1Filter = filter; + + spectrum_descr.tims_frame_list.clear(); + spectrum_descr.tims_frame_list.push_back( + qprecursor_list.value(0).toLongLong()); + // mass_spectrum.setPrecursorCharge(q.value(11).toInt()); + // mass_spectrum.setPrecursorMz(q.value(10).toDouble()); + // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble()); + spectrum_descr.precursor_ion_data = + PrecursorIonData(qprecursor_list.value(10).toDouble(), + qprecursor_list.value(11).toInt(), + qprecursor_list.value(13).toDouble()); + + spectrum_descr.precursor_id = qprecursor_list.value(6).toLongLong(); + spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1; + spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2; + + spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong(); + spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong(); + + spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble(); + spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble(); + spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat(); + spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong(); } -std::vector -TimsData::extractXicListByPrecursorIds( - const std::vector &precursor_id_list, - PrecisionPtr precision_ptr, - XicExtractMethod xicExtractMethod, - double rtRange) const + +void +pappso::TimsData::rawReaderSpectrumCollectionByMsLevel( + const pappso::MsRunIdCstSPtr &msrun_id, + pappso::SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level) { - qDebug(); - std::vector xic_list; + if(!m_hasPrecursorTable) + { + throw PappsoException( + QObject::tr("unable to read spectrum list : this data file does not " + "contain MS2 data, no precursor found.")); + } - try + // We'll need it to perform the looping in the spectrum list. + std::size_t spectrum_list_size = getTotalNumberOfScans(); + + // qDebug() << "The spectrum list has size:" << spectrum_list_size; + + // Inform the handler of the spectrum list so that it can handle feedback to + // the user. + handler.spectrumListHasSize(spectrum_list_size); + + QSqlDatabase qdb = openDatabaseConnection(); + QSqlQuery qprecursor_list = qdb.exec(QString( + "SELECT DISTINCT " + "PasefFrameMsMsInfo.Frame, " // 0 + "PasefFrameMsMsInfo.ScanNumBegin, " // 1 + "PasefFrameMsMsInfo.ScanNumEnd, " // 2 + "PasefFrameMsMsInfo.IsolationMz, " // 3 + "PasefFrameMsMsInfo.IsolationWidth, " // 4 + "PasefFrameMsMsInfo.CollisionEnergy, " // 5 + "PasefFrameMsMsInfo.Precursor, " // 6 + "Precursors.Id, " // 7 + "Precursors.LargestPeakMz, " // 8 + "Precursors.AverageMz, " // 9 + "Precursors.MonoisotopicMz, " // 10 + "Precursors.Charge, " // 11 + "Precursors.ScanNumber, " // 12 + "Precursors.Intensity, " // 13 + "Precursors.Parent " // 14 + "FROM PasefFrameMsMsInfo " + "INNER JOIN Precursors ON " + "PasefFrameMsMsInfo.Precursor=Precursors.Id " + "ORDER BY PasefFrameMsMsInfo.Frame, PasefFrameMsMsInfo.ScanNumBegin ;")); + if(qprecursor_list.lastError().isValid()) { - QSqlDatabase qdb = openDatabaseConnection(); + throw PappsoException( + QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL " + "command %2:\n%3\n%4\n%5") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) + .arg(qprecursor_list.lastQuery()) + .arg(qdb.lastError().databaseText()) + .arg(qdb.lastError().driverText()) + .arg(qdb.lastError().nativeErrorCode())); + } - for(auto precursor_id : precursor_id_list) + + std::size_t i = 0; // iterate on each Spectrum + + qprecursor_list.last(); // strange bug : get the last sql record and get + // back, unless it will not retrieve all records. + + qDebug() << "qprecursor_list.at()=" << qprecursor_list.at(); + qprecursor_list.first(); + + TimsFrameBaseCstSPtr tims_frame; + SpectrumDescr spectrum_descr; + + for(FrameIdDescr ¤t_frame : m_frameIdDescrList) + { + + // If the user of this reader instance wants to stop reading the + // spectra, then break this loop. + if(handler.shouldStop()) { - QSqlQuery q = qdb.exec( - QString("SELECT Frames.Time, " - "PasefFrameMsMsInfo.Frame,PasefFrameMsMsInfo.ScanNumBegin," - "PasefFrameMsMsInfo.ScanNumEnd, Precursors.MonoisotopicMz, " - "Precursors.Charge FROM " - "PasefFrameMsMsInfo INNER JOIN Precursors ON " - "PasefFrameMsMsInfo.Precursor=Precursors.Id INNER JOIN " - "Frames ON PasefFrameMsMsInfo.Frame=Frames.Id where " - "Precursors.Id=%1;") - .arg(precursor_id)); - if(q.lastError().isValid()) + qDebug() << "The operation was cancelled. Breaking the loop."; + throw ExceptionInterrupted( + QObject::tr("reading TimsTOF job cancelled by the user :\n%1") + .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))); + } + + tims_frame = getTimsFrameBaseCstSPtrCached(current_frame.m_frameId); + unsigned int tims_ms_level = tims_frame.get()->getMsLevel(); + + if((ms_level != 0) && (ms_level != tims_ms_level)) + { // bypass + i += current_frame.m_size; + } + else + { + bool want_binary_data = handler.needMsLevelPeakList(tims_ms_level); + qDebug() << "want_binary_data=" << want_binary_data; + if(want_binary_data) { - qDebug(); - throw PappsoException( - QObject::tr( - "ERROR in TIMS sqlite database file %1, executing SQL " - "command %2:\n%3\n%4\n%5") - .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")) - .arg(q.lastQuery()) - .arg(qdb.lastError().databaseText()) - .arg(qdb.lastError().driverText()) - .arg(qdb.lastError().nativeErrorCode())); + qDebug() << "bindec"; + tims_frame = getTimsFrameCstSPtrCached(current_frame.m_frameId); } - while(q.next()) + bool possible_precursor = false; + if(tims_ms_level == 2) { - // Frame, ScanNumBegin, ScanNumEnd, IsolationMz, ColliqionEnergy, - // Precursor - // Id, LargestPeakMz, AverageMz, MonoisotopicMz, Charge, - // ScanNumber, Intensity, Parent - TimsXicStructure xic_structure; - - xic_structure.precursorId = precursor_id; - xic_structure.mzRange = - MzRange(q.value(4).toDouble(), precision_ptr); - xic_structure.scanNumBegin = q.value(2).toUInt(); - xic_structure.scanNumEnd = q.value(3).toUInt(); - xic_structure.rtTarget = q.value(0).toDouble(); - // xic_structure.charge = q.value(5).toUInt(); + // seek the precursor record: + while(qprecursor_list.value(0).toULongLong() < + current_frame.m_frameId) + { + qprecursor_list.next(); - xic_list.push_back(xic_structure); + if(qprecursor_list.value(0).toULongLong() == + current_frame.m_frameId) + { + possible_precursor = true; + } + fillSpectrumDescriptionWithSqlRecord(spectrum_descr, + qprecursor_list); + } } - } - qDebug(); - TimsXicExtractorInterface *extractor_p = new TimsDirectXicExtractor(this); - extractor_p->setXicExtractMethod(xicExtractMethod); - extractor_p->extractTimsXicList(xic_list, rtRange); - } - catch(PappsoException &error) - { - throw error; - } - catch(std::exception &error) - { - qDebug() << QString("Failure %1 ").arg(error.what()); + for(std::size_t scan_num = 0; scan_num < current_frame.m_size; + scan_num++) + { + bool has_a_precursor = false; + if(possible_precursor) + { + if(spectrum_descr.scan_mobility_end < scan_num) + { + // seek the precursor record: + while(qprecursor_list.value(0).toULongLong() < + current_frame.m_frameId) + { + qprecursor_list.next(); + + if(qprecursor_list.value(0).toULongLong() != + current_frame.m_frameId) + { + possible_precursor = false; + } + fillSpectrumDescriptionWithSqlRecord(spectrum_descr, + qprecursor_list); + } + } + + if(possible_precursor && + (spectrum_descr.scan_mobility_start < scan_num)) + { + // we are in + has_a_precursor = true; + } + } // end to determine if we are in a precursor for this + // spectrum + + QualifiedMassSpectrum mass_spectrum; + + + MassSpectrumId spectrum_id; + + spectrum_id.setSpectrumIndex(i); + spectrum_id.setMsRunId(msrun_id); + spectrum_id.setNativeId(QString("frame=%1 scan=%2 index=%3") + .arg(current_frame.m_frameId) + .arg(scan_num) + .arg(i)); + + mass_spectrum.setMassSpectrumId(spectrum_id); + + mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel()); + mass_spectrum.setRtInSeconds(tims_frame.get()->getTime()); + + mass_spectrum.setDtInMilliSeconds( + tims_frame.get()->getDriftTime(scan_num)); + // 1/K0 + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::OneOverK0, + tims_frame.get()->getOneOverK0Transformation(scan_num)); + + mass_spectrum.setEmptyMassSpectrum(true); + if(want_binary_data) + { + try + { + mass_spectrum.setMassSpectrumSPtr( + tims_frame.get()->getMassSpectrumSPtr(scan_num)); + } + catch(PappsoException &error) + { + throw PappsoException( + QObject::tr( + "ERROR in %1 (scan_num=%2 spectrum_index=%3):\n%4") + .arg(__FUNCTION__) + .arg(scan_num) + .arg(spectrum_id.getSpectrumIndex()) + .arg(error.qwhat())); + } + if(mass_spectrum.size() > 0) + { + mass_spectrum.setEmptyMassSpectrum(false); + } + } + else + { + // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0) + //{ + mass_spectrum.setEmptyMassSpectrum(false); + // } + } + if(has_a_precursor) + { + if(spectrum_descr.precursor_id > 0) + { + + mass_spectrum.appendPrecursorIonData( + spectrum_descr.precursor_ion_data); + + std::size_t prec_spectrum_index = + getRawIndexFromCoordinate(spectrum_descr.parent_frame, + scan_num); + + mass_spectrum.setPrecursorSpectrumIndex( + prec_spectrum_index); + mass_spectrum.setPrecursorNativeId( + QString("frame=%1 scan=%2 index=%3") + .arg(spectrum_descr.parent_frame) + .arg(scan_num) + .arg(prec_spectrum_index)); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationMz, + spectrum_descr.isolationMz); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::IsolationWidth, + spectrum_descr.isolationWidth); + + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::CollisionEnergy, + spectrum_descr.collisionEnergy); + mass_spectrum.setParameterValue( + QualifiedMassSpectrumParameter::BrukerPrecursorIndex, + (quint64)spectrum_descr.precursor_id); + } + } + + handler.setQualifiedMassSpectrum(mass_spectrum); + i++; + } + } } +} - qDebug(); - return xic_list; +std::map +pappso::TimsData::getRawMsBySpectrumIndex(std::size_t spectrum_index) +{ + + qDebug() << " spectrum_index=" << spectrum_index; + auto coordinate = getScanCoordinateFromRawIndex(spectrum_index); + TimsFrameBaseCstSPtr tims_frame; + tims_frame = getTimsFrameCstSPtrCached(coordinate.first); + + std::map raw_spectrum; + tims_frame.get()->cumulateScansInRawMap( + raw_spectrum, coordinate.second, coordinate.second); + return raw_spectrum; } +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsdata.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsdata.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsdata.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsdata.h 2022-10-27 09:16:15.000000000 +0000 @@ -6,7 +6,7 @@ */ /******************************************************************************* - * Copyright (c) 2019 Olivier Langella . +œ* Copyright (c) 2019 Olivier Langella . * * This file is part of the PAPPSOms++ library. * @@ -33,6 +33,8 @@ #include "timsframe.h" #include "../../massspectrum/qualifiedmassspectrum.h" #include "../../processing/filters/filterinterface.h" +#include "../../msrun/xiccoord/xiccoordtims.h" +#include "../../msrun/msrunreader.h" #include #include #include @@ -41,23 +43,6 @@ namespace pappso { - -/** @brief structure needed to extract XIC from Tims data - */ - -struct TimsXicStructure -{ - TimsXicStructure() - : mzRange(pappso_double(1), PrecisionFactory::getPpmInstance(10.0)){}; - std::size_t precursorId; - MzRange mzRange; - std::size_t scanNumBegin; - std::size_t scanNumEnd; - pappso::pappso_double rtTarget; - XicSPtr xicSptr = nullptr; - unsigned int charge; -}; - class TimsData; /** \brief shared pointer on a TimsData object @@ -84,7 +69,7 @@ /** * Destructor */ - ~TimsData(); + virtual ~TimsData(); /** @brief get a mass spectrum given its spectrum index @@ -119,18 +104,39 @@ unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index); - QualifiedMassSpectrum - getQualifiedMassSpectrumByRawIndex(std::size_t spectrum_index, - bool want_binary_data); + void getQualifiedMassSpectrumByRawIndex(const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + std::size_t spectrum_index, + bool want_binary_data); + + Trace getTicChromatogram(); + + struct SpectrumDescr + { + std::size_t parent_frame = 0; + std::size_t precursor_id = 0; + std::size_t scan_mobility_start = 0; + std::size_t scan_mobility_end = 0; + std::size_t ms1_index = 0; + std::size_t ms2_index = 0; + double isolationMz = 0; + double isolationWidth = 0; + float collisionEnergy = 0; + std::vector tims_frame_list; + PrecursorIonData precursor_ion_data; + }; void - getQualifiedMs2MassSpectrumByPrecursorId(QualifiedMassSpectrum &mass_spectrum, - std::size_t ms2_index, - std::size_t precursor_index, + getQualifiedMs2MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + SpectrumDescr &spectrum_descr, bool want_binary_data); - QualifiedMassSpectrum getQualifiedMs1MassSpectrumByPrecursorId( - std::size_t ms2_index, std::size_t precursor_index, bool want_binary_data); + void + getQualifiedMs1MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id, + QualifiedMassSpectrum &mass_spectrum, + SpectrumDescr &spectrum_descr, + bool want_binary_data); /** @brief filter interface to apply just after raw MS2 specturm extraction * the filter can be a list of filters inside a FilterSuite object @@ -158,10 +164,85 @@ /** @brief get a Tims frame with his database ID + * but look in the cache first + * + * thread safe + */ + TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId); + + /** @brief get a Tims frame with his database ID + * + * this function is not thread safe + */ + TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId); + + XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id, + PrecisionPtr precision_ptr); + + + /** @brief function to visit an MsRunReader and get each Spectrum in a + * spectrum collection handler by Ms Levels + * + * this function will retrieve processed qualified spectrum depending on each + * Bruker precursors + */ + void ms2ReaderSpectrumCollectionByMsLevel( + const MsRunIdCstSPtr &msrun_id, + SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level); + + + /** @brief function to visit an MsRunReader and get each raw Spectrum in a + * spectrum collection handler by Ms Levels + * + * this function will retrieve every scans as a qualified mass spectrum + */ + void rawReaderSpectrumCollectionByMsLevel( + const MsRunIdCstSPtr &msrun_id, + SpectrumCollectionHandlerInterface &handler, + unsigned int ms_level); + + /** @brief get cumulated raw signal for a given precursor + * only to use to see the raw signal + * + * @param precursor_index precursor index to extract signal from + * @result a map of integers, x=time of flights, y= intensities + */ + std::map + getRawMs2ByPrecursorId(std::size_t precursor_index); + + /** @brief get raw signal for a spectrum index + * only to use to see the raw signal + * + * @param spectrum_index spcetrum index + * @result a map of integers, x=time of flights, y= intensities + */ + std::map + getRawMsBySpectrumIndex(std::size_t spectrum_index); + + + /** @brief retention timeline + * get retention times along the MSrun in seconds + * @return vector of retention times (seconds) */ - TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId) const; + virtual std::vector getRetentionTimeLine() const; + + /** @brief get an intermediate structure describing a spectrum + */ + SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id); + + /** @brief set only one is_mono_thread to true + * + * this avoid to use qtconcurrent + */ + void setMonoThread(bool is_mono_thread); + private: + SpectrumDescr getSpectrumDescrWithScanCoordinate( + const std::pair &scan_coordinate); + + std::pair getScanCoordinateFromRawIndex(std::size_t spectrum_index) const; @@ -174,31 +255,11 @@ /** @brief get a Tims frame base (no binary data file access) with his * database ID */ - TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr(std::size_t timsId) const; + TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr(std::size_t timsId); - /** @brief get a Tims frame with his database ID - * but look in the cache first - */ - TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId); - TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtrCached(std::size_t timsId); - /** @brief extract a list of XICs from Tims data - * - * @param precursor_id_list the list of precursors to extract - * @param precision_ptr precision to compute the mz range to extract for each - * precursor mass - * @param xicExtractMethod XIC extraction method (sum or max) to use - * @param rtRange retention time range in seconds to extract XIC from rtTarget - * - rtRange to rtTarget + rtRange - * @result the corresponding XIC list as a specific structure - */ - std::vector extractXicListByPrecursorIds( - const std::vector &precursor_id_list, - PrecisionPtr precision_ptr, - XicExtractMethod xicExtractMethod, - double rtRange) const; std::vector getMatchPrecursorIdByKo(std::vector> ids, @@ -210,12 +271,30 @@ getClosestPrecursorIdByMz(std::vector> ids, double mz_value); + + /** @brief private function to fill m_frameIdDescrList + */ + void fillFrameIdDescrList(); + + + private: + void ms2ReaderGenerateMS1MS2Spectrum( + const MsRunIdCstSPtr &msrun_id, + std::vector &qualified_mass_spectrum_list, + SpectrumCollectionHandlerInterface &handler, + SpectrumDescr &spectrum_descr, + unsigned int ms_level); + + void fillSpectrumDescriptionWithSqlRecord(SpectrumDescr &spectrum_descr, + QSqlQuery &qprecursor_list); + private: QDir m_timsDataDirectory; TimsBinDec *mpa_timsBinDec = nullptr; // QSqlDatabase *mpa_qdb = nullptr; std::size_t m_totalNumberOfScans; std::size_t m_totalNumberOfPrecursors; + std::size_t m_totalNumberOfFrames; std::size_t m_cacheSize = 60; std::deque m_timsFrameCache; std::deque m_timsFrameBaseCache; @@ -229,8 +308,40 @@ std::map m_mapMzCalibrationRecord; + std::map m_mapTimsCalibrationRecord; + std::vector m_mapFramesRecord; + std::map m_mapXicCoordRecord; + + MzCalibrationStore *mpa_mzCalibrationStore; + + + struct FrameIdDescr + { + std::size_t m_frameId; // frame id + std::size_t m_size; // frame size (number of TOF scans in frame) + std::size_t m_cumulSize; // cumulative size + }; + + + /** @brief store every frame id and corresponding sizes + */ + std::vector m_frameIdDescrList; + + /** @brief index to find quickly a frameId in the description list with the + * raw index of spectrum modulo 1000 + * @key thousands of TOF scans + * @value corresponding m_frameIdDescrList index + */ + std::map m_thousandIndexToFrameIdDescrListIndex; + + + /** @brief tells if someone is loading a frame id + */ + std::vector m_someoneIsLoadingFrameId; + + bool m_isMonoThread = false; - MzCalibrationStore * mpa_mzCalibrationStore; + bool m_hasPrecursorTable; QMutex m_mutex; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframe.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframe.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframe.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframe.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -39,7 +39,7 @@ { TimsFrame::XicComputeStructure::XicComputeStructure( - const TimsFrame *fram_p, const TimsXicStructure &xic_struct) + const TimsFrame *fram_p, const XicCoordTims &xic_struct) { xic_ptr = xic_struct.xicSptr.get(); @@ -54,6 +54,12 @@ tmpIntensity = 0; } +TimsFrame::TimsFrame(std::size_t timsId, quint32 scanNum) + : TimsFrameBase(timsId, scanNum) +{ + // m_timsDataFrame.resize(10); +} + TimsFrame::TimsFrame(std::size_t timsId, quint32 scanNum, char *p_bytes, @@ -311,7 +317,8 @@ std::size_t scanNumBegin, std::size_t scanNumEnd) const { - qDebug(); + qDebug() << "begin scanNumBegin=" << scanNumBegin + << " scanNumEnd=" << scanNumEnd; if(m_timsDataFrame.size() == 0) return; @@ -337,6 +344,7 @@ .arg(scanNumEnd) .arg(error.what()); } + qDebug() << "end"; } @@ -375,7 +383,7 @@ qint32 previous = -1; qint32 tof_index; - std::vector index_list; + // std::vector index_list; DataPoint data_point; for(std::size_t i = 0; i < size; i++) { @@ -402,15 +410,26 @@ void TimsFrame::extractTimsXicListInRtRange( - std::vector::iterator &itXicListbegin, - std::vector::iterator &itXicListend, + std::vector::iterator &itXicListbegin, + std::vector::iterator &itXicListend, XicExtractMethod method) const { + qDebug() << std::distance(itXicListbegin, itXicListend); std::vector tmp_xic_list; for(auto it = itXicListbegin; it != itXicListend; it++) { - tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, *it)); + tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, **it)); + + qDebug() << " tmp_xic_struct.mobilityIndexBegin=" + << tmp_xic_list.back().mobilityIndexBegin + << " tmp_xic_struct.mobilityIndexEnd=" + << tmp_xic_list.back().mobilityIndexEnd; + + qDebug() << " tmp_xic_struct.mzIndexLowerBound=" + << tmp_xic_list.back().mzIndexLowerBound + << " tmp_xic_struct.mzIndexUpperBound=" + << tmp_xic_list.back().mzIndexUpperBound; } if(tmp_xic_list.size() == 0) return; @@ -424,7 +443,7 @@ for(auto &&struct_xic : tmp_xic_list) { for(std::size_t scan = struct_xic.mobilityIndexBegin; - scan <= struct_xic.mobilityIndexEnd; + (scan <= struct_xic.mobilityIndexEnd) && (scan < m_scanNumber); scan++) { unique_scan_num_list.push_back(scan); @@ -438,6 +457,7 @@ while(it_scan_num != it_scan_num_end) { TraceSPtr ms_spectrum = getRawTraceSPtr(*it_scan_num); + // qDebug() << ms_spectrum.get()->toString(); for(auto &&tmp_xic_struct : tmp_xic_list) { if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) && @@ -448,6 +468,9 @@ tmp_xic_struct.tmpIntensity += ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound, tmp_xic_struct.mzIndexUpperBound); + + qDebug() << "tmp_xic_struct.tmpIntensity=" + << tmp_xic_struct.tmpIntensity; } else { @@ -455,6 +478,8 @@ tmp_xic_struct.tmpIntensity += ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound, tmp_xic_struct.mzIndexUpperBound); + qDebug() << "tmp_xic_struct.tmpIntensity=" + << tmp_xic_struct.tmpIntensity; } } } @@ -465,10 +490,13 @@ { if(tmp_xic_struct.tmpIntensity != 0) { + qDebug() << tmp_xic_struct.xic_ptr; tmp_xic_struct.xic_ptr->push_back( {m_time, tmp_xic_struct.tmpIntensity}); } } + + qDebug(); } @@ -476,14 +504,14 @@ TimsFrame::getRawTraceSPtr(std::size_t scanNum) const { - qDebug(); + // qDebug(); pappso::TraceSPtr trace_sptr = std::make_shared(); // std::vector if(m_timsDataFrame.size() == 0) return trace_sptr; - qDebug(); + // qDebug(); std::size_t size = getNbrPeaks(scanNum); @@ -503,8 +531,9 @@ data_point.y *= 100.0 / m_accumulationTime; previous = data_point.x; + trace_sptr.get()->push_back(data_point); } - qDebug(); + // qDebug(); return trace_sptr; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframe.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframe.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframe.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframe.h 2022-10-27 09:16:15.000000000 +0000 @@ -33,6 +33,7 @@ #include "../../massspectrum/qualifiedmassspectrum.h" #include "timsframebase.h" #include "../../xic/xic.h" +#include "../../msrun/xiccoord/xiccoordtims.h" namespace pappso { @@ -43,7 +44,6 @@ class TimsBinDec; -struct TimsXicStructure; class TimsDirectXicExtractor; /** @@ -55,7 +55,10 @@ public: /** - * Default constructor + * @param timsId tims frame id + * @param scanNum total number of scans in this frame + * @param p_bytes pointer on the decompressed binary buffer + * @param len size of the decompressed binary buffer */ TimsFrame(std::size_t timsId, quint32 scanNum, @@ -71,7 +74,7 @@ /** * Destructor */ - ~TimsFrame(); + virtual ~TimsFrame(); virtual std::size_t getNbrPeaks(std::size_t scanNum) const override; @@ -93,57 +96,77 @@ std::size_t scanNumBegin, std::size_t scanNumEnd) const override; - /** @brief cumulate a scan list into a map of integers - * @param scanNumBegin first scan to cumulate - * @param scanNumEnd last scan to cumulate - * @param accumulate_into map of x and y integer values - */ - void cumulateScans(std::size_t scanNumBegin, - std::size_t scanNumEnd, - std::map &accumulate_into) const; /** @brief get raw index list for one given scan * index are not TOF nor m/z, just index on digitizer */ - std::vector getScanIndexList(std::size_t scanNum) const; + virtual std::vector getScanIndexList(std::size_t scanNum) const override; /** @brief get raw intensities without transformation from one scan * it needs intensity normalization */ - std::vector getScanIntensities(std::size_t scanNum) const; + virtual std::vector getScanIntensities(std::size_t scanNum) const override; /** @brief get the mass spectrum corresponding to a scan number * @param scanNum the scan number to retrieve * */ - pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const; + virtual pappso::MassSpectrumCstSPtr + getMassSpectrumCstSPtr(std::size_t scanNum) const; + virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override; protected: + /** @brief constructor for binary independant tims frame + * @param timsId tims frame identifier in the database + * @param scanNum the total number of scans contained in this frame + */ + TimsFrame(std::size_t timsId, quint32 scanNum); + void extractTimsXicListInRtRange( - std::vector::iterator &itXicListbegin, - std::vector::iterator &itXicListend, + std::vector::iterator &itXicListbegin, + std::vector::iterator &itXicListend, XicExtractMethod method) const; + + /** @brief cumulate a scan into a map + * + * @param scanNum scan number 0 to (m_scanNumber-1) + */ + virtual void cumulateScan(std::size_t scanNum, + std::map &accumulate_into) const; + + + /** @brief get the raw index tof_index and intensities (normalized) + * + * @param scanNum the scan number to extract + * @return trace vector + * + */ + virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const; + + private: + /** @brief unshuffle data packet of tims compression type 2 + * @param src is a zstd decompressed buffer pointer + */ void unshufflePacket(const char *src); - std::size_t getScanOffset(std::size_t scanNum) const; - - /** @brief cumulate a scan into a map + /** @brief get offset for this spectrum in the binary file + * + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 */ - void cumulateScan(std::size_t scanNum, - std::map &accumulate_into) const; - pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const; + std::size_t getScanOffset(std::size_t scanNum) const; private: struct XicComputeStructure { XicComputeStructure(const TimsFrame *fram_p, - const TimsXicStructure &xic_struct); + const XicCoordTims &xic_struct); Xic *xic_ptr = nullptr; @@ -154,7 +177,7 @@ double tmpIntensity = 0; }; - private: + protected: QByteArray m_timsDataFrame; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframebase.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframebase.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframebase.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframebase.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -30,6 +30,7 @@ #include "mzcalibration/mzcalibrationmodel1.h" #include #include +#include namespace pappso { @@ -103,8 +104,9 @@ if(scanNum >= m_scanNumber) { throw pappso::ExceptionOutOfRange( - QObject::tr("Invalid scan number : scanNum%1 > m_scanNumber") - .arg(scanNum)); + QObject::tr("Invalid scan number : scanNum %1 > m_scanNumber %2") + .arg(scanNum) + .arg(m_scanNumber)); } return true; @@ -119,6 +121,12 @@ .arg(scanNum)); } +std::size_t +TimsFrameBase::getTotalNumberOfScans() const +{ + return m_scanNumber; +} + MassSpectrumSPtr TimsFrameBase::getMassSpectrumSPtr(std::size_t scanNum) const { @@ -382,11 +390,11 @@ data_point_cumul.y *= 100.0 / m_accumulationTime; - qDebug() << "raw data x=" << data_point_cumul.x; + // qDebug() << "raw data x=" << data_point_cumul.x; // mz calibration data_point_cumul.x = mz_calibration_p->getMzFromTofIndex(data_point_cumul.x); - qDebug() << "mz=" << data_point_cumul.x; + // qDebug() << "mz=" << data_point_cumul.x; local_trace.push_back(data_point_cumul); } @@ -448,4 +456,105 @@ msp_mzCalibration = mzCalibration; } + +quint32 +TimsFrameBase::getMaximumRawMassIndex() const +{ + quint32 max_value = 0; + for(quint32 i = 0; i < m_scanNumber; i++) + { + qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i; + std::vector index_list = getScanIndexList(i); + auto it = std::max_element(index_list.begin(), index_list.end()); + if(it != index_list.end()) + { + max_value = std::max(max_value, *it); + } + } + return max_value; +} + +std::vector +TimsFrameBase::getScanIndexList(std::size_t scanNum) const +{ + throw PappsoException( + QObject::tr( + "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1") + .arg(scanNum)); +} + + +std::vector +TimsFrameBase::getScanIntensities(std::size_t scanNum) const +{ + throw PappsoException( + QObject::tr( + "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1") + .arg(scanNum)); +} + +Trace +TimsFrameBase::getIonMobilityTraceByMzIndexRange( + std::size_t mz_index_lower_bound, + std::size_t mz_index_upper_bound, + XicExtractMethod method) const +{ + Trace im_trace; + DataPoint data_point; + for(quint32 i = 0; i < m_scanNumber; i++) + { + data_point.x = i; + data_point.y = 0; + qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i; + std::vector index_list = getScanIndexList(i); + auto it_lower = std::find_if(index_list.begin(), + index_list.end(), + [mz_index_lower_bound](quint32 to_compare) { + if(to_compare < mz_index_lower_bound) + { + return false; + } + return true; + }); + + + if(it_lower == index_list.end()) + { + } + else + { + + + auto it_upper = + std::find_if(index_list.begin(), + index_list.end(), + [mz_index_upper_bound](quint32 to_compare) { + if(mz_index_upper_bound >= to_compare) + { + return false; + } + return true; + }); + std::vector intensity_list = getScanIntensities(i); + for(int j = std::distance(index_list.begin(), it_lower); + j < std::distance(index_list.begin(), it_upper); + j++) + { + if(method == XicExtractMethod::sum) + { + data_point.y += intensity_list[j]; + } + else + { + data_point.y = + std::max((double)intensity_list[j], data_point.y); + } + } + } + im_trace.push_back(data_point); + } + qDebug(); + return im_trace; +} +// namespace pappso } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframebase.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframebase.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframebase.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframebase.h 2022-10-27 09:16:15.000000000 +0000 @@ -62,28 +62,64 @@ /** * Destructor */ - ~TimsFrameBase(); + virtual ~TimsFrameBase(); /** @brief tells if 2 tims frame has the same calibration data * Usefull to know if raw data can be handled between frames */ virtual bool hasSameCalibrationData(const TimsFrameBase &other) const; + /** @brief get the number of peaks in this spectrum + * need the binary file + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + */ virtual std::size_t getNbrPeaks(std::size_t scanNum) const; + + /** @brief get the number of scans contained in this frame + * each scan represents an ion mobility slice + */ + + virtual std::size_t getTotalNumberOfScans() const; + + + /** @brief get the maximum raw mass index contained in this frame + */ + virtual quint32 getMaximumRawMassIndex() const; + + /** @brief get Mass spectrum with peaks for this scan number + * need the binary file + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + */ virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const; + + /** @brief cumulate spectrum given a scan number range + * need the binary file + * @param scanNumBegin scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + * @param scanNumEnd scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + */ virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const; /** @brief cumulate scan list into a trace into a raw spectrum map * @param rawSpectrum simple map of integers to cumulate raw counts - * @param scanNumBegin first scan to cumulate - * @param scanNumEnd last scan to cumulate + * @param scanNumBegin scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + * @param scanNumEnd scan number in the frame in the order it lies in binary + * file, from 0 to N-1 */ virtual void cumulateScansInRawMap(std::map &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const; + /** @brief check that this scan number exists + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + */ bool checkScanNum(std::size_t scanNum) const; @@ -120,24 +156,31 @@ std::size_t getId() const; /** @brief get drift time of a scan number in milliseconds - * @param scanNum the scan number + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 * @return time in milliseconds of mobility delay (drift time) * */ double getDriftTime(std::size_t scanNum) const; /** @brief get 1/K0 value of a given scan (mobility value) - * @param scanNum the scan number + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 * */ double getOneOverK0Transformation(std::size_t scanNum) const; /** @brief get the scan number from a given 1/Ko mobility value * @param one_over_k0 the mobility value to tranform - * @return integer the scan number + * @return integer the scan number in the frame in the order it lies in binary + * file, from 0 to N-1 */ std::size_t getScanNumFromOneOverK0(double one_over_k0) const; - + /** @brief get voltage for a given scan number + * @param scanNum scan number in the frame in the order it lies in binary + * file, from 0 to N-1 + * @return double volt measure + * */ double getVoltageTransformation(std::size_t scanNum) const; @@ -159,6 +202,29 @@ void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration); + + /** @brief get raw index list for one given scan + * index are not TOF nor m/z, just index on digitizer + */ + virtual std::vector getScanIndexList(std::size_t scanNum) const; + + /** @brief get raw intensities without transformation from one scan + * it needs intensity normalization + */ + virtual std::vector getScanIntensities(std::size_t scanNum) const; + + /** @brief get a mobility trace cumulating intensities inside the given mass + * index range + * @param mz_index_lower_bound raw mass index lower bound + * @param mz_index_upper_bound raw mass index upper bound + * @param method max or sum intensities + */ + virtual Trace + getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound, + std::size_t mz_index_upper_bound, + XicExtractMethod method) const; + + protected: /** @brief total number of scans contained in this frame */ diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerawdatachunck.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerawdatachunck.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerawdatachunck.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerawdatachunck.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,213 @@ +/** + * \file pappsomspp/vendors/tims/timsframerawdatachunck.cpp + * \date 18/6/2022 + * \author Olivier Langella + * \brief stores raw binary tims frame + */ + +/******************************************************************************* + * Copyright (c) 2022 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "timsframerawdatachunck.h" +#include + +#include "../../pappsoexception.h" + +using namespace pappso; + +TimsFrameRawDataChunck::TimsFrameRawDataChunck() +{ +} + +TimsFrameRawDataChunck::~TimsFrameRawDataChunck() +{ + if(mpa_memoryBuffer != nullptr) + delete[] mpa_memoryBuffer; +} + +bool +TimsFrameRawDataChunck::readTimsFrame( + QFile *p_file, + std::size_t frameId, + const std::vector &frame_record_list) +{ + + m_frameId = frameId; + qint64 position = p_file->pos(); + const pappso::TimsFrameRecord &frame_record = frame_record_list[frameId]; + if(frameId == 1) + { + bool seekpos_ok = p_file->seek(frame_record.tims_offset); + if(!seekpos_ok) + { + throw PappsoException(QObject::tr("ERROR reading TIMS frame %1 " + "m_timsBinFile.seek(%3) failed") + .arg(frameId) + .arg(frame_record.tims_offset)); + } + } + else + { + + if(position == (qint64)frame_record.tims_offset) + { + // OK + } + else + { + // need to move to frame position : + if(position > (qint64)frame_record.tims_offset) + { + // get back + p_file->seek(frame_record.tims_offset); + position = p_file->pos(); + } + else + { + const pappso::TimsFrameRecord &previous_frame_record = + frame_record_list[frameId - 1]; + if(position < (qint64)previous_frame_record.tims_offset) + { + + throw PappsoException( + QObject::tr("ERROR reading TIMS frame %1 " + "file position %2 is before previous frame %3") + .arg(frameId) + .arg(position) + .arg(previous_frame_record.tims_offset)); + } + else + { + // catch up current position + qint64 move_size = + (qint64)frame_record.tims_offset - position; + p_file->read(move_size); + position = p_file->pos(); + } + } + } + } + + if(position != (qint64)frame_record.tims_offset) + { + + throw PappsoException( + QObject::tr("ERROR reading TIMS frame %1 " + "file position %2 is different of frame offset %3") + .arg(frameId) + .arg(position) + .arg(frame_record.tims_offset)); + } + qDebug(); + p_file->read((char *)&m_frameLength, 4); + // frame_length = qToBigEndian(frame_length); + + // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + // << " frame_length=" << frame_length; + + qDebug(); + p_file->read((char *)&m_frameNumberOfScans, 4); + // scan_number = qToBigEndian(scan_number); + + // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + // << " pos=" << m_timsBinFile.pos(); + + // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + // << " scan_number=" << scan_number; + // m_timsBinFile.seek(m_indexArray.at(timsId) + 8); + + + qDebug(); + + // if (m_memoryBufferSize + if(mpa_memoryBuffer == nullptr) + { + qDebug() << "mpa_memoryBuffer == nullptr"; + m_memoryBufferSize = (qint64)m_frameLength + 10; + mpa_memoryBuffer = new char[m_memoryBufferSize]; + } + if((m_memoryBufferSize - 10) < m_frameLength) + { + if(mpa_memoryBuffer != nullptr) + { + delete[] mpa_memoryBuffer; + } + m_memoryBufferSize = (qint64)m_frameLength + 10; + mpa_memoryBuffer = new char[m_memoryBufferSize]; + } + + + // QByteArray frame_byte_array(mpa_memoryBuffer, m_memoryBufferSize); + + qDebug(); + qint64 read_length = + p_file->read(mpa_memoryBuffer, (qint64)m_frameLength - 8); + qDebug(); + + // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + // << " +frame_length-1=" + // << (quint8) * (frame_byte_array.constData() + frame_length - 1); + // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + // << " +frame_length=" + // << (quint8) * (frame_byte_array.constData() + frame_length); + // m_timsBinFile.seek(m_indexArray.at(timsId) + 8); + + if(read_length + 8 != (qint64)m_frameLength) + { + throw PappsoException(QObject::tr("ERROR reading TIMS frame %1: " + "read_length=%2 != %3frame_length") + .arg(frameId) + .arg(read_length) + .arg(m_frameLength)); + } + + return true; +} + +char * +pappso::TimsFrameRawDataChunck::getMemoryBuffer() const +{ + return mpa_memoryBuffer; +} + +quint32 +pappso::TimsFrameRawDataChunck::getCompressedSize() const +{ + return m_frameLength - 8; +} + +quint32 +pappso::TimsFrameRawDataChunck::getFrameNumberOfScans() const +{ + return m_frameNumberOfScans; +} + +quint32 +pappso::TimsFrameRawDataChunck::getFrameLength() const +{ + return m_frameLength; +} + +std::size_t +pappso::TimsFrameRawDataChunck::getFrameId() const +{ + return m_frameId; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerawdatachunck.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerawdatachunck.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerawdatachunck.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerawdatachunck.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,75 @@ +/** + * \file pappsomspp/vendors/tims/timsframerawdatachunck.h + * \date 18/6/2022 + * \author Olivier Langella + * \brief stores raw binary tims frame + */ + +/******************************************************************************* + * Copyright (c) 2022 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include "timsframerecord.h" +#include "../../exportinmportconfig.h" + +namespace pappso +{ +/** + * @todo write docs + */ +class PMSPP_LIB_DECL TimsFrameRawDataChunck +{ + public: + /** + * Default constructor + */ + TimsFrameRawDataChunck(); + + /** + * Destructor + */ + virtual ~TimsFrameRawDataChunck(); + + + bool + readTimsFrame(QFile *p_file, + std::size_t frameId, + const std::vector &frame_record_list); + + + quint32 getFrameNumberOfScans() const; + quint32 getCompressedSize() const; + quint32 getFrameLength() const; + char *getMemoryBuffer() const; + std::size_t getFrameId() const; + + private: + char *mpa_memoryBuffer = nullptr; + qint64 m_memoryBufferSize = 0; + + std::size_t m_frameId = 0; + quint32 m_frameLength = 0; + quint32 m_frameNumberOfScans = 0; +}; + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerecord.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerecord.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframerecord.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframerecord.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,45 @@ +/** + * \file pappsomspp/vendors/tims/timsframerecord.h + * \date 19/6/2022 + * \author Olivier Langella + * \brief simple structure to store SQL lite frame records + */ + +/******************************************************************************* + * Copyright (c) 2022 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + + +namespace pappso +{ +struct TimsFrameRecord +{ + std::size_t tims_offset = 0; + double accumulation_time = 0; + std::size_t mz_calibration_id = 0; + double frame_t1 = 0; + double frame_t2 = 0; + double frame_time = 0; + int msms_type = 0; + std::size_t tims_calibration_id = 0; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframetype1.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframetype1.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframetype1.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframetype1.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,512 @@ +/** + * \file pappsomspp/vendors/tims/timsframetype1.cpp + * \date 3/10/2021 + * \author Olivier Langella + * \brief handle a single Bruker's TimsTof frame type 1 compression + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +#include "timsframetype1.h" +#include "../../../pappsomspp/pappsoexception.h" +#include "../../../pappsomspp/exception/exceptionoutofrange.h" +#include "../../../pappsomspp/exception/exceptionnotimplemented.h" +#include +#include +#include + + +namespace pappso +{ +TimsFrameType1::TimsFrameType1(std::size_t timsId, + quint32 scanNum, + char *p_bytes, + std::size_t len) + : TimsFrame(timsId, scanNum) +{ + qDebug() << timsId; + m_timsDataFrame.resize(len * 2); + + if(p_bytes != nullptr) + { + qDebug() << timsId; + copyAndLzfDecompress(p_bytes, len); + qDebug() << timsId; + } + else + { + if(m_scanNumber == 0) + { + + throw pappso::PappsoException( + QObject::tr( + "TimsFrameType1::TimsFrameType1(%1,%2,nullptr,%3) FAILED") + .arg(m_timsId) + .arg(m_scanNumber) + .arg(len)); + } + } +} + +TimsFrameType1::TimsFrameType1(const TimsFrameType1 &other) : TimsFrame(other) +{ +} + +TimsFrameType1::~TimsFrameType1() +{ +} + + +void +TimsFrameType1::copyAndLzfDecompress(const char *src, std::size_t len) +{ + + qDebug() << " m_scanNumber=" << m_scanNumber << " len=" << len; + // the start position offset for each scan and the length of the last scan + // copy first m_scanNumber*4 bytes in qbyte array + std::size_t count = (m_scanNumber + 2) * 4; + + qDebug() << " count=" << count; + if(m_timsDataFrame.size() < (long)(count + count)) + { + qDebug() << " m_timsDataFrame.size()=" << m_timsDataFrame.size(); + m_timsDataFrame.resize(count + count); + } + + /* + std::size_t decompressed_size = + lzfDecompressScan(src + 3687 - 8, + 9, + m_timsDataFrame.data() + 3660, + m_timsDataFrame.size() - 3660); + + qDebug() << "decompressed_size=" << decompressed_size; + */ + // memcpy(m_timsDataFrame.data(), src, count); + + qDebug() << "offset begin at last :" << count + 4; + + // std::vector compressed_len_list; + std::size_t offset; + std::size_t previous_offset = (*(quint32 *)(src)); + qDebug() << "first offset= " << previous_offset; + std::size_t cumul_decompressed_size = 0; + + + for(quint32 i = 1; i <= m_scanNumber; i++) + { + offset = (*(quint32 *)(src + (i * 4))); + + std::size_t compressed_size = offset - previous_offset; + + qDebug() << "scan i=" << i << " previous_offset=" << previous_offset + << " offset=" << offset << " length=" << compressed_size; + // compressed_len_list.push_back(offset - previous_offset); + std::size_t remaining_size = m_timsDataFrame.size(); + + if(cumul_decompressed_size < remaining_size) + { + remaining_size = remaining_size - cumul_decompressed_size; + } + else + { + remaining_size = 0; + } + qDebug() << " remaining_size=" << remaining_size; + std::size_t decompressed_size = + lzfDecompressScan(src + previous_offset - 8, + compressed_size, + m_timsDataFrame.data() + cumul_decompressed_size, + remaining_size); + + + m_scanOffsetList.push_back(cumul_decompressed_size); + m_scanSizeList.push_back(decompressed_size / 4); + cumul_decompressed_size += decompressed_size; + qDebug() << " decompressed_size=" << decompressed_size; + + + previous_offset = offset; + } + /* + std::size_t last_offset = (*(quint32 *)(src + (m_scanNumber * 4))); + qDebug() << "last scan length :" << last_offset; + + qDebug() << "last scan length bonus:" + << (*(quint32 *)(src + (m_scanNumber + 1 * 4))); + + qDebug() << " m_scanOffsetList.size()=" << m_scanOffsetList.size() + << " m_scanNumber=" << m_scanNumber; + */ + /* + throw PappsoException( + QObject::tr("ERROR reading TimsFrameType1 ").arg(m_timsId)); + */ +} + + +unsigned int +TimsFrameType1::lzfDecompressScan(const char *src, + unsigned int src_len, + char *dest, + unsigned int dest_len) +{ + qDebug() << "src=" << src << " src_len=" << src_len + << " dest_len=" << dest_len; + if(src_len == 0) + return 0; + unsigned int decompressed_size; + unsigned int more_space = src_len * 2; + decompressed_size = lzf_decompress(src, src_len, dest, dest_len); + while(decompressed_size == 0) + { + qDebug() << "dest_len=" << dest_len; + qDebug() << "decompressed_size=" << decompressed_size; + + if(errno == EINVAL) + { + throw PappsoException( + QObject::tr("ERROR reading TimsFrameType1 %1 TIMS binary file %2: " + "LZF decompression error EINVAL") + .arg(m_timsId)); + } + else if(errno == E2BIG) + { + qDebug() << " m_timsDataFrame.size()=" << m_timsDataFrame.size() + << " more_space=" << more_space; + m_timsDataFrame.resize(m_timsDataFrame.size() + more_space); + dest_len += more_space; + qDebug(); + decompressed_size = lzf_decompress(src, src_len, dest, dest_len); + } + else + { + break; + } + } + return decompressed_size; +} + +std::size_t +TimsFrameType1::getNbrPeaks(std::size_t scanNum) const +{ + pappso::MassSpectrumSPtr mass_spectrum_sptr = getMassSpectrumSPtr(scanNum); + return mass_spectrum_sptr.get()->size(); +} + + +void +TimsFrameType1::cumulateScan(std::size_t scanNum, + std::map &accumulate_into) const +{ + if(m_timsDataFrame.size() == 0) + return; + // checkScanNum(scanNum); + + + std::size_t size = m_scanSizeList[scanNum]; + + std::size_t offset = m_scanOffsetList[scanNum]; + + // qDebug() << "begin offset=" << offset << " size=" << size; + qint32 value = 0; + qint32 tof_index = 0; + for(std::size_t i = 0; i < size; i++) + { + value = (*(qint32 *)(m_timsDataFrame.constData() + offset + (i * 4))); + // qDebug() << " i=" << i << " value=" << value; + + if(value < 0) + { + tof_index += -1 * value; + } + else + { + + quint32 x = tof_index; + quint32 y = value; + + auto ret = accumulate_into.insert(std::pair(x, y)); + + if(ret.second == false) + { + // already existed : cumulate + ret.first->second += y; + } + tof_index++; + } + } + qDebug() << "end"; +} + +std::vector +TimsFrameType1::getScanIndexList(std::size_t scanNum) const +{ + qDebug(); + checkScanNum(scanNum); + + std::vector mzindex_values; + + try + { + qDebug(); + + + if(m_timsDataFrame.size() == 0) + return mzindex_values; + qDebug(); + + std::size_t size = m_scanSizeList[scanNum]; + + std::size_t offset = m_scanOffsetList[scanNum]; + + qDebug() << " offset=" << offset << " size=" << size; + if(size == 0) + return mzindex_values; + + qint32 value = 0; + qint32 tof_index = 0; + // std::vector index_list; + for(std::size_t i = 0; i < size; i++) + { + value = (*(qint32 *)(m_timsDataFrame.constData() + offset + (i * 4))); + + if(value < 0) + { + tof_index += -1 * value; + } + else + { + mzindex_values.push_back(tof_index); + tof_index++; + } + } + + + qDebug(); + return mzindex_values; + } + catch(PappsoException &error) + { + throw pappso::PappsoException(QObject::tr("Error %1 frameId=%2 " + "scanNum=%3 :\n%4") + .arg(__FUNCTION__) + .arg(getId()) + .arg(scanNum) + .arg(error.qwhat())); + } + qDebug(); +} + +std::vector +TimsFrameType1::getScanIntensities(std::size_t scanNum) const +{ + + + qDebug() << " scanNum=" << scanNum; + + checkScanNum(scanNum); + + std::vector int_values; + + try + { + qDebug(); + + + if(m_timsDataFrame.size() == 0) + return int_values; + qDebug(); + + std::size_t size = m_scanSizeList[scanNum]; + + std::size_t offset = m_scanOffsetList[scanNum]; + + qDebug() << " offset=" << offset << " size=" << size; + if(size == 0) + return int_values; + + qint32 value = 0; + qint32 tof_index = 0; + // std::vector index_list; + for(std::size_t i = 0; i < size; i++) + { + value = (*(qint32 *)(m_timsDataFrame.constData() + offset + (i * 4))); + + if(value < 0) + { + tof_index += -1 * value; + } + else + { + int_values.push_back(value); + tof_index++; + } + } + + + qDebug(); + return int_values; + } + catch(PappsoException &error) + { + throw pappso::PappsoException(QObject::tr("Error %1 frameId=%2 " + "scanNum=%3 :\n%4") + .arg(__FUNCTION__) + .arg(getId()) + .arg(scanNum) + .arg(error.qwhat())); + } +} + +pappso::MassSpectrumSPtr +TimsFrameType1::getMassSpectrumSPtr(std::size_t scanNum) const +{ + + qDebug() << " scanNum=" << scanNum; + + checkScanNum(scanNum); + + try + { + qDebug(); + + pappso::MassSpectrumSPtr mass_spectrum_sptr = + std::make_shared(); + // std::vector + + if(m_timsDataFrame.size() == 0) + return mass_spectrum_sptr; + qDebug(); + + std::size_t size = m_scanSizeList[scanNum]; + + std::size_t offset = m_scanOffsetList[scanNum]; + + qDebug() << " offset=" << offset << " size=" << size; + if(size == 0) + return mass_spectrum_sptr; + + + MzCalibrationInterface *mz_calibration_p = + getMzCalibrationInterfaceSPtr().get(); + + + qint32 value = 0; + qint32 tof_index = 0; + // std::vector index_list; + DataPoint data_point; + for(std::size_t i = 0; i < size; i++) + { + value = (*(qint32 *)(m_timsDataFrame.constData() + offset + (i * 4))); + + if(value < 0) + { + tof_index += -1 * value; + } + else + { + data_point.y = value; + + // intensity normalization + data_point.y *= 100.0 / m_accumulationTime; + + + // mz calibration + data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index); + mass_spectrum_sptr.get()->push_back(data_point); + tof_index++; + } + } + + + qDebug() << mass_spectrum_sptr.get()->toString(); + return mass_spectrum_sptr; + } + catch(PappsoException &error) + { + throw pappso::PappsoException( + QObject::tr("Error TimsFrameType1::getMassSpectrumSPtr frameId=%1 " + "scanNum=%2 :\n%3") + .arg(getId()) + .arg(scanNum) + .arg(error.qwhat())); + } +} + + +pappso::TraceSPtr +TimsFrameType1::getRawTraceSPtr(std::size_t scanNum) const +{ + + // qDebug(); + + pappso::TraceSPtr trace_sptr = std::make_shared(); + // std::vector + + if(m_timsDataFrame.size() == 0) + return trace_sptr; + qDebug(); + + std::size_t size = m_scanSizeList[scanNum]; + + std::size_t offset = m_scanOffsetList[scanNum]; + + qDebug() << " offset=" << offset << " size=" << size; + if(size == 0) + return trace_sptr; + + // qDebug(); + qint32 value = 0; + qint32 tof_index = 0; + + // std::vector index_list; + DataPoint data_point; + for(std::size_t i = 0; i < size; i++) + { + value = (*(qint32 *)(m_timsDataFrame.constData() + offset + (i * 4))); + + if(value < 0) + { + tof_index += -1 * value; + } + else + { + data_point.y = value; + + // intensity normalization + data_point.y *= 100.0 / m_accumulationTime; + + + // mz calibration + data_point.x = tof_index; + trace_sptr.get()->push_back(data_point); + tof_index++; + } + } + + + // qDebug(); + return trace_sptr; +} + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframetype1.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframetype1.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsframetype1.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsframetype1.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,130 @@ +/** + * \file pappsomspp/vendors/tims/timsframetype1.h + * \date 3/10/2021 + * \author Olivier Langella + * \brief handle a single Bruker's TimsTof frame type 1 compression + */ + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include "timsframe.h" + +namespace pappso +{ +/** + * @todo write docs + */ +class TimsFrameType1 : public TimsFrame +{ + public: + /** + * @param timsId tims frame id + * @param scanNum total number of scans in this frame + * @param p_bytes pointer on the decompressed binary buffer + * @param len size of the decompressed binary buffer + */ + TimsFrameType1(std::size_t timsId, + quint32 scanNum, + char *p_bytes, + std::size_t len); + + /** + * Copy constructor + * + * @param other TODO + */ + TimsFrameType1(const TimsFrameType1 &other); + + /** + * Destructor + */ + virtual ~TimsFrameType1(); + + + virtual std::size_t getNbrPeaks(std::size_t scanNum) const override; + + + /** @brief get raw index list for one given scan + * index are not TOF nor m/z, just index on digitizer + */ + virtual std::vector + getScanIndexList(std::size_t scanNum) const override; + + /** @brief get raw intensities without transformation from one scan + * it needs intensity normalization + */ + virtual std::vector + getScanIntensities(std::size_t scanNum) const override; + + /** @brief get the mass spectrum corresponding to a scan number + * @param scanNum the scan number to retrieve + * */ + + virtual pappso::MassSpectrumSPtr + getMassSpectrumSPtr(std::size_t scanNum) const override; + + + protected: + /** @brief cumulate a scan into a map + * + * @param scanNum scan number 0 to (m_scanNumber-1) + */ + virtual void + cumulateScan(std::size_t scanNum, + std::map &accumulate_into) const override; + + + /** @brief get the raw index tof_index and intensities (normalized) + * + * @param scanNum the scan number to extract + * @return trace vector + * + */ + virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const override; + + private: + /** @brief copy buffer header and lzf decompress each scan for tims + * compression type 1 + * @param src raw data buffer containing scan offsets and LZF compressed scans + * @param len length of the data buffer + */ + void copyAndLzfDecompress(const char *src, std::size_t len); + + /** @brief decompress a single LZF compressed scan buffer + * @param src pointer on the LZF compressed buffer + * @param src_len length of the source buffer + * @param dest pointer to the destination buffer (in the qbyte array) + * @param dest_len length of the destination buffer (max possible in the + * qbytearray) + * @return scan decompressed size + */ + unsigned int lzfDecompressScan(const char *src, + unsigned int src_len, + char *dest, + unsigned int dest_len); + + private: + std::vector m_scanOffsetList; + std::vector m_scanSizeList; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsms2centroidfilter.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsms2centroidfilter.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/timsms2centroidfilter.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/timsms2centroidfilter.h 2022-10-27 09:16:15.000000000 +0000 @@ -49,7 +49,7 @@ /** * Destructor */ - ~TimsMs2CentroidFilter(); + virtual ~TimsMs2CentroidFilter(); MassSpectrum &filter(MassSpectrum &data_points) const; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,11 +26,14 @@ ******************************************************************************/ #include "timsdirectxicextractor.h" +#include "../../../msrun/xiccoord/xiccoordtims.h" +#include "../../../exception/exceptioninterrupted.h" +#include using namespace pappso; -TimsDirectXicExtractor::TimsDirectXicExtractor(const TimsData *mp_tims_data) - : pappso::TimsXicExtractorInterface(mp_tims_data) +TimsDirectXicExtractor::TimsDirectXicExtractor(MsRunReaderSPtr &msrun_reader) + : pappso::TimsXicExtractorInterface(msrun_reader) { } @@ -40,39 +43,94 @@ void -TimsDirectXicExtractor::extractTimsXicList( - std::vector &timsXicList, double rtRange) const +pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) { - if(timsXicList.size() == 0) + qDebug(); + std::size_t xic_total_number = + std::distance(it_xic_coord_list_begin, it_xic_coord_list_end); + if(xic_total_number == 0) return; - std::sort(timsXicList.begin(), - timsXicList.end(), - [](const TimsXicStructure &a, const TimsXicStructure &b) { - return a.rtTarget < b.rtTarget; - }); - std::vector tims_frameid_list = - mp_timsData->getTimsMS1FrameIdRange(timsXicList[0].rtTarget - rtRange, - timsXicList.back().rtTarget + rtRange); + std::vector xic_coord_tims_list; + xic_coord_tims_list.reserve(xic_total_number); - std::vector::iterator itXicListbegin = timsXicList.begin(); - std::vector::iterator itXicListend = timsXicList.begin(); + for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++) + { + XicCoordTims *p_xic_coord_tims = dynamic_cast(it->get()); + if(p_xic_coord_tims == nullptr) + { + } + else + { + xic_coord_tims_list.push_back(p_xic_coord_tims); + } + } + std::sort(xic_coord_tims_list.begin(), + xic_coord_tims_list.end(), + [](const XicCoordTims *pa, const XicCoordTims *pb) { + return pa->rtTarget < pb->rtTarget; + }); + + + std::vector tims_frameid_list = + mp_timsData->getTimsMS1FrameIdRange( + xic_coord_tims_list[0]->rtTarget - m_retentionTimeAroundTarget, + xic_coord_tims_list.back()->rtTarget + m_retentionTimeAroundTarget); + + monitor.setStatus(QObject::tr("extracting %1 XICs on %2 Tims frames") + .arg(xic_total_number) + .arg(tims_frameid_list.size())); + monitor.setTotalSteps(tims_frameid_list.size()); + + qDebug() << " tims_frameid_list.size()=" << tims_frameid_list.size(); + qDebug() << " rt begin=" << xic_coord_tims_list[0]->rtTarget; + qDebug() << " rt end=" << xic_coord_tims_list.back()->rtTarget; for(std::size_t frame_id : tims_frameid_list) { - TimsFrameCstSPtr frame_sptr = mp_timsData->getTimsFrameCstSPtr(frame_id); - double rt = frame_sptr.get()->getTime(); - while((itXicListbegin != timsXicList.end()) && - ((itXicListbegin->rtTarget - rtRange) < rt)) + std::vector::iterator itXicListbegin = + xic_coord_tims_list.begin(); + std::vector::iterator itXicListend = + xic_coord_tims_list.end(); + qDebug(); + TimsFrameCstSPtr frame_sptr = + mp_timsData->getTimsFrameCstSPtrCached(frame_id); + qDebug(); + double rtframe = frame_sptr.get()->getTime(); + qDebug(); + + double rtbeginframe = rtframe - m_retentionTimeAroundTarget; + double rtendframe = rtframe + m_retentionTimeAroundTarget; + + if(rtbeginframe < 0) + rtbeginframe = 0; + + qDebug() << rtbeginframe; + while((itXicListbegin != itXicListend) && + ((*itXicListbegin)->rtTarget < rtbeginframe)) { itXicListbegin++; } - while((itXicListend != timsXicList.end()) && - (rt < (itXicListend->rtTarget + rtRange))) + qDebug(); + itXicListend = itXicListbegin; + while((itXicListend != xic_coord_tims_list.end()) && + ((*itXicListend)->rtTarget < rtendframe)) { itXicListend++; } frame_sptr.get()->extractTimsXicListInRtRange( itXicListbegin, itXicListend, m_xicExtractMethod); + + qDebug() << "" << frame_sptr.get()->getId(); + monitor.count(); + if(monitor.shouldIstop()) + { + throw pappso::ExceptionInterrupted( + QObject::tr("Xic extraction process interrupted")); + } } + qDebug(); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.h 2022-10-27 09:16:15.000000000 +0000 @@ -28,7 +28,6 @@ #pragma once #include "timsxicextractorinterface.h" - namespace pappso { /** @@ -40,16 +39,17 @@ /** * Default constructor */ - TimsDirectXicExtractor(const TimsData *mp_tims_data); + TimsDirectXicExtractor(MsRunReaderSPtr &msrun_reader); /** * Destructor */ virtual ~TimsDirectXicExtractor(); - protected: - virtual void extractTimsXicList(std::vector &timsXicList, - double rtRange) const override; + void protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) override; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxic.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxic.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxic.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxic.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -#include "timsxic.h" - -TimsXic::TimsXic() -{ -} - -TimsXic::TimsXic(const TimsXic &other) -{ -} - -TimsXic::~TimsXic() -{ -} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxic.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxic.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxic.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxic.h 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -#ifndef TIMSXIC_H -#define TIMSXIC_H - -/** - * @todo write docs - */ -class TimsXic -{ - public: - /** - * Default constructor - */ - TimsXic(); - - /** - * Copy constructor - * - * @param other TODO - */ - TimsXic(const TimsXic &other); - - /** - * Destructor - */ - ~TimsXic(); -}; - -#endif // TIMSXIC_H diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,21 +26,29 @@ ******************************************************************************/ #include "timsxicextractorinterface.h" +#include "../../../msrun/private/timsmsrunreaderms2.h" +#include "../../../exception/exceptionnotpossible.h" using namespace pappso; TimsXicExtractorInterface::TimsXicExtractorInterface( - const TimsData *mp_tims_data) - : mp_timsData(mp_tims_data) + MsRunReaderSPtr &msrun_reader) + : MsRunXicExtractorInterface(msrun_reader) { -} -TimsXicExtractorInterface::~TimsXicExtractorInterface() -{ + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(msrun_reader.get()); + if(tims2_reader != nullptr) + { + mp_timsData = tims2_reader->getTimsDataSPtr().get(); + } + else + { + throw pappso::ExceptionNotPossible(QObject::tr( + "error: TimsXicExtractorInterface must use a TimsMsRunReaderMs2")); + } } -void -TimsXicExtractorInterface::setXicExtractMethod(XicExtractMethod method) +TimsXicExtractorInterface::~TimsXicExtractorInterface() { - m_xicExtractMethod = method; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -31,6 +31,7 @@ #include "../../../mzrange.h" #include "../../../xic/xic.h" #include "../timsdata.h" +#include "../../../xicextractor/msrunxicextractorinterface.h" namespace pappso { @@ -38,33 +39,16 @@ /** * @todo set of minimum functions to build XICs using Tims data */ -class TimsXicExtractorInterface +class TimsXicExtractorInterface : public MsRunXicExtractorInterface { friend TimsData; public: - TimsXicExtractorInterface(const TimsData *mp_tims_data); + TimsXicExtractorInterface(MsRunReaderSPtr &msrun_reader); virtual ~TimsXicExtractorInterface(); - /** @brief set the XIC extraction method - */ - void setXicExtractMethod(XicExtractMethod method); // sum or max - - - protected: - /** @brief extract XICs for given coordinates - * XICs are extracted given their coordinates : retention time target, - * mobility range, mz range - * @param timsXicList list of TIMS XIC structures (XIC coordinates) - * @param rtRange the range in seconds that will be applied before and after - * XIC rtTarget to extract signal - */ - virtual void extractTimsXicList(std::vector &timsXicList, - double rtRange) const = 0; - protected: - const TimsData *mp_timsData; - XicExtractMethod m_xicExtractMethod = XicExtractMethod::max; + TimsData *mp_timsData; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/CMakeLists.txt libpappsomspp-0.8.58/src/pappsomspp/widget/CMakeLists.txt --- libpappsomspp-0.8.15/src/pappsomspp/widget/CMakeLists.txt 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/CMakeLists.txt 2022-10-27 09:16:15.000000000 +0000 @@ -5,6 +5,10 @@ message(\n${BoldRed}"Now configuring src/widget for ${PROJECT_NAME}"${ColourReset}\n) +# Find includes in corresponding build directories + +set(CMAKE_INCLUDE_CURRENT_DIR ON) + find_package(Qt5 COMPONENTS Core Gui PrintSupport Svg REQUIRED) @@ -20,12 +24,20 @@ # Files SET(PAPPSOWIDGET_CPP_FILES graphicdevicewidget.cpp + httpbutton/httpbutton.cpp precisionwidget/precisionwidget.cpp massspectrumwidget/qcpspectrum.cpp massspectrumwidget/massspectrumwidget.cpp + obo/obochooserwidget/obochooserwidget.cpp + obo/obolistwidget/obolistmodel.cpp + obo/obolistwidget/obolistproxymodel.cpp + obo/obolistwidget/obolistwidget.cpp + obo/obotermform/obotermform.cpp xicwidget/qcpxic.cpp xicwidget/xicwidget.cpp - plotwidget/colormapplotconfig.cpp + plotwidget/baseplotcontext.cpp + plotwidget/massspectraceplotcontext.cpp + plotwidget/colormapplotconfig.cpp plotwidget/baseplotwidget.cpp plotwidget/basetraceplotwidget.cpp plotwidget/ticxicchromtraceplotwidget.cpp @@ -35,12 +47,23 @@ plotwidget/ticxicchrommassspeccolormapplotwidget.cpp plotwidget/ticxicchromdriftspeccolormapplotwidget.cpp plotwidget/driftspecmassspeccolormapplotwidget.cpp + switchbuttonwidget/switchbuttonwidget.cpp ) +set(GUI_UIS + ./obo/obochooserwidget/uiobochooserwidget.ui + ./obo/obolistwidget/uiobolistwidget.ui + ./obo/obotermform/uiobotermform.ui +) + + +# this will run uic on .ui files: +qt5_wrap_ui( GUI_UI_HDRS ${GUI_UIS} ) + ############################################################# # Build the static lib -add_library(pappsomspp-widget-static STATIC ${PAPPSOWIDGET_CPP_FILES}) +add_library(pappsomspp-widget-static STATIC ${PAPPSOWIDGET_CPP_FILES} ${GUI_UI_HDRS}) set_target_properties(pappsomspp-widget-static PROPERTIES OUTPUT_NAME pappsomspp-widget @@ -58,6 +81,7 @@ Boost::thread Boost::chrono PwizLite::PwizLite + liblzf::liblzf ) @@ -72,7 +96,7 @@ ############################################################# # Build the shared lib -add_library(pappsomspp-widget-shared SHARED ${PAPPSOWIDGET_CPP_FILES}) +add_library(pappsomspp-widget-shared SHARED ${PAPPSOWIDGET_CPP_FILES} ${GUI_UI_HDRS}) set_target_properties(pappsomspp-widget-shared PROPERTIES OUTPUT_NAME pappsomspp-widget @@ -95,6 +119,7 @@ Boost::thread Boost::chrono PwizLite::PwizLite + liblzf::liblzf ) diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/httpbutton/httpbutton.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/httpbutton/httpbutton.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/httpbutton/httpbutton.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/httpbutton/httpbutton.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,142 @@ +/** + * \file pappsomspp/widget/httpbutton/httpbutton.cpp + * \date 20/04/2021 + * \author Olivier Langella + * \brief push button to trigger web browser on URL + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "httpbutton.h" +#include "../../utils.h" + +#include +#include + +using namespace pappso; + +HttpButton::HttpButton(QWidget *parent) : QPushButton(parent) +{ + qDebug(); +} + +pappso::HttpButton::~HttpButton() +{ +} + +void +pappso::HttpButton::mousePressEvent(QMouseEvent *e) +{ + if(!text().isEmpty()) + { + if(text().startsWith("MOD:")) + { + QDesktopServices::openUrl(getOlsUrl(this->text())); + // qDebug() << getOlsUrl(this->text()); + } + else if(text().startsWith("PubMed:")) + { + QDesktopServices::openUrl(getPubMedUrl(this->text())); + // qDebug() << getPubMedUrl(this->text()); + } + else if(text().startsWith("RESID:")) + { + QDesktopServices::openUrl(getRESIDUrl(this->text())); + // qDebug() << getPubMedUrl(this->text()); + } + else if(text().startsWith("ChEBI:")) + { + QDesktopServices::openUrl(getChEBIUrl(this->text())); + // qDebug() << getPubMedUrl(this->text()); + } + else if(text().startsWith("Unimod:")) + { + QDesktopServices::openUrl(getUnimodUrl(this->text())); + // qDebug() << getPubMedUrl(this->text()); + } + else + { + qDebug() << "unknown" << this->text(); + } + } + QPushButton::mousePressEvent(e); +} + +void +pappso::HttpButton::setText(const QString &text) +{ + QPushButton::setText(text); +} + + +const QUrl +HttpButton::getOlsUrl(QString psimod_accession) +{ + + QString iri(QString("http://purl.obolibrary.org/obo/%1") + .arg(psimod_accession.replace(":", "_"))); + QUrl url( + QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri)); + return url; +} + +const QUrl +HttpButton::getPubMedUrl(QString accession) +{ + // https://pubmed.ncbi.nlm.nih.gov/18688235/ + QUrl url(QString("https://pubmed.ncbi.nlm.nih.gov/%1/") + .arg(accession.replace("PubMed:", ""))); + return url; +} + + +const QUrl +HttpButton::getRESIDUrl(QString accession) +{ + // https://annotation.dbi.udel.edu/cgi-bin/resid?id=AA0470 + QUrl url(QString("https://annotation.dbi.udel.edu/cgi-bin/resid?id=%1") + .arg(accession.replace("RESID:", ""))); + return url; +} + + +const QUrl +HttpButton::getChEBIUrl(QString accession) +{ + // ChEBI:37629 + // https://www.ebi.ac.uk/chebi/searchId.do?chebiId=37628 + QUrl url(QString("https://www.ebi.ac.uk/chebi/searchId.do?chebiId=%1") + .arg(accession.replace("ChEBI:", ""))); + return url; +} + + +const QUrl +HttpButton::getUnimodUrl(QString accession) +{ + // Unimod:23 + // http://www.unimod.org/modifications_view.php?editid1=23 + QUrl url(QString("http://www.unimod.org/modifications_view.php?editid1=%1") + .arg(accession.replace("Unimod:", ""))); + return url; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/httpbutton/httpbutton.h libpappsomspp-0.8.58/src/pappsomspp/widget/httpbutton/httpbutton.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/httpbutton/httpbutton.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/httpbutton/httpbutton.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,65 @@ +/** + * \file pappsomspp/widget/httpbutton/httpbutton.h + * \date 20/04/2021 + * \author Olivier Langella + * \brief push button to trigger web browser on URL + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + + +#include +#include +#include "../../exportinmportconfig.h" + +namespace pappso +{ + +class PMSPP_LIB_DECL HttpButton : public QPushButton +{ + Q_OBJECT + public: + /** + * Default constructor + */ + explicit HttpButton(QWidget *parent = nullptr); + + /** + * Destructor + */ + ~HttpButton(); + + void setText(const QString &text); + + protected: + void mousePressEvent(QMouseEvent *e) override; + + const QUrl getOlsUrl(QString psimod_accession); + const QUrl getPubMedUrl(QString accession); + const QUrl getRESIDUrl(QString accession); + const QUrl getChEBIUrl(QString accession); + const QUrl getUnimodUrl(QString accession); +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -202,7 +202,9 @@ _max_isotope_number, _max_isotope_rank); - _peak_ion_isotope_match_list = psm_match.getPeakIonIsotopeMatchList(); + _peak_ion_isotope_match_list = std::list( + psm_match.getPeakIonIsotopeMatchList().begin(), + psm_match.getPeakIonIsotopeMatchList().end()); } else { @@ -318,12 +320,17 @@ } else { - + qDebug(); _peak_ion_isotope_match_list.sort( [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { - return a.getPeak().y > b.getPeak().y; + qDebug() << a.getPeak().y << " > "; + qDebug() << b.getPeak().y << " . "; + return (a.getPeak().y > b.getPeak().y); }); + qDebug(); unsigned int i = 0; + + qDebug(); for(const PeakIonIsotopeMatch &peak_ion_match : _peak_ion_isotope_match_list) { @@ -334,8 +341,6 @@ // peak_ion_match.getPeak().y); if(i < _tag_nmost_intense) { - QString plusstr = "+"; - plusstr = plusstr.repeated(peak_ion_match.getCharge()); QCPItemText *text_label = new QCPItemText(_custom_plot); text_label->setVisible(true); //_custom_plot->addItem(text_label); @@ -348,12 +353,9 @@ .y); // place position at center/top of axis rect text_label->setFont(QFont(font().family(), 8)); text_label->setText( - QString("%1%2%3") - .arg(peak_ion_match.getPeptideFragmentIonSp() - .get() - ->getPeptideIonName()) - .arg(peak_ion_match.getPeptideFragmentIonSp().get()->size()) - .arg(plusstr)); + peak_ion_match.getPeptideFragmentIonSp() + .get() + ->getCompletePeptideIonName(peak_ion_match.getCharge())); // text_label->setPen(QPen(PeptideFragmentIon::getPeptideIonColor(peak_ion_match.getPeptideIonType()), // 1)); // show black border around text text_label->setColor( @@ -364,6 +366,7 @@ } } + qDebug(); _custom_plot->replot(); qDebug(); } @@ -455,3 +458,18 @@ } } } + +void +pappso::MassSpectrumWidget::highlightPrecursorPeaks() +{ + + if(_ms_level > 1) + { + pappso_double precursor_mz_1 = _peptide_sp->getMz(1); + _custom_plot->highlightPrecursorPeaks( + precursor_mz_1, 1, _p_ms2_precision); + pappso_double precursor_mz_charge = _peptide_sp->getMz(_peptide_charge); + _custom_plot->highlightPrecursorPeaks( + precursor_mz_charge, _peptide_charge, _p_ms2_precision); + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -1,5 +1,5 @@ /** - * \file pappsomspp/widget/spectrumwidget/massspectrumwidget.h + * \file pappsomspp/widget/massspectrumwidget/massspectrumwidget.h * \date 22/12/2017 * \author Olivier Langella * \brief plot a sectrum and annotate with peptide @@ -68,6 +68,7 @@ bool savePdf(const QString &fileName, int width = 0, int height = 0); void toQPaintDevice(QPaintDevice *device, const QSize &size) override; + void highlightPrecursorPeaks(); // void setIsotopeMassList(std::vector // & isotope_mass_list); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -68,6 +68,12 @@ _p_peak_bars_isotope->setPen(QPen(red, 1)); _p_peak_bars_isotope->setBrush(QBrush(red)); + mp_peak_bars_precursor = new QCPBars(xAxis, yAxis); + mp_peak_bars_precursor->setWidthType(QCPBars::WidthType::wtAbsolute); + mp_peak_bars_precursor->setWidth(_bar_width * 1.5); + mp_peak_bars_precursor->setPen(QPen(Qt::cyan, 1)); + mp_peak_bars_precursor->setVisible(true); + connect(this->xAxis, SIGNAL(rangeChanged(QCPRange)), this, @@ -244,6 +250,8 @@ _p_peak_bars_isotope->setData(QVector(), QVector()); _p_peak_bars_isotope->data().clear(); qDebug(); + mp_peak_bars_precursor->setData(QVector(), QVector()); + mp_peak_bars_precursor->data().clear(); for(std::pair pair_ion_bar : _map_ion_type_bars) { pair_ion_bar.second->setData(QVector(), QVector()); @@ -458,3 +466,31 @@ total_intensity); } } + +void +pappso::QCPSpectrum::highlightPrecursorPeaks(double precursor_mz, + int charge, + PrecisionPtr ms2_precision) +{ + MzRange range(precursor_mz, ms2_precision); + double precursor_mz_c13 = precursor_mz + (DIFFC12C13 / charge); + MzRange range_c13(precursor_mz_c13, ms2_precision); + + for(const DataPoint &peak : *_p_spectrum) + { + if(((peak.x > range.lower()) && (peak.x < range.upper())) || + ((peak.x > range_c13.lower()) && (peak.x < range_c13.upper()))) + { + mp_peak_bars_precursor->addData(peak.x, peak.y); + QCPItemText *text_label = new QCPItemText(this); + text_label->setVisible(true); + text_label->setPositionAlignment(Qt::AlignBottom | Qt::AlignHCenter); + text_label->position->setType(QCPItemPosition::ptPlotCoords); + text_label->position->setCoords(peak.x, peak.y); + // place position at center/top of axis rect + text_label->setFont(QFont(font().family(), 8)); + text_label->setText("precursor"); + text_label->setColor(Qt::cyan); + } + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h 2022-10-27 09:16:15.000000000 +0000 @@ -60,6 +60,9 @@ &isotope_mass_list, pappso_double intensity); void addPeakIonIsotopeMatch(const PeakIonIsotopeMatch &peak_ion_match); + void highlightPrecursorPeaks(double precursor_mz, + int charge, + PrecisionPtr ms2_precision); virtual void mouseMoveEvent(QMouseEvent *event) override; virtual void mousePressEvent(QMouseEvent *event) override; virtual void mouseReleaseEvent(QMouseEvent *event) override; @@ -83,6 +86,7 @@ QCPRange _mass_delta_range; QCPBars *_p_peak_bars; QCPBars *_p_peak_bars_isotope; + QCPBars *mp_peak_bars_precursor; std::map _map_ion_type_bars; QCPAxisRect *_p_delta_axis_rect; QCPGraph *_p_delta_graph; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,88 @@ +/** + * \file pappsomspp/widget/obo/obochooserwidget/obochooserwidget.cpp + * \date 19/04/2021 + * \author Olivier Langella + * \brief display obo term list and choose items + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "obochooserwidget.h" + +#include "ui_uiobochooserwidget.h" +#include "../../../exception/exceptionnotfound.h" +#include + +using namespace pappso; + +OboChooserWidget::OboChooserWidget(QWidget *parent) + : QWidget(parent), ui(new Ui::OboChooserWidgetForm) +{ + qDebug(); + ui->setupUi(this); + + + connect(ui->oboListWidget, + &OboListWidget::oboTermChanged, + ui->oboTermForm, + &OboTermForm::displayOboTerm); +} + +pappso::OboChooserWidget::~OboChooserWidget() +{ + delete ui; +} + +bool +pappso::OboChooserWidget::isOboTermSelected() const +{ + return ui->oboTermForm->isOboTerm(); +} + +const pappso::OboPsiModTerm & +pappso::OboChooserWidget::getOboPsiModTermSelected() const +{ + if(ui->oboTermForm->isOboTerm()) + { + } + else + { + throw pappso::ExceptionNotFound(tr("OBO term not available")); + } + return ui->oboTermForm->getOboPsiModTerm(); +} + +void +pappso::OboChooserWidget::setMzTarget(double target_mz) +{ + qDebug(); + ui->oboListWidget->filterMzPrecision(target_mz, + ui->oboListWidget->getPrecisionPtr()); +} + +void +pappso::OboChooserWidget::setPrecision(pappso::PrecisionPtr precision) +{ + ui->oboListWidget->filterMzPrecision(ui->oboListWidget->getMzTarget(), + precision); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,81 @@ +/** + * \file pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h + * \date 19/04/2021 + * \author Olivier Langella + * \brief display obo term list and choose items + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + + +#include +#include "../../../exportinmportconfig.h" +#include "../../../obo/obopsimodterm.h" +#include "../../../precision.h" +namespace Ui +{ +class OboChooserWidgetForm; +} + +namespace pappso +{ + +class PMSPP_LIB_DECL OboChooserWidget : public QWidget +{ + Q_OBJECT + public: + /** + * Default constructor + */ + explicit OboChooserWidget(QWidget *parent = nullptr); + + /** + * Destructor + */ + ~OboChooserWidget(); + + + /** @brief tells if an OBO term has been selected + */ + bool isOboTermSelected() const; + + /** @brief get the selected obo term or an exception + */ + const OboPsiModTerm &getOboPsiModTermSelected() const; + + /** @brief set mz target to filter among possible modifications + */ + void setMzTarget(double target_mz); + + + /** @brief set mz precision to filter among possible modifications + */ + void setPrecision(PrecisionPtr precision); + + + private: + Ui::OboChooserWidgetForm *ui; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/uiobochooserwidget.ui libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/uiobochooserwidget.ui --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obochooserwidget/uiobochooserwidget.ui 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obochooserwidget/uiobochooserwidget.ui 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,114 @@ + + + OboChooserWidgetForm + + + + 0 + 0 + 761 + 458 + + + + Form + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Qt::Horizontal + + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + + + + pappso::OboListWidget + QWidget +
obo/obolistwidget/obolistwidget.h
+ 1 + + onOboTermChanged(pappso::OboPsiModTerm) + + + + pappso::OboTermForm + QWidget +
obo/obotermform/obotermform.h
+ 1 + + displayOboTerm(pappso::OboPsiModTerm) + + + + + + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,135 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistmodel.h + * \date 19/04/2021 + * \author Olivier Langella + * \brief MVC model of OBO term list + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "obolistmodel.h" +#include "../../../obo/obopsimod.h" +#include "obolistwidget.h" +#include "../../../exception/exceptionnotfound.h" + +#include +#include + +using namespace pappso; + +OboListModel::OboListModel(QObject *parent) : QStringListModel(parent) +{ +} + +OboListModel::~OboListModel() +{ +} + +pappso::OboListModel::OboPsiModHandler::OboPsiModHandler( + pappso::OboListModel *parent) +{ + mp_parent = parent; +} + +pappso::OboListModel::OboPsiModHandler::~OboPsiModHandler() +{ +} + +void +pappso::OboListModel::OboPsiModHandler::setOboPsiModTerm( + const pappso::OboPsiModTerm &term) +{ + mp_parent->m_oboPsiModTermList.push_back(term); +} + + +void +OboListModel::loadPsiMod() +{ + OboPsiModHandler handler(this); + OboPsiMod reader(handler); + + qDebug() << m_oboPsiModTermList.size(); +} + +QVariant +pappso::OboListModel::data(const QModelIndex &index, int role) const +{ + + // generate a log message when this method gets called + std::size_t row = index.row(); + // int col = index.column(); + // qDebug() << QString("row %1, col%2, role %3") + // .arg(row).arg(col).arg(role); + if(row < m_oboPsiModTermList.size()) + { + + switch(role) + { + case Qt::CheckStateRole: + + break; + case Qt::BackgroundRole: + // return QVariant(QColor("grey")); + break; + case Qt::SizeHintRole: + // qDebug() << "ProteinTableModel::headerData " << + // ProteinTableModel::getColumnWidth(section); + // return QSize(PeptideTableModel::getColumnWidth(col), 30); + break; + case Qt::ToolTipRole: + break; + case Qt::DisplayRole: + return QVariant(QString("%1 %2 %3") + .arg(m_oboPsiModTermList[row].m_accession) + .arg(m_oboPsiModTermList[row].m_diffMono) + .arg(m_oboPsiModTermList[row].m_name)); + break; + case Qt::UserRole: + QVariant value; + value.setValue(m_oboPsiModTermList[row]); + return value; + break; + } + } + return QVariant(); +} + +int +pappso::OboListModel::rowCount(const QModelIndex &parent [[maybe_unused]]) const +{ + return (int)m_oboPsiModTermList.size(); +} + +const pappso::OboPsiModTerm & +pappso::OboListModel::getOboPsiModTerm(int row) const +{ + if(row < (int) m_oboPsiModTermList.size()) + { + return m_oboPsiModTermList[row]; + } + else + { + throw pappso::ExceptionNotFound(tr("OBO term not found")); + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.h libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistmodel.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,85 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistmodel.h + * \date 19/04/2021 + * \author Olivier Langella + * \brief MVC model of OBO term list + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include "../../../exportinmportconfig.h" +#include "../../../obo/obopsimodterm.h" +#include "../../../obo/obopsimodhandlerinterface.h" +#include + + +namespace pappso +{ + +/** + * @todo write docs + */ +class PMSPP_LIB_DECL OboListModel : public QStringListModel +{ + public: + /** + * Default constructor + */ + OboListModel(QObject *parent = nullptr); + + /** + * Destructor + */ + ~OboListModel(); + + void loadPsiMod(); + + + QVariant data(const QModelIndex &index, + int role = Qt::DisplayRole) const override; + + int rowCount(const QModelIndex &parent = QModelIndex()) const override; + + + const OboPsiModTerm &getOboPsiModTerm(int row) const; + + protected: + class OboPsiModHandler : public OboPsiModHandlerInterface + { + + public: + OboPsiModHandler(OboListModel *parent); + virtual ~OboPsiModHandler(); + + void setOboPsiModTerm(const OboPsiModTerm &term) override; + + private: + pappso::OboListModel *mp_parent; + }; + + std::vector m_oboPsiModTermList; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,97 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistproxymodel.cpp + * \date 19/04/2021 + * \author Olivier Langella + * \brief MVC proxy model of OBO term list + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "obolistproxymodel.h" +#include "../../../obo/obopsimod.h" +#include "../../../mzrange.h" +#include + +using namespace pappso; + +OboListProxyModel::OboListProxyModel(OboListModel *source_model, + QObject *parent) + : QSortFilterProxyModel(parent) +{ + setFilterRole(Qt::DisplayRole); + mp_sourceModel = source_model; +} + +OboListProxyModel::~OboListProxyModel() +{ +} + +bool +pappso::OboListProxyModel::lessThan(const QModelIndex &source_left, + const QModelIndex &source_right) const +{ + // qDebug(); + + QVariant leftData = sourceModel()->data(source_left, Qt::UserRole); + QVariant rightData = sourceModel()->data(source_right, Qt::UserRole); + + return leftData.value().m_diffMono < + rightData.value().m_diffMono; +} + +void +pappso::OboListProxyModel::filterMzPrecision(double target_mz, + pappso::PrecisionPtr precision) +{ + m_precisionPtr = precision; + m_mzTarget = target_mz; + invalidateFilter(); +} + +bool +pappso::OboListProxyModel::filterAcceptsRow(int source_row, + const QModelIndex &source_parent + [[maybe_unused]]) const +{ + // qDebug(); + if(m_precisionPtr != nullptr) + { + MzRange range(m_mzTarget, m_precisionPtr); + OboPsiModTerm term = mp_sourceModel->getOboPsiModTerm(source_row); + /* + qDebug() << source_row << " " << source_parent.row() << " " + << range.toString() << " " << term.m_diffMono << " " + << term.m_accession; + */ + if(range.contains(term.m_diffMono)) + { + // qDebug(); + } + else + { + // qDebug() << "false"; + return false; + } + } + return true; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.h libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistproxymodel.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,69 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistproxymodel.h + * \date 19/04/2021 + * \author Olivier Langella + * \brief MVC proxy model of OBO term list + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include +#include "obolistwidget.h" +#include "obolistmodel.h" + +namespace pappso +{ + +/** + * @todo write docs + */ +class OboListProxyModel : public QSortFilterProxyModel +{ + public: + /** + * Default constructor + */ + OboListProxyModel(OboListModel *source_model, QObject *parent = nullptr); + + /** + * Destructor + */ + ~OboListProxyModel(); + + void filterMzPrecision(double target_mz, PrecisionPtr precision); + + protected: + bool lessThan(const QModelIndex &source_left, + const QModelIndex &source_right) const override; + bool filterAcceptsRow(int source_row, + const QModelIndex &source_parent) const override; + + private: + PrecisionPtr m_precisionPtr = nullptr; + double m_mzTarget = 0; + OboListModel *mp_sourceModel; +}; + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,147 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistwidget.cpp + * \date 17/04/2021 + * \author Olivier Langella + * \brief handles a list of obo term, select and click + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "obolistwidget.h" +#include "ui_uiobolistwidget.h" +#include +#include "obolistproxymodel.h" +#include "../../../mzrange.h" + +using namespace pappso; + +OboListWidget::OboListWidget(QWidget *parent) + : QWidget(parent), ui(new Ui::OboListWidgetForm) +{ + qDebug(); + ui->setupUi(this); + + mpa_oboListModel = new OboListModel(this); + mpa_oboListModel->loadPsiMod(); + + mpa_oboListProxyModel = new OboListProxyModel(mpa_oboListModel, this); + mpa_oboListProxyModel->setSourceModel(mpa_oboListModel); + // mpa_oboListProxyModel->setSortRole(Qt::UserRole); + + ui->oboTermListView->setModel(mpa_oboListProxyModel); + + mpa_oboListProxyModel->sort(Qt::AscendingOrder); + + connect(ui->oboTermListView->selectionModel(), + &QItemSelectionModel::selectionChanged, + this, + &OboListWidget::onSelectionChanged); +} + +OboListWidget::~OboListWidget() +{ + delete ui; + if(mpa_oboListProxyModel != nullptr) + { + delete mpa_oboListProxyModel; + } + if(mpa_oboListModel != nullptr) + { + delete mpa_oboListModel; + } +} + +void +pappso::OboListWidget::onSelectionChanged(const QItemSelection &selected, + const QItemSelection &deselected + [[maybe_unused]]) +{ + QModelIndexList index_list = + mpa_oboListProxyModel->mapSelectionToSource(selected).indexes(); + + if(index_list.size() > 0) + { + QModelIndex index = index_list.first(); + OboPsiModTerm term = + mpa_oboListModel->data(index, Qt::UserRole).value(); + qDebug() << term.m_accession; + emit oboTermChanged(term); + } +} + +void +pappso::OboListWidget::filterMzPrecision(double target_mz, + pappso::PrecisionPtr precision) +{ + qDebug(); + mpa_oboListProxyModel->filterMzPrecision(target_mz, precision); + if(precision == nullptr) + { + ui->massFilterGroupBox->setChecked(false); + ui->mzSpinBox->setValue(target_mz); + } + else + { + ui->massFilterGroupBox->setChecked(true); + ui->precisionWidget->setPrecision(precision); + ui->mzSpinBox->setValue(target_mz); + } +} + +void +pappso::OboListWidget::onFilterChanged() +{ + qDebug(); + if(ui->massFilterGroupBox->isChecked()) + { + mpa_oboListProxyModel->filterMzPrecision( + ui->mzSpinBox->value(), ui->precisionWidget->getPrecision()); + } + else + { + mpa_oboListProxyModel->filterMzPrecision(0, nullptr); + } +} + +void +pappso::OboListWidget::onFilterChanged(pappso::PrecisionPtr precision + [[maybe_unused]]) +{ + onFilterChanged(); +} + +double +pappso::OboListWidget::getMzTarget() const +{ + return ui->mzSpinBox->value(); +} + +pappso::PrecisionPtr +pappso::OboListWidget::getPrecisionPtr() const +{ + if(ui->massFilterGroupBox->isChecked()) + { + return ui->precisionWidget->getPrecision(); + } + return nullptr; +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/obolistwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,93 @@ +/** + * \file pappsomspp/widget/obo/obolistwidget/obolistwidget.h + * \date 17/04/2021 + * \author Olivier Langella + * \brief handles a list of obo term, select and click + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + + +#include +#include "../../../exportinmportconfig.h" +#include "../../../precision.h" +#include "obolistmodel.h" +#include + +namespace Ui +{ +class OboListWidgetForm; +} + +namespace pappso +{ + +class OboListProxyModel; + +class PMSPP_LIB_DECL OboListWidget : public QWidget +{ + Q_OBJECT + public: + /** + * Default constructor + */ + explicit OboListWidget(QWidget *parent = nullptr); + + /** + * Destructor + */ + ~OboListWidget(); + + void filterMzPrecision(double target_mz, PrecisionPtr precision); + + /** @brief get the current mz value used to filter term list + */ + double getMzTarget() const; + + /** @brief get the current precision used to filter term list + */ + PrecisionPtr getPrecisionPtr() const; + + signals: + void oboTermChanged(OboPsiModTerm oboTerm) const; + + private slots: + void onSelectionChanged(const QItemSelection &selected, + const QItemSelection &deselected); + void onFilterChanged(); + + void onFilterChanged(pappso::PrecisionPtr precision); + + + private: + Ui::OboListWidgetForm *ui; + + OboListModel *mpa_oboListModel = nullptr; + OboListProxyModel *mpa_oboListProxyModel = nullptr; +}; + +} // namespace pappso + +Q_DECLARE_METATYPE(pappso::OboPsiModTerm); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/uiobolistwidget.ui libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/uiobolistwidget.ui --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obolistwidget/uiobolistwidget.ui 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obolistwidget/uiobolistwidget.ui 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,166 @@ + + + OboListWidgetForm + + + + 0 + 0 + 400 + 300 + + + + Form + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + &Mass filter + + + true + + + false + + + + + + 4 + + + -500.000000000000000 + + + 6000.000000000000000 + + + 0.010000000000000 + + + + + + + + + + + + + + + + + pappso::PrecisionWidget + QWidget +
precisionwidget/precisionwidget.h
+ 1 + + precisionChanged(pappso::PrecisionPtr) + + + + + + + massFilterGroupBox + clicked() + OboListWidgetForm + onFilterChanged() + + + 120 + 22 + + + 594 + 60 + + + + + mzSpinBox + editingFinished() + OboListWidgetForm + onFilterChanged() + + + 129 + 53 + + + 673 + 174 + + + + + precisionWidget + precisionChanged() + OboListWidgetForm + onFilterChanged() + + + 287 + 59 + + + 698 + 128 + + + + + precisionWidget + precisionChanged(pappso::PrecisionPtr) + OboListWidgetForm + onFilterChanged(pappso::PrecisionPtr) + + + 254 + 52 + + + 616 + 139 + + + + + mzSpinBox + valueChanged(double) + OboListWidgetForm + onFilterChanged() + + + 176 + 53 + + + 680 + 202 + + + + + + onFilterChanged() + onFilterChanged(pappso::PrecisionPtr) + + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/obotermform.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/obotermform.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,136 @@ +/** + * \file pappsomspp/widget/obo/obotermform/obotermform.cpp + * \date 20/04/2021 + * \author Olivier Langella + * \brief display an obo term form + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "obotermform.h" + +#include "ui_uiobotermform.h" +#include +#include "../../../exception/exceptionnotfound.h" + +using namespace pappso; + +//"Oxidation of methionine to methionine sulfoxide with neutral loss of CH3SOH." +//[PubMed:18688235, PubMed:9004526] +QRegularExpression OboTermForm::m_findExternalLinks("^(.*)\\s\\[(.*)\\]$"); + + +OboTermForm::OboTermForm(QWidget *parent) + : QWidget(parent), ui(new Ui::OboTermForm) +{ + qDebug(); + ui->setupUi(this); + + OboPsiModTerm empty; + displayOboTerm(empty); +} + +pappso::OboTermForm::~OboTermForm() +{ + delete ui; +} + +void +pappso::OboTermForm::displayOboTerm(pappso::OboPsiModTerm oboTerm) +{ + qDebug() << oboTerm.m_accession; + ui->accessionHttpButton->setText(oboTerm.m_accession); + ui->nameLabel->setText(oboTerm.m_name); + ui->definitionLabel->setText(oboTerm.m_definition); + ui->diffFormulaLabel->setText(oboTerm.m_diffFormula); + if(oboTerm.isValid()) + { + ui->diffMonoLabel->setText(QString::number(oboTerm.m_diffMono, 'f', 4)); + parseDefinitionLabel(); + } + else + { + ui->diffMonoLabel->setText(""); + } + ui->originLabel->setText(oboTerm.m_origin); + ui->psiModLabel->setText(oboTerm.m_psiModLabel); + + + m_oboPsiModTerm = oboTerm; +} + +const pappso::OboPsiModTerm & +pappso::OboTermForm::getOboPsiModTerm() const +{ + if(isOboTerm()) + { + } + else + { + throw pappso::ExceptionNotFound(tr("OBO term not available")); + } + return m_oboPsiModTerm; +} + +bool +pappso::OboTermForm::isOboTerm() const +{ + return m_oboPsiModTerm.isValid(); +} + +void +pappso::OboTermForm::parseDefinitionLabel() +{ + QString label = ui->definitionLabel->text(); + //"Oxidation of methionine to methionine sulfoxide with neutral loss of + // CH3SOH." [PubMed:18688235, PubMed:9004526] + + QLayoutItem *child; + while((child = ui->xrefScrollAreaLayout->takeAt(0)) != 0) + { + if(child->widget() != NULL) + { + delete(child->widget()); + } + delete child; + } + + ui->xrefScrollArea->hide(); + QRegularExpressionMatch match = m_findExternalLinks.match(label); + if(match.hasMatch()) + { + QStringList pline = match.capturedTexts(); + ui->definitionLabel->setText(pline[1]); + + QStringList list_xref = pline[2].split(","); + + ui->xrefScrollArea->show(); + for(auto xref : list_xref) + { + HttpButton *newButton = new HttpButton; + newButton->setText(xref.trimmed()); + newButton->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed); + ui->xrefScrollAreaLayout->addWidget(newButton); + } + } +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/obotermform.h libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/obotermform.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/obotermform.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,85 @@ +/** + * \file pappsomspp/widget/obo/obotermform/obotermform.h + * \date 20/04/2021 + * \author Olivier Langella + * \brief display an obo term form + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + + +#include +#include "../../../exportinmportconfig.h" +#include "../../../obo/obopsimodterm.h" +namespace Ui +{ +class OboTermForm; +} + +namespace pappso +{ + +class PMSPP_LIB_DECL OboTermForm : public QWidget +{ + Q_OBJECT + public: + /** + * Default constructor + */ + explicit OboTermForm(QWidget *parent = nullptr); + + /** + * Destructor + */ + ~OboTermForm(); + + + /** @brief tells if an OBO term is displayed + */ + bool isOboTerm() const; + + /** @brief get the obo term or an exception + */ + const OboPsiModTerm &getOboPsiModTerm() const; + + public slots: + void displayOboTerm(OboPsiModTerm oboTerm); + + + protected: + /** @brief parse the definition label to extract external links + * */ + void parseDefinitionLabel(); + + + private: + Ui::OboTermForm *ui; + + OboPsiModTerm m_oboPsiModTerm; + + + static QRegularExpression m_findExternalLinks; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/uiobotermform.ui libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/uiobotermform.ui --- libpappsomspp-0.8.15/src/pappsomspp/widget/obo/obotermform/uiobotermform.ui 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/obo/obotermform/uiobotermform.ui 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,166 @@ + + + OboTermForm + + + + 0 + 0 + 582 + 368 + + + + Form + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + diffFormulaLabel + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + diffMonoLabel + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + originLabel + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + nameLabel + + + true + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + psiModLabel + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + definitionLabel + + + true + + + Qt::LinksAccessibleByMouse|Qt::TextSelectableByMouse + + + + + + + + + + + 0 + 0 + + + + QFrame::NoFrame + + + true + + + + + 0 + 0 + 582 + 68 + + + + + 0 + 0 + + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + 0 + + + + + + + + + + + + pappso::HttpButton + QWidget +
httpbutton/httpbutton.h
+ 1 + + + + + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -46,6 +46,50 @@ const QString &y_axis_label) : BasePlotWidget(parent, x_axis_label, y_axis_label) { + // Do not call createAllAncillaryItems() in this base class because all the + // items will have been created *before* the addition of plots and then the + // rendering order will hide them to the viewer, since the rendering order is + // according to the order in which the items have been created. + // + // The fact that the ancillary items are created before trace plots is not a + // problem because the trace plots are sparse and do not effectively hide the + // data. + // + // But, in the color map plot widgets, we cannot afford to create the + // ancillary items *before* the plot itself because then, the rendering of the + // plot (created after) would screen off the ancillary items (created before). + // + // So, the createAllAncillaryItems() function needs to be called in the + // derived classes at the most appropriate moment in the setting up of the + // widget. + // + // In the present case, the function needs to be called right after addition + // of the color map plot. +} + + +BaseColorMapPlotWidget::BaseColorMapPlotWidget(QWidget *parent) + : BasePlotWidget(parent, "x", "y") +{ + // Do not call createAllAncillaryItems() in this base class because all the + // items will have been created *before* the addition of plots and then the + // rendering order will hide them to the viewer, since the rendering order is + // according to the order in which the items have been created. + // + // The fact that the ancillary items are created before trace plots is not a + // problem because the trace plots are sparse and do not effectively hide the + // data. + // + // But, in the color map plot widgets, we cannot afford to create the + // ancillary items *before* the plot itself because then, the rendering of the + // plot (created after) would screen off the ancillary items (created before). + // + // So, the createAllAncillaryItems() function needs to be called in the + // derived classes at the most appropriate moment in the setting up of the + // widget. + // + // In the present case, the function needs to be called right after addition + // of the color map plot. } @@ -58,6 +102,11 @@ */ BaseColorMapPlotWidget::~BaseColorMapPlotWidget() { + if(mpa_origColorMapData != nullptr) + delete mpa_origColorMapData; + + if(mpa_origColorMapPlotConfig != nullptr) + delete mpa_origColorMapPlotConfig; } @@ -69,6 +118,13 @@ } +const ColorMapPlotConfig * +BaseColorMapPlotWidget::getOrigColorMapPlotConfig() +{ + return mpa_origColorMapPlotConfig; +} + + const ColorMapPlotConfig & BaseColorMapPlotWidget::getColorMapPlotConfig() { @@ -79,7 +135,7 @@ QCPColorMap * BaseColorMapPlotWidget::addColorMap( std::shared_ptr> double_map_trace_map_sp, - ColorMapPlotConfig color_map_plot_config, + const ColorMapPlotConfig color_map_plot_config, const QColor &color) { // qDebug() << "Adding color map with config:" << @@ -91,25 +147,36 @@ QCPColorMap *color_map_p = new QCPColorMap(xAxis, yAxis); - // Do not forget to copy the config! + color_map_p->setLayer("plotsLayer"); + // Do not forget to copy the config! m_colorMapPlotConfig = color_map_plot_config; + // Immediately create a copy of the original data for backup. + mpa_origColorMapPlotConfig = new ColorMapPlotConfig(color_map_plot_config); + #if 0 - // This is the code on the QCustomPlot documentation and it works fine. - QCPColorMap *color_map_p = new QCPColorMap(xAxis, yAxis); + // This is the code on the QCustomPlot documentation and it works fine. + QCPColorMap *color_map_p = new QCPColorMap(xAxis, yAxis); - color_map_p->data()->setSize(50, 50); - color_map_p->data()->setRange(QCPRange(0, 2), QCPRange(0, 2)); - for(int x = 0; x < 50; ++x) - for(int y = 0; y < 50; ++y) - color_map_p->data()->setCell(x, y, qCos(x / 10.0) + qSin(y / 10.0)); - color_map_p->setGradient(QCPColorGradient::gpPolar); - color_map_p->rescaleDataRange(true); - rescaleAxes(); - replot(); + color_map_p->data()->setSize(50, 50); + color_map_p->data()->setRange(QCPRange(0, 2), QCPRange(0, 2)); + for(int x = 0; x < 50; ++x) + for(int y = 0; y < 50; ++y) + color_map_p->data()->setCell(x, y, qCos(x / 10.0) + qSin(y / 10.0)); + color_map_p->setGradient(QCPColorGradient::gpPolar); + color_map_p->rescaleDataRange(true); + rescaleAxes(); + replot(); #endif + // Only now can afford to call createAllAncillaryItems() in this derived class + // because the color map has been created already. The rendering order will + // thus not hide the ancillary items, since they have been created after the + // color map plot (since the rendering order is according to the + // order in which the items have been created). See contructor note. + createAllAncillaryItems(); + // Connect the signal of selection change so that we can re-emit it for the // widget that is using *this widget. @@ -156,13 +223,23 @@ // color map plot cells. double prev_intensity = color_map_p->data()->data(dt_or_rt_key, mz); + double new_intensity = prev_intensity + intensity; + + // Record the min/max cell intensity value (origM(in/ax)ZValue). We + // will need that later. Also update the lastM(in/ax)ZValue because + // when doing this kind of data conversion it is assume that the user + // actually changes the data. + m_colorMapPlotConfig.setOrigAndLastMinZValue( + std::min(m_colorMapPlotConfig.origMinZValue, new_intensity)); + + m_colorMapPlotConfig.setOrigAndLastMaxZValue( + std::max(m_colorMapPlotConfig.origMaxZValue, new_intensity)); // qDebug() << "Setting tri-point:" << dt_or_rt_key << "," << mz << // "," - //<< prev_intensity + intensity; + //<< new_intensity; - color_map_p->data()->setData( - dt_or_rt_key, mz, prev_intensity + intensity); + color_map_p->data()->setData(dt_or_rt_key, mz, new_intensity); } } @@ -197,15 +274,186 @@ color_map_p->setPen(pen); - // Copy the color map's data into a backup copy. + // Copy the original color map's data into a backup copy. - mpa_backupColorMapData = new QCPColorMapData(*(color_map_p->data())); + mpa_origColorMapData = new QCPColorMapData(*(color_map_p->data())); replot(); return color_map_p; } +QCPColorMap * +BaseColorMapPlotWidget::addColorMap( + const TimsFrame &tims_frame, + const ColorMapPlotConfig color_map_plot_config, + const QColor &color) +{ + qDebug(); + if(!color.isValid()) + throw PappsoException( + QString("The color to be used for the plot graph is invalid.")); + + QCPColorMap *color_map_p = new QCPColorMap(xAxis, yAxis); + + color_map_p->setLayer("plotsLayer"); + + // Do not forget to copy the config! + m_colorMapPlotConfig = color_map_plot_config; + + // Immediately create a copy of the original data for backup. + mpa_origColorMapPlotConfig = new ColorMapPlotConfig(color_map_plot_config); + + qDebug(); +#if 0 + // This is the code on the QCustomPlot documentation and it works fine. + QCPColorMap *color_map_p = new QCPColorMap(xAxis, yAxis); + + color_map_p->data()->setSize(50, 50); + color_map_p->data()->setRange(QCPRange(0, 2), QCPRange(0, 2)); + for(int x = 0; x < 50; ++x) + for(int y = 0; y < 50; ++y) + color_map_p->data()->setCell(x, y, qCos(x / 10.0) + qSin(y / 10.0)); + color_map_p->setGradient(QCPColorGradient::gpPolar); + color_map_p->rescaleDataRange(true); + rescaleAxes(); + replot(); +#endif + + // Only now can afford to call createAllAncillaryItems() in this derived class + // because the color map has been created already. The rendering order will + // thus not hide the ancillary items, since they have been created after the + // color map plot (since the rendering order is according to the + // order in which the items have been created). See contructor note. + createAllAncillaryItems(); + + qDebug(); + // Connect the signal of selection change so that we can re-emit it for the + // widget that is using *this widget. + + connect(color_map_p, + static_cast( + &QCPAbstractPlottable::selectionChanged), + [this, color_map_p]() { + emit plottableSelectionChangedSignal(color_map_p, + color_map_p->selected()); + }); + + // qDebug() << "Configuring the color map with this config:" + //<< color_map_plot_config.toString(); + + color_map_p->data()->setSize(color_map_plot_config.keyCellCount, + color_map_plot_config.mzCellCount); + + color_map_p->data()->setRange(QCPRange(color_map_plot_config.minKeyValue, + color_map_plot_config.maxKeyValue), + QCPRange(color_map_plot_config.minMzValue, + color_map_plot_config.maxMzValue)); + color_map_p->data()->fill(0.0); + // double max_intensity = 0; + qDebug(); + // We have now to fill the color map. + std::size_t number_of_scans = tims_frame.getTotalNumberOfScans(); + for(std::size_t i = 0; i < number_of_scans; i++) + { + std::vector mz_index_vector = tims_frame.getScanIndexList(i); + std::vector intensity_index_vector = + tims_frame.getScanIntensities(i); + + + // The first value is the key and the second value is the MapTrace into + // which we need to iterated and for each point (double mz, double + // intensity) create a map cell. + + double dt_or_rt_key = i; + std::size_t vector_index = 0; + for(quint32 mzindex : mz_index_vector) + { + double mz = mzindex; + double intensity = intensity_index_vector.at(vector_index); + // max_intensity = std::max(max_intensity, intensity); + // We are filling dynamically the color map. If a cell had already + // something in, then we need to take that into account. This is + // because we let QCustomPlot handle the fuzzy transition between + // color map plot cells. + + double prev_intensity = color_map_p->data()->data(dt_or_rt_key, mz); + double new_intensity = prev_intensity + intensity; + + // qDebug() << "mz=" << mz << " int=" << intensity; + + // Record the min/max cell intensity value (origM(in/ax)ZValue). We + // will need that later. Also update the lastM(in/ax)ZValue because + // when doing this kind of data conversion it is assume that the user + // actually changes the data. + m_colorMapPlotConfig.setOrigAndLastMinZValue( + std::min(m_colorMapPlotConfig.origMinZValue, new_intensity)); + + m_colorMapPlotConfig.setOrigAndLastMaxZValue( + std::max(m_colorMapPlotConfig.origMaxZValue, new_intensity)); + + // qDebug() << "Setting tri-point:" << dt_or_rt_key << "," << mz << + // "," + //<< new_intensity; + + color_map_p->data()->setCell(dt_or_rt_key, mz, new_intensity); + + // qDebug() << "dt_or_rt_key=" << dt_or_rt_key << " mz=" << mz + // << " new_intensity=" << new_intensity; + + vector_index++; + } + } + + // At this point we have finished filling-up the color map. + + // The gpThermal is certainly one of the best. + + color_map_p->setGradient(QCPColorGradient::gpThermal); + + color_map_p->data()->recalculateDataBounds(); + color_map_p->rescaleDataRange(true); + + color_map_p->rescaleAxes(); + resetAxesRangeHistory(); + + // The pen of the color map itself is of no use. Instead the user will see the + // color of the axes' labels. + + qDebug(); + QPen pen = xAxis->basePen(); + pen.setColor(color); + + xAxis->setBasePen(pen); + xAxis->setLabelColor(color); + xAxis->setTickLabelColor(color); + + yAxis->setBasePen(pen); + yAxis->setLabelColor(color); + yAxis->setTickLabelColor(color); + + // And now set the color map's pen to the same color, even if we do not use + // it, we need it for coloring the plots that might be integrated from this + // color map. + + color_map_p->setPen(pen); + + // Copy the original color map's data into a backup copy. + + mpa_origColorMapData = new QCPColorMapData(*(color_map_p->data())); + + color_map_p->setInterpolate(false); + color_map_p->setTightBoundary(false); + + replot(); + + + qDebug() << color_map_p->data()->keyRange(); + qDebug() << color_map_p->data()->valueRange(); + qDebug() << color_map_p->data()->dataBounds(); + qDebug(); + return color_map_p; +} void BaseColorMapPlotWidget::transposeAxes() @@ -282,6 +530,9 @@ void BaseColorMapPlotWidget::zAxisScaleToLog10() { + // The user wants to rescale the intensity values of the color map according + // to: new_int = log10(orig_int). + // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" ; if(m_colorMapPlotConfig.zAxisScale == AxisScale::log10) @@ -292,25 +543,44 @@ return; } + // qDebug() << "m_colorMapPlotConfig:" << m_colorMapPlotConfig.toString(); + QCPColorMap *color_map_p = static_cast(plottable(0)); - QCPColorMapData *origData = color_map_p->data(); + QCPColorMapData *map_data = color_map_p->data(); - int keySize = origData->keySize(); - int valueSize = origData->valueSize(); + int keySize = map_data->keySize(); + int valueSize = map_data->valueSize(); - QCPRange keyRange = origData->keyRange(); - QCPRange valueRange = origData->valueRange(); + QCPRange keyRange = map_data->keyRange(); + QCPRange valueRange = map_data->valueRange(); + + // Make a copy of the current config so that we can modify + // the xxxZvalue values. + ColorMapPlotConfig new_color_map_plot_config(m_colorMapPlotConfig); + + // But we need to reset these two values to be able to update them using + // std::min() and std::max() below. + new_color_map_plot_config.setOrigAndLastMinZValue( + std::numeric_limits::max()); + + new_color_map_plot_config.setOrigAndLastMaxZValue( + std::numeric_limits::min()); + + // qDebug() << "new_color_map_plot_config" + //<< new_color_map_plot_config.toString(); // Log-ified heat map. - QCPColorMapData *newData = + QCPColorMapData *new_map_data = new QCPColorMapData(keySize, valueSize, keyRange, valueRange); + // qDebug() << "Starting iteration in the color map."; + for(int iter = 0; iter < keySize; ++iter) { for(int jter = 0; jter < valueSize; ++jter) { - double cell_data = origData->cell(iter, jter); + double cell_data = map_data->cell(iter, jter); double new_cell_data = 0; @@ -322,24 +592,163 @@ else new_cell_data = std::log10(cell_data); + // Store the new values here. Should we change the last or orig or + // both ? + new_color_map_plot_config.lastMinZValue = + //(new_cell_data < new_color_map_plot_config.minZValue + //? new_cell_data + //: new_color_map_plot_config.minZValue); + std::min(new_color_map_plot_config.lastMinZValue, new_cell_data); + + new_color_map_plot_config.lastMaxZValue = + //(new_cell_data > new_color_map_plot_config.maxZValue + //? new_cell_data + //: new_color_map_plot_config.maxZValue); + std::max(new_color_map_plot_config.lastMaxZValue, new_cell_data); + // qDebug() << "cell_data:" << cell_data - //<< "new_cell_data:" << new_cell_data; + //<< "new_cell_data:" << new_cell_data + //<< "new_color_map_plot_config.minZValue:" + //<< new_color_map_plot_config.minZValue + //<< "new_color_map_plot_config.maxZValue:" + //<< new_color_map_plot_config.maxZValue; - newData->setCell(iter, jter, new_cell_data); + new_map_data->setCell(iter, jter, new_cell_data); } } + // qDebug() << "Finished iteration in the color map."; + color_map_p->data()->clear(); - // Now we need to document the change. + // Will take ownership of the new_map_data. + color_map_p->setData(new_map_data); + + color_map_p->data()->recalculateDataBounds(); + color_map_p->rescaleDataRange(true); + + // At this point the new color map data have taken their place, we can update + // the config. This, way any new filtering can take advantage of the new + // values and compute the threshold correctly. + m_colorMapPlotConfig = new_color_map_plot_config; + + // Now we need to document the change. m_colorMapPlotConfig.zAxisScale = AxisScale::log10; - // Will take ownership of the newData. - color_map_p->setData(newData); + // qDebug() << "new_color_map_plot_config" + //<< new_color_map_plot_config.toString(); + + // qDebug() << "m_colorMapPlotConfig:" << m_colorMapPlotConfig.toString(); + + // We should not do this, as the user might have zoomed to a region of + // interest. + // color_map_p->rescaleAxes(); + + replot(); +} + +void +BaseColorMapPlotWidget::zAxisFilterLowPassPercentage( + double threshold_percentage) +{ + // This filter allows all the values smaller than a threshold to remain + // unchanged. Instead, all the values above the threshold will be reset to + // that threshold. + // + // The effect of this filter is to enhance the high-intensity signal. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + + QCPColorMapData *map_data = color_map_p->data(); + + int keySize = map_data->keySize(); + int valueSize = map_data->valueSize(); + + QCPRange keyRange = map_data->keyRange(); + QCPRange valueRange = map_data->valueRange(); + + double minZValue = m_colorMapPlotConfig.lastMinZValue; + double maxZValue = m_colorMapPlotConfig.lastMaxZValue; + + double amplitude = maxZValue - minZValue; + + double amplitude_fraction = amplitude * threshold_percentage / 100; + + double threshold = minZValue + amplitude_fraction; + + // qDebug() << "Before filtering minZValue:" << minZValue + //<< "maxZValue:" << maxZValue << "fraction:" << fraction + //<< "threshold:" << threshold + //<< "new threshold percentage:" << new_threshold_percentage; + + // Make a copy of the current config so that we can modify + // the xxxZvalue values. + ColorMapPlotConfig new_color_map_plot_config(m_colorMapPlotConfig); + + // But we need to reset these two values to be able to update them using + // std::min() and std::max() below. + new_color_map_plot_config.lastMinZValue = std::numeric_limits::max(); + new_color_map_plot_config.lastMaxZValue = std::numeric_limits::min(); + + // Filtered + QCPColorMapData *new_map_data = + new QCPColorMapData(keySize, valueSize, keyRange, valueRange); + + for(int iter = 0; iter < keySize; ++iter) + { + for(int jter = 0; jter < valueSize; ++jter) + { + double cell_data = map_data->cell(iter, jter); + + double new_cell_data = 0; + + if(cell_data < threshold) + // Keep the value, we are in low-pass + new_cell_data = cell_data; + else + new_cell_data = threshold; + + // Store the new values here. + new_color_map_plot_config.lastMinZValue = + //(new_cell_data < new_color_map_plot_config.minZValue + //? new_cell_data + //: new_color_map_plot_config.minZValue); + std::min(new_color_map_plot_config.lastMinZValue, new_cell_data); + + new_color_map_plot_config.lastMaxZValue = + //(new_cell_data > new_color_map_plot_config.maxZValue + //? new_cell_data + //: new_color_map_plot_config.maxZValue); + std::max(new_color_map_plot_config.lastMaxZValue, new_cell_data); + + // qDebug() << "cell_data:" << cell_data + //<< "new_cell_data:" << new_cell_data + //<< "new_color_map_plot_config.minZValue:" + //<< new_color_map_plot_config.minZValue + //<< "new_color_map_plot_config.maxZValue:" + //<< new_color_map_plot_config.maxZValue; + + new_map_data->setCell(iter, jter, new_cell_data); + } + } + + color_map_p->data()->clear(); + + // Will take ownership of the new_map_data. + color_map_p->setData(new_map_data); color_map_p->data()->recalculateDataBounds(); color_map_p->rescaleDataRange(true); + + // At this point the new color map data have taken their place, we can update + // the config. This, way any new filtering can take advantage of the new + // values and compute the threshold correctly. + m_colorMapPlotConfig = new_color_map_plot_config; + + // qDebug() << "Member colormap plot config is now, after filter was applied:" + //<< m_colorMapPlotConfig.toString(); + // We should not do this, as the user might have zoomed to a region of // interest. // color_map_p->rescaleAxes(); @@ -349,19 +758,235 @@ void -BaseColorMapPlotWidget::zAxisScaleResetToOriginal() +BaseColorMapPlotWidget::zAxisFilterLowPassThreshold(double threshold) { + + // This filter allows all the values smaller than a threshold to remain + // unchanged. Instead, all the values above the threshold will be reset to + // that threshold. + QCPColorMap *color_map_p = static_cast(plottable(0)); + + QCPColorMapData *map_data = color_map_p->data(); + + int keySize = map_data->keySize(); + int valueSize = map_data->valueSize(); + + QCPRange keyRange = map_data->keyRange(); + QCPRange valueRange = map_data->valueRange(); + + // qDebug() << "Before filtering minZValue:" << minZValue + //<< "maxZValue:" << maxZValue << "fraction:" << fraction + //<< "threshold:" << threshold + //<< "new threshold percentage:" << new_threshold_percentage; + + // Make a copy of the current config so that we can modify + // the xxxZvalue values. + ColorMapPlotConfig new_color_map_plot_config(m_colorMapPlotConfig); + + // But we need to reset these two values to be able to update them using + // std::min() and std::max() below. + new_color_map_plot_config.lastMinZValue = std::numeric_limits::max(); + new_color_map_plot_config.lastMaxZValue = std::numeric_limits::min(); + + // Filtered + QCPColorMapData *new_map_data = + new QCPColorMapData(keySize, valueSize, keyRange, valueRange); + + for(int iter = 0; iter < keySize; ++iter) + { + for(int jter = 0; jter < valueSize; ++jter) + { + double cell_data = map_data->cell(iter, jter); + + double new_cell_data = 0; + + if(cell_data < threshold) + // Keep the value, we are in low-pass + new_cell_data = cell_data; + else + new_cell_data = threshold; + + // Store the new values here. + new_color_map_plot_config.lastMinZValue = + //(new_cell_data < new_color_map_plot_config.minZValue + //? new_cell_data + //: new_color_map_plot_config.minZValue); + std::min(new_color_map_plot_config.lastMinZValue, new_cell_data); + + new_color_map_plot_config.lastMaxZValue = + //(new_cell_data > new_color_map_plot_config.maxZValue + //? new_cell_data + //: new_color_map_plot_config.maxZValue); + std::max(new_color_map_plot_config.lastMaxZValue, new_cell_data); + + // qDebug() << "cell_data:" << cell_data + //<< "new_cell_data:" << new_cell_data + //<< "new_color_map_plot_config.minZValue:" + //<< new_color_map_plot_config.minZValue + //<< "new_color_map_plot_config.maxZValue:" + //<< new_color_map_plot_config.maxZValue; + + new_map_data->setCell(iter, jter, new_cell_data); + } + } + color_map_p->data()->clear(); - if(mpa_backupColorMapData == nullptr) + // Will take ownership of the new_map_data. + color_map_p->setData(new_map_data); + + color_map_p->data()->recalculateDataBounds(); + color_map_p->rescaleDataRange(true); + + + // At this point the new color map data have taken their place, we can update + // the config. This, way any new filtering can take advantage of the new + // values and compute the threshold correctly. + m_colorMapPlotConfig = new_color_map_plot_config; + + // qDebug() << "Member colormap plot config is now, after filter was applied:" + //<< m_colorMapPlotConfig.toString(); + + // We should not do this, as the user might have zoomed to a region of + // interest. + // color_map_p->rescaleAxes(); + + replot(); +} + +void +BaseColorMapPlotWidget::zAxisFilterHighPassPercentage( + double threshold_percentage) +{ + // This filter allows all the value greater than a threshold to remain + // unchanged. Instead, all the values below the threshold will be reset to + // that threshold value. + // + // The effect of this filter is to reduce the low-intensity signal: reduce + // noise. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + + QCPColorMapData *map_data = color_map_p->data(); + + int keySize = map_data->keySize(); + int valueSize = map_data->valueSize(); + + QCPRange keyRange = map_data->keyRange(); + QCPRange valueRange = map_data->valueRange(); + + double minZValue = m_colorMapPlotConfig.lastMinZValue; + double maxZValue = m_colorMapPlotConfig.lastMaxZValue; + + double amplitude = maxZValue - minZValue; + + double amplitude_fraction = amplitude * threshold_percentage / 100; + + double threshold = minZValue + amplitude_fraction; + + // qDebug() << "Before filtering minZValue:" << minZValue + //<< "maxZValue:" << maxZValue << "fraction:" << fraction + //<< "threshold:" << threshold + //<< "new threshold percentage:" << new_threshold_percentage; + + // Make a copy of the current config so that we can modify + // the xxxZvalue values. + ColorMapPlotConfig new_color_map_plot_config(m_colorMapPlotConfig); + + // But we need to reset these two values to be able to update them using + // std::min() and std::max() below. + new_color_map_plot_config.lastMinZValue = std::numeric_limits::max(); + new_color_map_plot_config.lastMaxZValue = std::numeric_limits::min(); + + // Filtered + QCPColorMapData *new_map_data = + new QCPColorMapData(keySize, valueSize, keyRange, valueRange); + + for(int iter = 0; iter < keySize; ++iter) + { + for(int jter = 0; jter < valueSize; ++jter) + { + double cell_data = map_data->cell(iter, jter); + + double new_cell_data = 0; + + if(cell_data > threshold) + // Keep the value, we are in high-pass + new_cell_data = cell_data; + else + new_cell_data = threshold; + + // Store the new values here. + new_color_map_plot_config.lastMinZValue = + //(new_cell_data < new_color_map_plot_config.minZValue + //? new_cell_data + //: new_color_map_plot_config.minZValue); + std::min(new_color_map_plot_config.lastMinZValue, new_cell_data); + + new_color_map_plot_config.lastMaxZValue = + //(new_cell_data > new_color_map_plot_config.maxZValue + //? new_cell_data + //: new_color_map_plot_config.maxZValue); + std::max(new_color_map_plot_config.lastMaxZValue, new_cell_data); + + // qDebug() << "cell_data:" << cell_data + //<< "new_cell_data:" << new_cell_data + //<< "new_color_map_plot_config.minZValue:" + //<< new_color_map_plot_config.minZValue + //<< "new_color_map_plot_config.maxZValue:" + //<< new_color_map_plot_config.maxZValue; + + new_map_data->setCell(iter, jter, new_cell_data); + } + } + + color_map_p->data()->clear(); + + // Will take ownership of the new_map_data. + color_map_p->setData(new_map_data); + + color_map_p->data()->recalculateDataBounds(); + color_map_p->rescaleDataRange(true); + + + // At this point the new color map data have taken their place, we can update + // the config. This, way any new filtering can take advantage of the new + // values and compute the threshold correctly. + m_colorMapPlotConfig = new_color_map_plot_config; + + // qDebug() << "Member colormap plot config is now, after filter was applied:" + //<< m_colorMapPlotConfig.toString(); + + // We should not do this, as the user might have zoomed to a region of + // interest. + // color_map_p->rescaleAxes(); + + replot(); +} + + +void +BaseColorMapPlotWidget::zAxisDataResetToOriginal() +{ + // The user might have changed to the axis scale to log10, for example. + // While doing this, the original data were still available in + // mpa_origColorMapData,with mpa_origColorMapPlotConfig. We need to reset the + // current data to the original data. + // + // Same thing for filters that might have been applied to the data. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + color_map_p->data()->clear(); + + if(mpa_origColorMapData == nullptr) throw(PappsoException( - "Not possible that the mpa_backupColorMapData pointer is null.")); + "Not possible that the mpa_origColorMapData pointer be null.")); // We do no want that the color_map_p takes ownership of the data, because // these must remain there always, so pass true, to say that we want to copy // the data not transfer the pointer. - color_map_p->setData(mpa_backupColorMapData, true); + color_map_p->setData(mpa_origColorMapData, true); color_map_p->data()->recalculateDataBounds(); color_map_p->rescaleDataRange(true); @@ -370,7 +995,9 @@ // interest. // color_map_p->rescaleAxes(); - m_colorMapPlotConfig.zAxisScale = AxisScale::orig; + // Reset the current plot config to what it was originally. The member + // m_colorMapPlotConfig.zAxisScale is now AxisScale::orig. + m_colorMapPlotConfig = *mpa_origColorMapPlotConfig; replot(); } @@ -471,4 +1098,284 @@ } +void +BaseColorMapPlotWidget::currentXaxisRangeIndices(int &lower, int &upper) +{ + // We want to limit the ranges to the visible data range in the plot widget. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + QCPColorMapData *map_data = color_map_p->data(); + + bool found_range = false; + + // Get the full data set DT values range because if the context contains no + // values for the currently displayed ranges, then we fall back to them; + QCPRange full_data_range = color_map_p->getKeyRange(found_range); + + if(!found_range) + { + qDebug() << "The range was not found"; + return; + } + + // qDebug() << "Full key data range:" << full_data_range.lower << "-" + //<< full_data_range.upper; + + // But what we actually want is the currently visible axes ranges. And these + // are stored in the context. + + double visible_data_range_lower = m_context.m_xRange.lower; + double visible_data_range_upper = m_context.m_xRange.upper; + + // qDebug() << "Visible key data range:" << visible_data_range_lower << "-" + //<< visible_data_range_upper; + + // Note that if there has been *no* panning, rescale, nothing, with the color + // map, then the context has no idea of the ranges. So we need to check that. + // If that is the case, then we use the full key range as the full plot is + // displayed full scale upon its first showing. + + if(!visible_data_range_lower || !visible_data_range_upper) + { + visible_data_range_lower = full_data_range.lower; + visible_data_range_upper = full_data_range.upper; + } + + // qDebug() << "Visible key range:" << visible_data_range_lower << "-" + //<< visible_data_range_upper; + + // And now convert the double value ranges into cell indices, which is what we + // are being asked for. + + map_data->coordToCell(visible_data_range_lower, 0, &lower, nullptr); + map_data->coordToCell(visible_data_range_upper, 0, &upper, nullptr); + + // qDebug() << "Cell indices for currently visible key range:" << lower << "-" + //<< upper; +} + + +void +BaseColorMapPlotWidget::currentYaxisRangeIndices(int &lower, int &upper) +{ + // We want to limit the ranges to the visible data range in the plot widget. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + QCPColorMapData *map_data = color_map_p->data(); + + bool found_range = false; + + // Get the full data set MZ values range because if the context contains no + // values for the currently displayed ranges, then we fall back to them; + QCPRange full_data_range = color_map_p->getValueRange(found_range); + + if(!found_range) + { + qDebug() << "The range was not found"; + return; + } + + // qDebug() << "Full value data range:" << full_data_range.lower << "-" + //<< full_data_range.upper; + + // But what we actually want is the currently visible axes ranges. And these + // are stored in the context. + + double visible_data_range_lower = m_context.m_yRange.lower; + double visible_data_range_upper = m_context.m_yRange.upper; + + // qDebug() << "Visible value data range:" << visible_data_range_lower << "-" + //<< visible_data_range_upper; + + // Note that if there has been *no* panning, rescale, nothing, with the color + // map, then the context has no idea of the ranges. So we need to check that. + // If that is the case, then we use the full key range as the full plot is + // displayed full scale upon its first showing. + + if(!visible_data_range_lower || !visible_data_range_upper) + { + visible_data_range_lower = full_data_range.lower; + visible_data_range_upper = full_data_range.upper; + } + + // qDebug() << "Final visible value data range:" << visible_data_range_lower + //<< "-" << visible_data_range_upper; + + // And now convert the double value ranges into cell indices, which is what we + // are being asked for. + + map_data->coordToCell(0, visible_data_range_lower, nullptr, &lower); + map_data->coordToCell(0, visible_data_range_upper, nullptr, &upper); + + // qDebug() << "Cell indices for currently visible value range:" << lower << + // "-" + //<< upper; +} + + +void +BaseColorMapPlotWidget::dataTo3ColString(QString &data_string) +{ + // We want to export the data to a string in the x y z format, with + // x=key (cell's x coordinate) + // y=value (cell's y coordinate) + // z=intensity (cell value) + + QCPColorMap *color_map_p = static_cast(plottable(0)); + QCPColorMapData *map_data = color_map_p->data(); + + int key_index_lower_range; + int key_index_upper_range; + currentXaxisRangeIndices(key_index_lower_range, key_index_upper_range); + + // qDebug() << "Cell indices for currently visible key range:" + //<< key_index_lower_range << "-" << key_index_upper_range; + + int value_index_lower_range; + int value_index_upper_range; + currentYaxisRangeIndices(value_index_lower_range, value_index_upper_range); + + // qDebug() << "Cell indices for currently visible value range:" + //<< value_index_lower_range << "-" << value_index_upper_range; + + data_string.clear(); + QString debug_string; + + // Iterate in the matrix' key axis (DT, for example) + for(int key_iter = key_index_lower_range; key_iter < key_index_upper_range; + ++key_iter) + { + // Iterate in the matrix' value axis (MZ, for example) + for(int value_iter = value_index_lower_range; + value_iter < value_index_upper_range; + ++value_iter) + { + // This would be the DT value (x axis) + double key; + + // This would be the MZ value (y axis) + double value; + + map_data->cellToCoord(key_iter, value_iter, &key, &value); + + data_string += + QString("%1 %2 %3\n") + .arg(key, 0, 'f', 6, ' ') + .arg(value, 0, 'f', 6, ' ') + // The intensity without decimals + .arg(map_data->cell(key_iter, value_iter), 0, 'f', 0, ' '); + } + } + + // qDebug() << "The completed data string has size: " << data_string.size(); +} + + +void +BaseColorMapPlotWidget::dataToMatrixString(QString &data_string, bool detailed) +{ + // We want to export the data in the form of a matrix, exactly as the data + // appear within the colormap, unless the color is replaced with the intensity + // value. + + // We want to limit the export to the visible data range in the plot widget. + + QCPColorMap *color_map_p = static_cast(plottable(0)); + QCPColorMapData *map_data = color_map_p->data(); + + int key_index_lower_range; + int key_index_upper_range; + currentXaxisRangeIndices(key_index_lower_range, key_index_upper_range); + + // qDebug() << "Cell indices for currently visible key range:" + //<< key_index_lower_range << "-" << key_index_upper_range; + + int value_index_lower_range; + int value_index_upper_range; + currentYaxisRangeIndices(value_index_lower_range, value_index_upper_range); + + // qDebug() << "Cell indices for currently visible value range:" + //<< value_index_lower_range << "-" << value_index_upper_range; + + data_string.clear(); + + // At this point, we can write the header of the key data (that is the dt + // key values). + + for(int key_iter = key_index_lower_range; key_iter < key_index_upper_range; + ++key_iter) + { + double current_key_value; + map_data->cellToCoord(key_iter, 0, ¤t_key_value, nullptr); + + data_string += QString("%1 ").arg(current_key_value, 0, 'f', 6, ' '); + } + + // Finally call the newline + data_string += "\n"; + + // Now fill in the matrix, from top to down, that is from higher m/z values to + // lower values. + + // The matrix we are exporting looks like this: + + // | + // | + // | + // | + // | + // | + // m/z | + // | + // | + // | + // | + // |______________________________ + // dt + + // Because we want the matrix to be presented the same, we need to fill in the + // matrix from top to bottom starting from higher m/z values. + + for(int value_iter = value_index_upper_range; + value_iter >= value_index_lower_range; + --value_iter) + { + + for(int key_iter = key_index_lower_range; + key_iter < key_index_upper_range; + ++key_iter) + { + double intensity = map_data->cell(key_iter, value_iter); + + // Only to report debug messages + double key_double; + double value_double; + map_data->cellToCoord( + key_iter, value_iter, &key_double, &value_double); + + // qDebug() << "Currently iterated cell: " << key_iter << "," + //<< value_iter << "with values:" << key_double << "," + //<< value_double << "with intensity:" << intensity; + + // The intensity without decimals + if(detailed) + data_string += QString("%1/%2/%3 ") + .arg(key_double, 0, 'f', 6, ' ') + .arg(value_double, 0, 'f', 6, ' ') + .arg(intensity); + else + data_string += QString("%1 ").arg(intensity, 0, 'f', 0, ' '); + } + + data_string += "\n"; + } + + // qDebug().noquote() << "The matrix: " << data_string; + // qDebug() << "The completed data string has size: " << + // data_string.size(); + + data_string += "\n"; +} + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -38,6 +38,7 @@ /////////////////////// QCustomPlot +#include #include @@ -46,6 +47,7 @@ #include "baseplotwidget.h" #include "colormapplotconfig.h" #include "../../trace/trace.h" +#include "../../vendors/tims/timsframe.h" namespace pappso @@ -63,6 +65,7 @@ Q_OBJECT; public: + explicit BaseColorMapPlotWidget(QWidget *parent); explicit BaseColorMapPlotWidget(QWidget *parent, const QString &x_axis_label, const QString &y_axis_label); @@ -72,16 +75,31 @@ virtual void setColorMapPlotConfig(const ColorMapPlotConfig &color_map_config); virtual const ColorMapPlotConfig &getColorMapPlotConfig(); + const ColorMapPlotConfig *getOrigColorMapPlotConfig(); virtual QCPColorMap *addColorMap( std::shared_ptr> double_map_trace_map_sp, - ColorMapPlotConfig color_map_plot_config, + const ColorMapPlotConfig color_map_plot_config, const QColor &color); + virtual QCPColorMap * + addColorMap(const TimsFrame &tims_frame, + const ColorMapPlotConfig color_map_plot_config, + const QColor &color); + virtual void transposeAxes(); + // Change the scale of the intensity to log10 (color, z virtual axis) virtual void zAxisScaleToLog10(); - virtual void zAxisScaleResetToOriginal(); + virtual void zAxisFilterLowPassPercentage(double threshold_percentage); + + /** @brief fix maximum value for the intensity + */ + virtual void zAxisFilterLowPassThreshold(double threshold); + + virtual void zAxisFilterHighPassPercentage(double threshold_percentage); + + virtual void zAxisDataResetToOriginal(); DataKind xAxisDataKind() const; DataKind yAxisDataKind() const; @@ -95,12 +113,19 @@ const QColor &new_color) override; virtual QColor getPlottingColor(int index = 0) const override; + void dataTo3ColString(QString &data_string); + void dataToMatrixString(QString &data_string, bool detailed = false); + + void currentXaxisRangeIndices(int &lower, int &upper); + void currentYaxisRangeIndices(int &lower, int &upper); signals: protected: - QCPColorMapData *mpa_backupColorMapData = nullptr; + QCPColorMapData *mpa_origColorMapData = nullptr; + ColorMapPlotConfig m_colorMapPlotConfig; + ColorMapPlotConfig *mpa_origColorMapPlotConfig = nullptr; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotcontext.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotcontext.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,257 @@ +// Copyright 2021 Filippo Rusconi +// GPL3+ + +#include "baseplotcontext.h" + +namespace pappso +{ + +BasePlotContext::BasePlotContext() +{ +} + + +BasePlotContext::BasePlotContext(const BasePlotContext &other) +{ + m_dataKind = other.m_dataKind; + + m_isMouseDragging = other.m_isMouseDragging; + m_wasMouseDragging = other.m_wasMouseDragging; + + m_isKeyBoardDragging = other.m_isKeyBoardDragging; + m_isLeftPseudoButtonKeyPressed = other.m_isLeftPseudoButtonKeyPressed; + m_isRightPseudoButtonKeyPressed = other.m_isRightPseudoButtonKeyPressed; + m_wassKeyBoardDragging = other.m_wassKeyBoardDragging; + + m_startDragPoint = other.m_startDragPoint; + m_currentDragPoint = other.m_currentDragPoint; + m_lastCursorHoveredPoint = other.m_lastCursorHoveredPoint; + + m_selectionPolygon = other.m_selectionPolygon; + m_selectRectangleWidth = other.m_selectRectangleWidth; + + // The effective range of the axes. + m_xRange = other.m_xRange; + m_yRange = other.m_yRange; + + // Tell if the mouse move was started onto either axis, because that will + // condition if some calculations needs to be performed or not (for example, + // if the mouse cursor motion was started on an axis, there is no point to + // perform deconvolutions). + m_wasClickOnXAxis = other.m_wasClickOnXAxis; + m_wasClickOnYAxis = other.m_wasClickOnYAxis; + + m_isMeasuringDistance = other.m_isMeasuringDistance; + + // The user-selected region over the plot. + // Note that we cannot use QCPRange structures because these are normalized by + // QCustomPlot in such a manner that lower is actually < upper. But we need + // for a number of our calculations (specifically for the deconvolutions) to + // actually have the lower value be start drag point.x even if the drag + // direction was from right to left. + m_xRegionRangeStart = other.m_xRegionRangeStart; + m_xRegionRangeEnd = other.m_xRegionRangeEnd; + + m_yRegionRangeStart = other.m_yRegionRangeStart; + m_yRegionRangeEnd = other.m_yRegionRangeEnd; + + m_xDelta = other.m_xDelta; + m_yDelta = other.m_yDelta; + + m_pressedKeyCode = other.m_pressedKeyCode; + m_releasedKeyCode = other.m_releasedKeyCode; + + m_keyboardModifiers = other.m_keyboardModifiers; + + m_lastPressedMouseButton = other.m_lastPressedMouseButton; + m_lastReleasedMouseButton = other.m_lastReleasedMouseButton; + + m_pressedMouseButtons = other.m_pressedMouseButtons; + + m_mouseButtonsAtMousePress = other.m_mouseButtonsAtMousePress; + m_mouseButtonsAtMouseRelease = other.m_mouseButtonsAtMouseRelease; +} + + +BasePlotContext & +BasePlotContext::operator=(const BasePlotContext &other) +{ + if(this == &other) + return *this; + + m_dataKind = other.m_dataKind; + + m_isMouseDragging = other.m_isMouseDragging; + m_wasMouseDragging = other.m_wasMouseDragging; + + m_isKeyBoardDragging = other.m_isKeyBoardDragging; + m_isLeftPseudoButtonKeyPressed = other.m_isLeftPseudoButtonKeyPressed; + m_isRightPseudoButtonKeyPressed = other.m_isRightPseudoButtonKeyPressed; + m_wassKeyBoardDragging = other.m_wassKeyBoardDragging; + + m_startDragPoint = other.m_startDragPoint; + m_currentDragPoint = other.m_currentDragPoint; + m_lastCursorHoveredPoint = other.m_lastCursorHoveredPoint; + + m_selectionPolygon = other.m_selectionPolygon; + m_selectRectangleWidth = other.m_selectRectangleWidth; + + // The effective range of the axes. + m_xRange = other.m_xRange; + m_yRange = other.m_yRange; + + // Tell if the mouse move was started onto either axis, because that will + // condition if some calculations needs to be performed or not (for example, + // if the mouse cursor motion was started on an axis, there is no point to + // perform deconvolutions). + m_wasClickOnXAxis = other.m_wasClickOnXAxis; + m_wasClickOnYAxis = other.m_wasClickOnYAxis; + + m_isMeasuringDistance = other.m_isMeasuringDistance; + + // The user-selected region over the plot. + // Note that we cannot use QCPRange structures because these are normalized by + // QCustomPlot in such a manner that lower is actually < upper. But we need + // for a number of our calculations (specifically for the deconvolutions) to + // actually have the lower value be start drag point.x even if the drag + // direction was from right to left. + m_xRegionRangeStart = other.m_xRegionRangeStart; + m_xRegionRangeEnd = other.m_xRegionRangeEnd; + + m_yRegionRangeStart = other.m_yRegionRangeStart; + m_yRegionRangeEnd = other.m_yRegionRangeEnd; + + m_xDelta = other.m_xDelta; + m_yDelta = other.m_yDelta; + + m_pressedKeyCode = other.m_pressedKeyCode; + m_releasedKeyCode = other.m_releasedKeyCode; + + m_keyboardModifiers = other.m_keyboardModifiers; + + m_lastPressedMouseButton = other.m_lastPressedMouseButton; + m_lastReleasedMouseButton = other.m_lastReleasedMouseButton; + + m_pressedMouseButtons = other.m_pressedMouseButtons; + + m_mouseButtonsAtMousePress = other.m_mouseButtonsAtMousePress; + m_mouseButtonsAtMouseRelease = other.m_mouseButtonsAtMouseRelease; + + return *this; +} + + +BasePlotContext::~BasePlotContext() +{ +} + + +DragDirections +BasePlotContext::recordDragDirections() +{ + int drag_directions = static_cast(DragDirections::NOT_SET); + + if(m_currentDragPoint.x() > m_startDragPoint.x()) + drag_directions |= static_cast(DragDirections::LEFT_TO_RIGHT); + else + drag_directions |= static_cast(DragDirections::RIGHT_TO_LEFT); + + if(m_currentDragPoint.y() > m_startDragPoint.y()) + drag_directions |= static_cast(DragDirections::BOTTOM_TO_TOP); + else + drag_directions |= static_cast(DragDirections::TOP_TO_BOTTOM); + + //qDebug() << "DragDirections:" << drag_directions; + + m_dragDirections = static_cast(drag_directions); + + return static_cast(drag_directions); +} + + +QString +BasePlotContext::toString() const +{ + QString text("Context:"); + + text += QString("data kind: %1").arg(static_cast(m_dataKind)); + + text += QString(" isMouseDragging: %1 -- wasMouseDragging: %2") + .arg(m_isMouseDragging ? "true" : "false") + .arg(m_wasMouseDragging ? "true" : "false"); + + text += QString(" -- startDragPoint : (%1, %2)") + .arg(m_startDragPoint.x()) + .arg(m_startDragPoint.y()); + + text += QString(" -- currentDragPoint : (%1, %2)") + .arg(m_currentDragPoint.x()) + .arg(m_currentDragPoint.y()); + + text += QString(" -- lastCursorHoveredPoint : (%1, %2)") + .arg(m_lastCursorHoveredPoint.x()) + .arg(m_lastCursorHoveredPoint.y()); + + // Document how the mouse cursor is being dragged. + if(m_isMouseDragging) + { + if(static_cast(m_dragDirections) & static_cast(DragDirections::LEFT_TO_RIGHT)) + text += " -- dragging from left to right"; + else if(static_cast(m_dragDirections) & static_cast(DragDirections::RIGHT_TO_LEFT)) + text += " -- dragging from right to left"; + if(static_cast(m_dragDirections) & static_cast(DragDirections::TOP_TO_BOTTOM)) + text += " -- dragging from top to bottom"; + if(static_cast(m_dragDirections) & static_cast(DragDirections::BOTTOM_TO_TOP)) + text += " -- dragging from bottom to top"; + } + + // The selection polygon. + text += m_selectionPolygon.toString(); + + text += + QString(" -- xRange: (%1, %2)").arg(m_xRange.lower).arg(m_xRange.upper); + + text += + QString(" -- yRange: (%1, %2)").arg(m_yRange.lower).arg(m_yRange.upper); + + text += QString(" -- wasClickOnXAxis: %1") + .arg(m_wasClickOnXAxis ? "true" : "false"); + text += QString(" -- wasClickOnYAxis: %1") + .arg(m_wasClickOnYAxis ? "true" : "false"); + text += QString(" -- isMeasuringDistance: %1") + .arg(m_isMeasuringDistance ? "true" : "false"); + + text += QString(" -- xRegionRangeStart: %1 -- xRegionRangeEnd: %2") + .arg(m_xRegionRangeStart) + .arg(m_xRegionRangeEnd); + + text += QString(" -- yRegionRangeStart: %1 -- yRegionRangeEnd: %2") + .arg(m_yRegionRangeStart) + .arg(m_yRegionRangeEnd); + + text += QString(" -- xDelta: %1 -- yDelta: %2").arg(m_xDelta).arg(m_yDelta); + + text += QString(" -- pressedKeyCode: %1").arg(m_pressedKeyCode); + + text += QString(" -- keyboardModifiers: %1").arg(m_keyboardModifiers); + + text += + QString(" -- lastPressedMouseButton: %1").arg(m_lastPressedMouseButton); + + text += + QString(" -- lastReleasedMouseButton: %1").arg(m_lastReleasedMouseButton); + + text += QString(" -- pressedMouseButtons: %1").arg(m_pressedMouseButtons); + + text += + QString(" -- mouseButtonsAtMousePress: %1").arg(m_mouseButtonsAtMousePress); + + text += QString(" -- mouseButtonsAtMouseRelease: %1") + .arg(m_mouseButtonsAtMouseRelease); + + return text; +} + + +} // namespace pappso + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotcontext.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotcontext.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotcontext.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,108 @@ +// Copyright 2021 Filippo Rusconi +// GPL3+ + +#pragma once + +/////////////////////// StdLib includes + + +/////////////////////// Qt includes +#include +#include + +////////////////////// Other includes +#include "qcustomplot.h" + +/////////////////////// Local includes +#include "../../types.h" +#include "../../exportinmportconfig.h" +#include "../../processing/combiners/selectionpolygon.h" + + +namespace pappso +{ + +enum class DragDirections +{ + NOT_SET = 0x0000, + LEFT_TO_RIGHT = 1 << 0, + RIGHT_TO_LEFT = 1 << 1, + TOP_TO_BOTTOM = 1 << 2, + BOTTOM_TO_TOP = 1 << 3 +}; + + +class PMSPP_LIB_DECL BasePlotContext +{ + public: + BasePlotContext(); + BasePlotContext(const BasePlotContext &other); + virtual ~BasePlotContext(); + + BasePlotContext &operator=(const BasePlotContext &other); + + DataKind m_dataKind = DataKind::unset; + + bool m_isMouseDragging = false; + bool m_wasMouseDragging = false; + + bool m_isKeyBoardDragging = false; + bool m_isLeftPseudoButtonKeyPressed = false; + bool m_isRightPseudoButtonKeyPressed = false; + bool m_wassKeyBoardDragging = false; + + QPointF m_startDragPoint; + QPointF m_currentDragPoint; + QPointF m_lastCursorHoveredPoint; + DragDirections m_dragDirections = DragDirections::NOT_SET; + + SelectionPolygon m_selectionPolygon; + double m_selectRectangleWidth = 0; + + // The effective range of the axes. + QCPRange m_xRange; + QCPRange m_yRange; + + // Tell if the mouse move was started onto either axis, because that will + // condition if some calculations needs to be performed or not (for example, + // if the mouse cursor motion was started on an axis, there is no point to + // perform deconvolutions). + bool m_wasClickOnXAxis = false; + bool m_wasClickOnYAxis = false; + + bool m_isMeasuringDistance = false; + + // The user-selected region over the plot. + // Note that we cannot use QCPRange structures because these are normalized by + // QCustomPlot in such a manner that lower is actually < upper. But we need + // for a number of our calculations (specifically for the deconvolutions) to + // actually have the lower value be start drag point.x even if the drag + // direction was from right to left. + double m_xRegionRangeStart = std::numeric_limits::min(); + double m_xRegionRangeEnd = std::numeric_limits::min(); + + double m_yRegionRangeStart = std::numeric_limits::min(); + double m_yRegionRangeEnd = std::numeric_limits::min(); + + double m_xDelta = 0; + double m_yDelta = 0; + + int m_pressedKeyCode; + int m_releasedKeyCode; + + Qt::KeyboardModifiers m_keyboardModifiers; + + Qt::MouseButtons m_lastPressedMouseButton; + Qt::MouseButtons m_lastReleasedMouseButton; + + Qt::MouseButtons m_pressedMouseButtons; + + Qt::MouseButtons m_mouseButtonsAtMousePress; + Qt::MouseButtons m_mouseButtonsAtMouseRelease; + + DragDirections recordDragDirections(); + QString toString() const; +}; + + +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -32,6 +32,7 @@ /////////////////////// Local includes +#include "../../types.h" #include "baseplotwidget.h" #include "../../pappsoexception.h" #include "../../exception/exceptionnotpossible.h" @@ -45,76 +46,8 @@ namespace pappso { - -QString -BasePlotContext::toString() const -{ - QString text("Context:"); - - text += QString("data kind: %1").arg(static_cast(dataKind)); - - text += QString(" isMouseDragging: %1 -- wasMouseDragging: %2") - .arg(isMouseDragging ? "true" : "false") - .arg(wasMouseDragging ? "true" : "false"); - - text += QString(" -- startDragPoint : (%1, %2)") - .arg(startDragPoint.x()) - .arg(startDragPoint.y()); - - text += QString(" -- currentDragPoint : (%1, %2)") - .arg(currentDragPoint.x()) - .arg(currentDragPoint.y()); - - text += QString(" -- lastCursorHoveredPoint : (%1, %2)") - .arg(lastCursorHoveredPoint.x()) - .arg(lastCursorHoveredPoint.y()); - - text += QString(" -- xRange: (%1, %2)").arg(xRange.lower).arg(xRange.upper); - - text += QString(" -- yRange: (%1, %2)").arg(yRange.lower).arg(yRange.upper); - - text += - QString(" -- wasClickOnXAxis: %1").arg(wasClickOnXAxis ? "true" : "false"); - text += - QString(" -- wasClickOnYAxis: %1").arg(wasClickOnYAxis ? "true" : "false"); - text += QString(" -- isMeasuringDistance: %1") - .arg(isMeasuringDistance ? "true" : "false"); - - text += QString(" -- xRegionRangeStart: %1 -- xRegionRangeEnd: %2") - .arg(xRegionRangeStart) - .arg(xRegionRangeEnd); - - text += QString(" -- yRegionRangeStart: %1 -- yRegionRangeEnd: %2") - .arg(yRegionRangeStart) - .arg(yRegionRangeEnd); - - text += QString(" -- xDelta: %1 -- yDelta: %2").arg(xDelta).arg(yDelta); - - text += QString(" -- pressedKeyCode: %1").arg(pressedKeyCode); - - text += QString(" -- keyboardModifiers: %1").arg(keyboardModifiers); - - text += QString(" -- lastPressedMouseButton: %1").arg(lastPressedMouseButton); - - text += - QString(" -- lastReleasedMouseButton: %1").arg(lastReleasedMouseButton); - - text += QString(" -- pressedMouseButtons: %1").arg(pressedMouseButtons); - - text += - QString(" -- mouseButtonsAtMousePress: %1").arg(mouseButtonsAtMousePress); - - text += QString(" -- mouseButtonsAtMouseRelease: %1") - .arg(mouseButtonsAtMouseRelease); - - return text; -} - - BasePlotWidget::BasePlotWidget(QWidget *parent) : QCustomPlot(parent) { - // qDebug(); - if(parent == nullptr) qFatal("Programming error."); @@ -123,9 +56,53 @@ m_pen.setBrush(Qt::black); m_pen.setWidth(1); + // qDebug() << "Created new BasePlotWidget with" << layerCount() + //<< "layers before setting up widget."; + // qDebug().noquote() << "All layer names:\n" << allLayerNamesToString(); + + // As of today 20210313, the QCustomPlot is created with the following 6 + // layers: + // + // All layers' name: + // + // Layer index 0 name: background + // Layer index 1 name: grid + // Layer index 2 name: main + // Layer index 3 name: axes + // Layer index 4 name: legend + // Layer index 5 name: overlay + if(!setupWidget()) qFatal("Programming error."); + // Do not call createAllAncillaryItems() in this base class because all the + // items will have been created *before* the addition of plots and then the + // rendering order will hide them to the viewer, since the rendering order is + // according to the order in which the items have been created. + // + // The fact that the ancillary items are created before trace plots is not a + // problem because the trace plots are sparse and do not effectively hide the + // data. + // + // But, in the color map plot widgets, we cannot afford to create the + // ancillary items *before* the plot itself because then, the rendering of the + // plot (created after) would screen off the ancillary items (created before). + // + // So, the createAllAncillaryItems() function needs to be called in the + // derived classes at the most appropriate moment in the setting up of the + // widget. + // + // All this is only a workaround of a bug in QCustomPlot. See + // https://www.qcustomplot.com/index.php/support/forum/2283. + // + // I initially wanted to have a plots layer on top of the default background + // layer and a items layer on top of it. But that setting prevented the + // selection of graphs. + + // qDebug() << "Created new BasePlotWidget with" << layerCount() + //<< "layers after setting up widget."; + // qDebug().noquote() << "All layer names:\n" << allLayerNamesToString(); + show(); } @@ -148,9 +125,29 @@ xAxis->setLabel(x_axis_label); yAxis->setLabel(y_axis_label); + // qDebug() << "Created new BasePlotWidget with" << layerCount() + //<< "layers before setting up widget."; + // qDebug().noquote() << "All layer names:\n" << allLayerNamesToString(); + + // As of today 20210313, the QCustomPlot is created with the following 6 + // layers: + // + // All layers' name: + // + // Layer index 0 name: background + // Layer index 1 name: grid + // Layer index 2 name: main + // Layer index 3 name: axes + // Layer index 4 name: legend + // Layer index 5 name: overlay + if(!setupWidget()) qFatal("Programming error."); + // qDebug() << "Created new BasePlotWidget with" << layerCount() + //<< "layers after setting up widget."; + // qDebug().noquote() << "All layer names:\n" << allLayerNamesToString(); + show(); } @@ -168,23 +165,61 @@ m_xAxisRangeHistory.clear(); m_yAxisRangeHistory.clear(); + + // Note that the QCustomPlot xxxItem objects are allocated with (this) which + // means their destruction is automatically handled upon *this' destruction. } -bool -BasePlotWidget::setupWidget() +QString +BasePlotWidget::allLayerNamesToString() const { - // qDebug(); - // By default the widget comes with a graph. Remove it. + QString text; - if(graphCount()) - removeGraph(0); + for(int iter = 0; iter < layerCount(); ++iter) + { + text += + QString("Layer index %1: %2\n").arg(iter).arg(layer(iter)->name()); + } + + return text; +} + + +QString +BasePlotWidget::layerableLayerName(QCPLayerable *layerable_p) const +{ + if(layerable_p == nullptr) + qFatal("Programming error."); + + QCPLayer *layer_p = layerable_p->layer(); + + return layer_p->name(); +} + + +int +BasePlotWidget::layerableLayerIndex(QCPLayerable *layerable_p) const +{ + if(layerable_p == nullptr) + qFatal("Programming error."); + + QCPLayer *layer_p = layerable_p->layer(); + + for(int iter = 0; iter < layerCount(); ++iter) + { + if(layer(iter) == layer_p) + return iter; + } + + return -1; +} - // This is required so that we get the keyboard events. - setFocusPolicy(Qt::StrongFocus); - setInteractions(QCP::iRangeZoom | QCP::iSelectPlottables | QCP::iMultiSelect); +void +BasePlotWidget::createAllAncillaryItems() +{ // Make a copy of the pen to just change its color and set that color to // the tracer line. QPen pen = m_pen; @@ -197,19 +232,22 @@ // becomes the tracer that is being anchored at the region start. The second // line i horizontal and is always black. - pen.setColor(QColor("black")); + pen.setColor(QColor("steelblue")); // The set of tracers (horizontal and vertical) that track the position of the // mouse cursor. + mp_vPosTracerItem = new QCPItemLine(this); - mp_vPosTracerItem->setPen(m_pen); + mp_vPosTracerItem->setLayer("plotsLayer"); + mp_vPosTracerItem->setPen(pen); mp_vPosTracerItem->start->setType(QCPItemPosition::ptPlotCoords); mp_vPosTracerItem->end->setType(QCPItemPosition::ptPlotCoords); mp_vPosTracerItem->start->setCoords(0, 0); mp_vPosTracerItem->end->setCoords(0, 0); mp_hPosTracerItem = new QCPItemLine(this); - mp_hPosTracerItem->setPen(m_pen); + mp_hPosTracerItem->setLayer("plotsLayer"); + mp_hPosTracerItem->setPen(pen); mp_hPosTracerItem->start->setType(QCPItemPosition::ptPlotCoords); mp_hPosTracerItem->end->setType(QCPItemPosition::ptPlotCoords); mp_hPosTracerItem->start->setCoords(0, 0); @@ -222,6 +260,7 @@ pen.setColor(QColor("green")); mp_vStartTracerItem = new QCPItemLine(this); + mp_vStartTracerItem->setLayer("plotsLayer"); mp_vStartTracerItem->setPen(pen); mp_vStartTracerItem->start->setType(QCPItemPosition::ptPlotCoords); mp_vStartTracerItem->end->setType(QCPItemPosition::ptPlotCoords); @@ -232,31 +271,108 @@ pen.setColor(QColor("red")); mp_vEndTracerItem = new QCPItemLine(this); + mp_vEndTracerItem->setLayer("plotsLayer"); mp_vEndTracerItem->setPen(pen); mp_vEndTracerItem->start->setType(QCPItemPosition::ptPlotCoords); mp_vEndTracerItem->end->setType(QCPItemPosition::ptPlotCoords); mp_vEndTracerItem->start->setCoords(0, 0); mp_vEndTracerItem->end->setCoords(0, 0); - mp_zoomRectItem = new QCPItemRect(this); - mp_zoomRectItem->setPen(m_pen); - mp_zoomRectItem->topLeft->setType(QCPItemPosition::ptPlotCoords); - mp_zoomRectItem->bottomRight->setType(QCPItemPosition::ptPlotCoords); - mp_zoomRectItem->setVisible(false); - - mp_selectLineItem = new QCPItemLine(this); - mp_selectLineItem->setPen(m_pen); - mp_selectLineItem->start->setType(QCPItemPosition::ptPlotCoords); - mp_selectLineItem->end->setType(QCPItemPosition::ptPlotCoords); - mp_selectLineItem->setVisible(false); - // When the user click-drags the mouse, the X distance between the drag start // point and the drag end point (current point) is the xDelta. mp_xDeltaTextItem = new QCPItemText(this); + mp_xDeltaTextItem->setLayer("plotsLayer"); + mp_xDeltaTextItem->setColor(QColor("steelblue")); mp_xDeltaTextItem->setPositionAlignment(Qt::AlignBottom | Qt::AlignCenter); mp_xDeltaTextItem->position->setType(QCPItemPosition::ptPlotCoords); mp_xDeltaTextItem->setVisible(false); + // Same for the y delta + mp_yDeltaTextItem = new QCPItemText(this); + mp_yDeltaTextItem->setLayer("plotsLayer"); + mp_yDeltaTextItem->setColor(QColor("steelblue")); + mp_yDeltaTextItem->setPositionAlignment(Qt::AlignBottom | Qt::AlignCenter); + mp_yDeltaTextItem->position->setType(QCPItemPosition::ptPlotCoords); + mp_yDeltaTextItem->setVisible(false); + + // Make sure we prepare the four lines that will be needed to + // draw the selection rectangle. + pen = m_pen; + + pen.setColor("steelblue"); + + mp_selectionRectangeLine1 = new QCPItemLine(this); + mp_selectionRectangeLine1->setLayer("plotsLayer"); + mp_selectionRectangeLine1->setPen(pen); + mp_selectionRectangeLine1->start->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine1->end->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine1->start->setCoords(0, 0); + mp_selectionRectangeLine1->end->setCoords(0, 0); + mp_selectionRectangeLine1->setVisible(false); + + mp_selectionRectangeLine2 = new QCPItemLine(this); + mp_selectionRectangeLine2->setLayer("plotsLayer"); + mp_selectionRectangeLine2->setPen(pen); + mp_selectionRectangeLine2->start->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine2->end->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine2->start->setCoords(0, 0); + mp_selectionRectangeLine2->end->setCoords(0, 0); + mp_selectionRectangeLine2->setVisible(false); + + mp_selectionRectangeLine3 = new QCPItemLine(this); + mp_selectionRectangeLine3->setLayer("plotsLayer"); + mp_selectionRectangeLine3->setPen(pen); + mp_selectionRectangeLine3->start->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine3->end->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine3->start->setCoords(0, 0); + mp_selectionRectangeLine3->end->setCoords(0, 0); + mp_selectionRectangeLine3->setVisible(false); + + mp_selectionRectangeLine4 = new QCPItemLine(this); + mp_selectionRectangeLine4->setLayer("plotsLayer"); + mp_selectionRectangeLine4->setPen(pen); + mp_selectionRectangeLine4->start->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine4->end->setType(QCPItemPosition::ptPlotCoords); + mp_selectionRectangeLine4->start->setCoords(0, 0); + mp_selectionRectangeLine4->end->setCoords(0, 0); + mp_selectionRectangeLine4->setVisible(false); +} + + +bool +BasePlotWidget::setupWidget() +{ + // qDebug(); + + // By default the widget comes with a graph. Remove it. + + if(graphCount()) + { + // QCPLayer *layer_p = graph(0)->layer(); + // qDebug() << "The graph was on layer:" << layer_p->name(); + + // As of today 20210313, the graph is created on the currentLayer(), that + // is "main". + + removeGraph(0); + } + + // The general idea is that we do want custom layers for the trace|colormap + // plots. + + // qDebug().noquote() << "Right before creating the new layer, layers:\n" + //<< allLayerNamesToString(); + + // Add the layer that will store all the plots and all the ancillary items. + addLayer( + "plotsLayer", layer("background"), QCustomPlot::LayerInsertMode::limAbove); + // qDebug().noquote() << "Added new plotsLayer, layers:\n" + //<< allLayerNamesToString(); + + // This is required so that we get the keyboard events. + setFocusPolicy(Qt::StrongFocus); + setInteractions(QCP::iRangeZoom | QCP::iSelectPlottables | QCP::iMultiSelect); + // We want to capture the signals emitted by the QCustomPlot base class. connect( this, &QCustomPlot::mouseMove, this, &BasePlotWidget::mouseMoveHandler); @@ -269,6 +385,9 @@ this, &BasePlotWidget::mouseReleaseHandler); + connect( + this, &QCustomPlot::mouseWheel, this, &BasePlotWidget::mouseWheelHandler); + connect(this, &QCustomPlot::axisDoubleClick, this, @@ -399,8 +518,7 @@ // qDebug() << "axes history size:" << m_xAxisRangeHistory.size() //<< "current index:" << m_lastAxisRangeHistoryIndex - //<< xAxis->range().lower << "--" << xAxis->range().upper - //<< "and" + //<< xAxis->range().lower << "--" << xAxis->range().upper << "and" //<< yAxis->range().lower << "--" << yAxis->range().upper; } @@ -425,7 +543,7 @@ return; } - // qDebug() << "setting index to:" << m_lastAxisRangeHistoryIndex - 1 + // qDebug() << "Setting index to:" << m_lastAxisRangeHistoryIndex - 1 //<< "and restoring axes history to that index"; restoreAxesRangeHistory(--m_lastAxisRangeHistoryIndex); @@ -443,7 +561,7 @@ void BasePlotWidget::restoreAxesRangeHistory(std::size_t index) { - // qDebug() << "axes history size:" << m_xAxisRangeHistory.size() + // qDebug() << "Axes history size:" << m_xAxisRangeHistory.size() //<< "current index:" << m_lastAxisRangeHistoryIndex //<< "asking to restore index:" << index; @@ -453,6 +571,15 @@ return; } + // We want to go back to the range history item at index, which means we want + // to pop back all the items between index+1 and size-1. + + while(m_xAxisRangeHistory.size() > index + 1) + m_xAxisRangeHistory.pop_back(); + + if(m_xAxisRangeHistory.size() - 1 != index) + qFatal("Programming error."); + xAxis->setRange(*(m_xAxisRangeHistory.at(index))); yAxis->setRange(*(m_yAxisRangeHistory.at(index))); @@ -465,7 +592,7 @@ mp_vEndTracerItem->setVisible(false); - // The start trace will keep beeing represented at the last position and last + // The start tracer will keep beeing represented at the last position and last // size even if we call this function repetitively. So actually do not show, // it will reappare as soon as the mouse is moved. // if(m_shouldTracersBeVisible) @@ -475,7 +602,7 @@ replot(); - updateContextRanges(); + updateContextXandYAxisRanges(); // qDebug() << "restored axes history to index:" << index //<< "with values:" << xAxis->range().lower << "--" @@ -494,8 +621,8 @@ // qDebug() << "ENTER"; // We need this because some keys modify our behaviour. - m_context.pressedKeyCode = event->key(); - m_context.keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); + m_context.m_pressedKeyCode = event->key(); + m_context.m_keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); if(event->key() == Qt::Key_Left || event->key() == Qt::Key_Right || event->key() == Qt::Key_Up || event->key() == Qt::Key_Down) @@ -520,15 +647,18 @@ void BasePlotWidget::keyReleaseEvent(QKeyEvent *event) { - m_context.releasedKeyCode = event->key(); + m_context.m_releasedKeyCode = event->key(); // The keyboard key is being released, set the key code to 0. - m_context.pressedKeyCode = 0; - m_context.keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); + m_context.m_pressedKeyCode = 0; + + m_context.m_keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); // Now test if the key that was released is one of the housekeeping keys. if(event->key() == Qt::Key_Backspace) { + // qDebug(); + // The user wants to iterate back in the x/y axis range history. restorePreviousAxesRangeHistory(); @@ -629,7 +759,17 @@ { return mousePseudoButtonKeyReleaseEvent(event); } + else if(event->key() == Qt::Key_S) + { + // The user has asked to measure the horizontal size of the rectangle and + // to start making a skewed selection rectangle. + + m_context.m_selectRectangleWidth = + abs(m_context.m_currentDragPoint.x() - m_context.m_startDragPoint.x()); + // qDebug() << "Set m_context.selectRectangleWidth to" + //<< m_context.m_selectRectangleWidth << "upon release of S key"; + } // At this point emit the signal, since we did not treat it. Maybe the // consumer widget wants to know that the keyboard key was released. @@ -665,9 +805,9 @@ int pixel_increment = 0; - if(m_context.keyboardModifiers == Qt::NoModifier) + if(m_context.m_keyboardModifiers == Qt::NoModifier) pixel_increment = 1; - else if(m_context.keyboardModifiers == Qt::AltModifier) + else if(m_context.m_keyboardModifiers == Qt::AltModifier) pixel_increment = 50; // The user is moving the positional markers. This is equivalent to a @@ -708,8 +848,8 @@ { QPointF pixel_coordinates( - xAxis->coordToPixel(m_context.lastCursorHoveredPoint.x()), - yAxis->coordToPixel(m_context.lastCursorHoveredPoint.y())); + xAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.x()), + yAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.y())); Qt::MouseButton button = Qt::NoButton; QEvent::Type q_event_type = QEvent::MouseButtonPress; @@ -720,10 +860,10 @@ button = Qt::LeftButton; - m_context.isLeftPseudoButtonKeyPressed = - !m_context.isLeftPseudoButtonKeyPressed; + m_context.m_isLeftPseudoButtonKeyPressed = + !m_context.m_isLeftPseudoButtonKeyPressed; - if(m_context.isLeftPseudoButtonKeyPressed) + if(m_context.m_isLeftPseudoButtonKeyPressed) q_event_type = QEvent::MouseButtonPress; else q_event_type = QEvent::MouseButtonRelease; @@ -734,10 +874,10 @@ button = Qt::RightButton; - m_context.isRightPseudoButtonKeyPressed = - !m_context.isRightPseudoButtonKeyPressed; + m_context.m_isRightPseudoButtonKeyPressed = + !m_context.m_isRightPseudoButtonKeyPressed; - if(m_context.isRightPseudoButtonKeyPressed) + if(m_context.m_isRightPseudoButtonKeyPressed) q_event_type = QEvent::MouseButtonPress; else q_event_type = QEvent::MouseButtonRelease; @@ -755,7 +895,7 @@ mapToGlobal(pixel_coordinates.toPoint()), button, button, - m_context.keyboardModifiers, + m_context.m_keyboardModifiers, Qt::MouseEventSynthesizedByApplication); if(q_event_type == QEvent::MouseButtonPress) @@ -771,6 +911,396 @@ /// MOUSE-related EVENTS void +BasePlotWidget::mouseMoveHandler(QMouseEvent *event) +{ + + // If we have no focus, then get it. See setFocus() to understand why asking + // for focus is cosly and thus why we want to make this decision first. + if(!hasFocus()) + setFocus(); + + qDebug() << (graph() != nullptr); + // if(graph(0) != nullptr) + // { // check if the widget contains some graphs + + // The event->button() must be by Qt instructions considered to be 0. + + // Whatever happens, we want to store the plot coordinates of the current + // mouse cursor position (will be useful later for countless needs). + + QPointF mousePoint = event->localPos(); + qDebug(); + qDebug() << "local mousePoint position in pixels:" << mousePoint; + + m_context.m_lastCursorHoveredPoint.setX(xAxis->pixelToCoord(mousePoint.x())); + qDebug(); + m_context.m_lastCursorHoveredPoint.setY(yAxis->pixelToCoord(mousePoint.y())); + qDebug(); + + // qDebug() << "lastCursorHoveredPoint coord:" + //<< m_context.lastCursorHoveredPoint; + + // Now, depending on the button(s) (if any) that are pressed or not, we + // have a different processing. + + qDebug(); + if(m_context.m_pressedMouseButtons & Qt::LeftButton || + m_context.m_pressedMouseButtons & Qt::RightButton) + mouseMoveHandlerDraggingCursor(); + else + mouseMoveHandlerNotDraggingCursor(); + // } + qDebug(); + event->accept(); +} + + +void +BasePlotWidget::mouseMoveHandlerNotDraggingCursor() +{ + + qDebug(); + m_context.m_isMouseDragging = false; + + qDebug(); + // We are not dragging the mouse (no button pressed), simply let this + // widget's consumer know the position of the cursor and update the markers. + // The consumer of this widget will update mouse cursor position at + // m_context.m_lastCursorHoveredPoint if so needed. + + emit lastCursorHoveredPointSignal(m_context.m_lastCursorHoveredPoint); + + qDebug(); + + // We are not dragging, so we do not show the region end tracer we only + // show the anchoring start trace that might be of use if the user starts + // using the arrow keys to move the cursor. + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(false); + + qDebug(); + // Only bother with the tracers if the user wants them to be visible. + // Their crossing point must be exactly at the last cursor-hovered point. + + if(m_shouldTracersBeVisible) + { + // We are not dragging, so only show the position markers (v and h); + + qDebug(); + if(mp_hPosTracerItem != nullptr) + { + // Horizontal position tracer. + mp_hPosTracerItem->setVisible(true); + mp_hPosTracerItem->start->setCoords( + xAxis->range().lower, m_context.m_lastCursorHoveredPoint.y()); + mp_hPosTracerItem->end->setCoords( + xAxis->range().upper, m_context.m_lastCursorHoveredPoint.y()); + } + + qDebug(); + // Vertical position tracer. + if(mp_vPosTracerItem != nullptr) + { + mp_vPosTracerItem->setVisible(true); + + mp_vPosTracerItem->setVisible(true); + mp_vPosTracerItem->start->setCoords( + m_context.m_lastCursorHoveredPoint.x(), yAxis->range().upper); + mp_vPosTracerItem->end->setCoords( + m_context.m_lastCursorHoveredPoint.x(), yAxis->range().lower); + } + + qDebug(); + replot(); + } + + + return; +} + + +void +BasePlotWidget::mouseMoveHandlerDraggingCursor() +{ + qDebug(); + m_context.m_isMouseDragging = true; + + // Now store the mouse position data into the the current drag point + // member datum, that will be used in countless occasions later. + m_context.m_currentDragPoint = m_context.m_lastCursorHoveredPoint; + m_context.m_keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); + + // When we drag (either keyboard or mouse), we hide the position markers + // (black) and we show the start and end vertical markers for the region. + // Then, we draw the horizontal region range marker that delimits + // horizontally the dragged-over region. + + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); + + // Only bother with the tracers if the user wants them to be visible. + if(m_shouldTracersBeVisible && (mp_vEndTracerItem != nullptr)) + { + + // The vertical end tracer position must be refreshed. + mp_vEndTracerItem->start->setCoords(m_context.m_currentDragPoint.x(), + yAxis->range().upper); + + mp_vEndTracerItem->end->setCoords(m_context.m_currentDragPoint.x(), + yAxis->range().lower); + + mp_vEndTracerItem->setVisible(true); + } + + // Whatever the button, when we are dealing with the axes, we do not + // want to show any of the tracers. + + if(m_context.m_wasClickOnXAxis || m_context.m_wasClickOnYAxis) + { + qDebug(); + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); + + if(mp_vStartTracerItem != nullptr) + mp_vStartTracerItem->setVisible(false); + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(false); + } + else + { + qDebug(); + // Since we are not dragging the mouse cursor over the axes, make sure + // we store the drag directions in the context, as this might be + // useful for later operations. + + m_context.recordDragDirections(); + + // qDebug() << m_context.toString(); + } + + // Because when we drag the mouse button (whatever the button) we need to + // know what is the drag delta (distance between start point and current + // point of the drag operation) on both axes, ask that these x|y deltas be + // computed. + qDebug(); + calculateDragDeltas(); + + // Now deal with the BUTTON-SPECIFIC CODE. + + if(m_context.m_mouseButtonsAtMousePress & Qt::LeftButton) + { + qDebug(); + return mouseMoveHandlerLeftButtonDraggingCursor(); + } + else if(m_context.m_mouseButtonsAtMousePress & Qt::RightButton) + { + qDebug(); + return mouseMoveHandlerRightButtonDraggingCursor(); + } + + qDebug(); +} + + +void +BasePlotWidget::mouseMoveHandlerLeftButtonDraggingCursor() +{ + qDebug() << "the left button is dragging."; + + // Set the context.m_isMeasuringDistance to false, which later might be set to + // true if effectively we are measuring a distance. This is required because + // the derived widget classes might want to know if they have to perform + // some action on the basis that context is measuring a distance, for + // example the mass spectrum-specific widget might want to compute + // deconvolutions. + + m_context.m_isMeasuringDistance = false; + + // Let's first check if the mouse drag operation originated on either + // axis. In that case, the user is performing axis reframing or rescaling. + + if(m_context.m_wasClickOnXAxis || m_context.m_wasClickOnYAxis) + { + qDebug() << "Click was on one of the axes."; + + if(m_context.m_keyboardModifiers & Qt::ControlModifier) + { + // The user is asking a rescale of the plot. + + // We know that we do not want the tracers when we perform axis + // rescaling operations. + + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); + + if(mp_vStartTracerItem != nullptr) + mp_vStartTracerItem->setVisible(false); + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(false); + + // This operation is particularly intensive, thus we want to + // reduce the number of calculations by skipping this calculation + // a number of times. The user can ask for this feature by + // clicking the 'Q' letter. + + if(m_context.m_pressedKeyCode == Qt::Key_Q) + { + if(m_mouseMoveHandlerSkipCount < m_mouseMoveHandlerSkipAmount) + { + m_mouseMoveHandlerSkipCount++; + return; + } + else + { + m_mouseMoveHandlerSkipCount = 0; + } + } + + qDebug() << "Asking that the axes be rescaled."; + + axisRescale(); + } + else + { + // The user was simply dragging the axis. Just pan, that is slide + // the plot in the same direction as the mouse movement and with the + // same amplitude. + + qDebug() << "Asking that the axes be panned."; + + axisPan(); + } + + return; + } + + // At this point we understand that the user was not performing any + // panning/rescaling operation by clicking on any one of the axes.. Go on + // with other possibilities. + + // Let's check if the user is actually drawing a rectangle (covering a + // real area) or is drawing a line. + + // qDebug() << "The mouse dragging did not originate on an axis."; + + if(isVerticalDisplacementAboveThreshold()) + { + qDebug() << "Apparently the selection is a real rectangle."; + + // When we draw a rectangle the tracers are of no use. + + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); + + if(mp_vStartTracerItem != nullptr) + mp_vStartTracerItem->setVisible(false); + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(false); + + // Draw the rectangle, false, not as line segment and + // false, not for integration + drawSelectionRectangleAndPrepareZoom(false, false); + + // Draw the selection width/height text + drawXDeltaFeatures(); + drawYDeltaFeatures(); + + // qDebug() << "The selection polygon:" + //<< m_context.m_selectionPolygon.toString(); + } + else + { + qDebug() << "Apparently we are measuring a delta."; + + // Draw the rectangle, true, as line segment and + // false, not for integration + drawSelectionRectangleAndPrepareZoom(true, false); + + // qDebug() << "The selection polygon:" + //<< m_context.m_selectionPolygon.toString(); + + // The pure position tracers should be hidden. + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(true); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(true); + + // Then, make sure the region range vertical tracers are visible. + if(mp_vStartTracerItem != nullptr) + mp_vStartTracerItem->setVisible(true); + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(true); + + // Draw the selection width text + drawXDeltaFeatures(); + } + qDebug(); +} + + +void +BasePlotWidget::mouseMoveHandlerRightButtonDraggingCursor() +{ + qDebug() << "the right button is dragging."; + + // Set the context.m_isMeasuringDistance to false, which later might be set to + // true if effectively we are measuring a distance. This is required because + // the derived widgets might want to know if they have to perform some + // action on the basis that context is measuring a distance, for example the + // mass spectrum-specific widget might want to compute deconvolutions. + + m_context.m_isMeasuringDistance = false; + + if(isVerticalDisplacementAboveThreshold()) + { + // qDebug() << "Apparently the selection is a real rectangle."; + + // When we draw a rectangle the tracers are of no use. + + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); + + if(mp_vStartTracerItem != nullptr) + mp_vStartTracerItem->setVisible(false); + if(mp_vEndTracerItem != nullptr) + mp_vEndTracerItem->setVisible(false); + + // Draw the rectangle, false for as_line_segment and true, for + // integration. + drawSelectionRectangleAndPrepareZoom(false, true); + + // Draw the selection width/height text + drawXDeltaFeatures(); + drawYDeltaFeatures(); + } + else + { + // qDebug() << "Apparently the selection is a not a rectangle."; + + // Draw the rectangle, true, as line segment and + // false, true for integration + drawSelectionRectangleAndPrepareZoom(true, true); + + // Draw the selection width text + drawXDeltaFeatures(); + } + + // Draw the selection width text + drawXDeltaFeatures(); +} + + +void BasePlotWidget::mousePressHandler(QMouseEvent *event) { // When the user clicks this widget it has to take focus. @@ -778,35 +1308,35 @@ QPointF mousePoint = event->localPos(); - m_context.lastPressedMouseButton = event->button(); - m_context.mouseButtonsAtMousePress = event->buttons(); + m_context.m_lastPressedMouseButton = event->button(); + m_context.m_mouseButtonsAtMousePress = event->buttons(); - // The pressedMouseButtons must continually inform on the status of pressed - // buttons so add the pressed button. - m_context.pressedMouseButtons |= event->button(); + // The pressedMouseButtons must continually inform on the status of + // pressed buttons so add the pressed button. + m_context.m_pressedMouseButtons |= event->button(); - // qDebug().noquote() << m_context.toString(); + qDebug().noquote() << m_context.toString(); // In all the processing of the events, we need to know if the user is // clicking somewhere with the intent to change the plot ranges (reframing // or rescaling the plot). // - // Reframing the plot means that the new x and y axes ranges are modified so - // that they match the region that the user has encompassed by left clicking - // the mouse and dragging it over the plot. That is we reframe the plot so - // that it contains only the "selected" region. - // - // Rescaling the plot means the the new x|y axis range is modified such that - // the lower axis range is constant and the upper axis range is moved either - // left or right by the same amont as the x|y delta encompassed by the user - // moving the mouse. The axis is thus either compressed (mouse movement is - // leftwards) or un-compressed (mouse movement is rightwards). + // Reframing the plot means that the new x and y axes ranges are modified + // so that they match the region that the user has encompassed by left + // clicking the mouse and dragging it over the plot. That is we reframe + // the plot so that it contains only the "selected" region. + // + // Rescaling the plot means the the new x|y axis range is modified such + // that the lower axis range is constant and the upper axis range is moved + // either left or right by the same amont as the x|y delta encompassed by + // the user moving the mouse. The axis is thus either compressed (mouse + // movement is leftwards) or un-compressed (mouse movement is rightwards). // There are two ways to perform axis range modifications: // // 1. By clicking on any of the axes - // 2. By clicking on the plot region but using keyboard key modifiers, like - // Alt and Ctrl. + // 2. By clicking on the plot region but using keyboard key modifiers, + // like Alt and Ctrl. // // We need to know both cases separately which is why we need to perform a // number of tests below. @@ -820,7 +1350,7 @@ // qDebug() << __FILE__ << __LINE__ //<< "Layout element is axisRect and actually on an X axis part."; - m_context.wasClickOnXAxis = true; + m_context.m_wasClickOnXAxis = true; // int currentInteractions = interactions(); // currentInteractions |= QCP::iRangeDrag; @@ -828,7 +1358,7 @@ // axisRect()->setRangeDrag(xAxis->orientation()); } else - m_context.wasClickOnXAxis = false; + m_context.m_wasClickOnXAxis = false; if(isClickOntoYAxis(mousePoint)) { @@ -836,7 +1366,7 @@ // qDebug() << __FILE__ << __LINE__ //<< "Layout element is axisRect and actually on an Y axis part."; - m_context.wasClickOnYAxis = true; + m_context.m_wasClickOnYAxis = true; // int currentInteractions = interactions(); // currentInteractions |= QCP::iRangeDrag; @@ -844,11 +1374,11 @@ // axisRect()->setRangeDrag(yAxis->orientation()); } else - m_context.wasClickOnYAxis = false; + m_context.m_wasClickOnYAxis = false; // At this point, let's see if we need to remove the QCP::iRangeDrag bit: - if(!m_context.wasClickOnXAxis && !m_context.wasClickOnYAxis) + if(!m_context.m_wasClickOnXAxis && !m_context.m_wasClickOnYAxis) { // qDebug() << __FILE__ << __LINE__ // << "Click outside of axes."; @@ -858,18 +1388,21 @@ // setInteractions((QCP::Interaction)currentInteractions); } - m_context.startDragPoint.setX(xAxis->pixelToCoord(mousePoint.x())); - m_context.startDragPoint.setY(yAxis->pixelToCoord(mousePoint.y())); + m_context.m_startDragPoint.setX(xAxis->pixelToCoord(mousePoint.x())); + m_context.m_startDragPoint.setY(yAxis->pixelToCoord(mousePoint.y())); // Now install the vertical start tracer at the last cursor hovered // position. - if(m_shouldTracersBeVisible) + if((m_shouldTracersBeVisible) && (mp_vStartTracerItem != nullptr)) mp_vStartTracerItem->setVisible(true); - mp_vStartTracerItem->start->setCoords(m_context.lastCursorHoveredPoint.x(), - yAxis->range().upper); - mp_vStartTracerItem->end->setCoords(m_context.lastCursorHoveredPoint.x(), - yAxis->range().lower); + if(mp_vStartTracerItem != nullptr) + { + mp_vStartTracerItem->start->setCoords( + m_context.m_lastCursorHoveredPoint.x(), yAxis->range().upper); + mp_vStartTracerItem->end->setCoords( + m_context.m_lastCursorHoveredPoint.x(), yAxis->range().lower); + } replot(); } @@ -878,27 +1411,29 @@ void BasePlotWidget::mouseReleaseHandler(QMouseEvent *event) { - m_context.lastReleasedMouseButton = event->button(); + // Now the real code of this function. + + m_context.m_lastReleasedMouseButton = event->button(); // The event->buttons() is the description of the buttons that are pressed at // the moment the handler is invoked, that is now. If left and right were // pressed, and left was released, event->buttons() would be right. - m_context.mouseButtonsAtMouseRelease = event->buttons(); + m_context.m_mouseButtonsAtMouseRelease = event->buttons(); // The pressedMouseButtons must continually inform on the status of pressed // buttons so remove the released button. - m_context.pressedMouseButtons ^= event->button(); + m_context.m_pressedMouseButtons ^= event->button(); // qDebug().noquote() << m_context.toString(); // We'll need to know if modifiers were pressed a the moment the user // released the mouse button. - m_context.keyboardModifiers = QGuiApplication::keyboardModifiers(); + m_context.m_keyboardModifiers = QGuiApplication::keyboardModifiers(); - if(!m_context.isMouseDragging) + if(!m_context.m_isMouseDragging) { // Let the user know that the mouse was *not* being dragged. - m_context.wasMouseDragging = false; + m_context.m_wasMouseDragging = false; event->accept(); @@ -906,18 +1441,16 @@ } // Let the user know that the mouse was being dragged. - m_context.wasMouseDragging = true; + m_context.m_wasMouseDragging = true; // We cannot hide all items in one go because we rely on their visibility // to know what kind of dragging operation we need to perform (line-only // X-based zoom or rectangle-based X- and Y-based zoom, for example). The // only thing we know is that we can make the text invisible. - // We would not want to still see the selection line item. - mp_selectLineItem->setVisible(false); - // Same for the x delta text item mp_xDeltaTextItem->setVisible(false); + mp_yDeltaTextItem->setVisible(false); // We do not show the end vertical region range marker. mp_vEndTracerItem->setVisible(false); @@ -925,17 +1458,17 @@ // Horizontal position tracer. mp_hPosTracerItem->setVisible(true); mp_hPosTracerItem->start->setCoords(xAxis->range().lower, - m_context.lastCursorHoveredPoint.y()); + m_context.m_lastCursorHoveredPoint.y()); mp_hPosTracerItem->end->setCoords(xAxis->range().upper, - m_context.lastCursorHoveredPoint.y()); + m_context.m_lastCursorHoveredPoint.y()); // Vertical position tracer. mp_vPosTracerItem->setVisible(true); mp_vPosTracerItem->setVisible(true); - mp_vPosTracerItem->start->setCoords(m_context.lastCursorHoveredPoint.x(), + mp_vPosTracerItem->start->setCoords(m_context.m_lastCursorHoveredPoint.x(), yAxis->range().upper); - mp_vPosTracerItem->end->setCoords(m_context.lastCursorHoveredPoint.x(), + mp_vPosTracerItem->end->setCoords(m_context.m_lastCursorHoveredPoint.x(), yAxis->range().lower); // Force replot now because later that call might not be performed. @@ -946,25 +1479,18 @@ // the count to 0. m_mouseMoveHandlerSkipCount = 0; - // Compute the delta values, X and Y, that correspond to the movement that - // was done by the user while pressing the mouse button, that is get the - // geometry of the drag movement. - - calculateDragDeltasAndUnSortedRegionCorners(); - // Now that we have computed the useful ranges, we need to check what to do // depending on the button that was pressed. - if(m_context.lastReleasedMouseButton == Qt::LeftButton) + if(m_context.m_lastReleasedMouseButton == Qt::LeftButton) { return mouseReleaseHandlerLeftButton(); } - else if(m_context.lastReleasedMouseButton == Qt::RightButton) + else if(m_context.m_lastReleasedMouseButton == Qt::RightButton) { return mouseReleaseHandlerRightButton(); } - // By definition we are stopping the drag operation by releasing the mouse // button. Whatever that mouse button was pressed before and if there was // one pressed before. We cannot set that boolean value to false before @@ -972,7 +1498,7 @@ // that dragging was occurring. Like mouseReleaseHandledEvent(event) for // example. - m_context.isMouseDragging = false; + m_context.m_isMouseDragging = false; event->accept(); @@ -984,7 +1510,7 @@ BasePlotWidget::mouseReleaseHandlerLeftButton() { - if(m_context.wasClickOnXAxis || m_context.wasClickOnYAxis) + if(m_context.m_wasClickOnXAxis || m_context.m_wasClickOnYAxis) { // When the mouse move handler pans the plot, we cannot store each axes @@ -1004,38 +1530,71 @@ return; } - // Start handling the zoom rectangle so that we can skip any keyboard - // modified, like Ctrl that would not mean anything anyway. - if(mp_zoomRectItem->visible()) + // There are two possibilities: + // + // 1. The full selection polygon (four lines) were currently drawn, which + // means the user was willing to perform a zoom operation + // + // 2. Only the first top line was drawn, which means the user was dragging + // the cursor horizontally. That might have two ends, as shown below. + + // So, first check what is drawn of the selection polygon. + + PolygonType current_selection_polygon_type = + whatIsVisibleOfTheSelectionRectangle(); + + // Now that we know what was currently drawn of the selection polygon, we can + // remove it. true to reset the values to 0. + hideSelectionRectangle(true); + + // Force replot now because later that call might not be performed. + replot(); + + if(current_selection_polygon_type == PolygonType::FULL_POLYGON) { + // qDebug() << "Yes, the full polygon was visible"; // If we were dragging with the left button pressed and could draw a - // rectangle, then we were preparing a zoom operation. Let's bring - // that operation to an end. - - mp_zoomRectItem->setVisible(false); + // rectangle, then we were preparing a zoom operation. Let's bring that + // operation to its accomplishment. axisZoom(); + // qDebug() << "The selection polygon:" + //<< m_context.m_selectionPolygon.toString(); + return; } + else if(current_selection_polygon_type == PolygonType::TOP_LINE) + { + // qDebug() << "No, only the top line of the full polygon was visible"; - // If the user started by clicking in the plot region, dragged the mouse - // cursor with the left button and pressed the Ctrl modifier, then that - // means that they wanted to do a rescale over the x-axis in the form of a - // reframing. + // The user was dragging the left mouse cursor and that may mean they were + // measuring a distance or willing to perform a special zoom operation if + // the Ctrl key was down. - if(m_context.keyboardModifiers & Qt::ControlModifier) - { - return axisReframe(); + // If the user started by clicking in the plot region, dragged the mouse + // cursor with the left button and pressed the Ctrl modifier, then that + // means that they wanted to do a rescale over the x-axis in the form of a + // reframing. + + if(m_context.m_keyboardModifiers & Qt::ControlModifier) + { + return axisReframe(); + + // qDebug() << "The selection polygon:" + //<< m_context.m_selectionPolygon.toString(); + } } + // else + // qDebug() << "Another possibility."; } void BasePlotWidget::mouseReleaseHandlerRightButton() { - + qDebug(); // The right button is used for the integrations. Not for axis range // operations. So all we have to do is remove the various graphics items and // send a signal with the context that contains all the data required by the @@ -1043,315 +1602,68 @@ // Whatever we were doing we need to make the selection line invisible: - if(mp_selectLineItem->visible()) - mp_selectLineItem->setVisible(false); - if(mp_xDeltaTextItem->visible()) mp_xDeltaTextItem->setVisible(false); + if(mp_yDeltaTextItem->visible()) + mp_yDeltaTextItem->setVisible(false); // Also make the vertical end tracer invisible. mp_vEndTracerItem->setVisible(false); + // Once the integration is asked for, then the selection rectangle if of no + // more use. + hideSelectionRectangle(); + // Force replot now because later that call might not be performed. replot(); // Note that we only request an integration if the x-axis delta is enough. double x_delta_pixel = - fabs(xAxis->coordToPixel(m_context.currentDragPoint.x()) - - xAxis->coordToPixel(m_context.startDragPoint.x())); + fabs(xAxis->coordToPixel(m_context.m_currentDragPoint.x()) - + xAxis->coordToPixel(m_context.m_startDragPoint.x())); if(x_delta_pixel > 3) emit integrationRequestedSignal(m_context); // else - // qDebug() << "Not asking for integration."; + qDebug() << "Not asking for integration."; } void -BasePlotWidget::mouseMoveHandler(QMouseEvent *event) +BasePlotWidget::mouseWheelHandler([[maybe_unused]] QWheelEvent *event) { + // We should record the new range values each time the wheel is used to + // zoom/unzoom. - // If we have no focus, then get it. See setFocus() to understand why asking - // for focus is cosly and thus why we want to make this decision first. - if(!hasFocus()) - setFocus(); - - // The event->button() must be by Qt instructions considered to be 0. - - // Whatever happens, we want to store the plot coordinates of the current - // mouse cursor position (will be useful later for countless needs). - - QPointF mousePoint = event->localPos(); - - // qDebug() << "local mousePoint position in pixels:" << mousePoint; - - m_context.lastCursorHoveredPoint.setX(xAxis->pixelToCoord(mousePoint.x())); - m_context.lastCursorHoveredPoint.setY(yAxis->pixelToCoord(mousePoint.y())); + m_context.m_xRange = QCPRange(xAxis->range()); + m_context.m_yRange = QCPRange(yAxis->range()); - // qDebug() << "lastCursorHoveredPoint coord:" - //<< m_context.lastCursorHoveredPoint; + // qDebug() << "New x range: " << m_context.m_xRange; + // qDebug() << "New y range: " << m_context.m_yRange; - // Now, depending on the button(s) (if any) that are pressed or not, we have - // a different processing. + updateAxesRangeHistory(); - if(m_context.pressedMouseButtons & Qt::LeftButton || - m_context.pressedMouseButtons & Qt::RightButton) - mouseMoveHandlerDraggingCursor(); - else - mouseMoveHandlerNotDraggingCursor(); + emit plotRangesChangedSignal(m_context); + emit mouseWheelEventSignal(m_context); event->accept(); } void -BasePlotWidget::mouseMoveHandlerNotDraggingCursor() -{ - - m_context.isMouseDragging = false; - - // We are not dragging the mouse (no button pressed), simply let this - // widget's consumer know the position of the cursor and update the markers. - - emit lastCursorHoveredPointSignal(m_context.lastCursorHoveredPoint); - - // We are not dragging, so we do not show the region end tracer we only show - // the anchoring start trace that might be of use if the user starts using - // the arrow keys to move the cursor. - mp_vEndTracerItem->setVisible(false); - - // Only bother with the tracers if the user wants them to be visible. Their - // crossing point must be exactly at the last cursor-hovered point. - - if(m_shouldTracersBeVisible) - { - // We are not dragging, so only show the position markers (v and h); - - // Horizontal position tracer. - mp_hPosTracerItem->setVisible(true); - mp_hPosTracerItem->start->setCoords(xAxis->range().lower, - m_context.lastCursorHoveredPoint.y()); - mp_hPosTracerItem->end->setCoords(xAxis->range().upper, - m_context.lastCursorHoveredPoint.y()); - - // Vertical position tracer. - mp_vPosTracerItem->setVisible(true); - - mp_vPosTracerItem->setVisible(true); - mp_vPosTracerItem->start->setCoords(m_context.lastCursorHoveredPoint.x(), - yAxis->range().upper); - mp_vPosTracerItem->end->setCoords(m_context.lastCursorHoveredPoint.x(), - yAxis->range().lower); - - replot(); - } - - return; -} - - -void -BasePlotWidget::mouseMoveHandlerDraggingCursor() -{ - - m_context.isMouseDragging = true; - - // Now store the mouse position data into the the current drag point - // member datum, that will be used in countless occasions later. - m_context.currentDragPoint = m_context.lastCursorHoveredPoint; - m_context.keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); - - // When we drag (either keyboard or mouse), we hide the position markers - // (black) and we show the start and end vertical markers for the region. - // Then, we draw the horizontal region range marker that delimits - // horizontally the dragged-over region. - - mp_hPosTracerItem->setVisible(false); - mp_vPosTracerItem->setVisible(false); - - // Only bother with the tracers if the user wants them to be visible. - if(m_shouldTracersBeVisible) - { - - // The vertical end tracer position must be refreshed. - mp_vEndTracerItem->start->setCoords(m_context.currentDragPoint.x(), - yAxis->range().upper); - - mp_vEndTracerItem->end->setCoords(m_context.currentDragPoint.x(), - yAxis->range().lower); - - mp_vEndTracerItem->setVisible(true); - } - - // Whatever the button, when we are dealing with the axes, we do not - // want to show any of the tracers. - - if(m_context.wasClickOnXAxis || m_context.wasClickOnYAxis) - { - mp_hPosTracerItem->setVisible(false); - mp_vPosTracerItem->setVisible(false); - - mp_vStartTracerItem->setVisible(false); - mp_vEndTracerItem->setVisible(false); - } - - // We will need the axes ranges matching the region being selected by the - // user while left-mouse-dragging the cursor. - - calculateDragDeltasAndUnSortedRegionCorners(); - - // Now deal with the BUTTON-SPECIFIC CODE. - - if(m_context.mouseButtonsAtMousePress & Qt::LeftButton) - { - return mouseMoveHandlerLeftButtonDraggingCursor(); - } - else if(m_context.mouseButtonsAtMousePress & Qt::RightButton) - { - return mouseMoveHandlerRightButtonDraggingCursor(); - } -} - - -void -BasePlotWidget::mouseMoveHandlerLeftButtonDraggingCursor() -{ - // qDebug() << "the left button is dragging."; - - // Set the context.isMeasuringDistance to false, which later might be set to - // true if effectively we are measuring a distance. This is required because - // the derived widget classes might want to know if they have to perform - // some action on the basis that context is measuring a distance, for - // example the mass spectrum-specific widget might want to compute - // deconvolutions. - - m_context.isMeasuringDistance = false; - - // Let's first check if the mouse drag operation originated on either - // axis. In that case, the user is performing axis reframing or rescaling. - - if(m_context.wasClickOnXAxis || m_context.wasClickOnYAxis) - { - // qDebug() << __FILE__ << __LINE__ << "Click was on one of the axes."; - - if(m_context.keyboardModifiers & Qt::ControlModifier) - { - // The user is asking a rescale of the plot. - - // We know that we do not want the tracers when we perform axis - // rescaling operations. - - mp_hPosTracerItem->setVisible(false); - mp_vPosTracerItem->setVisible(false); - - mp_vStartTracerItem->setVisible(false); - mp_vEndTracerItem->setVisible(false); - - // This operation is particularly intensive, thus we want to - // reduce the number of calculations by skipping this calculation - // a number of times. The user can ask for this feature by - // clicking the 'Q' letter. - - if(m_context.pressedKeyCode == Qt::Key_Q) - { - if(m_mouseMoveHandlerSkipCount < m_mouseMoveHandlerSkipAmount) - { - m_mouseMoveHandlerSkipCount++; - return; - } - else - { - m_mouseMoveHandlerSkipCount = 0; - } - } - - // qDebug() << "Asking that the axes be rescaled."; - - axisRescale(); - } - else - { - // The user was simply dragging the axis. Just pan, that is slide - // the plot in the same direction as the mouse movement and with the - // same amplitude. - - // qDebug() << "Asking that the axes be panned."; - - axisPan(); - } - - return; - } - - // At this point we understand that the user was not performing any - // panning/rescaling operation by clicking on any one of the axes.. Go on - // with other possibilities. - - // Let's check if the user is actually drawing a rectangle (covering a - // real area) or is drawing a line. - - // qDebug() << "The mouse dragging did not originate on an axis."; - - if(isProperSelectionRectangle()) - { - // qDebug() << "Apparently the selection is a real rectangle."; - - // When we draw a rectangle the tracers are of no use. - - mp_hPosTracerItem->setVisible(false); - mp_vPosTracerItem->setVisible(false); - - mp_vStartTracerItem->setVisible(false); - mp_vEndTracerItem->setVisible(false); - - drawRectangleAndPrepareZoom(); - } - else - { - // qDebug() << "Apparently we are measuring a delta."; - - // The pure position tracers should be hidden. - mp_hPosTracerItem->setVisible(true); - mp_vPosTracerItem->setVisible(true); - - // Then, make sure the region range vertical tracers are visible. - mp_vStartTracerItem->setVisible(true); - mp_vEndTracerItem->setVisible(true); - - drawXDeltaLineAndMeasure(); - } -} - - -void -BasePlotWidget::mouseMoveHandlerRightButtonDraggingCursor() -{ - // qDebug() << "the right button is dragging."; - - // Set the context.isMeasuringDistance to false, which later might be set to - // true if effectively we are measuring a distance. This is required because - // the derived widgets might want to know if they have to perform some - // action on the basis that context is measuring a distance, for example the - // mass spectrum-specific widget might want to compute deconvolutions. - - m_context.isMeasuringDistance = false; - - drawXDeltaLineForIntegration(); -} - - -void BasePlotWidget::axisDoubleClickHandler( QCPAxis *axis, [[maybe_unused]] QCPAxis::SelectablePart part, QMouseEvent *event) { + // qDebug(); - m_context.keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); + m_context.m_keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); - if(m_context.keyboardModifiers & Qt::ControlModifier) + if(m_context.m_keyboardModifiers & Qt::ControlModifier) { + // qDebug(); // If the Ctrl modifiers is active, then both axes are to be reset. Also // the histories are reset also. @@ -1361,6 +1673,8 @@ } else { + // qDebug(); + // Only the axis passed as parameter is to be rescaled. // Reset the range of that axis to the max view possible. @@ -1376,9 +1690,9 @@ // "pressed". We need to remove manually the button from the pressed buttons // context member. - m_context.pressedMouseButtons ^= event->button(); + m_context.m_pressedMouseButtons ^= event->button(); - updateContextRanges(); + updateContextXandYAxisRanges(); emit plotRangesChangedSignal(m_context); @@ -1458,12 +1772,12 @@ // positions to pixels. double x_delta_pixel = - fabs(xAxis->coordToPixel(m_context.currentDragPoint.x()) - - xAxis->coordToPixel(m_context.startDragPoint.x())); + fabs(xAxis->coordToPixel(m_context.m_currentDragPoint.x()) - + xAxis->coordToPixel(m_context.m_startDragPoint.x())); double y_delta_pixel = - fabs(yAxis->coordToPixel(m_context.currentDragPoint.y()) - - yAxis->coordToPixel(m_context.startDragPoint.y())); + fabs(yAxis->coordToPixel(m_context.m_currentDragPoint.y()) - + yAxis->coordToPixel(m_context.m_startDragPoint.y())); if(x_delta_pixel > y_delta_pixel) return Qt::Horizontal; @@ -1512,8 +1826,8 @@ BasePlotWidget::horizontalGetGraphCoordNewPointCountPixels(int pixel_count) { QPointF pixel_coordinates( - xAxis->coordToPixel(m_context.lastCursorHoveredPoint.x()) + pixel_count, - yAxis->coordToPixel(m_context.lastCursorHoveredPoint.y())); + xAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.x()) + pixel_count, + yAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.y())); // Now convert back to local coordinates. @@ -1545,8 +1859,8 @@ BasePlotWidget::verticalGetGraphCoordNewPointCountPixels(int pixel_count) { QPointF pixel_coordinates( - xAxis->coordToPixel(m_context.lastCursorHoveredPoint.x()), - yAxis->coordToPixel(m_context.lastCursorHoveredPoint.y()) + pixel_count); + xAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.x()), + yAxis->coordToPixel(m_context.m_lastCursorHoveredPoint.y()) + pixel_count); // Now convert back to local coordinates. @@ -1586,7 +1900,7 @@ QCPRange -BasePlotWidget::getRange(PlotAxis axis, +BasePlotWidget::getRange(Axis axis, RangeType range_type, bool &found_range) const { @@ -1620,9 +1934,9 @@ // Depending on the axis param, select the key or value range. - if(axis == PlotAxis::x_axis) + if(axis == Axis::x) temp_range = graph_p->getKeyRange(found_range_for_iter); - else if(axis == PlotAxis::y_axis) + else if(axis == Axis::y) temp_range = graph_p->getValueRange(found_range_for_iter); else qFatal("Cannot reach this point. Programming error."); @@ -1681,14 +1995,14 @@ BasePlotWidget::getInnermostRangeX(bool &found_range) const { - return getRange(PlotAxis::x_axis, RangeType::innermost, found_range); + return getRange(Axis::x, RangeType::innermost, found_range); } QCPRange BasePlotWidget::getOutermostRangeX(bool &found_range) const { - return getRange(PlotAxis::x_axis, RangeType::outermost, found_range); + return getRange(Axis::x, RangeType::outermost, found_range); } @@ -1696,14 +2010,14 @@ BasePlotWidget::getInnermostRangeY(bool &found_range) const { - return getRange(PlotAxis::y_axis, RangeType::innermost, found_range); + return getRange(Axis::y, RangeType::innermost, found_range); } QCPRange BasePlotWidget::getOutermostRangeY(bool &found_range) const { - return getRange(PlotAxis::y_axis, RangeType::outermost, found_range); + return getRange(Axis::y, RangeType::outermost, found_range); } @@ -1715,26 +2029,29 @@ void BasePlotWidget::axisRescale() { + // Get the current x lower/upper range, that is, leftmost/rightmost x + // coordinate. double xLower = xAxis->range().lower; double xUpper = xAxis->range().upper; - // Get the current y lower/upper range. + // Get the current y lower/upper range, that is, bottommost/topmost y + // coordinate. double yLower = yAxis->range().lower; double yUpper = yAxis->range().upper; // This function is called only when the user has clicked on the x/y axis or // when the user has dragged the left mouse button with the Ctrl key - // modifier. The m_context.wasClickOnXAxis is then simulated in the mouse + // modifier. The m_context.m_wasClickOnXAxis is then simulated in the mouse // move handler. So we need to test which axis was clicked-on. - if(m_context.wasClickOnXAxis) + if(m_context.m_wasClickOnXAxis) { // We are changing the range of the X axis. // What is the x delta ? double xDelta = - m_context.currentDragPoint.x() - m_context.startDragPoint.x(); + m_context.m_currentDragPoint.x() - m_context.m_startDragPoint.x(); // If xDelta is < 0, the we were dragging from right to left, we are // compressing the view on the x axis, by adding new data to the right @@ -1750,14 +2067,14 @@ xAxis->setRange(xLower, xUpper - xDelta); } // End of - // if(m_context.wasClickOnXAxis) - else // that is, if(m_context.wasClickOnYAxis) + // if(m_context.m_wasClickOnXAxis) + else // that is, if(m_context.m_wasClickOnYAxis) { // We are changing the range of the Y axis. // What is the y delta ? double yDelta = - m_context.currentDragPoint.y() - m_context.startDragPoint.y(); + m_context.m_currentDragPoint.y() - m_context.m_startDragPoint.y(); // See above for an explanation of the computation. @@ -1782,11 +2099,11 @@ //} } // End of - // else // that is, if(m_context.wasClickOnYAxis) + // else // that is, if(m_context.m_wasClickOnYAxis) // Update the context with the current axes ranges - updateContextRanges(); + updateContextXandYAxisRanges(); emit plotRangesChangedSignal(m_context); @@ -1799,27 +2116,27 @@ { // double sorted_start_drag_point_x = - // std::min(m_context.startDragPoint.x(), m_context.currentDragPoint.x()); + // std::min(m_context.m_startDragPoint.x(), m_context.m_currentDragPoint.x()); // xAxis->setRange(sorted_start_drag_point_x, - // sorted_start_drag_point_x + fabs(m_context.xDelta)); + // sorted_start_drag_point_x + fabs(m_context.m_xDelta)); xAxis->setRange( - QCPRange(m_context.xRegionRangeStart, m_context.xRegionRangeEnd)); + QCPRange(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd)); // Note that the y axis should be rescaled from current lower value to new // upper value matching the y-axis position of the cursor when the mouse // button was released. - yAxis->setRange( - xAxis->range().lower, - std::max(m_context.yRegionRangeStart, m_context.yRegionRangeEnd)); + yAxis->setRange(xAxis->range().lower, + std::max(m_context.m_yRegionRangeStart, + m_context.m_yRegionRangeEnd)); // qDebug() << "xaxis:" << xAxis->range().lower << "-" << // xAxis->range().upper //<< "yaxis:" << yAxis->range().lower << "-" << yAxis->range().upper; - updateContextRanges(); + updateContextXandYAxisRanges(); updateAxesRangeHistory(); emit plotRangesChangedSignal(m_context); @@ -1832,18 +2149,18 @@ BasePlotWidget::axisZoom() { - // Use the m_context.xRegionRangeStart/End values, but we need to sort the + // Use the m_context.m_xRegionRangeStart/End values, but we need to sort the // values before using them, because now we want to really have the lower x // value. Simply craft a QCPRange that will swap the values if lower is not // < than upper QCustomPlot calls this normalization). xAxis->setRange( - QCPRange(m_context.xRegionRangeStart, m_context.xRegionRangeEnd)); + QCPRange(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd)); yAxis->setRange( - QCPRange(m_context.yRegionRangeStart, m_context.yRegionRangeEnd)); + QCPRange(m_context.m_yRegionRangeStart, m_context.m_yRegionRangeEnd)); - updateContextRanges(); + updateContextXandYAxisRanges(); updateAxesRangeHistory(); emit plotRangesChangedSignal(m_context); @@ -1851,29 +2168,40 @@ replot(); } + void BasePlotWidget::axisPan() { - if(m_context.wasClickOnXAxis) + qDebug(); + + // Sanity check + if(!m_context.m_wasClickOnXAxis && !m_context.m_wasClickOnYAxis) + qFatal( + "This function can only be called if the mouse click was on one of the " + "axes"); + + if(m_context.m_wasClickOnXAxis) { - xAxis->setRange(m_context.xRange.lower - m_context.xDelta, - m_context.xRange.upper - m_context.xDelta); + xAxis->setRange(m_context.m_xRange.lower - m_context.m_xDelta, + m_context.m_xRange.upper - m_context.m_xDelta); } - if(m_context.wasClickOnYAxis) + if(m_context.m_wasClickOnYAxis) { - yAxis->setRange(m_context.yRange.lower - m_context.yDelta, - m_context.yRange.upper - m_context.yDelta); + yAxis->setRange(m_context.m_yRange.lower - m_context.m_yDelta, + m_context.m_yRange.upper - m_context.m_yDelta); } - updateContextRanges(); + updateContextXandYAxisRanges(); + + // qDebug() << "The updated context:" << m_context.toString(); // We cannot store the new ranges in the history, because the pan operation // involved a huge quantity of micro-movements elicited upon each mouse move // cursor event so we would have a huge history. // updateAxesRangeHistory(); - // Now that the contex has the right range values, we can emit the + // Now that the context has the right range values, we can emit the // signal that will be used by this plot widget users, typically to // abide by the x/y range lock required by the user. @@ -1886,14 +2214,16 @@ void BasePlotWidget::replotWithAxesRanges(QCPRange xAxisRange, QCPRange yAxisRange, - PlotAxis axis) + Axis axis) { - if(static_cast(axis) & static_cast(PlotAxis::x_axis)) + // qDebug() << "With axis:" << (int)axis; + + if(static_cast(axis) & static_cast(Axis::x)) { xAxis->setRange(xAxisRange.lower, xAxisRange.upper); } - if(static_cast(axis) & static_cast(PlotAxis::y_axis)) + if(static_cast(axis) & static_cast(Axis::y)) { yAxis->setRange(yAxisRange.lower, yAxisRange.upper); } @@ -1937,11 +2267,11 @@ void BasePlotWidget::hideAllPlotItems() { - mp_selectLineItem->setVisible(false); - mp_xDeltaTextItem->setVisible(false); + mp_yDeltaTextItem->setVisible(false); - mp_zoomRectItem->setVisible(false); + // mp_zoomRectItem->setVisible(false); + hideSelectionRectangle(); // Force a replot to make sure the action is immediately visible by the // user, even without moving the mouse. @@ -1985,39 +2315,28 @@ void -BasePlotWidget::drawRectangleAndPrepareZoom() +BasePlotWidget::drawSelectionRectangleAndPrepareZoom(bool as_line_segment, + bool for_integration) { - // The user has drawn the mouse left button on the graph, which means he is - // willing to draw a zoom rectangle. - - mp_selectLineItem->setVisible(false); - - mp_xDeltaTextItem->setVisible(false); + // The user has dragged the mouse left button on the graph, which means he + // is willing to draw a selection rectangle, either for zooming-in or for + // integration. - mp_zoomRectItem->topLeft->setCoords(m_context.startDragPoint.x(), - m_context.startDragPoint.y()); - mp_zoomRectItem->bottomRight->setCoords(m_context.currentDragPoint.x(), - m_context.currentDragPoint.y()); - - mp_zoomRectItem->setVisible(true); - - // Now set the geometry of the rectangle to the context so that upon the - // mouse button release, if the zoom rectanble is visible we know how to - // reframe the plot axes. Note that we do not sort the values, if that is - // required the user needs to use the sortAscendingRange() function. + if(mp_xDeltaTextItem != nullptr) + mp_xDeltaTextItem->setVisible(false); + if(mp_yDeltaTextItem != nullptr) + mp_yDeltaTextItem->setVisible(false); - m_context.xRegionRangeStart = m_context.startDragPoint.x(); - m_context.xRegionRangeEnd = m_context.currentDragPoint.x(); + // Ensure the right selection rectangle is drawn. - m_context.yRegionRangeStart = m_context.startDragPoint.y(); - m_context.yRegionRangeEnd = m_context.currentDragPoint.y(); + updateSelectionRectangle(as_line_segment, for_integration); // Note that if we draw a zoom rectangle, then we are certainly not // measuring anything. So set the boolean value to false so that the user of // this widget or derived classes know that there is nothing to perform upon // (like deconvolution, for example). - m_context.isMeasuringDistance = false; + m_context.m_isMeasuringDistance = false; // Also remove the delta value from the pipeline by sending a simple // distance without measurement signal. @@ -2029,90 +2348,152 @@ void -BasePlotWidget::prepareXDeltaLineAndMeasure() +BasePlotWidget::drawXDeltaFeatures() { - // The user has dragged the mouse left button on the graph in such a way - // that the xDelta is big and the yDelta is almost nothing, that - // means that he does not want to draw a rectangle but a line to - // measure the delta between two points of the graph. + // The user is dragging the mouse over the graph and we want them to know what + // is the x delta value, that is the span between the point at the start of + // the drag and the current drag position. - mp_zoomRectItem->setVisible(false); + // FIXME: is this still true? + // + // We do not want to show the position markers because the only horiontal + // line to be visible must be contained between the start and end vertiacal + // tracer items. + if(mp_hPosTracerItem != nullptr) + mp_hPosTracerItem->setVisible(false); + if(mp_vPosTracerItem != nullptr) + mp_vPosTracerItem->setVisible(false); - // We also want to show the span as a text item. + // We want to draw the text in the middle position of the leftmost-rightmost + // point, even with skewed rectangle selection. - // m_context.xDelta is not an absolute value. - double m_xDeltaHalf = fabs(m_context.xDelta / 2); + QPointF leftmost_point = m_context.m_selectionPolygon.getLeftMostPoint(); - // Use the m_context.xRegionRangeStart/End values, but we need to sort the - // values before using them, because now we want to really have the lower x - // value. Simply craft a QCPRange that will swap the values if lower is not - // < than upper QCustomPlot calls this normalization). + // qDebug() << "leftmost_point:" << leftmost_point; - QCPRange sorted_range(m_context.xRegionRangeStart, m_context.xRegionRangeEnd); + QPointF rightmost_point = m_context.m_selectionPolygon.getRightMostPoint(); - // qDebug() << "sorted range:" << sorted_range.lower << "-" << - // sorted_range.upper - //<< "xrangedeltahalf:" << m_xDeltaHalf; + // qDebug() << "rightmost_point:" << rightmost_point; - mp_xDeltaTextItem->position->setCoords(sorted_range.lower + m_xDeltaHalf, - m_context.currentDragPoint.y()); + double x_axis_center_position = + leftmost_point.x() + (rightmost_point.x() - leftmost_point.x()) / 2; - mp_xDeltaTextItem->setText(QString("%1").arg(m_context.xDelta, 0, 'f', 3)); + // qDebug() << "x_axis_center_position:" << x_axis_center_position; - mp_xDeltaTextItem->setFont(QFont(font().family(), 7)); + // We want the text to print inside the rectangle, always at the current drag + // point so the eye can follow the delta value while looking where to drag the + // mouse. To position the text inside the rectangle, we need to know what is + // the drag direction. - mp_xDeltaTextItem->setVisible(true); + // Set aside a point instance to store the pixel coordinates of the text. + QPointF pixel_coordinates; - // We do not want to show the position markers because the only horiontal - // line to be visible must be contained between the start and end vertiacal - // tracer items. - mp_hPosTracerItem->setVisible(false); - mp_vPosTracerItem->setVisible(false); + // What is the distance between the rectangle line at current drag point and + // the text itself. + int pixels_away_from_line = 15; - mp_selectLineItem->setVisible(true); + // ATTENTION: the pixel coordinates for the vertical direction go in reverse + // order with respect to the y axis values !!! That is pixel(0,0) is top left + // of the graph. + if(static_cast(m_context.m_dragDirections) & + static_cast(DragDirections::TOP_TO_BOTTOM)) + { + // We need to print inside the rectangle, that is pixels_above_line pixels + // to the bottom, so with pixel y value decremented of that + // pixels_above_line value (one would have expected to increment that + // value, along the y axis, but the coordinates in pixel go in reverse + // order). - mp_selectLineItem->start->setCoords(m_context.startDragPoint.x(), - m_context.startDragPoint.y()); - // But we want the line to be horizontal, thus we keep the original y - // value. - mp_selectLineItem->end->setCoords(m_context.currentDragPoint.x(), - m_context.startDragPoint.y()); + pixels_away_from_line *= -1; + } + + double y_axis_pixel_coordinate = + yAxis->coordToPixel(m_context.m_currentDragPoint.y()); + + double y_axis_modified_pixel_coordinate = + y_axis_pixel_coordinate + pixels_away_from_line; + + pixel_coordinates.setX(x_axis_center_position); + pixel_coordinates.setY(y_axis_modified_pixel_coordinate); + + // Now convert back to graph coordinates. + + QPointF graph_coordinates(xAxis->pixelToCoord(pixel_coordinates.x()), + yAxis->pixelToCoord(pixel_coordinates.y())); + if(mp_xDeltaTextItem != nullptr) + { + mp_xDeltaTextItem->position->setCoords(x_axis_center_position, + graph_coordinates.y()); + mp_xDeltaTextItem->setText( + QString("%1").arg(m_context.m_xDelta, 0, 'f', 3)); + mp_xDeltaTextItem->setFont(QFont(font().family(), 9)); + mp_xDeltaTextItem->setVisible(true); + } // Set the boolean to true so that derived widgets know that something is // being measured, and they can act accordingly, for example by computing // deconvolutions in a mass spectrum. - m_context.isMeasuringDistance = true; + m_context.m_isMeasuringDistance = true; + + replot(); + + // Let the caller know that we were measuring something. + emit xAxisMeasurementSignal(m_context, true); return; } void -BasePlotWidget::drawXDeltaLineAndMeasure() +BasePlotWidget::drawYDeltaFeatures() { - prepareXDeltaLineAndMeasure(); + if(m_context.m_selectionPolygon.is1D()) + return; - // Also, we do not want arrows, because we are not integrating anything - // here. - mp_selectLineItem->setHead(QCPLineEnding::esNone); - mp_selectLineItem->setTail(QCPLineEnding::esNone); + // The user is dragging the mouse over the graph and we want them to know what + // is the y delta value, that is the span between the point at the top of + // the selection polygon and the point at its bottom. - replot(); + // FIXME: is this still true? + // + // We do not want to show the position markers because the only horiontal + // line to be visible must be contained between the start and end vertiacal + // tracer items. + mp_hPosTracerItem->setVisible(false); + mp_vPosTracerItem->setVisible(false); - // Let the caller know that we were measuring something. - emit xAxisMeasurementSignal(m_context, true); -} + // We want to draw the text in the middle position of the leftmost-rightmost + // point, even with skewed rectangle selection. + QPointF leftmost_point = m_context.m_selectionPolygon.getLeftMostPoint(); + QPointF topmost_point = m_context.m_selectionPolygon.getTopMostPoint(); -void -BasePlotWidget::drawXDeltaLineForIntegration() -{ - prepareXDeltaLineAndMeasure(); + // qDebug() << "leftmost_point:" << leftmost_point; + + QPointF rightmost_point = m_context.m_selectionPolygon.getRightMostPoint(); + QPointF bottommost_point = m_context.m_selectionPolygon.getBottomMostPoint(); + + // qDebug() << "rightmost_point:" << rightmost_point; + + double x_axis_center_position = + leftmost_point.x() + (rightmost_point.x() - leftmost_point.x()) / 2; - // Since we draw the selection line with the xDelta text for integration, we - // let the user guess it by the arrows at the ends of the line. - mp_selectLineItem->setHead(QCPLineEnding::esSpikeArrow); - mp_selectLineItem->setTail(QCPLineEnding::esSpikeArrow); + double y_axis_center_position = + bottommost_point.y() + (topmost_point.y() - bottommost_point.y()) / 2; + + // qDebug() << "x_axis_center_position:" << x_axis_center_position; + + mp_yDeltaTextItem->position->setCoords(x_axis_center_position, + y_axis_center_position); + mp_yDeltaTextItem->setText(QString("%1").arg(m_context.m_yDelta, 0, 'f', 3)); + mp_yDeltaTextItem->setFont(QFont(font().family(), 9)); + mp_yDeltaTextItem->setVisible(true); + mp_yDeltaTextItem->setRotation(90); + + // Set the boolean to true so that derived widgets know that something is + // being measured, and they can act accordingly, for example by computing + // deconvolutions in a mass spectrum. + m_context.m_isMeasuringDistance = true; replot(); @@ -2130,52 +2511,692 @@ // Compute the xAxis differential: - m_context.xDelta = - m_context.currentDragPoint.x() - m_context.startDragPoint.x(); + m_context.m_xDelta = + m_context.m_currentDragPoint.x() - m_context.m_startDragPoint.x(); // Same with the Y-axis range: - m_context.yDelta = - m_context.currentDragPoint.y() - m_context.startDragPoint.y(); + m_context.m_yDelta = + m_context.m_currentDragPoint.y() - m_context.m_startDragPoint.y(); - // qDebug() << "xDelta:" << m_context.xDelta - //<< "and yDelta:" << m_context.yDelta; + // qDebug() << "xDelta:" << m_context.m_xDelta + //<< "and yDelta:" << m_context.m_yDelta; return; } +bool +BasePlotWidget::isVerticalDisplacementAboveThreshold() +{ + // First get the height of the plot. + double plotHeight = yAxis->range().upper - yAxis->range().lower; + + double heightDiff = + fabs(m_context.m_startDragPoint.y() - m_context.m_currentDragPoint.y()); + + double heightDiffRatio = (heightDiff / plotHeight) * 100; + + if(heightDiffRatio > 10) + { + // qDebug() << "isVerticalDisplacementAboveThreshold: true"; + return true; + } + + // qDebug() << "isVerticalDisplacementAboveThreshold: false"; + return false; +} + + void -BasePlotWidget::calculateDragDeltasAndUnSortedRegionCorners() +BasePlotWidget::update1DSelectionRectangle(bool for_integration) { - calculateDragDeltas(); + // if(for_integration) + // qDebug() << "for_integration:" << for_integration; - // Note that we do not sort the x value nor the y values. If the user of the - // ranges need them to be sorted, they can use the sortAscendingRange(). + // When we make a linear selection, the selection polygon is a polygon that + // has the following characteristics: + // + // the x range is the linear selection span + // + // the y range is the widest std::min -> std::max possible. - m_context.xRegionRangeStart = m_context.startDragPoint.x(); - m_context.xRegionRangeEnd = m_context.currentDragPoint.x(); + // This is how the selection polygon logic knows if its is mono- + // two-dimensional. - m_context.yRegionRangeStart = m_context.startDragPoint.y(); - m_context.yRegionRangeEnd = m_context.currentDragPoint.y(); + // We want the top left point to effectively be the top left point, so check + // the direction of the mouse cursor drag. - return; + double x_range_start = + std::min(m_context.m_currentDragPoint.x(), m_context.m_startDragPoint.x()); + double x_range_end = + std::max(m_context.m_currentDragPoint.x(), m_context.m_startDragPoint.x()); + + double y_position = m_context.m_startDragPoint.y(); + + m_context.m_selectionPolygon.set1D(x_range_start, x_range_end); + + // Top line + mp_selectionRectangeLine1->start->setCoords( + QPointF(x_range_start, y_position)); + mp_selectionRectangeLine1->end->setCoords(QPointF(x_range_end, y_position)); + + // Only if we are drawing a selection rectangle for integration, do we set + // arrow heads to the line. + if(for_integration) + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esSpikeArrow); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esSpikeArrow); + } + else + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esNone); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esNone); + } + mp_selectionRectangeLine1->setVisible(true); + + // Right line: does not exist, start and end are the same end point of the top + // line. + mp_selectionRectangeLine2->start->setCoords(QPointF(x_range_end, y_position)); + mp_selectionRectangeLine2->end->setCoords(QPointF(x_range_end, y_position)); + mp_selectionRectangeLine2->setVisible(false); + + // Bottom line: identical to the top line, but invisible + mp_selectionRectangeLine3->start->setCoords( + QPointF(x_range_start, y_position)); + mp_selectionRectangeLine3->end->setCoords(QPointF(x_range_end, y_position)); + mp_selectionRectangeLine3->setVisible(false); + + // Left line: does not exist: start and end are the same end point of the top + // line. + mp_selectionRectangeLine4->start->setCoords(QPointF(x_range_end, y_position)); + mp_selectionRectangeLine4->end->setCoords(QPointF(x_range_end, y_position)); + mp_selectionRectangeLine4->setVisible(false); } -bool -BasePlotWidget::isProperSelectionRectangle() +void +BasePlotWidget::update2DSelectionRectangleSquare(bool for_integration) { - // First get the height of the plot. - double plotHeight = yAxis->range().upper - yAxis->range().lower; - double heightDiff = - fabs(m_context.startDragPoint.y() - m_context.currentDragPoint.y()); + // if(for_integration) + // qDebug() << "for_integration:" << for_integration; - double heightDiffRatio = (heightDiff / plotHeight) * 100; + // We are handling a conventional rectangle. Just create four points + // from top left to bottom right. But we want the top left point to be + // effectively the top left point and the bottom point to be the bottom point. + // So we need to try all four direction combinations, left to right or + // converse versus top to bottom or converse. - if(heightDiffRatio > 10) + m_context.m_selectionPolygon.resetPoints(); + + if(m_context.m_currentDragPoint.x() < m_context.m_startDragPoint.x()) + { + // qDebug() << "Dragging from right to left"; + + if(m_context.m_currentDragPoint.y() < m_context.m_startDragPoint.y()) + { + // qDebug() << "Dragging from top to bottom"; + + // TOP_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_startDragPoint.y()); + + // TOP_RIGHT_POINT + m_context.m_selectionPolygon.setPoint(PointSpecs::TOP_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // BOTTOM_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // BOTTOM_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + } + // End of + // if(m_context.m_currentDragPoint.y() < m_context.m_startDragPoint.y()) + else + { + // qDebug() << "Dragging from bottom to top"; + + // TOP_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // TOP_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // BOTTOM_RIGHT_POINT + m_context.m_selectionPolygon.setPoint(PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // BOTTOM_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_startDragPoint.y()); + } + } + // End of + // if(m_context.m_currentDragPoint.x() < m_context.m_startDragPoint.x()) + else + { + // qDebug() << "Dragging from left to right"; + + if(m_context.m_currentDragPoint.y() < m_context.m_startDragPoint.y()) + { + // qDebug() << "Dragging from top to bottom"; + + // TOP_LEFT_POINT + m_context.m_selectionPolygon.setPoint(PointSpecs::TOP_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // TOP_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_startDragPoint.y()); + + // BOTTOM_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // BOTTOM_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_currentDragPoint.y()); + } + else + { + // qDebug() << "Dragging from bottom to top"; + + // TOP_LEFT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // TOP_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // BOTTOM_RIGHT_POINT + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_startDragPoint.y()); + + // BOTTOM_LEFT_POINT + m_context.m_selectionPolygon.setPoint(PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + } + } + + // qDebug() << "Now draw the lines with points:" + //<< m_context.m_selectionPolygon.toString(); + + // Top line + mp_selectionRectangeLine1->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT)); + mp_selectionRectangeLine1->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT)); + + // Only if we are drawing a selection rectangle for integration, do we + // set arrow heads to the line. + if(for_integration) + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esSpikeArrow); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esSpikeArrow); + } + else + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esNone); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esNone); + } + + mp_selectionRectangeLine1->setVisible(true); + + // Right line + mp_selectionRectangeLine2->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT)); + mp_selectionRectangeLine2->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT)); + mp_selectionRectangeLine2->setVisible(true); + + // Bottom line + mp_selectionRectangeLine3->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT)); + mp_selectionRectangeLine3->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT)); + mp_selectionRectangeLine3->setVisible(true); + + // Left line + mp_selectionRectangeLine4->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT)); + mp_selectionRectangeLine4->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT)); + mp_selectionRectangeLine4->setVisible(true); +} + + +void +BasePlotWidget::update2DSelectionRectangleSkewed(bool for_integration) +{ + + // if(for_integration) + // qDebug() << "for_integration:" << for_integration; + + // We are handling a skewed rectangle, that is a rectangle that is + // tilted either to the left or to the right. + + // qDebug() << "m_context.m_selectRectangleWidth: " + //<< m_context.m_selectRectangleWidth; + + // Top line + // start + + // qDebug() << "m_context.m_startDragPoint: " << + // m_context.m_startDragPoint.x() + //<< "-" << m_context.m_startDragPoint.y(); + + // qDebug() << "m_context.m_currentDragPoint: " + //<< m_context.m_currentDragPoint.x() << "-" + //<< m_context.m_currentDragPoint.y(); + + m_context.m_selectionPolygon.resetPoints(); + + if(m_context.m_currentDragPoint.x() < m_context.m_startDragPoint.x()) + { + // qDebug() << "Dragging from right to left"; + + if(m_context.m_currentDragPoint.y() < m_context.m_startDragPoint.y()) + { + // qDebug() << "Dragging from top to bottom"; + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_startDragPoint.x() - m_context.m_selectRectangleWidth, + m_context.m_startDragPoint.y()); + + // m_context.m_selRectTopLeftPoint.setX( + // m_context.m_startDragPoint.x() - + // m_context.m_selectRectangleWidth); + // m_context.m_selRectTopLeftPoint.setY(m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint(PointSpecs::TOP_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // m_context.m_selRectTopRightPoint.setX(m_context.m_startDragPoint.x()); + // m_context.m_selRectTopRightPoint.setY(m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_currentDragPoint.x() + m_context.m_selectRectangleWidth, + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectBottomRightPoint.setX( + // m_context.m_currentDragPoint.x() + + // m_context.m_selectRectangleWidth); + // m_context.m_selRectBottomRightPoint.setY( + // m_context.m_currentDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectBottomLeftPoint.setX( + // m_context.m_currentDragPoint.x()); + // m_context.m_selRectBottomLeftPoint.setY( + // m_context.m_currentDragPoint.y()); + } + else + { + // qDebug() << "Dragging from bottom to top"; + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectTopLeftPoint.setX( + // m_context.m_currentDragPoint.x()); + // m_context.m_selRectTopLeftPoint.setY( + // m_context.m_currentDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_currentDragPoint.x() + m_context.m_selectRectangleWidth, + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectTopRightPoint.setX( + // m_context.m_currentDragPoint.x() + + // m_context.m_selectRectangleWidth); + // m_context.m_selRectTopRightPoint.setY( + // m_context.m_currentDragPoint.y()); + + + m_context.m_selectionPolygon.setPoint(PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // m_context.m_selRectBottomRightPoint.setX( + // m_context.m_startDragPoint.x()); + // m_context.m_selRectBottomRightPoint.setY( + // m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_startDragPoint.x() - m_context.m_selectRectangleWidth, + m_context.m_startDragPoint.y()); + + // m_context.m_selRectBottomLeftPoint.setX( + // m_context.m_startDragPoint.x() - + // m_context.m_selectRectangleWidth); + // m_context.m_selRectBottomLeftPoint.setY( + // m_context.m_startDragPoint.y()); + } + } + // End of + // Dragging from right to left. + else + { + // qDebug() << "Dragging from left to right"; + + if(m_context.m_currentDragPoint.y() < m_context.m_startDragPoint.y()) + { + // qDebug() << "Dragging from top to bottom"; + + m_context.m_selectionPolygon.setPoint(PointSpecs::TOP_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // m_context.m_selRectTopLeftPoint.setX(m_context.m_startDragPoint.x()); + // m_context.m_selRectTopLeftPoint.setY(m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_startDragPoint.x() + m_context.m_selectRectangleWidth, + m_context.m_startDragPoint.y()); + + // m_context.m_selRectTopRightPoint.setX( + // m_context.m_startDragPoint.x() + + // m_context.m_selectRectangleWidth); + // m_context.m_selRectTopRightPoint.setY(m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectBottomRightPoint.setX( + // m_context.m_currentDragPoint.x()); + // m_context.m_selRectBottomRightPoint.setY( + // m_context.m_currentDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_currentDragPoint.x() - m_context.m_selectRectangleWidth, + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectBottomLeftPoint.setX( + // m_context.m_currentDragPoint.x() - + // m_context.m_selectRectangleWidth); + // m_context.m_selRectBottomLeftPoint.setY( + // m_context.m_currentDragPoint.y()); + } + else + { + // qDebug() << "Dragging from bottom to top"; + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_LEFT_POINT, + m_context.m_currentDragPoint.x() - m_context.m_selectRectangleWidth, + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectTopLeftPoint.setX( + // m_context.m_currentDragPoint.x() - + // m_context.m_selectRectangleWidth); + // m_context.m_selRectTopLeftPoint.setY( + // m_context.m_currentDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::TOP_RIGHT_POINT, + m_context.m_currentDragPoint.x(), + m_context.m_currentDragPoint.y()); + + // m_context.m_selRectTopRightPoint.setX( + // m_context.m_currentDragPoint.x()); + // m_context.m_selRectTopRightPoint.setY( + // m_context.m_currentDragPoint.y()); + + m_context.m_selectionPolygon.setPoint( + PointSpecs::BOTTOM_RIGHT_POINT, + m_context.m_startDragPoint.x() + m_context.m_selectRectangleWidth, + m_context.m_startDragPoint.y()); + + // m_context.m_selRectBottomRightPoint.setX( + // m_context.m_startDragPoint.x() + + // m_context.m_selectRectangleWidth); + // m_context.m_selRectBottomRightPoint.setY( + // m_context.m_startDragPoint.y()); + + m_context.m_selectionPolygon.setPoint(PointSpecs::BOTTOM_LEFT_POINT, + m_context.m_startDragPoint.x(), + m_context.m_startDragPoint.y()); + + // m_context.m_selRectBottomLeftPoint.setX( + // m_context.m_startDragPoint.x()); + // m_context.m_selRectBottomLeftPoint.setY( + // m_context.m_startDragPoint.y()); + } + } + // End of Dragging from left to right. + + // qDebug() << "Now draw the lines with points:" + //<< m_context.m_selectionPolygon.toString(); + + // Top line + mp_selectionRectangeLine1->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT)); + mp_selectionRectangeLine1->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT)); + + // Only if we are drawing a selection rectangle for integration, do we set + // arrow heads to the line. + if(for_integration) + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esSpikeArrow); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esSpikeArrow); + } + else + { + mp_selectionRectangeLine1->setHead(QCPLineEnding::esNone); + mp_selectionRectangeLine1->setTail(QCPLineEnding::esNone); + } + + mp_selectionRectangeLine1->setVisible(true); + + // Right line + mp_selectionRectangeLine2->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT)); + mp_selectionRectangeLine2->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT)); + mp_selectionRectangeLine2->setVisible(true); + + // Bottom line + mp_selectionRectangeLine3->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT)); + mp_selectionRectangeLine3->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT)); + mp_selectionRectangeLine3->setVisible(true); + + // Left line + mp_selectionRectangeLine4->end->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT)); + mp_selectionRectangeLine4->start->setCoords( + m_context.m_selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT)); + mp_selectionRectangeLine4->setVisible(true); +} + + +void +BasePlotWidget::updateSelectionRectangle(bool as_line_segment, + bool for_integration) +{ + + // qDebug() << "as_line_segment:" << as_line_segment; + // qDebug() << "for_integration:" << for_integration; + + // We now need to construct the selection rectangle, either for zoom or for + // integration. + + // There are two situations : + // + // 1. if the rectangle should look like a line segment + // + // 2. if the rectangle should actually look like a rectangle. In this case, + // there are two sub-situations: + // + // a. if the S key is down, then the rectangle is + // skewed, that is its vertical sides are not parallel to the y axis. + // + // b. otherwise the rectangle is conventional. + + if(as_line_segment) + { + update1DSelectionRectangle(for_integration); + } + else + { + if(!(m_context.m_keyboardModifiers & Qt::AltModifier)) + { + update2DSelectionRectangleSquare(for_integration); + } + else if(m_context.m_keyboardModifiers & Qt::AltModifier) + { + update2DSelectionRectangleSkewed(for_integration); + } + } + + // This code automatically sorts the ranges (range start is always less than + // range end) even if the user actually selects from high to low (right to + // left or bottom to top). This has implications in code that uses the + // m_context data to perform some computations. This is why it is important + // that m_dragDirections be set correctly to establish where the current drag + // point is actually located (at which point). + + m_context.m_xRegionRangeStart = + m_context.m_selectionPolygon.getLeftMostPoint().x(); + m_context.m_xRegionRangeEnd = + m_context.m_selectionPolygon.getRightMostPoint().x(); + + m_context.m_yRegionRangeStart = + m_context.m_selectionPolygon.getBottomMostPoint().y(); + m_context.m_yRegionRangeEnd = + m_context.m_selectionPolygon.getTopMostPoint().y(); + + // At this point, draw the text describing the widths. + + // We want the x-delta on the bottom of the rectangle, inside it + // and the y-delta on the vertical side of the rectangle, inside it. + + // Draw the selection width text + drawXDeltaFeatures(); +} + +void +BasePlotWidget::hideSelectionRectangle(bool reset_values) +{ + mp_selectionRectangeLine1->setVisible(false); + mp_selectionRectangeLine2->setVisible(false); + mp_selectionRectangeLine3->setVisible(false); + mp_selectionRectangeLine4->setVisible(false); + + if(reset_values) + { + resetSelectionRectangle(); + } +} + + +void +BasePlotWidget::resetSelectionRectangle() +{ + m_context.m_selectionPolygon.resetPoints(); +} + + +PolygonType +BasePlotWidget::whatIsVisibleOfTheSelectionRectangle() +{ + // There are four lines that make the selection polygon. We want to know + // which lines are visible. + + int current_selection_polygon = static_cast(PolygonType::NOT_SET); + + if(mp_selectionRectangeLine1->visible()) + { + current_selection_polygon |= static_cast(PolygonType::TOP_LINE); + // qDebug() << "current_selection_polygon:" << current_selection_polygon; + } + if(mp_selectionRectangeLine2->visible()) + { + current_selection_polygon |= static_cast(PolygonType::RIGHT_LINE); + // qDebug() << "current_selection_polygon:" << current_selection_polygon; + } + if(mp_selectionRectangeLine3->visible()) + { + current_selection_polygon |= static_cast(PolygonType::BOTTOM_LINE); + // qDebug() << "current_selection_polygon:" << current_selection_polygon; + } + if(mp_selectionRectangeLine4->visible()) + { + current_selection_polygon |= static_cast(PolygonType::LEFT_LINE); + // qDebug() << "current_selection_polygon:" << current_selection_polygon; + } + + // qDebug() << "returning visibility:" << current_selection_polygon; + + return static_cast(current_selection_polygon); +} + + +bool +BasePlotWidget::isSelectionRectangleVisible() +{ + // Sanity check + int check = 0; + + check += mp_selectionRectangeLine1->visible(); + check += mp_selectionRectangeLine2->visible(); + check += mp_selectionRectangeLine3->visible(); + check += mp_selectionRectangeLine4->visible(); + + if(check > 0) return true; return false; @@ -2201,7 +3222,8 @@ { if(focusedPlotWidget == nullptr) throw ExceptionNotPossible( - "baseplotwidget.cpp @ redrawPlotBackground(QWidget *focusedPlotWidget -- " + "baseplotwidget.cpp @ redrawPlotBackground(QWidget *focusedPlotWidget " + "-- " "ERROR focusedPlotWidget cannot be nullptr."); if(dynamic_cast(this) != focusedPlotWidget) @@ -2222,10 +3244,12 @@ void -BasePlotWidget::updateContextRanges() +BasePlotWidget::updateContextXandYAxisRanges() { - m_context.xRange = QCPRange(xAxis->range().lower, xAxis->range().upper); - m_context.yRange = QCPRange(yAxis->range().lower, yAxis->range().upper); + m_context.m_xRange = QCPRange(xAxis->range().lower, xAxis->range().upper); + m_context.m_yRange = QCPRange(yAxis->range().lower, yAxis->range().upper); + + // qDebug() << "The new updated context: " << m_context.toString(); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/baseplotwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/baseplotwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -45,88 +45,19 @@ /////////////////////// Local includes #include "../../exportinmportconfig.h" #include "../../types.h" +#include "../../processing/combiners/selectionpolygon.h" +#include "baseplotcontext.h" namespace pappso { -enum class PlotAxis -{ - none = 0x000, - x_axis = 1 << 1, - y_axis = 1 << 2, - both = (x_axis | y_axis) -}; - - enum class RangeType { outermost = 1, innermost = 2, }; - -struct PMSPP_LIB_DECL BasePlotContext -{ - DataKind dataKind = DataKind::unset; - - bool isMouseDragging = false; - bool wasMouseDragging = false; - - bool isKeyBoardDragging = false; - bool isLeftPseudoButtonKeyPressed = false; - bool isRightPseudoButtonKeyPressed = false; - bool wassKeyBoardDragging = false; - - QPointF startDragPoint; - QPointF currentDragPoint; - QPointF lastCursorHoveredPoint; - - // The effective range of the axes. - QCPRange xRange; - QCPRange yRange; - - // Tell if the mouse move was started onto either axis, because that will - // condition if some calculations needs to be performed or not (for example, - // if the mouse cursor motion was started on an axis, there is no point to - // perform deconvolutions). - bool wasClickOnXAxis = false; - bool wasClickOnYAxis = false; - - bool isMeasuringDistance = false; - - // The user-selected region over the plot. - // Note that we cannot use QCPRange structures because these are normalized by - // QCustomPlot in such a manner that lower is actually < upper. But we need - // for a number of our calculations (specifically for the deconvolutions) to - // actually have the lower value be start drag point.x even if the drag - // direction was from right to left. - double xRegionRangeStart = std::numeric_limits::min(); - double xRegionRangeEnd = std::numeric_limits::min(); - - double yRegionRangeStart = std::numeric_limits::min(); - double yRegionRangeEnd = std::numeric_limits::min(); - - double xDelta = 0; - double yDelta = 0; - - int pressedKeyCode; - int releasedKeyCode; - - Qt::KeyboardModifiers keyboardModifiers; - - Qt::MouseButtons lastPressedMouseButton; - Qt::MouseButtons lastReleasedMouseButton; - - Qt::MouseButtons pressedMouseButtons; - - Qt::MouseButtons mouseButtonsAtMousePress; - Qt::MouseButtons mouseButtonsAtMouseRelease; - - QString toString() const; -}; - - class BasePlotWidget; typedef std::shared_ptr BasePlotWidgetSPtr; @@ -187,6 +118,8 @@ virtual void mouseReleaseHandlerLeftButton(); virtual void mouseReleaseHandlerRightButton(); + virtual void mouseWheelHandler(QWheelEvent *event); + virtual void mouseMoveHandler(QMouseEvent *event); virtual void mouseMoveHandlerNotDraggingCursor(); virtual void mouseMoveHandlerDraggingCursor(); @@ -215,8 +148,7 @@ /// RANGE-related functions virtual QCPRange getRangeX(bool &found_range, int index) const; virtual QCPRange getRangeY(bool &found_range, int index) const; - QCPRange - getRange(PlotAxis axis, RangeType range_type, bool &found_range) const; + QCPRange getRange(Axis axis, RangeType range_type, bool &found_range) const; virtual QCPRange getInnermostRangeX(bool &found_range) const; virtual QCPRange getOutermostRangeX(bool &found_range) const; @@ -239,7 +171,8 @@ virtual void replotWithAxesRanges(QCPRange xAxisRange, QCPRange yAxisRange, - PlotAxis whichAxis); + Axis axis); + virtual void replotWithAxisRangeX(double lower, double upper); virtual void replotWithAxisRangeY(double lower, double upper); /// PLOTTING / REPLOTTING functions @@ -251,16 +184,25 @@ virtual void showTracers(); virtual void hideTracers(); - virtual void drawRectangleAndPrepareZoom(); - - virtual void prepareXDeltaLineAndMeasure(); - virtual void drawXDeltaLineAndMeasure(); - virtual void drawXDeltaLineForIntegration(); + virtual void drawXDeltaFeatures(); + virtual void drawYDeltaFeatures(); virtual void calculateDragDeltas(); - virtual void calculateDragDeltasAndUnSortedRegionCorners(); - virtual bool isProperSelectionRectangle(); + virtual bool isVerticalDisplacementAboveThreshold(); + + virtual void + drawSelectionRectangleAndPrepareZoom(bool as_line_segment = false, + bool for_integration = false); + + virtual void updateSelectionRectangle(bool as_line_segment = false, + bool for_integration = false); + + virtual void resetSelectionRectangle(); + virtual void hideSelectionRectangle(bool reset_values = false); + virtual bool isSelectionRectangleVisible(); + virtual PolygonType whatIsVisibleOfTheSelectionRectangle(); + /// PLOT ITEMS : TRACER TEXT ITEMS... @@ -268,7 +210,7 @@ virtual void redrawPlotBackground(QWidget *focusedPlotWidget); - virtual void updateContextRanges(); + virtual void updateContextXandYAxisRanges(); virtual const BasePlotContext &getContext() const; @@ -287,6 +229,8 @@ void mouseReleaseEventSignal(const BasePlotContext &context); + void mouseWheelEventSignal(const BasePlotContext &context); + void plottableSelectionChangedSignal(QCPAbstractPlottable *plottable_p, bool selected); @@ -315,28 +259,32 @@ int m_rightMousePseudoButtonKey = Qt::Key_Greater; //! Rectangle defining the borders of zoomed-in/out data. - QCPItemRect *mp_zoomRectItem = nullptr; + // QCPItemRect *mp_zoomRectItem = nullptr; - //! Line that is printed when the user selects a range. - QCPItemLine *mp_selectLineItem = nullptr; + // The four lines that are needed to craft the selection rectangle. + QCPItemLine *mp_selectionRectangeLine1 = nullptr; + QCPItemLine *mp_selectionRectangeLine2 = nullptr; + QCPItemLine *mp_selectionRectangeLine3 = nullptr; + QCPItemLine *mp_selectionRectangeLine4 = nullptr; //! Text describing the x-axis delta value during a drag operation. QCPItemText *mp_xDeltaTextItem = nullptr; + QCPItemText *mp_yDeltaTextItem = nullptr; //! Tells if the tracers should be visible. bool m_shouldTracersBeVisible = true; //! Horizontal position tracer - QCPItemLine *mp_hPosTracerItem; + QCPItemLine *mp_hPosTracerItem = nullptr; //! Vertical position tracer - QCPItemLine *mp_vPosTracerItem; + QCPItemLine *mp_vPosTracerItem = nullptr; //! Vertical selection start tracer (typically in green). - QCPItemLine *mp_vStartTracerItem; + QCPItemLine *mp_vStartTracerItem = nullptr; //! Vertical selection end tracer (typically in red). - QCPItemLine *mp_vEndTracerItem /*only vertical*/; + QCPItemLine *mp_vEndTracerItem = nullptr /*only vertical*/; //! Index of the last axis range history item. /*! @@ -390,6 +338,14 @@ //! Pen used to draw the graph and textual elements in the plot widget. QPen m_pen; + + virtual void createAllAncillaryItems(); + virtual void update1DSelectionRectangle(bool for_integration = false); + virtual void update2DSelectionRectangleSquare(bool for_integration = false); + virtual void update2DSelectionRectangleSkewed(bool for_integration = false); + virtual QString allLayerNamesToString() const; + virtual QString layerableLayerName(QCPLayerable *layerable_p) const; + virtual int layerableLayerIndex(QCPLayerable *layerable_p) const; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -44,6 +44,24 @@ BaseTracePlotWidget::BaseTracePlotWidget(QWidget *parent) : BasePlotWidget(parent) { + // We can afford to call createAllAncillaryItems() in this derived class + // because all the items will have been created *before* the addition of plots + // and then the rendering order will hide them to the viewer, since the + // rendering order is according to the order in which the items have been + // created. + // + // The fact that the ancillary items are created before trace plots is not a + // problem because the trace plots are sparse and do not effectively hide the + // data. + // + // But, in the color map plot widgets, we cannot afford to create the + // ancillary items *before* the plot itself because then, the rendering of the + // plot (created after) would screen off the ancillary items (created before). + // + // So, the createAllAncillaryItems() function needs to be called in the + // derived classes at the most appropriate moment in the setting up of the + // widget. + createAllAncillaryItems(); } @@ -52,6 +70,24 @@ const QString &y_axis_label) : BasePlotWidget(parent, x_axis_label, y_axis_label) { + // We can afford to call createAllAncillaryItems() in this derived class + // because all the items will have been created *before* the addition of plots + // and then the rendering order will hide them to the viewer, since the + // rendering order is according to the order in which the items have been + // created. + // + // The fact that the ancillary items are created before trace plots is not a + // problem because the trace plots are sparse and do not effectively hide the + // data. + // + // But, in the color map plot widgets, we cannot afford to create the + // ancillary items *before* the plot itself because then, the rendering of the + // plot (created after) would screen off the ancillary items (created before). + // + // So, the createAllAncillaryItems() function needs to be called in the + // derived classes at the most appropriate moment in the setting up of the + // widget. + createAllAncillaryItems(); } @@ -159,9 +195,11 @@ QCPGraph *graph_p = addGraph(); + graph_p->setLayer("plotsLayer"); + // Now depracated as of 20200924 - //graph_p->setData(QVector::fromStdVector(trace.xValues()), - //QVector::fromStdVector(trace.yValues())); + // graph_p->setData(QVector::fromStdVector(trace.xValues()), + // QVector::fromStdVector(trace.yValues())); QVector key_qvector; QVector value_qvector; @@ -469,11 +507,13 @@ [[maybe_unused]] QCPAxis::SelectablePart part, QMouseEvent *event) { + //qDebug(); - m_context.keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); + m_context.m_keyboardModifiers = QGuiApplication::queryKeyboardModifiers(); - if(m_context.keyboardModifiers & Qt::ControlModifier) + if(m_context.m_keyboardModifiers & Qt::ControlModifier) { + //qDebug(); // If the Ctrl modifiers is active, then both axes are to be reset. Also // the histories are reset also. @@ -483,6 +523,8 @@ } else { + //qDebug(); + // Only the axis passed as parameter is to be rescaled. // Reset the range of that axis to the max view possible, but for the y // axis check if the Shift keyboard key is pressed. If so the full scale @@ -490,7 +532,7 @@ if(axis->orientation() == Qt::Vertical) { - if(m_context.keyboardModifiers & Qt::ShiftModifier) + if(m_context.m_keyboardModifiers & Qt::ShiftModifier) { // In this case, we want to make a rescale of the Y axis such @@ -519,9 +561,9 @@ // "pressed". We need to remove manually the button from the pressed buttons // context member. - m_context.pressedMouseButtons ^= event->button(); + m_context.m_pressedMouseButtons ^= event->button(); - updateContextRanges(); + updateContextXandYAxisRanges(); emit plotRangesChangedSignal(m_context); @@ -541,17 +583,17 @@ // This function is called only when the user has clicked on the x/y axis or // when the user has dragged the left mouse button with the Ctrl key - // modifier. The m_context.wasClickOnXAxis is then simulated in the mouse + // modifier. The m_context.m_wasClickOnXAxis is then simulated in the mouse // move handler. So we need to test which axis was clicked-on. - if(m_context.wasClickOnXAxis) + if(m_context.m_wasClickOnXAxis) { // We are changing the range of the X axis. // What is the x delta ? double xDelta = - m_context.currentDragPoint.x() - m_context.startDragPoint.x(); + m_context.m_currentDragPoint.x() - m_context.m_startDragPoint.x(); // If xDelta is < 0, the we were dragging from right to left, we are // compressing the view on the x axis, by adding new data to the right @@ -590,7 +632,7 @@ // data displayed in the new X axis range are full scale on the Y // axis. For this, the Shift modifier key should be pressed. - if(m_context.keyboardModifiers & Qt::ShiftModifier) + if(m_context.m_keyboardModifiers & Qt::ShiftModifier) { // In this case, we want to make a rescale of the Y axis such that @@ -605,14 +647,14 @@ // else, do leave the Y axis range unchanged. } // End of - // if(m_context.wasClickOnXAxis) - else // that is, if(m_context.wasClickOnYAxis) + // if(m_context.m_wasClickOnXAxis) + else // that is, if(m_context.m_wasClickOnYAxis) { // We are changing the range of the Y axis. // What is the y delta ? double yDelta = - m_context.currentDragPoint.y() - m_context.startDragPoint.y(); + m_context.m_currentDragPoint.y() - m_context.m_startDragPoint.y(); // See above for an explanation of the computation. @@ -637,11 +679,11 @@ //} } // End of - // else // that is, if(m_context.wasClickOnYAxis) + // else // that is, if(m_context.m_wasClickOnYAxis) // Update the context with the current axes ranges - updateContextRanges(); + updateContextXandYAxisRanges(); emit plotRangesChangedSignal(m_context); @@ -652,23 +694,24 @@ void BaseTracePlotWidget::axisReframe() { + //qDebug(); // double sorted_start_drag_point_x = - // std::min(m_context.startDragPoint.x(), m_context.currentDragPoint.x()); + // std::min(m_context.m_startDragPoint.x(), m_context.m_currentDragPoint.x()); // xAxis->setRange(sorted_start_drag_point_x, - // sorted_start_drag_point_x + fabs(m_context.xDelta)); + // sorted_start_drag_point_x + fabs(m_context.m_xDelta)); xAxis->setRange( - QCPRange(m_context.xRegionRangeStart, m_context.xRegionRangeEnd)); + QCPRange(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd)); // Note that the y axis should be rescaled from current lower value to new // upper value matching the y-axis position of the cursor when the mouse // button was released. - yAxis->setRange( - xAxis->range().lower, - std::max(m_context.yRegionRangeStart, m_context.yRegionRangeEnd)); + yAxis->setRange(xAxis->range().lower, + std::max(m_context.m_yRegionRangeStart, + m_context.m_yRegionRangeEnd)); // qDebug() << "xaxis:" << xAxis->range().lower << "-" << // xAxis->range().upper @@ -676,7 +719,7 @@ // If the shift modifier key is pressed, then the user want the y axis // to be full scale. - if(m_context.keyboardModifiers & Qt::ShiftModifier) + if(m_context.m_keyboardModifiers & Qt::ShiftModifier) { bool ok = false; @@ -687,7 +730,7 @@ } // else do nothing, let the y axis range as is. - updateContextRanges(); + updateContextXandYAxisRanges(); updateAxesRangeHistory(); emit plotRangesChangedSignal(m_context); @@ -700,17 +743,17 @@ BaseTracePlotWidget::axisZoom() { - // Use the m_context.xRegionRangeStart/End values, but we need to sort the + // Use the m_context.m_xRegionRangeStart/End values, but we need to sort the // values before using them, because now we want to really have the lower x // value. Simply craft a QCPRange that will swap the values if lower is not // < than upper QCustomPlot calls this normalization). xAxis->setRange( - QCPRange(m_context.xRegionRangeStart, m_context.xRegionRangeEnd)); + QCPRange(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd)); // If the shift modifier key is pressed, then the user want the y axis // to be full scale. - if(m_context.keyboardModifiers & Qt::ShiftModifier) + if(m_context.m_keyboardModifiers & Qt::ShiftModifier) { bool ok = false; @@ -721,9 +764,9 @@ } else yAxis->setRange( - QCPRange(m_context.yRegionRangeStart, m_context.yRegionRangeEnd)); + QCPRange(m_context.m_yRegionRangeStart, m_context.m_yRegionRangeEnd)); - updateContextRanges(); + updateContextXandYAxisRanges(); updateAxesRangeHistory(); emit plotRangesChangedSignal(m_context); @@ -734,14 +777,22 @@ void BaseTracePlotWidget::axisPan() { - if(m_context.wasClickOnXAxis) + //qDebug(); + + // Sanity check + if(!m_context.m_wasClickOnXAxis && !m_context.m_wasClickOnYAxis) + qFatal( + "This function can only be called if the mouse click was on one of the " + "axes"); + + if(m_context.m_wasClickOnXAxis) { - xAxis->setRange(m_context.xRange.lower - m_context.xDelta, - m_context.xRange.upper - m_context.xDelta); + xAxis->setRange(m_context.m_xRange.lower - m_context.m_xDelta, + m_context.m_xRange.upper - m_context.m_xDelta); // If the shift modifier key is pressed, then the user want the y axis // to be full scale. - if(m_context.keyboardModifiers & Qt::ShiftModifier) + if(m_context.m_keyboardModifiers & Qt::ShiftModifier) { bool ok = false; @@ -753,13 +804,15 @@ // else nothing to do we do not change the y axis scale. } - if(m_context.wasClickOnYAxis) + if(m_context.m_wasClickOnYAxis) { - yAxis->setRange(m_context.yRange.lower - m_context.yDelta, - m_context.yRange.upper - m_context.yDelta); + yAxis->setRange(m_context.m_yRange.lower - m_context.m_yDelta, + m_context.m_yRange.upper - m_context.m_yDelta); } - updateContextRanges(); + updateContextXandYAxisRanges(); + + //qDebug() << "The updated context:" << m_context.toString(); // We cannot store the new ranges in the history, because the pan operation // involved a huge quantity of micro-movements elicited upon each mouse move diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -110,10 +110,6 @@ pappso::Trace toTrace(const QCPRange &x_axis_range, int index) const; pappso::Trace toTrace(const QCPRange &x_axis_range, const QCPGraph *graph_p) const; - - signals: - - protected: }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,7 +31,10 @@ double max_key_value, double min_mz_value, - double max_mz_value) + double max_mz_value, + + double orig_min_z_value, + double orig_max_z_value) : xAxisDataKind(x_axis_data_kind), yAxisDataKind(y_axis_data_kind), @@ -46,8 +49,102 @@ maxKeyValue(max_key_value), minMzValue(min_mz_value), - maxMzValue(max_mz_value) + maxMzValue(max_mz_value), + + // Initialize both orig and last to the same value. + origMinZValue(orig_min_z_value), + lastMinZValue(orig_min_z_value), + + // Initialize both orig and last to the same value. + origMaxZValue(orig_max_z_value), + lastMaxZValue(orig_max_z_value) +{ +} + + +ColorMapPlotConfig::ColorMapPlotConfig(const ColorMapPlotConfig &other) +{ + xAxisDataKind = other.xAxisDataKind; + yAxisDataKind = other.yAxisDataKind; + + xAxisScale = other.xAxisScale; + yAxisScale = other.yAxisScale; + zAxisScale = other.zAxisScale; + + keyCellCount = other.keyCellCount; + mzCellCount = other.mzCellCount; + + minKeyValue = other.minKeyValue; + maxKeyValue = other.maxKeyValue; + + minMzValue = other.minMzValue; + maxMzValue = other.maxMzValue; + + origMinZValue = other.origMinZValue; + lastMinZValue = other.lastMinZValue; + + origMaxZValue = other.origMaxZValue; + lastMaxZValue = other.lastMaxZValue; +} + + +ColorMapPlotConfig & +ColorMapPlotConfig::operator=(const ColorMapPlotConfig &other) +{ + if(this == &other) + return *this; + + xAxisDataKind = other.xAxisDataKind; + yAxisDataKind = other.yAxisDataKind; + + xAxisScale = other.xAxisScale; + yAxisScale = other.yAxisScale; + zAxisScale = other.zAxisScale; + + keyCellCount = other.keyCellCount; + mzCellCount = other.mzCellCount; + + minKeyValue = other.minKeyValue; + maxKeyValue = other.maxKeyValue; + + minMzValue = other.minMzValue; + maxMzValue = other.maxMzValue; + + origMinZValue = other.origMinZValue; + lastMinZValue = other.lastMinZValue; + + origMaxZValue = other.origMaxZValue; + lastMaxZValue = other.lastMaxZValue; + + return *this; +} + + +void +ColorMapPlotConfig::setOrigMinZValue(double value) +{ + origMinZValue = value; +} + +void +ColorMapPlotConfig::setOrigAndLastMinZValue(double value) +{ + origMinZValue = value; + lastMinZValue = value; +} + + +void +ColorMapPlotConfig::setOrigMaxZValue(double value) +{ + origMaxZValue = value; +} + +void +ColorMapPlotConfig::setOrigAndLastMaxZValue(double value) { + origMaxZValue = value; + lastMaxZValue = value; } @@ -67,13 +164,15 @@ .arg(mzCellCount) .arg(minKeyValue); - text += - QString( - "minKeyValue: %8 - maxKeyValue: %9 - minMzValue: %10 - maxMzValue: %11") - .arg(keyCellCount) - .arg(maxKeyValue) - .arg(minMzValue) - .arg(maxMzValue); + text += QString( + "minKeyValue: %8 - maxKeyValue: %9 - minMzValue: %10 - maxMzValue: " + "%11 - lastMinZValue: %12 - lastMaxZValue: %13") + .arg(keyCellCount) + .arg(maxKeyValue) + .arg(minMzValue) + .arg(maxMzValue) + .arg(lastMinZValue) + .arg(lastMaxZValue); return text; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/colormapplotconfig.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/colormapplotconfig.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/colormapplotconfig.h 2022-10-27 09:16:15.000000000 +0000 @@ -31,14 +31,25 @@ std::size_t keyCellCount = 0; std::size_t mzCellCount = 0; + double lastMinZFilterThresholdPercentage = 0.0; + double lastMaxZFilterThresholdPercentage = 0.0; + double minKeyValue = std::numeric_limits::max(); double maxKeyValue = std::numeric_limits::min(); double minMzValue = std::numeric_limits::max(); - double maxMzValue = std::numeric_limits::min(); + double maxMzValue = std::numeric_limits::max(); + + double origMinZValue = std::numeric_limits::max(); + double lastMinZValue = std::numeric_limits::max(); + + double origMaxZValue = std::numeric_limits::min(); + double lastMaxZValue = std::numeric_limits::min(); ColorMapPlotConfig(); + ColorMapPlotConfig(const ColorMapPlotConfig &other); + ColorMapPlotConfig(DataKind x_axis_data_kind, DataKind y_axis_data_kind, @@ -53,7 +64,18 @@ double max_key_value, double min_mz_value, - double max_mz_value); + double max_mz_value, + + double orig_min_z_value, + double orig_max_z_value); + + ColorMapPlotConfig &operator=(const ColorMapPlotConfig &other); + + void setOrigMinZValue(double value); + void setOrigAndLastMinZValue(double value); + + void setOrigMaxZValue(double value); + void setOrigAndLastMaxZValue(double value); QString toString() const; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -47,9 +47,9 @@ { // Set the context to be of kind DataKind::dt - m_context.dataKind = DataKind::dt; + m_context.m_dataKind = DataKind::dt; - // qDebug() << "Data kind:" << static_cast(m_context.dataKind); + // qDebug() << "Data kind:" << static_cast(m_context.m_dataKind); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,82 @@ +// Copyright 2021 Filippo Rusconi +// GPLv3+ + +/////////////////////// StdLib includes + + +/////////////////////// Qt includes +#include + + +/////////////////////// Local includes +#include "../../exportinmportconfig.h" +#include "massspectraceplotcontext.h" + +namespace pappso +{ + + +MassSpecTracePlotContext::MassSpecTracePlotContext() +{ +} + + +MassSpecTracePlotContext::MassSpecTracePlotContext( + const MassSpecTracePlotContext &other) + : BasePlotContext(other.m_baseContext), + m_lastZ(other.m_lastZ), + m_lastMz(other.m_lastMz), + m_lastTicIntensity(other.m_lastTicIntensity), + m_lastMr(other.m_lastMr), + m_lastResolvingPower(other.m_lastResolvingPower) +{ +} + + +MassSpecTracePlotContext::~MassSpecTracePlotContext() +{ +} + + +MassSpecTracePlotContext & +MassSpecTracePlotContext::operator=(const MassSpecTracePlotContext &other) +{ + if(this == &other) + return *this; + + m_baseContext = other.m_baseContext; + + m_lastZ = other.m_lastZ; + m_lastMz = other.m_lastMz; + m_lastTicIntensity = other.m_lastTicIntensity; + m_lastMr = other.m_lastMr; + m_lastResolvingPower = other.m_lastResolvingPower; + + return *this; +} + + +QString +MassSpecTracePlotContext::toString() const +{ + QString text("Base context:\n"); + + text += m_baseContext.toString(); + + text += "\n"; + + text += QString("last z: %1").arg(m_lastZ); + text += QString("last m/z: %1").arg(m_lastMz, 0, 'f', 6); + text += QString("last TIC intensity: %1").arg(m_lastTicIntensity, 0, 'g', 0); + text += QString("last Mr: %1").arg(m_lastMr, 0, 'f', 6); + text += + QString("last resolving power: %1").arg(m_lastResolvingPower, 0, 'g', 0); + + text += "\n"; + + return text; +} + + +} // namespace pappso + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotcontext.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,43 @@ +// Copyright 2021 Filippo Rusconi +// GPLv3+ + +#pragma once + + +/////////////////////// StdLib includes + + +/////////////////////// Qt includes +#include + + +/////////////////////// Local includes +#include "../../exportinmportconfig.h" +#include "baseplotcontext.h" + +namespace pappso +{ + +class PMSPP_LIB_DECL MassSpecTracePlotContext : public BasePlotContext +{ + public: + MassSpecTracePlotContext(); + MassSpecTracePlotContext(const MassSpecTracePlotContext &other); + + virtual ~MassSpecTracePlotContext(); + + MassSpecTracePlotContext &operator=(const MassSpecTracePlotContext &other); + + BasePlotContext m_baseContext; + + int m_lastZ = -1; + double m_lastMz = std::numeric_limits::min(); + double m_lastTicIntensity = std::numeric_limits::min(); + double m_lastMr = std::numeric_limits::min(); + double m_lastResolvingPower = std::numeric_limits::min(); + + QString toString() const; +}; + +} // namespace pappso + diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -38,6 +38,7 @@ #include "massspectraceplotwidget.h" #include "../../pappsoexception.h" +#include "massspectraceplotcontext.h" int massSpecTracePlotContextMetaTypeId = @@ -52,40 +53,18 @@ namespace pappso { - -QString -MassSpecTracePlotContext::toString() const -{ - QString text("Base context:\n"); - - text += baseContext.toString(); - - text += "\n"; - - text += QString("last z: %1").arg(lastZ); - text += QString("last m/z: %1").arg(lastMz, 0, 'f', 6); - text += QString("last TIC intensity: %1").arg(lastTicIntensity, 0, 'g', 0); - text += QString("last Mr: %1").arg(lastMr, 0, 'f', 6); - text += - QString("last resolving power: %1").arg(lastResolvingPower, 0, 'g', 0); - - text += "\n"; - - return text; -} - MassSpecTracePlotWidget::MassSpecTracePlotWidget(QWidget *parent) : BaseTracePlotWidget(parent) { // Set the base context to be of kind DataKind::mz; - BasePlotWidget::m_context.dataKind = DataKind::mz; + BasePlotWidget::m_context.m_dataKind = DataKind::mz; // And then initialize ours with the base class' one. - m_context.baseContext = BasePlotWidget::m_context; + m_context.m_baseContext = BasePlotWidget::m_context; // qDebug() << "Data kind:" << - // static_cast(m_context.baseContext.dataKind); + // static_cast(m_context.m_baseContext.m_dataKind); } MassSpecTracePlotWidget::MassSpecTracePlotWidget(QWidget *parent, @@ -95,13 +74,13 @@ { // Set the base context to be of kind DataKind::mz; - BasePlotWidget::m_context.dataKind = DataKind::mz; + BasePlotWidget::m_context.m_dataKind = DataKind::mz; // And then initialize ours with the base class' one. - m_context.baseContext = BasePlotWidget::m_context; + m_context.m_baseContext = BasePlotWidget::m_context; // qDebug() << "Data kind:" << - // static_cast(m_context.baseContext.dataKind); + // static_cast(m_context.m_baseContext.m_dataKind); } @@ -126,8 +105,8 @@ emit keyPressEventSignal(m_context); emit testKeyPressEventSignal(m_context); emit newKeyPressEventSignal( - pappso::DataPoint(m_context.baseContext.currentDragPoint.x(), - m_context.baseContext.currentDragPoint.y())); + pappso::DataPoint(m_context.m_baseContext.m_currentDragPoint.x(), + m_context.m_baseContext.m_currentDragPoint.y())); } @@ -187,13 +166,13 @@ // to get it from the base class and refresh our local context with it. refreshBaseContext(); - if(m_context.baseContext.mouseButtonsAtMousePress & Qt::LeftButton) + if(m_context.m_baseContext.m_mouseButtonsAtMousePress & Qt::LeftButton) { - if(!m_context.baseContext.isMeasuringDistance) + if(!m_context.m_baseContext.m_isMeasuringDistance) return; // qDebug() << "lastMovingMouseButtons:" - //<< m_context.baseContext.lastMovingMouseButtons; + //<< m_context.m_baseContext.m_lastMovingMouseButtons; deconvolute(); computeResolvingPower(); @@ -228,7 +207,7 @@ const MassSpecTracePlotContext & MassSpecTracePlotWidget::refreshBaseContext() const { - m_context.baseContext = BasePlotWidget::m_context; + m_context.m_baseContext = BasePlotWidget::m_context; return m_context; } @@ -281,11 +260,11 @@ // on the fractional part of the deconvoluted charge value. This value is set // in the parent window's double spin box. - if(fabs(m_context.baseContext.xDelta) >= 0 && - fabs(m_context.baseContext.xDelta) <= 1.1) + if(fabs(m_context.m_baseContext.m_xDelta) >= 0 && + fabs(m_context.m_baseContext.m_xDelta) <= 1.1) { // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" - //<< "m_xDelta:" << m_context.baseContext.xDelta + //<< "m_xDelta:" << m_context.m_baseContext.m_xDelta //<< "trying isotope-based deconvolution."; return deconvoluteIsotopicCluster(); @@ -325,26 +304,26 @@ // That parameter defaults to 1, that is the two peaks are immediately // consecutive, that is, there is only one interval. - // We use the m_contex.baseContext.xRegionRange structure that is unsorted. + // We use the m_contex.basecontext.m_xRegionRange structure that is unsorted. // That is, lower is the start drag point.x and upper is the current drag // point.x. If dragging occurs from left to right, start.x < cur.x. // We use the unsorted values, because we need to know in which direction // the user has drug the mouse, because we want to provide the Mr value // for the peak currently under the mouse cursor, that is under // currentDragPoint, that is the value in - // m_context.baseContext.xRegionRange.upper. + // m_context.m_baseContext.m_xRegionRange.upper. - double startMz = m_context.baseContext.xRegionRangeStart; - double curMz = m_context.baseContext.xRegionRangeEnd; + double startMz = m_context.m_baseContext.m_xRegionRangeStart; + double curMz = m_context.m_baseContext.m_xRegionRangeEnd; // qDebug() << "startMz:" << startMz << "curMz:" << curMz; if(startMz == curMz) { - m_context.lastZ = -1; - m_context.lastMz = std::numeric_limits::min(); - m_context.lastTicIntensity = std::numeric_limits::min(); - m_context.lastMr = std::numeric_limits::min(); + m_context.m_lastZ = -1; + m_context.m_lastMz = std::numeric_limits::min(); + m_context.m_lastTicIntensity = std::numeric_limits::min(); + m_context.m_lastMr = std::numeric_limits::min(); return false; } @@ -407,10 +386,10 @@ (1 - m_chargeMinimalFractionalPart /* that is >= 0.01 */) && chargeFracPart <= m_chargeMinimalFractionalPart /* that is <= 0.99 */) { - m_context.lastZ = -1; - m_context.lastMz = std::numeric_limits::min(); - m_context.lastTicIntensity = std::numeric_limits::min(); - m_context.lastMr = std::numeric_limits::min(); + m_context.m_lastZ = -1; + m_context.m_lastMz = std::numeric_limits::min(); + m_context.m_lastTicIntensity = std::numeric_limits::min(); + m_context.m_lastMr = std::numeric_limits::min(); // qDebug() << __FILE__ << __LINE__ //<< "Not a charge state family peak," @@ -420,9 +399,9 @@ } if(chargeFracPart > m_chargeMinimalFractionalPart) - m_context.lastZ = chargeIntPart + 1; + m_context.m_lastZ = chargeIntPart + 1; else - m_context.lastZ = chargeIntPart; + m_context.m_lastZ = chargeIntPart; // Now, to actually compute the molecular mass based on the charge and on // the currently displayed m/z value, we need to have some thinking: @@ -437,19 +416,19 @@ { // The drag was from right to left, that is curMz is less than startMz. // So we want to show the charge of the curMz, that is, z + span. - m_context.lastZ = m_context.lastZ + span; + m_context.m_lastZ = m_context.m_lastZ + span; } - m_context.lastMz = curMz; - m_context.lastMr = - (m_context.lastMz * m_context.lastZ) - (m_context.lastZ * MPROTON); + m_context.m_lastMz = curMz; + m_context.m_lastMr = + (m_context.m_lastMz * m_context.m_lastZ) - (m_context.m_lastZ * MPROTON); // qDebug() << __FILE__ << __LINE__ //<< "startMz:" << QString("%1").arg(startMz, 0, 'f', 6) //<< "m_lastMz (curMz):" - //<< QString("%1").arg(m_context.lastMz, 0, 'f', 6) - //<< "m_lastMass:" << QString("%1").arg(m_context.lastMr, 0, 'f', 6) - //<< "m_lastZ:" << QString("%1").arg(m_context.lastZ); + //<< QString("%1").arg(m_context.m_lastMz, 0, 'f', 6) + //<< "m_lastMass:" << QString("%1").arg(m_context.m_lastMr, 0, 'f', 6) + //<< "m_lastZ:" << QString("%1").arg(m_context.m_lastZ); // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" //<< "returning true"; @@ -480,8 +459,8 @@ MassSpecTracePlotWidget::deconvoluteIsotopicCluster() { - if(m_context.baseContext.xRegionRangeStart == - m_context.baseContext.xRegionRangeEnd) + if(m_context.m_baseContext.m_xRegionRangeStart == + m_context.m_baseContext.m_xRegionRangeEnd) { // qDebug() << __FILE__ << __LINE__ //<< "Same xRegionRange.upper and xRegionRange.lower:" @@ -490,13 +469,13 @@ return false; } - double chargeTemp = 1 / fabs(m_context.baseContext.xDelta); + double chargeTemp = 1 / fabs(m_context.m_baseContext.m_xDelta); // Make a judicious roundup. double chargeIntPart; double chargeFracPart = modf(chargeTemp, &chargeIntPart); - // qDebug() << "m_xDelta:" << m_context.baseContext.xDelta + // qDebug() << "m_xDelta:" << m_context.m_baseContext.m_xDelta //<< "chargeTemp:" << QString("%1").arg(chargeTemp, 0, 'f', 6) //<< "chargeIntPart:" << chargeIntPart //<< "chargeFracPart:" << QString("%1").arg(chargeFracPart, 0, 'f', 6) @@ -505,10 +484,10 @@ if(chargeFracPart >= (1 - m_chargeMinimalFractionalPart) && chargeFracPart <= m_chargeMinimalFractionalPart) { - m_context.lastZ = -1; - m_context.lastMz = std::numeric_limits::min(); - m_context.lastTicIntensity = std::numeric_limits::min(); - m_context.lastMr = std::numeric_limits::min(); + m_context.m_lastZ = -1; + m_context.m_lastMz = std::numeric_limits::min(); + m_context.m_lastTicIntensity = std::numeric_limits::min(); + m_context.m_lastMr = std::numeric_limits::min(); // qDebug() << "Not in a isotopic cluster peak:" //<< "returning from deconvoluteIsotopicCluster"; @@ -518,19 +497,19 @@ if(chargeFracPart > m_chargeMinimalFractionalPart) { - m_context.lastZ = chargeIntPart + 1; + m_context.m_lastZ = chargeIntPart + 1; // qDebug() << "chargeFracPart > m_chargeMinimalFractionalPart -> m_lastZ // = " - //<< m_context.lastZ; + //<< m_context.m_lastZ; } else { - m_context.lastZ = chargeIntPart; + m_context.m_lastZ = chargeIntPart; // qDebug() //<< "chargeFracPart <= m_chargeMinimalFractionalPart -> m_lastZ = " - //<< m_context.lastZ; + //<< m_context.m_lastZ; } // Now that we have the charge in the form of an int, we can compute the @@ -540,11 +519,11 @@ // We need to sort the xRegionRange before being certain that lower is indeed // the left value of the drag span. - m_context.lastMz = std::min(m_context.baseContext.xRegionRangeStart, - m_context.baseContext.xRegionRangeEnd); + m_context.m_lastMz = std::min(m_context.m_baseContext.m_xRegionRangeStart, + m_context.m_baseContext.m_xRegionRangeEnd); - m_context.lastMr = - (m_context.lastMz * m_context.lastZ) - (m_context.lastZ * MPROTON); + m_context.m_lastMr = + (m_context.m_lastMz * m_context.m_lastZ) - (m_context.m_lastZ * MPROTON); // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()" //<< "returning true"; @@ -565,20 +544,20 @@ // during mouve movement handling. Note that the range values *are // sorted*. - if(!m_context.baseContext.xDelta || m_context.baseContext.xDelta > 1) + if(!m_context.m_baseContext.m_xDelta || m_context.m_baseContext.m_xDelta > 1) { - m_context.lastResolvingPower = std::numeric_limits::min(); + m_context.m_lastResolvingPower = std::numeric_limits::min(); return false; } // Resolving power is m/z / Delta(m/z), for singly-charged species. - m_context.lastResolvingPower = - (std::min(m_context.baseContext.xRegionRangeStart, - m_context.baseContext.xRegionRangeEnd) + - (m_context.baseContext.xDelta / 2)) / - m_context.baseContext.xDelta; + m_context.m_lastResolvingPower = + (std::min(m_context.m_baseContext.m_xRegionRangeStart, + m_context.m_baseContext.m_xRegionRangeEnd) + + (m_context.m_baseContext.m_xDelta / 2)) / + m_context.m_baseContext.m_xDelta; // The m_context was refreshed with the base class context in the calling // chain. diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -47,26 +47,13 @@ /////////////////////// Local includes #include "../../exportinmportconfig.h" #include "basetraceplotwidget.h" +#include "massspectraceplotcontext.h" namespace pappso { -struct PMSPP_LIB_DECL MassSpecTracePlotContext -{ - BasePlotContext baseContext; - - int lastZ = -1; - double lastMz = std::numeric_limits::min(); - double lastTicIntensity = std::numeric_limits::min(); - double lastMr = std::numeric_limits::min(); - double lastResolvingPower = std::numeric_limits::min(); - - QString toString() const; -}; - - class PMSPP_LIB_DECL MassSpecTracePlotWidget : public BaseTracePlotWidget { Q_OBJECT diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -46,9 +46,9 @@ { // Set the context to be of kind DataKind::rt - m_context.dataKind = DataKind::rt; + m_context.m_dataKind = DataKind::rt; - // qDebug() << "Data kind:" << static_cast(m_context.dataKind); + // qDebug() << "Data kind:" << static_cast(m_context.m_dataKind); } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -1,5 +1,5 @@ /** - * \file pappsomspp/widget/precision/precisionwidget.cpp + * \file pappsomspp/widget/precisionwidget/precisionwidget.cpp * \date 5/1/2018 * \author Olivier Langella * \brief edit presicion in ppm or dalton diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/precisionwidget/precisionwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/precisionwidget/precisionwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/precisionwidget/precisionwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -1,5 +1,5 @@ /** - * \file pappsomspp/widget/precision/precisionwidget.h + * \file pappsomspp/widget/precisionwidget/precisionwidget.h * \date 5/1/2018 * \author Olivier Langella * \brief edit presicion in ppm or dalton diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,73 @@ +/** + * \file pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.cpp + * \date 26/07/2021 + * \author Thomas Renne + * \brief widget to transform a push button to a switch button + */ + + +/******************************************************************************* + * Copyright (c) 2021 Thomas Renne . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + * Contributors: + * Thomas Renne - initial API and + *implementation + ******************************************************************************/ + +#include "switchbuttonwidget.h" + +pappso::SwitchWidget::SwitchWidget(QWidget *parent) : QPushButton(parent) +{ + setSwitchValue(false); + setIconSize(QSize(40, 16)); + setFlat(true); + setMaximumSize(40, 16); + + connect(this, &SwitchWidget::clicked, this, &SwitchWidget::updateSwitchValue); +} + +pappso::SwitchWidget::~SwitchWidget() +{ +} + +void +pappso::SwitchWidget::setSwitchValue(bool switch_value) +{ + m_switchButtonValue = switch_value; + if(m_switchButtonValue) + { + setIcon(QIcon(":/icons/resources/icons/switch_on.svg")); + } + else + { + setIcon(QIcon(":/icons/resources/icons/switch_off.svg")); + } +} + + +bool +pappso::SwitchWidget::getSwitchValue() +{ + return m_switchButtonValue; +} + +void +pappso::SwitchWidget::updateSwitchValue() +{ + setSwitchValue(!m_switchButtonValue); +} diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,63 @@ +/** + * \file pappsomspp/widget/switchbuttonwidget/switchbuttonwidget.h + * \date 26/07/2021 + * \author Thomas Renne + * \brief widget to transform a push button to a switch button + */ + + +/******************************************************************************* + * Copyright (c) 2021 Thomas Renne . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + * Contributors: + * Thomas Renne - initial API and + *implementation + ******************************************************************************/ + +#pragma once + +#include +#include "../../exportinmportconfig.h" + +namespace pappso +{ + +class PMSPP_LIB_DECL SwitchWidget : public QPushButton +{ + Q_OBJECT + public: + SwitchWidget(QWidget *parent = 0); + ~SwitchWidget(); + + /** @brief get the state of the switch button (on/off) + * @return boolean true or false + * */ + bool getSwitchValue(); + + /** @brief set the state of the switch button (on/off) + * @param switch_value boolean true or false + * */ + void setSwitchValue(bool switch_value); + + private slots: + void updateSwitchValue(); + + private: + bool m_switchButtonValue = false; +}; +} // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/qcpxic.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/qcpxic.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -179,7 +179,7 @@ } } -void +QCPGraph * QCPXic::addXicP(const Xic *xic_p) { @@ -207,6 +207,8 @@ if(_intensity_range.upper < xic_p->maxYDataPoint().y) _intensity_range.upper = xic_p->maxYDataPoint().y; } + + return graph_xic; } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/qcpxic.h libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/qcpxic.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/qcpxic.h 2022-10-27 09:16:15.000000000 +0000 @@ -49,7 +49,7 @@ protected: void clear(); void rescale(); - void addXicP(const Xic *xic_p); + QCPGraph *addXicP(const Xic *xic_p); void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt); void addXicPeakList(const Xic *xic_p, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/xicwidget.cpp libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.cpp --- libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/xicwidget.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -63,11 +63,11 @@ _qcp_xic->addMsMsEvent(xic_p, rt); _map_xic_msms_event[xic_p] = rt; } -void -XicWidget::addXicSp(XicCstSPtr &xic_sp) +QCPGraph * +XicWidget::addXicSp(XicCstSPtr xic_sp) { _xic_sp_list.push_back(xic_sp); - _qcp_xic->addXicP(xic_sp.get()); + return _qcp_xic->addXicP(xic_sp.get()); } const QString & diff -Nru libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/xicwidget.h libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.h --- libpappsomspp-0.8.15/src/pappsomspp/widget/xicwidget/xicwidget.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/widget/xicwidget/xicwidget.h 2022-10-27 09:16:15.000000000 +0000 @@ -52,7 +52,7 @@ ~XicWidget(); - void addXicSp(XicCstSPtr &xic_sp); + QCPGraph *addXicSp(XicCstSPtr xic_sp); void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt); void addXicPeakList(const Xic *xic_p, diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xic/xic.cpp libpappsomspp-0.8.58/src/pappsomspp/xic/xic.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xic/xic.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xic/xic.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -38,6 +38,10 @@ qDebug() << "Xic::Xic end"; } +Xic::Xic(const Trace &other) : Trace(other) +{ +} + Xic::~Xic() { } diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xic/xic.h libpappsomspp-0.8.58/src/pappsomspp/xic/xic.h --- libpappsomspp-0.8.15/src/pappsomspp/xic/xic.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xic/xic.h 2022-10-27 09:16:15.000000000 +0000 @@ -44,6 +44,7 @@ { public: Xic(); + Xic(const Trace & other); virtual ~Xic(); diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -32,6 +32,8 @@ #include "private/msrunxicextractor.h" #include "private/msrunxicextractordisk.h" #include "private/msrunxicextractordiskbuffer.h" +#include "../vendors/tims/xicextractor/timsdirectxicextractor.h" +#include "../msrun/private/timsmsrunreaderms2.h" namespace pappso { @@ -59,36 +61,60 @@ { m_tmpDirName = dir_name; } -MsRunXicExtractorInterfaceSp -MsRunXicExtractorFactory::buildMsRunXicExtractorSp( - MsRunReaderSPtr &msrun_reader) const +void +MsRunXicExtractorFactory::setMsRunXicExtractorFactoryType( + pappso::MsRunXicExtractorFactoryType type) { - std::shared_ptr msrun_xic_extractor_sp = - std::make_shared(MsRunXicExtractor(msrun_reader)); - return (msrun_xic_extractor_sp); + m_type = type; } MsRunXicExtractorInterfaceSp -MsRunXicExtractorFactory::buildMsRunXicExtractorDiskSp( +MsRunXicExtractorFactory::buildMsRunXicExtractorSp( MsRunReaderSPtr &msrun_reader) const { - std::shared_ptr msrun_xic_extractor_sp = - std::make_shared( - MsRunXicExtractorDisk(msrun_reader, QDir(m_tmpDirName))); - msrun_xic_extractor_sp.get()->prepareExtractor(); - return (msrun_xic_extractor_sp); + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(msrun_reader.get()); + if(tims2_reader == nullptr) + { + // NO TIMS + if((m_type == MsRunXicExtractorFactoryType::nose) || + (m_type == MsRunXicExtractorFactoryType::direct)) + { + std::shared_ptr msrun_xic_extractor_sp = + std::make_shared( + MsRunXicExtractor(msrun_reader)); + return (msrun_xic_extractor_sp); + } + else if(m_type == MsRunXicExtractorFactoryType::disk) + { + + std::shared_ptr msrun_xic_extractor_sp = + std::make_shared( + MsRunXicExtractorDisk(msrun_reader, QDir(m_tmpDirName))); + + msrun_xic_extractor_sp.get()->prepareExtractor(); + return (msrun_xic_extractor_sp); + } + else if(m_type == MsRunXicExtractorFactoryType::diskbuffer) + { + + std::shared_ptr msrun_xic_extractor_sp = + std::make_shared( + MsRunXicExtractorDiskBuffer(msrun_reader, QDir(m_tmpDirName))); + msrun_xic_extractor_sp.get()->prepareExtractor(); + return (msrun_xic_extractor_sp); + } + } + else + { + // TIMS + std::shared_ptr msrun_xic_extractor_sp = + std::make_shared(msrun_reader); + return (msrun_xic_extractor_sp); + } + return nullptr; } -MsRunXicExtractorInterfaceSp -MsRunXicExtractorFactory::buildMsRunXicExtractorDiskBufferSp( - MsRunReaderSPtr &msrun_reader) const -{ - std::shared_ptr msrun_xic_extractor_sp = - std::make_shared( - MsRunXicExtractorDiskBuffer(msrun_reader, QDir(m_tmpDirName))); - msrun_xic_extractor_sp.get()->prepareExtractor(); - return (msrun_xic_extractor_sp); -} } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorfactory.h libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.h --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorfactory.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorfactory.h 2022-10-27 09:16:15.000000000 +0000 @@ -35,17 +35,37 @@ namespace pappso { -/** @brief factory to build different kinds of XIC extractors + + +/** \def MsRunXicExtractorFactoryType the kind of xic extractor you want + * this may be usefull to choose if you want a direct extraction (no buffer, no + * temporary file) or an optimized xic extraction to save memory or cpu + * */ -class PMSPP_LIB_DECL MsRunXicExtractorFactory +enum class MsRunXicExtractorFactoryType : std::int8_t { - private: - static MsRunXicExtractorFactory m_instance; - QString m_tmpDirName; + nose = 0, ///< default factory + direct = 1, ///< build a simple XIC extractor that directly uses Proeowizard + ///< library to read and extract XICs building the xic extractor + ///< is fast, but extracting each XIC is slow + disk = 2, ///< build Xic extractor that first read the whole MsRun, put it on + ///< disk and extract XICs more quickly This needs some space on + ///< disk to store slices (1 dalton each) building the XIC extractor + ///< is slow extracting XIC from slices is a very quick operation + diskbuffer = + 3, ///< build Xic extractor that first read the whole MsRun, put it on disk + ///< using a write cache and extract XICs more quickly This needs some + ///< space on disk to store slices (1 dalton each) building the XIC + ///< extractor is slower than buildMsRunXicExtractorPwizSp, but faster + ///< than buildMsRunXicExtractorDiskSp extracting XIC from slices is a + ///< very quick operation +}; - MsRunXicExtractorFactory(); - virtual ~MsRunXicExtractorFactory(); +/** @brief factory to build different kinds of XIC extractors + */ +class PMSPP_LIB_DECL MsRunXicExtractorFactory +{ public: /** @brief singleton to get the only instance of the factory */ @@ -59,28 +79,24 @@ MsRunXicExtractorInterfaceSp buildMsRunXicExtractorSp(MsRunReaderSPtr &msrun_reader) const; - /** @brief build Xic extractor that first read the whole MsRun, put it on disk - * and extract XICs more quickly This needs some space on disk to store slices - * (1 dalton each) building the XIC extractor is slow extracting XIC from - * slices is a very quick operation - * @param msrun_reader the MsRun reader on which the XIC extractor will run - */ - MsRunXicExtractorInterfaceSp - buildMsRunXicExtractorDiskSp(MsRunReaderSPtr &msrun_reader) const; + /// set the temporary working directory + void setTmpDir(const QString &dir_name); - /** @brief build Xic extractor that first read the whole MsRun, put it on disk - * using a write cache and extract XICs more quickly This needs some space on - * disk to store slices (1 dalton each) building the XIC extractor is slower - * than buildMsRunXicExtractorPwizSp, but faster than - * buildMsRunXicExtractorDiskSp extracting XIC from slices is a very quick - * operation - * @param msrun_reader the MsRun reader on which the XIC extractor will run + /** @brief sets the xic extractor type + * @param type see the documentation of enumerations */ - MsRunXicExtractorInterfaceSp - buildMsRunXicExtractorDiskBufferSp(MsRunReaderSPtr &msrun_reader) const; + void + setMsRunXicExtractorFactoryType(pappso::MsRunXicExtractorFactoryType type); - /// set the temporary working directory - void setTmpDir(const QString &dir_name); + private: + MsRunXicExtractorFactory(); + virtual ~MsRunXicExtractorFactory(); + + + private: + static MsRunXicExtractorFactory m_instance; + QString m_tmpDirName; + MsRunXicExtractorFactoryType m_type = MsRunXicExtractorFactoryType::nose; }; } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,6 +29,9 @@ ******************************************************************************/ #include "msrunxicextractorinterface.h" +#include +#include +#include "../processing/uimonitor/uimonitorvoid.h" namespace pappso { @@ -52,20 +55,161 @@ { } -XicCstSPtr -MsRunXicExtractorInterface::getXicCstSPtr(const MzRange &mz_range) +void +MsRunXicExtractorInterface::setXicExtractMethod(XicExtractMethod method) { - return getXicCstSPtr(mz_range, 0, 100000000); + m_xicExtractMethod = method; } void -MsRunXicExtractorInterface::setXicExtractMethod(XicExtractMethod method) +MsRunXicExtractorInterface::setRetentionTimeAroundTarget( + double range_in_seconds) { - m_xicExtractMethod = method; + m_retentionTimeAroundTarget = range_in_seconds; } + const MsRunIdCstSPtr & MsRunXicExtractorInterface::getMsRunId() const { return msp_msrun_reader.get()->getMsRunId(); } + +const MsRunReaderSPtr & +MsRunXicExtractorInterface::getMsRunReaderSPtr() const +{ + return msp_msrun_reader; +} + +void +MsRunXicExtractorInterface::setPostExtractionTraceFilterCstSPtr( + pappso::FilterInterfaceCstSPtr &filter) +{ + mcsp_postExtractionTraceFilter = filter; +} + + +void +MsRunXicExtractorInterface::extractXicCoordSPtrListParallelized( + UiMonitorInterface &monitor, std::vector &xic_coord_list) +{ + qDebug(); + // get the number of available threads : + int number_of_threads = QThreadPool::globalInstance()->maxThreadCount(); + + if(number_of_threads == 1) + { + extractXicCoordSPtrList(monitor, xic_coord_list); + } + else + { + monitor.setStatus(QObject::tr("parallelized extraction of %1 XICs") + .arg(xic_coord_list.size())); + + std::size_t chunck_size = xic_coord_list.size() / number_of_threads; + chunck_size += 1; + if(chunck_size < 1000) + chunck_size = 1000; + + struct parallelExtractChunck + { + std::vector::iterator it_xic_coord_begin; + std::vector::iterator it_xic_coord_end; + }; + + std::vector chunck_list; + qDebug(); + for(auto it = xic_coord_list.begin(); it != xic_coord_list.end();) + { + qDebug() << "chunck_size=" << chunck_size; + parallelExtractChunck chunck; + chunck.it_xic_coord_begin = it; + for(std::size_t i = 0; i < chunck_size && it != xic_coord_list.end(); + i++) + { + it++; + } + chunck.it_xic_coord_end = it; + chunck_list.push_back(chunck); + } + qDebug(); + auto self = this; + + qDebug(); + std::function extractChunck = + [self](const parallelExtractChunck &extract_chunck) { + qDebug(); + UiMonitorVoid monitor; + self->protectedExtractXicCoordSPtrList( + monitor, + extract_chunck.it_xic_coord_begin, + extract_chunck.it_xic_coord_end); + self->postExtractionProcess(monitor, + extract_chunck.it_xic_coord_begin, + extract_chunck.it_xic_coord_end); + qDebug(); + return 1; + }; + qDebug(); + monitor.setTotalSteps(chunck_list.size()); + UiMonitorInterface *monitorRef = &monitor; + std::function + monitorExtract2 = + [monitorRef](std::size_t &result [[maybe_unused]], + const std::size_t &value + [[maybe_unused]]) { monitorRef->count(); }; + qDebug(); + + QFuture res = + QtConcurrent::mappedReduced(chunck_list.begin(), + chunck_list.end(), + extractChunck, + monitorExtract2, + QtConcurrent::UnorderedReduce); + qDebug(); + + /* + QFuture res = + QtConcurrent::mapped(chunck_list.begin(), chunck_list.end(), + extractChunck); + */ + res.waitForFinished(); + monitor.setTotalSteps(0); + } +} + +void +MsRunXicExtractorInterface::extractXicCoordSPtrList( + UiMonitorInterface &monitor, std::vector &xic_coord_list) +{ + + monitor.setStatus( + QObject::tr("extracting %1 XICs").arg(xic_coord_list.size())); + monitor.setTotalSteps(xic_coord_list.size()); + protectedExtractXicCoordSPtrList( + monitor, xic_coord_list.begin(), xic_coord_list.end()); + monitor.setTotalSteps(0); + postExtractionProcess(monitor, xic_coord_list.begin(), xic_coord_list.end()); +} + +void +MsRunXicExtractorInterface::postExtractionProcess( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) +{ + + if(mcsp_postExtractionTraceFilter != nullptr) + { + monitor.setStatus( + QObject::tr("filtering %1 XICs") + .arg(std::distance(it_xic_coord_list_begin, it_xic_coord_list_end))); + for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++) + { + mcsp_postExtractionTraceFilter.get()->filter( + *(it->get()->xicSptr.get())); + } + } +} + + } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorinterface.h libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.h --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/msrunxicextractorinterface.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/msrunxicextractorinterface.h 2022-10-27 09:16:15.000000000 +0000 @@ -31,8 +31,11 @@ #include "../msrun/msrunreader.h" #include #include +#include +#include #include "../mzrange.h" #include "../xic/xic.h" +#include "../processing/uimonitor/uimonitorinterface.h" namespace pappso @@ -50,78 +53,79 @@ */ void setXicExtractMethod(XicExtractMethod method); // sum or max - /** @brief get a XIC on this MsRun at the given mass range - * @param mz_range mz range to extract - */ - virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range) final; + /** @brief set the retention time range in seconds around the target rt + * + * only the interesting part of the xic will be extracted, form the rt target + * - range_in_seconds to rt target + range in seconds by default, all the LC + * run time is extracted + * + * @param range_in_seconds range in seconds + */ + void setRetentionTimeAroundTarget(double range_in_seconds); + + + /** @brief extract a list of XIC given a list of xic coordinates to extract + * + * XicCoord is a vessel containing the xic to fill and coordinates of this XIC + * in the MS run + * + * @param monitor process monitoring + * @param xic_coord_list list of xic coordinates to extract. The order of xic + * coordinates may change. + */ + virtual void + extractXicCoordSPtrList(UiMonitorInterface &monitor, + std::vector &xic_coord_list) final; + + + /** @brief multithreaded XIC extraction + * + * divide xic_coord_list and run extractXicCoordSPtrList separated threads + * + * @param monitor process monitoring + * @param xic_coord_list list of xic coordinates to extract. The order of xic + * coordinates may change. + */ + virtual void extractXicCoordSPtrListParallelized( + UiMonitorInterface &monitor, + std::vector &xic_coord_list) final; + + const MsRunIdCstSPtr &getMsRunId() const; - /** @brief get a XIC on this MsRun at the given mass range - * @param mz_range mz range to extract - * @param rt_begin begining of the XIC in seconds - * @param rt_end end of the XIC in seconds + /** @brief get the msrunreader currently used for XIC extraction */ - virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, - pappso::pappso_double rt_begin, - pappso::pappso_double rt_end) = 0; + const MsRunReaderSPtr &getMsRunReaderSPtr() const; - /** @brief extract a list of XIC given a list of mass to extract + /** @brief filter interface to apply just after XIC extration on each trace */ - virtual std::vector - getXicCstSPtrList(const std::vector &mz_range_list) = 0; + void + setPostExtractionTraceFilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter); - const MsRunIdCstSPtr &getMsRunId() const; protected: - struct MsRunXicExtractorPoints - { - std::size_t spectrum_index; - double rt; - }; - - /** @brief class to read retention time points of MsRun - */ - class MsRunXicExtractorReadPoints : public SpectrumCollectionHandlerInterface - { - private: - std::vector &m_msrun_points; - - public: - MsRunXicExtractorReadPoints( - std::vector &msrun_points) - : m_msrun_points(msrun_points){}; - - virtual void - setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override - { - if(spectrum.getMsLevel() == 1) - { - m_msrun_points.push_back( - {spectrum.getMassSpectrumId().getSpectrumIndex(), - spectrum.getRtInSeconds()}); - } - } - virtual bool - needPeakList() const override - { - return false; - } - virtual void - loadingEnded() override - { - } - }; - - /** @brief constructor is private, use the MsRunXicExtractorFactory */ MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader); MsRunXicExtractorInterface(const MsRunXicExtractorInterface &other); virtual ~MsRunXicExtractorInterface(); - - + + /** @brief possible post extraction process, eventually trace filters + */ + virtual void postExtractionProcess(UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end); + + virtual void protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) = 0; + + protected: MsRunReaderSPtr msp_msrun_reader; XicExtractMethod m_xicExtractMethod = XicExtractMethod::max; + double m_retentionTimeAroundTarget = std::numeric_limits::max(); + pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter = nullptr; }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunslice.cpp libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunslice.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunslice.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunslice.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -156,8 +156,8 @@ operator>>(QDataStream &instream, MsRunSlice &slice) { - quint32 vector_size; - quint32 slice_number; + quint32 vector_size = 0; + quint32 slice_number = 0; quint32 spectrum_position = 0; DataPoint peak; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -31,6 +31,7 @@ #include "msrunxicextractor.h" #include #include "../../pappsoexception.h" +#include "../../exception/exceptioninterrupted.h" #include "../../processing/filters/filterresample.h" namespace pappso @@ -67,17 +68,49 @@ m_msrun_points = other.m_msrun_points; } -XicCstSPtr -MsRunXicExtractor::getXicCstSPtr(const MzRange &mz_range, - pappso::pappso_double rt_begin, - pappso::pappso_double rt_end) + +void +MsRunXicExtractor::protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) +{ + + // sort xic by mz: + std::sort(it_xic_coord_list_begin, + it_xic_coord_list_end, + [](XicCoordSPtr &a, XicCoordSPtr &b) { + return a.get()->rtTarget < b.get()->rtTarget; + }); + + for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++) + { + // XicCoord *p_xic_coord = sp_xic_coord.get(); + extractOneXicCoord(*(it->get())); + monitor.count(); + if(monitor.shouldIstop()) + { + throw pappso::ExceptionInterrupted( + QObject::tr("Xic extraction process interrupted")); + } + } +} + + +void +MsRunXicExtractor::extractOneXicCoord(XicCoord &xic_coord) { - FilterResampleKeepXRange keep_range(mz_range.lower(), mz_range.upper()); - std::shared_ptr msrunxic_sp = std::make_shared(Xic()); + FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(), + xic_coord.mzRange.upper()); + std::shared_ptr msrunxic_sp = xic_coord.xicSptr; + + double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget; + double rt_end = xic_coord.rtTarget + m_retentionTimeAroundTarget; auto itpoints = m_msrun_points.begin(); + // find startint retention time : while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin)) { itpoints++; @@ -91,11 +124,9 @@ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " // << spectrum->size(); spectrum->debugPrintValues(); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " spectrum->size()=" << spectrum->size(); + qDebug() << " spectrum->size()=" << spectrum->size(); keep_range.filter(*(spectrum.get())); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " spectrum->size()=" << spectrum->size(); + qDebug() << " spectrum->size()=" << spectrum->size(); peak.x = itpoints->rt; @@ -106,8 +137,7 @@ { peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y; - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " peak.y=" << peak.y + qDebug() << " peak.y=" << peak.y << " spectrum->size()=" << spectrum->size(); } } @@ -119,30 +149,6 @@ itpoints++; } - - - return (msrunxic_sp); -} - -std::vector -MsRunXicExtractor::getXicCstSPtrList(const std::vector &mz_range_list) -{ - - std::vector> xic_list_return; - std::vector xic_list; - for(std::size_t i = 0; i < mz_range_list.size(); i++) - { - xic_list_return.push_back(std::make_shared(Xic())); - xic_list.push_back(xic_list_return.back().get()); - xic_list_return.back().get()->reserve(m_msrun_points.size()); - } - getXicFromPwizMSDataFile(xic_list, mz_range_list, 0, 100000000); - std::vector xic_list_return_b; - for(auto &xic : xic_list_return) - { - xic_list_return_b.push_back(xic); - } - return xic_list_return_b; } void @@ -152,18 +158,17 @@ pappso::pappso_double rt_begin, pappso::pappso_double rt_end) { - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); std::vector peak_for_mass; for(const MzRange &mass_range : mass_range_list) { peak_for_mass.push_back(DataPoint()); - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << " mass_range=" << mass_range.getMz(); + qDebug() << " mass_range=" << mass_range.getMz(); } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); auto itpoints = m_msrun_points.begin(); @@ -220,7 +225,7 @@ } - qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; + qDebug(); } // namespace pappso diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractor.h libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.h --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractor.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractor.h 2022-10-27 09:16:15.000000000 +0000 @@ -45,12 +45,6 @@ public: MsRunXicExtractor(const MsRunXicExtractor &other); virtual ~MsRunXicExtractor(); - virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, - pappso::pappso_double rt_begin, - pappso::pappso_double rt_end) override; - - virtual std::vector - getXicCstSPtrList(const std::vector &mz_range_list) override; protected: MsRunXicExtractor(MsRunReaderSPtr &msrun_reader); @@ -61,8 +55,58 @@ pappso::pappso_double rt_begin, pappso::pappso_double rt_end); + virtual void protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) override; + + + protected: + struct MsRunXicExtractorPoints + { + std::size_t spectrum_index; + double rt; + }; + + /** @brief class to read retention time points of MsRun + */ + class MsRunXicExtractorReadPoints : public SpectrumCollectionHandlerInterface + { + private: + std::vector &m_msrun_points; + + public: + MsRunXicExtractorReadPoints( + std::vector &msrun_points) + : m_msrun_points(msrun_points){}; + + virtual void + setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override + { + if(spectrum.getMsLevel() == 1) + { + m_msrun_points.push_back( + {spectrum.getMassSpectrumId().getSpectrumIndex(), + spectrum.getRtInSeconds()}); + } + } + virtual bool + needPeakList() const override + { + return false; + } + virtual void + loadingEnded() override + { + } + }; + + protected: std::vector m_msrun_points; + + private: + void extractOneXicCoord(XicCoord &xic_coord); }; diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -90,15 +90,38 @@ } } -XicCstSPtr -MsRunXicExtractorDisk::getXicCstSPtr(const MzRange &mz_range, - pappso::pappso_double rt_begin, - pappso::pappso_double rt_end) + +void +MsRunXicExtractorDisk::protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) +{ + // sort xic by mz: + std::sort(it_xic_coord_list_begin, + it_xic_coord_list_end, + [](XicCoordSPtr &a, XicCoordSPtr &b) { + return a.get()->mzRange.getMz() < b.get()->mzRange.getMz(); + }); + + for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++) + { + extractOneXicCoord(*(it->get())); + monitor.count(); + } +} + +void +MsRunXicExtractorDisk::extractOneXicCoord(XicCoord &xic_coord) { - std::shared_ptr msrunxic_sp = std::make_shared(Xic()); + std::shared_ptr msrunxic_sp = xic_coord.xicSptr; + + double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget; + double rt_end = xic_coord.rtTarget + m_retentionTimeAroundTarget; + std::vector slice_list; - slice_list = acquireSlices(mz_range); + slice_list = acquireSlices(xic_coord.mzRange); if(slice_list.size() == 0) { @@ -120,7 +143,7 @@ const MassSpectrum &spectrum = msrun_slice.get()->getSpectrum(i); for(auto &&peak : spectrum) { - if(mz_range.contains(peak.x)) + if(xic_coord.mzRange.contains(peak.x)) { if(m_xicExtractMethod == XicExtractMethod::sum) { @@ -138,21 +161,6 @@ } msrunxic_sp.get()->push_back(xic_element); } - - return (msrunxic_sp); -} - -std::vector -MsRunXicExtractorDisk::getXicCstSPtrList( - const std::vector &mz_range_list) -{ - - std::vector xic_list_return; - for(auto &range : mz_range_list) - { - xic_list_return.push_back(getXicCstSPtr(range, 0, 40000000)); - } - return xic_list_return; } void diff -Nru libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h --- libpappsomspp-0.8.15/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h 2022-10-27 09:16:15.000000000 +0000 @@ -49,17 +49,18 @@ MsRunXicExtractorDisk(MsRunReaderSPtr &msrun_reader); MsRunXicExtractorDisk(const MsRunXicExtractorDisk &other); virtual ~MsRunXicExtractorDisk(); - virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, - pappso::pappso_double rt_begin, - pappso::pappso_double rt_end) override; - virtual std::vector - getXicCstSPtrList(const std::vector &mz_range_list) override; protected: MsRunXicExtractorDisk(MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir); + virtual void protectedExtractXicCoordSPtrList( + UiMonitorInterface &monitor, + std::vector::iterator it_xic_coord_list_begin, + std::vector::iterator it_xic_coord_list_end) override; + + void prepareExtractor(); void serializeMsRun(); @@ -107,6 +108,10 @@ std::deque m_msRunSliceListCache; QMutex m_mutex; + + + private: + void extractOneXicCoord(XicCoord &xic_coord); }; diff -Nru libpappsomspp-0.8.15/src/resources/PSI-MOD.obo libpappsomspp-0.8.58/src/resources/PSI-MOD.obo --- libpappsomspp-0.8.15/src/resources/PSI-MOD.obo 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/src/resources/PSI-MOD.obo 2022-10-27 09:16:15.000000000 +0000 @@ -1,7 +1,7 @@ format-version: 1.2 -date: 30:05:2014 00:48 -saved-by: John S. Garavelli -auto-generated-by: FormulaOBO.PL +ontology: mod +date: 10:03:2021 14:36 +saved-by: Paul M. Thomas subsetdef: PSI-MOD-slim "subset of protein modifications" synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT synonymtypedef: OMSSA-label "Short label from OMSSA" EXACT @@ -12,23 +12,24 @@ synonymtypedef: RESID-misnomer "Misnomer tagged alternate name from RESID" RELATED synonymtypedef: RESID-name "Name from RESID" EXACT synonymtypedef: RESID-systematic "Systematic name from RESID" EXACT -synonymtypedef: UniMod-alternate "Alternate name from UniMod" RELATED -synonymtypedef: UniMod-description "Description (full_name) from UniMod" RELATED -synonymtypedef: UniMod-interim "Interim label from UniMod" RELATED +synonymtypedef: Unimod-alternate "Alternate name from Unimod" RELATED +synonymtypedef: Unimod-description "Description (full_name) from Unimod" RELATED +synonymtypedef: Unimod-interim "Interim label from Unimod" RELATED synonymtypedef: UniProt-feature "Protein feature description from UniProtKB" EXACT default-namespace: PSI-MOD -remark: PSI-MOD version: 1.013.0 +remark: PSI-MOD version: 1.031.2 remark: RESID release: 75.00 -remark: ISO-8601 date: 2014-01-28 14:22Z -remark: Annotation note 1 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235. -remark: Annotation note 2 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var". -remark: Annotation note 3 - When an entry in the UniMod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the UniMod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term". -remark: Annotation note 4 - The elemental formulas are in strict alphabetical order, not in CAS ("C" and "H" first) order. Isotope numbers are in parentheses before the element symbol, and an element should not occur in a formula both with and without an isotope number. In difference formulas, counts can be zero or negative. -remark: Annotation note 5 - In entries with an isotope indicator in the formula, average masses are meaningless and are assigned the value equal to the monoisotopic mass, but rounded to a lower precision; monoisotopic masses are calculated by using the masses for the indicated isotopes and the most common isotopes for other elements without isotope indicators in the formulas. -remark: Annotation note 6 - For cross-link modifications, the number following "Cross-link" in the comment record indicates the number of amino acid residues that appear in the origin record, used to check the difference formula and masses. This usage differs from RESID, where the cross-link number indicates the maximum number of peptide chains that can be cross-linked. -remark: Annotation note 7 - The synonym cross-reference "MOD:old name" has been replaced by "MOD:alternate name". -remark: Annotation note 8 - The DeltaMass listings for free amino acids have been removed. Most UniMod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter. -remark: Annotation note 9 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references. +remark: ISO-8601 date: 2021-03-10 14:36Z +remark: Annotation note 01 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235. +remark: Annotation note 02 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var". +remark: Annotation note 03 - When an entry in the Unimod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the Unimod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term". +remark: Annotation note 04 - The elemental formulas are in strict alphabetical order, not in CAS ("C" and "H" first) order. Isotope numbers are in parentheses before the element symbol, and an element should not occur in a formula both with and without an isotope number. In difference formulas, counts can be zero or negative. +remark: Annotation note 05 - In entries with an isotope indicator in the formula, average masses are meaningless and are assigned the value equal to the monoisotopic mass, but rounded to a lower precision; monoisotopic masses are calculated by using the masses for the indicated isotopes and the most common isotopes for other elements without isotope indicators in the formulas. +remark: Annotation note 06 - For cross-link modifications, the number following "Cross-link" in the comment record indicates the number of amino acid residues that appear in the origin record, used to check the difference formula and masses. This usage differs from RESID, where the cross-link number indicates the maximum number of peptide chains that can be cross-linked. +remark: Annotation note 07 - The synonym cross-reference "MOD:old name" has been replaced by "MOD:alternate name". +remark: Annotation note 08 - The DeltaMass listings for free amino acids have been removed. Most Unimod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter. +remark: Annotation note 09 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references. +remark: Annotation note 10 - GNOme is the Glycan Naming and Subsumption Ontology (https://gnome.glyomics.org/), an ontology for the support of glycomics. PSI-MOD does not have all possible glycans in its entries, just the ones that are noted to be on proteins and have been requested for addition. GNOme uses GlyTouCan (http://glytoucan.org/) to provide stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). [Term] id: MOD:00000 @@ -60,8 +61,8 @@ [Term] id: MOD:00003 -name: UniMod -def: "Entry from UniMod." [PubMed:18688235] +name: Unimod +def: "Entry from Unimod." [PubMed:18688235] comment: This term is for organizational use only and should not be assigned. [JSG] xref: Source: "none" is_a: MOD:00032 ! uncategorized protein modification @@ -69,7 +70,7 @@ [Term] id: MOD:00004 name: artifact -def: "Artifact entry from UniMod - OBSOLETE because organizational use is no longer required." [PubMed:18688235] +def: "Artifact entry from Unimod - OBSOLETE because organizational use is no longer required." [PubMed:18688235] is_obsolete: true [Term] @@ -96,10 +97,10 @@ [Term] id: MOD:00007 name: selenium substitution for sulfur -def: "A protein modification that effectively substitutes a selenium atom for a sulfur atom." [PubMed:12148805, UniMod:162] +def: "A protein modification that effectively substitutes a selenium atom for a sulfur atom." [PubMed:12148805, Unimod:162] synonym: "Delta:S(-1)Se(1)" RELATED PSI-MS-label [] synonym: "Se(S)Res" EXACT PSI-MOD-label [] -synonym: "Selenium replaces sulphur" RELATED UniMod-description [] +synonym: "Selenium replaces sulphur" RELATED Unimod-description [] xref: DiffAvg: "46.91" xref: DiffFormula: "C 0 H 0 N 0 O 0 S -1 Se 1" xref: DiffMono: "47.944450" @@ -107,14 +108,15 @@ xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" -xref: Source: "artifact" +xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:162" is_a: MOD:00745 ! selenium containing residue [Term] id: MOD:00008 name: common -def: "Entry from UniMod representing one or more entries in RESID. OBSOLETE because organizational use is no longer required." [PubMed:18688235] +def: "Entry from Unimod representing one or more entries in RESID. OBSOLETE because organizational use is no longer required." [PubMed:18688235] is_obsolete: true [Term] @@ -623,13 +625,12 @@ [Term] id: MOD:00030 name: N-formyl-L-methionine residue -def: "A protein modification that effectively converts a source amino acid residue to an N-formyl-L-methionine, a natural pretranslational modification." [ChEBI:33718, OMSSA:22, PubMed:10825024, PubMed:11152118, PubMed:2165784, PubMed:3042771, PubMed:8758896, RESID:AA0021#FMET, UniMod:107#N-term] +def: "A protein modification that effectively converts a source amino acid residue to an N-formyl-L-methionine, a natural pretranslational modification." [ChEBI:33718, OMSSA:22, PubMed:10825024, PubMed:11152118, PubMed:2165784, PubMed:3042771, PubMed:8758896, RESID:AA0021#FMET] subset: PSI-MOD-slim synonym: "(2S)-2-formylamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-formamido-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] synonym: "2-formylamino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "2-formylazanyl-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] -synonym: "Addition of N-formyl met" RELATED UniMod-description [] synonym: "fMet" EXACT PSI-MOD-label [] synonym: "FormylMet" RELATED PSI-MS-label [] synonym: "MOD_RES N-formylmethionine" EXACT UniProt-feature [] @@ -645,9 +646,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00409 ! N-formylated residue is_a: MOD:00868 ! natural, non-standard encoded residue -is_a: MOD:01696 ! alpha-amino acylated residue [Term] id: MOD:00031 @@ -730,7 +729,7 @@ [Term] id: MOD:00035 name: (2S,3R)-3-hydroxyasparagine -def: "A protein modification that effectively converts an L-asparagine residue to (2S,3R)-3-hydroxyasparagine." [PubMed:11823643, PubMed:2820791, RESID:AA0026] +def: "A protein modification that effectively converts an L-asparagine residue to (2S,3R)-3-hydroxyasparagine." [PubMed:11823643, PubMed:2820791, RESID:AA0026, ChEBI:141853] subset: PSI-MOD-slim synonym: "(2S,3R)-2,4-diamino-3-hydroxy-4-oxobutanoic acid" EXACT RESID-alternate [] synonym: "(2S,3R)-2-amino-3-hydroxy-4-butanediamic acid" EXACT RESID-systematic [] @@ -749,12 +748,13 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0369" is_a: MOD:01688 ! 3-hydroxy-L-asparagine [Term] id: MOD:00036 name: (2S,3R)-3-hydroxyaspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to (2S,3R)-3-hydroxyaspartic acid." [OMSSA:59, PubMed:6572939, PubMed:6871167, PubMed:8355279, RESID:AA0027, UniMod:35#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to (2S,3R)-3-hydroxyaspartic acid." [OMSSA:59, PubMed:6572939, PubMed:6871167, PubMed:8355279, RESID:AA0027, Unimod:35#D, ChEBI:141848] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-hydroxybutanedioic acid" EXACT RESID-systematic [] synonym: "(2S,3R)-3-hydroxyaspartic acid" EXACT RESID-name [] @@ -776,6 +776,8 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" +xref: UniProt: "PTM-0371" is_a: MOD:01926 ! 3-hydroxy-L-aspartic acid [Term] @@ -794,6 +796,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0044" is_a: MOD:01047 ! monohydroxylated lysine [Term] @@ -818,6 +821,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0030" is_a: MOD:01024 ! monohydroxylated proline [Term] @@ -843,12 +847,13 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0043" is_a: MOD:01024 ! monohydroxylated proline [Term] id: MOD:00040 name: 2-pyrrolidone-5-carboxylic acid (Gln) -def: "A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid." [ChEBI:30652, DeltaMass:123, OMSSA:110, PubMed:10214721, PubMed:1836357, PubMed:26343, PubMed:3473473, RESID:AA0031#GLN, UniMod:28#Q] +def: "A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid." [ChEBI:30652, DeltaMass:123, OMSSA:110, PubMed:10214721, PubMed:1836357, PubMed:26343, PubMed:3473473, RESID:AA0031#GLN, Unimod:28#Q] comment: DeltaMass gives a formula C 5 H 5 N 1 O 2 with mass 111.1 subset: PSI-MOD-slim synonym: "(2S)-5-oxo-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] @@ -863,7 +868,7 @@ synonym: "ntermpeppyroq" EXACT OMSSA-label [] synonym: "PCA" EXACT RESID-alternate [] synonym: "PyrGlu(Gln)" EXACT PSI-MOD-label [] -synonym: "Pyro-glu from Q" RELATED UniMod-description [] +synonym: "Pyro-glu from Q" RELATED Unimod-description [] synonym: "pyroglutamic acid" EXACT RESID-alternate [] synonym: "Pyroglutamic Acid formed from Gln" EXACT DeltaMass-label [] synonym: "Pyroglutamyl" EXACT DeltaMass-label [] @@ -876,6 +881,8 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:28" +xref: UniProt: "PTM-0261" is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:01048 ! 2-pyrrolidone-5-carboxylic acid is_a: MOD:01160 ! deaminated residue @@ -883,7 +890,7 @@ [Term] id: MOD:00041 name: L-gamma-carboxyglutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to L-gamma-carboxyglutamic acid." [DeltaMass:217, OMSSA:48, PubMed:10517147, PubMed:1807167, PubMed:3263814, PubMed:4528109, PubMed:7457858, PubMed:8135347, PubMed:8868490, PubMed:9188685, RESID:AA0032, UniMod:299#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to L-gamma-carboxyglutamic acid." [DeltaMass:217, OMSSA:48, PubMed:10517147, PubMed:1807167, PubMed:3263814, PubMed:4528109, PubMed:7457858, PubMed:8135347, PubMed:8868490, PubMed:9188685, RESID:AA0032, Unimod:299#E] comment: DeltaMass has an incorrect formula C 6 H 7 N 5 O 1 (N and O reversed) with mass 173. subset: PSI-MOD-slim synonym: "(3S)-3-aminopropane-1,1,3-tricarboxylic acid" EXACT RESID-systematic [] @@ -894,9 +901,9 @@ synonym: "4-carboxyglutamic acid" EXACT RESID-alternate [] synonym: "4CbxGlu" EXACT PSI-MOD-label [] synonym: "Carboxy" RELATED PSI-MS-label [] -synonym: "Carboxy" RELATED UniMod-interim [] +synonym: "Carboxy" RELATED Unimod-interim [] synonym: "Carboxy Glutamyl" EXACT DeltaMass-label [] -synonym: "Carboxylation" RELATED UniMod-description [] +synonym: "Carboxylation" RELATED Unimod-description [] synonym: "gamma-carboxylated L-glutamic acid" EXACT PSI-MOD-alternate [] synonym: "gammacarboxyle" EXACT OMSSA-label [] synonym: "L-gamma-carboxyglutamic acid" EXACT RESID-name [] @@ -910,13 +917,15 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:299" +xref: UniProt: "PTM-0039" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00042 name: L-aspartic 4-phosphoric anhydride -def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartic 4-phosphoric anhydride." [ChEBI:15836, PubMed:4357737, RESID:AA0033, UniMod:21#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartic 4-phosphoric anhydride." [ChEBI:15836, PubMed:4357737, RESID:AA0033, Unimod:21#D] synonym: "(2S)-2-amino-4-oxo-4-(phosphonooxy)butanoic acid" EXACT RESID-systematic [] synonym: "2-aminobutanedioic 4-phosphoric anhydride" EXACT RESID-alternate [] synonym: "2-azanyl-4-oxo-4-(phosphonooxy)butanoic acid" EXACT RESID-alternate [] @@ -929,7 +938,7 @@ synonym: "MOD_RES 4-aspartylphosphate" EXACT UniProt-feature [] synonym: "PAsp" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" @@ -939,13 +948,15 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0038" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01455 ! O-phosphorylated residue [Term] id: MOD:00043 name: S-phospho-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-phospho-L-cysteine." [PubMed:3142516, PubMed:7961745, PubMed:8128219, RESID:AA0034, UniMod:21#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-phospho-L-cysteine." [PubMed:3142516, PubMed:7961745, PubMed:8128219, RESID:AA0034, Unimod:21#C] synonym: "(2R)-2-amino-3-(phosphonosulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-azanyl-3-(phosphonosulfanyl)propanoic acid" EXACT RESID-alternate [] synonym: "ACT_SITE Phosphocysteine intermediate" EXACT UniProt-feature [] @@ -953,7 +964,7 @@ synonym: "MOD_RES Phosphocysteine" EXACT UniProt-feature [] synonym: "PCys" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "S-phospho-L-cysteine" EXACT RESID-name [] synonym: "S-phosphonocysteine" EXACT RESID-alternate [] synonym: "S-phosphorylated L-cysteine" EXACT PSI-MOD-alternate [] @@ -967,6 +978,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0251" is_a: MOD:00696 ! phosphorylated residue is_a: MOD:00777 ! residues isobaric at 182.96-182.98 Da is_a: MOD:00905 ! modified L-cysteine residue @@ -990,7 +1003,7 @@ synonym: "Ntau-phosphorylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "NtPHis" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "tele-phosphohistidine" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" @@ -1001,6 +1014,7 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0325" is_a: MOD:00890 ! phosphorylated L-histidine [Term] @@ -1022,7 +1036,7 @@ synonym: "Npi-phosphorylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "NpPHis" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "pros-phosphohistidine" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" @@ -1033,12 +1047,13 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0260" is_a: MOD:00890 ! phosphorylated L-histidine [Term] id: MOD:00046 name: O-phospho-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-phospho-L-serine." [ChEBI:15811, DeltaMass:0, OMSSA:6, PubMed:12923550, PubMed:4065410, PubMed:8061611, RESID:AA0037, UniMod:21#S] +def: "A protein modification that effectively converts an L-serine residue to O-phospho-L-serine." [ChEBI:15811, DeltaMass:0, OMSSA:6, PubMed:12923550, PubMed:4065410, PubMed:8061611, RESID:AA0037, Unimod:21#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(phosphonooxy)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate" EXACT RESID-alternate [] @@ -1052,7 +1067,7 @@ synonym: "OPSer" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Seryl" EXACT DeltaMass-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "phosphorylations" EXACT OMSSA-label [] synonym: "serine phosphate ester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" @@ -1064,6 +1079,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0253" is_a: MOD:00771 ! residues isobaric at 166.98-167.00 Da is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01455 ! O-phosphorylated residue @@ -1071,7 +1088,7 @@ [Term] id: MOD:00047 name: O-phospho-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine." [ChEBI:21967, DeltaMass:0, OMSSA:7, PubMed:12923550, PubMed:7678926, RESID:AA0038, UniMod:21#T] +def: "A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine." [ChEBI:21967, DeltaMass:0, OMSSA:7, PubMed:12923550, PubMed:7678926, RESID:AA0038, Unimod:21#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(phosphonooxy)butanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxybutanoic acid 3-phosphate" EXACT RESID-alternate [] @@ -1083,7 +1100,7 @@ synonym: "OPThr" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Threonyl" EXACT DeltaMass-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "phosphorylationt" EXACT OMSSA-label [] synonym: "threonine phosphate ester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" @@ -1095,6 +1112,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0254" is_a: MOD:00773 ! residues isobaric at 181.00-181.02 Da is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01455 ! O-phosphorylated residue @@ -1102,7 +1121,7 @@ [Term] id: MOD:00048 name: O4'-phospho-L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine." [DeltaMass:0, OMSSA:8, PubMed:10226369, PubMed:1725475, RESID:AA0039, UniMod:21#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine." [DeltaMass:0, OMSSA:8, PubMed:10226369, PubMed:1725475, RESID:AA0039, Unimod:21#Y] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate" EXACT RESID-alternate [] @@ -1114,7 +1133,7 @@ synonym: "OPTyr" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Tyrosinyl" EXACT DeltaMass-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "phosphorylationy" EXACT OMSSA-label [] synonym: "tyrosine phosphate" EXACT RESID-alternate [] xref: DiffAvg: "79.98" @@ -1126,6 +1145,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0255" is_a: MOD:00774 ! residues isobaric at 243.02-243.03 Da is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01455 ! O-phosphorylated residue @@ -1133,7 +1154,7 @@ [Term] id: MOD:00049 name: 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to diphthamide." [ChEBI:16692, DeltaMass:122, PubMed:15316019, PubMed:7430147, RESID:AA0040, UniMod:375#H] +def: "A protein modification that effectively converts an L-histidine residue to diphthamide." [ChEBI:16692, DeltaMass:122, PubMed:15316019, PubMed:7430147, RESID:AA0040, Unimod:375#H] synonym: "(2R)-1-amino-4-(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl)-N,N,N-trimethyl-1-oxobutan-2-aminium" EXACT RESID-systematic [] synonym: "(3-[4-(2-amino-2-carboxy-ethyl)-1H-imidazol-2-yl]-1-carbamoyl-propyl)-trimethylammonium" EXACT RESID-alternate [] synonym: "1-azanyl-4-(4-[2-azanyl-2-carboxyethyl]-1H-imidazol-2-yl)-N,N,N-trimethyl-1-oxobutan-2-azanium" EXACT RESID-alternate [] @@ -1145,7 +1166,7 @@ synonym: "alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium" EXACT RESID-alternate [] synonym: "Diphth" EXACT PSI-MOD-label [] synonym: "Diphthamide" RELATED PSI-MS-label [] -synonym: "Diphthamide" RELATED UniMod-description [] +synonym: "Diphthamide" RELATED Unimod-description [] synonym: "diphthamide" EXACT RESID-alternate [] synonym: "diphthamide (from histidine)" EXACT DeltaMass-label [] synonym: "MOD_RES Diphthamide" EXACT UniProt-feature [] @@ -1159,6 +1180,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:375" +xref: UniProt: "PTM-0118" is_a: MOD:00909 ! modified L-histidine residue [Term] @@ -1183,6 +1206,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0199" is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1208,6 +1232,7 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0200" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1236,6 +1261,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0201" is_a: MOD:00646 ! acetylated L-cysteine is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1261,6 +1287,7 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0202" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1312,6 +1339,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0203" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1336,6 +1364,7 @@ xref: Origin: "I" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0204" is_a: MOD:00910 ! modified L-isoleucine residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1388,6 +1417,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0205" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1413,6 +1443,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0206" is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1439,6 +1470,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0207" is_a: MOD:00647 ! acetylated L-serine is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1451,7 +1483,7 @@ synonym: "2-acetylamino-3-hydroxybutanoic acid" EXACT RESID-alternate [] synonym: "2-acetylazanyl-3-hydroxybutanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "MOD_RES N-acetylthreonine" EXACT UniProt-feature [] synonym: "N-acetyl-L-threonine" EXACT RESID-name [] synonym: "N-acetylated L-threonine" EXACT PSI-MOD-alternate [] @@ -1467,6 +1499,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0208" is_a: MOD:01186 ! acetylated L-threonine is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1492,6 +1525,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0209" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01458 ! alpha-amino acetylated residue @@ -1517,19 +1551,20 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0210" is_a: MOD:00920 ! modified L-valine residue is_a: MOD:01458 ! alpha-amino acetylated residue [Term] id: MOD:00064 name: N6-acetyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-acetyl-L-lysine." [ChEBI:17752, DeltaMass:214, OMSSA:24, PubMed:11369851, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1680872, PubMed:670159, RESID:AA0055, UniMod:1#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-acetyl-L-lysine." [ChEBI:17752, DeltaMass:214, OMSSA:24, PubMed:11369851, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1680872, PubMed:670159, RESID:AA0055, Unimod:1#K] subset: PSI-MOD-slim synonym: "(2S)-6-acetamido-2-aminohexanoic acid" EXACT RESID-systematic [] synonym: "6-acetylamino-2-aminohexanoic acid" EXACT RESID-alternate [] synonym: "6-acetylazanyl-2-aminohexanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "acetylk" EXACT OMSSA-label [] synonym: "epsilon-acetyllysine" EXACT RESID-alternate [] synonym: "MOD_RES N6-acetyllysine" EXACT UniProt-feature [] @@ -1546,19 +1581,21 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:1" +xref: UniProt: "PTM-0190" is_a: MOD:00723 ! N-acetylated L-lysine is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00065 name: S-acetyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-acetyl-L-cysteine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:1310545, PubMed:14730666, PubMed:15350136, RESID:AA0056, UniMod:1#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-acetyl-L-cysteine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:1310545, PubMed:14730666, PubMed:15350136, RESID:AA0056, Unimod:1#C] subset: PSI-MOD-slim synonym: "(2R)-3-acetylsulfanyl-2-aminopropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(acetylthio)propanoic acid" EXACT RESID-alternate [] synonym: "2-azanyl-3-(acetylsulfanyl)propanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "ACT_SITE S-acetylcysteine intermediate" EXACT UniProt-feature [] synonym: "cysteine acetate thioester" EXACT RESID-alternate [] synonym: "S-acetyl-L-cysteine" EXACT RESID-name [] @@ -1573,8 +1610,9 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00645 ! S-acetylated residue -is_a: MOD:00646 ! acetylated L-cysteine +xref: Unimod: "Unimod:1" +is_a: MOD:00645 ! mono S-acetylated residue +is_a: MOD:00646 ! monoacetylated L-cysteine [Term] id: MOD:00066 @@ -1599,6 +1637,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0211" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00908 ! modified glycine residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -1623,18 +1662,19 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0331" is_a: MOD:00447 ! N-glucuronylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00068 name: N-myristoylglycine -def: "A protein modification that effectively converts a glycine residue to N-myristoylglycine." [OMSSA:80, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059, UniMod:45#G] +def: "A protein modification that effectively converts a glycine residue to N-myristoylglycine." [OMSSA:80, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059, Unimod:45#G] subset: PSI-MOD-slim synonym: "(tetradecanoylamino)ethanoic acid" EXACT RESID-systematic [] synonym: "LIPID N-myristoyl glycine" EXACT UniProt-feature [] synonym: "Myristoyl" RELATED PSI-MS-label [] -synonym: "Myristoylation" RELATED UniMod-description [] +synonym: "Myristoylation" RELATED Unimod-description [] synonym: "N-(1-oxotetradecyl)glycine" EXACT RESID-alternate [] synonym: "N-(C14:0 aliphatic acyl)glycine" EXACT PSI-MOD-alternate [] synonym: "N-myristoyl-glycine" EXACT RESID-name [] @@ -1652,6 +1692,8 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:45" +xref: UniProt: "PTM-0221" is_a: MOD:00650 ! N-myristoylated residue is_a: MOD:00908 ! modified glycine residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -1669,9 +1711,10 @@ synonym: "N-(1-oxahexadecyl)-L-cysteine" EXACT RESID-alternate [] synonym: "N-palmitoyl-L-cysteine" EXACT RESID-name [] synonym: "N-palmitoylated L-cysteine" EXACT PSI-MOD-alternate [] +synonym: "N-hexadecanoylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "NPamCys" EXACT PSI-MOD-label [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" @@ -1681,6 +1724,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0222" is_a: MOD:01684 ! palmitoylated-L-cysteine is_a: MOD:01685 ! alpha-amino palmitoylated residue @@ -1693,7 +1737,7 @@ synonym: "(2S)-2-methylaminopropanoic acid" EXACT RESID-systematic [] synonym: "2-methylazanylpropanoic acid" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N-methylalanine" EXACT UniProt-feature [] synonym: "N-methyl-L-alanine" EXACT RESID-name [] synonym: "N-methylalanine" EXACT RESID-alternate [] @@ -1707,7 +1751,8 @@ xref: MassMono: "85.052764" xref: Origin: "A" xref: Source: "natural" -xref: TermSpec: "none" +xref: TermSpec: "N-term" +xref: UniProt: "PTM-0214" is_a: MOD:01461 ! N-methylated alanine is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -1726,7 +1771,7 @@ synonym: "N,N,N-trimethylated L-alanine" EXACT PSI-MOD-alternate [] synonym: "N2Me3+Ala" EXACT PSI-MOD-label [] synonym: "NMe3Ala" EXACT PSI-MOD-label [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0" @@ -1738,6 +1783,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0177" is_a: MOD:01461 ! N-methylated alanine is_a: MOD:01698 ! alpha-amino trimethylated protonated-residue @@ -1750,13 +1796,14 @@ synonym: "Methyl" RELATED PSI-MS-label [] synonym: "methylaminoacetic acid" EXACT RESID-alternate [] synonym: "methylaminoethanoic acid" EXACT RESID-systematic [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "N-methylated glycine" EXACT PSI-MOD-alternate [] synonym: "N-methylglycine" EXACT RESID-name [] synonym: "NMe1Gly" EXACT PSI-MOD-label [] synonym: "Sar" EXACT DeltaMass-label [] synonym: "Sarcosine" EXACT DeltaMass-label [] synonym: "Sarcosyl" EXACT DeltaMass-label [] +synonym: "MOD_RES N-methylglycine" EXACT UniProt-feature [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" @@ -1765,7 +1812,8 @@ xref: MassMono: "71.037114" xref: Origin: "G" xref: Source: "natural" -xref: TermSpec: "none" +xref: TermSpec: "N-term" +xref: UniProt: "PTM-0483" is_a: MOD:00570 ! residues isobaric at 71.037114 Da is_a: MOD:00714 ! methylated glycine is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -1780,7 +1828,7 @@ synonym: "2-methylamino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methyl Methionyl" EXACT DeltaMass-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N-methylmethionine" EXACT UniProt-feature [] synonym: "N-methyl-L-methionine" EXACT RESID-name [] synonym: "N-methylated L-methionine" EXACT PSI-MOD-alternate [] @@ -1794,7 +1842,8 @@ xref: MassMono: "145.056135" xref: Origin: "M" xref: Source: "natural" -xref: TermSpec: "none" +xref: TermSpec: "N-term" +xref: UniProt: "PTM-0217" is_a: MOD:01463 ! N-methylated methionine is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -1806,7 +1855,7 @@ subset: PSI-MOD-slim synonym: "(2S)-2-methylamino-3-phenylpropanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N-methylphenylalanine" EXACT UniProt-feature [] synonym: "N-methyl-L-phenylalanine" EXACT RESID-name [] synonym: "N-methylated L-phenylalanine" EXACT PSI-MOD-alternate [] @@ -1820,21 +1869,22 @@ xref: MassMono: "161.084064" xref: Origin: "F" xref: Source: "natural" -xref: TermSpec: "none" +xref: TermSpec: "N-term" +xref: UniProt: "PTM-0218" is_a: MOD:01063 ! monomethylated phenylalanine is_a: MOD:01680 ! alpha-amino monomethylated residue [Term] id: MOD:00075 name: N,N-dimethyl-L-proline -def: "A protein modification that effectively converts an L-proline residue to N,N-dimethyl-L-proline." [ChEBI:21451, PubMed:12964758, PubMed:14570711, PubMed:193025, PubMed:3882426, PubMed:6254758, RESID:AA0066, UniMod:529] -comment: UniMod terminal specification corrected [JSG]. +def: "A protein modification that effectively converts an L-proline residue to N,N-dimethyl-L-proline." [ChEBI:21451, PubMed:12964758, PubMed:14570711, PubMed:193025, PubMed:3882426, PubMed:6254758, RESID:AA0066, Unimod:529] +comment: Unimod terminal specification corrected [JSG]. subset: PSI-MOD-slim synonym: "(2S)-2-carboxy-1,1-dimethylpyrrolidinium" EXACT RESID-systematic [] synonym: "1,1-dimethyl-L-prolinium" EXACT RESID-alternate [] -synonym: "Delta:H(5)C(2)" RELATED UniMod-interim [] +synonym: "Delta:H(5)C(2)" RELATED Unimod-interim [] synonym: "Dimethyl" RELATED PSI-MS-label [] -synonym: "Dimethylation of proline residue" RELATED UniMod-description [] +synonym: "Dimethylation of proline residue" RELATED Unimod-description [] synonym: "MOD_RES N,N-dimethylproline" EXACT UniProt-feature [] synonym: "N,N-dimethyl-L-proline" EXACT RESID-name [] synonym: "N,N-dimethyl-L-prolinium" EXACT RESID-alternate [] @@ -1851,16 +1901,18 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:529" +xref: UniProt: "PTM-0179" is_a: MOD:00710 ! protonated-dimethylated residue is_a: MOD:01462 ! N-methylated proline [Term] id: MOD:00076 name: symmetric dimethyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to symmetric dimethylarginine, N(omega),N'(omega)-dimethyl-L-arginine." [PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:2426402, PubMed:5128665, RESID:AA0067, UniMod:36#R] +def: "A protein modification that effectively converts an L-arginine residue to symmetric dimethylarginine, N(omega),N'(omega)-dimethyl-L-arginine." [PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:2426402, PubMed:5128665, RESID:AA0067, Unimod:36#R] subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-[((methylamino)(methylimino)methyl)amino]pentanoic acid" EXACT RESID-systematic [] -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "MOD_RES Omega-N-methylated arginine" EXACT UniProt-feature [] synonym: "MOD_RES Symmetric dimethylarginine" EXACT UniProt-feature [] @@ -1880,17 +1932,19 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" +xref: UniProt: "PTM-0287" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00783 ! dimethylated L-arginine [Term] id: MOD:00077 name: asymmetric dimethyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to asymmetric dimethylarginine, N(omega),N(omega)-dimethyl-L-arginine." [ChEBI:17929, PubMed:11152131, PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:3032834, RESID:AA0068, UniMod:36#R] +def: "A protein modification that effectively converts an L-arginine residue to asymmetric dimethylarginine, N(omega),N(omega)-dimethyl-L-arginine." [ChEBI:17929, PubMed:11152131, PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:3032834, RESID:AA0068, Unimod:36#R] subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-([(dimethylamino)(imino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "asymmetric dimethylarginine" EXACT RESID-alternate [] -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "MOD_RES Asymmetric dimethylarginine" EXACT UniProt-feature [] synonym: "MOD_RES Omega-N-methylated arginine" EXACT UniProt-feature [] @@ -1908,6 +1962,8 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" +xref: UniProt: "PTM-0066" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00783 ! dimethylated L-arginine @@ -1918,7 +1974,7 @@ subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Omega-N-methylarginine" EXACT UniProt-feature [] synonym: "MOD_RES Omega-N-methylated arginine" EXACT UniProt-feature [] synonym: "NG-methylarginine" EXACT RESID-alternate [] @@ -1934,19 +1990,20 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0237" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00602 ! N-methylated residue [Term] id: MOD:00079 name: N4-methyl-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N4-methyl-L-asparagine." [OMSSA:75, PubMed:11875433, PubMed:2356973, PubMed:3782095, RESID:AA0070, UniMod:34#N] +def: "A protein modification that effectively converts an L-asparagine residue to N4-methyl-L-asparagine." [OMSSA:75, PubMed:11875433, PubMed:2356973, PubMed:3782095, RESID:AA0070, Unimod:34#N] subset: PSI-MOD-slim synonym: "(2S)-2-amino-N4-methylbutanediamic acid" EXACT RESID-systematic [] synonym: "beta-aspartyl methylamide" EXACT RESID-alternate [] synonym: "beta-methylasparagine" RELATED RESID-misnomer [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "methyln" EXACT OMSSA-label [] synonym: "MOD_RES N4-methylasparagine" EXACT UniProt-feature [] synonym: "N(gamma)-methylasparagine" EXACT RESID-alternate [] @@ -1963,6 +2020,8 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0183" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00673 ! methylated asparagine @@ -1977,7 +2036,7 @@ synonym: "2-amino-N5-methylpentanediamic acid" EXACT RESID-alternate [] synonym: "gamma-methylglutamine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N5-methylglutamine" EXACT UniProt-feature [] synonym: "N(delta)-methylglutamine" EXACT RESID-alternate [] synonym: "N-methylglutamine" EXACT RESID-alternate [] @@ -1993,13 +2052,14 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0185" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00722 ! monomethylated L-glutamine [Term] id: MOD:00081 name: L-glutamic acid 5-methyl ester (Glu) -def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamate 5-methyl ester." [DeltaMass:167, OMSSA:17, OMSSA:70, PubMed:16888, PubMed:6300110, RESID:AA0072#GLU, UniMod:34#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamate 5-methyl ester." [DeltaMass:167, OMSSA:17, OMSSA:70, PubMed:16888, PubMed:6300110, RESID:AA0072#GLU, Unimod:34#E] comment: DeltaMass gives the formula "C 6 H 9 O 1 N 3" with mass 143 (formula incorrect, N and O reversed) [JSG]. subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-methoxy-5-oxopentanoic acid" EXACT RESID-systematic [] @@ -2013,8 +2073,8 @@ synonym: "L-glutamic acid 5-methyl ester" EXACT RESID-name [] synonym: "meestere" EXACT OMSSA-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "methyl ester" RELATED UniMod-alternate [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "methyl ester" RELATED Unimod-alternate [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "methyle" EXACT OMSSA-label [] synonym: "MOD_RES Glutamate methyl ester (Glu)" EXACT UniProt-feature [] synonym: "O-methyl Glutamyl" EXACT DeltaMass-label [] @@ -2028,6 +2088,8 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0128" is_a: MOD:01453 ! L-glutamic acid 5-methyl ester [Term] @@ -2039,7 +2101,7 @@ synonym: "1-methylhistidine" RELATED RESID-misnomer [] synonym: "3'-methyl-L-histidine" EXACT RESID-name [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Pros-methylhistidine" EXACT UniProt-feature [] synonym: "N(delta)-methylhistidine" EXACT RESID-alternate [] synonym: "N(pi)-methylhistidine" EXACT RESID-alternate [] @@ -2055,6 +2117,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0259" +is_a: MOD:02038 ! monomethylated L-histidine is_a: MOD:00724 ! N-methylated L-histidine [Term] @@ -2075,7 +2139,7 @@ synonym: "N6,N6,N6-trimethyllysin-N6-ium" EXACT RESID-alternate [] synonym: "N6,N6,N6-trimethyllysine cation" EXACT RESID-alternate [] synonym: "N6Me3+Lys" EXACT PSI-MOD-label [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0" @@ -2087,6 +2151,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0187" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00663 ! methylated lysine is_a: MOD:00711 ! trimethylated protonated-residue @@ -2094,10 +2159,10 @@ [Term] id: MOD:00084 name: N6,N6-dimethyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6,N6-dimethyl-L-lysine." [OMSSA:36, PubMed:10550045, PubMed:12964758, PubMed:14570711, PubMed:3100523, PubMed:8453381, RESID:AA0075, UniMod:36#K] +def: "A protein modification that effectively converts an L-lysine residue to N6,N6-dimethyl-L-lysine." [OMSSA:36, PubMed:10550045, PubMed:12964758, PubMed:14570711, PubMed:3100523, PubMed:8453381, RESID:AA0075, Unimod:36#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(dimethylamino)hexanoic acid" EXACT RESID-systematic [] -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "dimethylk" EXACT OMSSA-label [] synonym: "epsilon-dimethyllysine" EXACT RESID-alternate [] @@ -2116,6 +2181,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" +xref: UniProt: "PTM-0188" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00663 ! methylated lysine @@ -2123,12 +2190,12 @@ [Term] id: MOD:00085 name: N6-methyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, UniMod:34#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, Unimod:34#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-methylaminohexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-methyllysine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N6-methyllysine" EXACT UniProt-feature [] synonym: "N(zeta)-methyllysine" EXACT RESID-alternate [] synonym: "N-methyl Lysyl" EXACT DeltaMass-label [] @@ -2144,13 +2211,15 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0194" is_a: MOD:00602 ! N-methylated residue is_a: MOD:01683 ! monomethylated L-lysine [Term] id: MOD:00086 name: N6-palmitoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-palmitoyl-L-lysine." [OMSSA:93, PubMed:2498336, PubMed:7801126, PubMed:7939682, RESID:AA0077, UniMod:47#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-palmitoyl-L-lysine." [OMSSA:93, PubMed:2498336, PubMed:7801126, PubMed:7939682, RESID:AA0077, Unimod:47#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(hexadecanoylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-(hexadecanamido)hexanoic acid" EXACT RESID-alternate [] @@ -2160,9 +2229,10 @@ synonym: "N6-(1-oxohexadecyl)-L-lysine" EXACT RESID-alternate [] synonym: "N6-palmitoyl-L-lysine" EXACT RESID-name [] synonym: "N6-palmitoylated L-lysine" EXACT PSI-MOD-alternate [] +synonym: "N6-hexadecanoylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6PamLys" EXACT PSI-MOD-label [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "palmitoylationk" EXACT OMSSA-label [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1" @@ -2173,20 +2243,22 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:47" +xref: UniProt: "PTM-0197" is_a: MOD:00651 ! N-palmitoylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00087 name: N6-myristoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-myristoyl-L-lysine." [OMSSA:81, PubMed:1402651, PubMed:8346241, RESID:AA0078, UniMod:45#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-myristoyl-L-lysine." [OMSSA:81, PubMed:1402651, PubMed:8346241, RESID:AA0078, Unimod:45#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(tetradecanoylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-(tetradecanamido)hexanoic acid" EXACT RESID-alternate [] synonym: "epsilon-myristoyllysine" EXACT RESID-alternate [] synonym: "LIPID N6-myristoyl lysine" EXACT UniProt-feature [] synonym: "Myristoyl" RELATED PSI-MS-label [] -synonym: "Myristoylation" RELATED UniMod-description [] +synonym: "Myristoylation" RELATED Unimod-description [] synonym: "myristoylationk" EXACT OMSSA-label [] synonym: "N(zeta)-myristoyllysine" EXACT RESID-alternate [] synonym: "N6-(1-oxotetradecyl)-L-lysine" EXACT RESID-alternate [] @@ -2203,23 +2275,26 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:45" +xref: UniProt: "PTM-0196" is_a: MOD:00650 ! N-myristoylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00088 name: O-palmitoyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-palmitoyl-L-threonine." [OMSSA:95, PubMed:6642431, PubMed:8413602, RESID:AA0079, UniMod:47#T] +def: "A protein modification that effectively converts an L-threonine residue to O-palmitoyl-L-threonine." [OMSSA:95, PubMed:6642431, PubMed:8413602, RESID:AA0079, Unimod:47#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(hexadecanoyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "L-threonine hexadecanoate ester" EXACT RESID-alternate [] synonym: "LIPID O-palmitoyl threonine" EXACT UniProt-feature [] synonym: "O-palmitoyl-L-threonine" EXACT RESID-name [] synonym: "O-palmitoylated L-threonine" EXACT PSI-MOD-alternate [] +synonym: "O-hexadecanoylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-palmitoyl-threonine" EXACT RESID-alternate [] synonym: "OPamThr" EXACT PSI-MOD-label [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "palmitoylationt" EXACT OMSSA-label [] synonym: "threonine palmitate ester" EXACT RESID-alternate [] xref: DiffAvg: "238.41" @@ -2231,13 +2306,15 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:47" +xref: UniProt: "PTM-0242" is_a: MOD:00652 ! O-palmitoylated residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine [Term] id: MOD:00089 name: O-palmitoyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-palmitoyl-L-serine." [OMSSA:94, PubMed:3467339, RESID:AA0080, UniMod:47#S] +def: "A protein modification that effectively converts an L-serine residue to O-palmitoyl-L-serine." [OMSSA:94, PubMed:3467339, RESID:AA0080, Unimod:47#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(hexadecanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "ACT_SITE O-palmitoyl serine intermediate" EXACT UniProt-feature [] @@ -2245,10 +2322,11 @@ synonym: "LIPID O-palmitoyl serine" EXACT UniProt-feature [] synonym: "O-palmitoyl-L-serine" EXACT RESID-name [] synonym: "O-palmitoylated L-serine" EXACT PSI-MOD-alternate [] +synonym: "O-hexadecanoylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-palmitoyl-serine" EXACT RESID-alternate [] synonym: "OPamSer" EXACT PSI-MOD-label [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "palmitoylations" EXACT OMSSA-label [] synonym: "serine palmitate ester" EXACT RESID-alternate [] xref: DiffAvg: "238.41" @@ -2260,8 +2338,10 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:47" +xref: UniProt: "PTM-0241" is_a: MOD:00652 ! O-palmitoylated residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine [Term] id: MOD:00090 @@ -2283,13 +2363,14 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0057" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00091 name: L-arginine amide -def: "A protein modification that effectively converts an L-arginine residue to L-arginine amide." [PubMed:2229025, PubMed:2753890, PubMed:743209, RESID:AA0082] +def: "A protein modification that effectively converts an L-arginine residue to L-arginine amide." [PubMed:2229025, PubMed:2753890, PubMed:743209, RESID:AA0082, ChEBI:145897] subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-[(diaminomethylidene)amino]pentanamide" EXACT RESID-systematic [] synonym: "2-amino-5-carbamimidamidopentanamide" EXACT RESID-alternate [] @@ -2308,13 +2389,14 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0060" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00092 name: L-asparagine amide -def: "A protein modification that effectively converts an L-asparagine residue to L-asparagine amide." [PubMed:2753132, PubMed:279902, PubMed:3415690, RESID:AA0083] +def: "A protein modification that effectively converts an L-asparagine residue to L-asparagine amide." [PubMed:2753132, PubMed:279902, PubMed:3415690, RESID:AA0083, ChEBI:145898] subset: PSI-MOD-slim synonym: "(2S)-2-aminobutanediamide" EXACT RESID-systematic [] synonym: "amidated L-asparagine" EXACT PSI-MOD-alternate [] @@ -2331,6 +2413,7 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0062" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00903 ! modified L-asparagine residue @@ -2357,6 +2440,7 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0063" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00904 ! modified L-aspartic acid residue @@ -2381,6 +2465,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0102" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00905 ! modified L-cysteine residue @@ -2404,6 +2489,7 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0130" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00907 ! modified L-glutamine residue @@ -2428,6 +2514,7 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0129" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00906 ! modified L-glutamic acid residue @@ -2453,6 +2540,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0132" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00908 ! modified glycine residue @@ -2476,6 +2564,7 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0148" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00909 ! modified L-histidine residue @@ -2499,6 +2588,7 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0161" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00910 ! modified L-isoleucine residue @@ -2525,6 +2615,7 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0166" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00911 ! modified L-leucine residue @@ -2548,6 +2639,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0168" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00912 ! modified L-lysine residue @@ -2572,6 +2664,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0164" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00913 ! modified L-methionine residue @@ -2595,6 +2688,7 @@ xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0248" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00914 ! modified L-phenylalanine residue @@ -2618,6 +2712,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0257" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00915 ! modified L-proline residue @@ -2641,6 +2736,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0275" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00916 ! modified L-serine residue @@ -2664,6 +2760,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0293" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00917 ! modified L-threonine residue @@ -2687,6 +2784,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0296" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00918 ! modified L-tryptophan residue @@ -2710,6 +2808,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0302" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00919 ! modified L-tyrosine residue @@ -2732,26 +2831,27 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0303" is_a: MOD:00883 ! C1-amidated residue is_a: MOD:00920 ! modified L-valine residue [Term] id: MOD:00110 name: L-cysteine methyl disulfide -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide." [OMSSA:179, PubMed:10555576, PubMed:163643, PubMed:2056535, PubMed:6381494, RESID:AA0101, UniMod:39#C] -comment: Produced artifactually by reaction of cysteine residues with methyl methanethiosulfonate (MMTS) [JSG]. +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide." [OMSSA:179, PubMed:10555576, PubMed:163643, PubMed:2056535, PubMed:6381494, RESID:AA0101, Unimod:39#C] +comment: Produced artifactually by reaction of cysteine residues with methyl methanethiosulfonate (MMTS) [JSG], but also naturally in bacteria [PMT]. synonym: "(2R)-2-amino-3-(methyldisulfanediyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(methyldisulfanediyl)propanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-(methyldithio)propanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-methyldisulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "2-azanyl-3-(methyldisulfanediyl)-propanoic acid" EXACT RESID-alternate [] -synonym: "Beta-methylthiolation" RELATED UniMod-description [] +synonym: "Beta-methylthiolation" RELATED Unimod-description [] synonym: "L-3-(methyldithio)alanine" EXACT RESID-alternate [] synonym: "L-cysteine methyl disulfide" EXACT RESID-name [] synonym: "methyl methanethiolsulfonate derivatized cysteine" EXACT PSI-MOD-alternate [] synonym: "methyl methanethiosulfonate derivatized cysteine" EXACT PSI-MOD-alternate [] synonym: "Methylthio" RELATED PSI-MS-label [] -synonym: "Methylthio" RELATED UniMod-interim [] +synonym: "Methylthio" RELATED Unimod-interim [] synonym: "mmts" EXACT OMSSA-label [] synonym: "MOD_RES Cysteine methyl disulfide" EXACT UniProt-feature [] synonym: "S-methylthio-L-cysteine" EXACT RESID-alternate [] @@ -2763,8 +2863,10 @@ xref: MassAvg: "149.23" xref: MassMono: "148.996906" xref: Origin: "C" -xref: Source: "hypothetical" +xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:39" +xref: UniProt: "PTM-0104" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01153 ! methylthiolated residue @@ -2773,13 +2875,13 @@ [Term] id: MOD:00111 name: S-farnesyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-farnesyl-L-cysteine." [DeltaMass:293, OMSSA:42, PubMed:1409665, PubMed:15609361, PubMed:1872463, PubMed:2684976, RESID:AA0102, UniMod:44#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-farnesyl-L-cysteine." [DeltaMass:293, OMSSA:42, PubMed:1409665, PubMed:15609361, PubMed:1872463, PubMed:2684976, RESID:AA0102, Unimod:44#C] comment: From DeltaMass: (name misspelled "S-farnesyl cystenyl") subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-([(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Farnesyl" RELATED PSI-MS-label [] -synonym: "Farnesylation" RELATED UniMod-description [] +synonym: "Farnesylation" RELATED Unimod-description [] synonym: "farnesylationc" EXACT OMSSA-label [] synonym: "LIPID S-farnesyl cysteine" EXACT UniProt-feature [] synonym: "S-farnesyl Cystenyl" EXACT DeltaMass-label [] @@ -2794,17 +2896,19 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:44" +xref: UniProt: "PTM-0277" is_a: MOD:00437 ! farnesylated residue is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00112 name: S-12-hydroxyfarnesyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-12-hydroxyfarnesyl-L-cysteine." [PubMed:17790543, RESID:AA0103, UniMod:376] +def: "A protein modification that effectively converts an L-cysteine residue to S-12-hydroxyfarnesyl-L-cysteine." [PubMed:17790543, RESID:AA0103, Unimod:376] synonym: "(2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Hydroxyfarnesyl" RELATED PSI-MS-label [] -synonym: "hydroxyfarnesyl" RELATED UniMod-description [] +synonym: "hydroxyfarnesyl" RELATED Unimod-description [] synonym: "LIPID S-12-hydroxyfarnesyl cysteine" EXACT UniProt-feature [] synonym: "S-12-hydroxyfarnesyl-L-cysteine" EXACT RESID-name [] synonym: "S12HyFarnCys" EXACT PSI-MOD-label [] @@ -2817,17 +2921,19 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:376" +xref: UniProt: "PTM-0269" is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00113 name: S-geranylgeranyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-geranylgeranyl-L-cysteine." [DeltaMass:0, OMSSA:49, PubMed:1483450, PubMed:15609361, RESID:AA0104, UniMod:48#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-geranylgeranyl-L-cysteine." [DeltaMass:0, OMSSA:49, PubMed:1483450, PubMed:15609361, RESID:AA0104, Unimod:48#C] comment: DeltaMass calculates the mass with two double bonds rather than four subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid" EXACT RESID-alternate [] -synonym: "Geranyl-geranyl" RELATED UniMod-description [] +synonym: "Geranyl-geranyl" RELATED Unimod-description [] synonym: "GeranylGeranyl" RELATED PSI-MS-label [] synonym: "geranylgeranylc" EXACT OMSSA-label [] synonym: "LIPID S-geranylgeranyl cysteine" EXACT UniProt-feature [] @@ -2843,13 +2949,15 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:48" +xref: UniProt: "PTM-0278" is_a: MOD:00441 ! geranylgeranylated residue is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00114 name: L-cysteine methyl ester -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl ester." [PubMed:11875433, PubMed:1872463, RESID:AA0105, UniMod:34#C-term] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl ester." [PubMed:11875433, PubMed:1872463, RESID:AA0105, Unimod:34#C-term] comment: Secondary to RESID:AA0102; secondary to RESID:AA0103; secondary to RESID:AA0104. subset: PSI-MOD-slim synonym: "2-amino-3-mercaptopropanoic methyl ester" EXACT RESID-alternate [] @@ -2860,7 +2968,7 @@ synonym: "methyl (2R)-2-amino-3-sulfanylpropanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-cysteine" EXACT PSI-MOD-alternate [] synonym: "methyl L-cysteinate" EXACT RESID-alternate [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Cysteine methyl ester" EXACT UniProt-feature [] synonym: "OMeCys" EXACT PSI-MOD-label [] xref: DiffAvg: "14.03" @@ -2872,13 +2980,15 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0105" is_a: MOD:01682 ! monomethylated L-cysteine is_a: MOD:01689 ! alpha-carboxyl methylated residue [Term] id: MOD:00115 name: S-palmitoyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoyl-L-cysteine." [DeltaMass:303, PubMed:1872406, PubMed:3166978, PubMed:8180229, PubMed:8824274, RESID:AA0106, UniMod:47#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoyl-L-cysteine." [DeltaMass:303, PubMed:1872406, PubMed:3166978, PubMed:8180229, PubMed:8824274, RESID:AA0106, Unimod:47#C] comment: From DeltaMass: (name misspelled "S-palmityl Cystenyl" and formula incorrect, N and O reversed) Formula: C19H35O1N2S1 Monoisotopic Mass Change: 341.239 Average Mass Change: 341.556 subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid" EXACT RESID-systematic [] @@ -2888,9 +2998,10 @@ synonym: "cysteine palmitate thioester" EXACT RESID-alternate [] synonym: "LIPID S-palmitoyl cysteine" EXACT UniProt-feature [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "S-palmitoyl-L-cysteine" EXACT RESID-name [] synonym: "S-palmitoylated L-cysteine" EXACT PSI-MOD-alternate [] +synonym: "S-hexadecanoylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S-palmityl Cystenyl" EXACT DeltaMass-label [] synonym: "SPamCys" EXACT PSI-MOD-label [] xref: DiffAvg: "238.41" @@ -2902,24 +3013,27 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:47" +xref: UniProt: "PTM-0281" is_a: MOD:00653 ! S-palmitoylated residue is_a: MOD:01684 ! palmitoylated-L-cysteine [Term] id: MOD:00116 name: S-diacylglycerol-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-diacylglycerol-L-cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107, UniMod:377#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-diacylglycerol-L-cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107, Unimod:377#C] comment: Incidental to RESID:AA0060. subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-[(2S)-2-((9Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-[(S)-2-((Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]thiopropanoic acid" EXACT RESID-alternate [] synonym: "Diacylglycerol" RELATED PSI-MS-label [] -synonym: "diacylglycerol" RELATED UniMod-description [] +synonym: "diacylglycerol" RELATED Unimod-description [] synonym: "LIPID S-diacylglycerol cysteine" EXACT UniProt-feature [] synonym: "S-(1-2'-oleoyl-3'-palmitoyl-glycerol)cysteine" EXACT RESID-alternate [] synonym: "S-(2',3'-diacylglycerol)-L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S-diacylglycerol-L-cysteine" EXACT RESID-name [] synonym: "SAcyl2GlyceroCys" EXACT PSI-MOD-label [] +xref: UniProt: "PTM-0274" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" @@ -2949,8 +3063,9 @@ xref: Origin: "C, Q" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0156" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00907 ! modified L-glutamine residue +is_a: MOD:02046 ! crosslinked L-glutamine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] @@ -2974,8 +3089,9 @@ xref: Origin: "C, H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0005" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02048 ! crosslinked L-histidine residue [Term] id: MOD:00119 @@ -3000,7 +3116,7 @@ xref: Origin: "C, S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01839 ! L-lanthionine @@ -3032,7 +3148,8 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0164" +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01841 ! lanthionine @@ -3061,6 +3178,7 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0067" is_a: MOD:01981 ! 3-methyllanthionine [Term] @@ -3086,18 +3204,19 @@ xref: Origin: "C, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0019" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00123 name: N6-carboxy-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-carboxy-L-lysine." [PubMed:11369851, PubMed:4436319, PubMed:637859, PubMed:7754395, RESID:AA0114, UniMod:299#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-carboxy-L-lysine." [PubMed:11369851, PubMed:4436319, PubMed:637859, PubMed:7754395, RESID:AA0114, Unimod:299#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(carboxyamino)hexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-carbamic hexanoic acid" EXACT RESID-alternate [] -synonym: "Carboxy" RELATED UniMod-interim [] -synonym: "Carboxylation" RELATED UniMod-description [] +synonym: "Carboxy" RELATED Unimod-interim [] +synonym: "Carboxylation" RELATED Unimod-description [] synonym: "lysine NZ-carboxylic acid" EXACT RESID-alternate [] synonym: "MOD_RES N6-carboxylysine" EXACT UniProt-feature [] synonym: "N6-carbamyllysine" RELATED RESID-misnomer [] @@ -3113,17 +3232,19 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:299" +xref: UniProt: "PTM-0191" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00124 name: N6-1-carboxyethyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-1-carboxyethyl-L-lysine." [PubMed:3123486, PubMed:8253186, PubMed:8421682, RESID:AA0115, UniMod:378#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-1-carboxyethyl-L-lysine." [PubMed:3123486, PubMed:8253186, PubMed:8421682, RESID:AA0115, Unimod:378#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-([(1S)-1-carboxyethyl]amino)hexanoic acid" EXACT RESID-systematic [] synonym: "Carboxyethyl" RELATED PSI-MS-label [] -synonym: "carboxyethyl" RELATED UniMod-description [] +synonym: "carboxyethyl" RELATED Unimod-description [] synonym: "MOD_RES N6-1-carboxyethyl lysine" EXACT UniProt-feature [] synonym: "N6-(1-carboxyethyl)-L-lysine" EXACT RESID-name [] synonym: "N6-(1-carboxyethyl)lysine" EXACT RESID-alternate [] @@ -3138,12 +3259,14 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:378" +xref: UniProt: "PTM-0189" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00125 name: hypusine -def: "A protein modification that effectively converts an L-lysine residue to hypusine, N6-(4-amino-2-hydroxybutyl)-L-lysine." [DeltaMass:0, PubMed:6806267, PubMed:8108861, RESID:AA0116, UniMod:379#K] +def: "A protein modification that effectively converts an L-lysine residue to hypusine, N6-(4-amino-2-hydroxybutyl)-L-lysine." [DeltaMass:0, PubMed:6806267, PubMed:8108861, RESID:AA0116, Unimod:379#K] comment: This modification occurs uniquely in translation initiation factor eIF-5A [JSG]. subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-([(2R)-4-amino-2-hydroxybutyl]amino)hexanoic acid" EXACT RESID-systematic [] @@ -3152,7 +3275,7 @@ synonym: "2-azanyl-6-[(4-azanyl-2-hydroxybutyl)azanyl]hexanoic acid" EXACT RESID-alternate [] synonym: "Hypu" EXACT PSI-MOD-label [] synonym: "Hypusine" RELATED PSI-MS-label [] -synonym: "hypusine" RELATED UniMod-description [] +synonym: "hypusine" RELATED Unimod-description [] synonym: "L-hypusine" EXACT RESID-name [] synonym: "MOD_RES Hypusine" EXACT UniProt-feature [] synonym: "N-(4-NH2-2-OH-butyl)- (of Lysine)" EXACT DeltaMass-label [] @@ -3166,6 +3289,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:379" +xref: UniProt: "PTM-0150" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01884 ! 4-aminobutylated residue relationship: derives_from MOD:01880 ! L-deoxyhypusine @@ -3173,7 +3298,7 @@ [Term] id: MOD:00126 name: N6-biotinyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-biotinyl-L-lysine." [DeltaMass:305, PubMed:16109483, PubMed:3178228, PubMed:7948875, PubMed:8747466, RESID:AA0117, UniMod:3#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-biotinyl-L-lysine." [DeltaMass:305, PubMed:16109483, PubMed:3178228, PubMed:7948875, PubMed:8747466, RESID:AA0117, Unimod:3#K] comment: From DeltaMass: Average Mass: 354 Formula:C 16 H 26 O 4 N 3 S 1 (formula incorrect, N and O reversed) Monoisotopic Mass Change:354.172 Average Mass Change:354.471 References:PE Sciex. subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoylamino)hexanoic acid" EXACT RESID-systematic [] @@ -3181,7 +3306,7 @@ synonym: "biocytin" EXACT RESID-alternate [] synonym: "Biotin" RELATED PSI-MS-label [] synonym: "biotinyl lysyl" EXACT DeltaMass-label [] -synonym: "Biotinylation" RELATED UniMod-description [] +synonym: "Biotinylation" RELATED Unimod-description [] synonym: "epsilon-N-biotinyllysine" EXACT RESID-alternate [] synonym: "MOD_RES N6-biotinyllysine" EXACT UniProt-feature [] synonym: "N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine" EXACT RESID-alternate [] @@ -3197,20 +3322,22 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:3" +xref: UniProt: "PTM-0382" is_a: MOD:01875 ! N6-acylated L-lysine is_a: MOD:01885 ! biotinylated residue [Term] id: MOD:00127 name: N6-lipoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-lipoyl-L-lysine." [DeltaMass:0, OMSSA:67, PubMed:3421911, PubMed:3522581, PubMed:7719855, RESID:AA0118, UniMod:42#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-lipoyl-L-lysine." [DeltaMass:0, OMSSA:67, PubMed:3421911, PubMed:3522581, PubMed:7719855, RESID:AA0118, Unimod:42#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(5-[(3R)-1,2-dithiolan-3-yl]pentanamido)hexanoic acid" EXACT RESID-alternate [] synonym: "(2S)-2-amino-6-[(5-[(3R)-1,2-dithiolan-3-yl]pentanoyl)amino]hexanoic acid" EXACT RESID-systematic [] synonym: "(2S,6'R)-2-amino-6-(6,8-dithiooctanamido)hexanoic acid" EXACT RESID-alternate [] synonym: "2-amino-6-(5-[1,2-dithiolan-3-yl]-1-oxopentyl)aminohexanoic acid" EXACT RESID-alternate [] synonym: "Lipoyl" RELATED PSI-MS-label [] -synonym: "Lipoyl" RELATED UniMod-description [] +synonym: "Lipoyl" RELATED Unimod-description [] synonym: "lipoylk" EXACT OMSSA-label [] synonym: "MOD_RES N6-lipoyllysine" EXACT UniProt-feature [] synonym: "N-Lipoyl- (on Lysine)" EXACT DeltaMass-label [] @@ -3227,19 +3354,21 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:42" +xref: UniProt: "PTM-0383" is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00128 name: N6-pyridoxal phosphate-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-pyridoxal phosphate-L-lysine." [DeltaMass:0, PubMed:1544460, RESID:AA0119, UniMod:46#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-pyridoxal phosphate-L-lysine." [DeltaMass:0, PubMed:1544460, RESID:AA0119, Unimod:46#K] comment: From DeltaMass: Average Mass: 231 subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-[([3-hydroxy-2-methyl-5-phosphonooxymethylpyridin-4-yl]methylidene)amino]hexanoic acid" EXACT RESID-systematic [] synonym: "MOD_RES N6-(pyridoxal phosphate)lysine" EXACT UniProt-feature [] synonym: "N6-pyridoxal phosphate-L-lysine" EXACT RESID-name [] synonym: "N6PydoxLys" EXACT PSI-MOD-label [] -synonym: "Pyridoxal phosphate" RELATED UniMod-description [] +synonym: "Pyridoxal phosphate" RELATED Unimod-description [] synonym: "Pyridoxal phosphate (Schiff Base formed to lysine)" EXACT DeltaMass-label [] synonym: "PyridoxalPhosphate" RELATED PSI-MS-label [] xref: DiffAvg: "229.13" @@ -3251,12 +3380,14 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:46" +xref: UniProt: "PTM-0387" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00129 name: N6-retinylidene-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-retinylidene-L-lysine, the adduct of retinal." [PubMed:6794028, PubMed:6870827, RESID:AA0120, UniMod:380#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-retinylidene-L-lysine, the adduct of retinal." [PubMed:6794028, PubMed:6870827, RESID:AA0120, Unimod:380#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT RESID-systematic [] synonym: "MOD_RES N6-(retinylidene)lysine" EXACT UniProt-feature [] @@ -3264,7 +3395,7 @@ synonym: "N6-retinyl-lysine" EXACT RESID-alternate [] synonym: "N6-retinylidene-L-lysine" EXACT RESID-name [] synonym: "N6RetalLys" EXACT PSI-MOD-label [] -synonym: "retinal" RELATED UniMod-description [] +synonym: "retinal" RELATED Unimod-description [] synonym: "Retinylidene" RELATED PSI-MS-label [] xref: DiffAvg: "266.43" xref: DiffFormula: "C 20 H 26 N 0 O 0" @@ -3275,12 +3406,14 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:380" +xref: UniProt: "PTM-0388" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00130 name: L-allysine -def: "A protein modification that effectively converts an L-lysine residue to L-allysine." [ChEBI:17917, DeltaMass:0, PubMed:11120890, PubMed:11332453, PubMed:358196, PubMed:5337886, PubMed:5529814, RESID:AA0121, UniMod:352#K] +def: "A protein modification that effectively converts an L-lysine residue to L-allysine." [ChEBI:17917, DeltaMass:0, PubMed:11120890, PubMed:11332453, PubMed:358196, PubMed:5337886, PubMed:5529814, RESID:AA0121, Unimod:352#K] comment: From DeltaMass: Average Mass: -1 subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-oxohexanoic acid" EXACT RESID-systematic [] @@ -3295,7 +3428,7 @@ synonym: "L-allysine" EXACT RESID-name [] synonym: "Lys->Allysine" RELATED PSI-MS-label [] synonym: "Lysal" EXACT PSI-MOD-label [] -synonym: "Lysine oxidation to aminoadipic semialdehyde" RELATED UniMod-description [] +synonym: "Lysine oxidation to aminoadipic semialdehyde" RELATED Unimod-description [] synonym: "MOD_RES Allysine" EXACT UniProt-feature [] synonym: "Oxidation of lysine (to aminoadipic semialdehyde)" EXACT DeltaMass-label [] xref: DiffAvg: "-1.03" @@ -3307,17 +3440,19 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:352" +xref: UniProt: "PTM-0059" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00131 name: L-2-aminoadipic acid -def: "A protein modification that effectively converts an L-lysine residue to L-2-aminoadipic acid." [DeltaMass:353, PubMed:336041, PubMed:358196, PubMed:7419498, RESID:AA0122, UniMod:381#K] +def: "A protein modification that effectively converts an L-lysine residue to L-2-aminoadipic acid." [DeltaMass:353, PubMed:336041, PubMed:358196, PubMed:7419498, RESID:AA0122, Unimod:381#K] comment: From DeltaMass: References:Amici A, Levine, RL, Tsai, L, and Stadtman, ER: Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions. Journal of Biological Chemistry 264: 3341-3346 1989.Requena JR, Chao CC, Levine RL, and Stadtman ER: Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins. Proceedings of the National Academy of Sciences USA 98: 69-74 2001. Notes:Expected reaction following oxidation of lysine to aminoadipic semialdehyde. Not proven experimentally but deduced by reference to the similar known reaction of oxidation of Arg to Glu via the semialdehyde. [This has been observed as a natural modification, see RESID:AA0122. JSG] subset: PSI-MOD-slim synonym: "(2S)-2-aminohexanedioic acid" EXACT RESID-systematic [] synonym: "2-amino-1,4-butanedicarboxylic acid" EXACT RESID-alternate [] -synonym: "alpha-amino adipic acid" RELATED UniMod-description [] +synonym: "alpha-amino adipic acid" RELATED Unimod-description [] synonym: "L-2-aminoadipic acid" EXACT RESID-name [] synonym: "L-alpha-aminoadipic acid" EXACT RESID-alternate [] synonym: "Lys->AminoadipicAcid" RELATED PSI-MS-label [] @@ -3332,6 +3467,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:381" is_a: MOD:00912 ! modified L-lysine residue [Term] @@ -3358,7 +3494,9 @@ xref: Origin: "K, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0172" +is_a: MOD:02055 ! crosslinked L-serine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01853 ! L-lysinoalanine @@ -3385,7 +3523,8 @@ xref: Origin: "K, Q" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00907 ! modified L-glutamine residue +xref: UniProt: "PTM-0158" +is_a: MOD:02046 ! crosslinked L-glutamine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia is_a: MOD:01630 ! N6-(L-isoglutamyl)-L-lysine @@ -3399,6 +3538,8 @@ synonym: "N6-(glycyl)-L-lysine" EXACT RESID-name [] synonym: "N6-glycyllysine" EXACT RESID-alternate [] synonym: "XLNK-N6Lys-1Gly" EXACT PSI-MOD-label [] +synonym: "CROSSLNK Glycyl lysine isopeptide (Gly-Lys) (interchain with K-...)" EXACT UniProt-feature [] +synonym: "CROSSLNK Glycyl lysine isopeptide (Lys-Gly) (interchain with G-...)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" @@ -3408,8 +3549,10 @@ xref: Origin: "G, K" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0134" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01875 ! N6-acylated L-lysine @@ -3436,14 +3579,15 @@ xref: Origin: "G, N" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00903 ! modified L-asparagine residue +xref: UniProt: "PTM-0489" +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia is_a: MOD:01928 ! N-(L-isoaspartyl)-glycine [Term] id: MOD:00136 name: pyruvic acid (Cys) -def: "A protein modification that effectively converts an L-cysteine residue to pyruvic acid." [PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127#CYS, UniMod:382] +def: "A protein modification that effectively converts an L-cysteine residue to pyruvic acid." [PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127#CYS, Unimod:382] subset: PSI-MOD-slim synonym: "2-oxopropanoic acid" EXACT RESID-systematic [] synonym: "MOD_RES Pyruvic acid (Cys)" EXACT UniProt-feature [] @@ -3458,17 +3602,19 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:382" +xref: UniProt: "PTM-0265" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01154 ! pyruvic acid [Term] id: MOD:00137 name: L-3-phenyllactic acid -def: "A protein modification that effectively converts an L-phenylalanine residue into L-3-phenyllactic acid." [PubMed:1973541, RESID:AA0128, UniMod:7#F] +def: "A protein modification that effectively converts an L-phenylalanine residue into L-3-phenyllactic acid." [PubMed:1973541, RESID:AA0128, Unimod:7#F] comment: This modification is not the result of deamidation, instead the alpha amino group is replaced with an hydroxyl group. synonym: "(2S)-2-hydroxy-3-phenylpropanoic acid" EXACT RESID-systematic [] -synonym: "Deamidated" RELATED UniMod-interim [] -synonym: "Deamidation" RELATED UniMod-description [] +synonym: "Deamidated" RELATED Unimod-interim [] +synonym: "Deamidation" RELATED Unimod-description [] synonym: "L-3-phenyllactic acid" EXACT RESID-name [] synonym: "MOD_RES 3-phenyllactic acid" EXACT UniProt-feature [] xref: DiffAvg: "0.98" @@ -3479,18 +3625,20 @@ xref: MassMono: "149.060255" xref: Origin: "F" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:7" +xref: UniProt: "PTM-0035" is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00138 name: 2-oxobutanoic acid -def: "A protein modification that effectively converts an L-threonine residue into 2-oxobutanoic acid." [PubMed:15023056, PubMed:1680314, PubMed:2253617, PubMed:2764678, RESID:AA0129, UniMod:385#T] +def: "A protein modification that effectively converts an L-threonine residue into 2-oxobutanoic acid." [PubMed:15023056, PubMed:1680314, PubMed:2253617, PubMed:2764678, RESID:AA0129, Unimod:385#T, ChEBI:149508] synonym: "2-ketobutyric acid" EXACT RESID-alternate [] synonym: "2-oxobutanoic acid" EXACT RESID-name [] synonym: "2-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-oxobutyric acid" EXACT RESID-alternate [] -synonym: "Ammonia-loss" RELATED UniMod-interim [] -synonym: "Loss of ammonia" RELATED UniMod-description [] +synonym: "Ammonia-loss" RELATED Unimod-interim [] +synonym: "Loss of ammonia" RELATED Unimod-description [] synonym: "MOD_RES 2-oxobutanoic acid" EXACT UniProt-feature [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" @@ -3500,18 +3648,20 @@ xref: MassMono: "85.028954" xref: Origin: "T" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:385" +xref: UniProt: "PTM-0017" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01160 ! deaminated residue [Term] id: MOD:00139 name: N2-succinyl-L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to N2-succinyl-L-tryptophan." [PubMed:11857757, PubMed:12175151, PubMed:8471040, RESID:AA0130, UniMod:64#N-term] +def: "A protein modification that effectively converts an L-tryptophan residue to N2-succinyl-L-tryptophan." [PubMed:11857757, PubMed:12175151, PubMed:8471040, RESID:AA0130, Unimod:64#N-term] synonym: "(2S)-2-(3-carboxypropanoyl)amino-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "(2S)-2-amino-(6,7-dihydro-6,7-dioxo-1H-indole)-3-propanoic acid" EXACT RESID-alternate [] synonym: "MOD_RES N2-succinyltryptophan" EXACT UniProt-feature [] synonym: "N2-succinyl-L-tryptophan" EXACT RESID-name [] -synonym: "Succinic anhydride labeling reagent light form (N-term)" RELATED UniMod-description [] +synonym: "Succinic anhydride labeling reagent light form (N-term)" RELATED Unimod-description [] synonym: "Succinyl" RELATED PSI-MS-label [] xref: DiffAvg: "100.07" xref: DiffFormula: "C 4 H 4 N 0 O 3" @@ -3520,14 +3670,17 @@ xref: MassAvg: "287.29" xref: MassMono: "287.103182" xref: Origin: "W" +xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00457 ! alpha-amino succinylated residue +xref: Unimod: "Unimod:64" +xref: UniProt: "PTM-0181" +is_a: MOD:02081 ! alpha-amino succinylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00140 name: S-phycocyanobilin-L-cysteine -def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycocyanobilin." [ChEBI:15617, DeltaMass:0, PubMed:16644722, PubMed:3208761, PubMed:3838747, PubMed:7918400, RESID:AA0131, UniMod:387#C] +def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycocyanobilin." [ChEBI:15617, DeltaMass:0, PubMed:16644722, PubMed:3208761, PubMed:3838747, PubMed:7918400, RESID:AA0131, Unimod:387#C] comment: From DeltaMass: Average Mass: 587. synonym: "(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-ethyl-1,2,3,19,21,22,24-heptahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] @@ -3535,7 +3688,7 @@ synonym: "PCB" EXACT RESID-alternate [] synonym: "phycobilin cysteine" EXACT RESID-alternate [] synonym: "Phycocyanobilin" RELATED PSI-MS-label [] -synonym: "phycocyanobilin" RELATED UniMod-description [] +synonym: "phycocyanobilin" RELATED Unimod-description [] synonym: "phycocyanobilin cysteine adduct" EXACT RESID-alternate [] synonym: "S-Phycocyanobilin (on Cysteine)" EXACT DeltaMass-label [] synonym: "S-phycocyanobilin-L-cysteine" EXACT RESID-name [] @@ -3548,19 +3701,20 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:387" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00141 name: S-phycoerythrobilin-L-cysteine -def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoerythrobilin." [ChEBI:15618, PubMed:14588022, PubMed:3208761, PubMed:3838747, PubMed:8876649, RESID:AA0132, UniMod:388#C] +def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoerythrobilin." [ChEBI:15618, PubMed:14588022, PubMed:3208761, PubMed:3838747, PubMed:8876649, RESID:AA0132, Unimod:388#C] synonym: "(2S,3R,16R)-18-ethenyl-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "BINDING Phycoerythrobilin chromophore (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "PEB" EXACT RESID-alternate [] synonym: "Phycoerythrobilin" RELATED PSI-MS-label [] -synonym: "phycoerythrobilin" RELATED UniMod-description [] +synonym: "phycoerythrobilin" RELATED Unimod-description [] synonym: "phycoerythrobilin cysteine adduct" EXACT RESID-alternate [] synonym: "S-phycoerythrobilin-L-cysteine" EXACT RESID-name [] xref: DiffAvg: "588.70" @@ -3572,19 +3726,20 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:388" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00142 name: S-phytochromobilin-L-cysteine -def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phytochromobilin." [ChEBI:15619, PubMed:1634523, PubMed:16593380, PubMed:3208761, PubMed:7918400, RESID:AA0133, UniMod:389#C] +def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phytochromobilin." [ChEBI:15619, PubMed:1634523, PubMed:16593380, PubMed:3208761, PubMed:7918400, RESID:AA0133, Unimod:389#C] synonym: "(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-1,2,3,19,22,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "BINDING Phytochromobilin chromophore (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "phytochrome chromophore" EXACT RESID-alternate [] synonym: "Phytochromobilin" RELATED PSI-MS-label [] -synonym: "phytochromobilin" RELATED UniMod-description [] +synonym: "phytochromobilin" RELATED Unimod-description [] synonym: "phytochromobilin cysteine adduct" EXACT RESID-alternate [] synonym: "S-phytochromobilin-L-cysteine" EXACT RESID-name [] xref: DiffAvg: "584.67" @@ -3596,6 +3751,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:389" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue @@ -3621,12 +3777,12 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00144 name: heme-L-cysteine -def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [ChEBI:17627, DeltaMass:0, PubMed:170910, PubMed:192772, PubMed:2536325, PubMed:9535866, RESID:AA0135, UniMod:390#C] +def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [ChEBI:17627, DeltaMass:0, PubMed:170910, PubMed:192772, PubMed:2536325, PubMed:9535866, RESID:AA0135, Unimod:390#C] comment: From DeltaMass: Average Mass: 617. subset: PSI-MOD-slim synonym: "(12-ethenyl-7-[(1S)-1-([(2R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis[2-carboxyethyl]-N21,N22,N23,N24)-ferrate" EXACT RESID-systematic [] @@ -3634,7 +3790,7 @@ synonym: "BINDING Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "cysteinyl heme" EXACT RESID-alternate [] synonym: "Heme" RELATED PSI-MS-label [] -synonym: "heme" RELATED UniMod-description [] +synonym: "heme" RELATED Unimod-description [] synonym: "heme-L-cysteine" EXACT RESID-name [] synonym: "HemeCys1" EXACT PSI-MOD-label [] synonym: "S-Heme (on Cysteine)" EXACT DeltaMass-label [] @@ -3647,8 +3803,9 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:390" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00145 @@ -3669,7 +3826,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00738 ! iron containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00146 @@ -3691,7 +3848,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00147 @@ -3712,7 +3869,7 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00148 @@ -3738,7 +3895,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00149 @@ -3761,7 +3918,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00150 @@ -3782,13 +3939,13 @@ xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00743 ! molybdenum containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00151 name: L-cysteinyl molybdopterin -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl molybdopterin." [PubMed:14527393, PubMed:7878465, PubMed:9428520, RESID:AA0142, UniMod:391#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl molybdopterin." [PubMed:14527393, PubMed:7878465, PubMed:9428520, RESID:AA0142, Unimod:391#C] subset: PSI-MOD-slim synonym: "(4R,5aR,11aR)-8-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-4,5a,6,9,10,11,11a-heptahydro-4-(phosphoric acid)methyl-2,2,10-trioxo-pteridino[6,7-5,6]pyrano[3,4-4,3][1,2,5]molybdadithiolene" EXACT RESID-systematic [] synonym: "cysteinyl Mo-molybdopterin" EXACT RESID-alternate [] @@ -3797,7 +3954,7 @@ synonym: "METAL Molybdenum-pterin" EXACT UniProt-feature [] synonym: "molybdoenzyme molybdenum cofactor" EXACT RESID-alternate [] synonym: "Molybdopterin" RELATED PSI-MS-label [] -synonym: "molybdopterin" RELATED UniMod-description [] +synonym: "molybdopterin" RELATED Unimod-description [] synonym: "MoPterCys" EXACT PSI-MOD-label [] xref: DiffAvg: "520.27" xref: DiffFormula: "C 10 H 11 Mo 1 N 5 O 8 P 1 S 2" @@ -3808,19 +3965,20 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:391" is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:00861 ! phosphorus containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00152 name: S-(8alpha-FAD)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S'-(8alpha-FAD)-L-cystine." [PubMed:10220347, RESID:AA0143, UniMod:50#C] +def: "A protein modification that effectively converts an L-cysteine residue to S'-(8alpha-FAD)-L-cystine." [PubMed:10220347, RESID:AA0143, Unimod:50#C] subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(S-cysteinyl)FAD" EXACT RESID-alternate [] synonym: "FAD" RELATED PSI-MS-label [] -synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] +synonym: "Flavin adenine dinucleotide" RELATED Unimod-description [] synonym: "MOD_RES S-8alpha-FAD cysteine" EXACT UniProt-feature [] synonym: "S-(8alpha-FAD)-L-cysteine" EXACT RESID-name [] synonym: "S8aFADCys" EXACT PSI-MOD-label [] @@ -3833,13 +3991,15 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:50" +xref: UniProt: "PTM-0272" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00153 name: 3'-(8alpha-FAD)-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to 3'-(8alpha-FAD)-L-histidine." [PubMed:241294, PubMed:8076, RESID:AA0144, UniMod:50#H] +def: "A protein modification that effectively converts an L-histidine residue to 3'-(8alpha-FAD)-L-histidine." [PubMed:241294, PubMed:8076, RESID:AA0144, Unimod:50#H] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3'-(8alpha-FAD)-L-histidine" EXACT RESID-name [] @@ -3847,7 +4007,7 @@ synonym: "8alpha-(N3'-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-N1-histidyl FAD" RELATED RESID-misnomer [] synonym: "FAD" RELATED PSI-MS-label [] -synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] +synonym: "Flavin adenine dinucleotide" RELATED Unimod-description [] synonym: "MOD_RES Pros-8alpha-FAD histidine" EXACT UniProt-feature [] synonym: "N(pi)-(8alpha-FAD)-histidine" EXACT RESID-alternate [] synonym: "Np8aFADHis" EXACT PSI-MOD-label [] @@ -3861,19 +4021,21 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:50" +xref: UniProt: "PTM-0258" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00154 name: O4'-(8alpha-FAD)-L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to O4'-(8alpha-FAD)-L-tyrosine." [DeltaMass:0, PubMed:7391034, RESID:AA0145, UniMod:50#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to O4'-(8alpha-FAD)-L-tyrosine." [DeltaMass:0, PubMed:7391034, RESID:AA0145, Unimod:50#Y] comment: From DeltaMass: Average Mass: 783 subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]oxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(O4'-tyrosyl)FAD" EXACT RESID-alternate [] synonym: "FAD" RELATED PSI-MS-label [] -synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] +synonym: "Flavin adenine dinucleotide" RELATED Unimod-description [] synonym: "MOD_RES O-8alpha-FAD tyrosine" EXACT UniProt-feature [] synonym: "O-8 alpha-Flavin [FAD])- (of Tyrosine)" EXACT DeltaMass-label [] synonym: "O4'-(8alpha-FAD)-L-tyrosine" EXACT RESID-name [] @@ -3887,13 +4049,15 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:50" +xref: UniProt: "PTM-0231" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00155 -name: 3'-hydroxylation of L-tyrosine to L-3',4'-dihydroxyphenylalanine -def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4'-dihydroxyphenylalanine." [DeltaMass:0, OMSSA:194, OMSSA:64, PubMed:1610822, PubMed:1903612, PubMed:3734192, RESID:AA0146, UniMod:35#Y] +name: L-3',4'-dihydroxyphenylalanine +def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4'-dihydroxyphenylalanine." [DeltaMass:0, OMSSA:194, OMSSA:64, PubMed:1610822, PubMed:1903612, PubMed:3734192, RESID:AA0146, Unimod:35#Y, ChEBI:141815] comment: incidental to RESID:AA0368 From DeltaMass: Average Mass: 16 subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" EXACT RESID-systematic [] @@ -3915,13 +4079,15 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" +xref: UniProt: "PTM-0023" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00707 ! hydroxylated tyrosine [Term] id: MOD:00156 -name: oxidation of tyrosine to L-2',4',5'-topaquinone -def: "A protein modification that effectively converts an L-tyrosine residue to an L-2',4',5'-topaquinone." [ChEBI:21187, PubMed:10387067, PubMed:1457410, PubMed:1569055, PubMed:2111581, RESID:AA0147, UniMod:392#Y] +name: L-2',4',5'-topaquinone +def: "A protein modification that effectively converts an L-tyrosine residue to an L-2',4',5'-topaquinone." [ChEBI:21187, PubMed:10387067, PubMed:1457410, PubMed:1569055, PubMed:2111581, RESID:AA0147, Unimod:392#Y] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(5-hydroxy-2,5-cyclohexadien-1,4-dion-2-yl)propanoic acid" EXACT RESID-systematic [] synonym: "2,4,5-trihydroxyphenylalanine quinone" EXACT RESID-alternate [] @@ -3930,7 +4096,7 @@ synonym: "L-2,4,5-TOPAquinone" EXACT RESID-alternate [] synonym: "MOD_RES 2',4',5'-topaquinone" EXACT UniProt-feature [] synonym: "Quinone" RELATED PSI-MS-label [] -synonym: "quinone" RELATED UniMod-description [] +synonym: "quinone" RELATED Unimod-description [] synonym: "TopaQ" EXACT PSI-MOD-label [] synonym: "TPQ" EXACT RESID-alternate [] xref: DiffAvg: "29.98" @@ -3942,13 +4108,15 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:392" +xref: UniProt: "PTM-0009" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00157 -name: oxidation of tryptophan to L-tryptophyl quinone -def: "A protein modification that effectively converts an L-tryptophan residue to an L-tryptophan quinone." [DeltaMass:0, PubMed:2028257, RESID:AA0148, UniMod:392#W] +name: L-tryptophyl quinone +def: "A protein modification that effectively converts an L-tryptophan residue to an L-tryptophan quinone." [DeltaMass:0, PubMed:2028257, RESID:AA0148, Unimod:392#W] comment: incidental to RESID:AA0149; incidental to RESID:AA0313; From DeltaMass: Average Mass: 30. subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(6,7-dioxo-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] @@ -3959,7 +4127,7 @@ synonym: "MOD_RES Tryptophylquinone" EXACT UniProt-feature [] synonym: "N-(3-carboxy-1-oxopropyl)-L-tryptophan" EXACT RESID-alternate [] synonym: "Quinone" RELATED PSI-MS-label [] -synonym: "quinone" RELATED UniMod-description [] +synonym: "quinone" RELATED Unimod-description [] synonym: "TrpQ" EXACT PSI-MOD-label [] xref: DiffAvg: "29.98" xref: DiffFormula: "C 0 H -2 N 0 O 2" @@ -3970,6 +4138,8 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:392" +xref: UniProt: "PTM-0299" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00918 ! modified L-tryptophan residue @@ -3998,14 +4168,15 @@ xref: Origin: "W, W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0298" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00918 ! modified L-tryptophan residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue [Term] id: MOD:00159 name: O-phosphopantetheine-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-phosphopantetheine-L-serine." [DeltaMass:0, PubMed:10320345, PubMed:10997907, PubMed:12057197, PubMed:12869567, PubMed:4568609, RESID:AA0150, UniMod:49#S] -comment: UniMod has DiffFormula C 11 H 20 N 2 O 6 P 1 S 1 From DeltaMass: Average Mass: 339 +def: "A protein modification that effectively converts an L-serine residue to O-phosphopantetheine-L-serine." [DeltaMass:0, PubMed:10320345, PubMed:10997907, PubMed:12057197, PubMed:12869567, PubMed:4568609, RESID:AA0150, Unimod:49#S] +comment: Unimod has DiffFormula C 11 H 20 N 2 O 6 P 1 S 1 From DeltaMass: Average Mass: 339 subset: PSI-MOD-slim synonym: "(2R)-2-hydroxy-3,3-dimethyl-4-[(2S)-2-amino-2-carboxyethyl]phosphonato-N-(3-oxo-3-[(2-sulfanylethyl)amino]propyl)butanamide" EXACT RESID-systematic [] synonym: "4'-Phosphopantetheine" EXACT DeltaMass-label [] @@ -4013,7 +4184,7 @@ synonym: "O-phosphopantetheine-L-serine" EXACT RESID-name [] synonym: "OPpantSer" EXACT PSI-MOD-label [] synonym: "Phosphopantetheine" RELATED PSI-MS-label [] -synonym: "Phosphopantetheine" RELATED UniMod-description [] +synonym: "Phosphopantetheine" RELATED Unimod-description [] xref: DiffAvg: "340.33" xref: DiffFormula: "C 11 H 21 N 2 O 6 P 1 S 1" xref: DiffMono: "340.085794" @@ -4023,6 +4194,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:49" +xref: UniProt: "PTM-0391" is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -4041,11 +4214,11 @@ [Term] id: MOD:00161 name: S-glucosyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-glucosylated L-cysteine." [PubMed:1145128, PubMed:15279557, PubMed:5286858, RESID:AA0152, UniMod:41#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-glucosylated L-cysteine." [PubMed:1145128, PubMed:15279557, PubMed:5286858, RESID:AA0152, Unimod:41#C] synonym: "(2R)-2-amino-3-[(beta-D-glucopyranosyl)sulfanyl]propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD S-linked (Glc)" EXACT UniProt-feature [] +synonym: "CARBOHYD S-linked (Glc) cysteine" EXACT UniProt-feature [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] synonym: "S-(beta-D-glucopyranosyl)cysteine" EXACT RESID-alternate [] synonym: "S-glucosyl-L-cysteine" EXACT RESID-name [] synonym: "S-glycosyl-cysteine" EXACT RESID-alternate [] @@ -4059,21 +4232,22 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" +xref: UniProt: "PTM-0626" is_a: MOD:00426 ! S-glycosylated residue -is_a: MOD:00433 ! glucosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00433 ! monoglucosylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00162 name: O5-glucosylgalactosyl-L-hydroxylysine -def: "A protein modification that effectively converts an L-lysine residue to O5-glucosylgalactosyl-L-hydroxylysine." [PubMed:15149698, PubMed:4288358, PubMed:4319110, RESID:AA0153, UniMod:393] +def: "A protein modification that effectively converts an L-lysine residue to O5-glucosylgalactosyl-L-hydroxylysine." [PubMed:15149698, PubMed:4288358, PubMed:4319110, RESID:AA0153, Unimod:393] comment: Secondary to RESID:AA0028. subset: PSI-MOD-slim synonym: "(2S,5R)-2,6-diamino-5-[2-O-(alpha-D-glucopyranosyl)-beta-D-galactopyranosyloxy]hexanoic acid" EXACT RESID-systematic [] synonym: "5-(2-O-alpha-D-glucopyranosyl-beta-D-galactopyranosyl)oxy-L-lysine" EXACT RESID-alternate [] synonym: "Glucosylgalactosyl" RELATED PSI-MS-label [] -synonym: "glucosylgalactosyl hydroxylysine" RELATED UniMod-description [] +synonym: "glucosylgalactosyl hydroxylysine" RELATED Unimod-description [] synonym: "O5-glucosylgalactosyl-L-hydroxylysine" EXACT RESID-name [] synonym: "OGlcGal5HyLys" EXACT PSI-MOD-label [] xref: DiffAvg: "340.28" @@ -4085,10 +4259,10 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00037 ! 5-hydroxy-L-lysine +xref: Unimod: "Unimod:393" +relationship: derives_from MOD:00037 ! 5-hydroxy-L-lysine +is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00396 ! O-glycosylated residue -is_a: MOD:00476 ! galactosylated residue -is_a: MOD:00726 ! glucosylated [Term] id: MOD:00163 @@ -4096,7 +4270,7 @@ def: "A protein modification that effectively converts an L-serine residue to O-(N-acetylaminogalactosyl)-L-serine." [PubMed:115869, PubMed:16005634, PubMed:3086323, PubMed:8948436, PubMed:9092502, RESID:AA0154] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GalNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GalNAc) serine" EXACT UniProt-feature [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "mucin type O-glycosylserine" EXACT RESID-alternate [] synonym: "O-(N-acetylamino)galactosyl-L-serine" EXACT RESID-name [] @@ -4111,7 +4285,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00563 ! N-acetylaminogalactosylated residue +xref: UniProt: "PTM-0564" +is_a: MOD:00563 ! mono-N-acetylaminogalactosylated residue is_a: MOD:01675 ! O-(N-acetylamino)hexosyl-L-serine [Term] @@ -4120,7 +4295,7 @@ def: "A protein modification that effectively converts an L-asparagine residue to O-(N-acetylaminogalactosyl)-L-threonine." [PubMed:16005634, PubMed:1997327, PubMed:3086323, PubMed:8948436, PubMed:9092502, RESID:AA0155] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GalNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GalNAc) threonine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (HexNAc)" EXACT UniProt-feature [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "mucin type O-glycosylthreonine" EXACT RESID-alternate [] @@ -4136,7 +4311,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00563 ! N-acetylaminogalactosylated residue +xref: UniProt: "PTM-0567" +is_a: MOD:00563 ! mono-N-acetylaminogalactosylated residue is_a: MOD:01676 ! O-(N-acetylamino)hexosyl-L-threonine [Term] @@ -4147,7 +4323,7 @@ synonym: "(2S)-2-amino-3-(1-D-mannopyranosyloxy-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "1'-glycosyl-L-tryptophan" EXACT RESID-alternate [] synonym: "1'-mannosyl-L-tryptophan" EXACT RESID-name [] -synonym: "CARBOHYD N-linked (Man)" EXACT UniProt-feature [] +synonym: "CARBOHYD N-linked (Man) tryptophan" EXACT UniProt-feature [] synonym: "N-mannosyl-tryptophan" EXACT RESID-alternate [] synonym: "N1'ManTrp" EXACT PSI-MOD-label [] synonym: "N1-mannosyl-tryptophan" EXACT RESID-alternate [] @@ -4160,21 +4336,22 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0535" is_a: MOD:00006 ! N-glycosylated residue -is_a: MOD:00595 ! mannosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00595 ! monomannosylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00166 name: O4'-glucosyl-L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to O4'-glucosyl-tyrosine." [PubMed:15279557, PubMed:3181138, RESID:AA0157, UniMod:41#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to O4'-glucosyl-tyrosine." [PubMed:15279557, PubMed:3181138, RESID:AA0157, Unimod:41#Y] synonym: "(2S)-2-amino-3-(4-alpha-D-glucopyranosyloxy)phenylpropanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] synonym: "O4'-glucosyl-L-tyrosine" EXACT RESID-name [] synonym: "O4'-glycosyl-L-tyrosine" EXACT RESID-alternate [] synonym: "O4GlcTyr" EXACT PSI-MOD-label [] +synonym: "CARBOHYD O-linked (Glc) tyrosine" EXACT UniProt-feature [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" @@ -4184,8 +4361,9 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00433 ! glucosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +xref: Unimod: "Unimod:41" +xref: UniProt: "PTM-0575" +is_a: MOD:00433 ! monoglucosylated residue is_a: MOD:01927 ! O-glycosyl-L-tyrosine [Term] @@ -4204,6 +4382,7 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0137" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00903 ! modified L-asparagine residue @@ -4223,6 +4402,7 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0138" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00904 ! modified L-aspartic acid residue @@ -4242,6 +4422,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0140" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00905 ! modified L-cysteine residue @@ -4261,6 +4442,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0141" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00908 ! modified glycine residue @@ -4280,6 +4462,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0142" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00916 ! modified L-serine residue @@ -4299,6 +4482,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0136" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00901 ! modified L-alanine residue @@ -4318,6 +4502,7 @@ xref: Origin: "T" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0143" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00917 ! modified L-threonine residue @@ -4337,6 +4522,7 @@ xref: Origin: "G" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0146" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00908 ! modified glycine residue @@ -4356,13 +4542,14 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0147" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00176 name: O-(phosphoribosyl dephospho-coenzyme A)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(phosphoribosyl dephospho-coenzyme A)-L-serine." [PubMed:10924139, PubMed:11052675, PubMed:179809, PubMed:180526, PubMed:368065, RESID:AA0167, UniMod:395#S] +def: "A protein modification that effectively converts an L-serine residue to O-(phosphoribosyl dephospho-coenzyme A)-L-serine." [PubMed:10924139, PubMed:11052675, PubMed:179809, PubMed:180526, PubMed:368065, RESID:AA0167, Unimod:395#S] comment: pRibodePcoA subset: PSI-MOD-slim synonym: "MOD_RES O-(phosphoribosyl dephospho-coenzyme A)serine" EXACT UniProt-feature [] @@ -4371,7 +4558,7 @@ synonym: "O3-(phosphoribosyl dephospho-coenzyme A)-L-serine" EXACT RESID-alternate [] synonym: "O3-2'-(5''-phosphoribosyl-3'-dephosphocoenzyme A)-L-serine" EXACT RESID-alternate [] synonym: "OPRibdPCoASer" EXACT PSI-MOD-label [] -synonym: "phosphoribosyl dephospho-coenzyme A" RELATED UniMod-description [] +synonym: "phosphoribosyl dephospho-coenzyme A" RELATED Unimod-description [] synonym: "PhosphoribosyldephosphoCoA" RELATED PSI-MS-label [] xref: DiffAvg: "881.63" xref: DiffFormula: "C 26 H 42 N 7 O 19 P 3 S 1" @@ -4382,6 +4569,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:395" +xref: UniProt: "PTM-0389" is_a: MOD:00860 ! sulfur containing modified residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -4389,11 +4578,11 @@ [Term] id: MOD:00177 name: omega-N-(ADP-ribosyl)-L-arginine -def: "A protein modification that effectively converts an L-argininine residue to omega-N-(ADP-ribosyl)-L-arginine." [DeltaMass:0, PubMed:15842200, PubMed:209022, PubMed:3090031, PubMed:3923473, PubMed:6582062, RESID:AA0168, UniMod:213#R] +def: "A protein modification that effectively converts an L-argininine residue to omega-N-(ADP-ribosyl)-L-arginine." [DeltaMass:0, PubMed:15842200, PubMed:209022, PubMed:3090031, PubMed:3923473, PubMed:6582062, RESID:AA0168, Unimod:213#R] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD-slim synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] -synonym: "ADP Ribose addition" RELATED UniMod-description [] +synonym: "ADP Ribose addition" RELATED Unimod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADPRibArg" EXACT PSI-MOD-label [] synonym: "MOD_RES ADP-ribosylarginine" EXACT UniProt-feature [] @@ -4410,17 +4599,19 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: Unimod: "Unimod:213" +xref: UniProt: "PTM-0053" +is_a: MOD:00752 ! monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00178 name: S-(ADP-ribosyl)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(ADP-ribosyl)-L-cysteine." [DeltaMass:0, PubMed:15842200, PubMed:3863818, RESID:AA0169, UniMod:213#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-(ADP-ribosyl)-L-cysteine." [DeltaMass:0, PubMed:15842200, PubMed:3863818, RESID:AA0169, Unimod:213#C] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD-slim synonym: "(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid" EXACT RESID-systematic [] -synonym: "ADP Ribose addition" RELATED UniMod-description [] +synonym: "ADP Ribose addition" RELATED Unimod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADPRibCys" EXACT PSI-MOD-label [] synonym: "MOD_RES ADP-ribosylcysteine" EXACT UniProt-feature [] @@ -4437,20 +4628,22 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: Unimod: "Unimod:213" +xref: UniProt: "PTM-0055" +is_a: MOD:00752 ! monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00179 name: L-glutamyl 5-glycerylphosphorylethanolamine -def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl 5-glycerylphosphorylethanolamine." [PubMed:2511205, PubMed:2569467, PubMed:9662537, RESID:AA0170, UniMod:396#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl 5-glycerylphosphorylethanolamine." [PubMed:2511205, PubMed:2569467, PubMed:9662537, RESID:AA0170, Unimod:396#E] comment: glycerylPE subset: PSI-MOD-slim synonym: "(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "5-L-glutamyl glycerylphosphorylethanolamine" EXACT RESID-name [] synonym: "5GlyceroPEtAGlu" EXACT PSI-MOD-label [] synonym: "GlycerylPE" RELATED PSI-MS-label [] -synonym: "glycerylphosphorylethanolamine" RELATED UniMod-description [] +synonym: "glycerylphosphorylethanolamine" RELATED Unimod-description [] synonym: "L-glutamyl 5-glycerophosphoethanolamine" EXACT RESID-alternate [] synonym: "L-glutamyl 5-glycerophosphorylethanolamine" EXACT RESID-alternate [] synonym: "L-glutamyl 5-glycerylphosphorylethanolamine" EXACT RESID-alternate [] @@ -4464,18 +4657,20 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:396" +xref: UniProt: "PTM-0403" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00180 name: S-sulfo-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-sulfo-L-cysteine." [PubMed:12876326, PubMed:14752058, PubMed:643076, RESID:AA0171, UniMod:40#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-sulfo-L-cysteine." [PubMed:12876326, PubMed:14752058, PubMed:643076, RESID:AA0171, Unimod:40#C] synonym: "(2R)-2-amino-3-(sulfosulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(sulfothio)propanoic acid" EXACT RESID-alternate [] synonym: "3-(sulfosulfanyl)-L-alanine" EXACT RESID-alternate [] synonym: "cysteine sulfate thioester" EXACT RESID-alternate [] synonym: "cysteine-S-sulfonic acid" EXACT RESID-alternate [] -synonym: "O-Sulfonation" RELATED UniMod-description [] +synonym: "O-Sulfonation" RELATED Unimod-description [] synonym: "S-sulfo-L-cysteine" EXACT RESID-name [] synonym: "S-sulfocysteine" EXACT PSI-MOD-alternate [] synonym: "S-sulfocysteine" EXACT RESID-alternate [] @@ -4490,6 +4685,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:40" is_a: MOD:00695 ! sulfated residue is_a: MOD:00777 ! residues isobaric at 182.96-182.98 Da is_a: MOD:00905 ! modified L-cysteine residue @@ -4497,13 +4693,13 @@ [Term] id: MOD:00181 name: O4'-sulfo-L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to O4'-sulfo-L-tyrosine." [DeltaMass:88, OMSSA:114, PubMed:10226369, PubMed:14752058, PubMed:2303439, PubMed:3778455, PubMed:3801003, RESID:AA0172, UniMod:40#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to O4'-sulfo-L-tyrosine." [DeltaMass:88, OMSSA:114, PubMed:10226369, PubMed:14752058, PubMed:2303439, PubMed:3778455, PubMed:3801003, RESID:AA0172, Unimod:40#Y] comment: From DeltaMass: Average Mass: 80 Average Mass Change:80 PubMed:9624161. subset: PSI-MOD-slim synonym: "(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate" EXACT RESID-alternate [] synonym: "MOD_RES Sulfotyrosine" EXACT UniProt-feature [] -synonym: "O-Sulfonation" RELATED UniMod-description [] +synonym: "O-Sulfonation" RELATED Unimod-description [] synonym: "O4'-sulfo-L-tyrosine" EXACT RESID-name [] synonym: "O4-sulfotyrosine" EXACT RESID-alternate [] synonym: "OSulfTyr" EXACT PSI-MOD-label [] @@ -4523,6 +4719,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:40" +xref: UniProt: "PTM-0286" is_a: MOD:00695 ! sulfated residue is_a: MOD:00774 ! residues isobaric at 243.02-243.03 Da is_a: MOD:00919 ! modified L-tyrosine residue @@ -4530,9 +4728,9 @@ [Term] id: MOD:00182 name: L-bromohistidine -def: "A protein modification that effectively converts an L-histidine residue to L-bromohistidine." [PubMed:2076468, PubMed:9033387, RESID:AA0173, UniMod:340#H] +def: "A protein modification that effectively converts an L-histidine residue to L-bromohistidine." [PubMed:2076468, PubMed:9033387, RESID:AA0173, Unimod:340#H] synonym: "Br1His" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "L-bromohistidine" EXACT RESID-name [] synonym: "MOD_RES Bromohistidine" EXACT UniProt-feature [] @@ -4545,6 +4743,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:340" +xref: UniProt: "PTM-0089" is_a: MOD:01049 ! halogenated histidine is_a: MOD:01912 ! monobrominated residue @@ -4555,7 +4755,7 @@ comment: From DeltaMass: Average Mass: 78 Average Mass Change:78 References:Yoshino,K et.al. Biochemistry Vol. 30 pg 6203-9 (1991) Identifidation of a novel amino acid, o-bromo-L-phenylananine, in egg-associated peptides that activate spermatozoa. synonym: "(S)-2-amino-3-(2-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2'BrPhe" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "L-2'-bromophenylalanine" EXACT RESID-name [] synonym: "L-o-bromination of Phe with 79Br" EXACT DeltaMass-label [] @@ -4578,7 +4778,7 @@ def: "A protein modification that effectively converts an L-phenylalanine residue to L-3'-bromophenylalanine." [PubMed:2076468, PubMed:9033387, RESID:AA0175] synonym: "(S)-2-amino-3-(3-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "3'BrPhe" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "L-3'-bromophenylalanine" EXACT RESID-name [] synonym: "m-bromophenylalanine" EXACT RESID-alternate [] @@ -4600,7 +4800,7 @@ def: "A protein modification that effectively converts an L-phenylalanine residue to L-4'-bromophenylalanine." [PubMed:2076468, PubMed:9033387, RESID:AA0176] synonym: "(2S)-2-amino-3-(4-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "4'BrPhe" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "L-4'-bromophenylalanine" EXACT RESID-name [] synonym: "p-bromophenylalanine" EXACT RESID-alternate [] @@ -4618,8 +4818,8 @@ [Term] id: MOD:00186 -name: 3',3'',5'-triiodo-L-thyronine -def: "A protein modification that effectively substitutes an L-tyrosine residue with 3',3'',5'-triiodo-L-thyronine." [ChEBI:18258, DeltaMass:0, RESID:AA0177, UniMod:397] +name: 3,3',5-triiodo-L-thyronine +def: "A protein modification that effectively substitutes an L-tyrosine residue with 3,3',5-triiodo-L-thyronine." [ChEBI:18258, DeltaMass:0, RESID:AA0177, Unimod:397] comment: From DeltaMass: Average Mass: 470. subset: PSI-MOD-slim synonym: "(S)-2-amino-3-[4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]propanoic acid" EXACT RESID-systematic [] @@ -4633,7 +4833,7 @@ synonym: "MOD_RES Triiodothyronine" EXACT UniProt-feature [] synonym: "O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine" EXACT RESID-alternate [] synonym: "T3" EXACT RESID-alternate [] -synonym: "triiodo" RELATED UniMod-description [] +synonym: "triiodo" RELATED Unimod-description [] synonym: "Triiodothyronine" RELATED PSI-MS-label [] xref: DiffAvg: "469.79" xref: DiffFormula: "C 6 H 1 I 3 N 0 O 1" @@ -4644,13 +4844,14 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00502 ! triiodinated residue +xref: Unimod: "Unimod:397" +xref: UniProt: "PTM-0295" is_a: MOD:00998 ! iodinated tyrosine [Term] id: MOD:00187 name: L-thyroxine -def: "A protein modification that effectively substitutes an L-tyrosine residue with L-thyroxine." [ChEBI:18332, PubMed:6704086, RESID:AA0178, UniMod:398] +def: "A protein modification that effectively substitutes an L-tyrosine residue with L-thyroxine." [ChEBI:18332, PubMed:6704086, RESID:AA0178, Unimod:398] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]propanoic acid" EXACT RESID-systematic [] synonym: "3',3'',5',5''-tetraiodo-L-thyronine" EXACT RESID-alternate [] @@ -4662,7 +4863,7 @@ synonym: "MOD_RES Thyroxine" EXACT UniProt-feature [] synonym: "O-(4-hydroxy-3,5-diiodophenyl)-3,5-diiodo-L-tyrosine" EXACT RESID-alternate [] synonym: "T4" EXACT RESID-alternate [] -synonym: "tetraiodo" RELATED UniMod-description [] +synonym: "tetraiodo" RELATED Unimod-description [] synonym: "Thyroxine" RELATED PSI-MS-label [] xref: DiffAvg: "595.68" xref: DiffFormula: "C 6 H 0 I 4 N 0 O 1" @@ -4673,16 +4874,18 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:398" +xref: UniProt: "PTM-0294" is_a: MOD:00998 ! iodinated tyrosine [Term] id: MOD:00188 name: 6'-bromo-L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to 6'-bromo-L-tryptophan." [PubMed:12118011, PubMed:9030520, PubMed:9033387, PubMed:9434739, RESID:AA0179, UniMod:340#W] +def: "A protein modification that effectively converts an L-tryptophan residue to 6'-bromo-L-tryptophan." [PubMed:12118011, PubMed:9030520, PubMed:9033387, PubMed:9434739, RESID:AA0179, Unimod:340#W] synonym: "(2S)-2-amino-3-(6-bromo-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "6'-bromo-L-tryptophan" EXACT RESID-name [] synonym: "6'-BrTrp" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "MOD_RES 6'-bromotryptophan" EXACT UniProt-feature [] xref: DiffAvg: "78.90" @@ -4694,13 +4897,15 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:398" +xref: UniProt: "PTM-0051" is_a: MOD:01068 ! halogenated tryptophan is_a: MOD:01912 ! monobrominated residue [Term] id: MOD:00189 name: dehydroalanine (Ser) -def: "A protein modification that effectively converts an L-serine residue to dehydroalanine." [DeltaMass:0, OMSSA:140, OMSSA:164, OMSSA:96, PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:7947813, PubMed:8239649, RESID:AA0181#SER, UniMod:23#S] +def: "A protein modification that effectively converts an L-serine residue to dehydroalanine." [DeltaMass:0, OMSSA:140, OMSSA:164, OMSSA:96, PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:7947813, PubMed:8239649, RESID:AA0181#SER, Unimod:23#S] subset: PSI-MOD-slim synonym: "2,3-didehydroalanine" EXACT RESID-alternate [] synonym: "2-aminoacrylic acid" EXACT RESID-alternate [] @@ -4724,6 +4929,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:23" +xref: UniProt: "PTM-0006" is_a: MOD:00416 ! phosphorylation of an hydroxyl amino acid with prompt loss of phosphate is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01168 ! dehydroalanine @@ -4731,7 +4938,7 @@ [Term] id: MOD:00190 name: dehydrobutyrine (Thr) -def: "A protein modification that effectively converts an L-threonine residue to dehydrobutyrine." [DeltaMass:0, OMSSA:141, OMSSA:164, OMSSA:97, PubMed:1547888, PubMed:3769923, RESID:AA0182, UniMod:23#T] +def: "A protein modification that effectively converts an L-threonine residue to dehydrobutyrine." [DeltaMass:0, OMSSA:141, OMSSA:164, OMSSA:97, PubMed:1547888, PubMed:3769923, RESID:AA0182, Unimod:23#T] subset: PSI-MOD-slim synonym: "(2Z)-2-aminobut-2-enoic acid" EXACT RESID-systematic [] synonym: "(Z)-2-amino-2-butenoic acid" EXACT RESID-alternate [] @@ -4743,8 +4950,8 @@ synonym: "anhydrothreonine" EXACT RESID-alternate [] synonym: "beta-elim-t" EXACT OMSSA-label [] synonym: "Dehydrated" RELATED PSI-MS-label [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "dehydro" EXACT OMSSA-label [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "Dhb" EXACT RESID-alternate [] @@ -4761,6 +4968,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:23" +xref: UniProt: "PTM-0007" is_a: MOD:00416 ! phosphorylation of an hydroxyl amino acid with prompt loss of phosphate is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01703 ! dehydrobutyrine @@ -4774,7 +4983,7 @@ synonym: "(2Z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acid" EXACT RESID-systematic [] synonym: "(Z)-2,3-didehydrogenated tyrosine" EXACT PSI-MOD-alternate [] synonym: "(Z)-2,3-didehydrotyrosine" EXACT RESID-name [] -synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] +synonym: "2-amino-3-oxo-butanoic_acid" RELATED Unimod-description [] synonym: "amino-(para-hydroxybenzylidenyl)acetic acid" EXACT RESID-alternate [] synonym: "cis-dehydrotyrosine" EXACT RESID-alternate [] synonym: "Didehydro" RELATED PSI-MS-label [] @@ -4792,6 +5001,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0002" is_a: MOD:00706 ! dehydrogenated tyrosine [Term] @@ -4816,14 +5026,16 @@ xref: Origin: "G, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0049" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00193 name: L-3-oxoalanine (Cys) -def: "A protein modification that effectively converts an L-cysteine residue to L-oxoalanine." [DeltaMass:350, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9478923, RESID:AA0185#CYS, UniMod:402#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-oxoalanine." [DeltaMass:350, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9478923, RESID:AA0185#CYS, Unimod:402#C] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxopropionic acid" EXACT RESID-alternate [] @@ -4843,18 +5055,20 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:402" +xref: UniProt: "PTM-0034" is_a: MOD:01169 ! L-3-oxoalanine [Term] id: MOD:00194 name: lactic acid -def: "A protein modification that effectively converts an L-serine residue to an amino-terminal lactic acid." [PubMed:7607233, RESID:AA0186, UniMod:403#S] +def: "A protein modification that effectively converts an L-serine residue to an amino-terminal lactic acid." [PubMed:7607233, RESID:AA0186, Unimod:403#S] synonym: "(2R)-2-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "2-hydroxypropionic acid" EXACT RESID-alternate [] synonym: "alpha-hydroxypropionic acid" EXACT RESID-alternate [] synonym: "Lac(Ser)" EXACT PSI-MOD-label [] synonym: "lactic acid" EXACT RESID-name [] -synonym: "lactic acid from N-term Ser" RELATED UniMod-description [] +synonym: "lactic acid from N-term Ser" RELATED Unimod-description [] synonym: "MOD_RES Lactic acid" EXACT UniProt-feature [] synonym: "Ser->LacticAcid" RELATED PSI-MS-label [] xref: DiffAvg: "-15.02" @@ -4865,6 +5079,8 @@ xref: MassMono: "73.028954" xref: Origin: "S" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:403" +xref: UniProt: "PTM-0163" is_a: MOD:00916 ! modified L-serine residue [Term] @@ -4889,9 +5105,11 @@ xref: Origin: "A, G" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00901 ! modified L-alanine residue -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0045" +is_a: MOD:02040 ! crosslinked L-alanine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00196 @@ -4915,9 +5133,11 @@ xref: Origin: "C, G" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0047" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00197 @@ -4942,8 +5162,9 @@ xref: Origin: "G, Q" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00907 ! modified L-glutamine residue -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0013" +is_a: MOD:02046 ! crosslinked L-glutamine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) [Term] @@ -4963,6 +5184,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0112" is_a: MOD:00570 ! residues isobaric at 71.037114 Da is_a: MOD:00862 ! D-alanine is_a: MOD:00901 ! modified L-alanine residue @@ -4989,6 +5211,7 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0114" is_a: MOD:00306 ! residues isobaric at 113.084064 Da is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00910 ! modified L-isoleucine residue @@ -5012,6 +5235,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0120" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00913 ! modified L-methionine residue @@ -5032,6 +5256,7 @@ xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0121" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00914 ! modified L-phenylalanine residue @@ -5042,6 +5267,7 @@ synonym: "(R)-2-amino-3-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "D-Ser(Ser)" EXACT PSI-MOD-label [] synonym: "D-serine" EXACT RESID-name [] +synonym: "MOD_RES D-serine (Ser)" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" @@ -5051,6 +5277,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0308" is_a: MOD:00891 ! D-serine is_a: MOD:00916 ! modified L-serine residue @@ -5072,7 +5299,9 @@ xref: MassMono: "114.042927" xref: Origin: "N" xref: Source: "natural" +xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0115" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00903 ! modified L-asparagine residue @@ -5094,6 +5323,7 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0119" is_a: MOD:00306 ! residues isobaric at 113.084064 Da is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00911 ! modified L-leucine residue @@ -5116,6 +5346,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0123" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00918 ! modified L-tryptophan residue @@ -5126,15 +5357,10 @@ synonym: "gamma-glutamylpolyglycine" EXACT RESID-alternate [] synonym: "L-isoglutamyl-polyglycine" EXACT RESID-name [] synonym: "MOD_RES 5-glutamyl polyglycine" EXACT UniProt-feature [] -xref: DiffAvg: "57.05" -xref: DiffFormula: "C 2 H 3 N 1 O 1" -xref: DiffMono: "57.021464" -xref: Formula: "C 7 H 10 N 2 O 4" -xref: MassAvg: "186.17" -xref: MassMono: "186.064057" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0394" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] @@ -5143,27 +5369,21 @@ def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl-polyglutamic acid, forming an isopeptide bond with a polyglutamic acid." [PubMed:10747868, PubMed:1680872, RESID:AA0202] synonym: "gamma-glutamylpolyglutamic acid" EXACT RESID-alternate [] synonym: "L-isoglutamyl-polyglutamic acid" EXACT RESID-name [] -xref: DiffAvg: "129.12" -xref: DiffFormula: "C 5 H 7 N 1 O 3" -xref: DiffMono: "129.042593" -xref: Formula: "C 10 H 14 N 2 O 6" -xref: MassAvg: "258.23" -xref: MassMono: "258.085186" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00674 ! amidated residue +xref: UniProt: "PTM-0395" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00208 name: O4'-(phospho-5'-adenosine)-L-tyrosine -def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphoadenosine through a phosphodiester bond to form O4'-(phospho-5'-adenosine)-L-tyrosine." [DeltaMass:0, PubMed:5543675, RESID:AA0203, UniMod:405#Y] +def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphoadenosine through a phosphodiester bond to form O4'-(phospho-5'-adenosine)-L-tyrosine." [DeltaMass:0, PubMed:5543675, RESID:AA0203, Unimod:405#Y] comment: From DeltaMass: Average Mass: 329. subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-[4-(5'-adenosine phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-O-tyrosine" EXACT RESID-alternate [] -synonym: "AMP binding site" RELATED UniMod-description [] +synonym: "AMP binding site" RELATED Unimod-description [] synonym: "hydrogen 5'-adenylate tyrosine ester" EXACT RESID-alternate [] synonym: "MOD_RES O-AMP-tyrosine" EXACT UniProt-feature [] synonym: "O-5'-Adenosylation ( of Tyrosine)" EXACT DeltaMass-label [] @@ -5180,6 +5400,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:405" +xref: UniProt: "PTM-0332" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01165 ! adenylated residue @@ -5201,13 +5423,14 @@ xref: MassMono: "143.027909" xref: Origin: "C, S" xref: TermSpec: "C-term" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0268" +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01850 ! S-(2-aminovinyl)-D-cysteine [Term] id: MOD:00210 name: L-cysteine sulfenic acid -def: "A protein modification that effectively monooxygenates an L-cysteine residue to L-cysteine sulfenic acid." [DeltaMass:41, OMSSA:193, PubMed:10964927, PubMed:2501303, PubMed:8756456, PubMed:9214307, PubMed:9586994, PubMed:9587003, RESID:AA0205, UniMod:35#C] +def: "A protein modification that effectively monooxygenates an L-cysteine residue to L-cysteine sulfenic acid." [DeltaMass:41, OMSSA:193, PubMed:10964927, PubMed:2501303, PubMed:8756456, PubMed:9214307, PubMed:9586994, PubMed:9587003, RESID:AA0205, Unimod:35#C] comment: From DeltaMass: Average Mass: 16 Average Mass Change:16 Notes:Green et al. in J. B. C. 270, 18209-18211 (1995) quote Kim and Raines in Eur. J. Biochem. 224, 109-114 (1994). Kim and Raines using ESI-MS and sulfhydryl group titration found that bovine seminal ribonuclease contains a single oxidized sulfhydryl group, which cannot participate in a disulfide bond. This form of cysteine is called sulfenic acid (-SOH). subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-(hydroxysulfanyl)propanoic acid" EXACT RESID-systematic [] @@ -5237,6 +5460,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" +xref: UniProt: "PTM-0107" is_a: MOD:00708 ! sulfur oxygenated L-cysteine is_a: MOD:01854 ! sulfur monooxygenated residue @@ -5244,7 +5469,7 @@ id: MOD:00211 name: S-(glycyl)-L-cysteine (Cys-Gly) def: "A protein modification that effectively crosslinks an L-cysteine residue and a glycine residue by a thioester bond to form S-glycyl-L-cysteine." [ChEBI:22050, PubMed:3306404, RESID:AA0206] -comment: Cross-link 2. For the modification of a C-terminal glycine by formation of a thioester bond with free L-cycteine see MOD:01777 [JSG]. +comment: Cross-link 2. For the modification of a C-terminal glycine by formation of a thioester bond with free L-cysteine see MOD:01777 [JSG]. subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-[(aminoacetyl)sulfanyl]propanoic acid" EXACT RESID-systematic [] synonym: "1-(cystein-S-yl)-glycinate" EXACT RESID-alternate [] @@ -5261,18 +5486,19 @@ xref: MassMono: "159.022823" xref: Origin: "C, G" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0429" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00212 name: S-4-hydroxycinnamyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-4-hydroxycinnamyl-L-cysteine." [PubMed:7947803, PubMed:7981196, RESID:AA0207, UniMod:407] +def: "A protein modification that effectively converts an L-cysteine residue to S-4-hydroxycinnamyl-L-cysteine." [PubMed:7947803, PubMed:7981196, RESID:AA0207, Unimod:407] synonym: "(2R)-2-amino-3-([(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "cinnamate cysteine thioester" EXACT RESID-alternate [] synonym: "Hydroxycinnamyl" RELATED PSI-MS-label [] -synonym: "hydroxycinnamyl" RELATED UniMod-description [] +synonym: "hydroxycinnamyl" RELATED Unimod-description [] synonym: "MOD_RES S-(4-hydroxycinnamyl)cysteine" EXACT UniProt-feature [] synonym: "S-4-hydroxycinnamyl-L-cysteine" EXACT RESID-name [] synonym: "S-para-coumaryl-L-cysteine" EXACT RESID-alternate [] @@ -5285,6 +5511,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:407" +xref: UniProt: "PTM-0414" is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -5295,12 +5523,6 @@ synonym: "chondroitin 6-sulfate (chondroitin sulfate C)" EXACT RESID-alternate [] synonym: "chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine" EXACT RESID-name [] synonym: "poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-6-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] -xref: DiffAvg: "-1.01" -xref: DiffFormula: "C 0 H -1 N 0 O 0" -xref: DiffMono: "-1.007825" -xref: Formula: "C 3 H 4 N 1 O 2" -xref: MassAvg: "86.07" -xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" @@ -5314,12 +5536,6 @@ synonym: "chondroitin sulfate B" EXACT RESID-alternate [] synonym: "dermatan 4-sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine" EXACT RESID-name [] synonym: "poly[beta-1,4-L-idopyranuronosyl-alpha-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] -xref: DiffAvg: "-1.01" -xref: DiffFormula: "C 0 H -1 N 0 O 0" -xref: DiffMono: "-1.007825" -xref: Formula: "C 3 H 4 N 1 O 2" -xref: MassAvg: "86.07" -xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" @@ -5333,12 +5549,6 @@ synonym: "heparin" EXACT RESID-alternate [] synonym: "heparitin sulfate" EXACT RESID-alternate [] synonym: "poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] -xref: DiffAvg: "-1.01" -xref: DiffFormula: "C 0 H -1 N 0 O 0" -xref: DiffMono: "-1.007825" -xref: Formula: "C 3 H 4 N 1 O 2" -xref: MassAvg: "86.07" -xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" @@ -5347,12 +5557,12 @@ [Term] id: MOD:00216 name: N6-formyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-formyl-L-lysine." [OMSSA:43, PubMed:15799070, RESID:AA0211, UniMod:122#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-formyl-L-lysine." [OMSSA:43, PubMed:15799070, RESID:AA0211, Unimod:122#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(formylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-formyllysine" EXACT RESID-alternate [] synonym: "Formyl" RELATED PSI-MS-label [] -synonym: "Formylation" RELATED UniMod-description [] +synonym: "Formylation" RELATED Unimod-description [] synonym: "formylk" EXACT OMSSA-label [] synonym: "MOD_RES N6-formyllysine" EXACT UniProt-feature [] synonym: "N(zeta)-formyllysine" EXACT RESID-alternate [] @@ -5368,13 +5578,15 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:122" +xref: UniProt: "PTM-0192" is_a: MOD:00409 ! N-formylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00217 name: O4-arabinosyl-L-hydroxyproline -def: "A protein modification that effectively converts an L-proline residue to O4-arabinosyl-L-hydroxyproline." [DeltaMass:0, PubMed:666730, PubMed:7852316, RESID:AA0212, UniMod:408] +def: "A protein modification that effectively converts an L-proline residue to O4-arabinosyl-L-hydroxyproline." [DeltaMass:0, PubMed:666730, PubMed:7852316, RESID:AA0212, Unimod:408] comment: secondary to RESID:AA0030; From DeltaMass: Average Mass: 147. subset: PSI-MOD-slim synonym: "(2S,4R)-4-(beta-L-arabinofuranosyloxy)pyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] @@ -5382,7 +5594,7 @@ synonym: "4-Glycosyloxy- (pentosyl,C5) (of Proline)" EXACT DeltaMass-label [] synonym: "beta-arabinofuranosyl-4-hydroxyproline" EXACT RESID-alternate [] synonym: "Glycosyl" RELATED PSI-MS-label [] -synonym: "glycosyl-L-hydroxyproline" RELATED UniMod-description [] +synonym: "glycosyl-L-hydroxyproline" RELATED Unimod-description [] synonym: "O4-arabinosyl-L-hydroxyproline" EXACT RESID-name [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] synonym: "OAra4HyPro" EXACT PSI-MOD-label [] @@ -5395,6 +5607,8 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:408" +xref: UniProt: "PTM-0545" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00915 ! modified L-proline residue @@ -5407,22 +5621,17 @@ synonym: "O-(phospho-5'-RNA)-L-serine" EXACT RESID-name [] synonym: "O3-(phospho-5'-RNA)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 5'-RNA phosphodiester" EXACT RESID-alternate [] -xref: DiffAvg: "78.97" -xref: DiffFormula: "C 0 H 0 N 0 O 3 P 1" -xref: DiffMono: "78.958505" -xref: Formula: "C 3 H 5 N 1 O 5 P 1" -xref: MassAvg: "166.05" -xref: MassMono: "165.990534" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0227" is_a: MOD:00751 ! ribonucleic acid linked residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00219 name: L-citrulline -def: "A protein modification that effectively converts an L-arginine residue to L-citrulline." [DeltaMass:0, OMSSA:33, PubMed:2466844, RESID:AA0214, UniMod:7#R] +def: "A protein modification that effectively converts an L-arginine residue to L-citrulline." [DeltaMass:0, OMSSA:33, PubMed:2466844, RESID:AA0214, Unimod:7#R] comment: This modification is not the result of deamidation, instead the guanidino group is replaced with an ureido group. subset: PSI-MOD-slim synonym: "(S)-2-amino-5-(carbamoylamino)pentanoic acid" EXACT RESID-systematic [] @@ -5432,8 +5641,8 @@ synonym: "citrullinationr" EXACT OMSSA-label [] synonym: "Citrulline" EXACT DeltaMass-label [] synonym: "Deamidated" RELATED PSI-MS-label [] -synonym: "Deamidated" RELATED UniMod-interim [] -synonym: "Deamidation" RELATED UniMod-description [] +synonym: "Deamidated" RELATED Unimod-interim [] +synonym: "Deamidation" RELATED Unimod-description [] synonym: "delta-ureidonorvaline" EXACT RESID-alternate [] synonym: "L-citrulline" EXACT RESID-name [] synonym: "MOD_RES Citrulline" EXACT UniProt-feature [] @@ -5449,6 +5658,8 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:7" +xref: UniProt: "PTM-0092" is_a: MOD:00902 ! modified L-arginine residue [Term] @@ -5474,6 +5685,7 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0042" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00682 ! hydroxylated arginine @@ -5498,20 +5710,23 @@ xref: Origin: "C, N" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00903 ! modified L-asparagine residue -is_a: MOD:00905 ! modified L-cysteine residue +xref: UniProt: "PTM-0151" +is_a: MOD:02042 ! crosslinked L-asparagine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:00946 ! crosslinked residues with loss of ammonia +is_a: MOD:00688 ! isopeptide crosslinked residues [Term] id: MOD:00222 name: 2'-alpha-mannosyl-L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to 2'-alpha-mannosyl-L-tryptophan." [PubMed:15279557, PubMed:7547911, PubMed:7947762, RESID:AA0217, UniMod:41#W] +def: "A protein modification that effectively converts an L-tryptophan residue to 2'-alpha-mannosyl-L-tryptophan." [PubMed:15279557, PubMed:7547911, PubMed:7947762, RESID:AA0217, Unimod:41#W] synonym: "(2S)-2-amino-3-(2-beta-D-mannopyranosyl-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "2'-mannosyl-L-tryptophan" EXACT RESID-name [] synonym: "2'-tryptophan C-mannoside" EXACT RESID-alternate [] synonym: "C2'ManTrp" EXACT PSI-MOD-label [] -synonym: "CARBOHYD C-linked (Man)" EXACT UniProt-feature [] +synonym: "CARBOHYD C-linked (Man) tryptophan" EXACT UniProt-feature [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" @@ -5521,9 +5736,10 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" +xref: UniProt: "PTM-0505" is_a: MOD:00421 ! C-glycosylated residue -is_a: MOD:00595 ! mannosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00595 ! monomannosylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] @@ -5533,15 +5749,10 @@ synonym: "MOD_RES N6-murein peptidoglycan lysine" EXACT UniProt-feature [] synonym: "N6-[(2R,6S)-2-(N-(N-mureinyl-(R)-alanyl)-(S)-glutamyl)amino-6-amino-6-carboxy-1-oxohex-1-yl]lysine" EXACT RESID-alternate [] synonym: "N6-mureinyl-L-lysine" EXACT RESID-name [] -xref: DiffAvg: "-1.01" -xref: DiffFormula: "C 0 H -1 N 0 O 0" -xref: DiffMono: "-1.007825" -xref: Formula: "C 6 H 11 N 2 O 1" -xref: MassAvg: "127.17" -xref: MassMono: "127.087138" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0195" is_a: MOD:01159 ! peptidoglycanated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -5554,25 +5765,20 @@ synonym: "MOD_RES Aspartate 1-(chondroitin 4-sulfate)-ester" EXACT UniProt-feature [] synonym: "poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-6-(1-L-aspartyl)-D-galactose)" EXACT RESID-alternate [] synonym: "protein-glycosaminoglycan-protein cross-link" EXACT RESID-alternate [] -xref: DiffAvg: "441.36" -xref: DiffFormula: "C 14 H 19 N 1 O 13 S 1" -xref: DiffMono: "441.057711" -xref: Formula: "C 18 H 25 N 2 O 17 S 1" -xref: MassAvg: "573.45" -xref: MassMono: "573.087393" xref: Origin: "D" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0334" is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00225 name: S-(6-FMN)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(6-FMN)-L-cysteine." [PubMed:10869173, PubMed:1551870, PubMed:620783, RESID:AA0220, UniMod:409#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-(6-FMN)-L-cysteine." [PubMed:10869173, PubMed:1551870, PubMed:620783, RESID:AA0220, Unimod:409#C] subset: PSI-MOD-slim synonym: "(R)-2-amino-3-[6-riboflavin 5'-dihydrogen phosphate]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "6-[S-cysteinyl]flavin mononucleotide" EXACT RESID-alternate [] synonym: "6-[S-cysteinyl]FMN" EXACT RESID-alternate [] -synonym: "flavin mononucleotide" RELATED UniMod-description [] +synonym: "flavin mononucleotide" RELATED Unimod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "MOD_RES S-6-FMN cysteine" EXACT UniProt-feature [] synonym: "S-(6-FMN)-L-cysteine" EXACT RESID-name [] @@ -5586,13 +5792,15 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue +xref: Unimod: "Unimod:409" +xref: UniProt: "PTM-0271" +is_a: MOD:02084 ! 6-FMN modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00226 name: 1'-(8alpha-FAD)-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to 1'-(8alpha-FAD)-L-histidine." [DeltaMass:0, PubMed:10585424, PubMed:1396672, PubMed:4339951, PubMed:9261083, RESID:AA0221, UniMod:50#H] +def: "A protein modification that effectively converts an L-histidine residue to 1'-(8alpha-FAD)-L-histidine." [DeltaMass:0, PubMed:10585424, PubMed:1396672, PubMed:4339951, PubMed:9261083, RESID:AA0221, Unimod:50#H] comment: From DeltaMass: Average Mass: 784 subset: PSI-MOD-slim synonym: "(S)-2-amino-3-(1-[8alpha riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] @@ -5601,7 +5809,7 @@ synonym: "8alpha-(N1'-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-N3-histidyl FAD" RELATED RESID-misnomer [] synonym: "FAD" RELATED PSI-MS-label [] -synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] +synonym: "Flavin adenine dinucleotide" RELATED Unimod-description [] synonym: "MOD_RES Tele-8alpha-FAD histidine" EXACT UniProt-feature [] synonym: "N theta and N pi-(8alpha-Flavin) (on Histidine)" EXACT DeltaMass-label [] synonym: "N(tau)-(8alpha-FAD)-histidine" EXACT RESID-alternate [] @@ -5616,13 +5824,15 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:50" +xref: UniProt: "PTM-0288" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00227 name: omega-N-phospho-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to omega-N-phospho-L-arginine." [PubMed:8300603, RESID:AA0222, UniMod:21#R] +def: "A protein modification that effectively converts an L-arginine residue to omega-N-phospho-L-arginine." [PubMed:8300603, RESID:AA0222, Unimod:21#R] subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-([amino(phosphonoamino)methylidene]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "(2S)-2-amino-5-(N'-phosphonocarbamimidamido)pentanoic acid" EXACT RESID-alternate [] @@ -5635,7 +5845,7 @@ synonym: "PArg" EXACT PSI-MOD-label [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "phosphoarginine" EXACT RESID-alternate [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" @@ -5645,13 +5855,15 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0250" is_a: MOD:00902 ! modified L-arginine residue is_a: MOD:01456 ! N-phosphorylated residue [Term] id: MOD:00228 name: S-diphytanylglycerol diether-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-diphytanylglycerol diether-L-cysteine." [PubMed:7797461, PubMed:8195126, RESID:AA0223, UniMod:410] +def: "A protein modification that effectively converts an L-cysteine residue to S-diphytanylglycerol diether-L-cysteine." [PubMed:7797461, PubMed:8195126, RESID:AA0223, Unimod:410] comment: incidental to RESID:AA0043. subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-([(2S)-2,3-bis(3,7,11,15-tetramethylhexadecanyloxy)propyl]sulfanyl)propanoic acid" EXACT RESID-systematic [] @@ -5660,7 +5872,7 @@ synonym: "S-(diphytanylglyceryl)-L-cysteine" EXACT RESID-name [] synonym: "S-[2',3'-bis(phytanyloxy)propyl]cysteine" EXACT RESID-alternate [] synonym: "S-archaeol cysteine" EXACT RESID-alternate [] -synonym: "S-diphytanylglycerol diether" RELATED UniMod-description [] +synonym: "S-diphytanylglycerol diether" RELATED Unimod-description [] synonym: "SPhyt2GlyceroCys" EXACT PSI-MOD-label [] xref: DiffAvg: "635.16" xref: DiffFormula: "C 43 H 86 N 0 O 2 S 0" @@ -5671,6 +5883,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:410" +xref: UniProt: "PTM-0273" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue @@ -5690,7 +5904,7 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:00230 @@ -5713,8 +5927,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00231 @@ -5736,17 +5950,17 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00232 name: N6-(phospho-5'-adenosine)-L-lysine -def: "A protein modification that effectively crosslinks an L-lysine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form N6-(phospho-5'-adenosine)-L-lysine." [DeltaMass:316, PubMed:3882425, PubMed:4944632, RESID:AA0227, UniMod:405#K] +def: "A protein modification that effectively crosslinks an L-lysine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form N6-(phospho-5'-adenosine)-L-lysine." [DeltaMass:316, PubMed:3882425, PubMed:4944632, RESID:AA0227, Unimod:405#K] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(5'-adenosine phosphonamino)hexanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-N6-L-lysine" EXACT RESID-alternate [] synonym: "ACT_SITE N6-AMP-lysine intermediate" EXACT UniProt-feature [] -synonym: "AMP binding site" RELATED UniMod-description [] +synonym: "AMP binding site" RELATED Unimod-description [] synonym: "AMP Lysyl" EXACT DeltaMass-label [] synonym: "epsilon-5'-adenylic-L-lysine" EXACT RESID-alternate [] synonym: "L-lysine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] @@ -5764,13 +5978,14 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:405" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00233 name: N6-(phospho-5'-guanosine)-L-lysine -def: "A protein modification that effectively crosslinks an L-lysine residue and 5'-phosphoguanosine through a phosphoramide ester bond to form N6-(phospho-5'-guanosine)-L-lysine." [DeltaMass:304, PubMed:6092377, PubMed:6264433, RESID:AA0228, UniMod:413#K] +def: "A protein modification that effectively crosslinks an L-lysine residue and 5'-phosphoguanosine through a phosphoramide ester bond to form N6-(phospho-5'-guanosine)-L-lysine." [DeltaMass:304, PubMed:6092377, PubMed:6264433, RESID:AA0228, Unimod:413#K] comment: From DeltaMass: Average Mass: 345 Formula:C10H12O5N7P1 Monoisotopic Mass Change:345.047 Average Mass Change:345.209 References:PE Sciex subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(5'-guanosine phosphonamino)hexanoic acid" EXACT RESID-systematic [] @@ -5785,7 +6000,7 @@ synonym: "N6-(phospho-5'-guanosine)-L-lysine" EXACT RESID-name [] synonym: "N6-L-lysine 5'-guanosine phosphoramidester" EXACT RESID-alternate [] synonym: "N6GMPLys" EXACT PSI-MOD-label [] -synonym: "phospho-guanosine" RELATED UniMod-description [] +synonym: "phospho-guanosine" RELATED Unimod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] xref: DiffAvg: "345.21" xref: DiffFormula: "C 10 H 12 N 5 O 7 P 1" @@ -5796,20 +6011,22 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:413" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01163 ! guanylated residue [Term] id: MOD:00234 name: L-cysteine glutathione disulfide -def: "A protein modification that effectively converts an L-cysteine residue to S-glutathionyl-L-cysteine." [ChEBI:21264, DeltaMass:0, OMSSA:51, PubMed:3083866, PubMed:8344916, RESID:AA0229, UniMod:55] +def: "A protein modification that effectively converts an L-cysteine residue to S-glutathionyl-L-cysteine." [ChEBI:21264, DeltaMass:0, OMSSA:51, PubMed:3083866, PubMed:8344916, RESID:AA0229, Unimod:55] comment: From DeltaMass: Average Mass: 305 +comment: Glutamyl-transpeptidase cleaves glutathione into cysteinylglycine (Cys-Gly) and a Glu residue. [PubMed: 28537416] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-((2S)-2-((4R)-4-amino-4-carboxyl-1-oxobutyl)amino-3-(carboxylmethyl)amino-3-oxo-propyl)dithio-propanoic acid" EXACT RESID-systematic [] synonym: "cysteinyl glutathione" EXACT RESID-alternate [] synonym: "Glutathionation" EXACT DeltaMass-label [] synonym: "Glutathione" RELATED PSI-MS-label [] -synonym: "glutathione disulfide" RELATED UniMod-description [] +synonym: "glutathione disulfide" RELATED Unimod-description [] synonym: "glutathionec" EXACT OMSSA-label [] synonym: "L-cysteine glutathione disulfide" EXACT RESID-name [] synonym: "L-gamma-glutamyl-L-cysteinyl-glycine (2-1')-disulfide with L-cysteine" EXACT RESID-alternate [] @@ -5825,13 +6042,16 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:55" +xref: UniProt: "PTM-0311" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01862 ! disulfide conjugated residue +relationship: contains MOD:02026 ! S-(cysteinyl-glycyl)-L-cysteine [Term] id: MOD:00235 name: S-nitrosyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-nitrosyl-L-cysteine." [PubMed:10442087, PubMed:11562475, PubMed:15688001, PubMed:8626764, PubMed:8637569, RESID:AA0230, UniMod:275] +def: "A protein modification that effectively converts an L-cysteine residue to S-nitrosyl-L-cysteine." [PubMed:10442087, PubMed:11562475, PubMed:15688001, PubMed:8626764, PubMed:8637569, RESID:AA0230, Unimod:275] subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-nitrososulfanyl-propanoic acid" EXACT RESID-systematic [] synonym: "L-cysteine nitrite ester" EXACT RESID-alternate [] @@ -5839,7 +6059,7 @@ synonym: "Nitrosyl" RELATED PSI-MS-label [] synonym: "S-nitrosocysteine" EXACT RESID-alternate [] synonym: "S-nitrosyl-L-cysteine" EXACT RESID-name [] -synonym: "S-nitrosylation" RELATED UniMod-description [] +synonym: "S-nitrosylation" RELATED Unimod-description [] synonym: "SNOCys" EXACT PSI-MOD-label [] xref: DiffAvg: "29.00" xref: DiffFormula: "C 0 H -1 N 1 O 1 S 0" @@ -5850,14 +6070,17 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:275" +xref: UniProt: "PTM-0280" is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02077 ! nitrosylated residue [Term] id: MOD:00236 name: N4-(ADP-ribosyl)-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N4-(ADP-ribosyl)-L-asparagine." [PubMed:15842200, PubMed:2498316, RESID:AA0231, UniMod:213#N] +def: "A protein modification that effectively converts an L-asparagine residue to N4-(ADP-ribosyl)-L-asparagine." [PubMed:15842200, PubMed:2498316, RESID:AA0231, Unimod:213#N] synonym: "(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid" EXACT RESID-systematic [] -synonym: "ADP Ribose addition" RELATED UniMod-description [] +synonym: "ADP Ribose addition" RELATED Unimod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "MOD_RES ADP-ribosylasparagine" EXACT UniProt-feature [] synonym: "N4-(ADP-ribosyl)-L-asparagine" EXACT RESID-name [] @@ -5872,13 +6095,15 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: Unimod: "Unimod:213" +xref: UniProt: "PTM-0054" +is_a: MOD:00752 ! monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00237 name: L-beta-methylthioaspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-methylthioaspartic acid." [DeltaMass:61, OMSSA:13, OMSSA:26, PubMed:15473684, PubMed:8844851, RESID:AA0232, UniMod:39#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-methylthioaspartic acid." [DeltaMass:61, OMSSA:13, OMSSA:26, PubMed:15473684, PubMed:8844851, RESID:AA0232, Unimod:39#D, ChEBI:73599] subset: PSI-MOD-slim synonym: "(2R,3Xi)-2-amino-3-(methylsulfanyl)butanedioic acid" EXACT RESID-systematic [] synonym: "3-(methylthio)-L-aspartic acid" EXACT RESID-name [] @@ -5887,9 +6112,9 @@ synonym: "3MeSAsp" EXACT PSI-MOD-label [] synonym: "beta-Methylthio-aspartic acid" EXACT DeltaMass-label [] synonym: "beta-methylthio-aspartic acid" EXACT RESID-alternate [] -synonym: "Beta-methylthiolation" RELATED UniMod-description [] +synonym: "Beta-methylthiolation" RELATED Unimod-description [] synonym: "bmethylthiold" EXACT OMSSA-label [] -synonym: "Methylthio" RELATED UniMod-interim [] +synonym: "Methylthio" RELATED Unimod-interim [] synonym: "methythiold" EXACT OMSSA-label [] synonym: "MOD_RES 3-methylthioaspartic acid" EXACT UniProt-feature [] xref: DiffAvg: "46.09" @@ -5901,6 +6126,8 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:39" +xref: UniProt: "PTM-0032" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01153 ! methylthiolated residue @@ -5925,20 +6152,21 @@ xref: Origin: "K, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0171" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00912 ! modified L-lysine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00239 name: S-methyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-methyl-L-cysteine." [PubMed:10660523, PubMed:11875433, PubMed:1339288, RESID:AA0234, UniMod:34#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-methyl-L-cysteine." [PubMed:10660523, PubMed:11875433, PubMed:1339288, RESID:AA0234, Unimod:34#C] subset: PSI-MOD-slim synonym: "(R)-2-amino-3-(methylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "ACT_SITE S-methylcysteine intermediate" EXACT UniProt-feature [] synonym: "L-3-(methylthio)alanine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES S-methylcysteine" EXACT UniProt-feature [] synonym: "S-methyl-L-cysteine" EXACT RESID-name [] synonym: "S-methylated L-cysteine" EXACT PSI-MOD-alternate [] @@ -5952,13 +6180,15 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0636" is_a: MOD:00654 ! S-methylated residue is_a: MOD:01682 ! monomethylated L-cysteine [Term] id: MOD:00240 name: 4-hydroxy-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4-hydroxy-L-lysine." [PubMed:4005040, RESID:AA0235] +def: "A protein modification that effectively converts an L-lysine residue to 4-hydroxy-L-lysine." [PubMed:4005040, RESID:AA0235, ChEBI:141495] comment: This modification was not structurally confirmed. Later 5-hydroxy-L-lysine was found at a homologous position in the same protein from closely related species. This is a deprecated entry in RESID. It probably does not occur naturally [JSG]. synonym: "(2S,4R)-2,6-diamino-4-hydroxyhexanoic acid" EXACT RESID-systematic [] synonym: "4-hydroxy-L-lysine" EXACT RESID-name [] @@ -5966,6 +6196,7 @@ synonym: "4HyLys" EXACT PSI-MOD-label [] synonym: "alpha,epsilon-diamino-gamma-hydroxycaproic acid" EXACT RESID-alternate [] synonym: "L-threo-gamma-hydroxylysine" EXACT RESID-alternate [] +synonym: "MOD_RES 4-hydroxylysine" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -5975,18 +6206,19 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: UniProt: "PTM-0664" is_a: MOD:01047 ! monohydroxylated lysine [Term] id: MOD:00241 name: N4-hydroxymethyl-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N4-hydroxymethyl-L-asparagine." [RESID:AA0236, UniMod:414] +def: "A protein modification that effectively converts an L-asparagine residue to N4-hydroxymethyl-L-asparagine." [RESID:AA0236, Unimod:414] comment: N4-methyl-L-asparagine, see MOD:0079, was found at a homologous position of the same protein in a closely related species. Since the peptide containing this modification was obtained by enzymatic cleavage, not cyanogen bromide cleavage, it could have experienced oxidation of the following methionine residue, leading to the erroneous attribution of a mass of 29 for the modification rather than 14. comment: This is a deprecated entry in RESID. It probably does not occur naturally [JSG]. synonym: "(2S)-2-amino-4-[(hydroxymethyl)amino]-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-amino-N4-hydroxymethylbutanediamic acid" EXACT RESID-alternate [] synonym: "beta-hydroxymethylasparagine" EXACT RESID-alternate [] synonym: "Hydroxymethyl" RELATED PSI-MS-label [] -synonym: "hydroxymethyl" RELATED UniMod-description [] +synonym: "hydroxymethyl" RELATED Unimod-description [] synonym: "N(gamma)-hydroxymethylasparagine" EXACT RESID-alternate [] synonym: "N4-hydroxymethyl-L-asparagine" EXACT RESID-name [] synonym: "N4-hydroxymethylasparagine" EXACT RESID-alternate [] @@ -5999,15 +6231,16 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:414" is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00242 name: O-(ADP-ribosyl)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(ADP-ribosyl)-L-serine." [PubMed:15842200, PubMed:3141412, RESID:AA0237, UniMod:213#S] +def: "A protein modification that effectively converts an L-serine residue to O-(ADP-ribosyl)-L-serine." [PubMed:15842200, PubMed:3141412, RESID:AA0237, Unimod:213#S] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid" EXACT RESID-systematic [] -synonym: "ADP Ribose addition" RELATED UniMod-description [] +synonym: "ADP Ribose addition" RELATED Unimod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "MOD_RES ADP-ribosylserine" EXACT UniProt-feature [] synonym: "O-(ADP-ribosyl)-L-serine" EXACT RESID-name [] @@ -6024,7 +6257,9 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: Unimod: "Unimod:213" +xref: UniProt: "PTM-0056" +is_a: MOD:00752 ! monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00916 ! modified L-serine residue [Term] @@ -6045,9 +6280,10 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +xref: UniProt: "PTM-0376" +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:01421 ! oxazole/oxazoline ring crosslinked residues (Ser) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00244 @@ -6067,8 +6303,10 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +xref: UniProt: "PTM-0381" +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:01421 ! oxazole/oxazoline ring crosslinked residues (Ser) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00245 @@ -6088,9 +6326,10 @@ xref: Origin: "G, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0377" +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01421 ! oxazole/oxazoline ring crosslinked residues (Ser) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00246 @@ -6110,9 +6349,10 @@ xref: Origin: "C, G" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0378" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00247 @@ -6132,9 +6372,10 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0363" +is_a: MOD:02055 ! crosslinked L-serine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00248 @@ -6154,9 +6395,10 @@ xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00914 ! modified L-phenylalanine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0375" +is_a: MOD:02053 ! crosslinked L-phenylalanine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00249 @@ -6176,8 +6418,9 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0360" +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00250 @@ -6196,9 +6439,9 @@ xref: Origin: "C, K" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00912 ! modified L-lysine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:00251 @@ -6210,15 +6453,10 @@ synonym: "O-(phospho-5'-DNA)-L-serine" EXACT RESID-name [] synonym: "O3-(phospho-5'-DNA)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 5'-DNA phosphodiester" EXACT RESID-alternate [] -xref: DiffAvg: "78.97" -xref: DiffFormula: "C 0 H 0 N 0 O 3 P 1" -xref: DiffMono: "78.958505" -xref: Formula: "C 3 H 5 N 1 O 5 P 1" -xref: MassAvg: "166.05" -xref: MassMono: "165.990534" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0226" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00916 ! modified L-serine residue @@ -6229,12 +6467,6 @@ synonym: "keratan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threonine" EXACT RESID-name [] synonym: "keratosulfate" EXACT RESID-alternate [] synonym: "poly[beta-1,4-(2-acetamido-2-deoxy-6-sulfate D-glucosyl)-beta-1,3-D-galactosyl]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-threonine" EXACT RESID-systematic [] -xref: DiffAvg: "-1.01" -xref: DiffFormula: "C 0 H -1 N 0 O 0" -xref: DiffMono: "-1.007825" -xref: Formula: "C 4 H 6 N 1 O 2" -xref: MassAvg: "100.10" -xref: MassMono: "100.039853" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" @@ -6243,7 +6475,7 @@ [Term] id: MOD:00253 name: L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide) (Sec) -def: "A protein modification that effectively converts an L-selenocysteine residue to L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)." [PubMed:14235557, PubMed:2211698, PubMed:8052647, PubMed:9036855, RESID:AA0248#SEC, UniMod:415] +def: "A protein modification that effectively converts an L-selenocysteine residue to L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)." [PubMed:14235557, PubMed:2211698, PubMed:8052647, PubMed:9036855, RESID:AA0248#SEC, Unimod:415] xref: DiffAvg: "1572.02" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4 Se 0" xref: DiffMono: "1572.985775" @@ -6253,6 +6485,7 @@ xref: Origin: "U" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:415" is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:01158 ! modified L-selenocysteine residue @@ -6264,15 +6497,10 @@ synonym: "MOD_RES O-(5'-phospho-RNA)-tyrosine" EXACT UniProt-feature [] synonym: "O4'-(phospho-5'-RNA)-L-tyrosine" EXACT RESID-name [] synonym: "O4'-L-tyrosine 5'-RNA phosphodiester" EXACT RESID-alternate [] -xref: DiffAvg: "79.98" -xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" -xref: DiffMono: "79.966331" -xref: Formula: "C 9 H 10 N 1 O 5 P 1" -xref: MassAvg: "243.15" -xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0229" is_a: MOD:00751 ! ribonucleic acid linked residue is_a: MOD:00919 ! modified L-tyrosine residue @@ -6298,18 +6526,19 @@ xref: Origin: "H, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0027" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02048 ! crosslinked L-histidine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00256 name: L-methionine sulfone -def: "A protein modification that dioxygenates an L-methionine residue to L-methionine sulfone." [DeltaMass:205, OMSSA:115, PubMed:12686488, PubMed:7786407, PubMed:7791219, PubMed:9252331, RESID:AA0251, UniMod:425#M] +def: "A protein modification that dioxygenates an L-methionine residue to L-methionine sulfone." [DeltaMass:205, OMSSA:115, PubMed:12686488, PubMed:7786407, PubMed:7791219, PubMed:9252331, RESID:AA0251, Unimod:425#M] comment: DeltaMass gives the formula C 5 H 9 N 3 O 1 S 1 with mass 163 subset: PSI-MOD-slim synonym: "(2S)-2-amino-4-(methylsulfonyl)butanoic acid" EXACT RESID-systematic [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "L-methionine S,S-dioxide" EXACT RESID-alternate [] synonym: "L-methionine sulfone" EXACT RESID-name [] @@ -6328,18 +6557,21 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0175" is_a: MOD:00709 ! sulfur oxygenated L-methionine is_a: MOD:01855 ! sulfur dioxygenated residue + [Term] id: MOD:00257 name: dipyrrolylmethanemethyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to dipyrrolylmethanemethyl-L-cysteine." [PubMed:3042456, PubMed:3196304, PubMed:3421931, PubMed:8727319, RESID:AA0252, UniMod:416] +def: "A protein modification that effectively converts an L-cysteine residue to dipyrrolylmethanemethyl-L-cysteine." [PubMed:3042456, PubMed:3196304, PubMed:3421931, PubMed:8727319, RESID:AA0252, Unimod:416] synonym: "(2S)-3-[5-[4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methyl-4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methylthio-2-aminopropanoic acid" EXACT RESID-systematic [] synonym: "3-[5-(3-acetic acid-4-propanoic acid-1-pyrrol-2-yl)methyl-3-acetic acid-4-propanoic acid-1-pyrrol-2-yl]methylthio-2-aminopropanoic acid" EXACT RESID-alternate [] synonym: "dipyrrole cofactor" EXACT RESID-alternate [] synonym: "Dipyrrolylmethanemethyl" RELATED PSI-MS-label [] -synonym: "dipyrrolylmethanemethyl" RELATED UniMod-description [] +synonym: "dipyrrolylmethanemethyl" RELATED Unimod-description [] synonym: "dipyrrolylmethanemethyl-L-cysteine" EXACT RESID-name [] synonym: "dipyrrolylmethyl-L-cysteine" EXACT RESID-alternate [] synonym: "dipyrromethane cofactor" EXACT RESID-alternate [] @@ -6354,6 +6586,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:416" +xref: UniProt: "PTM-0421" is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -6375,8 +6609,9 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0267" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue [Term] id: MOD:00259 @@ -6387,15 +6622,10 @@ synonym: "MOD_RES O-(5'-phospho-DNA)-tyrosine" EXACT UniProt-feature [] synonym: "O4'-(phospho-5'-DNA)-L-tyrosine" EXACT RESID-name [] synonym: "O4'-L-tyrosine 5'-DNA phosphodiester" EXACT RESID-alternate [] -xref: DiffAvg: "79.98" -xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" -xref: DiffMono: "79.966331" -xref: Formula: "C 9 H 10 N 1 O 5 P 1" -xref: MassAvg: "243.15" -xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0228" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00919 ! modified L-tyrosine residue @@ -6422,7 +6652,7 @@ [Term] id: MOD:00261 name: O4'-(phospho-5'-uridine)-L-tyrosine -def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphouridine through a phosphodiester bond to form O4'-(phospho-5'-uridine)-L-tyrosine." [DeltaMass:0, PubMed:11467524, PubMed:2885322, RESID:AA0256, UniMod:417#Y] +def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphouridine through a phosphodiester bond to form O4'-(phospho-5'-uridine)-L-tyrosine." [DeltaMass:0, PubMed:11467524, PubMed:2885322, RESID:AA0256, Unimod:417#Y] comment: From DeltaMass: Average Mass: 306. subset: PSI-MOD-slim synonym: "(S)-2-amino-3-[4-(5'-uridine phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] @@ -6434,7 +6664,7 @@ synonym: "O4'-L-tyrosine 5'-uridine phosphodiester" EXACT RESID-alternate [] synonym: "OUMPTyr" EXACT PSI-MOD-label [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] -synonym: "uridine phosphodiester" RELATED UniMod-description [] +synonym: "uridine phosphodiester" RELATED Unimod-description [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" @@ -6444,6 +6674,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:417" +xref: UniProt: "PTM-0333" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01166 ! uridylated residue @@ -6465,13 +6697,13 @@ xref: Origin: "E, Y" xref: Source: "natural" xref: TermSpec: "C-term" -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00263 name: S-phycoviolobilin-L-cysteine -def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoviolobilin." [PubMed:2106585, PubMed:3208761, RESID:AA0258, UniMod:387] +def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoviolobilin." [PubMed:2106585, PubMed:3208761, RESID:AA0258, Unimod:387] synonym: "(4S)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-4,5-dihydro-2,7,13,17-tetramethyl-(21H,22H,24H)-biladiene-bc-1,19-dione" EXACT RESID-systematic [] synonym: "BINDING Phycoviolobilin chromophore (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "cryptobiliviolin" EXACT RESID-alternate [] @@ -6479,7 +6711,7 @@ synonym: "cryptoviolobilin" EXACT RESID-alternate [] synonym: "PBV" EXACT RESID-alternate [] synonym: "Phycocyanobilin" RELATED PSI-MS-label [] -synonym: "phycocyanobilin" RELATED UniMod-description [] +synonym: "phycocyanobilin" RELATED Unimod-description [] synonym: "PVB" EXACT RESID-alternate [] synonym: "PXB" EXACT RESID-alternate [] synonym: "S-phycobiliviolin-L-cysteine" EXACT RESID-alternate [] @@ -6493,6 +6725,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:387" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue @@ -6517,7 +6750,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:00265 @@ -6540,18 +6773,12 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:00266 name: N-L-glutamyl-poly-L-glutamic acid def: "A protein modification that effectively forms a peptide bond between a C-terminal L-glutamic acid residue and one or more free L-glutamic acid molecules to form N-(L-glutamyl)-poly-L-glutamic acid." [PubMed:2570347, PubMed:328274, RESID:AA0261] -xref: DiffAvg: "0.00" -xref: DiffFormula: "C 0 H 0 N 0 O 0" -xref: DiffMono: "0.000000" -xref: Formula: "C 10 H 15 N 2 O 7" -xref: MassAvg: "275.24" -xref: MassMono: "275.087926" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "C-term" @@ -6560,7 +6787,7 @@ [Term] id: MOD:00267 name: L-cysteine sulfinic acid -def: "A protein modification that effectively dioxygenates an L-cysteine residue to L-cysteine sulfinic acid." [ChEBI:16345, OMSSA:162, PubMed:12686488, PubMed:9252331, PubMed:9586994, RESID:AA0262, UniMod:425#C] +def: "A protein modification that effectively dioxygenates an L-cysteine residue to L-cysteine sulfinic acid." [ChEBI:16345, OMSSA:162, PubMed:12686488, PubMed:9252331, PubMed:9586994, RESID:AA0262, Unimod:425#C] comment: "Hyun Ae Woo, et. al., Science 300 (5619), 653-656" subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-sulfinopropanoic acid" EXACT RESID-systematic [] @@ -6572,7 +6799,7 @@ synonym: "CysO2H" EXACT PSI-MOD-label [] synonym: "cysteine sulphinic acid" EXACT RESID-alternate [] synonym: "cysteine-S,S-dioxide [tautomer]" EXACT RESID-alternate [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "L-cysteine sulfinic acid" EXACT RESID-name [] synonym: "MOD_RES Cysteine sulfinic acid (-SO2H)" EXACT UniProt-feature [] @@ -6588,21 +6815,24 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0108" is_a: MOD:00708 ! sulfur oxygenated L-cysteine is_a: MOD:01855 ! sulfur dioxygenated residue [Term] id: MOD:00268 name: L-3',4',5'-trihydroxyphenylalanine -def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4',5'-trihydroxyphenylalanine." [DeltaMass:0, PubMed:12686488, PubMed:12771378, PubMed:8554314, PubMed:9252331, PubMed:9434739, RESID:AA0263, UniMod:425#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4',5'-trihydroxyphenylalanine." [DeltaMass:0, PubMed:12686488, PubMed:12771378, PubMed:8554314, PubMed:9252331, PubMed:9434739, RESID:AA0263, Unimod:425#Y, ChEBI:141811] comment: From DeltaMass: Average Mass: 32 synonym: "(S)-2-amino-3-(3,4,5-trihydroxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "3,4,6-Trihydroxy-Phenylalanine (from Tyrosine) (TOPA)" EXACT DeltaMass-label [] synonym: "35Hy2Tyr" EXACT PSI-MOD-label [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "L-3',4',5'-trihydroxyphenylalanine" EXACT RESID-name [] synonym: "L-3,4,5-TOPA" EXACT RESID-alternate [] +synonym: "MOD_RES 3',4',5'-trihydroxyphenylalanine" EXACT UniProt-feature [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" @@ -6612,18 +6842,20 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0667" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00707 ! hydroxylated tyrosine [Term] id: MOD:00269 name: O-(sn-1-glycerophosphoryl)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(sn-1-glycerophosphoryl)-L-serine." [PubMed:8645220, RESID:AA0264, UniMod:419#S] +def: "A protein modification that effectively converts an L-serine residue to O-(sn-1-glycerophosphoryl)-L-serine." [PubMed:8645220, RESID:AA0264, Unimod:419#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-[(2Xi)-2,3-dihydroxypropyl]phosphonoxypropanoic acid" EXACT RESID-systematic [] synonym: "alpha-glycerophosphoryl serine" EXACT RESID-alternate [] synonym: "Glycerophospho" RELATED PSI-MS-label [] -synonym: "glycerophospho" RELATED UniMod-description [] +synonym: "glycerophospho" RELATED Unimod-description [] synonym: "glycerophosphoserine" EXACT RESID-alternate [] synonym: "MOD_RES O-(sn-1-glycerophosphoryl)serine" EXACT UniProt-feature [] synonym: "O-(sn-1-glycerophosphoryl)-L-serine" EXACT RESID-name [] @@ -6639,6 +6871,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:419" +xref: UniProt: "PTM-0230" is_a: MOD:00916 ! modified L-serine residue [Term] @@ -6656,7 +6890,7 @@ synonym: "Carboxy->Thiocarboxy" RELATED PSI-MS-label [] synonym: "MOD_RES 1-thioglycine" EXACT UniProt-feature [] synonym: "S(O)Gly" EXACT PSI-MOD-label [] -synonym: "thiocarboxylic acid" RELATED UniMod-description [] +synonym: "thiocarboxylic acid" RELATED Unimod-description [] xref: DiffAvg: "16.06" xref: DiffFormula: "C 0 H 0 N 0 O -1 S 1" xref: DiffMono: "15.977156" @@ -6666,6 +6900,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0004" is_a: MOD:01625 ! 1-thioglycine [Term] @@ -6687,18 +6922,18 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02075 ! metal or metal cluster coordinated L-tyrosine residue [Term] id: MOD:00272 name: O-(phospho-5'-adenosine)-L-threonine -def: "A protein modification that effectively crosslinks an L-threonine residue and 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-threonine." [PubMed:2989287, PubMed:8917428, RESID:AA0267, UniMod:405#T] +def: "A protein modification that effectively crosslinks an L-threonine residue and 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-threonine." [PubMed:2989287, PubMed:8917428, RESID:AA0267, Unimod:405#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(5'-adenosine phosphonoxy)butanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-O3-L-threonine" EXACT RESID-alternate [] synonym: "ACT_SITE O-AMP-threonine intermediate" EXACT UniProt-feature [] -synonym: "AMP binding site" RELATED UniMod-description [] +synonym: "AMP binding site" RELATED Unimod-description [] synonym: "beta-5'-adenylic-L-threonine" EXACT RESID-alternate [] synonym: "L-threonine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] synonym: "MOD_RES O-AMP-threonine" EXACT UniProt-feature [] @@ -6716,6 +6951,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:405" +xref: UniProt: "PTM-0393" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01165 ! adenylated residue @@ -6742,14 +6979,14 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00274 name: L-cysteine persulfide -def: "A protein modification that effectively replaces the hydrogen atom of a cysteine sulfanyl group with a sulfanyl group, forming a disulfanyl group, and converting an L-cysteine residue to L-cysteine persulfide." [ChEBI:28839, PubMed:15096637, PubMed:4276457, PubMed:8161529, RESID:AA0269, UniMod:421] +def: "A protein modification that effectively replaces the hydrogen atom of a cysteine sulfanyl group with a sulfanyl group, forming a disulfanyl group, and converting an L-cysteine residue to L-cysteine persulfide." [ChEBI:28839, PubMed:15096637, PubMed:4276457, PubMed:8161529, RESID:AA0269, Unimod:421] subset: PSI-MOD-slim synonym: "(R)-2-amino-3-disulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-disulfanylpropanoic acid" EXACT RESID-alternate [] @@ -6761,7 +6998,7 @@ synonym: "ACT_SITE Cysteine persulfide intermediate" EXACT UniProt-feature [] synonym: "L-cysteine persulfide" EXACT RESID-name [] synonym: "MOD_RES Cysteine persulfide" EXACT UniProt-feature [] -synonym: "persulfide" RELATED UniMod-description [] +synonym: "persulfide" RELATED Unimod-description [] synonym: "S-mercaptocysteine" EXACT RESID-alternate [] synonym: "S-sulfanylcysteine" EXACT RESID-alternate [] synonym: "Sulfide" RELATED PSI-MS-label [] @@ -6775,6 +7012,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:421" +xref: UniProt: "PTM-0106" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01886 ! thiolated residue @@ -6800,9 +7039,10 @@ xref: Origin: "H, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0003" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02048 ! crosslinked L-histidine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00276 @@ -6823,8 +7063,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00912 ! modified L-lysine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02074 ! metal or metal cluster coordinated L-lysine residue [Term] id: MOD:00277 @@ -6838,7 +7078,7 @@ synonym: "C5Me1Arg" EXACT PSI-MOD-label [] synonym: "delta-methylarginine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES 5-methylarginine" EXACT UniProt-feature [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" @@ -6849,6 +7089,7 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0050" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00656 ! C-methylated residue @@ -6863,7 +7104,7 @@ synonym: "alpha-methylglutamine" EXACT RESID-alternate [] synonym: "C2MeGln" EXACT PSI-MOD-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES 2-methylglutamine" EXACT UniProt-feature [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" @@ -6874,17 +7115,18 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0016" is_a: MOD:00656 ! C-methylated residue is_a: MOD:00722 ! monomethylated L-glutamine [Term] id: MOD:00279 name: N-pyruvic acid 2-iminyl-L-cysteine -def: "A protein modification that effectively converts an Lcysteline residue to N-pyruvic acid 2-iminyl-L-cysteine." [PubMed:1388164, RESID:AA0274, UniMod:422#C] +def: "A protein modification that effectively converts an L-cysteine residue to N-pyruvic acid 2-iminyl-L-cysteine." [PubMed:1388164, RESID:AA0274, Unimod:422#C] subset: PSI-MOD-slim synonym: "(R)-2-(1-carboxy-2-sulfanylethanimino)propanoic acid" EXACT RESID-systematic [] synonym: "MOD_RES N-pyruvate 2-iminyl-cysteine" EXACT UniProt-feature [] -synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] +synonym: "N-pyruvic acid 2-iminyl" RELATED Unimod-description [] synonym: "N-pyruvic acid 2-iminyl-L-cysteine" EXACT RESID-name [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" @@ -6896,17 +7138,19 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:422" +xref: UniProt: "PTM-0224" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01170 ! pyruvic acid iminylated residue [Term] id: MOD:00280 name: N-pyruvic acid 2-iminyl-L-valine -def: "A protein modification that effectively converts an L-valine residue to N-pyruvic acid 2-iminyl-L-valine." [PubMed:2071591, RESID:AA0275, UniMod:422#V] +def: "A protein modification that effectively converts an L-valine residue to N-pyruvic acid 2-iminyl-L-valine." [PubMed:2071591, RESID:AA0275, Unimod:422#V] subset: PSI-MOD-slim synonym: "(S)-2-(1-carboxy-2-methylpropanimino)propanoic acid" EXACT RESID-systematic [] synonym: "MOD_RES N-pyruvate 2-iminyl-valine" EXACT UniProt-feature [] -synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] +synonym: "N-pyruvic acid 2-iminyl" RELATED Unimod-description [] synonym: "N-pyruvic acid 2-iminyl-L-valine" EXACT RESID-name [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" @@ -6918,6 +7162,8 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:422" +xref: UniProt: "PTM-0225" is_a: MOD:00920 ! modified L-valine residue is_a: MOD:01170 ! pyruvic acid iminylated residue @@ -6943,12 +7189,12 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00282 name: S-selenyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-selenyl-L-cysteine." [PubMed:10430865, PubMed:10966817, PubMed:11827487, PubMed:12716131, PubMed:14594807, RESID:AA0277, UniMod:423#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-selenyl-L-cysteine." [PubMed:10430865, PubMed:10966817, PubMed:11827487, PubMed:12716131, PubMed:14594807, RESID:AA0277, Unimod:423#C] synonym: "(R)-2-amino-3-(selanylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroselenosulfidopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-hydroselenylsulfidopropanoic acid" EXACT RESID-alternate [] @@ -6956,11 +7202,11 @@ synonym: "ACT_SITE S-selanylcysteine intermediate" EXACT UniProt-feature [] synonym: "cysteine perselenide" RELATED RESID-misnomer [] synonym: "Delta:Se(1)" RELATED PSI-MS-label [] -synonym: "MOD_RES S-selanylcysteine" EXACT UniProt-feature [] +synonym: "MOD_RES S-selenylcysteine" EXACT UniProt-feature [] synonym: "S-selanyl-L-cysteine" EXACT RESID-name [] synonym: "S-selanylcysteine" EXACT RESID-alternate [] synonym: "S-selenylcysteine" EXACT RESID-alternate [] -synonym: "selenyl" RELATED UniMod-description [] +synonym: "selenyl" RELATED Unimod-description [] xref: DiffAvg: "78.97" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0 Se 1" xref: DiffMono: "79.916521" @@ -6970,6 +7216,8 @@ xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:423" +xref: UniProt: "PTM-0282" is_a: MOD:00745 ! selenium containing residue is_a: MOD:00778 ! residues isobaric at 182.9-183.0 Da is_a: MOD:00905 ! modified L-cysteine residue @@ -6984,15 +7232,10 @@ synonym: "N6-[3-([(omega)-(dimethyl)aminopropyl-poly(3-[methylamino]propyl)]amino)propyl]lysine" EXACT RESID-alternate [] synonym: "N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysine" EXACT RESID-name [] synonym: "silaffin polycationic lysine derivative" EXACT RESID-alternate [] -xref: DiffAvg: "426.74" -xref: DiffFormula: "C 24 H 54 N 6 O 0" -xref: DiffMono: "426.440996" -xref: Formula: "C 30 H 66 N 8 O 1" -xref: MassAvg: "554.91" -xref: MassMono: "554.535959" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0198" is_a: MOD:00912 ! modified L-lysine residue [Term] @@ -7015,8 +7258,8 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue [Term] id: MOD:00285 @@ -7039,18 +7282,18 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00913 ! modified L-methionine residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02071 ! metal or metal cluster coordinated L-methionine residue [Term] id: MOD:00286 name: L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide) -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide)." [RESID:AA0281, UniMod:424#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide)." [RESID:AA0281, Unimod:424#C] synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-cystein-S-yl-molybdenum" EXACT RESID-systematic [] synonym: "L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" EXACT RESID-name [] -synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] +synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED Unimod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] xref: DiffAvg: "1572.02" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4" @@ -7061,13 +7304,14 @@ xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +xref: Unimod: "Unimod:424" +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue is_a: MOD:01167 ! molybdopterin guanine dinucleotide [Term] id: MOD:00287 name: (2S,3R,4S)-3,4-dihydroxyproline -def: "A protein modification that effectively converts an L-proline residue to a (2S,3R,4S)-3,4-dihydroxyproline." [DeltaMass:0, PubMed:12686488, RESID:AA0282, UniMod:425#P] +def: "A protein modification that effectively converts an L-proline residue to a (2S,3R,4S)-3,4-dihydroxyproline." [DeltaMass:0, PubMed:12686488, RESID:AA0282, Unimod:425#P, ChEBI:141803] comment: From DeltaMass: Average Mass: 32. synonym: "(2S,3R,4S)-3,4-dihydroxyproline" EXACT RESID-name [] synonym: "(2S,3R,4S)-3,4-dihydroxypyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] @@ -7076,7 +7320,7 @@ synonym: "3,4-dihydroxylated L-proline" EXACT PSI-MOD-alternate [] synonym: "3,4-Dihydroxylation (of Proline)" EXACT DeltaMass-label [] synonym: "34Hy2Pro" EXACT PSI-MOD-label [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "MOD_RES (3R,4S)-3,4-dihydroxyproline" EXACT UniProt-feature [] synonym: "trans-2,3-cis-3,4-dihydroxy-L-proline" EXACT RESID-alternate [] @@ -7089,6 +7333,8 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0306" is_a: MOD:00866 ! dihydroxylated proline [Term] @@ -7112,9 +7358,10 @@ xref: Origin: "E, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0263" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00289 @@ -7136,8 +7383,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00290 @@ -7159,8 +7406,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00291 @@ -7181,16 +7428,16 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00292 name: N6-pyruvic acid 2-iminyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-pyruvic acid 2-iminyl-L-lysine." [PubMed:1463470, PubMed:7853400, PubMed:9047371, RESID:AA0287, UniMod:422#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-pyruvic acid 2-iminyl-L-lysine." [PubMed:1463470, PubMed:7853400, PubMed:9047371, RESID:AA0287, Unimod:422#K] synonym: "(2S)-2-amino-6-([1-carboxyethylidene]amino)hexanoic acid" EXACT RESID-systematic [] synonym: "ACT_SITE Schiff-base intermediate with substrate" EXACT UniProt-feature [] -synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] +synonym: "N-pyruvic acid 2-iminyl" RELATED Unimod-description [] synonym: "N6-pyruvic acid 2-iminyl-L-lysine" EXACT RESID-name [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" @@ -7202,6 +7449,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:422" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01170 ! pyruvic acid iminylated residue @@ -7223,8 +7471,8 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02072 ! metal or metal cluster coordinated L-serine residue [Term] id: MOD:00294 @@ -7246,14 +7494,14 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue +is_a: MOD:02072 ! metal or metal cluster coordinated L-serine residue [Term] id: MOD:00295 name: O-octanoyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-octanoyl-L-serine." [PubMed:10604470, PubMed:12716131, RESID:AA0290, UniMod:426#S] +def: "A protein modification that effectively converts an L-serine residue to O-octanoyl-L-serine." [PubMed:10604470, PubMed:12716131, RESID:AA0290, Unimod:426#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(octanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "L-serine octanoate ester" EXACT RESID-alternate [] @@ -7262,7 +7510,7 @@ synonym: "O-octanoylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-octanoyl-L-serine" EXACT RESID-alternate [] synonym: "Octanoyl" RELATED PSI-MS-label [] -synonym: "octanoyl" RELATED UniMod-description [] +synonym: "octanoyl" RELATED Unimod-description [] synonym: "OOctSer" EXACT PSI-MOD-label [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" @@ -7273,18 +7521,20 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:426" +xref: UniProt: "PTM-0239" is_a: MOD:00669 ! O-octanoylated residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine [Term] id: MOD:00296 name: O-D-glucuronosyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-D-glucuronosyl-L-serine." [PubMed:10858503, PubMed:12716131, PubMed:7398618, RESID:AA0291, UniMod:54#S] +def: "A protein modification that effectively converts an L-serine residue to O-D-glucuronosyl-L-serine." [PubMed:10858503, PubMed:12716131, PubMed:7398618, RESID:AA0291, Unimod:54#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(beta-D-glucopyranuronosyl)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GlcA)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GlcA) serine" EXACT UniProt-feature [] synonym: "Glucuronyl" RELATED PSI-MS-label [] -synonym: "N-glucuronylation" RELATED UniMod-description [] +synonym: "N-glucuronylation" RELATED Unimod-description [] synonym: "O-D-glucuronosyl-L-serine" EXACT RESID-name [] synonym: "O3-D-glucuronosyl-L-serine" EXACT RESID-alternate [] xref: DiffAvg: "176.12" @@ -7296,6 +7546,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:54" +xref: UniProt: "PTM-0577" is_a: MOD:00447 ! N-glucuronylated residue is_a: MOD:00916 ! modified L-serine residue @@ -7320,9 +7572,9 @@ xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00298 @@ -7345,10 +7597,10 @@ xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue +is_a: MOD:02072 ! metal or metal cluster coordinated L-serine residue [Term] id: MOD:00299 @@ -7372,45 +7624,42 @@ xref: Origin: "K, N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue +xref: UniProt: "PTM-0153" +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia is_a: MOD:01929 ! N6-(L-isoaspartyl)-L-lysine [Term] id: MOD:00300 name: L-glutamyl-5-poly(ADP-ribose) -def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl-5-poly(ADP-ribose)." [DeltaMass:0, PubMed:11246023, PubMed:15842200, PubMed:8533153, RESID:AA0295, UniMod:213#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl-5-poly(ADP-ribose)." [DeltaMass:0, PubMed:11246023, PubMed:15842200, PubMed:8533153, RESID:AA0295, Unimod:213#E] synonym: "(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid" EXACT RESID-systematic [] -synonym: "ADP Ribose addition" RELATED UniMod-description [] +synonym: "ADP Ribose addition" RELATED Unimod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "L-glutamyl-5-poly(ADP-ribose)" EXACT RESID-name [] synonym: "L-isoglutamyl-poly(ADP-ribose)" EXACT RESID-alternate [] synonym: "MOD_RES PolyADP-ribosyl glutamic acid" EXACT UniProt-feature [] synonym: "O-ADP-ribosylation (on Glutamate or C terminus)" EXACT DeltaMass-label [] -xref: DiffAvg: "541.30" -xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" -xref: DiffMono: "541.061109" -xref: Formula: "C 20 H 28 N 6 O 16 P 2" -xref: MassAvg: "670.42" -xref: MassMono: "670.103702" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: Unimod: "Unimod:213" +is_a: MOD:02087 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00301 name: O-(N-acetylglucosamine-1-phosphoryl)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(N-acetylglucosamine-1-phosphoryl)-L-serine." [DeltaMass:0, PubMed:6438439, PubMed:6993483, PubMed:8631906, RESID:AA0296, UniMod:428] +def: "A protein modification that effectively converts an L-serine residue to O-(N-acetylglucosamine-1-phosphoryl)-L-serine." [DeltaMass:0, PubMed:6438439, PubMed:6993483, PubMed:8631906, RESID:AA0296, Unimod:428] synonym: "(2S)-2-amino-3-[([(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)oxy][hydroxy]phosphoryl)oxy]propanoic acid" EXACT RESID-systematic [] -synonym: "N-acetylglucosamine-1-phosphoryl" RELATED UniMod-description [] +synonym: "N-acetylglucosamine-1-phosphoryl" RELATED Unimod-description [] synonym: "O-(N-acetylglucosamine-1-phosphoryl)-L-serine" EXACT RESID-name [] synonym: "O-beta(N-acetyl-glucosamine-alpha1-phosphate)serine" EXACT RESID-alternate [] synonym: "O-GlcNAc-1-phosphorylation (of Serine)" EXACT DeltaMass-label [] synonym: "O3-(N-acetylglucosamine-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 2-(acetylamino)-2-deoxy-D-glucopyranose 1-phosphodiester" EXACT RESID-alternate [] synonym: "PhosphoHexNAc" RELATED PSI-MS-label [] +synonym: "CARBOHYD O-linked (GalNAcP) serine" EXACT UniProt-feature [] xref: DiffAvg: "283.17" xref: DiffFormula: "C 8 H 14 N 1 O 8 P 1" xref: DiffMono: "283.045703" @@ -7420,20 +7669,23 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:428" +xref: UniProt: "PTM-0586" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01804 ! glycosylphosphorylated residue [Term] id: MOD:00302 name: O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine." [PubMed:10037765, PubMed:15649890, RESID:AA0297, UniMod:429] +def: "A protein modification that effectively converts an L-serine residue to O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine." [PubMed:10037765, PubMed:15649890, RESID:AA0297, Unimod:429] synonym: "O-(alpha-D-mannosyl-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O-(D-mannose-1-phosphoryl)-L-serine" EXACT RESID-name [] synonym: "O-[alpha-D-mannopyranosyloxy(hydroxy)phosphoryl]-L-serine" EXACT RESID-systematic [] synonym: "O3-(D-mannose-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine alpha-D-mannopyranose 1-phosphodiester" EXACT RESID-alternate [] -synonym: "phosphoglycosyl-D-mannose-1-phosphoryl" RELATED UniMod-description [] +synonym: "phosphoglycosyl-D-mannose-1-phosphoryl" RELATED Unimod-description [] synonym: "PhosphoHex" RELATED PSI-MS-label [] +synonym: "CARBOHYD O-linked (Man1P) serine" EXACT UniProt-feature [] xref: DiffAvg: "242.12" xref: DiffFormula: "C 6 H 11 N 0 O 8 P 1" xref: DiffMono: "242.019154" @@ -7443,6 +7695,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:429" +xref: UniProt: "PTM-0594" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01804 ! glycosylphosphorylated residue @@ -7466,12 +7720,12 @@ xref: TermSpec: "none" is_a: MOD:00742 ! copper containing modified residue is_a: MOD:00860 ! sulfur containing modified residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00304 name: L-leucine methyl ester -def: "A protein modification that effectively converts an L-leucine residue to L-leucine methyl ester." [PubMed:10191253, PubMed:11875433, PubMed:8206937, RESID:AA0299, UniMod:34#C-term] +def: "A protein modification that effectively converts an L-leucine residue to L-leucine methyl ester." [PubMed:10191253, PubMed:11875433, PubMed:8206937, RESID:AA0299, Unimod:34#C-term] comment: incidental to RESID:AA0039 subset: PSI-MOD-slim synonym: "2-amino-4-methylpentanoic methyl ester" EXACT RESID-alternate [] @@ -7481,7 +7735,7 @@ synonym: "methyl (2S)-2-amino-4-methylpentanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-leucine" EXACT PSI-MOD-alternate [] synonym: "methyl L-leucinate" EXACT RESID-alternate [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Leucine methyl ester" EXACT UniProt-feature [] synonym: "OMeLeu" EXACT PSI-MOD-label [] xref: DiffAvg: "14.03" @@ -7493,6 +7747,8 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0167" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00662 ! methylated leucine is_a: MOD:01689 ! alpha-carboxyl methylated residue @@ -7517,8 +7773,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02072 ! metal or metal cluster coordinated L-serine residue [Term] id: MOD:00306 @@ -7542,14 +7798,14 @@ [Term] id: MOD:00307 name: L-aspartimide -def: "A protein modification that effectively cyclizes an L-asparagine residue to form a carboxyl-terminal L-aspartimide." [DeltaMass:18, PubMed:12771378, PubMed:2378679, PubMed:7662664, PubMed:7988548, PubMed:9309583, RESID:AA0302, UniMod:23#N] +def: "A protein modification that effectively cyclizes an L-asparagine residue to form a carboxyl-terminal L-aspartimide." [DeltaMass:18, PubMed:12771378, PubMed:2378679, PubMed:7662664, PubMed:7988548, PubMed:9309583, RESID:AA0302, Unimod:23#N] comment: From DeltaMass: Average Mass: -17 Average Mass Change:-17 References:Clarke, S., Lability of Aspargine and Aspartic Acid Residues in Protein and Peptides, in: Stability of Protein Pharmaceuticals : Chemical and Physical Paths of Protein Degradation, Part A (T.J. Ahern and M.C. Manning, eds.), 1992,Plenum Press, New York, pp.1-29Xie, M.; Vander Velde, D.; Morton, M.; Borchardt, R.T.; Schowen,R.L.: pH-Induced Change in the Rate-Determining Step for the Hydrolysis of the Asp/Asn-Derived Cyclic-Imide Intermediate in Protein Degradation. (1996) J. Am. Chem. Soc. 118: 8955-8956. synonym: "(3S)-3-amino-2,5-pyrrolidinedione" EXACT RESID-systematic [] synonym: "2-amino-butanimide" EXACT RESID-alternate [] synonym: "alpha-aminosuccinimide" EXACT RESID-alternate [] synonym: "ASI" EXACT RESID-alternate [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "L-2-aminosuccinimide" EXACT RESID-alternate [] synonym: "L-3-aminosuccinimide" RELATED RESID-misnomer [] synonym: "L-asparaginimide" EXACT RESID-alternate [] @@ -7564,6 +7820,7 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:23" is_a: MOD:00601 ! cyclized residue is_a: MOD:00704 ! dehydrated residue is_a: MOD:00903 ! modified L-asparagine residue @@ -7571,13 +7828,13 @@ [Term] id: MOD:00308 name: L-glutamimide -def: "A protein modification that effectively cyclizes an L-glutamine residue to form a carboxyl-terminal L-glutamimide." [PubMed:12771378, PubMed:14593103, RESID:AA0303, UniMod:23#Q] +def: "A protein modification that effectively cyclizes an L-glutamine residue to form a carboxyl-terminal L-glutamimide." [PubMed:12771378, PubMed:14593103, RESID:AA0303, Unimod:23#Q] synonym: "(3S)-3-aminopiperidine-2,6-dione" EXACT RESID-systematic [] synonym: "2-aminopentanimide" EXACT RESID-alternate [] synonym: "3-amino-2,6-piperidinedione" EXACT RESID-alternate [] synonym: "alpha-aminoglutarimide" EXACT RESID-alternate [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "L-glutamimide" EXACT RESID-name [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" @@ -7588,6 +7845,7 @@ xref: Origin: "Q" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:23" is_a: MOD:00601 ! cyclized residue is_a: MOD:00704 ! dehydrated residue is_a: MOD:00907 ! modified L-glutamine residue @@ -7595,7 +7853,7 @@ [Term] id: MOD:00309 name: L-beta-carboxyaspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-carboxyaspartic acid." [OMSSA:47, PubMed:6390094, PubMed:7138832, PubMed:7457858, PubMed:8135347, RESID:AA0304, UniMod:299#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-carboxyaspartic acid." [OMSSA:47, PubMed:6390094, PubMed:7138832, PubMed:7457858, PubMed:8135347, RESID:AA0304, Unimod:299#D] comment: References to this modification as a gamma-carboxylation are in error [JSG]. synonym: "(2S)-2-aminoethane-1,1,2-tricarboxylic acid" EXACT RESID-systematic [] synonym: "2-amino-3-carboxybutanedioic acid" EXACT RESID-alternate [] @@ -7604,8 +7862,8 @@ synonym: "3CbxAsp" EXACT PSI-MOD-label [] synonym: "beta-carboxyaspartic acid" EXACT RESID-alternate [] synonym: "Carboxy" RELATED PSI-MS-label [] -synonym: "Carboxy" RELATED UniMod-interim [] -synonym: "Carboxylation" RELATED UniMod-description [] +synonym: "Carboxy" RELATED Unimod-interim [] +synonym: "Carboxylation" RELATED Unimod-description [] synonym: "gammacarboxyld" EXACT OMSSA-label [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" @@ -7616,6 +7874,7 @@ xref: Origin: "D" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:299" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01152 ! carboxylated residue @@ -7626,7 +7885,7 @@ synonym: "(2S)-2-amino-5-(N-methylcarbamimidamido)pentanoic acid" EXACT RESID-systematic [] synonym: "delta-N-methylarginine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N5-methylarginine" EXACT UniProt-feature [] synonym: "N5-carbamimidoyl-N5-methyl-L-ornithine" EXACT RESID-alternate [] synonym: "N5-methyl-L-arginine" EXACT RESID-name [] @@ -7641,18 +7900,19 @@ xref: Origin: "R" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0185" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00602 ! N-methylated residue [Term] id: MOD:00311 name: L-cysteine coenzyme A disulfide -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine coenzyme A disulfide." [DeltaMass:0, PubMed:1734967, RESID:AA0306, UniMod:281#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine coenzyme A disulfide." [DeltaMass:0, PubMed:1734967, RESID:AA0306, Unimod:281#C] comment: DeltaMass gives no formula with mass as 454. synonym: "(2R)-2-amino-3-(2-((3-(((2R)-2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)amino)-1-oxopropyl)amino)ethyl)dithio-propanoic acid 4'-ester with adenosine 5'-(trihydrogen diphosphate) 3'-(dihydrogen phosphate)" EXACT RESID-systematic [] synonym: "coenzyme A L-cysteine mixed disulfide" EXACT RESID-alternate [] synonym: "CoenzymeA" RELATED PSI-MS-label [] -synonym: "Cysteine modified Coenzyme A" RELATED UniMod-description [] +synonym: "Cysteine modified Coenzyme A" RELATED Unimod-description [] synonym: "L-cysteine coenzyme A disulfide" EXACT RESID-name [] synonym: "SCoACys" EXACT PSI-MOD-label [] xref: DiffAvg: "765.52" @@ -7664,6 +7924,7 @@ xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:281" is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01862 ! disulfide conjugated residue @@ -7671,11 +7932,11 @@ [Term] id: MOD:00312 name: S-myristoyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-myristoyl-L-cysteine." [PubMed:10026218, PubMed:10080938, PubMed:8824274, RESID:AA0307, UniMod:45#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-myristoyl-L-cysteine." [PubMed:10026218, PubMed:10080938, PubMed:8824274, RESID:AA0307, Unimod:45#C] synonym: "(R)-2-amino-3-(tetradecanoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "LIPID S-myristoyl cysteine" EXACT UniProt-feature [] synonym: "Myristoyl" RELATED PSI-MS-label [] -synonym: "Myristoylation" RELATED UniMod-description [] +synonym: "Myristoylation" RELATED Unimod-description [] synonym: "S-(C14:1 aliphatic acyl)cysteine" EXACT PSI-MOD-alternate [] synonym: "S-myristoyl-L-cysteine" EXACT RESID-name [] synonym: "S-myristoylated L-cysteine" EXACT PSI-MOD-alternate [] @@ -7690,18 +7951,19 @@ xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:45" is_a: MOD:00655 ! S-myristoylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00313 name: S-palmitoleyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoleyl-L-cysteine." [OMSSA:187, PubMed:8294460, RESID:AA0308, UniMod:431#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoleyl-L-cysteine." [OMSSA:187, PubMed:8294460, RESID:AA0308, Unimod:431#C] synonym: "(R)-2-amino-3-((Z)-9-hexadecenoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "cis-9-hexadecenoate cysteine thioester" EXACT RESID-alternate [] synonym: "mod187" EXACT OMSSA-label [] synonym: "Palmitoleyl" RELATED PSI-MS-label [] -synonym: "palmitoleyl" RELATED UniMod-description [] +synonym: "palmitoleyl" RELATED Unimod-description [] synonym: "S-palmitoleyl-L-cysteine" EXACT RESID-name [] synonym: "S-palmitoleylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "SPamD1Cys" EXACT PSI-MOD-label [] @@ -7714,18 +7976,19 @@ xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00672 ! S-acylated residue +xref: Unimod: "Unimod:431" +xref: UniProt: "PTM-0645" +is_a: MOD:02002 ! S-palmitoleylated residue is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:01423 ! palmitoleylated residue [Term] id: MOD:00314 name: glycine cholesterol ester -def: "A protein modification that effectively converts a glycine residue to glycine cholesterol ester." [PubMed:11111088, PubMed:8824192, RESID:AA0309, UniMod:432#C-term] -comment: Incidental to RESID:AA0060. UniMod origin corrected [JSG]. +def: "A protein modification that effectively converts a glycine residue to glycine cholesterol ester." [PubMed:11111088, PubMed:8824192, RESID:AA0309, Unimod:432#C-term, ChEBI:143135] +comment: Incidental to RESID:AA0060. Unimod origin corrected [JSG]. subset: PSI-MOD-slim -synonym: "C-cholesterol" RELATED UniMod-interim [] -synonym: "cholesterol ester" RELATED UniMod-description [] +synonym: "C-cholesterol" RELATED Unimod-interim [] +synonym: "cholesterol ester" RELATED Unimod-description [] synonym: "cholesteryl glycinate" EXACT RESID-alternate [] synonym: "glycine cholest-5-en-3beta-ol ester" EXACT RESID-systematic [] synonym: "glycine cholesterol ester" EXACT RESID-name [] @@ -7740,6 +8003,8 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:432" +xref: UniProt: "PTM-0090" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01155 ! lipoconjugated residue @@ -7765,17 +8030,17 @@ xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00316 name: N4,N4-dimethyl-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N4,N4-dimethyl-L-asparagine." [PubMed:12964758, PubMed:14570711, PubMed:8783012, RESID:AA0311, UniMod:36#N] +def: "A protein modification that effectively converts an L-asparagine residue to N4,N4-dimethyl-L-asparagine." [PubMed:12964758, PubMed:14570711, PubMed:8783012, RESID:AA0311, Unimod:36#N] synonym: "(2S)-2-amino-4-(dimethylamino)-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-amino-N4,N4-dimethylbutanediamic acid" EXACT RESID-alternate [] synonym: "beta-dimethylasparagine" RELATED RESID-misnomer [] -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "MOD_RES N4,N4-dimethylasparagine" EXACT UniProt-feature [] synonym: "N(gamma),N(gamma)-dimethylasparagine" EXACT RESID-alternate [] @@ -7791,6 +8056,8 @@ xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" +xref: UniProt: "PTM-0182" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00673 ! methylated asparagine @@ -7798,9 +8065,9 @@ [Term] id: MOD:00317 name: N6-3,4-didehydroretinylidene-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-3,4-didehydroretinylidene-L-lysine." [PubMed:10717661, PubMed:3257009, PubMed:4056688, RESID:AA0312, UniMod:433#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-3,4-didehydroretinylidene-L-lysine." [PubMed:10717661, PubMed:3257009, PubMed:4056688, RESID:AA0312, Unimod:433#K] synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT RESID-systematic [] -synonym: "3,4-didehydroretinylidene" RELATED UniMod-description [] +synonym: "3,4-didehydroretinylidene" RELATED Unimod-description [] synonym: "Didehydroretinylidene" RELATED PSI-MS-label [] synonym: "N6-(3,4-didehydroretinylidene)-L-lysine" EXACT RESID-name [] synonym: "N6-3-dehydroretinal-L-lysine" EXACT RESID-alternate [] @@ -7814,6 +8081,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:433" is_a: MOD:00912 ! modified L-lysine residue [Term] @@ -7837,8 +8105,9 @@ xref: Origin: "C, W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0041" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00918 ! modified L-tryptophan residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue [Term] id: MOD:00319 @@ -7859,7 +8128,8 @@ xref: Origin: "C, D" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +xref: UniProt: "PTM-0025" +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:01993 ! beta-carbon thioether crosslinked residues [Term] @@ -7880,18 +8150,19 @@ xref: Origin: "C, E" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0040" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue [Term] id: MOD:00321 name: cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester -def: "A protein modification that effectively converts an L-aspartic acid residue to cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester." [PubMed:11435437, PubMed:7949339, RESID:AA0316, UniMod:434#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester." [PubMed:11435437, PubMed:7949339, RESID:AA0316, Unimod:434#D] synonym: "(7Z,14Xi)-14-[(S)-3-amino-3-carboxy-propanoyl]oxy-10,13-dioxo-7-heptadecenoic acid" EXACT RESID-systematic [] synonym: "barley lipid transfer protein modification" EXACT RESID-alternate [] synonym: "CHDH" RELATED PSI-MS-label [] synonym: "cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester" EXACT RESID-name [] -synonym: "cis-14-hydroxy-10,13-dioxo-7-heptadecenoic ester" RELATED UniMod-description [] +synonym: "cis-14-hydroxy-10,13-dioxo-7-heptadecenoic ester" RELATED Unimod-description [] synonym: "LIPID Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester" EXACT UniProt-feature [] xref: DiffAvg: "294.39" xref: DiffFormula: "C 17 H 26 N 0 O 4" @@ -7902,6 +8173,8 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:434" +xref: UniProt: "PTM-0091" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01155 ! lipoconjugated residue @@ -7915,7 +8188,7 @@ synonym: "3-methylhistidine" RELATED RESID-misnomer [] synonym: "4-methyl-histidine" RELATED RESID-misnomer [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Tele-methylhistidine" EXACT UniProt-feature [] synonym: "N(epsilon)-methylhistidine" EXACT RESID-alternate [] synonym: "N(tau)-methylhistidine" EXACT RESID-alternate [] @@ -7931,12 +8204,14 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0290" +is_a: MOD:02038 ! monomethylated L-histidine is_a: MOD:00724 ! N-methylated L-histidine [Term] id: MOD:00323 name: L-lysine methyl ester -def: "A protein modification that effectively converts an L-lysine residue to L-lysine methyl ester." [PubMed:10973948, PubMed:11875433, RESID:AA0318, UniMod:34#C-term] +def: "A protein modification that effectively converts an L-lysine residue to L-lysine methyl ester." [PubMed:10973948, PubMed:11875433, RESID:AA0318, Unimod:34#C-term] subset: PSI-MOD-slim synonym: "2,6-diaminohexanoic methyl ester" EXACT RESID-alternate [] synonym: "alpha,epsilon-diaminocaproic methyl ester" EXACT RESID-alternate [] @@ -7945,7 +8220,7 @@ synonym: "methyl (S)-2,6-diaminohexanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-lysine" EXACT PSI-MOD-alternate [] synonym: "methyl L-lysinate" EXACT RESID-alternate [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES Lysine methyl ester" EXACT UniProt-feature [] synonym: "OMeLys" EXACT PSI-MOD-label [] xref: DiffAvg: "14.03" @@ -7957,6 +8232,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0170" is_a: MOD:01683 ! monomethylated L-lysine is_a: MOD:01689 ! alpha-carboxyl methylated residue @@ -7977,20 +8254,20 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00744 ! molybdenum pterin containing modification -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02072 ! metal or metal cluster coordinated L-serine residue [Term] id: MOD:00325 name: L-beta-methylthioasparagine -def: "A protein modification that effectively converts an L-asparagine residue to L-beta-methylthioasparagine." [RESID:AA0320, UniMod:39#N] +def: "A protein modification that effectively converts an L-asparagine residue to L-beta-methylthioasparagine." [RESID:AA0320, Unimod:39#N] comment: This modification was predicted for ribosomal protein S12 in Bacillus subtilis when the sequence in the original version of the genome was reported to have asparagine rather than aspartic acid at the position of the methylthioaspartic acid modification (see MOD:00237). Two groups independently confirmed that the genome sequence was incorrect. The sequence in the revised genome has aspartic acid at that position. This is a deprecated entry in RESID. It probably does not occur naturally [JSG]. synonym: "(2R,3Xi)-2-amino-3-(methylsulfanyl)-4-butanediamic acid" EXACT RESID-systematic [] synonym: "2,4-diamino-3-(methylsulfanyl)-4-oxobutanoic acid" EXACT RESID-alternate [] synonym: "3-(methylthio)-L-asparagine" EXACT RESID-name [] synonym: "3-carboxamido-S-methyl-cysteine" EXACT RESID-alternate [] synonym: "beta-(methylthio)asparagine" EXACT RESID-alternate [] -synonym: "Beta-methylthiolation" RELATED UniMod-description [] -synonym: "Methylthio" RELATED UniMod-interim [] +synonym: "Beta-methylthiolation" RELATED Unimod-description [] +synonym: "Methylthio" RELATED Unimod-interim [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" @@ -8000,13 +8277,14 @@ xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:39" is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:01153 ! methylthiolated residue [Term] id: MOD:00326 name: L-pyrrolysine (Lys) -def: "A protein modification that effectively converts an L-lysine residue to L-pyrrolysine (not known as a natural, post-translational modification process)." [PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321#LYS, UniMod:435#K] +def: "A protein modification that effectively converts an L-lysine residue to L-pyrrolysine (not known as a natural, post-translational modification process)." [PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321#LYS, Unimod:435#K] comment: This entry is for the artifactual formation of L-pyrrolysine from lysine. For encoded L-pyrrolysine, use MOD:01187 [JSG]. synonym: "(2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acid" EXACT RESID-systematic [] synonym: "2-azanyl-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]azanylhexanoic acid" EXACT RESID-alternate [] @@ -8026,13 +8304,13 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:435" is_a: MOD:00912 ! modified L-lysine residue -is_a: MOD:01187 ! L-pyrrolysine residue [Term] id: MOD:00327 name: 3-hydroxy-L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to a 3-hydroxy-L-tryptophan." [PubMed:10024453, PubMed:11457355, RESID:AA0322] +def: "A protein modification that effectively converts an L-tryptophan residue to a 3-hydroxy-L-tryptophan." [PubMed:10024453, PubMed:11457355, RESID:AA0322, ChEBI:141794] synonym: "(2S,3S)-2-amino-3-hydroxy-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3-hydroxy-L-tryptophan" EXACT RESID-name [] synonym: "3-hydroxylated L-tryptophan" EXACT PSI-MOD-alternate [] @@ -8049,6 +8327,7 @@ xref: Origin: "W" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0031" is_a: MOD:01622 ! monohydroxylated tryptophan [Term] @@ -8059,12 +8338,6 @@ synonym: "ACT_SITE O-(3'-phospho-DNA)-tyrosine intermediate" EXACT UniProt-feature [] synonym: "O4'-(phospho-3'-DNA)-L-tyrosine" EXACT RESID-name [] synonym: "O4'-L-tyrosine 3'-DNA phosphodiester" EXACT RESID-alternate [] -xref: DiffAvg: "79.98" -xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" -xref: DiffMono: "79.966331" -xref: Formula: "C 9 H 10 N 1 O 5 P 1" -xref: MassAvg: "243.15" -xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" @@ -8074,13 +8347,13 @@ [Term] id: MOD:00329 name: hydroxyheme-L-glutamate ester -def: "A protein modification that effectively results from forming an adduct between a glutamic acid residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:11139583, PubMed:11821421, PubMed:11980497, RESID:AA0324, UniMod:436#E] +def: "A protein modification that effectively results from forming an adduct between a glutamic acid residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:11139583, PubMed:11821421, PubMed:11980497, RESID:AA0324, Unimod:436#E] synonym: "5-hydroxymethyl protoporphyrin IX 5-glutamate ester" EXACT RESID-alternate [] synonym: "[3-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-7,12-diethenyl-8,13,17-trimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "BINDING Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "cytochrome P450 CYP4A family heme cofactor" EXACT RESID-alternate [] synonym: "Hydroxyheme" RELATED PSI-MS-label [] -synonym: "hydroxyheme" RELATED UniMod-description [] +synonym: "hydroxyheme" RELATED Unimod-description [] synonym: "hydroxyheme-L-glutamate ester" EXACT RESID-name [] xref: DiffAvg: "614.48" xref: DiffFormula: "C 34 Fe 1 H 30 N 4 O 4" @@ -8091,13 +8364,14 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:436" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue [Term] id: MOD:00330 name: (phospho-5'-guanosine)-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to a (phospho-5'-guanosine)-L-histidine." [PubMed:10529169, PubMed:10869342, PubMed:7559521, RESID:AA0325, UniMod:413#H] +def: "A protein modification that effectively converts an L-histidine residue to a (phospho-5'-guanosine)-L-histidine." [PubMed:10529169, PubMed:10869342, PubMed:7559521, RESID:AA0325, Unimod:413#H] synonym: "(2S)-2-amino-3-(1-(5'-adenosine phosphono)imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "1'-(phospho-5'-guanosine)-L-histidine" EXACT RESID-name [] synonym: "ACT_SITE GMP-histidine intermediate" EXACT UniProt-feature [] @@ -8105,7 +8379,7 @@ synonym: "L-histidine monoanhydride with 5'-guanylic acid" EXACT RESID-alternate [] synonym: "N(tau)-5'-guanylic-L-histidine" EXACT RESID-alternate [] synonym: "N1'-guanylylated histidine" EXACT RESID-alternate [] -synonym: "phospho-guanosine" RELATED UniMod-description [] +synonym: "phospho-guanosine" RELATED Unimod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] synonym: "tele-5'-guanylic-L-histidine" EXACT RESID-alternate [] xref: DiffAvg: "345.21" @@ -8117,6 +8391,7 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:413" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01163 ! guanylated residue @@ -8142,19 +8417,20 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00332 name: omega-N-glucosyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to N4-glucosyl-arginine." [PubMed:15279557, PubMed:8521968, PubMed:9536051, RESID:AA0327, UniMod:41#R] +def: "A protein modification that effectively converts an L-arginine residue to N4-glucosyl-arginine." [PubMed:15279557, PubMed:8521968, PubMed:9536051, RESID:AA0327, Unimod:41#R] synonym: "(2S)-2-amino-5-(beta-D-glucopyranosyl[imino(methylamino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] synonym: "NG-beta-D-glucosylarginine" EXACT RESID-alternate [] synonym: "omega-N-(beta-D-glucosyl)-L-arginine" EXACT RESID-alternate [] synonym: "omega-N-glucosyl-L-arginine" EXACT RESID-name [] synonym: "omega-N-glycosyl-L-arginine" EXACT RESID-alternate [] +synonym: "CARBOHYD N-linked (Glc) arginine" EXACT UniProt-feature [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" @@ -8164,20 +8440,21 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00433 ! glucosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +xref: Unimod: "Unimod:41" +xref: UniProt: "PTM-0515" +is_a: MOD:00433 ! monoglucosylated residue is_a: MOD:01980 ! omega-N-glycosyl-L-arginine [Term] id: MOD:00333 name: (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine -def: "A protein modification that effectively converts an L-asparagine residue to (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine." [PubMed:7559516, PubMed:7835418, PubMed:8183363, RESID:AA0328, UniMod:437#C-term] -comment: UniMod origin shown as C-term [JSG]. +def: "A protein modification that effectively converts an L-asparagine residue to (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine." [PubMed:7559516, PubMed:7835418, PubMed:8183363, RESID:AA0328, Unimod:437#C-term] +comment: Unimod origin shown as C-term [JSG]. synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine" EXACT RESID-name [] -synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5-adenosine" RELATED UniMod-description [] +synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5-adenosine" RELATED Unimod-description [] synonym: "5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]adenosine" EXACT RESID-systematic [] synonym: "9-(5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]-beta-D-ribofuranosyl)adenine" EXACT RESID-alternate [] -synonym: "C-Asn-deriv" RELATED UniMod-interim [] +synonym: "C-Asn-deriv" RELATED Unimod-interim [] synonym: "microcin C7 asparagine modification" EXACT RESID-alternate [] synonym: "MOD_RES Aspartic acid 1-[(3-aminopropyl)(5'-adenosyl)phosphono]amide" EXACT UniProt-feature [] synonym: "N-(aspart-1-yl)-O-(3-aminopropyl)-O-(5'-adenosyl)phosphoramide" EXACT RESID-alternate [] @@ -8190,19 +8467,21 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:437" +xref: UniProt: "PTM-0335" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00334 name: 1'-heme-L-histidine -def: "A protein modification that effectively results from forming an adduct between the tele nitrogen of a histidine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:12033922, PubMed:12121092, RESID:AA0329, UniMod:390#H] +def: "A protein modification that effectively results from forming an adduct between the tele nitrogen of a histidine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:12033922, PubMed:12121092, RESID:AA0329, Unimod:390#H] synonym: "(S)-[7-ethenyl-12-[1-((2-amino-2-carboxyethyl)-1H-imidazol-1-yl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "1'-heme-L-histidine" EXACT RESID-name [] synonym: "2-[1-(N1'-histidyl)ethyl]protoporphyrin IX" EXACT RESID-alternate [] synonym: "BINDING Heme (covalent; via tele nitrogen)" EXACT UniProt-feature [] synonym: "Heme" RELATED PSI-MS-label [] -synonym: "heme" RELATED UniMod-description [] +synonym: "heme" RELATED Unimod-description [] synonym: "N(epsilon)-histidyl heme" EXACT RESID-alternate [] synonym: "N(tau)-histidyl heme" EXACT RESID-alternate [] synonym: "N1'-histidyl heme" EXACT RESID-alternate [] @@ -8216,8 +8495,9 @@ xref: Origin: "H" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:390" is_a: MOD:00699 ! porphyrin modified residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00335 @@ -8239,7 +8519,8 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +xref: UniProt: "PTM-0069" +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01993 ! beta-carbon thioether crosslinked residues relationship: has_functional_parent MOD:01981 ! 3-methyllanthionine @@ -8262,13 +8543,13 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00337 name: S-carbamoyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-carbamoyl-L-cysteine." [PubMed:12586941, PubMed:240389, RESID:AA0332, UniMod:5#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-carbamoyl-L-cysteine." [PubMed:12586941, PubMed:240389, RESID:AA0332, Unimod:5#C] synonym: "(R)-2-amino-3-(carbamoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(aminocarbonyl)sulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-(aminocarbonyl)thiopropanoic acid" EXACT RESID-alternate [] @@ -8290,18 +8571,20 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:5" +xref: UniProt: "PTM-0649" is_a: MOD:00398 ! carbamoylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00338 name: S-cyano-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-cyano-L-cysteine." [PubMed:12586941, PubMed:4808702, RESID:AA0333, UniMod:438#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-cyano-L-cysteine." [PubMed:12586941, PubMed:4808702, RESID:AA0333, Unimod:438#C] synonym: "(2R)-2-amino-3-thiocyanatopropanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-thiocyanatopropionic acid" EXACT RESID-alternate [] synonym: "beta-thiocyanatoalanine" EXACT RESID-alternate [] synonym: "Cyano" RELATED PSI-MS-label [] -synonym: "cyano" RELATED UniMod-description [] +synonym: "cyano" RELATED Unimod-description [] synonym: "MOD_RES S-cyanocysteine" EXACT UniProt-feature [] synonym: "S-cyano-L-cysteine" EXACT RESID-name [] synonym: "S-cyanocysteine" EXACT RESID-alternate [] @@ -8315,17 +8598,19 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:438" +xref: UniProt: "PTM-0650" is_a: MOD:00893 ! residues isobaric at 128.0-128.1 is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00339 name: L-cysteinyl hydrogenase diiron subcluster -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl hydrogenase diiron subcluster." [PubMed:10694885, PubMed:9836629, RESID:AA0334, UniMod:439#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl hydrogenase diiron subcluster." [PubMed:10694885, PubMed:9836629, RESID:AA0334, Unimod:439#C] comment: incidental to RESID:AA0140. synonym: "1,7-biscarbonyl-1-(cystein-S-yl)-8-oxo-4-aza-2lambda(3),6 lambda(3)-dithia-1,7-diferratricyclo[4.2.0.0(2,7)]octane-1,7-dicarbonitrile" EXACT RESID-alternate [] synonym: "Diironsubcluster" RELATED PSI-MS-label [] -synonym: "hydrogenase diiron subcluster" RELATED UniMod-description [] +synonym: "hydrogenase diiron subcluster" RELATED Unimod-description [] synonym: "L-cysteinyl hydrogenase diiron subcluster" EXACT RESID-name [] synonym: "METAL Diiron subcluster" EXACT UniProt-feature [] synonym: "mu-carbonyl-dicarbonyl-1kappaC,2kappaC-dicyanido-1kappaC,2kappaC-cysteinato-1kS-1,2-azadimethanthiol-1kS,2kS'-diiron" EXACT RESID-systematic [] @@ -8338,20 +8623,21 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:439" is_a: MOD:00738 ! iron containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00340 name: S-amidino-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-amidino-L-cysteine." [PubMed:9148748, RESID:AA0335, UniMod:440#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-amidino-L-cysteine." [PubMed:9148748, RESID:AA0335, Unimod:440#C] synonym: "(2R)-2-amino-3-(carbamimidoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-amidinosulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-amidinothiopropanoic acid" EXACT RESID-alternate [] synonym: "ACT_SITE Amidino-cysteine intermediate" EXACT UniProt-feature [] synonym: "alpha-amino-beta-amidinothiopropionic acid" EXACT RESID-alternate [] synonym: "Amidino" RELATED PSI-MS-label [] -synonym: "amidino" RELATED UniMod-description [] +synonym: "amidino" RELATED Unimod-description [] synonym: "beta-(S-isothiourea)alanine" EXACT RESID-alternate [] synonym: "beta-amidinothioalanine" EXACT RESID-alternate [] synonym: "S-amidino-L-cysteine" EXACT RESID-name [] @@ -8365,6 +8651,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:440" is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -8374,7 +8661,7 @@ comment: Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence [JSG]. synonym: "(2S,3S)-2-methylamino-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N-methylisoleucine" EXACT UniProt-feature [] synonym: "N-methyl-L-isoleucine" EXACT RESID-name [] synonym: "N-methylated L-isoleucine" EXACT PSI-MOD-alternate [] @@ -8389,6 +8676,7 @@ xref: Origin: "I" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0215" is_a: MOD:00715 ! methylated isoleucine is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -8400,7 +8688,7 @@ synonym: "(S)-2-methylamino-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "2-(methylamino)-4-methyl-valeric acid" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "MOD_RES N-methylleucine" EXACT UniProt-feature [] synonym: "N-methyl-L-leucine" EXACT RESID-name [] synonym: "N-methylated L-leucine" EXACT PSI-MOD-alternate [] @@ -8415,6 +8703,7 @@ xref: Origin: "L" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0216" is_a: MOD:01680 ! alpha-amino monomethylated residue is_a: MOD:01808 ! N-methylated leucine @@ -8440,6 +8729,7 @@ xref: Origin: "Y" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0220" is_a: MOD:00718 ! methylated tyrosine is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -8456,6 +8746,7 @@ synonym: "N-(1-oxohexadecyl)glycine" EXACT RESID-alternate [] synonym: "N-palmitoyl-glycine" EXACT RESID-name [] synonym: "N-palmitoylated glycine" EXACT PSI-MOD-alternate [] +synonym: "N-hexadecanoylated glycine" EXACT PSI-MOD-alternate [] synonym: "NPamGly" EXACT PSI-MOD-label [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" @@ -8466,6 +8757,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0223" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01685 ! alpha-amino palmitoylated residue @@ -8488,7 +8780,8 @@ xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00914 ! modified L-phenylalanine residue +xref: UniProt: "PTM-0012" +is_a: MOD:02053 ! crosslinked L-phenylalanine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -8510,8 +8803,9 @@ xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0011" is_a: MOD:00664 ! stereoisomerized residue -is_a: MOD:00914 ! modified L-phenylalanine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -8533,8 +8827,9 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0010" is_a: MOD:00664 ! stereoisomerized residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -8556,6 +8851,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0374" is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:01679 ! alpha-aminocarbamoylated residue @@ -8580,8 +8876,9 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0037" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01861 ! isothiazolidinone ring crosslinked residues [Term] @@ -8591,15 +8888,10 @@ synonym: "(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(threonyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanine" EXACT RESID-alternate [] synonym: "L-threonyl-pentaglycyl-murein peptidoglycan" EXACT RESID-name [] synonym: "MOD_RES Pentaglycyl murein peptidoglycan amidated threonine" EXACT UniProt-feature [] -xref: DiffAvg: "268.25" -xref: DiffFormula: "C 10 H 14 N 5 O 4" -xref: DiffMono: "268.104579" -xref: Formula: "C 14 H 22 N 6 O 7" -xref: MassAvg: "386.37" -xref: MassMono: "386.154997" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0246" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01159 ! peptidoglycanated residue @@ -8620,6 +8912,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0249" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01155 ! lipoconjugated residue @@ -8640,6 +8933,7 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0236" is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:01155 ! lipoconjugated residue @@ -8660,21 +8954,22 @@ xref: Origin: "M, W, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0328" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00913 ! modified L-methionine residue -is_a: MOD:00918 ! modified L-tryptophan residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02052 ! crosslinked L-methionine residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00354 name: O-(riboflavin phosphoryl)-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-(riboflavin phosphoryl)-L-threonine." [PubMed:10587447, PubMed:11163785, PubMed:11248234, RESID:AA0349, UniMod:442#T] +def: "A protein modification that effectively converts an L-threonine residue to O-(riboflavin phosphoryl)-L-threonine." [PubMed:10587447, PubMed:11163785, PubMed:11248234, RESID:AA0349, Unimod:442#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)butanoic acid" EXACT RESID-systematic [] synonym: "FMN" RELATED PSI-MS-label [] synonym: "MOD_RES FMN phosphoryl threonine" EXACT UniProt-feature [] synonym: "O-(riboflavin phosphoryl)-L-threonine" EXACT RESID-name [] -synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] +synonym: "O3-(riboflavin phosphoryl)" RELATED Unimod-description [] synonym: "O3-threonyl flavin mononucleotide" EXACT RESID-alternate [] synonym: "O3-threonyl FMN" EXACT RESID-alternate [] synonym: "OFMNThr" EXACT PSI-MOD-label [] @@ -8685,21 +8980,23 @@ xref: MassAvg: "539.44" xref: MassMono: "539.141729" xref: Origin: "T" -xref: Source: "hypothetical" +xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:442" +xref: UniProt: "PTM-0126" is_a: MOD:00917 ! modified L-threonine residue -is_a: MOD:01164 ! riboflavin-phosphoryl +is_a: MOD:01164 ! riboflavin-phosphorylated residue [Term] id: MOD:00355 name: O-(riboflavin phosphoryl)-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-(riboflavin phosphoryl)-L-serine." [RESID:AA0350, UniMod:442#S] +def: "A protein modification that effectively converts an L-serine residue to O-(riboflavin phosphoryl)-L-serine." [RESID:AA0350, Unimod:442#S] subset: PSI-MOD-slim synonym: "(R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)propanoic acid" EXACT RESID-systematic [] synonym: "FMN" RELATED PSI-MS-label [] synonym: "MOD_RES FMN phosphoryl serine" EXACT UniProt-feature [] synonym: "O-(riboflavin phosphoryl)-L-serine" EXACT RESID-name [] -synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] +synonym: "O3-(riboflavin phosphoryl)" RELATED Unimod-description [] synonym: "O3-seryl flavin mononucleotide" EXACT RESID-alternate [] synonym: "O3-seryl FMN" EXACT RESID-alternate [] synonym: "OFMNSer" EXACT PSI-MOD-label [] @@ -8710,22 +9007,24 @@ xref: MassAvg: "525.41" xref: MassMono: "525.126079" xref: Origin: "S" -xref: Source: "hypothetical" +xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:442" +xref: UniProt: "PTM-0125" is_a: MOD:00916 ! modified L-serine residue -is_a: MOD:01164 ! riboflavin-phosphoryl +is_a: MOD:01164 ! riboflavin-phosphorylated residue [Term] id: MOD:00356 -name: S-(4a-FMN)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(4a-FMN)-L-cysteine." [PubMed:12668455, PubMed:12846567, PubMed:7692961, RESID:AA0351, UniMod:443#C] +name: S-(4alpha-FMN)-L-cysteine +def: "A protein modification that effectively converts an L-cysteine residue to S-(4a-FMN)-L-cysteine." [PubMed:12668455, PubMed:12846567, PubMed:7692961, RESID:AA0351, Unimod:443#C] subset: PSI-MOD-slim synonym: "(R)-2-amino-3-(4a-riboflavin 5'-dihydrogen phosphate)sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "4a-(S-cysteinyl)flavin mononucleotide" EXACT RESID-alternate [] synonym: "4a-(S-cysteinyl)FMN" EXACT RESID-alternate [] synonym: "FMNC" RELATED PSI-MS-label [] synonym: "MOD_RES S-4a-FMN cysteine" EXACT UniProt-feature [] -synonym: "S-(4a-FMN)" RELATED UniMod-description [] +synonym: "S-(4a-FMN)" RELATED Unimod-description [] synonym: "S-(4a-FMN)-L-cysteine" EXACT RESID-name [] synonym: "S4aFMNCys" EXACT PSI-MOD-label [] xref: DiffAvg: "456.35" @@ -8737,19 +9036,21 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue +xref: Unimod: "Unimod:443" +xref: UniProt: "PTM-0270" +is_a: MOD:02083 ! 4alpha-FMN modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00357 name: 1'-(8alpha-FMN)-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to 1'-(8alpha-FMN)-L-histidine." [PubMed:11902668, PubMed:8611516, RESID:AA0352, UniMod:409#H] +def: "A protein modification that effectively converts an L-histidine residue to 1'-(8alpha-FMN)-L-histidine." [PubMed:11902668, PubMed:8611516, RESID:AA0352, Unimod:409#H] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-(1-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "1'-(8alpha-FMN)-L-histidine" EXACT RESID-name [] synonym: "8alpha-(N(epsilon)-histidyl)FMN" EXACT RESID-alternate [] synonym: "8alpha-(N1'-histidyl)FMN" EXACT RESID-alternate [] -synonym: "flavin mononucleotide" RELATED UniMod-description [] +synonym: "flavin mononucleotide" RELATED Unimod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "MOD_RES Tele-8alpha-FMN histidine" EXACT UniProt-feature [] synonym: "N(tau)-(8alpha-FMN)-histidine" EXACT RESID-alternate [] @@ -8764,20 +9065,22 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue +xref: Unimod: "Unimod:409" +xref: UniProt: "PTM-0289" +is_a: MOD:02085 ! 8alpha-FMN modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00358 name: 3'-(8alpha-FMN)-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to 3'-(8alpha-FMN)-L-histidine." [PubMed:12417325, RESID:AA0353, UniMod:409#H] +def: "A protein modification that effectively converts an L-histidine residue to 3'-(8alpha-FMN)-L-histidine." [PubMed:12417325, RESID:AA0353, Unimod:409#H] comment: In a later publication, PubMed:19438211, the authors changed the enzyme activity, the connection from a histidine nitrogen to a cysteine sulfur, and the identity of the flavin from FMN to FAD. They now believe the modification is S-(8alpha-FAD)-L-cysteine, see MOD:00152. This is a deprecated entry in RESID. It probably does not occur naturally [JSG]. subset: PSI-MOD-slim synonym: "(S)-2-amino-3-(3-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3'-(8alpha-FMN)-L-histidine" EXACT RESID-name [] synonym: "8alpha-(N(delta)-histidyl)FMN" EXACT RESID-alternate [] synonym: "8alpha-(N3'-histidyl)FMN" EXACT RESID-alternate [] -synonym: "flavin mononucleotide" RELATED UniMod-description [] +synonym: "flavin mononucleotide" RELATED Unimod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "N(pi)-(8alpha-FMN)-histidine" EXACT RESID-alternate [] synonym: "Npros8aFMNHis" EXACT PSI-MOD-label [] @@ -8791,7 +9094,8 @@ xref: Origin: "H" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue +xref: Unimod: "Unimod:409" +is_a: MOD:02085 ! 8alpha-FMN modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] @@ -8817,15 +9121,16 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0180" is_a: MOD:00902 ! modified L-arginine residue is_a: MOD:01458 ! alpha-amino acetylated residue [Term] id: MOD:00360 name: L-cysteinyl copper sulfido molybdopterin cytosine dinuncleotide -def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl copper sulfido molybdopterin cytosine dinuncleotide." [PubMed:12475995, RESID:AA0355, UniMod:444#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-cysteinyl copper sulfido molybdopterin cytosine dinuncleotide." [PubMed:12475995, RESID:AA0355, Unimod:444#C] synonym: "[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with cytosine)methyl-6-oxo-3,4-dimercapto-pteridino[6,7-5,6]pyranoato-S3,S4]-cysteinyl-S-copper-mu-sulfido-molybdenum hydroxide oxide" EXACT RESID-systematic [] -synonym: "copper sulfido molybdopterin cytosine dinuncleotide" RELATED UniMod-description [] +synonym: "copper sulfido molybdopterin cytosine dinuncleotide" RELATED Unimod-description [] synonym: "CuSMo" RELATED PSI-MS-label [] synonym: "cysteinyl copper mu-sulfido Mo-pterin cytosine dinucleotide" EXACT RESID-alternate [] synonym: "L-cysteinyl copper sulfido molybdopterin cytosine dinucleotide" EXACT RESID-name [] @@ -8838,10 +9143,11 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:444" is_a: MOD:00742 ! copper containing modified residue is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:00860 ! sulfur containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00361 @@ -8862,7 +9168,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00362 @@ -8883,8 +9189,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00902 ! modified L-arginine residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02076 ! metal or metal cluster coordinated L-arginine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:00363 @@ -8905,19 +9211,20 @@ xref: Origin: "C, U" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:01158 ! modified L-selenocysteine residue +xref: UniProt: "PTM-0109" +is_a: MOD:02061 ! crosslinked L-selenocysteine residue is_a: MOD:01627 ! L-cysteinyl-L-selenocysteine [Term] id: MOD:00364 name: 5-hydroxy-N6,N6,N6-trimethyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 5-hydroxy-N6,N6,N6-trimethyl-L-lysine." [PubMed:11349130, PubMed:14661085, RESID:AA0359, UniMod:445#K] +def: "A protein modification that effectively converts an L-lysine residue to 5-hydroxy-N6,N6,N6-trimethyl-L-lysine." [PubMed:11349130, PubMed:14661085, RESID:AA0359, Unimod:445#K] comment: Incidental to RESID:AA0278; secondary to RESID:AA0028; secondary to RESID:AA0074. synonym: "(2R,5Xi)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentan-1-aminium" EXACT RESID-systematic [] synonym: "(2Xi,5S)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentanaminium" EXACT RESID-alternate [] synonym: "(2Xi,5S)-5-azanyl-5-carboxy-2-hydroxy-N,N,N-trimethylpentanazanium" EXACT RESID-alternate [] synonym: "5-hydroxy-N(zeta)-trimethyllysine" EXACT RESID-alternate [] -synonym: "5-hydroxy-N6,N6,N6-trimethyl" RELATED UniMod-description [] +synonym: "5-hydroxy-N6,N6,N6-trimethyl" RELATED Unimod-description [] synonym: "5-hydroxy-N6,N6,N6-trimethyl-L-lysine" EXACT RESID-name [] synonym: "5-hydroxy-N6,N6,N6-trimethyllysin-N6-ium" EXACT RESID-alternate [] synonym: "5-hydroxy-N6,N6,N6-trimethyllysine cation" EXACT RESID-alternate [] @@ -8938,6 +9245,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:445" +xref: UniProt: "PTM-0186" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00912 ! modified L-lysine residue relationship: has_functional_parent MOD:00037 ! 5-hydroxy-L-lysine @@ -8963,21 +9272,22 @@ xref: Origin: "E, G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0157" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00366 name: O-sulfo-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-sulfo-L-serine." [PubMed:14752058, RESID:AA0361, UniMod:40#S] +def: "A protein modification that effectively converts an L-serine residue to O-sulfo-L-serine." [PubMed:14752058, RESID:AA0361, Unimod:40#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(sulfooxy)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxypropanoic acid 3-sulfate" EXACT RESID-alternate [] synonym: "MOD_RES Sulfoserine" EXACT UniProt-feature [] synonym: "O-sulfo-L-serine" EXACT RESID-name [] -synonym: "O-Sulfonation" RELATED UniMod-description [] +synonym: "O-Sulfonation" RELATED Unimod-description [] synonym: "O3-sulfonoserine" EXACT RESID-alternate [] synonym: "O3-sulfoserine" EXACT RESID-alternate [] synonym: "serine sulfate ester" EXACT RESID-alternate [] @@ -8991,6 +9301,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:40" +xref: UniProt: "PTM-0284" is_a: MOD:00695 ! sulfated residue is_a: MOD:00771 ! residues isobaric at 166.98-167.00 Da is_a: MOD:00916 ! modified L-serine residue @@ -8998,13 +9310,13 @@ [Term] id: MOD:00367 name: O-sulfo-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-sulfo-L-threonine." [PubMed:14752058, RESID:AA0362, UniMod:40#T] +def: "A protein modification that effectively converts an L-threonine residue to O-sulfo-L-threonine." [PubMed:14752058, RESID:AA0362, Unimod:40#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(sulfooxy)butanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxybutanoic acid 3-sulfate" EXACT RESID-alternate [] synonym: "MOD_RES Sulfothreonine" EXACT UniProt-feature [] synonym: "O-sulfo-L-threonine" EXACT RESID-name [] -synonym: "O-Sulfonation" RELATED UniMod-description [] +synonym: "O-Sulfonation" RELATED Unimod-description [] synonym: "O3-sulfonothreonine" EXACT RESID-alternate [] synonym: "O3-sulfothreonine" EXACT RESID-alternate [] synonym: "Sulfo" RELATED PSI-MS-label [] @@ -9018,6 +9330,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:40" +xref: UniProt: "PTM-0285" is_a: MOD:00695 ! sulfated residue is_a: MOD:00773 ! residues isobaric at 181.00-181.02 Da is_a: MOD:00917 ! modified L-threonine residue @@ -9025,13 +9339,13 @@ [Term] id: MOD:00368 name: N-carboxy-L-methionine -def: "A protein modification that effectively converts an L-methionine residue to N-carboxy-L-methionine." [PubMed:10368287, PubMed:11120890, PubMed:12595263, PubMed:8312270, RESID:AA0363, UniMod:299#M] +def: "A protein modification that effectively converts an L-methionine residue to N-carboxy-L-methionine." [PubMed:10368287, PubMed:11120890, PubMed:12595263, PubMed:8312270, RESID:AA0363, Unimod:299#M] comment: At least three protein crystallographic structures have been reported with this modification. However, no chemical evidence for this modification is provided, there were no reports of this modification before these crystallographic reports, and there is no metabolic explanation for the conversion of a formyl group to a carboxy group. There is confusion in its description, and misnaming is common. This modification is probably a misidentification of N-(dihydroxymethyl)methionine, the hydrated form of N-formylmethionine. See MOD:01446 [JSG]. synonym: "(S)-2-carboxyamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-carbamic-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] synonym: "2-carbamic-4-(methylthio)butanoic acid" EXACT RESID-alternate [] -synonym: "Carboxy" RELATED UniMod-interim [] -synonym: "Carboxylation" RELATED UniMod-description [] +synonym: "Carboxy" RELATED Unimod-interim [] +synonym: "Carboxylation" RELATED Unimod-description [] synonym: "N-carboxy-L-methionine" EXACT RESID-name [] synonym: "N-carboxymethionine" EXACT RESID-alternate [] xref: DiffAvg: "44.01" @@ -9043,18 +9357,19 @@ xref: Origin: "M" xref: Source: "hypothetical" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:299" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00369 name: O-acetyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-acetyl-L-serine." [ChEBI:17981, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:16731519, PubMed:489587, PubMed:7309355, RESID:AA0364, UniMod:1#S] +def: "A protein modification that effectively converts an L-serine residue to O-acetyl-L-serine." [ChEBI:17981, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:16731519, PubMed:489587, PubMed:7309355, RESID:AA0364, Unimod:1#S] comment: incidental to RESID:AA0051 subset: PSI-MOD-slim synonym: "(2S)-3-(acetyloxy)-2-aminopropanoic acid" EXACT RESID-systematic [] synonym: "Acetyl" RELATED PSI-MS-label [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "MOD_RES O-acetylserine" EXACT UniProt-feature [] synonym: "O-acetyl-L-serine" EXACT RESID-name [] synonym: "O-acetylated L-serine" EXACT PSI-MOD-alternate [] @@ -9070,8 +9385,11 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00644 ! O-acetylated residue -is_a: MOD:00647 ! acetylated L-serine +xref: Unimod: "Unimod:1" +xref: UniProt: "PTM-0232" +is_a: MOD:00644 ! mono O-acetylated residue +is_a: MOD:00647 ! monoacetylated L-serine +is_a: MOD:02003 ! O3-acylated L-serine [Term] id: MOD:00370 @@ -9082,7 +9400,7 @@ synonym: "(2E)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acid" EXACT RESID-systematic [] synonym: "(E)-2,3-didehydrogenated tyrosine" EXACT PSI-MOD-alternate [] synonym: "(E)-2,3-didehydrotyrosine" EXACT RESID-name [] -synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] +synonym: "2-amino-3-oxo-butanoic_acid" RELATED Unimod-description [] synonym: "amino-(para-hydroxybenzylidenyl)acetic acid" EXACT RESID-alternate [] synonym: "blue non-fluorescent pocilloporin chromophore" EXACT RESID-alternate [] synonym: "Didehydro" RELATED PSI-MS-label [] @@ -9099,6 +9417,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0001" is_a: MOD:00706 ! dehydrogenated tyrosine [Term] @@ -9120,9 +9439,9 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00740 ! manganese containing modified residue -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue is_a: MOD:01482 ! calcium containing modified residue [Term] @@ -9147,7 +9466,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00373 @@ -9170,20 +9489,21 @@ xref: Origin: "Y, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0155" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00374 name: 3,4-dihydroxy-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to 3,4-dihydroxy-L-arginine." [PubMed:10978343, PubMed:12686488, RESID:AA0369, UniMod:425#R] +def: "A protein modification that effectively converts an L-arginine residue to 3,4-dihydroxy-L-arginine." [PubMed:10978343, PubMed:12686488, RESID:AA0369, Unimod:425#R, ChEBI:141829] synonym: "(2S,3Xi,4Xi)-2-amino-5-carbamimidamido-3,4-dihydroxypentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-guanidino-3,4-dihydroxypentanoic acid" EXACT RESID-alternate [] synonym: "3,4-dihydroxy-L-arginine" EXACT RESID-name [] synonym: "3,4-dihydroxylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "34Hy2Arg" EXACT PSI-MOD-label [] synonym: "beta,gamma-dihydroxyarginine" EXACT RESID-alternate [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "MOD_RES 3,4-dihydroxyarginine" EXACT UniProt-feature [] xref: DiffAvg: "32.00" @@ -9195,20 +9515,22 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0022" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00682 ! hydroxylated arginine [Term] id: MOD:00375 name: 4,5-dihydroxy-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4,5-dihydroxy-L-lysine." [PubMed:10978343, PubMed:12686488, RESID:AA0370, UniMod:425#K] +def: "A protein modification that effectively converts an L-lysine residue to 4,5-dihydroxy-L-lysine." [PubMed:10978343, PubMed:12686488, RESID:AA0370, Unimod:425#K] synonym: "(2S,4Xi,5Xi)-2,6-diamino-4,5-dihydroxyhexanoic acid" EXACT RESID-systematic [] synonym: "4,5-dihydroxy-L-lysine" EXACT RESID-name [] synonym: "4,5-dihydroxylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "45Hy2Lys" EXACT PSI-MOD-label [] synonym: "alpha,epsilon-diamino-delta,gamma-dihydroxycaproic acid" EXACT RESID-alternate [] synonym: "delta,gamma-dihydroxylysine" EXACT RESID-alternate [] -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "MOD_RES 4,5-dihydroxylysine" EXACT UniProt-feature [] xref: DiffAvg: "32.00" @@ -9220,18 +9542,20 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: UniProt: "PTM-0036" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00681 ! hydroxylated lysine [Term] id: MOD:00376 name: 1'-(phospho-5'-adenosine)-L-histidine -def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form 1'-(phospho-5'-adenosine)-L-histidine." [PubMed:15182206, PubMed:9323207, RESID:AA0371, UniMod:405#H] +def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form 1'-(phospho-5'-adenosine)-L-histidine." [PubMed:15182206, PubMed:9323207, RESID:AA0371, Unimod:405#H] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-[1-(5'-adenosine phosphono)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "1'-(phospho-5'-adenosine)-L-histidine" EXACT RESID-name [] synonym: "ACT_SITE Tele-AMP-histidine intermediate" EXACT UniProt-feature [] -synonym: "AMP binding site" RELATED UniMod-description [] +synonym: "AMP binding site" RELATED Unimod-description [] synonym: "L-histidine 5'-adenosine phosphoramidester" EXACT RESID-alternate [] synonym: "L-histidine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] synonym: "N(tau)-5'-adenylic-L-histidine" EXACT RESID-alternate [] @@ -9247,13 +9571,14 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:405" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00377 name: 1'-(phospho-5'-uridine)-L-histidine -def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphouridine through a phosphoramide ester bond to form 1'-(phospho-5'-uridine)-L-histidine." [PubMed:11467524, PubMed:321007, PubMed:380639, PubMed:8794735, RESID:AA0372, UniMod:417#H] +def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphouridine through a phosphoramide ester bond to form 1'-(phospho-5'-uridine)-L-histidine." [PubMed:11467524, PubMed:321007, PubMed:380639, PubMed:8794735, RESID:AA0372, Unimod:417#H] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-[1-(5'-uridine phosphono)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "1'-(phospho-5'-uridine)-L-histidine" EXACT RESID-name [] @@ -9264,7 +9589,8 @@ synonym: "N1'-uridylylated histidine" EXACT RESID-alternate [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] synonym: "tele-5'-uridylic-L-histidine" EXACT RESID-alternate [] -synonym: "uridine phosphodiester" RELATED UniMod-description [] +synonym: "uridine phosphodiester" RELATED Unimod-description [] +synonym: "MOD_RES O-UMP-histidine" EXACT UniProt-feature [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" @@ -9274,13 +9600,15 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:417" +xref: UniProt: "PTM-0500" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01166 ! uridylated residue [Term] id: MOD:00378 name: L-aspartyl semialdehyde -def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl semialdehyde." [PubMed:1093385, PubMed:14235557, PubMed:15237995, RESID:AA0373, UniMod:447#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl semialdehyde." [PubMed:1093385, PubMed:14235557, PubMed:15237995, RESID:AA0373, Unimod:447#D] subset: PSI-MOD-slim synonym: "(S)-2-amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "aspartyl 4-semialdehyde" EXACT PSI-MOD-alternate [] @@ -9293,7 +9621,7 @@ synonym: "L-aspartyl aldehyde" EXACT RESID-name [] synonym: "L-beta-formylalanine" EXACT RESID-alternate [] synonym: "MOD_RES Aspartyl aldehyde" EXACT UniProt-feature [] -synonym: "reduction" RELATED UniMod-description [] +synonym: "reduction" RELATED Unimod-description [] xref: DiffAvg: "-16.00" xref: DiffFormula: "C 0 H 0 N 0 O -1" xref: DiffMono: "-15.994915" @@ -9303,17 +9631,19 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:447" +xref: UniProt: "PTM-0064" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01161 ! deoxygenated residue [Term] id: MOD:00379 name: L-serine microcin E492 siderophore ester -def: "A protein modification that effectively converts an L-serine residue to L-serine microcin E492 siderophore ester." [PubMed:15102848, RESID:AA0374, UniMod:448#C-term] -comment: UniMod origin corrected [JSG]. +def: "A protein modification that effectively converts an L-serine residue to L-serine microcin E492 siderophore ester." [PubMed:15102848, RESID:AA0374, Unimod:448#C-term] +comment: Unimod origin corrected [JSG]. synonym: "L-serine microcin E492 siderophore ester" EXACT RESID-name [] synonym: "Microcin" RELATED PSI-MS-label [] -synonym: "microcin E492 siderophore ester from serine" RELATED UniMod-description [] +synonym: "microcin E492 siderophore ester from serine" RELATED Unimod-description [] synonym: "MOD_RES Serine microcin E492 siderophore ester" EXACT UniProt-feature [] synonym: "N-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serine" EXACT RESID-systematic [] xref: DiffAvg: "831.69" @@ -9325,16 +9655,18 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:448" +xref: UniProt: "PTM-0276" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00380 name: L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide) -def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)." [PubMed:12910261, PubMed:14725769, RESID:AA0375, UniMod:424#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)." [PubMed:12910261, PubMed:14725769, RESID:AA0375, Unimod:424#D] synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-aspartyl-molybdenum" EXACT RESID-systematic [] synonym: "L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)" EXACT RESID-name [] -synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] +synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED Unimod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] synonym: "nitrate reductase A aspartyl Mo-bisMGD cofactor" EXACT RESID-alternate [] synonym: "phosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate ester" EXACT RESID-alternate [] @@ -9347,7 +9679,8 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +xref: Unimod: "Unimod:424" +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue is_a: MOD:01167 ! molybdopterin guanine dinucleotide [Term] @@ -9365,7 +9698,7 @@ xref: TermSpec: "none" is_a: MOD:00746 ! tungsten containing modified residue is_a: MOD:00748 ! pterin modified residue -is_a: MOD:01158 ! modified L-selenocysteine residue +is_a: MOD:02073 ! metal or metal cluster coordinated L-selenocysteine residue [Term] id: MOD:00382 @@ -9386,8 +9719,8 @@ xref: Origin: "M, Y" xref: Source: "hypothetical" xref: TermSpec: "N-term" -is_a: MOD:00913 ! modified L-methionine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02052 ! crosslinked L-methionine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:00383 @@ -9411,8 +9744,9 @@ xref: Origin: "E, G" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0014" +is_a: MOD:02045 ! crosslinked L-glutamic acid residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) [Term] @@ -9439,8 +9773,9 @@ xref: Origin: "G, M" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:00913 ! modified L-methionine residue +xref: UniProt: "PTM-0015" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02052 ! crosslinked L-methionine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) [Term] @@ -9465,9 +9800,11 @@ xref: Origin: "G, N" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue -is_a: MOD:00908 ! modified glycine residue +xref: UniProt: "PTM-0046" +is_a: MOD:02042 ! crosslinked L-asparagine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00386 @@ -9491,9 +9828,11 @@ xref: Origin: "G, K" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:00912 ! modified L-lysine residue +xref: UniProt: "PTM-0048" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00387 @@ -9517,8 +9856,9 @@ xref: Origin: "G, K" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:00912 ! modified L-lysine residue +xref: UniProt: "PTM-0018" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) [Term] @@ -9528,22 +9868,17 @@ synonym: "(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(alanyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanine" EXACT RESID-alternate [] synonym: "L-alanyl-pentaglycyl-murein peptidoglycan" EXACT RESID-name [] synonym: "MOD_RES Pentaglycyl murein peptidoglycan amidated alanine" EXACT UniProt-feature [] -xref: DiffAvg: "268.25" -xref: DiffFormula: "C 10 H 14 N 5 O 4" -xref: DiffMono: "268.104579" -xref: Formula: "C 13 H 20 N 6 O 6" -xref: MassAvg: "356.34" -xref: MassMono: "356.144432" xref: Origin: "A" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0245" is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:01159 ! peptidoglycanated residue [Term] id: MOD:00389 name: N-formyl-L-proline -def: "A protein modification that effectively converts an L-proline residue to N-formyl-L-proline." [PubMed:12051774, PubMed:5464655, RESID:AA0384, UniMod:122#N-term] +def: "A protein modification that effectively converts an L-proline residue to N-formyl-L-proline." [PubMed:12051774, PubMed:5464655, RESID:AA0384, Unimod:122#N-term] comment: CAUTION - observations of this modification can be attributed to unintended artifactual production, or to spurious peptide MS identification. This modification is probably not a natural post-translational modification [JSG]. synonym: "(2S)-1-formylpyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "1-formyl-2-pyrrolidinecarboxylic acid" EXACT RESID-alternate [] @@ -9560,6 +9895,7 @@ xref: Origin: "P" xref: Source: "hypothetical" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:122" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -9567,11 +9903,11 @@ [Term] id: MOD:00390 name: O-decanoyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-decanoyl-L-serine." [PubMed:12630926, RESID:AA0385, UniMod:449#S] +def: "A protein modification that effectively converts an L-serine residue to O-decanoyl-L-serine." [PubMed:12630926, RESID:AA0385, Unimod:449#S] synonym: "(2S)-2-amino-3-(decanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "Decanoyl" RELATED PSI-MS-label [] synonym: "L-serine decanoate ester" EXACT RESID-alternate [] -synonym: "lipid" RELATED UniMod-description [] +synonym: "lipid" RELATED Unimod-description [] synonym: "LIPID O-decanoyl serine" EXACT UniProt-feature [] synonym: "O-decanoyl-L-serine" EXACT RESID-name [] synonym: "O-decanoylated L-serine" EXACT PSI-MOD-alternate [] @@ -9586,13 +9922,15 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:449" +xref: UniProt: "PTM-0234" is_a: MOD:00668 ! O-decanoylated residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine [Term] id: MOD:00391 name: O-octanoyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-octanoyl-L-threonine." [PubMed:11546772, PubMed:12716131, RESID:AA0386, UniMod:426#T] +def: "A protein modification that effectively converts an L-threonine residue to O-octanoyl-L-threonine." [PubMed:11546772, PubMed:12716131, RESID:AA0386, Unimod:426#T] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(octanoyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "L-threonine octanoate ester" EXACT RESID-alternate [] @@ -9601,7 +9939,7 @@ synonym: "O-octanoylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-octanoyl-L-threonine" EXACT RESID-alternate [] synonym: "Octanoyl" RELATED PSI-MS-label [] -synonym: "octanoyl" RELATED UniMod-description [] +synonym: "octanoyl" RELATED Unimod-description [] synonym: "OOctThr" EXACT PSI-MOD-label [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" @@ -9612,17 +9950,19 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:426" +xref: UniProt: "PTM-0240" is_a: MOD:00669 ! O-octanoylated residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine [Term] id: MOD:00392 name: O-decanoyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-decanoyl-L-threonine." [PubMed:11546772, RESID:AA0387, UniMod:449#T] +def: "A protein modification that effectively converts an L-threonine residue to O-decanoyl-L-threonine." [PubMed:11546772, RESID:AA0387, Unimod:449#T] synonym: "(2S)-2-amino-3-(decanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "Decanoyl" RELATED PSI-MS-label [] synonym: "L-threonine decanoate ester" EXACT RESID-alternate [] -synonym: "lipid" RELATED UniMod-description [] +synonym: "lipid" RELATED Unimod-description [] synonym: "LIPID O-decanoyl threonine" EXACT UniProt-feature [] synonym: "O-decanoyl-L-threonine" EXACT RESID-name [] synonym: "O-decanoylated L-threonine" EXACT PSI-MOD-alternate [] @@ -9637,8 +9977,10 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:449" +xref: UniProt: "PTM-0235" is_a: MOD:00668 ! O-decanoylated residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine [Term] id: MOD:00393 @@ -9650,14 +9992,14 @@ [Term] id: MOD:00394 -name: acetylated residue -def: "A protein modification that effectively replaces a hydrogen atom with an acetyl group." [DeltaMass:0, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, UniMod:1] +name: monoacetylated residue +def: "A protein modification that effectively replaces one hydrogen atom with one acetyl group." [DeltaMass:0, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, Unimod:1] comment: Amino hydrogens are replaced to produce amides; hydroxyl hydrogens are replaced to produce esters; and hydrosulfanyl (thiol) hydrogens are replaced to produce sulfanyl esters (thiol esters). From DeltaMass: Average Mass: 42 subset: PSI-MOD-slim synonym: "Acetyl" RELATED PSI-MS-label [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "Acetylation (N terminus, N epsilon of Lysine, O of Serine) (Ac)" EXACT DeltaMass-label [] -synonym: "AcRes" EXACT PSI-MOD-label [] +synonym: "Ac1Res" EXACT PSI-MOD-label [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 O 1" xref: DiffMono: "42.010565" @@ -9667,7 +10009,8 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00649 ! acylated residue +xref: Unimod: "Unimod:1" +is_a: MOD:02078 ! acetylated residue [Term] id: MOD:00395 @@ -9675,7 +10018,7 @@ def: "A protein modification that crosslinks two residues by formation of a thioester bond between a cysteine thiol and either an alpha-carbonyl, as in S-(L-methionyl-L-cysteine), or a sidechain carbonyl, as in S-(L-isoglutamyl)-L-cysteine." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:00033 ! crosslinked residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:00396 @@ -9688,10 +10031,10 @@ [Term] id: MOD:00397 name: iodoacetamide derivatized residue -def: "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group." [PubMed:11327326, PubMed:11510821, PubMed:12422359, UniMod:4] +def: "A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group." [PubMed:11327326, PubMed:11510821, PubMed:12422359, Unimod:4] subset: PSI-MOD-slim synonym: "Carbamidomethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -9701,17 +10044,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:4" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00398 name: carbamoylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a carbamoyl (carboxamido) group. Replacement of an amino hydrogen produces a ureido group." [DeltaMass:56, PubMed:10978403, PubMed:12203680, UniMod:5] +def: "A protein modification that effectively replaces a hydrogen atom with a carbamoyl (carboxamido) group. Replacement of an amino hydrogen produces a ureido group." [DeltaMass:56, PubMed:10978403, PubMed:12203680, Unimod:5] comment: This modification can be produced by hydrogen cyanate, either used as a reagent or as released by urea degradation in solution [JSG]. subset: PSI-MOD-slim -synonym: "Carbamyl" RELATED UniMod-interim [] +synonym: "Carbamyl" RELATED Unimod-interim [] synonym: "Carbamylation" EXACT DeltaMass-label [] -synonym: "Carbamylation" RELATED UniMod-description [] +synonym: "Carbamylation" RELATED Unimod-description [] xref: DiffAvg: "43.02" xref: DiffFormula: "C 1 H 1 N 1 O 1" xref: DiffMono: "43.005814" @@ -9721,17 +10065,18 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:5" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00399 name: iodoacetic acid derivatized residue -def: "A protein modification that is produced by reaction with iodoacetic acid, usually replacement of a reactive hydrogen with a methylcarboxy group." [DeltaMass:64, UniMod:6] +def: "A protein modification that is produced by reaction with iodoacetic acid, usually replacement of a reactive hydrogen with a methylcarboxy group." [DeltaMass:64, Unimod:6] comment: From DeltaMass: Average Mass: 58 Abbreviation:CmC Average Mass Change:58 Notes:Cysteine reacts with iodoacetic acid to produce carboxymethyl cysteine. subset: PSI-MOD-slim synonym: "Carboxymethyl" RELATED PSI-MS-label [] synonym: "Carboxymethyl (on Cysteine)" EXACT DeltaMass-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -9741,16 +10086,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:6" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00400 name: deamidated residue -def: "A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen." [DeltaMass:32, OMSSA:4, UniMod:7] +def: "A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen." [DeltaMass:32, OMSSA:4, Unimod:7] comment: From DeltaMass: References:Vish Katta. subset: PSI-MOD-slim synonym: "Deamidated" RELATED PSI-MS-label [] -synonym: "Deamidation" RELATED UniMod-description [] +synonym: "Deamidation" RELATED Unimod-description [] synonym: "Deamidation of Asparagine and Glutamine to Aspartate and Glutamate" EXACT DeltaMass-label [] synonym: "deamidationkq" EXACT OMSSA-label [] synonym: "dNRes" EXACT PSI-MOD-label [] @@ -9763,13 +10109,14 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:7" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00401 name: Gygi ICAT(TM) d0 modified cysteine -def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Gygi isotope-coded affinity tag d0 reagent." [PubMed:10504701, UniMod:8#C] -synonym: "Gygi ICAT(TM) d0" RELATED UniMod-description [] +def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Gygi isotope-coded affinity tag d0 reagent." [PubMed:10504701, Unimod:8#C] +synonym: "Gygi ICAT(TM) d0" RELATED Unimod-description [] synonym: "ICAT-G" RELATED PSI-MS-label [] xref: DiffAvg: "486.63" xref: DiffFormula: "C 22 H 38 N 4 O 6 S 1" @@ -9780,14 +10127,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:8" is_a: MOD:01426 ! isotope tagged reagent derivatized residue is_a: MOD:01820 ! isotope tagged sufhydryl reagent modified cysteine [Term] id: MOD:00402 name: Gygi ICAT(TM) d8 modified cysteine -def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Gygi isotope-coded affinity tag d8 reagent." [PubMed:10504701, UniMod:9#C] -synonym: "Gygi ICAT(TM) d8" RELATED UniMod-description [] +def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Gygi isotope-coded affinity tag d8 reagent." [PubMed:10504701, Unimod:9#C] +synonym: "Gygi ICAT(TM) d8" RELATED Unimod-description [] synonym: "ICAT-G:2H(8)" RELATED PSI-MS-label [] xref: DiffAvg: "494.30" xref: DiffFormula: "C 22 (1)H 30 (2)H 8 N 4 O 6 S 1" @@ -9798,17 +10146,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:9" is_a: MOD:01431 ! (2)H deuterium tagged reagent is_a: MOD:01820 ! isotope tagged sufhydryl reagent modified cysteine [Term] id: MOD:00403 name: homoserine -def: "A protein modification that effectively converts an L-methionine residue to homoserine." [DeltaMass:113, OMSSA:56, UniMod:10#M] +def: "A protein modification that effectively converts an L-methionine residue to homoserine." [DeltaMass:113, OMSSA:56, Unimod:10#M] comment: Usually formed from methionine by reaction with cyanogen bromide, CNBr, which cleaves the peptide at the methionine carboxyl group and the following residue amino group. subset: PSI-MOD-slim synonym: "ctermpephsem" EXACT OMSSA-label [] -synonym: "Homoserine" RELATED UniMod-description [] +synonym: "Homoserine" RELATED Unimod-description [] synonym: "Homoserine formed from Met by CNBr treatment" EXACT DeltaMass-label [] synonym: "Met->Hse" RELATED PSI-MS-label [] xref: DiffAvg: "-30.09" @@ -9820,17 +10169,18 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:10" is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00404 name: homoserine lactone -def: "A protein modification that effectively converts an L-methionine residue to homoserine lactone." [DeltaMass:90, OMSSA:57, UniMod:11#M] +def: "A protein modification that effectively converts an L-methionine residue to homoserine lactone." [DeltaMass:90, OMSSA:57, Unimod:11#M] comment: Usually formed from methionine by reaction with cyanogen bromide, CNBr, which cleaves the peptide at the methionine carboxyl group. Under acid conditions the homoserine dehydrates to form the cyclic lactone. subset: PSI-MOD-slim synonym: "ctermpephselactm" EXACT OMSSA-label [] -synonym: "Homoserine lactone" RELATED UniMod-description [] -synonym: "Met->Hsl" RELATED UniMod-interim [] +synonym: "Homoserine lactone" RELATED Unimod-description [] +synonym: "Met->Hsl" RELATED Unimod-interim [] xref: DiffAvg: "-48.10" xref: DiffFormula: "C -1 H -4 S -1" xref: DiffMono: "-48.003371" @@ -9840,15 +10190,16 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:11" is_a: MOD:00601 ! cyclized residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00405 name: Applied Biosystems original ICAT(TM) d8 modified cysteine -def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Applied Biosystems original isotope-coded affinity tag d8 reagent." [UniMod:12#C] +def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Applied Biosystems original isotope-coded affinity tag d8 reagent." [Unimod:12#C] subset: PSI-MOD-slim -synonym: "Applied Biosystems original ICAT(TM) d8" RELATED UniMod-description [] +synonym: "Applied Biosystems original ICAT(TM) d8" RELATED Unimod-description [] synonym: "ICAT-D:2H(8)" RELATED PSI-MS-label [] xref: DiffAvg: "450.28" xref: DiffFormula: "C 20 (1)H 26 (2)H 8 N 4 O 5 S 1" @@ -9859,15 +10210,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:12" is_a: MOD:01431 ! (2)H deuterium tagged reagent is_a: MOD:01820 ! isotope tagged sufhydryl reagent modified cysteine + [Term] id: MOD:00406 name: Applied Biosystems original ICAT(TM) d0 modified cysteine -def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Applied Biosystems original isotope-coded affinity tag d0 reagent." [UniMod:13#C] +def: "A protein modification that is produced by formation of an adduct of a cysteine residue with the Applied Biosystems original isotope-coded affinity tag d0 reagent." [Unimod:13#C] subset: PSI-MOD-slim -synonym: "Applied Biosystems original ICAT(TM) d0" RELATED UniMod-description [] +synonym: "Applied Biosystems original ICAT(TM) d0" RELATED Unimod-description [] synonym: "ICAT-D" RELATED PSI-MS-label [] xref: DiffAvg: "442.22" xref: DiffFormula: "C 20 (1)H 34 N 4 O 5 S 1" @@ -9878,13 +10231,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:13" is_a: MOD:01426 ! isotope tagged reagent derivatized residue is_a: MOD:01820 ! isotope tagged sufhydryl reagent modified cysteine [Term] id: MOD:00407 name: residue methyl ester -def: "A protein modification that effectively replaces a carboxyl group with a carboxy methyl ester group. OBSOLETE because UniMod:14 merged with entry 34, remap to MOD:00599." [PubMed:18688235] +def: "A protein modification that effectively replaces a carboxyl group with a carboxy methyl ester group. OBSOLETE because Unimod:14 merged with entry 34, remap to MOD:00599." [PubMed:18688235] synonym: "ResOMe" EXACT PSI-MOD-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2" @@ -9895,11 +10249,12 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00599" is_obsolete: true [Term] id: MOD:00408 -name: N-acetylated residue +name: mono N-acetylated residue def: "A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "N-Acetyl" EXACT PSI-MOD-alternate [] @@ -9914,7 +10269,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00670 ! N-acylated residue [Term] @@ -9941,8 +10296,8 @@ [Term] id: MOD:00410 name: S-(N-isopropylcarboxamidomethyl)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(N-isopropylcarboxamidomethyl)-L-cysteine." [OMSSA:84, PubMed:11465505, PubMed:8465942, UniMod:17#C] -synonym: "N-isopropylcarboxamidomethyl" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-cysteine residue to S-(N-isopropylcarboxamidomethyl)-L-cysteine." [OMSSA:84, PubMed:11465505, PubMed:8465942, Unimod:17#C] +synonym: "N-isopropylcarboxamidomethyl" RELATED Unimod-description [] synonym: "NIPCAM" RELATED PSI-MS-label [] synonym: "nipcam" EXACT OMSSA-label [] xref: DiffAvg: "99.13" @@ -9954,14 +10309,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:17" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00411 name: O18 label -def: "modification from UniMod Isotopic label. OBSOLETE because UniMod:18 is now merged with entry 258 remap to MOD:00581 'single 018 label'" [PubMed:18688235] -comment: A modification from UniMod:18 +def: "modification from Unimod Isotopic label. OBSOLETE because Unimod:18 is now merged with entry 258 remap to MOD:00581 'single 018 label'" [PubMed:18688235] +comment: A modification from Unimod:18 xref: DiffAvg: "2.00" xref: DiffFormula: "(16)O -1 (18)O 1" xref: DiffMono: "2.004246" @@ -9971,12 +10327,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00581" is_obsolete: true [Term] id: MOD:00412 name: oxidation -def: "modification from UniMod artifact. OBSOLETE because UniMod entry 19 is now merged with UniMod 35 remap to MOD:00425 'monohydroxylated residue'." [PubMed:18688235] +def: "modification from Unimod artifact. OBSOLETE because Unimod entry 19 is now merged with Unimod 35 remap to MOD:00425 'monohydroxylated residue'." [PubMed:18688235] xref: DiffAvg: "16.00" xref: DiffFormula: "O 1" xref: DiffMono: "15.994915" @@ -9986,14 +10343,15 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00425" is_obsolete: true [Term] id: MOD:00413 name: biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine derivatized cysteine -def: "A protein modification that is produced by reaction of a cysteine residue with biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine." [UniMod:20#C] -synonym: "Biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine" RELATED UniMod-description [] -synonym: "PEO-Iodoacetyl-LC-Biotin" RELATED UniMod-interim [] +def: "A protein modification that is produced by reaction of a cysteine residue with biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine." [Unimod:20#C] +synonym: "Biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine" RELATED Unimod-description [] +synonym: "PEO-Iodoacetyl-LC-Biotin" RELATED Unimod-interim [] xref: DiffAvg: "414.52" xref: DiffFormula: "C 18 H 30 N 4 O 5 S 1" xref: DiffMono: "414.193691" @@ -10003,13 +10361,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:20" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00414 name: monomethylated L-arginine -def: "A protein modification that effectively replaces one hydrogen atom of an L-arginine residue with one methyl group." [DeltaMass:215, OMSSA:77, UniMod:34#R] +def: "A protein modification that effectively replaces one hydrogen atom of an L-arginine residue with one methyl group." [DeltaMass:215, OMSSA:77, Unimod:34#R] comment: From DeltaMass: formula incorrect, N and O reversed subset: PSI-MOD-slim synonym: "Me1Arg" EXACT PSI-MOD-label [] @@ -10025,13 +10384,14 @@ xref: Origin: "R" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00658 ! methylated arginine [Term] id: MOD:00415 name: phosphorylation without neutral loss -def: "modification from UniMod - OBSOLETE because UniMod entry 22 is now merged with entry 21 remap to MOD:00696 'phosphorylated residue'." [PubMed:18688235] +def: "modification from Unimod - OBSOLETE because Unimod entry 22 is now merged with entry 21 remap to MOD:00696 'phosphorylated residue'." [PubMed:18688235] xref: DiffAvg: "79.98" xref: DiffFormula: "H 1 O 3 P 1" xref: DiffMono: "79.966331" @@ -10041,16 +10401,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00696" is_obsolete: true [Term] id: MOD:00416 name: phosphorylation of an hydroxyl amino acid with prompt loss of phosphate -def: "A change resulting in an alteration of the measured molecular mass of a peptide or protein hydroxyl amino acid phosphorylated promptly followed by secondary loss of a neutral trihydrogen phosphate molecular fragment." [UniMod:23] -comment: O4-phosphotyrosine does not lose phosphate by this mechanism. UniMod does not provide a citation for this particular modification [JSG]. +def: "A change resulting in an alteration of the measured molecular mass of a peptide or protein hydroxyl amino acid phosphorylated promptly followed by secondary loss of a neutral trihydrogen phosphate molecular fragment." [Unimod:23] +comment: O4-phosphotyrosine does not lose phosphate by this mechanism. Unimod does not provide a citation for this particular modification [JSG]. subset: PSI-MOD-slim -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "H -2 O -1" xref: DiffMono: "-18.010565" @@ -10060,15 +10421,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:23" is_a: MOD:00432 ! modified residue with neutral loss of phosphate is_a: MOD:00704 ! dehydrated residue [Term] id: MOD:00417 name: S-carboxamidoethyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-carboxamidoethyl-L-cysteine." [DeltaMass:72, OMSSA:5, PubMed:1481983, UniMod:24#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-carboxamidoethyl-L-cysteine." [DeltaMass:72, OMSSA:5, PubMed:1481983, Unimod:24#C] comment: From DeltaMass: References: Anal. Biochem. Vol 216 No. 1 p131 (citation not found) Notes: Residual acrylamide in SDS gels can label free cysteines to produce propionamido-Cys (also known as PAM-Cys) -synonym: "Acrylamide adduct" RELATED UniMod-description [] +synonym: "Acrylamide adduct" RELATED Unimod-description [] synonym: "PAM-Cys" EXACT DeltaMass-label [] synonym: "Propionamide" RELATED PSI-MS-label [] synonym: "Propionamide or Acrylamide adduct" EXACT DeltaMass-label [] @@ -10085,15 +10447,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:24" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00418 name: pyridylacetylated residue -def: "A protein modification that effectively replaces a hydrogen atom with an (pyridin-3-yl)acetyl group." [PubMed:9276974, UniMod:25] +def: "A protein modification that effectively replaces a hydrogen atom with an (pyridin-3-yl)acetyl group." [PubMed:9276974, Unimod:25] comment: Produced by reaction with N-[(pyrid-3-yl)acetyl]oxy-succinimide [JSG]. synonym: "Pyridylacetyl" RELATED PSI-MS-label [] -synonym: "pyridylacetyl" RELATED UniMod-description [] +synonym: "pyridylacetyl" RELATED Unimod-description [] xref: DiffAvg: "119.12" xref: DiffFormula: "C 7 H 5 N 1 O 1" xref: DiffMono: "119.037114" @@ -10103,20 +10466,21 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:25" is_a: MOD:00649 ! acylated residue is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00419 name: (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid -def: "A protein modification that effectively converts an L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid." [DeltaMass:336, PubMed:12643538, UniMod:26#C] +def: "A protein modification that effectively converts an L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid." [DeltaMass:336, PubMed:12643538, Unimod:26#C] comment: From DeltaMass: A secondary modification affecting peptides with S-carbamoylmethyl-L-cysteine (CamC) at the N-terminus. These exist in enzymatic digests of proteins that have been S-alkylated with iodoacetamide. Cyclization of N-terminal CamC gives a residue of (R)-5-oxoperhydro-1,4-thiazine-3-carboxylic acid. Peptides in which this has occurred become more hydrophobic, and lose 17 Da from the N-terminal residue. synonym: "(R)-5-oxoperhydro-1,4-thiazine-3-carboxylic acid" EXACT DeltaMass-label [] synonym: "5-oxothiomorpholine-3-carboxylic acid" EXACT PSI-MOD-alternate [] synonym: "Otc" EXACT DeltaMass-label [] -synonym: "Pyro-carbamidomethyl" RELATED UniMod-interim [] +synonym: "Pyro-carbamidomethyl" RELATED Unimod-interim [] synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" EXACT DeltaMass-label [] -synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED UniMod-description [] +synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED Unimod-description [] xref: DiffAvg: "40.02" xref: DiffFormula: "C 2 H 0 N 0 O 1 S 0" xref: DiffMono: "39.994915" @@ -10126,13 +10490,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:26" is_a: MOD:00601 ! cyclized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00420 name: 2-pyrrolidone-5-carboxylic acid (Glu) -def: "A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid." [DeltaMass:16, OMSSA:109, PubMed:10214721, PubMed:1836357, PubMed:3473473, PubMed:8382902, RESID:AA0031#GLU, UniMod:27#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid." [DeltaMass:16, OMSSA:109, PubMed:10214721, PubMed:1836357, PubMed:3473473, PubMed:8382902, RESID:AA0031#GLU, Unimod:27#E] comment: From DeltaMass: References: The conversion of glutamic acid to pyroglutamic was reported for the beta-amyloid protein. Miller et al. Arch. Biochem. Biophy. (1993) 301, 41-52 [DeltaMass]. The modification in amyloid protein is probably an artifact of treatment with strong acid under anhydrous conditions. Peptides with N-terminal glutamic acid isolated from single cells of Aplysia neurons show partial conversion to pyroglutamic acid, possibly dependent on a temperature sensitive factor [JSG]. synonym: "(2S)-5-oxo-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "2-oxopyrrolidine-5-carboxylic acid" EXACT RESID-alternate [] @@ -10145,7 +10510,7 @@ synonym: "ntermpeppyroe" EXACT OMSSA-label [] synonym: "PCA" EXACT RESID-alternate [] synonym: "PyrGlu(Glu)" EXACT PSI-MOD-label [] -synonym: "Pyro-glu from E" RELATED UniMod-description [] +synonym: "Pyro-glu from E" RELATED Unimod-description [] synonym: "pyroglutamic acid" EXACT RESID-alternate [] synonym: "Pyroglutamic Acid formed from Glutamic Acid" EXACT DeltaMass-label [] xref: DiffAvg: "-18.02" @@ -10157,6 +10522,8 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:27" +xref: UniProt: "PTM-0262" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01048 ! 2-pyrrolidone-5-carboxylic acid @@ -10171,9 +10538,9 @@ [Term] id: MOD:00422 name: alpha-amino morpholine-2-acetylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a morpholine-2-acetyl group." [PubMed:10446193, UniMod:29#N-term] -comment: The UniMod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. -synonym: "N-Succinimidyl-2-morpholine acetate" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a morpholine-2-acetyl group." [PubMed:10446193, Unimod:29#N-term] +comment: The Unimod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. +synonym: "N-Succinimidyl-2-morpholine acetate" RELATED Unimod-description [] synonym: "N-succinimidylmorpholine-2-acetate alpha-amino derivative" EXACT PSI-MOD-alternate [] synonym: "SMA" RELATED PSI-MS-label [] xref: DiffAvg: "127.14" @@ -10185,18 +10552,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:29" is_a: MOD:01696 ! alpha-amino acylated residue is_a: MOD:01813 ! morpholine-2-acetylated residue [Term] id: MOD:00423 name: monosodium salt -def: "A protein modification that effectively substitutes one sodium atom for one hydrogen atom." [DeltaMass:0, UniMod:30] +def: "A protein modification that effectively substitutes one sodium atom for one hydrogen atom." [DeltaMass:0, Unimod:30] subset: PSI-MOD-slim synonym: "Cation:Na" RELATED PSI-MS-label [] synonym: "Na1Res" EXACT PSI-MOD-label [] synonym: "Sodium" EXACT DeltaMass-label [] -synonym: "Sodium adduct" RELATED UniMod-description [] +synonym: "Sodium adduct" RELATED Unimod-description [] xref: DiffAvg: "21.98" xref: DiffFormula: "H -1 Na 1" xref: DiffMono: "21.981944" @@ -10205,18 +10573,19 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:30" is_a: MOD:00747 ! sodium containing modified residue [Term] id: MOD:00424 name: S-pyridylethyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-pyridylethyl-L-cysteine." [DeltaMass:253, OMSSA:112, PubMed:11760118, PubMed:626389, PubMed:8297018, PubMed:8783016, UniMod:31#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-pyridylethyl-L-cysteine." [DeltaMass:253, OMSSA:112, PubMed:11760118, PubMed:626389, PubMed:8297018, PubMed:8783016, Unimod:31#C] comment: From DeltaMass: Formula:C10H12O2N1S1 (formula incorrect, N and O reversed) Monoisotopic Mass Change:208.067 Average Mass Change:208.286 (mass incorrect, aggregate not delta) References:PE Sciex synonym: "PECys" EXACT DeltaMass-label [] synonym: "Pyridylethyl" RELATED PSI-MS-label [] synonym: "Pyridylethyl Cystenyl" EXACT DeltaMass-label [] synonym: "S-pyridinylethyl-L-cysteine" EXACT PSI-MOD-alternate [] -synonym: "S-pyridylethylation" RELATED UniMod-description [] +synonym: "S-pyridylethylation" RELATED Unimod-description [] synonym: "spyridylethylc" EXACT OMSSA-label [] synonym: "vinylpyridine derivatized cysteine residue" EXACT PSI-MOD-alternate [] xref: DiffAvg: "105.14" @@ -10228,17 +10597,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:31" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00425 name: monohydroxylated residue -def: "A protein modification that effectively replaces one hydrogen atom with a hydroxyl group." [UniMod:35] +def: "A protein modification that effectively replaces one hydrogen atom with a hydroxyl group." [Unimod:35] subset: PSI-MOD-slim synonym: "Hy1Res" EXACT PSI-MOD-label [] -synonym: "Oxidation" RELATED UniMod-interim [] -synonym: "Oxidation or Hydroxylation" RELATED UniMod-description [] +synonym: "Oxidation" RELATED Unimod-interim [] +synonym: "Oxidation or Hydroxylation" RELATED Unimod-description [] xref: DiffAvg: "16.00" xref: DiffFormula: "O 1" xref: DiffMono: "15.994915" @@ -10247,7 +10617,8 @@ xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" -xref: TermSpec: "C-term" +xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00677 ! hydroxylated residue [Term] @@ -10270,9 +10641,9 @@ [Term] id: MOD:00428 name: dihydroxylated residue -def: "A protein modification that effectively replaces two hydrogen atoms with two hydroxyl groups." [PubMed:12686488, UniMod:425] +def: "A protein modification that effectively replaces two hydrogen atoms with two hydroxyl groups." [PubMed:12686488, Unimod:425] subset: PSI-MOD-slim -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "Hy2Res" EXACT PSI-MOD-label [] xref: DiffAvg: "32.00" @@ -10284,15 +10655,16 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" is_a: MOD:00677 ! hydroxylated residue [Term] id: MOD:00429 name: dimethylated residue -def: "A protein modification that effectively replaces two hydrogen atoms with two methyl groups." [DeltaMass:0, PubMed:12964758, PubMed:14570711, UniMod:36] +def: "A protein modification that effectively replaces two hydrogen atoms with two methyl groups." [DeltaMass:0, PubMed:12964758, PubMed:14570711, Unimod:36] comment: For amino-terminal proline residues, dimethylation can effectively only be accomplished with a protonated imino group. This process accounts only for dimethylation and not protonation. The alternative Me2+Res process accounts for both protonation and dimethylation [JSG]. subset: PSI-MOD-slim -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "Me2Res" EXACT PSI-MOD-label [] synonym: "N,N dimethylation (of Arginine or Lysine)" EXACT DeltaMass-label [] @@ -10305,16 +10677,17 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" is_a: MOD:00427 ! methylated residue [Term] id: MOD:00430 name: trimethylated residue -def: "A protein modification that effectively replaces three hydrogen atoms with three methyl groups." [PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, UniMod:37] +def: "A protein modification that effectively replaces three hydrogen atoms with three methyl groups." [PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, Unimod:37] comment: For amino acids residues, amine trimethylation can effectively only be accomplished with an aminium, protonated primary amino, group. This process accounts only for trimethylation and not protonation. The alternative Me3+Res process accounts for both protonation and trimethylation. subset: PSI-MOD-slim synonym: "Me3Res" EXACT PSI-MOD-label [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "42.08" xref: DiffFormula: "C 3 H 6" @@ -10325,6 +10698,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:37" is_a: MOD:00427 ! methylated residue [Term] @@ -10345,7 +10719,7 @@ [Term] id: MOD:00433 -name: glucosylated residue +name: monoglucosylated residue def: "A protein modification that effectively replaces a hydrogen atom with an glucose group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD-slim synonym: "GlcRes" EXACT PSI-MOD-label [] @@ -10358,18 +10732,18 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00434 ! hexosylated residue -is_a: MOD:00726 ! glucosylated +is_a: MOD:00761 ! monohexosylated residue +is_a: MOD:00726 ! glucosylated residue [Term] id: MOD:00434 name: hexosylated residue -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexose sugar group through a glycosidic bond." [DeltaMass:203, PubMed:15279557, UniMod:41] +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexose sugar group through a glycosidic bond." [DeltaMass:203, PubMed:15279557, Unimod:41] comment: From DeltaMass: Average Mass: 162 Formula:C6 H10 05 Monoisotopic Mass Change:162.053 Average Mass Change:162.143 References:PE Sciex. subset: PSI-MOD-slim synonym: "Hex" EXACT PSI-MOD-label [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] synonym: "Hexoses (Fru, Gal, Glc, Man)" EXACT DeltaMass-label [] synonym: "O-Glycosyl-" EXACT DeltaMass-label [] xref: DiffAvg: "none" @@ -10381,6 +10755,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" is_a: MOD:00693 ! glycosylated residue [Term] @@ -10403,12 +10778,12 @@ [Term] id: MOD:00436 -name: N-acetylhexosaminylated +name: N-acetylhexosaminylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with an N-acetylhexosamine group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD-slim synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "HexNAc" EXACT PSI-MOD-label [] -synonym: "N-Acetylhexosamine" RELATED UniMod-description [] +synonym: "N-Acetylhexosamine" RELATED Unimod-description [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" @@ -10418,17 +10793,18 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: GNOme: "GNO:G29068FM" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00437 name: farnesylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a farnesyl group." [DeltaMass:0, PubMed:15609361, UniMod:44] +def: "A protein modification that effectively replaces a hydrogen atom with a farnesyl group." [DeltaMass:0, PubMed:15609361, Unimod:44] comment: From DeltaMass: Average Mass: 204 subset: PSI-MOD-slim synonym: "Farnesyl" RELATED PSI-MS-label [] synonym: "Farnesylation" EXACT DeltaMass-label [] -synonym: "Farnesylation" RELATED UniMod-description [] +synonym: "Farnesylation" RELATED Unimod-description [] synonym: "FarnRes" EXACT PSI-MOD-label [] xref: DiffAvg: "204.36" xref: DiffFormula: "C 15 H 24" @@ -10439,18 +10815,19 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:44" is_a: MOD:00703 ! isoprenylated residue [Term] id: MOD:00438 name: myristoylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a myristoyl group." [DeltaMass:0, UniMod:45] +def: "A protein modification that effectively replaces a hydrogen atom with a myristoyl group." [DeltaMass:0, Unimod:45] comment: From DeltaMass: Average Mass: 210 subset: PSI-MOD-slim synonym: "C14:0 aliphatic acylated residue" EXACT PSI-MOD-alternate [] synonym: "Myristoyl" RELATED PSI-MS-label [] synonym: "Myristoylation" EXACT DeltaMass-label [] -synonym: "Myristoylation" RELATED UniMod-description [] +synonym: "Myristoylation" RELATED Unimod-description [] synonym: "MyrRes" EXACT PSI-MOD-label [] xref: DiffAvg: "210.36" xref: DiffFormula: "C 14 H 26 O 1" @@ -10461,6 +10838,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:45" is_a: MOD:00649 ! acylated residue is_a: MOD:01155 ! lipoconjugated residue @@ -10491,8 +10869,9 @@ subset: PSI-MOD-slim synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" EXACT DeltaMass-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "PamRes" EXACT PSI-MOD-label [] +synonym: "Hexadecanoylated residue" EXACT PSI-MOD-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 O 1" xref: DiffMono: "238.229666" @@ -10508,10 +10887,10 @@ [Term] id: MOD:00441 name: geranylgeranylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a geranylgeranyl group." [DeltaMass:0, PubMed:15609361, UniMod:48] +def: "A protein modification that effectively replaces a hydrogen atom with a geranylgeranyl group." [DeltaMass:0, PubMed:15609361, Unimod:48] comment: From DeltaMass: Average Mass: 272 subset: PSI-MOD-slim -synonym: "Geranyl-geranyl" RELATED UniMod-description [] +synonym: "Geranyl-geranyl" RELATED Unimod-description [] synonym: "GeranylGeranyl" RELATED PSI-MS-label [] synonym: "Geranylgeranylation" EXACT DeltaMass-label [] synonym: "GergerRes" EXACT PSI-MOD-label [] @@ -10524,6 +10903,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:48" is_a: MOD:00703 ! isoprenylated residue [Term] @@ -10563,8 +10943,8 @@ [Term] id: MOD:00444 name: N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine -def: "A protein modification that effectively converts an L-cysteine residue to N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine." [OMSSA:118, PubMed:10356335, UniMod:51] -synonym: "N-acyl diglyceride cysteine" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-cysteine residue to N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine." [OMSSA:118, PubMed:10356335, Unimod:51] +synonym: "N-acyl diglyceride cysteine" RELATED Unimod-description [] synonym: "ntermpeptripalmitatec" EXACT OMSSA-label [] synonym: "Tripalmitate" RELATED PSI-MS-label [] xref: DiffAvg: "789.32" @@ -10576,15 +10956,16 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:51" is_a: MOD:00899 ! N-palmitoyl-S-diacylglycerol-L-cysteine relationship: has_functional_parent MOD:01144 ! S-(sn-1-2,3-dipalmitoylglycerol)-L-cysteine [Term] id: MOD:00445 name: L-homoarginine -def: "A protein modification that effectively converts an L-lysine residue to L-homoarginine, such as reaction with O-methylisourea." [OMSSA:53, PubMed:11078590, PubMed:11085420, PubMed:11821862, UniMod:52] +def: "A protein modification that effectively converts an L-lysine residue to L-homoarginine, such as reaction with O-methylisourea." [OMSSA:53, PubMed:11078590, PubMed:11085420, PubMed:11821862, Unimod:52] subset: PSI-MOD-slim -synonym: "Guanidination" RELATED UniMod-description [] +synonym: "Guanidination" RELATED Unimod-description [] synonym: "guanidinationk" EXACT OMSSA-label [] synonym: "Guanidinyl" RELATED PSI-MS-label [] xref: DiffAvg: "42.04" @@ -10596,15 +10977,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:52" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00446 name: 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of a residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, UniMod:53] +def: "A protein modification produced by formation of an adduct of a residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, Unimod:53] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. -synonym: "4-hydroxynonenal (HNE)" RELATED UniMod-description [] +synonym: "4-hydroxynonenal (HNE)" RELATED Unimod-description [] synonym: "HNE" RELATED PSI-MS-label [] xref: DiffAvg: "156.22" xref: DiffFormula: "C 9 H 16 O 2" @@ -10615,16 +10997,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:53" is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00447 name: N-glucuronylated residue -def: "A protein modification that effectively results from forming an adduct with a glucuronic acid either through a carboxyl group amide or ester bond, or through C1-glycosylation." [DeltaMass:0, PubMed:7398618, UniMod:54#N-term] +def: "A protein modification that effectively results from forming an adduct with a glucuronic acid either through a carboxyl group amide or ester bond, or through C1-glycosylation." [DeltaMass:0, PubMed:7398618, Unimod:54#N-term] subset: PSI-MOD-slim synonym: "Glucuronyl" RELATED PSI-MS-label [] synonym: "N-Glucuronyl (N terminus)" EXACT DeltaMass-label [] -synonym: "N-glucuronylation" RELATED UniMod-description [] +synonym: "N-glucuronylation" RELATED Unimod-description [] xref: DiffAvg: "176.12" xref: DiffFormula: "C 6 H 8 O 6" xref: DiffMono: "176.032088" @@ -10634,11 +11017,12 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:54" is_a: MOD:00764 ! glycoconjugated residue [Term] id: MOD:00448 -name: N-acetylaminoglucosylated residue +name: mono-N-acetylaminoglucosylated residue def: "A protein modification that effectively replaces a hydrogen atom with an N-acetylaminoglucose group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD-slim synonym: "GlcNAcRes" EXACT PSI-MOD-label [] @@ -10658,8 +11042,8 @@ [Term] id: MOD:00449 name: acetate labeling reagent (N-term) (heavy form, +3amu) -def: "modification from UniMod Isotopic label" [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:56] -synonym: "Acetate labeling reagent (N-term & K) (heavy form, +3amu)" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:56] +synonym: "Acetate labeling reagent (N-term & K) (heavy form, +3amu)" RELATED Unimod-description [] synonym: "Acetyl:2H(3)" RELATED PSI-MS-label [] xref: DiffAvg: "45.03" xref: DiffFormula: "C 2 (1)H -1 (2)H 3 O 1" @@ -10670,12 +11054,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:56" is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00450 name: acetate labeling reagent light form (K) -def: "OBSOLETE because this isotopic label from UniMod entry 57 is deprecated" [PubMed:11857757] +def: "OBSOLETE because this isotopic label from Unimod entry 57 is deprecated" [PubMed:11857757] xref: DiffAvg: "42.01" xref: DiffFormula: "C 2 (1)H 2 O 1" xref: DiffMono: "42.010565" @@ -10690,8 +11075,8 @@ [Term] id: MOD:00451 name: alpha-amino propanoylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:58#N-term] -synonym: "Propionate labeling reagent light form (N-term & K)" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:58#N-term] +synonym: "Propionate labeling reagent light form (N-term & K)" RELATED Unimod-description [] synonym: "Propionyl" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -10702,13 +11087,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:58" is_a: MOD:01894 ! propanoylated residue [Term] id: MOD:00452 name: alpha-amino 3x(13)C-labeled propanoylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 3x(13)C-labeled propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:59#N-term] -synonym: "Propionate labeling reagent heavy form (+3amu), N-term & K" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 3x(13)C-labeled propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:59#N-term] +synonym: "Propionate labeling reagent heavy form (+3amu), N-term & K" RELATED Unimod-description [] synonym: "Propionyl:13C(3)" RELATED PSI-MS-label [] xref: DiffAvg: "59.04" xref: DiffFormula: "(13)C 3 H 4 O 1" @@ -10716,17 +11102,21 @@ xref: Formula: "(12)C 6 (13)C 3 H 16 N 2 O 2" xref: MassAvg: "187.13" xref: MassMono: "187.131242" -xref: Origin: "K" +xref: Origin: "X" xref: Source: "artifact" -xref: TermSpec: "none" -is_a: MOD:00451 ! alpha-amino propanoylated residue +xref: TermSpec: "N-term" +xref: Unimod: "Unimod:59" +relationship: derives_from MOD:00451 ! alpha-amino propanoylated residue +is_a: MOD:01428 ! (13)C isotope tagged reagent +is_a: MOD:01426 ! isotope tagged reagent derivatized residue + [Term] id: MOD:00453 name: quaternary amine labeling reagent light form (N-term & K) -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent light form group." [PubMed:11857757, UniMod:60] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent light form group." [PubMed:11857757, Unimod:60] synonym: "GIST-Quat" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent light form (N-term & K)" RELATED Unimod-description [] xref: DiffAvg: "127.19" xref: DiffFormula: "C 7 H 13 N 1 O 1" xref: DiffMono: "127.099714" @@ -10736,14 +11126,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:60" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00454 name: quaternary amine labeling reagent heavy form (+3amu) (N-term & K) -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+3amu) form group." [PubMed:11857757, UniMod:61] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+3amu) form group." [PubMed:11857757, Unimod:61] synonym: "GIST-Quat:2H(3)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy (+3amu) form, N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy (+3amu) form, N-term & K" RELATED Unimod-description [] xref: DiffAvg: "130.12" xref: DiffFormula: "C 7 (1)H 10 (2)H 3 N 1 O 1" xref: DiffMono: "130.118544" @@ -10753,14 +11144,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:61" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00455 name: quaternary amine labeling reagent heavy form (+6amu) (N-term & K) -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+6amu) form group." [PubMed:11857757, UniMod:62] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+6amu) form group." [PubMed:11857757, Unimod:62] synonym: "GIST-Quat:2H(6)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy form (+6amu), N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy form (+6amu), N-term & K" RELATED Unimod-description [] xref: DiffAvg: "133.14" xref: DiffFormula: "C 7 H 7 (2)H 6 N 1 O 1" xref: DiffMono: "133.137375" @@ -10770,14 +11162,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:62" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00456 name: quaternary amine labeling reagent heavy form (+9amu) (N-term & K) -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+9amu) form group." [PubMed:11857757, UniMod:63] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a quaternary amine reagent heavy (+9amu) form group." [PubMed:11857757, Unimod:63] synonym: "GIST-Quat:2H(9)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy form (+9amu), N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy form (+9amu), N-term & K" RELATED Unimod-description [] xref: DiffAvg: "136.16" xref: DiffFormula: "C 7 (1)H 4 (2)H 9 N 1 O 1" xref: DiffMono: "136.156205" @@ -10787,15 +11180,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:63" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00457 -name: alpha-amino succinylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a succinyl group." [PubMed:11857757, PubMed:12175151, UniMod:64#N-term] -synonym: "Succinic anhydride labeling reagent light form (N-term)" RELATED UniMod-description [] +name: 4x(12)C, 4x(1)H labeled alpha-amino succinylated residue +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a light succinyl group." [PubMed:11857757, PubMed:12175151, Unimod:64#N-term] +synonym: "Succinic anhydride labeling reagent light form (N-term)" RELATED Unimod-description [] synonym: "Succinyl" RELATED PSI-MS-label [] -xref: DiffAvg: "100.02" +xref: DiffAvg: "100.03" xref: DiffFormula: "(12)C 4 (1)H 4 O 3" xref: DiffMono: "100.016044" xref: Formula: "none" @@ -10804,15 +11198,16 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00848 ! reagent derivatized residue -is_a: MOD:01029 ! succinylated residue +xref: Unimod: "Unimod:64" +relationship: derives_from MOD:01029 ! succinylated residue is_a: MOD:01696 ! alpha-amino acylated residue +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00458 name: 4x(2)H labeled alpha-amino succinylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 4x(2)H labeled succinyl group." [PubMed:11857757, PubMed:12175151, UniMod:65#N-term] -synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 4x(2)H labeled succinyl group." [PubMed:11857757, PubMed:12175151, Unimod:65#N-term] +synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term" RELATED Unimod-description [] synonym: "Succinyl:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "104.04" xref: DiffFormula: "C 4 (2)H 4 O 3" @@ -10823,13 +11218,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00457 ! alpha-amino succinylated residue +xref: Unimod: "Unimod:65" +relationship: derives_from MOD:01029 ! succinylated residue +is_a: MOD:01696 ! alpha-amino acylated residue +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00459 name: 4x(13)C labeled alpha-amino succinylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 4x(13)C labeled succinyl group." [PubMed:11857757, PubMed:12175151, UniMod:66#N-term] -synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), N-term & K" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 4x(13)C labeled succinyl group." [PubMed:11857757, PubMed:12175151, Unimod:66#N-term] +synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), N-term & K" RELATED Unimod-description [] synonym: "Succinyl:13C(4)" RELATED PSI-MS-label [] xref: DiffAvg: "104.03" xref: DiffFormula: "(13)C 4 H 4 O 3" @@ -10839,12 +11237,16 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" -is_a: MOD:00457 ! alpha-amino succinylated residue +xref: Unimod: "Unimod:66" +relationship: derives_from MOD:01029 ! succinylated residue +is_a: MOD:01696 ! alpha-amino acylated residue +is_a: MOD:01428 ! (13)C isotope tagged reagent +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00460 name: L-cysteic acid (L-cysteine sulfonic acid) -def: "A protein modification that effectively trioxygenates an L-cysteine residue to L-cysteine sulfonic acid." [ChEBI:17285, DeltaMass:334, OMSSA:34, PubMed:14678012, PubMed:18306178, PubMed:19522542, PubMed:9252331, RESID:AA0556, UniMod:345#C] +def: "A protein modification that effectively trioxygenates an L-cysteine residue to L-cysteine sulfonic acid." [ChEBI:17285, DeltaMass:334, OMSSA:34, PubMed:14678012, PubMed:18306178, PubMed:19522542, PubMed:9252331, RESID:AA0556, Unimod:345#C] comment: From DeltaMass: Notes:Treatment of cysteine by strongly oxidising reagents such as performic acid results in the complete oxidation of the sulphur atom. Such treatment is often carried out prior to amino acid analysis as the resulting cysteic acid is then resistant to acid degradation during the hydrolysis procedure. subset: PSI-MOD-slim synonym: "(2R)-2-amino-3-sulfopropanoic acid" EXACT RESID-systematic [] @@ -10856,10 +11258,11 @@ synonym: "cysteic acid" EXACT RESID-alternate [] synonym: "Cysteic acid, oxidation of cysteine" EXACT DeltaMass-label [] synonym: "cysteicacidc" EXACT OMSSA-label [] -synonym: "cysteine oxidation to cysteic acid" RELATED UniMod-description [] +synonym: "cysteine oxidation to cysteic acid" RELATED Unimod-description [] synonym: "cysteine sulphonic acid" EXACT RESID-alternate [] synonym: "L-cysteine sulfonic acid" EXACT RESID-name [] synonym: "Trioxidation" RELATED PSI-MS-label [] +synonym: "MOD_RES Cysteine sulfonic acid (-SO3H)" EXACT UniProt-feature [] xref: DiffAvg: "48.00" xref: DiffFormula: "C 0 H 0 N 0 O 3 S 0" xref: DiffMono: "47.984744" @@ -10869,17 +11272,19 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:345" +xref: UniProt: "PTM-0634" is_a: MOD:00708 ! sulfur oxygenated L-cysteine [Term] id: MOD:00461 -name: nitrosylation -def: "A protein modification that effectively substitutes a nitrite (NO2) group for a hydrogen atom." [DeltaMass:0, PubMed:8839040, PubMed:9252331, UniMod:354] +name: nitrated residue +def: "A protein modification that effectively substitutes a nitrite (NO2) group for a hydrogen atom." [DeltaMass:0, PubMed:8839040, PubMed:9252331, Unimod:354] comment: Note, this is often misrepresented as the introduction of a nitrate (NO3) group [JSG]. subset: PSI-MOD-slim synonym: "Nitro" RELATED PSI-MS-label [] synonym: "Nitro (NO2)" EXACT DeltaMass-label [] -synonym: "Oxidation to nitro" RELATED UniMod-description [] +synonym: "Oxidation to nitro" RELATED Unimod-description [] xref: DiffAvg: "45.00" xref: DiffFormula: "H -1 N 1 O 2" xref: DiffMono: "44.985078" @@ -10888,17 +11293,18 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:354" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00462 name: L-kynurenine -def: "A protein modification that effectively converts an L-tryptophan residue to L-kynurenine." [DeltaMass:357, OMSSA:66, PubMed:11029593, PubMed:9252331, UniMod:351#W] +def: "A protein modification that effectively converts an L-tryptophan residue to L-kynurenine." [DeltaMass:357, OMSSA:66, PubMed:11029593, PubMed:9252331, Unimod:351#W] subset: PSI-MOD-slim synonym: "(2S)-2-amino-4-(2-aminophenyl)-4-oxo-butanoic acid" EXACT PSI-MOD-alternate [] synonym: "kynureninw" EXACT OMSSA-label [] synonym: "Trp->Kynurenin" RELATED PSI-MS-label [] -synonym: "tryptophan oxidation to kynurenin" RELATED UniMod-description [] +synonym: "tryptophan oxidation to kynurenin" RELATED Unimod-description [] xref: DiffAvg: "3.99" xref: DiffFormula: "C -1 O 1" xref: DiffMono: "3.994915" @@ -10908,16 +11314,17 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:351" is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00463 name: 3'-hydroxy-L-kynurenine -def: "A protein modification that effectively converts an L-tryptophan residue to 3'-hydroxy-L-kynurenine." [OMSSA:58, PubMed:9252331, UniMod:350#W] +def: "A protein modification that effectively converts an L-tryptophan residue to 3'-hydroxy-L-kynurenine." [OMSSA:58, PubMed:9252331, Unimod:350#W] subset: PSI-MOD-slim synonym: "hydroxykynureninw" EXACT OMSSA-label [] synonym: "Trp->Hydroxykynurenin" RELATED PSI-MS-label [] -synonym: "tryptophan oxidation to hydroxykynurenin" RELATED UniMod-description [] +synonym: "tryptophan oxidation to hydroxykynurenin" RELATED Unimod-description [] xref: DiffAvg: "19.99" xref: DiffFormula: "C -1 O 2" xref: DiffMono: "19.989829" @@ -10927,20 +11334,21 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:350" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00464 name: N'-formyl-L-kynurenine -def: "A protein modification that effectively converts an L-tryptophan residue to N'-formyl-L-kynurenine." [DeltaMass:356, OMSSA:45, PubMed:12124932, PubMed:12686488, PubMed:9252331, UniMod:425#W] +def: "A protein modification that effectively converts an L-tryptophan residue to N'-formyl-L-kynurenine." [DeltaMass:356, OMSSA:45, PubMed:12124932, PubMed:12686488, PubMed:9252331, Unimod:425#W] comment: From DeltaMass: References:Willy V. Bienvenut, Catherine Déon, Carla Pasquarello, Jennifer M. Campbell, Jean-Charles Sanchez, Marvin L. Vestal, Denis F. Hochstrasser Matrix-assisted laser desorption/ionization-tandemmass spectrometry with high resolution andsensitivity for identification and characterizationof proteins. Proteomics 2002, 2, 868-876 Notes: A double oxidation of tryptophan for which the N-formylkynurenine (+32) structure can be proposed. Many minor peaks accompanying the main peak might also be attributed to other oxidation products of the tryptophan such as kynurenine (+4), an unknown by-product found in all oxidized tryptophan patterns (+13), hydroxytryptophan (+16), 3-hydroxykynurenine (+20) and hydroxy-N-formylkynurenine (+48). See proposed structures at http://www.abrf.org/images/misc/dmass32.jpg. subset: PSI-MOD-slim -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "Double oxidation of Trp" EXACT DeltaMass-label [] synonym: "formylkynureninw" EXACT OMSSA-label [] -synonym: "tryptophan oxidation to formylkynurenin" RELATED UniMod-alternate [] +synonym: "tryptophan oxidation to formylkynurenin" RELATED Unimod-alternate [] xref: DiffAvg: "32.00" xref: DiffFormula: "O 2" xref: DiffMono: "31.989829" @@ -10950,16 +11358,17 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00465 name: dihydroxyphenylalanine (Phe) -def: "A protein modification that effectively converts an L-phenylalanine residue to a dihydroxyphenylalanine." [OMSSA:39, PubMed:1610822, PubMed:1903612, PubMed:3734192, PubMed:9252331, RESID:AA0146#var, UniMod:425#F] +def: "A protein modification that effectively converts an L-phenylalanine residue to a dihydroxyphenylalanine." [OMSSA:39, PubMed:1610822, PubMed:1903612, PubMed:3734192, PubMed:9252331, RESID:AA0146#var, Unimod:425#F] comment: Dihydroxyphenyalanines with a 4'-hydroxyl orginate naturally by a monohydroxylation of tyrosine, and not by dihydroxylation of phenylalanine [JSG]. subset: PSI-MOD-slim -synonym: "dihydroxy" RELATED UniMod-description [] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "dihydroxyf" EXACT OMSSA-label [] synonym: "Dioxidation" RELATED PSI-MS-label [] xref: DiffAvg: "32.00" @@ -10971,6 +11380,7 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00914 ! modified L-phenylalanine residue @@ -10985,9 +11395,9 @@ [Term] id: MOD:00467 name: iminobiotinyl modified residue -def: "A protein modification that effectively substitutes an iminobiotinyl group for a hydrogen atom." [PubMed:9750125, UniMod:89] +def: "A protein modification that effectively substitutes an iminobiotinyl group for a hydrogen atom." [PubMed:9750125, Unimod:89] synonym: "Iminobiotin" RELATED PSI-MS-label [] -synonym: "Iminobiotinylation" RELATED UniMod-description [] +synonym: "Iminobiotinylation" RELATED Unimod-description [] xref: DiffAvg: "225.31" xref: DiffFormula: "C 10 H 15 N 3 O 1 S 1" xref: DiffMono: "225.093583" @@ -10997,14 +11407,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:89" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00468 name: ESP-Tag light d0 -def: "modification from UniMod Isotopic label" [UniMod:90] +def: "modification from Unimod Isotopic label" [Unimod:90] synonym: "ESP" RELATED PSI-MS-label [] -synonym: "ESP-Tag light d0" RELATED UniMod-description [] +synonym: "ESP-Tag light d0" RELATED Unimod-description [] xref: DiffAvg: "338.47" xref: DiffFormula: "C 16 H 26 N 4 O 2 S 1" xref: DiffMono: "338.177647" @@ -11014,13 +11425,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:90" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00469 name: ESP-Tag heavy d10 -def: "modification from UniMod Isotopic label" [UniMod:91] -synonym: "ESP-Tag heavy d10" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [Unimod:91] +synonym: "ESP-Tag heavy d10" RELATED Unimod-description [] synonym: "ESP:2H(10)" RELATED PSI-MS-label [] xref: DiffAvg: "348.24" xref: DiffFormula: "C 16 (1)H 16 (2)H 10 N 4 O 2 S 1" @@ -11031,14 +11443,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:91" is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00470 name: NHS-LC-Biotin -def: "modification from UniMod Chemical derivative" [UniMod:92] -synonym: "NHS-LC-Biotin" RELATED UniMod-interim [] -synonym: "NHS-LC-Biotin" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:92] +synonym: "NHS-LC-Biotin" RELATED Unimod-interim [] +synonym: "NHS-LC-Biotin" RELATED Unimod-description [] xref: DiffAvg: "339.45" xref: DiffFormula: "C 16 H 25 N 3 O 3 S 1" xref: DiffMono: "339.161663" @@ -11048,14 +11461,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:92" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00471 name: EDT-maleimide-PEO-biotin -def: "modification from UniMod Chemical derivative" [UniMod:93] -synonym: "EDT-maleimide-PEO-biotin" RELATED UniMod-interim [] -synonym: "EDT-maleimide-PEO-biotin" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:93] +synonym: "EDT-maleimide-PEO-biotin" RELATED Unimod-interim [] +synonym: "EDT-maleimide-PEO-biotin" RELATED Unimod-description [] xref: DiffAvg: "601.80" xref: DiffFormula: "C 25 H 39 N 5 O 6 S 3" xref: DiffMono: "601.206247" @@ -11065,14 +11479,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:93" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00472 name: IMID d0 -def: "modification from UniMod Isotopic label" [PubMed:11746907, UniMod:94, URL:http\://dx.doi.org/10.1002/rcm.517] +def: "modification from Unimod Isotopic label" [PubMed:11746907, Unimod:94, URL:http\://dx.doi.org/10.1002/rcm.517] synonym: "IMID" RELATED PSI-MS-label [] -synonym: "IMID d0" RELATED UniMod-description [] +synonym: "IMID d0" RELATED Unimod-description [] xref: DiffAvg: "68.04" xref: DiffFormula: "C 3 (1)H 4 N 2" xref: DiffMono: "68.037448" @@ -11082,13 +11497,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:94" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00473 name: IMID d4 -def: "modification from UniMod Isotopic label" [PubMed:11746907, UniMod:95, URL:http\://dx.doi.org/10.1002/rcm.517] -synonym: "IMID d4" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [PubMed:11746907, Unimod:95, URL:http\://dx.doi.org/10.1002/rcm.517] +synonym: "IMID d4" RELATED Unimod-description [] synonym: "IMID:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "72.06" xref: DiffFormula: "C 3 (2)H 4 N 2" @@ -11099,13 +11515,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:95" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00474 name: S-([1,1,2-(2)H3]-carboxamidoethyl)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(1,1,2-(2)H3)-propanamide-L-cysteine." [UniMod:97#C] -synonym: "Acrylamide d3" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-cysteine residue to S-(1,1,2-(2)H3)-propanamide-L-cysteine." [Unimod:97#C] +synonym: "Acrylamide d3" RELATED Unimod-description [] synonym: "Propionamide:2H(3)" RELATED PSI-MS-label [] synonym: "S-([1,1,2-(2)H3]-3-amino-3-oxopropyl)cysteine" EXACT PSI-MOD-alternate [] synonym: "S-([1,1,2-(2)H3]-carbamoylethyl)-L-cysteine" EXACT PSI-MOD-alternate [] @@ -11119,16 +11536,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00417 ! S-carboxamidoethyl-L-cysteine +xref: Unimod: "Unimod:97" +relationship: derives_from MOD:00417 ! S-carboxamidoethyl-L-cysteine is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00475 -name: tyrosine oxidation to 2-aminotyrosine -def: "modification from UniMod Chemical derivative" [PubMed:8839040, PubMed:9252331, UniMod:342#Y] -comment: May be misdescribed. Name (if not misdescribed) should be 2'-aminotyrosine [JSG]. +name: 2-amino-L-tyrosine +def: "A protein modification that effectively converts an L-tyrosine residue to 2-amino-L-tyrosine." [PubMed:8839040, PubMed:9252331, Unimod:342#Y] synonym: "Amino" RELATED PSI-MS-label [] -synonym: "Tyrosine oxidation to 2-aminotyrosine" RELATED UniMod-description [] +synonym: "Tyrosine oxidation to 2-aminotyrosine" RELATED Unimod-description [] xref: DiffAvg: "15.02" xref: DiffFormula: "H 1 N 1" xref: DiffMono: "15.010899" @@ -11138,24 +11555,35 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:342" +is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02039 ! aminated residue [Term] id: MOD:00476 -name: galactosylated residue +name: monogalactosylated residue def: "A protein modification that effectively replaces a hydrogen atom with an galactose group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD-slim synonym: "GalRes" EXACT PSI-MOD-label [] -is_a: MOD:00434 ! hexosylated residue -is_a: MOD:00728 ! galactosylated +xref: DiffAvg: "162.14" +xref: DiffFormula: "C 6 H 10 O 5" +xref: DiffMono: "162.052823" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00761 ! monohexosylated residue +is_a: MOD:00728 ! galactosylated residue [Term] id: MOD:00477 name: 2-pyrrolidone -def: "A protein modification that effectively converts, by oxidative decarboxylation, an L-proline residue to 2-pyrrolidone with breakage of the peptide chain." [PubMed:2161657, PubMed:9252331, UniMod:360#P] -comment: The oxidative decarboxylation of a proline residue results in breaking of the peptide chain, leaving a peptidyl-2-pyrrolidone at the C-terminus. The difference formula, derived from the result in the original citation, has been corrected from the UniMod entry. +def: "A protein modification that effectively converts, by oxidative decarboxylation, an L-proline residue to 2-pyrrolidone with breakage of the peptide chain." [PubMed:2161657, PubMed:9252331, Unimod:360#P] +comment: The oxidative decarboxylation of a proline residue results in breaking of the peptide chain, leaving a peptidyl-2-pyrrolidone at the C-terminus. The difference formula, derived from the result in the original citation, has been corrected from the Unimod entry. synonym: "Pro->Pyrrolidinone" RELATED PSI-MS-label [] -synonym: "Proline oxidation to pyrrolidinone" RELATED UniMod-description [] +synonym: "Proline oxidation to pyrrolidinone" RELATED Unimod-description [] xref: DiffAvg: "-13.02" xref: DiffFormula: "C -1 H -1 N 0 O 0" xref: DiffMono: "-13.007825" @@ -11165,20 +11593,20 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:360" is_a: MOD:00683 ! dehydrogenated residue is_a: MOD:00915 ! modified L-proline residue -is_a: MOD:00960 ! decarboxylated residue [Term] id: MOD:00478 name: glutamyl semialdehyde (Pro) -def: "A protein modification that effectively converts an L-proline residue to L-glutamyl semialdehyde." [DeltaMass:354, PubMed:11120890, PubMed:2563380, PubMed:9252331, UniMod:35#P] +def: "A protein modification that effectively converts an L-proline residue to L-glutamyl semialdehyde." [DeltaMass:354, PubMed:11120890, PubMed:2563380, PubMed:9252331, Unimod:35#P] synonym: "gamma-glutamyl semialdehyde" EXACT PSI-MOD-alternate [] synonym: "glutamyl 5-semialdehyde" EXACT PSI-MOD-alternate [] synonym: "glutamyl aldehyde" EXACT PSI-MOD-alternate [] -synonym: "Oxidation" RELATED UniMod-interim [] +synonym: "Oxidation" RELATED Unimod-interim [] synonym: "Oxidation of proline to gamma-glutamyl semialdehyde" EXACT DeltaMass-label [] -synonym: "Oxidation or Hydroxylation" RELATED UniMod-description [] +synonym: "Oxidation or Hydroxylation" RELATED Unimod-description [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -11188,6 +11616,7 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01440 ! glutamyl semialdehyde @@ -11195,10 +11624,10 @@ [Term] id: MOD:00479 name: glutamyl semialdehyde (Arg) -def: "A protein modification that effectively converts an L-arginine residue to L-glutamyl semialdehyde." [DeltaMass:351, PubMed:11120890, PubMed:1680314, PubMed:9252331, UniMod:344#R] +def: "A protein modification that effectively converts an L-arginine residue to L-glutamyl semialdehyde." [DeltaMass:351, PubMed:11120890, PubMed:1680314, PubMed:9252331, Unimod:344#R] comment: From DeltaMass: Average Mass: -27 Monoisotopic Mass Change:-27.06 Average Mass Change:-27.07 References:Amici A, Levine, RL, Tsai, L, and Stadtman, ER: Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions. Journal of Biological Chemistry 264: 3341-3346 1989.Requena JR, Chao CC, Levine RL, and Stadtman ER: Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins. Proceedings of the National Academy of Sciences USA 98: 69-74 2001. synonym: "Arg->GluSA" RELATED PSI-MS-label [] -synonym: "Arginine oxidation to glutamic semialdehyde" RELATED UniMod-description [] +synonym: "Arginine oxidation to glutamic semialdehyde" RELATED Unimod-description [] synonym: "Oxidation of arginine (to glutamic acid)" EXACT DeltaMass-label [] xref: DiffAvg: "-43.07" xref: DiffFormula: "C -1 H -5 N -3 O 1" @@ -11209,15 +11638,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:344" is_a: MOD:00902 ! modified L-arginine residue is_a: MOD:01440 ! glutamyl semialdehyde [Term] id: MOD:00480 name: Applied Biosystems cleavable ICAT(TM) light -def: "modification from UniMod Isotopic label" [OMSSA:129, UniMod:105#C, URL:http\://www.appliedbiosystems.com/products/productdetail.cfm?prod_id=153] +def: "modification from Unimod Isotopic label" [OMSSA:129, Unimod:105#C, URL:http\://www.appliedbiosystems.com/products/productdetail.cfm?prod_id=153] subset: PSI-MOD-slim -synonym: "Applied Biosystems cleavable ICAT(TM) light" RELATED UniMod-description [] +synonym: "Applied Biosystems cleavable ICAT(TM) light" RELATED Unimod-description [] synonym: "ICAT-C" RELATED PSI-MS-label [] synonym: "icatlight" EXACT OMSSA-label [] xref: DiffAvg: "227.26" @@ -11229,14 +11659,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:105" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00481 name: Applied Biosystems cleavable ICAT(TM) heavy -def: "modification from UniMod Isotopic label" [OMSSA:130, UniMod:106#C, URL:http\://www.appliedbiosystems.com/products/productdetail.cfm?prod_id=153] +def: "modification from Unimod Isotopic label" [OMSSA:130, Unimod:106#C, URL:http\://www.appliedbiosystems.com/products/productdetail.cfm?prod_id=153] subset: PSI-MOD-slim -synonym: "Applied Biosystems cleavable ICAT(TM) heavy" RELATED UniMod-description [] +synonym: "Applied Biosystems cleavable ICAT(TM) heavy" RELATED Unimod-description [] synonym: "ICAT-C:13C(9)" RELATED PSI-MS-label [] synonym: "icatheavy" EXACT OMSSA-label [] xref: DiffAvg: "236.16" @@ -11248,12 +11679,13 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:106" is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:00482 name: N-formyl-L-methionine (Met) -def: "A protein modification that effectively converts an L-methionine residue to N-formyl-L-methionine (not known as a natural, post-translational modification process)." [PubMed:11152118, PubMed:2165784, PubMed:3042771, RESID:AA0021#MET] +def: "A protein modification that effectively converts an L-methionine residue to N-formyl-L-methionine (not known as a natural, post-translational modification process)." [PubMed:11152118, PubMed:2165784, PubMed:3042771, Unimod:122#M, RESID:AA0021#MET] comment: This entry is for the artifactual formation of N-formyl-L-methionine from methionine. For encoded N-formyl-L-methionine, use MOD:00030 [JSG]. synonym: "(2S)-2-formylamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-formamido-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] @@ -11272,14 +11704,15 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00030 ! N-formyl-L-methionine residue +xref: Unimod: "Unimod:122" +xref: UniProt: "PTM-0212" is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00483 name: N-ethylmaleimide derivatized cysteine -def: "A protein modification that is produced by reaction with N-ethylmaleimide." [OMSSA:83, PubMed:11813307, PubMed:12777388, UniMod:108#C] -synonym: "N-ethylmaleimide on cysteines" RELATED UniMod-description [] +def: "A protein modification that is produced by reaction with N-ethylmaleimide." [OMSSA:83, PubMed:11813307, PubMed:12777388, Unimod:108#C] +synonym: "N-ethylmaleimide on cysteines" RELATED Unimod-description [] synonym: "nemc" EXACT OMSSA-label [] synonym: "Nethylmaleimide" RELATED PSI-MS-label [] xref: DiffAvg: "125.13" @@ -11291,15 +11724,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:108" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00484 name: oxidized lysine biotinylated with biotin-LC-hydrazide, reduced -def: "modification from UniMod Chemical derivative" [UniMod:112#K] -synonym: "Oxidized lysine biotinylated with biotin-LC-hydrazide, reduced" RELATED UniMod-description [] -synonym: "OxLysBiotinRed" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:112#K] +synonym: "Oxidized lysine biotinylated with biotin-LC-hydrazide, reduced" RELATED Unimod-description [] +synonym: "OxLysBiotinRed" RELATED Unimod-interim [] xref: DiffAvg: "354.47" xref: DiffFormula: "C 16 H 26 N 4 O 3 S 1" xref: DiffMono: "354.172562" @@ -11309,15 +11743,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:112" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00485 name: oxidized lysine biotinylated with biotin-LC-hydrazide -def: "modification from UniMod Chemical derivative" [UniMod:113#K] -synonym: "Oxidized lysine biotinylated with biotin-LC-hydrazide" RELATED UniMod-description [] -synonym: "OxLysBiotin" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:113#K] +synonym: "Oxidized lysine biotinylated with biotin-LC-hydrazide" RELATED Unimod-description [] +synonym: "OxLysBiotin" RELATED Unimod-interim [] xref: DiffAvg: "352.45" xref: DiffFormula: "C 16 H 24 N 4 O 3 S 1" xref: DiffMono: "352.156912" @@ -11327,15 +11762,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:113" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00486 name: oxidized proline biotinylated with biotin-LC-hydrazide, reduced -def: "modification from UniMod Chemical derivative" [UniMod:114#C] -synonym: "Oxidized proline biotinylated with biotin-LC-hydrazide, reduced" RELATED UniMod-description [] -synonym: "OxProBiotinRed" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:114#C] +synonym: "Oxidized proline biotinylated with biotin-LC-hydrazide, reduced" RELATED Unimod-description [] +synonym: "OxProBiotinRed" RELATED Unimod-interim [] xref: DiffAvg: "371.50" xref: DiffFormula: "C 16 H 29 N 5 O 3 S 1" xref: DiffMono: "371.199111" @@ -11345,15 +11781,16 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:114" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00487 name: oxidized proline biotinylated with biotin-LC-hydrazide -def: "modification from UniMod Chemical derivative" [UniMod:115#C] -synonym: "Oxidized Proline biotinylated with biotin-LC-hydrazide" RELATED UniMod-description [] -synonym: "OxProBiotin" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:115#C] +synonym: "Oxidized Proline biotinylated with biotin-LC-hydrazide" RELATED Unimod-description [] +synonym: "OxProBiotin" RELATED Unimod-interim [] xref: DiffAvg: "369.48" xref: DiffFormula: "C 16 H 27 N 5 O 3 S 1" xref: DiffMono: "369.183461" @@ -11363,15 +11800,16 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:115" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00488 name: oxidized arginine biotinylated with biotin-LC-hydrazide -def: "modification from UniMod Chemical derivative" [UniMod:116#C] -synonym: "OxArgBiotin" RELATED UniMod-interim [] -synonym: "Oxidized arginine biotinylated with biotin-LC-hydrazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:116#C] +synonym: "OxArgBiotin" RELATED Unimod-interim [] +synonym: "Oxidized arginine biotinylated with biotin-LC-hydrazide" RELATED Unimod-description [] xref: DiffAvg: "310.41" xref: DiffFormula: "C 15 H 22 N 2 O 3 S 1" xref: DiffMono: "310.135114" @@ -11387,9 +11825,9 @@ [Term] id: MOD:00489 name: oxidized arginine biotinylated with biotin-LC-hydrazide, reduced -def: "modification from UniMod Chemical derivative" [UniMod:117#C] -synonym: "OxArgBiotinRed" RELATED UniMod-interim [] -synonym: "Oxidized arginine biotinylated with biotin-LC-hydrazide, reduced" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:117#C] +synonym: "OxArgBiotinRed" RELATED Unimod-interim [] +synonym: "Oxidized arginine biotinylated with biotin-LC-hydrazide, reduced" RELATED Unimod-description [] xref: DiffAvg: "312.43" xref: DiffFormula: "C 15 H 24 N 2 O 3 S 1" xref: DiffMono: "312.150764" @@ -11399,14 +11837,15 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:117" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00490 name: EDT-iodo-PEO-biotin -def: "modification from UniMod Chemical derivative" [UniMod:118] -synonym: "EDT-iodo-PEO-biotin" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:118] +synonym: "EDT-iodo-PEO-biotin" RELATED Unimod-description [] synonym: "EDT-iodoacetyl-PEO-biotin" RELATED PSI-MS-label [] xref: DiffAvg: "490.70" xref: DiffFormula: "C 20 H 34 N 4 O 4 S 3" @@ -11416,14 +11855,15 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:118" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00491 name: thio ether formation - BTP Adduct -def: "modification from UniMod Chemical derivative" [PubMed:11861642, UniMod:119#C] +def: "modification from Unimod Chemical derivative" [PubMed:11861642, Unimod:119#C] synonym: "IBTP" RELATED PSI-MS-label [] -synonym: "Thio Ether Formation - BTP Adduct" RELATED UniMod-description [] +synonym: "Thio Ether Formation - BTP Adduct" RELATED Unimod-description [] xref: DiffAvg: "316.38" xref: DiffFormula: "C 22 H 21 P 1" xref: DiffMono: "316.138087" @@ -11433,6 +11873,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:119" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00905 ! modified L-cysteine residue @@ -11440,12 +11881,12 @@ [Term] id: MOD:00492 name: ubiquitination signature dipeptidyl lysine -def: "A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin." [OMSSA:52, PubMed:11125103, PubMed:12612601, PubMed:12872131, RESID:AA0125#var, UniMod:121#K] +def: "A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin." [OMSSA:52, PubMed:11125103, PubMed:12612601, PubMed:12872131, RESID:AA0125#var, Unimod:121#K] synonym: "GlyGly" RELATED PSI-MS-label [] synonym: "glyglyk" EXACT OMSSA-label [] synonym: "N6-(glycylglycyl)lysine" EXACT PSI-MOD-alternate [] synonym: "N6-glycylglycyl-L-lysine" EXACT PSI-MOD-alternate [] -synonym: "ubiquitinylation residue" RELATED UniMod-description [] +synonym: "ubiquitinylation residue" RELATED Unimod-description [] xref: DiffAvg: "114.10" xref: DiffFormula: "C 4 H 6 N 2 O 2" xref: DiffMono: "114.042927" @@ -11455,19 +11896,21 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +xref: Unimod: "Unimod:121" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01875 ! N6-acylated L-lysine relationship: derives_from MOD:01148 ! ubiquitinylated lysine [Term] id: MOD:00493 name: formylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a formyl group." [DeltaMass:0, PubMed:15799070, UniMod:122] +def: "A protein modification that effectively replaces a hydrogen atom with a formyl group." [DeltaMass:0, PubMed:15799070, Unimod:122] comment: From DeltaMass: Average Mass: 28 subset: PSI-MOD-slim synonym: "FoRes" EXACT PSI-MOD-label [] synonym: "Formyl" RELATED PSI-MS-label [] -synonym: "Formylation" RELATED UniMod-description [] +synonym: "Formylation" RELATED Unimod-description [] synonym: "Formylation (CHO)" EXACT DeltaMass-label [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" @@ -11477,14 +11920,15 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:122" is_a: MOD:00649 ! acylated residue [Term] id: MOD:00494 name: N-iodoacetyl, p-chlorobenzyl-12C6-glucamine -def: "modification from UniMod Isotopic label" [PubMed:12185208, UniMod:123#C] +def: "modification from Unimod Isotopic label" [PubMed:12185208, Unimod:123#C] synonym: "ICAT-H" RELATED PSI-MS-label [] -synonym: "N-iodoacetyl, p-chlorobenzyl-12C6-glucamine" RELATED UniMod-description [] +synonym: "N-iodoacetyl, p-chlorobenzyl-12C6-glucamine" RELATED Unimod-description [] xref: DiffAvg: "345.78" xref: DiffFormula: "C 15 Cl 1 H 20 N 1 O 6 S 0" xref: DiffMono: "345.097915" @@ -11494,15 +11938,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:123" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00495 name: N-iodoacetyl, p-chlorobenzyl-13C6-glucamine -def: "modification from UniMod Isotopic label" [PubMed:12185208, UniMod:124#C] +def: "modification from Unimod Isotopic label" [PubMed:12185208, Unimod:124#C] synonym: "ICAT-H:13C(6)" RELATED PSI-MS-label [] -synonym: "N-iodoacetyl, p-chlorobenzyl-13C6-glucamine" RELATED UniMod-description [] +synonym: "N-iodoacetyl, p-chlorobenzyl-13C6-glucamine" RELATED Unimod-description [] xref: DiffAvg: "351.12" xref: DiffFormula: "(12)C 9 (13)C 6 Cl 1 H 20 N 1 O 6 S 0" xref: DiffMono: "351.118044" @@ -11512,13 +11957,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:124" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00496 name: reductive amination-D -def: "OBSOLETE because UniMod entry 125 is merged with entry 199, remap to id: MOD:00552" [UniMod:125] +def: "OBSOLETE because Unimod entry 125 is merged with entry 199, remap to id: MOD:00552" [Unimod:125] xref: DiffAvg: "32.06" xref: DiffFormula: "C 2 (2)H 4" xref: DiffMono: "32.056407" @@ -11528,15 +11974,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00552" +xref: Unimod: "Unimod:125" is_obsolete: true [Term] id: MOD:00497 name: 3-sulfanylpropanoyl (N-term and Lys) -def: "modification from UniMod [(35)S]dithiobis(succinimidyl propionate) crosslinking" [PubMed:957432, UniMod:126] -comment: The name "thioacylation of primary amines" in UniMod was a misdescription [JSG]. -synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED UniMod-alternate [] -synonym: "3-sulfanylpropanoyl" RELATED UniMod-description [] +def: "modification from Unimod [(35)S]dithiobis(succinimidyl propionate) crosslinking" [PubMed:957432, Unimod:126] +comment: The name "thioacylation of primary amines" in Unimod was a misdescription [JSG]. +synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED Unimod-alternate [] +synonym: "3-sulfanylpropanoyl" RELATED Unimod-description [] synonym: "Thioacyl" RELATED PSI-MS-label [] xref: DiffAvg: "88.12" xref: DiffFormula: "C 3 H 4 O 1 S 1" @@ -11547,6 +11995,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:126" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue @@ -11555,7 +12004,7 @@ name: fluorinated residue def: "A protein modification that effectively substitutes a hydrogen of a residue with a fluorine atom." [PubMed:18688235] synonym: "Fluoro" RELATED PSI-MS-label [] -synonym: "fluorophenylalanine replacement of phenylalanine" RELATED UniMod-description [] +synonym: "fluorophenylalanine replacement of phenylalanine" RELATED Unimod-description [] synonym: "Fluorophenylalanyl" EXACT DeltaMass-label [] synonym: "FRes" EXACT PSI-MOD-label [] xref: Origin: "X" @@ -11566,8 +12015,8 @@ [Term] id: MOD:00499 name: 5-iodoacetamidofluorescein -def: "modification from UniMod Chemical derivative" [PubMed:3311742, PubMed:3578767, UniMod:128#C] -synonym: "5-Iodoacetamidofluorescein (Molecular Probe, Eugene, OR)" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:3311742, PubMed:3578767, Unimod:128#C] +synonym: "5-Iodoacetamidofluorescein (Molecular Probe, Eugene, OR)" RELATED Unimod-description [] synonym: "Fluorescein" RELATED PSI-MS-label [] xref: DiffAvg: "388.35" xref: DiffFormula: "C 22 H 14 N 1 O 6" @@ -11578,17 +12027,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:128" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00500 name: monoiodinated residue -def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one iodine atom." [DeltaMass:0, PubMed:15627961, PubMed:2026710, UniMod:129] +def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one iodine atom." [DeltaMass:0, PubMed:15627961, PubMed:2026710, Unimod:129] comment: From DeltaMass: Average Mass: 126 subset: PSI-MOD-slim synonym: "I1Res" EXACT PSI-MOD-label [] -synonym: "Iodination" RELATED UniMod-description [] +synonym: "Iodination" RELATED Unimod-description [] synonym: "Iodination (of Histidine[C4] or Tyrosine[C3])" EXACT DeltaMass-label [] synonym: "Iodo" RELATED PSI-MS-label [] xref: DiffAvg: "125.90" @@ -11599,15 +12049,16 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:129" is_a: MOD:00755 ! iodinated residue [Term] id: MOD:00501 name: diiodinated residue -def: "A protein modification that effectively substitutes two hydrogen atoms of a residue with two iodine atoms." [UniMod:130] +def: "A protein modification that effectively substitutes two hydrogen atoms of a residue with two iodine atoms." [Unimod:130] comment: From DeltaMass: Average Mass: 252 subset: PSI-MOD-slim -synonym: "di-Iodination" RELATED UniMod-description [] +synonym: "di-Iodination" RELATED Unimod-description [] synonym: "Diiodo" RELATED PSI-MS-label [] synonym: "I2Res" EXACT PSI-MOD-label [] xref: DiffAvg: "251.79" @@ -11618,16 +12069,17 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" +xref: Unimod: "Unimod:130" is_a: MOD:00755 ! iodinated residue [Term] id: MOD:00502 name: triiodinated residue -def: "A protein modification that effectively substitutes three hydrogen atoms of a residue with three iodine atoms." [OMSSA:116, PubMed:15627961, PubMed:2026710, UniMod:131] -comment: From UniMod. In PubMed:2026710, mono- and diiodination of tyrosine are discussed, but triiodination of tyrosine is not mentioned. In PubMed:15627961, triiodothyronine (see MOD:00186) is discussed, but triiodotyrosine is not mentioned. This modification probably does not exist, and may be a confusion of "tyrosine" for "thyronine", a common error [JSG]. +def: "A protein modification that effectively substitutes three hydrogen atoms of a residue with three iodine atoms." [OMSSA:116, PubMed:15627961, PubMed:2026710, Unimod:131] +comment: From Unimod. In PubMed:2026710, mono- and diiodination of tyrosine are discussed, but triiodination of tyrosine is not mentioned. In PubMed:15627961, triiodothyronine (see MOD:00186) is discussed, but triiodotyrosine is not mentioned. This modification probably does not exist, and may be a confusion of "tyrosine" for "thyronine", a common error [JSG]. subset: PSI-MOD-slim synonym: "I3Res" EXACT PSI-MOD-label [] -synonym: "tri-Iodination" RELATED UniMod-description [] +synonym: "tri-Iodination" RELATED Unimod-description [] synonym: "triiodinationy" EXACT OMSSA-label [] synonym: "Triiodo" RELATED PSI-MS-label [] xref: DiffAvg: "377.69" @@ -11639,13 +12091,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:131" is_a: MOD:00755 ! iodinated residue [Term] id: MOD:00503 name: N-(cis-delta 5)-tetradecaenoylglycine -def: "A protein modification that effectively converts a glycine residue to N-(cis-delta 5)-tetradecaenoylglycine." [OMSSA:78, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059#var, UniMod:134#G] -synonym: "(cis-delta 5)-tetradecaenoyl" RELATED UniMod-description [] +def: "A protein modification that effectively converts a glycine residue to N-(cis-delta 5)-tetradecaenoylglycine." [OMSSA:78, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059#var, Unimod:134#G] +synonym: "(cis-delta 5)-tetradecaenoyl" RELATED Unimod-description [] synonym: "Myristoleyl" RELATED PSI-MS-label [] synonym: "myristoleylation (one double bond)" EXACT DeltaMass-label [] synonym: "N-(C14:1 aliphatic acyl)glycine" EXACT PSI-MOD-alternate [] @@ -11659,14 +12112,15 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:134" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01696 ! alpha-amino acylated residue [Term] id: MOD:00504 name: N-(cis,cis-delta 5,delta 8)-tetradecadienoylglycine -def: "A protein modification that effectively converts a glycine residue to N-(cis,cis-delta 5,delta 8)-tetradecadienoylglycine." [OMSSA:79, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059#var, UniMod:135#G] -synonym: "(cis,cis-delta 5, delta 8)-tetradecadienoyl" RELATED UniMod-description [] +def: "A protein modification that effectively converts a glycine residue to N-(cis,cis-delta 5,delta 8)-tetradecadienoylglycine." [OMSSA:79, PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059#var, Unimod:135#G] +synonym: "(cis,cis-delta 5, delta 8)-tetradecadienoyl" RELATED Unimod-description [] synonym: "Myristoyl+Delta:H(-4)" RELATED PSI-MS-label [] synonym: "myristoylation-4H (two double bonds)" EXACT DeltaMass-label [] synonym: "N-(C14:2 aliphatic acyl)glycine" EXACT PSI-MOD-alternate [] @@ -11680,17 +12134,18 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:135" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01696 ! alpha-amino acylated residue [Term] id: MOD:00505 name: benzoyl labeling reagent light form (N-term and K) -def: "modification from UniMod Isotopic label" [DeltaMass:0, PubMed:15456300, UniMod:136] +def: "modification from Unimod Isotopic label" [DeltaMass:0, PubMed:15456300, Unimod:136] comment: From DeltaMass: Average Mass: 104 synonym: "Benzoyl" RELATED PSI-MS-label [] synonym: "Benzoyl (Bz)" EXACT DeltaMass-label [] -synonym: "labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "labeling reagent light form (N-term & K)" RELATED Unimod-description [] xref: DiffAvg: "104.11" xref: DiffFormula: "C 7 H 4 O 1" xref: DiffMono: "104.026215" @@ -11700,14 +12155,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:136" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00506 -name: N-linked glycan core -def: "modification from UniMod N-linked glycosylation, Hex(5) HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:137#N] +name: N-linked glycan core N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, Hex(5) HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:137#N] synonym: "Hex(5)HexNAc(2)" RELATED PSI-MS-label [] -synonym: "N-linked glycan core" RELATED UniMod-description [] +synonym: "N-linked glycan core" RELATED Unimod-description [] xref: DiffAvg: "1217.09" xref: DiffFormula: "C 46 H 76 N 2 O 35" xref: DiffMono: "1216.422862" @@ -11717,15 +12173,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:137" +xref: GNOme: "GNO:G02815KT" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00507 name: 5-dimethylaminonaphthalene-1-sulfonyl -def: "OBSOLETE because redundant, replaced by MOD:01653. Remap to MOD:01653." [DeltaMass:0, UniMod:139] +def: "OBSOLETE because redundant, replaced by MOD:01653. Remap to MOD:01653." [DeltaMass:0, Unimod:139] comment: From DeltaMass: Average Mass: 233 -synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED UniMod-description [] +synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED Unimod-description [] synonym: "Dansyl" RELATED PSI-MS-label [] synonym: "Dansyl (Dns)" EXACT DeltaMass-label [] xref: DiffAvg: "233.29" @@ -11737,31 +12195,35 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:139" +xref: Remap: "MOD:01653" is_obsolete: true [Term] id: MOD:00508 name: ISD a-series (C-Term) -def: "modification from UniMod Other" [PubMed:14588022, UniMod:140] +def: "OBSOLETE because this is an ion type and is not a biological or chemical modification to a polypeptide, can be handled by PSI-MS CV term, MS:1001229" [PubMed:14588022, Unimod:140] comment: Virtual Modification for MS/MS of a-type ions, by decarboxylation of C-terminus as reaction inside the mass spectrometer. synonym: "a-type-ion" RELATED PSI-MS-label [] -synonym: "ISD a-series (C-Term)" RELATED UniMod-description [] -xref: DiffAvg: "-29.02" -xref: DiffFormula: "C -1 H -1 O -1" -xref: DiffMono: "-29.002740" +synonym: "ISD a-series (C-Term)" RELATED Unimod-description [] +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:140" +is_obsolete: true + [Term] id: MOD:00509 name: amidination of lysines or N-terminal amines with methyl acetimidate -def: "modification from UniMod Chemical derivative" [PubMed:12643539, PubMed:6273432, UniMod:141] -synonym: "amidination of lysines or N-terminal amines with methyl acetimidate" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:12643539, PubMed:6273432, Unimod:141] +synonym: "amidination of lysines or N-terminal amines with methyl acetimidate" RELATED Unimod-description [] synonym: "Amidine" RELATED PSI-MS-label [] xref: DiffAvg: "41.05" xref: DiffFormula: "C 2 H 3 N 1" @@ -11772,15 +12234,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:141" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00510 -name: HexNAc1dHex1 -def: "modification from UniMod N-linked glycosylation, dHex HexNAc" [OMSSA:183, PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:142] +name: HexNAc1dHex1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex HexNAc" [OMSSA:183, PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:142] synonym: "dHexHexNAcN" EXACT OMSSA-label [] synonym: "HexNAc(1)dHex(1)" RELATED PSI-MS-label [] -synonym: "HexNAc1dHex1" RELATED UniMod-description [] +synonym: "HexNAc1dHex1" RELATED Unimod-description [] xref: DiffAvg: "349.34" xref: DiffFormula: "C 14 H 23 N 1 O 9" xref: DiffMono: "349.137281" @@ -11790,15 +12253,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:142" +xref: GNOme: "GNO:G00194GV" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00511 -name: HexNAc2 -def: "modification from UniMod N-linked glycosylation, HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:143] +name: HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:143] synonym: "HexNAc(2)" RELATED PSI-MS-label [] -synonym: "HexNAc2" RELATED UniMod-description [] +synonym: "HexNAc2" RELATED Unimod-description [] xref: DiffAvg: "406.39" xref: DiffFormula: "C 16 H 26 N 2 O 10" xref: DiffMono: "406.158745" @@ -11808,15 +12273,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:143" +xref: GNOme: "GNO:G27391WQ" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00512 -name: Hex3 -def: "modification from UniMod N-linked glycosylation, Hex3" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:144] +name: Hex3 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, Hex3" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:144] synonym: "Hex(3)" RELATED PSI-MS-label [] -synonym: "Hex3" RELATED UniMod-description [] +synonym: "Hex3" RELATED Unimod-description [] xref: DiffAvg: "486.42" xref: DiffFormula: "C 18 H 30 O 15" xref: DiffMono: "486.158470" @@ -11826,15 +12293,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:144" +xref: GNOme: "GNO:G39365VM" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00513 -name: HexNAc1dHex2 -def: "modification from UniMod N-linked glycosylation, dHex(2) HexNAc" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:145] +name: HexNAc1dHex2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex(2) HexNAc" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:145] synonym: "HexNAc(1)dHex(2)" RELATED PSI-MS-label [] -synonym: "HexNAc1dHex2" RELATED UniMod-description [] +synonym: "HexNAc1dHex2" RELATED Unimod-description [] xref: DiffAvg: "495.48" xref: DiffFormula: "C 20 H 33 N 1 O 13" xref: DiffMono: "495.195190" @@ -11844,15 +12313,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:145" +xref: GNOme: "GNO:G74392IM" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00514 -name: Hex1HexNAc1dHex1 -def: "modification from UniMod N-linked glycosylation, dHex Hex HexNAc" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:146] +name: Hex1HexNAc1dHex1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex Hex HexNAc" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:146] synonym: "Hex(1)HexNAc(1)dHex(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1dHex1" RELATED UniMod-description [] +synonym: "Hex1HexNAc1dHex1" RELATED Unimod-description [] xref: DiffAvg: "511.48" xref: DiffFormula: "C 20 H 33 N 1 O 14" xref: DiffMono: "511.190105" @@ -11862,15 +12333,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:146" +xref: GNOme: "GNO:G54129SE" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00515 -name: HexNAc2dHex1 -def: "modification from UniMod N-linked glycosylation, dHex HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, UniMod:147] +name: HexNAc2dHex1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex HexNAc(2)" [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151#var, Unimod:147] synonym: "HexNAc(2)dHex(1)" RELATED PSI-MS-label [] -synonym: "HexNAc2dHex1" RELATED UniMod-description [] +synonym: "HexNAc2dHex1" RELATED Unimod-description [] xref: DiffAvg: "552.53" xref: DiffFormula: "C 22 H 36 N 2 O 14" xref: DiffMono: "552.216654" @@ -11880,15 +12353,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:147" +xref: GNOme: "GNO:G06042JP" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00516 -name: Hex1HexNAc2 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:148] +name: Hex1HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:148] synonym: "Hex(1)HexNAc(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc2" RELATED UniMod-description [] +synonym: "Hex1HexNAc2" RELATED Unimod-description [] xref: DiffAvg: "568.53" xref: DiffFormula: "C 22 H 36 N 2 O 15" xref: DiffMono: "568.211568" @@ -11898,16 +12373,18 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:148" +xref: GNOme: "GNO:G58001LT" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00517 name: Hex1HexNAc1NeuAc1 glycosylated residue -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [DeltaMass:0, UniMod:149] +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [DeltaMass:0, Unimod:149] comment: From DeltaMass: Average Mass: 657 synonym: "Hex(1)HexNAc(1)NeuAc(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc1" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc1" RELATED Unimod-description [] synonym: "NeuAc-Hex-HexNAc" EXACT DeltaMass-label [] xref: DiffAvg: "657.60" xref: DiffFormula: "C 25 H 41 N 2 O 18" @@ -11918,14 +12395,15 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: GNOme: "GNO:G17015OC" is_a: MOD:00725 ! complex glycosylation [Term] id: MOD:00518 -name: HexNAc2dHex2 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:150] +name: HexNAc2dHex2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:150] synonym: "HexNAc(2)dHex(2)" RELATED PSI-MS-label [] -synonym: "HexNAc2dHex2" RELATED UniMod-description [] +synonym: "HexNAc2dHex2" RELATED Unimod-description [] xref: DiffAvg: "698.67" xref: DiffFormula: "C 28 H 46 N 2 O 18" xref: DiffMono: "698.274563" @@ -11935,14 +12413,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:150" +xref: GNOme: "GNO:G90423UY" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00519 -name: Hex1HexNAc2Pent1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:151] +name: Hex1HexNAc2Pent1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:151] synonym: "Hex(1)HexNAc(2)Pent(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc2Pent1" RELATED UniMod-description [] +synonym: "Hex1HexNAc2Pent1" RELATED Unimod-description [] xref: DiffAvg: "700.64" xref: DiffFormula: "C 27 H 44 N 2 O 19" xref: DiffMono: "700.253827" @@ -11952,14 +12433,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:151" +xref: GNOme: "GNO:G54968WM" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00520 -name: Hex1HexNAc2dHex1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:152] +name: Hex1HexNAc2dHex1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:152] synonym: "Hex(1)HexNAc(2)dHex(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc2dHex1" RELATED UniMod-description [] +synonym: "Hex1HexNAc2dHex1" RELATED Unimod-description [] xref: DiffAvg: "714.67" xref: DiffFormula: "C 28 H 46 N 2 O 19" xref: DiffMono: "714.269477" @@ -11969,14 +12453,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:152" +xref: GNOme: "GNO:G94583DZ" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00521 -name: Hex2HexNAc2 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:153] +name: Hex2HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:153] synonym: "Hex(2)HexNAc(2)" RELATED PSI-MS-label [] -synonym: "Hex2HexNAc2" RELATED UniMod-description [] +synonym: "Hex2HexNAc2" RELATED Unimod-description [] xref: DiffAvg: "730.67" xref: DiffFormula: "C 28 H 46 N 2 O 20" xref: DiffMono: "730.264392" @@ -11986,14 +12473,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:153" +xref: GNOme: "GNO:G53434XO" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00522 -name: Hex3HexNAc1Pent1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:154] +name: Hex3HexNAc1Pent1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:154] synonym: "Hex(3)HexNAc(1)Pent(1)" RELATED PSI-MS-label [] -synonym: "Hex3HexNAc1Pent1" RELATED UniMod-description [] +synonym: "Hex3HexNAc1Pent1" RELATED Unimod-description [] xref: DiffAvg: "821.73" xref: DiffFormula: "C 31 H 51 N 1 O 24" xref: DiffMono: "821.280102" @@ -12003,31 +12493,37 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:154" +xref: GNOme: "GNO:G64686LL" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00523 -name: Hex1HexNAc2dHex1Pent1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:155] +name: Hex1HexNAc2dHex1Pent1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:155] synonym: "Hex(1)HexNAc(2)dHex(1)Pent(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc2dHex1Pent1" RELATED UniMod-description [] +synonym: "Hex1HexNAc2dHex1Pent1" RELATED Unimod-description [] xref: DiffAvg: "846.79" xref: DiffFormula: "C 33 H 54 N 2 O 23" xref: DiffMono: "846.311736" xref: Formula: "C 35 H 57 N 3 O 26" -xref: MassAvg: "935.84" -xref: MassMono: "935.323029" +xref: MassAvg: "960.89" +xref: MassMono: "960.354663" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:155" +xref: GNOme: "GNO:G84825UQ" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00524 -name: Hex1HexNAc2dHex2 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:156] +name: Hex1HexNAc2dHex2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:156] synonym: "Hex(1)HexNAc(2)dHex(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc2dHex2" RELATED UniMod-description [] +synonym: "Hex1HexNAc2dHex2" RELATED Unimod-description [] xref: DiffAvg: "860.81" xref: DiffFormula: "C 34 H 56 N 2 O 23" xref: DiffMono: "860.327386" @@ -12037,14 +12533,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:156" +xref: GNOme: "GNO:G05460KC" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00525 -name: Hex2HexNAc2Pent1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:157] +name: Hex2HexNAc2Pent1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:157] synonym: "Hex(2)HexNAc(2)Pent(1)" RELATED PSI-MS-label [] -synonym: "Hex2HexNAc2Pent1" RELATED UniMod-description [] +synonym: "Hex2HexNAc2Pent1" RELATED Unimod-description [] xref: DiffAvg: "862.79" xref: DiffFormula: "C 33 H 54 N 2 O 24" xref: DiffMono: "862.306651" @@ -12054,14 +12553,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:157" +xref: GNOme: "GNO:G18999EB" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00526 -name: Hex2HexNAc2dHex1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:158] +name: Hex2HexNAc2dHex1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:158] synonym: "Hex(2)HexNAc(2)dHex(1)" RELATED PSI-MS-label [] -synonym: "Hex2HexNAc2dHex1" RELATED UniMod-description [] +synonym: "Hex2HexNAc2dHex1" RELATED Unimod-description [] xref: DiffAvg: "876.81" xref: DiffFormula: "C 34 H 56 N 2 O 24" xref: DiffMono: "876.322301" @@ -12071,16 +12573,19 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:158" +xref: GNOme: "GNO:G93579XB" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00527 -name: Hex3HexNAc2 -def: "modification from UniMod N-linked glycosylation" [DeltaMass:0, RESID:AA0151#var, UniMod:159] +name: Hex3HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [DeltaMass:0, RESID:AA0151#var, Unimod:159] comment: From DeltaMass: Average Mass: 893 synonym: "(Hex)3-HexNAc-HexNAc" EXACT DeltaMass-label [] synonym: "Hex(3)HexNAc(2)" RELATED PSI-MS-label [] -synonym: "Hex3HexNAc2" RELATED UniMod-description [] +synonym: "Hex3HexNAc2" RELATED Unimod-description [] xref: DiffAvg: "892.81" xref: DiffFormula: "C 34 H 56 N 2 O 25" xref: DiffMono: "892.317215" @@ -12090,14 +12595,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:159" +xref: GNOme: "GNO:G28681TP" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] -id: MOD:00528 +id: MOD:00528 name: Hex1HexNAc1NeuAc2 glycosylated residue -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [UniMod:160] +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [Unimod:160] synonym: "Hex(1)HexNAc(1)NeuAc(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc2" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc2" RELATED Unimod-description [] xref: DiffAvg: "947.85" xref: DiffFormula: "C 36 H 57 N 3 O 26" xref: DiffMono: "947.323029" @@ -12107,14 +12615,16 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:160" +xref: GNOme: "GNO:G23729WG" is_a: MOD:00725 ! complex glycosylation [Term] id: MOD:00529 -name: Hex3HexNAc2P1 -def: "modification from UniMod N-linked glycosylation" [RESID:AA0151#var, UniMod:161] +name: Hex3HexNAc2P1 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [RESID:AA0151#var, Unimod:161] synonym: "Hex(3)HexNAc(2)P(1)" RELATED PSI-MS-label [] -synonym: "Hex3HexNAc2P1" RELATED UniMod-description [] +synonym: "Hex3HexNAc2P1" RELATED Unimod-description [] xref: DiffAvg: "972.79" xref: DiffFormula: "C 34 H 57 N 2 O 28 P 1" xref: DiffMono: "972.283546" @@ -12124,15 +12634,18 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:161" +xref: GNOme: "GNO:G88520YF" is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00530 name: L-selenomethionine -def: "A protein modification that effectively converts an L-methionine residue to L-selenomethionine." [OMSSA:113, PubMed:12148805, UniMod:162#M] +def: "A protein modification that effectively converts an L-methionine residue to L-selenomethionine." [OMSSA:113, PubMed:12148805, Unimod:162#M] synonym: "Delta:S(-1)Se(1)" RELATED PSI-MS-label [] synonym: "Se(S)Met" EXACT PSI-MOD-label [] -synonym: "Selenium replaces sulphur" RELATED UniMod-description [] +synonym: "Selenium replaces sulphur" RELATED Unimod-description [] synonym: "semetm" EXACT OMSSA-label [] xref: DiffAvg: "46.91" xref: DiffFormula: "C 0 H 0 N 0 S -1 Se 1" @@ -12143,16 +12656,17 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:162" is_a: MOD:00007 ! selenium substitution for sulfur is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00531 name: (18)O labeled deglycosylated asparagine -def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O as the result of having been deglycosylated in (18)O water." [PubMed:14435542, UniMod:170] +def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O as the result of having been deglycosylated in (18)O water." [PubMed:14435542, Unimod:170] subset: PSI-MOD-slim synonym: "Delta:H(1)O(-1)18O(1)" RELATED PSI-MS-label [] -synonym: "glycosylated asparagine 18O labeling" RELATED UniMod-description [] +synonym: "glycosylated asparagine 18O labeling" RELATED Unimod-description [] xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" xref: DiffMono: "2.988262" @@ -12162,14 +12676,15 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:170" is_a: MOD:01293 ! 1x(18)O labeled deamidated L-asparagine [Term] id: MOD:00532 name: Shimadzu 13CNBS -def: "modification from UniMod Chemical derivative" [PubMed:12845591, UniMod:171] -synonym: "NBS:13C(6)" RELATED UniMod-interim [] -synonym: "Shimadzu NBS-13C" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:12845591, Unimod:171] +synonym: "NBS:13C(6)" RELATED Unimod-interim [] +synonym: "Shimadzu NBS-13C" RELATED Unimod-description [] xref: DiffAvg: "159.01" xref: DiffFormula: "(13)C 6 H 3 N 1 O 2 S 1" xref: DiffMono: "159.008578" @@ -12179,14 +12694,15 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:171" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00533 name: Shimadzu 12CNBS -def: "modification from UniMod Chemical derivative" [PubMed:12845591, UniMod:172] -synonym: "NBS" RELATED UniMod-interim [] -synonym: "Shimadzu NBS-12C" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:12845591, Unimod:172] +synonym: "NBS" RELATED Unimod-interim [] +synonym: "Shimadzu NBS-12C" RELATED Unimod-description [] xref: DiffAvg: "152.99" xref: DiffFormula: "(12)C 6 H 3 N 1 O 2 S 1" xref: DiffMono: "152.988449" @@ -12196,15 +12712,16 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:172" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00534 name: Michael addition of BHT quinone methide to cysteine and lysine -def: "modification from UniMod Post-translational" [PubMed:9448752, UniMod:176] +def: "modification from Unimod Post-translational" [PubMed:9448752, Unimod:176] comment: Butylated Hydroxytoluene adduct. synonym: "BHT" RELATED PSI-MS-label [] -synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED UniMod-description [] +synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED Unimod-description [] xref: DiffAvg: "218.34" xref: DiffFormula: "C 15 H 22 O 1" xref: DiffMono: "218.167065" @@ -12214,15 +12731,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:176" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00535 name: phosphorylation to amine thiol -def: "modification from UniMod Chemical derivative" [PubMed:12216740, UniMod:178] +def: "modification from Unimod Chemical derivative" [PubMed:12216740, Unimod:178] comment: DAET = 2-(dimethylamino)ethanethiol. The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site. synonym: "DAET" RELATED PSI-MS-label [] -synonym: "phosphorylation to amine thiol" RELATED UniMod-description [] +synonym: "phosphorylation to amine thiol" RELATED Unimod-description [] xref: DiffAvg: "87.18" xref: DiffFormula: "C 4 H 9 N 1 O -1 S 1" xref: DiffMono: "87.050656" @@ -12232,12 +12750,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:178" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00536 name: L-serine to L-alanine replacement -def: "OBSOLETE because UniMod 179 merged wth UniMod 447 remap to ??? a protein modification that replaces an L-serine residue with an L-alanine residue" [UniMod:179] +def: "OBSOLETE because Unimod 179 merged with Unimod 447 remap to ??? a protein modification that replaces an L-serine residue with an L-alanine residue" [Unimod:179] synonym: "Ser_Ala" EXACT PSI-MOD-label [] xref: DiffAvg: "-16.00" xref: DiffFormula: "O -1" @@ -12248,16 +12767,17 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:179" is_obsolete: true [Term] id: MOD:00537 name: L-alanine residue (Thr) -def: "A protein modification that effectively converts an L-threonine residue to L-alanine." [UniMod:659] +def: "A protein modification that effectively converts an L-threonine residue to L-alanine." [Unimod:659] comment: This could represent either an engineered replacement or a chemical modification. synonym: "Thr(Ala)" EXACT PSI-MOD-label [] -synonym: "Thr->Ala" RELATED UniMod-interim [] -synonym: "Thr->Ala substitution" RELATED UniMod-description [] +synonym: "Thr->Ala" RELATED Unimod-interim [] +synonym: "Thr->Ala substitution" RELATED Unimod-description [] xref: DiffAvg: "-30.03" xref: DiffFormula: "C -1 H -2 O -1" xref: DiffMono: "-30.010565" @@ -12267,7 +12787,7 @@ xref: Origin: "T" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00010 ! L-alanine residue +xref: Unimod: "Unimod:659" is_a: MOD:00917 ! modified L-threonine residue [Term] @@ -12280,7 +12800,7 @@ [Term] id: MOD:00539 name: threonine reduced to aminobutynate -def: "OBSOLETE because UniMod 179 merged wth UniMod 447 remap to ??? modification from UniMod O-linked glycosylation" [UniMod:182] +def: "OBSOLETE because Unimod 179 merged wth Unimod 447 remap to ??? modification from Unimod O-linked glycosylation" [Unimod:182] xref: DiffAvg: "-17.01" xref: DiffFormula: "H -1 O -1" xref: DiffMono: "-17.002740" @@ -12290,13 +12810,14 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:182" is_obsolete: true [Term] id: MOD:00540 name: 9x(13)C labeled residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 9x(13)C labeled residue." [PubMed:12716131, UniMod:184] -synonym: "13C(9) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue containing common isotopes to a 9x(13)C labeled residue." [PubMed:12716131, Unimod:184] +synonym: "13C(9) Silac label" RELATED Unimod-description [] synonym: "Label:13C(9)" RELATED PSI-MS-label [] xref: DiffAvg: "9.03" xref: DiffFormula: "(12)C -9 (13)C 9" @@ -12307,13 +12828,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:184" is_a: MOD:00842 ! (13)C labeled residue [Term] id: MOD:00541 name: 9x(13)C labeled L-phosphotyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to 9x(13)C labeled L-phosphotyrosine." [PubMed:12716131, UniMod:185] -synonym: "C13 label (Phosphotyrosine)" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-tyrosine residue to 9x(13)C labeled L-phosphotyrosine." [PubMed:12716131, Unimod:185] +synonym: "C13 label (Phosphotyrosine)" RELATED Unimod-description [] synonym: "Label:13C(9)+Phospho" RELATED PSI-MS-label [] xref: DiffAvg: "89.00" xref: DiffFormula: "(12)C -9 (13)C 9 H 1 O 3 P 1" @@ -12324,16 +12846,18 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00540 ! 9x(13)C labeled residue +xref: Unimod: "Unimod:185" is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:00842 ! (13)C labeled residue +relationship: derives_from MOD:00540 ! 9x(13)C labeled residue relationship: derives_from MOD:00048 ! O4'-phospho-L-tyrosine [Term] id: MOD:00542 name: hydroxyphenylglyoxal arginine -def: "modification from UniMod Chemical derivative" [PubMed:11698400, PubMed:11914093, UniMod:186] +def: "modification from Unimod Chemical derivative" [PubMed:11698400, PubMed:11914093, Unimod:186] synonym: "HPG" RELATED PSI-MS-label [] -synonym: "Hydroxyphenylglyoxal arginine" RELATED UniMod-description [] +synonym: "Hydroxyphenylglyoxal arginine" RELATED Unimod-description [] xref: DiffAvg: "132.12" xref: DiffFormula: "C 8 H 4 O 2" xref: DiffMono: "132.021129" @@ -12343,15 +12867,17 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:186" +is_a: MOD:00902 ! modified L-arginine residue +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00543 name: bis(hydroxyphenylglyoxal) arginine -def: "modification from UniMod Chemical derivative" [PubMed:11698400, UniMod:187] -comment: OH-PGO and PGO react with arginine at a stoichiometry of 2:1 [UniMod]. +def: "modification from Unimod Chemical derivative" [PubMed:11698400, Unimod:187] +comment: OH-PGO and PGO react with arginine at a stoichiometry of 2:1 [Unimod]. synonym: "2HPG" RELATED PSI-MS-label [] -synonym: "bis(hydroxphenylglyoxal) arginine" RELATED UniMod-description [] +synonym: "bis(hydroxphenylglyoxal) arginine" RELATED Unimod-description [] xref: DiffAvg: "282.25" xref: DiffFormula: "C 16 H 10 O 5" xref: DiffMono: "282.052823" @@ -12361,14 +12887,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:187" +is_a: MOD:00902 ! modified L-arginine residue +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00544 name: 6x(13)C labeled residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 6x(13)C labeled residue." [PubMed:12716131, UniMod:188] +def: "A protein modification that effectively converts a residue containing common isotopes to a 6x(13)C labeled residue." [PubMed:12716131, Unimod:188] subset: PSI-MOD-slim -synonym: "13C(6) Silac label" RELATED UniMod-description [] +synonym: "13C(6) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "6.02" xref: DiffFormula: "(12)C -6 (13)C 6" @@ -12379,31 +12907,27 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:188" is_a: MOD:00842 ! (13)C labeled residue [Term] id: MOD:00545 name: deuterated dimethyl labeling (D) def: "OBSOLETE because redundant with MOD:00927. Remap to MOD:00927." [PubMed:14670044] -xref: DiffAvg: "34.07" -xref: DiffFormula: "C 2 (1)H -2 (2)H 6" -xref: DiffMono: "34.068961" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Remap: "MOD:00927" is_obsolete: true [Term] id: MOD:00546 name: (18)O label at both C-terminal oxygens -def: "A protein modification that effectively substitutes two (18)O atom for the two (16)O atoms of an alpha-carboxyl (1-carboxyl) group." [OMSSA:88, PubMed:11467524, UniMod:193] +def: "A protein modification that effectively substitutes two (18)O atom for the two (16)O atoms of an alpha-carboxyl (1-carboxyl) group." [OMSSA:88, PubMed:11467524, Unimod:193] subset: PSI-MOD-slim synonym: "ctermpepdio18" EXACT OMSSA-label [] synonym: "Label:18O(2)" RELATED PSI-MS-label [] -synonym: "O18 label at both C-terminal oxygens" RELATED UniMod-description [] +synonym: "O18 label at both C-terminal oxygens" RELATED Unimod-description [] xref: DiffAvg: "4.01" xref: DiffFormula: "(16)O -2 (18)O 2" xref: DiffMono: "4.008493" @@ -12413,13 +12937,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:193" is_a: MOD:00847 ! (18)O disubstituted residue [Term] id: MOD:00547 name: 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate -def: "modification from UniMod Chemical derivative" [PubMed:14997490, UniMod:194] -synonym: "6-aminoquinolyl-N-hydroxysuccinimidyl carbamate" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative used for amino acid analysis" [PubMed:14997490, Unimod:194] +synonym: "6-aminoquinolyl-N-hydroxysuccinimidyl carbamate" RELATED Unimod-description [] synonym: "AccQTag" RELATED PSI-MS-label [] xref: DiffAvg: "170.17" xref: DiffFormula: "C 10 H 6 N 2 O 1" @@ -12430,14 +12955,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:194" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00548 -name: APTA-d0 -def: "modification from UniMod Chemical derivative" [PubMed:15283597, UniMod:195] +name: APTA +def: "modification from Unimod Chemical derivative" [PubMed:15283597, Unimod:195] comment: Derivatization of cysteine with 3-acrylamidopropyl)trimethylammonium chloride [JSG]. -synonym: "APTA-d0" RELATED UniMod-description [] +synonym: "APTA-d0" RELATED Unimod-description [] synonym: "QAT" RELATED PSI-MS-label [] xref: DiffAvg: "171.26" xref: DiffFormula: "C 9 H 19 N 2 O 1" @@ -12448,15 +12974,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +xref: Unimod: "Unimod:195" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00549 name: APTA d3 -def: "modification from UniMod Isotopic label" [PubMed:15283597, UniMod:196] +def: "modification from Unimod Isotopic label" [PubMed:15283597, Unimod:196] comment: Derivatization of cysteine with 3-acrylamidopropyl)trimethylammonium chloride (difference formula correct) [JSG]. -synonym: "(3-acrylamidopropyl)trimethylammonium" RELATED UniMod-description [] -synonym: "APTA d3" RELATED UniMod-description [] +synonym: "(3-acrylamidopropyl)trimethylammonium" RELATED Unimod-description [] +synonym: "APTA d3" RELATED Unimod-description [] synonym: "QAT:2H(3)" RELATED PSI-MS-label [] xref: DiffAvg: "174.17" xref: DiffFormula: "C 9 (1)H 16 (2)H 3 N 2 O 1" @@ -12467,13 +12994,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:196" is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00550 name: EAPTA d0 -def: "modification from UniMod Chemical derivative" [UniMod:197] -synonym: "EAPTA d0" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:197] +synonym: "EAPTA d0" RELATED Unimod-description [] synonym: "EQAT" RELATED PSI-MS-label [] xref: DiffAvg: "184.28" xref: DiffFormula: "C 10 H 20 N 2 O 1" @@ -12484,13 +13012,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:197" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00551 name: EAPTA d5 -def: "modification from UniMod Isotopic label" [UniMod:198] -synonym: "EAPTA d5" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [Unimod:198] +synonym: "EAPTA d5" RELATED Unimod-description [] synonym: "EQAT:2H(5)" RELATED PSI-MS-label [] xref: DiffAvg: "189.19" xref: DiffFormula: "C 10 (1)H 15 (2)H 5 N 2 O 1" @@ -12501,15 +13030,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:198" is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00552 name: 4x(2)H labeled dimethylated residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 4x(2)H labeled dimethylated residue." [PubMed:14670044, UniMod:199] +def: "A protein modification that effectively converts a residue containing common isotopes to a 4x(2)H labeled dimethylated residue." [PubMed:14670044, Unimod:199] comment: Supposed to be alpha-amino and Lys-N6 derivatized by C(2)H2O and reduction. subset: PSI-MOD-slim -synonym: "DiMethyl-CHD2" RELATED UniMod-description [] +synonym: "DiMethyl-CHD2" RELATED Unimod-description [] synonym: "Dimethyl:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "32.06" xref: DiffFormula: "C 2 (2)H 4" @@ -12520,15 +13050,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:199" is_a: MOD:00839 ! (2)H deuterium labeled residue [Term] id: MOD:00553 name: 1,2-ethanedithiol modified residue -def: "A protein modification that effectively substitutes a (2-sulfanylethyl)sulfanyl (or thioethylthiol) group for a hydroxy group." [DeltaMass:0, PubMed:11507762, UniMod:200] +def: "A protein modification that effectively substitutes a (2-sulfanylethyl)sulfanyl (or thioethylthiol) group for a hydroxy group." [DeltaMass:0, PubMed:11507762, Unimod:200] comment: From DeltaMass: Average Mass: 93; supposed to be derivatization of serine and threonine. synonym: "1,2-ethanedithiol (EDT)" EXACT DeltaMass-label [] -synonym: "EDT" RELATED UniMod-description [] +synonym: "EDT" RELATED Unimod-description [] synonym: "Ethanedithiol" RELATED PSI-MS-label [] xref: DiffAvg: "76.18" xref: DiffFormula: "C 2 H 4 O -1 S 2" @@ -12539,12 +13070,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:200" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00554 name: APTA-d0 with no neutral loss -def: "OBSOLETE because UniMod entry 202 was merged with entry 195, remap to MOD:00548. modification from UniMod Chemical derivative" [UniMod:202] +def: "OBSOLETE because Unimod entry 202 was merged with entry 195, remap to MOD:00548. modification from Unimod Chemical derivative" [Unimod:202] xref: DiffAvg: "170.26" xref: DiffFormula: "C 9 H 18 N 2 O 1" xref: DiffMono: "170.141913" @@ -12554,12 +13086,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00548" +xref: Unimod: "Unimod:202" is_obsolete: true [Term] id: MOD:00555 name: APTA-d0 with quaternary amine loss -def: "OBSOLETE because UniMod entry 202 was merged with entry 195, remap to MOD:00548. modification from UniMod Chemical derivative" [UniMod:203] +def: "OBSOLETE because Unimod entry 202 was merged with entry 195, remap to MOD:00548. modification from Unimod Chemical derivative" [Unimod:203] xref: DiffAvg: "170.26" xref: DiffFormula: "C 9 H 18 N 2 O 1" xref: DiffMono: "170.141913" @@ -12569,13 +13103,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00548" +xref: Unimod: "Unimod:203" is_obsolete: true [Term] id: MOD:00556 name: acrolein addition +94 -def: "modification from UniMod Other" [UniMod:205] -synonym: "Acrolein addition +94" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by any literature that I can find[PMT]" [Unimod:205] +synonym: "Acrolein addition +94" RELATED Unimod-description [] synonym: "Delta:H(6)C(6)O(1)" RELATED PSI-MS-label [] xref: DiffAvg: "94.11" xref: DiffFormula: "C 6 H 6 O 1" @@ -12586,13 +13122,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:205" +is_obsolete: true [Term] id: MOD:00557 name: acrolein addition +56 -def: "modification from UniMod Other" [PubMed:10825247, PubMed:15541752, UniMod:206] -synonym: "Acrolein addition +56" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by the papers listed or any other that I can find[PMT]" [PubMed:10825247, PubMed:15541752, Unimod:206] +synonym: "Acrolein addition +56" RELATED Unimod-description [] synonym: "Delta:H(4)C(3)O(1)" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -12603,13 +13140,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:206" +is_obsolete: true [Term] id: MOD:00558 name: acrolein addition +38 -def: "modification from UniMod Other" [UniMod:207] -synonym: "Acrolein addition +38" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by any literature that I can find[PMT]" [Unimod:207] +synonym: "Acrolein addition +38" RELATED Unimod-description [] synonym: "Delta:H(2)C(3)" RELATED PSI-MS-label [] xref: DiffAvg: "38.05" xref: DiffFormula: "C 3 H 2" @@ -12620,13 +13158,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:207" +is_obsolete: true [Term] id: MOD:00559 name: acrolein addition +76 -def: "modification from UniMod Other" [UniMod:208] -synonym: "Acrolein addition +76" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by any literature that I can find[PMT]" [Unimod:208] +synonym: "Acrolein addition +76" RELATED Unimod-description [] synonym: "Delta:H(4)C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "76.10" xref: DiffFormula: "C 6 H 4" @@ -12637,13 +13176,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:208" +is_obsolete: true [Term] id: MOD:00560 name: acrolein addition +112 -def: "modification from UniMod Other" [UniMod:209] -synonym: "Acrolein addition +112" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by any literature that I can find[PMT]" [Unimod:209] +synonym: "Acrolein addition +112" RELATED Unimod-description [] synonym: "Delta:H(8)C(6)O(2)" RELATED PSI-MS-label [] xref: DiffAvg: "112.13" xref: DiffFormula: "C 6 H 8 O 2" @@ -12654,13 +13194,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:209" +is_obsolete: true [Term] id: MOD:00561 -name: N-ethyl iodoacetamide-d0 -def: "modification from UniMod Isotopic label" [PubMed:12766232, UniMod:211] -synonym: "N-ethyl iodoacetamide-d0" RELATED UniMod-description [] +name: N-ethyl iodoacetamide- +def: "modification from Unimod Isotopic label" [PubMed:12766232, Unimod:211] +synonym: "N-ethyl iodoacetamide-d0" RELATED Unimod-description [] synonym: "NEIAA" RELATED PSI-MS-label [] xref: DiffAvg: "85.11" xref: DiffFormula: "C 4 H 7 N 1 O 1" @@ -12671,13 +13212,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +xref: Unimod: "Unimod:211" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00562 name: N-ethyl iodoacetamide-d5 -def: "modification from UniMod Isotopic label" [PubMed:12766232, UniMod:212] -synonym: "N-ethyl iodoacetamide-d5" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [PubMed:12766232, Unimod:212] +synonym: "N-ethyl iodoacetamide-d5" RELATED Unimod-description [] synonym: "NEIAA:2H(5)" RELATED PSI-MS-label [] xref: DiffAvg: "90.08" xref: DiffFormula: "C 4 (1)H 2 (2)H 5 N 1 O 1" @@ -12688,11 +13230,12 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:212" is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00563 -name: N-acetylaminogalactosylated residue +name: mono-N-acetylaminogalactosylated residue def: "A protein modification that effectively replaces a hydrogen atom with an N-acetylaminogalactose group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD-slim synonym: "GalNAcRes" EXACT PSI-MOD-label [] @@ -12712,27 +13255,23 @@ [Term] id: MOD:00564 name: Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry -def: "Modification from UniMod Isotopic label. The UniMod term was extracted when it had not been approved. OBSOLETE because redundant to MOD:01505. Remap to MOD:01505, or one of the child terms MOD:01493 or MOD:01497." [UniMod:214, URL:http\://docs.appliedbiosystems.com/pebiodocs/04351918.pdf] -synonym: "iTRAQ4plex" RELATED UniMod-interim [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] -xref: DiffAvg: "144.10" -xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 O 1" -xref: DiffMono: "144.102062" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" +def: "Modification from Unimod Isotopic label. The Unimod term was extracted when it had not been approved. OBSOLETE because redundant to MOD:01505. Remap to MOD:01505, or one of the child terms MOD:01493 or MOD:01497." [Unimod:214, URL:http\://docs.appliedbiosystems.com/pebiodocs/04351918.pdf] +synonym: "iTRAQ4plex" RELATED Unimod-interim [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01505" +xref: Unimod: "Unimod:214" is_obsolete: true [Term] id: MOD:00565 name: deglycosylated asparagine -def: "modification from UniMod N-linked glycosylation" [UniMod:7#N] +def: "modification from Unimod N-linked glycosylation" [Unimod:7#N] comment: Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in H2O. CAUTION - the difference formula appears to be based on a partial structure [JSG]. -synonym: "Deamidated" RELATED UniMod-interim [] -synonym: "Deamidation" RELATED UniMod-description [] +synonym: "Deamidated" RELATED Unimod-interim [] +synonym: "Deamidation" RELATED Unimod-description [] xref: DiffAvg: "0.98" xref: DiffFormula: "H -1 N -1 O 1" xref: DiffMono: "0.984016" @@ -12742,15 +13281,16 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:7" is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00566 name: label cysteine with IGBP reagent -def: "modification from UniMod Chemical derivative" [UniMod:243] +def: "modification from Unimod Chemical derivative" [Unimod:243] comment: "IDBEST tag for quantitation, http://www.targetdiscovery.com/index.php?topic=prod.idbe" synonym: "IGBP" RELATED PSI-MS-label [] -synonym: "Light IDBEST tag for quantitation" RELATED UniMod-description [] +synonym: "Light IDBEST tag for quantitation" RELATED Unimod-description [] xref: DiffAvg: "297.15" xref: DiffFormula: "Br 1 C 12 H 13 N 2 O 2" xref: DiffMono: "296.016040" @@ -12760,12 +13300,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:243" +is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00567 name: histidine oxidation to asparagine -def: "OBSOLETE because UniMod entry 244 is redundant with UniMod 348. Remap to MOD:00775." [ChEBI:29956, PubMed:15736973, PubMed:5681232, PubMed:6692818, PubMed:9789001, RESID:AA0003, UniMod:244] +def: "OBSOLETE because Unimod entry 244 is redundant with Unimod 348. Remap to MOD:00775." [ChEBI:29956, PubMed:15736973, PubMed:5681232, PubMed:6692818, PubMed:9789001, RESID:AA0003, Unimod:244] xref: DiffAvg: "-23.04" xref: DiffFormula: "C -2 H -1 N -1 O 1" xref: DiffMono: "-23.015984" @@ -12775,12 +13317,13 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:244" is_obsolete: true [Term] id: MOD:00568 name: histidine oxidation to aspartic acid -def: "OBSOLETE because UniMod entry 245 is redundant with UniMod 349. Remap to MOD:00776" [PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, UniMod:245] +def: "OBSOLETE because Unimod entry 245 is redundant with Unimod 349. Remap to MOD:00776" [PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, Unimod:245] xref: DiffAvg: "-22.05" xref: DiffFormula: "C -2 H -2 N -2 O 2" xref: DiffMono: "-22.031969" @@ -12790,6 +13333,8 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00776" +xref: UinMod: "Unimod:245" is_obsolete: true [Term] @@ -12809,11 +13354,11 @@ [Term] id: MOD:00571 name: 2-pyrrolidone-5-carboxylic acid (Pro) -def: "A modification that effectively oxygenates C5 of an L-proline residue to form a 2-pyrrolidone-5-carboxylic acid, pyroglutamic acid." [OMSSA:111, PubMed:9252331, UniMod:359] +def: "A modification that effectively oxygenates C5 of an L-proline residue to form a 2-pyrrolidone-5-carboxylic acid, pyroglutamic acid." [OMSSA:111, PubMed:9252331, Unimod:359] comment: The review article PubMed:9252331 does not provide an original citation for this modification [JSG]. synonym: "Pro->pyro-Glu" RELATED PSI-MS-label [] synonym: "PyrGlu(Pro)" EXACT PSI-MOD-label [] -synonym: "Pyroglutamic" RELATED UniMod-interim [] +synonym: "Pyroglutamic" RELATED Unimod-interim [] synonym: "pyroglutamicp" EXACT OMSSA-label [] xref: DiffAvg: "13.98" xref: DiffFormula: "H -2 O 1" @@ -12824,6 +13369,7 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:359" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01048 ! 2-pyrrolidone-5-carboxylic acid @@ -12831,9 +13377,9 @@ [Term] id: MOD:00572 name: oxidized arginine biotinylated with biotin hydrazide -def: "modification from UniMod Chemical derivative" [PubMed:15174056, PubMed:15828771, UniMod:343] -synonym: "Argbiotinhydrazide" RELATED UniMod-interim [] -synonym: "oxidized Arginine biotinylated with biotin hydrazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:15174056, PubMed:15828771, Unimod:343] +synonym: "Argbiotinhydrazide" RELATED Unimod-interim [] +synonym: "oxidized Arginine biotinylated with biotin hydrazide" RELATED Unimod-description [] xref: DiffAvg: "199.27" xref: DiffFormula: "C 9 H 13 N 1 O 2 S 1" xref: DiffMono: "199.066700" @@ -12843,15 +13389,17 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:343" +is_a: MOD:00848 ! reagent derivatized residue +is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00573 name: oxidized lysine biotinylated with biotin hydrazide -def: "modification from UniMod Chemical derivative" [PubMed:15174056, UniMod:353] +def: "modification from Unimod Chemical derivative" [PubMed:15174056, Unimod:353] comment: "http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB" -synonym: "Lysbiotinhydrazide" RELATED UniMod-interim [] -synonym: "oxidized Lysine biotinylated with biotin hydrazide" RELATED UniMod-description [] +synonym: "Lysbiotinhydrazide" RELATED Unimod-interim [] +synonym: "oxidized Lysine biotinylated with biotin hydrazide" RELATED Unimod-description [] xref: DiffAvg: "241.31" xref: DiffFormula: "C 10 H 15 N 3 O 2 S 1" xref: DiffMono: "241.088498" @@ -12861,15 +13409,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:353" +is_a: MOD:00848 ! reagent derivatized residue +is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00574 name: oxidized proline biotinylated with biotin hydrazide -def: "modification from UniMod Chemical derivative" [PubMed:15174056, UniMod:357] +def: "modification from Unimod Chemical derivative" [PubMed:15174056, Unimod:357] comment: "http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB" -synonym: "oxidized proline biotinylated with biotin hydrazide" RELATED UniMod-description [] -synonym: "probiotinhydrazide" RELATED UniMod-interim [] +synonym: "oxidized proline biotinylated with biotin hydrazide" RELATED Unimod-description [] +synonym: "probiotinhydrazide" RELATED Unimod-interim [] xref: DiffAvg: "258.34" xref: DiffFormula: "C 10 H 18 N 4 O 2 S 1" xref: DiffMono: "258.115047" @@ -12879,15 +13429,17 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:357" +is_a: MOD:00848 ! reagent derivatized residue +is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00575 name: oxidized threonine biotinylated with biotin hydrazide -def: "modification from UniMod Chemical derivative" [PubMed:15174056, UniMod:361] +def: "modification from Unimod Chemical derivative" [PubMed:15174056, Unimod:361] comment: "http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB" -synonym: "oxidized Threonine biotinylated with biotin hydrazide" RELATED UniMod-description [] -synonym: "Thrbiotinhydrazide" RELATED UniMod-interim [] +synonym: "oxidized Threonine biotinylated with biotin hydrazide" RELATED Unimod-description [] +synonym: "Thrbiotinhydrazide" RELATED Unimod-interim [] xref: DiffAvg: "240.32" xref: DiffFormula: "C 10 H 16 N 4 O 1 S 1" xref: DiffMono: "240.104482" @@ -12897,14 +13449,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:361" +is_a: MOD:00848 ! reagent derivatized residue +is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00576 -name: crotonaldehyde -def: "modification from UniMod Other" [PubMed:11283024, UniMod:253] +name: crotonylated residue +def: "modification from Unimod Other" [PubMed:11283024, PubMed:25907603, Unimod:253] synonym: "Crotonaldehyde" RELATED PSI-MS-label [] -synonym: "Crotonaldehyde" RELATED UniMod-description [] +synonym: "Crotonaldehyde" RELATED Unimod-description [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 O 1" xref: DiffMono: "70.041865" @@ -12914,48 +13468,52 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:253" +is_a: MOD:00649 ! acylated residue [Term] id: MOD:00577 -name: acetaldehyde +26 -def: "modification from UniMod Other" [PubMed:7744761, UniMod:254] -synonym: "Acetaldehyde +26" RELATED UniMod-description [] +name: acetaldehyde crosslinked penta-L-lysine +def: "modification occurs as a Schiff base in the presence of pentalysine" [PubMed:7744761, Unimod:254] +synonym: "Acetaldehyde +26" RELATED Unimod-description [] synonym: "Delta:H(2)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "26.04" xref: DiffFormula: "C 2 H 2" xref: DiffMono: "26.015650" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" -xref: Origin: "X" +xref: Formula: "C 8 H 14 N 2 O 1" +xref: MassAvg: "666.91" +xref: MassMono: "666.490465" +xref: Origin: "K, K, K, K, K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:254" +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:00692 ! uncategorized crosslinked residues [Term] id: MOD:00578 name: acetaldehyde +28 -def: "modification from UniMod Other" [UniMod:255] -synonym: "Acetaldehyde +28" RELATED UniMod-description [] +def: "OBSOLETE because this modification not supported by any literature that I can find [PMT]" [Unimod:255] +synonym: "Acetaldehyde +28" RELATED Unimod-description [] synonym: "Delta:H(4)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" xref: DiffMono: "28.031300" -xref: Formula: "none" +xref: Formula: "C " xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:255" +is_obsolete: true [Term] id: MOD:00579 name: propionaldehyde +40 -def: "modification from UniMod Other" [UniMod:256] +def: "OBSOLETE because not supported by the linked literature [PMT]. modification from Unimod Other" [Unimod:256] synonym: "Delta:H(4)C(3)" RELATED PSI-MS-label [] -synonym: "Propionaldehyde +40" RELATED UniMod-description [] +synonym: "Propionaldehyde +40" RELATED Unimod-description [] xref: DiffAvg: "40.06" xref: DiffFormula: "C 3 H 4" xref: DiffMono: "40.031300" @@ -12965,12 +13523,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:256" +is_obsolete: true [Term] id: MOD:00580 name: propionaldehyde +42 -def: "OBSOLETE because entry removed from UniMod. Remap potentially to MOD:00579 propionaldehyde +40" [UniMod:257] +def: "OBSOLETE because entry removed from Unimod. Remap potentially to MOD:00579 propionaldehyde +40" [Unimod:257] xref: DiffAvg: "42.08" xref: DiffFormula: "C 3 H 6" xref: DiffMono: "42.046950" @@ -12980,16 +13539,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00579" +xref: Unimod: "Unimod:257" is_obsolete: true [Term] id: MOD:00581 name: (18)O monosubstituted residue -def: "A protein modification that effectively substitutes one (18)O atom for one (16)O atom." [OMSSA:87, PubMed:11467524, UniMod:258] +def: "A protein modification that effectively substitutes one (18)O atom for one (16)O atom." [OMSSA:87, PubMed:11467524, Unimod:258] subset: PSI-MOD-slim synonym: "ctermpepo18" EXACT OMSSA-label [] synonym: "Label:18O(1)" RELATED PSI-MS-label [] -synonym: "O18 Labeling" RELATED UniMod-description [] +synonym: "O18 Labeling" RELATED Unimod-description [] xref: DiffAvg: "2.00" xref: DiffFormula: "(16)O -1 (18)O 1" xref: DiffMono: "2.004246" @@ -12999,13 +13560,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:258" is_a: MOD:00845 ! (18)O substituted residue [Term] id: MOD:00582 name: 6x(13)C,2x(15)N labeled L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 6x(13)C,2x(15)N labeled L-lysine." [OMSSA:181, PubMed:12716131, UniMod:259] -synonym: "13C(6) 15N(2) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 6x(13)C,2x(15)N labeled L-lysine." [OMSSA:181, PubMed:12716131, Unimod:259] +synonym: "13C(6) 15N(2) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)15N(2)" RELATED PSI-MS-label [] synonym: "lys-13C615N2" EXACT OMSSA-label [] xref: DiffAvg: "8.01" @@ -13017,6 +13579,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:259" is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00843 ! (15)N labeled residue is_a: MOD:00912 ! modified L-lysine residue @@ -13024,9 +13587,9 @@ [Term] id: MOD:00583 name: thiophosphorylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a thiophosphono group (H2PO2S, 'thiophosphate')." [PubMed:12110917, UniMod:260] +def: "A protein modification that effectively replaces a hydrogen atom with a thiophosphono group (H2PO2S, 'thiophosphate')." [PubMed:12110917, Unimod:260] synonym: "Thiophospho" RELATED PSI-MS-label [] -synonym: "Thiophosphorylation" RELATED UniMod-description [] +synonym: "Thiophosphorylation" RELATED Unimod-description [] xref: DiffAvg: "96.04" xref: DiffFormula: "H 1 O 2 P 1 S 1" xref: DiffMono: "95.943487" @@ -13036,14 +13599,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:260" is_a: MOD:00860 ! sulfur containing modified residue is_a: MOD:00861 ! phosphorus containing modified residue [Term] id: MOD:00584 name: 4-sulfophenyl isothiocyanate derivatized residue -def: "A protein modification produced by formation of an adduct with 4-sulfophenyl isothiocyanate." [PubMed:14689565, PubMed:14745769, PubMed:16526082, UniMod:261] -synonym: "4-sulfophenyl isothiocyanate" RELATED UniMod-description [] +def: "A protein modification produced by formation of an adduct with 4-sulfophenyl isothiocyanate." [PubMed:14689565, PubMed:14745769, PubMed:16526082, Unimod:261] +synonym: "4-sulfophenyl isothiocyanate" RELATED Unimod-description [] synonym: "SPITC" RELATED PSI-MS-label [] xref: DiffAvg: "215.24" xref: DiffFormula: "C 7 H 5 N 1 O 3 S 2" @@ -13054,15 +13618,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:261" is_a: MOD:00841 ! isothiocyanate reagent derivatized residue [Term] id: MOD:00585 name: deuterium trisubstituted residue -def: "A protein modification that effectively substitutes three (2)H deuterium atoms for three (1)H protium atoms." [UniMod:262] +def: "A protein modification that effectively substitutes three (2)H deuterium atoms for three (1)H protium atoms." [Unimod:262] synonym: "D(H)3Res" EXACT PSI-MOD-label [] synonym: "Label:2H(3)" RELATED PSI-MS-label [] -synonym: "Trideuteration" RELATED UniMod-description [] +synonym: "Trideuteration" RELATED Unimod-description [] xref: DiffAvg: "3.02" xref: DiffFormula: "(1)H -3 (2)H 3" xref: DiffMono: "3.018830" @@ -13072,14 +13637,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:262" is_a: MOD:00786 ! deuterium substituted residue [Term] id: MOD:00586 -name: phosphorylation to pyridyl thiol -def: "modification from UniMod Chemical derivative" [UniMod:264] +name: pyridyl thiol modified residue +def: "modification from Unimod Chemical derivative" [Unimod:264] synonym: "PET" RELATED PSI-MS-label [] -synonym: "phosphorylation to pyridyl thiol" RELATED UniMod-description [] +synonym: "phosphorylation to pyridyl thiol" RELATED Unimod-description [] xref: DiffAvg: "121.20" xref: DiffFormula: "C 7 H 7 N 1 O -1 S 1" xref: DiffMono: "121.035006" @@ -13089,14 +13655,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:264" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00587 name: 6x(13)C,4x(15)N labeled L-arginine -def: "A protein modification that effectively converts an L-arginine residue to 6x(13)C, 4x(15)N labeled L-arginine." [OMSSA:137, PubMed:12716131, UniMod:267] +def: "A protein modification that effectively converts an L-arginine residue to 6x(13)C, 4x(15)N labeled L-arginine." [OMSSA:137, PubMed:12716131, Unimod:267] subset: PSI-MOD-slim -synonym: "13C(6) 15N(4) Silac label" RELATED UniMod-description [] +synonym: "13C(6) 15N(4) Silac label" RELATED Unimod-description [] synonym: "arg-13c6-15n4" EXACT OMSSA-label [] synonym: "Label:13C(6)15N(4)" RELATED PSI-MS-label [] xref: DiffAvg: "10.01" @@ -13108,6 +13675,7 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:267" is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00843 ! (15)N labeled residue is_a: MOD:00902 ! modified L-arginine residue @@ -13115,8 +13683,8 @@ [Term] id: MOD:00588 name: 5x(13)C,1x(15)N labeled L-valine -def: "A protein modification that effectively converts an L-valine residue to 5x(13)C,1x(15)N labeled L-valine." [PubMed:12771378, UniMod:268#V] -synonym: "13C(5) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-valine residue to 5x(13)C,1x(15)N labeled L-valine." [PubMed:12771378, Unimod:268#V] +synonym: "13C(5) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "6.01" xref: DiffFormula: "(12)C -5 (13)C 5 (14)N -1 (15)N 1" @@ -13127,14 +13695,15 @@ xref: Origin: "V" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:268" is_a: MOD:00920 ! modified L-valine residue is_a: MOD:01809 ! 5x(13)C,1x(15)N labeled residue [Term] id: MOD:00589 -name: 1x(13)C,1x(15)N labeled L-phenylalanine -def: "A protein modification that effectively converts an L-phenylalanine residue to (13)C,(15)N labeled L-phenylalanine." [PubMed:12771378, UniMod:269] -synonym: "13C(9) 15N(1) Silac label" RELATED UniMod-description [] +name: 9x(13)C,1x(15)N labeled L-phenylalanine +def: "A protein modification that effectively converts an L-phenylalanine residue to (13)C,(15)N labeled L-phenylalanine." [PubMed:12771378, Unimod:269] +synonym: "13C(9) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(9)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "10.03" xref: DiffFormula: "(12)C -9 (13)C 9 (14)N -1 (15)N 1" @@ -13145,6 +13714,7 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:269" is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00843 ! (15)N labeled residue is_a: MOD:00914 ! modified L-phenylalanine residue @@ -13152,9 +13722,9 @@ [Term] id: MOD:00590 name: nucleophilic addtion to cytopiloyne -def: "modification from UniMod Chemical derivative" [PubMed:15549660, UniMod:270] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative" [PubMed:15549660, Unimod:270] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -13164,14 +13734,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:00591 name: nucleophilic addition to cytopiloyne+H2O -def: "modification from UniMod Chemical derivative" [PubMed:15549660, UniMod:271] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative" [PubMed:15549660, Unimod:271] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -13181,14 +13752,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:00592 name: sulfonation of N-terminal -def: "modification from UniMod Chemical derivative" [PubMed:12705581, PubMed:15732931, PubMed:16046801, UniMod:272] +def: "modification from Unimod Chemical derivative" [PubMed:12705581, PubMed:15732931, PubMed:16046801, Unimod:272] synonym: "CAF" RELATED PSI-MS-label [] -synonym: "sulfonation of N-terminus" RELATED UniMod-description [] +synonym: "sulfonation of N-terminus" RELATED Unimod-description [] xref: DiffAvg: "136.12" xref: DiffFormula: "C 3 H 4 O 4 S 1" xref: DiffMono: "135.983030" @@ -13198,14 +13770,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:272" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00593 name: covalent modification of lysine by omega-maleimido alkanoyl N-hydroxysuccinimido esters -def: "modification from UniMod Chemical derivative" [UniMod:273] +def: "OBSOLETE because removed from Unimod. modification from Unimod Chemical derivative" [Unimod:273] comment: J. Prot. Chem. 2, 263-277, 1983 -synonym: "covalent modification of lysine by cross-linking reagent" RELATED UniMod-description [] +synonym: "covalent modification of lysine by cross-linking reagent" RELATED Unimod-description [] synonym: "Xlink:SSD" RELATED PSI-MS-label [] xref: DiffAvg: "253.25" xref: DiffFormula: "C 12 H 15 N 1 O 5" @@ -13216,7 +13789,8 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:273" +is_obsolete: true [Term] id: MOD:00594 @@ -13228,30 +13802,30 @@ [Term] id: MOD:00595 -name: mannosylated residue +name: monomannosylated residue def: "A protein modification that effectively replaces a hydrogen atom with an manose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD-slim synonym: "ManRes" EXACT PSI-MOD-label [] xref: DiffAvg: "162.14" -xref: DiffFormula: "C 6 H 10 N 0 O 5" +xref: DiffFormula: "C 6 H 10 O 5" xref: DiffMono: "162.052823" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" -xref: Source: "none" +xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00434 ! hexosylated residue -is_a: MOD:00727 ! mannosylated +is_a: MOD:00727 ! mannosylated residue +is_a: MOD:00761 ! monohexosylated residue [Term] id: MOD:00596 name: 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue -def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS." [DeltaMass:235, PubMed:8597590, UniMod:276] +def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS." [DeltaMass:235, PubMed:8597590, Unimod:276] comment: From DeltaMass: Average Mass: 183 Average Mass Change:183 References:We have found that AEBSF modifies many proteins by covalent attachment, preferentially on Tyr, and to a lesser extent on Lys, His, and the amino-terminus. These modifications were identified by electrospray MS of the proteins (adds 183 Da per AEBS-group) and by peptide mapping and MS/MS. All the proteins we examined were modified after 24 hrs. at 4 C with 1 mM AEBSF in TRIS, pH 8.0. The reaction is 10-20x slower at pH 7; however AEBSF is quite stable in aqueous solution and the extent of to which the protein is modified continues to increase for several days. We have seen the addition of 10 or more AEBS-groups to proteins after prolonged storage. We found no equivalent modification from PMSF, probably because it degrades so quickly. We no longer use AEBSF, and urge caution to those who do. To address the problem, Boehringer Mannheim (now Roche Molecular Biochemicals) introduced Pefabloc PLUS which includes an additional component to compete for these side reactions. In our limited experience with Pefabloc PLUS, it reduces the +183 modifications, but does not always eliminate them. As a result, we prefer PMSF, despite its own set of drawbacks. We have never found PMSF-induced modification of proteins (except trypsin), probably due to its short half-life in aqeous solution. synonym: "AEBS" RELATED PSI-MS-label [] synonym: "AEBSF" EXACT DeltaMass-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -13261,12 +13835,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:276" is_a: MOD:01652 ! sulfonyl halide reagent derivatized residue [Term] id: MOD:00597 name: methyl methanethiosulfonate -def: "OBSOLETE because UniMod entry 277 redundant with UniMod 39. Remap to MOD:00110." [UniMod:277] +def: "OBSOLETE because Unimod entry 277 redundant with Unimod 39. Remap to MOD:00110." [Unimod:277] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 S 1" xref: DiffMono: "45.987721" @@ -13276,15 +13851,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00110" +xref: Unimod: "Unimod:277" is_obsolete: true [Term] id: MOD:00598 name: S-(2-hydroxyethyl)cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(2-hydroxyethyl)cysteine" [PubMed:15351294, UniMod:278] +def: "A protein modification that effectively converts an L-cysteine residue to S-(2-hydroxyethyl)cysteine" [PubMed:15351294, Unimod:278] comment: This modification of cysteine is produced by the reagent iodoethanol with triethylphosphine [JSG]. subset: PSI-MOD-slim -synonym: "Ethanolation of Cys" RELATED UniMod-description [] +synonym: "Ethanolation of Cys" RELATED Unimod-description [] synonym: "Ethanolyl" RELATED PSI-MS-label [] xref: DiffAvg: "44.05" xref: DiffFormula: "C 2 H 4 O 1" @@ -13295,16 +13872,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:278" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00599 name: monomethylated residue -def: "A protein modification that effectively replaces one hydrogen atom with one methyl group." [PubMed:11875433, UniMod:34] +def: "A protein modification that effectively replaces one hydrogen atom with one methyl group." [PubMed:11875433, Unimod:34] subset: PSI-MOD-slim synonym: "Me1Res" EXACT PSI-MOD-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2" xref: DiffMono: "14.015650" @@ -13314,16 +13892,17 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00427 ! methylated residue [Term] id: MOD:00600 name: L-glutamic acid 5-ethyl ester -def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamate 5-ethyl ester." [DeltaMass:0, PubMed:9629898, UniMod:280#E] -comment: From DeltaMass: Average Mass: 28 with no citation. The UniMod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation. For dimethylated residues, see MOD:00429 and its children [JSG]. +def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamate 5-ethyl ester." [DeltaMass:0, PubMed:9629898, Unimod:280#E] +comment: From DeltaMass: Average Mass: 28 with no citation. The Unimod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation. For dimethylated residues, see MOD:00429 and its children [JSG]. synonym: "Ethyl" EXACT DeltaMass-label [] synonym: "Ethyl" RELATED PSI-MS-label [] -synonym: "Ethylation" RELATED UniMod-description [] +synonym: "Ethylation" RELATED Unimod-description [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" xref: DiffMono: "28.031300" @@ -13333,6 +13912,7 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:280" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01339 ! ethylated residue @@ -13355,7 +13935,7 @@ [Term] id: MOD:00603 name: N-ethylation -def: "OBSOLETE because UniMod entry 283 is redundant with UniMod 280. Remap to MOD:00600" [UniMod:283] +def: "OBSOLETE because Unimod entry 283 is redundant with Unimod 280. Remap to MOD:00600" [Unimod:283] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" xref: DiffMono: "28.031300" @@ -13365,13 +13945,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Remap: "MOD:00600" +xref: Unimod: "Unimod:283" is_obsolete: true [Term] id: MOD:00604 name: 2x(2)H monomethylated L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 2x(2)H labeled monomethylated L-lysine." [PubMed:15525938, UniMod:284] -synonym: "Deuterium Methylation of Lysine" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 2x(2)H labeled monomethylated L-lysine." [PubMed:15525938, Unimod:284] +synonym: "Deuterium Methylation of Lysine" RELATED Unimod-description [] synonym: "Methyl:2H(2)" RELATED PSI-MS-label [] xref: DiffAvg: "16.03" xref: DiffFormula: "C 1 (2)H 2" @@ -13382,6 +13964,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:284" is_a: MOD:00839 ! (2)H deuterium labeled residue is_a: MOD:00912 ! modified L-lysine residue relationship: derives_from MOD:00085 ! N6-methyl-L-lysine @@ -13389,11 +13972,11 @@ [Term] id: MOD:00605 name: Sulfanilic Acid (SA), light C12 -def: "modification from UniMod Chemical derivative, C-Terminal/Glutamate/Aspartate sulfonation" [UniMod:285] -synonym: "Light Sulfanilic Acid (SA) C12" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative, C-Terminal/Glutamate/Aspartate sulfonation" [Unimod:285] +synonym: "Light Sulfanilic Acid (SA) C12" RELATED Unimod-description [] synonym: "SulfanilicAcid" RELATED PSI-MS-label [] -xref: DiffAvg: "155.17" -xref: DiffFormula: "C 6 H 5 N 1 O 2 S 1" +xref: DiffAvg: "155.00" +xref: DiffFormula: "(12)C 6 H 5 N 1 O 2 S 1" xref: DiffMono: "155.004099" xref: Formula: "none" xref: MassAvg: "none" @@ -13401,13 +13984,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:285" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00606 name: Sulfanilic Acid (SA), heavy C13 -def: "modification from UniMod Chemical derivative" [PubMed:9254591, UniMod:286] -synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:9254591, Unimod:286] +synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED Unimod-description [] synonym: "SulfanilicAcid:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "161.02" xref: DiffFormula: "(13)C 6 H 5 N 1 O 2 S 1" @@ -13418,15 +14002,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +xref: Unimod: "Unimod:286" +is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:00607 name: dioxoindolealanine lactone -def: "modification from UniMod Chemical derivative" [PubMed:7949339, UniMod:288] -comment: UniMod name, formula, and terminal specification corrected. Formula corresponded to uncleaved intermediate [JSG]. +def: "modification from Unimod Chemical derivative" [PubMed:7949339, Unimod:288] +comment: Unimod name, formula, and terminal specification corrected. Formula corresponded to uncleaved intermediate [JSG]. synonym: "Trp->Oxolactone" RELATED PSI-MS-label [] -synonym: "Tryptophan oxidation to oxolactone" RELATED UniMod-description [] +synonym: "Tryptophan oxidation to oxolactone" RELATED Unimod-description [] xref: DiffAvg: "30.99" xref: DiffFormula: "H -1 O 2" xref: DiffMono: "30.982004" @@ -13436,31 +14021,33 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:288" is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00608 name: biotin polyethyleneoxide amine -def: "modification from UniMod Chemical derivative" [UniMod:289] -synonym: "Biotin polyethyleneoxide amine" RELATED UniMod-description [] -synonym: "Biotin-PEO-Amine" RELATED UniMod-interim [] -xref: DiffAvg: "356.49" -xref: DiffFormula: "C 16 H 28 N 4 O 3 S 1" -xref: DiffMono: "356.188212" +def: "modification from Unimod Chemical derivative" [Unimod:289] +synonym: "Biotin polyethyleneoxide amine" RELATED Unimod-description [] +synonym: "Biotin-PEO-Amine" RELATED Unimod-interim [] +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:289" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00609 -name: Pierce EZ-Link Biotin-HPDP -def: "modification from UniMod Chemical derivative" [UniMod:290] -synonym: "Biotin-HPDP" RELATED UniMod-interim [] -synonym: "Pierce EZ-Link Biotin-HPDP" RELATED UniMod-description [] +name: Pierce EZ-Link Biotin-HPDP modified L-cysteine +def: "modification from Unimod Chemical derivative" [Unimod:290] +synonym: "Biotin-HPDP" RELATED Unimod-interim [] +synonym: "Pierce EZ-Link Biotin-HPDP" RELATED Unimod-description [] xref: DiffAvg: "428.61" xref: DiffFormula: "C 19 H 32 N 4 O 3 S 2" xref: DiffMono: "428.191583" @@ -13470,14 +14057,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:290" +is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00610 name: cysteinyl mercury -def: "modification from UniMod Chemical derivative" [PubMed:10695144, UniMod:291] +def: "modification from Unimod Chemical derivative" [PubMed:10695144, Unimod:291] synonym: "Delta:Hg(1)" RELATED PSI-MS-label [] -synonym: "Mercury Mercaptan" RELATED UniMod-description [] +synonym: "Mercury Mercaptan" RELATED Unimod-description [] xref: DiffAvg: "200.59" xref: DiffFormula: "Hg 1" xref: DiffMono: "201.970643" @@ -13487,15 +14076,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:291" is_a: MOD:00848 ! reagent derivatized residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue is_a: MOD:01075 ! mercury containing modified residue [Term] id: MOD:00611 name: iodouridine monophosphate derivatized residue -def: "A protein modification that is produced by reaction of iodouridine monophosphate, or a polynucleotide containing iodouridine, with a residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, UniMod:292] -synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED UniMod-description [] +def: "A protein modification that is produced by reaction of iodouridine monophosphate with a residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, Unimod:292] +synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED Unimod-description [] synonym: "IodoU-AMP" RELATED PSI-MS-label [] xref: DiffAvg: "322.17" xref: DiffFormula: "C 9 H 11 N 2 O 9 P 1" @@ -13506,13 +14096,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:292" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00612 name: 3-(carboxamidomethylthio)propanoylated residue -def: "A protein modification that is produced by derivatization of a residue with 3,3-dithiobis[sulfosuccinimidyl propanoate], DTSSP, or with Pierce EZ-Link Sulfo-NHS-SS-Biotin reagent, sulfosuccinimidyl 3-[(2-[biotinamido]ethyl)disulfanyl]propanoate, followed by reduction with dithiothreitol and then reaction with iodoacetamide." [PubMed:15121203, UniMod:293] -synonym: "3-(carbamidomethylthio)propanoyl" RELATED UniMod-description [] +def: "A protein modification that is produced by derivatization of a residue with 3,3-dithiobis[sulfosuccinimidyl propanoate], DTSSP, or with Pierce EZ-Link Sulfo-NHS-SS-Biotin reagent, sulfosuccinimidyl 3-[(2-[biotinamido]ethyl)disulfanyl]propanoate, followed by reduction with dithiothreitol and then reaction with iodoacetamide." [PubMed:15121203, Unimod:293] +synonym: "3-(carbamidomethylthio)propanoyl" RELATED Unimod-description [] synonym: "CAMthiopropanoyl" RELATED PSI-MS-label [] xref: DiffAvg: "145.18" xref: DiffFormula: "C 5 H 7 N 1 O 2 S 1" @@ -13523,14 +14114,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:293" is_a: MOD:00649 ! acylated residue is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00613 name: biotinoyl-iodoacetyl-ethylenediamine -def: "modification from UniMod Chemical derivative" [PubMed:10906242, UniMod:294] -synonym: "biotinoyl-iodoacetyl-ethylenediamine" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:10906242, Unimod:294] +synonym: "biotinoyl-iodoacetyl-ethylenediamine" RELATED Unimod-description [] synonym: "IED-Biotin" RELATED PSI-MS-label [] xref: DiffAvg: "326.42" xref: DiffFormula: "C 14 H 22 N 4 O 3 S 1" @@ -13541,17 +14133,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:294" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00614 -name: fucosylated -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a fucose (6-deoxy-D-galactose) group through a glycosidic bond." [PubMed:11344537, PubMed:15189151, UniMod:295] +name: fucosylated residue +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a fucose (6-deoxy-D-galactose) group through a glycosidic bond." [PubMed:11344537, PubMed:15189151, Unimod:295] subset: PSI-MOD-slim synonym: "dHex" RELATED PSI-MS-label [] synonym: "Fuc" EXACT PSI-MOD-label [] -synonym: "Fucose" RELATED UniMod-description [] +synonym: "Fucose" RELATED Unimod-description [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 O 4" xref: DiffMono: "146.057909" @@ -13561,12 +14154,14 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00736 ! deoxyhexosylated +xref: Unimod: "Unimod:295" +xref: GNOme: "GNO:G49112ZN" +is_a: MOD:00736 ! deoxyhexosylated residue [Term] id: MOD:00615 name: 4-sulfophenyl isothiocyante modification to N-term R -def: "OBSOLETE because entry UniMod:261 site N-term R was abandoned. Remap to MOD:00584" [PubMed:14689565, UniMod:261] +def: "OBSOLETE because entry Unimod:261 site N-term R was abandoned. Remap to MOD:00584" [PubMed:14689565, Unimod:261] xref: DiffAvg: "215.24" xref: DiffFormula: "C 7 H 5 N 1 O 3 S 2" xref: DiffMono: "214.971085" @@ -13576,6 +14171,8 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Remap: "MOD:00584" +xref: Unimod: "Unimod:261" is_obsolete: true [Term] @@ -13588,9 +14185,9 @@ [Term] id: MOD:00617 name: 3x(2)H residue methyl ester -def: "A protein modification that effectively converts a residue containing common isotopes to a 3x(2)H labeled residue methyl ester." [OMSSA:21, UniMod:298] +def: "A protein modification that effectively converts a residue containing common isotopes to a 3x(2)H labeled residue methyl ester." [OMSSA:21, Unimod:298] synonym: "ctermpeptrideuteromethyl" EXACT OMSSA-label [] -synonym: "deuterated methyl ester" RELATED UniMod-description [] +synonym: "deuterated methyl ester" RELATED Unimod-description [] synonym: "Methyl:2H(3)" RELATED PSI-MS-label [] xref: DiffAvg: "17.03" xref: DiffFormula: "C 1 (1)H -1 (2)H 3" @@ -13601,15 +14198,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:298" is_a: MOD:00839 ! (2)H deuterium labeled residue [Term] id: MOD:00618 name: tryptophan carboxylation -def: "modification from UniMod Chemical derivative" [UniMod:299#W] -comment: There is no literature citation for this UniMod entry [JSG]. -synonym: "Carboxy" RELATED UniMod-interim [] -synonym: "Carboxylation" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:299#W] +comment: There is no literature citation for this Unimod entry [JSG]. +synonym: "Carboxy" RELATED Unimod-interim [] +synonym: "Carboxylation" RELATED Unimod-description [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 O 2" xref: DiffMono: "43.989829" @@ -13619,13 +14217,14 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:299" is_a: MOD:00918 ! modified L-tryptophan residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00619 name: hydroxylethanone -def: "OBSOLETE because entry 300 is redundant with UniMod 6 remap to MOD:01328" [UniMod:300] +def: "OBSOLETE because entry 300 is redundant with Unimod 6 remap to MOD:01328" [Unimod:300] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -13635,15 +14234,17 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01328" +xref: Unimod: "Unimod:300" is_obsolete: true [Term] id: MOD:00620 name: cysteine monobromobimane derivative -def: "modification from UniMod Chemical derivative" [PubMed:7856876, UniMod:301] +def: "modification from Unimod Chemical derivative" [PubMed:7856876, Unimod:301] comment: 1-(bromomethyl)-2,6,7-trimethylpyrazolo[1,2-a]pyrazole-3,5-dione, C 10 H 11 Br 1 N 2 O 2. synonym: "Bromobimane" RELATED PSI-MS-label [] -synonym: "Monobromobimane derivative" RELATED UniMod-description [] +synonym: "Monobromobimane derivative" RELATED Unimod-description [] xref: DiffAvg: "190.20" xref: DiffFormula: "C 10 H 10 N 2 O 2" xref: DiffMono: "190.074228" @@ -13653,15 +14254,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:301" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00621 name: menadione quinone derivative -def: "modification from UniMod Chemical derivative" [PubMed:15939799, UniMod:302] -synonym: "Menadione" RELATED UniMod-interim [] -synonym: "Menadione quinone derivative" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:15939799, Unimod:302] +synonym: "Menadione" RELATED Unimod-interim [] +synonym: "Menadione quinone derivative" RELATED Unimod-description [] xref: DiffAvg: "170.17" xref: DiffFormula: "C 11 H 6 O 2" xref: DiffMono: "170.036779" @@ -13671,15 +14273,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:302" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00622 name: cysteine mercaptoethanol -def: "modification from UniMod Chemical derivative" [DeltaMass:80, PubMed:12442261, UniMod:303] +def: "modification from Unimod Chemical derivative" [DeltaMass:80, PubMed:12442261, Unimod:303] comment: From DeltaMass: Average Mass: 76 Average Mass Change:76 PubMed:8019414. synonym: "Beta mercaptoethanol adduct" EXACT DeltaMass-label [] -synonym: "Cysteine mercaptoethanol" RELATED UniMod-description [] +synonym: "Cysteine mercaptoethanol" RELATED Unimod-description [] synonym: "DeStreak" RELATED PSI-MS-label [] xref: DiffAvg: "76.11" xref: DiffFormula: "C 2 H 4 O 1 S 1" @@ -13690,15 +14293,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:303" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00623 -name: fucosylated biantennary (-2 galactose) -def: "modification from UniMod N-linked glycosylation" [UniMod:305] +name: fucosylated biantennary (-2 galactose) N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [Unimod:305] synonym: "dHex(1)Hex(3)HexNAc(4)" RELATED PSI-MS-label [] -synonym: "Fucosylated biantennary (-2 galactose)" RELATED UniMod-description [] +synonym: "Fucosylated biantennary (-2 galactose)" RELATED Unimod-description [] xref: DiffAvg: "1443.33" xref: DiffFormula: "C 56 H 90 N 4 O 39" xref: DiffMono: "1442.518219" @@ -13708,8 +14312,10 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:305" +xref: GNOme: "GNO:G25987BV" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00624 @@ -13721,9 +14327,9 @@ [Term] id: MOD:00625 name: N-methylmaleimide derivatized residue -def: "modification from UniMod Chemical derivative" [UniMod:314] +def: "modification from Unimod Chemical derivative" [Unimod:314] synonym: "Nmethylmaleimide" RELATED PSI-MS-label [] -synonym: "Nmethylmaleimide" RELATED UniMod-description [] +synonym: "Nmethylmaleimide" RELATED Unimod-description [] xref: DiffAvg: "111.10" xref: DiffFormula: "C 5 H 5 N 1 O 2" xref: DiffMono: "111.032028" @@ -13733,13 +14339,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:314" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00626 -name: fluorescein-5-thiosemicarbazide -def: "modification from UniMod Chemical derivative" [PubMed:2883911, UniMod:478] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +name: fluorescein-5-thiosemicarbazide modified residue +def: "modification from Unimod Chemical derivative" [PubMed:2883911, Unimod:478] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -13750,15 +14357,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:478" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00627 name: 2,5-dimethylpyrrole lysine from 2,5-hexanedione adduct -def: "modification from UniMod Chemical derivative" [UniMod:316] -comment: There is no citation for this UniMod entry. Add PubMed:7981420, correct spelling [JSG]. +def: "modification from Unimod Chemical derivative" [Unimod:316] +comment: There is no citation for this Unimod entry. Add PubMed:7981420, correct spelling [JSG]. synonym: "(2S)-2-amino-6-(2,5-dimethylpyrrolidin-1-yl)hexanoic acid" EXACT PSI-MOD-alternate [] -synonym: "2,5-dimethypyrrole" RELATED UniMod-description [] +synonym: "2,5-dimethypyrrole" RELATED Unimod-description [] synonym: "6-(2,5-dimethylpyrrolidin-1-yl)norleucine" EXACT PSI-MOD-alternate [] synonym: "DimethylpyrroleAdduct" RELATED PSI-MS-label [] xref: DiffAvg: "78.11" @@ -13770,6 +14378,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:316" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue @@ -13786,15 +14395,16 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: GNOme: "GNO:G90627TW" is_a: MOD:00725 ! complex glycosylation [Term] id: MOD:00629 name: MDA adduct +62 -def: "modification from UniMod Chemical derivative" [UniMod:318] +def: "modification from Unimod Chemical derivative" [Unimod:318] comment: Usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues [UniProt]. synonym: "Delta:H(2)C(5)" RELATED PSI-MS-label [] -synonym: "MDA adduct +62" RELATED UniMod-description [] +synonym: "MDA adduct +62" RELATED Unimod-description [] xref: DiffAvg: "62.07" xref: DiffFormula: "C 5 H 2" xref: DiffMono: "62.015650" @@ -13804,16 +14414,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:318" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00630 name: C3-H2-O adduct (+54 amu) of malondialdehyde with lysine or methylglyoxal with arginine. -def: "modification from UniMod Chemical derivative" [PubMed:9328283, UniMod:319] +def: "modification from Unimod Chemical derivative" [PubMed:9328283, Unimod:319] comment: This is not a legitimate ontological entry and will become obsolete when the children are reassigned [JSG] synonym: "Delta:H(2)C(3)O(1)" RELATED PSI-MS-label [] -synonym: "MDA adduct +54" RELATED UniMod-description [] +synonym: "MDA adduct +54" RELATED Unimod-description [] xref: DiffAvg: "54.05" xref: DiffFormula: "C 3 H 2 O 1" xref: DiffMono: "54.010565" @@ -13823,15 +14434,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:319" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00631 name: hydrolyzed N-ethylmaleimide adduct -def: "modification from UniMod Chemical derivative" [UniMod:320] +def: "modification from Unimod Chemical derivative" [Unimod:320] comment: N-ethylmaeimide adduct + H20 (a mixture of isobaric products) [JSG]. synonym: "Nethylmaleimide+water" RELATED PSI-MS-label [] -synonym: "Nethylmaleimidehydrolysis" RELATED UniMod-description [] +synonym: "Nethylmaleimidehydrolysis" RELATED Unimod-description [] xref: DiffAvg: "143.14" xref: DiffFormula: "C 6 H 9 N 1 O 3" xref: DiffMono: "143.058243" @@ -13841,12 +14453,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:320" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00632 name: N-succinimide -def: "OBSOLETE because this chemical derivative modification from UniMod 321 is deprecated." [UniMod:321] +def: "OBSOLETE because this chemical derivative modification from Unimod 321 is deprecated." [Unimod:321] xref: DiffAvg: "-17.01" xref: DiffFormula: "H -1 O -1" xref: DiffMono: "-17.002740" @@ -13856,15 +14469,16 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:321" is_obsolete: true [Term] id: MOD:00633 name: bis-N-I-sulfonerahodamine -def: "modification from UniMod Chemical derivative" [UniMod:323] -comment: Invitrogen B-10621, a red fluorescent cross-linking reagent (only link to Cys is indicated) [UniMod]. +def: "modification from Unimod Chemical derivative" [Unimod:323] +comment: Invitrogen B-10621, a red fluorescent cross-linking reagent (only link to Cys is indicated) [Unimod]. synonym: "bis-((N-iodoacetyl)piperazinyl)sulfonerhodamine" EXACT PSI-MOD-alternate [] -synonym: "bis-N-I-sulfonerahodamine" RELATED UniMod-description [] +synonym: "bis-N-I-sulfonerahodamine" RELATED Unimod-description [] synonym: "Xlink:B10621" RELATED PSI-MS-label [] xref: DiffAvg: "713.57" xref: DiffFormula: "C 31 H 30 I 1 N 4 O 6 S 1" @@ -13875,16 +14489,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:323" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00634 name: dimethyl 3,3'-dithiobispropionimidate -def: "modification from UniMod Chemical derivative" [PubMed:770170, UniMod:324] +def: "modification from Unimod Chemical derivative" [PubMed:770170, Unimod:324] comment: Pierce reagent, needs sites for N, Q, R, K, and N-term [JSG]. -synonym: "dimethyl 3,3'-dithiobispropionimidate" RELATED UniMod-description [] -synonym: "DTBP" RELATED UniMod-interim [] +synonym: "dimethyl 3,3'-dithiobispropionimidate" RELATED Unimod-description [] +synonym: "DTBP" RELATED Unimod-interim [] xref: DiffAvg: "123.60" xref: DiffFormula: "C 3 Cl 1 H 6 N 1 S 1" xref: DiffMono: "122.990948" @@ -13894,14 +14509,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:324" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00635 name: 10-fluoroethoxyphosphinyl-N-(biotinamidopentyl)decanamide -def: "modification from UniMod Chemical derivative" [PubMed:10611275, UniMod:325] -synonym: "10-ethoxyphosphinyl-N-(biotinamidopentyl)decanamide" RELATED UniMod-description [] -synonym: "FP-Biotin" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [PubMed:10611275, Unimod:325] +synonym: "10-ethoxyphosphinyl-N-(biotinamidopentyl)decanamide" RELATED Unimod-description [] +synonym: "FP-Biotin" RELATED Unimod-interim [] xref: DiffAvg: "572.75" xref: DiffFormula: "C 27 H 49 N 4 O 5 P 1 S 1" xref: DiffMono: "572.316128" @@ -13911,6 +14527,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:325" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -13918,10 +14535,10 @@ [Term] id: MOD:00636 name: S-ethylcysteine (Ser) -def: "A protein modification that effectively converts an L-serine residue to S-ethylcysteine." [UniMod:327] -comment: Modification from UniMod. Phosphoserine is converted to dehydroalanine then by Michael addition of ethanethiol to S-ethylcysteine. Needs parent and sibling for S-ethyl-cysteine. +def: "A protein modification that effectively converts an L-serine residue to S-ethylcysteine." [Unimod:327] +comment: Modification from Unimod. Phosphoserine is converted to dehydroalanine then by Michael addition of ethanethiol to S-ethylcysteine. Needs parent and sibling for S-ethyl-cysteine. synonym: "Delta:H(4)C(2)O(-1)S(1)" RELATED PSI-MS-label [] -synonym: "S-Ethylcystine from Serine" RELATED UniMod-description [] +synonym: "S-Ethylcystine from Serine" RELATED Unimod-description [] xref: DiffAvg: "44.11" xref: DiffFormula: "C 2 H 4 O -1 S 1" xref: DiffMono: "44.008457" @@ -13931,14 +14548,15 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:327" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00637 name: 1x(13)C,3x(2)H labeled monomethylated L-arginine -def: "A protein modification that effectively replaces one hydrogen atom of an L-arginine residue with a (13)C,3x(2)H labeled methyl group to form a 1x(13)C,3x(2)H labeled monomethylated L-arginine." [UniMod:329] +def: "A protein modification that effectively replaces one hydrogen atom of an L-arginine residue with a (13)C,3x(2)H labeled methyl group to form a 1x(13)C,3x(2)H labeled monomethylated L-arginine." [Unimod:329] synonym: "Methyl:2H(3)13C(1)" RELATED PSI-MS-label [] -synonym: "monomethylated arginine" RELATED UniMod-description [] +synonym: "monomethylated arginine" RELATED Unimod-description [] xref: DiffAvg: "18.04" xref: DiffFormula: "(13)C 1 (1)H -1 (2)H 3" xref: DiffMono: "18.037835" @@ -13948,6 +14566,7 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:329" is_a: MOD:00839 ! (2)H deuterium labeled residue is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00902 ! modified L-arginine residue @@ -13956,9 +14575,9 @@ [Term] id: MOD:00638 name: 2x(13)C,6x(2)H labeled dimethylated L-arginine -def: "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated L-arginine." [PubMed:15782174, UniMod:330] +def: "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated L-arginine." [PubMed:15782174, Unimod:330] synonym: "Dimethyl:2H(6)13C(2)" RELATED PSI-MS-label [] -synonym: "dimethylated arginine" RELATED UniMod-description [] +synonym: "dimethylated arginine" RELATED Unimod-description [] xref: DiffAvg: "36.08" xref: DiffFormula: "(13)C 2 (1)H -2 (2)H 6" xref: DiffMono: "36.075670" @@ -13968,6 +14587,7 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:330" is_a: MOD:00839 ! (2)H deuterium labeled residue is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00902 ! modified L-arginine residue @@ -13976,9 +14596,9 @@ [Term] id: MOD:00639 name: thiophosphate labeled with biotin-HPDP -def: "modification from UniMod Chemical derivative" [UniMod:332] +def: "modification from Unimod Chemical derivative" [Unimod:332] synonym: "Thiophos-S-S-biotin" RELATED PSI-MS-label [] -synonym: "thiophosphate labeled with biotin-HPDP" RELATED UniMod-description [] +synonym: "thiophosphate labeled with biotin-HPDP" RELATED Unimod-description [] xref: DiffAvg: "525.66" xref: DiffFormula: "C 19 H 34 N 4 O 5 P 1 S 3" xref: DiffMono: "525.142895" @@ -13988,15 +14608,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:332" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue [Term] id: MOD:00640 name: 6-N-biotinylaminohexyl isopropyl phosphorofluoridate -def: "modification from UniMod Chemical derivative" [UniMod:333] -synonym: "6-N-biotinylaminohexyl isopropyl phosphate" RELATED UniMod-description [] -synonym: "Can-FP-biotin" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:333] +synonym: "6-N-biotinylaminohexyl isopropyl phosphate" RELATED Unimod-description [] +synonym: "Can-FP-biotin" RELATED Unimod-interim [] xref: DiffAvg: "467.54" xref: DiffFormula: "C 19 F 1 H 35 N 3 O 5 P 1 S 1" xref: DiffMono: "467.201907" @@ -14006,6 +14627,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:333" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -14013,7 +14635,7 @@ [Term] id: MOD:00641 name: CAMthiopropanoyl of Lys -def: "OBSOLETE because UniMod entry 334 is merged with UniMod 293. Remap to MOD:00612" [UniMod:334] +def: "OBSOLETE because Unimod entry 334 is merged with Unimod 293. Remap to MOD:00612" [Unimod:334] xref: DiffAvg: "146.18" xref: DiffFormula: "C 5 H 8 N 1 O 2 S 1" xref: DiffMono: "146.027574" @@ -14023,15 +14645,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00612" +xref: Unimod: "Unimod:334" is_obsolete: true [Term] id: MOD:00642 name: reduced 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of a residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:15133838, UniMod:335] +def: "A protein modification produced by formation of an adduct of a residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:15133838, Unimod:335] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. synonym: "HNE+Delta:H(2)" RELATED PSI-MS-label [] -synonym: "reduced 4-Hydroxynonenal" RELATED UniMod-description [] +synonym: "reduced 4-Hydroxynonenal" RELATED Unimod-description [] xref: DiffAvg: "158.24" xref: DiffFormula: "C 9 H 18 O 2" xref: DiffMono: "158.130680" @@ -14041,6 +14665,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:335" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:01155 ! lipoconjugated residue relationship: derives_from MOD:00446 ! 4-hydroxynonenal adduct @@ -14048,9 +14673,9 @@ [Term] id: MOD:00643 name: methylamine Michael addition derivatized residue -def: "modification from UniMod Artifact" [PubMed:11968134, UniMod:337] +def: "modification from Unimod Artifact" [PubMed:11968134, Unimod:337] synonym: "Methylamine" RELATED PSI-MS-label [] -synonym: "Michael addition with methylamine" RELATED UniMod-description [] +synonym: "Michael addition with methylamine" RELATED Unimod-description [] xref: DiffAvg: "13.04" xref: DiffFormula: "C 1 H 3 N 1 O -1" xref: DiffMono: "13.031634" @@ -14060,11 +14685,12 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:337" +is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00644 -name: O-acetylated residue +name: mono O-acetylated residue def: "A protein modification that effectively replaces a residue hydroxyl group with an acetoxy group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "OAcRes" EXACT PSI-MOD-label [] @@ -14077,12 +14703,12 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00645 -name: S-acetylated residue +name: mono S-acetylated residue def: "A protein modification that effectively replaces a residue sulfanyl group with an acetylsulfanyl group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "SAcRes" EXACT PSI-MOD-label [] @@ -14095,12 +14721,12 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00672 ! S-acylated residue [Term] id: MOD:00646 -name: acetylated L-cysteine +name: monoacetylated L-cysteine def: "A protein modification that effectively converts an L-cysteine residue to either N-acetyl-L-cysteine or S-acetyl-L-cysteine." [PubMed:18688235] subset: PSI-MOD-slim synonym: "AcCys" EXACT PSI-MOD-label [] @@ -14112,12 +14738,12 @@ xref: MassMono: "145.019749" xref: Origin: "C" xref: Source: "natural" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00647 -name: acetylated L-serine +name: monoacetylated L-serine def: "A protein modification that effectively converts an L-serine residue to either N-acetyl-L-serine, O-acetyl-L-serine, or N,O-diacetyl-L-serine." [PubMed:18688235] subset: PSI-MOD-slim synonym: "AcSer" EXACT PSI-MOD-label [] @@ -14129,14 +14755,14 @@ xref: MassMono: "none" xref: Origin: "S" xref: Source: "natural" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00648 name: N,O-diacetylated L-serine def: "A protein modification that effectively converts an L-serine residue to N,O-diacetyl-L-serine." [PubMed:16731519, PubMed:489587, PubMed:7309355, RESID:AA0051#var, RESID:AA0364#var] -comment: The samples were prepared using glacial acetic acid, and were probably artifactual [JSG]. +comment: In one paper, the samples were prepared using glacial acetic acid, and were probably artifactual [JSG]. synonym: "(S)-2-acetamido-3-acetyloxypropanoic acid" EXACT PSI-MOD-alternate [] synonym: "N,O-diacetyl-L-serine" EXACT PSI-MOD-alternate [] synonym: "N,O-diacetylserine" EXACT PSI-MOD-alternate [] @@ -14150,9 +14776,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00408 ! N-acetylated residue -is_a: MOD:00644 ! O-acetylated residue -is_a: MOD:00647 ! acetylated L-serine +is_a: MOD:02080 ! diacetylated L-serine relationship: has_functional_parent MOD:00060 ! N-acetyl-L-serine relationship: has_functional_parent MOD:00369 ! O-acetyl-L-serine @@ -14188,6 +14812,7 @@ def: "A protein modification that effectively replaces a residue amino group with a palmitoylamino group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "NPamRes" EXACT PSI-MOD-label [] +synonym: "N-hexadecanoylated residue" EXACT PSI-MOD-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 O 1" xref: DiffMono: "238.229666" @@ -14206,6 +14831,7 @@ def: "A protein modification that effectively replaces a residue hydroxyl group with a palmitoyloxy group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "OPamRes" EXACT PSI-MOD-label [] +synonym: "O-hexadecanoylated residue" EXACT PSI-MOD-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 O 1" xref: DiffMono: "238.229666" @@ -14224,6 +14850,7 @@ def: "A protein modification that effectively replaces a residue sulfanyl group with an palmitoylsulfanyl group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "SPamRes" EXACT PSI-MOD-label [] +synonym: "S-hexadecanoylated residue" EXACT PSI-MOD-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 O 1 S 0" xref: DiffMono: "238.229666" @@ -14271,7 +14898,7 @@ [Term] id: MOD:00657 name: L-glutamic acid 5-methyl ester (Gln) -def: "A protein modification that effectively converts an L-glutamine residue to L-glutamate 5-methyl ester." [PubMed:16888, PubMed:6300110, RESID:AA0072#GLN, UniMod:528] +def: "A protein modification that effectively converts an L-glutamine residue to L-glutamate 5-methyl ester." [PubMed:16888, PubMed:6300110, RESID:AA0072#GLN, Unimod:528] comment: This is known to be a natural modification of glutamine in prokaryotes. subset: PSI-MOD-slim synonym: "(2S)-2-amino-5-methoxy-5-oxopentanoic acid" EXACT RESID-systematic [] @@ -14280,7 +14907,7 @@ synonym: "5-methyl L-2-aminoglutarate" EXACT RESID-alternate [] synonym: "5-methyl L-glutamate" EXACT RESID-alternate [] synonym: "deamidated 5-methyl esterified glutamine" EXACT PSI-MOD-alternate [] -synonym: "Deamidation followed by a methylation" RELATED UniMod-description [] +synonym: "Deamidation followed by a methylation" RELATED Unimod-description [] synonym: "glutamic acid 5-methyl ester" EXACT RESID-alternate [] synonym: "glutamic acid gamma-methyl ester" EXACT RESID-alternate [] synonym: "L-glutamic acid 5-methyl ester" EXACT RESID-name [] @@ -14296,6 +14923,8 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:528" +xref: UniProt: "PTM-0127" is_a: MOD:01369 ! deamidated and methyl esterified residue is_a: MOD:01453 ! L-glutamic acid 5-methyl ester relationship: has_functional_parent MOD:00659 ! methylated glutamine @@ -14307,6 +14936,7 @@ subset: PSI-MOD-slim synonym: "MeArg" EXACT PSI-MOD-label [] xref: Origin: "R" +xref: UniProt: "PTM-0238" is_a: MOD:00427 ! methylated residue is_a: MOD:00902 ! modified L-arginine residue @@ -14367,6 +14997,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0193" is_a: MOD:00427 ! methylated residue is_a: MOD:00912 ! modified L-lysine residue @@ -14427,9 +15058,9 @@ [Term] id: MOD:00668 name: O-decanoylated residue -def: "A protein modification that effectively replaces a residue hydroxyl group with a decanoyloxy group." [UniMod:449] +def: "A protein modification that effectively replaces a residue hydroxyl group with a decanoyloxy group." [Unimod:449] synonym: "Decanoyl" RELATED PSI-MS-label [] -synonym: "lipid" RELATED UniMod-description [] +synonym: "lipid" RELATED Unimod-description [] synonym: "ODecRes" EXACT PSI-MOD-label [] xref: DiffAvg: "154.25" xref: DiffFormula: "C 10 H 18 N 0 O 1" @@ -14440,16 +15071,17 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:449" is_a: MOD:00667 ! decanoylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00669 name: O-octanoylated residue -def: "A protein modification that effectively replaces a residue hydroxyl group with a octanoyloxy group." [UniMod:426] +def: "A protein modification that effectively replaces a residue hydroxyl group with a octanoyloxy group." [Unimod:426] subset: PSI-MOD-slim synonym: "Octanoyl" RELATED PSI-MS-label [] -synonym: "octanoyl" RELATED UniMod-description [] +synonym: "octanoyl" RELATED Unimod-description [] synonym: "OOctRes" EXACT PSI-MOD-label [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" @@ -14460,6 +15092,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:426" is_a: MOD:00666 ! octanoylated residue is_a: MOD:00671 ! O-acylated residue @@ -14594,6 +15227,7 @@ def: "A protein modification that effectively converts an L-arginine residue to a hydroxylated L-arginine." [PubMed:18688235] synonym: "HyArg" EXACT PSI-MOD-label [] xref: Origin: "R" +xref: UniProt: "PTM-0498" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00902 ! modified L-arginine residue @@ -14609,7 +15243,7 @@ [Term] id: MOD:00684 name: deamidated L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid." [PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, RESID:AA0004#ASN, UniMod:7#N] +def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid." [PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, RESID:AA0004#ASN, Unimod:7#N] comment: incidental to RESID:AA0059 subset: PSI-MOD-slim synonym: "(2S)-2-aminobutanedioic acid" EXACT RESID-systematic [] @@ -14627,14 +15261,15 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00013 ! L-aspartic acid residue +xref: Unimod: "Unimod:7" +xref: UniProt: "PTM-0116" is_a: MOD:00400 ! deamidated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00685 name: deamidated L-glutamine -def: "A protein modification that effectively converts an L-glutamine residue to L-glutamic acid." [PubMed:1881881, PubMed:4565668, PubMed:4922541, PubMed:6692818, PubMed:9192900, PubMed:957425, RESID:AA0006#GLN, UniMod:7#Q] +def: "A protein modification that effectively converts an L-glutamine residue to L-glutamic acid." [PubMed:1881881, PubMed:4565668, PubMed:4922541, PubMed:6692818, PubMed:9192900, PubMed:957425, RESID:AA0006#GLN, Unimod:7#Q] subset: PSI-MOD-slim synonym: "(2S)-2-aminopentanedioic acid" EXACT RESID-systematic [] synonym: "1-aminopropane-1,3-dicarboxylic acid" EXACT RESID-alternate [] @@ -14654,13 +15289,15 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00015 ! L-glutamic acid residue +xref: Unimod: "Unimod:7" +xref: UniProt: "PTM-0117" is_a: MOD:00400 ! deamidated residue +is_a: MOD:00907 ! modified L-glutamine residue [Term] id: MOD:00686 name: L-selenocysteine (Cys) -def: "A protein modification that effectively converts an L-cysteine residue to L-selenocysteine (not known as a natural, post-translational modification process)." [PubMed:10523135, PubMed:2037562, PubMed:2963330, PubMed:6217842, PubMed:6714945, RESID:AA0022#CYS, UniMod:162#C] +def: "A protein modification that effectively converts an L-cysteine residue to L-selenocysteine (not known as a natural, post-translational modification process)." [PubMed:10523135, PubMed:2037562, PubMed:2963330, PubMed:6217842, PubMed:6714945, RESID:AA0022#CYS, Unimod:162#C] comment: This entry is for the artifactual formation of L-selenocysteine from cysteine. For encoded L-selenocysteine, use MOD:00031 [JSG]. synonym: "(2R)-2-amino-3-selanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-azanyl-3-selanylpropanoic acid" EXACT RESID-alternate [] @@ -14679,8 +15316,8 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:162" is_a: MOD:00007 ! selenium substitution for sulfur -is_a: MOD:00031 ! L-selenocysteine residue is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -14688,7 +15325,7 @@ name: thioether crosslinked residues def: "A protein modification that crosslinks two residues by formation of a thioether bond between a cysteine thiol and either an alkyl C as in lanthionine, or an aryl C as 2'-(S-cysteinyl)-L-histidine." [PubMed:18688235] is_a: MOD:00033 ! crosslinked residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:00688 @@ -14744,10 +15381,10 @@ [Term] id: MOD:00695 name: sulfated residue -def: "A protein modification that effectively substitutes a sulfonyl group for the hydrogen atom of a hydroxyl or sulfanyl group." [DeltaMass:0, PubMed:14752058, UniMod:40] +def: "A protein modification that effectively substitutes a sulfonyl group for the hydrogen atom of a hydroxyl or sulfanyl group." [DeltaMass:0, PubMed:14752058, Unimod:40] comment: From DeltaMass: Average Mass: 80. subset: PSI-MOD-slim -synonym: "O-Sulfonation" RELATED UniMod-description [] +synonym: "O-Sulfonation" RELATED Unimod-description [] synonym: "Sulfo" RELATED PSI-MS-label [] synonym: "SulfRes" EXACT PSI-MOD-label [] synonym: "Sulphonation (SO3H) (of PMC group)" EXACT DeltaMass-label [] @@ -14760,16 +15397,17 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:40" is_a: MOD:00860 ! sulfur containing modified residue [Term] id: MOD:00696 name: phosphorylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate')." [DeltaMass:0, UniMod:21] +def: "A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate')." [DeltaMass:0, Unimod:21] comment: From DeltaMass: Average Mass: 80. subset: PSI-MOD-slim synonym: "Phospho" RELATED PSI-MS-label [] -synonym: "Phosphorylation" RELATED UniMod-description [] +synonym: "Phosphorylation" RELATED Unimod-description [] synonym: "Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine)" EXACT DeltaMass-label [] synonym: "PhosRes" EXACT PSI-MOD-label [] xref: DiffAvg: "79.98" @@ -14781,19 +15419,20 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" is_a: MOD:00861 ! phosphorus containing modified residue [Term] id: MOD:00697 name: flavin modified residue -def: "A protein modification that effectively results from forming an adduct with a compound containing a flavin group." [UniMod:50] +def: "A protein modification that effectively results from forming an adduct with a compound containing a flavin group." [] subset: PSI-MOD-slim synonym: "FAD" RELATED PSI-MS-label [] -synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] +synonym: "Flavin adenine dinucleotide" RELATED Unimod-description [] synonym: "FlavRes" EXACT PSI-MOD-label [] -xref: DiffAvg: "783.54" -xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2 S 0" -xref: DiffMono: "783.141485" +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" @@ -14855,10 +15494,10 @@ [Term] id: MOD:00704 name: dehydrated residue -def: "A protein modification that effectively forms a double bond by removing a molecule of water from a residue." [DeltaMass:0, UniMod:23] +def: "A protein modification that effectively forms a double bond by removing a molecule of water from a residue." [DeltaMass:0, Unimod:23] subset: PSI-MOD-slim -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" @@ -14868,6 +15507,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:23" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] @@ -14889,14 +15529,16 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0124" is_a: MOD:00664 ! stereoisomerized residue [Term] id: MOD:00706 name: dehydrogenated tyrosine -def: "A protein modification that effectively converts L-tyrosine to 2,3-didehydrotyrosine." [UniMod:401#Y] +def: "A protein modification that effectively converts L-tyrosine to 2,3-didehydrotyrosine." [Unimod:401#Y] subset: PSI-MOD-slim synonym: "dHTyr" EXACT PSI-MOD-label [] +synonym: "MOD_RES 2,3-didehydrotyrosine" EXACT UniProt-feature [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" @@ -14906,6 +15548,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:401" +xref: UniProt: "PTM-0008" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01888 ! didehydrogenated residue @@ -14970,8 +15614,8 @@ xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" -xref: TermSpec: "N-term" -is_a: MOD:00430 ! trimethylated residue +xref: TermSpec: "none" +is_a: MOD:00427 ! methylated residue [Term] id: MOD:00712 @@ -15057,7 +15701,7 @@ [Term] id: MOD:00719 name: L-methionine sulfoxide -def: "A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues." [DeltaMass:177, OMSSA:1, PubMed:21406390, PubMed:22116028, RESID:AA0581, UniMod:35#M] +def: "A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues." [DeltaMass:177, OMSSA:1, PubMed:21406390, PubMed:22116028, RESID:AA0581, Unimod:35#M] comment: From DeltaMass: Average Mass: 147 Formula:C5H9O1N2S Monoisotopic Mass Change:147.035 Average Mass Change:147.195 (formula incorrect, N and O reversed) References:PE Sciex. subset: PSI-MOD-slim synonym: "(2S)-2-amino-4-[(R)-methylsulfinyl]butanoic acid" EXACT RESID-systematic [] @@ -15067,7 +15711,7 @@ synonym: "L-methionine sulfoxide" EXACT PSI-MOD-alternate [] synonym: "Methionyl Sulfoxide" EXACT DeltaMass-label [] synonym: "MetO" EXACT PSI-MOD-label [] -synonym: "MOD_RES Methionine (R)-sulfoxide" EXACT UniProt-feature [] +synonym: "MOD_RES Methionine sulfoxide" EXACT UniProt-feature [] synonym: "Oxidation" RELATED PSI-MS-label [] synonym: "oxym" EXACT OMSSA-label [] xref: DiffAvg: "16.00" @@ -15079,6 +15723,8 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" +xref: UniProt: "PTM-0469" is_a: MOD:00709 ! sulfur oxygenated L-methionine is_a: MOD:01854 ! sulfur monooxygenated residue @@ -15100,6 +15746,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0480" is_a: MOD:00719 ! L-methionine sulfoxide [Term] @@ -15107,6 +15754,7 @@ name: L-methionine (S)-sulfoxide def: "A protein modification that effectively oxygenates an L-methionine residue to L-methionine sulfoxide S-diastereomer." [PubMed:18688235] synonym: "S-MetO" EXACT PSI-MOD-label [] +synonym: "MOD_RES Methionine (S)-sulfoxide" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1 S 0" xref: DiffMono: "15.994915" @@ -15116,12 +15764,13 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: UniProt: "PTM-0481" is_a: MOD:00719 ! L-methionine sulfoxide [Term] id: MOD:00722 name: monomethylated L-glutamine -def: "A protein modification that effectively replaces one hydrogen atom of an L-glutamine residue with one methyl group." [OMSSA:14, UniMod:34#Q] +def: "A protein modification that effectively replaces one hydrogen atom of an L-glutamine residue with one methyl group." [OMSSA:14, Unimod:34#Q] subset: PSI-MOD-slim synonym: "Me1Gln" EXACT PSI-MOD-label [] synonym: "methylq" EXACT OMSSA-label [] @@ -15134,6 +15783,7 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00659 ! methylated glutamine @@ -15152,13 +15802,13 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00408 ! N-acetylated residue +is_a: MOD:00408 ! mono N-acetylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00724 name: N-methylated L-histidine -def: "A protein modification that effectively replaces one hydrogen atom on a nitrogen of an L-histidine residue with one methyl group." [OMSSA:74, UniMod:34#H] +def: "A protein modification that effectively replaces one hydrogen atom on a nitrogen of an L-histidine residue with one methyl group." [OMSSA:74, Unimod:34#H] subset: PSI-MOD-slim synonym: "Methyl" RELATED PSI-MS-label [] synonym: "methylh" EXACT OMSSA-label [] @@ -15172,6 +15822,7 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00661 ! methylated histidine @@ -15184,28 +15835,29 @@ [Term] id: MOD:00726 -name: glucosylated +name: glucosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a glucose group through a glycosidic bond." [PubMed:18688235] synonym: "Glc" EXACT PSI-MOD-label [] -xref: DiffAvg: "162.14" -xref: DiffFormula: "C 6 H 10 O 5" -xref: DiffMono: "162.052823" +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00433" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00727 -name: mannosylated +name: mannosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a mannose group through a glycosidic bond," [PubMed:18688235] synonym: "Man" EXACT PSI-MOD-label [] -xref: DiffAvg: "162.14" -xref: DiffFormula: "C 6 H 10 O 5" -xref: DiffMono: "162.052823" +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" @@ -15216,12 +15868,12 @@ [Term] id: MOD:00728 -name: galactosylated +name: galactosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a galactose group through a glycosidic bond." [PubMed:18688235] synonym: "Gal" EXACT PSI-MOD-label [] -xref: DiffAvg: "162.14" -xref: DiffFormula: "C 6 H 10 O 5" -xref: DiffMono: "162.052823" +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" @@ -15251,7 +15903,7 @@ [Term] id: MOD:00730 -name: arabinosylated +name: arabinosylated residue def: "a protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a arabinose sugar group through a glycosidic bond" [PubMed:18688235] synonym: "Ara" EXACT PSI-MOD-label [] xref: DiffAvg: "132.12" @@ -15267,7 +15919,7 @@ [Term] id: MOD:00731 -name: ribosylated +name: ribosylated residue def: "a protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a ribose sugar group through a glycosidic bond" [PubMed:18688235] synonym: "Rib" EXACT PSI-MOD-label [] xref: DiffAvg: "132.12" @@ -15283,7 +15935,7 @@ [Term] id: MOD:00732 -name: xylosylated +name: xylosylated residue def: "a protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a xylose sugar group through a glycosidic bond" [PubMed:18688235] synonym: "Xyl" EXACT PSI-MOD-label [] xref: DiffAvg: "132.12" @@ -15299,7 +15951,7 @@ [Term] id: MOD:00733 -name: N-acetylaminoglucosylated +name: N-acetylaminoglucosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with an N-acetylglucosamine group through a glycosidic bond." [PubMed:18688235] synonym: "GlcNAc" EXACT PSI-MOD-label [] xref: DiffAvg: "203.19" @@ -15311,11 +15963,11 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00436 ! N-acetylhexosaminylated +is_a: MOD:00436 ! N-acetylhexosaminylated residue [Term] id: MOD:00734 -name: N-acetylaminogalactosylated +name: N-acetylaminogalactosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with an N-acetylgalactosamine group through a glycosidic bond." [DeltaMass:247] comment: From DeltaMass: Average Mass: 203 Formula:C8H13O5N1 Monoisotopic Mass Change:203.079 Average Mass Change:203.196 References:PE Sciex synonym: "GalNAc" EXACT PSI-MOD-label [] @@ -15329,11 +15981,11 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00436 ! N-acetylhexosaminylated +is_a: MOD:00436 ! N-acetylhexosaminylated residue [Term] id: MOD:00735 -name: hexosuronylated +name: hexosuronylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexosuronic acid group through a glycosidic bond." [PubMed:18688235] synonym: "HexA" EXACT PSI-MOD-label [] xref: DiffAvg: "176.12" @@ -15349,7 +16001,7 @@ [Term] id: MOD:00736 -name: deoxyhexosylated +name: deoxyhexosylated residue def: "a protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a deoxyhexose group through a glycosidic bond" [DeltaMass:0] comment: From DeltaMass: Average Mass: 146 subset: PSI-MOD-slim @@ -15364,11 +16016,12 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: GNOme: "GNO:G02438LG" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00737 -name: N-acetylneuraminylated +name: N-acetylneuraminylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with an N-acetylneuraminic acid (sialic acid) group through a glycosidic bond." [DeltaMass:0] comment: From DeltaMass: Average Mass: 291 synonym: "N-acetylneuraminic acid (Sialic acid, NeuAc, NANA, SA)" EXACT DeltaMass-label [] @@ -15382,6 +16035,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: GNOme: "GNO:G76685HR" is_a: MOD:00693 ! glycosylated residue [Term] @@ -15492,12 +16146,12 @@ [Term] id: MOD:00752 -name: adenosine diphosphoribosyl (ADP-ribosyl) modified residue -def: "A protein modification that effectively results from forming an adduct with ADP-ribose through formation of a glycosidic bond." [DeltaMass:0] +name: monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue +def: "A protein modification that effectively results from forming an adduct with one ADP-ribose through formation of a glycosidic bond." [DeltaMass:0] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD-slim synonym: "ADP-rybosylation (from NAD)" EXACT DeltaMass-label [] -synonym: "ADPRibRes" EXACT PSI-MOD-label [] +synonym: "ADPRib1Res" EXACT PSI-MOD-label [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" xref: DiffMono: "541.061109" @@ -15507,7 +16161,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00701 ! nucleotide or nucleic acid modified residue +is_a: MOD:02087 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue [Term] id: MOD:00753 @@ -15558,6 +16212,7 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0111" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00664 ! stereoisomerized residue @@ -15572,6 +16227,7 @@ synonym: "beta-galactopyranosyl-4-hydroxyproline" EXACT RESID-alternate [] synonym: "O4-galactosyl-L-hydroxyproline" EXACT RESID-name [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] +synonym: "CARBOHYD O-linked (Gal) hydroxyproline" EXACT UniProt-feature [] xref: DiffAvg: "178.14" xref: DiffFormula: "C 6 H 10 N 0 O 6" xref: DiffMono: "178.047738" @@ -15581,6 +16237,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0558" is_a: MOD:00915 ! modified L-proline residue [Term] @@ -15596,6 +16253,7 @@ synonym: "O4-(N-acetylamino)glucosyl-L-hydroxyproline" EXACT RESID-name [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] synonym: "O4GlcNAcHyPro" EXACT PSI-MOD-label [] +synonym: "CARBOHYD O-linked (GlcNAc) hydroxyproline" EXACT UniProt-feature [] xref: DiffAvg: "219.19" xref: DiffFormula: "C 8 H 13 N 1 O 6" xref: DiffMono: "219.074287" @@ -15605,15 +16263,15 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +xref: UniProt: "PTM-0578" is_a: MOD:01677 ! O4-(N-acetylamino)hexosyl-L-hydroxyproline [Term] id: MOD:00759 -name: fucosylated biantennary (-1 galactose) -def: "modification from UniMod N-linked glycosylation" [UniMod:307] +name: fucosylated biantennary (-1 galactose) N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation" [Unimod:307] synonym: "dHex(1)Hex(4)HexNAc(4)" RELATED PSI-MS-label [] -synonym: "Fucosylated biantennary (-1 galactose)" RELATED UniMod-description [] +synonym: "Fucosylated biantennary (-1 galactose)" RELATED Unimod-description [] xref: DiffAvg: "1607.48" xref: DiffFormula: "C 62 H 102 N 4 O 44" xref: DiffMono: "1606.586693" @@ -15623,14 +16281,16 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:307" +xref: GNOme: "GNO:G59937CP" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00760 -name: biantennary -def: "modification from UniMod N-linked glycosylation - missing ref" [UniMod:311] -synonym: "Biantennary" RELATED UniMod-description [] +name: biantennary N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation - missing ref" [Unimod:311] +synonym: "Biantennary" RELATED Unimod-description [] synonym: "Hex(5)HexNAc(4)" RELATED PSI-MS-label [] xref: DiffAvg: "1623.48" xref: DiffFormula: "C 62 H 102 N 4 O 45" @@ -15641,12 +16301,14 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:311" +xref: GNOme: "GNO:G10486CT" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00761 -name: monohexosylated (Hex1) +name: monohexosylated residue def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with one hexose sugar group through a glycosidic bond." [PubMed:18688235] synonym: "Hex1" EXACT PSI-MOD-alternate [] xref: DiffAvg: "162.14" @@ -15658,13 +16320,14 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: GNOme: "GNO:G81399MY" is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:00762 -name: biantennary (-2 galactose) -def: "modification from UniMod N-linked glycosylation - missing ref" [UniMod:309] -synonym: "Biantennary (-2 galactose)" RELATED UniMod-description [] +name: biantennary (-2 galactose) N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation - missing ref" [Unimod:309] +synonym: "Biantennary (-2 galactose)" RELATED Unimod-description [] synonym: "Hex(3)HexNAc(4)" RELATED PSI-MS-label [] xref: DiffAvg: "1299.20" xref: DiffFormula: "C 50 H 82 N 4 O 35" @@ -15675,14 +16338,16 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:309" +xref: GNOme: "GNO:G35029YA" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00763 -name: biantennary (-1 galactose) -def: "modification from UniMod N-linked glycosylation - missing ref" [UniMod:310] -synonym: "Biantennary (-1 galactose)" RELATED UniMod-description [] +name: biantennary (-1 galactose) N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation - missing ref" [Unimod:310] +synonym: "Biantennary (-1 galactose)" RELATED Unimod-description [] synonym: "Hex(4)HexNAc(4)" RELATED PSI-MS-label [] xref: DiffAvg: "1461.34" xref: DiffFormula: "C 56 H 92 N 4 O 40" @@ -15693,8 +16358,10 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:310" +xref: GNOme: "GNO:G72787SB" is_a: MOD:00725 ! complex glycosylation -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:00764 @@ -15706,7 +16373,7 @@ [Term] id: MOD:00765 name: cysteinylation (disulfide with free L-cysteine) -def: "A protein modification that effectively converts an L-cysteine residue to S-(L-cysteinyl)-L-cysteine, forming a disulfide bond with free cysteine." [DeltaMass:260, PubMed:1988019, PubMed:2001356, PubMed:2076469, PubMed:3083866, PubMed:366603, PubMed:7918467, PubMed:8344916, RESID:AA0025#CYS1, UniMod:312] +def: "A protein modification that effectively converts an L-cysteine residue to S-(L-cysteinyl)-L-cysteine, forming a disulfide bond with free cysteine." [DeltaMass:260, PubMed:1988019, PubMed:2001356, PubMed:2076469, PubMed:3083866, PubMed:366603, PubMed:7918467, PubMed:8344916, RESID:AA0025#CYS1, Unimod:312] comment: This entry is for formation of a disulfide bond between a peptide cysteine and a free cysteine. For the cystine cross-link, see MOD:00234. From DeltaMass: (name misspelled and formula incorrect, N and O reversed) Formula: C6H10O2N3S2 Monoisotopic Mass Change: 222.013 Average Mass Change: 222.283 subset: PSI-MOD-slim synonym: "(2R,2'R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)" EXACT RESID-systematic [] @@ -15734,14 +16401,16 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:312" +xref: UniProt: "PTM-0415" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01862 ! disulfide conjugated residue [Term] id: MOD:00766 name: C terminal -K from HC of MAb -def: "modification from UniMod Post-translational - C-terminal loss of lysine" [PubMed:16078144, UniMod:313] -synonym: "Loss of C-terminal K from Heavy Chain of MAb" RELATED UniMod-description [] +def: "modification from Unimod Post-translational - C-terminal loss of lysine OBSOLETE because the idenical to MOD:01642. Remap to MOD:01642" [PubMed:16078144, Unimod:313] +synonym: "Loss of C-terminal K from Heavy Chain of MAb" RELATED Unimod-description [] synonym: "Lys-loss" RELATED PSI-MS-label [] xref: DiffAvg: "-128.18" xref: DiffFormula: "C -6 H -12 N -2 O -1" @@ -15751,7 +16420,9 @@ xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "C-term" -is_a: MOD:00003 ! UniMod +xref: Unimod: "Unimod:313" +xref: Remap: "MOD:01642" +is_obsolete: true [Term] id: MOD:00767 @@ -15764,7 +16435,7 @@ id: MOD:00768 name: methionine oxidation with neutral loss of 80 Da def: "Oxidation of methionine to methionine sulfone with neutral loss of CH3SO2H." [PubMed:18688235, PubMed:9004526] -comment: Originally created from UniMod:508 that was later deleted. +comment: Originally created from Unimod:508 that was later deleted. xref: DiffAvg: "-80.10" xref: DiffFormula: "C -1 H -4 N 0 O -2 S -1" xref: DiffMono: "-79.993200" @@ -15821,10 +16492,10 @@ [Term] id: MOD:00775 name: L-asparagine (His) -def: "An artifactual protein modification that converts an L-histidine residue to L-asparagine by oxidative degradation." [OMSSA:54, PubMed:9252331, UniMod:348] +def: "An artifactual protein modification that converts an L-histidine residue to L-asparagine by oxidative degradation." [OMSSA:54, PubMed:9252331, Unimod:348] synonym: "His->Asn" RELATED PSI-MS-label [] synonym: "his2asnh" EXACT OMSSA-label [] -synonym: "histidine oxidation to aspargine" RELATED UniMod-description [] +synonym: "histidine oxidation to aspargine" RELATED Unimod-description [] xref: DiffAvg: "-23.04" xref: DiffFormula: "C -2 H -1 N -1 O 1" xref: DiffMono: "-23.015984" @@ -15834,17 +16505,18 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00012 ! L-asparagine residue +xref: Unimod: "Unimod:348" is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02088 ! natural, standard, encoded residue substitution [Term] id: MOD:00776 name: L-aspartic acid (His) -def: "An artifactual protein modification that converts an L-histidine residue to L-aspartic acid by oxidative degradation." [OMSSA:55, PubMed:9252331, UniMod:349] +def: "An artifactual protein modification that converts an L-histidine residue to L-aspartic acid by oxidative degradation." [OMSSA:55, PubMed:9252331, Unimod:349] comment: From OMSSA: desc="oxidation of H to D" monomass= -23.015984 (this is the same mass difference as OMSSA:54, his2asnh) [JSG]. synonym: "His->Asp" RELATED PSI-MS-label [] synonym: "his2asph" EXACT OMSSA-label [] -synonym: "histidine oxidation to aspartic acid" RELATED UniMod-description [] +synonym: "histidine oxidation to aspartic acid" RELATED Unimod-description [] xref: DiffAvg: "-22.05" xref: DiffFormula: "C -2 H -2 N -2 O 2" xref: DiffMono: "-22.031969" @@ -15854,8 +16526,9 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00013 ! L-aspartic acid residue +xref: Unimod: "Unimod:349" is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02088 ! natural, standard, encoded residue substitution [Term] id: MOD:00777 @@ -15874,7 +16547,7 @@ [Term] id: MOD:00779 name: lysine oxidation to aminoadipic semialdehyde -def: "OBSOLETE because redundant with MOD:00130. Remap to MOD:00130." [DeltaMass:352, PubMed:11332453, PubMed:358196, PubMed:5337886, PubMed:5529814, UniMod:352] +def: "OBSOLETE because redundant with MOD:00130. Remap to MOD:00130." [DeltaMass:352, PubMed:11332453, PubMed:358196, PubMed:5337886, PubMed:5529814, Unimod:352] comment: From DeltaMass: Average Mass: -1 Average Mass Change:-1 References:Amici A, Levine, RL, Tsai, L, and Stadtman, ER: Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions. Journal of Biological Chemistry 264: 3341-3346 1989.Requena JR, Chao CC, Levine RL, and Stadtman ER: Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins. Proceedings of the National Academy of Sciences USA 98: 69-74 2001. synonym: "Oxidation of lysine (to aminoadipic semialdehyde)" EXACT DeltaMass-label [] xref: DiffAvg: "-1.03" @@ -15886,6 +16559,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00130" +xref: Unimod: "Unimod:352" is_obsolete: true [Term] @@ -15945,7 +16620,7 @@ [Term] id: MOD:00783 name: dimethylated L-arginine -def: "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two methyl groups." [OMSSA:37, UniMod:36#R] +def: "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two methyl groups." [OMSSA:37, Unimod:36#R] subset: PSI-MOD-slim synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "dimethylr" EXACT OMSSA-label [] @@ -15959,6 +16634,8 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:36" +xref: UniProt: "PTM-0341" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00658 ! methylated arginine @@ -16009,9 +16686,9 @@ [Term] id: MOD:00787 name: diisopropylphosphoserine -def: "modification from UniMod - label for the active site serine of the serine esterase/protease family also shown to label tyrosine in serum albumin" [UniMod:362] -synonym: "Diisopropylphosphate" RELATED UniMod-interim [] -synonym: "O-Diisopropylphosphorylation" RELATED UniMod-description [] +def: "modification from Unimod - label for the active site serine of the serine esterase/protease family also shown to label tyrosine in serum albumin" [Unimod:362] +synonym: "Diisopropylphosphate" RELATED Unimod-interim [] +synonym: "O-Diisopropylphosphorylation" RELATED Unimod-description [] xref: DiffAvg: "164.14" xref: DiffFormula: "C 6 H 13 O 3 P 1" xref: DiffMono: "164.060231" @@ -16021,6 +16698,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:362" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -16028,9 +16706,9 @@ [Term] id: MOD:00788 name: isopropylphosphotyrosine -def: "modification from UniMod" [UniMod:363] -synonym: "Isopropylphospho" RELATED UniMod-interim [] -synonym: "O-Isopropylphosphorylation" RELATED UniMod-description [] +def: "modification from Unimod" [Unimod:363] +synonym: "Isopropylphospho" RELATED Unimod-interim [] +synonym: "O-Isopropylphosphorylation" RELATED Unimod-description [] xref: DiffAvg: "122.06" xref: DiffFormula: "C 3 H 7 O 3 P 1" xref: DiffMono: "122.013281" @@ -16040,6 +16718,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:363" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00919 ! modified L-tyrosine residue @@ -16047,8 +16726,8 @@ [Term] id: MOD:00789 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form -def: "modification from UniMod - isotopic label ICPL method - The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy. The digest is typically applied AFTER ICPL_light/heavy labeling, only Protein N-term labeling and Lys-specific labeling is applied." [PubMed:15602776, UniMod:364, URL:http\://www.serva.de/products/sheets/39230-E.pdf] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form" RELATED UniMod-description [] +def: "modification from Unimod - isotopic label ICPL method - The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy. The digest is typically applied AFTER ICPL_light/heavy labeling, only Protein N-term labeling and Lys-specific labeling is applied." [PubMed:15602776, Unimod:364, URL:http\://www.serva.de/products/sheets/39230-E.pdf] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form" RELATED Unimod-description [] synonym: "ICPL:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "111.04" xref: DiffFormula: "(13)C 6 H 3 N 1 O 1" @@ -16059,13 +16738,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +xref: Unimod: "Unimod:364" +is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:00790 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form -def: "modification from UniMod - isotopic label ICPL method - The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy. The digest is typically applied AFTER ICPL_light/heavy labeling, only Protein N-term labeling and Lys-specific labeling is applied." [PubMed:15602776, UniMod:365, URL:http\://www.serva.de/products/sheets/39230-E.pdf] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form" RELATED UniMod-description [] +def: "modification from Unimod - isotopic label ICPL method - The paper describes an H/D labeling strategy whereas the commercial product follows a C/13C labeling strategy. The digest is typically applied AFTER ICPL_light/heavy labeling, only Protein N-term labeling and Lys-specific labeling is applied." [PubMed:15602776, Unimod:365, URL:http\://www.serva.de/products/sheets/39230-E.pdf] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form" RELATED Unimod-description [] synonym: "ICPL" RELATED PSI-MS-label [] xref: DiffAvg: "105.02" xref: DiffFormula: "(12)C 6 H 3 N 1 O 1" @@ -16076,15 +16756,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:365" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:00791 name: 1x(18)O labeled deamidated L-glutamine -def: "A protein modification that effectively converts an L-glutamine residue to L-glutamic acid with one (18)O." [PubMed:8382902, UniMod:366#Q] +def: "A protein modification that effectively converts an L-glutamine residue to L-glutamic acid with one (18)O." [PubMed:8382902, Unimod:366#Q] subset: PSI-MOD-slim synonym: "Deamidated:18O(1)" RELATED PSI-MS-label [] -synonym: "Deamidation in presence of O18" RELATED UniMod-description [] +synonym: "Deamidation in presence of O18" RELATED Unimod-description [] xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" xref: DiffMono: "2.988262" @@ -16094,7 +16775,8 @@ xref: Origin: "Q" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00685 ! deamidated L-glutamine +xref: Unimod: "Unimod:366" +relationship: derives_from MOD:00685 ! deamidated L-glutamine is_a: MOD:00852 ! 1x(18)O labeled deamidated residue [Term] @@ -16108,7 +16790,7 @@ [Term] id: MOD:00793 name: dehydroalanine (Cys) -def: "A protein modification that effectively converts an L-cysteine residue to dehydroalanine." [ChEBI:17123, DeltaMass:8, PubMed:10220322, PubMed:11212008, PubMed:1547888, PubMed:15799070, PubMed:1815586, PubMed:20805503, PubMed:2914619, PubMed:7947813, PubMed:8239649, RESID:AA0181#CYS, UniMod:368] +def: "A protein modification that effectively converts an L-cysteine residue to dehydroalanine." [ChEBI:17123, DeltaMass:8, PubMed:10220322, PubMed:11212008, PubMed:1547888, PubMed:15799070, PubMed:1815586, PubMed:20805503, PubMed:2914619, PubMed:7947813, PubMed:8239649, RESID:AA0181#CYS, Unimod:368] comment: From DeltaMass: In an attempt to clarfiy the difference between the modification of cysteine to lanthionine and cysteine to dehydroalanine, the following contributions from the ABRF email forum are presented:Structurally speaking lanthionine is like cystine but lacks one S atom. I imagine one can think of it as a condensation of cysteine and dehydroalanine but I do not know how it is made biologically. Dehydroalanine could be derived from either serine or cysteine. If I recall Biochem 101 correctly lanthionine was first found in wool.-Lowell Ericsson (ERICSSONLH@U.WASHINGTON.EDU)As far as I know, the structure of lanthionine is two Ala's joined by a single sulphur with the loss of two hydrogens from the methyl group of the Ala.Stephen Bayne (sbay@novo.dk)Regarding the structure of lanthionine and dehydroalanine: dehydroalanine is formed by the loss of one sulfur atom and two hydrogen atoms from ONE cysteine residue. lanthionine is formed from TWO cysteines, is a thioether, and contains one sulfur atom less than the amino acid cystine. Dan McCormick (MCCORMICK@rcf.mayo.edu) [DeltaMass]. Most bacterially produced lanthionine crosslinks are made by dehydration of L-serine to dehydroalanine, and then reaction with L-cysteine so as to produce chiral inversion at the alpha-carbon of the original L-serine; the lanthionine is a meso-diastereomer with L-configuration of the original cysteine alpha-carbon and D-configuration of the original L-serine alpha-carbon. In cypemycin dehydroalanine has been shown to be produced by loss of hydrogen sulfide from cysteine. Beta-elimination of hydrogen sulfide does occur during treatment with performic acid [JSG]. subset: PSI-MOD-slim synonym: "2,3-didehydroalanine" EXACT RESID-alternate [] @@ -16119,7 +16801,7 @@ synonym: "Cys->Dha" RELATED PSI-MS-label [] synonym: "dehydroalanine" EXACT RESID-name [] synonym: "Dehydroalanine (from Cysteine)" EXACT DeltaMass-label [] -synonym: "Dehydroalanine (from Cysteine)" RELATED UniMod-description [] +synonym: "Dehydroalanine (from Cysteine)" RELATED Unimod-description [] synonym: "Dha" EXACT RESID-alternate [] synonym: "dHAla(Cys)" EXACT PSI-MOD-label [] synonym: "MOD_RES 2,3-didehydroalanine (Cys)" EXACT UniProt-feature [] @@ -16131,17 +16813,19 @@ xref: MassMono: "69.021464" xref: Origin: "C" xref: Source: "natural" +xref: Unimod: "Unimod:368" xref: TermSpec: "none" +xref: UniProt: "PTM-0468" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01168 ! dehydroalanine [Term] id: MOD:00794 name: pyrrolidone from proline -def: "OBSOLETE because redundant and identical to MOD:00477. Remap to MOD:00477." [PubMed:9252331, UniMod:369] -comment: This UniMod entry appears to have come from the same description in PubMed:9252331 as UniMod:360. This entry was not annotated as being approved. Neither difference formula corresponds to the result described in the original citation PubMed:2161657. -synonym: "Pro->Pyrrolidone" RELATED UniMod-interim [] -synonym: "Pyrrolidone from Proline" RELATED UniMod-description [] +def: "OBSOLETE because redundant and identical to MOD:00477. Remap to MOD:00477." [PubMed:9252331, Unimod:369] +comment: This Unimod entry appears to have come from the same description in PubMed:9252331 as Unimod:360. This entry was not annotated as being approved. Neither difference formula corresponds to the result described in the original citation PubMed:2161657. +synonym: "Pro->Pyrrolidone" RELATED Unimod-interim [] +synonym: "Pyrrolidone from Proline" RELATED Unimod-description [] xref: DiffAvg: "-28.01" xref: DiffFormula: "C -1 O -1" xref: DiffMono: "-27.994915" @@ -16151,14 +16835,16 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00477" +xref: Unimod: "Unimod:369" is_obsolete: true [Term] id: MOD:00795 name: Michael addition of hydroxymethylvinyl ketone to cysteine -def: "modification from UniMod" [PubMed:11743741, UniMod:371] +def: "modification from Unimod" [PubMed:11743741, Unimod:371] synonym: "HMVK" RELATED PSI-MS-label [] -synonym: "Michael addition of hydroxymethylvinyl ketone to cysteine" RELATED UniMod-description [] +synonym: "Michael addition of hydroxymethylvinyl ketone to cysteine" RELATED Unimod-description [] xref: DiffAvg: "86.09" xref: DiffFormula: "C 4 H 6 O 2" xref: DiffMono: "86.036779" @@ -16168,17 +16854,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:371" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00796 name: L-ornithine (Arg) -def: "A protein modification that effectively converts an L-arginine residue to L-ornithine." [DeltaMass:129, OMSSA:163, PubMed:15489230, UniMod:372] +def: "A protein modification that effectively converts an L-arginine residue to L-ornithine." [DeltaMass:129, OMSSA:163, PubMed:15489230, Unimod:372] subset: PSI-MOD-slim synonym: "Arg->Orn" RELATED PSI-MS-label [] synonym: "arg2orn" EXACT OMSSA-label [] synonym: "Ornithine (from Arginine)" EXACT DeltaMass-label [] -synonym: "Ornithine from Arginine" RELATED UniMod-description [] +synonym: "Ornithine from Arginine" RELATED Unimod-description [] synonym: "Ornithyl" EXACT DeltaMass-label [] xref: DiffAvg: "-42.04" xref: DiffFormula: "C -1 H -2 N -2" @@ -16189,12 +16876,13 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:372" is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00797 name: 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal -def: "a protein modification that effectively converts an L-cysteine residue to the PEP adduct, 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal" [PubMed:4696757, PubMed:7999765, PubMed:8664284, RESID:AA0391] +def: "a protein modification that effectively converts an L-cysteine residue to the PEP adduct, 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal" [PubMed:4696757, PubMed:7999765, PubMed:8664284, RESID:AA0391, ChEBI:149496] synonym: "(2R)-2-amino-3-[1-carboxy-1-(phosphonooxy)ethyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acid" EXACT RESID-alternate [] synonym: "2-([(2R)-2-azanyl-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acid" EXACT RESID-alternate [] @@ -16214,15 +16902,16 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0424" is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00798 name: half cystine -def: "A protein modification that can be regarded as effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed." [PubMed:1988019, PubMed:2001356, PubMed:2076469, PubMed:3083866, PubMed:366603, PubMed:7918467, PubMed:8344916, UniMod:374] +def: "A protein modification that can be regarded as effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed." [PubMed:1988019, PubMed:2001356, PubMed:2076469, PubMed:3083866, PubMed:366603, PubMed:7918467, PubMed:8344916, Unimod:374] synonym: "Dehydro" RELATED PSI-MS-label [] -synonym: "Half of a disulfide bridge" RELATED UniMod-description [] +synonym: "Half of a disulfide bridge" RELATED Unimod-description [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0 S 0" xref: DiffMono: "-1.007825" @@ -16232,6 +16921,7 @@ xref: Origin: "C" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:374" is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -16244,6 +16934,7 @@ synonym: "S-galactosyl-L-cysteine" EXACT RESID-name [] synonym: "S-glycosyl-cysteine" EXACT RESID-alternate [] synonym: "SGalCys" EXACT PSI-MOD-label [] +synonym: "CARBOHYD S-linked (Gal) cysteine" EXACT UniProt-feature [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5 S 0" xref: DiffMono: "162.052823" @@ -16253,9 +16944,9 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: UniProt: "PTM-0624" is_a: MOD:00426 ! S-glycosylated residue -is_a: MOD:00476 ! galactosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00476 ! monogalactosylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -16277,8 +16968,8 @@ xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00772 ! vanadium containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00801 @@ -16299,8 +16990,8 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00802 @@ -16329,7 +17020,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00772 ! vanadium containing modified residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00803 @@ -16351,7 +17042,8 @@ xref: Origin: "C, Y" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00919 ! modified L-tyrosine residue +xref: UniProt: "PTM-0020" +is_a: MOD:02058 ! crosslinked L-tyrosine residue is_a: MOD:01993 ! beta-carbon thioether crosslinked residues [Term] @@ -16360,7 +17052,7 @@ def: "A protein modification that effectively converts an L-serine residue to O3-beta-glucosylated L-serine." [PubMed:10734111, PubMed:2105311, PubMed:2511201, RESID:AA0397] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(beta-D-glucopyranosyloxy)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (Glc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Glc) serine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (Hex)" EXACT UniProt-feature [] synonym: "O-glucosyl-L-serine" EXACT RESID-name [] synonym: "O-glycosylserine" EXACT RESID-alternate [] @@ -16375,9 +17067,9 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0573" is_a: MOD:00002 ! O-glycosyl-L-serine -is_a: MOD:00433 ! glucosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00433 ! monoglucosylated residue [Term] id: MOD:00805 @@ -16385,7 +17077,7 @@ def: "A protein modification that effectively converts an L-serine residue to O3-(N-acetylaminoglucosyl)-L-serine." [PubMed:3086323, PubMed:8404891, RESID:AA0398] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GlcNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GlcNAc) serine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (HexNAc)" EXACT UniProt-feature [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-serine" EXACT RESID-alternate [] @@ -16405,7 +17097,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +xref: UniProt: "PTM-0580" +is_a: MOD:00448 ! mono-N-acetylaminoglucosylated residue is_a: MOD:01675 ! O-(N-acetylamino)hexosyl-L-serine [Term] @@ -16414,7 +17107,7 @@ def: "A protein modification that effectively converts an L-threonine residue to O3-(N-acetylaminoglucosyl)-L-threonine." [PubMed:3086323, PubMed:8404891, RESID:AA0399] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)butanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GlcNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GlcNAc) threonine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (HexNAc)" EXACT UniProt-feature [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-threonine" EXACT RESID-alternate [] @@ -16434,13 +17127,14 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +xref: UniProt: "PTM-0582" +is_a: MOD:00448 ! mono-N-acetylaminoglucosylated residue is_a: MOD:01676 ! O-(N-acetylamino)hexosyl-L-threonine [Term] id: MOD:00807 name: pyruvic acid (Ser) -def: "A protein modification that effectively converts an L-serine residue to pyruvic acid." [DeltaMass:23, PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127#SER, UniMod:385#S] +def: "A protein modification that effectively converts an L-serine residue to pyruvic acid." [DeltaMass:23, PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127#SER, Unimod:385#S] comment: DeltaMass gives mass 70 and difference mass -16 with no formula subset: PSI-MOD-slim synonym: "2-oxopropanoic acid" EXACT RESID-systematic [] @@ -16457,6 +17151,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:385" +xref: UniProt: "PTM-0266" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01154 ! pyruvic acid is_a: MOD:01160 ! deaminated residue @@ -16466,7 +17162,7 @@ name: O-galactosyl-L-serine def: "A protein modification that effectively converts an L-serine residue to O3-galactosylserine." [PubMed:666730, RESID:AA0400] synonym: "(2S)-2-amino-3-(alpha-D-galactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (Gal)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Gal) serine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (Hex)" EXACT UniProt-feature [] synonym: "O-galactosyl-L-serine" EXACT RESID-name [] synonym: "O-glycosylserine" EXACT RESID-alternate [] @@ -16481,16 +17177,16 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0560" is_a: MOD:00002 ! O-glycosyl-L-serine -is_a: MOD:00476 ! galactosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00476 ! monogalactosylated residue [Term] id: MOD:00809 name: O-galactosyl-L-threonine def: "A protein modification that effectively converts an L-threonine residue to O3-galactosylthreonine." [PubMed:2673008, RESID:AA0401] synonym: "(2S,3R)-2-amino-3-(alpha-D-galactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (Gal)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Gal) threonine" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (Hex)" EXACT UniProt-feature [] synonym: "O-galactosyl-L-threonine" EXACT RESID-name [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] @@ -16505,8 +17201,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00476 ! galactosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +xref: UniProt: "PTM-0562" +is_a: MOD:00476 ! monogalactosylated residue is_a: MOD:01348 ! O-hexosylated threonine [Term] @@ -16515,7 +17211,7 @@ def: "A protein modification that effectively converts an L-serine residue to O3-mannosylserine." [PubMed:391559, RESID:AA0402] synonym: "(2S)-2-amino-3-(alpha-D-mannopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "CARBOHYD O-linked (Hex)" EXACT UniProt-feature [] -synonym: "CARBOHYD O-linked (Man)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Man) serine" EXACT UniProt-feature [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O-mannopyranosylserine" EXACT RESID-alternate [] synonym: "O-mannosyl-L-serine" EXACT RESID-name [] @@ -16530,9 +17226,9 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0588" is_a: MOD:00002 ! O-glycosyl-L-serine -is_a: MOD:00595 ! mannosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +is_a: MOD:00595 ! monomannosylated residue [Term] id: MOD:00811 @@ -16540,7 +17236,7 @@ def: "a protein modification that effectively forms a O3-mannosylthreonine" [PubMed:391559, RESID:AA0403] synonym: "(2S,3R)-2-amino-3-(alpha-D-mannopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "CARBOHYD O-linked (Hex)" EXACT UniProt-feature [] -synonym: "CARBOHYD O-linked (Man)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Man) threonine" EXACT UniProt-feature [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O-mannosyl-L-threonine" EXACT RESID-name [] synonym: "O3-mannosylthreonine" EXACT RESID-alternate [] @@ -16554,24 +17250,25 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00595 ! mannosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +xref: UniProt: "PTM-0591" +is_a: MOD:00595 ! monomannosylated residue is_a: MOD:01348 ! O-hexosylated threonine [Term] id: MOD:00812 name: O-fucosyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to an O-fucosylserine." [PubMed:10734111, PubMed:11067851, PubMed:11344537, PubMed:12096136, PubMed:1517205, PubMed:15189151, PubMed:1904059, PubMed:3311742, PubMed:3578767, RESID:AA0404, UniMod:295#S] +def: "A protein modification that effectively converts an L-serine residue to an O-fucosylserine." [PubMed:10734111, PubMed:11067851, PubMed:11344537, PubMed:12096136, PubMed:1517205, PubMed:15189151, PubMed:1904059, PubMed:3311742, PubMed:3578767, RESID:AA0404, Unimod:295#S] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "CARBOHYD O-linked (dHex)" EXACT UniProt-feature [] synonym: "CARBOHYD O-linked (Fuc)" EXACT UniProt-feature [] synonym: "dHex" RELATED PSI-MS-label [] -synonym: "Fucose" RELATED UniMod-description [] +synonym: "Fucose" RELATED Unimod-description [] synonym: "O-fucosyl-L-serine" EXACT RESID-name [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O3-fucosylserine" EXACT RESID-alternate [] synonym: "OFucSer" EXACT PSI-MOD-label [] +synonym: "CARBOHYD O-linked (Fuc) serine" EXACT UniProt-feature [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 N 0 O 4" xref: DiffMono: "146.057909" @@ -16581,19 +17278,21 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:295" +xref: UniProt: "PTM-0550" is_a: MOD:00002 ! O-glycosyl-L-serine -is_a: MOD:00614 ! fucosylated +is_a: MOD:00614 ! fucosylated residue [Term] id: MOD:00813 name: O-fucosyl-L-threonine -def: "A protein modification that effectively converts an threonine residue to an O-fucosylthreonine." [PubMed:11344537, PubMed:11857757, PubMed:15189151, PubMed:1740125, PubMed:1900431, RESID:AA0405, UniMod:295#T] +def: "A protein modification that effectively converts an threonine residue to an O-fucosylthreonine." [PubMed:11344537, PubMed:11857757, PubMed:15189151, PubMed:1740125, PubMed:1900431, RESID:AA0405, Unimod:295#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "CARBOHYD O-linked (dHex)" EXACT UniProt-feature [] -synonym: "CARBOHYD O-linked (Fuc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (Fuc) threonine" EXACT UniProt-feature [] synonym: "dHex" RELATED PSI-MS-label [] -synonym: "Fucose" RELATED UniMod-description [] +synonym: "Fucose" RELATED Unimod-description [] synonym: "O-fucosyl-L-threonine" EXACT RESID-name [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O3-fucosylthreonine" EXACT RESID-alternate [] @@ -16607,8 +17306,10 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:295" +xref: UniProt: "PTM-0552" is_a: MOD:00005 ! O-glycosyl-L-threonine -is_a: MOD:00614 ! fucosylated +is_a: MOD:00614 ! fucosylated residue [Term] id: MOD:00814 @@ -16621,6 +17322,7 @@ synonym: "O-xylosyl-L-serine" EXACT RESID-name [] synonym: "O3-xylosylserine" EXACT RESID-alternate [] synonym: "OXylSer" EXACT PSI-MOD-label [] +synonym: "CARBOHYD O-linked (Xyl) serine" EXACT UniProt-feature [] xref: DiffAvg: "132.12" xref: DiffFormula: "C 5 H 8 N 0 O 4" xref: DiffMono: "132.042259" @@ -16630,6 +17332,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: UniProt: "PTM-0598" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] @@ -16645,6 +17348,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00151" is_obsolete: true [Term] @@ -16670,9 +17374,9 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00672 ! S-acylated residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:01155 ! lipoconjugated residue +xref: UniProt: "PTM-0283" +is_a: MOD:02005 ! S-acylated L-cysteine +is_a: MOD:02006 ! S-stearoylated residue [Term] id: MOD:00817 @@ -16692,16 +17396,18 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0026" is_a: MOD:00601 ! cyclized residue is_a: MOD:01115 ! isoprenylated tryptophan [Term] id: MOD:00818 name: glycosylphosphatidylinositolated residue -def: "A protein modification that effectively converts a residue to a glycosylphosphatidylinositolethanolamidated." [PubMed:12643538, UniMod:394#C-term] -synonym: "glycosylphosphatidylinositol" RELATED UniMod-description [] -synonym: "GPIanchor" RELATED UniMod-interim [] +def: "A protein modification that effectively converts a residue to a glycosylphosphatidylinositolethanolamidated." [PubMed:12643538, Unimod:394#C-term] +synonym: "glycosylphosphatidylinositol" RELATED Unimod-description [] +synonym: "GPIanchor" RELATED Unimod-interim [] synonym: "GPIRes" EXACT PSI-MOD-label [] +synonym: "LIPID GPI-anchor amidated carboxyl end" EXACT UniProt-feature [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" @@ -16711,6 +17417,8 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:394" +xref: UniProt: "PTM-0139" is_a: MOD:00764 ! glycoconjugated residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:01155 ! lipoconjugated residue @@ -16766,8 +17474,8 @@ xref: Origin: "D, G" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02043 ! crosslinked L-aspartic acid residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01882 ! 5-imidazolinone ring crosslinked residues (Gly) [Term] @@ -16791,7 +17499,7 @@ xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00901 ! modified L-alanine residue +is_a: MOD:02040 ! crosslinked L-alanine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16815,7 +17523,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00911 ! modified L-leucine residue +is_a: MOD:02050 ! crosslinked L-leucine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16839,13 +17547,13 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00913 ! modified L-methionine residue +is_a: MOD:02052 ! crosslinked L-methionine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00824 name: dehydroalanine (Tyr) -def: "A protein modification that effectively converts an L-tyrosine residue to dehydroalanine." [PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:6838602, PubMed:7947813, PubMed:8239649, RESID:AA0181#TYR, UniMod:400] +def: "A protein modification that effectively converts an L-tyrosine residue to dehydroalanine." [PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:6838602, PubMed:7947813, PubMed:8239649, RESID:AA0181#TYR, Unimod:400] comment: incidental to RESID:AA0178 synonym: "2,3-didehydroalanine" EXACT RESID-alternate [] synonym: "2-aminoacrylic acid" EXACT RESID-alternate [] @@ -16864,6 +17572,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:400" +xref: UniProt: "PTM-0647" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01168 ! dehydroalanine @@ -16888,7 +17598,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00914 ! modified L-phenylalanine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16912,7 +17622,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16936,7 +17646,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16960,7 +17670,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00918 ! modified L-tryptophan residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -16984,8 +17694,8 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00914 ! modified L-phenylalanine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -17010,6 +17720,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0219" is_a: MOD:01417 ! monomethylated proline is_a: MOD:01462 ! N-methylated proline is_a: MOD:01680 ! alpha-amino monomethylated residue @@ -17021,6 +17732,7 @@ subset: PSI-MOD-slim synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "N4GlcNAcAsn" EXACT PSI-MOD-label [] +synonym: "CARBOHYD N-linked (GlcNAc) asparagine" EXACT UniProt-feature [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" @@ -17030,7 +17742,8 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +xref: UniProt: "PTM-0527" +is_a: MOD:00448 ! mono-N-acetylaminoglucosylated residue is_a: MOD:01674 ! N4-(N-acetylamino)hexosyl-L-asparagine [Term] @@ -17047,6 +17760,7 @@ synonym: "N4-glycosyl-L-asparagine" EXACT RESID-alternate [] synonym: "N4-glycosylasparagine" EXACT RESID-alternate [] synonym: "N4GalNAcAsn" EXACT PSI-MOD-label [] +synonym: "CARBOHYD N-linked (GalNAc) asparagine" EXACT UniProt-feature [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" @@ -17056,7 +17770,8 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00563 ! N-acetylaminogalactosylated residue +xref: UniProt: "PTM-0512" +is_a: MOD:00563 ! mono-N-acetylaminogalactosylated residue is_a: MOD:01674 ! N4-(N-acetylamino)hexosyl-L-asparagine [Term] @@ -17072,6 +17787,7 @@ synonym: "N4-glycosyl-L-asparagine" EXACT RESID-alternate [] synonym: "N4-glycosylasparagine" EXACT RESID-alternate [] synonym: "N4GlcAsn" EXACT PSI-MOD-label [] +synonym: "CARBOHYD N-linked (Glc) asparagine" EXACT UniProt-feature [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" @@ -17081,8 +17797,8 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00433 ! glucosylated residue -is_a: MOD:00761 ! monohexosylated (Hex1) +xref: UniProt: "PTM-0517" +is_a: MOD:00433 ! monoglucosylated residue is_a: MOD:01346 ! N4-hexosylated asparagine [Term] @@ -17098,6 +17814,7 @@ synonym: "O3-(2-acetamido-2-deoxy-beta-D-fucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O3-(N-acetylfucosaminyl)serine" EXACT RESID-alternate [] synonym: "OFucNAcSer" EXACT PSI-MOD-label [] +synonym: "CARBOHYD O-linked (FucNAc) serine" EXACT UniProt-feature [] xref: DiffAvg: "187.19" xref: DiffFormula: "C 8 H 13 N 1 O 4" xref: DiffMono: "187.084458" @@ -17107,26 +17824,27 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0553" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00835 name: L-3-oxoalanine (Ser) -def: "A protein modification that effectively converts an L-serine residue to L-oxoalanine." [DeltaMass:349, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9276974, PubMed:9478923, RESID:AA0185#SER, UniMod:401#S] +def: "A protein modification that effectively converts an L-serine residue to L-oxoalanine." [DeltaMass:349, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9276974, PubMed:9478923, RESID:AA0185#SER, Unimod:401#S] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxopropionic acid" EXACT RESID-alternate [] synonym: "C(alpha)-formylglycine" RELATED RESID-misnomer [] -synonym: "dehydrogenated serine residue" RELATED UniMod-description [] +synonym: "dehydrogenated serine residue" RELATED Unimod-description [] synonym: "Didehydro" RELATED PSI-MS-label [] -synonym: "formylglycine" RELATED UniMod-alternate [] +synonym: "formylglycine" RELATED Unimod-alternate [] synonym: "formylglycine (from serine)" EXACT DeltaMass-label [] synonym: "L-3-oxoalanine" EXACT RESID-name [] synonym: "L-amino-malonic acid semialdehyde" EXACT RESID-alternate [] synonym: "L-aminomalonaldehydic acid" EXACT RESID-alternate [] synonym: "L-serinesemialdehyde" RELATED RESID-misnomer [] synonym: "MOD_RES 3-oxoalanine (Ser)" EXACT UniProt-feature [] -synonym: "oxoalanine" RELATED UniMod-alternate [] +synonym: "oxoalanine" RELATED Unimod-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" @@ -17136,6 +17854,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:401" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01169 ! L-3-oxoalanine is_a: MOD:01888 ! didehydrogenated residue @@ -17158,10 +17877,10 @@ [Term] id: MOD:00838 name: 3x(2)H labeled L-leucine -def: "A protein modification that effectively substitutes three (1)H protium atoms with three (2)H deuterium atoms to produce 3x(2)H labeled L-leucine." [UniMod:262#L] +def: "A protein modification that effectively substitutes three (1)H protium atoms with three (2)H deuterium atoms to produce 3x(2)H labeled L-leucine." [Unimod:262#L] synonym: "D(H)3Leu" EXACT PSI-MOD-label [] synonym: "Label:2H(3)" RELATED PSI-MS-label [] -synonym: "Trideuteration" RELATED UniMod-description [] +synonym: "Trideuteration" RELATED Unimod-description [] xref: DiffAvg: "3.02" xref: DiffFormula: "(1)H -3 (2)H 3" xref: DiffMono: "3.018830" @@ -17171,6 +17890,7 @@ xref: Origin: "L" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:262" is_a: MOD:00585 ! deuterium trisubstituted residue is_a: MOD:00911 ! modified L-leucine residue @@ -17272,7 +17992,7 @@ [Term] id: MOD:00852 name: 1x(18)O labeled deamidated residue -def: "A protein modification that effectively replaces a carboxamido group with a carboxyl group labeled with one (18)O." [PubMed:8382902, UniMod:366] +def: "A protein modification that effectively replaces a carboxamido group with a carboxyl group labeled with one (18)O." [PubMed:8382902, Unimod:366] subset: PSI-MOD-slim xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" @@ -17283,6 +18003,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:366" is_a: MOD:00851 ! (18)O labeled deamidated residue [Term] @@ -17323,7 +18044,7 @@ [Term] id: MOD:00855 name: N6,N6,N6-trimethyl-L-lysine (from L-lysinium residue) -def: "A protein modification that effectively converts an L-lysinium (N6-protonated L-lysine) residue to an N6,N6,N6-trimethyl-L-lysine." [DeltaMass:0, OMSSA:15, PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, UniMod:37#K] +def: "A protein modification that effectively converts an L-lysinium (N6-protonated L-lysine) residue to an N6,N6,N6-trimethyl-L-lysine." [DeltaMass:0, OMSSA:15, PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, Unimod:37#K] comment: For amino acids residues, amine trimethylation can effectively only be accomplished with an aminium, protonated primary amino, group. This process accounts only for trimethylation and not protonation. The alternative N6Me3+Lys process (MOD:00083) accounts for both protonation and trimethylation. subset: PSI-MOD-slim synonym: "N6Me3Lys" EXACT PSI-MOD-label [] @@ -17338,6 +18059,7 @@ xref: Origin: "MOD:00854" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:37" is_a: MOD:00430 ! trimethylated residue relationship: derives_from MOD:00854 ! protonated L-lysine (L-lysinium) residue @@ -17362,7 +18084,7 @@ [Term] id: MOD:00857 name: N,N,N-trimethyl-L-alanine (from L-alaninium) -def: "A protein modification that effectively converts an L-alaninium (protonated L-alanine) residue to an N,N,N-trimethyl-L-alanine." [PubMed:12590383, PubMed:332162, PubMed:3979397, PubMed:6778808, PubMed:7715456, UniMod:37#A] +def: "A protein modification that effectively converts an L-alaninium (protonated L-alanine) residue to an N,N,N-trimethyl-L-alanine." [PubMed:12590383, PubMed:332162, PubMed:3979397, PubMed:6778808, PubMed:7715456, Unimod:37#A] comment: For amino acids residues, amine trimethylation can effectively only be accomplished with an aminium, protonated primary amino, group. This process accounts only for trimethylation and not protonation. The alternative N2Me3+Ala process (MOD:00071) accounts for both protonation and trimethylation. subset: PSI-MOD-slim synonym: "N2Me3Ala" EXACT PSI-MOD-label [] @@ -17376,6 +18098,7 @@ xref: Origin: "MOD:00856" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:37" is_a: MOD:01687 ! alpha-amino trimethylated residue relationship: derives_from MOD:00856 ! protonated L-alanine (L-alaninium) residue @@ -17396,6 +18119,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0113" is_a: MOD:00862 ! D-alanine is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01161 ! deoxygenated residue @@ -17461,6 +18185,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0310" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00917 ! modified L-threonine residue @@ -17485,8 +18210,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:00865 @@ -17504,6 +18229,7 @@ xref: Origin: "D" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0322" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00904 ! modified L-aspartic acid residue @@ -17521,6 +18247,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0024" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00678 ! hydroxylated proline @@ -17542,7 +18269,6 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00007 ! selenium substitution for sulfur is_a: MOD:01627 ! L-cysteinyl-L-selenocysteine [Term] @@ -17577,16 +18303,17 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00010 ! L-alanine residue +xref: UniProt: "PTM-0314" is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02088 ! natural, standard, encoded residue substitution [Term] id: MOD:00870 name: phenyl isocyanate derivatized residue -def: "A protein modification produced by formation of an adduct with phenyl isocyanate." [UniMod:411] -comment: From UniMod with no citation. +def: "A protein modification produced by formation of an adduct with phenyl isocyanate." [Unimod:411] +comment: From Unimod with no citation. subset: PSI-MOD-slim -synonym: "phenyl isocyanate" RELATED UniMod-description [] +synonym: "phenyl isocyanate" RELATED Unimod-description [] synonym: "Phenylisocyanate" RELATED PSI-MS-label [] xref: DiffAvg: "119.12" xref: DiffFormula: "C 7 H 5 N 1 O 1" @@ -17597,15 +18324,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:411" is_a: MOD:00840 ! isocyanate reagent derivatized residue [Term] id: MOD:00871 name: (2)H5-phenyl isocyanate derivatized residue -def: "A protein modification produced by formation of an adduct with (2)H5-phenyl isocyanate." [UniMod:412] -comment: From UniMod with no citation. +def: "A protein modification produced by formation of an adduct with (2)H5-phenyl isocyanate." [Unimod:412] +comment: From Unimod with no citation. subset: PSI-MOD-slim -synonym: "d5-phenyl isocyanate" RELATED UniMod-description [] +synonym: "d5-phenyl isocyanate" RELATED Unimod-description [] synonym: "Phenylisocyanate:2H(5)" RELATED PSI-MS-label [] xref: DiffAvg: "124.07" xref: DiffFormula: "C 7 (2)H 5 N 1 O 1" @@ -17616,15 +18344,16 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00870 ! phenyl isocyanate derivatized residue +xref: Unimod: "Unimod:412" +relationship: derives_from MOD:00870 ! phenyl isocyanate derivatized residue is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] id: MOD:00872 name: L-isoglutamyl monoglutamic acid -def: "OBSOLETE because redundant and identical to MOD:01970. Remap to MOD:01970." [PubMed:10747868, PubMed:15525938, PubMed:1680872, RESID:AA0202#var, UniMod:450] -synonym: "Glu" RELATED UniMod-interim [] -synonym: "monoglutamyl" RELATED UniMod-description [] +def: "OBSOLETE because redundant and identical to MOD:01970. Remap to MOD:01970." [PubMed:10747868, PubMed:15525938, PubMed:1680872, RESID:AA0202#var, Unimod:450] +synonym: "Glu" RELATED Unimod-interim [] +synonym: "monoglutamyl" RELATED Unimod-description [] synonym: "N alpha -(gamma-Glutamyl)-Glu" EXACT DeltaMass-label [] xref: DiffAvg: "129.12" xref: DiffFormula: "C 5 H 7 N 1 O 3" @@ -17635,14 +18364,16 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:01970" +xref: Unimod: "Unimod:450" is_obsolete: true [Term] id: MOD:00873 name: L-isoglutamyl diglutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamic acid, forming an isopeptide bond with a diglutamic acid." [DeltaMass:0, PubMed:10747868, PubMed:1680872, RESID:AA0202#var, UniMod:451] -synonym: "diglutamyl" RELATED UniMod-description [] -synonym: "GluGlu" RELATED UniMod-interim [] +def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamic acid, forming an isopeptide bond with a diglutamic acid." [DeltaMass:0, PubMed:10747868, PubMed:1680872, RESID:AA0202#var, Unimod:451] +synonym: "diglutamyl" RELATED Unimod-description [] +synonym: "GluGlu" RELATED Unimod-interim [] xref: DiffAvg: "258.23" xref: DiffFormula: "C 10 H 14 N 2 O 6" xref: DiffMono: "258.085186" @@ -17652,16 +18383,17 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:451" is_a: MOD:00207 ! L-isoglutamyl-polyglutamic acid [Term] id: MOD:00874 name: L-isoglutamyl triglutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamyl-glutamic acid, forming an isopeptide bond with a triglutamic acid." [DeltaMass:0, PubMed:10747868, PubMed:1680872, RESID:AA0202#var, UniMod:452] +def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamyl-glutamic acid, forming an isopeptide bond with a triglutamic acid." [DeltaMass:0, PubMed:10747868, PubMed:1680872, RESID:AA0202#var, Unimod:452] comment: From DeltaMass: Average Mass: 388. -synonym: "GluGluGlu" RELATED UniMod-interim [] +synonym: "GluGluGlu" RELATED Unimod-interim [] synonym: "N alpha -(gamma-Glutamyl)-Glu3" EXACT DeltaMass-label [] -synonym: "triglutamyl" RELATED UniMod-description [] +synonym: "triglutamyl" RELATED Unimod-description [] xref: DiffAvg: "387.35" xref: DiffFormula: "C 15 H 21 N 3 O 9" xref: DiffMono: "387.127779" @@ -17671,14 +18403,15 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:452" is_a: MOD:00207 ! L-isoglutamyl-polyglutamic acid [Term] id: MOD:00875 name: L-isoglutamyl tetraglutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamyl-glutamyl-glutamic acid, forming an isopeptide bond with a tetraglutamic acid." [PubMed:10747868, PubMed:1680872, RESID:AA0202#var, UniMod:453] -synonym: "GluGluGluGlu" RELATED UniMod-interim [] -synonym: "tetraglutamyl" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl glutamyl-glutamyl-glutamyl-glutamic acid, forming an isopeptide bond with a tetraglutamic acid." [PubMed:10747868, PubMed:1680872, RESID:AA0202#var, Unimod:453] +synonym: "GluGluGluGlu" RELATED Unimod-interim [] +synonym: "tetraglutamyl" RELATED Unimod-description [] xref: DiffAvg: "516.46" xref: DiffFormula: "C 20 H 28 N 4 O 12" xref: DiffMono: "516.170372" @@ -17688,14 +18421,15 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:453" is_a: MOD:00207 ! L-isoglutamyl-polyglutamic acid [Term] id: MOD:00876 name: hexosaminylated residue -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexosamine sugar group through a glycosidic bond." [UniMod:454] +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexosamine sugar group through a glycosidic bond." [Unimod:454] synonym: "HexN" RELATED PSI-MS-label [] -synonym: "Hexosamine" RELATED UniMod-description [] +synonym: "Hexosamine" RELATED Unimod-description [] synonym: "Hexosamines (GalN, GlcN)" EXACT DeltaMass-label [] xref: DiffAvg: "161.16" xref: DiffFormula: "C 6 H 11 N 1 O 4" @@ -17706,14 +18440,15 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:454" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00877 name: imidoester crosslink dimethyl pimelimidate singly attached -def: "dimethyl pimelimidate modification from UniMod" [UniMod:455, URL:http\://www.piercenet.com/files/0668ss5.pdf] -synonym: "One end of crosslink attached, one end free" RELATED UniMod-description [] -synonym: "Xlink:DMP-s" RELATED UniMod-interim [] +def: "dimethyl pimelimidate modification from Unimod" [Unimod:455, URL:http\://www.piercenet.com/files/0668ss5.pdf] +synonym: "One end of crosslink attached, one end free" RELATED Unimod-description [] +synonym: "Xlink:DMP-s" RELATED Unimod-interim [] xref: DiffAvg: "154.21" xref: DiffFormula: "C 8 H 14 N 2 O 1" xref: DiffMono: "154.110613" @@ -17723,14 +18458,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:455" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00878 name: imidoester crosslink dimethyl pimelimidate doubly attached -def: "dimethyl pimelimidate modification from UniMod - Mechanism of the reaction of imidoesters with amines" [PubMed:7171546, UniMod:456, URL:http\://dx.doi.org/10.1021/ja00877a017] -synonym: "Both ends of crosslink attached to same peptide" RELATED UniMod-description [] -synonym: "Xlink:DMP" RELATED UniMod-interim [] +def: "dimethyl pimelimidate modification from Unimod - Mechanism of the reaction of imidoesters with amines" [PubMed:7171546, Unimod:456, URL:http\://dx.doi.org/10.1021/ja00877a017] +synonym: "Both ends of crosslink attached to same peptide" RELATED Unimod-description [] +synonym: "Xlink:DMP" RELATED Unimod-interim [] xref: DiffAvg: "122.17" xref: DiffFormula: "C 7 H 10 N 2" xref: DiffMono: "122.084398" @@ -17740,14 +18476,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:456" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00879 name: naphthalene-2,3-dicarboxaldehyde -def: "modification from UniMod" [PubMed:2081203, UniMod:457] -synonym: "naphthalene-2,3-dicarboxaldehyde" RELATED UniMod-description [] -synonym: "NDA" RELATED UniMod-interim [] +def: "modification from Unimod" [PubMed:2081203, Unimod:457] +synonym: "naphthalene-2,3-dicarboxaldehyde" RELATED Unimod-description [] +synonym: "NDA" RELATED Unimod-interim [] xref: DiffAvg: "175.19" xref: DiffFormula: "C 13 H 5 N 1" xref: DiffMono: "175.042199" @@ -17757,13 +18494,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:457" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00880 name: 6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized residue -def: "A protein modification produced by formation of an adduct with 6x(13)C labeled 4-sulfophenyl isothiocyanate." [PubMed:15536630, PubMed:16526082, UniMod:464] -synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED UniMod-description [] +def: "A protein modification produced by formation of an adduct with 6x(13)C labeled 4-sulfophenyl isothiocyanate." [PubMed:15536630, PubMed:16526082, Unimod:464] +synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED Unimod-description [] synonym: "SPITC:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "220.99" xref: DiffFormula: "(12)C 1 (13)C 6 H 5 N 1 O 3 S 2" @@ -17774,13 +18512,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00584 ! 4-sulfophenyl isothiocyanate derivatized residue +xref: Unimod: "Unimod:464" +relationship: derives_from MOD:00584 ! 4-sulfophenyl isothiocyanate derivatized residue is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:00881 name: N-reductive amination-D -def: "OBSOLETE because UniMod entry 465 megerd with 199. Remap to MOD:00552 DiMethyl-CH2D." [PubMed:9252331, UniMod:465] +def: "OBSOLETE because Unimod entry 465 megerd with 199. Remap to MOD:00552 DiMethyl-CH2D." [PubMed:9252331, Unimod:465] xref: DiffAvg: "32.06" xref: DiffFormula: "C 2 (2)H 4" xref: DiffMono: "32.056407" @@ -17790,16 +18529,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00552" +xref: Unimod: "Unimod:465" is_obsolete: true [Term] id: MOD:00882 name: S-(2-aminoethyl)cysteine (Ser) -def: "A protein modification that effectively converts an L-serine residue to S-(2-aminoethyl)cysteine." [DeltaMass:171, PubMed:12923550, UniMod:472#S] +def: "A protein modification that effectively converts an L-serine residue to S-(2-aminoethyl)cysteine." [DeltaMass:171, PubMed:12923550, Unimod:472#S] comment: From DeltaMass: Average Mass: 146 Abbreviation:-AECys_ Formula:C5H10O2N1S1 Monoisotopic Mass Change:146.051 Average Mass Change:146.214 References:PE Sciex. -synonym: "AEC-MAEC" RELATED UniMod-interim [] +synonym: "AEC-MAEC" RELATED Unimod-interim [] synonym: "Aminoethyl Cysteinyl (AECys)" EXACT DeltaMass-label [] -synonym: "aminoethylcysteine" RELATED UniMod-description [] +synonym: "aminoethylcysteine" RELATED Unimod-description [] xref: DiffAvg: "59.13" xref: DiffFormula: "C 2 H 5 N 1 O -1 S 1" xref: DiffMono: "59.019356" @@ -17809,17 +18550,18 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:472" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00883 name: C1-amidated residue -def: "A protein modification that effectively replaces a 1-carboxyl group (usually referred to as the alpha-carboxyl) with a carboxamido group." [DeltaMass:0, OMSSA:25, UniMod:2] +def: "A protein modification that effectively replaces a 1-carboxyl group (usually referred to as the alpha-carboxyl) with a carboxamido group." [DeltaMass:0, OMSSA:25, Unimod:2] comment: The normal biological process involves formation of an amide of an amino acid residue in a peptide sequence where it is followed by a glycine and two basic residues, either arginine or lysine, although in some taxa only one basic residue is required. The peptide is cleaved after the basic residues, glycine is oxidized to hydroxyglycine, which decomposes to release a carboxamide C-terminal [JSG]. subset: PSI-MOD-slim synonym: "alpha-amidated residue" EXACT PSI-MOD-alternate [] synonym: "Amidated" RELATED PSI-MS-label [] -synonym: "Amidation" RELATED UniMod-description [] +synonym: "Amidation" RELATED Unimod-description [] synonym: "Amide formation (C terminus)" EXACT DeltaMass-label [] synonym: "ctermamide" EXACT OMSSA-label [] synonym: "ResN" EXACT PSI-MOD-label [] @@ -17832,6 +18574,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:2" is_a: MOD:00674 ! amidated residue [Term] @@ -17864,8 +18607,8 @@ [Term] id: MOD:00886 name: 6'-chloro-L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to 6'-chloro-L-tryptophan." [PubMed:9033387, RESID:AA0180, UniMod:936#W] -comment: The UniMod:340 cross-reference to RESID:AA0180 is incorrect. RESID:AA0180 should be cross-referenced by UniMod:936 [JSG]. +def: "A protein modification that effectively converts an L-tryptophan residue to 6'-chloro-L-tryptophan." [PubMed:9033387, RESID:AA0180, Unimod:936#W] +comment: The Unimod:340 cross-reference to RESID:AA0180 is incorrect. RESID:AA0180 should be cross-referenced by Unimod:936 [JSG]. synonym: "(2S)-2-amino-3-(6-chloro-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "6'-chloro-L-tryptophan" EXACT RESID-name [] synonym: "6'-ClTrp" EXACT PSI-MOD-label [] @@ -17879,6 +18622,8 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:936" +xref: UniProt: "PTM-0052" is_a: MOD:01913 ! monochlorinated L-tryptophan [Term] @@ -17909,7 +18654,7 @@ [Term] id: MOD:00889 name: N,N-dimethyl-L-proline (from L-prolinium) -def: "A protein modification that effectively converts an L-prolinium (charged L-proline) residue to N,N-dimethyl-L-proline." [UniMod:36#P] +def: "A protein modification that effectively converts an L-prolinium (charged L-proline) residue to N,N-dimethyl-L-proline." [Unimod:36#P] subset: PSI-MOD-slim xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" @@ -17921,13 +18666,17 @@ xref: Origin: "MOD:00888" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00075 ! N,N-dimethyl-L-proline +xref: Unimod: "Unimod:36" +relationship: derives_from MOD:00075 ! N,N-dimethyl-L-proline relationship: derives_from MOD:00888 ! protonated L-proline (L-prolinium) residue +is_a: MOD:00712 ! methylated proline +is_a: MOD:00710 ! protonated-dimethylated residue +is_a: MOD:01686 ! alpha-amino dimethylated residue [Term] id: MOD:00890 name: phosphorylated L-histidine -def: "A protein modification that effectively converts an L-histidine residue to a phosphorylated L-histidine, such as pros-phosphohistidine, or tele-phosphohistidine." [OMSSA:192, UniMod:21#H] +def: "A protein modification that effectively converts an L-histidine residue to a phosphorylated L-histidine, such as pros-phosphohistidine, or tele-phosphohistidine." [OMSSA:192, Unimod:21#H] subset: PSI-MOD-slim synonym: "mod192" EXACT OMSSA-label [] synonym: "NPhosHis" EXACT PSI-MOD-label [] @@ -17942,6 +18691,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:21" +xref: UniProt: "PTM-0252" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01456 ! N-phosphorylated residue @@ -17970,6 +18721,7 @@ def: "A protein modification that effectively converts an L-cysteine residue to D-serine." [PubMed:18025465, PubMed:6893271, RESID:AA0195#CYS] synonym: "(R)-2-amino-3-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "D-serine" EXACT RESID-name [] +synonym: "MOD_RES D-serine (Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-16.06" xref: DiffFormula: "C 0 H 0 N 0 O 1 S -1" xref: DiffMono: "-15.977156" @@ -17979,6 +18731,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0309" is_a: MOD:00891 ! D-serine is_a: MOD:00905 ! modified L-cysteine residue @@ -18002,6 +18755,16 @@ name: FAD modified residue def: "A protein modification that effectively results from forming an adduct with a compound containing a flavin adenine dinucleotide (FAD) group." [PubMed:18688235] subset: PSI-MOD-slim +synonym: "FADRes" EXACT PSI-MOD-label [] +xref: DiffAvg: "783.54" +xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2" +xref: DiffMono: "783.141485" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" is_a: MOD:00697 ! flavin modified residue is_a: MOD:00861 ! phosphorus containing modified residue @@ -18010,6 +18773,16 @@ name: FMN modified residue def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group." [PubMed:18688235] subset: PSI-MOD-slim +synonym: "FMNRes" EXACT PSI-MOD-label [] +xref: DiffAvg: "none" +xref: DiffFormula: "none" +xref: DiffMono: "none" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" is_a: MOD:00697 ! flavin modified residue is_a: MOD:00861 ! phosphorus containing modified residue @@ -18033,10 +18806,10 @@ [Term] id: MOD:00898 name: S-(sn-1-2-oleoyl-3-palmitoyl-glycerol)cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(sn-1-2-oleoyl-3-palmitoyl-glycerol)cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107#var, UniMod:377] +def: "A protein modification that effectively converts an L-cysteine residue to S-(sn-1-2-oleoyl-3-palmitoyl-glycerol)cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107#var, Unimod:377] comment: Incidental to RESID:AA0060. synonym: "Diacylglycerol" RELATED PSI-MS-label [] -synonym: "diacylglycerol" RELATED UniMod-description [] +synonym: "diacylglycerol" RELATED Unimod-description [] xref: DiffAvg: "576.95" xref: DiffFormula: "C 37 H 68 N 0 O 4 S 0" xref: DiffMono: "576.511761" @@ -18046,6 +18819,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:377" is_a: MOD:00116 ! S-diacylglycerol-L-cysteine [Term] @@ -18260,16 +19034,16 @@ [Term] id: MOD:00921 -name: new uncategorized UniMod entries -def: "New uncategorized UniMod. OBSOLETE because organizational use is no longer required." [PubMed:18688235] +name: new uncategorized Unimod entries +def: "New uncategorized Unimod. OBSOLETE because organizational use is no longer required." [PubMed:18688235] is_obsolete: true [Term] id: MOD:00922 name: Cy3 CyDye DIGE Fluor saturation dye -def: "modification from UniMod Chemical derivative" [UniMod:494] -synonym: "Cy3 CyDye DIGE Fluor saturation dye" RELATED UniMod-description [] -synonym: "CyDye-Cy3" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:494] +synonym: "Cy3 CyDye DIGE Fluor saturation dye" RELATED Unimod-description [] +synonym: "CyDye-Cy3" RELATED Unimod-interim [] xref: DiffAvg: "672.84" xref: DiffFormula: "C 37 H 44 N 4 O 6 S 1" xref: DiffMono: "672.298156" @@ -18279,15 +19053,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:494" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00923 name: Cy5 CyDye DIGE Fluor saturation dye -def: "modification from UniMod Chemical derivative" [UniMod:495] -synonym: "Cy5 CyDye DIGE Fluor saturation dye" RELATED UniMod-description [] -synonym: "CyDye-Cy5" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [Unimod:495] +synonym: "Cy5 CyDye DIGE Fluor saturation dye" RELATED Unimod-description [] +synonym: "CyDye-Cy5" RELATED Unimod-interim [] xref: DiffAvg: "684.85" xref: DiffFormula: "C 38 H 44 N 4 O 6 S 1" xref: DiffMono: "684.298156" @@ -18297,6 +19072,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:495" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue @@ -18317,18 +19093,20 @@ xref: Origin: "K, T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0326" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:00925 name: heptosylated residue -def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a heptose sugar group through a glycosidic bond." [UniMod:490] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a heptose sugar group through a glycosidic bond." [Unimod:490] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -18338,14 +19116,15 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00926 name: Bisphenol A diglycidyl ether derivative -def: "Modification from UniMod Non-standard residue. OBSOLETE because not an amino acid modification. From UniMod not an approved entry." [PubMed:11225353, UniMod:493] -synonym: "BADGE" RELATED UniMod-interim [] -synonym: "Bisphenol A diglycidyl ether derivative" RELATED UniMod-description [] +def: "Modification from Unimod Non-standard residue. OBSOLETE because not an amino acid modification. From Unimod not an approved entry." [PubMed:11225353, Unimod:493] +synonym: "BADGE" RELATED Unimod-interim [] +synonym: "Bisphenol A diglycidyl ether derivative" RELATED Unimod-description [] xref: DiffAvg: "340.42" xref: DiffFormula: "C 21 H 24 O 4" xref: DiffMono: "340.167459" @@ -18355,13 +19134,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:493" is_obsolete: true [Term] id: MOD:00927 name: 2x(13)C,4x(2)H labeled dimethylated residue -def: "A protein modification that effectively replaces two hydrogen atoms of a residue containing common isotopes with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated residue." [PubMed:16335955, PubMed:3802193, UniMod:510] -synonym: "DiMethyl-C13HD2" RELATED UniMod-description [] +def: "A protein modification that effectively replaces two hydrogen atoms of a residue containing common isotopes with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated residue." [PubMed:16335955, PubMed:3802193, Unimod:510] +synonym: "DiMethyl-C13HD2" RELATED Unimod-description [] synonym: "Dimethyl:2H(4)13C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "34.06" xref: DiffFormula: "(13)C 2 (2)H 4" @@ -18372,16 +19152,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: UnMod: "Unimod:510" is_a: MOD:00839 ! (2)H deuterium labeled residue is_a: MOD:00842 ! (13)C labeled residue [Term] id: MOD:00928 name: [3-(2,5)-dioxopyrrolidin-1-yloxycarbonyl)-propyl]dimethyloctylammonium -def: "modification from UniMod Chemical derivative" [PubMed:16771548, UniMod:513] +def: "modification from Unimod Chemical derivative" [PubMed:16771548, Unimod:513] comment: Should have children for K and X-N-term [JSG]. -synonym: "[3-(2,5)-Dioxopyrrolidin-1-yloxycarbonyl)-propyl]dimethyloctylammonium" RELATED UniMod-description [] -synonym: "C8-QAT" RELATED UniMod-interim [] +synonym: "[3-(2,5)-Dioxopyrrolidin-1-yloxycarbonyl)-propyl]dimethyloctylammonium" RELATED Unimod-description [] +synonym: "C8-QAT" RELATED Unimod-interim [] xref: DiffAvg: "227.39" xref: DiffFormula: "C 14 H 29 N 1 O 1" xref: DiffMono: "227.224915" @@ -18391,15 +19172,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:513" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00929 name: lactose glycated lysine -def: "A modification produced in a non-enzymatic reaction between a lactose carbonyl group and an L-lysine to form a Schiff-base or an Amadori ketosamine lysine adduct." [PubMed:9606156, UniMod:512] +def: "A modification produced in a non-enzymatic reaction between a lactose carbonyl group and an L-lysine to form a Schiff-base or an Amadori ketosamine lysine adduct." [PubMed:9606156, Unimod:512] comment: The term lactosylation used with this meaning is a misnomer [JSG]. -synonym: "Hex(2)" RELATED UniMod-interim [] -synonym: "Lactosylation" RELATED UniMod-description [] +synonym: "Hex(2)" RELATED Unimod-interim [] +synonym: "Lactosylation" RELATED Unimod-description [] +synonym: "CARBOHYD N-linked (Lac) (glycation) lysine" EXACT UniProt-feature [] xref: DiffAvg: "342.30" xref: DiffFormula: "C 12 H 22 O 11" xref: DiffMono: "342.116212" @@ -18409,13 +19192,15 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:512" +xref: UniProt: "PTM-0511" is_a: MOD:00767 ! glycated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00930 name: propyl-NAG tyrosine adduct -def: "tyrosine adduct with substrate analog inhibitor 1,2-dideoxy-2'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2'-thiazoline." [PubMed:15795231, UniMod:514] +def: "tyrosine adduct with substrate analog inhibitor 1,2-dideoxy-2'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2'-thiazoline." [PubMed:15795231, Unimod:514] xref: DiffAvg: "232.27" xref: DiffFormula: "C 9 H 14 N 1 O 4 S 1" xref: DiffMono: "232.064354" @@ -18425,15 +19210,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:514" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00931 name: Michael addition of t-butyl hydroxylated BHT (BHTOH) to C, H or K -def: "modification from UniMod Other - BHTOH is formed upon metabolism of BHT with P450 enzymes. The BHTOH is further metabolized to its quinone methide (electrophile) which reacts with -SH and -NH2 groups" [PubMed:11085420, UniMod:498] -synonym: "BHTOH" RELATED UniMod-interim [] -synonym: "Michael addition of t-butyl hydroxylated BHT (BHTOH) to C, H or K" RELATED UniMod-description [] +def: "modification from Unimod Other - BHTOH is formed upon metabolism of BHT with P450 enzymes. The BHTOH is further metabolized to its quinone methide (electrophile) which reacts with -SH and -NH2 groups" [PubMed:11085420, Unimod:498] +synonym: "BHTOH" RELATED Unimod-interim [] +synonym: "Michael addition of t-butyl hydroxylated BHT (BHTOH) to C, H or K" RELATED Unimod-description [] xref: DiffAvg: "234.34" xref: DiffFormula: "C 15 H 22 O 2" xref: DiffMono: "234.161980" @@ -18443,13 +19229,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:498" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00932 name: IDBEST tag for quantitation -def: "modification from UniMod Isotopic label" [PubMed:11821862, UniMod:499] -synonym: "Heavy IDBEST tag for quantitation" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label" [PubMed:11821862, Unimod:499] +synonym: "Heavy IDBEST tag for quantitation" RELATED Unimod-description [] synonym: "IGBP:13C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "298.02" xref: DiffFormula: "Br 1 (12)C 10 (13)C 2 H 13 N 2 O 2" @@ -18460,16 +19247,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:499" is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:00933 name: methylglyoxal arginine adduct (+54 amu) -def: "modification from UniMod Chemical derivative - 5-hydro-5-methylimidazol-4-one, arginine methylglyoxal arginine adduct (+54 amu)" [UniMod:319#R] +def: "modification from Unimod Chemical derivative - 5-hydro-5-methylimidazol-4-one, arginine methylglyoxal arginine adduct (+54 amu)" [Unimod:319#R] comment: Ref. Uchida K, Sakai K, Itakura K, Osawa T, Toyokuni S. 1977. Protein modification by lipid peroxidation products: formation of malondialdehyde-derived N(epsilon)-(2-propenol)lysine in proteins. Arch Biochem Biophys. 346(1):45-52. synonym: "Delta:H(2)C(3)O(1)" RELATED PSI-MS-label [] -synonym: "MDA adduct +54" RELATED UniMod-description [] +synonym: "MDA adduct +54" RELATED Unimod-description [] xref: DiffAvg: "54.05" xref: DiffFormula: "C 3 H 2 O 1" xref: DiffMono: "54.010565" @@ -18479,15 +19267,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:319" is_a: MOD:00630 ! C3-H2-O adduct (+54 amu) of malondialdehyde with lysine or methylglyoxal with arginine. is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00934 name: Levuglandinyl - arginine hydroxylactam adduct -def: "modification from UniMod Post-translational" [UniMod:506] -synonym: "Levuglandinyl - arginine hydroxylactam adduct" RELATED UniMod-description [] -synonym: "LG-Hlactam-R" RELATED UniMod-interim [] +def: "modification from Unimod Post-translational" [Unimod:506] +synonym: "Levuglandinyl - arginine hydroxylactam adduct" RELATED Unimod-description [] +synonym: "LG-Hlactam-R" RELATED Unimod-interim [] xref: DiffAvg: "306.40" xref: DiffFormula: "C 19 H 26 N -2 O 5" xref: DiffMono: "306.171876" @@ -18497,6 +19286,7 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:506" is_a: MOD:00846 ! levuglandinyl (prostaglandin H2) adduct is_a: MOD:00902 ! modified L-arginine residue @@ -18504,7 +19294,7 @@ id: MOD:00935 name: methionine oxidation with neutral loss of 64 Da def: "Oxidation of methionine to methionine sulfoxide with neutral loss of CH3SOH." [PubMed:18688235, PubMed:9004526] -comment: Originally created from UniMod:507 that was later deleted. +comment: Originally created from Unimod:507 that was later deleted. xref: DiffAvg: "-64.10" xref: DiffFormula: "C -1 H -4 N 0 O -1 S -1" xref: DiffMono: "-63.998286" @@ -18520,9 +19310,9 @@ [Term] id: MOD:00936 name: Levuglandinyl - hydroxylactam adduct, K and N-term -def: "modification from UniMod Post-translational" [UniMod:504] -synonym: "Levuglandinyl - lysine hydroxylactam adduct" RELATED UniMod-description [] -synonym: "LG-Hlactam-K" RELATED UniMod-interim [] +def: "modification from Unimod Post-translational" [Unimod:504] +synonym: "Levuglandinyl - lysine hydroxylactam adduct" RELATED Unimod-description [] +synonym: "LG-Hlactam-K" RELATED Unimod-interim [] xref: DiffAvg: "348.44" xref: DiffFormula: "C 20 H 28 O 5" xref: DiffMono: "348.193674" @@ -18532,14 +19322,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:504" is_a: MOD:00846 ! levuglandinyl (prostaglandin H2) adduct [Term] id: MOD:00937 name: Levuglandinyl - arginine lactam adduct -def: "modification from UniMod Post-translational" [UniMod:505] -synonym: "Levuglandinyl - arginine lactam adduct" RELATED UniMod-description [] -synonym: "LG-lactam-R" RELATED UniMod-interim [] +def: "modification from Unimod Post-translational" [Unimod:505] +synonym: "Levuglandinyl - arginine lactam adduct" RELATED Unimod-description [] +synonym: "LG-lactam-R" RELATED Unimod-interim [] xref: DiffAvg: "290.40" xref: DiffFormula: "C 19 H 26 N -2 O 4" xref: DiffMono: "290.176961" @@ -18549,15 +19340,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:505" is_a: MOD:00846 ! levuglandinyl (prostaglandin H2) adduct is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00938 name: Levuglandinyl - lactam adduct, K and N-term -def: "modification from UniMod Post-translational" [PubMed:12590383, UniMod:503] -synonym: "Levuglandinyl - lysine lactam adduct" RELATED UniMod-description [] -synonym: "LG-lactam-K" RELATED UniMod-interim [] +def: "modification from Unimod Post-translational" [PubMed:12590383, Unimod:503] +synonym: "Levuglandinyl - lysine lactam adduct" RELATED Unimod-description [] +synonym: "LG-lactam-K" RELATED Unimod-interim [] xref: DiffAvg: "332.44" xref: DiffFormula: "C 20 H 28 O 4" xref: DiffMono: "332.198759" @@ -18567,14 +19359,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:503" is_a: MOD:00846 ! levuglandinyl (prostaglandin H2) adduct [Term] id: MOD:00939 name: hydrolyzed N-methylmaleimide cysteine adduct -def: "modification from UniMod Chemical derivative" [UniMod:500] -synonym: "Nmethylmaleimide+water" RELATED UniMod-interim [] -synonym: "Nmethylmaleimidehydrolysis" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [Unimod:500] +synonym: "Nmethylmaleimide+water" RELATED Unimod-interim [] +synonym: "Nmethylmaleimidehydrolysis" RELATED Unimod-description [] xref: DiffAvg: "129.12" xref: DiffFormula: "C 5 H 7 N 1 O 3" xref: DiffMono: "129.042593" @@ -18584,15 +19377,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:500" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00940 name: 3-methyl-2-pyridyl isocyanate derivatized residue -def: "A protein modification produced by formation of an adduct with 3-methyl-2-pyridyl isocyanate." [PubMed:11078590, UniMod:501] -synonym: "3-methyl-2-pyridyl isocyanate" RELATED UniMod-description [] -synonym: "PyMIC" RELATED UniMod-interim [] +def: "A protein modification produced by formation of an adduct with 3-methyl-2-pyridyl isocyanate." [PubMed:11078590, Unimod:501] +synonym: "3-methyl-2-pyridyl isocyanate" RELATED Unimod-description [] +synonym: "PyMIC" RELATED Unimod-interim [] xref: DiffAvg: "134.14" xref: DiffFormula: "C 7 H 6 N 2 O 1" xref: DiffMono: "134.048013" @@ -18602,14 +19396,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:501" is_a: MOD:00840 ! isocyanate reagent derivatized residue [Term] id: MOD:00941 name: dehydropyrrolizidine alkaloid (dehydroretronecine) derivatized cysteine -def: "modification from UniMod Chemical derivative" [PubMed:12175151, UniMod:488] -synonym: "Dehydropyrrolizidine alkaloid (dehydroretronecine) on cysteines" RELATED UniMod-description [] -synonym: "DHP" RELATED UniMod-interim [] +def: "modification from Unimod Chemical derivative" [PubMed:12175151, Unimod:488] +synonym: "Dehydropyrrolizidine alkaloid (dehydroretronecine) on cysteines" RELATED Unimod-description [] +synonym: "DHP" RELATED Unimod-interim [] xref: DiffAvg: "118.16" xref: DiffFormula: "C 8 H 8 N 1" xref: DiffMono: "118.065674" @@ -18619,17 +19414,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:488" is_a: MOD:00848 ! reagent derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00942 name: (4,4,5,5-(2)H4)-L-lysine -def: "A protein modification that effectively substitutes four (1)H protium atoms with four (2)H deuterium atoms to produce (4,4,5,5-(2)H4)-L-lysine." [OMSSA:180, UniMod:481] +def: "A protein modification that effectively substitutes four (1)H protium atoms with four (2)H deuterium atoms to produce (4,4,5,5-(2)H4)-L-lysine." [OMSSA:180, Unimod:481] comment: For SILAC experiments. -synonym: "4,4,5,5-D4 Lysine" RELATED UniMod-description [] +synonym: "4,4,5,5-D4 Lysine" RELATED Unimod-description [] synonym: "4,4,5,5-tetradeuterolysine" EXACT PSI-MOD-alternate [] -synonym: "Label:2H(4)" RELATED UniMod-interim [] +synonym: "Label:2H(4)" RELATED Unimod-interim [] synonym: "lys-2H4" EXACT OMSSA-label [] xref: DiffAvg: "4.03" xref: DiffFormula: "(1)H -4 (2)H 4" @@ -18640,15 +19436,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:481" is_a: MOD:00837 ! deuterium tetrasubstituted residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00943 name: 4-trimethylammoniumbutanoyl derivatized residue -def: "modification from UniMod Isotopic label" [PubMed:12643539, UniMod:476] -synonym: "4-trimethyllammoniumbutyryl-" RELATED UniMod-description [] -synonym: "TMAB" RELATED UniMod-interim [] +def: "modification from Unimod Isotopic label" [PubMed:12643539, Unimod:476] +synonym: "4-trimethyllammoniumbutyryl-" RELATED Unimod-description [] +synonym: "TMAB" RELATED Unimod-interim [] xref: DiffAvg: "128.19" xref: DiffFormula: "C 7 H 14 N 1 O 1" xref: DiffMono: "128.107539" @@ -18658,14 +19455,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:476" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00944 name: d9-4-trimethylammoniumbutanoyl derivatized residue -def: "modification from UniMod Isotopic label" [UniMod:477] -synonym: "d9-4-trimethyllammoniumbutyryl-" RELATED UniMod-description [] -synonym: "TMAB:2H(9)" RELATED UniMod-interim [] +def: "modification from Unimod Isotopic label" [Unimod:477] +synonym: "d9-4-trimethyllammoniumbutyryl-" RELATED Unimod-description [] +synonym: "TMAB:2H(9)" RELATED Unimod-interim [] xref: DiffAvg: "137.16" xref: DiffFormula: "C 7 (1)H 5 (2)H 9 N 1 O 1" xref: DiffMono: "137.164030" @@ -18675,7 +19473,8 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00943 ! 4-trimethylammoniumbutanoyl derivatized residue +xref: Unimod: "Unimod:477" +relationship: derives_from MOD:00943 ! 4-trimethylammoniumbutanoyl derivatized residue is_a: MOD:01431 ! (2)H deuterium tagged reagent [Term] @@ -18691,6 +19490,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00626" is_obsolete: true [Term] @@ -18709,7 +19509,7 @@ [Term] id: MOD:00948 name: 5'-dephospho -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: -79 xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -18720,7 +19520,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:00949 @@ -18736,12 +19536,13 @@ xref: Origin: "K" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +xref: Remap: "MOD:01933" +is_obsolete: true [Term] id: MOD:00950 name: decomposed carboxymethylated methionine -def: "modification from DeltaMass" [DeltaMass:3] +def: "OBSOLETE because this modification has not been seen/reported on since this original publication in 1994 and carboxymethylation of proteins is common enough for this mass shift to have been seen in the intervening 25+ years. modification from DeltaMass" [DeltaMass:3] comment: From DeltaMass: Average Mass: -48 Average Mass Change:-48 References:Anal. Biochem. Vol 216 No.1 p141 xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -18752,7 +19553,7 @@ xref: Origin: "M" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:00951 @@ -18769,7 +19570,6 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00015 ! L-glutamic acid residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00957 ! modified residue with neutral loss of carbon dioxide is_a: MOD:00960 ! decarboxylated residue @@ -18796,7 +19596,8 @@ xref: Origin: "D, G" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +xref: UniProt: "PTM-0312" +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01628 ! (2-aminosuccinimidyl)acetic acid @@ -18820,7 +19621,7 @@ xref: Origin: "E, S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01977 ! O-(L-isoglutamyl)-L-serine @@ -18846,8 +19647,8 @@ xref: Origin: "H, S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02048 ! crosslinked L-histidine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -18896,7 +19697,7 @@ xref: Origin: "H, R" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_a: MOD:00692 ! uncategorized crosslinked residues [Term] id: MOD:00959 @@ -18979,6 +19780,7 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00462" is_obsolete: true [Term] @@ -19046,12 +19848,12 @@ xref: Origin: "K, K" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_a: MOD:02051 ! crosslinked L-lysine residue [Term] id: MOD:00968 name: CM-Cys vs PAM-Cys -def: "modification from DeltaMass" [DeltaMass:347] +def: "OBSOLETE because this isn't a protein modification, but rather the difference between two known modifications. modification from DeltaMass" [DeltaMass:347] comment: From DeltaMass: Average Mass: 13 Formula:C2H2O2 vs C3H5ON Monoisotopic Mass Change:13.03 Average Mass Change:13.05 Notes:Residual acrylamide in SDS gels can partly label cysteine residues in proteins (propionamido-Cys, PAM-Cys, DeltaMass +71Da; see entry). Subsequent alkylation of protein bands with iodoacetic acid e.g. in preparation for proteomic analysis, will convert remaining free cysteines into carboxymethyl-Cys (CM-Cys, DeltaMass +58Da; see entry). Peptide mass fingerprinting may therefore potentially reveal the same cysteine-containing peptide in two forms, differing in mass by 13Da. The relative ratios of the peaks will depend on the initial degree of labelling with acrylamide. Use of high quality, deionised acrylamide in the SDS gel will minimise modification of cysteine through this route. Where it remains a problem, deliberate alkylation using acrylamide instead of iodoacetamide will ensure chemical homogeneity of the final product. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -19062,12 +19864,12 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:00969 name: CAM-Cys vs PAM-Cys -def: "modification from DeltaMass" [DeltaMass:346] +def: "OBSOLETE because this isn't a protein modification, but rather the difference between two known modifications. modification from DeltaMass" [DeltaMass:346] comment: From DeltaMass: Average Mass: 14 Formula:CH2 Monoisotopic Mass Change:14.016 Average Mass Change:14.027 Notes: Residual acrylamide in SDS gels can partly label cysteine residues in proteins (propionamido-Cys, PAM-Cys, DeltaMass +71Da; see entry). Subsequent alkylation of protein bands with iodoacetamide e.g. in preparation for proteomic analysis, will convert remaining free cysteines into carboxamidomethyl-Cys (CAM-Cys, DeltaMass +57Da; see entry). Peptide mass fingerprinting may therefore potentially reveal the same cysteine-containing peptide in two forms, differing in mass by 14Da. The relative ratios of the peaks will depend on the initial degree of labelling with acrylamide. Use of high quality, deionised acrylamide in the SDS gel will minimise modification of cysteine through this route. Where it remains a problem, deliberate alkylation using acrylamide instead of iodoacetamide will ensure chemical homogeneity of the final product. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -19078,7 +19880,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:00970 @@ -19098,27 +19900,28 @@ [Term] id: MOD:00971 -name: Oxohistidine (from histidine) -def: "modification from DeltaMass" [DeltaMass:38] +name: 2-Oxohistidine +def: "A protein modification that effectively converts an L-histidine residue to 2-oxohistidine." [PubMed:8405458, DeltaMass:38] comment: From DeltaMass: Average Mass: 16 Average Mass Change:16 References:Lewisch, S. A. and Levine, R. L. (1995) Anal. Biochem. 231, 440-446. Determination of 2-oxo-histidine by amino acid analysis Notes:Rod LevineNIHBldg 3, Room 106 MSC 0320Bethesda, MD 20892-0320email: rlevine@nih.govvoice: 1 (301) 496-2310fax: 1 (301) 496-0599 -xref: DiffAvg: "none" -xref: DiffFormula: "none" -xref: DiffMono: "none" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" +xref: DiffAvg: "16" +xref: DiffFormula: "C 0 H 0 N 0 O 1" +xref: DiffMono: "15.994915" +xref: Formula: "C 6 H 7 N 3 O 2" +xref: MassAvg: "153.14" +xref: MassMono: "153.053826" xref: Origin: "H" -xref: Source: "none" +xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:00677 ! hydroxylated residue [Term] id: MOD:00972 name: monobrominated L-phenylalanine -def: "A protein modification that effectively converts an L-phenylalanine residue to a monobrominated L-phenylalanine, such as L-2'-bromophenylalanine." [UniMod:340#F] +def: "A protein modification that effectively converts an L-phenylalanine residue to a monobrominated L-phenylalanine, such as L-2'-bromophenylalanine." [Unimod:340#F] comment: From DeltaMass: Average Mass: 78 Average Mass Change:78 References:Yoshino,K et.al. Biochemistry Vol. 30 pg 6203-9 (1991) Identifidation of a novel amino acid, o-bromo-L-phenylananine, in egg-associated peptides that activate spermatozoa synonym: "Br1Phe" EXACT PSI-MOD-label [] -synonym: "bromination" RELATED UniMod-description [] +synonym: "bromination" RELATED Unimod-description [] synonym: "Bromo" RELATED PSI-MS-label [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" @@ -19129,7 +19932,8 @@ xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:01066 ! halogenated phenylalanine +xref: Unimod: "Unimod:340" +is_a: MOD:02086 ! brominated phenylalanine is_a: MOD:01912 ! monobrominated residue [Term] @@ -19162,7 +19966,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01046 ! 3'-chloro-L-tyrosine +relationship: derives_from MOD:01046 ! 3'-chloro-L-tyrosine +is_a: MOD:00987 ! chlorinated tyrosine [Term] id: MOD:00975 @@ -19178,7 +19983,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01046 ! 3'-chloro-L-tyrosine +relationship: derives_from MOD:01046 ! 3'-chloro-L-tyrosine +is_a: MOD:00987 ! chlorinated tyrosine [Term] id: MOD:00976 @@ -19194,6 +20000,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01072" is_obsolete: true [Term] @@ -19259,6 +20066,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01060" is_obsolete: true [Term] @@ -19295,8 +20103,8 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00031 ! L-selenocysteine residue is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02088 ! natural, standard, encoded residue substitution [Term] id: MOD:00983 @@ -19328,7 +20136,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01045 ! 3',5'-dichloro-L-tyrosine +relationship: derives_from MOD:01045 ! 3',5'-dichloro-L-tyrosine +is_a: MOD:00987 ! chlorinated tyrosine [Term] id: MOD:00985 @@ -19356,7 +20165,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01045 ! 3',5'-dichloro-L-tyrosine +relationship: derives_from MOD:01045 ! 3',5'-dichloro-L-tyrosine +is_a: MOD:00987 ! chlorinated tyrosine [Term] id: MOD:00987 @@ -19394,6 +20204,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01079" is_obsolete: true [Term] @@ -19410,7 +20221,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01045 ! 3',5'-dichloro-L-tyrosine +relationship: derives_from MOD:01045 ! 3',5'-dichloro-L-tyrosine +is_a: MOD:00987 ! chlorinated tyrosine [Term] id: MOD:00991 @@ -19475,7 +20287,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01025 ! 3'-bromo-L-tyrosine +relationship: derives_from MOD:01025 ! 3'-bromo-L-tyrosine +is_a: MOD:01000 ! monobrominated tyrosine [Term] id: MOD:00995 @@ -19491,7 +20304,8 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00183 ! L-2'-bromophenylalanine +relationship: derives_from MOD:00183 ! L-2'-bromophenylalanine +is_a: MOD:02086 ! brominated phenylalanine [Term] id: MOD:00996 @@ -19507,7 +20321,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01025 ! 3'-bromo-L-tyrosine +relationship: derives_from MOD:01025 ! 3'-bromo-L-tyrosine +is_a: MOD:01000 ! monobrominated tyrosine [Term] id: MOD:00997 @@ -19552,6 +20367,7 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00404" is_obsolete: true [Term] @@ -19655,19 +20471,14 @@ [Term] id: MOD:01006 name: dibrominated tyrosine -def: "A protein modification that effectively substitutes two hydrogen atoms of an L-tyrosine residue with two bromine atoms." [UniMod:534] +def: "A protein modification that effectively substitutes two hydrogen atoms of an L-tyrosine residue with two bromine atoms." [Unimod:534] synonym: "Br2Tyr" EXACT PSI-MOD-label [] synonym: "Dibromo" RELATED PSI-MS-label [] -synonym: "Dibromo" RELATED UniMod-description [] -xref: DiffAvg: "157.79" -xref: DiffFormula: "Br 2 C 0 H -2 N 0 O 0" -xref: DiffMono: "155.821024" -xref: Formula: "Br 2 C 9 H 7 N 1 O 2" -xref: MassAvg: "320.97" -xref: MassMono: "318.884353" +synonym: "Dibromo" RELATED Unimod-description [] xref: Origin: "Y" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:534" is_a: MOD:00988 ! brominated tyrosine [Term] @@ -19767,8 +20578,8 @@ xref: Origin: "MOD:00034" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00460 ! L-cysteic acid (L-cysteine sulfonic acid) relationship: derives_from MOD:00034 ! L-cystine (cross-link) +is_a: MOD:00675 ! oxidized residue [Term] id: MOD:01013 @@ -19851,6 +20662,7 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00403" is_obsolete: true [Term] @@ -19956,7 +20768,7 @@ [Term] id: MOD:01024 name: monohydroxylated proline -def: "A protein modification that effectively converts an L-proline residue to one of several monohydroxylated proline residues, including 3-hydroxy-L-proline and 4-hydroxy-L-proline." [DeltaMass:0, OMSSA:62, UniMod:35#P] +def: "A protein modification that effectively converts an L-proline residue to one of several monohydroxylated proline residues, including 3-hydroxy-L-proline and 4-hydroxy-L-proline." [DeltaMass:0, OMSSA:62, Unimod:35#P] comment: From DeltaMass: Average Mass: 131. This is the mass of the free amino acid [JSG]. subset: PSI-MOD-slim synonym: "Hy1Pro" EXACT PSI-MOD-label [] @@ -19973,6 +20785,8 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" +xref: UniProt: "PTM-0149" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00594 ! residues isobaric at 113.047678 Da is_a: MOD:00678 ! hydroxylated proline @@ -20008,6 +20822,7 @@ xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00850 ! unnatural residue +is_a: MOD:00306 ! residues isobaric at 113.084064 Da [Term] id: MOD:01027 @@ -20046,10 +20861,10 @@ [Term] id: MOD:01029 name: succinylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a succinyl group linked through a carbonyl carbon." [DeltaMass:0, UniMod:64] +def: "A protein modification that effectively replaces a hydrogen atom with a succinyl group linked through a carbonyl carbon." [DeltaMass:0, Unimod:64] comment: From DeltaMass with no citation or formula, Average Mass: 117 [JSG]. subset: PSI-MOD-slim -synonym: "Succinic anhydride labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "Succinic anhydride labeling reagent light form (N-term & K)" RELATED Unimod-description [] xref: DiffAvg: "100.07" xref: DiffFormula: "C 4 H 4 O 3" xref: DiffMono: "100.016044" @@ -20059,6 +20874,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:64" is_a: MOD:00649 ! acylated residue [Term] @@ -20176,6 +20992,7 @@ xref: Origin: "D" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01181" is_obsolete: true [Term] @@ -20224,6 +21041,7 @@ xref: Origin: "D" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00036" is_obsolete: true [Term] @@ -20311,6 +21129,7 @@ xref: Origin: "Q" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00080" is_obsolete: true [Term] @@ -20348,7 +21167,7 @@ [Term] id: MOD:01047 name: monohydroxylated lysine -def: "A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine." [DeltaMass:168, OMSSA:60, UniMod:35#K] +def: "A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine." [DeltaMass:168, OMSSA:60, Unimod:35#K] comment: From DeltaMass: Average Mass: 144 Abbreviation:-Hyl- Formula:C6H12N2O2 Monoisotopic Mass Change:144.09 Average Mass Change:144.174. subset: PSI-MOD-slim synonym: "Hy1Lys" EXACT PSI-MOD-label [] @@ -20364,6 +21183,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00681 ! hydroxylated lysine @@ -20513,7 +21333,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01023 ! 3',5'-dibromo-L-tyrosine +relationship: derives_from MOD:01023 ! 3',5'-dibromo-L-tyrosine +is_a: MOD:01006 ! dibrominated tyrosine [Term] id: MOD:01057 @@ -20529,7 +21350,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01023 ! 3',5'-dibromo-L-tyrosine +relationship: derives_from MOD:01023 ! 3',5'-dibromo-L-tyrosine +is_a: MOD:01006 ! dibrominated tyrosine [Term] id: MOD:01058 @@ -20562,12 +21384,13 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01023 ! 3',5'-dibromo-L-tyrosine +relationship: derives_from MOD:01023 ! 3',5'-dibromo-L-tyrosine +is_a: MOD:01006 ! dibrominated tyrosine [Term] id: MOD:01060 name: S-carboxamidomethyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine." [DeltaMass:196, DeltaMass:337, OMSSA:3, PubMed:10504701, PubMed:11510821, PubMed:12422359, PubMed:18306178, UniMod:4#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine." [DeltaMass:196, DeltaMass:337, OMSSA:3, PubMed:10504701, PubMed:11510821, PubMed:12422359, PubMed:18306178, Unimod:4#C] comment: From DeltaMass: (name misspelled "Carboxyamidomethyl Cystenyl") [JSG]. subset: PSI-MOD-slim synonym: "amidocarboxymethylcysteine" EXACT DeltaMass-label [] @@ -20578,7 +21401,7 @@ synonym: "carbamoylmethylcysteine" EXACT DeltaMass-label [] synonym: "Carboxamidomethyl (on Cysteine)" EXACT DeltaMass-label [] synonym: "Carboxyamidomethyl Cystenyl" EXACT DeltaMass-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] synonym: "S-carbamoylmethyl-L-cysteine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1 S 0" @@ -20589,13 +21412,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01061 name: S-carboxymethyl-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-carboxymethyl-L-cysteine." [DeltaMass:0, DeltaMass:197, OMSSA:2, UniMod:6#C] +def: "A protein modification that effectively converts an L-cysteine residue to S-carboxymethyl-L-cysteine." [DeltaMass:0, DeltaMass:197, OMSSA:2, Unimod:6#C] comment: From DeltaMass with no citation, name misspelled "Carboxymethyl Cystenyl", and formula incorrect, N and O reversed: Average Mass: 161 Abbreviation: -Cmc- Formula: C5H7O1N3S1 Monoisotopic Mass Change: 161.015 Average Mass Change: 161.179 [JSG]. subset: PSI-MOD-slim synonym: "Carboxymethyl" RELATED PSI-MS-label [] @@ -20603,7 +21427,7 @@ synonym: "Carboxymethyl Cystenyl" EXACT DeltaMass-label [] synonym: "carboxymethylc" EXACT OMSSA-label [] synonym: "CmC" EXACT PSI-MOD-alternate [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 N 0 O 2 S 0" xref: DiffMono: "58.005479" @@ -20613,6 +21437,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:6" is_a: MOD:00399 ! iodoacetic acid derivatized residue is_a: MOD:00905 ! modified L-cysteine residue @@ -20631,6 +21456,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01061" is_obsolete: true [Term] @@ -20671,7 +21497,7 @@ [Term] id: MOD:01065 name: hexose glycated N-terminal -def: "A modification produced in a non-enzymatic reaction between a carbohydrate carbonyl group (C1 of aldohexose or C2 of fructose) and a protein N-terminal amino group to form a Schiff-base or an Amadori ketosamine (or aminoketose) residue adduct." [DeltaMass:0, UniMod:41#N-term] +def: "A modification produced in a non-enzymatic reaction between a carbohydrate carbonyl group (C1 of aldohexose or C2 of fructose) and a protein N-terminal amino group to form a Schiff-base or an Amadori ketosamine (or aminoketose) residue adduct." [DeltaMass:0, Unimod:41#N-term] comment: From DeltaMass: Average Mass: 162 xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 O 5" @@ -20682,6 +21508,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:41" is_a: MOD:00767 ! glycated residue [Term] @@ -20840,6 +21667,7 @@ xref: Origin: "R" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00414" is_obsolete: true [Term] @@ -20861,11 +21689,11 @@ [Term] id: MOD:01078 name: S-(2-aminoethyl)-3-methylcysteine (Thr) -def: "A protein modification that effectively converts an L-threonine residue to S-(2-aminoethyl)-3-methylcysteine." [PubMed:12923550, UniMod:472#T] +def: "A protein modification that effectively converts an L-threonine residue to S-(2-aminoethyl)-3-methylcysteine." [PubMed:12923550, Unimod:472#T] comment: From DeltaMass: Average Mass: 146 Abbreviation:-AECys_ Formula:C5H10O2N1S1 Monoisotopic Mass Change:146.051 Average Mass Change:146.214 References:PE Sciex. synonym: "2-amino-3-(2-aminoethyl)sulfanyl-3-methylbutanoic acid" EXACT PSI-MOD-alternate [] -synonym: "AEC-MAEC" RELATED UniMod-interim [] -synonym: "beta-methylaminoethylcysteine" RELATED UniMod-description [] +synonym: "AEC-MAEC" RELATED Unimod-interim [] +synonym: "beta-methylaminoethylcysteine" RELATED Unimod-description [] synonym: "S-aminoethyl-3-methylcysteine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "59.13" xref: DiffFormula: "C 2 H 5 N 1 O -1 S 1" @@ -20876,6 +21704,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:472" is_a: MOD:00917 ! modified L-threonine residue [Term] @@ -20902,7 +21731,7 @@ [Term] id: MOD:01080 name: acrylamidyl cysteinyl -def: "modification from DeltaMass" [DeltaMass:219] +def: "OBSOLETE because this is identical to MOD:00417. modification from DeltaMass" [DeltaMass:219] comment: From DeltaMass: (name misspelled "Acrylamidyl Cystenyl") Average Mass: 174 Formula: C6H10O2N2S1 Monoisotopic Mass Change: 174.046 Average Mass Change: 174.221 synonym: "Acrylamidyl Cystenyl" EXACT DeltaMass-label [] xref: DiffAvg: "none" @@ -20913,8 +21742,8 @@ xref: MassMono: "174.046299" xref: Origin: "C" xref: Source: "artifact" -xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +xref: Remap: "MOD:00417" +is_obsolete: true [Term] id: MOD:01081 @@ -20935,7 +21764,7 @@ [Term] id: MOD:01082 name: 4-glycosyloxy- (hexosyl, C6) (of proline) -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because redundant with MOD:00757, remap. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: 177. Caution: Formula does not match mass. The natural glycosylating sugar of hydroxyproline is galactose. xref: DiffAvg: "178.14" xref: DiffFormula: "C 6 H 10 O 6" @@ -20946,7 +21775,8 @@ xref: Origin: "P" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +xref: Remap: "MOD:00757" +is_obsolete: true [Term] id: MOD:01083 @@ -20967,11 +21797,11 @@ [Term] id: MOD:01084 name: iodoacetic acid derivatized amino-terminal residue -def: "A protein modification that by reaction of iodoacetic acid effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxymethyl group." [UniMod:6#N-term] +def: "A protein modification that by reaction of iodoacetic acid effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxymethyl group." [Unimod:6#N-term] subset: PSI-MOD-slim synonym: "Carboxymethyl" RELATED PSI-MS-label [] synonym: "Carboxymethyl (on Cysteine)" EXACT DeltaMass-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -20981,23 +21811,25 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:6" is_a: MOD:00399 ! iodoacetic acid derivatized residue [Term] id: MOD:01085 -name: alpha-N-gluconoylation (His Tagged proteins) -def: "modification from DeltaMass" [DeltaMass:226] -comment: From DeltaMass: Average Mass: 178 Formula: C6H10O6 Monoisotopic Mass Change: 178.05 Average Mass Change: 178.14 References: Geoghegan, K. F., H. B. Dixon, et al. (1999). Spontaneous alpha-N-6-phosphogluconoylation of a His tag in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem 267(1): 169-84. -xref: DiffAvg: "none" -xref: DiffFormula: "none" -xref: DiffMono: "none" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" -xref: Origin: "none" -xref: Source: "none" -xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +name: alpha-N-gluconoylated L-histidine +def: "A protein modification that effectively replaces the N-terminal hydrogen atom of a N-terminal histidine residue with a gluconoyl group linked through a glycosidic bond. modification from DeltaMass" [PubMed:9918669, DeltaMass:226] +comment: Occurs on His-tagged proteins expresssed in E. coli. From DeltaMass: Average Mass: 178 Formula: C6H10O6 Monoisotopic Mass Change: 178.05 Average Mass Change: 178.14 References: Geoghegan, K. F., H. B. Dixon, et al. (1999). Spontaneous alpha-N-6-phosphogluconoylation of a His tag in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem 267(1): 169-84. Mass listed here is 179 because it's N-terminal. +xref: DiffAvg: "179.15" +xref: DiffFormula: "C 6 H 11 O 6" +xref: DiffMono: "179.055563" +xref: Formula: "C 12 H 18 N 3 O 7" +xref: MassAvg: "316.29" +xref: MassMono: "316.114475" +xref: Origin: "H" +xref: Source: "natural" +xref: TermSpec: "N-term" +is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:00006 ! N-glycosylated residue [Term] id: MOD:01086 @@ -21067,11 +21899,11 @@ [Term] id: MOD:01090 name: iodoacetamide derivatized amino-terminal residue -def: "A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group." [PubMed:11327326, PubMed:11510821, PubMed:12422359, UniMod:4#N-term] +def: "A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group." [PubMed:11327326, PubMed:11510821, PubMed:12422359, Unimod:4#N-term] subset: PSI-MOD-slim synonym: "(carbamoylmethyl)amino" EXACT PSI-MOD-alternate [] synonym: "Carbamidomethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -21081,6 +21913,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue [Term] @@ -21137,12 +21970,12 @@ [Term] id: MOD:01094 name: N6-carboxymethyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-carboxymethyl-L-lysine." [DeltaMass:237, UniMod:6#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-carboxymethyl-L-lysine." [DeltaMass:237, Unimod:6#K] comment: From DeltaMass:237 (with no citation, formula incorrect, N and O reversed) Average Mass: 186 Formula: C8H14O2N3 Monoisotopic Mass Change: 186.1 Average Mass Change: 186.211 [JSG]. subset: PSI-MOD-slim synonym: "Carboxymethyl" RELATED PSI-MS-label [] synonym: "Carboxymethyl Lysyl" EXACT DeltaMass-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -21152,6 +21985,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:6" is_a: MOD:00399 ! iodoacetic acid derivatized residue [Term] @@ -21235,7 +22069,6 @@ xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:01029 ! succinylated residue [Term] id: MOD:01100 @@ -21267,6 +22100,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:00111" is_obsolete: true [Term] @@ -21283,6 +22117,7 @@ xref: Origin: "none" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00504" is_obsolete: true [Term] @@ -21299,6 +22134,7 @@ xref: Origin: "none" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00503" is_obsolete: true [Term] @@ -21548,19 +22384,20 @@ [Term] id: MOD:01118 -name: alpha-N-6-phosphogluconoylation (His Tagged proteins) -def: "modification from DeltaMass" [DeltaMass:275] -comment: From DeltaMass: Average Mass: 258 Formula: C6H10O6HPO3 Monoisotopic Mass Change: 258.01 Average Mass Change: 258.12 References: Geoghegan, K. F., H. B. Dixon, et al. (1999). Spontaneous alpha-N-6-phosphogluconoylation of a His tag in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem 267(1): 169-84. -xref: DiffAvg: "none" -xref: DiffFormula: "none" -xref: DiffMono: "none" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" -xref: Origin: "none" -xref: Source: "none" -xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +name: alpha-N-6-phosphogluconoylated L-histidine +def: "A protein modification that effectively replaces the N-terminal hydrogen atom of a N-terminal histidine residue with a 6-phosphogluconoyl group linked through a glycosidic bond. modification from DeltaMass" [PubMed:9918669, DeltaMass:275] +comment: Occurs on His-tagged proteins expresssed in E. coli.From DeltaMass: Average Mass: 258 Formula: C6H10O6HPO3 Monoisotopic Mass Change: 258.01 Average Mass Change: 258.12 References: Geoghegan, K. F., H. B. Dixon, et al. (1999). Spontaneous alpha-N-6-phosphogluconoylation of a His tag in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem 267(1): 169-84. Mass is one Da higher because this is an N-terminal modification +xref: DiffAvg: "259.12" +xref: DiffFormula: "C 6 H 12 O 9 P 1" +xref: DiffMono: "259.021894" +xref: Formula: "C 12 H 19 N 3 O 10 P 1" +xref: MassAvg: "396.27" +xref: MassMono: "396.080806" +xref: Origin: "H" +xref: Source: "natural" +xref: TermSpec: "N-term" +is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:00006 ! N-glycosylated residue [Term] id: MOD:01119 @@ -21625,7 +22462,7 @@ [Term] id: MOD:01122 name: 5'phos dCytidinyl -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: 289 with no citation. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21636,7 +22473,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01123 @@ -21652,6 +22489,7 @@ xref: Origin: "Y" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01123" is_obsolete: true [Term] @@ -21673,7 +22511,7 @@ [Term] id: MOD:01125 name: 5'phos dThymidinyl -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: 304 with no citation. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21684,12 +22522,12 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01126 name: 5'phos Cytidinyl -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: 305 with no citation. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21700,7 +22538,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01127 @@ -21716,6 +22554,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01166" is_obsolete: true [Term] @@ -21738,7 +22577,7 @@ [Term] id: MOD:01129 name: 5'phos dAdenosyl -def: "modification from DeltaMass" [DeltaMass:295] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:295] comment: From DeltaMass: Average Mass: 313 Formula: C10H12O5N5P1 Monoisotopic Mass Change: 313.058 Average Mass Change: 313.211 xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21749,7 +22588,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01130 @@ -21770,7 +22609,7 @@ [Term] id: MOD:01131 name: 5'phos dGuanosyl -def: "modification from DeltaMass" [DeltaMass:0] +def: "OBSOLETE because this is a modification that occurs to DNA/RNA and not proteins. modification from DeltaMass" [DeltaMass:0] comment: From DeltaMass: Average Mass: 329 xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21781,7 +22620,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01132 @@ -21797,6 +22636,7 @@ xref: Origin: "none" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01165" is_obsolete: true [Term] @@ -21852,7 +22692,7 @@ [Term] id: MOD:01136 name: dioctyl phthalate -def: "modification from DeltaMass" [DeltaMass:309] +def: "OBSOLETE because this is a small molecule contaminant and not a modification to a polypeptide. modification from DeltaMass" [DeltaMass:309] comment: From DeltaMass: Average Mass: 391 Average Mass Change: 391 Notes: A common plasticizer, and, unfortunaltely, a common contaminate. A sodium adduct is often associated with this peak at 413. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21863,7 +22703,7 @@ xref: Origin: "none" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01137 @@ -21887,7 +22727,7 @@ [Term] id: MOD:01138 name: Aedans Cystenyl -def: "modification from DeltaMass" [DeltaMass:311] +def: "OBSOLETE because no evidence has been seen for this protein modification. modification from DeltaMass" [DeltaMass:311] comment: [probably aminoethyldansyl, JSG] From DeltaMass: (name misspelled "Aedans Cystenyl", and formula incorrect, N and O reversed) Average Mass: 409 Abbreviation: Aedans-Cys Formula: C17H19O3N5S2 Monoisotopic Mass Change: 409.077 Average Mass Change: 409.482 xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21898,12 +22738,12 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01139 name: dioctyl phthalate sodium adduct -def: "modification from DeltaMass" [DeltaMass:312] +def: "OBSOLETE because this is a MS contaminant, not a known modification to a polypeptide. modification from DeltaMass" [DeltaMass:312] comment: From DeltaMass: Mass: Average Mass Change: 413 Notes: A common plasticizer, and, unfortunaltely, a common contaminate. A sodium adduct is often associated with this peak at 413. xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -21914,15 +22754,15 @@ xref: Origin: "none" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +is_obsolete: true [Term] id: MOD:01140 name: diiodinated tyrosine -def: "A protein modification that effectively substitutes two hydrogen atoms of an L-tyrosine residue with two iodine atoms." [DeltaMass:0, OMSSA:35, PubMed:15627961, UniMod:130#Y] +def: "A protein modification that effectively substitutes two hydrogen atoms of an L-tyrosine residue with two iodine atoms." [DeltaMass:0, OMSSA:35, PubMed:15627961, Unimod:130#Y] subset: PSI-MOD-slim synonym: "3,5-Diiodination (of Tyrosine)" EXACT DeltaMass-label [] -synonym: "di-Iodination" RELATED UniMod-description [] +synonym: "di-Iodination" RELATED Unimod-description [] synonym: "diiodinationy" EXACT OMSSA-label [] synonym: "Diiodo" RELATED PSI-MS-label [] synonym: "I2Tyr" EXACT PSI-MOD-label [] @@ -21935,6 +22775,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:130" is_a: MOD:00501 ! diiodinated residue is_a: MOD:00998 ! iodinated tyrosine @@ -22008,7 +22849,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:01144 @@ -22031,8 +22872,9 @@ [Term] id: MOD:01145 name: N-tau-(ADP-ribosyl)diphthamide -def: "A protein modification that effectively converts an L-histidine residue to N-tau-(ADP-ribosyl)diphthamide." [DeltaMass:0] +def: "A protein modification that effectively converts an L-histidine residue to N-tau-(ADP-ribosyl)diphthamide." [DeltaMass:0, ChEBI:82697] comment: From DeltaMass: (name misspelled "N theta -(ADP-ribosyl) diphthamide (of Histidine)") Average Mass: 648 +synonym: "MOD_RES ADP-ribosyldiphthamide" EXACT UniProt-feature [] xref: DiffAvg: "684.51" xref: DiffFormula: "C 22 H 36 N 7 O 14 P 2" xref: DiffMono: "684.178999" @@ -22043,7 +22885,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +xref: UniProt: "PTM-0672" +is_a: MOD:02087 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00909 ! modified L-histidine residue relationship: derives_from MOD:00049 ! 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine @@ -22069,19 +22912,22 @@ [Term] id: MOD:01147 -name: (Hex)3-HexNAc-(dHex)HexNAc -def: "modification from DeltaMass" [DeltaMass:0] +name: dHex1Hex3HexNAc2 N4-glycosylated asparagine +def: "modification from DeltaMass" [DeltaMass:0, Unimod:1761] comment: From DeltaMass: Average Mass: 1,039 -xref: DiffAvg: "none" -xref: DiffFormula: "none" -xref: DiffMono: "none" -xref: Formula: "none" -xref: MassAvg: "none" -xref: MassMono: "none" -xref: Origin: "none" -xref: Source: "none" +xref: DiffAvg: "1038.95" +xref: DiffFormula: "C 40 H 66 N 2 O 29" +xref: DiffMono: "1038.375124" +xref: Formula: "C 44 H 72 N 4 O 31" +xref: MassAvg: "1153.06" +xref: MassMono: "1152.418052" +xref: Origin: "N" +xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00947 ! DeltaMass +xref: Unimod: "Unimod:1761" +xref: GNOme: "GNO:G20956ZV" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:01148 @@ -22091,7 +22937,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01875 ! N6-acylated L-lysine relationship: contains MOD:00134 ! N6-glycyl-L-lysine @@ -22103,7 +22950,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01875 ! N6-acylated L-lysine relationship: contains MOD:00134 ! N6-glycyl-L-lysine @@ -22115,7 +22963,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01875 ! N6-acylated L-lysine relationship: contains MOD:00134 ! N6-glycyl-L-lysine @@ -22138,10 +22987,10 @@ [Term] id: MOD:01152 name: carboxylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a carboxylic acid group." [UniMod:299] +def: "A protein modification that effectively replaces a hydrogen atom with a carboxylic acid group." [Unimod:299] subset: PSI-MOD-slim -synonym: "Carboxy" RELATED UniMod-interim [] -synonym: "Carboxylation" RELATED UniMod-description [] +synonym: "Carboxy" RELATED Unimod-interim [] +synonym: "Carboxylation" RELATED Unimod-description [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" xref: DiffMono: "43.989829" @@ -22151,15 +23000,16 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:299" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01153 name: methylthiolated residue -def: "A protein modification that effectively replaces a hydrogen atom with an methylsulfanyl group (thiomethyl group)." [UniMod:39] +def: "A protein modification that effectively replaces a hydrogen atom with an methylsulfanyl group (thiomethyl group)." [Unimod:39] subset: PSI-MOD-slim -synonym: "Beta-methylthiolation" RELATED UniMod-description [] -synonym: "Methylthio" RELATED UniMod-interim [] +synonym: "Beta-methylthiolation" RELATED Unimod-description [] +synonym: "Methylthio" RELATED Unimod-interim [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" @@ -22169,6 +23019,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:39" is_a: MOD:01886 ! thiolated residue [Term] @@ -22235,10 +23086,10 @@ [Term] id: MOD:01160 name: deaminated residue -def: "A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen." [UniMod:385] +def: "A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen." [Unimod:385] subset: PSI-MOD-slim -synonym: "Ammonia-loss" RELATED UniMod-interim [] -synonym: "Loss of ammonia" RELATED UniMod-description [] +synonym: "Ammonia-loss" RELATED Unimod-interim [] +synonym: "Loss of ammonia" RELATED Unimod-description [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" @@ -22248,16 +23099,17 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:385" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01161 name: deoxygenated residue -def: "A protein modification that effectively removes oxygen atoms from a residue without the removal of hydrogen atoms." [PubMed:14235557, UniMod:447] +def: "A protein modification that effectively removes oxygen atoms from a residue without the removal of hydrogen atoms." [PubMed:14235557, Unimod:447] subset: PSI-MOD-slim synonym: "Deoxy" RELATED PSI-MS-label [] synonym: "dOxyRes" EXACT PSI-MOD-label [] -synonym: "reduction" RELATED UniMod-description [] +synonym: "reduction" RELATED Unimod-description [] xref: DiffAvg: "-16.00" xref: DiffFormula: "C 0 H 0 N 0 O -1" xref: DiffMono: "-15.994915" @@ -22267,14 +23119,15 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:447" is_a: MOD:01472 ! reduced residue [Term] id: MOD:01162 name: fucosylated biantennary -def: "modification from UniMod N-linked glycosylation" [UniMod:308] +def: "modification from Unimod N-linked glycosylation" [Unimod:308] synonym: "dHex(1)Hex(5)HexNAc(4)" RELATED PSI-MS-label [] -synonym: "Fucosylated biantennary" RELATED UniMod-description [] +synonym: "Fucosylated biantennary" RELATED Unimod-description [] xref: DiffAvg: "1769.62" xref: DiffFormula: "C 68 H 112 N 4 O 49" xref: DiffMono: "1768.639516" @@ -22284,15 +23137,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:308" +xref: GNOme: "GNO:G83555HU" is_a: MOD:00725 ! complex glycosylation [Term] id: MOD:01163 name: guanylated residue -def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoguanosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:304, UniMod:413] +def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoguanosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:304, Unimod:413] comment: From DeltaMass: (formula incorrect, N and O reversed) Average Mass: 345 Formula: C10H12O5N7P1 Monoisotopic Mass Change: 345.047 Average Mass Change: 345.209. synonym: "5'phos Guanosyl" EXACT DeltaMass-label [] -synonym: "phospho-guanosine" RELATED UniMod-description [] +synonym: "phospho-guanosine" RELATED Unimod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] xref: DiffAvg: "345.21" xref: DiffFormula: "C 10 H 12 N 5 O 7 P 1" @@ -22303,15 +23158,16 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:413" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01164 -name: riboflavin-phosphoryl -def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through a phosphodiester bond." [UniMod:442] +name: riboflavin-phosphorylated residue +def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through a phosphodiester bond." [Unimod:442] subset: PSI-MOD-slim synonym: "FMN" RELATED PSI-MS-label [] -synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] +synonym: "O3-(riboflavin phosphoryl)" RELATED Unimod-description [] xref: DiffAvg: "438.33" xref: DiffFormula: "C 17 H 19 N 4 O 8 P 1" xref: DiffMono: "438.094050" @@ -22321,16 +23177,17 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue +xref: Unimod: "Unimod:442" +is_a: MOD:00697 ! flavin modified residue [Term] id: MOD:01165 name: adenylated residue -def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoadenosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:0, UniMod:405] +def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoadenosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:0, Unimod:405] comment: From DeltaMass: (name misspelled "5'phos adenosinyl") Average Mass: 329 subset: PSI-MOD-slim synonym: "5'phos Adenosinyl" EXACT DeltaMass-label [] -synonym: "AMP binding site" RELATED UniMod-description [] +synonym: "AMP binding site" RELATED Unimod-description [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" @@ -22341,16 +23198,17 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:405" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01166 name: uridylated residue -def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphouridine through either a phosphodiester or a phosphoramide bond." [DeltaMass:292, UniMod:417] +def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphouridine through either a phosphodiester or a phosphoramide bond." [DeltaMass:292, Unimod:417] comment: From DeltaMass: (name misspelled "5'phos Uridinyl" and formula incorrect, N and O reversed) Average Mass: 306 Formula: C9H11O2N8P1 Monoisotopic Mass Change: 306.025 Average Mass Change: 306.17 synonym: "5'phos Uridinyl" EXACT DeltaMass-label [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] -synonym: "uridine phosphodiester" RELATED UniMod-description [] +synonym: "uridine phosphodiester" RELATED Unimod-description [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" @@ -22360,13 +23218,14 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:417" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01167 name: molybdopterin guanine dinucleotide -def: "modification from UniMod" [UniMod:424] -synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] +def: "modification from Unimod" [Unimod:424] +synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED Unimod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] xref: DiffAvg: "1572.02" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4" @@ -22377,6 +23236,7 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:424" is_a: MOD:00744 ! molybdenum pterin containing modification [Term] @@ -22433,8 +23293,8 @@ [Term] id: MOD:01170 name: pyruvic acid iminylated residue -def: "A protein modification that effectively forms a 2-ketoimine of pyruvicacid with a residue amino group." [UniMod:422] -synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] +def: "A protein modification that effectively forms a 2-ketoimine of pyruvicacid with a residue amino group." [Unimod:422] +synonym: "N-pyruvic acid 2-iminyl" RELATED Unimod-description [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" xref: DiffFormula: "C 3 H 2 N 0 O 2" @@ -22445,15 +23305,16 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:422" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01171 name: O-acetyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-acetyl-L-threonine." [PubMed:16728640, RESID:AA0423, UniMod:1#T] +def: "A protein modification that effectively converts an L-threonine residue to O-acetyl-L-threonine." [PubMed:16728640, RESID:AA0423, Unimod:1#T] subset: PSI-MOD-slim synonym: "(2S,3R)-3-(acetyloxy)-2-aminobutanoic acid" EXACT RESID-systematic [] -synonym: "Acetylation" RELATED UniMod-description [] +synonym: "Acetylation" RELATED Unimod-description [] synonym: "ACT_SITE O-acetylthreonine intermediate" EXACT UniProt-feature [] synonym: "MOD_RES O-acetylthreonine" EXACT UniProt-feature [] synonym: "O-acetyl-L-threonine" EXACT RESID-name [] @@ -22469,8 +23330,10 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00644 ! O-acetylated residue -is_a: MOD:01186 ! acetylated L-threonine +xref: Unimod: "Unimod:1" +xref: UniProt: "PTM-0233" +is_a: MOD:00644 ! mono O-acetylated residue +is_a: MOD:01186 ! monoacetylated L-threonine [Term] id: MOD:01172 @@ -22488,6 +23351,7 @@ xref: Origin: "A" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0144" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00901 ! modified L-alanine residue @@ -22507,6 +23371,7 @@ xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0145" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00903 ! modified L-asparagine residue @@ -22528,6 +23393,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0447" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue @@ -22578,7 +23444,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00912 ! modified L-lysine residue +is_a: MOD:02051 ! crosslinked L-lysine residue [Term] id: MOD:01177 @@ -22601,6 +23467,7 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0416" is_a: MOD:00909 ! modified L-histidine residue [Term] @@ -22643,6 +23510,7 @@ xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0178" is_a: MOD:01461 ! N-methylated alanine is_a: MOD:01686 ! alpha-amino dimethylated residue @@ -22671,7 +23539,7 @@ [Term] id: MOD:01181 name: L-aspartic acid 4-methyl ester -def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartate 4-methyl ester." [OMSSA:69, PubMed:1556110, PubMed:16888766, PubMed:9629898, RESID:AA0435, UniMod:34#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartate 4-methyl ester." [OMSSA:69, PubMed:1556110, PubMed:16888766, PubMed:9629898, RESID:AA0435, Unimod:34#D] comment: CAUTION - observations of this modifation are attributable to artifacts produced in preparation. It is extremely unlikely that eukaryotes produce this modification, because an enzyme acting to form the methyl ester of L-aspartyl peptides would interfere with the D-aspartyl peptide repair mechanism [JSG]. synonym: "(2S)-2-amino-4-methoxy-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-aminobutanedioic acid 4-methyl ester" EXACT RESID-alternate [] @@ -22693,6 +23561,7 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00393 ! O-methylated residue is_a: MOD:01681 ! monomethylated L-aspartic acid @@ -22710,6 +23579,7 @@ synonym: "6-(S-L-cysteinyl)-8alpha-(N3'-L-histidino)-FAD" EXACT RESID-name [] synonym: "BINDING FAD (covalent; via 2 links)" EXACT UniProt-feature [] synonym: "BINDING FAD (covalent; via 2 links, pros nitrogen)" EXACT UniProt-feature [] +synonym: "CROSSLNK 6-(S-cysteinyl)-8alpha-(pros-histidyl)-FAD (His-Cys)" EXACT UniProt-feature [] synonym: "SCys6-NprosHis8a-FAD" EXACT PSI-MOD-label [] xref: DiffAvg: "781.52" xref: DiffFormula: "C 27 H 29 N 9 O 15 P 2 S 0" @@ -22720,9 +23590,9 @@ xref: Origin: "C, H" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00895 ! FAD modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +xref: UniProt: "PTM-0681" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02048 ! crosslinked L-histidine residue is_a: MOD:01621 ! flavin crosslinked residues [Term] @@ -22783,7 +23653,6 @@ xref: Origin: "C, C" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00007 ! selenium substitution for sulfur is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -22814,13 +23683,12 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00012 ! L-asparagine residue is_a: MOD:00674 ! amidated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:01186 -name: acetylated L-threonine +name: monoacetylated L-threonine def: "A protein modification that effectively converts an L-threonine residue to either N-acetyl-L-threonne, or O-acetyl-Lthreonine." [PubMed:18688235] subset: PSI-MOD-slim synonym: "AcThr" EXACT PSI-MOD-label [] @@ -22832,13 +23700,13 @@ xref: MassMono: "none" xref: Origin: "T" xref: Source: "natural" -is_a: MOD:00394 ! acetylated residue +is_a: MOD:00394 ! monoacetylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01187 name: L-pyrrolysine residue -def: "A protein modification that inserts or replaces a residue with an L-pyrrolysine residue, a natural pretranslational modification." [ChEBI:21860, PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321, UniMod:435] +def: "A protein modification that inserts or replaces a residue with an L-pyrrolysine residue, a natural pretranslational modification." [ChEBI:21860, PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321, Unimod:435] subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acid" EXACT RESID-systematic [] synonym: "2-azanyl-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]azanylhexanoic acid" EXACT RESID-alternate [] @@ -22858,13 +23726,14 @@ xref: Origin: "O" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:435" is_a: MOD:00868 ! natural, non-standard encoded residue [Term] id: MOD:01188 name: N-ethyl iodoacetamide-d5 - site Y -def: "modification from UniMod Isotopic label -" [PubMed:11710128, PubMed:12766232, PubMed:3155470, PubMed:957432, UniMod:212#Y] -synonym: "N-ethyl iodoacetamide-d5" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:11710128, PubMed:12766232, PubMed:3155470, PubMed:957432, Unimod:212#Y] +synonym: "N-ethyl iodoacetamide-d5" RELATED Unimod-description [] synonym: "NEIAA:2H(5)" RELATED PSI-MS-label [] xref: DiffAvg: "90.08" xref: DiffFormula: "C 4 (1)H 2 (2)H 5 N 1 O 1" @@ -22875,13 +23744,14 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:212" is_a: MOD:00562 ! N-ethyl iodoacetamide-d5 [Term] id: MOD:01189 name: N-ethyl iodoacetamide-d5 - site C -def: "modification from UniMod Isotopic label -" [PubMed:12766232, UniMod:212#C] -synonym: "N-ethyl iodoacetamide-d5" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:12766232, Unimod:212#C] +synonym: "N-ethyl iodoacetamide-d5" RELATED Unimod-description [] synonym: "NEIAA:2H(5)" RELATED PSI-MS-label [] xref: DiffAvg: "90.08" xref: DiffFormula: "C 4 (1)H 2 (2)H 5 N 1 O 1" @@ -22892,14 +23762,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:212" is_a: MOD:00562 ! N-ethyl iodoacetamide-d5 [Term] id: MOD:01190 name: dibromo -def: "Modification from UniMod Chemical derivative. OBSOLETE because duplicate and redundant with MOD:01006. Remap to MOD:01006." [UniMod:534] +def: "Modification from Unimod Chemical derivative. OBSOLETE because duplicate and redundant with MOD:01006. Remap to MOD:01006." [Unimod:534] synonym: "Dibromo" RELATED PSI-MS-label [] -synonym: "Dibromo" RELATED UniMod-description [] +synonym: "Dibromo" RELATED Unimod-description [] xref: DiffAvg: "157.79" xref: DiffFormula: "Br 2 H -2" xref: DiffMono: "155.821024" @@ -22909,13 +23780,15 @@ xref: Origin: "Y" xref: Source: "none" xref: TermSpec: "none" +xref: Remap: "MOD:01006" +xref: Unimod: "Unimod:534" is_obsolete: true [Term] id: MOD:01191 name: N-ethyl iodoacetamide-d0 - site C -def: "modification from UniMod Isotopic label -" [PubMed:12766232, UniMod:211#C] -synonym: "N-ethyl iodoacetamide-d0" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:12766232, Unimod:211#C] +synonym: "N-ethyl iodoacetamide-d0" RELATED Unimod-description [] synonym: "NEIAA" RELATED PSI-MS-label [] xref: DiffAvg: "85.11" xref: DiffFormula: "C 4 H 7 N 1 O 1" @@ -22926,13 +23799,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:211" is_a: MOD:00561 ! N-ethyl iodoacetamide-d0 [Term] id: MOD:01192 name: N-ethyl iodoacetamide-d0 - site Y -def: "modification from UniMod Isotopic label -" [PubMed:11760118, PubMed:12766232, UniMod:211#Y] -synonym: "N-ethyl iodoacetamide-d0" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:11760118, PubMed:12766232, Unimod:211#Y] +synonym: "N-ethyl iodoacetamide-d0" RELATED Unimod-description [] synonym: "NEIAA" RELATED PSI-MS-label [] xref: DiffAvg: "85.11" xref: DiffFormula: "C 4 H 7 N 1 O 1" @@ -22943,14 +23817,15 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:211" is_a: MOD:00561 ! N-ethyl iodoacetamide-d0 [Term] id: MOD:01193 -name: phosphorylation to pyridyl thiol - site T -def: "modification from UniMod Chemical derivative -" [PubMed:1093385, UniMod:264#T] +name: pyridyl thiol modified L-threonine +def: "modification from Unimod Chemical derivative -" [PubMed:1093385, Unimod:264#T] synonym: "PET" RELATED PSI-MS-label [] -synonym: "phosphorylation to pyridyl thiol" RELATED UniMod-description [] +synonym: "phosphorylation to pyridyl thiol" RELATED Unimod-description [] xref: DiffAvg: "121.20" xref: DiffFormula: "C 7 H 7 N 1 O -1 S 1" xref: DiffMono: "121.035006" @@ -22960,14 +23835,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00586 ! phosphorylation to pyridyl thiol +xref: Unimod: "Unimod:264" +is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:00586 ! pyridyl thiol modified residue [Term] id: MOD:01194 -name: phosphorylation to pyridyl thiol - site S -def: "modification from UniMod Chemical derivative -" [PubMed:15279557, UniMod:264#S] +name: pyridyl thiol modified L-serine +def: "modification from Unimod Chemical derivative -" [PubMed:15279557, Unimod:264#S] synonym: "PET" RELATED PSI-MS-label [] -synonym: "phosphorylation to pyridyl thiol" RELATED UniMod-description [] +synonym: "phosphorylation to pyridyl thiol" RELATED Unimod-description [] xref: DiffAvg: "121.20" xref: DiffFormula: "C 7 H 7 N 1 O -1 S 1" xref: DiffMono: "121.035006" @@ -22977,14 +23854,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00586 ! phosphorylation to pyridyl thiol +xref: Unimod: "Unimod:264" +is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:00586 ! pyridyl thiol modified residue [Term] id: MOD:01195 name: benzoyl labeling reagent light form - site K -def: "modification from UniMod Isotopic label -" [PubMed:11813307, PubMed:12777388, PubMed:15456300, UniMod:136#K] +def: "modification from Unimod Isotopic label -" [PubMed:11813307, PubMed:12777388, PubMed:15456300, Unimod:136#K] synonym: "Benzoyl" RELATED PSI-MS-label [] -synonym: "labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "labeling reagent light form (N-term & K)" RELATED Unimod-description [] xref: DiffAvg: "104.11" xref: DiffFormula: "C 7 H 4 O 1" xref: DiffMono: "104.026215" @@ -22994,13 +23873,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:136" is_a: MOD:00505 ! benzoyl labeling reagent light form (N-term and K) [Term] id: MOD:01196 name: 5-dimethylaminonaphthalene-1-sulfonyl - site K -def: "OBSOLETE because redundant, replaced with MOD:01654. Remap to MOD:01654." [UniMod:139] -synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED UniMod-description [] +def: "OBSOLETE because redundant, replaced with MOD:01654. Remap to MOD:01654." [Unimod:139] +synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED Unimod-description [] synonym: "Dansyl" RELATED PSI-MS-label [] xref: DiffAvg: "233.29" xref: DiffFormula: "C 12 H 11 N 1 O 2 S 1" @@ -23011,15 +23891,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01654" +xref: Unimod: "Unimod:139" is_obsolete: true [Term] id: MOD:01197 name: N-heptosyl-L-glutamine -def: "A protein modification that effectively converts an L-glutamine residue to N-heptosyl-L-glutamine." [UniMod:490#Q] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-glutamine residue to N-heptosyl-L-glutamine." [Unimod:490#Q] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23029,15 +23911,16 @@ xref: Origin: "Q" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01198 name: O-heptosyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-heptosyl-L-serine." [UniMod:490#S] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-serine residue to O-heptosyl-L-serine." [Unimod:490#S] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23047,15 +23930,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01199 name: N-heptosyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to an N-heptosyl-L-arginine." [UniMod:490#R] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-arginine residue to an N-heptosyl-L-arginine." [Unimod:490#R] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23065,15 +23949,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01200 name: O-heptosyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-heptosyl-L-threonine." [UniMod:490#T] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-threonine residue to O-heptosyl-L-threonine." [Unimod:490#T] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23083,15 +23968,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01201 name: N6-heptosyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-heptosyl-L-lysine." [UniMod:490#K] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-lysine residue to N6-heptosyl-L-lysine." [Unimod:490#K] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23101,15 +23987,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01202 name: N-heptosyl-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N-heptosyl-L-asparagine." [UniMod:490#N] -comment: From UniMod with no citation [JSG]. +def: "A protein modification that effectively converts an L-asparagine residue to N-heptosyl-L-asparagine." [Unimod:490#N] +comment: From Unimod with no citation [JSG]. synonym: "Hep" RELATED PSI-MS-label [] -synonym: "Heptose" RELATED UniMod-description [] +synonym: "Heptose" RELATED Unimod-description [] xref: DiffAvg: "192.17" xref: DiffFormula: "C 7 H 12 O 6" xref: DiffMono: "192.063388" @@ -23119,15 +24006,16 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:490" is_a: MOD:00925 ! heptosylated residue [Term] id: MOD:01203 name: N6-(pyridylacetyl)lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-[(pyrid-3-yl)acetyl]lysine." [PubMed:9276974, UniMod:25#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-[(pyrid-3-yl)acetyl]lysine." [PubMed:9276974, Unimod:25#K] comment: Produced by reaction with N-[(pyrid-3-yl)acetyl]oxy-succinimide [JSG]. synonym: "Pyridylacetyl" RELATED PSI-MS-label [] -synonym: "pyridylacetyl" RELATED UniMod-description [] +synonym: "pyridylacetyl" RELATED Unimod-description [] xref: DiffAvg: "119.12" xref: DiffFormula: "C 7 H 5 N 1 O 1" xref: DiffMono: "119.037114" @@ -23137,15 +24025,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:25" is_a: MOD:00418 ! pyridylacetylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01204 name: prompt loss of methanethiol from oxidixed methionine -def: "modification from UniMod Artifact -" [PubMed:9004526, UniMod:526] +def: "modification from Unimod Artifact -" [PubMed:9004526, Unimod:526] synonym: "Dethiomethyl" RELATED PSI-MS-label [] -synonym: "Prompt loss of side chain from oxidised Met" RELATED UniMod-description [] +synonym: "Prompt loss of side chain from oxidised Met" RELATED Unimod-description [] xref: DiffAvg: "-48.10" xref: DiffFormula: "C -1 H -4 S -1" xref: DiffMono: "-48.003371" @@ -23155,14 +24044,15 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:526" is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:01205 name: Hex1HexNAc1NeuAc2 O-glycosylated serine -def: "A protein modification that effectively replaces an O3 hydrogen atom of a serine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [PubMed:7949339, UniMod:160#S] +def: "A protein modification that effectively replaces an O3 hydrogen atom of a serine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [PubMed:7949339, Unimod:160#S] synonym: "Hex(1)HexNAc(1)NeuAc(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc2" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc2" RELATED Unimod-description [] xref: DiffAvg: "947.85" xref: DiffFormula: "C 36 H 57 N 3 O 26" xref: DiffMono: "947.323029" @@ -23172,15 +24062,16 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:160" is_a: MOD:00528 ! Hex1HexNAc1NeuAc2 glycosylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01206 name: Hex1HexNAc1NeuAc2 O-glycosylated threonine -def: "A protein modification that effectively replaces an O3 hydrogen atom of a threonine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [UniMod:160#T] +def: "A protein modification that effectively replaces an O3 hydrogen atom of a threonine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [Unimod:160#T] synonym: "Hex(1)HexNAc(1)NeuAc(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc2" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc2" RELATED Unimod-description [] xref: DiffAvg: "947.85" xref: DiffFormula: "C 36 H 57 N 3 O 26" xref: DiffMono: "947.323029" @@ -23190,15 +24081,16 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:160" is_a: MOD:00528 ! Hex1HexNAc1NeuAc2 glycosylated residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:00005 ! O-glycosyl-L-threonine [Term] id: MOD:01207 name: Hex1HexNAc1NeuAc2 N4-glycosylated asparagine -def: "A protein modification that effectively replaces an N4 hydrogen atom of an asparagine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [UniMod:160#N] +def: "A protein modification that effectively replaces an N4 hydrogen atom of an asparagine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc2 linked through a glycosidic bond." [Unimod:160#N] synonym: "Hex(1)HexNAc(1)NeuAc(2)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc2" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc2" RELATED Unimod-description [] xref: DiffAvg: "947.85" xref: DiffFormula: "C 36 H 57 N 3 O 26" xref: DiffMono: "947.323029" @@ -23208,16 +24100,17 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:160" is_a: MOD:00528 ! Hex1HexNAc1NeuAc2 glycosylated residue -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:01208 name: copper(1+) carboxylate C-terminal residue -def: "A protein modification that effectively converts a C-terminal residue to the copper(1+) carboxylate salt." [UniMod:531#C-term] +def: "A protein modification that effectively converts a C-terminal residue to the copper(1+) carboxylate salt." [Unimod:531#C-term] synonym: "Cation:Cu[I]" RELATED PSI-MS-label [] synonym: "cuprous salt" EXACT PSI-MOD-alternate [] -synonym: "Replacement of proton by copper" RELATED UniMod-description [] +synonym: "Replacement of proton by copper" RELATED Unimod-description [] xref: DiffAvg: "62.54" xref: DiffFormula: "Cu 1 H -1" xref: DiffMono: "61.921772" @@ -23227,15 +24120,16 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:531" is_a: MOD:00742 ! copper containing modified residue [Term] id: MOD:01209 name: copper(1+) L-aspartate -def: "A protein modification that effectively converts an L-aspartic acid residue to the copper(1+) aspartate salt." [UniMod:531#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to the copper(1+) aspartate salt." [Unimod:531#D] synonym: "Cation:Cu[I]" RELATED PSI-MS-label [] synonym: "cuprous salt" EXACT PSI-MOD-alternate [] -synonym: "Replacement of proton by copper" RELATED UniMod-description [] +synonym: "Replacement of proton by copper" RELATED Unimod-description [] xref: DiffAvg: "62.54" xref: DiffFormula: "Cu 1 H -1" xref: DiffMono: "61.921772" @@ -23245,16 +24139,17 @@ xref: Origin: "D" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:531" is_a: MOD:00742 ! copper containing modified residue -is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue [Term] id: MOD:01210 name: copper(1+) L-glutamate -def: "A protein modification that effectively converts an L-glutamic acid residue to the copper(1+) glutamate salt." [UniMod:531#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to the copper(1+) glutamate salt." [Unimod:531#E] synonym: "Cation:Cu[I]" RELATED PSI-MS-label [] synonym: "cuprous salt" EXACT PSI-MOD-alternate [] -synonym: "Replacement of proton by copper" RELATED UniMod-description [] +synonym: "Replacement of proton by copper" RELATED Unimod-description [] xref: DiffAvg: "62.54" xref: DiffFormula: "Cu 1 H -1" xref: DiffMono: "61.921772" @@ -23264,15 +24159,16 @@ xref: Origin: "E" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:531" is_a: MOD:00742 ! copper containing modified residue -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue [Term] id: MOD:01211 name: N6-(morpholine-2-acetyl)-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-(morpholine-2-acetyl)-lysine." [PubMed:10446193, UniMod:29#K] -comment: The UniMod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. -synonym: "N-Succinimidyl-2-morpholine acetate" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to N6-(morpholine-2-acetyl)-lysine." [PubMed:10446193, Unimod:29#K] +comment: The Unimod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. +synonym: "N-Succinimidyl-2-morpholine acetate" RELATED Unimod-description [] synonym: "N-succinimidylmorpholine-2-acetate N6-derivatized lysine" EXACT PSI-MOD-alternate [] synonym: "SMA" RELATED PSI-MS-label [] xref: DiffAvg: "127.14" @@ -23284,17 +24180,18 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:29" is_a: MOD:01813 ! morpholine-2-acetylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01212 name: iodoacetamide N6-derivatized lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-(carboxamidomethyl)lysine." [OMSSA:27, PubMed:11510821, PubMed:12422359, PubMed:12686488, UniMod:4#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-(carboxamidomethyl)lysine." [OMSSA:27, PubMed:11510821, PubMed:12422359, PubMed:12686488, Unimod:4#K] subset: PSI-MOD-slim synonym: "Carbamidomethyl" RELATED PSI-MS-label [] synonym: "carbamidomethylk" EXACT OMSSA-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] synonym: "N6-(2-amino-2-oxoethyl)lysine" EXACT PSI-MOD-alternate [] synonym: "N6-(carbamoylmethyl)lysine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "57.05" @@ -23306,17 +24203,18 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01213 name: iodoacetamide derivatized histidine -def: "A protein modification that effectively converts an L-histidine residue to an iodoacetamide derivatized histidine, either 1'- or 3'-(carboxamidolmethyl)histidine." [OMSSA:28, PubMed:11510821, PubMed:12422359, PubMed:15627961, PubMed:2026710, UniMod:4#H] +def: "A protein modification that effectively converts an L-histidine residue to an iodoacetamide derivatized histidine, either 1'- or 3'-(carboxamidolmethyl)histidine." [OMSSA:28, PubMed:11510821, PubMed:12422359, PubMed:15627961, PubMed:2026710, Unimod:4#H] subset: PSI-MOD-slim synonym: "Carbamidomethyl" RELATED PSI-MS-label [] synonym: "carbamidometylh" EXACT OMSSA-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -23326,15 +24224,16 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:01214 name: iodoacetamide - site C -def: "modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060." [PubMed:10504701, PubMed:11510821, PubMed:12422359, UniMod:4#C] +def: "modification from Unimod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060." [PubMed:10504701, PubMed:11510821, PubMed:12422359, Unimod:4#C] synonym: "Carbamidomethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -23344,16 +24243,18 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01060" +xref: Unimod: "Unimod:4" is_obsolete: true [Term] id: MOD:01215 name: iodoacetamide derivatized aspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to O4-(carboxamidomethyl)aspartate." [OMSSA:29, PubMed:11510821, PubMed:12422359, PubMed:16526082, UniMod:4#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to O4-(carboxamidomethyl)aspartate." [OMSSA:29, PubMed:11510821, PubMed:12422359, PubMed:16526082, Unimod:4#D] subset: PSI-MOD-slim synonym: "Carbamidomethyl" RELATED PSI-MS-label [] synonym: "carbamidomethyld" EXACT OMSSA-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -23363,17 +24264,18 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:01216 name: iodoacetamide derivatized glutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to O5-(carboxamidomethyl)glutamate." [OMSSA:30, PubMed:11510821, PubMed:12422359, UniMod:4#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to O5-(carboxamidomethyl)glutamate." [OMSSA:30, PubMed:11510821, PubMed:12422359, Unimod:4#E] subset: PSI-MOD-slim synonym: "Carbamidomethyl" RELATED PSI-MS-label [] synonym: "carbamidomethyle" EXACT OMSSA-label [] -synonym: "Iodoacetamide derivative" RELATED UniMod-description [] +synonym: "Iodoacetamide derivative" RELATED Unimod-description [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" @@ -23383,14 +24285,15 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: UniMo: "Unimod:4" is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:01217 name: Sulfanilic Acid (SA), light C12 - site D -def: "modification from UniMod Isotopic label -" [PubMed:12872131, UniMod:285#D] -synonym: "Light Sulfanilic Acid (SA) C12" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:12872131, Unimod:285#D] +synonym: "Light Sulfanilic Acid (SA) C12" RELATED Unimod-description [] synonym: "SulfanilicAcid" RELATED PSI-MS-label [] xref: DiffAvg: "155.00" xref: DiffFormula: "(12)C 6 H 5 N 1 O 2 S 1" @@ -23401,13 +24304,14 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:285" is_a: MOD:00605 ! Sulfanilic Acid (SA), light C12 [Term] id: MOD:01218 name: Sulfanilic Acid (SA), light C12 - site E -def: "modification from UniMod Isotopic label -" [PubMed:15283597, UniMod:285#E] -synonym: "Light Sulfanilic Acid (SA) C12" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:15283597, Unimod:285#E] +synonym: "Light Sulfanilic Acid (SA) C12" RELATED Unimod-description [] synonym: "SulfanilicAcid" RELATED PSI-MS-label [] xref: DiffAvg: "155.00" xref: DiffFormula: "(12)C 6 H 5 N 1 O 2 S 1" @@ -23418,13 +24322,14 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:285" is_a: MOD:00605 ! Sulfanilic Acid (SA), light C12 [Term] id: MOD:01219 name: Sulfanilic Acid (SA), heavy C13 - site D -def: "modification from UniMod Chemical derivative -" [PubMed:9254591, PubMed:9750125, UniMod:286#D] -synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:9254591, PubMed:9750125, Unimod:286#D] +synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED Unimod-description [] synonym: "SulfanilicAcid:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "161.02" xref: DiffFormula: "(13)C 6 H 5 N 1 O 2 S 1" @@ -23435,13 +24340,14 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:286" is_a: MOD:00606 ! Sulfanilic Acid (SA), heavy C13 [Term] id: MOD:01220 name: Sulfanilic Acid (SA), heavy C13 - site E -def: "modification from UniMod Chemical derivative -" [PubMed:15121203, PubMed:9254591, UniMod:286#E] -synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:15121203, PubMed:9254591, Unimod:286#E] +synonym: "Heavy Sulfanilic Acid (SA) C13" RELATED Unimod-description [] synonym: "SulfanilicAcid:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "161.02" xref: DiffFormula: "(13)C 6 H 5 N 1 O 2 S 1" @@ -23452,15 +24358,16 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:286" is_a: MOD:00606 ! Sulfanilic Acid (SA), heavy C13 [Term] id: MOD:01221 name: O-formyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-formyl-L-threonine." [PubMed:11861642, PubMed:15799070, UniMod:122#T] -comment: From UniMod: Can occur under CNBr cleavage conditions (70% HCOOH). +def: "A protein modification that effectively converts an L-threonine residue to O-formyl-L-threonine." [PubMed:11861642, PubMed:15799070, Unimod:122#T] +comment: From Unimod: Can occur under CNBr cleavage conditions (70% HCOOH). synonym: "Formyl" RELATED PSI-MS-label [] -synonym: "Formylation" RELATED UniMod-description [] +synonym: "Formylation" RELATED Unimod-description [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" xref: DiffMono: "27.994915" @@ -23470,16 +24377,17 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +xref: Unimod: "Unimod:122" +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01483 ! O-formylated residue [Term] id: MOD:01222 name: O-formyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-formyl-L-serine." [PubMed:15627961, PubMed:15799070, UniMod:122#S] -comment: From UniMod: Can occur under CNBr cleavage conditions (70% HCOOH). +def: "A protein modification that effectively converts an L-serine residue to O-formyl-L-serine." [PubMed:15627961, PubMed:15799070, Unimod:122#S] +comment: From Unimod: Can occur under CNBr cleavage conditions (70% HCOOH). synonym: "Formyl" RELATED PSI-MS-label [] -synonym: "Formylation" RELATED UniMod-description [] +synonym: "Formylation" RELATED Unimod-description [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" xref: DiffMono: "27.994915" @@ -23489,18 +24397,19 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: Unimod: "Unimod:122" +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01483 ! O-formylated residue [Term] id: MOD:01223 name: thioacylation of primary amines - site N-term -def: "modification from UniMod Other -" [OMSSA:41, PubMed:11710128, PubMed:3155470, PubMed:957432, UniMod:126#N-term] -comment: This UniMod entry is misdescribed as "thioacylation" [JSG]. -synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED UniMod-alternate [] +def: "modification from Unimod Other -" [OMSSA:41, PubMed:11710128, PubMed:3155470, PubMed:957432, Unimod:126#N-term] +comment: This Unimod entry is misdescribed as "thioacylation" [JSG]. +synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED Unimod-alternate [] synonym: "ntermpeptioacetyl" EXACT OMSSA-label [] synonym: "Thioacyl" RELATED PSI-MS-label [] -synonym: "thioacylation of primary amines (N-term and Lys)" RELATED UniMod-description [] +synonym: "thioacylation of primary amines (N-term and Lys)" RELATED Unimod-description [] xref: DiffAvg: "88.12" xref: DiffFormula: "C 3 H 4 O 1 S 1" xref: DiffMono: "87.998286" @@ -23510,17 +24419,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:126" is_a: MOD:00497 ! 3-sulfanylpropanoyl (N-term and Lys) [Term] id: MOD:01224 name: thioacylation of primary amines - site K -def: "modification from UniMod Other -" [OMSSA:40, PubMed:11710128, PubMed:3155470, PubMed:957432, UniMod:126#K] -comment: This UniMod entry is misdescribed as "thioacylation" [JSG]. -synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED UniMod-alternate [] +def: "modification from Unimod Other -" [OMSSA:40, PubMed:11710128, PubMed:3155470, PubMed:957432, Unimod:126#K] +comment: This Unimod entry is misdescribed as "thioacylation" [JSG]. +synonym: "3,3-Dithio-bis-(sulfosuccinimidyl)propionate" RELATED Unimod-alternate [] synonym: "thioacetylk" EXACT OMSSA-label [] synonym: "Thioacyl" RELATED PSI-MS-label [] -synonym: "thioacylation of primary amines (N-term and Lys)" RELATED UniMod-description [] +synonym: "thioacylation of primary amines (N-term and Lys)" RELATED Unimod-description [] xref: DiffAvg: "88.12" xref: DiffFormula: "C 3 H 4 O 1 S 1" xref: DiffMono: "87.998286" @@ -23530,15 +24440,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:126" is_a: MOD:00497 ! 3-sulfanylpropanoyl (N-term and Lys) [Term] id: MOD:01225 name: monofluorinated L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue into an L-fluorotyrosine." [OMSSA:46, PubMed:8069568, UniMod:127#Y] -comment: From UniMod: the citation appears to be correct, but the PMID is not and has been corrected [JSG]. +def: "A protein modification that effectively converts an L-tyrosine residue into an L-fluorotyrosine." [OMSSA:46, PubMed:8069568, Unimod:127#Y] +comment: From Unimod: the citation appears to be correct, but the PMID is not and has been corrected [JSG]. synonym: "Fluoro" RELATED PSI-MS-label [] -synonym: "fluorophenylalanine replacement of phenylalanine" RELATED UniMod-description [] +synonym: "fluorophenylalanine replacement of phenylalanine" RELATED Unimod-description [] synonym: "phef" EXACT OMSSA-label [] xref: DiffAvg: "17.99" xref: DiffFormula: "F 1 H -1" @@ -23549,16 +24460,17 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:127" is_a: MOD:00498 ! fluorinated residue is_a: MOD:00985 ! halogenated tyrosine [Term] id: MOD:01226 name: monofluorinated L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to an L-fluorotryptophan." [PubMed:8069568, UniMod:127#W] -comment: From UniMod: the citation appears to be correct, but the PMID is not and has been corrected [JSG]. +def: "A protein modification that effectively converts an L-tryptophan residue to an L-fluorotryptophan." [PubMed:8069568, Unimod:127#W] +comment: From Unimod: the citation appears to be correct, but the PMID is not and has been corrected [JSG]. synonym: "Fluoro" RELATED PSI-MS-label [] -synonym: "fluorophenylalanine replacement of phenylalanine" RELATED UniMod-description [] +synonym: "fluorophenylalanine replacement of phenylalanine" RELATED Unimod-description [] xref: DiffAvg: "17.99" xref: DiffFormula: "F 1 H -1" xref: DiffMono: "17.990578" @@ -23568,16 +24480,17 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:127" is_a: MOD:00498 ! fluorinated residue is_a: MOD:01068 ! halogenated tryptophan [Term] id: MOD:01227 name: monofluorinated L-phenylalanine -def: "A protein modification that effectively converts an L-phenylalanine residue to an L-fluorophenylalanine." [DeltaMass:181, OMSSA:46, PubMed:8069568, UniMod:127#F] -comment: From UniMod: the citation appears to be correct, but the PMID is not and has been corrected. From DeltaMass: (element abbreviation in formula incorrect, mass incorrect, and aggregate not delta) Average Mass: 149 Formula: C9H8O1N1Fl1 Average Mass Change: 149 References:PE Sciex with no citation [JSG]. +def: "A protein modification that effectively converts an L-phenylalanine residue to an L-fluorophenylalanine." [DeltaMass:181, OMSSA:46, PubMed:8069568, Unimod:127#F] +comment: From Unimod: the citation appears to be correct, but the PMID is not and has been corrected. From DeltaMass: (element abbreviation in formula incorrect, mass incorrect, and aggregate not delta) Average Mass: 149 Formula: C9H8O1N1Fl1 Average Mass Change: 149 References:PE Sciex with no citation [JSG]. synonym: "Fluoro" RELATED PSI-MS-label [] -synonym: "fluorophenylalanine replacement of phenylalanine" RELATED UniMod-description [] +synonym: "fluorophenylalanine replacement of phenylalanine" RELATED Unimod-description [] synonym: "phef" EXACT OMSSA-label [] xref: DiffAvg: "17.99" xref: DiffFormula: "C 0 F 1 H -1 N 0 O 0" @@ -23588,17 +24501,18 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:127" is_a: MOD:00498 ! fluorinated residue is_a: MOD:01066 ! halogenated phenylalanine [Term] id: MOD:01228 name: monoiodinated tyrosine -def: "A protein modification that effectively substitutes one hydrogen atom of an L-tyrosine residue with one iodine atom." [DeltaMass:0, OMSSA:65, PubMed:1326520, PubMed:15627961, PubMed:2026710, UniMod:129#Y] +def: "A protein modification that effectively substitutes one hydrogen atom of an L-tyrosine residue with one iodine atom." [DeltaMass:0, OMSSA:65, PubMed:1326520, PubMed:15627961, PubMed:2026710, Unimod:129#Y] comment: From DeltaMass: Average Mass: 289 [name misspelled "monoiodated" - JSG]. subset: PSI-MOD-slim synonym: "I1Tyr" EXACT PSI-MOD-label [] -synonym: "Iodination" RELATED UniMod-description [] +synonym: "Iodination" RELATED Unimod-description [] synonym: "iodinationy" EXACT OMSSA-label [] synonym: "Iodo" RELATED PSI-MS-label [] xref: DiffAvg: "125.90" @@ -23610,15 +24524,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:129" is_a: MOD:00500 ! monoiodinated residue is_a: MOD:00998 ! iodinated tyrosine [Term] id: MOD:01229 name: L-iodohistidine -def: "A protein modification that effectively converts an L-histidine residue to an L-iodohistidine." [PubMed:15627961, PubMed:2026710, UniMod:129#H] +def: "A protein modification that effectively converts an L-histidine residue to an L-iodohistidine." [PubMed:15627961, PubMed:2026710, Unimod:129#H] synonym: "I1His" EXACT PSI-MOD-label [] -synonym: "Iodination" RELATED UniMod-description [] +synonym: "Iodination" RELATED Unimod-description [] synonym: "Iodo" RELATED PSI-MS-label [] xref: DiffAvg: "125.90" xref: DiffFormula: "C 0 H -1 I 1 N 0 O 0" @@ -23629,14 +24544,15 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:129" is_a: MOD:00500 ! monoiodinated residue is_a: MOD:01049 ! halogenated histidine [Term] id: MOD:01230 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form - site K -def: "modification from UniMod Isotopic label -" [PubMed:15602776, UniMod:365#K] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:15602776, Unimod:365#K] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form" RELATED Unimod-description [] synonym: "ICPL" RELATED PSI-MS-label [] xref: DiffAvg: "105.02" xref: DiffFormula: "(12)C 6 H 3 N 1 O 1" @@ -23647,14 +24563,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:365" is_a: MOD:00790 ! Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, light form [Term] id: MOD:01231 name: 3x(13)C labeled N6-propanoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 3x(13)C labeled N6-propanoyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:12442261, UniMod:59#K] +def: "A protein modification that effectively converts an L-lysine residue to 3x(13)C labeled N6-propanoyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:12442261, Unimod:59#K] subset: PSI-MOD-slim -synonym: "Propionate labeling reagent heavy form (+3amu), N-term & K" RELATED UniMod-description [] +synonym: "Propionate labeling reagent heavy form (+3amu), N-term & K" RELATED Unimod-description [] synonym: "Propionyl:13C(3)" RELATED PSI-MS-label [] xref: DiffAvg: "59.04" xref: DiffFormula: "(13)C 3 H 4 O 1" @@ -23665,14 +24582,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01398 ! N6-propanoyl-L-lysine +xref: Unimod: "Unimod:59" +relationship: derives_from MOD:01398 ! N6-propanoyl-L-lysine +is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:01232 name: 3x(12)C labeled N6-propanoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 3x(12)C labeled N6-propanoyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:58#K] +def: "A protein modification that effectively converts an L-lysine residue to 3x(12)C labeled N6-propanoyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:58#K] subset: PSI-MOD-slim -synonym: "Propionate labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "Propionate labeling reagent light form (N-term & K)" RELATED Unimod-description [] synonym: "Propionyl" RELATED PSI-MS-label [] xref: DiffAvg: "56.03" xref: DiffFormula: "(12)C 3 H 4 O 1" @@ -23683,14 +24602,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01398 ! N6-propanoyl-L-lysine +xref: Unimod: "Unimod:58" +relationship: derives_from MOD:01398 ! N6-propanoyl-L-lysine +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01233 name: 3x(2)H labeled N6-acetyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled N6-acetyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:56#K] +def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled N6-acetyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:56#K] subset: PSI-MOD-slim -synonym: "Acetate labeling reagent (N-term & K) (heavy form, +3amu)" RELATED UniMod-description [] +synonym: "Acetate labeling reagent (N-term & K) (heavy form, +3amu)" RELATED Unimod-description [] synonym: "Acetyl:2H(3)" RELATED PSI-MS-label [] xref: DiffAvg: "45.03" xref: DiffFormula: "C 2 (1)H -1 (2)H 3 O 1" @@ -23701,16 +24622,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00064 ! N6-acetyl-L-lysine +xref: Unimod: "Unimod:56" +relationship: derives_from MOD:00064 ! N6-acetyl-L-lysine is_a: MOD:00449 ! acetate labeling reagent (N-term) (heavy form, +3amu) [Term] id: MOD:01234 name: (18)O monosubstituted L-serine -def: "modification from UniMod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, UniMod:258#S] +def: "modification from Unimod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, Unimod:258#S] subset: PSI-MOD-slim synonym: "Label:18O(1)" RELATED PSI-MS-label [] -synonym: "O18 Labeling" RELATED UniMod-description [] +synonym: "O18 Labeling" RELATED Unimod-description [] xref: DiffAvg: "2.00" xref: DiffFormula: "(16)O -1 (18)O 1" xref: DiffMono: "2.004246" @@ -23720,16 +24642,17 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:258" is_a: MOD:00581 ! (18)O monosubstituted residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01235 name: (18)O monosubstituted L-threonine -def: "modification from UniMod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, PubMed:15549660, UniMod:258#T] +def: "modification from Unimod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, PubMed:15549660, Unimod:258#T] subset: PSI-MOD-slim synonym: "Label:18O(1)" RELATED PSI-MS-label [] -synonym: "O18 Labeling" RELATED UniMod-description [] +synonym: "O18 Labeling" RELATED Unimod-description [] xref: DiffAvg: "2.00" xref: DiffFormula: "(16)O -1 (18)O 1" xref: DiffMono: "2.004246" @@ -23739,16 +24662,17 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:258" is_a: MOD:00581 ! (18)O monosubstituted residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01236 name: (18)O monosubstituted L-tyrosine -def: "modification from UniMod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, PubMed:15549660, UniMod:258#Y] +def: "modification from Unimod Isotopic label - alkaline phosphatase to dephosphorylate" [PubMed:11467524, PubMed:15549660, Unimod:258#Y] subset: PSI-MOD-slim synonym: "Label:18O(1)" RELATED PSI-MS-label [] -synonym: "O18 Labeling" RELATED UniMod-description [] +synonym: "O18 Labeling" RELATED Unimod-description [] xref: DiffAvg: "2.00" xref: DiffFormula: "(16)O -1 (18)O 1" xref: DiffMono: "2.004246" @@ -23758,15 +24682,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:258" is_a: MOD:00581 ! (18)O monosubstituted residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01237 name: cysteine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-cysteine residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, PubMed:9629898, UniMod:53#C] +def: "A protein modification produced by formation of an adduct of an L-cysteine residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, PubMed:9629898, Unimod:53#C] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. -synonym: "4-hydroxynonenal (HNE)" RELATED UniMod-description [] +synonym: "4-hydroxynonenal (HNE)" RELATED Unimod-description [] synonym: "HNE" RELATED PSI-MS-label [] xref: DiffAvg: "156.22" xref: DiffFormula: "C 9 H 16 O 2" @@ -23777,14 +24702,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:53" is_a: MOD:00446 ! 4-hydroxynonenal adduct [Term] id: MOD:01238 name: lysine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-lysine residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, PubMed:9629898, UniMod:53#K] +def: "A protein modification produced by formation of an adduct of an L-lysine residue with 4-hydroxynonenal." [PubMed:11327326, PubMed:15133838, PubMed:9629898, Unimod:53#K] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. -synonym: "4-hydroxynonenal (HNE)" RELATED UniMod-description [] +synonym: "4-hydroxynonenal (HNE)" RELATED Unimod-description [] synonym: "HNE" RELATED PSI-MS-label [] xref: DiffAvg: "156.22" xref: DiffFormula: "C 9 H 16 O 2" @@ -23795,14 +24721,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:53" is_a: MOD:00446 ! 4-hydroxynonenal adduct [Term] id: MOD:01239 name: histidine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal." [PubMed:10717661, PubMed:11327326, PubMed:15133838, UniMod:53#H] +def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal." [PubMed:10717661, PubMed:11327326, PubMed:15133838, Unimod:53#H] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. -synonym: "4-hydroxynonenal (HNE)" RELATED UniMod-description [] +synonym: "4-hydroxynonenal (HNE)" RELATED Unimod-description [] synonym: "HNE" RELATED PSI-MS-label [] xref: DiffAvg: "156.22" xref: DiffFormula: "C 9 H 16 O 2" @@ -23813,14 +24740,15 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:53" is_a: MOD:00446 ! 4-hydroxynonenal adduct [Term] id: MOD:01240 name: ubiquitination signature tetrapeptidyl lysine -def: "A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of leucyl-arginyl-glycyl-glycine, the C-terminal tetrapeptide of ubiquitin." [PubMed:10504701, UniMod:535] +def: "A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of leucyl-arginyl-glycyl-glycine, the C-terminal tetrapeptide of ubiquitin." [PubMed:10504701, Unimod:535] synonym: "LeuArgGlyGly" RELATED PSI-MS-label [] -synonym: "Ubiquitination" RELATED UniMod-description [] +synonym: "Ubiquitination" RELATED Unimod-description [] xref: DiffAvg: "383.45" xref: DiffFormula: "C 16 H 29 N 7 O 4" xref: DiffMono: "383.228102" @@ -23830,15 +24758,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +xref: Unimod: "Unimod:535" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01875 ! N6-acylated L-lysine relationship: derives_from MOD:01148 ! ubiquitinylated lysine [Term] id: MOD:01241 name: 3x(2)H labeled L-aspartic acid 4-methyl ester -def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled L-aspartic acid 4-methyl ester." [OMSSA:19, PubMed:12185208, UniMod:298#D] -synonym: "deuterated methyl ester" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled L-aspartic acid 4-methyl ester." [OMSSA:19, PubMed:12185208, Unimod:298#D] +synonym: "deuterated methyl ester" RELATED Unimod-description [] synonym: "Methyl:2H(3)" RELATED PSI-MS-label [] synonym: "trideuteromethyld" EXACT OMSSA-label [] xref: DiffAvg: "17.03" @@ -23850,6 +24780,7 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:298" is_a: MOD:00617 ! 3x(2)H residue methyl ester is_a: MOD:00904 ! modified L-aspartic acid residue relationship: derives_from MOD:01181 ! L-aspartic acid 4-methyl ester @@ -23857,8 +24788,8 @@ [Term] id: MOD:01242 name: 3x(2)H labeled L-glutamic acid 5-methyl ester -def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled L-glutamic acid 5-methyl ester." [OMSSA:20, PubMed:1326520, UniMod:298#E] -synonym: "deuterated methyl ester" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 3x(2)H labeled L-glutamic acid 5-methyl ester." [OMSSA:20, PubMed:1326520, Unimod:298#E] +synonym: "deuterated methyl ester" RELATED Unimod-description [] synonym: "Methyl:2H(3)" RELATED PSI-MS-label [] synonym: "trideuteromethyle" EXACT OMSSA-label [] xref: DiffAvg: "17.03" @@ -23870,6 +24801,7 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:298" is_a: MOD:00617 ! 3x(2)H residue methyl ester is_a: MOD:00906 ! modified L-glutamic acid residue relationship: derives_from MOD:00081 ! L-glutamic acid 5-methyl ester (Glu) @@ -23877,9 +24809,9 @@ [Term] id: MOD:01243 name: potassium carboxylate C-terminal residue -def: "A protein modification that effectively converts a C-terminal residue to the potassium carboxylate salt." [UniMod:530#C-term] +def: "A protein modification that effectively converts a C-terminal residue to the potassium carboxylate salt." [Unimod:530#C-term] synonym: "Cation:K" RELATED PSI-MS-label [] -synonym: "Replacement of proton by potassium" RELATED UniMod-description [] +synonym: "Replacement of proton by potassium" RELATED Unimod-description [] xref: DiffAvg: "38.09" xref: DiffFormula: "H -1 K 1" xref: DiffMono: "37.955882" @@ -23889,14 +24821,15 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:530" is_a: MOD:01072 ! monopotassium salt [Term] id: MOD:01244 name: potassium L-glutamate -def: "A protein modification that effectively converts an L-glutamioc acid residue to the potassium glutamate salt." [UniMod:530#E] +def: "A protein modification that effectively converts an L-glutamioc acid residue to the potassium glutamate salt." [Unimod:530#E] synonym: "Cation:K" RELATED PSI-MS-label [] -synonym: "Replacement of proton by potassium" RELATED UniMod-description [] +synonym: "Replacement of proton by potassium" RELATED Unimod-description [] xref: DiffAvg: "38.09" xref: DiffFormula: "H -1 K 1" xref: DiffMono: "37.955882" @@ -23906,15 +24839,16 @@ xref: Origin: "E" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:530" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01072 ! monopotassium salt [Term] id: MOD:01245 name: potassium L-aspartate -def: "A protein modification that effectively converts an L-aspartic acid residue to the potassium aspartate salt." [UniMod:530#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to the potassium aspartate salt." [Unimod:530#D] synonym: "Cation:K" RELATED PSI-MS-label [] -synonym: "Replacement of proton by potassium" RELATED UniMod-description [] +synonym: "Replacement of proton by potassium" RELATED Unimod-description [] xref: DiffAvg: "38.09" xref: DiffFormula: "H -1 K 1" xref: DiffMono: "37.955882" @@ -23924,15 +24858,16 @@ xref: Origin: "D" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:530" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01072 ! monopotassium salt [Term] id: MOD:01246 name: fucosylated -site S -def: "OBSOLETE because redundant and identical to MOD:00812 after formula correction. Remap to MOD:00812." [PubMed:11344537, PubMed:15189151, PubMed:3311742, PubMed:3578767, UniMod:295#S] +def: "OBSOLETE because redundant and identical to MOD:00812 after formula correction. Remap to MOD:00812." [PubMed:11344537, PubMed:15189151, PubMed:3311742, PubMed:3578767, Unimod:295#S] synonym: "dHex" RELATED PSI-MS-label [] -synonym: "Fucose" RELATED UniMod-description [] +synonym: "Fucose" RELATED Unimod-description [] xref: DiffAvg: "147.15" xref: DiffFormula: "C 6 H 11 O 4" xref: DiffMono: "147.065734" @@ -23942,14 +24877,16 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00812" +xref: Unimod: "Unimod:295" is_obsolete: true [Term] id: MOD:01247 name: fucosylated -site T -def: "OBSOLETE because redundant and identical to MOD:00813 after formula correction. Remap to MOD:00813." [PubMed:11344537, PubMed:11857757, PubMed:15189151, UniMod:295#T] +def: "OBSOLETE because redundant and identical to MOD:00813 after formula correction. Remap to MOD:00813." [PubMed:11344537, PubMed:11857757, PubMed:15189151, Unimod:295#T] synonym: "dHex" RELATED PSI-MS-label [] -synonym: "Fucose" RELATED UniMod-description [] +synonym: "Fucose" RELATED Unimod-description [] xref: DiffAvg: "147.15" xref: DiffFormula: "C 6 H 11 O 4" xref: DiffMono: "147.065734" @@ -23959,14 +24896,16 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00813" +xref: Unimod: "Unimod:295" is_obsolete: true [Term] id: MOD:01248 name: iodouridine monophosphate derivatized tyrosine -def: "A protein modification that is produced by reaction of iodouridine monophosphate, or a polynucleotide containing iodouridine, with an L-tyrosine residue to form an ether linkage." [PubMed:11112526, PubMed:11567090, PubMed:6540775, UniMod:292#Y] +def: "A protein modification that is produced by reaction of iodouridine monophosphate with an L-tyrosine residue to form an ether linkage." [PubMed:11112526, PubMed:11567090, PubMed:6540775, Unimod:292#Y] comment: This has an ether linkage and not a phosphodiester linkage with UMP. -synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED UniMod-description [] +synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED Unimod-description [] synonym: "IodoU-AMP" RELATED PSI-MS-label [] xref: DiffAvg: "322.17" xref: DiffFormula: "C 9 H 11 N 2 O 9 P 1" @@ -23977,15 +24916,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:292" is_a: MOD:00611 ! iodouridine monophosphate derivatized residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01249 name: iodouridine monophosphate derivatized tryptophan -def: "A protein modification that is produced by reaction of iodouridine monophosphate, or a polynucleotide containing iodouridine, with an L-tryptophan residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, UniMod:292#W] +def: "A protein modification that is produced by reaction of iodouridine monophosphate with an L-tryptophan residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, Unimod:292#W] comment: This has a carbon-nitrogen linkage and not a phosphodiester linkage with UMP. -synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED UniMod-description [] +synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED Unimod-description [] synonym: "IodoU-AMP" RELATED PSI-MS-label [] xref: DiffAvg: "322.17" xref: DiffFormula: "C 9 H 11 N 2 O 9 P 1" @@ -23996,15 +24936,16 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:292" is_a: MOD:00611 ! iodouridine monophosphate derivatized residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:01250 name: iodouridine monophosphate derivatized phenylalanine -def: "A protein modification that is produced by reaction of iodouridine monophosphate, or a polynucleotide containing iodouridine, with an L-phenylalanine residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, UniMod:292#F] +def: "A protein modification that is produced by reaction of iodouridine monophosphate with an L-phenylalanine residue." [PubMed:11112526, PubMed:11567090, PubMed:6540775, Unimod:292#F] comment: This has a carbon-carbon linkage and not a phosphodiester linkage with UMP. -synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED UniMod-description [] +synonym: "Cross-link of (Iodo)-uracil MP with W,F,Y" RELATED Unimod-description [] synonym: "IodoU-AMP" RELATED PSI-MS-label [] xref: DiffAvg: "322.17" xref: DiffFormula: "C 9 H 11 N 2 O 9 P 1" @@ -24015,14 +24956,15 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:292" is_a: MOD:00611 ! iodouridine monophosphate derivatized residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:01251 name: N6-[3-(carboxamidomethylthio)propanoyl]lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-[3-(carboxamidomethylthio)propanoyl]lysine." [PubMed:15121203, UniMod:293#K] -synonym: "3-(carbamidomethylthio)propanoyl" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to N6-[3-(carboxamidomethylthio)propanoyl]lysine." [PubMed:15121203, Unimod:293#K] +synonym: "3-(carbamidomethylthio)propanoyl" RELATED Unimod-description [] synonym: "CAMthiopropanoyl" RELATED PSI-MS-label [] xref: DiffAvg: "145.18" xref: DiffFormula: "C 5 H 7 N 1 O 2 S 1" @@ -24033,15 +24975,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:293" is_a: MOD:00612 ! 3-(carboxamidomethylthio)propanoylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01252 name: 5-hydro-5-methylimidazol-4-one, methylglyoxal arginine adduct (+54 amu) -def: "OBSOLETE because redundant and identical to MOD:00933. Remap to MOD:00933." [PubMed:9448752, UniMod:319#R] +def: "OBSOLETE because redundant and identical to MOD:00933. Remap to MOD:00933." [PubMed:9448752, Unimod:319#R] synonym: "Delta:H(2)C(3)O(1)" RELATED PSI-MS-label [] -synonym: "MDA adduct +54" RELATED UniMod-description [] +synonym: "MDA adduct +54" RELATED Unimod-description [] xref: DiffAvg: "54.05" xref: DiffFormula: "C 3 H 2 O 1" xref: DiffMono: "54.010565" @@ -24051,14 +24994,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00933" +xref: Unimod: "Unimod:319" is_obsolete: true [Term] id: MOD:01253 name: malondialdehyde lysine adduct (+54 amu) -def: "modification from UniMod Chemical derivative - Malondialdehyde (MDA) adduct" [UniMod:319#K] +def: "modification from Unimod Chemical derivative - Malondialdehyde (MDA) adduct" [Unimod:319#K] synonym: "Delta:H(2)C(3)O(1)" RELATED PSI-MS-label [] -synonym: "MDA adduct +54" RELATED UniMod-description [] +synonym: "MDA adduct +54" RELATED Unimod-description [] xref: DiffAvg: "54.05" xref: DiffFormula: "C 3 H 2 O 1" xref: DiffMono: "54.010565" @@ -24068,15 +25013,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:319" is_a: MOD:00630 ! C3-H2-O adduct (+54 amu) of malondialdehyde with lysine or methylglyoxal with arginine. is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01254 name: 4x(2)H labeled dimethylated L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4x(2)H labeled dimethylated L-lysine." [OMSSA:189, PubMed:14670044, UniMod:199#K] +def: "A protein modification that effectively converts an L-lysine residue to 4x(2)H labeled dimethylated L-lysine." [OMSSA:189, PubMed:14670044, Unimod:199#K] subset: PSI-MOD-slim -synonym: "DiMethyl-CHD2" RELATED UniMod-description [] +synonym: "DiMethyl-CHD2" RELATED Unimod-description [] synonym: "Dimethyl:2H(4)" RELATED PSI-MS-label [] synonym: "mod189" EXACT OMSSA-label [] xref: DiffAvg: "32.06" @@ -24088,6 +25034,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:199" is_a: MOD:00552 ! 4x(2)H labeled dimethylated residue is_a: MOD:00912 ! modified L-lysine residue relationship: derives_from MOD:00084 ! N6,N6-dimethyl-L-lysine @@ -24095,8 +25042,8 @@ [Term] id: MOD:01255 name: S-(2-sulfanylethyl)cysteine (Ser) -def: "A protein modification that effectively converts an L-serine residue to S-(2-sulfanylethyl)cysteine." [PubMed:11507762, UniMod:200#S] -synonym: "EDT" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-serine residue to S-(2-sulfanylethyl)cysteine." [PubMed:11507762, Unimod:200#S] +synonym: "EDT" RELATED Unimod-description [] synonym: "Ethanedithiol" RELATED PSI-MS-label [] synonym: "S-(2-mercaptoethyl)cysteine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "76.18" @@ -24108,15 +25055,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:200" is_a: MOD:00553 ! 1,2-ethanedithiol modified residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01256 name: 3-methyl-S-(2-sulfanylethyl)cysteine (Thr) -def: "A protein modification that effectively converts an L-threonine residue to 3-methyl-S-(2-sulfanylethyl)cysteine." [PubMed:11507762, UniMod:200#T] +def: "A protein modification that effectively converts an L-threonine residue to 3-methyl-S-(2-sulfanylethyl)cysteine." [PubMed:11507762, Unimod:200#T] synonym: "beta-methyl-S-(2-mercaptoethyl)cysteine" EXACT PSI-MOD-alternate [] -synonym: "EDT" RELATED UniMod-description [] +synonym: "EDT" RELATED Unimod-description [] synonym: "Ethanedithiol" RELATED PSI-MS-label [] xref: DiffAvg: "76.18" xref: DiffFormula: "C 2 H 4 O -1 S 2" @@ -24127,14 +25075,15 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:200" is_a: MOD:00553 ! 1,2-ethanedithiol modified residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01257 name: 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate - site K -def: "modification from UniMod Chemical derivative -" [PubMed:12716131, PubMed:14997490, UniMod:194#K] -synonym: "6-aminoquinolyl-N-hydroxysuccinimidyl carbamate" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:12716131, PubMed:14997490, Unimod:194#K] +synonym: "6-aminoquinolyl-N-hydroxysuccinimidyl carbamate" RELATED Unimod-description [] synonym: "AccQTag" RELATED PSI-MS-label [] xref: DiffAvg: "170.17" xref: DiffFormula: "C 10 H 6 N 2 O 1" @@ -24145,14 +25094,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:194" is_a: MOD:00547 ! 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate [Term] id: MOD:01258 -name: N-methylmaleimide - site C -def: "modification from UniMod Chemical derivative -" [PubMed:9448752, UniMod:314#C] +name: N-methylmaleimide modified L-cysteine +def: "modification from Unimod Chemical derivative -" [PubMed:9448752, Unimod:314#C] synonym: "Nmethylmaleimide" RELATED PSI-MS-label [] -synonym: "Nmethylmaleimide" RELATED UniMod-description [] +synonym: "Nmethylmaleimide" RELATED Unimod-description [] xref: DiffAvg: "111.10" xref: DiffFormula: "C 5 H 5 N 1 O 2" xref: DiffMono: "111.032028" @@ -24162,15 +25112,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:314" is_a: MOD:00625 ! N-methylmaleimide derivatized residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01259 -name: N-methylmaleimide - site K -def: "modification from UniMod Chemical derivative -" [PubMed:9448752, UniMod:314#K] +name: N-methylmaleimide modified L-lysine +def: "modification from Unimod Chemical derivative -" [PubMed:9448752, Unimod:314#K] synonym: "Nmethylmaleimide" RELATED PSI-MS-label [] -synonym: "Nmethylmaleimide" RELATED UniMod-description [] +synonym: "Nmethylmaleimide" RELATED Unimod-description [] xref: DiffAvg: "111.10" xref: DiffFormula: "C 5 H 5 N 1 O 2" xref: DiffMono: "111.032028" @@ -24180,15 +25131,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:314" is_a: MOD:00625 ! N-methylmaleimide derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01260 name: nucleophilic addtion to cytopiloyne - site Y -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:270#Y] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:270#Y] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24198,15 +25150,15 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00919 ! modified L-tyrosine residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01261 name: nucleophilic addtion to cytopiloyne - site S -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:270#C] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:270#C] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24216,15 +25168,15 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00916 ! modified L-serine residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01262 -name: nucleophilic addtion to cytopiloyne - site R -def: "modification from UniMod Chemical derivative -" [PubMed:12590383, PubMed:15549660, UniMod:270#R] +name: nucleophilic addition to cytopiloyne - site R +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:12590383, PubMed:15549660, Unimod:270#R] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24234,15 +25186,15 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00902 ! modified L-arginine residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01263 name: nucleophilic addtion to cytopiloyne - site K -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:270#K] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:270#K] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24252,15 +25204,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01264 name: nucleophilic addtion to cytopiloyne - site C -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:270#C] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:270#C] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24270,15 +25222,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00905 ! modified L-cysteine residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01265 name: nucleophilic addtion to cytopiloyne - site P -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:270#P] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:270#P] synonym: "Cytopiloyne" RELATED PSI-MS-label [] -synonym: "nucleophilic addtion to cytopiloyne" RELATED UniMod-description [] +synonym: "nucleophilic addtion to cytopiloyne" RELATED Unimod-description [] xref: DiffAvg: "362.38" xref: DiffFormula: "C 19 H 22 O 7" xref: DiffMono: "362.136553" @@ -24288,15 +25240,15 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00590 ! nucleophilic addtion to cytopiloyne -is_a: MOD:00915 ! modified L-proline residue +xref: Unimod: "Unimod:270" +is_obsolete: true [Term] id: MOD:01266 name: nucleophilic addition to cytopiloyne+H2O - site C -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:271#C] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:271#C] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24306,15 +25258,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00905 ! modified L-cysteine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01267 name: nucleophilic addition to cytopiloyne+H2O - site K -def: "modification from UniMod Chemical derivative -" [PubMed:11746907, PubMed:15549660, UniMod:271#K] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:11746907, PubMed:15549660, Unimod:271#K] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24324,15 +25276,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01268 name: nucleophilic addition to cytopiloyne+H2O - site T -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:271#T] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:271#T] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24342,15 +25294,15 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00917 ! modified L-threonine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01269 name: nucleophilic addition to cytopiloyne+H2O - site R -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:271#R] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:271#R] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24360,15 +25312,15 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00902 ! modified L-arginine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01270 name: nucleophilic addition to cytopiloyne+H2O - site S -def: "modification from UniMod Chemical derivative -" [PubMed:14670044, PubMed:15549660, UniMod:271#S] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:14670044, PubMed:15549660, Unimod:271#S] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24378,15 +25330,15 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00916 ! modified L-serine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01271 name: nucleophilic addition to cytopiloyne+H2O - site Y -def: "modification from UniMod Chemical derivative -" [PubMed:15549660, UniMod:271#Y] +def: "OBSOLETE because there is no evidence in the literature of covalent modification of polypeptides with cytopiloyne or cytopiloyne+H2O. Modifications could potentially happen, but are not experimentally verified. [PMT] modification from Unimod Chemical derivative -" [PubMed:15549660, Unimod:271#Y] synonym: "Cytopiloyne+water" RELATED PSI-MS-label [] -synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED UniMod-description [] +synonym: "nucleophilic addition to cytopiloyne+H2O" RELATED Unimod-description [] xref: DiffAvg: "380.39" xref: DiffFormula: "C 19 H 24 O 8" xref: DiffMono: "380.147118" @@ -24396,15 +25348,15 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00591 ! nucleophilic addition to cytopiloyne+H2O -is_a: MOD:00919 ! modified L-tyrosine residue +xref: Unimod: "Unimod:271" +is_obsolete: true [Term] id: MOD:01272 name: iminobiotinylation - site K -def: "modification from UniMod Chemical derivative -" [PubMed:9750125, UniMod:89#K] +def: "modification from Unimod Chemical derivative -" [PubMed:9750125, Unimod:89#K] synonym: "Iminobiotin" RELATED PSI-MS-label [] -synonym: "Iminobiotinylation" RELATED UniMod-description [] +synonym: "Iminobiotinylation" RELATED Unimod-description [] xref: DiffAvg: "225.31" xref: DiffFormula: "C 10 H 15 N 3 O 1 S 1" xref: DiffMono: "225.093583" @@ -24414,15 +25366,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:89" is_a: MOD:00467 ! iminobiotinyl modified residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01273 name: O-[4-(2-aminoethyl)benzenesulfonyl] serine -def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-serine residue." [PubMed:15283597, PubMed:8597590, UniMod:276#S] +def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-serine residue." [PubMed:15283597, PubMed:8597590, Unimod:276#S] synonym: "AEBS" RELATED PSI-MS-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -24432,15 +25385,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:276" is_a: MOD:00596 ! 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01274 name: N'-[4-(2-aminoethyl)benzenesulfonyl] derivatized histidine -def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-histidine residue." [PubMed:8597590, UniMod:276#H] +def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-histidine residue." [PubMed:8597590, Unimod:276#H] synonym: "AEBS" RELATED PSI-MS-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -24450,15 +25404,16 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:276" is_a: MOD:00596 ! 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:01275 name: N6-[4-(2-aminoethyl)benzenesulfonyl]lysine -def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-lysine residue." [PubMed:8597590, UniMod:276#K] +def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-lysine residue." [PubMed:8597590, Unimod:276#K] synonym: "AEBS" RELATED PSI-MS-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -24468,15 +25423,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:276" is_a: MOD:00596 ! 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01276 name: O4'-[4-(2-aminoethyl)benzenesulfonyl]tyrosine -def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-tyrosine residue." [PubMed:10906242, PubMed:8597590, UniMod:276#Y] +def: "A protein modification that is produced by formation of an adduct with 4-(2-aminoethyl)benzenesulfonyl fluoride, AEBS, and an L-tyrosine residue." [PubMed:10906242, PubMed:8597590, Unimod:276#Y] synonym: "AEBS" RELATED PSI-MS-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -24486,15 +25442,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:276" is_a: MOD:00596 ! 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01277 -name: crotonaldehyde - site C -def: "modification from UniMod Other -" [PubMed:11283024, UniMod:253#C] +name: crotonylated L-cysteine +def: "modification from Unimod Other -" [PubMed:11283024, Unimod:253#C] synonym: "Crotonaldehyde" RELATED PSI-MS-label [] -synonym: "Crotonaldehyde" RELATED UniMod-description [] +synonym: "Crotonaldehyde" RELATED Unimod-description [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 O 1" xref: DiffMono: "70.041865" @@ -24504,15 +25461,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00576 ! crotonaldehyde +xref: Unimod: "Unimod:253" +is_a: MOD:00576 ! crotonylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01278 -name: crotonaldehyde - site K -def: "modification from UniMod Other -" [PubMed:11283024, UniMod:253#K] +name: crotonylated L-lysine +def: "modification from Unimod Other -" [PubMed:11283024, Unimod:253#K] synonym: "Crotonaldehyde" RELATED PSI-MS-label [] -synonym: "Crotonaldehyde" RELATED UniMod-description [] +synonym: "Crotonaldehyde" RELATED Unimod-description [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 O 1" xref: DiffMono: "70.041865" @@ -24522,15 +25480,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00576 ! crotonaldehyde +xref: Unimod: "Unimod:253" +is_a: MOD:00576 ! crotonylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01279 -name: crotonaldehyde - site H -def: "modification from UniMod Other -" [PubMed:11283024, PubMed:1443554, UniMod:253#H] +name: crotonylated L-histidine +def: "modification from Unimod Other -" [PubMed:11283024, PubMed:1443554, Unimod:253#H] synonym: "Crotonaldehyde" RELATED PSI-MS-label [] -synonym: "Crotonaldehyde" RELATED UniMod-description [] +synonym: "Crotonaldehyde" RELATED Unimod-description [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 O 1" xref: DiffMono: "70.041865" @@ -24540,14 +25499,15 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00576 ! crotonaldehyde +xref: Unimod: "Unimod:253" +is_a: MOD:00576 ! crotonylated residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:01280 name: EDT-iodo-PEO-biotin - site T -def: "modification from UniMod Chemical derivative -" [PubMed:11857757, PubMed:12175151, UniMod:118#T] -synonym: "EDT-iodo-PEO-biotin" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:11857757, PubMed:12175151, Unimod:118#T] +synonym: "EDT-iodo-PEO-biotin" RELATED Unimod-description [] synonym: "EDT-iodoacetyl-PEO-biotin" RELATED PSI-MS-label [] xref: DiffAvg: "490.70" xref: DiffFormula: "C 20 H 34 N 4 O 4 S 3" @@ -24558,14 +25518,15 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:118" is_a: MOD:00490 ! EDT-iodo-PEO-biotin is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01281 name: EDT-iodo-PEO-biotin - site S -def: "modification from UniMod Chemical derivative -" [PubMed:16335955, UniMod:118#S] -synonym: "EDT-iodo-PEO-biotin" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:16335955, Unimod:118#S] +synonym: "EDT-iodo-PEO-biotin" RELATED Unimod-description [] synonym: "EDT-iodoacetyl-PEO-biotin" RELATED PSI-MS-label [] xref: DiffAvg: "490.70" xref: DiffFormula: "C 20 H 34 N 4 O 4 S 3" @@ -24576,14 +25537,15 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:118" is_a: MOD:00490 ! EDT-iodo-PEO-biotin is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01282 name: acrolein addition +56 - site H -def: "modification from UniMod Other -" [PubMed:10825247, PubMed:15541752, UniMod:206#H] -synonym: "Acrolein addition +56" RELATED UniMod-description [] +def: "OBSOLETE because this modification is not supported by the linked literature [PMT]" [PubMed:10825247, PubMed:15541752, Unimod:206#H] +synonym: "Acrolein addition +56" RELATED Unimod-description [] synonym: "Delta:H(4)C(3)O(1)" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -24594,14 +25556,14 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00557 ! acrolein addition +56 -is_a: MOD:00909 ! modified L-histidine residue +xref: Unimod: "Unimod:206" +is_obsolete: true [Term] id: MOD:01283 name: acrolein addition +56 - site K -def: "modification from UniMod Other -" [PubMed:10825247, PubMed:15541752, UniMod:206#K] -synonym: "Acrolein addition +56" RELATED UniMod-description [] +def: "OBSOLETE because this modification is not supported by the linked literature [PMT]" [PubMed:10825247, PubMed:15541752, Unimod:206#K] +synonym: "Acrolein addition +56" RELATED Unimod-description [] synonym: "Delta:H(4)C(3)O(1)" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -24612,14 +25574,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00557 ! acrolein addition +56 -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:206" +is_obsolete: true [Term] id: MOD:01284 name: acrolein addition +56 - site C -def: "modification from UniMod Other -" [PubMed:10825247, PubMed:15541752, PubMed:9254591, UniMod:206#C] -synonym: "Acrolein addition +56" RELATED UniMod-description [] +def: "OBSOLETE because this modification is not supported by the linked literature [PMT]" [PubMed:10825247, PubMed:15541752, PubMed:9254591, Unimod:206#C] +synonym: "Acrolein addition +56" RELATED Unimod-description [] synonym: "Delta:H(4)C(3)O(1)" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -24630,14 +25592,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00557 ! acrolein addition +56 -is_a: MOD:00905 ! modified L-cysteine residue +xref: Unimod: "Unimod:206" +is_obsolete: true [Term] id: MOD:01285 name: 6x(13)C,1x(15)N labeled L-leucine -def: "A protein modification that effectively converts an L-leucine residue to 6x(13)C,1x(15)N isotope labeled L-leucine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:695#L] -synonym: "13C(6) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-leucine residue to 6x(13)C,1x(15)N isotope labeled L-leucine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:695#L] +synonym: "13C(6) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "7.02" xref: DiffFormula: "(12)C -6 (13)C 6 (14)N -1 (15)N 1" @@ -24648,14 +25610,15 @@ xref: Origin: "L" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:695" is_a: MOD:00911 ! modified L-leucine residue is_a: MOD:01370 ! 6x(13)C,1x(15)N labeled residue [Term] id: MOD:01286 name: 6x(13)C,1x(15)N labeled L-isoleucine -def: "A protein modification that effectively converts an L-isoleucine residue to 6x(13)C,1x(15)N isotope labeled L-isoleucine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:695#I] -synonym: "13C(6) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-isoleucine residue to 6x(13)C,1x(15)N isotope labeled L-isoleucine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:695#I] +synonym: "13C(6) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "7.02" xref: DiffFormula: "(12)C -6 (13)C 6 (14)N -1 (15)N 1" @@ -24666,14 +25629,15 @@ xref: Origin: "I" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:695" is_a: MOD:00910 ! modified L-isoleucine residue is_a: MOD:01370 ! 6x(13)C,1x(15)N labeled residue [Term] id: MOD:01287 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form - site K -def: "modification from UniMod Isotopic label -" [PubMed:11857757, PubMed:15602776, UniMod:364#K] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:11857757, PubMed:15602776, Unimod:364#K] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form" RELATED Unimod-description [] synonym: "ICPL:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "111.04" xref: DiffFormula: "(13)C 6 H 3 N 1 O 1" @@ -24684,14 +25648,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:364" is_a: MOD:00789 ! Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, heavy form is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01288 name: acetaldehyde +28 - site H -def: "modification from UniMod Other -" [UniMod:255#H] -synonym: "Acetaldehyde +28" RELATED UniMod-description [] +def: "OBSOLETE because this is not supported by the literature [PMT]" [Unimod:255#H] +synonym: "Acetaldehyde +28" RELATED Unimod-description [] synonym: "Delta:H(4)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" @@ -24702,14 +25667,14 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00578 ! acetaldehyde +28 -is_a: MOD:00909 ! modified L-histidine residue +xref: Unimod: "Unimod:255" +is_obsolete: true [Term] id: MOD:01289 name: acetaldehyde +28 - site K -def: "modification from UniMod Other -" [UniMod:255#K] -synonym: "Acetaldehyde +28" RELATED UniMod-description [] +def: "OBSOLETE because this is not supported by the literature [PMT]" [Unimod:255#K] +synonym: "Acetaldehyde +28" RELATED Unimod-description [] synonym: "Delta:H(4)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" @@ -24720,14 +25685,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00578 ! acetaldehyde +28 -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:255" +is_obsolete: true [Term] id: MOD:01290 name: dihydroxylated residue - site F -def: "OBSOLETE because redundant and identical to MOD:00465. Remap to MOD:00465." [PubMed:11857757, PubMed:12175151, PubMed:12686488, PubMed:9252331, UniMod:425] -synonym: "dihydroxy" RELATED UniMod-description [] +def: "OBSOLETE because redundant and identical to MOD:00465. Remap to MOD:00465." [PubMed:11857757, PubMed:12175151, PubMed:12686488, PubMed:9252331, Unimod:425] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] xref: DiffAvg: "32.00" xref: DiffFormula: "O 2" @@ -24738,13 +25703,15 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:425" +xref: Remap: "MOD:00465" is_obsolete: true [Term] id: MOD:01291 name: dihydroxylated residue - site W -def: "OBSOLETE because redundant and identical to MOD:00464. Remap to MOD:00464." [PubMed:12643539, PubMed:12686488, PubMed:6273432, PubMed:9252331, UniMod:425] -synonym: "dihydroxy" RELATED UniMod-description [] +def: "OBSOLETE because redundant and identical to MOD:00464. Remap to MOD:00464." [PubMed:12643539, PubMed:12686488, PubMed:6273432, PubMed:9252331, Unimod:425] +synonym: "dihydroxy" RELATED Unimod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] xref: DiffAvg: "32.00" xref: DiffFormula: "O 2" @@ -24755,14 +25722,16 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00464" +xref: Unimod: "Unimod:425" is_obsolete: true [Term] id: MOD:01292 name: dimethylation of proline residue -def: "OBSOLETE because redundant and identical to MOD:00075. Map to MOD:00075." [UniMod:529] +def: "OBSOLETE because redundant and identical to MOD:00075. Map to MOD:00075." [Unimod:529] synonym: "Delta:H(5)C(2)" RELATED PSI-MS-label [] -synonym: "Dimethylation of proline residue" RELATED UniMod-description [] +synonym: "Dimethylation of proline residue" RELATED Unimod-description [] xref: DiffAvg: "29.06" xref: DiffFormula: "C 2 H 5" xref: DiffMono: "29.039125" @@ -24772,15 +25741,17 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00075" +xref: Unimod: "Unimod:529" is_obsolete: true [Term] id: MOD:01293 name: 1x(18)O labeled deamidated L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O." [OMSSA:139, PubMed:8382902, UniMod:366#N] +def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O." [OMSSA:139, PubMed:8382902, Unimod:366#N] subset: PSI-MOD-slim synonym: "Deamidated:18O(1)" RELATED PSI-MS-label [] -synonym: "Deamidation in presence of O18" RELATED UniMod-description [] +synonym: "Deamidation in presence of O18" RELATED Unimod-description [] synonym: "oxy18" EXACT OMSSA-label [] xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" @@ -24791,6 +25762,7 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:366" is_a: MOD:00852 ! 1x(18)O labeled deamidated residue relationship: derives_from MOD:00684 ! deamidated L-asparagine @@ -24799,7 +25771,7 @@ name: deamidation in presence of O18 -site Q def: "OBSOLETE identical and redundant with MOD:00791. Remap to MOD:00791." [PubMed:8382902] synonym: "Deamidated:18O(1)" RELATED PSI-MS-label [] -synonym: "Deamidation in presence of O18" RELATED UniMod-description [] +synonym: "Deamidation in presence of O18" RELATED Unimod-description [] xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" xref: DiffMono: "2.988262" @@ -24809,16 +25781,17 @@ xref: Origin: "Q" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00791" is_obsolete: true [Term] id: MOD:01295 name: monosodium L-aspartate -def: "A protein modification that effectively converts an L-aspartic acid residue to monosodium L-aspartate." [PubMed:12216740, UniMod:30#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to monosodium L-aspartate." [PubMed:12216740, Unimod:30#D] subset: PSI-MOD-slim synonym: "Cation:Na" RELATED PSI-MS-label [] synonym: "Na1Asp" EXACT PSI-MOD-label [] -synonym: "Sodium adduct" RELATED UniMod-description [] +synonym: "Sodium adduct" RELATED Unimod-description [] xref: DiffAvg: "21.98" xref: DiffFormula: "H -1 Na 1" xref: DiffMono: "21.981944" @@ -24828,18 +25801,19 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:30" is_a: MOD:00423 ! monosodium salt is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:01296 name: monosodium L-glutamate -def: "A protein modification that effectively converts an L-glutamic acid residue to monosodium L-glutamate." [PubMed:12216740, UniMod:30#E] +def: "A protein modification that effectively converts an L-glutamic acid residue to monosodium L-glutamate." [PubMed:12216740, Unimod:30#E] subset: PSI-MOD-slim synonym: "Cation:Na" RELATED PSI-MS-label [] synonym: "MSG" EXACT PSI-MOD-alternate [] synonym: "Na1Glu" EXACT PSI-MOD-label [] -synonym: "Sodium adduct" RELATED UniMod-description [] +synonym: "Sodium adduct" RELATED Unimod-description [] xref: DiffAvg: "21.98" xref: DiffFormula: "H -1 Na 1" xref: DiffMono: "21.981944" @@ -24849,15 +25823,16 @@ xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:30" is_a: MOD:00423 ! monosodium salt is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:01297 name: 5x(13)C labeled L-proline -def: "A protein modification that effectively converts an L-proline residue to 5x(13)C labeled L-proline." [PubMed:12716131, UniMod:772#P] +def: "A protein modification that effectively converts an L-proline residue to 5x(13)C labeled L-proline." [PubMed:12716131, Unimod:772#P] comment: In PubMed:12716131, fully (13)C labeled proline apparently resulted from the catabolic conversion of (13)C labeled L-arginine during SILAC. -synonym: "13C(5) Silac label" RELATED UniMod-description [] +synonym: "13C(5) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)" RELATED PSI-MS-label [] xref: DiffAvg: "5.02" xref: DiffFormula: "(12)C -5 (13)C 5" @@ -24868,16 +25843,17 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:772" is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01832 ! 5x(13)C-labeled residue [Term] id: MOD:01298 name: reduced cysteine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-cysteine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:15133838, UniMod:335#C] +def: "A protein modification produced by formation of an adduct of an L-cysteine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:15133838, Unimod:335#C] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. synonym: "HNE+Delta:H(2)" RELATED PSI-MS-label [] -synonym: "reduced 4-Hydroxynonenal" RELATED UniMod-description [] +synonym: "reduced 4-Hydroxynonenal" RELATED Unimod-description [] xref: DiffAvg: "158.24" xref: DiffFormula: "C 9 H 18 O 2" xref: DiffMono: "158.130680" @@ -24887,6 +25863,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:335" is_a: MOD:00642 ! reduced 4-hydroxynonenal adduct is_a: MOD:00905 ! modified L-cysteine residue relationship: derives_from MOD:01237 ! cysteine 4-hydroxynonenal adduct @@ -24894,10 +25871,10 @@ [Term] id: MOD:01299 name: reduced lysine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:12148805, PubMed:15133838, UniMod:335#K] +def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:12148805, PubMed:15133838, Unimod:335#K] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. synonym: "HNE+Delta:H(2)" RELATED PSI-MS-label [] -synonym: "reduced 4-Hydroxynonenal" RELATED UniMod-description [] +synonym: "reduced 4-Hydroxynonenal" RELATED Unimod-description [] xref: DiffAvg: "158.24" xref: DiffFormula: "C 9 H 18 O 2" xref: DiffMono: "158.130680" @@ -24907,6 +25884,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:335" is_a: MOD:00642 ! reduced 4-hydroxynonenal adduct is_a: MOD:00912 ! modified L-lysine residue relationship: derives_from MOD:01238 ! lysine 4-hydroxynonenal adduct @@ -24914,10 +25892,10 @@ [Term] id: MOD:01300 name: reduced histidine 4-hydroxynonenal adduct -def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:12148805, PubMed:15133838, UniMod:335#H] +def: "A protein modification produced by formation of an adduct of an L-histidine residue with 4-hydroxynonenal artificially reduced by a reagent such as NaBH4." [PubMed:11910026, PubMed:12148805, PubMed:15133838, Unimod:335#H] comment: 4-hydroxynonenal, a toxic lipid aldehyde, is a product of the hydroperoxide beta-cleavage degradation of omega-6 polyunsaturated fatty acids, such as arachidonic and linoleic acids [JSG]. synonym: "HNE+Delta:H(2)" RELATED PSI-MS-label [] -synonym: "reduced 4-Hydroxynonenal" RELATED UniMod-description [] +synonym: "reduced 4-Hydroxynonenal" RELATED Unimod-description [] xref: DiffAvg: "158.24" xref: DiffFormula: "C 9 H 18 O 2" xref: DiffMono: "158.130680" @@ -24927,6 +25905,7 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:335" is_a: MOD:00642 ! reduced 4-hydroxynonenal adduct is_a: MOD:00909 ! modified L-histidine residue relationship: derives_from MOD:01239 ! histidine 4-hydroxynonenal adduct @@ -24934,10 +25913,10 @@ [Term] id: MOD:01301 name: methylamine Michael addition derivatized threonine -def: "A protein modification that effectively converts an L-threonine residue to 2-amino-3-(methylamino)butanoic acid." [PubMed:11743741, UniMod:337#T] +def: "A protein modification that effectively converts an L-threonine residue to 2-amino-3-(methylamino)butanoic acid." [PubMed:11743741, Unimod:337#T] comment: In PubMed:11743741 phosphothreonine is converted to dehydrobutyrine in base, then by Michael addition of methylamine to 2-amino-3-(methylamino)butanoic acid. synonym: "Methylamine" RELATED PSI-MS-label [] -synonym: "Michael addition with methylamine" RELATED UniMod-description [] +synonym: "Michael addition with methylamine" RELATED Unimod-description [] xref: DiffAvg: "13.04" xref: DiffFormula: "C 1 H 3 N 1 O -1" xref: DiffMono: "13.031634" @@ -24947,16 +25926,17 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:337" is_a: MOD:00643 ! methylamine Michael addition derivatized residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01302 name: methylamine Michael addition derivatized serine -def: "A protein modification that effectively converts an L-serine residue to 2-amino-3-(methylamino)propanoic acid." [PubMed:11743741, UniMod:337#S] +def: "A protein modification that effectively converts an L-serine residue to 2-amino-3-(methylamino)propanoic acid." [PubMed:11743741, Unimod:337#S] comment: In PubMed:11743741 phosphoserine is converted to dehydroalanine in base, then by Michael addition of methylamine to 2-amino-3-(methylamino)propanoic acid. synonym: "Methylamine" RELATED PSI-MS-label [] -synonym: "Michael addition with methylamine" RELATED UniMod-description [] +synonym: "Michael addition with methylamine" RELATED Unimod-description [] xref: DiffAvg: "13.04" xref: DiffFormula: "C 1 H 3 N 1 O -1" xref: DiffMono: "13.031634" @@ -24966,16 +25946,17 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:337" is_a: MOD:00643 ! methylamine Michael addition derivatized residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01303 name: N4-hexosaminylated asparagine -def: "A protein modification that effectively converts an L-asparagine residue to an N4-hexosaminyl-L-asparagine." [PubMed:11467524, UniMod:454#N] +def: "A protein modification that effectively converts an L-asparagine residue to an N4-hexosaminyl-L-asparagine." [PubMed:11467524, Unimod:454#N] comment: The natural modifications are N4-(N-acetylamino)galactosyl-L-asparagine (MOD:00832) or N4-(N-acetylamino)glucosyl-L-asparagine (MOD:00831) [JSG]. synonym: "HexN" RELATED PSI-MS-label [] -synonym: "Hexosamine" RELATED UniMod-description [] +synonym: "Hexosamine" RELATED Unimod-description [] xref: DiffAvg: "161.16" xref: DiffFormula: "C 6 H 11 N 1 O 4" xref: DiffMono: "161.068808" @@ -24985,15 +25966,16 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:454" is_a: MOD:00160 ! N4-glycosyl-L-asparagine is_a: MOD:00876 ! hexosaminylated residue [Term] id: MOD:01304 name: N6-hexosaminylated lysine -def: "A protein modification that effectively converts an L-lysine residue to an N4-hexosaminyl-L-lysine, as a synthetic peptide protectting group." [UniMod:454#K] +def: "A protein modification that effectively converts an L-lysine residue to an N4-hexosaminyl-L-lysine, as a synthetic peptide protectting group." [Unimod:454#K] synonym: "HexN" RELATED PSI-MS-label [] -synonym: "Hexosamine" RELATED UniMod-description [] +synonym: "Hexosamine" RELATED Unimod-description [] xref: DiffAvg: "161.16" xref: DiffFormula: "C 6 H 11 N 1 O 4" xref: DiffMono: "161.068808" @@ -25003,16 +25985,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:454" is_a: MOD:00876 ! hexosaminylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01305 name: N1'-hexosaminylated tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to N1'-hexosaminyl-L-tryptophan." [UniMod:454#W] +def: "A protein modification that effectively converts an L-tryptophan residue to N1'-hexosaminyl-L-tryptophan." [Unimod:454#W] comment: The natural modification is N1'-mannosyl-L-tryptophan (MOD:00165) [JSG]. synonym: "HexN" RELATED PSI-MS-label [] -synonym: "Hexosamine" RELATED UniMod-description [] +synonym: "Hexosamine" RELATED Unimod-description [] xref: DiffAvg: "161.16" xref: DiffFormula: "C 6 H 11 N 1 O 4" xref: DiffMono: "161.068808" @@ -25022,16 +26005,17 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:454" is_a: MOD:00876 ! hexosaminylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:01306 name: O-hexosaminylated threonine -def: "A protein modification that effectively converts an L-threonine residue to O-hexosaminyl-L-threonine." [UniMod:454#T] +def: "A protein modification that effectively converts an L-threonine residue to O-hexosaminyl-L-threonine." [Unimod:454#T] comment: The natural modifications are O-(N-acetylaminogalactosyl)-L-threonine (MOD:00164) or O-(N-acetylaminoglucosyl)-L-threonine (MOD:00806) [JSG]. synonym: "HexN" RELATED PSI-MS-label [] -synonym: "Hexosamine" RELATED UniMod-description [] +synonym: "Hexosamine" RELATED Unimod-description [] xref: DiffAvg: "161.16" xref: DiffFormula: "C 6 H 11 N 1 O 4" xref: DiffMono: "161.068808" @@ -25041,15 +26025,16 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:454" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00876 ! hexosaminylated residue [Term] id: MOD:01307 name: thiophosphate labeled with biotin-HPDP -site S -def: "modification from UniMod Chemical derivative -" [UniMod:332#S] +def: "modification from Unimod Chemical derivative -" [Unimod:332#S] synonym: "Thiophos-S-S-biotin" RELATED PSI-MS-label [] -synonym: "thiophosphate labeled with biotin-HPDP" RELATED UniMod-description [] +synonym: "thiophosphate labeled with biotin-HPDP" RELATED Unimod-description [] xref: DiffAvg: "525.66" xref: DiffFormula: "C 19 H 34 N 4 O 5 P 1 S 3" xref: DiffMono: "525.142895" @@ -25059,15 +26044,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:332" is_a: MOD:00639 ! thiophosphate labeled with biotin-HPDP is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01308 name: thiophosphate labeled with biotin-HPDP -site T -def: "modification from UniMod Chemical derivative -" [UniMod:332#T] +def: "modification from Unimod Chemical derivative -" [Unimod:332#T] synonym: "Thiophos-S-S-biotin" RELATED PSI-MS-label [] -synonym: "thiophosphate labeled with biotin-HPDP" RELATED UniMod-description [] +synonym: "thiophosphate labeled with biotin-HPDP" RELATED Unimod-description [] xref: DiffAvg: "525.66" xref: DiffFormula: "C 19 H 34 N 4 O 5 P 1 S 3" xref: DiffMono: "525.142895" @@ -25077,15 +26063,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:332" is_a: MOD:00639 ! thiophosphate labeled with biotin-HPDP is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01309 name: thiophosphate labeled with biotin-HPDP - site Y -def: "modification from UniMod Chemical derivative - " [UniMod:332#Y] +def: "modification from Unimod Chemical derivative - " [Unimod:332#Y] synonym: "Thiophos-S-S-biotin" RELATED PSI-MS-label [] -synonym: "thiophosphate labeled with biotin-HPDP" RELATED UniMod-description [] +synonym: "thiophosphate labeled with biotin-HPDP" RELATED Unimod-description [] xref: DiffAvg: "525.66" xref: DiffFormula: "C 19 H 34 N 4 O 5 P 1 S 3" xref: DiffMono: "525.142895" @@ -25095,15 +26082,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:332" is_a: MOD:00639 ! thiophosphate labeled with biotin-HPDP is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01310 name: quaternary amine labeling reagent light form N6-L-lysine -def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent light form group." [PubMed:11857757, UniMod:60#K] +def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent light form group." [PubMed:11857757, Unimod:60#K] synonym: "GIST-Quat" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent light form (N-term & K)" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent light form (N-term & K)" RELATED Unimod-description [] xref: DiffAvg: "59.07" xref: DiffFormula: "C 3 (1)H 9 N 1" xref: DiffMono: "59.073499" @@ -25113,15 +26101,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:60" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01311 name: quaternary amine labeling reagent heavy form (+3amu) N6-L-lysine -def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+3amu) form group." [PubMed:11698400, PubMed:11857757, PubMed:11914093, UniMod:61#K] +def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+3amu) form group." [PubMed:11698400, PubMed:11857757, PubMed:11914093, Unimod:61#K] synonym: "GIST-Quat:2H(3)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy (+3amu) form, N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy (+3amu) form, N-term & K" RELATED Unimod-description [] xref: DiffAvg: "62.09" xref: DiffFormula: "C 3 (1)H 6 (2)H 3 N 1" xref: DiffMono: "62.092330" @@ -25131,16 +26120,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:61" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01312 name: quaternary amine labeling reagent heavy form (+6amu) N6-L-lysine -def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+6amu) form group." [PubMed:11857757, UniMod:62#K] +def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+6amu) form group." [PubMed:11857757, Unimod:62#K] comment: Apparently incorrect parent [JSG]. synonym: "GIST-Quat:2H(6)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy form (+6amu), N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy form (+6amu), N-term & K" RELATED Unimod-description [] xref: DiffAvg: "65.11" xref: DiffFormula: "C 3 (1)H 3 (2)H 6 N 1" xref: DiffMono: "65.111160" @@ -25150,15 +26140,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:62" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01313 name: quaternary amine labeling reagent heavy form (+9amu) N6-L-lysine -def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+9amu) form group." [PubMed:11857757, UniMod:63#K] +def: "A protein modification that effectively replaces a lysine N6-hydrogen with a quaternary amine reagent heavy (+9amu) form group." [PubMed:11857757, Unimod:63#K] synonym: "GIST-Quat:2H(9)" RELATED PSI-MS-label [] -synonym: "Quaternary amine labeling reagent heavy form (+9amu), N-term & K" RELATED UniMod-description [] +synonym: "Quaternary amine labeling reagent heavy form (+9amu), N-term & K" RELATED Unimod-description [] xref: DiffAvg: "68.13" xref: DiffFormula: "C 3 (2)H 9 N 1" xref: DiffMono: "68.129990" @@ -25168,14 +26159,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:63" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01314 name: 4x(1)H,4x(12)C-labeled N6-succinyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4x(1)H,4x(12)C-labeled N6-succinyl-L-lysine." [PubMed:11857757, PubMed:12175151, PubMed:12716131, UniMod:64#K] -synonym: "Succinic anhydride labeling reagent light form (K)" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 4x(1)H,4x(12)C-labeled N6-succinyl-L-lysine." [PubMed:11857757, PubMed:12175151, PubMed:12716131, Unimod:64#K] +synonym: "Succinic anhydride labeling reagent light form (K)" RELATED Unimod-description [] synonym: "Succinyl" RELATED PSI-MS-label [] xref: DiffAvg: "100.02" xref: DiffFormula: "(12)C 4 (1)H 4 O 3" @@ -25186,14 +26178,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:64" +relationship: derives_from MOD:01819 ! N6-succinyl-L-lysine +is_a: MOD:00670 ! N-acylated residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue -is_a: MOD:01819 ! N6-succinyl-L-lysine [Term] id: MOD:01315 name: 4x(2)H labeled N6-succinyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4x(2)H-labeled N6-succinyl-L-lysine." [PubMed:11344537, PubMed:11857757, PubMed:12175151, PubMed:15189151, UniMod:65#K] -synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term & K" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 4x(2)H-labeled N6-succinyl-L-lysine." [PubMed:11344537, PubMed:11857757, PubMed:12175151, PubMed:15189151, Unimod:65#K] +synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4H2), N-term & K" RELATED Unimod-description [] synonym: "Succinyl:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "104.04" xref: DiffFormula: "C 4 (2)H 4 O 3" @@ -25204,13 +26198,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01819 ! N6-succinyl-L-lysine +xref: Unimod: "Unimod:65" +relationship: derives_from MOD:01819 ! N6-succinyl-L-lysine +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01316 name: 4x(13)C labeled N6-succinyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 4x(13)C labeled N6-succinyl-L-lysine." [PubMed:11344537, PubMed:11857757, PubMed:12175151, PubMed:15189151, UniMod:66#K] -synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), K" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to 4x(13)C labeled N6-succinyl-L-lysine." [PubMed:11344537, PubMed:11857757, PubMed:12175151, PubMed:15189151, Unimod:66#K] +synonym: "Succinic anhydride labeling reagent, heavy form (+4amu, 4C13), K" RELATED Unimod-description [] synonym: "Succinyl:13C(4)" RELATED PSI-MS-label [] xref: DiffAvg: "104.03" xref: DiffFormula: "(13)C 4 H 4 O 3" @@ -25221,14 +26218,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01819 ! N6-succinyl-L-lysine +xref: Unimod: "Unimod:66" +relationship: derives_from MOD:01819 ! N6-succinyl-L-lysine +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:01428 ! (13)C isotope tagged reagent [Term] id: MOD:01317 name: phosphorylation to amine thiol - site T -def: "modification from UniMod Chemical derivative -" [PubMed:12216740, UniMod:178#T] +def: "modification from Unimod Chemical derivative -" [PubMed:12216740, Unimod:178#T] synonym: "DAET" RELATED PSI-MS-label [] -synonym: "phosphorylation to amine thiol" RELATED UniMod-description [] +synonym: "phosphorylation to amine thiol" RELATED Unimod-description [] xref: DiffAvg: "87.18" xref: DiffFormula: "C 4 H 9 N 1 O -1 S 1" xref: DiffMono: "87.050656" @@ -25238,15 +26238,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:178" is_a: MOD:00535 ! phosphorylation to amine thiol is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01318 name: phosphorylation to amine thiol - site S -def: "modification from UniMod Chemical derivative -" [PubMed:11510821, PubMed:12216740, PubMed:12422359, UniMod:178#S] +def: "modification from Unimod Chemical derivative -" [PubMed:11510821, PubMed:12216740, PubMed:12422359, Unimod:178#S] synonym: "DAET" RELATED PSI-MS-label [] -synonym: "phosphorylation to amine thiol" RELATED UniMod-description [] +synonym: "phosphorylation to amine thiol" RELATED Unimod-description [] xref: DiffAvg: "87.18" xref: DiffFormula: "C 4 H 9 N 1 O -1 S 1" xref: DiffMono: "87.050656" @@ -25256,16 +26257,17 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:178" is_a: MOD:00535 ! phosphorylation to amine thiol is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01319 name: Michael addition of BHT quinone methide to histidine -def: "modification from UniMod Other" [PubMed:11510821, PubMed:12422359, PubMed:9448752, UniMod:176#H] -comment: Secondary adduct, much less common than cysteine. [UniMod] +def: "modification from Unimod Other" [PubMed:11510821, PubMed:12422359, PubMed:9448752, Unimod:176#H] +comment: Secondary adduct, much less common than cysteine. [Unimod] synonym: "BHT" RELATED PSI-MS-label [] -synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED UniMod-description [] +synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED Unimod-description [] xref: DiffAvg: "218.34" xref: DiffFormula: "C 15 H 22 O 1" xref: DiffMono: "218.167065" @@ -25275,16 +26277,17 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:176" is_a: MOD:00534 ! Michael addition of BHT quinone methide to cysteine and lysine is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:01320 name: Michael addition of BHT quinone methide to lysine -def: "modification from UniMod Other" [PubMed:16078144, PubMed:9448752, UniMod:176#K] -comment: Secondary adduct, much less common than cysteine. [UniMod] +def: "modification from Unimod Other" [PubMed:16078144, PubMed:9448752, Unimod:176#K] +comment: Secondary adduct, much less common than cysteine. [Unimod] synonym: "BHT" RELATED PSI-MS-label [] -synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED UniMod-description [] +synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED Unimod-description [] xref: DiffAvg: "218.34" xref: DiffFormula: "C 15 H 22 O 1" xref: DiffMono: "218.167065" @@ -25294,16 +26297,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:176" is_a: MOD:00534 ! Michael addition of BHT quinone methide to cysteine and lysine is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01321 name: Michael addition of BHT quinone methide to cysteine -def: "modification from UniMod Other" [PubMed:11510821, PubMed:12422359, PubMed:9448752, UniMod:176#C] -comment: Primary adduct formed. [UniMod] +def: "modification from Unimod Other" [PubMed:11510821, PubMed:12422359, PubMed:9448752, Unimod:176#C] +comment: Primary adduct formed. [Unimod] synonym: "BHT" RELATED PSI-MS-label [] -synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED UniMod-description [] +synonym: "Michael addition of BHT quinone methide to Cysteine and Lysine" RELATED Unimod-description [] xref: DiffAvg: "218.34" xref: DiffFormula: "C 15 H 22 O 1" xref: DiffMono: "218.167065" @@ -25313,15 +26317,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:176" is_a: MOD:00534 ! Michael addition of BHT quinone methide to cysteine and lysine is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01322 name: propionaldehyde +40 - site K -def: "modification from UniMod Other -" [PubMed:15549660, UniMod:256#K] +def: "OBSOLETE because not supported by the linked literature [PMT]. modification from Unimod Other -" [PubMed:15549660, Unimod:256#K] synonym: "Delta:H(4)C(3)" RELATED PSI-MS-label [] -synonym: "Propionaldehyde +40" RELATED UniMod-description [] +synonym: "Propionaldehyde +40" RELATED Unimod-description [] xref: DiffAvg: "40.06" xref: DiffFormula: "C 3 H 4" xref: DiffMono: "40.031300" @@ -25331,15 +26336,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00579 ! propionaldehyde +40 -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:256" +is_obsolete: true [Term] id: MOD:01323 name: propionaldehyde +40 - site H -def: "modification from UniMod Other -" [UniMod:256#H] +def: "OBSOLETE because not supported by the linked literature [PMT]. modification from Unimod Other -" [Unimod:256#H] synonym: "Delta:H(4)C(3)" RELATED PSI-MS-label [] -synonym: "Propionaldehyde +40" RELATED UniMod-description [] +synonym: "Propionaldehyde +40" RELATED Unimod-description [] xref: DiffAvg: "40.06" xref: DiffFormula: "C 3 H 4" xref: DiffMono: "40.031300" @@ -25349,14 +26354,14 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00579 ! propionaldehyde +40 -is_a: MOD:00909 ! modified L-histidine residue +xref: Unimod: "Unimod:256" +is_obsolete: true [Term] id: MOD:01324 name: acetaldehyde +26 - site H -def: "modification from UniMod Other -" [PubMed:7744761, UniMod:254#H] -synonym: "Acetaldehyde +26" RELATED UniMod-description [] +def: "OBSOLETE because this is not supported by the linked literature [PMT]" [PubMed:7744761, Unimod:254#H] +synonym: "Acetaldehyde +26" RELATED Unimod-description [] synonym: "Delta:H(2)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "26.04" xref: DiffFormula: "C 2 H 2" @@ -25367,14 +26372,14 @@ xref: Origin: "H" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00577 ! acetaldehyde +26 -is_a: MOD:00909 ! modified L-histidine residue +xref: Unimod: "Unimod:254" +is_obsolete: true [Term] id: MOD:01325 name: acetaldehyde +26 - site K -def: "modification from UniMod Other -" [PubMed:7744761, UniMod:254#K] -synonym: "Acetaldehyde +26" RELATED UniMod-description [] +def: "OBSOLETE because this is not supported by the linked literature [PMT]" [PubMed:7744761, Unimod:254#K] +synonym: "Acetaldehyde +26" RELATED Unimod-description [] synonym: "Delta:H(2)C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "26.04" xref: DiffFormula: "C 2 H 2" @@ -25385,14 +26390,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00577 ! acetaldehyde +26 -is_a: MOD:00912 ! modified L-lysine residue +xref: Unimod: "Unimod:254" +is_obsolete: true [Term] id: MOD:01326 name: 9x(13)C labeled L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to 9x(13)C labeled L-tyrosine." [PubMed:11510821, PubMed:12422359, PubMed:12716131, UniMod:184#Y] -synonym: "13C(9) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-tyrosine residue to 9x(13)C labeled L-tyrosine." [PubMed:11510821, PubMed:12422359, PubMed:12716131, Unimod:184#Y] +synonym: "13C(9) Silac label" RELATED Unimod-description [] synonym: "Label:13C(9)" RELATED PSI-MS-label [] xref: DiffAvg: "9.03" xref: DiffFormula: "(12)C -9 (13)C 9" @@ -25403,14 +26408,15 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:184" is_a: MOD:00540 ! 9x(13)C labeled residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01327 name: 9x(13)C labeled L-phenylalanine -def: "A protein modification that effectively converts an L-phenylalanine residue to 9x(13)C labeled L-phenylalanine." [PubMed:12716131, UniMod:184#F] -synonym: "13C(9) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-phenylalanine residue to 9x(13)C labeled L-phenylalanine." [PubMed:12716131, Unimod:184#F] +synonym: "13C(9) Silac label" RELATED Unimod-description [] synonym: "Label:13C(9)" RELATED PSI-MS-label [] xref: DiffAvg: "9.03" xref: DiffFormula: "(12)C -9 (13)C 9" @@ -25421,16 +26427,17 @@ xref: Origin: "F" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:184" is_a: MOD:00540 ! 9x(13)C labeled residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:01328 name: iodoacetic acid - site W -def: "modification from UniMod Chemical derivative - hydroxylethanone" [PubMed:17525468, UniMod:6#W] -comment: There is no citation for this UniMod entry. Iodoacetic acid derivatization of tryptophan is not mentioned in the citation [JSG]. +def: "modification from Unimod Chemical derivative - hydroxylethanone" [PubMed:17525468, Unimod:6#W] +comment: There is no citation for this Unimod entry. Iodoacetic acid derivatization of tryptophan is not mentioned in the citation [JSG]. synonym: "Carboxymethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -25440,6 +26447,7 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:6" is_a: MOD:00399 ! iodoacetic acid derivatized residue is_a: MOD:00918 ! modified L-tryptophan residue @@ -25447,9 +26455,9 @@ id: MOD:01329 name: iodoacetic acid - site C def: "OBSOLETE because duplicate and redundant with MOD:01061. Remap to MOD:01061" [DeltaMass:197] -comment: Modification from UniMod Chemical derivative, UniMod:6 site C +comment: Modification from Unimod Chemical derivative, Unimod:6 site C synonym: "Carboxymethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -25459,15 +26467,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01061" +xref: Unimod: "Unimod:6" is_obsolete: true [Term] id: MOD:01330 name: iodoacetic acid -site K def: "OBSOLETE because identical with MOD:01094. Remap to MOD:01094" [PubMed:18688235] -comment: a modification from UniMod:6 +comment: a modification from Unimod:6 synonym: "Carboxymethyl" RELATED PSI-MS-label [] -synonym: "Iodoacetic acid derivative" RELATED UniMod-description [] +synonym: "Iodoacetic acid derivative" RELATED Unimod-description [] xref: DiffAvg: "58.04" xref: DiffFormula: "C 2 H 2 O 2" xref: DiffMono: "58.005479" @@ -25477,14 +26487,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:01094" +xref: Unimod: "Unimod:6" is_obsolete: true [Term] id: MOD:01331 name: 6x(13)C labeled L-arginine -def: "A protein modification that effectively converts an L-arginine residue to 6x(13)C labeled L-arginine." [OMSSA:136, PubMed:12716131, UniMod:188#R] +def: "A protein modification that effectively converts an L-arginine residue to 6x(13)C labeled L-arginine." [OMSSA:136, PubMed:12716131, Unimod:188#R] subset: PSI-MOD-slim -synonym: "13C(6) Silac label" RELATED UniMod-description [] +synonym: "13C(6) Silac label" RELATED Unimod-description [] synonym: "arg-13c6" EXACT OMSSA-label [] synonym: "Label:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "6.02" @@ -25496,14 +26508,15 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:188" is_a: MOD:00544 ! 6x(13)C labeled residue [Term] id: MOD:01332 name: 6x(13)C labeled L-leucine -def: "A protein modification that effectively converts an L-leucine residue to 6x(13)C labeled L-leucine." [PubMed:12716131, UniMod:188#L] +def: "A protein modification that effectively converts an L-leucine residue to 6x(13)C labeled L-leucine." [PubMed:12716131, Unimod:188#L] subset: PSI-MOD-slim -synonym: "13C(6) Silac label" RELATED UniMod-description [] +synonym: "13C(6) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "6.02" xref: DiffFormula: "(12)C -6 (13)C 6" @@ -25514,14 +26527,15 @@ xref: Origin: "L" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:188" is_a: MOD:00544 ! 6x(13)C labeled residue [Term] id: MOD:01333 name: 6x(13)C labeled L-isoleucine -def: "A protein modification that effectively converts an L-isoleucine residue to 6x(13)C labeled L-isoleucine." [PubMed:12716131, PubMed:12766232, UniMod:188#I] +def: "A protein modification that effectively converts an L-isoleucine residue to 6x(13)C labeled L-isoleucine." [PubMed:12716131, PubMed:12766232, Unimod:188#I] subset: PSI-MOD-slim -synonym: "13C(6) Silac label" RELATED UniMod-description [] +synonym: "13C(6) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "6.02" xref: DiffFormula: "(12)C -6 (13)C 6" @@ -25532,14 +26546,15 @@ xref: Origin: "I" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:188" is_a: MOD:00544 ! 6x(13)C labeled residue [Term] id: MOD:01334 name: 6x(13)C labeled L-lysine -def: "A protein modification that effectively converts an L-lysine residue to 6x(13)C labeled L-lysine." [OMSSA:138, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:12716131, UniMod:188#K] +def: "A protein modification that effectively converts an L-lysine residue to 6x(13)C labeled L-lysine." [OMSSA:138, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:12716131, Unimod:188#K] subset: PSI-MOD-slim -synonym: "13C(6) Silac label" RELATED UniMod-description [] +synonym: "13C(6) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)" RELATED PSI-MS-label [] synonym: "lys-13c6" EXACT OMSSA-label [] xref: DiffAvg: "6.02" @@ -25551,13 +26566,14 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:188" is_a: MOD:00544 ! 6x(13)C labeled residue [Term] id: MOD:01335 name: 6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized lysine -def: "modification from UniMod Chemical derivative -" [PubMed:11467524, PubMed:16526082, UniMod:464#K] -synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:11467524, PubMed:16526082, Unimod:464#K] +synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED Unimod-description [] synonym: "SPITC:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "220.99" xref: DiffFormula: "(12)C 1 (13)C 6 H 5 N 1 O 3 S 2" @@ -25568,6 +26584,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:464" is_a: MOD:00880 ! 6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized residue is_a: MOD:00912 ! modified L-lysine residue @@ -25575,8 +26592,8 @@ id: MOD:01336 name: deamidation followed by a methylation -site Q def: "OBSOLETE - identical and redundant with MOD:00657. Remap to MOD:00657." [PubMed:18688235] -comment: Modification from UniMod Post-translational - UniMod:528. -synonym: "Deamidation followed by a methylation" RELATED UniMod-description [] +comment: Modification from Unimod Post-translational - Unimod:528. +synonym: "Deamidation followed by a methylation" RELATED Unimod-description [] synonym: "Methyl+Deamidated" RELATED PSI-MS-label [] xref: DiffAvg: "15.01" xref: DiffFormula: "C 1 H 1 N -1 O 1" @@ -25587,14 +26604,16 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00657" +xref: Unimod: "Unimod:528" is_obsolete: true [Term] id: MOD:01337 name: deamidated 4-methyl esterified asparagine -def: "A protein modification that effectively converts an L-asparagine residue to L-aspartate 4-methyl ester." [UniMod:528#N] +def: "A protein modification that effectively converts an L-asparagine residue to L-aspartate 4-methyl ester." [Unimod:528#N] comment: The deamidation and methylation of L-asparagine has not been reported as a natural modification. It is extremely unlikely that eukaryotes produce this modification, because a natural process that would form L-aspartic acid 4-methyl ester from either L-aspartic acid or L-asparagine would interfere with the D-aspartyl peptide repair mechanism [JSG]. -synonym: "Deamidation followed by a methylation" RELATED UniMod-description [] +synonym: "Deamidation followed by a methylation" RELATED Unimod-description [] synonym: "Methyl+Deamidated" RELATED PSI-MS-label [] xref: DiffAvg: "15.01" xref: DiffFormula: "C 1 H 1 N -1 O 1" @@ -25605,16 +26624,17 @@ xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01181 ! L-aspartic acid 4-methyl ester +xref: Unimod: "Unimod:528" +relationship: derives_from MOD:01181 ! L-aspartic acid 4-methyl ester is_a: MOD:01369 ! deamidated and methyl esterified residue [Term] id: MOD:01338 name: N6-ethyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-ethyl-L-lysine." [PubMed:9629898, UniMod:280#K] -comment: The UniMod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation [JSG]. +def: "A protein modification that effectively converts an L-lysine residue to N6-ethyl-L-lysine." [PubMed:9629898, Unimod:280#K] +comment: The Unimod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation [JSG]. synonym: "Ethyl" RELATED PSI-MS-label [] -synonym: "Ethylation" RELATED UniMod-description [] +synonym: "Ethylation" RELATED Unimod-description [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" xref: DiffMono: "28.031300" @@ -25624,16 +26644,17 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:280" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01339 ! ethylated residue [Term] id: MOD:01339 name: ethylated residue -def: "A protein modification that effectively replaces a hydrogen atom with an ethyl group." [PubMed:9629898, UniMod:280] -comment: From DeltaMass: Average Mass: 28 with no citation. The UniMod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation [JSG]. +def: "A protein modification that effectively replaces a hydrogen atom with an ethyl group." [PubMed:9629898, Unimod:280] +comment: From DeltaMass: Average Mass: 28 with no citation. The Unimod citation refers to the formation of glutamate ethyl ester and not to either lysine or N-terminal alkylation [JSG]. synonym: "Ethyl" RELATED PSI-MS-label [] -synonym: "Ethylation" RELATED UniMod-description [] +synonym: "Ethylation" RELATED Unimod-description [] synonym: "EtRes" EXACT PSI-MOD-label [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" @@ -25644,13 +26665,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:280" is_a: MOD:00001 ! alkylated residue [Term] id: MOD:01340 name: ESP-Tag heavy d10 - site K -def: "modification from UniMod Isotopic label -" [PubMed:11078590, PubMed:11085420, PubMed:11821862, UniMod:91#K] -synonym: "ESP-Tag heavy d10" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label -" [PubMed:11078590, PubMed:11085420, PubMed:11821862, Unimod:91#K] +synonym: "ESP-Tag heavy d10" RELATED Unimod-description [] synonym: "ESP:2H(10)" RELATED PSI-MS-label [] xref: DiffAvg: "348.24" xref: DiffFormula: "C 16 (1)H 16 (2)H 10 N 4 O 2 S 1" @@ -25661,15 +26683,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:91" is_a: MOD:00469 ! ESP-Tag heavy d10 is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01341 name: ESP-Tag light d0 - site K -def: "modification from UniMod Isotopic label -" [UniMod:90#K] +def: "modification from Unimod Isotopic label -" [Unimod:90#K] synonym: "ESP" RELATED PSI-MS-label [] -synonym: "ESP-Tag light d0" RELATED UniMod-description [] +synonym: "ESP-Tag light d0" RELATED Unimod-description [] xref: DiffAvg: "338.47" xref: DiffFormula: "C 16 H 26 N 4 O 2 S 1" xref: DiffMono: "338.177647" @@ -25679,15 +26702,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:90" is_a: MOD:00468 ! ESP-Tag light d0 is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01342 name: selenium substitution for sulfur - site M -def: "OBSOLETE because redundant and identical to MOD:00530. Remap to MOD:00530." [PubMed:12148805, UniMod:162] +def: "OBSOLETE because redundant and identical to MOD:00530. Remap to MOD:00530." [PubMed:12148805, Unimod:162] synonym: "Delta:S(-1)Se(1)" RELATED PSI-MS-label [] -synonym: "Selenium replaces sulphur" RELATED UniMod-description [] +synonym: "Selenium replaces sulphur" RELATED Unimod-description [] xref: DiffAvg: "46.91" xref: DiffFormula: "S -1 Se 1" xref: DiffMono: "47.944450" @@ -25697,14 +26721,16 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00530" +xref: Unimod: "Unimod:162" is_obsolete: true [Term] id: MOD:01343 name: selenium substitution for sulfur - site C -def: "OBSOLETE because redundant and identical to MOD:00686. Remap to MOD:00686." [PubMed:12148805, UniMod:162] +def: "OBSOLETE because redundant and identical to MOD:00686. Remap to MOD:00686." [PubMed:12148805, Unimod:162] synonym: "Delta:S(-1)Se(1)" RELATED PSI-MS-label [] -synonym: "Selenium replaces sulphur" RELATED UniMod-description [] +synonym: "Selenium replaces sulphur" RELATED Unimod-description [] xref: DiffAvg: "46.91" xref: DiffFormula: "S -1 Se 1" xref: DiffMono: "47.944450" @@ -25714,13 +26740,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00686" +xref: Unimod: "Unimod:162" is_obsolete: true [Term] id: MOD:01344 name: dehydrogenated residue - site S -def: "OBSOLETE because redundant and identical with MOD:00835. Remap to MOD:00835." [PubMed:9252331, PubMed:9276974, UniMod:401] -synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] +def: "OBSOLETE because redundant and identical with MOD:00835. Remap to MOD:00835." [PubMed:9252331, PubMed:9276974, Unimod:401] +synonym: "2-amino-3-oxo-butanoic_acid" RELATED Unimod-description [] synonym: "Didehydro" RELATED PSI-MS-label [] xref: DiffAvg: "-2.02" xref: DiffFormula: "H -2" @@ -25731,15 +26759,17 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00835" +xref: Unimod: "Unimod:401" is_obsolete: true [Term] id: MOD:01345 name: 2-amino-3-oxobutanoic acid -def: "A protein modification that effectively converts an L-threonine residue to 2-amino-3-oxobutanoic acid." [OMSSA:23, PubMed:12716131, PubMed:9252331, UniMod:401#T] -comment: There is no citation for this modification in the UniMod entry. Although mentioned in PubMed:9252331, there is no citation for it there [JSG]. +def: "A protein modification that effectively converts an L-threonine residue to 2-amino-3-oxobutanoic acid." [OMSSA:23, PubMed:12716131, PubMed:9252331, Unimod:401#T] +comment: There is no citation for this modification in the Unimod entry. Although mentioned in PubMed:9252331, there is no citation for it there [JSG]. synonym: "2-amino-3-ketobutyric acid" EXACT PSI-MOD-alternate [] -synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] +synonym: "2-amino-3-oxo-butanoic_acid" RELATED Unimod-description [] synonym: "3-ketobutyrine" EXACT PSI-MOD-alternate [] synonym: "Didehydro" RELATED PSI-MS-label [] synonym: "twoamino3oxobutanoicacid" EXACT OMSSA-label [] @@ -25752,15 +26782,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:401" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01888 ! didehydrogenated residue [Term] id: MOD:01346 name: N4-hexosylated asparagine -def: "A protein modification that effectively converts an L-asparagine residue to an N4-hexosyl-L-asparagine." [PubMed:11112526, PubMed:11567090, PubMed:15279557, PubMed:6540775, UniMod:41#N] +def: "A protein modification that effectively converts an L-asparagine residue to an N4-hexosyl-L-asparagine." [PubMed:11112526, PubMed:11567090, PubMed:15279557, PubMed:6540775, Unimod:41#N] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 O 5" xref: DiffMono: "162.052823" @@ -25770,15 +26801,16 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" is_a: MOD:00160 ! N4-glycosyl-L-asparagine is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:01347 name: hexose glycated L-lysine -def: "A modification produced in a non-enzymatic reaction between a carbohydrate carbonyl group (C1 of aldohexose or C2 of fructose) and an L-lysine residue to form a Schiff-base or an Amadori ketosamine lysine adduct." [DeltaMass:0, PubMed:15279557, UniMod:41#K] +def: "A modification produced in a non-enzymatic reaction between a carbohydrate carbonyl group (C1 of aldohexose or C2 of fructose) and an L-lysine residue to form a Schiff-base or an Amadori ketosamine lysine adduct." [DeltaMass:0, PubMed:15279557, Unimod:41#K] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 O 5" xref: DiffMono: "162.052823" @@ -25788,15 +26820,16 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" is_a: MOD:00767 ! glycated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01348 name: O-hexosylated threonine -def: "A protein modification that effectively converts an L-threonine residue to an O-hexosyl-L-threonine." [PubMed:15279557, PubMed:8597590, UniMod:41#T] +def: "A protein modification that effectively converts an L-threonine residue to an O-hexosyl-L-threonine." [PubMed:15279557, PubMed:8597590, Unimod:41#T] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 O 5" xref: DiffMono: "162.052823" @@ -25806,16 +26839,17 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:01349 name: hydrolyzed N-ethylmaleimide cysteine adduct -def: "modification from UniMod Chemical derivative -" [UniMod:320#C] +def: "modification from Unimod Chemical derivative -" [Unimod:320#C] comment: Hydolyzed N-ethylmaeimide adduct, a mixture of isobaric 2- and 3-(S-cysteinyl)-4-(ethylamino)-4-oxobutanoic acid [JSG]. synonym: "Nethylmaleimide+water" RELATED PSI-MS-label [] -synonym: "Nethylmaleimidehydrolysis" RELATED UniMod-description [] +synonym: "Nethylmaleimidehydrolysis" RELATED Unimod-description [] xref: DiffAvg: "143.14" xref: DiffFormula: "C 6 H 9 N 1 O 3" xref: DiffMono: "143.058243" @@ -25825,16 +26859,17 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:320" is_a: MOD:00631 ! hydrolyzed N-ethylmaleimide adduct is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01350 name: hydrolyzed N-ethylmaleimide lysine adduct -def: "modification from UniMod Chemical derivative -" [UniMod:320#K] +def: "modification from Unimod Chemical derivative -" [Unimod:320#K] comment: Hydolyzed N-ethylmaeimide adduct, a mixture of isobaric 2- and 3-(N6-lysyl)-4-(ethylamino)-4-oxobutanoic acid [JSG]. synonym: "Nethylmaleimide+water" RELATED PSI-MS-label [] -synonym: "Nethylmaleimidehydrolysis" RELATED UniMod-description [] +synonym: "Nethylmaleimidehydrolysis" RELATED Unimod-description [] xref: DiffAvg: "143.14" xref: DiffFormula: "C 6 H 9 N 1 O 3" xref: DiffMono: "143.058243" @@ -25844,16 +26879,17 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:320" is_a: MOD:00631 ! hydrolyzed N-ethylmaleimide adduct [Term] id: MOD:01351 name: nitrated L-tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to a nitrated L-tryptophan." [OMSSA:85, PubMed:8839040, PubMed:9252331, UniMod:354#W] +def: "A protein modification that effectively converts an L-tryptophan residue to a nitrated L-tryptophan." [OMSSA:85, PubMed:8839040, PubMed:9252331, Unimod:354#W] comment: One or more isobaric isomers are produced by nitration with peroxynitrite reagent [JSG]. synonym: "Nitro" RELATED PSI-MS-label [] synonym: "nitrow" EXACT OMSSA-label [] -synonym: "Oxidation to nitro" RELATED UniMod-description [] +synonym: "Oxidation to nitro" RELATED Unimod-description [] xref: DiffAvg: "45.00" xref: DiffFormula: "H -1 N 1 O 2" xref: DiffMono: "44.985078" @@ -25863,18 +26899,19 @@ xref: Origin: "W" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00461 ! nitrosylation +xref: Unimod: "Unimod:354" +is_a: MOD:00461 ! nitrated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:01352 name: nitrated L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to a nitrated L-tyrosine." [OMSSA:86, PubMed:14678012, PubMed:8839040, PubMed:9252331, UniMod:354#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to a nitrated L-tyrosine." [OMSSA:86, PubMed:14678012, PubMed:8839040, PubMed:9252331, Unimod:354#Y] comment: One or more isobaric isomers are produced by nitration with peroxynitrite reagent [JSG]. subset: PSI-MOD-slim synonym: "Nitro" RELATED PSI-MS-label [] synonym: "nitroy" EXACT OMSSA-label [] -synonym: "Oxidation to nitro" RELATED UniMod-description [] +synonym: "Oxidation to nitro" RELATED Unimod-description [] xref: DiffAvg: "45.00" xref: DiffFormula: "H -1 N 1 O 2" xref: DiffMono: "44.985078" @@ -25884,14 +26921,16 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00461 ! nitrosylation +xref: Unimod: "Unimod:354" +xref: UniProt: "PTM-0213" +is_a: MOD:00461 ! nitrated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01353 name: amidination of lysines or N-terminal amines with methyl acetimidate - site K -def: "modification from UniMod Chemical derivative -" [PubMed:12643539, PubMed:15602776, PubMed:6273432, UniMod:141#K] -synonym: "amidination of lysines or N-terminal amines with methyl acetimidate" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:12643539, PubMed:15602776, PubMed:6273432, Unimod:141#K] +synonym: "amidination of lysines or N-terminal amines with methyl acetimidate" RELATED Unimod-description [] synonym: "Amidine" RELATED PSI-MS-label [] xref: DiffAvg: "41.05" xref: DiffFormula: "C 2 H 3 N 1" @@ -25902,15 +26941,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:141" is_a: MOD:00509 ! amidination of lysines or N-terminal amines with methyl acetimidate is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01354 name: Hex1HexNAc1NeuAc1 N4-glycosylated asparagine -def: "A protein modification that effectively replaces an N4 hydrogen atom of an asparagine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [PubMed:11698400, UniMod:149#N] +def: "A protein modification that effectively replaces an N4 hydrogen atom of an asparagine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [PubMed:11698400, Unimod:149#N] synonym: "Hex(1)HexNAc(1)NeuAc(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc1" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc1" RELATED Unimod-description [] xref: DiffAvg: "657.60" xref: DiffFormula: "C 25 H 41 N 2 O 18" xref: DiffMono: "657.235437" @@ -25920,15 +26960,16 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:149" is_a: MOD:00517 ! Hex1HexNAc1NeuAc1 glycosylated residue -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] id: MOD:01355 -name: Hex1HexNAc1NeuAc1O-glycosylated threonine -def: "A protein modification that effectively replaces an O3 hydrogen atom of a threonine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [UniMod:149#T] +name: Hex1HexNAc1NeuAc1 O-glycosylated threonine +def: "A protein modification that effectively replaces an O3 hydrogen atom of a threonine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [Unimod:149#T] synonym: "Hex(1)HexNAc(1)NeuAc(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc1" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc1" RELATED Unimod-description [] xref: DiffAvg: "657.60" xref: DiffFormula: "C 25 H 41 N 2 O 18" xref: DiffMono: "657.235437" @@ -25938,15 +26979,16 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:149" is_a: MOD:00517 ! Hex1HexNAc1NeuAc1 glycosylated residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:00005 ! O-glycosyl-L-threonine [Term] id: MOD:01356 name: Hex1HexNAc1NeuAc1 O-glycosylated serine -def: "A protein modification that effectively replaces an O3 hydrogen atom of a serine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [PubMed:7856876, UniMod:149#S] +def: "A protein modification that effectively replaces an O3 hydrogen atom of a serine residue with a carbohydrate-like group composed of Hex1HexNAc1NeuAc1 linked through a glycosidic bond." [PubMed:7856876, Unimod:149#S] synonym: "Hex(1)HexNAc(1)NeuAc(1)" RELATED PSI-MS-label [] -synonym: "Hex1HexNAc1NeuAc1" RELATED UniMod-description [] +synonym: "Hex1HexNAc1NeuAc1" RELATED Unimod-description [] xref: DiffAvg: "657.60" xref: DiffFormula: "C 25 H 41 N 2 O 18" xref: DiffMono: "657.235437" @@ -25956,14 +26998,15 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:149" is_a: MOD:00517 ! Hex1HexNAc1NeuAc1 glycosylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01357 name: 2x(13)C,4x(2)H labeled dimethylated L-lysine -def: "A protein modification that effectively replaces two hydrogen atoms of an L-lysine residue containing common isotopes with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated L-lysine." [PubMed:12686488, PubMed:16335955, UniMod:510#K] -synonym: "DiMethyl-C13HD2" RELATED UniMod-description [] +def: "A protein modification that effectively replaces two hydrogen atoms of an L-lysine residue containing common isotopes with two (13)C,3x(2)H labeled methyl groups to form a 2x(13)C,6x(2)H labeled dimethylated L-lysine." [PubMed:12686488, PubMed:16335955, Unimod:510#K] +synonym: "DiMethyl-C13HD2" RELATED Unimod-description [] synonym: "Dimethyl:2H(4)13C(2)" RELATED PSI-MS-label [] xref: DiffAvg: "34.06" xref: DiffFormula: "(13)C 2 (2)H 4" @@ -25974,6 +27017,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:510" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00927 ! 2x(13)C,4x(2)H labeled dimethylated residue relationship: derives_from MOD:00084 ! N6,N6-dimethyl-L-lysine @@ -25981,8 +27025,8 @@ [Term] id: MOD:01358 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form - site N-term -def: "modification from UniMod Isotopic label - Use when labelling post-digest" [PubMed:15602776, UniMod:687#N-term] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label - Use when labelling post-digest" [PubMed:15602776, Unimod:687#N-term] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form" RELATED Unimod-description [] synonym: "ICPL:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "109.05" xref: DiffFormula: "C 6 (1)H -1 (2)H 4 N 1 O 1" @@ -25993,13 +27037,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:687" is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01359 name: Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form - site K -def: "modification from UniMod Isotopic label - Use when labelling post-digest" [PubMed:15602776, UniMod:687#K] -synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form" RELATED UniMod-description [] +def: "modification from Unimod Isotopic label - Use when labelling post-digest" [PubMed:15602776, Unimod:687#K] +synonym: "Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form" RELATED Unimod-description [] synonym: "ICPL:2H(4)" RELATED PSI-MS-label [] xref: DiffAvg: "109.05" xref: DiffFormula: "C 6 (1)H -1 (2)H 4 N 1 O 1" @@ -26010,14 +27055,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:687" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01360 name: 4-sulfophenyl isothiocyanate N6-derivatized lysine -def: "A protein modification that effectively converts an L-lysine residue to the 4-sulfophenyl isothiocyanate adduct, N6-[(4-sulfophenyl)carbamothioyl]lysine." [PubMed:14689565, PubMed:14745769, PubMed:15549660, PubMed:16526082, UniMod:261#K] -synonym: "4-sulfophenyl isothiocyanate" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-lysine residue to the 4-sulfophenyl isothiocyanate adduct, N6-[(4-sulfophenyl)carbamothioyl]lysine." [PubMed:14689565, PubMed:14745769, PubMed:15549660, PubMed:16526082, Unimod:261#K] +synonym: "4-sulfophenyl isothiocyanate" RELATED Unimod-description [] synonym: "N6-[(4-sulfophenyl)carbamothioyl]lysine" EXACT PSI-MOD-alternate [] synonym: "SPITC" RELATED PSI-MS-label [] xref: DiffAvg: "215.24" @@ -26029,15 +27075,16 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:261" is_a: MOD:00584 ! 4-sulfophenyl isothiocyanate derivatized residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01361 name: O-thiophospho-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-thiophospho-L-threonine." [PubMed:11507762, PubMed:12110917, UniMod:260#T] +def: "A protein modification that effectively converts an L-threonine residue to O-thiophospho-L-threonine." [PubMed:11507762, PubMed:12110917, Unimod:260#T] synonym: "Thiophospho" RELATED PSI-MS-label [] -synonym: "Thiophosphorylation" RELATED UniMod-description [] +synonym: "Thiophosphorylation" RELATED Unimod-description [] xref: DiffAvg: "96.04" xref: DiffFormula: "H 1 O 2 P 1 S 1" xref: DiffMono: "95.943487" @@ -26047,15 +27094,16 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:260" is_a: MOD:00583 ! thiophosphorylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01362 name: O-thiophospho-L-serine -def: "A protein modification that effectively converts an L-serine residue to O-thiophospho-L-serine." [PubMed:11507762, PubMed:12110917, UniMod:260#S] +def: "A protein modification that effectively converts an L-serine residue to O-thiophospho-L-serine." [PubMed:11507762, PubMed:12110917, Unimod:260#S] synonym: "Thiophospho" RELATED PSI-MS-label [] -synonym: "Thiophosphorylation" RELATED UniMod-description [] +synonym: "Thiophosphorylation" RELATED Unimod-description [] xref: DiffAvg: "96.04" xref: DiffFormula: "H 1 O 2 P 1 S 1" xref: DiffMono: "95.943487" @@ -26065,15 +27113,16 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:260" is_a: MOD:00583 ! thiophosphorylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01363 name: O4'-thiophospho-L-tyrosine -def: "A protein modification that effectively converts an L-tyrosine residue to O4'-thiophospho-L-tyrosine." [PubMed:12110917, PubMed:15549660, UniMod:260#Y] +def: "A protein modification that effectively converts an L-tyrosine residue to O4'-thiophospho-L-tyrosine." [PubMed:12110917, PubMed:15549660, Unimod:260#Y] synonym: "Thiophospho" RELATED PSI-MS-label [] -synonym: "Thiophosphorylation" RELATED UniMod-description [] +synonym: "Thiophosphorylation" RELATED Unimod-description [] xref: DiffAvg: "96.04" xref: DiffFormula: "H 1 O 2 P 1 S 1" xref: DiffMono: "95.943487" @@ -26083,14 +27132,15 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:260" is_a: MOD:00583 ! thiophosphorylated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01364 name: fluorescein-5-thiosemicarbazide - site S -def: "modification from UniMod Chemical derivative -" [PubMed:11467524, UniMod:478#S] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:11467524, Unimod:478#S] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -26101,14 +27151,15 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide +xref: Unimod: "Unimod:478" +is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide modified residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01365 name: fluorescein-5-thiosemicarbazide - site C -def: "modification from UniMod Chemical derivative -" [UniMod:478#C] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [Unimod:478#C] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -26119,14 +27170,15 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide +xref: Unimod: "Unimod:478" +is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01366 name: fluorescein-5-thiosemicarbazide - site K -def: "modification from UniMod Chemical derivative -" [UniMod:478#K] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [Unimod:478#K] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -26137,14 +27189,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide +xref: Unimod: "Unimod:478" +is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide modified residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01367 name: fluorescein-5-thiosemicarbazide - site P -def: "modification from UniMod Chemical derivative -" [UniMod:478#P] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [Unimod:478#P] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -26155,14 +27208,15 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide +xref: Unimod: "Unimod:478" +is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide modified residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:01368 name: fluorescein-5-thiosemicarbazide - site R -def: "modification from UniMod Chemical derivative -" [PubMed:15525938, UniMod:478#R] -synonym: "fluorescein-5-thiosemicarbazide" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative -" [PubMed:15525938, Unimod:478#R] +synonym: "fluorescein-5-thiosemicarbazide" RELATED Unimod-description [] synonym: "FTC" RELATED PSI-MS-label [] xref: DiffAvg: "421.43" xref: DiffFormula: "C 21 H 15 N 3 O 5 S 1" @@ -26173,15 +27227,16 @@ xref: Origin: "R" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide +xref: Unimod: "Unimod:478" +is_a: MOD:00626 ! fluorescein-5-thiosemicarbazide modified residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:01369 name: deamidated and methyl esterified residue -def: "A protein modification that effectively replaces a carboxamido group with a carboxyl methyl ester group." [UniMod:528] +def: "A protein modification that effectively replaces a carboxamido group with a carboxyl methyl ester group." [Unimod:528] subset: PSI-MOD-slim -synonym: "Deamidation followed by a methylation" RELATED UniMod-description [] +synonym: "Deamidation followed by a methylation" RELATED Unimod-description [] synonym: "Methyl+Deamidated" RELATED PSI-MS-label [] xref: DiffAvg: "15.01" xref: DiffFormula: "C 1 H 1 N -1 O 1" @@ -26192,14 +27247,15 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:528" is_a: MOD:00393 ! O-methylated residue -is_a: MOD:00400 ! deamidated residue +relationship: contains MOD:00400 ! deamidated residue [Term] id: MOD:01370 name: 6x(13)C,1x(15)N labeled residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 6x(13)C,1x(15)N labeled residue." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:695] -synonym: "13C(6) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue containing common isotopes to a 6x(13)C,1x(15)N labeled residue." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:695] +synonym: "13C(6) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(6)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "7.02" xref: DiffFormula: "(12)C -6 (13)C 6 (14)N -1 (15)N 1" @@ -26210,6 +27266,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:695" is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00843 ! (15)N labeled residue @@ -26218,7 +27275,7 @@ name: deamidation in presence of O18 def: "OBSOLETE bcecause identical and redundant with MOD:00851. Remap to MOD:00851." [PubMed:8382902] synonym: "Deamidated:18O(1)" RELATED PSI-MS-label [] -synonym: "Deamidation in presence of O18" RELATED UniMod-description [] +synonym: "Deamidation in presence of O18" RELATED Unimod-description [] xref: DiffAvg: "2.99" xref: DiffFormula: "H -1 N -1 (18)O 1" xref: DiffMono: "2.988262" @@ -26228,15 +27285,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00851" is_obsolete: true [Term] id: MOD:01372 name: (2S)-4-hydroxyleucine -def: "A protein modification that effectively converts an L-leucine residue to a (2S)-4-hydroxyleucine." [PubMed:363352, PubMed:9164839, RESID:AA0442] +def: "A protein modification that effectively converts an L-leucine residue to a (2S)-4-hydroxyleucine." [PubMed:363352, PubMed:9164839, RESID:AA0442, ChEBI:141825] synonym: "(2S)-2-amino-4-hydroxy-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S)-4-hydroxyleucine" EXACT RESID-name [] synonym: "gamma-hydroxyleucine" EXACT RESID-alternate [] +synonym: "MOD_RES (2S)-4-hydroxyleucine" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -26246,16 +27305,18 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0665" is_a: MOD:01411 ! monohydroxylated leucine [Term] id: MOD:01373 name: (2S,4R)-5-hydroxyleucine -def: "A protein modification that effectively converts an L-leucine residue to a (2S,4R)-5-hydroxyleucine." [PubMed:16858410, PubMed:7690768, PubMed:9164839, RESID:AA0443] +def: "A protein modification that effectively converts an L-leucine residue to a (2S,4R)-5-hydroxyleucine." [PubMed:16858410, PubMed:7690768, PubMed:9164839, RESID:AA0443, ChEBI:141824] synonym: "(2S,4R)-2-amino-5-hydroxy-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,4R)-5-hydroxyleucine" EXACT RESID-name [] synonym: "(4R)-5-hydroxyleucine" EXACT RESID-alternate [] synonym: "delta-hydroxyleucine" EXACT RESID-alternate [] +synonym: "MOD_RES (4R)-5-hydroxyleucine" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -26265,6 +27326,7 @@ xref: Origin: "L" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0491" is_a: MOD:01411 ! monohydroxylated leucine [Term] @@ -26283,13 +27345,14 @@ xref: Origin: "L" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0492" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00911 ! modified L-leucine residue [Term] id: MOD:01375 name: (2S,4R)-4,5-dihydroxyleucine -def: "A protein modification that effectively converts an L-leucine residue to a (2S,4R)-4,5-dihydroxyleucine." [PubMed:6010785, PubMed:6893271, RESID:AA0445] +def: "A protein modification that effectively converts an L-leucine residue to a (2S,4R)-4,5-dihydroxyleucine." [PubMed:6010785, PubMed:6893271, RESID:AA0445, ChEBI:141823] synonym: "(2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,4R)-4,5-dihydroxyleucine" EXACT RESID-name [] synonym: "(4R)-4,5-dihydroxyleucine" EXACT RESID-alternate [] @@ -26304,12 +27367,13 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0340" is_a: MOD:01412 ! dihydroxylated leucine [Term] id: MOD:01376 name: (2S,3S,4R)-3,4-dihydroxyisoleucine -def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3S,4R)-3,4-dihydroxyisoleucine." [PubMed:11320328, RESID:AA0447] +def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3S,4R)-3,4-dihydroxyisoleucine." [PubMed:11320328, RESID:AA0447, ChEBI:141827] synonym: "(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,3S,4R)-3,4-dihydroxyisoleucine" EXACT RESID-name [] synonym: "(3S,4R)-3,4-dihydroxyisoleucine" EXACT RESID-alternate [] @@ -26324,12 +27388,13 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0343" is_a: MOD:01416 ! dihydroxylated isoleucine [Term] id: MOD:01377 name: (2S,3R,4S)-4-hydroxyisoleucine -def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3R,4S)-4-hydroxyisoleucine." [PubMed:363352, RESID:AA0448] +def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3R,4S)-4-hydroxyisoleucine." [PubMed:363352, RESID:AA0448, ChEBI:141844] synonym: "(2S,3R,4S)-2-amino-3-methyl-4-hydroxyvaleric acid" EXACT RESID-alternate [] synonym: "(2S,3R,4S)-2-amino-4-hydroxy-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,3R,4S)-4-hydroxyisoleucine" EXACT RESID-name [] @@ -26345,12 +27410,13 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0337" is_a: MOD:01415 ! monohydroxylated isoleucine [Term] id: MOD:01378 name: (2S,3R,4R)-4,5-dihydroxyisoleucine -def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3R,4R)-4,5-dihydroxyisoleucine." [PubMed:11805306, PubMed:18552824, PubMed:363352, RESID:AA0449] +def: "A protein modification that effectively converts an L-isoleucine residue to a (2S,3R,4R)-4,5-dihydroxyisoleucine." [PubMed:11805306, PubMed:18552824, PubMed:363352, RESID:AA0449, ChEBI:141826] synonym: "(2S,3R,4R)-2-amino-4,5-dihydroxy-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,3R,4R)-4,5-dihydroxyisoleucine" EXACT RESID-name [] synonym: "(3R,4R)-4,5-dihydroxyisoleucine" EXACT RESID-alternate [] @@ -26365,6 +27431,7 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0336" is_a: MOD:01416 ! dihydroxylated isoleucine [Term] @@ -26383,6 +27450,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0304" is_a: MOD:00918 ! modified L-tryptophan residue [Term] @@ -26403,8 +27471,9 @@ xref: Origin: "C, W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0338" is_a: MOD:00687 ! thioether crosslinked residues -is_a: MOD:00918 ! modified L-tryptophan residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue [Term] id: MOD:01381 @@ -26426,7 +27495,8 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0493" +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01768 ! O-palmitoleylated residue [Term] @@ -26452,6 +27522,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0503" is_a: MOD:01463 ! N-methylated methionine is_a: MOD:01698 ! alpha-amino trimethylated protonated-residue @@ -26475,6 +27546,8 @@ xref: Origin: "C, C" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0324" +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:00689 ! disulfide crosslinked residues [Term] @@ -26495,6 +27568,7 @@ xref: Origin: "S" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0321" is_a: MOD:00916 ! modified L-serine residue [Term] @@ -26520,13 +27594,14 @@ xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0346" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:01386 name: 3-hydroxy-L-valine -def: "A protein modification that effectively converts an L-valine residue to 3-hydroxy-L-valine." [PubMed:7328054, RESID:AA0463] +def: "A protein modification that effectively converts an L-valine residue to 3-hydroxy-L-valine." [PubMed:7328054, RESID:AA0463, ChEBI:141793] synonym: "(2S)-2-amino-3-hydroxy-3-methylbutanoic acid" EXACT RESID-systematic [] synonym: "3-hydroxy-L-valine" EXACT RESID-name [] synonym: "3-hydroxyvaline" EXACT RESID-alternate [] @@ -26541,6 +27616,7 @@ xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0347" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00920 ! modified L-valine residue @@ -26563,6 +27639,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0356" is_a: MOD:01803 ! O-methylated threonine [Term] @@ -26592,6 +27669,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0354" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:00960 ! decarboxylated residue @@ -26613,9 +27691,10 @@ xref: Origin: "C, I" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00910 ! modified L-isoleucine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0361" +is_a: MOD:02049 ! crosslinked L-isoleucine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01390 @@ -26635,9 +27714,10 @@ xref: Origin: "C, V" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00920 ! modified L-valine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0365" +is_a: MOD:02059 ! crosslinked L-valine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01391 @@ -26657,9 +27737,9 @@ xref: Origin: "C, V" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00920 ! modified L-valine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0373" +is_a: MOD:02059 ! crosslinked L-valine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues [Term] id: MOD:01392 @@ -26679,9 +27759,9 @@ xref: Origin: "C, N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0352" +is_a: MOD:02042 ! crosslinked L-asparagine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues relationship: derives_from MOD:00656 ! C-methylated residue [Term] @@ -26700,6 +27780,9 @@ xref: Origin: "C, S, S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0358" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01425 ! pyridinyl ring crosslinked residues [Term] @@ -26710,6 +27793,7 @@ synonym: "(5R,6R)-5-amino-6-[(1R)-1-amino-2-sulfanylethyl]-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic acid" EXACT RESID-systematic [] synonym: "L-cysteine 5-amino-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic acid" EXACT RESID-name [] synonym: "L-cysteine 5-aminopiperideine-2,5-dicarboxylic acid" EXACT RESID-alternate [] +synonym: "CROSSLNK 5-amino-piperideine-2,5-dicarboxylic acid" RELATED UniProt-feature [] xref: DiffAvg: "-53.04" xref: DiffFormula: "C 0 H -5 N 0 O -3 S 0" xref: DiffMono: "-53.023869" @@ -26719,6 +27803,9 @@ xref: Origin: "C, S, S" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0348" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01425 ! pyridinyl ring crosslinked residues [Term] @@ -26738,8 +27825,8 @@ xref: Origin: "I, T" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00910 ! modified L-isoleucine residue -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02049 ! crosslinked L-isoleucine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01424 ! quinaldate modified residue [Term] @@ -26784,14 +27871,15 @@ xref: Origin: "S, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0386" +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01422 ! oxazole/oxazoline ring crosslinked residues (Thr) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01398 name: N6-propanoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-propanoyl-L-lysine." [PubMed:17267393, PubMed:17684016, PubMed:20715035, RESID:AA0475, UniMod:58#K] +def: "A protein modification that effectively converts an L-lysine residue to N6-propanoyl-L-lysine." [PubMed:17267393, PubMed:17684016, PubMed:20715035, RESID:AA0475, Unimod:58#K] comment: The binding of histone peptides with propanoylated lysine to nuclear bromodomain proteins is non-specific and weaker than binding to the corresponding acetylated lysine peptides [JSG]. subset: PSI-MOD-slim synonym: "(2S)-2-amino-6-(propanoylamino)hexanoic acid" EXACT RESID-systematic [] @@ -26802,6 +27890,7 @@ synonym: "N6-(1-oxopropyl)-L-lysine" EXACT RESID-alternate [] synonym: "N6-propanoyl-L-lysine" EXACT RESID-name [] synonym: "N6-propionyllysine" EXACT RESID-alternate [] +synonym: "MOD_RES N6-propionyllysine" EXACT UniProt-feature [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 N 0 O 1" xref: DiffMono: "56.026215" @@ -26811,6 +27900,8 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:58" +xref: UniProt: "PTM-0642" is_a: MOD:01155 ! lipoconjugated residue is_a: MOD:01875 ! N6-acylated L-lysine is_a: MOD:01894 ! propanoylated residue @@ -26836,6 +27927,7 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0355" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00912 ! modified L-lysine residue @@ -26846,22 +27938,16 @@ synonym: "L-lysyl-poly(ADP-ribose)" EXACT RESID-name [] synonym: "MOD_RES Lysyl poly(ADP-ribose)" EXACT UniProt-feature [] synonym: "poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl] (2S)-2,6-diaminohexanoate" EXACT RESID-systematic [] -xref: DiffAvg: "541.30" -xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" -xref: DiffMono: "541.061109" -xref: Formula: "C 21 H 34 N 7 O 15 P 2" -xref: MassAvg: "686.48" -xref: MassMono: "686.158812" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "C-term" -is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue +is_a: MOD:02087 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01401 name: (2S,3S)-3-hydroxyasparagine -def: "A protein modification that effectively converts an L-asparagine residue to a (2S,3S)-3-hydroxyasparagine." [ChEBI:50789, PubMed:11823643, PubMed:12042299, PubMed:12215170, PubMed:17573339, RESID:AA0478] +def: "A protein modification that effectively converts an L-asparagine residue to a (2S,3S)-3-hydroxyasparagine." [ChEBI:50789, PubMed:11823643, PubMed:12042299, PubMed:12215170, PubMed:17573339, RESID:AA0478, ChEBI:138107] subset: PSI-MOD-slim synonym: "(2S,3S)-2,4-diamino-3-hydroxy-4-oxobutanoic acid" EXACT RESID-alternate [] synonym: "(2S,3S)-2-amino-3-hydroxy-4-butanediamic acid" EXACT RESID-systematic [] @@ -26878,12 +27964,13 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0370" is_a: MOD:01688 ! 3-hydroxy-L-asparagine [Term] id: MOD:01402 name: (2S,3R,4R)-3,4-dihydroxyproline -def: "A protein modification that effectively converts an L-proline residue to a (2S,3R,4R)-3,4-dihydroxyproline." [PubMed:6893271, RESID:AA0479] +def: "A protein modification that effectively converts an L-proline residue to a (2S,3R,4R)-3,4-dihydroxyproline." [PubMed:6893271, RESID:AA0479, ChEBI:141805] synonym: "(2S,3R,4R)-3,4-dihydroxyproline" EXACT RESID-name [] synonym: "(2S,3R,4R)-3,4-dihydroxypyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "2,3-trans-3,4-trans-3,4-dihydroxy-L-proline" EXACT RESID-alternate [] @@ -26898,6 +27985,7 @@ xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0368" is_a: MOD:00866 ! dihydroxylated proline [Term] @@ -26918,6 +28006,7 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0372" is_a: MOD:01413 ! trihydroxylated leucine [Term] @@ -26938,9 +28027,10 @@ xref: Origin: "C, N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0359" +is_a: MOD:02042 ! crosslinked L-asparagine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01405 @@ -26959,9 +28049,9 @@ xref: Origin: "C, P" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00915 ! modified L-proline residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02054 ! crosslinked L-proline residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01406 @@ -26981,9 +28071,10 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0364" +is_a: MOD:02056 ! crosslinked L-threonine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01407 @@ -27003,8 +28094,10 @@ xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00914 ! modified L-phenylalanine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues +xref: UniProt: "PTM-0366" +is_a: MOD:02053 ! crosslinked L-phenylalanine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01408 @@ -27024,8 +28117,10 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues +xref: UniProt: "PTM-0392" +is_a: MOD:02056 ! crosslinked L-threonine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01409 @@ -27205,7 +28300,7 @@ [Term] id: MOD:01420 -name: thiazole/thiazoline ring croslinked residues +name: thiazole/thiazoline ring crosslinked residues def: "A protein modification that crosslinks two residues by condensation of a cysteine thiol with the carbonyl of the preceding residue to form a thiazole or thiazoline ring." [PubMed:18688235] xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -27232,7 +28327,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01419 ! oxazole/oxazoline ring crosslinked residues [Term] @@ -27248,13 +28343,13 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01419 ! oxazole/oxazoline ring crosslinked residues [Term] id: MOD:01423 name: palmitoleylated residue -def: "A protein modification that effectively replaces a hydrogen atom with a palmitoleyl group." [UniMod:431] +def: "A protein modification that effectively replaces a hydrogen atom with a palmitoleyl group." [Unimod:431] subset: PSI-MOD-slim xref: DiffAvg: "236.40" xref: DiffFormula: "C 16 H 28 N 0 O 1" @@ -27265,7 +28360,9 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:431" is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:01424 @@ -27284,12 +28381,10 @@ xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" -xref: Origin: "C, S, S" +xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00033 ! crosslinked residues -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:01426 @@ -27312,6 +28407,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Remap: "MOD:00819" is_obsolete: true [Term] @@ -27320,6 +28416,7 @@ def: "A protein modification that forms an adduct with a (13)C labeled compound used as a reagent." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:00842 ! (13)C labeled residue [Term] id: MOD:01429 @@ -27327,6 +28424,7 @@ def: "A protein modification that forms an adduct with a (15)N labeled compound used as a reagent." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:00843 ! (15)N labeled residue [Term] id: MOD:01430 @@ -27334,6 +28432,7 @@ def: "A protein modification that forms an adduct with a (13)C labeled compound used as a reagent." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:00844 ! (18)O labeled residue [Term] id: MOD:01431 @@ -27341,15 +28440,17 @@ def: "A protein modification that forms an adduct with a (2)H labeled compound used as a reagent." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:00839 ! (2)H deuterium labeled residue [Term] id: MOD:01432 name: (2S,4S)-4,5-dihydroxyleucine -def: "A protein modification that effectively converts an L-leucine residue to a (2S,4S)-4,5-dihydroxyleucine." [PubMed:3718926, RESID:AA0446] +def: "A protein modification that effectively converts an L-leucine residue to a (2S,4S)-4,5-dihydroxyleucine." [PubMed:3718926, RESID:AA0446, ChEBI:141819] synonym: "(2S,4S)-2-amino-4,5-dihydroxy-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "(2S,4S)-4,5-dihydroxyleucine" EXACT RESID-name [] synonym: "(4S)-4,5-dihydroxyleucine" EXACT RESID-alternate [] synonym: "gamma,delta-dihydroxyleucine" EXACT RESID-alternate [] +synonym: "MOD_RES (4S)-4,5-dihydroxyleucine" EXACT UniProt-feature [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" @@ -27359,6 +28460,7 @@ xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0666" is_a: MOD:01412 ! dihydroxylated leucine [Term] @@ -27379,14 +28481,14 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0379" is_a: MOD:00683 ! dehydrogenated residue is_a: MOD:00917 ! modified L-threonine residue -is_a: MOD:00960 ! decarboxylated residue [Term] id: MOD:01434 name: 4-hydroxy-L-glutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to a 4-hydroxy-L-glutamic acid." [PubMed:893891, RESID:AA0487] +def: "A protein modification that effectively converts an L-glutamic acid residue to a 4-hydroxy-L-glutamic acid." [PubMed:893891, RESID:AA0487, ChEBI:141845] synonym: "(2S,4Xi)-2-amino-4-hydroxypentanedioic acid" EXACT RESID-systematic [] synonym: "4-hydroxy-L-glutamic acid" EXACT RESID-name [] synonym: "gamma-hydroxy glutaminic acid" EXACT RESID-alternate [] @@ -27401,6 +28503,7 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0453" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00906 ! modified L-glutamic acid residue @@ -27423,8 +28526,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00672 ! S-acylated residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue [Term] id: MOD:01436 @@ -27463,9 +28566,11 @@ xref: Origin: "C, P, S" xref: Source: "natural" xref: TermSpec: "C-term" -is_a: MOD:00915 ! modified L-proline residue -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0380" +is_a: MOD:02054 ! crosslinked L-proline residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01629 ! cyclo[(prolylserin)-O-yl] cysteinate +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01438 @@ -27477,7 +28582,7 @@ synonym: "Pyridylethyl" RELATED PSI-MS-label [] synonym: "Pyridylethyl Cystenyl" EXACT DeltaMass-label [] synonym: "S-(pyridin-2-ylethyl)-L-cysteine" EXACT PSI-MOD-alternate [] -synonym: "S-pyridylethylation" RELATED UniMod-description [] +synonym: "S-pyridylethylation" RELATED Unimod-description [] xref: DiffAvg: "105.14" xref: DiffFormula: "C 7 H 7 N 1" xref: DiffMono: "105.057849" @@ -27497,7 +28602,7 @@ synonym: "Pyridylethyl" RELATED PSI-MS-label [] synonym: "Pyridylethyl Cystenyl" EXACT DeltaMass-label [] synonym: "S-(pyridin-4-ylethyl)-L-cysteine" EXACT PSI-MOD-alternate [] -synonym: "S-pyridylethylation" RELATED UniMod-description [] +synonym: "S-pyridylethylation" RELATED Unimod-description [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -27525,6 +28630,7 @@ xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues +is_a: MOD:00594 ! residues isobaric at 113.047678 Da [Term] id: MOD:01441 @@ -27553,9 +28659,10 @@ xref: Origin: "V, Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0390" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue -is_a: MOD:00920 ! modified L-valine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue +is_a: MOD:02059 ! crosslinked L-valine residue [Term] id: MOD:01443 @@ -27572,11 +28679,11 @@ xref: Origin: "E, E, E, E, H, H" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00438 ! myristoylated residue +relationship: contains MOD:00438 ! myristoylated residue is_a: MOD:00738 ! iron containing modified residue is_a: MOD:00740 ! manganese containing modified residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:01444 @@ -27726,7 +28833,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00046 ! O-phospho-L-serine +is_a: MOD:00916 ! modified L-serine is_a: MOD:00431 ! modified residue with a secondary neutral loss relationship: derives_from MOD:00159 ! O-phosphopantetheine-L-serine @@ -27745,7 +28852,7 @@ xref: Origin: "MOD:00159" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00046 ! O-phospho-L-serine +is_a: MOD:00916 ! modified L-serine is_a: MOD:00431 ! modified residue with a secondary neutral loss relationship: derives_from MOD:00159 ! O-phosphopantetheine-L-serine @@ -27787,13 +28894,7 @@ synonym: "(1Z,2S)-2-carboxy-1-[(3R,4R)-3,4-dihydroxy-5-(phosphonooxy)pentylidene]pyrrolidinium" EXACT RESID-systematic [] synonym: "DNA glycosylase proline Schiff base intermediate" RELATED RESID-misnomer [] synonym: "N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium" EXACT RESID-name [] -xref: DiffAvg: "179.09" -xref: DiffFormula: "C 5 H 8 N 0 O 5 P 1" -xref: DiffMono: "179.010386" xref: FormalCharge: "1+" -xref: Formula: "C 10 H 16 N 1 O 6 P 1" -xref: MassAvg: "277.21" -xref: MassMono: "277.070975" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" @@ -27822,7 +28923,7 @@ name: N-phosphorylated residue def: "A protein modification that effectively replaces a hydrogen atom of a residue amino or imino group with a phosphono group (H2PO3 or 'phosphate')." [PubMed:18688235] subset: PSI-MOD-slim -synonym: "OPhosRes" EXACT PSI-MOD-label [] +synonym: "NPhosRes" EXACT PSI-MOD-label [] xref: DiffAvg: "79.98" xref: DiffFormula: "H 1 O 3 P 1" xref: DiffMono: "79.966331" @@ -27848,14 +28949,14 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00014 ! L-cysteine residue is_a: MOD:00749 ! sulfur substitution for oxygen is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02088 ! natural, standard, encoded residue substitution [Term] id: MOD:01458 name: alpha-amino acetylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an acetyl group." [OMSSA:10, UniMod:1#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an acetyl group." [OMSSA:10, Unimod:1#N-term] subset: PSI-MOD-slim synonym: "N2AcRes" EXACT PSI-MOD-label [] synonym: "ntermacetyl" EXACT OMSSA-label [] @@ -27868,16 +28969,17 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00408 ! N-acetylated residue +xref: Unimod: "Unimod:1" +is_a: MOD:00408 ! mono N-acetylated residue is_a: MOD:01696 ! alpha-amino acylated residue [Term] id: MOD:01459 name: 4x(2)H labeled alpha-dimethylamino N-terminal residue -def: "A protein modification that effectively converts an N-terminal residue to an 4x(2)H labeled alpha-dimethylamino N-terminal residue." [OMSSA:190, PubMed:14670044, UniMod:199#N-term] +def: "A protein modification that effectively converts an N-terminal residue to an 4x(2)H labeled alpha-dimethylamino N-terminal residue." [OMSSA:190, PubMed:14670044, Unimod:199#N-term] comment: Supposed to be alpha-amino and Lys-N6 derivatized by C(2)H2O and reduction. subset: PSI-MOD-slim -synonym: "DiMethyl-CHD2" RELATED UniMod-description [] +synonym: "DiMethyl-CHD2" RELATED Unimod-description [] synonym: "Dimethyl:2H(4)" RELATED PSI-MS-label [] synonym: "mod190" EXACT OMSSA-label [] xref: DiffAvg: "32.06" @@ -27889,6 +28991,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:199" is_a: MOD:00552 ! 4x(2)H labeled dimethylated residue [Term] @@ -27976,9 +29079,9 @@ [Term] id: MOD:01466 name: menadione quinone derivative - site C -def: "modification from UniMod Chemical derivative" [PubMed:15939799, UniMod:302#K] -synonym: "Menadione" RELATED UniMod-interim [] -synonym: "Menadione quinone derivative" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:15939799, Unimod:302#K] +synonym: "Menadione" RELATED Unimod-interim [] +synonym: "Menadione quinone derivative" RELATED Unimod-description [] xref: DiffAvg: "170.17" xref: DiffFormula: "C 11 H 6 O 2" xref: DiffMono: "170.036779" @@ -27988,15 +29091,16 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:302" is_a: MOD:00621 ! menadione quinone derivative is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01467 name: menadione quinone derivative - site K -def: "modification from UniMod Chemical derivative" [PubMed:15939799, UniMod:302#K] -synonym: "Menadione" RELATED UniMod-interim [] -synonym: "Menadione quinone derivative" RELATED UniMod-description [] +def: "modification from Unimod Chemical derivative" [PubMed:15939799, Unimod:302#K] +synonym: "Menadione" RELATED Unimod-interim [] +synonym: "Menadione quinone derivative" RELATED Unimod-description [] xref: DiffAvg: "170.17" xref: DiffFormula: "C 11 H 6 O 2" xref: DiffMono: "170.036779" @@ -28006,20 +29110,21 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:302" is_a: MOD:00621 ! menadione quinone derivative is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01468 name: L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide) (Cys) -def: "A protein modification that effectively converts an L-cysteine residue to L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide) (not known as a natural, post-translational modification process)." [PubMed:14235557, PubMed:2211698, PubMed:8052647, PubMed:9036855, RESID:AA0248#CYS, UniMod:415] +def: "A protein modification that effectively converts an L-cysteine residue to L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide) (not known as a natural, post-translational modification process)." [PubMed:14235557, PubMed:2211698, PubMed:8052647, PubMed:9036855, RESID:AA0248#CYS, Unimod:415] comment: This entry is for the artifactual formation of L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide) from cysteine. For natural formation from L-selenocysteine, use MOD:00253. synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-selenocysteinyl-Se-molybdenum" EXACT RESID-systematic [] synonym: "formate dehydrogenase selenocysteine molybdenum cofactor" EXACT RESID-alternate [] -synonym: "L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] +synonym: "L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" RELATED Unimod-description [] synonym: "L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" EXACT RESID-name [] -synonym: "molybdopterin-se" RELATED UniMod-interim [] +synonym: "molybdopterin-se" RELATED Unimod-interim [] synonym: "MolybdopterinGD+Delta:S(-1)Se(1)" RELATED PSI-MS-label [] xref: DiffAvg: "1618.93" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 3 Se 1" @@ -28030,8 +29135,9 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:415" is_a: MOD:00744 ! molybdenum pterin containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02073 ! metal or metal cluster coordinated L-selenocysteine residue [Term] id: MOD:01469 @@ -28049,7 +29155,7 @@ xref: TermSpec: "none" is_a: MOD:00746 ! tungsten containing modified residue is_a: MOD:00748 ! pterin modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02073 ! metal or metal cluster coordinated L-selenocysteine residue [Term] id: MOD:01470 @@ -28065,8 +29171,8 @@ synonym: "3-methyldehydroalanine" EXACT RESID-alternate [] synonym: "alpha,beta-dehydroaminobutyric acid" EXACT RESID-alternate [] synonym: "anhydrothreonine" EXACT RESID-alternate [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "Dhb" EXACT RESID-alternate [] synonym: "methyl-dehydroalanine" EXACT RESID-alternate [] @@ -28080,6 +29186,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0441" is_a: MOD:00190 ! dehydrobutyrine (Thr) [Term] @@ -28096,8 +29203,8 @@ synonym: "3-methyldehydroalanine" EXACT RESID-alternate [] synonym: "alpha,beta-dehydroaminobutyric acid" EXACT RESID-alternate [] synonym: "anhydrothreonine" EXACT RESID-alternate [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "Dhb" EXACT RESID-alternate [] synonym: "methyl-dehydroalanine" EXACT RESID-alternate [] @@ -28111,6 +29218,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0440" is_a: MOD:00190 ! dehydrobutyrine (Thr) [Term] @@ -28143,7 +29251,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00399 ! iodoacetic acid derivatized residue +relationship: derives_from MOD:00399 ! iodoacetic acid derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue relationship: derives_from MOD:00159 ! O-phosphopantetheine-L-serine @@ -28162,7 +29270,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00397 ! iodoacetamide derivatized residue +relationship: derives_from MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue relationship: derives_from MOD:00159 ! O-phosphopantetheine-L-serine @@ -28315,20 +29423,20 @@ xref: Origin: "K, E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01630 ! N6-(L-isoglutamyl)-L-lysine [Term] id: MOD:01485 name: iTRAQ4plex-114 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [UniMod:532] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [Unimod:532] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 114" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ114" RELATED UniMod-interim [] +synonym: "Accurate mass for 114" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ114" RELATED Unimod-interim [] synonym: "iTRAQ4plex114" RELATED PSI-MS-label [] xref: DiffAvg: "144.11" xref: DiffFormula: "(12)C 5 (13)C 2 H 12 N 2 (18)O 1" @@ -28339,6 +29447,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:532" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01430 ! (18)O isotope tagged reagent is_a: MOD:01516 ! modifications with monoisotopic mass diferences that are nominally equal at 144.099-144.106 Da. @@ -28347,13 +29456,13 @@ [Term] id: MOD:01486 name: iTRAQ4plex-114 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:167, UniMod:532#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:167, Unimod:532#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 114" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ114" RELATED UniMod-interim [] +synonym: "Accurate mass for 114" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ114" RELATED Unimod-interim [] synonym: "iTRAQ114nterm" EXACT OMSSA-label [] synonym: "iTRAQ4plex114" RELATED PSI-MS-label [] xref: DiffAvg: "144.11" @@ -28365,19 +29474,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:532" is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent acylated residue is_a: MOD:01711 ! iTRAQ4plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01487 name: iTRAQ4plex-114 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:168, UniMod:532#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:168, Unimod:532#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 114" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ114" RELATED UniMod-interim [] +synonym: "Accurate mass for 114" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ114" RELATED Unimod-interim [] synonym: "iTRAQ114K" EXACT OMSSA-label [] synonym: "iTRAQ4plex114" RELATED PSI-MS-label [] xref: DiffAvg: "144.11" @@ -28389,19 +29499,20 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent acylated residue +xref: Unimod: "Unimod:532" +is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent ac ylated residue is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01488 name: iTRAQ4plex-114 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:169, UniMod:532#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-114 reporter+balance group." [OMSSA:169, Unimod:532#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 114" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ114" RELATED UniMod-interim [] +synonym: "Accurate mass for 114" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ114" RELATED Unimod-interim [] synonym: "iTRAQ114Y" EXACT OMSSA-label [] synonym: "iTRAQ4plex114" RELATED PSI-MS-label [] xref: DiffAvg: "144.11" @@ -28413,6 +29524,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:532" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28453,7 +29565,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28473,20 +29585,20 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01485 ! iTRAQ4plex-114 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue [Term] id: MOD:01492 name: iTRAQ4plex-115 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [UniMod:533] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [Unimod:533] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ115" RELATED UniMod-interim [] +synonym: "Accurate mass for 115" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ115" RELATED Unimod-interim [] synonym: "iTRAQ4plex115" RELATED PSI-MS-label [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 6 (13)C 1 H 12 (14)N 1 (15)N 1 (18)O 1" @@ -28497,6 +29609,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:533" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01430 ! (18)O isotope tagged reagent @@ -28506,13 +29619,13 @@ [Term] id: MOD:01493 name: iTRAQ4plex-115 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:170, UniMod:533#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:170, Unimod:533#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ115" RELATED UniMod-interim [] +synonym: "Accurate mass for 115" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ115" RELATED Unimod-interim [] synonym: "iTRAQ115nterm" EXACT OMSSA-label [] synonym: "iTRAQ4plex115" RELATED PSI-MS-label [] xref: DiffAvg: "144.10" @@ -28524,19 +29637,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:533" is_a: MOD:01492 ! iTRAQ4plex-115 reporter+balance reagent acylated residue is_a: MOD:01711 ! iTRAQ4plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01494 name: iTRAQ4plex-115 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:171, UniMod:533#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:171, Unimod:533#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ115" RELATED UniMod-interim [] +synonym: "Accurate mass for 115" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ115" RELATED Unimod-interim [] synonym: "iTRAQ115K" EXACT OMSSA-label [] synonym: "iTRAQ4plex115" RELATED PSI-MS-label [] xref: DiffAvg: "144.10" @@ -28548,6 +29662,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:533" is_a: MOD:01492 ! iTRAQ4plex-115 reporter+balance reagent acylated residue is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -28555,12 +29670,12 @@ [Term] id: MOD:01495 name: iTRAQ4plex-115 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:172, UniMod:533#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-115 reporter+balance group." [OMSSA:172, Unimod:533#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ115" RELATED UniMod-interim [] +synonym: "Accurate mass for 115" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ115" RELATED Unimod-interim [] synonym: "iTRAQ115Y" EXACT OMSSA-label [] synonym: "iTRAQ4plex115" RELATED PSI-MS-label [] xref: DiffAvg: "144.10" @@ -28572,6 +29687,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:533" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01492 ! iTRAQ4plex-115 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28612,7 +29728,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01492 ! iTRAQ4plex-115 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28632,21 +29748,21 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01492 ! iTRAQ4plex-115 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue [Term] id: MOD:01499 name: iTRAQ4plex-116 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [UniMod:214] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [Unimod:214] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28656,6 +29772,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01517 ! modifications with monoisotopic mass differences that are nominally equal at 144.102062 Da @@ -28664,15 +29781,15 @@ [Term] id: MOD:01500 name: iTRAQ4plex-116 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:173, UniMod:214#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:173, Unimod:214#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ116nterm" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28682,21 +29799,22 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:214" is_a: MOD:01499 ! iTRAQ4plex-116 reporter+balance reagent acylated residue is_a: MOD:01711 ! iTRAQ4plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01501 name: iTRAQ4plex-116 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:174, UniMod:214#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:174, Unimod:214#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ116K" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28706,6 +29824,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:01499 ! iTRAQ4plex-116 reporter+balance reagent acylated residue is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -28713,14 +29832,14 @@ [Term] id: MOD:01502 name: iTRAQ4plex-116 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:175, UniMod:214#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group." [OMSSA:175, Unimod:214#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ116Y" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28730,6 +29849,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01499 ! iTRAQ4plex-116 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28770,7 +29890,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01499 ! iTRAQ4plex-116 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28790,23 +29910,23 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01499 ! iTRAQ4plex-116 reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue [Term] id: MOD:01506 name: iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [UniMod:214, UniMod:889] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [Unimod:214, Unimod:889] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "mTRAQ heavy" RELATED UniMod-description [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "mTRAQ heavy" RELATED Unimod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28816,6 +29936,8 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" +xref: Unimod: "Unimod:889" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01517 ! modifications with monoisotopic mass differences that are nominally equal at 144.102062 Da @@ -28825,18 +29947,18 @@ [Term] id: MOD:01507 name: iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:176, OMSSA:211, UniMod:214#N-term, UniMod:889N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:176, OMSSA:211, Unimod:214#N-term, Unimod:889#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ117nterm" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "mTRAQ heavy" RELATED UniMod-description [] +synonym: "mTRAQ heavy" RELATED Unimod-description [] synonym: "mTRAQ heavy on nterm" EXACT OMSSA-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28846,24 +29968,26 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:214" +xref: Unimod: "Unimod:889" is_a: MOD:01506 ! iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue is_a: MOD:01711 ! iTRAQ4plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01508 name: iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:177, OMSSA:212, UniMod:214#K, UniMod:889#K] +def: "A protein modification that effectively replaces the N6-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:177, OMSSA:212, Unimod:214#K, Unimod:889#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ117K" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "mTRAQ heavy" RELATED UniMod-description [] +synonym: "mTRAQ heavy" RELATED Unimod-description [] synonym: "mTRAQ heavy on K" EXACT OMSSA-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28873,6 +29997,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:01506 ! iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -28880,17 +30005,17 @@ [Term] id: MOD:01509 name: iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:178, OMSSA:213, UniMod:214#Y, UniMod:889#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ4plex-117 reporter+balance group." [OMSSA:178, OMSSA:213, Unimod:214#Y, Unimod:889#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "iTRAQ" RELATED UniMod-interim [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] synonym: "iTRAQ117Y" EXACT OMSSA-label [] synonym: "iTRAQ4plex" RELATED PSI-MS-label [] -synonym: "mTRAQ heavy" RELATED UniMod-description [] +synonym: "mTRAQ heavy" RELATED Unimod-description [] synonym: "mTRAQ heavy on Y" EXACT OMSSA-label [] -synonym: "Representative mass and accurate mass for 116 & 117" RELATED UniMod-description [] +synonym: "Representative mass and accurate mass for 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "144.10" xref: DiffFormula: "(12)C 4 (13)C 3 H 12 (14)N 1 (15)N 1 (16)O 1" xref: DiffMono: "144.102062" @@ -28900,6 +30025,8 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" +xref: Unimod: "Unimod:889" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01506 ! iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28940,7 +30067,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01506 ! iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -28960,7 +30087,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01506 ! iTRAQ4plex-117, mTRAQ heavy, reporter+balance reagent acylated residue is_a: MOD:01713 ! iTRAQ4plex reporter+balance reagent O-acylated residue @@ -29003,7 +30130,7 @@ [Term] id: MOD:01518 name: iTRAQ4plex reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [UniMod:214] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [Unimod:214] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] @@ -29016,6 +30143,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:01426 ! isotope tagged reagent derivatized residue is_a: MOD:01705 ! isotope tagged reagent acylated residue @@ -29121,7 +30249,7 @@ [Term] id: MOD:01526 name: iTRAQ8plex reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ8plex reagent reporter+balance groups." [UniMod:730] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ8plex reagent reporter+balance groups." [Unimod:730] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim xref: DiffAvg: "none" @@ -29133,6 +30261,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01426 ! isotope tagged reagent derivatized residue is_a: MOD:01705 ! isotope tagged reagent acylated residue @@ -29146,14 +30275,14 @@ [Term] id: MOD:01528 name: iTRAQ8plex-113 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [UniMod:730] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [Unimod:730] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29163,6 +30292,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29171,14 +30301,14 @@ [Term] id: MOD:01529 name: iTRAQ8plex-113 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [UniMod:730#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [Unimod:730#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29188,20 +30318,21 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:730" is_a: MOD:01528 ! iTRAQ8plex-113 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01530 name: iTRAQ8plex-113 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [UniMod:730#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [Unimod:730#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29211,6 +30342,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01528 ! iTRAQ8plex-113 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29218,13 +30350,13 @@ [Term] id: MOD:01531 name: iTRAQ8plex-113 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [UniMod:730#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [Unimod:730#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29234,6 +30366,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01528 ! iTRAQ8plex-113 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29244,10 +30377,10 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29267,10 +30400,10 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29280,7 +30413,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01528 ! iTRAQ8plex-113 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29290,10 +30423,10 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Applied Biosystems iTRAQ8plex-113 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29303,21 +30436,21 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01528 ! iTRAQ8plex-113 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01535 name: iTRAQ8plex-114 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [UniMod:730] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [Unimod:730] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29327,6 +30460,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29335,14 +30469,14 @@ [Term] id: MOD:01536 name: iTRAQ8plex-114 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [UniMod:730#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [Unimod:730#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29352,20 +30486,21 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:730" is_a: MOD:01535 ! iTRAQ8plex-114 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01537 name: iTRAQ8plex-114 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [UniMod:730#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [Unimod:730#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29375,6 +30510,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01535 ! iTRAQ8plex-114 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29382,13 +30518,13 @@ [Term] id: MOD:01538 name: iTRAQ8plex-114 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [UniMod:730#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [Unimod:730#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29398,6 +30534,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01535 ! iTRAQ8plex-114 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29408,10 +30545,10 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Applied Biosystems iTRAQ8plex-114 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29440,7 +30577,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01535 ! iTRAQ8plex-114 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29459,20 +30596,20 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01535 ! iTRAQ8plex-114 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01542 name: iTRAQ8plex-115 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [UniMod:731] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [Unimod:731] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29482,6 +30619,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29490,13 +30628,13 @@ [Term] id: MOD:01543 name: iTRAQ8plex-115 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [UniMod:731#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [Unimod:731#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29506,19 +30644,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:731" is_a: MOD:01542 ! iTRAQ8plex-115 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01544 name: iTRAQ8plex-115 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [UniMod:731#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [Unimod:731#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29528,6 +30667,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01542 ! iTRAQ8plex-115 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29535,12 +30675,12 @@ [Term] id: MOD:01545 name: iTRAQ8plex-115 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [UniMod:731#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-115 reporter+balance group." [Unimod:731#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29550,6 +30690,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01542 ! iTRAQ8plex-115 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29588,7 +30729,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01542 ! iTRAQ8plex-115 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29607,21 +30748,21 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01542 ! iTRAQ8plex-115 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01549 name: iTRAQ8plex-116 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [UniMod:730] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [Unimod:730] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29631,6 +30772,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29639,14 +30781,14 @@ [Term] id: MOD:01550 name: iTRAQ8plex-116 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [UniMod:730#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [Unimod:730#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29656,20 +30798,21 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:730" is_a: MOD:01549 ! iTRAQ8plex-116 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01551 name: iTRAQ8plex-116 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [UniMod:730#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [Unimod:730#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29679,6 +30822,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01549 ! iTRAQ8plex-116 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29686,13 +30830,13 @@ [Term] id: MOD:01552 name: iTRAQ8plex-116 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [UniMod:730#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-116 reporter+balance group." [Unimod:730#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29702,6 +30846,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01549 ! iTRAQ8plex-116 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29740,7 +30885,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01549 ! iTRAQ8plex-116 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29759,21 +30904,21 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01549 ! iTRAQ8plex-116 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01556 name: iTRAQ8plex-117 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [UniMod:730] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [Unimod:730] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29783,6 +30928,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29791,14 +30937,14 @@ [Term] id: MOD:01557 name: iTRAQ8plex-117 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [UniMod:730#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [Unimod:730#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29808,20 +30954,21 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:730" is_a: MOD:01556 ! iTRAQ8plex-117 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01558 name: iTRAQ8plex-117 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [UniMod:730#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [Unimod:730#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29831,6 +30978,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:01556 ! iTRAQ8plex-117 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29838,13 +30986,13 @@ [Term] id: MOD:01559 name: iTRAQ8plex-117 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [UniMod:730#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-117 reporter+balance group." [Unimod:730#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex" RELATED UniMod-interim [] -synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED UniMod-alternate [] -synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED UniMod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex" RELATED Unimod-interim [] +synonym: "iTRAQ8plex:13C(7)15N(1)" RELATED Unimod-alternate [] +synonym: "Representative mass and accurate mass for 113, 114, 116 & 117" RELATED Unimod-description [] xref: DiffAvg: "304.21" xref: DiffFormula: "(12)C 7 (13)C 7 H 24 (14)N 3 (15)N 1 (16)O 3" xref: DiffMono: "304.205359" @@ -29854,6 +31002,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:730" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01556 ! iTRAQ8plex-117 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29892,7 +31041,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01556 ! iTRAQ8plex-117 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -29911,20 +31060,20 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01556 ! iTRAQ8plex-117 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01563 name: iTRAQ8plex-118 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [UniMod:731] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [Unimod:731] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29934,6 +31083,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -29942,13 +31092,13 @@ [Term] id: MOD:01564 name: iTRAQ8plex-118 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [UniMod:731#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [Unimod:731#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29958,19 +31108,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:731" is_a: MOD:01563 ! iTRAQ8plex-118 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01565 name: iTRAQ8plex-118 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [UniMod:731#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [Unimod:731#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -29980,6 +31131,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01563 ! iTRAQ8plex-118 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -29987,12 +31139,12 @@ [Term] id: MOD:01566 name: iTRAQ8plex-118 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [UniMod:731#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-118 reporter+balance group." [Unimod:731#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30002,6 +31154,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01563 ! iTRAQ8plex-118 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30040,7 +31193,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01563 ! iTRAQ8plex-118 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30059,20 +31212,20 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01563 ! iTRAQ8plex-118 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01570 name: iTRAQ8plex-119 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [UniMod:731] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [Unimod:731] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30082,6 +31235,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -30090,13 +31244,13 @@ [Term] id: MOD:01571 name: iTRAQ8plex-119 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [UniMod:731#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [Unimod:731#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30106,19 +31260,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:731" is_a: MOD:01570 ! iTRAQ8plex-119 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01572 name: iTRAQ8plex-119 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [UniMod:731#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [Unimod:731#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30128,6 +31283,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01570 ! iTRAQ8plex-119 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -30135,12 +31291,12 @@ [Term] id: MOD:01573 name: iTRAQ8plex-119 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [UniMod:731#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-119 reporter+balance group." [Unimod:731#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30150,6 +31306,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01570 ! iTRAQ8plex-119 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30188,7 +31345,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01570 ! iTRAQ8plex-119 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30207,20 +31364,20 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01570 ! iTRAQ8plex-119 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue [Term] id: MOD:01577 name: iTRAQ8plex-121 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [UniMod:731] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [Unimod:731] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30230,6 +31387,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01526 ! iTRAQ8plex reporter+balance reagent acylated residue @@ -30238,13 +31396,13 @@ [Term] id: MOD:01578 name: iTRAQ8plex-121 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [UniMod:731#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [Unimod:731#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30254,19 +31412,20 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:731" is_a: MOD:01577 ! iTRAQ8plex-121 reporter+balance reagent acylated residue is_a: MOD:01712 ! iTRAQ8plex reporter+balance reagent acylated N-terminal [Term] id: MOD:01579 name: iTRAQ8plex-121 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [UniMod:731#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [Unimod:731#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30276,6 +31435,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:01577 ! iTRAQ8plex-121 reporter+balance reagent acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -30283,12 +31443,12 @@ [Term] id: MOD:01580 name: iTRAQ8plex-121 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [UniMod:731#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems iTRAQ8plex-121 reporter+balance group." [Unimod:731#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Accurate mass for 115, 118, 119 & 121" RELATED UniMod-description [] -synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED UniMod-alternate [] -synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED UniMod-interim [] +synonym: "Accurate mass for 115, 118, 119 & 121" RELATED Unimod-description [] +synonym: "Applied Biosystems iTRAQ(TM) multiplexed quantitation chemistry" RELATED Unimod-alternate [] +synonym: "iTRAQ8plex:13C(6)15N(2)" RELATED Unimod-interim [] xref: DiffAvg: "304.20" xref: DiffFormula: "(12)C 8 (13)C 6 H 24 (14)N 2 (15)N 2 (16)O 3" xref: DiffMono: "304.199039" @@ -30298,6 +31458,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:731" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01577 ! iTRAQ8plex-121 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30336,7 +31497,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01577 ! iTRAQ8plex-121 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30355,7 +31516,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01577 ! iTRAQ8plex-121 reporter+balance reagent acylated residue is_a: MOD:01714 ! iTRAQ8plex reporter+balance reagent O-acylated residue @@ -30376,6 +31537,8 @@ synonym: "O-(glycyl)-L-serine" EXACT RESID-name [] synonym: "O3-(aminoacetyl)serine" EXACT RESID-alternate [] synonym: "serine glycinate ester" EXACT RESID-alternate [] +synonym: "CROSSLNK Glycyl serine ester (Ser-Gly) (interchain with G-...)" EXACT UniProt-feature [] +synonym: "CROSSLNK Glycyl serine ester (Gly-Ser) (interchain with S-...)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" @@ -30385,9 +31548,10 @@ xref: Origin: "G, S" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0422" is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00908 ! modified glycine residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -30399,6 +31563,8 @@ synonym: "O-(glycyl)-L-threonine" EXACT RESID-name [] synonym: "O3-(2-aminoacetyl)threonine" EXACT RESID-alternate [] synonym: "threonine glycinate ester" EXACT RESID-alternate [] +synonym: "CROSSLNK Glycyl threonine ester (Thr-Gly) (interchain with G-...)" EXACT UniProt-feature [] +synonym: "CROSSLNK Glycyl threonine ester (Gly-Thr) (interchain with T-...)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" @@ -30408,8 +31574,9 @@ xref: Origin: "G, T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0423" is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water @@ -30433,6 +31600,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0399" is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -30458,6 +31626,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0400" is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00916 ! modified L-serine residue @@ -30472,6 +31641,7 @@ synonym: "O-[2,4-bis(acetylamino)]glucosyl-L-serine" EXACT RESID-alternate [] synonym: "O-seryl-beta-2,4-bis(acetylamino)glucoside" EXACT RESID-alternate [] synonym: "O3-(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)-L-serine" EXACT RESID-alternate [] +synonym: "CARBOHYD O-linked (DADDGlc) serine" EXACT UniProt-feature [] xref: DiffAvg: "244.25" xref: DiffFormula: "C 10 H 16 N 2 O 5" xref: DiffMono: "244.105922" @@ -30481,6 +31651,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0547" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] @@ -30696,8 +31867,9 @@ xref: Origin: "K, M" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00912 ! modified L-lysine residue -is_a: MOD:00913 ! modified L-methionine residue +xref: UniProt: "PTM-0401" +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:02052 ! crosslinked L-methionine residue [Term] id: MOD:01603 @@ -30713,6 +31885,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:995" is_a: MOD:00843 ! (15)N labeled residue is_a: MOD:00912 ! modified L-lysine residue @@ -30736,7 +31909,7 @@ [Term] id: MOD:01605 name: 5-glutamyl 2-aminoadipic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to 5-glutamyl 2-aminoadipic acid." [PubMed:19620981, RESID:AA0502] +def: "A protein modification that effectively converts an L-glutamic acid residue to 5-glutamyl 2-aminoadipic acid." [PubMed:19620981, RESID:AA0502, ChEBI:78503] synonym: "(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)hexanedioic acid" EXACT RESID-systematic [] synonym: "5-glutamyl 2-aminoadipic acid" EXACT RESID-name [] synonym: "MOD_RES 5-glutamyl 2-aminoadipic acid" EXACT UniProt-feature [] @@ -30751,7 +31924,7 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00674 ! amidated residue +xref: UniProt: "PTM-0406" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] @@ -30769,7 +31942,6 @@ xref: Origin: "E" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00674 ! amidated residue is_a: MOD:00861 ! phosphorus containing modified residue is_a: MOD:00906 ! modified L-glutamic acid residue @@ -30792,7 +31964,6 @@ xref: Origin: "E" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00674 ! amidated residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] @@ -30815,6 +31986,7 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0407" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] @@ -30823,7 +31995,7 @@ def: "A protein modification that effectively converts an L-tryptophan residue to 7'-hydroxy-2'-alpha-mannosyl-L-tryptophan." [PubMed:19584055, RESID:AA0506] synonym: "(2S)-2-amino-3-[7-hydroxy-2-(alpha-D-mannopyranosyl)-1H-indol-3-yl]propanoic acid" EXACT RESID-systematic [] synonym: "7'-hydroxy-2'-alpha-mannosyl-L-tryptophan" EXACT RESID-name [] -synonym: "MOD_RES 7'-hydroxytryptophan" EXACT UniProt-feature [] +synonym: "CARBOHYD C-linked (Man) hydroxytryptophan" EXACT UniProt-feature [] xref: DiffAvg: "178.14" xref: DiffFormula: "C 6 H 10 N 0 O 6" xref: DiffMono: "178.047738" @@ -30833,6 +32005,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0504" is_a: MOD:00918 ! modified L-tryptophan residue relationship: has_functional_parent MOD:00222 ! 2'-alpha-mannosyl-L-tryptophan relationship: has_functional_parent MOD:01664 ! 7'-hydroxy-L-tryptophan @@ -30844,6 +32017,7 @@ synonym: "L-threonine methyl ester" EXACT RESID-name [] synonym: "methyl (2S,3R)-2-amino-3-hydroxybutanoate" EXACT RESID-systematic [] synonym: "methyl L-threoninate" EXACT RESID-alternate [] +synonym: "MOD_RES Threonine methyl ester" EXACT UniProt-feature [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" @@ -30853,6 +32027,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0412" is_a: MOD:01689 ! alpha-carboxyl methylated residue is_a: MOD:01803 ! O-methylated threonine @@ -30879,9 +32054,8 @@ xref: Origin: "C, H" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00896 ! FMN modified residue -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00909 ! modified L-histidine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02048 ! crosslinked L-histidine residue is_a: MOD:01621 ! flavin crosslinked residues [Term] @@ -30905,6 +32079,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0411" is_a: MOD:01228 ! monoiodinated tyrosine [Term] @@ -30928,6 +32103,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0408" is_a: MOD:01140 ! diiodinated tyrosine [Term] @@ -30953,6 +32129,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0409" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01165 ! adenylated residue @@ -30976,8 +32153,9 @@ xref: Origin: "C, G" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0410" is_a: MOD:00395 ! thioester crosslinked residues -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] @@ -30998,6 +32176,7 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0417" is_a: MOD:01620 ! polysulfide crosslinked residues [Term] @@ -31007,6 +32186,7 @@ synonym: "(2S,3R)-2-amino-3-[6-phosphonooxy-alpha-D-mannopyranosyloxy]butanoic acid" EXACT RESID-systematic [] synonym: "O-(6-phosphomannosyl)-L-threonine" EXACT RESID-name [] synonym: "O3-(6-phosphomannosyl)threonine" EXACT RESID-alternate [] +synonym: "CARBOHYD O-linked (Man6P) threonine" EXACT UniProt-feature [] xref: DiffAvg: "242.12" xref: DiffFormula: "C 6 H 11 N 0 O 8 P 1" xref: DiffMono: "242.019154" @@ -31016,8 +32196,9 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0596" is_a: MOD:00005 ! O-glycosyl-L-threonine -is_a: MOD:00595 ! mannosylated residue +is_a: MOD:01804 ! glycosylphosphorylated residue [Term] id: MOD:01618 @@ -31037,9 +32218,10 @@ xref: Origin: "A, N" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0418" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00901 ! modified L-alanine residue -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:02040 ! crosslinked L-alanine residue +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] @@ -31048,7 +32230,7 @@ def: "A protein modification that crosslinks two cysteine residues by formation of a chain of two or more bonded sulfur atoms." [PubMed:18688235] subset: PSI-MOD-slim is_a: MOD:00033 ! crosslinked residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:01620 @@ -31068,7 +32250,7 @@ [Term] id: MOD:01622 name: monohydroxylated tryptophan -def: "A protein modification that effectively converts an L-tryptophan residue to one of several monohydroxylated tryptophan residues, including 3-hydroxy-L-tryptophan and 7'-hydroxy-L-tryptophan." [OMSSA:90, UniMod:35#W] +def: "A protein modification that effectively converts an L-tryptophan residue to one of several monohydroxylated tryptophan residues, including 3-hydroxy-L-tryptophan and 7'-hydroxy-L-tryptophan." [OMSSA:90, Unimod:35#W] synonym: "Oxidation" RELATED PSI-MS-label [] synonym: "oxyw" EXACT OMSSA-label [] xref: DiffAvg: "16.00" @@ -31080,6 +32262,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00918 ! modified L-tryptophan residue @@ -31121,7 +32304,8 @@ xref: Origin: "G, N" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue +xref: UniProt: "PTM-0450" +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia is_a: MOD:01628 ! (2-aminosuccinimidyl)acetic acid @@ -31138,7 +32322,7 @@ synonym: "Carboxy->Thiocarboxy" RELATED PSI-MS-label [] synonym: "MOD_RES 1-thioglycine" EXACT UniProt-feature [] synonym: "S(O)Gly" EXACT PSI-MOD-label [] -synonym: "thiocarboxylic acid" RELATED UniMod-description [] +synonym: "thiocarboxylic acid" RELATED Unimod-description [] xref: DiffAvg: "16.06" xref: DiffFormula: "C 0 H 0 N 0 O -1 S 1" xref: DiffMono: "15.977156" @@ -31198,7 +32382,7 @@ xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00859 ! modified residue that can arise from different natural residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:01628 @@ -31215,7 +32399,7 @@ xref: Origin: "G, X" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue is_a: MOD:01944 ! 2-aminosuccinimide ring crosslinked residues [Term] @@ -31236,7 +32420,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00859 ! modified residue that can arise from different natural residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue [Term] id: MOD:01630 @@ -31259,9 +32443,11 @@ xref: Origin: "K, X" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0397" +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:01875 ! N6-acylated L-lysine is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00859 ! modified residue that can arise from different natural residues -is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01631 @@ -31482,10 +32668,10 @@ [Term] id: MOD:01643 name: L-methionine removal -def: "A protein modification that effectively removes or replaces an L-methionine." [OMSSA:9, PubMed:3327521, UniMod:765] +def: "A protein modification that effectively removes or replaces an L-methionine." [OMSSA:9, PubMed:3327521, Unimod:765] comment: This represents the loss or replacement of an L-methionine residue in a polypeptide, including initiator methionine removal in eukaryotes. It may be combined with the formula or mass of another entry that is the replacement residue to represent a mutation or substitution [JSG]. subset: PSI-MOD-slim -synonym: "Met-loss" RELATED UniMod-interim [] +synonym: "Met-loss" RELATED Unimod-interim [] synonym: "ntermmcleave" EXACT OMSSA-label [] xref: DiffAvg: "-131.19" xref: DiffFormula: "C -5 H -9 N -1 O -1 S -1" @@ -31496,6 +32682,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:765" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:01651 ! natural, standard, encoded residue removal @@ -31628,13 +32815,14 @@ [Term] id: MOD:01651 name: natural, standard, encoded residue removal -def: "A protein modification that effectively removes or replaces a natural, standard, encoded residue." [PubMed:18688235] -comment: This represents the loss or replacement of an encoded residue in a polypeptide, and may be combined with the formula or mass of another entry that is the replacement residue to represent a mutation or substitution. +def: "A protein modification that effectively removes a natural, standard, encoded residue." [PubMed:18688235] +comment: This represents the loss of an encoded residue in a polypeptide. subset: PSI-MOD-slim xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00009 ! natural residue +is_a: MOD:01156 ! protein modification characterized by chemical process [Term] id: MOD:01652 @@ -31649,8 +32837,8 @@ [Term] id: MOD:01653 name: dansyl chloride derivatized residue -def: "A protein modification that is produced by formation of an adduct with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride." [DeltaMass:0, UniMod:139] -synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED UniMod-description [] +def: "A protein modification that is produced by formation of an adduct with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride." [DeltaMass:0, Unimod:139] +synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED Unimod-description [] synonym: "Dansyl" RELATED PSI-MS-label [] synonym: "Dansyl (Dns)" EXACT DeltaMass-label [] synonym: "DansylRes" EXACT PSI-MOD-label [] @@ -31663,13 +32851,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:139" is_a: MOD:01652 ! sulfonyl halide reagent derivatized residue [Term] id: MOD:01654 name: N6-Dansyl derivatized lysine -def: "A protein modification that is produced by reaction with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride, to form N6-Dansyl-lysine." [UniMod:139#K] -synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED UniMod-description [] +def: "A protein modification that is produced by reaction with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride, to form N6-Dansyl-lysine." [Unimod:139#K] +synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED Unimod-description [] synonym: "Dansyl" RELATED PSI-MS-label [] synonym: "N6DansylLys" EXACT PSI-MOD-label [] xref: DiffAvg: "233.29" @@ -31681,14 +32870,15 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:139" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01653 ! dansyl chloride derivatized residue [Term] id: MOD:01655 name: alpha-amino-Dansyl derivatized residue -def: "A protein modification that is produced by reaction with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride, to form an alpha-amino-Dansyl-derivatized residue." [UniMod:139#N-term] -synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED UniMod-description [] +def: "A protein modification that is produced by reaction with 5-dimethylaminonaphthalene-1-sulfonyl chloride, dansyl chloride, to form an alpha-amino-Dansyl-derivatized residue." [Unimod:139#N-term] +synonym: "5-dimethylaminonaphthalene-1-sulfonyl" RELATED Unimod-description [] synonym: "Dansyl" RELATED PSI-MS-label [] synonym: "N2DansylRes" EXACT PSI-MOD-label [] xref: DiffAvg: "233.29" @@ -31700,6 +32890,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:139" is_a: MOD:01653 ! dansyl chloride derivatized residue [Term] @@ -31810,6 +33001,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0662" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01154 ! pyruvic acid @@ -31870,6 +33062,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0427" is_a: MOD:01622 ! monohydroxylated tryptophan [Term] @@ -31880,12 +33073,6 @@ synonym: "ACT_SITE Schiff-base intermediate with DNA; via amino nitrogen" EXACT UniProt-feature [] synonym: "DNA glycosylase valine Schiff base intermediate" EXACT RESID-alternate [] synonym: "N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-valine" EXACT RESID-name [] -xref: DiffAvg: "178.08" -xref: DiffFormula: "C 5 H 7 N 0 O 5 P 1" -xref: DiffMono: "178.003110" -xref: Formula: "C 10 H 17 N 1 O 6 P 1" -xref: MassAvg: "278.22" -xref: MassMono: "278.079349" xref: Origin: "V" xref: Source: "hypothetical" xref: TermSpec: "N-term" @@ -31954,7 +33141,7 @@ [Term] id: MOD:01669 name: trimethyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to N(omega),N(omega),N'(omega)-trimethyl-L-arginine." [OMSSA:117, PubMed:11704273, PubMed:602668, RESID:AA0523, UniMod:37#R] +def: "A protein modification that effectively converts an L-arginine residue to N(omega),N(omega),N'(omega)-trimethyl-L-arginine." [OMSSA:117, PubMed:11704273, PubMed:602668, RESID:AA0523, Unimod:37#R] synonym: "(2S)-2-amino-5-([(dimethylamino)(methylamino)methylidene]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "(2S)-2-amino-5-([(dimethylamino)(methylimino)methyl]amino)pentanoic acid" EXACT RESID-alternate [] synonym: "2-[(4S)-4-amino-5-oxopentyl]-1,1,3-trimethylguanidine" EXACT RESID-alternate [] @@ -31962,7 +33149,7 @@ synonym: "N5-[(dimethylamino)(imino)methyl]ornithine" EXACT RESID-alternate [] synonym: "NoNoNo'Me3Arg" EXACT PSI-MOD-label [] synonym: "omega-N,omega-N,omega-N'-trimethyl-L-arginine" EXACT RESID-name [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] synonym: "trimethylationr" EXACT OMSSA-label [] xref: DiffAvg: "42.08" @@ -31974,6 +33161,7 @@ xref: Origin: "R" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:37" is_a: MOD:00430 ! trimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00658 ! methylated arginine @@ -32036,11 +33224,11 @@ [Term] id: MOD:01673 name: N-acetylaminohexosylated residue -def: "A protein modification that effectively replaces a hydrogen atom with an N-acetylaminohexose group through a glycosidic bond." [UniMod:43] +def: "A protein modification that effectively replaces a hydrogen atom with an N-acetylaminohexose group through a glycosidic bond." [Unimod:43] subset: PSI-MOD-slim synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "HexNAcRes" EXACT PSI-MOD-label [] -synonym: "N-Acetylhexosamine" RELATED UniMod-description [] +synonym: "N-Acetylhexosamine" RELATED Unimod-description [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" @@ -32050,18 +33238,19 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" -is_a: MOD:00436 ! N-acetylhexosaminylated +xref: Unimod: "Unimod:43" +is_a: MOD:00436 ! N-acetylhexosaminylated residue [Term] id: MOD:01674 name: N4-(N-acetylamino)hexosyl-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to N4-(N-acetaminohexosyl)-L-asparagine." [OMSSA:182, UniMod:43#N] +def: "A protein modification that effectively converts an L-asparagine residue to N4-(N-acetaminohexosyl)-L-asparagine." [OMSSA:182, Unimod:43#N] subset: PSI-MOD-slim synonym: "(S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-hexopyranosyl)amino-4-oxobutanoic acid" EXACT PSI-MOD-alternate [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "HexNAcAsn" EXACT PSI-MOD-label [] synonym: "hexNAcN" EXACT OMSSA-label [] -synonym: "N-Acetylhexosamine" RELATED UniMod-description [] +synonym: "N-Acetylhexosamine" RELATED Unimod-description [] synonym: "N4-(2-acetamido-2-deoxy-beta-D-hexopyranosyl)-L-asparagine" EXACT PSI-MOD-alternate [] synonym: "N4-(2-acetylamino-2-deoxy-beta-D-hexopyranosyl)-L-asparagine" EXACT PSI-MOD-alternate [] synonym: "N4-(N-acetylhexosaminyl)asparagine" EXACT PSI-MOD-alternate [] @@ -32078,18 +33267,19 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:43" is_a: MOD:00160 ! N4-glycosyl-L-asparagine is_a: MOD:01673 ! N-acetylaminohexosylated residue [Term] id: MOD:01675 name: O-(N-acetylamino)hexosyl-L-serine -def: "A protein modification that effectively converts an L-serine residue to O3-(N-acetylaminohexosyl)-L-serine." [OMSSA:184, UniMod:43#S] +def: "A protein modification that effectively converts an L-serine residue to O3-(N-acetylaminohexosyl)-L-serine." [OMSSA:184, Unimod:43#S] subset: PSI-MOD-slim synonym: "(S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-hexopyranosyloxy)propanoic acid" EXACT PSI-MOD-alternate [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "hexNAcS" EXACT OMSSA-label [] -synonym: "N-Acetylhexosamine" RELATED UniMod-description [] +synonym: "N-Acetylhexosamine" RELATED Unimod-description [] synonym: "O-(2-acetylamino-2-deoxy-beta-D-hexopyranosyl)-L-serine" EXACT PSI-MOD-alternate [] synonym: "O-(N-acetylhexosaminyl)serine" EXACT PSI-MOD-alternate [] synonym: "O-glycosylserine" EXACT PSI-MOD-alternate [] @@ -32105,18 +33295,19 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:43" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:01673 ! N-acetylaminohexosylated residue [Term] id: MOD:01676 name: O-(N-acetylamino)hexosyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O3-(N-acetylaminohexosyl)-L-threonine." [OMSSA:185, UniMod:43#T] +def: "A protein modification that effectively converts an L-threonine residue to O3-(N-acetylaminohexosyl)-L-threonine." [OMSSA:185, Unimod:43#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-(alpha-D-2-acetamido-2-deoxyhexopyranosyloxy)butanoic acid" EXACT PSI-MOD-alternate [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "hexNAcT" EXACT OMSSA-label [] -synonym: "N-Acetylhexosamine" RELATED UniMod-description [] +synonym: "N-Acetylhexosamine" RELATED Unimod-description [] synonym: "O-(N-acetylhexcosaminyl)-L-threonine" EXACT PSI-MOD-alternate [] synonym: "O-glycosylthreonine" EXACT PSI-MOD-alternate [] synonym: "O3-(N-acetylhexosaminyl)threonine" EXACT PSI-MOD-alternate [] @@ -32130,6 +33321,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:43" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:01673 ! N-acetylaminohexosylated residue @@ -32156,21 +33348,22 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00915 ! modified L-proline residue -is_a: MOD:01673 ! N-acetylaminohexosylated residue +relationship: contains MOD:01673 ! N-acetylaminohexosylated residue [Term] id: MOD:01678 name: N6-carbamoyl-L-lysine -def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, UniMod:5#K] +def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, Unimod:5#K, ChEBI:144369] comment: This modification can be produced by hydrogen cyanate, either as a reagent or as released by urea degradation in solution [JSG]. subset: PSI-MOD-slim synonym: "2-amino-6-ureido-hexanoic acid" EXACT PSI-MOD-alternate [] -synonym: "Carbamyl" RELATED UniMod-interim [] -synonym: "Carbamylation" RELATED UniMod-description [] +synonym: "Carbamyl" RELATED Unimod-interim [] +synonym: "Carbamylation" RELATED Unimod-description [] synonym: "carbamylk" EXACT OMSSA-label [] synonym: "homocitrulline" EXACT PSI-MOD-alternate [] synonym: "N6-(aminocarbonyl)-L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6CbmLys" EXACT PSI-MOD-label [] +synonym: "MOD_RES N6-carbamoyllysine" EXACT UniProt-feature [] xref: DiffAvg: "43.02" xref: DiffFormula: "C 1 H 1 N 1 O 1" xref: DiffMono: "43.005814" @@ -32180,16 +33373,19 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:5" +xref: UniProt: "PTM-0675" +is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00398 ! carbamoylated residue [Term] id: MOD:01679 name: alpha-aminocarbamoylated residue -def: "A protein modification that effectively replaces a residue alpha amino or imino hydrogen with a carbamoyl group." [DeltaMass:56, OMSSA:32, PubMed:10978403, PubMed:12203680, UniMod:5#N-term] +def: "A protein modification that effectively replaces a residue alpha amino or imino hydrogen with a carbamoyl group." [DeltaMass:56, OMSSA:32, PubMed:10978403, PubMed:12203680, Unimod:5#N-term] comment: This modification can be produced by hydrogen cyanate, either as a reagent or as released by urea degradation. This modification effectively blocks Edman degradation, and because it can dehydrate to a cyanate group and react with another peptide N-terminal, it can effectively block two peptide molecules [JSG]. subset: PSI-MOD-slim -synonym: "Carbamyl" RELATED UniMod-interim [] -synonym: "Carbamylation" RELATED UniMod-description [] +synonym: "Carbamyl" RELATED Unimod-interim [] +synonym: "Carbamylation" RELATED Unimod-description [] synonym: "N2CbmRes" EXACT PSI-MOD-label [] synonym: "ntermcarbamyl" EXACT OMSSA-label [] xref: DiffAvg: "43.02" @@ -32201,16 +33397,17 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:5" is_a: MOD:00398 ! carbamoylated residue [Term] id: MOD:01680 name: alpha-amino monomethylated residue -def: "A protein modification that effectively replaces one residue alpha amino or imino hydrogen with one methyl group." [OMSSA:11, OMSSA:76, UniMod:34#N-term] +def: "A protein modification that effectively replaces one residue alpha amino or imino hydrogen with one methyl group." [OMSSA:11, OMSSA:76, Unimod:34#N-term] comment: Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence [JSG]. subset: PSI-MOD-slim synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "N2Me1Res" EXACT PSI-MOD-label [] synonym: "ntermmethyl" EXACT OMSSA-label [] synonym: "ntermpepmethyl" EXACT OMSSA-label [] @@ -32223,16 +33420,17 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:01460 ! alpha-amino methylated residue [Term] id: MOD:01681 name: monomethylated L-aspartic acid -def: "A protein modification that effectively replaces one hydrogen atom of an L-aspartic acid residue with one methyl group." [OMSSA:16, UniMod:34#D] +def: "A protein modification that effectively replaces one hydrogen atom of an L-aspartic acid residue with one methyl group." [OMSSA:16, Unimod:34#D] synonym: "Me1Asp" EXACT PSI-MOD-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "methyld" EXACT OMSSA-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" @@ -32243,17 +33441,18 @@ xref: Origin: "D" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00887 ! methylated aspartic acid [Term] id: MOD:01682 name: monomethylated L-cysteine -def: "A protein modification that effectively replaces one hydrogen atom of an L-cysteine residue with one methyl group." [OMSSA:73, UniMod:34#C] +def: "A protein modification that effectively replaces one hydrogen atom of an L-cysteine residue with one methyl group." [OMSSA:73, Unimod:34#C] subset: PSI-MOD-slim synonym: "Me1Cys" EXACT PSI-MOD-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "methylc" EXACT OMSSA-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" @@ -32264,6 +33463,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:34" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00660 ! methylated cysteine @@ -32274,7 +33474,7 @@ subset: PSI-MOD-slim synonym: "Me1Lys" EXACT PSI-MOD-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methylation" RELATED UniMod-description [] +synonym: "Methylation" RELATED Unimod-description [] synonym: "methylk" EXACT OMSSA-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" @@ -32291,12 +33491,13 @@ [Term] id: MOD:01684 name: palmitoylated-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to a palmitoylated-L-cysteine, such as N-palmitoyl-L-cysteine or S-palmitoyl-L-cysteine." [OMSSA:92, UniMod:47] +def: "A protein modification that effectively converts an L-cysteine residue to a palmitoylated-L-cysteine, such as N-palmitoyl-L-cysteine or S-palmitoyl-L-cysteine." [OMSSA:92, Unimod:47] subset: PSI-MOD-slim synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] synonym: "palmitoylationc" EXACT OMSSA-label [] synonym: "PamCys" EXACT PSI-MOD-label [] +synonym: "Hexadecanoylated L-cysteine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" @@ -32306,17 +33507,17 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00440 ! palmitoylated residue +xref: Unimod: "Unimod:47" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01685 name: alpha-amino palmitoylated residue -def: "A protein modification that effectively replaces a residue alpha-amino group with a alpha-palmitoylamino group." [UniMod:47#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino group with a alpha-palmitoylamino group." [Unimod:47#N-term] subset: PSI-MOD-slim synonym: "N2PamRes" EXACT PSI-MOD-label [] synonym: "Palmitoyl" RELATED PSI-MS-label [] -synonym: "Palmitoylation" RELATED UniMod-description [] +synonym: "Palmitoylation" RELATED Unimod-description [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" @@ -32326,15 +33527,16 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:47" is_a: MOD:00651 ! N-palmitoylated residue is_a: MOD:01696 ! alpha-amino acylated residue [Term] id: MOD:01686 name: alpha-amino dimethylated residue -def: "A protein modification that effectively replaces two alpha amino hydrogen atoms with two methyl group." [OMSSA:38, UniMod:36#N-term] +def: "A protein modification that effectively replaces two alpha amino hydrogen atoms with two methyl group." [OMSSA:38, Unimod:36#N-term] comment: For alpha-amino acids, both N-alpha-monomethylation and complete N-alpha protonation and trimethylation have been observed, but incomplete dimethylation has not been reported as a natural process. For N-terminal proline residues, dimethylation can only be effectively accomplished with a protonated imino group, whereas this process accounts only for dimethylation and not protonation. See MOD:00889. -synonym: "di-Methylation" RELATED UniMod-description [] +synonym: "di-Methylation" RELATED Unimod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "N2Me2Res" EXACT PSI-MOD-label [] synonym: "ntermpepdimethyl" EXACT OMSSA-label [] @@ -32347,18 +33549,19 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:36" is_a: MOD:00429 ! dimethylated residue is_a: MOD:01460 ! alpha-amino methylated residue [Term] id: MOD:01687 name: alpha-amino trimethylated residue -def: "A protein modification that effectively replaces an alpha-aminium group with a trimethylaminium group." [OMSSA:12, UniMod:37#N-term] +def: "A protein modification that effectively replaces an alpha-aminium group with a trimethylaminium group." [OMSSA:12, Unimod:37#N-term] comment: For amino acids residues, amine trimethylation can effectively only be accomplished with an aminium, protonated primary amino, group. This process accounts only for trimethylation and not protonation. The alternative N2Me3+Res process (MOD:01698) accounts for both protonation and trimethylation. subset: PSI-MOD-slim synonym: "N2Me3Res" EXACT PSI-MOD-label [] synonym: "ntermtrimethyl" EXACT OMSSA-label [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "42.08" xref: DiffFormula: "C 3 H 6 N 0 O 0" @@ -32370,6 +33573,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:37" is_a: MOD:00430 ! trimethylated residue is_a: MOD:01460 ! alpha-amino methylated residue relationship: derives_from MOD:01700 ! alpha-amino protonated residue @@ -32377,7 +33581,7 @@ [Term] id: MOD:01688 name: 3-hydroxy-L-asparagine -def: "A protein modification that effectively converts an L-asparagine residue to one of the diastereomeric 3-hydroxy-L-asparagine residues." [OMSSA:61, UniMod:35#N] +def: "A protein modification that effectively converts an L-asparagine residue to one of the diastereomeric 3-hydroxy-L-asparagine residues." [OMSSA:61, Unimod:35#N] subset: PSI-MOD-slim synonym: "3HyAsn" EXACT PSI-MOD-label [] synonym: "hydroxylationn" EXACT OMSSA-label [] @@ -32392,19 +33596,20 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:01689 name: alpha-carboxyl methylated residue -def: "A protein modification that effectively converts a carboxyl-terminal residue to an alpha-carboxyl (1-carboxyl) methyl ester." [OMSSA:18, OMSSA:68, UniMod:34#C-term] +def: "A protein modification that effectively converts a carboxyl-terminal residue to an alpha-carboxyl (1-carboxyl) methyl ester." [OMSSA:18, OMSSA:68, Unimod:34#C-term] subset: PSI-MOD-slim synonym: "C1OMeRes" EXACT PSI-MOD-label [] synonym: "ctermpepmeester" EXACT OMSSA-label [] synonym: "ctermpepmethyl" EXACT OMSSA-label [] synonym: "Methyl" RELATED PSI-MS-label [] -synonym: "Methyl" RELATED UniMod-alternate [] +synonym: "Methyl" RELATED Unimod-alternate [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 0" xref: DiffMono: "14.015650" @@ -32414,6 +33619,7 @@ xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" +xref: Unimod: "Unimod:34" is_a: MOD:00393 ! O-methylated residue [Term] @@ -32433,6 +33639,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0419" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -32453,6 +33660,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0420" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -32480,11 +33688,11 @@ [Term] id: MOD:01693 name: alpha-amino pyridylacetylated residue -def: "A protein modification that effectively replaces a residue alpha amino or imino hydrogen with a (pyrid-3-yl)acetyl group." [OMSSA:107, PubMed:9276974, UniMod:25#N-term] +def: "A protein modification that effectively replaces a residue alpha amino or imino hydrogen with a (pyrid-3-yl)acetyl group." [OMSSA:107, PubMed:9276974, Unimod:25#N-term] comment: Produced by reaction with N-[(pyrid-3-yl)acetyl]oxy-succinimide [JSG]. synonym: "ntermpeppyridyl" EXACT OMSSA-label [] synonym: "Pyridylacetyl" RELATED PSI-MS-label [] -synonym: "pyridylacetyl" RELATED UniMod-description [] +synonym: "pyridylacetyl" RELATED Unimod-description [] xref: DiffAvg: "119.12" xref: DiffFormula: "C 7 H 5 N 1 O 1" xref: DiffMono: "119.037114" @@ -32494,6 +33702,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:25" is_a: MOD:00418 ! pyridylacetylated residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -32515,13 +33724,14 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0428" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01695 name: alpha-amino 3-(carboxamidomethylthio)propanoylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an 3-(carboxamidomethylthio)propanoyl group." [PubMed:15121203, UniMod:293#N-term] -synonym: "3-(carbamidomethylthio)propanoyl" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an 3-(carboxamidomethylthio)propanoyl group." [PubMed:15121203, Unimod:293#N-term] +synonym: "3-(carbamidomethylthio)propanoyl" RELATED Unimod-description [] synonym: "CAMthiopropanoyl" RELATED PSI-MS-label [] xref: DiffAvg: "145.18" xref: DiffFormula: "C 5 H 7 N 1 O 2 S 1" @@ -32532,6 +33742,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:293" is_a: MOD:00612 ! 3-(carboxamidomethylthio)propanoylated residue is_a: MOD:01696 ! alpha-amino acylated residue @@ -32548,10 +33759,10 @@ [Term] id: MOD:01697 name: alpha-amino 4-(2-aminoethyl)benzenesulfonylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an 4-(2-aminoethyl)benzenesulfonyl group." [DeltaMass:235, PubMed:8597590, UniMod:276#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with an 4-(2-aminoethyl)benzenesulfonyl group." [DeltaMass:235, PubMed:8597590, Unimod:276#N-term] comment: See the comment for MOD:00596 [JSG]. synonym: "AEBS" RELATED PSI-MS-label [] -synonym: "Aminoethylbenzenesulfonylation" RELATED UniMod-description [] +synonym: "Aminoethylbenzenesulfonylation" RELATED Unimod-description [] xref: DiffAvg: "183.23" xref: DiffFormula: "C 8 H 9 N 1 O 2 S 1" xref: DiffMono: "183.035400" @@ -32561,6 +33772,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:276" is_a: MOD:00596 ! 4-(2-aminoethyl)benzenesulfonyl fluoride derivatized residue [Term] @@ -32569,7 +33781,7 @@ def: "A protein modification that effectively replaces an amino group with a trimethylaminium group." [PubMed:18688235] subset: PSI-MOD-slim synonym: "N2Me3+Res" EXACT PSI-MOD-label [] -synonym: "tri-Methylation" RELATED UniMod-description [] +synonym: "tri-Methylation" RELATED Unimod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0 S 0" @@ -32663,8 +33875,8 @@ subset: PSI-MOD-slim synonym: "beta-elim-t" EXACT OMSSA-label [] synonym: "Dehydrated" RELATED PSI-MS-label [] -synonym: "Dehydrated" RELATED UniMod-interim [] -synonym: "Dehydration" RELATED UniMod-description [] +synonym: "Dehydrated" RELATED Unimod-interim [] +synonym: "Dehydration" RELATED Unimod-description [] synonym: "dehydro" EXACT OMSSA-label [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "dHAbu" EXACT PSI-MOD-label [] @@ -32778,7 +33990,7 @@ [Term] id: MOD:01711 name: iTRAQ4plex reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [UniMod:214#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [Unimod:214#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] @@ -32791,13 +34003,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:214" is_a: MOD:01708 ! isotope tagged reagent alpha-amino acylated residue is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue [Term] id: MOD:01712 name: iTRAQ8plex reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with one of the Applied Biosystems iTRAQ8plex reagent reporter+balance groups." [UniMod:214#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with one of the Applied Biosystems iTRAQ8plex reagent reporter+balance groups." [Unimod:214#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] @@ -32810,6 +34023,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:214" is_a: MOD:01708 ! isotope tagged reagent alpha-amino acylated residue is_a: MOD:01710 ! iTRAQ8plex reporter+balance reagent N-acylated residue @@ -32850,12 +34064,12 @@ [Term] id: MOD:01715 name: TMT6plex reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with a Proteome Sciences TMT6plex reporter+balance group." [UniMod:214] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with a Proteome Sciences TMT6plex reporter+balance group." [Unimod:214] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -32865,6 +34079,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:214" is_a: MOD:01426 ! isotope tagged reagent derivatized residue is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent @@ -32888,8 +34103,8 @@ comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -32904,12 +34119,12 @@ [Term] id: MOD:01718 name: TMT6plex reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a Proteome Sciences TMT6plex reporter+balance group." [UniMod:214#N-term] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a Proteome Sciences TMT6plex reporter+balance group." [Unimod:214#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -32919,6 +34134,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:214" is_a: MOD:01708 ! isotope tagged reagent alpha-amino acylated residue is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue @@ -32928,8 +34144,8 @@ def: "A protein modification that effectively replaces a residue hydroxyl with one of the Proteome Sciences TMT6plex reagent reporter+balance acyloxy groups." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -32944,12 +34160,12 @@ [Term] id: MOD:01720 name: TMT6plex-126 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -32959,17 +34175,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue [Term] id: MOD:01721 name: TMT6plex-126 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-126 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-126 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -32979,18 +34196,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:737" is_a: MOD:01718 ! TMT6plex reporter+balance reagent acylated N-terminal is_a: MOD:01720 ! TMT6plex-126 reporter+balance reagent acylated residue [Term] id: MOD:01722 name: TMT6plex-126 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33000,6 +34218,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01720 ! TMT6plex-126 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33007,11 +34226,11 @@ [Term] id: MOD:01723 name: TMT6plex-126 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33021,6 +34240,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01720 ! TMT6plex-126 reporter+balance reagent acylated residue @@ -33031,8 +34251,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33052,8 +34272,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33063,7 +34283,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01720 ! TMT6plex-126 reporter+balance reagent acylated residue @@ -33073,8 +34293,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-126 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33084,7 +34304,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01720 ! TMT6plex-126 reporter+balance reagent acylated residue @@ -33095,8 +34315,8 @@ subset: PSI-MOD-slim synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-126 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33115,12 +34335,12 @@ [Term] id: MOD:01728 name: TMT6plex-127 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33130,17 +34350,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue [Term] id: MOD:01729 name: TMT6plex-127 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-127 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-127 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33156,12 +34377,12 @@ [Term] id: MOD:01730 name: TMT6plex-127 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33171,6 +34392,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01728 ! TMT6plex-127 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33178,11 +34400,11 @@ [Term] id: MOD:01731 name: TMT6plex-127 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33202,8 +34424,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33223,8 +34445,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33234,7 +34456,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01728 ! TMT6plex-127 reporter+balance reagent acylated residue @@ -33244,8 +34466,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-127 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33255,7 +34477,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01728 ! TMT6plex-127 reporter+balance reagent acylated residue @@ -33266,8 +34488,8 @@ subset: PSI-MOD-slim synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-127 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33285,12 +34507,12 @@ [Term] id: MOD:01736 name: TMT6plex-128 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33300,17 +34522,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue [Term] id: MOD:01737 name: TMT6plex-128 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-128 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-128 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33320,18 +34543,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:737" is_a: MOD:01718 ! TMT6plex reporter+balance reagent acylated N-terminal is_a: MOD:01736 ! TMT6plex-128 reporter+balance reagent acylated residue [Term] id: MOD:01738 name: TMT6plex-128 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33341,6 +34565,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01736 ! TMT6plex-128 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33348,11 +34573,11 @@ [Term] id: MOD:01739 name: TMT6plex-128 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33362,6 +34587,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01736 ! TMT6plex-128 reporter+balance reagent acylated residue @@ -33372,8 +34598,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33393,8 +34619,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33404,7 +34630,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01736 ! TMT6plex-128 reporter+balance reagent acylated residue @@ -33414,8 +34640,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-128 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33425,7 +34651,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01736 ! TMT6plex-128 reporter+balance reagent acylated residue @@ -33436,8 +34662,8 @@ subset: PSI-MOD-slim synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-128 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33455,12 +34681,12 @@ [Term] id: MOD:01744 name: TMT6plex-129 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33470,17 +34696,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue [Term] id: MOD:01745 name: TMT6plex-129 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-129 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-129 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33490,18 +34717,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:737" is_a: MOD:01718 ! TMT6plex reporter+balance reagent acylated N-terminal is_a: MOD:01744 ! TMT6plex-129 reporter+balance reagent acylated residue [Term] id: MOD:01746 name: TMT6plex-129 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33511,6 +34739,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01744 ! TMT6plex-129 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33518,11 +34747,11 @@ [Term] id: MOD:01747 name: TMT6plex-129 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33532,6 +34761,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01744 ! TMT6plex-129 reporter+balance reagent acylated residue @@ -33542,8 +34772,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33563,8 +34793,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33574,7 +34804,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01744 ! TMT6plex-129 reporter+balance reagent acylated residue @@ -33584,8 +34814,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-129 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33595,7 +34825,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01744 ! TMT6plex-129 reporter+balance reagent acylated residue @@ -33606,8 +34836,8 @@ subset: PSI-MOD-slim synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-129 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33625,12 +34855,12 @@ [Term] id: MOD:01752 name: TMT6plex-130 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33640,18 +34870,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue relationship: derives_from MOD:01827 ! cysTMT6plex-130 reporter+balance reagent cysteine disulfide [Term] id: MOD:01753 name: TMT6plex-130 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-130 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-130 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33661,18 +34892,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:737" is_a: MOD:01718 ! TMT6plex reporter+balance reagent acylated N-terminal is_a: MOD:01752 ! TMT6plex-130 reporter+balance reagent acylated residue [Term] id: MOD:01754 name: TMT6plex-130 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33682,6 +34914,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01752 ! TMT6plex-130 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33689,11 +34922,11 @@ [Term] id: MOD:01755 name: TMT6plex-130 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33703,6 +34936,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01752 ! TMT6plex-130 reporter+balance reagent acylated residue @@ -33713,8 +34947,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33734,8 +34968,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33745,7 +34979,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01752 ! TMT6plex-130 reporter+balance reagent acylated residue @@ -33755,8 +34989,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-130 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33766,7 +35000,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01752 ! TMT6plex-130 reporter+balance reagent acylated residue @@ -33777,8 +35011,8 @@ subset: PSI-MOD-slim synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-130 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33795,13 +35029,13 @@ [Term] id: MOD:01760 name: TMT6plex-131 reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [UniMod:737] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [Unimod:737] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] synonym: "cysTMT6plex-131 reporter fragment" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33811,18 +35045,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01715 ! TMT6plex reporter+balance reagent acylated residue relationship: derives_from MOD:01828 ! cysTMT6plex-131 reporter+balance reagent cysteine disulfide [Term] id: MOD:01761 name: TMT6plex-131 reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-131 reporter+balance group." [UniMod:737#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Proteome Sciences TMT6plex-131 reporter+balance group." [Unimod:737#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33832,18 +35067,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:737" is_a: MOD:01718 ! TMT6plex reporter+balance reagent acylated N-terminal is_a: MOD:01760 ! TMT6plex-131 reporter+balance reagent acylated residue [Term] id: MOD:01762 name: TMT6plex-131 reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [UniMod:737#K] +def: "A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [Unimod:737#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33853,6 +35089,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:01717 ! TMT6plex reporter+balance reagent N-acylated residue is_a: MOD:01760 ! TMT6plex-131 reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -33860,11 +35097,11 @@ [Term] id: MOD:01763 name: TMT6plex-131 reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [UniMod:737#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [Unimod:737#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33874,6 +35111,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:737" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01760 ! TMT6plex-131 reporter+balance reagent acylated residue @@ -33884,8 +35122,8 @@ def: "A protein modification that effectively replaces an N'-hydrogen atom of a histidine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33905,8 +35143,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a serine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33916,7 +35154,7 @@ xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02003 ! O3-acylated L-serine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01760 ! TMT6plex-131 reporter+balance reagent acylated residue @@ -33926,8 +35164,8 @@ def: "A protein modification that effectively replaces an O3-hydrogen atom of a threonine residue with the Proteome Sciences TMT6plex-131 reporter+balance group." [PubMed:18688235] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "3-[(2,6-dimethylpiperidin-1-yl)acetyl]amino)propanoyl" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "229.16" xref: DiffFormula: "(12)C 8 (13)C 4 H 20 (14)N 1 (15)N 1 O 2" xref: DiffMono: "229.162932" @@ -33937,7 +35175,7 @@ xref: Origin: "T" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01719 ! TMT6plex reporter+balance reagent O-acylated residue is_a: MOD:01760 ! TMT6plex-131 reporter+balance reagent acylated residue @@ -33946,8 +35184,8 @@ name: TMT6plex-131 reporter fragment def: "The protein modification reporter fragment produced by an Proteome Sciences TMT6plex-131 reagent acylated residue." [PubMed:18688235] synonym: "2,6-dimethyl-1-methylidenepiperidinium" EXACT PSI-MOD-alternate [] -synonym: "Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "TMT6plex" RELATED UniMod-alternate [] +synonym: "Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "TMT6plex" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -33981,7 +35219,7 @@ [Term] id: MOD:01769 name: O-palmitoleyl-L-threonine -def: "A protein modification that effectively converts an L-threonine residue to O-palmitoleyl-L-threonine." [OMSSA:188, PubMed:6642431, PubMed:8413602, RESID:AA0079#var, UniMod:431#T] +def: "A protein modification that effectively converts an L-threonine residue to O-palmitoleyl-L-threonine." [OMSSA:188, PubMed:6642431, PubMed:8413602, RESID:AA0079#var, Unimod:431#T] subset: PSI-MOD-slim synonym: "(2S,3R)-2-amino-3-((Z)-9-hexadecenoyloxy)butanoic acid" EXACT PSI-MOD-alternate [] synonym: "L-threonine cis-9-hexadecenoate ester" EXACT PSI-MOD-alternate [] @@ -33989,7 +35227,7 @@ synonym: "O-palmitoleylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-palmitoleyl-threonine" EXACT PSI-MOD-alternate [] synonym: "Palmitoleyl" RELATED PSI-MS-label [] -synonym: "palmitoleyl" RELATED UniMod-description [] +synonym: "palmitoleyl" RELATED Unimod-description [] xref: DiffAvg: "236.40" xref: DiffFormula: "C 16 H 28 N 0 O 1" xref: DiffMono: "236.214016" @@ -33999,7 +35237,8 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +xref: Unimod: "Unimod:431" +is_a: MOD:02004 ! O3-acylated L-threonine is_a: MOD:01768 ! O-palmitoleylated residue [Term] @@ -34017,7 +35256,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02004 ! O3-acylated L-threonine relationship: has_functional_parent MOD:00088 ! O-palmitoyl-L-threonine relationship: has_functional_parent MOD:00106 ! L-threonine amide @@ -34184,6 +35423,7 @@ xref: Origin: "G" xref: Source: "hypothetical" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0433" is_a: MOD:00908 ! modified glycine residue [Term] @@ -34225,13 +35465,14 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00037 ! 5-hydroxy-L-lysine +xref: UniProt: "PTM-0474" +relationship: derives_from MOD:00037 ! 5-hydroxy-L-lysine is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01781 name: N6-butanoyl-L-lysine -def: "A protein modification that effectively converts an L-lysine residue to N6-butanoyl-L-lysine." [PubMed:17267393, PubMed:20715035, RESID:AA0532, UniMod:1289] +def: "A protein modification that effectively converts an L-lysine residue to N6-butanoyl-L-lysine." [PubMed:17267393, PubMed:20715035, RESID:AA0532, Unimod:1289] comment: The binding of histone peptides with butanoylated lysine to nuclear bromodomain proteins is non-specific and weaker than binding to the corresponding acetylated lysine peptides [JSG]. synonym: "(2S)-2-amino-6-(butanoylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "(2S)-2-azanyl-6-(butanoylamino)hexanoic acid" EXACT RESID-alternate [] @@ -34242,6 +35483,7 @@ synonym: "N6-(1-oxobutyl)-L-lysine" EXACT RESID-alternate [] synonym: "N6-butanoyl-L-lysine" EXACT RESID-name [] synonym: "N6-butyryllysine" EXACT RESID-alternate [] +synonym: "MOD_RES N6-butyryllysine" EXACT UniProt-feature [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 N 0 O 1" xref: DiffMono: "70.041865" @@ -34251,6 +35493,8 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: Unimod: "Unimod:1289" +xref: UniProt: "PTM-0637" is_a: MOD:01875 ! N6-acylated L-lysine is_a: MOD:01997 ! N-butanoylated residue @@ -34272,6 +35516,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0432" is_a: MOD:01680 ! alpha-amino monomethylated residue is_a: MOD:01800 ! N-methylated serine @@ -34292,6 +35537,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0431" is_a: MOD:01686 ! alpha-amino dimethylated residue is_a: MOD:01800 ! N-methylated serine @@ -34317,6 +35563,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0430" is_a: MOD:01698 ! alpha-amino trimethylated protonated-residue is_a: MOD:01800 ! N-methylated serine @@ -34364,6 +35611,7 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0434" is_a: MOD:01352 ! nitrated L-tyrosine [Term] @@ -34386,8 +35634,9 @@ xref: Origin: "Y, Y" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0320" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:01788 @@ -34506,7 +35755,6 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00708 ! sulfur oxygenated L-cysteine is_a: MOD:01854 ! sulfur monooxygenated residue relationship: derives_from MOD:01060 ! S-carboxamidomethyl-L-cysteine @@ -34543,8 +35791,8 @@ xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00839 ! (2)H deuterium labeled residue +is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00913 ! modified L-methionine residue -is_a: MOD:01794 ! 1x(13)C,3x(2)H labeled monomethylated residue [Term] id: MOD:01796 @@ -34561,7 +35809,6 @@ xref: TermSpec: "none" is_a: MOD:00839 ! (2)H deuterium labeled residue is_a: MOD:00913 ! modified L-methionine residue -is_a: MOD:01794 ! 1x(13)C,3x(2)H labeled monomethylated residue [Term] id: MOD:01797 @@ -34708,7 +35955,8 @@ xref: Origin: "D, G" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00904 ! modified L-aspartic acid residue +xref: UniProt: "PTM-0490" +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01928 ! N-(L-isoaspartyl)-glycine @@ -34731,6 +35979,7 @@ xref: Origin: "L" xref: Source: "hypothetical" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0435" is_a: MOD:01686 ! alpha-amino dimethylated residue is_a: MOD:01808 ! N-methylated leucine @@ -34768,8 +36017,8 @@ [Term] id: MOD:01809 name: 5x(13)C,1x(15)N labeled residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 5x(13)C,1x(15)N labeled residue." [PubMed:12771378, UniMod:268] -synonym: "13C(5) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue containing common isotopes to a 5x(13)C,1x(15)N labeled residue." [PubMed:12771378, Unimod:268] +synonym: "13C(5) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "6.01" xref: DiffFormula: "(12)C -5 (13)C 5 (14)N -1 (15)N 1" @@ -34780,14 +36029,15 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:268" is_a: MOD:00842 ! (13)C labeled residue is_a: MOD:00843 ! (15)N labeled residue [Term] id: MOD:01810 name: 5x(13)C,1x(15)N labeled L-proline -def: "A protein modification that effectively converts an L-proline residue to 5x(13)C,1x(15)N labeled L-proline." [PubMed:12771378, UniMod:268#P] -synonym: "13C(5) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-proline residue to 5x(13)C,1x(15)N labeled L-proline." [PubMed:12771378, Unimod:268#P] +synonym: "13C(5) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "6.01" xref: DiffFormula: "(12)C -5 (13)C 5 (14)N -1 (15)N 1" @@ -34798,14 +36048,15 @@ xref: Origin: "P" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:268" is_a: MOD:00915 ! modified L-proline residue is_a: MOD:01809 ! 5x(13)C,1x(15)N labeled residue [Term] id: MOD:01811 name: 5x(13)C,1x(15)N labeled L-methionine -def: "A protein modification that effectively converts an L-methionine residue to 5x(13)C,1x(15)N labeled L-methionine." [PubMed:12771378, UniMod:268#M] -synonym: "13C(5) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-methionine residue to 5x(13)C,1x(15)N labeled L-methionine." [PubMed:12771378, Unimod:268#M] +synonym: "13C(5) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "6.01" xref: DiffFormula: "(12)C -5 (13)C 5 (14)N -1 (15)N 1" @@ -34816,14 +36067,15 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:268" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:01809 ! 5x(13)C,1x(15)N labeled residue [Term] id: MOD:01812 name: 5x(13)C,1x(15)N labeled L-methionine sulfoxide -def: "A protein modification that effectively converts an L-methionine residue to 5x(13)C,1x(15)N labeled L-methionine sulfoxide." [PubMed:12771378, UniMod:268#M] -synonym: "13C(5) 15N(1) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts an L-methionine residue to 5x(13)C,1x(15)N labeled L-methionine sulfoxide." [PubMed:12771378, Unimod:268#M] +synonym: "13C(5) 15N(1) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)15N(1)" RELATED PSI-MS-label [] xref: DiffAvg: "6.01" xref: DiffFormula: "(12)C -5 (13)C 5 (14)N -1 (15)N 1" @@ -34834,15 +36086,16 @@ xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00719 ! L-methionine sulfoxide +xref: Unimod: "Unimod:268" +relationship: derives_from MOD:00719 ! L-methionine sulfoxide is_a: MOD:01809 ! 5x(13)C,1x(15)N labeled residue [Term] id: MOD:01813 name: morpholine-2-acetylated residue -def: "A protein modification that effectively substitutes a morpholine-2-acetyl group for a hydrogen atom." [PubMed:10446193, UniMod:29] -comment: The UniMod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. -synonym: "N-Succinimidyl-2-morpholine acetate" RELATED UniMod-description [] +def: "A protein modification that effectively substitutes a morpholine-2-acetyl group for a hydrogen atom." [PubMed:10446193, Unimod:29] +comment: The Unimod name "N-Succinimidyl-3-morpholine acetate" appears to have been a typographical error [JSG]. +synonym: "N-Succinimidyl-2-morpholine acetate" RELATED Unimod-description [] synonym: "N-succinimidylmorpholine-2-acetate derivative" EXACT PSI-MOD-alternate [] synonym: "SMA" RELATED PSI-MS-label [] xref: DiffAvg: "127.14" @@ -34853,6 +36106,7 @@ xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" +xref: Unimod: "Unimod:29" is_a: MOD:00649 ! acylated residue is_a: MOD:00848 ! reagent derivatized residue @@ -34864,6 +36118,7 @@ synonym: "6-[(1R)-1-amino-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acid" EXACT RESID-systematic [] synonym: "6-[1-azanyl-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acid" EXACT RESID-alternate [] synonym: "L-cysteine 3-hydroxy-2,5-pyridinedicarboxylic acid" EXACT RESID-name [] +synonym: "CROSSLNK 3-hydroxypyridine-2,5-dicarboxylic acid (Ser-Cys)" RELATED UniProt-feature [] xref: DiffAvg: "-54.07" xref: DiffFormula: "C 0 H -8 N -1 O -2 S 0" xref: DiffMono: "-54.055504" @@ -34873,6 +36128,9 @@ xref: Origin: "C, S, S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0454" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01425 ! pyridinyl ring crosslinked residues [Term] @@ -34893,9 +36151,10 @@ xref: Origin: "C, E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0456" +is_a: MOD:02045 ! crosslinked L-glutamic acid residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01816 @@ -34919,7 +36178,7 @@ [Term] id: MOD:01817 -name: oxidation of tryptophan to 2'-oxo-L-tryptophan +name: 2'-oxo-L-tryptophan def: "A protein modification that effectively converts an L-tryptophan residue to a 2'-oxo-L-tryptophan." [PubMed:9461080, RESID:AA0543] synonym: "(2S)-2-amino-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]propanoic acid" EXACT RESID-systematic [] synonym: "2'-oxo-L-tryptophan" EXACT RESID-name [] @@ -34958,8 +36217,9 @@ xref: Origin: "W, W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0544" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00918 ! modified L-tryptophan residue +is_a: MOD:02057 ! crosslinked L-tryptophan residue [Term] id: MOD:01819 @@ -34982,6 +36242,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0438" is_a: MOD:01029 ! succinylated residue is_a: MOD:01875 ! N6-acylated L-lysine @@ -34999,11 +36260,11 @@ [Term] id: MOD:01821 name: cysTMT6plex reporter+balance reagent cysteine disulfide -def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex reporter+balance group." [UniMod:985, URL:http\://www.piercenet.com/files/2162220.pdf] +def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex reporter+balance group." [Unimod:985, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" @@ -35014,6 +36275,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:985" is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01429 ! (15)N isotope tagged reagent is_a: MOD:01820 ! isotope tagged sufhydryl reagent modified cysteine @@ -35021,11 +36283,11 @@ [Term] id: MOD:01822 name: cysTMT6plex-zero reporter+balance reagent cysteine disulfide -def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-zero reporter+balance group." [UniMod:984, URL:http\://www.piercenet.com/files/2162220.pdf] +def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-zero reporter+balance group." [Unimod:984, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysTMT" RELATED UniMod-interim [] -synonym: "Native cysteine-reactive Tandem Mass Tag(TM)" RELATED UniMod-description [] +synonym: "cysTMT" RELATED Unimod-interim [] +synonym: "Native cysteine-reactive Tandem Mass Tag(TM)" RELATED Unimod-description [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "299.17" xref: DiffFormula: "(12)C 14 H 25 (14)N 3 O 2 S 1" @@ -35036,6 +36298,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:984" is_a: MOD:01821 ! cysTMT6plex reporter+balance reagent cysteine disulfide [Term] @@ -35044,8 +36307,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-126 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35056,6 +36319,7 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:985" is_a: MOD:01821 ! cysTMT6plex reporter+balance reagent cysteine disulfide [Term] @@ -35064,8 +36328,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-127 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35084,8 +36348,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-128 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35104,8 +36368,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-129 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35124,8 +36388,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-130 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35144,8 +36408,8 @@ def: "A protein modification that effectively replaces a residue sulfhydryl hydrogen with a Thermo Scientific cysTMT6plex-131 reporter+balance group." [PubMed:18688235, URL:http\://www.piercenet.com/files/2162220.pdf] comment: The reagent consists of a reporter group, a balance group and a protein sulfhydryl reactive pyridine disulfanyl group. The reporter group, an isotopically labeled 1,2,6-trimethylpiperidine, is connected to a 3-(carbonylamino)propanoyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim -synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED UniMod-description [] -synonym: "cysTMT6plex" RELATED UniMod-interim [] +synonym: "cysteine-reactive Sixplex Tandem Mass Tag(TM)" RELATED Unimod-description [] +synonym: "cysTMT6plex" RELATED Unimod-interim [] synonym: "S-(2-{3-[2-(2,6-dimethylpiperidin-1-yl)acetamido]propanamido}ethyl)sulfanyl" EXACT PSI-MOD-alternate [] xref: DiffAvg: "304.18" xref: DiffFormula: "(12)C 10 (13)C 4 H 25 (14)N 2 (15)N 1 O 2 S 1" @@ -35191,7 +36455,6 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00399 ! iodoacetic acid derivatized residue is_a: MOD:00708 ! sulfur oxygenated L-cysteine is_a: MOD:01855 ! sulfur dioxygenated residue relationship: derives_from MOD:01061 ! S-carboxymethyl-L-cysteine @@ -35211,7 +36474,6 @@ xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00397 ! iodoacetamide derivatized residue is_a: MOD:00708 ! sulfur oxygenated L-cysteine is_a: MOD:01855 ! sulfur dioxygenated residue relationship: derives_from MOD:01060 ! S-carboxamidomethyl-L-cysteine @@ -35219,8 +36481,8 @@ [Term] id: MOD:01832 name: 5x(13)C-labeled residue -def: "A protein modification that effectively converts a residue containing common isotopes to a 5x(13)C-labeled residue." [PubMed:12771378, UniMod:772] -synonym: "13C(5) Silac label" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue containing common isotopes to a 5x(13)C-labeled residue." [PubMed:12771378, Unimod:772] +synonym: "13C(5) Silac label" RELATED Unimod-description [] synonym: "Label:13C(5)" RELATED PSI-MS-label [] xref: DiffAvg: "5.02" xref: DiffFormula: "(12)C -5 (13)C 5" @@ -35231,6 +36493,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:772" is_a: MOD:00842 ! (13)C labeled residue [Term] @@ -35253,32 +36516,32 @@ id: MOD:01834 name: 5x(13)C-labeled L-methionine sulfoxide def: "A protein modification that effectively converts an L-methionine residue containing common isotopes to 5x(13)C-labeled L-methionine sulfoxide." [PubMed:18688235] -xref: DiffAvg: "21.01" -xref: DiffFormula: "(12)C -5 (13)C 5 H 0 N 0 O 1 S 0" -xref: DiffMono: "21.011689" +xref: DiffAvg: "5.02" +xref: DiffFormula: "(12)C -5 (13)C 5 H 0 N 0 O 0 S 0" +xref: DiffMono: "5.016774" xref: Formula: "(13)C 5 H 9 N 1 O 2 S 1" xref: MassAvg: "152.05" xref: MassMono: "152.052174" -xref: Origin: "M" +xref: Origin: "MOD:00719" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00719 ! L-methionine sulfoxide +relationship: derives_from MOD:00719 ! L-methionine sulfoxide is_a: MOD:01832 ! 5x(13)C-labeled residue [Term] id: MOD:01835 name: 5x(13)C-labeled L-methionine sulfone def: "A protein modification that effectively converts an L-methionine residue containing common isotopes to 5x(13)C-labeled L-methionine sulfone." [PubMed:18688235] -xref: DiffAvg: "37.01" -xref: DiffFormula: "(12)C -5 (13)C 5 H 0 N 0 O 2 S 0" -xref: DiffMono: "37.006603" +xref: DiffAvg: "5.02" +xref: DiffFormula: "(12)C -5 (13)C 5 H 0 N 0 O 0 S 0" +xref: DiffMono: "5.016774" xref: Formula: "(13)C 5 H 9 N 1 O 3 S 1" xref: MassAvg: "168.05" xref: MassMono: "168.047088" -xref: Origin: "M" +xref: Origin: "MOD:00256" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00256 ! L-methionine sulfone +relationship: derives_from MOD:00256 ! L-methionine sulfone is_a: MOD:01832 ! 5x(13)C-labeled residue [Term] @@ -35321,7 +36584,7 @@ xref: Origin: "C, C" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:01839 ! L-lanthionine +is_a: MOD:00687 ! thioether crosslinked residues [Term] id: MOD:01838 @@ -35346,6 +36609,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0439" is_a: MOD:01853 ! L-lysinoalanine [Term] @@ -35364,6 +36628,7 @@ xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01841 ! lanthionine +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01840 @@ -35386,8 +36651,10 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0442" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00910 ! modified L-isoleucine residue +is_a: MOD:00306 ! residues isobaric at 113.084064 Da [Term] id: MOD:01841 @@ -35411,6 +36678,7 @@ xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:01993 ! beta-carbon thioether crosslinked residues +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01842 @@ -35429,6 +36697,7 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0443" is_a: MOD:01851 ! S-(2-aminovinyl)-cysteine [Term] @@ -35447,6 +36716,7 @@ xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0444" is_a: MOD:01913 ! monochlorinated L-tryptophan [Term] @@ -35467,8 +36737,9 @@ xref: Origin: "C, L" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00911 ! modified L-leucine residue +xref: UniProt: "PTM-0448" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02050 ! crosslinked L-leucine residue is_a: MOD:01856 ! oxazole/oxazoline ring crosslinked residues (Cys) [Term] @@ -35489,8 +36760,9 @@ xref: Origin: "C, P" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00915 ! modified L-proline residue +xref: UniProt: "PTM-0449" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02054 ! crosslinked L-proline residue is_a: MOD:01856 ! oxazole/oxazoline ring crosslinked residues (Cys) [Term] @@ -35511,7 +36783,7 @@ xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00742 ! copper containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:01847 @@ -35570,6 +36842,7 @@ xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "C-term" +xref: UniProt: "PTM-0446" is_a: MOD:01850 ! S-(2-aminovinyl)-D-cysteine [Term] @@ -35625,7 +36898,8 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01853 ! L-lysinoalanine [Term] @@ -35675,8 +36949,9 @@ xref: Origin: "C, M" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00913 ! modified L-methionine residue +xref: UniProt: "PTM-0495" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02052 ! crosslinked L-methionine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -35684,7 +36959,7 @@ name: S-(N-acetylamino)glucosyl-L-cysteine def: "A protein modification that effectively converts an L-cysteine residue to S-(N-acetylamino)glucosyl-L-cysteine." [ChEBI:61631, PubMed:21251913, PubMed:21395300, RESID:AA0560] synonym: "(2R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosylsulfanyl)propanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD S-linked (GlcNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD S-linked (GlcNAc) cysteine" EXACT UniProt-feature [] synonym: "S-(N-acetylamino)glucosyl-L-cysteine" EXACT RESID-name [] synonym: "S-[(N-acetylamino)glycosyl]cysteine" EXACT RESID-alternate [] synonym: "S-[beta-D-(N-acetylamino)glucopyranosyl]cysteine" EXACT RESID-alternate [] @@ -35697,8 +36972,9 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0628" is_a: MOD:00426 ! S-glycosylated residue -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +is_a: MOD:00448 ! mono-N-acetylaminoglucosylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] @@ -35723,8 +36999,9 @@ xref: Origin: "C, F" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00914 ! modified L-phenylalanine residue +xref: UniProt: "PTM-0451" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue is_a: MOD:01861 ! isothiazolidinone ring crosslinked residues [Term] @@ -35744,6 +37021,7 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0452" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01862 ! disulfide conjugated residue @@ -35771,7 +37049,7 @@ comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" @@ -35787,12 +37065,12 @@ [Term] id: MOD:01864 name: mTRAQ light reporter+balance reagent acylated residue -def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems mTRAQ light reporter+balance group." [UniMod:888] +def: "A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems mTRAQ light reporter+balance group." [Unimod:888] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "mTRAQ heavy" RELATED UniMod-description [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "mTRAQ heavy" RELATED Unimod-description [] xref: DiffAvg: "140.09" xref: DiffFormula: "(12)C 7 H 12 (14)N 2 (16)O 1" xref: DiffMono: "140.094963" @@ -35802,18 +37080,19 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:888" is_a: MOD:01863 ! mTRAQ reporter+balance reagent acylated residue is_a: MOD:01868 ! modifications with monoisotopic mass differences that are nominally equal at 140.094963 Da [Term] id: MOD:01865 name: mTRAQ light reporter+balance reagent acylated N-terminal -def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:208, UniMod:888#N-term] +def: "A protein modification that effectively replaces a hydrogen atom of a protein N-terminal with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:208, Unimod:888#N-term] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "mTRAQ light" RELATED UniMod-description [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "mTRAQ light" RELATED Unimod-description [] synonym: "mTRAQ light on nterm" EXACT OMSSA-label [] xref: DiffAvg: "140.09" xref: DiffFormula: "(12)C 7 H 12 (14)N 2 (16)O 1" @@ -35824,17 +37103,18 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" +xref: Unimod: "Unimod:888" is_a: MOD:01864 ! mTRAQ light reporter+balance reagent acylated residue [Term] id: MOD:01866 name: mTRAQ light reporter+balance reagent N6-acylated lysine -def: "A protein modification that effectively replaces the N6-amino hydrogen atom of a lysine residue with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:209, UniMod:888#K] +def: "A protein modification that effectively replaces the N6-amino hydrogen atom of a lysine residue with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:209, Unimod:888#K] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. subset: PSI-MOD-slim synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "mTRAQ light" RELATED UniMod-description [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "mTRAQ light" RELATED Unimod-description [] synonym: "mTRAQ light on K" EXACT OMSSA-label [] xref: DiffAvg: "140.09" xref: DiffFormula: "(12)C 7 H 12 (14)N 2 (16)O 1" @@ -35845,17 +37125,18 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:888" is_a: MOD:01864 ! mTRAQ light reporter+balance reagent acylated residue is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01867 name: mTRAQ light reporter+balance reagent O4'-acylated tyrosine -def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:210, UniMod:888#Y] +def: "A protein modification that effectively replaces the O4'-hydrogen atom of a tyrosine residue with the Applied Biosystems mTRAQ light reporter+balance group." [OMSSA:210, Unimod:888#Y] comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] -synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED UniMod-alternate [] -synonym: "mTRAQ light" RELATED UniMod-description [] +synonym: "Applied Biosystems mTRAQ(TM) reagent" RELATED Unimod-alternate [] +synonym: "mTRAQ light" RELATED Unimod-description [] synonym: "mTRAQ light on Y" EXACT OMSSA-label [] xref: DiffAvg: "140.09" xref: DiffFormula: "(12)C 7 H 12 (14)N 2 (16)O 1" @@ -35866,6 +37147,7 @@ xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:888" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01864 ! mTRAQ light reporter+balance reagent acylated residue @@ -35905,13 +37187,13 @@ [Term] id: MOD:01871 name: cyclized N-terminal S-carboxamidomethyl-L-cysteine -def: "A protein modification that effectively cyclizes an S-carboxamidomethyl-L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid with the loss of ammonia." [DeltaMass:336, PubMed:12643538, UniMod:26] +def: "A protein modification that effectively cyclizes an S-carboxamidomethyl-L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid with the loss of ammonia." [DeltaMass:336, PubMed:12643538, Unimod:26] subset: PSI-MOD-slim synonym: "(R)-5-oxoperhydro-1,4-thiazine-3-carboxylic acid" EXACT DeltaMass-label [] synonym: "5-oxothiomorpholine-3-carboxylic acid" EXACT PSI-MOD-alternate [] synonym: "Otc" EXACT DeltaMass-label [] -synonym: "Pyro-carbamidomethyl" RELATED UniMod-interim [] -synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED UniMod-description [] +synonym: "Pyro-carbamidomethyl" RELATED Unimod-interim [] +synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED Unimod-description [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0 S 0" xref: DiffMono: "-17.026549" @@ -35921,21 +37203,22 @@ xref: Origin: "MOD:01060" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00397 ! iodoacetamide derivatized residue -is_a: MOD:00419 ! (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid +xref: Unimod: "Unimod:26" +is_a: MOD:01160 ! deaminated residue +relationship: contains MOD:00419 ! (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid relationship: derives_from MOD:01060 ! S-carboxamidomethyl-L-cysteine [Term] id: MOD:01872 name: cyclized N-terminal S-carboxymethyl-L-cysteine -def: "A protein modification that effectively cyclizes an S-carboxymethyl-L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid with the loss of water." [PubMed:12643538, UniMod:26] -comment: Contrary to the impression given in UniMod entry 26, the cyclization of N-terminal S-carboxymethyl-L-cysteine is not reported in PubMed:1263538. The cyclization would be expected to proceed under strongly acidic conditions [JSG]. +def: "A protein modification that effectively cyclizes an S-carboxymethyl-L-cysteine residue to (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid with the loss of water." [PubMed:12643538, Unimod:26] +comment: Contrary to the impression given in Unimod entry 26, the cyclization of N-terminal S-carboxymethyl-L-cysteine is not reported in PubMed:1263538. The cyclization would be expected to proceed under strongly acidic conditions [JSG]. subset: PSI-MOD-slim synonym: "(R)-5-oxoperhydro-1,4-thiazine-3-carboxylic acid" EXACT DeltaMass-label [] synonym: "5-oxothiomorpholine-3-carboxylic acid" EXACT PSI-MOD-alternate [] synonym: "Otc" EXACT DeltaMass-label [] -synonym: "Pyro-carbamidomethyl" RELATED UniMod-interim [] -synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED UniMod-description [] +synonym: "Pyro-carbamidomethyl" RELATED Unimod-interim [] +synonym: "S-carbamoylmethylcysteine cyclization (N-terminus)" RELATED Unimod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" @@ -35945,8 +37228,9 @@ xref: Origin: "MOD:01061" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00399 ! iodoacetic acid derivatized residue -is_a: MOD:00419 ! (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid +xref: Unimod: "Unimod:26" +is_a: MOD:00704 ! dehydrated residue +relationship: contains MOD:00419 ! (R)-5-oxo-1,4-tetrahydrothiazine-3-carboxylic acid relationship: derives_from MOD:01061 ! S-carboxymethyl-L-cysteine [Term] @@ -36004,9 +37288,7 @@ [Term] id: MOD:01876 name: 4x(1)H,4x(12)C-labeled alpha-amino succinylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 4x(12)C labeled succinyl group." [PubMed:11857757, PubMed:12175151, PubMed:12716131, UniMod:64] -synonym: "Succinic anhydride labeling reagent, light form (+4amu, 4H2) site N-term" RELATED UniMod-description [] -synonym: "Succinyl" RELATED PSI-MS-label [] +def: "OBSOLETE because identical to MOD:00457" [PubMed:18688235] xref: DiffAvg: "100.02" xref: DiffFormula: "(12)C 4 (1)H 4 O 3" xref: DiffMono: "100.016044" @@ -36016,8 +37298,8 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" -is_a: MOD:00457 ! alpha-amino succinylated residue -is_a: MOD:01426 ! isotope tagged reagent derivatized residue +xref: Remap: "MOD:00457" +is_obsolete: true [Term] id: MOD:01877 @@ -36038,8 +37320,9 @@ xref: Origin: "C, R" xref: Source: "natural" xref: TermSpec: "N-term" -is_a: MOD:00902 ! modified L-arginine residue -is_a: MOD:00905 ! modified L-cysteine residue +xref: UniProt: "PTM-0457" +is_a: MOD:02041 ! crosslinked L-arginine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:01883 ! 5-imidazolinone ring crosslinked residues (Cys) [Term] @@ -36060,8 +37343,9 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00917 ! modified L-threonine residue +xref: UniProt: "PTM-0458" +is_a: MOD:02044 ! crosslinked L-cysteine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01856 ! oxazole/oxazoline ring crosslinked residues (Cys) [Term] @@ -36082,7 +37366,7 @@ xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00742 ! copper containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:01880 @@ -36092,6 +37376,7 @@ synonym: "deoxyhypusine" EXACT RESID-alternate [] synonym: "L-deoxyhypusine" EXACT RESID-name [] synonym: "N6-(4-aminobutyl)lysine" EXACT RESID-alternate [] +synonym: "MOD_RES Deoxyhypusine" EXACT UniProt-feature [] xref: DiffAvg: "71.12" xref: DiffFormula: "C 4 H 9 N 1 O 0" xref: DiffMono: "71.073499" @@ -36101,6 +37386,7 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0684" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01884 ! 4-aminobutylated residue @@ -36122,8 +37408,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues -is_a: MOD:00914 ! modified L-phenylalanine residue -is_a: MOD:00920 ! modified L-valine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue +is_a: MOD:02059 ! crosslinked L-valine residue [Term] id: MOD:01882 @@ -36198,7 +37484,7 @@ [Term] id: MOD:01888 name: didehydrogenated residue -def: "A protein modification that effectively removes two neutral hydrogen atoms (proton and electron) from a residue." [UniMod:401] +def: "A protein modification that effectively removes two neutral hydrogen atoms (proton and electron) from a residue." [Unimod:401] subset: PSI-MOD-slim synonym: "2dHRes" EXACT PSI-MOD-label [] xref: DiffAvg: "-2.02" @@ -36210,12 +37496,13 @@ xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" +xref: Unimod: "Unimod:401" is_a: MOD:00683 ! dehydrogenated residue [Term] id: MOD:01889 name: S-(2-succinyl)-L-cysteine -def: "A protein modification that effectively converts an L-cysteine residue to S-(2-succinyl)-L-cysteine, by addition of either fumaric acid or maleic acid." [PubMed:16624247, PubMed:18448829, PubMed:20677745, RESID:AA0561, UniMod:957] +def: "A protein modification that effectively converts an L-cysteine residue to S-(2-succinyl)-L-cysteine, by addition of either fumaric acid or maleic acid." [PubMed:16624247, PubMed:18448829, PubMed:20677745, RESID:AA0561, Unimod:957] synonym: "(2R)-2-amino-3-([(1R)-1,2-dicarboxyethyl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "(2R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid" EXACT RESID-alternate [] synonym: "2-((2-amino-2-carboxyethyl)thio)butanedioic acid" EXACT RESID-alternate [] @@ -36224,6 +37511,7 @@ synonym: "S-(2-succinyl)-L-cysteine" EXACT RESID-name [] synonym: "S-(2-succinyl)cysteine" EXACT RESID-alternate [] synonym: "S-[(2R)-2-succinyl]-L-cysteine" EXACT RESID-alternate [] +synonym: "MOD_RES S-(2-succinyl)cysteine" EXACT UniProt-feature [] xref: DiffAvg: "116.07" xref: DiffFormula: "C 4 H 4 N 0 O 4 S 0" xref: DiffMono: "116.010959" @@ -36233,6 +37521,8 @@ xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:957" +xref: UniProt: "PTM-0674" is_a: MOD:00001 ! alkylated residue is_a: MOD:00905 ! modified L-cysteine residue @@ -36252,8 +37542,8 @@ xref: Origin: "H, MOD:00030" xref: Source: "hypothetical" xref: TermSpec: "N-term" -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:01450 ! modified N-formyl-L-methionine residue +is_a: MOD:02048 ! crosslinked L-histidine residue +is_a: MOD:02062 ! crosslinked N-formyl-L-methionine residue [Term] id: MOD:01891 @@ -36271,8 +37561,8 @@ xref: Origin: "H, M" xref: Source: "hypothetical" xref: TermSpec: "N-term" -is_a: MOD:00909 ! modified L-histidine residue -is_a: MOD:00913 ! modified L-methionine residue +is_a: MOD:02048 ! crosslinked L-histidine residue +is_a: MOD:02052 ! crosslinked L-methionine residue [Term] id: MOD:01892 @@ -36297,6 +37587,7 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0475" is_a: MOD:01875 ! N6-acylated L-lysine [Term] @@ -36320,13 +37611,14 @@ xref: Origin: "K" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0467" is_a: MOD:01875 ! N6-acylated L-lysine [Term] id: MOD:01894 name: propanoylated residue -def: "A protein modification that effectively replaces a hydrogen atom with an propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:58] -synonym: "Propionate labeling reagent light form (N-term & K)" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a hydrogen atom with an propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:58] +synonym: "Propionate labeling reagent light form (N-term & K)" RELATED Unimod-description [] synonym: "Propionyl" RELATED PSI-MS-label [] xref: DiffAvg: "56.06" xref: DiffFormula: "C 3 H 4 O 1" @@ -36337,13 +37629,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:58" is_a: MOD:00649 ! acylated residue [Term] id: MOD:01895 name: alpha-amino 3x(12)C-labeled propanoylated residue -def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 3x(12)C-labeled propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, UniMod:58#N-term] -synonym: "Propionate labeling reagent light form (N-term & K)" RELATED UniMod-description [] +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a 3x(12)C-labeled propanoyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, Unimod:58#N-term] +synonym: "Propionate labeling reagent light form (N-term & K)" RELATED Unimod-description [] synonym: "Propionyl" RELATED PSI-MS-label [] xref: DiffAvg: "56.03" xref: DiffFormula: "(12)C 3 H 4 O 1" @@ -36354,7 +37647,9 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00451 ! alpha-amino propanoylated residue +xref: Unimod: "Unimod:58" +relationship: derives_from MOD:00451 ! alpha-amino propanoylated residue +is_a: MOD:01426 ! isotope tagged reagent derivatized residue [Term] id: MOD:01896 @@ -36393,10 +37688,10 @@ xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0466" is_a: MOD:00601 ! cyclized residue is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00910 ! modified L-isoleucine residue -is_a: MOD:01888 ! didehydrogenated residue is_a: MOD:01905 ! 5-hydroxy-3-methyl-L-proline [Term] @@ -36418,6 +37713,7 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0459" is_a: MOD:00783 ! dimethylated L-arginine [Term] @@ -36437,9 +37733,10 @@ xref: Origin: "C, R" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00902 ! modified L-arginine residue -is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues -is_a: MOD:01888 ! didehydrogenated residue +xref: UniProt: "PTM-0460" +is_a: MOD:02041 ! crosslinked L-arginine residue +is_a: MOD:01420 ! thiazole/thiazoline ring crosslinked residues +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01900 @@ -36459,9 +37756,10 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +xref: UniProt: "PTM-0461" +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:01422 ! oxazole/oxazoline ring crosslinked residues (Thr) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01901 @@ -36481,8 +37779,9 @@ xref: Origin: "T, T" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0462" is_a: MOD:01422 ! oxazole/oxazoline ring crosslinked residues (Thr) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01902 @@ -36502,9 +37801,10 @@ xref: Origin: "I, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00910 ! modified L-isoleucine residue +xref: UniProt: "PTM-0463" +is_a: MOD:02049 ! crosslinked L-isoleucine residue is_a: MOD:01421 ! oxazole/oxazoline ring crosslinked residues (Ser) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01903 @@ -36524,8 +37824,9 @@ xref: Origin: "S, S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0464" is_a: MOD:01421 ! oxazole/oxazoline ring crosslinked residues (Ser) -is_a: MOD:01888 ! didehydrogenated residue +is_a: MOD:02082 ! didehydrogenated and dehydrated residue [Term] id: MOD:01904 @@ -36546,8 +37847,10 @@ xref: Origin: "S, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +xref: UniProt: "PTM-0465" +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01422 ! oxazole/oxazoline ring crosslinked residues (Thr) +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01905 @@ -36614,8 +37917,8 @@ [Term] id: MOD:01908 name: 4-sulfophenyl isothiocyanate alpha-amino derivatized residue -def: "A protein modification that effectively converts a residue to the 4-sulfophenyl isothiocyanate adduct, alpha-amino-[(4-sulfophenyl)carbamothioyl] residue." [PubMed:14689565, PubMed:14745769, PubMed:15549660, PubMed:16526082, UniMod:261#N-term] -synonym: "4-sulfophenyl isothiocyanate" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue to the 4-sulfophenyl isothiocyanate adduct, alpha-amino-[(4-sulfophenyl)carbamothioyl] residue." [PubMed:14689565, PubMed:14745769, PubMed:15549660, PubMed:16526082, Unimod:261#N-term] +synonym: "4-sulfophenyl isothiocyanate" RELATED Unimod-description [] synonym: "alpha-amino-[(4-sulfophenyl)carbamothioyl] residue" EXACT PSI-MOD-alternate [] synonym: "SPITC" RELATED PSI-MS-label [] xref: DiffAvg: "215.24" @@ -36627,13 +37930,14 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:261" is_a: MOD:00584 ! 4-sulfophenyl isothiocyanate derivatized residue [Term] id: MOD:01909 name: 6x(13)C labeled 4-sulfophenyl isothiocyanate alpha-amino derivatized residue -def: "A protein modification that effectively converts a residue to the 6x(13)C labeled 4-sulfophenyl isothiocyanate adduct, alpha-amino-[(4-sulfophenyl)carbamothioyl] residue." [PubMed:11467524, PubMed:16526082, UniMod:464#N-term] -synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED UniMod-description [] +def: "A protein modification that effectively converts a residue to the 6x(13)C labeled 4-sulfophenyl isothiocyanate adduct, alpha-amino-[(4-sulfophenyl)carbamothioyl] residue." [PubMed:11467524, PubMed:16526082, Unimod:464#N-term] +synonym: "4-sulfophenyl isothiocyanate (Heavy C13)" RELATED Unimod-description [] synonym: "SPITC:13C(6)" RELATED PSI-MS-label [] xref: DiffAvg: "220.99" xref: DiffFormula: "(12)C 1 (13)C 6 H 5 N 1 O 3 S 2" @@ -36644,12 +37948,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:464" is_a: MOD:00880 ! 6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized residue [Term] id: MOD:01910 name: monofluorinated residue -def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one fluorine atom." [UniMod:127] +def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one fluorine atom." [Unimod:127] synonym: "F1Res" EXACT PSI-MOD-label [] xref: DiffAvg: "17.99" xref: DiffFormula: "C 0 F 1 H -1 N 0 O 0" @@ -36660,12 +37965,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:127" is_a: MOD:00498 ! fluorinated residue [Term] id: MOD:01911 name: monochlorinated residue -def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one chlorine atom." [UniMod:936] +def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one chlorine atom." [Unimod:936] synonym: "Cl1Res" EXACT PSI-MOD-label [] xref: DiffAvg: "34.44" xref: DiffFormula: "C 0 Cl 1 H -1 N 0 O 0" @@ -36676,12 +37982,13 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:936" is_a: MOD:00753 ! chlorinated residue [Term] id: MOD:01912 name: monobrominated residue -def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one bromine atom." [UniMod:340] +def: "A protein modification that effectively substitutes one hydrogen atom of a residue with one bromine atom." [Unimod:340] synonym: "Br1Res" EXACT PSI-MOD-label [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" @@ -36692,6 +37999,7 @@ xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" +xref: Unimod: "Unimod:340" is_a: MOD:00754 ! brominated residue [Term] @@ -36714,23 +38022,25 @@ [Term] id: MOD:01914 name: O5-galactosyl-L-hydroxylysine -def: "A protein modification that effectively converts an L-lysine residue to O5-galactosyl-L-hydroxylysine." [PMID:743239, PubMed:17516569, UniMod:907] +def: "A protein modification that effectively converts a 5-hydroxy-L-lysine residue to O5-galactosyl-L-hydroxylysine." [PMID:743239, PubMed:17516569, Unimod:907] comment: Secondary to RESID:AA0028. This intermediate is rarely observed [JSG]. subset: PSI-MOD-slim -synonym: "Galactosyl hydroxylysine" RELATED UniMod-description [] +synonym: "Galactosyl hydroxylysine" RELATED Unimod-description [] synonym: "OGal5HyLys" EXACT PSI-MOD-label [] -xref: DiffAvg: "178.14" -xref: DiffFormula: "C 6 H 10 N 0 O 6" -xref: DiffMono: "178.047738" +synonym: "CARBOHYD O-linked (Gal) hydroxylysine" EXACT UniProt-feature [] +xref: DiffAvg: "162.14" +xref: DiffFormula: "C 6 H 10 O 5" +xref: DiffMono: "162.052823" xref: Formula: "C 16 H 22 N 2 O 7" xref: MassAvg: "354.36" xref: MassMono: "354.142701" -xref: Origin: "K" +xref: Origin: "MOD:00037" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00037 ! 5-hydroxy-L-lysine +xref: Unimod: "Unimod:907" +xref: UniProt: "PTM-0556" +is_a: MOD:00476 ! monogalactosylated residue is_a: MOD:00396 ! O-glycosylated residue -is_a: MOD:00476 ! galactosylated residue [Term] id: MOD:01915 @@ -36757,7 +38067,7 @@ name: O4'-(N-acetylamino)galactosyl-L-tyrosine def: "A protein modification that effectively converts an L-tyrosine residue to O4'-(N-acetylamino)galactosyl-L-tyrosine." [PubMed:21712440, PubMed:21983924, RESID:AA0577] synonym: "(2S)-2-amino-3-(D-2-acetamido-2-deoxygalactopyranosyloxy)phenylpropanoic acid" EXACT RESID-systematic [] -synonym: "CARBOHYD O-linked (GalNAc)" EXACT UniProt-feature [] +synonym: "CARBOHYD O-linked (GalNAc) tyrosine" EXACT UniProt-feature [] synonym: "mucin type O-glycosyltyrosine" EXACT RESID-alternate [] synonym: "O4'-(N-acetylamino)galactosyl-L-tyrosine" EXACT RESID-name [] synonym: "O4'-(N-acetylgalactosaminyl)tyrosine" EXACT RESID-alternate [] @@ -36771,7 +38081,8 @@ xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00563 ! N-acetylaminogalactosylated residue +xref: UniProt: "PTM-0570" +is_a: MOD:00563 ! mono-N-acetylaminogalactosylated residue is_a: MOD:01927 ! O-glycosyl-L-tyrosine [Term] @@ -36795,8 +38106,10 @@ xref: Origin: "D, K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +xref: UniProt: "PTM-0486" +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:01929 ! N6-(L-isoaspartyl)-L-lysine +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01918 @@ -36820,12 +38133,13 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0472" is_a: MOD:00037 ! 5-hydroxy-L-lysine [Term] id: MOD:01919 name: (2S,3S)-3-hydroxyaspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to (2S,3S)-3-hydroxyaspartic acid." [ChEBI:10696, PubMed:21177872, RESID:AA0579] +def: "A protein modification that effectively converts an L-aspartic acid residue to (2S,3S)-3-hydroxyaspartic acid." [ChEBI:10696, PubMed:21177872, RESID:AA0579, ChEBI:138111] subset: PSI-MOD-slim synonym: "(2S,3S)-2-amino-3-hydroxybutanedioic acid" EXACT RESID-systematic [] synonym: "(2S,3S)-3-hydroxyaspartic acid" EXACT RESID-name [] @@ -36845,15 +38159,16 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0473" is_a: MOD:01926 ! 3-hydroxy-L-aspartic acid [Term] id: MOD:01920 name: 3-hydroxy-L-histidine -def: "A protein modification that effectively converts an L-histidine residue to 3-hydroxy-L-histidine." [PubMed:21251231, RESID:AA0580] +def: "A protein modification that effectively converts an L-histidine residue to 3-hydroxy-L-histidine." [PubMed:21251231, RESID:AA0580, ChEBI:138021] synonym: "(2S)-2-amino-3-hydroxy-3-(1H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3-hydroxy-L-histidine" EXACT RESID-name [] -synonym: "MOD_RES 3-hydroxyhistidine" EXACT UniProt-feature [] +synonym: "MOD_RES (3S)-3-hydroxyhistidine" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -36863,6 +38178,8 @@ xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0477" +is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:00677 ! hydroxylated residue [Term] @@ -36925,7 +38242,7 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01875 ! N6-acylated L-lysine @@ -36974,12 +38291,13 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0471" is_a: MOD:00037 ! 5-hydroxy-L-lysine [Term] id: MOD:01926 name: 3-hydroxy-L-aspartic acid -def: "A protein modification that effectively converts an L-aspartic acid residue to one of the diastereomeric 3-hydroxy-L-aspartic acid residues." [OMSSA:59, UniMod:35#D] +def: "A protein modification that effectively converts an L-aspartic acid residue to one of the diastereomeric 3-hydroxy-L-aspartic acid residues." [OMSSA:59, Unimod:35#D] subset: PSI-MOD-slim synonym: "(2S)-2-amino-3-hydroxybutanedioic acid" EXACT PSI-MOD-alternate [] synonym: "(2S)-3-hydroxyaspartic acid" EXACT PSI-MOD-alternate [] @@ -36997,6 +38315,7 @@ xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:35" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00904 ! modified L-aspartic acid residue @@ -37034,7 +38353,7 @@ xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00688 ! isopeptide crosslinked residues -is_a: MOD:00908 ! modified glycine residue +is_a: MOD:02047 ! crosslinked glycine residue [Term] id: MOD:01929 @@ -37128,7 +38447,7 @@ xref: Origin: "K, K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00912 ! modified L-lysine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] @@ -37149,7 +38468,7 @@ xref: Origin: "K, K, K, K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00912 ! modified L-lysine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01425 ! pyridinyl ring crosslinked residues [Term] @@ -37170,7 +38489,7 @@ xref: Origin: "K, K, K, K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00912 ! modified L-lysine residue +is_a: MOD:02051 ! crosslinked L-lysine residue is_a: MOD:01425 ! pyridinyl ring crosslinked residues [Term] @@ -37179,6 +38498,7 @@ def: "modification from RESID" [PubMed:22045808, RESID:AA0589] synonym: "(D-glucopyranosyl)oxy-L-lysine" EXACT RESID-systematic [] synonym: "O-glucosyl-L-hydroxylysine" EXACT RESID-name [] +synonym: "CARBOHYD O-linked (Glc) hydroxylysine" EXACT UniProt-feature [] xref: DiffAvg: "178.14" xref: DiffFormula: "C 6 H 10 N 0 O 6" xref: DiffMono: "178.047738" @@ -37188,7 +38508,10 @@ xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:01047 ! monohydroxylated lysine +xref: UniProt: "PTM-0572" +relationship: derives_from MOD:01047 ! monohydroxylated lysine +is_a: MOD:00396 ! O-glycosylated residue +is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01936 @@ -37207,6 +38530,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02011 ! N-oleoylated residue [Term] id: MOD:01937 @@ -37246,8 +38570,9 @@ xref: Origin: "C, N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:01945 ! 2-(2-aminosuccinimidyl)-3-sulfanylpropanoic acid +is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:01939 @@ -37266,8 +38591,9 @@ xref: Origin: "C, D" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:01945 ! 2-(2-aminosuccinimidyl)-3-sulfanylpropanoic acid +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01940 @@ -37286,8 +38612,9 @@ xref: Origin: "E, N" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:02042 ! crosslinked L-asparagine residue is_a: MOD:01946 ! 2-(2-aminosuccinimidyl)pentanedioic acid +is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:01941 @@ -37306,8 +38633,9 @@ xref: Origin: "D, E" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:01946 ! 2-(2-aminosuccinimidyl)pentanedioic acid +is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:01942 @@ -37367,7 +38695,7 @@ xref: Origin: "C, X" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02044 ! crosslinked L-cysteine residue is_a: MOD:01944 ! 2-aminosuccinimide ring crosslinked residues [Term] @@ -37384,7 +38712,7 @@ xref: Origin: "E, X" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02045 ! crosslinked L-glutamic acid residue is_a: MOD:01944 ! 2-aminosuccinimide ring crosslinked residues [Term] @@ -37408,7 +38736,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00904 ! modified L-aspartic acid residue +is_a: MOD:02043 ! crosslinked L-aspartic acid residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01978 ! O-(L-isoaspartyl)-L-threonine @@ -37430,7 +38758,7 @@ xref: Origin: "C, S, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01993 ! beta-carbon thioether crosslinked residues [Term] @@ -37451,8 +38779,8 @@ xref: Source: "hypothetical" xref: TermSpec: "N-term" is_a: MOD:00033 ! crosslinked residues -is_a: MOD:00914 ! modified L-phenylalanine residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02053 ! crosslinked L-phenylalanine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue [Term] id: MOD:01950 @@ -37470,6 +38798,7 @@ xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0488" is_a: MOD:00907 ! modified L-glutamine residue [Term] @@ -37490,13 +38819,13 @@ xref: Origin: "Q, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00907 ! modified L-glutamine residue +is_a: MOD:02046 ! crosslinked L-glutamine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia is_a: MOD:01977 ! O-(L-isoglutamyl)-L-serine [Term] id: MOD:01952 -name: O-(L-isoglutamyl)-L-threonine (cross-link) +name: O-(L-isoglutamyl)-L-threonine (Gln-Thr) def: "A protein modification that effectively cross-links an L-threonine residue and an L-glutamine residue with an ester bond releasing ammonia to form O-(L-isoglutamyl)-L-threonine." [PubMed:17051152, RESID:AA0536#TQX] comment: Cross-link 2. synonym: "(2S)-2-amino-5-([(1S,2R)-1-amino-1-carboxypropan-2-yl]oxy)-5-oxopentanoic acid" EXACT RESID-systematic [] @@ -37514,9 +38843,11 @@ xref: Origin: "Q, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00907 ! modified L-glutamine residue +is_a: MOD:02046 ! crosslinked L-glutamine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01979 ! O-(L-isoglutamyl)-L-threonine +is_a: MOD:00885 ! ester crosslinked residues +is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:01953 @@ -37533,7 +38864,7 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00738 ! iron containing modified residue -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:01954 @@ -37577,11 +38908,11 @@ xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00740 ! manganese containing modified residue -is_a: MOD:00901 ! modified L-alanine residue -is_a: MOD:00904 ! modified L-aspartic acid residue -is_a: MOD:00906 ! modified L-glutamic acid residue -is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01482 ! calcium containing modified residue +is_a: MOD:02065 ! metal or metal cluster coordinated L-alanine residue +is_a: MOD:02066 ! metal or metal cluster coordinated L-aspartic acid residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue +is_a: MOD:02070 ! metal or metal cluster coordinated L-histidine residue [Term] id: MOD:01956 @@ -37604,16 +38935,18 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0476" is_a: MOD:00682 ! hydroxylated arginine [Term] id: MOD:01957 name: 2-hydroxyproline -def: "A protein modification that effectively converts an L-proline residue to 2-hydroxyproline." [PubMed:23385463, RESID:AA0602] +def: "A protein modification that effectively converts an L-proline residue to 2-hydroxyproline." [PubMed:23385463, RESID:AA0602, ChEBI:141809] synonym: "(2R)-2-hydroxypyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "2-hydroxyproline" EXACT RESID-name [] synonym: "2-oxidanylpyrrolidine-2-carboxylic acid" EXACT RESID-alternate [] synonym: "alpha-hydroxyproline" EXACT RESID-alternate [] +synonym: "MOD_RES 2-hydroxyproline" EXACT UniProt-feature [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" @@ -37623,6 +38956,7 @@ xref: Origin: "P" xref: Source: "hypothetical" xref: TermSpec: "none" +xref: UniProt: "PTM-0668" is_a: MOD:01024 ! monohydroxylated proline [Term] @@ -37644,7 +38978,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue [Term] id: MOD:01959 @@ -37663,8 +38997,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00906 ! modified L-glutamic acid residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02068 ! metal or metal cluster coordinated L-glutamic acid residue [Term] id: MOD:01960 @@ -37684,8 +39018,8 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification -is_a: MOD:00905 ! modified L-cysteine residue -is_a: MOD:00907 ! modified L-glutamine residue +is_a: MOD:02067 ! metal or metal cluster coordinated L-cysteine residue +is_a: MOD:02069 ! metal or metal cluster coordinated L-glutamine residue [Term] id: MOD:01961 @@ -37706,6 +39040,7 @@ xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:01785" is_obsolete: true [Term] @@ -37720,6 +39055,7 @@ synonym: "N4-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-asparagine" EXACT RESID-alternate [] synonym: "N4-[N,N-diacetylbacillosaminyl]asparagine" EXACT RESID-alternate [] synonym: "N4-[N2,N4-diacetylbacillosaminyl]asparagine" EXACT RESID-alternate [] +synonym: "CARBOHYD N-linked (DATDGlc) asparagine" EXACT UniProt-feature [] xref: DiffAvg: "228.25" xref: DiffFormula: "C 10 H 16 N 2 O 4" xref: DiffMono: "228.111007" @@ -37729,6 +39065,7 @@ xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0506" is_a: MOD:00160 ! N4-glycosyl-L-asparagine [Term] @@ -37743,6 +39080,7 @@ synonym: "O-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-serine" EXACT RESID-alternate [] synonym: "O-[N,N-diacetylbacillosaminyl]serine" EXACT RESID-alternate [] synonym: "O-[N2,N4-diacetylbacillosaminyl]serine" EXACT RESID-alternate [] +synonym: "CARBOHYD O-linked (DATDGlc) serine" EXACT UniProt-feature [] xref: DiffAvg: "228.25" xref: DiffFormula: "C 10 H 16 N 2 O 4" xref: DiffMono: "228.111007" @@ -37752,6 +39090,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0548" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] @@ -37763,6 +39102,7 @@ synonym: "O-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucosyl)-L-serine" EXACT RESID-name [] synonym: "O-(N2-acetyl-N4-glycerylbacillosaminyl)-L-serine" EXACT RESID-alternate [] +synonym: "CARBOHYD O-linked (GATDGlc) serine" EXACT UniProt-feature [] xref: DiffAvg: "274.27" xref: DiffFormula: "C 11 H 18 N 2 O 6" xref: DiffMono: "274.116486" @@ -37772,6 +39112,7 @@ xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0549" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] @@ -37789,7 +39130,7 @@ xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" -is_a: MOD:00064 ! N6-acetyl-L-lysine +relationship: derives_from MOD:00064 ! N6-acetyl-L-lysine is_a: MOD:01428 ! (13)C isotope tagged reagent is_a: MOD:01431 ! (2)H deuterium tagged reagent @@ -37810,6 +39151,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: Remap: "MOD:00720" is_obsolete: true [Term] @@ -37827,6 +39169,7 @@ synonym: "omega-N-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginine" EXACT RESID-alternate [] synonym: "omega-N-(2-N-acetylaminoglucosyl)arginine" EXACT RESID-alternate [] synonym: "omega-N-(N-acetylamino)glucosyl-L-arginine" EXACT RESID-name [] +synonym: "CARBOHYD N-linked (GlcNAc) arginine" EXACT UniProt-feature [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" @@ -37836,7 +39179,8 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00448 ! N-acetylaminoglucosylated residue +xref: UniProt: "PTM-0518" +is_a: MOD:00448 ! mono-N-acetylaminoglucosylated residue is_a: MOD:01980 ! omega-N-glycosyl-L-arginine [Term] @@ -37886,17 +39230,17 @@ [Term] id: MOD:01970 name: 5-glutamyl glutamic acid -def: "A protein modification that effectively converts an L-glutamic acid residue to 5-glutamyl glutamic acid, forming an isopeptide bond with a free glutamic acid." [PubMed:10747868, PubMed:15525938, PubMed:1680872, PubMed:23434852, RESID:AA0612, UniMod:450] +def: "A protein modification that effectively converts an L-glutamic acid residue to 5-glutamyl glutamic acid, forming an isopeptide bond with a free glutamic acid." [PubMed:10747868, PubMed:15525938, PubMed:1680872, PubMed:23434852, RESID:AA0612, Unimod:450] synonym: "(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanedioic acid" EXACT RESID-systematic [] synonym: "(2S)-2-[(4S)-4-amino-4-carboxybutanamido]pentanedioic acid" EXACT RESID-alternate [] synonym: "2-([4-azanyl-4-carboxybutanoyl]azanyl)pentanedioic acid" EXACT RESID-alternate [] synonym: "5-glutamyl glutamic acid" EXACT RESID-name [] synonym: "gamma-glutamylglutamate" EXACT RESID-alternate [] -synonym: "Glu" RELATED UniMod-interim [] +synonym: "Glu" RELATED Unimod-interim [] synonym: "isoglutamyl glutamic acid" EXACT RESID-alternate [] synonym: "isoglutamyl monoglutamic acid" EXACT RESID-alternate [] synonym: "MOD_RES 5-glutamyl glutamate" EXACT UniProt-feature [] -synonym: "monoglutamyl" RELATED UniMod-description [] +synonym: "monoglutamyl" RELATED Unimod-description [] synonym: "N alpha -(gamma-Glutamyl)-Glu" EXACT DeltaMass-label [] synonym: "N-(gamma-L-glutamyl)-L-glutamic acid" EXACT RESID-alternate [] xref: DiffAvg: "129.12" @@ -37908,12 +39252,14 @@ xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:450" +xref: UniProt: "PTM-0479" is_a: MOD:00207 ! L-isoglutamyl-polyglutamic acid [Term] id: MOD:01971 name: 5-glutamyl N2-ornithine -def: "A protein modification that effectively converts an L-glutamic acid residue to N2-ornithine." [PubMed:23434852, RESID:AA0613] +def: "A protein modification that effectively converts an L-glutamic acid residue to N2-ornithine." [PubMed:23434852, RESID:AA0613, ChEBI:136763] synonym: "(2S)-5-amino-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanoic acid" EXACT RESID-alternate [] synonym: "(2S)-5-amino-2-[(4S)-4-amino-4-carboxybutanamido]pentanoic acid" EXACT RESID-systematic [] synonym: "4-amino-5-[(4-amino-1-carboxy-butyl)amino]-5-ketovaleric acid" EXACT RESID-alternate [] @@ -37932,7 +39278,7 @@ xref: Origin: "E" xref: Source: "hypothetical" xref: TermSpec: "none" -is_a: MOD:00674 ! amidated residue +xref: UniProt: "PTM-0478" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] @@ -37998,6 +39344,7 @@ xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0636" is_a: MOD:00716 ! methylated methionine [Term] @@ -38012,15 +39359,11 @@ synonym: "S-poly(3-hydroxybutyric acid)cysteine" EXACT RESID-alternate [] synonym: "S-poly(beta-hydroxybutyrate)cysteine" EXACT RESID-alternate [] synonym: "S-poly[(R)-3-hydroxybutyrate]cysteine" EXACT RESID-alternate [] -xref: DiffAvg: "172.18" -xref: DiffFormula: "C 8 H 12 N 0 O 4 S 0" -xref: DiffMono: "172.073559" -xref: Formula: "C 11 H 17 N 1 O 5 S 1" -xref: MassAvg: "275.32" -xref: MassMono: "275.082744" +synonym: "MOD_RES S-poly(beta-hydroxybutyryl)lysine" EXACT UniProt-feature [] xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0641" is_a: MOD:00672 ! S-acylated residue is_a: MOD:00905 ! modified L-cysteine residue @@ -38037,15 +39380,11 @@ synonym: "O3-poly(3-hydroxybutyric acid)serine" EXACT RESID-alternate [] synonym: "O3-poly(beta-hydroxybutyrate)serine" EXACT RESID-alternate [] synonym: "O3-poly[(R)-3-hydroxybutyrate]serine" EXACT RESID-alternate [] -xref: DiffAvg: "172.18" -xref: DiffFormula: "C 8 H 12 N 0 O 4" -xref: DiffMono: "172.073559" -xref: Formula: "C 11 H 17 N 1 O 6" -xref: MassAvg: "259.26" -xref: MassMono: "259.105587" +synonym: "MOD_RES O3-poly(beta-hydroxybutyryl)lysine" EXACT UniProt-feature [] xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" +xref: UniProt: "PTM-0640" is_a: MOD:00671 ! O-acylated residue is_a: MOD:00916 ! modified L-serine residue @@ -38069,7 +39408,7 @@ xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:00885 ! ester crosslinked residues -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02055 ! crosslinked L-serine residue [Term] id: MOD:01978 @@ -38091,7 +39430,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue [Term] id: MOD:01979 @@ -38114,15 +39453,15 @@ xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue [Term] id: MOD:01980 name: omega-N-glycosyl-L-arginine -def: "A protein modification that effectively converts an L-arginine residue to N4-glycosyl-arginine." [PubMed:15279557, PubMed:8521968, PubMed:9536051, RESID:AA0327, UniMod:41#R] +def: "A protein modification that effectively converts an L-arginine residue to N4-glycosyl-arginine." [PubMed:15279557, PubMed:8521968, PubMed:9536051, RESID:AA0327, Unimod:41#R] synonym: "(2S)-2-amino-5-(beta-D-glucopyranosyl[imino(methylamino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] -synonym: "Hexose" RELATED UniMod-description [] +synonym: "Hexose" RELATED Unimod-description [] synonym: "NG-beta-D-glucosylarginine" EXACT RESID-alternate [] synonym: "omega-N-(beta-D-glucosyl)-L-arginine" EXACT RESID-alternate [] synonym: "omega-N-glucosyl-L-arginine" EXACT RESID-name [] @@ -38130,6 +39469,7 @@ xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" +xref: Unimod: "Unimod:41" is_a: MOD:00006 ! N-glycosylated residue is_a: MOD:00902 ! modified L-arginine residue @@ -38153,7 +39493,7 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water is_a: MOD:01993 ! beta-carbon thioether crosslinked residues @@ -38176,12 +39516,14 @@ xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0" xref: DiffMono: "43.054775" +xref: FormalCharge: "1+" xref: Formula: "C 5 H 11 N 1 O 1" xref: MassAvg: "101.15" xref: MassMono: "101.084064" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0485" is_a: MOD:00714 ! methylated glycine is_a: MOD:01698 ! alpha-amino trimethylated protonated-residue @@ -38203,6 +39545,7 @@ xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" +xref: UniProt: "PTM-0484" is_a: MOD:00714 ! methylated glycine is_a: MOD:01686 ! alpha-amino dimethylated residue @@ -38223,7 +39566,7 @@ xref: Origin: "A, C" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00901 ! modified L-alanine residue +is_a: MOD:02040 ! crosslinked L-alanine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38243,7 +39586,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue -is_a: MOD:00903 ! modified L-asparagine residue +is_a: MOD:02060 ! crosslinked D-asparagine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38262,7 +39605,7 @@ xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02055 ! crosslinked L-serine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38282,7 +39625,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue -is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:02064 ! crosslinked D-serine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38302,7 +39645,7 @@ xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" -is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:02056 ! crosslinked L-threonine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38323,7 +39666,7 @@ xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue -is_a: MOD:00919 ! modified L-tyrosine residue +is_a: MOD:02058 ! crosslinked L-tyrosine residue is_a: MOD:01992 ! alpha-carbon thioether crosslinked residues [Term] @@ -38417,7 +39760,7 @@ def: "A protein modification that effectively replaces a hydrogen atom with an butanoyl group." [PubMed:18688235] comment: Amino hydrogens are replaced to produce amides; hydroxyl hydrogens are replaced to produce esters; and hydrosulfanyl (thiol) hydrogens are replaced to produce sulfanyl esters (thiol esters). synonym: "ButRes" EXACT PSI-MOD-label [] -synonym: "Butyryl" RELATED UniMod-interim [] +synonym: "Butyryl" RELATED Unimod-interim [] synonym: "butyrylation" EXACT PSI-MOD-alternate [] xref: DiffAvg: "70.09" xref: DiffFormula: "C 4 H 6 O 1" @@ -38498,6 +39841,1328 @@ xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue +[Term] +id: MOD:02001 +name: stearoylated residue +def: "A protein modification that effectively replaces a hydrogen atom with a stearoyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "266.47" +xref: DiffFormula: "C 18 H 34 O 1" +xref: DiffMono: "266.260966" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02002 +name: S-palmitoleylated residue +def: "A protein modification that effectively replaces a residue sulfanyl group with a palmitoleylsulfanyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "236.40" +xref: DiffFormula: "C 16 H 28 N 0 O 1" +xref: DiffMono: "236.214016" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00672 ! S-acylated residue +is_a: MOD:01423 ! palmitoleylated residue + +[Term] +id: MOD:02003 +name: O3-acylated L-serine +def: "A protein modification that effectively replaces an O3-hydroxy hydrogen atom of L-serine with an acyl group." [] +subset: PSI-MOD-slim +xref: Origin: "S" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00671 ! O-acylated residue +is_a: MOD:00916 ! modified L-serine residue + +[Term] +id: MOD:02004 +name: O3-acylated L-threonine +def: "A protein modification that effectively replaces an O3-hydroxy hydrogen atom of L-threonine with an acyl group." [] +subset: PSI-MOD-slim +xref: Origin: "T" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00671 ! O-acylated residue +is_a: MOD:00917 ! modified L-threonine residue + +[Term] +id: MOD:02005 +name: S-acylated L-cysteine +def: "A protein modification that effectively replaces an sulfanyl hydrogen atom of L-cysteine with an acyl group." [] +subset: PSI-MOD-slim +xref: Origin: "C" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00672 ! S-acylated residue +is_a: MOD:00905 ! modified L-cysteine residue + +[Term] +id: MOD:02006 +name: S-stearoylated residue +def: "A protein modification that effectively replaces a residue sulfanyl group with a stearoylsulfanyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "266.47" +xref: DiffFormula: "C 18 H 34 O 1" +xref: DiffMono: "266.260966" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00672 ! S-acylated residue +is_a: MOD:02001 ! stearoylated residue + +[Term] +id: MOD:02007 +name: N6-palmitoleyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-palmitoleyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "236.40" +xref: DiffFormula: "C 16 H 28 N 0 O 1" +xref: DiffMono: "236.214016" +xref: Formula: "C 22 H 40 N 2 O 2" +xref: MassAvg: "364.58" +xref: MassMono: "364.308979" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02008 ! N-palmitoleylated residue + +[Term] +id: MOD:02008 +name: N-palmitoleylated residue +def: "A protein modification that effectively replaces a residue amino group with a palmitoleylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "236.40" +xref: DiffFormula: "C 16 H 28 N 0 O 1" +xref: DiffMono: "236.214016" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:01423 ! palmitoleylated residue + +[Term] +id: MOD:02009 +name: N6-stearoyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-stearoyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "266.47" +xref: DiffFormula: "C 18 H 34 O 1" +xref: DiffMono: "266.260966" +xref: Formula: "C 24 H 46 N 2 O 2" +xref: MassAvg: "394.65" +xref: MassMono: "394.355929" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02010 ! N-stearoylated residue + +[Term] +id: MOD:02010 +name: N-stearoylated residue +def: "A protein modification that effectively replaces a residue amino group with a stearoylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "266.47" +xref: DiffFormula: "C 18 H 34 O 1" +xref: DiffMono: "266.260966" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02001 ! stearoylated residue + +[Term] +id: MOD:02011 +name: N-oleoylated residue +def: "A protein modification that effectively replaces a residue amino group with a oleoylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "264.45" +xref: DiffFormula: "C 18 H 32 N 0 O 1" +xref: DiffMono: "264.245316" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02012 ! oleoylated residue + +[Term] +id: MOD:02012 +name: oleoylated residue +def: "A protein modification that effectively replaces a hydrogen atom with a oleoyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "264.45" +xref: DiffFormula: "C 18 H 32 N 0 O 1" +xref: DiffMono: "264.245316" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02013 +name: N6-linoloyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-linoloyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "262.45" +xref: DiffFormula: "C 18 H 30 N 0 O 1" +xref: DiffMono: "262.229666" +xref: Formula: "C 24 H 42 N 2 O 2" +xref: MassAvg: "390.63" +xref: MassMono: "390.324629" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02014 ! N-linoloylated residue + +[Term] +id: MOD:02014 +name: N-linoloylated residue +def: "A protein modification that effectively replaces a residue amino group with a linoloylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "262.45" +xref: DiffFormula: "C 18 H 30 N 0 O 1" +xref: DiffMono: "262.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02015 ! linoloylated residue + +[Term] +id: MOD:02015 +name: linoloylated residue +def: "A protein modification that effectively replaces a hydrogen atom with a linoloyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "262.45" +xref: DiffFormula: "C 18 H 30 N 0 O 1" +xref: DiffMono: "262.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02016 +name: N6-arachidonoyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-arachidonoyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "286.49" +xref: DiffFormula: "C 20 H 30 N 0 O 1" +xref: DiffMono: "286.229666" +xref: Formula: "C 26 H 42 N 2 O 2" +xref: MassAvg: "414.67" +xref: MassMono: "414.324629" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02017 ! N-arachidonoylated residue + +[Term] +id: MOD:02017 +name: N-arachidonoylated residue +def: "A protein modification that effectively replaces a residue amino group with an arachidonoylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "286.49" +xref: DiffFormula: "C 20 H 30 N 0 O 1" +xref: DiffMono: "286.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02018 ! arachidonoylated residue + +[Term] +id: MOD:02018 +name: arachidonoylated residue +def: "A protein modification that effectively replaces a hydrogen atom with an arachidonoyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "286.49" +xref: DiffFormula: "C 20 H 30 N 0 O 1" +xref: DiffMono: "286.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02019 +name: N6-timnodonoyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-timnodonoyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "284.48" +xref: DiffFormula: "C 20 H 28 N 0 O 1" +xref: DiffMono: "284.214016" +xref: Formula: "C 26 H 40 N 2 O 2" +xref: MassAvg: "412.66" +xref: MassMono: "412.308979" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02020 ! N-timnodonoylated residue + +[Term] +id: MOD:02020 +name: N-timnodonoylated residue +def: "A protein modification that effectively replaces a residue amino group with a timnodonoylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "284.48" +xref: DiffFormula: "C 20 H 28 N 0 O 1" +xref: DiffMono: "284.214016" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02021 ! timnodonoylated residue + +[Term] +id: MOD:02021 +name: timnodonoylated residue +def: "A protein modification that effectively replaces a hydrogen atom with a timnodonoyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "284.48" +xref: DiffFormula: "C 20 H 28 N 0 O 1" +xref: DiffMono: "284.214016" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02022 +name: N6-cervonoyl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-cervonoyl-L-lysine." [] +subset: PSI-MOD-slim +xref: DiffAvg: "310.53" +xref: DiffFormula: "C 22 H 30 N 0 O 1" +xref: DiffMono: "310.229666" +xref: Formula: "C 28 H 42 N 2 O 2" +xref: MassAvg: "438.71" +xref: MassMono: "438.324629" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:01875 ! N6-acylated L-lysine +is_a: MOD:02023 ! N-cervonoylated residue + +[Term] +id: MOD:02023 +name: N-cervonoylated residue +def: "A protein modification that effectively replaces a residue amino group with a cervonoylamino group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "310.53" +xref: DiffFormula: "C 22 H 30 N 0 O 1" +xref: DiffMono: "310.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00670 ! N-acylated residue +is_a: MOD:02024 ! cervonoylated residue + +[Term] +id: MOD:02024 +name: cervonoylated residue +def: "A protein modification that effectively replaces a hydrogen atom with a cervonoyl group." [] +subset: PSI-MOD-slim +xref: DiffAvg: "310.53" +xref: DiffFormula: "C 22 H 30 N 0 O 1" +xref: DiffMono: "310.229666" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue +is_a: MOD:01155 ! lipoconjugated residue + +[Term] +id: MOD:02025 +name: 5-glutaminyl glutamic acid +def: "A protein modification that effectively converts the alpha amino group of a glutamine residue to glutaminyl glutamic acid by forming an isopeptide bond with the side chain carboxyl group of a free glutamic acid." [PubMed:28801462] +xref: DiffAvg: "128.13" +xref: DiffFormula: "C 5 H 8 N 2 O 2" +xref: DiffMono: "128.058576" +xref: Formula: "C 10 H 15 N 3 O 5" +xref: MassAvg: "257.24" +xref: MassMono: "257.101167" +xref: Origin: "E" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00906 ! modified L-glutamic acid residue + +[Term] +id: MOD:02026 +name: S-(cysteinyl-glycyl)-L-cysteine +def: "A protein modification that effectively cross-links an L-cysteinyl-L-glycine dipeptide and an L-cysteine residue by a disulfide bond to form S-(cysteinyl-glycyl)-L-cysteine." [PubMed:27936627, PubMed:20594348, PubMed:29627744] +comment: Glutamyl-transpeptidase cleaves glutathione into cysteinylglycine (Cys-Gly) and a Glu residue. [PubMed:28537416] +xref: DiffAvg: "176.17" +xref: DiffFormula: "C 5 H 8 N 2 O 3 S 1" +xref: DiffMono: "176.025563" +xref: Formula: "C 8 H 13 N 3 O 4 S 2" +xref: MassAvg: "279.33" +xref: MassMono: "279.034748" +xref: Origin: "C" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:01862 ! disulfide conjugated residue +relationship: part_of MOD:00234 ! L-cysteine glutathione disulfide + +[Term] +id: MOD:02027 +name: urmylated lysine +def: "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a URM1 protein." [PubMed:10713047, PubMed:21209336] +subset: PSI-MOD-slim +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:02047 ! crosslinked glycine residue +is_a: MOD:02051 ! crosslinked L-lysine residue +is_a: MOD:01875 ! N6-acylated L-lysine +relationship: contains MOD:00134 ! N6-glycyl-L-lysine + +[Term] +id: MOD:02028 +name: iTRAQ4plex reporter+balance reagent acylated residue, average mass modification +def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [Unimod:214] +comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. Four versions of chemically identical iTRAQ4plex moyeties, but with different isotope distribution. This modification is calculated as the average of the four species. It has no isotopic distribution reality, the exact mass does not correspond to any real isotopic distribution. +subset: PSI-MOD-slim +synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate [] +synonym: "iTRAQ" RELATED Unimod-interim [] +xref: DiffAvg: "144.10" +xref: DiffFormula: "none" +xref: DiffMono: "144.102411" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "artifact" +xref: TermSpec: "none" +is_a: MOD:01426 ! isotope tagged reagent derivatized residue +is_a: MOD:01705 ! isotope tagged reagent acylated residue +is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue +is_a: MOD:01513 ! modifications with monoisotopic mass differences that are nominally equal at a resolution below 0.1 Da + +[Term] +id: MOD:02029 +name: cis-peptidyl-L-proline +def: "A protein modification that effectively specifies the boundary conformation of two adjacent source amino acid residues, the second (C-term side) being a L-proline, where the carbonyl group of the amide bond of the N-side of the L-proline is positioned such that the organodiyl group is in the cis orientation (omega=0)" [ChEBI:83833, PubMed:15735342, PubMed:15311922, PubMed:24116866, PubMed:5485910] +xref: DiffAvg: "0.00" +xref: DiffFormula: "C 0 H 0 N 0 O 0" +xref: DiffMono: "0.000000" +xref: Origin: "X, P" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00915 ! modified L-proline residue + +[Term] +id: MOD:02030 +name: trans-peptidyl-L-proline +def: "A protein modification that effectively specifies the boundary conformation of two adjacent source amino acid residues, the second (C-term side) being a L-proline, where the carbonyl group of the amide bond of the N-side of the L-proline is positioned such that the organodiyl group is in the trans orientation (omega=180)" [ChEBI:83834, PubMed:15735342, PubMed:15311922, PubMed:24116866, PubMed:5485910] +xref: DiffAvg: "0.00" +xref: DiffFormula: "C 0 H 0 N 0 O 0" +xref: DiffMono: "0.000000" +xref: Origin: "X, P" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00915 ! modified L-proline residue + +[Term] +id: MOD:02031 +name: dHex1Hex4HexNAc5 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex Hex(4) HexNAc(5)" [PubMed:33135055, Unimod:1519] +synonym: "dHex Hex(4) HexNAc(5)" RELATED Unimod-description [] +xref: DiffAvg: "1810.68" +xref: DiffFormula: "C 70 H 115 N 5 O 49" +xref: DiffMono: "1809.666065" +xref: Formula: "C 74 H 121 N 7 O 51" +xref: MassAvg: "1924.78" +xref: MassMono: "1923.708993" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1519" +xref: GNOme: "GNO:G03382KH" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02032 +name: dHex2Hex4HexNAc5 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex(2) Hex(4) HexNAc(5)" [PubMed:33135055, Unimod:1785] +synonym: "dHex(2) Hex(4) HexNAc(5)" RELATED Unimod-description [] +xref: DiffAvg: "1956.82" +xref: DiffFormula: "C 76 H 125 N 5 O 53" +xref: DiffMono: "1955.723974" +xref: Formula: "C 80 H 131 N 7 O 55" +xref: MassAvg: "2070.92" +xref: MassMono: "2069.766901" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1785" +xref: GNOme: "GNO:G70418MS" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02033 +name: dHex1Hex5HexNAc3 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex Hex(5) HexNAc(3)" [PubMed:33135055, Unimod:1484] +synonym: "dHex Hex(5) HexNAc(3)" RELATED Unimod-description [] +xref: DiffAvg: "1566.43" +xref: DiffFormula: "C 60 H 99 N 3 O 44" +xref: DiffMono: "1565.560143" +xref: Formula: "C 64 H 105 N 5 O 46" +xref: MassAvg: "1680.53" +xref: MassMono: "1679.603071" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1484" +xref: GNOme: "GNO:G82119TF" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02034 +name: dHex1Hex3HexNAc6 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex Hex(3) HexNAc(6)" [PubMed:33135055, Unimod:1781] +synonym: "dHex Hex(3) HexNAc(6)" RELATED Unimod-description [] +xref: DiffAvg: "1851.73" +xref: DiffFormula: "C 72 H 118 N 6 O 49" +xref: DiffMono: "1850.692614" +xref: Formula: "C 76 H 124 N 8 O 51" +xref: MassAvg: "1965.83" +xref: MassMono: "1964.735542" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1781" +xref: GNOme: "GNO:G50757KG" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02035 +name: dHex1Hex6HexNAc3 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, dHex Hex(6) HexNAc(3)" [PubMed:33135055, Unimod:1509] +synonym: "dHex Hex(6) HexNAc(3)" RELATED Unimod-description [] +xref: DiffAvg: "1728.57" +xref: DiffFormula: "C 66 H 109 N 3 O 49" +xref: DiffMono: "1727.612967" +xref: Formula: "C 70 H 115 N 5 O 51" +xref: MassAvg: "1842.67" +xref: MassMono: "1841.655894" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1509" +xref: GNOme: "GNO:G84820NF" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02036 +name: Hex9HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, Hex(9)HexNAc(2)" [PubMed:33135055, Unimod:1531] +synonym: "M9/Man9" RELATED Unimod-description [] +xref: DiffAvg: "1865.66" +xref: DiffFormula: "C 70 H 116 N 2 O 55" +xref: DiffMono: "1864.634156" +xref: Formula: "C 74 H 122 N 4 O 57" +xref: MassAvg: "1979.76" +xref: MassMono: "1978.677083" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1531" +xref: GNOme: "GNO:G70101JE" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02037 +name: Hex7HexNAc2 N4-glycosylated asparagine +def: "modification from Unimod N-linked glycosylation, Hex(7) HexNAc(2)" [PubMed:33135055, Unimod:1480] +synonym: "M7/Man7" RELATED Unimod-description [] +xref: DiffAvg: "1541.38" +xref: DiffFormula: "C 58 H 96 N 2 O 45" +xref: DiffMono: "1540.528509" +xref: Formula: "C 62 H 102 N 4 O 47" +xref: MassAvg: "1655.48" +xref: MassMono: "1654.571436" +xref: MassMono: "1654.571436" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1480" +xref: GNOme: "GNO:G05724UK" +is_a: MOD:00725 ! complex glycosylation +is_a: MOD:00160 ! N4-glycosyl-L-asparagine + +[Term] +id: MOD:02038 +name: monomethylated L-histidine +def: "A protein modification that effectively replaces one hydrogen atom of an L-histidine residue with one methyl group." [DeltaMass:215, OMSSA:77, Unimod:34#H] +subset: PSI-MOD-slim +synonym: "Me1His" EXACT PSI-MOD-label [] +synonym: "Methyl" RELATED PSI-MS-label [] +synonym: "methylh" EXACT OMSSA-label [] +synonym: "MOD_RES Methylhistidine" EXACT UniProt-feature [] +xref: DiffAvg: "14.03" +xref: DiffFormula: "C 1 H 2 N 0 O 0" +xref: DiffMono: "14.015650" +xref: Formula: "C 7 H 9 N 3 O 1" +xref: MassAvg: "151.17" +xref: MassMono: "151.074562" +xref: Origin: "H" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:34" +xref: UniProt: "PTM-0176" +is_a: MOD:00599 ! monomethylated residue +is_a: MOD:00661 ! methylated histidine + +[Term] +id: MOD:02039 +name: aminated residue +def: "A protein modification that effectively replaces a hydrogen group with a amino group" [] +synonym: "AmRes" EXACT PSI-MOD-label [] +xref: Origin: "X" +xref: Source: "none" +xref: TermSpec: "none" +is_a: MOD:01156 ! protein modification categorized by chemical process + +[Term] +id: MOD:02040 +name: crosslinked L-alanine residue +def: "A protein modification that contains an L-alanine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkAla" EXACT PSI-MOD-label [] +xref: Origin: "A" +is_a: MOD:00901 ! modified L-alanine residue + +[Term] +id: MOD:02041 +name: crosslinked L-arginine residue +def: "A protein modification that contains an L-arginine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkArg" EXACT PSI-MOD-label [] +xref: Origin: "R" +is_a: MOD:00902 ! modified L-arginine residue + +[Term] +id: MOD:02042 +name: crosslinked L-asparagine residue +def: "A protein modification that contains an L-asparagine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkAsn" EXACT PSI-MOD-label [] +xref: Origin: "N" +is_a: MOD:00903 ! modified L-asparagine residue + +[Term] +id: MOD:02043 +name: crosslinked L-aspartic acid residue +def: "A protein modification that contains an L-aspartic acid residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkAsp" EXACT PSI-MOD-label [] +xref: Origin: "D" +is_a: MOD:00904 ! modified L-aspartic acid residue + +[Term] +id: MOD:02044 +name: crosslinked L-cysteine residue +def: "A protein modification that contains an L-cysteine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkCys" EXACT PSI-MOD-label [] +xref: Origin: "C" +is_a: MOD:00905 ! modified L-cysteine residue + +[Term] +id: MOD:02045 +name: crosslinked L-glutamic acid residue +def: "A protein modification that contains an L-glutamic acid residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkGlu" EXACT PSI-MOD-label [] +xref: Origin: "E" +is_a: MOD:00906 ! modified L-glutamic acid residue + +[Term] +id: MOD:02046 +name: crosslinked L-glutamine residue +def: "A protein modification that contains an L-glutamine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkGln" EXACT PSI-MOD-label [] +xref: Origin: "Q" +is_a: MOD:00907 ! modified L-glutamine residue + +[Term] +id: MOD:02047 +name: crosslinked glycine residue +def: "A protein modification that contains a glycine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkGly" EXACT PSI-MOD-label [] +xref: Origin: "G" +is_a: MOD:00908 ! modified glycine residue + +[Term] +id: MOD:02048 +name: crosslinked L-histidine residue +def: "A protein modification that contains an L-histidine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkHis" EXACT PSI-MOD-label [] +xref: Origin: "H" +is_a: MOD:00909 ! modified L-histidine residue + +[Term] +id: MOD:02049 +name: crosslinked L-isoleucine residue +def: "A protein modification that contains an L-isoleucine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkIle" EXACT PSI-MOD-label [] +xref: Origin: "I" +is_a: MOD:00910 ! modified L-isoleucine residue + +[Term] +id: MOD:02050 +name: crosslinked L-leucine residue +def: "A protein modification that contains an L-leucine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkLeu" EXACT PSI-MOD-label [] +xref: Origin: "L" +is_a: MOD:00911 ! modified L-leucine residue + +[Term] +id: MOD:02051 +name: crosslinked L-lysine residue +def: "A protein modification that contains an L-lysine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkLys" EXACT PSI-MOD-label [] +xref: Origin: "K" +is_a: MOD:00912 ! modified L-lysine residue + +[Term] +id: MOD:02052 +name: crosslinked L-methionine residue +def: "A protein modification that contains an L-methionine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkMet" EXACT PSI-MOD-label [] +xref: Origin: "M" +is_a: MOD:00913 ! modified L-methionine residue + +[Term] +id: MOD:02053 +name: crosslinked L-phenylalanine residue +def: "A protein modification that contains an L-phenylalanine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkPhe" EXACT PSI-MOD-label [] +xref: Origin: "F" +is_a: MOD:00914 ! modified L-phenylalanine residue + +[Term] +id: MOD:02054 +name: crosslinked L-proline residue +def: "A protein modification that contains an L-proline residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkPro" EXACT PSI-MOD-label [] +xref: Origin: "P" +is_a: MOD:00915 ! modified L-proline residue + +[Term] +id: MOD:02055 +name: crosslinked L-serine residue +def: "A protein modification that contains an L-serine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkSer" EXACT PSI-MOD-label [] +xref: Origin: "S" +is_a: MOD:00916 ! modified L-serine residue + +[Term] +id: MOD:02056 +name: crosslinked L-threonine residue +def: "A protein modification that contains an L-threonine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkThr" EXACT PSI-MOD-label [] +xref: Origin: "T" +is_a: MOD:00917 ! modified L-threonine residue + +[Term] +id: MOD:02057 +name: crosslinked L-tryptophan residue +def: "A protein modification that contains an L-tryptophan residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkTrp" EXACT PSI-MOD-label [] +xref: Origin: "W" +is_a: MOD:00918 ! modified L-tryptophan residue + +[Term] +id: MOD:02058 +name: crosslinked L-tyrosine residue +def: "A protein modification that contains an L-tyrosine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkTyr" EXACT PSI-MOD-label [] +xref: Origin: "Y" +is_a: MOD:00919 ! modified L-tyrosine residue + +[Term] +id: MOD:02059 +name: crosslinked L-valine residue +def: "A protein modification that contains an L-valine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkVal" EXACT PSI-MOD-label [] +xref: Origin: "V" +is_a: MOD:00920 ! modified L-valine residue + +[Term] +id: MOD:02060 +name: crosslinked D-asparagine residue +def: "A protein modification that contains an D-asparagine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkDAsn" EXACT PSI-MOD-label [] +xref: Origin: "MOD:00203" +is_a: MOD:02097 ! modified D-asparagine residue + +[Term] +id: MOD:02061 +name: crosslinked L-selenocysteine residue +def: "A protein modification that contains an L-selenocysteine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "U" +is_a: MOD:01158 ! modified L-selenocysteine residue + +[Term] +id: MOD:02062 +name: crosslinked N-formyl-L-methionine residue +def: "A protein modification that contains an N-formyl-L-methionine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "MOD:00030" +is_a: MOD:01450 ! modified N-formyl-L-methionine residue + +[Term] +id: MOD:02063 +name: crosslinked D-phenylalanine residue +def: "A protein modification that contains an D-phenylalanine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkDPhe" EXACT PSI-MOD-label [] +xref: Origin: "F" +is_a: MOD:00201 ! D-phenylalanine + +[Term] +id: MOD:02064 +name: crosslinked D-serine residue +def: "A protein modification that contains an D-serine residue crosslinked to one or more amino acid residues." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "XlnkDSer" EXACT PSI-MOD-label [] +xref: Origin: "S" +is_a: MOD:00202 ! D-serine (Ser) + +[Term] +id: MOD:02065 +name: metal or metal cluster coordinated L-alanine residue +def: "A protein modification that contains an L-alanine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "A" +is_a: MOD:00901 ! modified L-alanine residue + +[Term] +id: MOD:02066 +name: metal or metal cluster coordinated L-aspartic acid residue +def: "A protein modification that contains an L-aspartic acid residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "D" +is_a: MOD:00904 ! modified L-aspartic acid residue + +[Term] +id: MOD:02067 +name: metal or metal cluster coordinated L-cysteine residue +def: "A protein modification that contains an L-cysteine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "C" +is_a: MOD:00905 ! modified L-cysteine residue + +[Term] +id: MOD:02068 +name: metal or metal cluster coordinated L-glutamic acid residue +def: "A protein modification that contains an L-glutamic acid residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "E" +is_a: MOD:00906 ! modified L-glutamic acid residue + +[Term] +id: MOD:02069 +name: metal or metal cluster coordinated L-glutamine residue +def: "A protein modification that contains an L-glutamine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "Q" +is_a: MOD:00907 ! modified L-glutamine residue + +[Term] +id: MOD:02070 +name: metal or metal cluster coordinated L-histidine residue +def: "A protein modification that contains an L-histidine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "H" +is_a: MOD:00909 ! modified L-histidine residue + +[Term] +id: MOD:02071 +name: metal or metal cluster coordinated L-methionine residue +def: "A protein modification that contains an L-methionine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "M" +is_a: MOD:00913 ! modified L-methionine residue + +[Term] +id: MOD:02072 +name: metal or metal cluster coordinated L-serine residue +def: "A protein modification that contains an L-serine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "S" +is_a: MOD:00916 ! modified L-serine residue + +[Term] +id: MOD:02073 +name: metal or metal cluster coordinated L-selenocysteine residue +def: "A protein modification that contains an L-selenocysteine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "U" +is_a: MOD:01158 ! modified L-selenocysteine residue + +[Term] +id: MOD:02074 +name: metal or metal cluster coordinated L-lysine residue +def: "A protein modification that contains an L-lysine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "K" +is_a: MOD:00912 ! modified L-lysine residue + +[Term] +id: MOD:02075 +name: metal or metal cluster coordinated L-tyrosine residue +def: "A protein modification that contains an L-tyrosine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "Y" +is_a: MOD:00919 ! modified L-tyrosine residue + +[Term] +id: MOD:02076 +name: metal or metal cluster coordinated L-arginine residue +def: "A protein modification that contains an L-arginine residue coordinated to one or more metal atoms or metal clusters." [PubMed:18688235] +subset: PSI-MOD-slim +xref: Origin: "R" +is_a: MOD:00902 ! modified L-arginine residue + +[Term] +id: MOD:02077 +name: nitrosylated residue +def: "A protein modification that effectively replaces a hydrogen atom with an nitrosyl (NO) group." [PubMed:10442087, PubMed:11562475, PubMed:15688001, PubMed:8626764, PubMed:8637569, Unimod:275] +subset: PSI-MOD-slim +synonym: "Nitrosyl" RELATED PSI-MS-label [] +xref: DiffAvg: "29.00" +xref: DiffFormula: "C 0 H -1 N 1 O 1 S 0" +xref: DiffMono: "28.990164" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:275" +is_a: MOD:01156 ! protein modification categorized by chemical process + +[Term] +id: MOD:02078 +name: acetylated residue +def: "A protein modification that effectively replaces one or more hydrogen atoms with one or more acetyl groups." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136] +subset: PSI-MOD-slim +synonym: "Acetyl" RELATED PSI-MS-label [] +synonym: "AcRes" EXACT PSI-MOD-label [] +xref: Origin: "X" +xref: Source: "artifact" +xref: TermSpec: "none" +is_a: MOD:00649 ! acylated residue + +[Term] +id: MOD:02079 +name: diacetylated residue +def: "A protein modification that effectively replaces one hydrogen atom with one acetyl group." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, Unimod:1] +comment: Amino hydrogens are replaced to produce amides; hydroxyl hydrogens are replaced to produce esters; and hydrosulfanyl (thiol) hydrogens are replaced to produce sulfanyl esters (thiol esters). From DeltaMass: Average Mass: 42 +subset: PSI-MOD-slim +synonym: "Diacetyl" RELATED PSI-MS-label [] +synonym: "Ac2Res" EXACT PSI-MOD-label [] +xref: DiffAvg: "84.07" +xref: DiffFormula: "C 4 H 4 N 0 O 2" +xref: DiffMono: "84.021129" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "artifact" +xref: TermSpec: "none" +is_a: MOD:02078 ! acetylated residue + +[Term] +id: MOD:02080 +name: diacetylated L-serine +def: "A protein modification that effectively converts an L-serine residue to either N-acetyl-L-serine, O-acetyl-L-serine, or N,O-diacetyl-L-serine." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "Ac2Ser" EXACT PSI-MOD-label [] +xref: DiffAvg: "84.07" +xref: DiffFormula: "C 4 H 4 N 0 O 2" +xref: DiffMono: "84.021129" +xref: Formula: "C 7 H 10 N 1 O 4" +xref: MassAvg: "172.16" +xref: MassMono: "172.060983" +xref: Origin: "S" +xref: Source: "natural" +is_a: MOD:02079 ! diacetylated residue +is_a: MOD:00916 ! modified L-serine residue + +[Term] +id: MOD:02081 +name: alpha-amino succinylated residue +def: "A protein modification that effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a succinyl group." [PubMed:11857757, PubMed:12175151, Unimod:64#N-term] +synonym: "Succinyl" RELATED PSI-MS-label [] +xref: DiffAvg: "100.07" +xref: DiffFormula: "C 4 H 4 O 3" +xref: DiffMono: "100.016044" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "N-term" +xref: Unimod: "Unimod:64" +is_a: MOD:01029 ! succinylated residue +is_a: MOD:01696 ! alpha-amino acylated residue +is_a: MOD:01426 ! isotope tagged reagent derivatized residue + +[Term] +id: MOD:02082 +name: didehydrogenated and dehydrated residue +def: "A protein modification that effectively removes two neutral hydrogen atoms (proton and electron) and a water moiety from a residue." [Unimod:401] +subset: PSI-MOD-slim +synonym: "2dHdH2ORes" EXACT PSI-MOD-label [] +xref: DiffAvg: "-20.03" +xref: DiffFormula: "C 0 H -4 N 0 O -1" +xref: DiffMono: "-20.026215" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "none" +xref: TermSpec: "none" +is_a: MOD:00683 ! dehydrogenated residue + +[Term] +id: MOD:02083 +name: 4alpha-FMN modified residue +def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through the 4-alpha position of FMN." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "4aFMNRes" EXACT PSI-MOD-label [] +xref: DiffFormula: "C 17 H 21 N 4 O 9 P 1" +xref: DiffAvg: "456.35" +xref: DiffMono: "456.104615" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00896 ! FMN modified residue + +[Term] +id: MOD:02084 +name: 6-FMN modified residue +def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through the 6 position of FMN." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "6-FMNRes" EXACT PSI-MOD-label [] +xref: DiffAvg: "454.33" +xref: DiffFormula: "C 17 H 19 N 4 O 9 P 1" +xref: DiffMono: "454.088965" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00896 ! FMN modified residue + +[Term] +id: MOD:02085 +name: 8alpha-FMN modified residue +def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through the 8-alpha position of FMN." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "8a-FMNRes" EXACT PSI-MOD-label [] +xref: DiffAvg: "454.33" +xref: DiffFormula: "C 17 H 19 N 4 O 9 P 1" +xref: DiffMono: "454.088965" +xref: Formula: "none" +xref: MassAvg: "none" +xref: MassMono: "none" +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00896 ! FMN modified residue + +[Term] +id: MOD:02086 +name: brominated phenylalanine +def: "A protein modification that effectively substitutes a hydrogen atom of an L-phenylalanine residue with a bromine atom." [PubMed:18688235] +synonym: "BrPhe" EXACT PSI-MOD-label [] +xref: Origin: "F" +xref: Source: "none" +xref: TermSpec: "none" +is_a: MOD:00754 ! brominated residue +is_a: MOD:01066 ! halogenated phenylalanine + +[Term] +id: MOD:02087 +name: adenosine diphosphoribosyl (ADP-ribosyl) modified residue +def: "A protein modification that effectively results from forming an adduct with one or more ADP-ribose moieties or to modified residues through formation of a glycosidic bond." [DeltaMass:0] +subset: PSI-MOD-slim +synonym: "ADPRibRes" EXACT PSI-MOD-label [] +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00701 ! nucleotide or nucleic acid modified residue + +[Term] +id: MOD:02088 +name: natural, standard, encoded residue substitution +def: "A protein modification that effectively replaces a natural, standard, encoded residue." [PubMed:18688235] +comment: This represents the replacement of an encoded residue in a polypeptide, and must be combined with the formula or mass of another entry that is the replacement residue to represent a mutation or substitution. +subset: PSI-MOD-slim +xref: Origin: "X" +xref: Source: "natural" +xref: TermSpec: "none" +is_a: MOD:00009 ! natural residue +is_a: MOD:01156 ! protein modification categorized by chemical process + +[Term] +id: MOD:02089 +name: O-(phospho-5'-uridine)-L-serine +def: "A protein modification that effectively crosslinks an L-serine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-serine." [DeltaMass:0, PubMed:22504181, Unimod:417#S, ChEBI:156051] +subset: PSI-MOD-slim +synonym: "MOD_RES O-UMP-serine" EXACT UniProt-feature [] +synonym: "OUMPSer" EXACT PSI-MOD-label [] +synonym: "PhosphoUridine" RELATED PSI-MS-label [] +xref: DiffAvg: "306.17" +xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" +xref: DiffMono: "306.025302" +xref: Formula: "C 12 H 16 N 3 O 9 P 1" +xref: MassAvg: "377.24" +xref: MassMono: "377.062416" +xref: Origin: "S" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:417" +xref: UniProt: "PTM-0501" +is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:01166 ! uridylated residue + +[Term] +id: MOD:02090 +name: O-(phospho-5'-uridine)-L-threonine +def: "A protein modification that effectively modifies an L-threonine residue with 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-threonine." [DeltaMass:0, PubMed:22504181, Unimod:417#T, ChEBI:156052] +subset: PSI-MOD-slim +synonym: "MOD_RES O-UMP-threonine" EXACT UniProt-feature [] +synonym: "OUMPThr" EXACT PSI-MOD-label [] +synonym: "PhosphoUridine" RELATED PSI-MS-label [] +xref: DiffAvg: "306.17" +xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" +xref: DiffMono: "306.025302" +xref: Formula: "C 13 H 18 N 3 O 9 P 1" +xref: MassAvg: "391.27" +xref: MassMono: "391.078066" +xref: Origin: "T" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:417" +xref: UniProt: "PTM-0502" +is_a: MOD:00917 ! modified L-threonine residue +is_a: MOD:01166 ! uridylated residue + +[Term] +id: MOD:02091 +name: O-(phospho-5'-adenosine)-L-serine +def: "A protein modification that effectively modifies an L-serine residue with 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-serine." [PubMed:21472612, Unimod:405#S] +subset: PSI-MOD-slim +synonym: "MOD_RES O-AMP-serine" EXACT UniProt-feature [] +synonym: "Phosphoadenosine" RELATED PSI-MS-label [] +xref: DiffAvg: "329.21" +xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" +xref: DiffMono: "329.052520" +xref: Formula: "C 13 H 17 N 6 O 8 P 1" +xref: MassAvg: "416.28" +xref: MassMono: "416.084549" +xref: Origin: "S" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:405" +xref: UniProt: "PTM-0651" +is_a: MOD:00916 ! modified L-serine residue +is_a: MOD:01165 ! adenylated residue + +[Term] +id: MOD:02092 +name: S-methylbutanedioic acid-L-cysteine +def: "A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine by alkylation with itaconate through a thioether bond." [PubMed:29590092] +subset: PSI-MOD-slim +synonym: "MOD_RES S-(2,3-dicarboxypropyl)cysteine" EXACT UniProt-feature [] +xref: DiffAvg: "130.10" +xref: DiffFormula: "C 5 H 6 N 0 O 4 P 0 S 0" +xref: DiffMono: "130.026609" +xref: Formula: "C 8 H 11 N 1 O 5 P 0 S 1" +xref: MassAvg: "233.24" +xref: MassMono: "233.035793" +xref: Origin: "C" +xref: Source: "natural" +xref: TermSpec: "none" +xref: UniProt: "PTM-0676" +is_a: MOD:00905 ! modified L-cysteine residue +is_a: MOD:00001 ! alkylated residue + +[Term] +id: MOD:02093 +name: N6-(2-hydroxyisobutanoyl)-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-(2-hydroxyisobutanoyl)-L-lysine." [PubMed:29775581, PubMed:24681537, ChEBI:144968, Unimod:1849] +synonym: "MOD_RES N6-(2-hydroxyisobutyryl)lysine" EXACT UniProt-feature [] +xref: DiffAvg: "86.09" +xref: DiffFormula: "C 4 H 6 N 0 O 2" +xref: DiffMono: "86.036779" +xref: Formula: "C 10 H 18 N 2 O 3" +xref: MassAvg: "214.27" +xref: MassMono: "214.131742" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +xref: Unimod: "Unimod:1849" +xref: UniProt: "PTM-0638" +is_a: MOD:01875 ! N6-acylated L-lysine + +[Term] +id: MOD:02094 +name: N6-((3R)-3-hydroxybutanoyl)-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-((3R)-3-hydroxybutanoyl)-L-lysine." [PubMed:27105115, ChEBI:149490] +synonym: "MOD_RES N6-(beta-hydroxybutyryl)lysine" EXACT UniProt-feature [] +xref: DiffAvg: "86.09" +xref: DiffFormula: "C 4 H 6 N 0 O 2" +xref: DiffMono: "86.036779" +xref: Formula: "C 10 H 18 N 2 O 3" +xref: MassAvg: "214.27" +xref: MassMono: "214.131742" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +xref: UniProt: "PTM-0499" +is_a: MOD:01875 ! N6-acylated L-lysine + +[Term] +id: MOD:02095 +name: N6-glutaryl-L-lysine +def: "A protein modification that effectively converts an L-lysine residue to N6-glutaryl-L-lysine." [PubMed:24703693, ChEBI:87828] +synonym: "MOD_RES N6-glutaryllysine" EXACT UniProt-feature [] +xref: DiffAvg: "114.10" +xref: DiffFormula: "C 5 H 6 N 0 O 3" +xref: DiffMono: "114.031694" +xref: Formula: "C 11 H 18 N 2 O 4" +xref: MassAvg: "242.28" +xref: MassMono: "242.126657" +xref: Origin: "K" +xref: Source: "natural" +xref: TermSpec: "none" +xref: UniProt: "PTM-0487" +is_a: MOD:01875 ! N6-acylated L-lysine + +[Term] +id: MOD:02096 +name: N4-methyl-D-asparagine +def: "A protein modification that effectively converts a D-asparagine residue to N4-methyl-D-asparagine." [PubMed:22983711, ChEBI:149514] +subset: PSI-MOD-slim +synonym: "MOD_RES N4-methyl-D-asparagine" EXACT UniProt-feature [] +synonym: "N4-methylated D-asparagine" EXACT PSI-MOD-alternate [] +xref: DiffAvg: "14.03" +xref: DiffFormula: "C 1 H 2 N 0 O 0" +xref: DiffMono: "14.015650" +xref: Formula: "C 5 H 8 N 2 O 2" +xref: MassAvg: "128.13" +xref: MassMono: "128.058578" +xref: Origin: "N" +xref: Source: "natural" +xref: TermSpec: "none" +xref: UniProt: "PTM-0691" +is_a: MOD:00599 ! monomethylated residue +is_a: MOD:00602 ! N-methylated residue +is_a: MOD:00673 ! methylated asparagine +is_a: MOD:02097 ! modified D-asparagine residue +is_a: MOD:00894 ! residues isobaric at 128.058578 Da + +[Term] +id: MOD:02097 +name: modified D-asparagine residue +def: "A protein modification that modifies a D-asparagine residue." [PubMed:18688235] +subset: PSI-MOD-slim +synonym: "ModDAsn" EXACT PSI-MOD-label [] +is_a: MOD:00203 ! D-asparagine + [Typedef] id: contains name: contains @@ -38523,3 +41188,4 @@ name: part of def: "'Entity A' part_of 'Entity B' implies that 'Entity A' is a part of the structure of 'Entity B'." [PubMed:18688235] is_transitive: true + diff -Nru libpappsomspp-0.8.15/src/resources/icons/switch_off.svg libpappsomspp-0.8.58/src/resources/icons/switch_off.svg --- libpappsomspp-0.8.15/src/resources/icons/switch_off.svg 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/resources/icons/switch_off.svg 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,86 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + OFF + + diff -Nru libpappsomspp-0.8.15/src/resources/icons/switch_on.svg libpappsomspp-0.8.58/src/resources/icons/switch_on.svg --- libpappsomspp-0.8.15/src/resources/icons/switch_on.svg 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/src/resources/icons/switch_on.svg 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,86 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + ON + + diff -Nru libpappsomspp-0.8.15/tests/CMakeLists.txt libpappsomspp-0.8.58/tests/CMakeLists.txt --- libpappsomspp-0.8.15/tests/CMakeLists.txt 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/CMakeLists.txt 2022-10-27 09:16:15.000000000 +0000 @@ -89,10 +89,32 @@ test_massspectrum.cpp test_mzintegrationparams.cpp test_massspectrumcombiner.cpp + test_timsxicextractor.cpp + test_timsxicextractor_based_masspec.cpp + test_trace_filters.cpp + test_xic.cpp + test_aa.cpp + test_protein.cpp + test_peptide.cpp + test_psm.cpp + test_uimonitor.cpp + test_timsframe.cpp + test_tims_data_xic_chromatogram.cpp + test_tandem_run_wrapper.cpp + test_msrunalignment.cpp + ) + + # These source files are compiled into a single Catch2-based test binary. + # tests dedicated to check memory usage and avoid memory leaks + set(catch2_only_cpp_memory_SRCS + memory/test_tandemwrapperrun.cpp + memory/test_timsdata_reader_memory.cpp ) add_executable(catch2-only-tests + common.cpp ${catch2_only_cpp_SRCS} + ${catch2_only_cpp_memory_SRCS} ) set_property(TARGET catch2-only-tests PROPERTY CXX_STANDARD 17) # we want C++17 @@ -108,6 +130,8 @@ set(required_target_link_libraries pappsomspp-shared Catch2::Catch2 + OdsStream::Core + liblzf::liblzf ) target_link_libraries(catch2-only-tests @@ -118,43 +142,22 @@ # the call. add_test(catch2-only-tests "catch2-only-tests") - add_executable(test_fasta_reader test_fasta_reader.cpp) target_link_libraries(test_fasta_reader Qt5::Core pappsomspp-shared) add_test(test_fasta_reader "test_fasta_reader") - - add_executable(test_protein test_protein.cpp) - target_link_libraries(test_protein Qt5::Core pappsomspp-shared) - add_test(test_protein "test_protein") - - add_executable(test_xic test_xic.cpp) - target_link_libraries(test_xic Qt5::Core pappsomspp-shared Qt5::Gui OdsStream::Core) - add_test(test_xic "test_xic") - - add_executable(test_massrange test_massrange.cpp) target_link_libraries(test_massrange Qt5::Core pappsomspp-shared) add_test(test_massrange "test_massrange") - add_executable(test_aa test_aa.cpp) - target_link_libraries(test_aa Qt5::Core pappsomspp-shared Catch2::Catch2) - add_test(test_aa "test_aa") - - add_executable(test_peptide test_peptide.cpp) - target_link_libraries(test_peptide Qt5::Core Qt5::Gui pappsomspp-shared) - add_test(test_peptide "test_peptide") - add_executable(test_peptidenaturalisotopelist test_peptidenaturalisotopelist.cpp) target_link_libraries(test_peptidenaturalisotopelist Qt5::Core Qt5::Gui pappsomspp-shared) add_test(test_peptidenaturalisotopelist "test_peptidenaturalisotopelist") - add_executable(test_natural_isotope_average test_natural_isotope_average.cpp) target_link_libraries(test_natural_isotope_average Qt5::Core pappsomspp-shared) add_test(test_natural_isotope_average "test_natural_isotope_average") - add_executable(test_peptidefragment test_peptidefragment.cpp) target_link_libraries(test_peptidefragment Qt5::Core Qt5::Gui pappsomspp-shared) add_test(test_peptidefragment "test_peptidefragment") @@ -169,70 +172,46 @@ add_test(test_big_hyperscore "test_big_hyperscore") #ENDIF(FALSE) - add_executable(test_rawmasslist test_rawmasslist.cpp) target_link_libraries(test_rawmasslist Qt5::Core Qt5::Gui pappsomspp-shared) add_test(test_rawmasslist "test_rawmasslist") - - add_executable(test_isotope_with_spectrum test_isotope_with_spectrum.cpp) + add_executable(test_isotope_with_spectrum common.cpp test_isotope_with_spectrum.cpp) target_link_libraries(test_isotope_with_spectrum Qt5::Core Qt5::Gui pappsomspp-shared ${Boost_LIBRARIES}) add_test(test_isotope_with_spectrum "test_isotope_with_spectrum") set(TEST_LIST ${TEST_LIST} test_isotope_with_spectrum) - add_executable(test_hyperscore test_hyperscore.cpp) + add_executable(test_hyperscore common.cpp test_hyperscore.cpp) target_link_libraries(test_hyperscore Qt5::Core pappsomspp-shared Qt5::Gui ${Boost_LIBRARIES}) add_test(test_hyperscore "test_hyperscore") set(TEST_LIST ${TEST_LIST} test_hyperscore) - add_executable(test_xtandem_spectrum test_xtandem_spectrum.cpp) + add_executable(test_xtandem_spectrum common.cpp test_xtandem_spectrum.cpp) target_link_libraries(test_xtandem_spectrum Qt5::Core pappsomspp-shared Qt5::Gui ${Boost_LIBRARIES}) add_test(test_xtandem_spectrum "test_xtandem_spectrum") set(TEST_LIST ${TEST_LIST} test_xtandem_spectrum) - add_executable(test_scan_15968 test_scan_15968.cpp) + add_executable(test_scan_15968 common.cpp test_scan_15968.cpp) target_link_libraries(test_scan_15968 Qt5::Core Qt5::Gui pappsomspp-shared ${Boost_LIBRARIES}) add_test(test_scan_15968 "test_scan_15968") set(TEST_LIST ${TEST_LIST} test_scan_15968) - add_executable(test_psm test_psm.cpp) - target_link_libraries(test_psm Qt5::Core pappsomspp-shared Qt5::Gui Qt5::Concurrent ${Boost_LIBRARIES}) - add_test(test_psm "test_psm") - set(TEST_LIST ${TEST_LIST} test_psm) - add_executable(test_xicextractor test_xicextractor.cpp) target_link_libraries(test_xicextractor Qt5::Core Qt5::Gui pappsomspp-shared ${Boost_LIBRARIES} OdsStream::Core) add_test(test_xicextractor "test_xicextractor") set(TEST_LIST ${TEST_LIST} test_xicextractor) - add_executable(test_trace_filters test_trace_filters.cpp) - target_link_libraries(test_trace_filters Qt5::Core Qt5::Gui Qt5::Concurrent pappsomspp-shared ${Boost_LIBRARIES}) - add_test(test_trace_filters "test_trace_filters") - set(TEST_LIST ${TEST_LIST} test_trace_filters) - - - add_executable(test_msrunalignment test_msrunalignment.cpp) - target_include_directories (test_msrunalignment PUBLIC ${QUAZIP_INCLUDE_DIR}) - target_link_libraries(test_msrunalignment Qt5::Core Qt5::Gui Qt5::Concurrent pappsomspp-shared ${Boost_LIBRARIES} OdsStream::Core) - add_test(test_msrunalignment "test_msrunalignment") - set(TEST_LIST ${TEST_LIST} test_msrunalignment) - add_executable(test_msrunoutput test_msrunoutput.cpp) target_link_libraries(test_msrunoutput Qt5::Core Qt5::Gui Qt5::Concurrent pappsomspp-shared ${Boost_LIBRARIES} OdsStream::Core Catch2::Catch2) add_test(test_msrunoutput "test_msrunoutput") set(TEST_LIST ${TEST_LIST} test_msrunoutput) - add_executable(test_timsframe test_timsframe.cpp) - target_link_libraries(test_timsframe Qt5::Core pappsomspp-shared Catch2::Catch2) - add_test(test_timsframe "test_timsframe") - if(UNIX) - set_property(TEST test_big_hyperscore test_xic test_protein test_fasta_reader - test_massrange test_aa test_peptide test_peptidenaturalisotopelist test_peptidefragment + set_property(TEST catch2-only-tests test_big_hyperscore test_fasta_reader + test_massrange test_peptidenaturalisotopelist test_peptidefragment test_fragmentationcid ${TEST_LIST} test_natural_isotope_average test_rawmasslist - test_timsframe PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src") endif() @@ -241,6 +220,10 @@ set(ENV{PATH} "$ENV{PATH};..\\src") endif() + + + add_subdirectory(widget) + else() message(STATUS "Tests are not built.") endif() diff -Nru libpappsomspp-0.8.15/tests/common.cpp libpappsomspp-0.8.58/tests/common.cpp --- libpappsomspp-0.8.15/tests/common.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/common.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,81 @@ + +#include "common.h" + +using namespace pappso; + +MassSpectrum +readMgf(const QString &filename) +{ + try + { + qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; + MsFileAccessor accessor(filename, "msrun"); + qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; + MsRunReaderSPtr reader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()" + << accessor.getMsRunIds().front().get()->getXmlId(); + std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " + << reader->spectrumListSize() << std::endl; + MassSpectrumSPtr spectrum_sp = reader->massSpectrumSPtr(0); + std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " + << spectrum_sp.get()->size() << std::endl; + spectrum_sp.get()->debugPrintValues(); + spectrum_sp.get()->sortMz(); + return *(spectrum_sp.get()); + } + catch(pappso::PappsoException &error) + { + std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + << QString("ERROR reading file %1 :") + .arg(filename) + .toStdString() + .c_str() + << " " << error.what(); + throw error; + } +} + +QualifiedMassSpectrum +readQualifiedMassSpectrumMgf(const QString &filename) +{ + try + { + qDebug(); + MsFileAccessor accessor(filename, "msrun"); + qDebug(); + MsRunReaderSPtr reader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + qDebug() << accessor.getMsRunIds().front().get()->getXmlId(); + std::cout << reader->spectrumListSize() << std::endl; + QualifiedMassSpectrum spectrum_sp = + reader->qualifiedMassSpectrum(0, true); + return spectrum_sp; + } + catch(pappso::PappsoException &error) + { + std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ + << QString("ERROR reading file %1 : %2") + .arg(filename) + .arg(error.qwhat()) + .toStdString() + .c_str(); + throw error; + } +} + +bool +compareTextFiles(const QString &file1, const QString &file2) +{ + + QFile fnew(file1); + fnew.open(QFile::ReadOnly | QFile::Text); + // REQUIRE(fnew.errorString().toStdString() == ""); + QTextStream infnew(&fnew); + + QFile fold(file2); + fold.open(QFile::ReadOnly | QFile::Text); + QTextStream infold(&fold); + + return (infold.readAll().toStdString() == infnew.readAll().toStdString()); +} diff -Nru libpappsomspp-0.8.15/tests/common.h libpappsomspp-0.8.58/tests/common.h --- libpappsomspp-0.8.15/tests/common.h 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/common.h 2022-10-27 09:16:15.000000000 +0000 @@ -5,66 +5,41 @@ #include #include #include +#include using namespace pappso; -MassSpectrum -readMgf(const QString &filename) -{ - try - { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; - MsFileAccessor accessor(filename, "msrun"); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; - MsRunReaderSPtr reader = - accessor.msRunReaderSp(accessor.getMsRunIds().front()); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()" - << accessor.getMsRunIds().front().get()->getXmlId(); - std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - << reader->spectrumListSize() << std::endl; - MassSpectrumSPtr spectrum_sp = reader->massSpectrumSPtr(0); - std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " - << spectrum_sp.get()->size() << std::endl; - spectrum_sp.get()->debugPrintValues(); - spectrum_sp.get()->sortMz(); - return *(spectrum_sp.get()); - } - catch(pappso::PappsoException &error) - { - std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << QString("ERROR reading file %1 :") - .arg(filename) - .toStdString() - .c_str() - << " " << error.what(); - throw error; - } -} +MassSpectrum readMgf(const QString &filename); + +QualifiedMassSpectrum readQualifiedMassSpectrumMgf(const QString &filename); -QualifiedMassSpectrum -readQualifiedMassSpectrumMgf(const QString &filename) + +class XicOdsWriter { - try - { - qDebug(); - MsFileAccessor accessor(filename, "msrun"); - qDebug(); - MsRunReaderSPtr reader = - accessor.msRunReaderSp(accessor.getMsRunIds().front()); - qDebug() << accessor.getMsRunIds().front().get()->getXmlId(); - std::cout << reader->spectrumListSize() << std::endl; - QualifiedMassSpectrum spectrum_sp = - reader->qualifiedMassSpectrum(0, true); - return spectrum_sp; - } - catch(pappso::PappsoException &error) - { - std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ - << QString("ERROR reading file %1 : %2") - .arg(filename) - .arg(error.qwhat()) - .toStdString() - .c_str(); - throw error; - } -} + public: + XicOdsWriter(CalcWriterInterface &output) : _output(output) + { + _output.writeCell("rt"); + _output.writeCell("intensity"); + _output.writeLine(); + }; + + void + write(const Trace &xic) + { + auto it = xic.begin(); + while(it != xic.end()) + { + + _output.writeCell(it->x); + _output.writeCell(it->y); + _output.writeLine(); + it++; + } + }; + + private: + CalcWriterInterface &_output; +}; + +bool compareTextFiles(const QString &file1, const QString &file2); diff -Nru libpappsomspp-0.8.15/tests/config.h.cmake libpappsomspp-0.8.58/tests/config.h.cmake --- libpappsomspp-0.8.15/tests/config.h.cmake 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/config.h.cmake 2022-10-27 09:16:15.000000000 +0000 @@ -1,5 +1,6 @@ #pragma once #cmakedefine CMAKE_SOURCE_DIR "@CMAKE_SOURCE_DIR@" +#cmakedefine CMAKE_BINARY_DIR "@CMAKE_BINARY_DIR@" #cmakedefine USEPAPPSOTREE @USEPAPPSOTREE@ Binary files /srv/release.debian.org/tmp/wp6jDaiuvp/libpappsomspp-0.8.15/tests/data/alignment/peptide_table.ods and /srv/release.debian.org/tmp/SxIFRls3td/libpappsomspp-0.8.58/tests/data/alignment/peptide_table.ods differ diff -Nru libpappsomspp-0.8.15/tests/data/alignment/result_delta_rt.tsv libpappsomspp-0.8.58/tests/data/alignment/result_delta_rt.tsv --- libpappsomspp-0.8.15/tests/data/alignment/result_delta_rt.tsv 1970-01-01 00:00:00.000000000 +0000 +++ 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2974.72470165 +2975.12 2975.03631668 +2975.43 2975.34793172 +2975.74 2975.65954675 +2976.05 2975.97190853 +2976.79 2976.71435713 +2977.15 2977.07689256 +2977.51 2977.43875072 +2977.86 2977.79066098 +2978.25 2978.18257124 +2978.61 2978.54479409 +2979.14 2979.07696483 +2979.5 2979.43906612 +2979.82 2979.76078535 +2980.13 2980.07241775 +2980.44 2980.38403279 +2980.75 2980.69564782 +2981.06 2981.00741915 +2981.46 2981.40925995 +2981.81 2981.76118757 +2982.17 2982.12309783 +2982.56 2982.51502545 +2982.92 2982.87695308 +2983.28 2983.23874177 +2983.59 2983.55044364 +2983.9 2983.86299644 +2984.75 2984.71568816 +2985.14 2985.10846672 +2985.5 2985.47110635 +2986.27 2986.24438852 +2987.03 2987.00767069 +2987.39 2987.37024086 +2987.75 2987.73296732 +2988.6 2988.58569377 +2988.96 2988.94845497 +2989.34 2989.33036522 +2989.7 2989.69227548 +2990.06 2990.05415101 +2990.42 2990.41633912 +2990.96 2990.9585967 +2991.36 2991.36085428 +2991.72 2991.72319868 +2992.31 2992.31594251 +2992.94 2992.94868633 +2993.3 2993.31169065 +2994.04 2994.05422608 +2994.4 2994.41681361 +2994.79 2994.80874124 +2995.15 2995.17066886 +2995.51 2995.5329438 +2996.1 2996.12520138 +2996.45 2996.47745896 +2996.81 2996.83931712 +2997.17 2997.20126211 +2997.57 2997.6032071 +2997.93 2997.96556887 +2998.53 2998.56784381 +2998.88 2998.92043134 +2999.42 2999.46260209 +2999.78 2999.82385244 diff -Nru libpappsomspp-0.8.15/tests/data/asr1_digested_peptides.txt libpappsomspp-0.8.58/tests/data/asr1_digested_peptides.txt --- libpappsomspp-0.8.15/tests/data/asr1_digested_peptides.txt 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/asr1_digested_peptides.txt 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,28 @@ +>prot1 +RT AE DY +>prot1b +RT AE DY +>prot2 +VC IP +>prot3 +AE YV RD +>prot4 +YV VC +>protL +VC AR +>GST-sans-ASR1 +HNMLGGCPK HHHHHLFHHK HNMLGGCPKER YEEHLYER RIEAIPQIDK LTQSMAIIR AEISMLEGAVLDIRYGVSR AEISMLEGAVLDIR IAYSKDFETLK YEEHLYERDEGDK GLVQPTR YIAWPLQGWQATFGGGDHPPK FELGLEFPNLPYYIDGDVK TYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPK MSPILGYWKIK DFETLKVDFLSK GLVQPTRLLLEYLEEK IKGLVQPTR MSPILGYWK IEAIPQIDK LLLEYLEEK YIADKHNMLGGCPK SSKYIAWPLQGWQATFGGGDHPPK SDLEVLFQGPLGSMAEEK FELGLEFPNLPYYIDGDVKLTQSMAIIR IEAIPQIDKYLK YGVSRIAYSK VDFLSKLPEMLK MFEDRLCHK LPEMLKMFEDR DEGDKWR LLLEYLEEKYEEHLYER LTQSMAIIRYIADK KFELGLEFPNLPYYIDGDVK ERAEISMLEGAVLDIR +>ASR1-clivee +DAEEAGGEKK KDPEHAHR IEEEVAAAAAVGSGGFAFHEHHEKK QHLGEAGAIAAGAFALYEK HHHHHLFHHK HHHHHLFHHKK DPEHAHRHK GPLGSMAEEK IEEEVAAAAAVGSGGFAFHEHHEK DPEHAHR GPLGSMAEEKHHHHHLFHHK HKIEEEVAAAAAVGSGGFAFHEHHEK HKQHLGEAGAIAAGAFALYEK DAEEAGGEK QHLGEAGAIAAGAFALYEKHEAK DHKDAEEAGGEK +>sp|Q940H6|SRK2E_ARATH Serine/threonine-protein kinase SRK2E OS=Arabidopsis thaliana GN=SRK2E PE=1 SV=1 +IDENVKR MDRPAVSGPMDLPIMHDSDR DLKLENTLLDGSPAPR IFVADPAK EIINHRSLR SSVLHSQPK GEKIDENVK LKICDFGYSK YIERGEK STVGTPAYIAPEVLLK EVILTPTHLAIVMEYASGGELFER FFFQQLISGVSYCHAMQVCHR NHEWFLK QSNELVAVK FSEDEARFFFQQLISGVSYCHAMQVCHR FSEDEAR HPNIVRFK ICNAGRFSEDEAR RISIPEIR ISIPEIRNHEWFLK ISIPEIR ILNVQYAIPDYVHISPECR ICDFGYSK DKQSNELVAVK SSVLHSQPKSTVGTPAYIAPEVLLK EVILTPTHLAIVMEYASGGELFERICNAGR DIGSGNFGVARLMR VADVWSCGVTLYVMLVGAYPFEDPEEPKNFR VADVWSCGVTLYVMLVGAYPFEDPEEPK QSNELVAVKYIER DIGSGNFGVAR ILNVQYAIPDYVHISPECRHLISR PAVSGPMDLPIMHDSDRYELVK PAVSGPMDLPIMHDSDR IFVADPAKR REIINHR HLISRIFVADPAK EYDGKVADVWSCGVTLYVMLVGAYPFEDPEEPK TIHRILNVQYAIPDYVHISPECR SLRHPNIVR LENTLLDGSPAPRLK FKEVILTPTHLAIVMEYASGGELFER LENTLLDGSPAPR FFFQQLISGVSYCHAMQVCHRDLK YELVKDIGSGNFGVAR ICDFGYSKSSVLHSQPK STVGTPAYIAPEVLLKK +>sp|P17948|VGFR1_HUMAN Vascular endothelial growth factor receptor 1 OS=Homo sapiens GN=FLT1 PE=1 SV=2 +EPITMEDLISYSFQVARGMEFLSSR ESERLSITK CDFCSNNEESFILDADSNMGNR QFCSTLTLNTAQANHTGFYSCK EHSITLNLTIMNVSLQDSGTYACR WMAPESIFDK RFTWTDSK MVSYWDTGVLLCALLSCLLLTGSSSGSK VQMTWSYPDEK ILTHIGHHLNVVNLLGACTK QGGPLMVIVEYCK DVTEEDAGNYTILLSIK NLTATLIVNVKPQIYEK DVTWILLRTVNNR KQQVLETVAGK IIWDSRK PFVEMYSEIPEIIHMTEGRELVIPCR DLFFLNKDAALHMEPK IDQSNSHANIFYSVLTIDK SLGRGAFGK LKDPELSLK PRFAELVEK WMAPESIFDKIYSTK VTSPNITVTLKK WSLPEMVSKESER LPYDASKWEFAR NKMASTLVVADSR DYIPINAILTGNSGFTYSTPAFSEDFFK NLSDHTVAISSSTTLDCHANGVPEPQITWFK ALMTELK ISGIYICIASNK AFPSPEVVWLKDGLPATEK MAITKEHSITLNLTIMNVSLQDSGTYACR TDYLSIIMDPDEVPLDEQCERLPYDASK ARNVYTGEEILQK DPELSLKGTQHIMQAGQTLHLQCR SPTCRTVAVK IQQEPGIILGPGSSTLFIERVTEEDEGVYHCK SSSEIKTDYLSIIMDPDEVPLDEQCER EPITMEDLISYSFQVAR NLTATLIVNVK MEPGLEQGKK TFEELLPNATSMFDDYQGDSSTLLASPMLKR MLKEGATASEYK LSITKSACGR MRAPEYSTPEIYQIMLDCWHR AVSSFPDPALYPLGSRQILTCTAYGIPQPTIK NPDYVRK ICDFGLARDIYK GMEFLSSR ALMTELKILTHIGHHLNVVNLLGACTK NISFYITDVPNGFHVNLEK VGTVGRNISFYITDVPNGFHVNLEK DAALHMEPKK TVNNRTMHYSISK IESITQRMAIIEGK SVNTSVHIYDK SGPSFKSVNTSVHIYDK YLAVPTSK YGNLSNYLK MPTEGEDLKLSCTVNK GFIISNATYK YGNLSNYLKSK EGATASEYKALMTELK MVSYWDTGVLLCALLSCLLLTGSSSGSKLK MASTLVVADSRISGIYICIASNK FAELVEK QTNTIIDVQISTPR TDYLSIIMDPDEVPLDEQCER DVTWILLR VVQASAFGIKK IESITQR ESGLSDVSR KFPLDTLIPDGK PSFCHSSCGHVSEGKR DLFFLNK ICDFGLAR ETESAIYIFISDTGR MPTEGEDLK LSCTVNKFLYR DVTEEDAGNYTILLSIKQSNVFK FTWTDSK EIGLLTCEATVNGHLYK GHTLVLNCTATTPLNTR GYSLIIK NVYTGEEILQK LPYDASK NNHKIQQEPGIILGPGSSTLFIER WEFARER APEYSTPEIYQIMLDCWHR GHTLVLNCTATTPLNTRVQMTWSYPDEK VKAFPSPEVVWLK TNYLTHRQTNTIIDVQISTPR DKGLYTCR LDSVTSSESFASSGFQEDK RIDQSNSHANIFYSVLTIDK FTWTDSKPK WFWHPCNHNHSEAR QQVLETVAGKR QTNTIIDVQISTPRPVK LSCTVNK ELVIPCR EHSITLNLTIMNVSLQDSGTYACRAR TMHYSISK VTEEDEGVYHCK QGGPLMVIVEYCKYGNLSNYLK ASLKIDLR NISFYITDVPNGFHVNLEKMPTEGEDLK FNSGSSDDVRYVNAFK SNLELITLTCTCVAATLFWLLLTLFIR NLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHK PSFCHSSCGHVSEGK WSLPEMVSK QSNVFKNLTATLIVNVK IDLRVTSK IACCSPPPDYNSVVLYSTPPI SARYLTR ILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCK NVYTGEEILQKK GTQHIMQAGQTLHLQCR QKMAITK DGLPATEK FTYDHAELERK DIYKNPDYVR MEPGLEQGK SVNTSVHIYDKAFITVK YVNAFKFMSLER LLRGHTLVLNCTATTPLNTR MASTLVVADSR LPLKWMAPESIFDK LGDLLQANVQQDGK ELVIPCRVTSPNITVTLK NILLSENNVVK SYRLSMK SACGRNGK ATNQKGSVESSAYLTVQGTSDK RSSSEIK VTSPNITVTLK FLYRDVTWILLR SLSDVEEEEDSDGFYK VTEEDEGVYHCKATNQK MAIIEGKNK KGFIISNATYK CDFCSNNEESFILDADSNMGNRIESITQR DGLPATEKSAR ISGIYICIASNKVGTVGR DQEAPYLLR IKTFEELLPNATSMFDDYQGDSSTLLASPMLK IDQSNSHANIFYSVLTIDKMQNK KIACCSPPPDYNSVVLYSTPPI SLSDVEEEEDSDGFYKEPITMEDLISYSFQVAR FNSGSSDDVR RDLFFLNK TMHYSISKQK GFIISNATYKEIGLLTCEATVNGHLYK EIGLLTCEATVNGHLYKTNYLTHR SKESGLSDVSR GLYTCRVR ESISAPKFNSGSSDDVR FAELVEKLGDLLQANVQQDGK QILTCTAYGIPQPTIKWFWHPCNHNHSEAR PFVEMYSEIPEIIHMTEGR SDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSR PQIYEKAVSSFPDPALYPLGSR TNYLTHR NILLSENNVVKICDFGLAR SDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLR GMEFLSSRK YLTRGYSLIIK GSVESSAYLTVQGTSDK VQMTWSYPDEKNK DYIPINAILTGNSGFTYSTPAFSEDFFKESISAPK CIHRDLAAR FTYDHAELER ETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGR EITIRDQEAPYLLR SNLELITLTCTCVAATLFWLLLTLFIRK LGKSLGR QILTCTAYGIPQPTIK KETESAIYIFISDTGR FMSLERIK EKMEPGLEQGK DPELSLK EGATASEYK QQVLETVAGK GAFGKVVQASAFGIK GTQHIMQAGQTLHLQCRGEAAHK DAALHMEPK LDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYK QFCSTLTLNTAQANHTGFYSCKYLAVPTSK MAIIEGK AFITVKHR RFTYDHAELER AFPSPEVVWLK VVQASAFGIK GEAAHKWSLPEMVSK FPLDTLIPDGK GYSLIIKDVTEEDAGNYTILLSIK TVAVKMLK AVSSFPDPALYPLGSR ESGLSDVSRPSFCHSSCGHVSEGK RIIWDSR NGKQFCSTLTLNTAQANHTGFYSCK ESISAPK FPLDTLIPDGKR IQQEPGIILGPGSSTLFIER VRSGPSFK YLAVPTSKK APEYSTPEIYQIMLDCWHRDPK GDTRLPLK DLAARNILLSENNVVK TFEELLPNATSMFDDYQGDSSTLLASPMLK PRLDSVTSSESFASSGFQEDK +>gi|27807057|ref|NP_777009.1| cAMP-dependent protein kinase catalytic subunit alpha [Bos taurus] +MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVML +PENLLIDQQGYIQVTDFGFAK GPGDTSNFDDYEEEEIRVSINEK QIEHTLNEK HMETGNHYAMKILDK ILQAVNFPFLVK IGRFSEPHAR DNSNLYMVMEYVPGGEMFSHLR DLKPENLLIDQQGYIQVTDFGFAK FKGPGDTSNFDDYEEEEIR VEAPFIPKFK FPSHFSSDLKDLLR FGNLKNGVNDIK AVDWWALGVLIYEMAAGYPPFFADQPIQIYEK WFATTDWIAIYQRK NLLQVDLTK GPGDTSNFDDYEEEEIR FSEPHARFYAAQIVLTFEYLHSLDLIYR LKQIEHTLNEK VEAPFIPK NGVNDIKNHK CGKEFSEF NLLQVDLTKR PENLLIDQQGYIQVTDFGFAKR QIEHTLNEKR VSINEKCGK ILQAVNFPFLVKLEFSFK KVEAPFIPK FYAAQIVLTFEYLHSLDLIYR DLLRNLLQVDLTK GRTWTLCGTPEYLAPEIILSK TWTLCGTPEYLAPEIILSKGYNK DNSNLYMVMEYVPGGEMFSHLRR HMETGNHYAMK IVSGKVR VRFPSHFSSDLK LEFSFKDNSNLYMVMEYVPGGEMFSHLR FYAAQIVLTFEYLHSLDLIYRDLK VKHMETGNHYAMK NHKWFATTDWIAIYQR RILQAVNFPFLVK FPSHFSSDLK FSEPHAR WFATTDWIAIYQR NGVNDIK TWTLCGTPEYLAPEIILSK +>Oliv1GST-sans-ASR1 +HNMLGGCPK HHHHHLFHHK HNMLGGCPKER YEEHLYER RIEAIPQIDK LTQSMAIIR AEISMLEGAVLDIRYGVSR AEISMLEGAVLDIR IAYSKDFETLK YEEHLYERDEGDK GLVQPTR YIAWPLQGWQATFGGGDHPPK FELGLEFPNLPYYIDGDVK TYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPK MSPILGYWKIK DFETLKVDFLSK GLVQPTRLLLEYLEEK IKGLVQPTR MSPILGYWK IEAIPQIDK LLLEYLEEK YIADKHNMLGGCPK SSKYIAWPLQGWQATFGGGDHPPK SDLEVLFQGPLGSMAEEK FELGLEFPNLPYYIDGDVKLTQSMAIIR IEAIPQIDKYLK YGVSRIAYSK VDFLSKLPEMLK MFEDRLCHK LPEMLKMFEDR DEGDKWR LLLEYLEEKYEEHLYER LTQSMAIIRYIADK KFELGLEFPNLPYYIDGDVK ERAEISMLEGAVLDIR +>Oliv2GST-sans-ASR1 +HNMLGGCPK HHHHHLFHHK HNMLGGCPKER YEEHLYER RIEAIPQIDK LTQSMAIIR AEISMLEGAVLDIRYGVSR AEISMLEGAVLDIR IAYSKDFETLK YEEHLYERDEGDK GLVQPTR YIAWPLQGWQATFGGGDHPPK FELGLEFPNLPYYIDGDVK TYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPK MSPILGYWKIK DFETLKVDFLSK GLVQPTRLLLEYLEEK IKGLVQPTR MSPILGYWK IEAIPQIDK LLLEYLEEK YIADKHNMLGGCPK SSKYIAWPLQGWQATFGGGDHPPK SDLEVLFQGPLGSMAEEK FELGLEFPNLPYYIDGDVKLTQSMAIIR IEAIPQIDKYLK YGVSRIAYSK VDFLSKLPEMLK MFEDRLCHK LPEMLKMFEDR DEGDKWR LLLEYLEEKYEEHLYER LTQSMAIIRYIADK KFELGLEFPNLPYYIDGDVK ERAEISMLEGAVLDIR + diff -Nru libpappsomspp-0.8.15/tests/data/fuzzy.fasta libpappsomspp-0.8.58/tests/data/fuzzy.fasta --- libpappsomspp-0.8.15/tests/data/fuzzy.fasta 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/fuzzy.fasta 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,9 @@ + +>YGR254W +MAVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL* + +>YGR255C +MFFSKVMLTRRILVRGLATAKSSAPKLTDVLIVGGGPAGLTLAASIKNSPQLKDLKTTLVDMVDLKDKLSDFYNSPPDYFTNRIVSVTPRSIHFLENNAGATLMHDRIQSYDGLYVTDGCSKATLDLARDSMLCMIEIINIQASLYNRISQYDSKKDSIDIIDNTKVVNIKHSDPNDPLSWPLVTLSNGEVYKTRLLVGADGFNSPTRRFSQIPSRGWMYNAYGVVASMKLEYPPFKLRGWQRFLPTGPIAHLPMPENNATLVWSSSERLSRLLLSLPPESFTALINAAFVLEDADMNYYYRTLEDGSMDTDKLIEDIKFRTEEIYATLKDESDIDEIYPPRVVSIIDKTRARFPLKLTHADRYCTDRVALVGDAAHTTHPLAGQGLNMGQTDVHGLVYALEKAMERGLDIGSSLSLEPFWAERYPSNNVLLGMADKLFKLYHTNFPPVVALRTFGLNLTNKIGPVKNMIIDTLGGNEK* +>YGR254Wb +IEKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL* + diff -Nru libpappsomspp-0.8.15/tests/data/peaklist_15046.mgf libpappsomspp-0.8.58/tests/data/peaklist_15046.mgf --- libpappsomspp-0.8.15/tests/data/peaklist_15046.mgf 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/peaklist_15046.mgf 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,405 @@ +BEGIN IONS +PEPMASS=628.86414 +CHARGE=2+ +TITLE=Elution from: 0.03 to 0.03 period: 0 experiment: 1 cycles: 1 +87.044518 18144.138672 +87.055824 8354.851562 +87.063744 2016.232910 +87.100098 18421.673828 +88.039680 9698.241211 +89.060104 44192.640625 +89.071327 2624.996826 +91.054779 2603.166260 +95.086212 1365.674316 +98.023689 3297.584717 +98.060287 12331.965820 +99.044670 2327.026611 +99.055923 1545.317993 +100.075584 1391.067993 +101.059868 1451.454834 +101.071022 13954.998047 +102.055191 21067.572266 +102.067963 1751.412842 +102.668068 1359.763184 +103.039200 24412.833984 +104.053139 11923.086914 +104.058647 1342.618530 +110.071404 38867.855469 +111.074142 1669.391968 +112.075729 11409.827148 +112.087006 8545.700195 +113.059448 2408.010254 +113.071121 2622.328857 +114.091179 1925.284790 +115.049995 1874.524780 +115.086487 11461.291992 +116.070557 6221.220703 +117.090759 1933.492676 +120.080780 69923.148438 +121.084206 6431.173340 +124.075020 3348.915283 +127.049965 5576.637207 +127.086334 11661.118164 +128.070465 2376.371094 +129.065613 5615.301270 +129.102066 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libpappsomspp-0.8.15/tests/data/tandem/database.xml libpappsomspp-0.8.58/tests/data/tandem/database.xml --- libpappsomspp-0.8.15/tests/data/tandem/database.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/database.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,7 @@ + + + + + + + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml libpappsomspp-0.8.58/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml --- libpappsomspp-0.8.15/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,81 @@ + + + 30 + yes + 0.05 + 0.05 + yes + yes + no + yes + yes + valid + yes + spectrum + yes + tandem-style.xsl + 0.0 + 0.0 + +17.00305 + +1.00794 + no + [RK]|{P} + + yes + yes + yes + yes + no + 0.01 + 57.02146@C + + + no + + +42.01056@[ + 15.99491@M + + + + + + yes + no + yes + 57.02146@C + + + 15.99491@M + + no + yes + no + yes + yes + 1 + 4 + no + yes + no + 100.0 + monoisotopic + 0.02 + Daltons + 4 + 150.0 + 500.0 + 15 + 18.01057 + 0.02 + 10 + 10 + ppm + yes + 1000 + 1 + 20000 2.0 4 10.0 + + 100 + no + yes + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/settings/timstofmgf.xml libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf.xml --- libpappsomspp-0.8.15/tests/data/tandem/settings/timstofmgf.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,87 @@ + + + 30 + yes + 0.1 + 0.01 + no + yes + yes + no + yes + yes + all + yes + spectrum + yes + tandem-style.xsl + 0.0 + 0.0 + +17.00305 + +1.00794 + no + [RK]|{P} + + yes + yes + yes + yes + yes + 0.01 + 57.02146@C + + + no + + + 15.99491@M + + + + + + yes + no + yes + 57.02146@C + + + 15.99491@M + + + + + + no + yes + no + yes + yes + 1 + 4 + no + yes + no + 100 + monoisotopic + 0.02 + Daltons + 4 + 150 + 300 + 15 + 18 + 0.02 + 15 + 15 + ppm + yes + 1000 + 5 + 50000 2.0 4 10.0 + 100 + no + no + yes + + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/settings/timstofmgf_wrong.xml libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf_wrong.xml --- libpappsomspp-0.8.15/tests/data/tandem/settings/timstofmgf_wrong.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/settings/timstofmgf_wrong.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,87 @@ + + + 30 + yes + 0.1 + 0.01 + no + yes + yes + no + yes + yes + all + yes + spectrum + yes + tandem-style.xsl + 0.0 + 0.0 + +17.00305 + +1.00794 + no + [RK]|{P} + + yes + yes + yes + yes + yes + 0.01 + 57.02146@C + + + no + + + 15.99491@M + + + + + + yes + no + yes + 57.02146@C + + + 15.99491@M + + + + + + no + yes + no + yes + yes + 1 + 4 + no + yes + no + 100 + monoisotopic + 0.02 + Daltons + 4 + 150 + 300 + 15 + 18 + 0.02 + 15 + 15 + ppm + yes + 1000 + 5 + 50000 2.0 4 10.0 + 100 + no + no + yes + + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/tandem_result_file.xml libpappsomspp-0.8.58/tests/data/tandem/tandem_result_file.xml --- libpappsomspp-0.8.15/tests/data/tandem/tandem_result_file.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/tandem_result_file.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,44302 @@ + + + + + +GRMZM2G121878_P01 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T01; parent_gene=GRMZM2G121878 + + + MSSCLCLPKK KEGPAKEKPS TDTPTSSLLQ NQKPSQPPPP PSKASSKGMD + PTVERLKSGF QKFKTEVYDK KPELFEPLKS GQSPRYMVFA CSDSRVCPSV + TLGLQPGEAF TVRNIASMVP PYDKIKYAGT GSAIEYAVCA LKVQVIVVIG + HSCCGGIRAL LSLKDGAPDN FHFVEDWVRI GSPAKNKVKK EHASVPFDDQ + CSILEKEAVN VSLQNLKSYP FVKEGLAGGT LKLVGAHYDF VKGQFVTWEP + PQDAIERLTS GFQQFKVNVY DKKPELFGPL KSGQAPKYMV FACSDSRVCP + SVTLGLQPGE AFTVRNIAAM VPGYDKTKYT GIGSAIEYAV CALKVEVLVV + IGHSCCGGIR ALLSLQDGAP DTFHFVEDWV KIGFIAKMKV KKEHASVPFD + DQCSILEKEA VNVSLENLKT YPFVKEGLAN GTLKLIGAHY DFVSGEFLTW + KK + + + + + +GRMZM2G121878_P02 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T02; parent_gene=GRMZM2G121878 + + + MSSCLCLPKK KEGPAKEKPS TDTPTSSLLQ NQKPSQPPPP PSKASSKGMD + PTVERLKSGF QKFKTEVYDK KPELFEPLKS GQSPRYMVFA CSDSRVCPSV + TLGLQPGEAF TVRNIASMVP PYDKIKYAGT GSAIEYAVCA LKVQVIVVIG + HSCCGGIRAL LSLKDGAPDN FHFVEDWVRI GSPAKNKVKK EHASVPFDDQ + CSILEKEAVN VSLQNLKSYP FVKEGLAGGT LKLVGAHYDF VKGQFVTWEP + PQDAIERLTS GFQQFKVNVY DKKPELFGPL KSGQAPKYMV FACSDSRVCP + SVTLGLQPGE AFTVRNIAAM VPGYDKTKYT GIGSAIEYAV CALKVEVLVV + IGHSCCGGIR ALLSLQDGAP DTFHFVEDWV KIGFIAKMKV KKEHASVPFD + DQCSILEKEA VNVSLENLKT YPFVKEGLAN GTLKLIGAHY DFVSGEFLTW + KK + + + + + +GRMZM2G121878_P05 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469087..215473931:-1; parent_transcript=GRMZM2G121878_T05; parent_gene=GRMZM2G121878 + + + MSSCLCLPKK KEGPAKEKPS TDTPTSSLLQ NQKPSQPPPP PSKASSKGMD + PTVERLKSGF QKFKTEVYDK KPELFEPLKS GQSPRYMVFA CSDSRVCPSV + TLGLQPGEAF TVRNIASMVP PYDKIKYAGT GSAIEYAVCA LKVQVIVVIG + HSCCGGIRAL LSLKDGAPDN FHFVEDWVRI GSPAKNKVKK EHASVPFDDQ + CSILEKEAVN VSLQNLKSYP FVKEGLAGGT LKLVGAHYDF VKGQFVTWEP + VGVHAHSSSF RATPID + + + + + +GRMZM2G121878_P06 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469442..215473931:-1; parent_transcript=GRMZM2G121878_T06; parent_gene=GRMZM2G121878 + + + MSSCLCLPKK KEGPAKEKPS TDTPTSSLLQ NQKPSQPPPP PSKASSKGMD + PTVERLKSGF QKFKTEVYDK KPELFEPLKS GQSPRYMVFA CSDSRVCPSV + TLGLQPGEAF TVRNIASMVP PYDKIKYAGT GSAIEYAVCA LKVQVIVVIG + HSCCGGIRAL LSLKDGAPDN FHFVEDWVRI GSPAKNKVKK EHASVPFDDQ + CSILEKEAVN VSLQNLKSYP FVKEGLAGGT LKLVGAHYDF VKGQFVTWEP + VGVHAHSSSF RATPID + + + + + + +7.72976 +-0.46847 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +1567 1567 1567 1567 1567 1567 1567 1222 1088 750 596 106 41 13 4 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1562 1562 1562 1562 1562 1562 1562 1217 1083 744 584 79 24 1 0 + + + + + + +0 1 2 3 4 + + + + +712 829 31 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +804 754 9 4 0 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2004 (charge 2) + +1401.75 +2 + + +161.706 195.115 209.055 226.083 243.108 331.197 337.153 370.792 428.25 466.756 525.303 683.727 719.409 1031.56 + + + + +26 26 34 38 36 32 37 34 100 32 94 29 59 60 + + + + + + +GRMZM2G121878_P01 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T01; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P02 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T02; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P05 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469087..215473931:-1; parent_transcript=GRMZM2G121878_T05; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P06 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469442..215473931:-1; parent_transcript=GRMZM2G121878_T06; parent_gene=GRMZM2G121878 + + + + + + + + +5.47408 +-0.267029 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +7983 7983 7964 7321 6505 5518 4378 3427 2622 1813 1180 792 328 186 91 28 13 6 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7988 7988 7964 7223 6196 5090 3908 2613 1830 985 395 89 24 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2316 3439 1615 444 138 34 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1126 3325 2304 950 185 52 43 7 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2019 (charge 3) + +1401.75 +3 + + +153.102 157.097 167.081 167.118 175.119 179.118 181.06 181.097 181.133 184.071 184.108 185.091 195.113 196.116 198.087 199.108 203.102 209.056 212.139 216.134 226.155 227.103 234.144 240.134 243.108 246.122 254.149 263.155 267.144 269.139 +278.113 282.144 286.627 292.128 295.139 300.155 307.633 309.155 311.681 316.644 318.171 320.124 324.657 326.182 331.197 332.199 337.15 338.152 351.165 354.176 355.186 360.207 365.174 371.202 373.183 379.198 383.194 397.207 398.204 402.174 +406.208 410.24 424.218 428.25 430.255 434.201 441.245 447.195 452.244 465.207 468.838 476.251 482.235 483.238 492.251 494.261 507.297 525.303 527.307 535.247 538.286 544.253 552.28 555.287 562.262 572.315 579.284 604.34 622.354 624.359 +638.33 648.306 652.337 666.321 683.348 695.405 719.408 721.411 830.44 + + + + +1 11 8 11 1 1 2 6 1 4 3 8 33 3 2 10 7 6 2 5 28 8 12 6 23 1 3 7 2 1 +7 5 3 3 15 24 1 8 20 3 1 5 2 3 34 7 12 1 2 8 1 16 1 2 1 6 1 9 1 1 +1 9 5 100 5 1 6 2 4 1 4 1 8 2 2 7 6 79 6 1 1 1 1 4 2 2 2 4 43 3 +1 1 1 3 8 2 13 1 1 + + + + + + +GRMZM2G140667_P01 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589206..218592127:-1; parent_transcript=GRMZM2G140667_T01; parent_gene=GRMZM2G140667 + + + MRTASPGWLP PNSFHPRLLR SDGPPGPAAG RIASAAMVKA YPTVNEDYLK + AVDKAKRKLR GLIAEKNCAP LMLRLAWHSA GTFDVATKTG GPFGTMKNPA + EQAHGANAGL EIAIRLLEPI KEQFPILSYA DFYQLAGVVA VEVTGGPDVP + FHPGRQDKPE PPPEGRLPDA TQGSDHLRQV FSTQMGLSDQ DIVALSGGHT + LGRCHKDRSG FEGAWTSNPL IFDNSYFKEL LSGEKEGLLQ LPSDKALLSD + PSFRPLVDKY AADEDAFFAD YAEAHLKLSE LGFAEA + + + + + +GRMZM2G140667_P02 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589352..218592127:-1; parent_transcript=GRMZM2G140667_T02; parent_gene=GRMZM2G140667 + + + MRTASPGWLP PNSFHPRLLR SDGPPGPAAG RIASAAMVKA YPTVNEDYLK + AVDKAKRKLR GLIAEKNCAP LMLRLAWHSA GTFDVATKTG GPFGTMKNPA + EQAHGANAGL EIAIRLLEPI KEQFPILSYA DFYQLAGVVA VEVTGGPDVP + FHPGRQDKPE PPPEGRLPDA TQGSDHLRQV FSTQMGLSDQ DIVALSGGHT + LGRCHKDRSG FEGAWTSNPL IFDNSYFKEL LSGEKEGLLQ LPSDKALLSD + PSFRPLVDKY AADEDAFFAD YAEAHLKLSE LG + + + + + +GRMZM2G140667_P04 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589294..218592021:-1; parent_transcript=GRMZM2G140667_T04; parent_gene=GRMZM2G140667 + + + MKNPAEQAHG ANAGLEIAIR LLEPIKEQFP ILSYADFYQL AGVVAVEVTG + GPDVPFHPGR QDKPEPPPEG RLPDATQGSD HLRQVFSTQM GLSDQDIVAL + SGGHTLGRCH KDRSGFEGAW TSNPLIFDNS YFKELLSGEK EGLLQLPSDK + ALLSDPSFRP LVDKYAADED AFFADYAEAH LKLSELGFAE A + + + + + + +5.38227 +-0.347243 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6644 6644 6644 6644 6235 5853 5330 3422 2506 929 411 163 77 23 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6646 6646 6646 6646 6237 5836 5300 3237 2289 616 220 53 20 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4042 2218 355 48 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1435 3942 1072 154 44 1 0 19 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2028 (charge 3) + +1249.62 +3 + + +158.093 167.118 169.134 175.119 181.061 195.112 197.128 199.107 209.092 212.139 215.139 220.003 227.102 232.141 238.013 248.035 249.042 262.05 266.044 271.1 273.043 278.148 284.008 290.045 322.188 327.515 337.186 361.185 372.161 441.211 +452.214 458.236 466.191 469.242 472.169 495.252 503.664 545.238 555.289 563.246 580.275 652.338 846.722 900.298 1056.68 + + + + +8 5 5 26 6 22 10 19 8 7 8 36 28 59 31 51 6 100 42 6 8 35 27 28 6 6 6 8 8 8 +28 94 12 8 6 6 6 8 54 20 9 20 6 6 6 + + + + + + +GRMZM2G052036_P01 NP_001143161 hypothetical protein LOC100275650 seq=translation; coord=10:60021321..60022270:1; parent_transcript=GRMZM2G052036_T01; parent_gene=GRMZM2G052036 + + + MQQIISACKL PHTQRAAAFL PPRPSLRRLP VPGLDRPAGG APPPRRLVVR + RRCQEENKQQ QEAEEGSGAD EQEQQKRTFL SLEEAGLVEM SGLSTHERFL + CRLTISSLNL LRVISEQEGV PIEELNAGRV CDWFLKDKLK REQNVGTAVL + QWDDPGF + + + + + + +5.82718 +-0.375947 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +2721 2721 2721 2721 2721 2721 2721 2478 1225 624 276 133 35 6 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2726 2726 2726 2726 2726 2726 2726 2483 1220 601 258 120 29 5 1 0 + + + + + + +0 1 2 3 + + + + +2030 670 28 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +470 2133 116 3 2 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2039 (charge 3) + +2174.95 +3 + + +151.218 163.267 168.643 175.12 201.087 240.098 241.081 257.126 284.859 299.061 359.023 368.157 431.278 559.333 666.813 689.376 816.431 945.476 951.415 1060.5 1078.51 1188.55 + + + + +18 19 18 43 24 100 33 35 21 32 29 38 28 41 43 32 48 44 32 43 31 56 + + + + + + +GRMZM2G449496_P01 NP_001169327 hypothetical protein LOC100383193 seq=translation; coord=8:85120975..85124082:1; parent_transcript=GRMZM2G449496_T01; parent_gene=GRMZM2G449496 + + + MAPALTSNPP SFRPLTSPLR RRAATVPCRV GKPGKDSSAA DDATGPNKRP + NLFADFGNAK SLIQAFPSQS LFAGGGRGRK DPQTVFVAGA TGQAGVRIAQ + TLLRQGFAVR AGVPDLASAQ ELARLAAAYR LISPAEARRL NAVEAGFGDP + DAIAKSIGPA AKVVVTVGSA EKGPEGGGVT TDDALRVVRA ADLASVAHVV + VVYDEGAASG GLGGGGSTYN VLDGFTSFFS NLFSREQQAL TLSQFLAKVA + ETDVRYTLVK ASLTDDYTPE SYYAQLVLTK EGVSPSDTGK VSRSQIAALV + ADVFSNVAVA ENKVVEVSTS SSATAKNIAE AFTAIPEDRR RTEYLEAAAK + AQAEEETLAS ERANKKAEAA ASKSEADTKT TPSEEAAATP SAVNGAQASL + ENLLSRAKVI SADFSWEKFS TQFADVTTPL TSSLEKEPNK AQIATVRGQE + KAKKLAPRIA VVKPAAQKAK QPDPKPEVRA LFGGLFKQET VYVDDD + + + + + + +3.85356 +-0.308285 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +3905 3905 3847 3398 2334 1685 980 576 194 66 2 1 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 + + + + +3912 3912 3854 3383 2251 1579 876 478 116 40 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1533 1892 440 48 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1120 2073 624 91 7 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2063 (charge 3) + +1615.73 +3 + + +157.061 159.077 167.055 167.081 168.056 169.052 175.071 175.119 184.108 185.055 187.071 203.066 212.103 215.103 223.064 226.118 230.114 239.095 241.092 244.165 245.095 254.077 258.106 272.088 281.052 283.049 299.061 301.059 303.057 345.975 +346.975 348.971 359.028 361.026 386.213 391.715 416.037 417.034 419.031 435.044 442.239 469.757 478.258 498.272 505.105 526.76 535.267 584.27 619.792 628.306 646.275 655.305 694.428 699.315 725.405 766.403 782.427 874.51 883.474 938.512 +1083.85 + + + + +5 5 42 4 11 13 11 1 2 5 2 5 7 2 10 6 5 12 8 2 1 2 1 4 2 6 74 100 5 7 +18 1 7 16 2 2 8 29 4 2 1 1 1 1 2 1 2 2 3 2 1 1 4 1 5 2 6 6 6 4 +1 + + + + + + +GRMZM2G121878_P01 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T01; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P02 NP_001147846 carbonic anhydrase seq=translation; coord=3:215466579..215473931:-1; parent_transcript=GRMZM2G121878_T02; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P05 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469087..215473931:-1; parent_transcript=GRMZM2G121878_T05; parent_gene=GRMZM2G121878 + + + + + + + +GRMZM2G121878_P06 NP_001147846 carbonic anhydrase seq=translation; coord=3:215469442..215473931:-1; parent_transcript=GRMZM2G121878_T06; parent_gene=GRMZM2G121878 + + + + + + + + +5.78782 +-0.330732 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +8324 8324 8324 8324 8324 5958 5182 3554 2294 1693 895 417 160 50 18 2 1 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +8336 8336 8336 8336 8336 5970 5173 3436 2170 1581 750 328 123 22 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +5880 2142 294 16 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1163 5759 1274 126 9 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2087 (charge 3) + +1529.81 +3 + + +152.056 167.08 175.119 181.06 195.113 199.071 199.108 210.025 226.154 244.165 258.078 293.23 300.156 311.681 314.099 331.198 354.142 360.208 379.2 428.249 448.185 464.243 525.304 530.274 577.34 622.352 719.403 1199.99 1295.2 1527.16 + + + + + +39 9 11 11 48 13 15 51 100 41 9 8 13 12 9 16 15 14 10 93 11 10 69 16 12 59 36 11 11 11 + + + + + + + +GRMZM2G401308_P03 NP_001105088 histone H1-like protein seq=translation; coord=7:11441042..11442532:-1; parent_transcript=GRMZM2G401308_T03; parent_gene=GRMZM2G401308 + + + MSTEEAVVAE VPVTEVPAEV PAAQVAEAPK AKKAPKEKKA PKEKKLSAAK + KPAAHPPYAE MIVEAIAALK ERKGSSSVAI SKYVEGKHGG KLPTNFRKQL + TVQLKKLAAA GKLTRVKNSF KLPATDAKPK AAKPKAPKAA PKPKPSPKAK + AKTAAKPKAA SPKPKAKAKA KPVAPAAASP KPRGRPPKVA KTSAKASPAK + AAKKAAAPAK KGKAAAAPKK VATPKKAAAA AAPARKGVAR KAKK + + + + + +GRMZM2G401308_P04 NP_001105088 histone H1-like protein seq=translation; coord=7:11441303..11442532:-1; parent_transcript=GRMZM2G401308_T04; parent_gene=GRMZM2G401308 + + + MSTEEAVVAE VPVTEVPAEV PAAQVAEAPK AKKAPKEKKA PKEKKLSAAK + KPAAHPPYAE VRFSPLRSSR FVASLGSSPL MESVGLILSL CSVHVREFDI + ESETQPVGSV WLQMIVEAIA ALKERKGSSS VAISKYVEGK HGGKLPTNFR + KQLTVQLKKL AAAGKLTRVK NSFKLPATDA KPKAAKPKAP KAAPKPKPSP + KAKAKTAAKP KAASPKPKAK AKAKPVAPAA ASPKPRGRPP KVAKTSAKAS + PAKAAKKAAA PAKKGKAAAA PKKVATPKKA AAAAAPARKG VARKAKK + + + + + +GRMZM2G401308_P01 NP_001105088 histone H1-like protein seq=translation; coord=7:11440921..11442532:-1; parent_transcript=GRMZM2G401308_T01; parent_gene=GRMZM2G401308 + + + PRCQRRSRRP RWPRRPRRRR RPRRRRRLRR RSFPRRRSRR RTLPTLSGKL + PTNFRKQLTV QLKKLAAAGK LTRVKNSFKL PATDAKPKAA KPKAPKAAPK + PKPSPKAKAK TAAKPKAASP KPKAKAKAKP VAPAAASPKP RGRPPKVAKT + SAKASPAKAA KKAAAPAKKG KAAAAPKKVA TPKKAAAAAA PARKGVARKA + KK + + + + + +GRMZM2G401308_P02 NP_001105088 histone H1-like protein seq=translation; coord=7:11441042..11445373:-1; parent_transcript=GRMZM2G401308_T02; parent_gene=GRMZM2G401308 + + + MMVTREHPMR SRECQLCHEN PLSSPSMTKM IVEAIAALKE RKGSSSVAIS + KYVEGKHGGK LPTNFRKQLT VQLKKLAAAG KLTRVKNSFK LPATDAKPKA + AKPKAPKAAP KPKPSPKAKA KTAAKPKAAS PKPKAKAKAK PVAPAAASPK + PRGRPPKVAK TSAKASPAKA AKKAAAPAKK GKAAAAPKKV ATPKKAAAAA + APARKGVARK AKK + + + + + + +4.02217 +-0.277391 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +2231 2231 2230 2161 1846 1321 1005 369 207 137 60 31 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2237 2237 2236 2163 1836 1315 945 296 159 86 25 13 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1296 710 206 26 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +411 1400 346 68 6 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2096 (charge 3) + +1360.8 +3 + + +154.085 158.092 169.097 169.133 170.137 171.112 173.092 175.119 183.112 185.164 197.128 198.125 199.107 226.155 239.161 244.165 249.041 254.15 268.165 305.957 309.204 311.171 324.203 326.011 338.197 341.141 355.196 443.25 447.761 453.342 +455.254 470.261 483.279 495.754 497.316 504.283 584.351 623.824 655.384 726.423 797.455 894.516 896.527 922.504 965.551 1179.3 + + + + +1 2 8 18 1 2 1 11 2 1 15 1 7 23 100 13 5 1 8 1 2 2 6 2 2 2 1 1 6 2 +4 4 4 2 7 1 5 2 6 2 5 12 2 1 2 2 + + + + + + +GRMZM5G845611_P01 B4F8L7 Glyceraldehyde-3-phosphate dehydrogenase BPutative uncharacterized protein ; seq=translation; coord=1:6410461..6413123:1; parent_transcript=GRMZM5G845611_T01; parent_gene=GRMZM5G845611 + + + MATHAALAAS RIPAGARLHS RAPASSRHGV QRLDFADFSG LRPGSCSVSA + AAREASFSDV LGAQLVAKAT GENAVRAPAE AKLKVAINGF GRIGRNFLRC + WHGREDSPID VVVVNDSGGV RNASHLLKYD SMLGTFKADV KIVDDTTISV + DGKPITVVSS RDPLKLPWGE LGIDIVIEGT GVFVDGPGAG KHIQAGAKKV + IITAPAKGAD IPTYVVGVNE GDYDHSVADI ISNASCTTNC LAPFVKILDE + EFGIVKGTMT TTHSYTGDQR LLDASHRDLR RARAAALNIV PTSTGAAKAV + ALVLPQLKGK LNGIALRVPT PNVSVVDLVI NTVKTGITAD DVNAAFRKAA + AGPLQGILEV CDVPLVSVDF RCSDVSCTID ASLSMVMGDD MVKVVAWYDN + EWGYSQRVVD LAHLVAAKWP GAAAAGSGDP LEDFCKDNPE TDECKVYEA + + + + + + +GRMZM2G337113_P02 P09315 Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic Precursor (EC 1.2.1.13)(NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) seq=translation; coord=2:42257261..42259297:-1; parent_transcript=GRMZM2G337113_T02; parent_gene=GRMZM2G337113 + + + MASSMLSATT VPLQQGGGLS EFSGLRSSAS LPMRRNATSD DFMSAVSFRT + HAVGTSGGSR RAPTEAKLKV AINGFGRIGR NFLRCWHGRG DASPLDVIAI + NDTGGVKQAS HLLKYDSTLG IFDADVKPVG DNAISVDGKV IKVVSDRNPS + NLPWGELGID LVIEGTGVFV DREGAGKHIQ AGAKKVLITA PGKGDIPTYV + VGVNADQYNP DEPIISNASC TTNCLAPFVK VLDQKFGIIK GTMTTTHSYT + GDQRLLDASH RDLRRARAAA LNIVPTSTGA AKAVSLVLPN LKGKLNGIAL + RVPTPNVSVV DLVVQVSKKT LAEEVNQAFR DAAANELTGI LEVCDVPLVS + VDFRCSDVSS TIDASLTMVM GDDMVKVISW YDNEWGYSQR VVDLADICAN + QWK + + + + + + + +3.12555 +-0.250044 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +2579 2579 2573 2400 1466 1194 696 432 235 76 28 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +2585 2585 2577 2403 1392 1154 520 262 80 32 7 1 0 + + + + + + +0 1 2 3 4 + + + + +1666 774 126 24 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +486 1406 599 85 8 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2100 (charge 3) + +1571.67 +3 + + +157.097 159.077 167.055 169.052 175.119 185.092 195.088 221.152 225.098 239.089 269.123 286.15 299.061 301.058 303.177 304.181 309.203 347.974 348.971 419.035 420.993 475.226 482.216 492.227 523.733 576.275 583.271 675.303 689.305 735.106 +739.329 826.363 944.377 963.448 1003.31 1445.5 + + + + +2 6 4 3 5 2 1 1 2 14 1 3 2 13 36 6 100 2 1 1 1 5 2 1 1 7 1 1 1 1 +6 12 1 1 1 1 + + + + + + +GRMZM2G027995_P01 Q41741 Eukaryotic initiation factor 4A (eIF-4A)(EC 3.6.4.13)(ATP-dependent RNA helicase eIF4A) seq=translation; coord=6:87119198..87122939:1; parent_transcript=GRMZM2G027995_T01; parent_gene=GRMZM2G027995 + + + MAGMAPEGSQ FDAKHYDSKM QELLSTGETE EFFTSYDEVF ESFDDMGLQE + NLLRGIYAYG FEKPSAIQQR GIVPFCKGLD VIQQAQSGTG KTATFCSGIL + QQLDYGLVEC QALVLAPTRE LAQQIEKVMR ALGDYLGVKV HACVGGTSVR + EDQRILASGV HVVVGTPGRV FDMLRRQSLR PDNIKMFVLD EADEMLSRGF + KDQIYDIFQL LPSKIQVGVF SATMPPEALE ITRKFMNKPV RILVKRDELT + LEGIKQFYVN VDKEDWKLDT LCDLYETLAI TQSVIFVNTR RKVDWLTDKM + RSRDHTVSAT HGDMDQNTRD IIMREFRSGS SRVLITTDLL ARGIDVQQVS + LVINYDLPTQ PENYLHRIGR SGRFGRKGVA INFVTRDDER MLFDIQKFYN + VLIEELPANV ADLL + + + + + +GRMZM2G027995_P02 Q41741 Eukaryotic initiation factor 4A (eIF-4A)(EC 3.6.4.13)(ATP-dependent RNA helicase eIF4A) seq=translation; coord=6:87119221..87123018:1; parent_transcript=GRMZM2G027995_T02; parent_gene=GRMZM2G027995 + + + MAGMAPEGSQ FDAKHYDSKM QELLSTGETE EFFTSYDEVF ESFDDMGLQE + NLLRGIYAYG FEKPSAIQQR GIVPFCKGLD VIQQAQSGTG KTATFCSGIL + QQLDYGLVEC QALVLAPTRE LAQQIEKVMR ALGDYLGVKV HACVGGTSVR + EDQRILASGV HVVVGTPGRV FDMLRRQSLR PDNIKMFVLD EADEMLSRGF + KDQIYDIFQL LPSKIQVGVF SATMPPEALE ITRKFMNKPV RILVKRDELT + LEGIKQFYVN VDKEDWKLDT LCDLYETLAI TQSVIFVNTR RKVDWLTDKM + RSRDHTVSAT HGDMDQNTRD IIMREFRSGS SRVLITTDLL ARGIDVQQVS + LVINYDLPTQ PENYLHRIGR SGRFGRKGVA INFVTRDDER MLFDIQKFYN + VLIEELPANV ADLL + + + + + +GRMZM2G116034_P02 NP_001104874 translation initiation factor seq=translation; coord=5:56777167..56780802:-1; parent_transcript=GRMZM2G116034_T02; parent_gene=GRMZM2G116034 + + + MAGMAPEGSQ FDAKHYDSKM QELLSTGETE EFFTSYDEVF ESFDDMGLQE + NLLRGIYAYG FEKPSAIQQR GIVPFCKGLD VIQQAQSGTG KTATFCSGIL + QQLDYGLVEC QALVLAPTRE LAQQIEKVMR ALGDYLGVKV HACVGGTSVR + EDQRILGSGV HVVVGTPGRV FDMLRRQSLR PDNIKMFVLD EADEMLSRGF + KDQIYDIFQL LPAKIQVGVF SATMPPEALE ITRKFMNKPV RILVKRDELT + LEGIKQFYVN VDKEDWKLDT LCDLYETLAI TQSVIFVNTR RKVDWLTDKM + RSRDHTVSAT HGDMDQNTRD IIMREFRSGS SRVLITTDLL ARGIDVQQVS + LVINYDLPTQ PENYLHRIGR SGRFGRKGVA INFVTRDDER MLFDIQKFYN + VLIEELPANV ADLL + + + + + +GRMZM2G116034_P01 NP_001104874 translation initiation factor seq=translation; coord=5:56776697..56780711:-1; parent_transcript=GRMZM2G116034_T01; parent_gene=GRMZM2G116034 + + + MAPEGSQFDA KHYDSKMQEL LSTGETEEFF TSYDEVFESF DDMGLQENLL + RGIYAYGFEK PSAIQQRGIV PFCKGLDVIQ QAQSGTGKTA TFCSGILQQL + DYGLVECQAL VLAPTRELAQ QIEKVMRALG DYLGVKVHAC VGGTSVREDQ + RILGSGVHVV VGTPGRVFDM LRRQSLRPDN IKMFVLDEAD EMLSRGFKDQ + IYDIFQLLPA KIQVGVFSAT MPPEALEITR KFMNKPVRIL VKRDELTLEG + IKQFYVNVDK EDWKLDTLCD LYETLAITQS VIFVNTRRKV DWLTDKMRSR + DHTVSATHGD MDQNTRDIIM REFRSGSSRV LITTDLLARG IDVQQVSLVI + NYDLPTQPEN YLHRIGRSGR FGRKGVAINF VTRDDERMLF DIQKFYNVLI + EELPANVADL L + + + + + + +5.81101 +-0.352182 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +3106 3106 3106 3106 3106 2856 1726 1367 623 220 115 37 19 8 2 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +3118 3118 3118 3118 3118 2868 1738 1316 591 196 95 35 22 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2295 750 60 1 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +467 2226 384 27 2 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2109 (charge 3) + +2027.89 +3 + + +150.319 152.226 157.463 175.119 276.166 299.137 310.116 348.674 359.166 470.669 518.267 537.227 553.237 555.228 580.464 650.294 764.335 774.34 826.434 911.448 927.461 936.388 938.407 955.452 1073.44 2074.33 + + + + +8 9 8 16 13 14 12 13 15 12 53 57 16 15 12 13 42 14 15 14 25 100 16 17 18 17 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + MASTKAPGPG EKHHSIDAQL RQLVPGKVSE DDKLIEYDAL LVDRFLNILQ + DLHGPSLREF VQECYEVSAD YEGKGDTTKL GELGAKLTGL APADAILVAS + SILHMLNLAN LAEEVQIAHR RRNSKLKKGG FADEGSATTE SDIEETLKRL + VSEVGKSPEE VFEALKNQTV DLVFTAHPTQ SARRSLLQKN ARIRNCLTQL + NAKDITDDDK QELDEALQRE IQAAFRTDEI RRAQPTPQDE MRYGMSYIHE + TVWKGVPKFL RRVDTALKNI GINERLPYNV SLIRFSSWMG GDRDGNPRVT + PEVTRDVCLL ARMMAANLYI DQIEELMFEL SMWRCNDELR VRAEELHSSS + GSKVTKYYIE FWKQIPPNEP YRVILGHVRD KLYNTRERAR HLLASGVSEI + SAESSFTSIE EFLEPLELCY KSLCDCGDKA IADGSLLDLL RQVFTFGLSL + VKLDIRQESE RHTDVIDAIT THLGIGSYRE WPEDKRQEWL LSELRGKRPL + LPPDLPQTDE IADVIGAFHV LAELPPDSFG PYIISMATAP SDVLAVELLQ + RECGVRQPLP VVPLFERLAD LQSAPASVER LFSVDWYMDR IKGKQQVMVG + YSDSGKDAGR LSAAWQLYRA QEEMAQVAKR YGVKLTLFHG RGGTVGRGGG + PTHLAILSQP PDTINGSIRV TVQGEVIEFC FGEEHLCFQT LQRFTAATLE + HGMHPPVSPK PEWRKLMDEM AVVATEEYRS VVVKEARFVE YFRSATPETE + YGRMNIGSRP AKRRPGGGIT TLRAIPWIFS WTQTRFHLPV WLGVGAAFKF + AIDKDVRNFQ VLKEMYNEWP FFRVTLDLLE MVFAKGDPGI AGLYDELLVA + EELKPFGKQL RDKYVETQQL LLQIAGHKDI LEGDPFLKQG LVLRNPYITT + LNVFQAYTLK RIRDPNFKVT PQPPLSKEFA DENKPAGLVK LNPASEYPPG + LEDTLILTMK GIAAGMQNTG + + + + + + + +4.9801 +-0.284577 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 + + + + +2740 2740 2725 2618 2477 1722 1572 1044 645 465 233 123 60 22 7 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +2750 2750 2735 2628 2479 1714 1415 922 528 327 96 44 19 8 3 1 0 + + + + + + +0 1 2 3 4 + + + + +1654 926 138 32 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +588 1722 364 68 1 0 1 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2135 (charge 2) + +1188.53 +2 + + +153.102 155.081 158.092 166.05 167.055 168.055 169.052 171.113 172.108 172.12 175.119 181.097 183.076 184.08 198.124 200.103 201.106 209.092 221.084 226.119 239.095 241.092 258.156 264.104 268.978 270.976 281.05 283.029 285.01 287.007 +297.155 299.061 301.06 303.02 305.018 309.204 322.153 341.144 344.976 346.974 355.07 357.068 359.031 364.172 369.19 373.081 375.08 387.198 396.171 401.984 415.037 417.035 419.994 420.992 443.169 446.695 451.2 470.187 495.22 502.226 +566.224 585.179 613.257 630.279 667.306 694.285 699.304 710.31 727.337 729.351 752.379 757.951 791.334 793.337 807.544 828.38 838.363 840.408 881.409 892.368 903.367 907.427 912.468 925.438 927.448 971.419 989.435 991.44 + + + + +4 8 2 28 44 9 1 53 6 1 12 11 66 5 2 62 5 6 2 11 75 14 15 1 17 4 1 1 100 30 +1 56 19 30 8 74 7 6 11 5 92 58 2 24 1 13 6 16 56 1 2 1 14 12 1 5 8 2 2 6 +11 1 2 8 2 9 1 5 57 3 1 1 39 5 1 4 2 1 4 2 1 6 1 68 10 2 16 2 + + + + + + +GRMZM2G153969_P01 NP_001149564 OB-fold nucleic acid binding domain containing protein seq=translation; coord=9:28603999..28607933:1; parent_transcript=GRMZM2G153969_T01; parent_gene=GRMZM2G153969 + + + MSTAPRRPFR GRGAPPPGTG YVRRGPAPAP GPADGAKTLR KPVFTTVDQL + RPQTHGHTLT ARVISARTVL DKPSTHIGRT RVAECLVGDS TGTVLVTARN + EQVDLLKPDT TVIFRNAKID MFKGTMRLVV DKWGRIEVTQ PADFKVNQDN + NMSLVEYELV DVDEEE + + + + + + +7.02473 +-0.453208 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +7715 7715 7715 7694 7396 6700 6206 3776 2739 1028 400 131 19 8 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7725 7725 7725 7704 7406 6709 6145 3631 2463 710 205 66 2 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3774 3174 592 154 30 3 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1917 4385 1206 203 12 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2141 (charge 3) + +1261.66 +3 + + +150.026 154.086 155.081 157.683 167.119 169.097 173.092 173.128 175.119 186.123 194.129 197.103 198.124 199.108 199.169 201.124 226.155 229.629 237.092 240.137 244.167 269.126 275.171 309.202 354.224 382.22 390.197 438.2 440.238 452.252 +458.25 472.287 522.316 550.308 558.292 615.311 712.359 942.41 + + + + +6 6 19 4 5 6 6 28 30 8 7 6 4 6 5 9 24 5 4 10 22 4 9 26 25 100 6 6 6 5 +6 5 32 17 8 21 7 5 + + + + + + +GRMZM2G167698_P01 seq=translation; coord=1:60966702..60970186:-1; parent_transcript=GRMZM2G167698_T01; parent_gene=GRMZM2G167698 + + + MDVALSTIVF VIAVFIPALL TLVQRSRSRH AGHNPPPPPE PRAIPLVGHL + HHLLRKKPLH RTLAHLAERH GDVLGLRFGS SRVAVVSSAS VAQQCLVALD + TSFGNRPRLP SARILSYEWS TMGHSNCGPY WRQARRTTST EFSSVERVQH + FADVHEQEAR AMARRLCRVA HASGGRALVD VKSRLLEMLM NGLLDMLFKR + TTSRSWSSDE KDEAVEVSEE ARCFMAMAEE TMELTLTVWD FLPPLARWLD + VDAVGRRLQR LQANRTEFLQ RLIEEHKEME KGGQVTRRTL VGVMLELQDK + DPEAYTDQLI RSLCVSALEA GTLSTGYTIE WVMSLLLNNP HIMKKARDEI + DACVGEPKRL LDATDLPKLP YLRCIILETL RLYPVVPLLV PRESSTNCTV + NGFNIAKGTM LLVNTFAIHR DPRTWDDPET FLPERFEDGS NQAGKTTTTT + DLSFGMGRRR CPAENLGMQL AGIALGTMIQ CFNWERVGTE LVDMAEGSGL + TMSKKVPLEA FCQPRASMVD LLANI + + + + + +GRMZM2G009232_P01 NP_001141257 hypothetical protein LOC100273344 seq=translation; coord=1:60675952..60678513:1; parent_transcript=GRMZM2G009232_T01; parent_gene=GRMZM2G009232 + + + MDVALSTIVF VIAIFIPALL TLVQRSRSRH AGHNPPPPPE PRAIPLVGHL + HHLLRKKPLH RCLAHLAERH GDVLGLRFGS SRVAVVSSAS VAQQCLVALD + TSFGNRPRLP SARILSYEWS TMGHSNCGPY WRQARRTTST EFSSVERVQH + FADVHEQEAR AMARRLCRVA HASGGRALVD VKSRLLEMLM NGLLDMLFRR + TTSRSRSSDE KDEAVEVSEE ARCFMAMAEE TMELTLTVWD FLPPLARWLD + VDAVGRRLQR LQANRTEFLQ RLIEEHKEME KSGQVTRRTL VGVMLELQDK + DPEAYTDQLI RSLCVSALEA GTLSTGYTIE WVMSLLLNNP HIMKKARDEI + DACVGEPKRL LDATDLPKLP YLRCIILETL RLYPVVPLLV PRESSTNCTV + NGFNIAKGTM LLVNTFAIHR DPRTWDDPET FLPERFEDGS NQSGKTTMDL + SFGMGRRRCP AENLGMQLAG IALGTMIQCF NWERVGTELV DMAEGSGLTM + AKKVPLEAFC QPRASMVDLL ANI + + + + + +GRMZM2G009232_P02 NP_001141257 hypothetical protein LOC100273344 seq=translation; coord=1:60675990..60678492:1; parent_transcript=GRMZM2G009232_T02; parent_gene=GRMZM2G009232 + + + MDVALSTIVF VIAIFIPALL TLVQRSRSRH AGHNPPPPPE PRAIPLVGHL + HHLLRKKPLH RCLAHLAERH GDVLGLRFGS SRVAVVSSAS VAQQCLVALD + TSFGNRPRLP SARILSYEWS TMGHSNCGPY WRQARRTTST EFSSVERVQH + FADVHEQEAR AMARRLCRVA HASGGRALVD VKSRLLEMLM NGLLDMLFRR + TTSRSRSSDE KDEAVEVSEE ARCFMAMAEE TMELTLTVWD FLPPLARWLD + VDAVGRRLQR LQANRTEFLQ RLIEEHKEME KSGQVTRRTL VGVMLELQDK + DPEAYTDQLI RSLVHSKLGH SVQAIQSSG + + + + + +GRMZM2G009232_P03 NP_001141257 hypothetical protein LOC100273344 seq=translation; coord=1:60675952..60677362:1; parent_transcript=GRMZM2G009232_T03; parent_gene=GRMZM2G009232 + + + MDVALSTIVF VIAIFIPALL TLVQRSRSRH AGHNPPPPPE PRAIPLVGHL + HHLLRKKPLH RCLAHLAERH GDVLGLRFGS SRVAVVSSAS VAQQCLVALD + TSFGNRPRLP SARILSYEWS TMGHSNCGPY WRQARRTTST EFSSVERVQH + FADVHEQEAR AMARRLCRVA HASGGRALVD VKSRLLEMLM NGLLDMLFRR + TTSRSRSSDE KDEAVEVSEE ARCFMAMAEE TMELTLTVWD FLPPLARWLD + VDAVGRRLQR LQANRTEFLQ RLIEEHKEME KSGQVTRRTL VGVMLELQDK + DPEAYTDQLI RSLCVVSIIL YVHSIHQFLI + + + + + + +5.78333 +-0.350505 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +6535 6535 6535 6535 6387 6064 5691 5250 3450 1989 1108 530 134 71 16 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6547 6547 6547 6547 6399 6076 5686 5242 3374 1865 650 268 72 27 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3697 2422 390 28 2 12 0 + + + + + + +0 1 2 3 4 5 + + + + +1126 3939 1292 169 25 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2164 (charge 3) + +1402.69 +3 + + +152.057 155.118 163.133 164.136 167.094 167.117 169.133 170.769 175.119 195.087 195.113 197.129 199.108 209.104 226.155 227.158 240.134 244.165 251.123 255.145 259.118 266.125 268.164 272.172 300.156 306.943 309.204 311.682 324.954 331.194 +334.949 348.967 364.024 403.18 428.25 469.099 517.223 525.303 545.482 579.292 595.32 642.33 692.367 785.397 937.207 + + + + +9 12 100 46 7 11 11 7 44 9 27 10 16 11 63 8 13 17 7 12 63 10 8 54 12 70 13 12 52 7 +11 11 12 14 39 30 26 29 9 9 29 10 16 9 10 + + + + + + +GRMZM2G071959_P01 P30755 Histone H2B.1 seq=translation; coord=7:119910222..119911045:1; parent_transcript=GRMZM2G071959_T01; parent_gene=GRMZM2G071959 + + + MAPKAEKKPA AKKPAEEEPA TEKVEKAPAG KKPKAEKRLP AGKSKEGGEG + KKGKKKAKKS VETYKIYIFK VLKQVHPDIG ISSKAMSIMN SFINDIFEKL + AAESAKLARY NKKPTITSRE IQTSVRLVLP GELAKHAVSE GTKAVTKFTS + S + + + + + + +6.03144 +-0.365542 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + + + + +9785 9785 9785 9785 9785 9594 8974 6732 4831 2534 1272 528 249 64 9 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9786 9786 9786 9786 9786 9595 8975 6701 4564 2126 875 305 136 13 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4420 4186 1015 153 15 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2453 5548 1640 142 7 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2171 (charge 3) + +1584.81 +3 + + +151.199 155.082 156.122 157.133 159.076 169.097 171.077 171.113 173.093 175.119 185.127 186.124 187.413 197.128 201.087 204.05 209.091 226.154 231.098 240.134 242.113 244.165 258.145 270.108 273.024 279.182 282.422 298.139 311.209 354.006 +375.227 412.181 427.184 430.158 451.752 458.262 466.231 477.732 490.242 520.274 537.257 555.276 632.359 666.306 684.318 733.41 794.387 805.456 885.495 938.414 1577.04 + + + + +11 15 11 29 13 71 56 15 20 29 11 13 9 11 13 11 16 82 18 26 19 13 14 51 12 14 14 20 14 13 +13 14 23 19 15 19 20 14 17 24 18 25 24 23 100 25 17 18 19 17 19 + + + + + + +GRMZM2G140667_P01 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589206..218592127:-1; parent_transcript=GRMZM2G140667_T01; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P02 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589352..218592127:-1; parent_transcript=GRMZM2G140667_T02; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P04 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589294..218592021:-1; parent_transcript=GRMZM2G140667_T04; parent_gene=GRMZM2G140667 + + + + + + + + +5.03355 +-0.245539 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +8369 8369 8306 8103 7608 7092 6135 4820 3369 2107 1314 788 477 301 160 98 39 12 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8371 8371 8308 8097 7535 6875 5709 3629 2049 689 203 57 20 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1541 3089 2317 1081 269 78 14 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1611 3512 2229 718 213 81 4 22 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2174 (charge 3) + +1249.62 +3 + + +155.082 157.108 158.092 167.118 172.108 173.092 175.119 181.061 181.097 181.133 195.113 196.117 198.087 198.123 199.071 199.108 203.608 209.092 212.139 215.114 217.082 220.003 226.118 228.106 229.621 232.14 235.124 244.128 248.034 262.05 +266.044 268.129 274.155 276.642 278.148 283.14 284.123 291.182 292.163 301.151 309.193 312.168 316.656 324.156 325.167 326.674 337.15 339.167 341.183 343.173 355.161 356.164 361.183 373.173 381.179 383.156 398.203 400.194 420.184 423.199 +424.224 434.204 435.889 438.196 441.208 442.211 452.214 453.214 458.235 460.241 466.193 467.197 469.24 471.239 480.21 484.203 485.207 495.256 517.24 535.252 538.261 539.268 545.235 549.267 552.277 555.288 557.293 563.246 566.293 567.295 +580.272 582.264 598.283 635.317 642.292 652.341 654.349 660.303 677.324 695.336 + + + + +1 3 11 4 5 2 19 3 5 6 20 2 2 4 4 12 2 4 5 6 2 2 22 2 6 61 2 2 2 4 +2 3 4 3 27 2 4 5 4 6 4 3 4 4 2 10 8 2 1 4 10 2 12 2 1 2 9 2 2 3 +5 2 1 3 8 2 33 6 100 5 16 4 18 2 1 9 2 7 3 2 7 1 14 4 2 61 4 22 6 2 +16 2 5 1 2 18 2 1 5 1 + + + + + + +GRMZM2G157462_P01 NP_001152484 dynamin-2A seq=translation; coord=6:115289930..115298874:1; parent_transcript=GRMZM2G157462_T01; parent_gene=GRMZM2G157462 + + + MEAMEELSEL AESMRQAASL LADDDPSDDA APRRPTTFLN AVALGNVGAG + KSAVLNSLIG HPVLPTGENG ATRAPIVVDL QREPGLSSKS IVLQIDSKSQ + QVSASALRHS LQDRLSRGAS GGSGRGRVDE IYLKLRTSTA PSLKLIDLPG + IDQRAVDDSM INEYAGHNDA ILLIVIPAMQ AADVASSRAL RLAKDIDADG + TRTVGVISKV DQANGDAKTI ACVQALLSNK GPKNLPDIEW VALIGQSVAI + ASAQSVGSEN SLETAWRAEA ESLKNILTGS PQNKLGRIAL VDTIAKQIRK + RMKVRVPNLL SGLQGKSQMV QDELARLGES MVQSAEGTRA VALELCREFE + DKFLAHITSG EGSGWKIVAS FEGKFPDRIK QLPLDRHFDL NNVKRIVLEA + DGYQPYLISP EKGLRSLIKI VLEMAKEPSR LCVEEVHRVL LDIVNASANA + TPGLGRYPPF KREVVAIASN ALETFKNDAK KMVVALVDME RAFVPPQHFI + RLVQRRMERQ RREDELRNRS SKKTQEAEQP TSKRASSPQT DAEQGGGSLK + SMKDKSGQQD KDTKEGSNLQ VAGPAGEITA GYLLKKSAKT NGWSKRWFVL + NEKSGKLGYT KKQEERHFRG VITLEECNLE EVEEEEPSKS SKDSKKANGS + EKISSLVFKI TNRVAYKTVL KAHSAVVLKA ESMADKVEWV NKIKAVIQSK + GGSFKGPSTE GSSMRQSNSD GALDTMARRP ADPEEELRWM SQEVRGYVEA + VLNSLAANVP KAIVLCQVEK AKEDMLNQLY SSISGQSNAK IEELLQEDHN + AKRRREKYQK QSSLLSKLTR QLSIHDNRAS VSSYSNDTTE AESPRTPTRS + GEDWRSAFDS ASNGPVAGST NSQSRSKSAD GRSRRYENGD VSSGANSGSR + RTPNRLPPAP PKY + + + + + +GRMZM5G811223_P01 seq=translation; coord=9:1743076..1749011:1; parent_transcript=GRMZM5G811223_T01; parent_gene=GRMZM5G811223 + + + MAFCLFGIDR MERQRREDEL RNRSSKKTQE AEQSTSKRAF SPQTDAEQGG + GSLKSMKDKS GQQDKDAKEG SNLQVAGPAG EITAGYLLKK SAKTNGWSKR + WFVLNEKSGK LGYTEKQEER HFRGVITLEE CNLEEVEEEE PSKSSKDSKK + ANGSEKPPSL VFKITNRVAY KTVLKAHSAV LLKAESMPDK VEWVNKIKAV + IQSKGGSFKG PSTEGGSMKQ SNSDGALDAM ARRPADPEEE LRWMSQEVRG + YVEAVLNSLA ANVPKAIVLC QVEKAKEDML NQLYSSISGQ SNAKIEELLQ + EDHNAKRRRE KYQKQSSLLS KLTRQLSIHD NRASVSSYSN DSTEVESPRT + PSRSGEDWRS AFDSSSNGPV ATSTNSESRS RSADGRSRRY ENGDVSSGAN + SGSRRTPNRL PPAPPKY + + + + + + +4.6853 +-0.302277 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + + + + +3664 3664 3664 3664 3568 2162 1982 1218 568 261 138 54 19 2 1 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +3679 3679 3679 3679 3583 2177 1979 1174 508 226 122 45 21 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +2648 968 67 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +541 2622 474 35 2 10 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2215 (charge 3) + +1655.73 +3 + + +155.081 167.056 169.097 171.077 173.092 175.119 199.107 201.123 225.042 239.095 241.093 244.166 283.945 299.061 355.071 520.246 563.263 648.305 661.853 684.323 718.277 735.305 737.324 745.406 822.369 925.203 1111.86 1370.24 + + + + +7 7 13 4 5 13 7 8 14 24 6 10 6 10 8 12 8 30 9 9 14 100 10 9 12 9 9 8 + + + + + + +GRMZM2G061876_P02 seq=translation; coord=5:128783450..128798039:1; parent_transcript=GRMZM2G061876_T02; parent_gene=GRMZM2G061876 + + + MQTQTLILRA GPSARRSTPP PASTVHLAAS GRCLLRAPSS LRRRRTRSLR + ASASLEQVKE VASSPAPSAG KSSQATRRDV RNIAIVAHVD HGKTTLVDSM + LRQAKVFRDN QVVQERIMDS NDLERERGIT ILSKNTSITY KGTKINIIDT + PGHSDFGGEV ERVLNMVEGV LLVVDSVEGP MPQTRFVLKK ALEFGHAVVV + VVNKIDRPTA RPEFVVNSTF ELFIELNATD EQCDFQTVYA SGIKGKASLS + PDNLADDLGP LFEAILRCIP EPRVEKDGAL QMLVSNTEYD EHKGRIAIGR + LHAGELQRGM EVKVCTPDDA CRVGKVSELF VYQNFSRAPV ESVSAGDICA + VCGIDDIMIG ETIADKVTGT PLPTIKVEEP TVRMSFSINT SPFVGREGKY + VTSRNLRDRL YRELERNLAM KVEDGETADT FLVSGRGTLH LTILIENMRR + EGYEFMIGPP KVINKTVDGK LLEPYEIAAV EVPEESMGSV VELLGKRRGQ + MVDMEANGTE GTTLLKYKIP TRGLIGLRNA ILTASRGRAI LNTIFDSYGP + WAGDLSSRDQ GSLVAFEDGS TTSYALLNAQ ERGMLFVQPG QDVYKGQIVG + IHQRPGDLAI NVCKKKAATN VRSNKETTVV LDEPLSYSLD DCIEFIQEDE + IVEVTPASIR MCKNPKVSKK K + + + + + + +5.78656 +-0.3507 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +5158 5158 5158 5158 4895 3222 2798 1735 1069 695 288 138 28 9 2 1 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5158 5158 5158 5158 4895 3218 2563 1604 786 444 166 94 2 1 1 0 + + + + + + +0 1 2 3 + + + + +3809 1276 92 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +792 3631 732 17 2 0 3 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2226 (charge 2) + +1100.56 +2 + + +157.061 167.055 167.081 169.097 171.114 175.12 183.113 199.107 201.124 204.134 211.108 218.82 221.084 225.042 229.118 235.063 239.095 240.096 244.166 246.126 247.99 256.128 272.171 275.172 282.145 295.102 299.06 321.445 459.259 525.745 +530.287 551.931 627.347 632.918 714.375 + + + + +6 36 7 9 6 8 25 13 68 6 7 5 7 32 11 11 100 8 11 6 5 9 13 6 11 9 26 6 60 7 +7 12 22 7 7 + + + + + + +GRMZM2G036464_P01 P38562 Glutamine synthetase root isozyme 4 (EC 6.3.1.2)(GS107)(Glutamate--ammonia ligase) seq=translation; coord=4:167081372..167084703:-1; parent_transcript=GRMZM2G036464_T01; parent_gene=GRMZM2G036464 + + + MACLTDLVNL NLSDTTEKII AEYIWIGGSG MDLRSKARTL PGPVTDPSKL + PKWNYDGSST GQAPGEDSEV ILYPQAIFKD PFRRGNNILV MCDCYTPAGE + PIPTNKRYSA AKIFSSLEVA AEEPWYGIEQ EYTLLQKDTN WPLGWPIGGF + PGPQGPYYCG IGAEKSFGRD IVDAHYKACL YAGINISGIN GEVMPGQWEF + QVGPSVGISS GDQVWVARYI LERITEIAGV VVTFDPKPIP GDWNGAGAHT + NYSTESMRKE GGYEVIKAAI EKLKLRHKEH IAAYGEGNER RLTGRHETAD + INTFSWGVAN RGASVRVGRE TEQNGKGYFE DRRPASNMDP YVVTSMIAET + TIVWKP + + + + + +GRMZM2G036464_P02 P38562 Glutamine synthetase root isozyme 4 (EC 6.3.1.2)(GS107)(Glutamate--ammonia ligase) seq=translation; coord=4:167081469..167084622:-1; parent_transcript=GRMZM2G036464_T02; parent_gene=GRMZM2G036464 + + + MACLTDLVNL NLSDTTEKII AEYIWIGGSG MDLRSKARTL PGPVTDPSKL + PKWNYDGSST GQAPGEDSEV ILYPQAIFKD PFRRGNNILV MCDCYTPAGE + PIPTNKRYSA AKIFSSLEVA AEEPWYGIEQ EYTLLQKDTN WPLGWPIGGF + PGPQGPYYCG IGAEKSFGRD IVDAHYKACL YAGINISGIN GEVMPGQWEF + QVGPSVGISS GDQVWVARYI LERITEIAGV VVTFDPKPIP GDWNGAGAHT + NYSTESMRKE GGYEVIKAAI EKLKLRHKEH IAAYGEGNER RLTGRHETAD + INTFSWVRF + + + + + +GRMZM2G050514_P01 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27977783..27980656:-1; parent_transcript=GRMZM2G050514_T01; parent_gene=GRMZM2G050514 + + + MASLTDLVNL DLSDCTDRII AEYIWIGGTG IDLRSKARTV KGPITDPSQL + PKWNYDGSST GQAPGEDSEV ILYPQAIFKD PFRKGNHILV MCDCYTPQGE + PIPTNKRYSA AKVFSHPDVA AEVPWYGIEQ EYTLLQKDVS WPLGWPVGGY + PGPQGPYYCA AGADKAFGRD VVDAHYKACL YAGINISGIN GEVMPGQWEF + QVGPSVGISA GDEIWVARYI LERITEMAGI VLSLDPKPIK GDWNGAGAHT + NYSTKSMREA GGYEVIKAAI DKLGKRHKEH IAAYGEGNER RLTGRHETAD + INTFKWGVAN RGASIRVGRD TEREGKGYFE DRRPASNMDP YVVTGMIAET + TILWNGN + + + + + +GRMZM2G050514_P02 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27977900..27980647:-1; parent_transcript=GRMZM2G050514_T02; parent_gene=GRMZM2G050514 + + + MASLTDLVNL DLSDCTDRII AEYIWIGGTG IDLRSKARTV KGPITDPSQL + PKWNYDGSST GQAPGEDSEV ILYPQAIFKD PFRKGNHILV SLCVVMCDCY + TPQGEPIPTN KRYSAAKVFS HPDVAAEVPW YGIEQEYTLL QKDVSWPLGW + PVGGYPGPQG PYYCAAGADK AFGRDVVDAH YKACLYAGIN ISGINGEVMP + GQWEFQVGPS VGISAGDEIW VARYILERIT EMAGIVLSLD PKPIKGDWNG + AGAHTNYSTK SMREAGGYEV IKAAIDKLGK RHKEHIAAYG EGNERRLTGR + HETADINTFK WGVANRGASI RVGRDTEREG KGYFEDRRPA SNMDPYVVTG + MIAETTILWN GN + + + + + +GRMZM2G050514_P03 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27978141..27981439:-1; parent_transcript=GRMZM2G050514_T03; parent_gene=GRMZM2G050514 + + + MEVGSVMASL TDLVNLDLSD CTDRIIAEYI WIGGTGIDLR SKARTVKGPI + TDPSQLPKWN YDGSSTGQAP GEDSEVILYP QAIFKDPFRK GNHILVMCDC + YTPQGEPIPT NKRYSAAKVF SHPDVAAEVP WYGIEQEYTL LQKDVSWPLG + WPVGGYPGPQ GPYYCAAGAD KAFGRDVVDA HYKACLYAGI NISGINGEVM + PGQWEFQVGP SVGISAGDEI WVARYILERI TEMAGIVLSL DPKPIKGDWN + GAGAHTNYST KSMREAGGYE VIKAAIDKLG KRHKEHIAAY GEGNERRLTG + RHETADINTF KWGVANRGAS IRVGRDTERE GKGYFEDRRP ASNMDPYVVT + GMIAETTILW NGN + + + + + + +5.86809 +-0.317194 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +9099 9099 8912 8419 7711 6964 4824 3453 1851 925 415 200 103 51 19 7 2 1 1 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +9109 9109 8916 8413 7674 6817 4501 2790 1131 334 79 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3208 4004 1536 292 53 31 3 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1970 4613 1913 483 103 13 9 25 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2249 (charge 3) + +1610.77 +3 + + +155.093 157.134 158.093 159.076 167.055 168.055 169.052 175.119 178.134 185.128 187.071 207.112 221.089 223.063 225.042 239.094 241.092 244.094 249.097 252.638 266.635 269.124 281.05 282.051 288.156 295.103 299.061 301.059 309.179 323.176 +324.177 337.672 344.698 346.973 350.183 360.028 361.026 377.193 380.216 384.152 390.71 395.206 401.179 416.037 417.034 423.202 448.23 458.197 461.75 466.24 475.225 480.292 494.237 504.267 508.29 514.253 532.262 558.277 575.307 586.265 +603.3 605.277 626.253 644.264 661.29 663.296 674.331 680.336 807.347 824.353 826.359 895.388 897.395 948.42 966.426 968.427 1079.52 + + + + +4 2 2 1 40 10 6 16 1 3 2 4 1 9 4 11 3 2 4 7 12 2 5 4 7 1 100 51 34 8 +2 4 22 9 2 12 9 6 4 1 1 7 2 23 19 5 1 3 2 2 20 2 3 7 2 3 6 2 3 1 +9 2 1 3 39 2 4 1 2 24 4 24 4 3 21 3 1 + + + + + + +GRMZM2G036464_P01 P38562 Glutamine synthetase root isozyme 4 (EC 6.3.1.2)(GS107)(Glutamate--ammonia ligase) seq=translation; coord=4:167081372..167084703:-1; parent_transcript=GRMZM2G036464_T01; parent_gene=GRMZM2G036464 + + + + + + + +GRMZM2G036464_P02 P38562 Glutamine synthetase root isozyme 4 (EC 6.3.1.2)(GS107)(Glutamate--ammonia ligase) seq=translation; coord=4:167081469..167084622:-1; parent_transcript=GRMZM2G036464_T02; parent_gene=GRMZM2G036464 + + + + + + + +GRMZM2G050514_P01 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27977783..27980656:-1; parent_transcript=GRMZM2G050514_T01; parent_gene=GRMZM2G050514 + + + + + + + +GRMZM2G050514_P02 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27977900..27980647:-1; parent_transcript=GRMZM2G050514_T02; parent_gene=GRMZM2G050514 + + + + + + + +GRMZM2G050514_P03 P38559 Glutamine synthetase root isozyme 1 (EC 6.3.1.2)(GS122)(Glutamate--ammonia ligase) seq=translation; coord=1:27978141..27981439:-1; parent_transcript=GRMZM2G050514_T03; parent_gene=GRMZM2G050514 + + + + + + + + +6.6034 +-0.338636 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +8872 8872 8790 8161 7440 5845 4236 2473 1402 778 390 199 81 36 19 3 2 2 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +8884 8884 8802 8140 7365 5623 3758 1889 713 237 40 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3080 3943 1498 297 44 9 31 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1781 4483 1958 513 122 13 6 28 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2254 (charge 3) + +1610.77 +3 + + +155.093 156.077 157.134 158.092 159.076 167.056 168.055 169.051 175.119 176.12 178.134 185.129 187.072 207.113 221.09 223.063 225.042 239.095 241.093 244.092 249.098 252.637 253.138 266.635 269.124 281.051 282.051 284.088 288.156 295.104 +299.062 301.06 309.179 323.177 336.185 344.698 346.974 359.028 361.026 367.209 377.193 380.223 390.711 394.215 401.177 405.194 415.036 417.035 423.202 433.048 441.175 448.23 458.203 466.24 475.226 480.293 494.234 504.267 508.29 514.252 +532.262 558.28 575.304 579.327 586.263 604.27 605.273 617.353 626.254 644.266 661.289 663.291 674.335 787.423 807.332 824.353 826.362 895.39 897.395 966.427 968.431 1079.52 + + + + +3 1 1 2 1 37 7 2 12 1 2 3 2 4 2 6 3 11 2 2 3 6 1 12 1 4 2 1 7 1 +100 27 29 7 4 19 4 10 5 1 5 4 2 5 2 1 15 11 4 1 1 2 1 3 18 1 3 4 1 2 +8 2 2 2 2 6 2 1 2 3 34 3 3 2 1 19 2 21 3 18 2 1 + + + + + + +GRMZM5G845611_P01 B4F8L7 Glyceraldehyde-3-phosphate dehydrogenase BPutative uncharacterized protein ; seq=translation; coord=1:6410461..6413123:1; parent_transcript=GRMZM5G845611_T01; parent_gene=GRMZM5G845611 + + + + + + + + +GRMZM2G337113_P02 P09315 Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic Precursor (EC 1.2.1.13)(NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) seq=translation; coord=2:42257261..42259297:-1; parent_transcript=GRMZM2G337113_T02; parent_gene=GRMZM2G337113 + + + + + + + + + +3.49696 +-0.279757 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 + + + + +2614 2614 2610 2520 1466 1245 753 296 123 78 4 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +2615 2615 2611 2520 1459 1234 523 187 62 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +1751 794 76 4 0 + + + + + + +0 1 2 3 4 5 6 + + + + +469 1642 481 27 0 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2260 (charge 3) + +1571.68 +3 + + +155.082 159.076 167.055 169.052 171.113 173.092 175.119 187.071 199.108 226.155 239.089 244.165 283.176 286.148 299.062 301.059 303.177 304.179 309.203 346.973 348.973 362.025 380.198 496.836 508.751 576.273 615.345 664.913 672.368 678.359 +696.412 739.343 759.401 774.803 826.363 830.433 901.473 1222.09 1333.11 + + + + +2 5 5 3 6 2 5 5 3 9 14 4 4 1 3 13 19 2 100 1 1 1 1 1 2 5 2 1 3 1 +1 2 4 1 7 5 1 1 1 + + + + + + +GRMZM2G140667_P01 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589206..218592127:-1; parent_transcript=GRMZM2G140667_T01; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P02 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589352..218592127:-1; parent_transcript=GRMZM2G140667_T02; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P04 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589294..218592021:-1; parent_transcript=GRMZM2G140667_T04; parent_gene=GRMZM2G140667 + + + + + + + + +4.43292 +-0.305719 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + + + + +4815 4815 4815 4815 4621 2503 2014 899 400 244 134 33 4 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4830 4830 4830 4830 4636 2518 2025 721 350 118 97 30 15 1 0 + + + + + + +0 1 2 3 + + + + +4186 617 33 0 + + + + + + +0 1 2 3 4 5 6 + + + + +375 4078 355 9 13 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2263 (charge 2) + +1249.62 +2 + + +167.055 169.097 175.119 198.087 198.124 199.108 226.119 232.141 239.094 244.092 278.148 299.06 326.674 337.15 367.275 555.29 652.342 687.324 878.448 879.44 + + + + +21 7 11 8 5 6 43 24 38 6 7 17 9 10 5 7 100 6 37 19 + + + + + + +GRMZM2G101938_P01 NP_001132839 hypothetical protein LOC100194331 seq=translation; coord=6:105424578..105432613:1; parent_transcript=GRMZM2G101938_T01; parent_gene=GRMZM2G101938 + + + MAAGYRAEDD YDYLFKVVLI GDSGVGKSNL LSRFTRNEFS LESKSTIGVE + FATRSLQVDG KVVKAQIWDT AGQERYRAIT SAYYRGAVGA LLVYDVTRHS + TFENVERWLK ELRDHTDPNI VVMLVGNKSD LRHLVAVQTD EGKAFAERES + LYFMETSALE STNVENAFAE VLTQIYRIVS KRAVEAGEDA ASGPGKGEKI + NIKDDVSAVK KGGCCSS + + + + + + +5.06064 +-0.349009 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6998 6998 6993 6678 4398 3467 1780 900 506 218 87 23 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +6996 6996 6991 6666 4312 3190 1508 650 289 65 19 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4193 2421 362 25 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1259 4323 1227 161 27 2 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2275 (charge 3) + +1572.75 +3 + + +152.057 155.082 159.077 167.055 169.134 171.113 173.092 175.119 183.076 185.092 187.072 199.107 226.155 239.089 244.165 258.108 283.176 302.06 303.178 309.204 333.177 383.193 452.248 461.266 475.221 480.259 576.272 615.346 672.364 678.354 +695.408 739.338 759.403 805.422 812.435 826.37 830.439 901.474 921.502 1016.5 1064.48 1191.21 + + + + +2 2 4 1 1 8 2 5 3 2 7 4 13 13 6 1 4 5 16 100 2 3 4 2 1 1 4 5 4 2 +2 4 8 1 1 5 5 1 1 1 2 1 + + + + + + +GRMZM2G001514_P01 NP_001149409 LOC100283035 seq=translation; coord=8:69592559..69594672:1; parent_transcript=GRMZM2G001514_T01; parent_gene=GRMZM2G001514 + + + MATTSTPRLA TLLVLLAAAS PLLSAAQKAA PKAPAAAKAA PGPAASSSSG + AGAADAAPPT DVNKALKDDQ FSEFKQLLHD TRVDTQINAQ LTDSYNGLTI + MAPTNAAFDK MKAGVLNGLS PQDQIQLVLY CVLPRFYSLS MLGTLDGKVN + TQGSGHDGPY RYDIKRSGNN VNVSTGVNWM LLGSPVSKDF PLAIYPVDKV + PLPYELFGPK PPTPAPAPAP APAKSKTKKK KKAAGIAEPP TADDDTSASD + DQKAAATPGA AGSWAAAALS ALAAAALGAG LF + + + + + +GRMZM2G021794_P01 NP_001147565 fasciclin-like arabinogalactan protein 7 seq=translation; coord=6:164551086..164552313:1; parent_transcript=GRMZM2G021794_T01; parent_gene=GRMZM2G021794 + + + MAGSASRLAI LLVLLAASPL LGATQKAAPG PASSSGSGAG AADAAPPTDV + NKALKDEQFS EFRQLLHDTR VDTQINAQLT DSYNGLTIMA PTNAAFDKMK + AGVLNGLSPQ EQIQMVLYCV LPRFYSLSML GTLSGKVNTQ GSGHDGPYRY + DIKRSGNNVN VSTGVNWMLL GSPVSKDFPL AIYPVDKVPL PYELFGPKPP + TPAPAPAPAP GPAKAKTKKK KKSAAIAEPP TADDDDTGST SDDQKAAAAP + PRASRAAAAL SVLGAAVLVG GLF + + + + + + +4.82692 +-0.35755 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +4067 4067 3911 3606 3205 2475 1507 917 507 159 59 14 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 + + + + +4064 4064 3904 3588 3139 2399 1345 601 198 32 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1503 1824 665 65 10 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +604 2345 967 110 39 3 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2293 (charge 3) + +1387.63 +3 + + +150.066 153.066 155.082 158.093 167.056 167.093 168.055 169.052 169.097 171.076 175.119 181.06 186.124 188.103 195.076 195.089 197.092 198.086 199.071 199.108 212.104 214.119 216.098 223.064 225.043 227.103 230.114 244.166 253.093 297.156 +299.063 311.147 338.182 341.017 342.999 359.029 361.026 372.675 383.667 401.185 422.179 429.089 431.087 435.236 444.702 450.176 454.169 464.205 473.213 475.23 492.257 494.266 519.723 528.731 565.202 590.262 607.283 744.344 801.366 888.399 +928.401 945.419 947.43 + + + + +1 1 2 2 27 2 3 1 7 2 10 1 3 2 2 1 5 2 1 1 1 6 3 6 6 1 3 1 2 1 +1 2 1 4 3 100 31 5 1 2 2 15 7 3 2 1 2 1 4 3 35 1 1 6 2 1 11 3 3 3 +1 8 2 + + + + + + +GRMZM2G156227_P01 NP_001140897 hypothetical protein LOC100272974 seq=translation; coord=2:12102598..12106650:-1; parent_transcript=GRMZM2G156227_T01; parent_gene=GRMZM2G156227 + + + MAGANFLSTA ALVARGVAAC SSISTPTRRH PQIRVCCRAD VEAMEAYAHE + ERLRFRRRDF IGTCVGTAIG LEMIDGSTSF SGVATAADLI ERRQRSEFQS + KIKDTLYVAI KAKPELVPSL LTMALNDAMT YDKTTKTGGA NGSIRLETSR + PENSGLSSAL DLLTEAKKEI DSFSKGGPIS FADLIQFAAQ SALKRSFLDA + AIAKCGGNEE KGRTLYSAYG SNGQWGLFDR TFGRADAQEA DPEGRVPDWS + KASVQEMKDR FVAVGLGPRQ LAVMSAFLGP DQAATEGRLI ADPDCRPWVE + KYQRSRETVS RTDYEVDLIT TLTKLSSLGQ KINYEAYTYP KQKIDLGKLK + L + + + + + + +4.62246 +-0.280149 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +1899 1899 1869 1680 1626 1440 961 751 395 181 101 59 24 12 6 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +1874 1874 1844 1655 1596 1402 879 657 252 63 31 3 2 2 1 0 + + + + + + +0 1 2 3 4 + + + + +1222 607 90 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +432 1219 244 21 4 0 5 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2301 (charge 2) + +1158.5 +2 + + +152.057 159.077 167.055 169.097 173.092 175.119 181.097 183.077 186.124 187.072 187.144 188.076 194.625 197.67 200.103 201.087 204.135 212.103 217.083 226.154 230.115 232.141 239.095 241.081 244.167 258.109 275.134 285.011 287.007 299.062 +301.156 302.663 312.117 319.605 327.241 329.145 337.403 355.069 357.068 369.179 371.215 411.951 418.996 420.992 427.183 441.21 456.285 458.236 460.24 470.189 489.219 515.284 546.733 573.263 621.438 628.333 644.299 684.325 773.339 885.382 +917.504 1093.15 + + + + +3 17 21 15 3 18 2 5 3 33 4 2 4 2 21 3 2 4 3 16 2 29 11 3 3 10 4 3 3 19 +3 9 4 2 2 4 2 4 10 3 3 3 3 3 3 4 3 100 4 4 3 8 9 4 3 4 16 3 15 3 +2 2 + + + + + + +GRMZM2G128056_P01 NP_001146398 hypothetical protein LOC100279978 seq=translation; coord=9:12571363..12580129:1; parent_transcript=GRMZM2G128056_T01; parent_gene=GRMZM2G128056 + + + MAYRSAVLLP ALLLAVAVVV ASAAAGDGRW REEQARDRVP RVPGQAFNTS + FAQYAGYVTV SEQRGAALFY WFFEAEKDPG SKPLVLWLNG GPGCSSIAFG + LGEEVGPFHV NADGKGVHVN PYSWNKVANL LFLDSPVGVG YSYSNTSDDA + LKNGDARTAT DSLAFLLKWL ERFPQYKERE FYLTGESYAG HYVPQLAQAI + KRHHEATGDK SINLKGYMVG NALTDDFHDH YGIFQFMWTT GLISDQTYKL + LNVFCDYESF VHSSPQCDKI MDIASTEAGN IDSYSIFTPT CHASFASSKN + KVMKRLHSAG KMGEQYDPCT EKHSTVYFNL AEVQKALHVN TVIGKSKWET + CSEAVNTHWG DCERSVLHIY HELIQYGLRI WVFSGDTDAV IPVTSTRYSI + DALKLPTITP WHAWYDDDGE VGGWTQGYRG LNFVTVRGAG HEVPLHRPKQ + ALTLIKSFLT GSPMPVQSST HSNM + + + + + + +6.3243 +-0.308503 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +5754 5754 5754 5754 5754 5415 5220 4799 4280 3239 2475 1038 519 198 95 66 29 13 6 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5752 5752 5752 5752 5752 5413 5214 4762 4149 3074 1929 544 245 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2602 2136 820 164 33 0 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1111 2731 1497 350 39 27 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2306 (charge 3) + +1297.71 +3 + + +154.087 155.081 157.108 158.093 159.077 166.061 167.093 169.097 171.077 173.128 175.119 178.061 181.097 183.149 185.092 186.087 186.123 189.087 190.436 195.088 195.113 197.126 199.108 201.123 208.954 210.95 217.083 221.104 223.999 226.156 +235.063 240.134 244.166 248.035 258.145 262.135 266.044 269.166 272.171 275.124 277.139 284.009 288.111 294.165 304.094 306.12 324.13 333.177 341.217 345.976 346.973 355.197 362.025 374.236 400.266 403.166 409.23 415.04 423.2 452.191 +470.246 486.761 518.267 537.329 551.261 650.407 747.463 1054.38 1139.04 1280.3 + + + + +13 12 30 11 12 14 19 18 12 15 100 14 13 32 13 14 13 18 8 55 12 9 50 17 60 77 11 13 20 98 +47 11 69 16 10 36 38 44 8 15 33 14 11 19 22 15 43 12 13 47 40 12 21 12 39 10 19 12 16 17 +12 10 10 87 50 15 47 11 12 10 + + + + + + +GRMZM2G102760_P01 NP_001105975 lipoxygenase seq=translation; coord=5:12274159..12279067:-1; parent_transcript=GRMZM2G102760_T01; parent_gene=GRMZM2G102760 + + + MFWHGVADRL TGKNKEAWSE GKIRGTVRLV KKEVLDVGDF NASLLDGVHR + ILGWDDGVAF QLVSATAADP SNGGRGKVGK AAHLEEAVVS LKSTADGETV + YRVSFEWDES QGIPGAVLVR NLQHAEFFLK TLTLEGVPGK GTVVFVANSW + VYPHKLYSQE RIFFANDTYL PSKMPAALVP YRQDELKILR GDDNPGPYQE + HDRVYRYDYY NDLGDPDKGE EHARPILGGS QEHPYPRRCR TGRHPTKKDP + NSESRLFLLN LNIYVPRDER FGHLKMSDFL GYSLKTIIEA VLPTLGTFVD + DTPKEFDSFE DILGLYELGP EAPNNPLIAE IRKKIPSEFL RSILPNGSHD + HPLKMPLPNV IKSDVLKKAP EFKFGWRTDE EFARETLAGV NPVIIKRLTE + FPAKSTLDPR QYGDHTSKIT EAHIRHNMGG LSVQNALRNK RLFILDHHDH + FMPYLDEINE LEGNFIYASR TLLFLKDDGT LKPLAIELSL PHPDGQQRGA + VSKVYTPAHT GVEGHVWQLA KAYACVNDSA WHQLISHWLN THAVIEPFVI + ATNRQLSVVH PVHKLLSPHY RDTLNINALA RQTLINAGGV FERTVFPAKY + ALGMSADVYK SWNFNEQALP ADLVKRGVAV PDQSSPYGVR LLIKDYPYAV + DGLVIWWAIE RWVKEYLDIY YPNDGELQRD VELQAWWKEV REEAHGDLKD + RDWWPRMDTV QQLARACTTI IWVASALHAA VNFGQYPYAG YLPNRPTASR + RPMPEPGSHD YKKLGAGQKE ADMVFIRTIT SQFQTILGIS LIEILSKHSS + DEVYLGQRDE PDRWTSDAKA LDAFKRFGSR LVQIENRIKT MNDSPDLKNR + KGPVEMPYML LYPNTSDVTG EKAEGLTAMG IPNSISI + + + + + +GRMZM2G102760_P02 NP_001105975 lipoxygenase seq=translation; coord=5:12274159..12279067:-1; parent_transcript=GRMZM2G102760_T02; parent_gene=GRMZM2G102760 + + + MPYLDEINEL EGNFIYASRT LLFLKDDGTL KPLAIELSLP HPDGQQRGAV + SKVYTPAHTG VEGHVWQLAK AYACVNDSAW HQLISHWLNT HAVIEPFVIA + TNRQLSVVHP VHKLLSPHYR DTLNINALAR QTLINAGGVF ERTVFPAKYA + LGMSADVYKS WNFNEQALPA DLVKRGVAVP DQSSPYGVRL LIKDYPYAVD + GLVIWWAIER WVKEYLDIYY PNDGELQRDV ELQAWWKEVR EEAHGDLKDR + DWWPRMDTVQ QLARACTTII WVASALHAAV NFGQYPYAGY LPNRPTASRR + PMPEPGSHDY KKLGAGQKEA DMVFIRTITS QFQTILGISL IEILSKHSSD + EVYLGQRDEP DRWTSDAKAL DAFKRFGSRL VQIENRIKTM NDSPDLKNRK + GPVEMPYMLL YPNTSDVTGE KAEGLTAMGI PNSISI + + + + + + +6.32748 +-0.36157 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +10513 10513 10513 10457 9743 9238 8256 5731 4146 1846 973 393 196 73 14 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +10519 10519 10519 10463 9749 9209 8144 5483 3731 1345 523 144 38 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4789 4385 1035 256 40 8 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1748 5994 2318 403 41 9 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2312 (charge 3) + +1541.75 +3 + + +152.057 153.103 155.081 155.118 157.109 157.134 158.137 161.093 166.061 171.076 175.119 181.097 183.113 185.092 185.128 189.087 193.105 195.113 197.103 199.108 199.182 204.134 207.087 215.138 218.15 223.155 226.155 227.103 229.099 237.134 +244.165 251.15 253.092 262.629 267.109 275.208 292.163 299.87 310.178 314.011 340.125 343.18 353.877 367.19 379.173 381.256 385.202 397.148 399.154 438.273 452.255 457.173 459.216 466.234 484.255 494.198 500.352 508.242 521.236 544.244 +553.745 566.275 583.304 585.311 611.299 613.296 629.268 690.342 765.367 834.404 852.398 871.441 931.459 + + + + +15 4 15 5 8 42 4 4 15 4 26 4 5 4 15 7 9 7 5 30 4 15 6 4 8 5 52 25 4 5 +24 22 30 4 8 5 9 5 5 4 15 24 4 6 6 4 100 16 4 8 6 5 4 5 5 25 4 7 7 4 +8 9 45 5 69 6 4 6 9 17 8 6 17 + + + + + + +GRMZM2G306732_P01 NP_001150706 fructose-1,6-bisphosphatase seq=translation; coord=1:38848595..38850785:-1; parent_transcript=GRMZM2G306732_T01; parent_gene=GRMZM2G306732 + + + MAAAATTSSS SHLLLLSRQQ AASLRCRLSF LGQPARRSGR VTAQAPAAKD + VRCMAAVDTA ASAAAAETSP KSSSYEIVTL TTWLLQQERT GAIDNEMTIV + LASISTACKQ IAALVQRAPI SNLTGVQGAV NVQGEDQKKL DVVSNEVFSN + CLKSSGRTGV IASEEEDVPV AVEQSYSGNY IVVFDPLDGS SNIDAAVSTG + SIFGIYNPND ECLADVDDND TLDSVEQRCI VNVCQPGSNL LAAGYCMYSS + SVIFVLTVGT GVYVFTLDPM YGEFVLTQEK VQIPKAGKIY AFNEGNYALW + DDKLKLYMDS LKEPGDSGKP YSARYIGSLV GDFHRTLLYG GIYGYPRDKK + SKNGKLRLLY ECAPMSFIVE QAGGKGSDGH QRILDITPTE IHQRVPLYIG + SVEEVDKVEK FLA + + + + + + +5.79765 +-0.351373 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +6216 6216 6104 5799 5472 4936 4378 4098 2524 1261 675 287 123 42 14 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6222 6222 6110 5805 5475 4916 4297 4052 2090 1000 395 92 39 4 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3376 2408 395 41 2 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +833 3577 1455 325 26 6 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2317 (charge 3) + +1263.6 +3 + + +152.057 154.087 155.082 157.061 157.108 158.093 159.076 166.061 169.097 169.134 171.113 173.056 173.093 173.129 175.119 181.097 182.101 185.056 186.124 187.107 193.098 194.128 195.089 197.129 204.135 209.092 213.088 226.155 233.129 235.119 +240.135 242.077 244.165 246.156 251.263 255.146 265.997 272.172 290.986 293.1 297.156 299.099 304.947 309.204 315.073 322.959 328.15 329.942 333.189 335.137 340.629 346.971 359.198 423.326 439.835 484.214 496.254 519.25 522.312 576.282 +593.305 595.309 619.368 672.406 730.325 778.416 881.377 1067.15 + + + + +3 3 5 3 2 9 3 3 5 4 4 8 3 4 43 53 9 2 36 3 16 3 2 4 5 70 3 11 12 2 +3 3 9 2 2 5 3 17 4 5 18 3 4 14 3 4 3 3 15 3 2 15 2 5 2 3 18 3 3 4 +100 4 3 4 3 4 3 3 + + + + + + +GRMZM2G033493_P01 NP_001131923 hypothetical protein LOC100193314 seq=translation; coord=7:157278232..157282868:-1; parent_transcript=GRMZM2G033493_T01; parent_gene=GRMZM2G033493 + + + MAAISSLPFA ALRGAAEWRP SSTAAAVSGA VVLSARSRRG SRSVVRCVAT + TGDVPPTVAE TKLNFLKSYK RPIPSIYSAV LQELLVQQHL MRYKKTYQYD + AVFALGFVTV YDQLMEGYPS NEDRDSIFKA YITALNEDPD QYRADALKME + EWARSQNGSS LVDFSSRDGE IEAILKDISE RAKGKGNFSY SRFFAVGLFR + LLELSNATEP TILDKLCAAL NVSKRSVDRD LDVYRNILSK LVQAKELLKE + YVDREKKKRE ERSEAPKPNE AVTKFDGNLY STRH + + + + + + +3.28282 +-0.226401 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +5551 5551 5551 3921 3758 2542 1965 1413 903 496 292 99 42 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5534 5534 5534 3904 3698 2401 1687 1121 526 307 169 21 1 0 0 1 0 + + + + + + +0 1 2 3 4 + + + + +3460 1867 220 16 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1096 3717 634 110 3 0 3 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2327 (charge 2) + +1270.67 +2 + + +154.051 155.082 159.077 169.098 171.076 171.114 175.119 181.109 187.072 189.087 199.109 201.124 209.104 212.103 217.083 226.155 230.15 244.166 248.161 254.152 279.034 288.12 290.163 322.917 341.146 355.198 379.701 383.194 395.155 412.184 +418.27 443.756 452.251 470.262 511.252 528.3 566.299 614.846 617.301 637.331 677.399 731.853 736.394 758.404 853.412 886.499 903.497 921.499 983.546 + + + + +3 3 3 5 5 3 4 10 4 21 25 5 31 5 52 100 8 14 33 3 3 6 11 2 9 3 3 9 3 17 +3 3 12 9 11 3 3 3 3 17 3 4 5 41 3 5 3 9 9 + + + + + + +GRMZM2G058173_P01 NP_001151824 undecaprenyl pyrophosphate synthetase seq=translation; coord=7:144837690..144838974:-1; parent_transcript=GRMZM2G058173_T01; parent_gene=GRMZM2G058173 + + + MMLLALHSPS TGTVAWRRRR PAPLPAISRR ARIIRPSPFA LSTAAATDTS + TGHAPATADR EAPLLQLLHS GVRAESLPRH VGLVIDGHAR WARARGLSVS + EGHAVGRRTV EHTVRLSRAW GIRVLTVFAC SHENMTTRPK AEMDFFMQLY + EGFIRDNVDQ FCREGIRLHL IGDSPGLPAS LLRAAREANQ LATQSESEMV + LMLAMGYSGR RDILRACQEL ATEVQRNLLR PEDIDEALIA GKLGTSIAGG + ELSYPDLVIR TSGELRLSNF LLWQSAFAEL FFSDVMWPDF GEDEYLGALR + SYQTRQRRFG QRK + + + + + + +6.83716 +-0.390695 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7977 7977 7977 7704 7112 6672 6098 5611 3377 2401 1127 443 128 53 20 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7953 7953 7953 7680 7088 6633 5996 5411 3175 1982 797 197 18 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4021 3033 773 113 35 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1709 4781 1225 237 25 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2342 (charge 3) + +1714.8 +3 + + +152.057 155.081 157.109 158.092 159.076 169.097 171.076 171.113 172.072 173.092 174.096 175.119 195.088 195.996 199.072 199.108 214.118 217.083 226.155 240.134 244.13 257.125 270.109 303.891 318.126 339.134 348.64 371.241 419.712 444.243 +451.729 466.793 469.221 513.959 551.35 556.199 566.64 581.826 604.354 613.307 630.321 650.809 670.305 677.399 687.834 696.273 701.357 704.339 736.339 757.873 771.876 812.394 824.375 838.414 895.444 903.487 996.483 1083.51 1111.4 1299.6 +1625.3 + + + + +5 7 4 5 3 5 6 6 9 93 4 64 6 3 4 23 4 8 61 6 31 4 6 4 4 4 5 40 7 4 +5 17 4 5 5 5 6 5 5 5 100 8 6 6 6 17 48 6 5 5 5 6 6 17 22 7 8 9 6 7 +6 + + + + + + +GRMZM2G024104_P01 P38560 Glutamine synthetase root isozyme 2 (EC 6.3.1.2)(Glutamate--ammonia ligase) seq=translation; coord=1:267894143..267897525:-1; parent_transcript=GRMZM2G024104_T01; parent_gene=GRMZM2G024104 + + + MALLSDLINL DLSGRTGKII AEYIWVGGSG MDVRSKARTL SGPVDDPSKL + PKWNFDGSST GQAPGDDSEV ILCPRAIFRD PFRKGQNILV MCDCYEPNGE + PIPSNKRHGA AKIFSHPDVK AEEPWFGIEQ EYTLLQKDTK WPLGWPLGGY + PGPQGPYYCA VGADKSYGRD IVDAHYKACL YAGIDISGIN GEVMPGQWEF + QVGPAVGVSA GDQLWVARYI LERITEIAGV VVSFDPKPIP GDWNGAGAHT + NYSTKSMRSD GGYEVIKKAI GKLGLRHREH IAAYGDGNER RLTGRHETAD + INTFVWGVAN RGASVRVGRD TEKEGKGYFE DRRPASNMDP YVVTSLIAET + TMLWEPSHSN GDGKGAAAP + + + + + +GRMZM2G024104_P02 P38560 Glutamine synthetase root isozyme 2 (EC 6.3.1.2)(Glutamate--ammonia ligase) seq=translation; coord=1:267894143..267897525:-1; parent_transcript=GRMZM2G024104_T02; parent_gene=GRMZM2G024104 + + + MALLSDLINL DLSGRTGKII AEYIWVGGSG MDVRSKARTL SGPVDDPSKL + PKWNFDGSST GQAPGDDSEV ILWDPFRKGQ NILVMCDCYE PNGEPIPSNK + RHGAAKIFSH PDVKAEEPWF GIEQEYTLLQ KDTKWPLGWP LGGYPGPQGP + YYCAVGADKS YGRDIVDAHY KACLYAGIDI SGINGEVMPG QWEFQVGPAV + GVSAGDQLWV ARYILERITE IAGVVVSFDP KPIPGDWNGA GAHTNYSTKS + MRSDGGYEVI KKAIGKLGLR HREHIAAYGD GNERRLTGRH ETADINTFVW + GVANRGASVR VGRDTEKEGK GYFEDRRPAS NMDPYVVTSL IAETTMLWEP + SHSNGDGKGA AAP + + + + + +GRMZM2G024104_P03 P38560 Glutamine synthetase root isozyme 2 (EC 6.3.1.2)(Glutamate--ammonia ligase) seq=translation; coord=1:267894143..267897157:-1; parent_transcript=GRMZM2G024104_T03; parent_gene=GRMZM2G024104 + + + MDVRSKARTL SGPVDDPSKL PKWNFDGSST GQAPGDDSEV ILCPRAIFRD + PFRKGQNILV MCDCYEPNGE PIPSNKRHGA AKIFSHPDVK AEEPWFGIEQ + EYTLLQKDTK WPLGWPLGGY PGPQGPYYCA VGADKSYGRD IVDAHYKACL + YAGIDISGIN GEVMPGQWEF QVGPAVGVSA GDQLWVARYI LERITEIAGV + VVSFDPKPIP GDWNGAGAHT NYSTKSMRSD GGYEVIKKAI GKLGLRHREH + IAAYGDGNER RLTGRHETAD INTFVWGVAN RGASVRVGRD TEKEGKGYFE + DRRPASNMDP YVVTSLIAET TMLWEPSHSN GDGKGAAAP + + + + + +GRMZM2G024104_P04 P38560 Glutamine synthetase root isozyme 2 (EC 6.3.1.2)(Glutamate--ammonia ligase) seq=translation; coord=1:267894143..267896770:-1; parent_transcript=GRMZM2G024104_T04; parent_gene=GRMZM2G024104 + + + MCDCYEPNGE PIPSNKRHGA AKIFSHPDVK AEEPWFGIEQ EYTLLQKDTK + WPLGWPLGGY PGPQGPYYCA VGADKSYGRD IVDAHYKACL YAGIDISGIN + GEVMPGQWEF QVGPAVGVSA GDQLWVARYI LERITEIAGV VVSFDPKPIP + GDWNGAGAHT NYSTKSMRSD GGYEVIKKAI GKLGLRHREH IAAYGDGNER + RLTGRHETAD INTFVWGVAN RGASVRVGRD TEKEGKGYFE DRRPASNMDP + YVVTSLIAET TMLWEPSHSN GDGKGAAAP + + + + + +GRMZM2G024104_P05 P38560 Glutamine synthetase root isozyme 2 (EC 6.3.1.2)(Glutamate--ammonia ligase) seq=translation; coord=1:267894143..267895292:-1; parent_transcript=GRMZM2G024104_T05; parent_gene=GRMZM2G024104 + + + MRSDGGYEVI KKAIGKLGLR HREHIAAYGD GNERRLTGRH ETADINTFVW + GVANRGASVR VGRDTEKEGK GYFEDRRPAS NMDPYVVTSL IAETTMLWEP + SHSNGDGKGA AAP + + + + + + +5.98252 +-0.32338 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +7264 7264 7264 7264 6949 6379 6026 4169 3289 1692 780 355 146 71 27 16 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7288 7288 7288 7288 6973 6403 6030 4096 3147 1468 529 187 49 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4002 2543 581 91 46 4 0 25 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1327 4660 1093 156 28 3 25 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2343 (charge 3) + +1624.76 +3 + + +152.058 153.481 155.082 157.097 159.077 159.092 166.06 167.082 169.051 169.097 170.278 173.056 175.119 184.072 185.091 185.128 199.107 202.899 226.155 244.166 253.132 266.64 280.638 294.166 296.136 300.064 302.06 304.059 309.2 323.183 +326.604 337.181 358.703 372.698 408.216 423.206 475.228 520.782 532.27 541.119 543.24 560.269 584.301 647.275 655.337 810.344 881.383 952.417 + + + + +6 5 12 7 8 6 5 8 7 9 6 6 42 7 7 7 10 6 56 18 12 42 43 9 11 9 13 11 7 57 +9 17 8 36 16 10 80 10 10 19 11 100 14 40 10 15 37 18 + + + + + + +GRMZM2G096153_P01 NM_001111509 glutathione transferase10 (gst10), mRNA seq=translation; coord=1:7866607..7868253:-1; parent_transcript=GRMZM2G096153_T01; parent_gene=GRMZM2G096153 + + + MAAPVTVYGP MLSPAVARVA ACLLEKDVPF QIEPVDMSKG EHKSPSFLKL + QPFGQVPAFK DHLTTVFESR AICRYICDQY ADSGNQALFG KKEDGAVGRA + AIEQWIESEG QSFNPPSLAI IFQLAFAPMM GRTTDLAVVE QNEAKLAKVL + DVYDQRLGES QYFAGDDFSL ADLVHLPNAD FLVNRTSKAG LITERKNLAR + WWDDVSSRPA WKKVTEMQST PRPS + + + + + + +GRMZM2G096153_P02 NM_001111509 glutathione transferase10 (gst10), mRNA seq=translation; coord=1:7866691..7868236:-1; parent_transcript=GRMZM2G096153_T02; parent_gene=GRMZM2G096153 + + + MQISLFFSLL SFFRQQRCNK NTDLQLRVQA EMHTFAKGQI AEALGYILGV + TSAYACLAGK RKPKRSYYLR RPISLLCVWC SSLTESRAIC RYICDQYADS + GNQALFGKKE DGAVGRAAIE QWIESEGQSF NPPSLAIIFQ LAFAPMMGRT + TDLAVVEQNE AKLAKVLDVY DQRLGESQYF AGDDFSLADL VHLPNADFLV + NRTSKAGLIT ERKNLARWWD DVSSRPAWKK VTEMQSTPRP S + + + + + + + +6.36476 +-0.385743 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + + + + +4069 4069 4069 4069 4069 4007 2261 1862 926 380 140 42 13 8 3 1 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4068 4068 4068 4068 4068 4006 2260 1770 776 306 115 25 1 0 + + + + + + +0 1 2 3 + + + + +2856 1149 68 0 + + + + + + +0 1 2 3 4 5 6 + + + + +706 3211 148 4 0 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2344 (charge 2) + +1248.59 +2 + + +152.057 157.011 157.098 167.055 169.061 173.128 175.119 183.113 185.092 195.089 199.108 201.124 203.102 212.103 216.098 225.043 230.114 239.095 244.165 295.101 299.062 312.156 323.308 387.137 401.831 456.257 540.784 557.305 644.331 652.337 +772.401 802.951 825.31 855.427 1274.32 + + + + +21 11 16 14 12 51 20 19 18 18 18 17 13 54 12 68 15 100 19 15 22 18 17 13 13 53 13 18 48 44 +21 13 16 23 13 + + + + + + +GRMZM2G140667_P01 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589206..218592127:-1; parent_transcript=GRMZM2G140667_T01; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P02 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589352..218592127:-1; parent_transcript=GRMZM2G140667_T02; parent_gene=GRMZM2G140667 + + + + + + + +GRMZM2G140667_P04 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589294..218592021:-1; parent_transcript=GRMZM2G140667_T04; parent_gene=GRMZM2G140667 + + + + + + + + +6.72101 +-0.344667 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +7934 7934 7934 7916 7246 6924 6213 5650 5086 3696 2750 1377 567 271 89 50 17 2 1 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7949 7949 7949 7931 7261 6906 6170 5533 4932 2733 1673 320 30 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2769 3759 1114 255 57 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1453 3618 1829 742 255 39 1 20 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2346 (charge 3) + +1249.62 +3 + + +154.086 155.082 158.092 159.076 169.097 171.113 171.149 172.108 173.092 173.13 175.119 181.06 181.097 181.133 190.976 194.624 195.088 195.113 197.129 199.072 199.107 202.39 207.113 220.003 223.153 227.103 230.128 232.141 235.12 238.012 +244.165 246.156 248.034 252.139 256.002 262.05 266.045 272.171 278.148 284.01 290.044 291.185 294.65 301.154 303.161 310.207 322.189 324.154 331.199 337.15 345.224 346.974 355.161 361.185 393.194 398.203 434.222 441.206 444.293 452.21 +458.236 460.243 466.192 470.243 495.255 515.327 538.276 555.286 563.247 582.261 586.366 590.284 592.312 626.028 647.305 652.338 1115.77 1222.79 + + + + +14 7 23 7 6 5 5 6 9 6 87 6 7 5 6 3 6 18 8 4 26 4 5 9 5 40 9 59 5 5 +21 9 21 32 7 56 15 6 18 13 7 6 6 5 17 7 7 15 5 8 9 5 8 9 16 14 5 7 14 30 +100 7 6 7 6 5 5 61 5 5 6 5 5 5 18 13 4 5 + + + + + + +GRMZM2G349062_P01 NP_001147604 pheophorbide a oxygenase seq=translation; coord=1:290135976..290138852:1; parent_transcript=GRMZM2G349062_T01; parent_gene=GRMZM2G349062 + + + MDPLSLLQLP RASRPPMPLA AAAAPLVSAR LSVSGGARSV RRRRRRRAAG + LSVFAVATET PRTEEQQPSP SGEERFDWLD QWYPLAPVCD LDPRAPHGKT + VLGLSVVAWY DRGAGEWRVF DDACPHRLAP LSEGRIDDRG RLQCVYHGWC + FDGAGACKFI PQAPALGPPV HTSSRACVAS YPCVVQNNIL WFYPRADPEH + SDVLQRKRPP LIPEIDDPDF VTVYGIRDLP YGYDILVENL MDPAHVPYAH + KGIMRGIRKK EDPGRVDYDK EGGGPVKMKI EQANIEGFVS PQERGYFQFV + APCTFFGTPF VQEGQKKKAP RVMLVFFCIP VGPGRSRVIW AFPRNVGVWL + HHITPRWLYH VGQNLILDSD IFLLHVEERK FAAAGLDNWQ RACYVPTSSD + AMVVAFRNWF RKFCKNQVGW ATLQVDQLPP TRTKDQLMER YWSHVVQCRS + CNAALKAMKA LEAALQVASV AVVGFLAVAK GTVLTSTVQR AAVVSATVLC + FAASRWLANF IQKNFYFQDY IHAYK + + + + + +GRMZM2G349062_P02 NP_001147604 pheophorbide a oxygenase seq=translation; coord=1:290135976..290138852:1; parent_transcript=GRMZM2G349062_T02; parent_gene=GRMZM2G349062 + + + MDPLSLLQLP RASRPPMPLA AAAAPLVSAR LSVSGGARSV RRRRRRRAAG + LSVFAVATET PRTEEQQPSP SGEERFDWLD QWYPLAPVCD LDPRAPHGKT + VLGLSVVAWY DRGAGEWRVF DDACPHRLAP LSEGRIDDRG RLQCVYHGWC + FDGAGACKFI PQAPALGPPV HTSSRACVAS YPCVVQNNIL WFYPRADPEH + SDVLQRKRPP LIPEIDDPDF VTVYGIRDLP YGYDILVENL MDPAHVPYAH + KGIMRGIRKK EDPGRVDYDK EGGGPVKMKI EQANIEGFVS PQERGYFQFV + APCTFFGTPF VQEKKKAPRV MLVFFCIPVG PGRSRVIWAF PRNVGVWLHH + ITPRWLYHVG QNLILDSDIF LLHVEERKFA AAGLDNWQRA CYVPTSSDAM + VVAFRNWFRK FCKNQVGWAT LQVDQLPPTR TKDQLMERYW SHVVQCRSCN + AALKAMKALE AALQVASVAV VGFLAVAKGT VLTSTVQRAA VVSATVLCFA + ASRWLANFIQ KNFYFQDYIH AYK + + + + + + +3.75082 +-0.258677 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +1842 1842 1842 1823 1773 1739 926 671 442 195 126 46 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1844 1844 1844 1825 1775 1741 914 651 320 151 111 33 5 1 0 + + + + + + +0 1 2 3 4 + + + + +1399 419 25 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +304 1363 174 2 0 0 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2368 (charge 2) + +1473.65 +2 + + +175.119 185.092 203.102 226.155 231.097 232.976 240.098 257.124 259.092 295.806 304.162 347.275 360.137 365.108 488.197 674.305 761.337 804.852 858.396 969.415 986.458 + + + + +15 6 24 6 38 3 38 8 4 4 8 4 6 4 13 15 6 4 100 14 5 + + + + + + +GRMZM2G039251_P01 NP_001149702 succinyl-CoA ligase alpha-chain 2 seq=translation; coord=2:207032350..207038547:1; parent_transcript=GRMZM2G039251_T01; parent_gene=GRMZM2G039251 + + + MAASSPRALQ SLGSAASRFL HARGFAAAAA AAPSPAVFVD KSTRVICQGI + TGKNGTFHTE QAIEYGTNMV GGVTPKKGGT EHLGLPVFNS VAEAKAETKA + NATVIYVPPP FAAAAIMEAM EAELDLAVCI TEGIPQHDMV KVKAALNSQS + KTRLIGPNCP GIIKPGECKI GIMPGYIHKP GRIGIVSRSG TLTYEAVFQT + TAVGLGQSTC VGIGGDPFNG TNFVDCLEKF VNDPQTEGIV LIGEIGGTAE + EDAATFIQES KTQKPVVAFI AGLTAPPGRR MGHAGAIVAG GKGTAQDKIK + ALREAGVTVV ESPAKIGSTM FEIFKQRGMV E + + + + + +GRMZM2G072054_P01 NP_001136494 hypothetical protein LOC100216609 seq=translation; coord=7:160283320..160289262:1; parent_transcript=GRMZM2G072054_T01; parent_gene=GRMZM2G072054 + + + MAASSRRASQ LLGSAASRLL LGRGFAAAAA AAPSPAVFVD KSTRVICQGI + TGKNGTFHTE QAIEYGTNMV GGVTPKKGGT EHLGLPVFNS VAEAKAETKA + NASVIYVPPP FAAAAIMEAM EAELDLVVCI TEGIPQHDMV KVKAALNRQS + KTRLIGPNCP GIIKPGECKI GIMPGYIHKP GRIGIVSRSG TLTYEAVFQT + TAVGLGQSTC VGIGGDPFNG TNFVDCLEKF VDDPQTEGIV LIGEIGGTAE + EDAATFIQES KTQKPVVAFI AGLTAPPGRR MGHAGAIVAG GKGTAQDKIK + ALREAGVTVV ESPAKIGSTM FEIFKQRGMV E + + + + + + +4.88671 +-0.296164 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +5545 5545 5545 5545 5545 5421 4206 3126 2359 1643 934 495 139 53 13 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5557 5557 5557 5557 5557 5433 4218 3123 2248 1483 738 315 48 22 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3117 1981 337 108 8 0 0 6 + + + + + + +0 1 2 3 4 5 6 + + + + +915 3785 726 117 7 7 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2369 (charge 3) + +1224.66 +3 + + +152.057 154.086 155.081 158.059 158.093 159.076 161.502 167.092 169.135 171.113 175.086 175.119 187.043 197.128 199.108 204.134 208.108 216.735 227.62 228.122 241.617 244.166 257.085 262.139 263.138 270.961 272.956 275.124 277.137 289.972 +296.133 302.662 305.648 309.203 324.954 332.192 341.166 345.171 397.708 431.263 482.228 555.305 681.33 747.377 + + + + +10 39 16 8 11 11 9 10 12 17 14 94 12 14 19 18 10 9 100 33 58 35 10 45 12 9 12 12 15 10 +9 15 83 19 17 45 57 41 19 14 37 11 16 10 + + + + + + +GRMZM5G872068_P01 P38561 Glutamine synthetase root isozyme 3 (EC 6.3.1.2)(GS112)(Glutamate--ammonia ligase) seq=translation; coord=5:205237019..205240533:-1; parent_transcript=GRMZM5G872068_T01; parent_gene=GRMZM5G872068 + + + MACLTDLVNL NLSDNTEKII AEYIWIGGSG MDLRSKARTL SGPVTDPSKL + PKWNYDGSST GQAPGEDSEV ILYPQAIFKD PFRRGNNILV MCDCYTPAGE + PIPTNKRYNA AKIFSSPEVA AEEPWYGIEQ EYTLLQKDTN WPLGWPIGGF + PGPQGPYYCG IGAEKSFGRD IVDAHYKACL YAGINISGIN GEVMPGQWEF + QVGPSVGISS GDQVWVARYI LERITEIAGV VVTFDPKPIP GDWNGAGAHT + NYSTESMRKE GGYEVIKAAI EKLKLRHREH IAAYGEGNER RLTGRHETAD + INTFSWGVAN RGASVRVGRE TEQNGKGYFE DRRPASNMDP YVVTSMIAET + TIIWKP + + + + + +GRMZM2G046601_P01 NM_001111827 glutamine synthetase (LOC542215), mRNA seq=translation; coord=9:146062602..146070481:1; parent_transcript=GRMZM2G046601_T01; parent_gene=GRMZM2G046601 + + + MASLTDLVNL DLSDCTDRII AEYIWVGGSG IDLRSKARVM CDCYTPQGEP + IPSNKRYKAA TVFSHPDVAA EVPWYGIEQE YTLLQKDVSW PLGWPVGGYP + GPQGPYYCAA GADKAFGRDV VDAHYKACLY AGINISGING EVMPGQWEFQ + VGPSVGISAG DEIWVARYIL ERITEMAGIV LSLDPKPIKG DWNGAGAHTN + YSTKSMREAG GYEVIKEAIE KLGKRHREHI AAYGEGNERR LTGRHETADI + NTFKWGVANR GASIRVGRDT EKEGKGYFED RRPASNMDPY VVTGMIADTT + ILWKGN + + + + + +GRMZM2G046601_P04 NM_001111827 glutamine synthetase (LOC542215), mRNA seq=translation; coord=9:146069111..146070481:1; parent_transcript=GRMZM2G046601_T04; parent_gene=GRMZM2G046601 + + + MPGQWEFQVG PSVGISAGDE IWVARYILER ITEMAGIVLS LDPKPIKGDW + NGAGAHTNYS TKSMREAGGY EVIKEAIEKL GKRHREHIAA YGEGNERRLT + GRHETADINT FKWGVANRGA SIRVGRDTEK EGKGYFEDRR PASNMDPYVV + TGMIADTTIL WKGN + + + + + + +5.20476 +-0.281338 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +7769 7769 7734 7379 6975 6549 6065 4095 2959 1601 726 343 174 105 62 25 6 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7783 7783 7748 7393 6972 6517 6017 4008 2692 1290 458 167 45 12 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3522 3042 929 205 65 5 1 15 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1690 4684 1118 211 50 16 0 15 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2390 (charge 3) + +1638.77 +3 + + +152.057 154.086 155.082 156.077 157.109 157.134 158.092 169.098 171.076 172.072 173.057 175.119 185.128 187.072 187.108 197.129 199.108 199.589 207.112 209.092 221.092 226.154 235.062 244.165 256.668 262.049 266.64 272.125 277.139 280.638 +294.167 315.179 323.182 337.18 358.701 372.699 401.177 408.216 413.189 423.209 452.25 470.261 475.219 516.28 532.278 543.246 560.269 604.269 626.253 644.273 661.289 744.383 757.85 780.365 824.352 843.892 895.389 899.426 903.487 966.42 +1501.94 + + + + +6 2 5 3 3 13 3 5 4 4 2 34 4 3 5 4 16 3 4 3 3 52 4 21 2 5 61 4 5 47 +5 4 66 43 15 45 5 18 4 13 13 5 27 5 22 4 100 5 4 6 61 5 4 4 31 4 37 4 7 34 +5 + + + + + + +GRMZM2G081037_P01 NP_001141129 hypothetical protein LOC100273215 seq=translation; coord=4:156953772..156958300:1; parent_transcript=GRMZM2G081037_T01; parent_gene=GRMZM2G081037 + + + MLAAAWRLSQ RAVTSPLLGI GRSQIRNPFS TMASLSPAAA SPKRLRVYSS + AAADGDGAGS GKRVGTHNGS FHCDEALGCF LIRLTSQFAG ADVVRTRDSQ + ILDTLDAVLD VGGVYDPSRH RYDHHQKGFS EVFGHGFNTK LSSAGLVYKH + FGKEIIAKEL GVNEDHEDVH CLYLAIYKSF VEALDAIDNG INQYDTDQPP + KYVNNTHLSS RVGRFNLDWT DPDQSLEKEN AAFEQAMVLA GSEFMESVRF + HVKSWLPARS IVLECLLSKG NIDPSGEIMV LDRFCPWKLH LFELEEELKT + DPLTKYVLYQ QDERSKSWRV QAVAVAPDRF ESRKALPEKW RGMRDDELSA + ETGIPGCVFV HMSGFIGGNK TYEGALEMAR AALKF + + + + + +GRMZM2G081037_P02 NP_001141129 hypothetical protein LOC100273215 seq=translation; coord=4:156953772..156958300:1; parent_transcript=GRMZM2G081037_T02; parent_gene=GRMZM2G081037 + + + MLAAAWRLSQ RAVTSPLLGI GRSQIRNPFS TMASLSPAAA SPKRLRVYSS + AAADGDGAGS GKRVGTHNGS FHCDEALGCF LIRLTSQFAG ADVVRTRDSQ + ILDTLDAVLD VGGVYDPSRH RYDHHQKGFS EVFGHGFNTK LSSAGLVYKH + FGKEIIAKEL GVNEDHEDVH CLYLAIYKSF VEALDAIDNG INQYDTDQPP + KYVNNTHLSS RVGRFNLDWT DPDQSLEKEN AAFEQAMVLA GSEFMESVRF + HVKSWLPARS IVLECLLSKG NIDPSGEIMV LDRFCPWKLH LFELEEELKT + DPLTKYVLYQ DERSKSWRVQ AVAVAPDRFE SRKALPEKWR GMRDDELSAE + TGIPGCVFVH MSGFIGGNKT YEGALEMARA ALKF + + + + + + +7.24773 +-0.439257 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +7046 7046 7043 6613 6276 5745 5251 3086 2086 897 314 100 24 10 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7065 7065 7062 6632 6271 5678 5149 2941 1781 596 111 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2965 3100 830 135 36 0 0 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1729 3935 1135 207 34 9 10 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2391 (charge 3) + +1568.73 +3 + + +151.042 155.081 157.061 157.097 157.109 159.076 167.055 168.056 169.051 169.097 170.052 171.793 175.072 175.119 180.063 183.077 185.092 186.124 187.07 195.111 199.054 199.107 210.087 223.063 226.155 228.097 230.113 235.144 239.092 241.092 +244.166 246.108 251.106 253.167 263.138 269.813 283.05 300.062 301.059 303.057 309.2 316.677 337.191 345.976 346.975 348.972 355.199 361.025 363.023 374.186 387.192 395.234 402.7 417.033 419.037 452.255 470.263 488.249 504.29 524.785 +596.327 632.345 678.339 739.336 741.349 747.378 804.394 826.368 919.421 990.466 1061.49 1442.15 + + + + +2 2 6 2 2 13 43 17 24 4 3 2 4 33 2 3 4 3 2 3 2 19 3 5 38 19 4 38 10 4 +20 12 3 3 5 2 3 55 100 33 13 3 3 9 21 16 3 11 3 3 3 3 4 11 4 6 3 3 18 3 +3 30 4 6 3 4 26 15 19 19 5 4 + + + + + + +GRMZM2G473788_P01 NP_001144729 hypothetical protein LOC100277773 seq=translation; coord=6:58445440..58450019:-1; parent_transcript=GRMZM2G473788_T01; parent_gene=GRMZM2G473788 + + + MSEQQQPLPQ PRSSMREALE KEDKEKAAAA AAAKEKAAVP KNGNGNGGKN + GGGAGSGNGG APPQSGEETA REIQVVREAY RRETAAPAYV IPEEPPAVVE + LVGWYIYGFC SYFITHLLLP VLFPAIITQV AFPNSDFTPD PKYTLKGVTC + SVHEMSMYQR LTKHSIVIDG SRMSPLGWSG LSWAIGILIV APLLTQTAHH + LDRGQYQSLI LIAATSFGSF FCLLTGFFKT VWVFLFYILF IAGSIIVAEA + VHTRNLGLMI RGLAAHDSGK HLVLRRRAAA SQLSLYCTAI GGIGAALMAA + FMYHMLRRTD QLTGLWVVSI FCGLIWFIGI CHGLFTNRPS SSSPTTAFEP + NFFTKLSYSM TLLRYPQAIG SLVAVFLSSF ATMCIFTSGT LYAIGGVCIK + PVLVLALWIL YFLFPLISLP LLHPIQIIIR ADAVRMQLLG FIICLFVSGA + GFYFKSHRWR AAHIIVIALV QSTANGILYA FGRILLLDAS PPGKEGAFSV + WYAFVRVTGA MIGFAASSAG PGRAGGSFAA AFLGSFLGII VLIFGNVSNI + GALKAAGHLK GMDDEKRMGG LGMEKGEGMG SAVADSGESR GRV + + + + + + + +4.39477 +-0.26635 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +1150 1150 1150 1150 1150 1150 744 727 448 257 161 55 33 26 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1142 1142 1142 1142 1142 1142 736 719 396 204 132 26 5 1 0 + + + + + + +0 1 2 3 + + + + +844 294 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +209 831 103 6 1 0 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2401 (charge 2) + +1425.59 +2 + + +175.119 187.072 196.759 205.064 224.548 226.155 244.092 262.15 287.17 313.916 423.481 535.245 650.275 721.311 820.378 891.414 978.442 1035.46 + + + + +24 19 14 15 11 15 42 22 13 10 10 100 38 74 51 19 46 58 + + + + + + +GRMZM2G141432_P01 B6T878 Histone H2B seq=translation; coord=2:215086749..215088308:1; parent_transcript=GRMZM2G141432_T01; parent_gene=GRMZM2G141432 + + + MAPKAEKKPA AKKPAEEEPA APAEKAPAGK KPKAEKRLPA GKSAGKEGGV + DKKGRKKAKK SVETYKIYIF KVLKQVHPDI GISSKAMSIM NSFINDIFEK + LAGEAAKLAR YNKKPTITSR EIQTSVRLVL PGELAKHAVS EGTKAVTKFT + SS + + + + + + +4.54745 +-0.245808 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +6129 6129 6034 5737 3988 3378 1958 1460 877 564 289 151 80 34 25 14 10 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6093 6093 5998 5701 3923 2972 1642 989 533 262 43 3 2 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3979 1897 235 20 0 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +823 4112 1008 166 22 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2403 (charge 2) + +1366.69 +2 + + +165.138 166.141 167.055 169.097 173.092 175.119 177.259 181.133 195.112 199.072 201.087 209.128 221.085 223.065 225.043 227.103 239.095 256.259 258.144 262.154 270.144 276.155 279.181 285.01 298.139 303.019 311.173 316.15 331.081 337.188 +341.019 342.996 347.194 355.069 359.028 369.175 373.079 381.179 388.135 399.188 408.224 418.995 427.183 429.089 444.246 481.196 497.272 515.283 534.188 537.268 556.223 619.801 656.314 666.298 674.841 685.311 710.334 724.316 795.344 812.413 +843.404 852.406 895.439 906.429 915.013 923.45 941.449 1070.5 1091.53 1141.53 1238.58 1240.57 1263.75 + + + + +5 2 23 48 2 6 1 2 2 2 7 7 2 2 22 3 28 1 25 3 3 17 9 12 37 3 2 2 3 2 +3 2 10 27 100 5 2 2 2 2 8 7 12 20 74 2 2 9 2 9 18 3 2 4 6 4 5 6 11 7 +2 7 3 3 2 24 3 6 3 7 6 2 2 + + + + + + +AC212835.3_FGP007 seq=translation; coord=2:21007540..21010895:1; parent_transcript=AC212835.3_FGT007; parent_gene=AC212835.3_FG007 + + + MEGLIKGLVH VAIDAVEDAV RERDHGRADD DEVPRRRAAQ SSDPDDDGEE + ERDERSRSTW AEVVSEQKGS DPDERRDHRS SGRDNRHERR DDEGWKRADG + RNQQQHHAGR QNQCEGEERW DGSGSRRRQQ QQQAQGYGNQ HQEEERINDG + GWQTVGEKKR HGRPQQSEAW NGYRKPPSEQ KYSEDVGHIH QGLNFEPTRE + ELNSLSKACS RLWELDMNRI VPGKDYIIDC GKGKKVYQKG DMASESLFSW + LGDDVLRKPT YSRFCALLDN YNPHQGYKEV VTQQDKHEEI AFVEEIARTA + PIKYLHRYLV QKGAVPQDYE DFKRMLTSLW FDLYGRGGNS SCSSAFEHVF + VGEIKGRGQG ESEVSGFHNW IQFYLEEAKG NVDYQGYIFP RRRGESPDSE + IQLLTVQFEW HGVLKSVSST LIGVSPEFEV ALYTLCFFVG GEDNRVDIGP + YSVNVKCYRL GNNKIGSAFP IVEN + + + + + + +6.00285 +-0.324479 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +4188 4188 4188 4188 4024 3570 3179 2832 1738 1017 585 323 156 73 23 9 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4150 4150 4150 4150 3986 3532 3107 2765 1590 800 322 73 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2153 1609 349 71 10 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1058 2315 640 142 36 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2404 (charge 3) + +2185.96 +3 + + +151.872 151.962 155.081 158.092 167.082 171.077 175.119 183.076 193.097 195.076 200.103 211.12 221.717 226.155 240.098 241.101 243.694 257.125 304.161 311.135 328.164 351.128 352.13 368.156 433.203 479.192 496.218 501.277 562.245 563.749 +567.257 588.308 607.249 609.181 616.454 624.272 637.273 639.653 656.294 665.282 673.788 674.286 690.309 694.32 712.572 776.394 827.361 829.362 938.399 955.417 1095.45 1126.48 1243.98 1346.57 + + + + +4 4 4 6 5 4 43 5 8 9 8 10 5 6 100 5 6 52 49 12 7 24 6 76 37 9 13 12 36 12 +7 13 9 23 6 13 9 8 7 9 14 23 51 10 22 14 73 14 13 12 9 44 7 26 + + + + + + +GRMZM5G872068_P01 P38561 Glutamine synthetase root isozyme 3 (EC 6.3.1.2)(GS112)(Glutamate--ammonia ligase) seq=translation; coord=5:205237019..205240533:-1; parent_transcript=GRMZM5G872068_T01; parent_gene=GRMZM5G872068 + + + + + + + +GRMZM2G046601_P01 NM_001111827 glutamine synthetase (LOC542215), mRNA seq=translation; coord=9:146062602..146070481:1; parent_transcript=GRMZM2G046601_T01; parent_gene=GRMZM2G046601 + + + + + + + +GRMZM2G046601_P04 NM_001111827 glutamine synthetase (LOC542215), mRNA seq=translation; coord=9:146069111..146070481:1; parent_transcript=GRMZM2G046601_T04; parent_gene=GRMZM2G046601 + + + + + + + + +4.91163 +-0.363824 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +5044 5044 5044 5044 5044 4909 4788 4646 1784 1388 334 31 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5068 5068 5068 5068 5068 4933 4812 4670 1802 1347 323 33 1 0 + + + + + + +0 1 2 3 + + + + +4521 544 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +275 4678 104 2 0 0 15 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2415 (charge 2) + +1638.77 +2 + + +158.647 161.524 175.119 200.732 212.424 238.524 252.146 277.14 294.167 324.555 362.332 409.461 475.225 525.479 543.24 811.384 820.89 895.396 966.412 1079.53 1345.61 + + + + +8 9 57 9 9 9 11 24 12 11 10 13 46 13 12 23 100 16 42 23 43 + + + + + + +GRMZM2G154595_P01 NP_001142100 hypothetical protein LOC100274264 seq=translation; coord=6:165631098..165635858:-1; parent_transcript=GRMZM2G154595_T01; parent_gene=GRMZM2G154595 + + + MRPALLKSTA ELLRRSRGYA SSANPERKVA ILGAAGGIGQ PLSLLMKLNP + LVSSLSLYDI AGTPGVAADV SHINSPALVK GFMGDDQLGE ALEGSDVVII + PAGVPRKPGM TRDDLFNINA GIVKGLCTAI AKHCPNALVN MISNPVNSTV + PIAAEVFKKA GTYDEKKLFG VTTLDVVRAK TFYAGKAGVP VTGVNVPVVG + GHAGITILPL FSQATPASNS LSQEDIEALT KRTQDGGTEV VEAKAGKGSA + TLSMAYAGAV FADACLKGLN GVPDIVECSF VQSTVTELPF FASKVRLGKN + GVEEVLGLGE LNEFEKKGLE NLKGELKSSI DKGIKFAHGN + + + + + +GRMZM2G466833_P01 NP_001140825 hypothetical protein LOC100272900 seq=translation; coord=3:213896741..213905427:1; parent_transcript=GRMZM2G466833_T01; parent_gene=GRMZM2G466833 + + + MVLVRDLPAQ WCSFEISLYA MLDSLPDWLR RAPRLPRLPP RRSPPPLRRA + RPKLYLKLAA ERQDPNPNST MRPSLMRSTS QLLRRRSYSS ASGQPERKVA + ILGAAGGIGQ PLSLLMKLNP LVSSLSLYDI AGTPGVAADV SHINSPALVK + GFMGDEQLGE ALEGSDVVII PAGVPRKPGM TRDDLFNINA GIVKNLSTAI + AKYCPNALVN MISNPVNSTV PIAAEVFKKA GTYDEKKLFG VTTLDVVRAK + TFYAGKANLP VTDVNVPVVG GHAGITILPL FSQATPATNA LSDEDIKALT + KRTQDGGTEV VEAKAGKGSA TLSMAYAGAV FADACLKGLN GVPDIVECSF + VQSTVTELPF FASKVRLGKN GVEEVLGLGE LSDFEKEGLE KLKSELKSSI + EKGIKFANDN + + + + + + +6.30828 +-0.38232 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +2346 2346 2346 2346 2346 2007 1723 1269 825 458 269 101 24 6 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2347 2347 2347 2347 2347 2008 1723 1254 773 406 180 53 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +694 1462 182 9 7 5 0 + + + + + + +0 1 2 3 4 5 + + + + +1346 969 32 6 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2425 (charge 2) + +1389.7 +2 + + +155.082 201.123 218.15 244.094 329.184 347.195 376.146 414.182 445.223 484.211 489.195 501.241 569.275 586.159 651.269 686.827 691.236 761.366 845.38 916.457 944.435 1015.51 1043.51 1049.44 1172.55 1230.77 1417.87 + + + + +12 10 66 11 14 9 8 18 10 11 11 52 10 9 9 10 10 9 100 12 47 33 16 11 18 12 11 + + + + + + +GRMZM2G156861_P02 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168699190:1; parent_transcript=GRMZM2G156861_T02; parent_gene=GRMZM2G156861 + + + MFGNIGKIPI IGDLTGSNKN AHLKGNLVLM RKTVLGFDVT SIAGSLMDGL + GEFLGRGVTC QLVSSTVVDP NNGNRGKVGQ EASLEQWLLH PPPLLAGEDQ + FRVTFDWEVE KHGVPGAIIV KNNHASEFFL KTITIDDVPG HGPIVFVANS + WVYPQYKYRY NRVFFSNDTY LPSQMPAALK PYRDDELRNL RGDDQQGPYQ + EHDRVYRYDV YNDLGNPDAK NPRPVLGGSK HHPYPRRGRT GRKPTQTDPN + SESRLTLTDG DVYVPRDERF GHIKNSDFYG YTIKAFVDGL VPILEGYLLG + IEFNSFKDIL QLYEGGIKLP DIPALEEFRK QFPLQMVKDL MPAGGDYVLK + LPMPKIIKED KKAWMSDEEF ARETLAGVNP LIIRRLTEFP PKSTLDPSKY + GDQTSTITEA HIAGSLEGLT VQQALDSNRL YILDHHDHYM PFLIEVNSLN + DNFIYATRTL LFLRGDGTLA PVAIEMSLPE LRDGITAAKS TVYTPAPPTA + GAEAWVWRLA KAYVNVNDYC WHQGISHWLN THAVMEPFVI ATNRQLSVTH + PVHRLLLPHY RDTMNINALA RQKLINAGGI FEMTVFPRKY AIEISSKVYG + SWNFTEQALP DDLIKRGMAV PDPSSPYKVR LLIEDYPYAS DGLAVWHAIE + QWVTEYLAIY YPNDGVLQAD VELQAWWKEA REVGHADLKD EHWWPKMQTV + PELVKACTTI IWIASALHAA VNFGQYPYCG YHPNRPSVSR RPMPVPGSDA + YKELEKNPEK FFVRSITAQF QAVVGISLLE ILSSHSSDEV YLGQRDTKEW + TSDAKAQEAF KRFGARLTEI EKRVEAMNKD PRFKNRYSAA QFPYTLLFPN + TSDKGDNTGV TAKGIPNSIS I + + + + + +GRMZM2G156861_P03 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168839001:1; parent_transcript=GRMZM2G156861_T03; parent_gene=GRMZM2G156861 + + + MFGNIGKIPI IGDLTGSNKN AHLKGNLVLM RKTVLGFDVT SIAGSLMDGL + GEFLGRGVTC QLVSSTVVDP NNGNRGKVGQ EASLEQWLLH PPPLLAGEDQ + FRVTFDWEVE KHGVPGAIIV KNNHASEFFL KTITIDDVPG HGPIVFVANS + WVYPQYKYRY NRVFFSNDTY LPSQMPAALK PYRDDELRNL RGDDQQGPYQ + EHDRVYRYDV YNDLGLPDSG NPRPVLGGTK ELPYPRRCRT GRKPTKSDPN + SESRLTLVDG DVYVPRDERF GHIKKSDFYG YAIKALVNAV IPAIRTYVDL + SPGEFDSFKD IMKLYEGGIQ LPKIPALEDL RKQFPLELVK DVLPVGGDYL + LKLPMPQIIK EDKTGWMTDE EFGREILAGV NPMLVKRLTE FPPRSSLDPS + KYGDHTSTIR EADLENKLEG LTVQQALHGN RLYILDHHDN FMPFLVRVNS + LEGNFIYATR TVLFLRGDGT LVPVAIELSL PELRDGLTTA KSTVYTPKST + TGAEAWVWHL AKAYANVNDY CWHQLISHWL NTHAVMEPFV IATNRQLSVT + HPVHKLLLPH YRDTMNINSN ARQMLVNAGG IFETTVFPRQ YAFEMSSVIY + KDWNFTEQAL PDDLIKRGMA VADPSSPYKV RLLVEDYPYA SDGLAIWHAI + EQWVTEYLAV YYPNDGVLRA DVELQAWWKE AREVGHADLK DAPWWPKMQT + VAELVKACTT IIWIASALHA AVNFGQYPYA GYLPNRPSVS RKPMPAPGSD + EYAELERKPE KVFVRTITSQ FQALVGISLL EILSSHSSDE VYLGQRDTKE + WTSDAKAQEA FKRFGARLTE IEKRVVTMNA DPRLKNRNGP AEFPYTLLYP + NTSDTKGDAA GITAKGIPNS ISI + + + + + +GRMZM2G156861_P01 NP_001105003 lipoxygenase seq=translation; coord=3:168835321..168839001:1; parent_transcript=GRMZM2G156861_T01; parent_gene=GRMZM2G156861 + + + MFGNIGKIPI IGDLTGSNKN AHLKGNVVLV RKTVLGLDVT SIAGSLLDGI + GEFLGRGVTC QLISSTVVDP NNGNRGKLGA EASLEQWLLN PPPLLSSENQ + FRVTFDWEVE KQGIPGAIIV KNNHASEFFL KTITLNDVPG HGTIVFVANS + WIYPQSKYRY NRVFFSNDTY LPSQMPAALK PYRDDELRNL RGDDQQGPYQ + EHDRVYRYDV YNDLGLPDSG NPRPVLGGTK ELPYPRRCRT GRKPTKSDPN + SESRLTLVDG DVYVPRDERF GHIKKSDFYG YAIKALVNAV IPAIRTYVDL + SPGEFDSFKD IMKLYEGGIQ LPKIPALEDL RKQFPLELVK DVLPVGGDYL + LKLPMPQIIK EDKTGWMTDE EFGREILAGV NPMLVKRLTE FPPRSSLDPS + KYGDHTSTIR EADLENKLEG LTVQQALHGN RLYILDHHDN FMPFLVRVNS + LEGNFIYATR TVLFLRGDGT LVPVAIELSL PELRDGLTTA KSTVYTPKST + TGAEAWVWHL AKAYANVNDY CWHQLISHWL NTHAVMEPFV IATNRQLSVT + HPVHKLLLPH YRDTMNINSN ARQMLVNAGG IFETTVFPRQ YAFEMSSVIY + KDWNFTEQAL PDDLIKRGMA VADPSSPYKV RLLVEDYPYA SDGLAIWHAI + EQWVTEYLAV YYPNDGVLRA DVELQAWWKE AREVGHADLK DAPWWPKMQT + VAELVKACTT IIWIASALHA AVNFGQYPYA GYLPNRPSVS RKPMPAPGSD + EYAELERKPE KVFVRTITSQ FQALVGISLL EILSSHSSDE VYLGQRDTKE + WTSDAKAQEA FKRFGARLTE IEKRVVTMNA DPRLKNRNGP AEFPYTLLYP + NTSDTKGDAA GITAKGIPNS ISI + + + + + +GRMZM2G109130_P01 NP_001105515 lipoxygenase seq=translation; coord=1:264200949..264205758:1; parent_transcript=GRMZM2G109130_T01; parent_gene=GRMZM2G109130 + + + MLSGIIDGLT GANKHARLKG TVVLMRKNVL DLNDFGATVV DSISEFLGKG + VTCQLISSTL VDANNGNRGR VGAEANLEQW LTSLPSLTTG ESKFGVTFDW + EVEKLGVPGA VVVKNNHAAE FFLKTITLDD VPGRGAVTFV ANSWVYPAGK + YRYNRVFFSN DTYLPSQMPA ALKPYRDDEL RNLRGDDQQG PYQEHDRVYR + YDVYNDLGEP DGGNPRPILG GSADHPYPRR CRTGRKPTKT DPNSESRLSL + VEQIYVPRDE RFGHLKMSDF LGYSIKAITQ GIIPAVRTYV DTTPGEFDSF + QDIINLYEGG IKLPKIQALE DMRKLFPLQL VKDLLPAGGD YLLKLPIPQI + IQEDKNAWRT DEEFAREVLA GVNPMVITRL TEFPPKSTLD PSKYGDHTST + ITAEHIEKNL EGLTVQQALD GNRLYILDHH DRFMPFLIDV NNLEGNFIYA + TRTLFFLRGD GRLAPLAIEL SEPYIDGDLT VAKSKVYTPA SSGVEAWVWQ + LAKAYVAVND SGWHQLVSHW LNTHAVMEPF VIATNRQLSV THPVHKLLSS + HFRDTMTINA LARQTLINGG GIFEMTVFPG KYALGMSSVV YKSWNFTEQG + LPADLVKRGV AVADPSSPYK VRLLIEDYPY ASDGLAIWHA IEQWVGEYLA + IYYPDDGALR GDEELQAWWK EVREVGHGDH KDAPWWPKMQ AVSELASACT + TIIWIASALH AAVNFGQYPY AGYLPNRPTV SRRRMPEPGS KEYEELERDP + ERGFIHTITS QIQTIIGISL IEILSKHSSD EVYLGQRDTP EWTSDARALA + AFKRFSDALV KIEGKVVGEN RDPQLRNRNG PAEFPYMLLY PNTSDHSGAA + AGLTAKGIPN SISI + + + + + +GRMZM2G109130_P02 NP_001105515 lipoxygenase seq=translation; coord=1:264202964..264205732:1; parent_transcript=GRMZM2G109130_T02; parent_gene=GRMZM2G109130 + + + MPAALKPYRD DELRNLRGDD QQGPYQEHDR VYRYDVYNDL GEPDGGNPRP + ILGGSADHPY PRRCRTGRKP TKTDPNSESR LSLVEQIYVP RDERFGHLKM + SDFLGYSIKA ITQGIIPAVR TYVDTTPGEF DSFQDIINLY EGGIKLPKIQ + ALEDMRKLFP LQLVKDLLPA GGDYLLKLPI PQIIQEDKNA WRTDEEFARE + VLAGVNPMVI TRLTEFPPKS TLDPSKYGDH TSTITAEHIE KNLEGLTVQQ + ALDGNRLYIL DHHDRFMPFL IDVNNLEGNF IYATRTLFFL RGDGRLAPLA + IELSEPYIDG DLTVAKSKVY TPASSGVEAW VWQLAKAYVA VNDSGWHQLV + SHWLNTHAVM EPFVIATNRQ LSVTHPVHKL LSSHFRDTMT INALARQTLI + NGGGIFEMTV FPGKYALGMS SVVYKSWNFT EQGLPADLVK RGVAVADPSS + PYKVRLLIED YPYASDGLAI WHAIEQWVGE YLAIYYPDDG ALRGDEELQA + WWKEVREVGH GDHKDAPWWP KMQAVSELAS ACTTIIWIAS ALHAAVNFGQ + YPYAGYLPNR PTVSRRRMPE PGSKEYEELE RDPERGFIHT ITSQIQTIIG + ISLIEILSKH SSDEVYLGQR DTPEWTSDAR ALAAFKRFSD ALVKIEGKVV + GENRDPQLRN RNGPAEFPYM LLYPNTSDHS GAAAGLTAKG IPNSISI + + + + + + +3.78982 +-0.244504 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +1360 1360 1360 1360 1360 1360 1073 988 458 373 136 78 60 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1359 1359 1359 1359 1359 1359 1072 987 456 351 117 40 10 1 0 + + + + + + +0 1 2 3 + + + + +903 438 32 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +371 922 66 2 0 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2434 (charge 2) + +1544.63 +2 + + +155.082 157.831 173.056 175.119 226.154 235.12 240.097 244.092 288.081 290.145 305.11 326.557 370.137 375.239 421.102 427.203 556.248 604.254 673.819 684.306 944.424 984.416 1001.43 + + + + +14 10 17 74 13 28 15 52 24 21 17 13 13 17 15 63 26 17 18 18 53 23 100 + + + + + + +AC212835.3_FGP007 seq=translation; coord=2:21007540..21010895:1; parent_transcript=AC212835.3_FGT007; parent_gene=AC212835.3_FG007 + + + + + + + + +3.86658 +-0.249456 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 + + + + +872 872 872 815 729 567 487 284 193 136 88 46 10 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +860 860 860 803 716 544 448 249 130 71 29 1 0 0 1 0 + + + + + + +0 1 2 3 4 5 + + + + +362 357 120 37 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +286 399 141 39 8 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2437 (charge 3) + +2020.8 +3 + + +155.082 157.061 159.076 160.108 170.092 171.077 175.119 181.061 183.076 185.092 188.103 198.088 200.103 213.087 216.098 226.119 242.114 269.125 271.14 283.14 287.134 295.141 299.135 304.162 313.151 328.114 337.111 340.161 352.669 356.193 +358.172 369.225 383.119 400.147 413.215 417.191 419.189 430.241 443.144 488.197 501.279 510.223 554.803 567.737 575.29 602.328 611.82 614.906 616.739 620.907 625.251 630.584 644.319 648.596 651.604 654.847 656.359 658.102 662.859 666.36 +669.622 673.368 682.765 687.754 704.341 716.285 722.781 731.29 774.411 776.413 788.798 816.344 825.413 832.315 833.327 875.834 889.441 891.442 931.855 946.326 959.412 972.481 990.487 992.486 1002.42 1019.44 1061.54 1141.4 1149.57 1158.42 +1160.44 1205.57 1232.48 1273.44 1287.48 1305.47 1347.5 1361.48 1447.51 1558.53 + + + + +3 3 1 3 2 6 24 2 2 4 2 12 13 5 7 3 4 10 8 2 8 2 2 100 4 6 3 4 4 3 +5 2 2 9 4 2 4 10 8 5 7 46 2 28 3 12 4 2 3 5 23 4 3 4 4 4 6 6 6 7 +3 11 8 2 4 15 9 89 18 3 3 5 2 8 3 10 19 2 3 9 3 2 25 2 5 4 11 1 3 29 +6 4 2 2 3 1 2 2 5 2 + + + + + + +GRMZM2G085019_P01 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T01; parent_gene=GRMZM2G085019 + + + MLSTRTAAVA ASASPASPWK LGGRSEGGAS CDGCRTYRNT LRRRAAPAKV + RALPPRRVDA VAMVSNAETE TEKEQEEAAA ASEELPVMPW ATSVASGYTL + LRDPHHNKGL AFTEEERDGH YLRGLLPPAV LSQELQIKKF MNTLRQYQTP + LQRYIAMMNL QETDERLFYK LLIDNVVELL PFVYTPTVGE ACQKYGSIFG + RPQGLYVSLK DKGKVLEVLR NWPHRNIQVI CVTDGERILG LGDLGCQGMG + IPVGKLALYT ALGGVDPSVC LPITIDVGTN NEKLLNDEFY IGLRQKRATG + EEYDELIEEF MSAVKQFYGE KVLIQFEDFA NHNAFDLLEK YSKSHLVFND + DIQGTASVVL AGLLAALKMV GGTLAEQTYL FLGAGEAGTG IAELIALEIS + KQTNAPIEEC RKKVWLVDSK GLIVDSRKGS LQPFKKPWAH EHEPLKTLYD + AVQSIKPTVL IGTSGVGRTF TKEIIEAMSS FNERPIIFSL SNPTSHSECT + AEQAYTWSQG RSIFASGSPF APVEYEGKTF VPGQSNNAYI FPGLGLGLVI + SGAVRVHEDM LLAASKALAD QATQDNFEKG SIFPPFTSIR KISAHIAAAV + AAKAYELGLA TRLPPPSDLV KYAENCMYTP VYRNYR + + + + + +GRMZM2G085019_P02 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T02; parent_gene=GRMZM2G085019 + + + MLSTRTAAVA ASASPASPWK LGGRSEGGAS CDGCRTYRNT LRRRAAPAKV + RALPPSEELP VMPWATSVAS GYTLLRDPHH NKGLAFTEEE RDGHYLRGLL + PPAVLSQELQ IKKFMNTLRQ YQTPLQRYIA MMNLQETDER LFYKLLIDNV + VELLPFVYTP TVGEACQKYG SIFGRPQGLY VSLKDKGKVL EVLRNWPHRN + IQVICVTDGE RILGLGDLGC QGMGIPVGKL ALYTALGGVD PSVCLPITID + VGTNNEKLLN DEFYIGLRQK RATGEEYDEL IEEFMSAVKQ FYGEKVLIQF + EDFANHNAFD LLEKYSKSHL VFNDDIQGTA SVVLAGLLAA LKMVGGTLAE + QTYLFLGAGE AGTGIAELIA LEISKQTNAP IEECRKKVWL VDSKGLIVDS + RKGSLQPFKK PWAHEHEPLK TLYDAVQSIK PTVLIGTSGV GRTFTKEIIE + AMSSFNERPI IFSLSNPTSH SECTAEQAYT WSQGRSIFAS GSPFAPVEYE + GKTFVPGQSN NAYIFPGLGL GLVISGAVRV HEDMLLAASK ALADQATQDN + FEKGSIFPPF TSIRKISAHI AAAVAAKAYE LGLATRLPPP SDLVKYAENC + MYTPVYRNYR + + + + + + +5.02163 +-0.271439 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +6688 6688 6688 6688 6603 6491 6115 5653 4673 3211 1923 1000 546 302 176 69 30 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6692 6692 6692 6692 6607 6495 6118 5636 4572 2899 1360 452 177 45 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2090 3066 1109 368 58 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1028 3589 1734 295 35 11 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2439 (charge 3) + +1499.81 +3 + + +152.056 155.081 156.077 157.097 158.092 159.077 159.092 162.102 166.061 167.081 167.093 169.097 169.134 171.077 171.113 173.092 173.129 175.12 181.096 181.11 183.149 185.092 186.124 187.108 194.129 195.089 197.128 199.107 202.054 204.134 +207.08 209.105 211.144 219.149 221.103 223.156 226.155 227.103 235.12 239.115 240.134 244.165 246.107 249.098 251.15 256.145 260.197 267.109 284.139 303.203 327.166 329.657 338.147 343.655 346.15 355.173 357.25 367.135 379.672 386.155 +396.152 436.23 444.194 454.164 457.201 462.266 464.237 466.207 468.28 471.196 475.208 482.233 486.293 492.719 514.25 533.303 549.247 567.25 570.297 572.285 574.291 604.241 622.317 623.35 647.37 701.299 727.387 730.34 752.395 756.424 +758.335 764.372 784.424 790.324 840.477 859.382 887.381 889.438 960.492 977.528 + + + + +18 36 7 30 7 14 27 6 18 9 8 22 18 18 7 8 19 55 9 7 64 6 34 20 22 8 9 33 8 100 +21 16 25 8 23 17 79 23 28 17 27 35 6 45 16 79 31 63 74 40 18 7 18 6 7 36 92 8 7 14 +20 7 26 9 9 19 20 8 7 8 22 15 8 35 7 17 8 7 18 18 7 30 40 31 18 7 39 6 18 15 +21 6 21 23 15 15 66 24 35 7 + + + + + + +GRMZM2G150474_P01 NP_001105626 glutathione S-transferase GST 15 seq=translation; coord=8:127719984..127722343:-1; parent_transcript=GRMZM2G150474_T01; parent_gene=GRMZM2G150474 + + + MATPAAVMKL YGWAISPFVS RALLALEEAG VDYELVPMSP QAGDHRRPEH + LARNPFAMVP VLEDGDLTLF ESRAIARHVL RKHRPELLGA GAGGSLERAA + MVDVWLEVEA HQLSPPAVAI VVECFAAPLL GRERDQTVVD ENVEKLRKVL + EVYEARLGEC RYLAGDFLSL ADLSPFTIMH CIMATEYAAA LVEALPRVSA + WWEGLAARPA AKKVAEFIPV GAAGLLEHPP KQQD + + + + + + + + + +7.32802 +-0.444122 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + + + + +3800 3800 3800 3800 3761 3653 3620 3425 1857 1394 640 158 45 15 3 1 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3804 3804 3804 3804 3765 3657 3620 3410 1821 1337 386 42 7 1 0 + + + + + + +0 1 2 3 + + + + +3145 635 26 0 + + + + + + +0 1 2 3 4 5 6 + + + + +435 2917 418 29 6 1 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2444 (charge 2) + +1326.63 +2 + + +152.056 158.094 169.097 175.119 199.072 212.103 222.088 226.154 239.114 257.125 258.11 262.151 351.131 360.151 367.17 434.735 483.261 587.292 602.358 633.813 687.342 775.378 868.46 942.462 965.507 1006.24 1071.51 + + + + +8 7 12 52 8 10 7 8 53 34 8 100 9 7 27 8 54 9 6 8 33 11 23 92 28 7 9 + + + + + + +GRMZM2G124576_P02 seq=translation; coord=1:59670870..59675001:-1; parent_transcript=GRMZM2G124576_T02; parent_gene=GRMZM2G124576 + + + MLVLFETPAG FALFKVLDEG KLDKVEDLWK EFTTSDSARK VVELKAFNKF + ENTSDALSAA TLIIDSKPSK GLRKFLQKHC EGETLAVADS KLGNAIKEKL + KIDCLHNSAV MELMRGLRNQ LTELITGLGA QDLGPMSLGL SHSLSRYKLK + FSPEKVDTMI IQAIGLLDDL DKELNTYAMR VREWYGWHFP ELTKIVTDNI + QYAKVVKMMG NRTNAVNLDF SEILSDEELE TQLKEAAVIS MGTEVSDLDL + SNIRELCDQV LALSEYRAQL YDYLKSRMNT IAPNLTALVG ELVGARLIAH + GGSLLNLAKQ PGSTIQILGA EKALFRALKT KHSTPKYGLI YHASLIGKAS + QKHKGKISRS LAAKTALAIR YDALGDGEDN SIGTESRLKL ETRLQVLEGR + ELGKSAGSTK GKPKIEVYEK DRKQGAGALT TPAKTYNPAA DLVLTEETPK + KSELASKKRK HHEVQTEPSA ELAEGAVQED RKKKKKNKES EEAPAAEGDG + EKKKKKKSKD VGEEPAVAAA AATEGEKKKK KKKSDADGEG VTTQTEESGK + KDKKKKKKRH ADDE + + + + + + +4.93314 +-0.340217 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + + + + +781 781 781 781 781 781 638 569 455 310 195 39 15 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +786 786 786 786 786 786 643 574 457 303 195 28 8 1 0 + + + + + + +0 1 2 3 + + + + +226 535 25 0 + + + + + + +0 1 2 3 4 5 6 + + + + +501 271 9 0 0 5 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2445 (charge 2) + +1418.59 +2 + + +152.056 155.082 158.091 164.914 169.098 171.076 183.075 199.072 201.087 217.082 226.154 241.081 259.092 328.113 333.176 359.715 437.197 486.141 505.221 596.538 634.265 705.298 807.266 873.394 1397.9 + + + + +22 20 23 16 27 25 18 61 23 32 19 36 22 26 24 17 19 18 21 19 29 27 21 100 22 + + + + + + +GRMZM2G077851_P01 NP_001136667 hypothetical protein LOC100216796 seq=translation; coord=1:151356484..151358622:1; parent_transcript=GRMZM2G077851_T01; parent_gene=GRMZM2G077851 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTDVIH + DPGRGAPLAK VTFRHPFRYK HQKELFVAAE GMYTGQFVYC GRRATLSIGN + VLPLRGIPEG AVVCNVEHHV GDRGVFARAS GDYAIVISHN PDNGTSRIKL + PSGAKKIVPS SCRAMIGQVA GGGRTEKPML KAGNAYHKYR VKRNSWPKVR + GVAMNPVEHP HGGGNHQHIG HASTVRRDAP PGQKVGLIAA RRTGRLRGQA + AATASKADKA T + + + + + + +GRMZM2G072729_P01 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34222504..34224841:1; parent_transcript=GRMZM2G072729_T01; parent_gene=GRMZM2G072729 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTDVIH + DPGRGAPLAK VTFRHPFRYK HQKELFVAAE GMYTGQFVYC GRRATLSIGN + VLPLRGIPEG AVVCNVEHHV GDRGVFARAS GDYAIVISHN PDNGTSRIKL + PSGAKKIVPS SCRAMIGQVA GGGRTEKPML KAGNAYHKYR VKRNSWPKVR + GVAMNPVEHP HGGGNHQHIG HASTVRRDAP PGQKVGLIAA RRTGRLRGQA + AATAAKADKA + + + + + + +GRMZM2G072729_P02 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34222942..34224888:1; parent_transcript=GRMZM2G072729_T02; parent_gene=GRMZM2G072729 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTDVIH + DPGRGAPLAK VTFRHPFRYK HQKELFVAAE GMYTGQFVYC GRRATLSIGN + VLPLRGIPEG AVVCNVEHHV GDRGVFARAS GDYAIVISHN PDNGTSRIKL + PSGAKKIVPS SCRAMIGQVA GGGRTEKPML KAGNAYHKYR VKRNSWPKVR + GVAMNPVEHP HGGGNHQHIG HASTVRRDAP PGQKVGLIAA RRTGRLRGQA + AATAAKADKA + + + + + + +GRMZM2G067456_P01 NP_001131396 hypothetical protein LOC100192723 seq=translation; coord=3:127004080..127006073:-1; parent_transcript=GRMZM2G067456_T01; parent_gene=GRMZM2G067456 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTDVIH + DPGRGAPLAK VTFRHPFRYK HQKELFVAAE GMYTGQFVYC GRRATLSIGN + VLPLRGIPEG AVVCNVEHHV GDRGVFARAS GDYAIVISHN PDNGTSRIKL + PSGAKKIVPS SCRAMIGQVA GGGRTEKPML KAGNAYHKYR VKRNSWPKVR + GVAMNPVEHP HGGGNHQHIG HASTVRRDAP PGQKVGLIAA RRTGRLRGQA + AATASKADKA T + + + + + + +GRMZM2G077851_P03 NP_001136667 hypothetical protein LOC100216796 seq=translation; coord=1:151356736..151358244:1; parent_transcript=GRMZM2G077851_T03; parent_gene=GRMZM2G077851 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTFRHP + FRYKHQKELF VAAEGMYTGQ FVYCGRRATL SIGNVLPLRG IPEGAVVCNV + EHHVGDRGVF ARASGDYAIV ISHNPDNGTS RIKLPSGAKK IVPSSCRAMI + GQVAGGGRTE KPMLKAGNAY HKYRVKRNSW PKVRGVAMNP VEHPHGGGNH + QHIGHASTVR RDAPPGQKVG LIAARRTGRL RGQAAATASK ADKAT + + + + + + +GRMZM2G072729_P03 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34223087..34224612:1; parent_transcript=GRMZM2G072729_T03; parent_gene=GRMZM2G072729 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTFRHP + FRYKHQKELF VAAEGMYTGQ FVYCGRRATL SIGNVLPLRG IPEGAVVCNV + EHHVGDRGVF ARASGDYAIV ISHNPDNGTS RIKLPSGAKK IVPSSCRAMI + GQVAGGGRTE KPMLKAGNAY HKYRVKRNSW PKVRGVAMNP VEHPHGGGNH + QHIGHASTVR RDAPPGQKVG LIAARRTGRL RGQAAATAAK ADKA + + + + + + +GRMZM2G067456_P02 NP_001131396 hypothetical protein LOC100192723 seq=translation; coord=3:127004341..127005956:-1; parent_transcript=GRMZM2G067456_T02; parent_gene=GRMZM2G067456 + + + MGRVIRAQRK GAGSVFKSHT HHRKGPARFR SLDFGERNGY LKGVVTFRHP + FRYKHQKELF VAAEGMYTGQ FVYCGRRATL SIGNVLPLRG IPEGAVVCNV + EHHVGDRGVF ARASGDYAIV ISHNPDNGTS RIKLPSGAKK IVPSSCRAMI + GQVAGGGRTE KPMLKAGNAY HKYRVKRNSW PKVRGVAMNP VEHPHGGGNH + QHIGHASTVR RDAPPGQKVG LIAARRTGRL RGQAAATASK ADKAT + + + + + + + +6.0928 +-0.393084 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + + + + +2961 2961 2961 2961 2961 2906 2412 1943 1297 694 410 100 37 9 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2973 2973 2973 2973 2973 2918 2424 1950 1281 667 387 90 44 18 1 0 + + + + + + +0 1 2 3 4 + + + + +1393 1429 144 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1417 1434 105 5 0 0 12 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2450 (charge 3) + +2712.3 +3 + + +210.591 226.155 228.133 235.951 327.167 523.076 526.726 529.409 594.472 635.314 727.382 764.37 824.377 840.464 847.086 874.893 881.433 883.398 903.487 906.427 977.53 984.515 1112.55 1314.47 1762.86 2045.92 + + + + +13 80 29 15 16 16 16 16 17 18 100 23 23 24 27 30 96 22 21 28 69 24 64 22 24 26 + + + + + + +GRMZM2G451224_P01 O65101 Photosystem I reaction center subunit VI, chloroplastic Precursor (PSI-H)(Light-harvesting complex I 11 kDa protein) seq=translation; coord=6:163973641..163974980:-1; parent_transcript=GRMZM2G451224_T01; parent_gene=GRMZM2G451224 + + + MASLAAVSVK PVAIKGLAGS SISGRKLAVA RPSARSIRRP RAAAVVAKYG + DKSVYFDLDD IGNTTGQWDL YGSDAPSPYN PLQSKFFETF AAPFTKRGLL + LKFLLLGGGS LLAYVSASAS PDLLPIKKGP QEPPQPGPRG KI + + + + + + +5.86224 +-0.316878 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +8428 8428 8361 8228 7662 7141 6566 5041 3809 1921 1015 514 221 78 42 19 5 1 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8432 8432 8365 8220 7644 7083 6394 4526 3049 904 247 71 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2844 3625 1354 487 101 24 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1556 3858 2198 618 175 21 6 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2453 (charge 3) + +1287.68 +3 + + +154.086 155.082 155.118 157.061 157.097 157.109 157.134 158.092 162.102 166.061 167.056 167.08 167.118 168.056 169.097 169.134 172.108 173.092 173.129 175.119 181.097 183.076 183.113 183.149 185.092 185.129 186.123 194.129 195.113 197.128 +198.087 198.124 199.108 199.169 201.123 208.954 212.139 213.627 221.104 226.119 227.102 235.119 240.134 243.144 249.098 252.097 255.146 258.145 269.161 272.171 274.014 284.009 287.01 296.166 300.203 312.166 317.67 323.172 324.986 329.194 +341.019 342.997 344.976 349.188 355.161 359.028 361.026 366.215 394.21 398.755 409.22 411.235 412.234 415.038 418.231 426.246 428.25 435.708 485.285 497.282 505.241 512.278 515.29 517.275 522.268 537.278 538.279 540.278 554.302 572.314 +594.335 616.32 619.318 632.302 637.33 639.325 651.355 727.38 733.349 782.291 + + + + +2 14 1 2 4 2 5 9 2 2 31 1 2 2 8 2 2 3 13 29 7 2 2 1 1 2 1 1 10 2 +1 2 6 1 4 18 22 11 2 23 4 5 5 5 4 2 13 6 4 7 4 23 7 6 2 10 4 7 2 12 +2 5 11 6 7 78 16 3 7 1 19 7 1 1 2 100 5 2 9 2 5 2 1 2 15 11 1 39 1 2 +3 4 2 1 22 2 5 2 2 1 + + + + + + +GRMZM2G169160_P01 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666220..5677820:-1; parent_transcript=GRMZM2G169160_T01; parent_gene=GRMZM2G169160 + + + MLTCGRFISS SAATSTASFF PFRTLTRSLV RRPAPHLLSS ASAAAATAVE + LDTNDGSAGG GAGVVRPQWK AAIDFKWIRD NRDAVADNIR TRNSTANLDL + VFELYDQYLT LQKEVERLRA ERNAVANKMK GKLDPSVRQA LVEEGKNLKE + GLIALEEDLV QLTDKLQLEA QSIPNTTHPD VPVGGEESSV LRKEVGSQRS + FNFAIKDHLQ LGKELDLFDF DAAAEVSGSK FYYLKNEAVL LEMALVNWAI + SEVSKKGFTP LITPEIVRSS VVEKCGFQPR AKNTQVYSIE DSDQCLIGTA + EIPVGGIHMD SILAESALPL KYVAYSHCFR TEAGAAGAAT RGLYRVHQFS + KVEMFIFCRP EESGKWHEEL ITIEEDLYAS LGLHFKTLDM ATGDLGAPAY + RKFDIEAWMP GLERYGEISS ASNCTDYQSR RLGIRYRPSP SEPPSTSTKK + GKGAASGPTQ FVHTLNATAV AVPRLIVCIL ENFQQGDGSI VVPEPLRPYM + GGLELLSPKF K + + + + + +GRMZM2G169160_P03 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666399..5677820:-1; parent_transcript=GRMZM2G169160_T03; parent_gene=GRMZM2G169160 + + + MLTCGRFISS SAATSTASFF PFRTLTRSLV RRPAPHLLSS ASAAAATAVE + LDTNGDGSAG GGAGVVRPQW KAAIDFKWIR DNRDAVADNI RTRNSTANLD + LVFELYDQYL TLQKEVERLR AERNAVANKM KGKLDPSVRQ ALVEEGKNLK + EGLIALEEDL VQLTDKLQLE AQSIPNTTHP DVPVGGEESS VLRKEVGSQR + SFNFAIKDHL QLGKELDLFD FDAAAEVSGS KFYYLKNEAV LLEMALVNWA + ISEVSKKGFT PLITPEIVRS SVVEKCGFQP RAKNTQVYSI EDSDQCLIGT + AEIPVGGIHM DSILAESALP LKYVAYSHCF RTEAGAAGAA TRGLYRVHQF + SKVEMFIFCR PEESGKWHEE LITIEEDLYA SLGLHFKTLD MATGDLGAPA + YRKFDIEAWM PGLERYGEIS SASNCTDYQS RRLGIRYRPS PSEPPSTSTK + KGKGAASGPT QFVHTLNATA VAVPRLIVCI LENFQQGDGS IVVPEPLRPY + MGGLELLSPK FK + + + + + + +6.24997 +-0.357141 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +11868 11868 11868 11638 11154 10476 9553 7642 5793 3436 1882 895 396 141 38 7 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +11875 11875 11875 11645 11161 10432 9470 7437 5107 2432 676 204 77 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4772 5010 1686 354 51 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2425 5820 2887 593 126 23 13 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2454 (charge 3) + +1661.85 +3 + + +150.767 154.675 155.082 157.098 158.092 159.076 167.081 169.098 169.135 172.889 175.119 180.102 183.151 185.092 187.071 187.107 195.114 197.128 199.108 201.124 208.83 212.141 214.083 226.155 229.581 231.123 240.098 244.166 249.098 255.143 +258.861 268.13 272.171 277.117 301.157 303.146 320.173 322.175 337.19 374.719 383.194 400.195 414.236 420.714 423.241 427.193 444.22 452.255 504.257 564.337 620.324 630.295 651.357 660.347 670.332 678.378 688.348 699.364 748.425 760.159 +789.39 791.394 817.382 845.476 903.487 1229.66 + + + + +3 3 5 17 4 4 4 7 4 3 38 26 3 8 4 3 4 6 29 5 4 5 4 100 5 9 5 30 8 4 +4 4 8 5 4 32 8 5 5 5 17 5 5 8 22 6 29 9 29 8 17 7 8 8 21 7 18 10 62 6 +51 9 54 23 6 6 + + + + + + +GRMZM2G015419_P04 NP_001105980 lipoxygenase seq=translation; coord=4:233625700..233629448:1; parent_transcript=GRMZM2G015419_T04; parent_gene=GRMZM2G015419 + + + MMNLNLKQPL VLPAHHSNVV GSRLSSSSGS RRHVRLPRIS CSATEEVSGA + VSSVTVERML TVTASVEASP AIGQMYFQRA VDDIGDLLGK TLLLELVSSE + LDAKSGVEKT RVTAYAHKTL REGHYEAEFK VPASFGPVGA VLVENEHHKE + VFIKEIKLVT GGDSSTAVTF DCNSWVHSKF DNPEKRIFFT LKSYLPSDTP + KGLEDLRKKD LQALRGDGHG ERKVFERVYD YDVYNDLGDP DKNPAHQRPV + LGGNKQYPYP RRCRTGRPRT KKDPETEMRE GHNYVPRDEQ FSEVKQLTFG + ATTLRSGLHA LLPALRPLLI NKKDLRFPHF PAIDDLFSDG IPLPAQTGFD + AIRTVVPRMV KLVEDTTDHV LRFEVPEMIE RDRFSWFKDE EFARQTIAGL + NPLCIQLLTE FPIKSKLDPE VYGPAESAIT KEILEKQMNG ALTVEQALAA + KRLFILDYHD VFLPYVHKVR ELQDATLYAS RTIFFLTDLG TLMPLAIELT + RPKSPTRPQW KRAFTHGPDA TDAWLWKLAK AHVLTHDTGY HQLVSHWLRT + HCCVEPYIIA ANRQLSRLHP VYRLLHPHFR YTMEINALAR EALINADGII + EESFWPGKYA VELSSVAYGA TWQFDTEALP NDLIKRGLAV RGEDGELELT + IKDYPYAHDG LLVWDSIRQW ASEYVNVYYK SDEAVAADPE LRAFWDEVRN + VGHGDKKDEP WWPVLDTRDS LVETLTTIMW VTSGHHSAVN FGQYHFAGYF + PNRPTTIRKN MPVEEGGPGE EMEKFLKQPE TTLLDMLPTQ MQAIKVMTTL + DILSSHSPDE EYMGEFAEPS WLAEPMVKAA FEKFGGRMKE IEGFIDECNN + NLDLKNRCGA GIVPYELLKP FSKPGVTGRG IPSSISI + + + + + +GRMZM2G015419_P02 NP_001105980 lipoxygenase seq=translation; coord=4:233625689..233629426:1; parent_transcript=GRMZM2G015419_T02; parent_gene=GRMZM2G015419 + + + MMNLNLKQPL VLPAHHSNVV GSRLSSSSPS AAAASRRTGG GVSSRSGSRR + HVRLPRISCS ATEEVSGAVS SVTVERMLTV TASVEASPAI GQMYFQRAVD + DIGDLLGKTL LLELVSSELD AKSGVEKTRV TAYAHKTLRE GHYEAEFKVP + ASFGPVGAVL VENEHHKEVF IKEIKLVTGG DSSTAVTFDC NSWVHSKFDN + PEKRIFFTLK SYLPSDTPKG LEDLRKKDLQ ALRGDGHGER KVFERVYDYD + VYNDLGDPDK NPAHQRPVLG GNKQYPYPRR CRTGRPRTKK DPETEMREGH + NYVPRDEQFS EVKQLTFGAT TLRSGLHALL PALRPLLINK KDLRFPHFPA + IDDLFSDGIP LPAQTGFDAI RTVVPRMVKL VEDTTDHVLR FEVPEMIERD + RFSWFKDEEF ARQTIAGLNP LCIQLLTEFP IKSKLDPEVY GPAESAITKE + ILEKQMNGAL TVEQALAAKR LFILDYHDVF LPYVHKVREL QDATLYASRT + IFFLTDLGTL MPLAIELTRP KSPTRPQWKR AFTHGPDATD AWLWKLAKAH + VLTHDTGYHQ LVSHWLRTHC CVEPYIIAAN RQLSRLHPVY RLLHPHFRYT + MEINALAREA LINADGIIEE SFWPGKYAVE LSSVAYGATW QFDTEALPND + LIKRGLAVRG EDGELELTIK DYPYAHDGLL VWDSIRQWAS EYVNVYYKSD + EAVAADPELR AFWDEVRNVG HGDKKDEPWW PVLDTRDSLV ETLTTIMWVT + SGHHSAVNFG QYHFAGYFPN RPTTIRKNMP VEEGGPGEEM EKFLKQPETT + LLDMLPTQMQ AIKVMTTLDI LSSHSPDEEY MGEFAEPSWL AEPMVKAAFE + KFGGRMKEIE GFIDECNNNL DLKNRCGAGI VPYELLKPFS KPGVTGRGIP + SSISI + + + + + +GRMZM2G015419_P05 NP_001105980 lipoxygenase seq=translation; coord=4:233625821..233629381:1; parent_transcript=GRMZM2G015419_T05; parent_gene=GRMZM2G015419 + + + MMNLNLKQPL VLPAHHSNVV GDLLGKTLLL ELVSSELDAK SGVEKTRVTA + YAHKTLREGH YEAEFKVPAS FGPVGAVLVE NEHHKEVFIK EIKLVTGGDS + STAVTFDCNS WVHSKFDNPE KRIFFTLKSY LPSDTPKGLE DLRKKDLQAL + RGDGHGERKV FERVYDYDVY NDLGDPDKNP AHQRPVLGGN KQYPYPRRCR + TGRPRTKKDP ETEMREGHNY VPRDEQFSEV KQLTFGATTL RSGLHALLPA + LRPLLINKKD LRFPHFPAID DLFSDGIPLP AQTGFDAIRT VVPRMVKLVE + DTTDHVLRFE VPEMIERDRF SWFKDEEFAR QTIAGLNPLC IQLLTEFPIK + SKLDPEVYGP AESAITKEIL EKQMNGALTV EQALAAKRLF ILDYHDVFLP + YVHKVRELQD ATLYASRTIF FLTDLGTLMP LAIELTRPKS PTRPQWKRAF + THGPDATDAW LWKLAKAHVL THDTGYHQLV SHWLRTHCCV EPYIIAANRQ + LSRLHPVYRL LHPHFRYTME INALAREALI NADGIIEESF WPGKYAVELS + SVAYGATWQF DTEALPNDLI KRGLAVRGED GELELTIKDY PYAHDGLLVW + DSIRQWASEY VNVYYKSDEA VAADPELRAF WDEVRNVGHG DKKDEPWWPV + LDTRDSLVET LTTIMWVTSG HHSAVNFGQY HFAGYFPNRP TTIRKNMPVE + EGGPGEEMEK FLKQPETTLL DMLPTQMQAI KVMTTLDILS SHSPDEEYMG + EFAEPSWLAE PMVKAAFEKF GGRMKEIEGF IDECNNNLDL KNRCGAGIVP + YELLKPFSKP GVTGRGIPSS ISI + + + + + +GRMZM2G015419_P03 NP_001105980 lipoxygenase seq=translation; coord=4:233625690..233628092:1; parent_transcript=GRMZM2G015419_T03; parent_gene=GRMZM2G015419 + + + MMNLNLKQPL VLPAHHSNVV GSRLSSSSPS AAAASRRTGG GVSSRSGSRR + HVRLPRISCS ATEEVSGAVS SVTVERMLTV TASVEASPAI GQMYFQRAVD + DIGDLLGKTL LLELVSSELD AKSGVEKTRV TAYAHKTLRE GHYEAEFKVP + ASFGPVGAVL VENEHHKEVF IKEIKLVTGG DSSTAVTFDC NSWVHSKFDN + PEKRIFFTLK SYLPSDTPKG LEDLRKKDLQ ALRGDGHGER KVFERVYDYD + VYNDLGDPDK NPAHQRPVLG GNKQYPYPRR CRTGRPRTKK DPETEMREGH + NYVPRDEQFS EVKQLTFGAT TLRSGLHALL PALRPLLINK KDLRFPHFPA + IDDLFSDGIP LPAQTGFDAI RTVVPRMVKL VEDTTDHVLR FEVPEMIESK + LASRRTHLRT ACYLNLKKNK + + + + + + +5.46753 +-0.331365 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +8789 8789 8753 8232 7763 7025 5018 3711 1809 863 361 166 84 25 6 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +8789 8789 8753 8232 7744 6949 4765 3086 1170 438 102 30 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3283 3854 1340 281 43 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2135 4659 1652 278 55 12 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2456 (charge 3) + +1727.93 +3 + + +153.102 157.097 159.077 167.055 169.097 169.133 175.119 181.097 184.108 185.092 185.601 187.07 197.129 199.108 201.086 208.108 213.087 226.119 230.113 235.119 239.095 243.146 244.131 256.129 283.141 285.01 296.027 299.062 303.019 306.155 +318.175 341.182 344.976 355.07 358.174 373.08 375.199 393.529 403.057 414.215 418.993 425.882 430.161 455.225 489.271 502.538 521.267 544.806 553.317 556.268 573.3 581.281 590.308 628.85 637.36 647.347 659.323 675.348 685.864 700.368 +705.331 752.368 758.437 827.423 840.497 968.562 996.513 1013.57 1128.61 1273.72 + + + + +5 2 3 12 5 3 16 2 3 15 2 3 4 4 4 11 12 23 5 6 38 3 9 3 4 38 2 30 4 4 +3 4 5 100 5 19 5 5 3 4 13 12 4 12 6 3 3 4 4 3 3 4 5 12 28 4 6 4 5 5 +12 5 4 4 5 4 5 5 5 6 + + + + + + +GRMZM2G044132_P01 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53846005:1; parent_transcript=GRMZM2G044132_T01; parent_gene=GRMZM2G044132 + + + MADEYGRSGY GRSGAGDDYD SGYNSKSGTD DYGRGEGGYN KSGGDDDYGR + SGGDGYGRSG GDDYGRGTGG GGYNKSGGGD DYGRSGGDDY GRGTGGGGYN + KSGNDGYDSG YNRSGTTNDD EYGRGTGGGY GSKPSGDDAY AGGGGGGYGK + QSGGGADEGG EYGSSRDDSE KYRKEEKEHK HKEHLGEMGA LAAGAFALYE + RHEAKKDPEH AQRHKIEEGV AAVAALGSGG FAFHEHHDKK EAKDAAEDAG + EEEESGRRGE GKKKHHFFG + + + + + +GRMZM2G044132_P02 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53845943:1; parent_transcript=GRMZM2G044132_T02; parent_gene=GRMZM2G044132 + + + MADEYGRSGY GRSGAGDDYD SGYNSKSGTD DYGRGEGGYN KSGGDDDYGR + SGGDGYGRSG GDDYGRGTGG GGYNKSGGGD DYGRSGGDDY GRGTGGGGYN + KSGNDGYDSG YNRSGTTNDD EYGRGTGGGY GSKPSGDDAY AGGGGGGYGK + QSGGGADEGG EYGSSRDDSE KYRKEEKEHK HKEHLGEMGA LAAGAFALVT + NQRPSFPSFL AHARTDERAD AVLCDCDCRA CSSCHCDNFR DDHVHACMID + RTDACSTRGT RRRRTRSTRS GTRSRRAWRR WLPWAAAASR STSTTTRRRP + KTRRRTPGRR RSPAAAARGR RSTTSSADRA AARSIYLRT + + + + + + +5.38943 +-0.276381 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 + + + + +1466 1466 1466 1466 1466 1388 1069 879 637 457 271 135 56 33 11 8 4 2 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1466 1466 1466 1466 1466 1388 1064 863 565 348 143 48 11 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +675 567 176 46 5 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +254 826 318 53 14 2 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2460 (charge 3) + +2087.84 +3 + + +169.06 170.092 171.077 172.071 173.056 175.119 181.061 187.071 188.103 189.087 198.088 199.071 210.087 213.087 216.098 217.081 226.118 228.097 238.082 240.133 244.093 256.092 258.145 268.092 274.103 285.119 295.103 301.112 313.114 325.113 +327.129 329.186 342.141 352.125 355.125 358.136 363.187 370.136 371.142 430.24 440.189 473.231 478.211 555.213 559.283 572.25 618.248 630.313 665.281 684.258 688.326 690.949 692.644 694.293 695.853 697.371 701.345 723.839 734.997 749.316 +758.311 767.681 773.34 777.309 781.309 798.295 807.325 815.824 818.357 834.331 836.379 845.375 852.338 855.331 899.349 905.404 923.406 927.344 931.425 936.865 945.456 946.46 963.402 980.428 982.425 1015.4 1020.41 1024.4 1038.44 1060.49 +1126.46 1143.49 1145.52 1153.44 1241.48 1329.54 1369.53 1386.57 1388.56 1515.62 + + + + +8 32 55 8 9 19 35 37 27 10 49 49 8 19 24 33 11 8 22 22 56 27 24 10 9 18 18 12 67 8 +8 11 34 20 10 9 67 92 34 28 18 9 28 58 31 55 25 23 12 20 48 35 11 67 32 10 8 8 8 34 +38 8 9 8 20 14 23 30 8 10 11 26 31 18 8 9 27 32 8 18 32 18 21 100 9 11 8 21 22 22 +18 65 11 10 8 21 10 45 11 8 + + + + + + +GRMZM2G105644_P01 NP_001149382 geranylgeranyl hydrogenase seq=translation; coord=5:206890298..206892838:1; parent_transcript=GRMZM2G105644_T01; parent_gene=GRMZM2G105644 + + + MTSLSSAVAL PSSCRARPAG GSRRARMVVT RAAASSPKLP NGRRLRVAVV + GGGPAGGAAA EALAKGGVET VLIERKMDNC KPCGGAIPLC MVSEFDLPLD + LVDRKVRKMK MISPSNVAVD IGRTLAPHEY IGMVRREVLD AYLRSRAQSV + GAEVVNGLFL RYEAPKEPNG SYVVHYNHYD GSNGKVGGEK RSFEVDAIVG + ADGANSRVAK DMGAGDYEYA IAFQERVKIP DDKMVYYEER AEMYVGDDVS + PDFYGWVFPK CDHVAVGTGT VTHKADIKKF QAATRLRAKD KIEGGKIIRV + EAHPIPEHPR PKRVSGRVTL VGDAAGYVTK CSGEGIYFAA KSGRMCAEAI + VAGSANGTRM VEESDLRKYL AEFDRLYWPT YKVLDILQKV FYRSNAAREA + FVEMCADDYV QKMTFDSYLY KRVVPGNPLD DIKLAVNTIG SLVRATALRR + EMEKVTL + + + + + + +7.31807 +-0.325248 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +10251 10251 10200 10022 9633 8957 8061 6566 5398 3580 2153 1162 609 348 170 66 39 8 3 2 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +10268 10268 10217 10039 9635 8931 7878 6165 4500 2417 1081 276 83 24 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2887 4638 1987 597 119 34 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2187 4232 2637 906 227 56 9 14 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2461 (charge 3) + +1506.82 +3 + + +155.081 156.076 158.092 159.076 164.118 166.061 167.055 167.08 168.056 169.06 169.097 173.092 175.119 181.109 183.077 183.134 183.149 184.153 185.104 186.087 192.077 193.096 194.128 195.075 195.113 197.128 199.108 199.169 201.123 209.104 +211.144 213.087 216.098 226.155 227.102 229.118 232.141 235.119 239.094 241.081 244.165 249.098 254.162 259.092 267.107 272.172 278.081 299.062 317.693 320.135 326.18 330.192 336.167 338.145 344.976 359.028 364.161 369.225 374.709 383.192 +391.252 409.218 415.036 426.246 430.74 437.213 452.246 455.248 464.253 469.312 480.243 497.32 501.607 506.28 520.291 533.301 534.269 540.293 564.785 575.358 595.322 617.326 629.333 634.377 647.352 651.363 680.335 686.376 703.408 732.374 +748.409 763.42 790.445 843.446 860.475 862.484 873.44 927.495 1070.61 1072.6 + + + + +13 2 6 6 8 9 52 4 2 3 7 9 32 22 3 2 39 3 2 2 10 4 6 2 8 3 20 6 27 29 +10 6 2 50 23 17 6 10 17 8 34 3 21 2 6 11 5 100 13 8 2 5 3 8 24 15 9 17 9 3 +2 15 17 8 30 17 8 3 6 5 7 63 3 2 2 2 2 3 20 12 2 2 6 18 12 3 8 3 7 7 +13 5 22 2 42 5 7 2 18 3 + + + + + + +GRMZM2G015419_P04 NP_001105980 lipoxygenase seq=translation; coord=4:233625700..233629448:1; parent_transcript=GRMZM2G015419_T04; parent_gene=GRMZM2G015419 + + + + + + + + + +GRMZM2G015419_P02 NP_001105980 lipoxygenase seq=translation; coord=4:233625689..233629426:1; parent_transcript=GRMZM2G015419_T02; parent_gene=GRMZM2G015419 + + + + + + + + + +GRMZM2G015419_P05 NP_001105980 lipoxygenase seq=translation; coord=4:233625821..233629381:1; parent_transcript=GRMZM2G015419_T05; parent_gene=GRMZM2G015419 + + + + + + + + + + +5.96141 +-0.340652 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +3551 3551 3551 3551 3447 3138 2560 1735 1174 567 315 117 57 17 9 6 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3556 3556 3556 3556 3452 3143 2561 1696 1077 443 211 43 9 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1365 1807 315 61 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +954 1987 514 86 9 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2462 (charge 3) + +1792.77 +3 + + +152.057 155.082 167.055 169.097 169.133 171.113 175.119 185.091 186.125 187.072 189.087 195.077 197.128 197.549 199.107 212.103 213.086 215.138 223.616 226.155 235.055 240.133 258.145 262.084 271.138 277.085 279.657 284.124 287.008 289.002 +301.058 308.171 320.224 326.173 357.07 359.191 386.179 390.18 402.233 418.178 423.19 470.22 488.233 552.229 580.768 586.302 625.364 674.296 715.344 720.284 738.296 768.387 771.36 774.325 825.402 835.349 852.43 923.464 949.394 1057.5 +1115.28 + + + + +7 32 9 6 31 12 18 7 6 10 7 11 11 6 11 8 7 8 6 33 8 13 8 8 9 13 37 14 17 8 +11 9 9 10 36 10 41 20 11 100 10 12 30 11 10 13 32 69 13 14 60 12 14 10 12 19 48 12 13 12 +13 + + + + + + +GRMZM2G021170_P01 NP_001141977 hypothetical protein LOC100274127 seq=translation; coord=10:96835856..96839456:-1; parent_transcript=GRMZM2G021170_T01; parent_gene=GRMZM2G021170 + + + MAAARMALVS CARRLPSLPS PLTLSRPRAG AVSFLAAQPS PATAPRSGRN + LALFCSLSPT SPSLTEAAVA LPPPKAAVEE TKPPVPSGDE KGEPTVEELA + GLLDVRVGRV VKAWRHPEAD TLYVEEVDVG EAEPRTICSG LVNFLPIEEL + QDRNVIVLAN LKPRNMRGIK SNGMLMAASD ASHENVELLI PSEGSFPGER + VWFGSEEEKN RQSDPASPNQ VQKKKIWEAV QPHLRTTDNC IAVLGDKQMR + TSAGLVFCKS LQGARVS + + + + + + +5.31876 +-0.322349 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +5148 5148 5148 5148 5051 4598 4466 2642 2050 934 492 200 107 31 2 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5158 5158 5158 5158 5061 4608 4446 2459 1851 769 338 100 30 15 1 0 + + + + + + +0 1 2 3 4 + + + + +3907 1128 122 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +626 3920 574 31 1 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2463 (charge 2) + +1298.64 +2 + + +152.056 154.049 155.082 159.077 169.097 170.091 171.077 175.119 181.061 188.103 189.087 198.087 199.072 199.108 210.215 212.103 217.082 226.155 227.103 239.114 244.166 248.159 256.129 258.145 271.104 275.173 281.125 293.54 295.104 313.115 +331.126 340.162 359.028 374.238 411.152 439.231 452.253 477.247 502.301 567.285 595.28 606.29 617.475 632.323 696.351 713.394 728.362 758.4 779.335 788.89 800.426 871.455 968.513 1146.52 + + + + +10 8 11 10 36 10 31 28 28 15 27 26 28 27 7 33 45 100 27 11 16 10 27 35 8 12 9 7 14 66 +15 63 59 13 44 40 9 8 9 11 9 7 14 10 15 98 16 9 9 9 44 14 45 8 + + + + + + +AC215244.3_FGP002 seq=translation; coord=4:193735481..193760758:1; parent_transcript=AC215244.3_FGT002; parent_gene=AC215244.3_FG002 + + + MASSGDPPGS ADEKKTPKSE GSSDERQGLP PAGFSNPFDF GSMQSLLNDP + SIKEMADQIA RDPAFNRMAE QLQRSAQSTG EQGTPPLNPQ QYMETMQKVM + ENPQFMTMAE RLGNALMQDP AMSSMLETFS SPSHKEQLEE RMSRIKEDPA + MKSILDELEN GGPSAMMKYW NDPDTLQKIG EAMGASFPFG AGSSAEPSGT + EETEEEGGDD DESIVHHTAS VGDEEGLKKA LDGGADKDEE DSEGRRALHF + ACGYGELKCA QILLEAGAAV DALDKNKNTP LHYAAGYGRK ECVDLLLKHG + AAVTLQNLDG KTPIDVAKLN NQDEVLKLLE KDAFL + + + + + + +4.55703 +-0.337557 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + + + + +3759 3759 3759 3630 3310 3149 2882 2724 1647 1077 348 92 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3771 3771 3771 3642 3322 3155 2887 2719 1457 943 208 67 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2274 1257 230 16 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +749 2389 511 95 33 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2464 (charge 3) + +1819.8 +3 + + +152.056 153.915 155.081 157.134 158.093 158.138 162.47 167.055 167.082 171.076 171.149 173.055 175.119 185.128 192.869 198.283 199.107 212.102 226.155 227.102 230.078 239.095 242.113 244.165 252.094 262.153 266.067 299.061 301.113 302.661 +452.251 456.202 470.262 489.218 507.557 544.237 546.73 588.288 604.313 610.779 624.085 659.267 679.356 684.973 695.405 732.824 752.321 760.833 805.425 809.836 818.841 1628.32 + + + + +3 3 4 100 5 7 3 23 3 4 3 6 47 18 3 4 22 4 56 20 19 74 4 23 4 4 4 18 6 9 +10 5 6 24 17 7 22 7 22 39 6 6 5 6 9 10 6 46 8 8 40 7 + + + + + + +GRMZM2G451224_P01 O65101 Photosystem I reaction center subunit VI, chloroplastic Precursor (PSI-H)(Light-harvesting complex I 11 kDa protein) seq=translation; coord=6:163973641..163974980:-1; parent_transcript=GRMZM2G451224_T01; parent_gene=GRMZM2G451224 + + + + + + + + +4.53019 +-0.312427 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6520 6520 6520 6213 6068 5511 3412 2832 1310 587 273 106 44 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6508 6508 6508 6201 6032 5475 3370 2449 853 150 42 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +4572 1819 110 26 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +853 4656 872 140 1 0 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2465 (charge 2) + +1287.68 +2 + + +152.056 155.081 158.092 159.076 167.117 171.077 172.071 172.789 173.129 175.119 181.134 186.088 186.124 187.071 195.088 195.112 198.124 199.108 201.124 212.138 226.119 240.099 244.166 255.143 269.125 284.009 303.178 323.17 349.188 355.162 +374.708 394.213 409.22 412.18 426.248 436.235 488.233 502.273 523.251 540.277 543.278 558.864 566.26 624.74 645.349 651.362 670.31 683.242 688.334 731.379 748.41 750.41 877.454 920.12 988.487 1005.5 1159.59 + + + + +3 9 2 3 2 2 5 2 3 23 2 3 4 5 3 3 3 13 3 4 31 3 4 2 3 4 2 4 3 16 +4 3 9 11 18 3 3 13 3 8 3 2 3 3 4 16 3 9 3 11 100 5 17 2 3 4 19 + + + + + + +GRMZM2G420436_P01 NP_001147873 GMN10 seq=translation; coord=1:260920191..260928400:-1; parent_transcript=GRMZM2G420436_T01; parent_gene=GRMZM2G420436 + + + MASVPLSSPS QAGLLGPPFP LLPPPFGACL RYRLPRLPTG LSSSVRKGGL + LPLPLLVPPR AAGGKDGRAV TKEELEEEEE EFEVTKEGEE VNQETGGGSG + ATKEAAARGS GRFAADYVSL GVREPVYEVI EVRSNGRMST KKISRRQLLK + SSGLRLRDTR SVDPSLWLMN SMPSLLVREQ AILLNLGSLR AIAMYARVLI + FNYNSPGGKA FLGLLLSRLN PRNINGGPAM PFQLEVVEAA LLSRIQRLEQ + RLMKIEPHVA TLLEVLPNRL TADVLEQLRL SKQALVELGS RAGDLKQMLI + DLLDDPHEIR RICIMGRNCT LDRLSDIVEC TVPLEKQIAE EEEEEIEMLL + ENYLQRCESC HGQAERLLNS AREMEDSISV NLSSRRLEVS RVELLLQVGT + FCVAIGALIA GIFGMNLKSY LETNAWAFWV TTGGIVVGAV AGFFVVYSYL + RARKIL + + + + + + +5.20852 +-0.29763 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +1624 1624 1624 1624 1624 1624 1541 1304 1020 713 506 319 227 68 21 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +1626 1626 1626 1626 1626 1626 1543 1304 1011 676 458 289 195 21 13 1 0 + + + + + + +0 1 2 3 4 + + + + +525 976 122 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1031 548 48 2 0 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2467 (charge 2) + +1649.73 +2 + + +159.077 168.066 169.061 177.811 187.071 195.089 204.087 212.204 241.082 248.161 259.093 270.109 298.102 316.115 344.585 361.925 376.22 381.141 384.568 409.136 420.692 427.146 445.157 520.274 577.287 634.316 735.358 823.364 846.393 864.408 +975.445 1106.51 1111.48 1639.63 1687.31 + + + + +13 25 28 12 75 34 82 13 84 19 20 21 84 68 18 16 29 18 17 35 17 39 31 31 25 94 97 25 24 69 +22 73 100 25 24 + + + + + + +GRMZM2G156861_P02 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168699190:1; parent_transcript=GRMZM2G156861_T02; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G156861_P03 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168839001:1; parent_transcript=GRMZM2G156861_T03; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G156861_P01 NP_001105003 lipoxygenase seq=translation; coord=3:168835321..168839001:1; parent_transcript=GRMZM2G156861_T01; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G109130_P01 NP_001105515 lipoxygenase seq=translation; coord=1:264200949..264205758:1; parent_transcript=GRMZM2G109130_T01; parent_gene=GRMZM2G109130 + + + + + + + +GRMZM2G109130_P02 NP_001105515 lipoxygenase seq=translation; coord=1:264202964..264205732:1; parent_transcript=GRMZM2G109130_T02; parent_gene=GRMZM2G109130 + + + + + + + + +5.26038 +-0.256604 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +2471 2471 2471 2422 2311 2088 1787 1337 1198 720 496 259 166 68 27 17 9 6 5 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2464 2464 2464 2415 2304 2062 1598 1252 1078 517 283 108 11 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +864 1067 391 98 63 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +579 931 798 123 24 15 4 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2469 (charge 3) + +1544.64 +3 + + +155.082 158.093 168.077 169.061 173.056 175.119 176.123 181.061 181.097 184.072 185.056 199.108 203.066 204.134 209.056 212.102 214.106 216.098 226.155 227.102 231.061 233.128 240.098 244.093 249.099 253.094 257.124 261.123 266.113 269.088 +288.081 290.147 291.15 295.105 297.12 300.133 305.11 315.478 318.146 323.099 329.191 334.145 337.116 349.153 353.109 355.125 378.141 380.119 383.192 389.182 398.128 401.182 402.186 406.671 410.176 416.141 421.169 424.188 427.205 429.17 +446.203 452.255 464.202 470.259 472.715 492.714 493.216 501.226 512.217 516.29 518.227 521.211 538.239 544.281 548.234 556.248 558.249 612.262 620.773 649.272 650.258 667.282 668.282 677.396 684.306 686.313 695.408 770.314 812.331 827.334 +830.353 847.37 849.372 903.491 921.499 927.406 944.424 946.43 1001.45 1003.45 + + + + +46 8 10 4 45 86 6 4 5 4 9 16 5 4 8 6 7 6 50 15 12 35 14 35 8 8 4 11 21 11 +21 39 6 5 4 5 13 5 8 12 4 16 7 6 4 5 4 8 6 10 6 17 5 5 8 6 4 17 69 6 +7 8 7 5 32 8 4 30 6 5 4 4 11 6 4 100 6 6 5 4 5 41 12 5 76 8 5 4 11 4 +6 58 6 7 4 4 25 4 22 4 + + + + + + +GRMZM2G058173_P01 NP_001151824 undecaprenyl pyrophosphate synthetase seq=translation; coord=7:144837690..144838974:-1; parent_transcript=GRMZM2G058173_T01; parent_gene=GRMZM2G058173 + + + + + + + + +6.62576 +-0.281947 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 + + + + +7929 7929 7863 7664 7222 6648 6058 4900 3911 2375 1404 800 465 248 152 88 38 12 8 3 2 2 1 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7930 7930 7864 7646 7174 6520 5802 4388 2679 1052 212 26 8 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2056 3126 1766 694 190 86 14 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1235 3344 2221 797 243 64 21 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2470 (charge 3) + +1801.83 +3 + + +153.066 155.082 158.093 161.092 162.096 167.093 169.097 171.077 172.08 173.092 173.128 175.119 175.134 183.076 189.087 195.088 197.092 198.124 199.109 203.103 209.103 214.119 217.082 224.103 226.118 240.097 242.114 244.13 260.124 266.124 +270.108 277.086 284.124 290.146 296.136 297.155 300.117 313.151 315.167 318.129 331.162 339.17 341.145 348.122 359.155 361.183 367.173 384.186 389.165 404.167 419.712 426.208 448.219 454.205 456.211 462.231 484.214 498.745 528.289 533.261 +542.259 555.25 583.783 586.291 592.789 599.237 613.299 614.292 630.321 632.328 650.3 670.282 684.332 691.82 701.358 702.359 727.837 736.344 743.331 753.318 762.845 771.327 807.342 814.369 824.365 838.416 840.433 842.36 852.431 885.411 +895.44 897.446 913.393 996.484 1047.51 1083.52 1085.53 1166.55 1184.56 1299.58 + + + + +2 7 4 24 2 4 6 74 5 11 2 33 2 4 25 6 7 2 3 2 5 9 11 2 8 2 52 8 19 4 +6 4 2 2 4 2 2 7 2 5 8 2 2 6 4 4 4 2 4 2 6 2 4 4 5 8 2 5 8 7 +4 2 4 2 12 2 5 2 100 7 7 4 2 4 54 17 2 11 7 4 2 8 4 2 2 19 2 4 8 4 +35 2 2 17 2 15 2 2 7 6 + + + + + + +GRMZM2G003565_P03 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49056549..49061498:-1; parent_transcript=GRMZM2G003565_T03; parent_gene=GRMZM2G003565 + + + MDSVMAAPDS PPQTVVLVSA GASHSVALLT GNVLCSWGRG EDGQLGHGDA + EDRLVPTVLS GFDAPAITSV ICGADHTTAY SEDELQVYSW GWGDFGRLGH + GNSSDVFTPQ PVKALQGLKI KQIACGDSHC LAVTMAGEVQ SWGRNQNGQL + GLGTTEDSLL PQKIQAFESV CVKMIAAGAE HTAAVTEDGD LYGWGWGRYG + NLGLGDRNDR LLPEKVSSVE GEKMVLVACG WRHTITVSDS GNLYTYGWSK + YGQLGHGDFE DHLVPHKVEA LKDSTISQIS GGWRHTMALT SEGKLYGWGW + NKFGQVGVGN NDDHSSPGQV SFPEDQKISQ VACGWRHTLA LSEKKNVFSW + GRGTSGQLGN GEIVDRNTPV LIDALSSDGS ACKKLESSTA APFAAKVWVS + PSERYAIVPD ENVRKAGGGT ARGNGADANV PENDVKRMRV QSS + + + + + +GRMZM2G003565_P01 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49060070..49061498:-1; parent_transcript=GRMZM2G003565_T01; parent_gene=GRMZM2G003565 + + + MDSVMAAPDS PPQTVVLVSA GASHSVALLT GNVLCSWGRG EDGQLGHGDA + EDRLVPTVLS GFDAPAITSV ICGADHTTAY SEDELQVYSW GWGDFGRLGH + GNSSDVFTPQ PVKALQGLKI KQIACGDSHC LAVTMAGEVQ SWGRNQNGQL + GLGTTEDSLL PQKIQAFEVT KGITKSSYRV IWIMIGKF + + + + + +GRMZM2G003565_P02 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49056549..49061498:-1; parent_transcript=GRMZM2G003565_T02; parent_gene=GRMZM2G003565 + + + MDSVMAAPDS PPQTVVLVSA GASHSVALLT GNVLCSWGRG EDGQLGHGDA + EDRLVPTVLS GFDAPAITSV ICGADHTTAY SEDELQVYSW GWGDFGRLGH + GNSSDVFTPQ PVKALQGLKI KQIACGDSHC LAVTMAGEVQ SWGRNQNGQL + GLGTTEDSLL PQKIQAFE + + + + + + +4.55806 +-0.246382 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +2060 2060 2060 1996 1883 1735 1596 1449 821 623 356 231 122 63 36 16 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2061 2061 2061 1995 1875 1728 1559 1395 736 461 239 87 8 1 0 + + + + + + +0 1 2 3 4 5 + + + + +630 1032 311 88 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +414 1079 380 158 17 12 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2471 (charge 3) + +1455.61 +3 + + +150.066 155.082 158.092 159.077 160.08 166.098 167.081 167.093 169.06 169.097 170.045 171.077 171.113 172.071 173.056 173.092 175.119 176.122 178.061 181.061 185.092 186.088 187.072 188.075 190.083 194.128 195.088 195.113 197.128 199.071 +199.108 201.086 204.135 209.092 212.103 214.155 217.081 226.155 227.102 239.115 240.134 242.148 244.166 252.134 254.162 260.035 266.077 273.119 283.104 284.085 290.145 301.115 308.172 310.114 316.114 337.187 359.239 361.207 367.135 380.23 +382.22 386.97 400.17 411.162 419.196 428.681 434.239 452.249 454.49 465.255 470.262 473.259 476.268 482.284 490.226 510.278 512.278 531.737 540.74 547.319 577.767 591.252 605.252 615.345 623.35 625.366 634.349 662.275 664.276 682.248 +685.367 712.395 720.408 721.392 799.333 817.456 856.354 858.363 866.341 969.435 + + + + +4 18 10 100 5 2 2 14 8 6 5 2 2 9 17 2 66 5 6 4 2 17 49 4 18 2 23 4 6 4 +8 2 4 2 2 4 2 28 11 4 2 2 7 4 11 5 4 5 14 6 26 18 6 3 2 2 2 2 4 6 +6 2 37 18 4 13 3 4 4 3 3 2 2 10 39 17 2 2 8 6 6 3 10 2 8 2 4 71 5 2 +2 2 8 15 15 6 38 5 2 12 + + + + + + +GRMZM2G103490_P01 NP_001168322 hypothetical protein LOC100382088 seq=translation; coord=9:139614346..139617289:1; parent_transcript=GRMZM2G103490_T01; parent_gene=GRMZM2G103490 + + + MSSSTIRKAL GAVKDQTSIS LAKVTSNIAP DLDVLIVKAT SHDDEPAEER + HIREILHLTS GSRAHVAAAV AGCSRRLSRT RDYVVALKSL MLVHRLLVDG + DPSFHRELLH GTRRGTRLLN LSDFRDEAHS GSWDHSAFVR TYALYLDQRL + EFFLHERKQG LNAGSSSSAN GPSPRDRDRW GSPDPYGRRS PSYSSPPGYG + GYDDYRERNG GNNDDKRPPT PVRDMKPERV LARMHHLQQL LDRFLACRPT + GGAKQSRMVL VALYQIVRES FQLYSDICEV LAVLLDRFFD MEYAECVKAF + EAYASAAKQI DELSAFYSWC KDTGVARSSE YPEVQRVTDK LLETLEEFMR + DRAKRPKSPP REPEPEPVKE EPEPDMNSIK ALPAPEDYKE PEPVKVEEEV + KPEPPPQPQG DLVDLREDTV SADEQGNRLA LALFQGPPAA GGNNGSWEAF + PSNGGNEVTS AWQNPAAEPG KADWELALVE TASNLSMQKP AMSGGMDPLL + LNGMYDQGVV RQHVSAQVTT GSASSVALPA PGQKTQMLAL PAPDGSMQTV + GGDPFAASLA VPPPSYVQMA DLEKKQQLLS QEQIMWQQYQ RDGMQGQSSL + NKLDQAYHNG FAPNPGMPYG MPAAYNTGYY YPTY + + + + + +GRMZM2G103490_P02 NP_001168322 hypothetical protein LOC100382088 seq=translation; coord=9:139614895..139617265:1; parent_transcript=GRMZM2G103490_T02; parent_gene=GRMZM2G103490 + + + MSSSTIRKAL GAVKDQTSIS LAKVTSNIAP DLDVLIVKAT SHDDEPAEER + HIREILHLTS GSRAHVAAAV AGCSRRLSRT RDYVVALKSL MLVHRLLVDG + DPSFHRELLH GTRRGTRLLN LSDFRDEAHS GSWDHSAFVR TYALYLDQRL + EFFLHERKQG LNAGSSSSAN GPSPRDRDRW GSPDPYGRRS PSYSSPPGYG + GYDDYRERNG GNNDDKRPPT PVRDMKPERV LARMHHLQQL LDRFLACRPT + GGAKQSRMVL VALYQIVRES FQLYSDICEV LAVLLDRFFD MEYAECVKAF + EAYASAAKQI DELSAFYSWC KDTGVARSSE YPEVQRVTDK LLETLEEFMR + DRAKRPKSPP REPEPEPVKE EPEPDMNSIK ALPAPEDYKE PEPVKVEEEV + KPEPPPQPQG DLVDLREDTV SADEQGNRLA LALFQGPPAA GGNNGSWEAF + PSNGGNEVTS AWQNPAAEPG KADWELALVE TASNLSMQKP AMSGGMDPLL + LNGMYDQGVV RQHVSAQVTT GSASSVALPA PGQKTQMLAL PAPDGSMQTV + GGDPFAASLA VPPPSYVQMA DLEKKQQLLS QEQIMWQQYQ RDGMQGQSSL + NKLDQAYHNG FAPNPGMPYG MPAAYNTGYY YPTY + + + + + + +6.13742 +-0.314739 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +9957 9957 9957 9957 9957 9437 9015 8279 5711 4241 2399 1324 850 341 146 44 19 9 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9958 9958 9958 9958 9958 9438 9009 8237 5579 4009 1805 573 242 77 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4876 3778 1103 172 29 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2046 5745 1895 221 47 3 2 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2474 (charge 3) + +1714.85 +3 + + +152.056 155.081 157.061 158.093 159.077 161.092 169.097 171.077 171.113 172.071 173.092 175.072 175.119 186.088 194.627 198.088 198.848 199.108 226.155 228.632 240.134 244.166 252.352 255.145 260.641 272.172 285.154 305.382 356.194 378.14 +382.182 456.257 513.277 524.284 571.3 610.294 627.323 629.318 658.339 669.376 681.33 698.357 738.386 756.404 768.363 773.362 785.384 870.402 872.405 923.441 + + + + +11 10 26 10 16 10 17 16 13 11 11 13 61 10 10 9 8 25 57 20 17 13 8 58 9 69 11 10 14 10 +10 66 96 13 13 43 100 17 18 14 17 53 19 16 17 43 45 25 16 14 + + + + + + +GRMZM2G001327_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695861:-1; parent_transcript=GRMZM2G001327_T01; parent_gene=GRMZM2G001327 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYEEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSAYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G001327_P03 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695738:-1; parent_transcript=GRMZM2G001327_T03; parent_gene=GRMZM2G001327 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYEEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSAYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G154218_P01 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515921..136519080:-1; parent_transcript=GRMZM2G154218_T01; parent_gene=GRMZM2G154218 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYDEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSAYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G154218_P02 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515968..136519018:-1; parent_transcript=GRMZM2G154218_T02; parent_gene=GRMZM2G154218 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYDEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSAYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G149768_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136568621..136572271:-1; parent_transcript=GRMZM2G149768_T01; parent_gene=GRMZM2G149768 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYEEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSAYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G110509_P01 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T01; parent_gene=GRMZM2G110509 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYDEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSQYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G110509_P02 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T02; parent_gene=GRMZM2G110509 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYDEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSQYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + +GRMZM2G110509_P03 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607316..84610225:1; parent_transcript=GRMZM2G110509_T03; parent_gene=GRMZM2G110509 + + + MGKEKSHINI VVIGHVDSGK STTTGHLIYK LGGIDKRVIE RFEKEAAEMN + KRSFKYAWVL DKLKAERERG ITIDIALWKF ETTKYYCTVI DAPGHRDFIK + NMITGTSQAD CAVLIIDSTT GGFEAGISKD GQTREHALLA FTLGVKQMIC + CCNKMDATTP KYSKARYDEI VKEVSSYLKK VGYNPDKIAF VPISGFEGDN + MIERSTNLDW YKGPTLLEAL DQITEPKRPS DKPLRLPLQD VYKIGGIGTV + PVGRVETGVI KPGMVVTFGP TGLTTEVKSV EMHHEALQEA LPGDNVGFNV + KNVAVKDLKR GFVASNSKDD PAKEAASFTS QVIIMNHPGQ IGNGYAPVLD + CHTSHIAVKF AELITKIDRR SGKELEKEPK FLKNGDAGMV KMIPTKPMVV + ETFSQYPPLG RFAVRDMRQT VAVGVIKSVE KKDPTGAKVT KAAAKKK + + + + + + +5.28383 +-0.234837 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +8757 8757 8757 8587 8408 7936 7395 5892 4733 3147 2003 1161 654 349 207 96 66 39 26 15 4 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8750 8750 8750 8580 8400 7912 7245 5604 4027 2149 795 304 95 16 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2694 3780 1568 540 140 35 0 6 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1606 3873 2032 947 249 48 1 7 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2476 (charge 3) + +1491.75 +3 + + +152.057 154.086 155.082 156.077 157.061 157.097 157.108 157.134 158.093 159.076 159.092 169.097 171.113 173.056 173.092 175.071 175.119 181.097 185.056 185.092 186.124 187.108 195.088 195.113 197.105 198.124 199.108 202.082 207.113 209.092 +213.087 216.134 218.15 226.155 240.133 244.166 254.153 280.669 282.169 284.125 313.152 315.203 319.173 323.134 328.115 333.203 338.181 341.218 355.198 359.156 361.198 369.226 372.224 383.194 406.205 428.177 430.231 432.272 438.272 443.243 +446.186 452.253 460.268 462.263 466.278 470.262 483.192 493.234 496.834 503.315 514.261 522.761 531.305 535.323 545.256 563.336 573.315 580.775 589.282 600.323 618.336 620.349 622.316 635.359 647.259 657.34 673.353 695.408 697.34 704.381 +715.351 719.363 732.383 760.382 774.388 780.377 791.411 801.395 819.412 836.441 + + + + +10 4 11 4 5 4 4 4 11 10 24 33 10 3 4 5 34 4 4 9 4 10 10 5 5 10 31 5 5 9 +4 9 37 78 4 50 4 8 4 3 8 100 3 3 4 10 5 8 11 5 30 5 3 11 5 4 5 37 8 4 +5 13 49 4 4 16 4 4 28 26 4 14 37 9 17 5 4 18 37 14 26 10 10 5 8 3 9 10 4 12 +4 11 26 11 5 3 16 9 24 17 + + + + + + +GRMZM2G373522_P01 NP_001105327 dehydrin seq=translation; coord=4:154310162..154311883:-1; parent_transcript=GRMZM2G373522_T01; parent_gene=GRMZM2G373522 + + + MEDERNTQQH QGGEQAQDQE NEVKDRGLLD SLLGRNKHDD QEKKNQQEEE + ELATGMEKVT VAEPDHKEEG HEAAEKKDSL LAKLHRTSSS SSSSSDDEEE + EVIDENGEIV KRKKKGLKEK VKEKLAAHKA HDEGDHHQPG VPAPAPAPPV + AVDTHAHHQE GEHKPHFPAP APPPHVETHH PVVVHKIEDD DTKTQTPPQA + PEEEKKGLLD KIKEKLPGGH KKPEDAAAAA AAPAVHAPPP PAPHAEVDVS + SPDGKKGLLG KIMDKIPGYH KSSGEEDRKD AAGEHKTSS + + + + + + +5.76363 +-0.311547 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +8770 8770 8704 8265 7850 7205 6529 4804 3429 1875 965 498 247 135 34 17 6 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8792 8792 8726 8287 7841 7153 6326 4277 2446 897 248 60 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2638 3659 1709 605 114 19 48 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1358 4239 2288 734 126 38 8 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2479 (charge 3) + +1482.74 +3 + + +153.102 155.081 156.077 157.061 157.134 158.092 159.077 159.092 160.076 166.06 167.081 169.097 171.113 173.056 173.092 173.129 175.071 175.119 184.072 185.092 187.087 189.087 195.091 195.113 198.123 199.108 201.087 204.135 207.112 209.092 +212.139 217.097 226.155 227.102 230.114 240.134 244.165 258.145 264.137 271.65 275.208 297.121 302.662 310.629 315.131 319.172 323.172 327.166 331.161 336.13 341.146 354.146 356.145 368.158 370.121 380.197 384.189 388.135 394.21 406.205 +428.213 432.172 452.249 465.183 469.251 479.24 483.193 485.188 493.235 495.834 525.271 527.767 533.253 540.289 542.219 544.248 546.732 549.295 577.29 580.267 593.252 611.328 613.283 631.291 644.327 662.332 668.291 698.366 704.325 706.355 +736.42 741.382 759.392 761.367 830.421 941.457 995.503 1055.53 1082.53 1372.75 + + + + +4 6 4 6 15 12 13 40 2 2 2 12 16 2 3 3 7 28 6 3 4 2 14 8 3 25 2 3 3 3 +11 3 32 22 19 15 17 7 3 3 10 12 8 4 3 7 9 3 3 2 3 4 10 4 2 8 9 2 7 20 +3 2 4 4 14 7 12 11 15 100 3 10 2 7 4 3 3 3 7 11 2 3 7 4 7 4 2 2 3 4 +6 3 27 2 11 3 3 7 3 2 + + + + + + +GRMZM2G003565_P03 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49056549..49061498:-1; parent_transcript=GRMZM2G003565_T03; parent_gene=GRMZM2G003565 + + + + + + + +GRMZM2G003565_P01 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49060070..49061498:-1; parent_transcript=GRMZM2G003565_T01; parent_gene=GRMZM2G003565 + + + + + + + +GRMZM2G003565_P02 NP_001141147 hypothetical protein LOC100273233 seq=translation; coord=2:49056549..49061498:-1; parent_transcript=GRMZM2G003565_T02; parent_gene=GRMZM2G003565 + + + + + + + + +4.86622 +-0.294922 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +1521 1521 1521 1521 1475 1439 1373 1302 1177 467 355 176 111 28 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1528 1528 1528 1528 1482 1446 1380 1303 1182 457 295 133 17 1 0 + + + + + + +0 1 2 3 + + + + +1070 428 37 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +339 1007 158 23 2 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2480 (charge 2) + +1455.61 +2 + + +158.093 159.077 167.093 169.061 172.071 173.055 175.119 186.087 187.072 190.082 195.088 212.103 226.154 244.095 260.417 283.105 290.146 302.099 341.109 358.134 389.268 400.17 412.099 452.135 470.155 485.228 490.226 510.196 553.301 565.221 +662.277 668.741 671.85 678.662 799.337 848.479 856.351 969.436 1310.08 1427.59 + + + + +14 31 10 7 6 8 100 23 48 27 11 7 7 6 6 6 42 26 6 12 6 31 6 8 11 9 74 7 7 7 +65 8 14 10 33 7 89 42 8 8 + + + + + + +GRMZM2G124455_P01 P41980 Superoxide dismutase [Mn] 3.4, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=8:91831315..91844753:1; parent_transcript=GRMZM2G124455_T01; parent_gene=GRMZM2G124455 + + + MALRTLASKN ALSFALGGAA RPSAASARGV TTVALPDLSY DFGALEPAIS + GEIMRLHHQK HHATYVANYN KALEQLDAAV AKGDASAVVQ LQGAIKFNGG + GHVNHSIFWK NLKPISEGGG EPPHGKLGWA IDEDFGSFEA LVKRMNAEGA + ALQGSGWVWL ALDKEAKKLS VETTANQDPL VTKGASLVPL LGIDVWEHAY + YLQYKNVRPD YLNNIWKVMN WKYAGEVYEN VLA + + + + + +GRMZM2G059991_P01 P09233 Superoxide dismutase [Mn] 3.1, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=6:135883373..135887597:1; parent_transcript=GRMZM2G059991_T01; parent_gene=GRMZM2G059991 + + + MALRTLASKK VLSFPFGGAG RPLAAAASAR GVTTVTLPDL SYDFIALEPA + ISGEIMRLHH QKHHATYVAN YNKALEQLDT AVSKGDASAV VQLQGAIKFN + GGGHVNHSIF WKNLKPISEG GGEPPHGKLG WAIDEDFGSF EALVKKMNAE + GAALQGSGWV WLALDKEAKK LSVETTANQD PLVTKGASLV PLLGIDVWEH + AYYLQYKNVR PDYLNNIWKV MNWKYAGEVY ENVLA + + + + + +GRMZM2G124455_P02 P41980 Superoxide dismutase [Mn] 3.4, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=8:91831315..91844753:1; parent_transcript=GRMZM2G124455_T02; parent_gene=GRMZM2G124455 + + + MALRTLASKN ALSFALGGAA RPSAASARGV TTVALPDLSY DFGALEPAIS + GEIMRLHHQK HHATYVANYN KALEQLDAAV AKGDASAVVQ LQGAIKFNGG + GHVNHSIFWK NLKPISEGGG EPPHGKLGWA IDEDFGSFEA LVKRMNAEGA + ALQGSGWVWL ALDKEAKKLS VETTANQVKG SSGD + + + + + + +5.89769 +-0.318794 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +7590 7590 7590 7429 7305 6909 6548 5424 4245 2954 1844 992 507 151 60 33 12 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7592 7592 7592 7431 7307 6892 6472 5238 3902 2224 996 332 19 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2448 3057 1549 441 80 22 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1058 3651 2095 668 116 10 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2484 (charge 3) + +1317.63 +3 + + +154.05 155.081 155.118 157.097 158.093 159.077 166.061 169.061 169.097 169.134 171.077 171.113 173.092 173.128 175.119 186.088 186.124 189.087 194.129 195.113 197.128 199.108 201.106 209.105 213.087 215.104 224.11 226.119 227.103 231.124 +233.092 235.145 237.097 240.134 244.129 247.13 250.12 253.093 255.108 258.099 261.156 266.157 272.171 275.125 276.129 278.113 284.009 285.156 292.141 294.12 297.198 299.009 304.131 313.689 320.133 328.152 338.146 346.161 349.15 353.182 +359.206 368.194 372.141 382.014 383.97 386.207 389.18 394.168 400.879 407.728 412.231 417.222 420.22 421.832 424.216 426.212 429.199 436.994 441.333 445.224 447.209 456.256 460.74 464.587 496.603 521.237 522.765 538.263 564.259 566.266 +582.277 592.264 593.266 597.332 609.301 611.278 653.355 678.351 681.341 709.354 + + + + +4 13 4 5 10 4 4 10 11 10 8 12 10 16 37 38 14 11 10 4 5 12 22 12 5 13 16 27 10 4 +5 9 3 9 19 12 19 4 19 39 44 3 22 100 16 21 19 8 14 3 3 15 4 8 5 39 14 12 5 5 +18 3 9 5 14 4 5 3 13 4 12 4 3 4 20 11 47 3 48 3 25 4 11 9 5 9 14 22 7 9 +14 28 9 4 37 4 4 3 3 3 + + + + + + +GRMZM2G085153_P02 NP_001140952 hypothetical protein LOC100273031 seq=translation; coord=2:165609242..165613195:-1; parent_transcript=GRMZM2G085153_T02; parent_gene=GRMZM2G085153 + + + MRGPWASSAL SLRLRLRGAR ARTNTSPMSS TAARVVHPAA AAPPPPRPRR + LAPARCAAGS ATDTATAGPT RVTTVSNRGD SLAICRVLNG MWQTSGGWGR + IDRDAAVDAM LAHADAGLST FDMADHYGPA EDLYGMFINR IRRERPPEFL + EEVKGLTKWV PPPVKMTRSY VEDNINRSRK RMDVTALDML QFHWWEYSNP + GYLDALKHIT DLKEEGKIKT VALTNFDTDR LQIILENGIP VVSNQVQHSI + VDMRPQQRMA ELCQLTGVRL ITYGTVMGGL LSEKFLDTNV SIPFAGPPLN + TPSLQKYKRM VDAWGGWSLF QTLLQTLKKV SLKHGVTIST VAVKYILNQT + SVAGSMVGVR LGLSEHIKDT NAIFSLELDE EDMNIITEVS KRGRNLIDII + GDCGDEYRA + + + + + +GRMZM2G085153_P03 NP_001140952 hypothetical protein LOC100273031 seq=translation; coord=2:165609278..165613195:-1; parent_transcript=GRMZM2G085153_T03; parent_gene=GRMZM2G085153 + + + MRGPWASSAL SLRLRLRGAR ARTNTSPMSS TAARVVHPAA AAPPPPRPRR + LAPARCAAGS ATDTATAGPT RVTTVSNRGD SLAICRVLNG MWQTSGGWGR + IDRDAAVDAM LAHADAGLST FDMADHYGPA EDLYGMFINR IRRERPPEFL + EEVKGLTKWV PPPVKMTRSY VEDNINRSRK RMDVTALDML QFHWWEYSNP + GYLDALKHIT DLKEEGKIKT VALTNFDTDR LQIILENGIP VVSNQVQHSI + VDMRPQQRMA ELCQLTGVRL ITYGTVMGGL LSEKFLDTNV SIPFAGPPLN + TPSLQKYKRM VDAWGGWSLF QTLLQTLKKV PWSV + + + + + + +5.20702 +-0.297544 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +4838 4838 4838 4838 4838 4745 4566 4402 2625 2161 1194 641 262 113 52 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4845 4845 4845 4845 4845 4752 4573 4408 2593 2009 963 226 31 14 1 0 + + + + + + +0 1 2 3 4 + + + + +3507 1206 128 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +726 3358 656 104 1 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2490 (charge 2) + +1347.65 +2 + + +155.081 158.092 159.077 171.076 171.113 173.092 175.12 185.093 198.088 200.103 212.103 216.098 224.103 226.119 242.113 256.127 269.125 275.988 281.126 284.01 287.135 295.139 304.161 313.025 356.194 373.222 413.216 415.141 430.241 484.245 +501.28 510.22 569.879 602.323 731.288 774.408 824.411 889.444 891.454 990.486 1061.53 1148.56 1152.65 1154.56 + + + + +21 14 12 12 14 13 73 15 70 80 37 20 12 13 23 19 77 10 17 21 36 13 47 22 20 16 19 11 55 13 +54 17 12 77 16 100 13 75 13 93 23 15 12 18 + + + + + + +GRMZM2G027995_P01 Q41741 Eukaryotic initiation factor 4A (eIF-4A)(EC 3.6.4.13)(ATP-dependent RNA helicase eIF4A) seq=translation; coord=6:87119198..87122939:1; parent_transcript=GRMZM2G027995_T01; parent_gene=GRMZM2G027995 + + + + + + + +GRMZM2G027995_P02 Q41741 Eukaryotic initiation factor 4A (eIF-4A)(EC 3.6.4.13)(ATP-dependent RNA helicase eIF4A) seq=translation; coord=6:87119221..87123018:1; parent_transcript=GRMZM2G027995_T02; parent_gene=GRMZM2G027995 + + + + + + + +GRMZM2G116034_P02 NP_001104874 translation initiation factor seq=translation; coord=5:56777167..56780802:-1; parent_transcript=GRMZM2G116034_T02; parent_gene=GRMZM2G116034 + + + + + + + +GRMZM2G116034_P01 NP_001104874 translation initiation factor seq=translation; coord=5:56776697..56780711:-1; parent_transcript=GRMZM2G116034_T01; parent_gene=GRMZM2G116034 + + + + + + + + +6.61414 +-0.377951 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +3421 3421 3379 3218 2965 2357 1682 1153 738 403 171 78 41 3 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3411 3411 3369 3196 2932 2258 1465 932 468 241 49 8 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1166 1565 577 116 12 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +522 1754 952 182 18 5 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2491 (charge 3) + +1784.76 +3 + + +155.082 158.092 159.077 161.092 165.077 166.062 166.098 167.056 167.093 168.056 169.052 169.099 171.113 173.092 173.129 175.072 175.119 176.123 180.077 183.077 183.113 183.148 187.108 190.061 195.088 199.108 201.123 208.072 211.119 217.072 +221.084 225.098 236.066 237.07 239.095 241.092 253.093 258.08 268.978 270.977 276.166 281.052 285.01 287.007 292.104 299.062 301.059 303.021 305.018 309.204 318.119 325.155 329.113 336.13 341.181 344.977 346.974 355.07 357.068 359.065 +364.17 374.082 375.078 396.171 402.192 417.035 419.995 420.993 435.198 459.181 493.706 500.264 502.217 518.269 522.226 537.226 575.254 593.266 633.295 666.786 668.29 676.309 694.312 704.323 727.339 764.334 766.841 791.336 801.375 879.365 +888.396 918.377 925.444 927.445 936.385 938.388 989.444 1074.45 1174.48 1333.57 + + + + +2 2 3 1 2 6 1 20 3 3 5 1 5 1 11 1 11 1 2 3 1 1 1 1 6 7 5 3 2 1 +3 20 13 1 40 17 60 1 11 5 7 2 57 40 2 35 25 19 15 100 2 1 2 12 2 6 6 75 88 3 +1 7 9 6 2 3 11 14 2 1 2 2 2 23 2 15 3 2 8 2 2 2 3 2 8 17 5 5 3 8 +2 2 10 2 42 7 3 7 2 3 + + + + + + +GRMZM5G859592_P01 seq=translation; coord=1:248587698..248589524:-1; parent_transcript=GRMZM5G859592_T01; parent_gene=GRMZM5G859592 + + + MKSDSEENRD EDSDEAGDKQ EGDYVSGKEK AGKFSEVKES SGKKKANTGS + GHQSGPPKKI IRSPVKKVSS KIHEEKESPN NSAKVFSRKK KPTAEKEIKE + KKSSGKKVTK GKGESVEAVL PSKDDLRKTI TEILKKVDFN TATFSDILKK + LDNHYKMDLA PKKEAIKVMI QDELTKLSEE DEGEGAGDTE KKQQQPQAKE + IEA + + + + + + +7.03374 +-0.380202 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +4183 4183 4183 4178 3878 3767 3497 2819 2212 1393 701 322 155 38 12 7 2 1 1 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4187 4187 4187 4182 3882 3765 3470 2767 1898 1016 292 93 24 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1670 1814 568 127 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +849 2126 899 258 50 3 5 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2500 (charge 3) + +1693.74 +3 + + +155.118 156.078 158.093 159.077 167.082 169.061 169.098 171.077 173.129 174.131 175.119 183.113 185.092 187.071 189.087 195.075 197.093 199.071 199.108 201.124 203.103 214.119 217.082 226.155 228.171 231.099 240.135 244.166 262.149 266.118 +272.172 275.208 283.14 286.141 296.128 302.097 310.106 328.117 346.127 356.109 367.122 383.189 385.132 424.698 438.239 446.234 452.25 458.177 486.212 499.073 505.299 517.237 527.768 551.75 576.295 621.743 662.312 666.24 677.348 695.411 +703.828 708.818 749.377 752.338 759.361 760.85 774.383 805.403 903.447 917.429 934.438 991.471 1038.51 1357.28 + + + + +4 5 7 7 5 8 9 7 35 4 37 9 5 25 24 5 8 25 31 20 5 20 50 100 7 5 35 26 7 6 +11 28 23 7 4 6 5 7 10 8 7 7 7 6 10 22 20 5 5 5 24 7 24 7 21 6 10 7 39 7 +27 7 8 20 69 32 39 56 20 23 9 32 6 7 + + + + + + +GRMZM2G119886_P01 NP_001150760 DNA binding protein seq=translation; coord=1:41759285..41762638:-1; parent_transcript=GRMZM2G119886_T01; parent_gene=GRMZM2G119886 + + + MASTAARRLR ELQAQTGNKT CVDCAQRNPQ WASVSYGVFM CLECSGKHRG + LGVHISFVRS VTMDSWTEAQ LRKMEAGGND RLNAFLTARG VPKETPHVAK + YNSNAAAAYR DRIAALAEGK PWTDPPVVKE TPGSGAPAPA RKPPVHTSAA + SGGGGWDDWD DDFRPDMRRN QSVGSFAAAG AQSGRQPPRS KSTQDMYTRQ + QLEASAANKE DFFARRMAEN ESKPDGIPPS QGGKYVGFGS SPPPSANRNG + GAAQGDVMQV VSQGFGRLSL VAASAAQSAA SAVQVGTKEI QSKMRDGGYD + QKVNETVSVV ANKTAEIGSR TWGIMRGVMA LASQKVEEYA KEGGVGGWGE + DWQHSEQKSE PYQRFEHETN GNSWNSSQNS SSKNNSSSWD DWDDPGKKDE + PAKPHQSSDS WAGWDDGKDD GFDSPSYNNH STSNKGSNQN GTSGGTFWTE + GGFR + + + + + +GRMZM2G368806_P01 seq=translation; coord=2:236772112..236773704:1; parent_transcript=GRMZM2G368806_T01; parent_gene=GRMZM2G368806 + + + MDSWTEAQLR KMEAGGNDRL NAFLTAWGVP KETSHVAKYN FNAATAYRDC + IASLIEGKPW TDPPVVKETP GSGAPAPARK PPLHASRGGG GWDDWDDDFR + PDMRRNQSVG SFAVAGAQSG RQPPRSKSTQ DIYTRQQLEA SVANKDDFFA + RRMAENESKP EGIPPSQGGK YVVFGSSPAP SANRNGGAAQ GDVLQVVSQE + NRTITMEYMF DYNGIWMPFI SCSLCCPVCC + + + + + +GRMZM2G368806_P02 seq=translation; coord=2:236772112..236773704:1; parent_transcript=GRMZM2G368806_T02; parent_gene=GRMZM2G368806 + + + MDSWTEAQLR KMEAGGNDRL NAFLTAWGVP KETSHVAKYN FNAATAYRDC + IASLIEGKPW TDPPVVKETP GSGAPAPARK PPLHASRGGG GWDDWDDDFR + PDMRRNQSVG SFAVAGAQSG RQPPRSKSTQ DIYTRQQLEA SVANKDDFFA + RRMAENESKP EGIPPSQGGK YVVFGSSPAP SANRNGGAAQ GDVLQVVSQG + FGCLSLVAAS AAQSAASVVQ VGTKEIQSKL KVIGDGGDPN GHYDKDDHQ + + + + + + +6.62758 +-0.323297 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +5386 5386 5292 5007 4814 4438 4282 2405 1771 830 328 198 79 34 15 11 3 2 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5397 5397 5303 5018 4817 4437 4263 2138 1468 462 142 53 14 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2961 2100 302 33 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1164 3551 572 92 12 0 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2515 (charge 2) + +1110.55 +2 + + +152.056 155.045 155.081 157.061 157.097 157.108 158.081 158.092 159.077 161.092 164.817 167.081 168.065 169.097 169.134 171.076 171.114 172.072 172.109 173.092 173.128 175.119 181.061 181.096 185.092 186.124 189.087 197.091 198.087 199.108 +201.088 203.103 209.091 213.087 217.081 224.104 226.155 231.097 240.135 242.114 244.164 256.153 259.093 273.12 281.125 283.176 286.139 299.135 300.136 311.17 324.165 326.182 333.783 337.186 342.182 352.161 370.173 373.208 408.229 414.245 +431.731 433.876 440.735 444.245 462.231 479.262 494.28 511.299 513.309 554.299 582.334 586.322 639.353 683.371 726.386 751.388 783.409 851.457 880.467 1047.78 + + + + +3 4 43 2 4 3 8 5 3 4 2 4 3 39 2 46 4 11 3 8 2 27 3 3 33 4 3 2 4 14 +4 12 4 13 2 5 38 5 16 31 8 10 3 4 11 9 3 11 2 5 4 15 2 3 28 10 16 15 3 3 +12 2 14 4 2 4 3 100 3 3 10 3 18 21 28 4 45 9 18 3 + + + + + + +GRMZM2G110063_P02 NP_001152272 LOC100285911 seq=translation; coord=8:14727821..14778423:1; parent_transcript=GRMZM2G110063_T02; parent_gene=GRMZM2G110063 + + + MAKALLYSSL LPGLPRAVGS SRSAAARLLL LPPLRLRRGR RAASACAVRA + GLHGLDSVGG PHLQAALERA EAALYTLADA AVAAADAAAG AGDDAGQAAA + AVQKNGGWFG FISEALEVVL KVLKDGLSAV HVPYSYGFAI ILLTIIVKAA + TLPLTKKQVE STMAMQNLQP QLKAIQQRYA GNQERIQLET ARLYRQAGVN + PLAGCFPTLA TIPVWIGLYQ ALSNVANEGL LTEGFFWIPS LGGPTTIAAR + QSGAGISWLF PFVDGHPPLG WYDTICYLVL PVLLVASQYV SMEIMKPPQS + DDPSQKNTLL VLKFLPFMIG YFSLSVPSGL SIYWFTNNVL STAQQVWLRK + MGGAKPVVSE GDRRIITAGR AKRSNAQPAG ERFRQLKEEE SMRKVNKALA + AGDSNASSST YDMEDEESDD ETTEEGGPVE EASSTGSDKK PPSYSGKKGK + RSKRKRMVQ + + + + + +GRMZM2G110063_P01 NP_001152272 LOC100285911 seq=translation; coord=8:14727847..14778423:1; parent_transcript=GRMZM2G110063_T01; parent_gene=GRMZM2G110063 + + + MAMQNLQPQL KAIQQRYAGN QERIQLETAR LYRQAGVNPL AGCFPTLATI + PVWIGLYQAL SNVANEGLLT EGFFWIPSLG GPTTIAARQS GAGISWLFPF + VDGHPPLGWY DTICYLVLPV LLVASQYVSM EIMKPPQSDD PSQKNTLLVL + KFLPFMIGYF SLSVPSGLSI YWFTNNVLST AQQVWLRKMG GAKPVVSEGD + RRIITAGRAK RSNAQPAGER FRQLKEEESM RKVNKALAAG DSNASSSTYD + MEDEESDDET TEEGGPVEEA SSTGSDKKPP SYSGKKGKRS KRKRMVQ + + + + + + +5.65614 +-0.305737 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 + + + + +7647 7647 7647 7487 7228 6847 6392 5720 5156 3292 2351 1029 547 228 112 58 19 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7666 7666 7666 7506 7247 6859 6356 5599 4961 2726 1572 296 34 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2561 3374 1257 401 61 14 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1542 3558 1626 646 211 74 3 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2516 (charge 3) + +1458.75 +3 + + +152.057 155.082 155.118 157.109 158.092 159.077 160.08 161.074 166.114 166.615 167.093 169.061 169.098 169.134 171.077 172.072 173.056 173.092 175.119 176.123 181.061 183.113 186.087 187.072 187.107 189.069 189.086 190.083 193.098 195.088 +197.129 198.088 198.132 199.072 200.139 201.124 212.103 221.092 226.155 227.103 231.098 239.151 244.166 246.09 252.137 260.035 271.187 273.121 283.104 290.145 296.201 301.114 308.173 313.212 317.127 331.22 360.176 400.169 411.161 421.427 +428.68 431.38 441.333 443.24 459.241 486.249 490.225 498.768 503.267 507.77 510.302 540.739 571.816 605.254 607.336 636.355 647.799 655.353 659.316 662.274 664.359 684.322 702.318 703.323 719.341 722.618 758.379 799.332 801.39 812.42 +818.415 840.427 856.355 858.439 917.471 954.5 969.431 997.506 998.502 1014.53 + + + + +8 4 3 4 10 49 3 7 30 4 7 5 4 37 3 5 9 3 80 7 4 13 15 21 8 16 2 6 4 14 +35 4 5 4 19 5 3 4 19 8 4 2 7 27 14 4 6 4 7 16 8 13 2 8 4 37 6 16 11 28 +6 17 45 17 10 5 21 6 4 100 3 5 11 6 5 8 6 5 4 31 33 9 12 4 7 7 4 10 12 4 +4 9 24 14 3 7 6 19 9 8 + + + + + + +GRMZM2G083418_P01 NP_001149063 LOC100282684 seq=translation; coord=3:9805845..9808735:-1; parent_transcript=GRMZM2G083418_T01; parent_gene=GRMZM2G083418 + + + MVGGGRRGGA AEEVKLNTGN VFAALESLKK KKKGDKGKAA GSSSRKKHGE + GAAQRQEPPQ KELFWAPAPL TTKSWADVED DDDDDYFATT APPRPVWGTA + GEPAKEEEDV DDAVRAALQE DIESDDGDLD DEVDDGPEDE PEHDAEDAPA + EPAIRTAAAP AAPPKDTERQ LSKKELKKKE LAELDAVLAE LGLSANSSST + AQDAEKKGTN QIGDAEKKED APAPPESKAS KKKKKKDKSS KEGKETQEAL + DGSEETASAG PDEDTSAVDV KERLKKMASM KKKKSSRETD TAAKIAAAEA + AARSARLAAA KKKEKSHYNQ QPVR + + + + + + +6.91677 +-0.354706 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +7715 7715 7650 7384 6910 6560 5940 5429 3821 2696 1311 671 357 174 35 17 7 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7721 7721 7656 7380 6883 6495 5863 5179 3198 2216 629 133 44 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2993 3219 1148 287 66 5 2 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1302 3687 1999 521 103 107 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2517 (charge 3) + +1395.72 +3 + + +152.057 154.086 155.082 157.109 157.134 158.093 159.076 159.092 163.133 164.136 167.055 167.081 167.117 168.055 169.053 169.097 170.101 171.077 173.092 174.096 175.119 185.092 185.129 186.124 187.072 195.113 197.129 199.109 199.169 201.123 +212.139 223.064 226.154 227.103 240.134 244.129 246.156 265.998 270.96 283.176 287.975 290.985 304.948 306.939 311.171 315.165 322.958 324.954 329.996 332.954 334.95 337.187 346.97 348.983 354.213 360.029 362.027 363.023 373.196 382.212 +384.182 386.21 389.196 405.209 418.241 421.722 432.087 438.235 446.235 452.252 457.24 467.102 502.301 515.258 519.296 521.236 541.787 573.331 590.326 648.329 659.352 668.326 677.357 686.338 704.365 730.372 745.385 748.396 749.396 764.282 +782.292 784.299 819.434 825.41 842.436 844.446 853.333 913.473 984.516 1081.56 + + + + +2 2 6 3 24 10 7 2 70 2 7 2 2 2 5 67 6 2 74 5 47 2 26 5 3 6 2 11 6 2 +5 4 21 6 54 27 2 2 35 8 28 9 100 11 15 2 84 10 7 32 3 5 12 6 2 11 42 18 16 2 +5 2 14 21 3 63 6 2 2 2 7 6 2 4 11 2 12 2 10 9 2 2 14 2 2 2 39 25 2 2 +21 6 9 6 65 8 6 15 11 6 + + + + + + +GRMZM2G055276_P01 B4FR90 Putative uncharacterized protein seq=translation; coord=3:202432697..202435947:1; parent_transcript=GRMZM2G055276_T01; parent_gene=GRMZM2G055276 + + + MATLNPFELL GADDNDDPTQ LIAAAAAAAQ KAEAKKSAVA PAGKAAQPAA + TTKFPTKPAP PSQTVRDARG GGSSARGGFG RGERGRGRGG RGYGQNRGFS + GDNGNEFQGG YGGGGYGDGA VTGGSEGERE RETRPPYRGG GRRGGYRNVE + FADDSERPPR RNYERHSGTG HGYEMKRDGA GRGNWGTATD ELIAQDAEDS + PKMEEAAPVA EKQGEQNDAP AADENKDNKD ATANEEEEKE EDKEMTLEEF + EKIREEKRKA LLALKAEERK VEVDKDLQSL QPLSNKKEND EVFIKLGSDK + DKKKENAERD ERAKKSVSIN EFLKPAEGER YYGGRGRGRG RGDRGGFRGG + YGGGYSRGPA AAAPSIEDQA QFPSLGGK + + + + + + +GRMZM2G055276_P02 B4FR90 Putative uncharacterized protein seq=translation; coord=3:202432697..202435928:1; parent_transcript=GRMZM2G055276_T02; parent_gene=GRMZM2G055276 + + + MATLNPFELL GADDNDDPTQ LIAAAAAAAQ KAEAKKSAVA PAGKAAQPAA + TTKFPTKPAP PSQTVRDARG GGSSARGGFG RGERGRGRGG RGYGQNRGFS + GDNGNEFQGG YGGGGYGDGA VTGGSEGERE RETRPPYRGG GRRGGYRNVE + FADDSERPPR RNYERHSGTG HGYEMKRDGA GRGNWGTATD ELIAQDAEDS + PKMEEAAPVA EKQGEQNDAP AADENKDNKD ATANEEEEKE EDKEMTLEEF + EKIREEKRKA LLALKAEERK VEVDKDLQSL QPLSNKKEND EVFIKLVSFP + VINALIP + + + + + + + +4.63562 +-0.319698 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +1227 1227 1227 1227 1227 1096 694 565 387 140 65 18 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1228 1228 1228 1228 1228 1097 695 562 360 123 40 7 5 1 0 + + + + + + +0 1 2 3 4 + + + + +615 559 52 17 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +544 659 24 0 0 0 0 16 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2527 (charge 2) + +1826.78 +2 + + +172.764 185.536 226.082 230.077 240.098 258.108 261.156 270.11 281.95 298.103 315.13 341.11 355.159 376.183 408.151 417.163 426.163 435.114 495.182 496.902 504.273 618.316 620.202 638.208 639.21 655.235 668.238 726.351 841.359 862.392 +933.421 1084.49 1101.52 1103.52 1172.55 + + + + +7 7 12 15 22 10 40 12 7 62 20 18 33 13 36 9 44 10 12 12 11 15 17 53 12 72 12 19 18 15 +17 19 100 18 39 + + + + + + +GRMZM2G149751_P01 C0P5Y3 Putative uncharacterized protein seq=translation; coord=1:176837841..176844200:1; parent_transcript=GRMZM2G149751_T01; parent_gene=GRMZM2G149751 + + + MASHIVGYPR MGPKRELKFA LESFWDGKST AEDLEKVATD LRASIWKQMA + DAGIKYIPSN TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG FDTYFSMARG + NATVPAMEMT KWFDTNYHFI VPELGPNTKF SYASHKAVNE YKEAKALGVD + TVPVLVGPVS YLLLSKPAKG VEKGFPLLSL LSSILPVYKE VIAELKAAGA + SWIQFDEPTL VLDLDSDKLA AFSAAYAELE SVLSGLNVLV ETYFADVPAE + SYKTLTSLSS VTAYGFDLVR GTQTLGLVTS AGFPAGKYLF AGVVDGRNIW + ADDLATSLST LQSLEAVVGK DKLVVSTSCS LMHTAVDLVN ETKLDSEIKS + WLAFAAQKVV EVDALAKALA GQKDEAYFAA NAAAQASRKS SPRVTNEEVQ + KAAAALKGSD HRRGTNVSAR LDAQQKKLNL PILPTTTIGS FPQTVELRRV + RREYKAKKIS EEEYVTAIKE EINKVVKLQE ELDIDVLVHG EPERNDMVEY + FGEQLSGFAF TANGWVQSYG SRCVKPPIIY GDVSRPNPMT VFWSKTAQSM + TSRPMKGMLT GPVTILNWSF VRNDQPRFET CYQIALAIKK EVEDLEAGGI + QVIQIDEAAL REGLPLRKAE HAFYLDWAVH SFRITNCEIQ DTTQIHTHMC + YSNFNDIIHS IIDMDADVIT IENSRSDEKL LSVFREGVKY GAGIGPGVYD + IHSPRIPSAE EIADRIDKML AVLDTNILWV NPDCGLKTRK YTEVKPALTN + MVSAAKLIRT QLASAK + + + + + +GRMZM2G149751_P03 C0P5Y3 Putative uncharacterized protein seq=translation; coord=1:176837893..176844200:1; parent_transcript=GRMZM2G149751_T03; parent_gene=GRMZM2G149751 + + + MASHIVGYPR MGPKRELKFA LESFWDGKST AEDLEKVATD LRASIWKQMA + DAGIKYIPSN TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG FDTYFSMARG + NATVPAMEMT KWFDTNYHFI VPELGPNTKF SYASHKAVNE YKEAKALGVD + TVPVLVGPVS YLLLSKPAKG VEKGFPLLSL LSSILPVYKE VIAELKAAGA + SWIQFDEPTL VLDLDSDKLA AFSAAYAELE SVLSGLNVLV ETYFADVPAE + SYKTLTSLSS VTAYGFDLVR GTQTLGLVTS AGFPAGKYLF AGVVDGRNIW + ADDLATSLST LQSLEAVVGK DKLVVSTSCS LMHTAVDLVN ETKLDSEIKS + WLAFAAQKVV EVDALAKALA GQKDEAYFAA NAAAQASRKS SPRVTNEEVQ + KAAAALKGSD HRRGTNVSAR LDAQQKKLNL PILPTTTIGS FPQTVELRRV + RREYKAKKIS EEEYVTAIKE EINKVVKLQE ELDIDVLVHG EPERNDMVEY + FGEQLSGFAF TANGWVQSYG SRCVKPPIIY GDVSRPNPMT VFWSKTAQSM + TSRPMKGMLT GPVTILNWSF VRNDQPRFET CYQIALAIKK EVEDLEAGGI + QVIQIDEAAL REGLPLRKAE HAFYLDWAVH SFRITNCEIQ DTTQIHTHMC + YSNFNDIIHS IIDMDADVIT IENSRSDEKL LSVFREGVKY GAGIGPGVYD + IHSPRIPSAE EIADRIDKML AVLDTNILWV NPDCGLKTRK YTEVKPALTN + MVSAAKLIRT QLASAK + + + + + +GRMZM2G149751_P05 C0P5Y3 Putative uncharacterized protein seq=translation; coord=1:176839355..176845518:1; parent_transcript=GRMZM2G149751_T05; parent_gene=GRMZM2G149751 + + + MASHIVGYPR MGPKRELKFA LESFWDGKST AEDLEKVATD LRASIWKQMA + DAGIKYIPSN TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG FDTYFSMARG + NATVPAMEMT KWFDTNYHFI VPELGPNTKF SYASHKAVNE YKEAKALGVD + TVPVLVGPVS YLLLSKPAKG VEKGFPLLSL LSSILPVYKE VIAELKAAGA + SWIQFDEPTL VLDLDSDKLA AFSAAYAELE SVLSGLNVLV ETYFADVPAE + SYKTLTSLSS VTAYGFDLVR GTQTLGLVTS AGFPAGKYLF AGVVDGRNIW + ADDLATSLST LQSLEAVVGK DKLVVSTSCS LMHTAVDLVN ETKLDSEIKS + WLAFAAQKVV EVDALAKALA GQKDEAYFAA NAAAQASRKS SPRVTNEEVQ + KAAAALKGSD HRRGTNVSAR LDAQQKKLNL PILPTTTIGS FPQTVELRRV + RREYKAKKIS EEEYVTAIKE EINKVVKLQE ELDIDVLVHG EPERNDMVEY + FGEQLSGFAF TANGWVQSYG SRCVKPPIIY GDVSRPNPMT VFWSKTAQSM + TSRPMKGMLT GPVTILNWSF VRNDQPRFET CYQIALAIKK EVEDLEAGGI + QVIQIDEAAL REGLPLRKAE HAFYLDWAVH SFRITNCEIQ DTTQIHTHMC + YSNFNDIIHS IIDMDADVIT IENSRSDEKL LSVFREGVKY GAGIGPGVYD + IHSPRIPSAE EIADRIDKML AVLDTNILWV NPDCGLKTRK YTEVKPALTN + MVSAAKLIRT QLASANGCGC FCLFFGCSSA P + + + + + +GRMZM2G149751_P06 C0P5Y3 Putative uncharacterized protein seq=translation; coord=1:176840387..176843727:1; parent_transcript=GRMZM2G149751_T06; parent_gene=GRMZM2G149751 + + + MHTAVDLVNE TKLDSEIKSW LAFAAQKVVE VDALAKALAG QKDEAYFAAN + AAAQASRKSS PRVTNEEVQK AAAALKGSDH RRGTNVSARL DAQQKKLNLP + ILPTTTIGSF PQTVELRRVR REYKAKKISE EEYVTAIKEE INKVVKLQEE + LDIDVLVHGE PERNDMVEYF GEQLSGFAFT ANGWVQSYGS RCVKPPIIYG + DVSRPNPMTV FWSKTAQSMT SRPMKGMLTG PVTILNWSFV RNDQPRFETC + YQIALAIKKE VEDLEAGGIQ VIQIDEAALR EGLPLRKAEH AFYLDWAVHS + FRITNCEIQD TTQIHTHMCY SNFNDIIHSI IDMDADVITI ENSRSDEKLL + SVFREGVKYG AGIGPGVYDI HSPRIPSAEE IADRIDKMLA VLDTNILWVN + PDCGLKTRKY TEVKPALTNM VSAAKLIRTQ LASAK + + + + + + +7.18625 +-0.350549 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +7631 7631 7631 7631 7351 7047 6500 5813 5158 3682 2699 1421 738 348 146 74 29 4 2 1 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7642 7642 7642 7642 7362 7055 6480 5580 4806 3015 1800 504 94 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2696 2951 1468 446 73 13 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1064 3240 2245 848 184 57 1 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2530 (charge 3) + +1237.6 +3 + + +153.067 154.05 154.086 155.082 156.076 157.097 157.108 158.092 159.076 160.079 165.102 166.05 166.062 167.081 169.097 169.134 170.093 171.077 171.113 173.092 173.13 175.119 181.097 183.076 183.113 183.15 188.103 191.085 194.128 195.088 +195.114 197.129 198.087 199.071 200.103 209.105 216.098 221.106 226.119 227.102 229.101 233.129 235.119 240.134 244.165 246.155 248.16 251.081 254.16 258.146 266.16 268.166 270.108 272.171 278.154 282.119 287.135 301.159 310.177 314.137 +320.169 323.208 327.167 328.155 341.218 345.187 357.198 361.81 375.206 379.708 386.691 408.704 411.85 415.199 419.239 431.162 438.274 460.218 464.254 469.232 473.27 475.224 490.242 507.748 525.256 535.322 563.262 574.286 591.294 601.31 +607.319 618.34 635.315 645.324 702.362 719.391 722.333 757.412 850.427 937.456 + + + + +6 7 8 45 6 9 17 19 40 7 8 7 7 10 18 7 28 31 31 66 6 100 7 28 10 7 6 31 10 9 +8 10 30 22 24 17 11 6 23 7 6 20 9 8 28 7 6 7 7 6 6 8 7 27 6 6 7 10 8 6 +6 8 9 6 19 10 7 7 22 11 20 8 12 9 8 6 11 8 8 6 31 7 8 6 11 8 7 6 22 6 +19 42 35 6 10 72 10 8 11 30 + + + + + + +GRMZM2G373522_P01 NP_001105327 dehydrin seq=translation; coord=4:154310162..154311883:-1; parent_transcript=GRMZM2G373522_T01; parent_gene=GRMZM2G373522 + + + + + + + +GRMZM2G373522_P02 NP_001105327 dehydrin seq=translation; coord=4:154310885..154311883:-1; parent_transcript=GRMZM2G373522_T02; parent_gene=GRMZM2G373522 + + + MEDERNTQQH QGGEQAQDQE NEVKDRGLLD SLLGRNKHDD QEKKNQQEEE + ELATGMEKVT VAEPDHKEEG HEAAEKKDSL LAKLHRTSSS SSSVSSS + + + + + + +8.04476 +-0.412552 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +3737 3737 3737 3737 3737 3737 3561 3275 2729 1681 1001 359 169 55 26 5 3 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3740 3740 3740 3740 3740 3740 3564 3278 2725 1652 881 249 33 1 0 + + + + + + +0 1 2 3 4 + + + + +2150 1446 148 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +793 2309 570 60 11 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2531 (charge 3) + +2439.09 +3 + + +175.119 176.124 216.098 221.103 232.84 244.092 248.538 261.924 266.126 290.145 311.68 355.071 377.153 418.239 517.307 590.239 609.28 646.35 715.776 721.644 757.632 760.406 852.204 889.428 971.442 1000.46 1017.49 1062.47 1132.53 1260.58 +1331.61 1498.65 + + + + +100 22 17 21 17 29 19 16 20 26 22 25 19 37 40 24 34 36 35 21 26 44 35 43 67 59 44 25 46 31 +29 27 + + + + + + +GRMZM2G044132_P01 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53846005:1; parent_transcript=GRMZM2G044132_T01; parent_gene=GRMZM2G044132 + + + + + + + +GRMZM2G044132_P02 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53845943:1; parent_transcript=GRMZM2G044132_T02; parent_gene=GRMZM2G044132 + + + + + + + + +6.81986 +-0.368641 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 + + + + +1533 1533 1533 1528 1471 1423 1251 869 674 384 162 71 15 7 3 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1542 1542 1542 1537 1480 1428 1257 862 513 237 87 26 11 1 0 + + + + + + +0 1 2 3 4 5 + + + + +947 485 98 11 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +339 967 202 27 2 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2534 (charge 2) + +1513.62 +2 + + +153.066 167.056 170.093 171.076 172.073 175.119 181.061 186.088 186.806 187.071 188.103 198.088 199.072 210.087 216.098 217.081 228.099 234.41 238.081 239.095 245.076 250.082 256.093 258.106 262.151 272.171 285.119 295.103 299.061 301.115 +313.114 325.115 330.14 342.141 349.184 352.126 355.071 359.028 370.135 371.135 373.133 406.205 429.088 441.175 552.237 556.208 569.268 698.308 739.302 748.306 755.331 788.013 812.355 923.385 941.392 1056.42 1127.46 1184.48 1241.5 1298.53 +1300.53 1386.56 + + + + +8 8 22 25 7 37 14 6 4 7 27 43 21 6 23 4 4 4 8 4 14 5 14 4 17 5 8 5 34 5 +41 4 7 15 5 19 4 14 85 8 4 39 5 17 13 7 54 13 7 34 21 4 100 18 60 47 7 5 16 28 +5 7 + + + + + + +GRMZM2G105644_P01 NP_001149382 geranylgeranyl hydrogenase seq=translation; coord=5:206890298..206892838:1; parent_transcript=GRMZM2G105644_T01; parent_gene=GRMZM2G105644 + + + + + + + + +4.26202 +-0.258305 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6709 6709 6709 6444 4281 3598 1840 1331 966 582 235 107 70 28 9 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6707 6707 6707 6442 4269 3449 1678 1186 813 475 114 49 32 1 0 + + + + + + +0 1 2 3 4 + + + + +5028 1582 88 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +862 5149 670 27 2 0 3 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2536 (charge 2) + +1506.82 +2 + + +155.645 164.118 175.119 175.402 181.108 183.15 192.113 209.103 229.118 235.12 244.166 254.162 307.765 310.152 313.156 321.156 323.367 330.191 338.145 364.163 366.139 409.22 430.739 437.213 480.293 497.32 595.332 619.359 634.376 647.344 +860.474 942.513 973.567 1053.58 1070.61 1072.61 + + + + +3 16 5 2 30 5 4 18 12 5 3 3 3 3 3 6 3 4 3 3 5 56 15 29 4 14 4 4 21 3 +49 11 5 5 100 14 + + + + + + +GRMZM2G059191_P01 NP_001149023 ferredoxin--NADP reductase, leaf isozyme seq=translation; coord=8:157455159..157458787:-1; parent_transcript=GRMZM2G059191_T01; parent_gene=GRMZM2G059191 + + + MAAVTAAAIS LSSSSASSPA AAAKAKAASP SSSPCRHLQF LSAASPRRRW + RAGARAVRAQ VSTTETAAAG PAKTSKKQDE GLVTNKYKPK EPYVGRCLSN + TRITGDDAPG ETWHMVFSTE GEIPYREGQS IGIIADGEDK NGKPHKLRLY + SIASSALGDF GDSKTVSLCV KRLVYTNDQG EIVKGVCSNF LCDLKPGADV + KITGPVGKEM LMPKDPNATV IMLATGTGIA PFRSFLWKMF LEEHEDYKFS + GLAWLFLGVP TSDSLLYKEE LEKMKEMAPD NFRLDFAVSR EQTNAAGEKM + YIQTRMAEYR EELWELLKKD NTYVYMCGLK GMEKGIDDIM LNLAAKDGID + WMQYKKQLKK GEQWNVEVY + + + + + + +4.3514 +-0.263721 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 + + + + +7136 7136 7136 6902 5112 4384 3088 2254 1585 1040 605 270 107 43 15 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7143 7143 7143 6909 5119 4342 3014 2058 1286 748 341 139 30 6 1 0 + + + + + + +0 1 2 3 4 + + + + +3685 2970 444 44 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1431 5104 558 45 4 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2540 (charge 2) + +1203.62 +2 + + +155.082 157.097 159.076 159.113 161.092 167.081 169.097 171.076 171.112 173.092 173.128 175.107 175.119 181.098 185.092 187.071 187.09 187.108 188.112 198.034 198.124 199.108 201.124 203.102 210.978 213.087 216.044 218.149 226.155 231.098 +240.099 242.113 244.166 249.039 252.135 254.112 270.145 272.123 288.154 295.14 297.157 299.133 315.202 316.207 323.173 341.143 353.186 372.224 373.227 383.192 400.183 443.262 458.725 478.995 497.83 514.302 522.871 546.912 555.244 585.338 +677.388 686.381 704.356 797.407 815.421 903.467 916.46 1017.51 1105.55 + + + + +6 7 3 100 4 5 19 7 4 4 3 6 16 3 48 5 5 71 4 5 5 30 5 21 3 35 5 3 86 31 +4 3 16 4 3 5 10 4 6 3 4 4 45 7 4 4 3 59 11 5 6 36 4 5 5 27 19 10 4 24 +13 40 46 4 30 4 17 12 11 + + + + + + +GRMZM2G174807_P01 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18133361..18135367:-1; parent_transcript=GRMZM2G174807_T01; parent_gene=GRMZM2G174807 + + + MEGKEEDVRL GANKFSERQP IGTAAQGTDD KDYKEPPPAP LFEPGELKSW + SFYRAGIAEF VATFLFLYIS ILTVMGVSKS TSKCATVGIQ GIAWSFGGMI + FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRAVFYIIM QCLGAICGAG + VVKGFQQGLY MGNGGGANVV APGYTKGDGL GAEIVGTFIL VYTVFSATDA + KRNARDSHVP ILAPLPIGFA VFLVHLATIP ITGTGINPAR SLGAAVIYNQ + HHAWADHWIF WVGPFIGAAL AAIYHQVIIR AIPFKSRS + + + + + + + +GRMZM2G174807_P02 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18134011..18135367:-1; parent_transcript=GRMZM2G174807_T02; parent_gene=GRMZM2G174807 + + + MEGKEEDVRL GANKFSERQP IGTAAQGTDD KDYKEPPPAP LFEPGELKSW + SFYRAGIAEF VATFLFLYIS ILTVMGVSKS TSKCATVGIQ GIAWSFGGMI + FALVYCTAGI SGTVHAARPA ASLASSSVSF FLCLPCLVVC ANWFADVSLS + LSLSLSLSLS LSLSLFSQLQ AGTSTRR + + + + + + + +GRMZM2G174807_P03 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18133344..18135342:-1; parent_transcript=GRMZM2G174807_T03; parent_gene=GRMZM2G174807 + + + MEGKEEDVRL GANKFSERQP IGTAAQGTDD KDYKEPPPAP LFEPGELKSW + SFYRAGIAEF VATFLFLYIS ILTVMGVSKS TSKCATVGIQ GIAWSFGGMI + FALVYCTAGI SVPGRHLRRG RRQGVPAGAV HGQRRRRQRR GARLHQGRRP + RRRDRRHLHP RLHRLLRHRR QEERQGLPCA DPRPSSNRVC RVPRPPGHHP + YHRHRHQPRA EPWRRRNLQP APCVG + + + + + + + +AC209208.3_FGP002 seq=translation; coord=5:193306422..193309271:1; parent_transcript=AC209208.3_FGT002; parent_gene=AC209208.3_FG002 + + + MEGKEEDVRL GANKFSERQP IGTAAQGAAD DKDYKEPPPA PLFEPGELKS + WSFYRAGIAE FVATFLFLYI TILTVMGVSK STSKCATVGI QGIAWSFGGM + IFALVYCTAG ISGGHINPAV TFGLFLARKL SLTRALFYII MQCLGAICGA + GVVKGFQQGL YMGNGGGANV VAPGYTKGDG LGAEIVGTFI LVYTVFSATD + AKRNARDSHV PILAPLPIGF AVFLVHLATI PITGTGINPA RSLGAAIIYN + RDHAWNDHWI FWVGPFIGAA LAAIYHQVII RAIPFKSRS + + + + + + + +GRMZM2G392975_P01 Q9AQU5 Aquaporin PIP1-3/PIP1-4 (Plasma membrane intrinsic protein 1-3)(ZmPIP1-3)(ZmPIP1;3)(Plasma membrane intrinsic protein 1-4)(ZmPIP1-4)(ZmPIP1;4) seq=translation; coord=4:153627243..153631088:1; parent_transcript=GRMZM2G392975_T01; parent_gene=GRMZM2G392975 + + + MEGKEEDVRL GANKFSERQP IGTAAQGAGA GDDDKDYKEP PPAPLFEPGE + LKSWSFYRAG IAEFVATFLF LYITVLTVMG VSKSTSKCAT VGIQGIAWSF + GGMIFALVYC TAGISGGHIN PAVTFGLFLA RKLSLTRAIF YIIMQCLGAI + CGAGVVKGFQ QGLYMGNGGG ANVVAPGYTK GDGLGAEIVG TFILVYTVFS + ATDAKRNARD SHVPILAPLP IGFAVFLVHL ATIPITGTGI NPARSLGAAI + IYNRDHAWSD HWIFWVGPFI GAALAAIYHQ VIIRAIPFKS RS + + + + + + + +GRMZM2G392975_P02 Q9AQU5 Aquaporin PIP1-3/PIP1-4 (Plasma membrane intrinsic protein 1-3)(ZmPIP1-3)(ZmPIP1;3)(Plasma membrane intrinsic protein 1-4)(ZmPIP1-4)(ZmPIP1;4) seq=translation; coord=4:153627262..153630840:1; parent_transcript=GRMZM2G392975_T02; parent_gene=GRMZM2G392975 + + + MEGKEEDVRL GANKFSERQP IGTAAQGAGA GDDDKDYKEP PPAPLFEPGE + LKSWSFYRAG IAEFVATFLF LYITVLTVMG VSKSTSKCAT VGIQGIAWSF + GGMIFALVYC TAGISGGHIN PAVTFGLFLA RKLSLTRAIF YIIMQCLGAI + CGAGVVKGFQ QGLYMGNGGG ANVVAPGYTK GDGLGAEIVG TFILVYTVFS + ATDAKRNARD SHVPILAPLP IGFAVFLVHL ATIPITGTGI NPARSLGAAI + IYNRDHAWSD HWIFWVGPFI GAALAAIYHQ VIIRAIPFKS RS + + + + + + + +GRMZM2G392975_P03 Q9AQU5 Aquaporin PIP1-3/PIP1-4 (Plasma membrane intrinsic protein 1-3)(ZmPIP1-3)(ZmPIP1;3)(Plasma membrane intrinsic protein 1-4)(ZmPIP1-4)(ZmPIP1;4) seq=translation; coord=4:153627517..153630684:1; parent_transcript=GRMZM2G392975_T03; parent_gene=GRMZM2G392975 + + + MEGKEEDVRL GANKFSERQP IGTAAQGAGA GDDDKDYKEP PPAPLFEPGE + LKSWSFYRAG IAEFVATFLF LYITVLTVMG VSKSTSKCAT VGIQGIAWSF + GGMIFALVYC TAGISGGHIN PAVTFGLFLA RKLSLTRAIF YIIMQCLGAI + CGAGVVKGFQ QGLYMGNGGG ANVVAPGYTK GDGLGAEIVG TFILVYTVFS + ATDAKRNARD SHVPILAPLP IGFAVFLVHL ATIPITGTGI NPARSLGAAI + IYHQVIIRAI PFKSRS + + + + + + + +GRMZM2G081843_P01 Q9AR14 Aquaporin PIP1-5 (Plasma membrane intrinsic protein 1-5)(ZmPIP1-5)(ZmPIP1;5)(ZmPIP1-5b) seq=translation; coord=4:169974857..169976357:-1; parent_transcript=GRMZM2G081843_T01; parent_gene=GRMZM2G081843 + + + MEGKEEDVRL GANRYSERQP IGTAAQGTEE KDYKEPPPAP LFEAEELTSW + SFYRAGIAEF VATFLFLYIS ILTVMGVSKS SSKCATVGIQ GIAWSFGGMI + FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRALFYMVM QCLGAICGAG + VVKGFQEGLY MGAGGGANAV NPGYTKGDGL GAEIVGTFVL VYTVFSATDA + KRSARDSHVP ILAPLPIGFA VFLVHLATIP ITGTGINPAR SLGAAIVYNR + SHAWNDHWIF WVGPFIGAAL AAIYHVVIIR ALPFKSRD + + + + + + + + +4.95818 +-0.283325 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +3241 3241 3207 2691 2575 2369 1330 859 412 218 107 62 21 16 9 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3248 3248 3214 2695 2566 2331 1247 677 258 70 17 5 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2097 959 173 18 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +569 2290 314 53 19 2 0 14 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2546 (charge 2) + +1150.5 +2 + + +153.102 158.092 162.058 169.061 169.097 175.119 176.122 181.097 186.124 187.107 190.053 191.057 195.113 198.124 199.108 204.134 207.124 226.155 235.119 239.15 241.082 244.165 255.098 257.161 259.092 274.187 285.009 297.156 312.118 315.166 +319.097 355.069 372.225 374.119 376.117 389.215 416.711 426.196 440.215 444.209 469.276 472.228 500.738 518.257 534.75 543.756 551.243 559.235 569.256 629.288 647.299 670.273 688.276 775.394 795.31 813.329 832.416 877.322 943.44 961.459 +979.556 + + + + +1 3 5 1 3 21 1 1 10 1 31 2 1 1 2 1 1 8 1 1 1 3 6 5 1 100 1 3 3 3 +2 2 2 1 1 4 3 2 1 1 1 3 2 6 1 4 2 3 2 2 13 2 1 4 1 3 10 1 2 6 +1 + + + + + + +GRMZM2G122937_P01 NP_001159012 remorin seq=translation; coord=2:22990515..22995670:1; parent_transcript=GRMZM2G122937_T01; parent_gene=GRMZM2G122937 + + + MAEEEAKKVE VEVTKEPEAA AKEDVADDKA VIPATDPPPP PPPADDSKAL + AIVEKVADEP APEKPAPAKQ GGSNDRDLAL ARVETEKRNS LIKAWEENEK + TKAENKAAKK VSAILSWENT KKANIEAELK KIEEQLEKKK AEYAEKMKNK + VAMIHKEAEE KRAMVEAKRG EEVLKAEEMA AKYRATGHAP KKLIGCFGA + + + + + +GRMZM2G122937_P03 NP_001159012 remorin seq=translation; coord=2:22990515..22995246:1; parent_transcript=GRMZM2G122937_T03; parent_gene=GRMZM2G122937 + + + MAEEEAKKVE VEVTKEPEAA AKEDVADDKA VIPATDPPPP PPPADDSKAL + AIVEKVADEP APEKPAPAKQ GGSNDRDLAL ARVETEKRNS LIKAWEENEK + TKAENKAAKK VSAILSWENT KKANIEAELK KIEEQLEKKK AEYAEKMKNK + VAMIHKEAEE KRAMVEAKRG EEVLKAEEMA AKYRATGHAP KKLIGCFGA + + + + + +GRMZM2G122937_P02 NP_001159012 remorin seq=translation; coord=2:22990515..22995669:1; parent_transcript=GRMZM2G122937_T02; parent_gene=GRMZM2G122937 + + + MAEEEAKKVE VEVTKEPEAA AKEDVADDKA VIPATDPPPP PPPADDSKAL + AIVEKVADEP APEKPAPAKQ GGSNDRDLAL ARVETEKRNS LIKAWEENEK + TKAENKAAKK VSAILSWENT KKANIEAELK KIEVCH + + + + + + +7.03561 +-0.312694 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 + + + + +8530 8530 8381 8282 8000 7587 6571 5629 4226 2968 2024 1275 717 350 177 115 38 12 3 2 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +8556 8556 8407 8306 8017 7548 6392 5136 3387 1813 994 408 132 67 25 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2586 3423 1631 711 188 11 4 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1738 3187 2276 875 414 54 6 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2550 (charge 3) + +1419.75 +3 + + +154.086 155.082 155.118 157.061 157.109 157.133 158.092 159.076 169.097 169.133 170.1 171.113 172.117 173.092 175.119 181.061 181.097 183.112 183.149 185.056 185.092 187.071 187.107 194.129 195.112 197.129 199.071 199.107 201.124 209.092 +211.143 213.086 217.082 218.15 227.102 228.105 232.14 240.134 245.077 252.134 258.144 266.15 272.172 284.123 286.139 290.986 297.192 305.956 313.26 315.203 324.119 337.186 342.129 343.132 345.215 355.198 361.181 367.16 381.213 383.194 +386.239 395.193 410.235 413.167 415.182 417.244 419.245 426.235 428.284 448.215 452.249 454.764 465.281 483.292 485.299 488.279 503.288 523.288 525.294 558.805 563.242 567.302 580.234 585.331 594.32 611.387 620.337 660.841 663.377 691.378 +709.38 740.434 762.419 802.398 819.47 837.482 839.488 908.52 1005.57 1007.57 + + + + +2 2 3 2 2 2 6 18 78 3 5 47 2 2 16 12 6 5 2 8 6 44 8 12 2 2 8 21 5 8 +3 6 38 17 59 8 9 14 40 6 6 2 9 2 11 3 16 6 5 75 2 13 14 2 3 37 2 2 2 2 +9 5 5 7 6 2 84 8 5 6 2 11 7 85 5 8 12 35 3 11 2 2 5 9 8 27 3 2 3 17 +5 14 2 2 6 100 16 19 22 3 + + + + + + +GRMZM2G124576_P02 seq=translation; coord=1:59670870..59675001:-1; parent_transcript=GRMZM2G124576_T02; parent_gene=GRMZM2G124576 + + + + + + + + +5.68182 +-0.344353 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +4781 4781 4781 4781 4667 3568 3079 2213 1485 1064 366 220 62 19 6 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +4786 4786 4786 4786 4672 3573 3074 2165 1337 902 269 148 45 6 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2030 2097 545 106 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1451 2765 545 20 0 0 5 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2551 (charge 3) + +1838.82 +3 + + +152.057 155.082 157.061 157.097 159.077 167.055 169.098 175.072 175.119 181.098 183.113 185.092 186.124 187.071 194.273 199.072 199.108 203.066 216.097 226.155 230.113 233.165 235.118 240.096 241.092 244.165 247.32 274.103 285.009 287.008 +297.157 300.062 301.06 303.017 315.167 336.278 356.072 357.068 359.121 375.082 379.777 419.259 421.993 470.27 514.223 543.249 548.301 638.347 665.784 678.349 731.305 778.389 844.912 906.455 1007.51 1108.55 1739.84 + + + + +8 7 64 8 16 7 9 42 12 6 7 7 13 45 6 7 11 63 6 62 8 36 8 30 16 32 5 8 16 14 +8 15 39 6 9 6 59 100 14 10 6 14 14 8 9 8 11 9 10 13 10 14 8 13 11 45 10 + + + + + + +GRMZM2G000489_P01 NP_001148081 gibberellin receptor GID1L2 seq=translation; coord=8:14933363..14934823:-1; parent_transcript=GRMZM2G000489_T01; parent_gene=GRMZM2G000489 + + + MSGDTAPHVV EDFFGAIQLL SDGTVVRGDE AALLPPKPFP DVPGVQWKDA + VYDAARGLKV RVYRPTADAG DSKLPVLVHF HGGGYCVGSY DELGGADYLR + RRLAADLPAL VLSVQYRLAP EHRLPAAIED GATFLAWLRG QAALAGAGGA + GAGVEQWLAE SADFARTFLS GVSAGANLAH HLAVRAGSGQ VDLAPARLAG + LVLLSLFLGG VERTATESAP PDGVSLTVAM SDQLWRMALP VGASMDHPLA + NPFGPGSPGL EPVALPPVLV EAPGVDVLRD RVLLYAARLR EMGKDVELAE + FPGEQHGFSV LRWGQANEEL MQILKRFLHR K + + + + + + +5.62602 +-0.321487 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +8010 8010 8010 7522 7245 6765 6160 4821 3613 2210 1083 505 234 98 48 14 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8020 8020 8020 7532 7252 6743 6073 4625 3118 1331 293 60 6 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3145 3311 1174 308 67 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1400 3839 1919 703 123 23 8 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2554 (charge 3) + +1279.63 +3 + + +153.102 154.086 155.081 155.118 157.061 157.097 157.108 158.056 158.092 159.077 166.061 169.097 169.133 170.137 171.076 171.113 173.129 175.072 175.119 176.122 181.096 181.11 182.129 183.113 183.149 184.116 185.117 187.072 187.108 192.077 +194.129 195.113 197.128 198.124 199.071 199.109 201.123 203.066 210.124 212.139 216.135 223.107 226.155 234.145 240.134 244.166 252.136 255.145 262.049 272.17 284.16 290.096 297.057 303.145 309.199 320.171 349.172 352.199 369.225 385.171 +388.182 403.174 406.194 409.856 419.241 426.246 430.739 433.216 438.248 449.25 466.278 472.272 477.229 490.279 497.319 500.252 509.25 529.268 534.255 541.273 561.31 581.779 590.782 592.26 594.375 599.333 601.276 617.34 628.252 634.378 +660.382 663.298 704.337 706.338 784.355 803.405 860.471 875.433 947.427 1058.52 + + + + +3 7 6 8 7 3 6 3 8 16 7 4 35 4 2 10 4 4 36 3 4 5 20 42 18 3 2 13 3 6 +3 7 10 7 3 17 2 8 15 7 30 3 34 100 3 11 3 10 3 8 4 3 3 40 8 21 9 6 23 8 +3 3 16 6 12 41 3 8 3 3 54 2 17 3 12 3 3 3 2 12 4 5 11 8 3 3 3 4 3 2 +2 3 35 3 8 7 8 3 23 4 + + + + + + +conta|P35527|K1CI_HUMAN Keratin, type I cytoskeletal 9 (Cytokeratin 9) (K9) (CK 9) - Homo sapiens (Human). + + + MSCRQFSSSY LTSGGGGGGG LGSGGSIRSS YSRFSSSGGR GGGGRFSSSS + GYGGGSSRVC GRGGGGSFGY SYGGGSGGGF SASSLGGGFG GGSRGFGGAS + GGGYSSSGGF GGGFGGGSGG GFGGGYGSGF GGLGGFGGGA GGGDGGILTA + NEKSTMQELN SRLASYLDKV QALEEANNDL ENKIQDWYDK KGPAAIQKNY + SPYYNTIDDL KDQIVDLTVG NNKTLLDIDN TRMTLDDFRI KFEMEQNLRQ + GVDADINGLR QVLDNLTMEK SDLEMQYETL QEELMALKKN HKEEMSQLTG + QNSGDVNVEI NVAPGKDLTK TLNDMRQEYE QLIAKNRKDI ENQYETQITQ + IEHEVSSSGQ EVQSSAKEVT QLRHGVQELE IELQSQLSKK AALEKSLEDT + KNRYCGQLQM IQEQISNLEA QITDVRQEIE CQNQEYSLLL SIKMRLEKEI + ETYHNLLEGG QEDFESSGAG KIGLGGRGGS GGSYGRGSRG GSGGSYGGGG + SGGGYGGGSG SRGGSGGSYG GGSGSGGGSG GGYGGGSGGG HSGGSGGGHS + GGSGGNYGGG SGSGGGSGGG YGGGSGSRGG SGGSHGGGSG FGGESGGSYG + GGEEASGSGG GYGGGSGKSS HS + + + + + + +6.09555 +-0.348317 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 + + + + +2238 2238 2238 2228 2045 1898 1544 1172 759 384 198 82 50 9 5 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2263 2263 2263 2253 2070 1917 1535 1087 614 199 54 16 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1016 885 231 102 17 4 6 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +499 1189 424 124 11 2 3 11 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2557 (charge 3) + +2091.88 +3 + + +152.057 155.082 159.077 172.072 173.092 175.119 184.071 185.092 193.097 202.082 205.098 217.082 221.09 226.119 233.188 241.093 244.13 246.138 255.146 259.103 298.117 316.125 319.172 343.518 367.135 383.538 421.721 463.225 486.239 520.247 +559.269 575.732 577.269 616.279 675.311 685.298 699.376 703.311 740.332 749.665 794.345 797.356 799.356 838.377 854.373 866.375 911.398 923.411 952.423 981.429 998.424 1055.45 1094.46 1169.49 1440.27 1601.49 + + + + +6 5 5 4 5 20 6 5 5 6 4 5 5 5 4 9 9 5 6 5 5 5 5 6 5 5 23 6 6 22 +8 6 100 9 17 21 8 27 24 8 7 29 7 27 28 20 41 11 11 12 20 9 8 8 7 8 + + + + + + +GRMZM2G432390_P01 B6U3G3 Putative uncharacterized protein seq=translation; coord=3:162813868..162819135:1; parent_transcript=GRMZM2G432390_T01; parent_gene=GRMZM2G432390 + + + MPPPAAMLLL TAASGPPTLS LTLAARRAPL RAPSRRRLRA LRPARIRAAA + AIGGEFGGLG RRRVVVGEFI ERLRNVLPGG SWWRLEDGDE AGDGAGRAEG + SGTTAVSALR RMWALVAGDR LVIYVGFASL VGAALSEIAI PHLLAASIFS + AQNGGAVFYR NAKLLVVLCL VSGVFRYANW LDKLYDVSFR QTVAYGGWSL + SLNYLYHSTQ VIGVVIGGLA IMSGKLTAEQ LTKFTLYAEW LILSTWWIGD + NWSSLMQSVG ASEKVFRLMD LLPSKQLSSE GLKLEKLKGQ IQYADVSFSY + PSRPTVPILG GLNLTLNPNE VVAIVGLSGS GKSTIINLLL RLYEPTNGQI + LIDGVPLTEL DIRWFRERIG FVGQEPRLFR MDISSNIKYG CPRDVSHEEV + IWAAKQAYAH DFIMALPDGY NTIVDDALLS GGQKQRVAIA RALLRDPSIL + LLDEATSALD AESEHYVKSV ITKVSRDSKA KRTVVIIAHR LSTIQTADRI + IVMENGNIVE DGKHIDLIEK GGLYSRLARR QNDDLK + + + + + + +4.07294 +-0.232739 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +1599 1599 1587 1466 1424 1308 957 709 379 250 150 94 56 30 11 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1592 1592 1580 1459 1411 1283 899 563 301 135 63 25 9 1 0 + + + + + + +0 1 2 3 4 + + + + +730 763 85 27 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +555 775 233 34 1 4 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2562 (charge 2) + +1261.53 +2 + + +152.057 152.107 155.081 157.108 157.133 158.093 159.076 169.097 170.045 171.076 171.113 172.117 173.056 173.092 175.119 180.102 183.077 183.113 186.088 186.124 187.072 194.128 197.129 198.087 199.071 199.107 199.181 201.087 204.133 212.103 +215.139 217.083 226.154 228.134 230.077 232.141 236.104 240.136 243.134 245.077 256.092 258.11 266.173 284.086 288.083 301.187 302.099 313.257 340.198 353.109 358.208 360.199 373.135 399.114 417.126 445.24 448.22 464.141 474.184 516.277 +532.247 545.184 581.29 585.325 587.318 603.285 702.342 714.317 717.345 732.328 734.331 821.319 835.385 847.352 888.4 904.376 912.481 936.343 938.506 960.444 1001.38 1019.4 1021.41 1071.48 1088.47 1148.44 + + + + +21 3 10 2 2 9 3 2 2 2 39 2 10 14 19 2 8 3 2 3 9 2 9 4 4 2 2 10 2 3 +100 2 15 3 4 16 4 2 39 12 4 3 2 8 10 15 9 2 2 3 22 97 3 12 3 20 3 3 10 10 +48 3 3 3 4 52 9 15 8 32 2 2 3 12 10 29 3 3 2 3 3 44 8 3 3 8 + + + + + + +GRMZM2G087570_P01 seq=translation; coord=6:44382950..44385913:-1; parent_transcript=GRMZM2G087570_T01; parent_gene=GRMZM2G087570 + + + MAAAAAAATS FTTLAVARSA GQRSLLASKA APSPLLSLRG ARIPSQAVSF + SGGLAASPSH SRARFATSAS AEPKEADLQS KITNKVYFDI SIGNPVGKNV + GRIVIGLYGD DVPQTAENFR ALCTGEKGFG YKGSSFHRVI SDFMIQGGDF + DKGNGTGGKS IYGRTFKDEN FKLVHTGPGV VSMANAGPNT NGSQFFICTV + KTPWLDGRHV VFGQVVEGMD IVRLIESQET DRGDRPKKKV VISECGELPV + V + + + + + +GRMZM2G076544_P01 NP_001149265 peptidyl-prolyl cis-trans isomerase seq=translation; coord=8:135138380..135140767:-1; parent_transcript=GRMZM2G076544_T01; parent_gene=GRMZM2G076544 + + + MAATATSFAT LAVARSAGQR FLLASKAAPS PLLSLRGARL PSQGVSLSGG + LAASPSHSRA RFATSASAEP KEAELQSKIT NKVYFDISIG NPVGKNVGRI + VIGLYGDDVP QTTENFRALC TGEKGFGYKG SSFHRVISDF MIQGGDFDKG + NGTGGKSIYG RTFKDENFKL VHTGPGVVSM ANAGPNTNGS QFFICTVKTP + WLDGRHVVFG QVLEGMDVVS LIESQETDRG DRPKKKVVIS ECGELPVV + + + + + + +4.52144 +-0.220558 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7658 7658 7580 5960 5078 4072 3372 2651 2164 1577 1010 486 281 196 95 77 26 6 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7656 7656 7578 5898 4773 3633 2872 2064 1510 892 451 79 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4162 2901 498 90 6 1 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1357 3999 1862 373 64 3 8 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2563 (charge 2) + +1643.83 +2 + + +151.061 152.057 157.108 175.118 176.285 199.07 199.163 199.181 202.082 216.097 227.176 228.179 244.166 254.16 272.172 300.663 327.129 329.157 338.021 341.218 345.141 356.217 364.711 383.239 400.266 408.702 443.247 456.171 472.75 485.258 +503.223 523.237 529.253 572.314 580.767 601.303 614.802 636.302 644.813 669.848 680.297 687.344 692.319 700.84 702.345 709.85 711.387 728.421 749.366 758.373 759.88 766.39 792.898 801.409 804.907 813.911 823.422 916.42 927.467 1056.51 +1146.57 1172.59 1185.56 1227.55 1244.58 1246.58 1261.6 1272.57 1358.64 1383.64 1400.64 + + + + +1 1 2 1 2 2 2 58 2 4 30 2 15 3 13 8 3 2 2 3 7 8 35 4 40 3 2 3 8 2 +2 4 2 9 8 3 2 8 31 2 2 13 3 43 3 10 9 19 8 100 7 2 3 8 4 66 78 7 3 8 +3 3 2 4 35 4 4 9 8 4 11 + + + + + + +GRMZM2G122937_P01 NP_001159012 remorin seq=translation; coord=2:22990515..22995670:1; parent_transcript=GRMZM2G122937_T01; parent_gene=GRMZM2G122937 + + + + + + + +GRMZM2G122937_P03 NP_001159012 remorin seq=translation; coord=2:22990515..22995246:1; parent_transcript=GRMZM2G122937_T03; parent_gene=GRMZM2G122937 + + + + + + + +GRMZM2G122937_P02 NP_001159012 remorin seq=translation; coord=2:22990515..22995669:1; parent_transcript=GRMZM2G122937_T02; parent_gene=GRMZM2G122937 + + + + + + + + +3.78937 +-0.204831 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +5962 5962 5962 5954 4160 3791 2547 2056 1688 1314 918 600 259 154 86 36 6 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5968 5968 5968 5960 4166 3752 2436 1970 1505 1118 737 468 134 73 35 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3718 1978 251 22 0 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1168 4107 618 69 5 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2564 (charge 2) + +1419.75 +2 + + +157.061 169.097 171.076 171.113 172.115 175.119 185.056 187.072 187.108 199.071 199.108 214.156 217.082 227.102 240.134 245.077 286.139 297.193 315.203 337.185 342.13 355.199 387.186 395.193 403.072 415.183 419.247 426.234 454.229 483.292 +503.289 509.592 523.289 554.893 558.804 593.371 599.404 611.386 645.794 691.373 709.351 740.427 837.483 839.483 859.462 908.526 1005.58 1007.58 1067.2 1249.63 + + + + +5 61 8 56 5 4 8 32 5 4 7 5 14 46 8 48 100 15 78 8 9 55 8 5 4 15 49 5 5 89 +7 5 40 9 15 4 8 25 5 19 4 6 72 5 5 12 71 7 5 5 + + + + + + +GRMZM2G137528_P01 NP_001140953 hypothetical protein LOC100273032 seq=translation; coord=5:158605385..158610074:1; parent_transcript=GRMZM2G137528_T01; parent_gene=GRMZM2G137528 + + + MATVAMDISK PTPVASGDEA AAAAKGRSGG GGEGLRQYYL QHIHDLQLQI + RQKTHNLNRL EAQRNDLNSR VRMLREELQL LQEPGSYVGE VVKVMGKSKV + LVKVHPEGKY VVDIDKSIDI TKITPSTRVA LRNDSYMLHL ILPSKVDPLV + NLMKVEKVPD STYDMIGGLD QQIKEIKEVI ELPIKHPELF ESLGIAQPKG + VLLYGPPGTG KTLLARAVAH HTDCTFIRVS GSELVQKYIG EGSRMVRELF + VMAREHAPSI IFMDEIDSIG SARMESGTGN GDSEVQRTML ELLNQLDGFE + ASNKIKVLMA TNRIDILDQA LLRPGRIDRK IEFPNPNEDS RFDILKIHSR + KMNLMRGIDL KKIAEKMNGA SGAELKAVCT EAGMFALRER RVHVTQEDFE + MAVAKVMKKD TEKNMSLRKL WK + + + + + +GRMZM2G137528_P02 NP_001140953 hypothetical protein LOC100273032 seq=translation; coord=5:158605242..158609659:1; parent_transcript=GRMZM2G137528_T02; parent_gene=GRMZM2G137528 + + + MATVAMDISK PTPVASGDEA AAAAKGRSGG GGEGLRQYYL QHIHDLQLQI + RQKTHNLNRL EAQRNDLNSR VRMLREELQL LQEPGSYVGE VVKVMGKSKV + LVKVHPEGKY VVDIDKSIDI TKITPSTRVA LRNDSYMLHL ILPSKVDPLV + NLMKVEKVPD STYDMIGGLD QQIKEIKEVI ELPIKHPELF ESLGIAQPKG + VLLYGPPGTG KTLLARAVAH HTDCTFIRVS GSELVQKYIG EGSRMVRELF + VMAREHAPSI IFMDEIDSIG SARMESGTGN GDSEVQRTML ELLNQLDGFE + ASNKIKVLMA TNRIDILDQA LLRPGRIDRK IEFPNPNEDS RFDILKIHSR + KMNLMRGIDL KKIAEKMNGA SGAELKAVCT EAGMFALRER RVHVTQEDFE + MAVAKVMKKD TEKNMSLRKL WK + + + + + +GRMZM2G107362_P02 NP_001142276 hypothetical protein LOC100274445 seq=translation; coord=4:231475847..231481286:1; parent_transcript=GRMZM2G107362_T02; parent_gene=GRMZM2G107362 + + + MATVAMDISK PTPAASGDEA AAAAKGRSGG GGEGLRQYYL QHIHDLQLQI + RQKTHNLNRL EAQRNDLNSR VRMLREELQL LQEPGSYVGE VVKVMGKSKV + LVKVHPEGKY VVDIDKSIDI TKITPSTRVA LRNDSYMLHL ILPSKVDPLV + NLMKVEKVPD STYDMIGGLD QQIKEIKEVI ELPIKHPELF ESLGIAQPKG + VLLYGPPGTG KTLLARAVAH HTDCTFIRVS GSELVQKYIG EGSRMVRELF + VMAREHAPSI IFMDEIDSIG SARMESGTGN GDSEVQRTML ELLNQLDGFE + ASNKIKVLMA TNRIDILDQA LLRPGRIDRK IEFPNPNEDS RFDILKIHSR + KMNLMRGIDL KKIAEKMNGA SGAELKAVCT EAGMFALRER RVHVTQEDFE + MAVAKVMKKD TEKNMSLRKL WK + + + + + +GRMZM2G107362_P04 NP_001142276 hypothetical protein LOC100274445 seq=translation; coord=4:231475809..231481211:1; parent_transcript=GRMZM2G107362_T04; parent_gene=GRMZM2G107362 + + + MATVAMDISK PTPAASGDEA AAAAKGRSGG GGEGLRQYYL QHIHDLQLQI + RQKTHNLNRL EAQRNDLNSR VRMLREELQL LQEPGSYVGE VVKVMGKSKV + LVKVHPEGKY VVDIDKSIDI TKITPSTRVA LRNDSYMLHL ILPSKVDPLV + NLMKVEKVPD STYDMIGGLD QQIKEIKEVI ELPIKHPELF ESLGIAQPKG + VLLYGPPGTG KTLLARAVAH HTDCTFIRVS GSELVQKYIG EGSRMVRELF + VMAREHAPSI IFMDEIDSIG SARMESGTGN GDSEVQRTML ELLNQLDGFE + ASNKIKVLMA TNRIDILDQA LLRPGRIDRK IEFPNPNEDS RFDILKIHSR + KMNLMRGIDL KKIAEKMNGA SGAELKAVCT EAGMFALRER RVHVTQEDFE + MAVAKVMKKD TEKNMSLRKL WNGSAFISIS FTKAVEWCNG MLWTMLSQVA + PRMLMFKIFL ITAVVCCCKV DWIYQIS + + + + + +GRMZM2G107362_P01 NP_001142276 hypothetical protein LOC100274445 seq=translation; coord=4:231479786..231481291:1; parent_transcript=GRMZM2G107362_T01; parent_gene=GRMZM2G107362 + + + MDEIDSIGSA RMESGTGNGD SEVQRTMLEL LNQLDGFEAS NKIKVLMATN + RIDILDQALL RPGRIDRKIE FPNPNEDSRF DILKIHSRKM NLMRGIDLKK + IAEKMNGASG AELKAVCTEA GMFALRERRV HVTQEDFEMA VAKVMKKDTE + KNMSLRKLWK + + + + + + +6.06837 +-0.418508 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +1311 1311 1311 1311 1311 1275 1225 1148 1007 426 217 62 15 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +1325 1325 1325 1325 1325 1289 1237 1160 1014 393 182 46 11 5 1 0 + + + + + + +0 1 2 3 + + + + +890 406 36 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +304 915 101 4 0 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2565 (charge 2) + +1466.62 +2 + + +152.057 157.061 158.093 159.076 172.072 175.119 188.074 191.18 199.071 216.099 226.155 233.095 242.3 244.064 245.606 261.091 286.152 292.878 303.178 348.122 402.247 531.288 600.309 618.32 790.369 838.511 904.402 961.431 982.328 1062.47 +1120.5 1182.4 1206.54 + + + + +11 12 9 16 9 79 55 7 11 11 15 100 7 10 8 74 17 7 43 14 51 16 10 98 80 9 28 75 9 9 +14 10 60 + + + + + + +GRMZM2G318635_P01 seq=translation; coord=5:213291570..213301733:-1; parent_transcript=GRMZM2G318635_T01; parent_gene=GRMZM2G318635 + + + MAPKAGKAKP KARGDRKKKE EKVLPTVLDV TVETPDYTLL TLKGISTDRI + LDIRKLLAVH VDTCHLTSFS LSHEVRGGQL KDTVEIAALK PCHLTIVEED + YTEELAVAHV RRLLDIVACT TVFGAKKPEP KPDAADAAAE SAKAGSPSPG + KTAPGGGEEP MYPPPKLEQF YDFFTFSHLT PPLHYIRRSS RPFVDDKRED + DFFQIDVRVC NGKPVTIVAS QEGFYPAGKR ALISRSLVGL LQQTSRAFDG + AYKALMKAFV EHNKFGNLPY GFRSNTWVAP PVVADSPSVF PPLPTEDETW + GGSGGGQGRD GKHDHRPWVK EFAILAAMPC KTAEERQIRD RKAFLLHSLF + VDVAVLKAVA SIQQLISNHT SLHETENGTI GSVLHTEQVG DMKIMITKDK + TDASSKLDVK LDGSQAPGMS SDELAQRNLL KGITADESAT VHDTATLGVV + IVKHCGYTAV VQVPVDTELP AASVAQQEIH IEDQPEGGSN ALNVNSLRML + LHKSCAQAPG VQRLQTSDPQ DNEATQTFVR KILTDSLQKL ENEVPIVTRP + IRWELGACWV QHLQNPTSEK TETKKSDETK DVPTVKGLGK QFGQLKEIKK + KTDDKGGKGT YVKGNNSPNT DNGHTDNTAS VKDDKDIILQ RLLPEAAFQR + LKESETGLHV KSLDELIEMS HKYYDDTALP KLVADFGSLE LSPVDGRTLT + DFMHTRGLQM RSLGRVVELS DKLPHIQSLC IHEMVVRAFK HIVRAVIAAV + DDINDMADSV ASCLNILLGP FLEENNDKDC GEDHNLRKRW LEVFLIKRFG + WKWKDEYCLD LRKYAILRGL CHKVGLELIT KDYDMDMPNP FRKSDIISVV + PIYKHVACSS ADGRTLLESS KTFLDKGKLE DAVSYGTKAL AKLVAVCGPY + HRMTAGAYSL LAVVLYHTGD FNQATIYQQK ALDINERELG LDHPDTMKSY + GDLAVFYYRL QHTELALKYV NRALYLLHLT CGPSHPNTAA TYINVAMMEE + GLGNVHVALR YLHEALKCNQ RLLGADHIQT AASYHAIAIA LSLMEAYSLS + VQHEKTTLRI LQAKLGSEDL RTQDASAWLE YFESKALEQQ EAARNGTPKP + DASIASRGHL SVSDLLDYIN PDDELKAKEM QRKQVRAKIK GRTGQNQSEL + VDDEDQRSPA PNNDKNLLTE NGNSGVKENG TFVEHVKDEI SSDTAIHIPQ + DGFTEECTSD EGWQAAVPKG RSTGSRRTGA GTRRPNLAKI NTSSLNSENG + RYKGRGISNF SSPRVSPSEA AVSIGSRPLA KKLAKSSSFN SKAVSTAVSS + NTGENSFNLN SKPASPAIAT AAAKVIPSTT PSASQTVRKS LSYKEVAIAA + PGTLAKASSD VHTEEKDTGD QGASPESSNS KSPKEINGHP SGEKDGAIEV + SPQDDTSQVS KSPDGGKPEQ TDVLIGSNQP DTVHKKSSDP AETSVAKDID + LPAPVISSGT QTEADTPNDE APTAIEANDS SSNDDERDSG ADTPEQLSSG + GENEKSSLSE SEKNDTPREG AKETTSKLSA AAAPFNPSSV PAFGSMAVPG + FREHGGLLPS PANVPPMLSI PLRKHPHQSA TARVPYGPRL AGGYNRSGHR + GLRKKPVLTS GEAPTETNTS GPRIMNPNAP EFVPGQSRSP NGHPASPNGP + LASPGGIPSS PQDLLSSPDS TLESPVTASP QVSECSQISP EGDVEGVGVK + QNMDDTNHPE SKDGEVEPEQ TKAPEGTEEG AAVKDAAEEL IAAEQPKSWA + DYSDGEVEVV EVAS + + + + + + +4.51323 +-0.257899 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +3306 3306 3306 3306 3143 1952 1570 1071 607 397 209 116 64 22 9 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3285 3285 3285 3285 3122 1930 1513 977 524 291 130 41 1 0 + + + + + + +0 1 2 3 4 + + + + +2071 1111 123 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +683 2414 194 15 2 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2567 (charge 2) + +1403.64 +2 + + +155.082 161.334 171.113 173.092 175.119 181.096 183.075 185.091 187.071 199.071 199.108 201.087 213.087 216.097 241.082 256.094 258.108 274.103 284.172 299.135 329.193 345.14 366.494 380.001 484.73 493.245 530.259 631.316 642.457 654.273 +732.361 861.41 962.461 986.432 1016.48 1059.51 1061.49 1128.57 1131.5 + + + + +9 5 23 7 10 8 5 7 25 8 23 52 7 8 6 9 20 85 9 9 10 11 5 6 6 5 10 12 7 6 +36 39 53 7 7 100 8 6 7 + + + + + + +GRMZM2G353213_P01 NM_001157997 translocon Tic40 (LOC100285102), mRNA seq=translation; coord=10:117993529..118000841:-1; parent_transcript=GRMZM2G353213_T01; parent_gene=GRMZM2G353213 + + + MQQAFKSMMT QSAPNSFGSN SPFPFSMPPQ ASPTAPSTYP YLEPKKDTSP + HVSTVDVSAN EVEATGTSKE VDVTETPKPS KKFAFVDVSP EELQQKNLQS + SPETVDVKHD STYSESKEDT EEQVPTISTN TESKEDTEEK VPTNGASFKL + NEGAAHGPTE SNNSASMLSV ETIEKMMEDP AVQKMVYPYL PEEMRNPNSF + KWMLQNPMYR QQLQDMLNNM GATPDQWDNR MLDHLKNFDL SSPEVRQQFA + QVGMTPEEVV SKIMANPDVA VAFQNPKIQT AIMDCSQNPL NIVKYQNDKE + VMDVFMKISQ IFPQING + + + + + +GRMZM2G353213_P02 NM_001157997 translocon Tic40 (LOC100285102), mRNA seq=translation; coord=10:117993529..118000841:-1; parent_transcript=GRMZM2G353213_T02; parent_gene=GRMZM2G353213 + + + MESLILASSC SASPRLPLLS SAARFRGLPV SVPPPSSASI SGAARKGPMR + PRLFVAAAAA PRGSGNVFEG LRAKGFASMS SSTGNENMST GTGTLPPMPP + TSSYIGSPVF WIGVGVALSV AFTTVSSMLK RYAMQQAFKS MMTQSAPNSF + GSNSPFPFSM PPQASPTAPS TYPYLEPKKD TSPHVSTVDV SANEVEATGT + SKEVDVTETP KPSKKFAFVD VSPEELQQKN LQSSPETVDV KHDSTYSESK + EDTEEQVPTI STNTESKEDT EEKVPTNGAS FKLNEGAAHG PTESNNSASM + LSVETIEKMM EDPAVQKMVY PYLPEEMRNP NSFKWMLQNP MYRQQLQDML + NNMGATPDQW DNRMLDHLKN FDLSSPEVRQ QFAQVGMTPE EVVSKIMANP + DVAVAFQNPK IQTAIMDCSQ NPLNIVKYQN DKEVMDVFMK ISQIFPQING + + + + + + +AC204045.3_FGP005 seq=translation; coord=10:24601518..24602602:-1; parent_transcript=AC204045.3_FGT005; parent_gene=AC204045.3_FG005 + + + MEQAFKSMMT QAPPNSFGSN SSFPFGMPQQ AYPTAPSSFS YLELKKDTSP + QVSTVDVSAT EVDAAGTSKE VDVTETPKPS KKFAFVDVSP EDLRQKDLQS + SLEMVDVKHD STESETKEDT EEKAPTNGVT FKLNEDAARG PTESSQSGPM + LSVETIEKMM EDPAVQKMVY P + + + + + + +5.25933 +-0.300533 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +7403 7403 7403 7329 7016 6755 6373 5782 4333 3323 1947 1144 524 178 74 30 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7413 7413 7413 7339 7026 6760 6338 5598 3915 2743 1143 373 77 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2039 3141 1633 509 86 8 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1734 3457 1666 452 94 5 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2569 (charge 3) + +1457.78 +3 + + +152.057 155.082 155.118 156.102 157.134 158.093 159.077 169.097 172.072 172.108 173.129 175.119 176.123 183.113 184.072 184.117 185.091 187.071 187.108 188.111 193.097 194.102 197.103 199.108 201.123 203.103 211.107 213.086 215.101 221.092 +226.155 227.102 229.093 231.098 233.093 241.094 244.165 254.124 260.035 276.636 278.113 286.115 289.163 290.115 298.141 311.145 313.186 316.15 326.135 327.202 332.145 342.724 346.185 360.184 393.247 397.206 403.204 441.283 448.767 456.231 +459.293 485.26 499.29 505.241 508.294 513.253 525.249 533.758 538.339 542.281 546.769 557.827 562.266 566.27 570.277 575.28 584.288 587.389 590.777 597.263 599.302 601.307 615.34 619.287 627.297 647.798 657.313 666.432 684.441 719.357 +737.336 762.366 785.489 794.356 804.369 869.476 914.531 1015.58 1104.49 1120.48 + + + + +16 5 6 5 4 19 8 8 12 6 6 49 4 100 9 9 9 4 66 5 25 4 4 11 52 27 21 7 15 19 +49 8 7 35 4 5 13 6 6 4 4 5 4 3 10 4 20 8 13 4 9 5 4 4 10 5 17 7 5 5 +41 5 12 10 16 5 4 7 10 8 8 4 10 5 6 37 5 6 9 7 25 6 5 16 33 30 4 6 39 6 +5 5 19 10 5 5 6 11 5 4 + + + + + + +GRMZM2G044132_P01 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53846005:1; parent_transcript=GRMZM2G044132_T01; parent_gene=GRMZM2G044132 + + + + + + + +GRMZM2G044132_P02 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53845943:1; parent_transcript=GRMZM2G044132_T02; parent_gene=GRMZM2G044132 + + + + + + + + +4.83413 +-0.333388 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + + + + +1518 1518 1518 1514 1399 1299 1143 972 753 535 251 75 19 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1528 1528 1528 1524 1409 1302 1143 961 719 487 182 36 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +659 612 212 41 4 0 + + + + + + +0 1 2 3 4 5 6 + + + + +378 721 380 40 3 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2574 (charge 3) + +1513.61 +3 + + +155.081 156.077 157.097 158.092 159.077 164.118 166.061 167.055 168.056 169.097 170.092 171.076 171.113 173.071 173.092 173.129 175.119 181.06 181.109 183.113 183.149 184.152 186.088 187.071 187.108 192.077 192.113 193.097 194.129 195.113 +197.128 198.088 199.071 199.108 199.181 201.123 204.135 209.105 211.144 213.087 216.098 226.155 229.118 230.12 235.119 237.135 240.097 244.166 254.162 267.109 272.172 278.082 299.061 301.059 313.115 318.194 320.136 327.13 330.191 338.146 +345.977 359.028 361.025 364.161 369.223 383.217 388.194 400.986 406.204 409.222 416.037 418.995 431.743 437.218 440.192 458.204 481.297 498.324 499.324 552.248 555.212 569.268 573.226 576.297 623.342 635.378 636.384 647.351 649.355 692.37 +732.389 734.387 764.417 812.358 844.459 861.48 862.482 864.483 1071.61 1072.63 + + + + +4 6 4 12 14 7 12 72 14 11 4 6 7 5 7 4 65 7 27 13 58 17 5 17 4 20 4 5 5 12 +5 4 4 23 6 40 4 42 16 5 13 35 27 6 14 6 11 29 27 6 19 7 60 37 5 14 14 4 10 10 +18 23 4 15 16 4 5 11 52 19 12 100 26 11 4 4 7 62 26 6 13 35 6 4 7 15 6 6 4 14 +5 10 4 6 5 39 38 4 16 24 + + + + + + +GRMZM2G423137_P01 NP_001145083 hypothetical protein LOC100278290 seq=translation; coord=4:238355940..238357484:-1; parent_transcript=GRMZM2G423137_T01; parent_gene=GRMZM2G423137 + + + MAAPLTAVRA RLLLLPVTCT AAGTTGRPAP PSKSSRPRLL PPGTTRCRCS + RPPMEAVAPV SAAAVAALLL LPADAALAVG GELGILEGRS FALLHPLIMG + GLFAYTLWAG YLGWQWRRVR TVQDEINALK KQLKPAAAAT PAAVGAGADS + SSTTTPPPAA ASKSPSPAEA RIEELTDERK ALLKGSFRDR HFNAGSLLLG + LGVLESVGGA LNTWFRTGKL FPGPHLFAGA AITVLWAAAA ALVPAMQKGD + ETARSLHIAL NAVNVLLFVW QIPTGLEIVG KVFEFTTWP + + + + + + +5.35038 +-0.368992 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + + + + +5848 5848 5848 5816 2818 2298 793 304 162 44 22 11 2 1 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5846 5846 5846 5814 2816 2280 777 262 140 36 18 2 1 1 0 + + + + + + +0 1 2 3 + + + + +4538 1291 20 0 + + + + + + +0 1 2 3 4 5 6 + + + + +891 4892 65 0 0 1 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2576 (charge 2) + +1616.78 +2 + + +152.057 168.007 171.077 175.119 185.092 195.113 203.066 212.169 216.099 226.082 240.135 244.095 278.493 300.169 305.18 313.619 315.128 356.159 425.17 544.312 641.367 738.416 839.46 875.912 + + + + +5 3 6 5 3 4 4 3 4 4 6 4 4 4 5 4 7 5 6 7 31 100 7 7 + + + + + + +GRMZM5G813217_P01 NP_001146412 hypothetical protein LOC100279992 seq=translation; coord=7:129966857..129971449:-1; parent_transcript=GRMZM5G813217_T01; parent_gene=GRMZM5G813217 + + + MAPALSRTLG PSSVAALRPS PSCRGLLRAA LAPQGRGASA RCAVGVRWEA + ARRRRMAGVR CDAAVAEKPA GEEETAGEKY EYQAEVTRLM DLIVHSLYSH + KEVFLRELVS NASDALDKLR FLSVTDPSVL ADGGELEIRI KPDLEAGTIT + ITDTGIGMTK DELKDCLGTI AQSGTSKFLK ALKENKDLGA DNGLIGQFGV + GFYSAFLVAE RVVVSTKSPK ADKQYVWEAE ADSSSYVIKE ENDPEKMLSR + GTEITLYLRD DDKYEFADPT RIQGLVKNYS QFVSFPIYTW QEKSRTVEVE + EEEESKGEEA TEESKSEEAT EGEKQKKKKT ITEKYWDWEL ANETKPIWMR + NPKEVEKTEY NEFYKKTFNE FLDPLAYTHF TTEGEVEFRS VLYVPGMAPL + SNEEIMNPKT KNIRLYVKRV FISDDFDGEL FPRYLSFVKG VVDSNDLPLN + VSREILQESR IVRIMRKRLV RKTFDMIQEI AEKDGKEDYN KFWESFGKFM + KLGCIEDTGN HKRLAPLLRF YSSKNETDLI SLDQYVENMP ENQKAIYYIA + TDSLQSAKTA PFLEKLVQKD IEVLYLIEPI DEVAIQNLQT YKEKKFVDIS + KEDLELGDED EDKEKESKQE YTLLCDWIKQ QLGDKVAKVQ ISKRLSSSPC + VLVSGKFGWS ANMERLMKAQ TLGDTSSLEF MRGRRIFEIN PDHPIIKDLN + AACKNEPEST EAKRAAELLY EAALISSGYT VSAANPRACC WPIYDCEYDV + IVHLCYPA + + + + + +GRMZM5G813217_P02 NP_001146412 hypothetical protein LOC100279992 seq=translation; coord=7:129966717..129971449:-1; parent_transcript=GRMZM5G813217_T02; parent_gene=GRMZM5G813217 + + + MAPALSRTLG PSSVAALRPS PSCRGLLRAA LAPQGRGASA RCAVGVRWEA + ARRRRMAGVR CDAAVAEKPA GEEETAGEKY EYQAEVTRLM DLIVHSLYSH + KEVFLRELVS NASDALDKLR FLSVTDPSVL ADGGELEIRI KPDLEAGTIT + ITDTGIGMTK DELKDCLGTI AQSGTSKFLK ALKENKDLGA DNGLIGQFGV + GFYSAFLVAE RVVVSTKSPK ADKQYVWEAE ADSSSYVIKE ENDPEKMLSR + GTEITLYLRD DDKYEFADPT RIQGLVKNYS QFVSFPIYTW QEKSRTVEVE + EEEESKGEEA TEESKSEEAT EGEKQKKKKT ITEKYWDWEL ANETKPIWMR + NPKEVEKTEY NEFYKKTFNE FLDPLAYTHF TTEGEVEFRS VLYVPGMAPL + SNEEIMNPKT KNIRLYVKRV FISDDFDGEL FPRYLSFVKG VVDSNDLPLN + VSREILQESR INYA + + + + + + +7.76038 +-0.360948 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +11334 11334 11334 11110 10755 10262 8744 7334 5332 3710 2350 1438 667 345 156 46 15 3 2 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +11345 11345 11345 11121 10766 10243 8660 6923 4440 2407 1153 326 102 44 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3696 4612 2045 839 135 14 3 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1650 5308 2932 1123 255 67 8 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2578 (charge 3) + +1686.82 +3 + + +155.082 155.118 159.076 167.081 169.097 169.134 171.113 173.092 175.119 178.086 179.091 181.06 185.093 187.071 187.109 195.076 195.113 197.129 198.088 199.072 199.108 199.181 201.125 204.134 209.091 213.088 216.098 219.116 221.103 223.108 +226.155 230.113 234.144 238.118 240.134 242.15 244.165 249.098 251.102 256.128 258.145 267.109 269.124 276.155 300.155 307.669 310.193 327.168 328.114 333.177 341.145 345.213 347.217 352.164 355.159 359.155 361.15 369.18 380.16 402.403 +404.214 418.714 427.717 438.237 443.238 460.252 467.708 487.241 493.247 505.261 509.23 516.285 518.285 533.239 559.319 584.288 596.32 614.336 615.337 623.301 634.304 653.34 684.336 696.283 723.329 726.373 743.376 763.34 822.41 855.414 +909.44 941.458 949.411 959.468 1020.45 1022.45 1099.48 1117.5 1119.51 1231.91 + + + + +20 14 6 4 14 8 40 8 16 21 5 6 4 7 5 7 6 24 4 3 27 23 10 3 4 8 23 8 8 45 +55 6 19 6 68 16 16 14 8 5 24 8 36 6 4 6 4 7 6 24 4 69 14 4 13 6 15 4 4 4 +17 8 7 4 5 5 4 4 4 29 5 7 6 5 12 6 8 99 100 17 17 5 5 6 5 19 8 8 6 18 +5 5 16 24 19 6 8 95 18 5 + + + + + + +GRMZM2G148744_P01 NP_001140409 hypothetical protein LOC100272465 seq=translation; coord=1:193791442..193794419:-1; parent_transcript=GRMZM2G148744_T01; parent_gene=GRMZM2G148744 + + + MVKYSQEPGN PTKSAKAMGR DLRVHFKNTR ETAFALRKLS LTKAKRYLED + VIAHKQAIPF RRYCGGVGRT AQAKSRHSNG QGRWPVKSAR FILDLLKNAE + SNADVKGLDV DNLYVSHIQV NQAQKQRRRT YRAHGRINPY MSSPCHIELI + LSEKEEPVKK EADNIVAARK Q + + + + + +GRMZM2G702426_P01 O48557 60S ribosomal protein L17 seq=translation; coord=4:44061937..44064386:-1; parent_transcript=GRMZM2G702426_T01; parent_gene=GRMZM2G702426 + + + MVKYSQEPGN PTKSAKAMGR DLRVHFKNTR ETAFALRKLP LTKAKRYLED + VIAHKQAIPF RRYCGGVGRT AQAKSRHSNG QGRWPVKSAR FILDLLKNAE + SNADVKGLDV DNLYVSHIQV NQAQKQRRRT YRAHGRINPY MSSPCHIELI + LSEKEEPVKK EADNIVAARK Q + + + + + + +4.92773 +-0.266364 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +4647 4647 4561 3533 3099 2297 1614 1127 817 381 193 135 63 36 19 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4618 4618 4532 3496 2971 2025 1255 840 566 137 41 1 0 0 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2764 1602 259 26 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +711 3017 799 84 37 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2585 (charge 2) + +1120.53 +2 + + +153.066 155.082 164.071 167.082 170.093 171.076 171.113 172.072 172.109 175.087 175.119 178.086 179.09 181.061 181.097 185.092 188.07 193.097 195.076 198.087 199.072 199.108 199.181 205.098 209.093 212.103 216.098 223.108 226.083 230.114 +233.092 238.083 241.082 244.166 248.161 251.102 252.106 258.109 269.125 292.128 295.141 307.169 310.104 327.203 331.16 335.135 345.213 349.152 352.161 355.125 361.15 366.178 380.156 398.207 426.715 432.189 442.23 450.201 459.255 467.227 +481.242 485.236 491.187 499.251 508.211 516.279 527.246 578.293 596.307 597.306 613.331 615.337 706.351 724.362 742.376 853.409 870.422 957.462 + + + + +1 10 1 2 2 1 9 3 3 3 1 23 3 8 3 1 2 1 7 5 4 13 1 4 3 9 27 49 3 12 +8 2 12 2 14 15 3 14 44 1 1 22 4 12 1 5 78 2 3 2 14 5 6 3 6 2 6 4 9 5 +1 4 1 2 6 13 2 1 9 3 100 7 1 14 7 8 1 6 + + + + + + +GRMZM2G067789_P01 seq=translation; coord=5:45333604..45337777:1; parent_transcript=GRMZM2G067789_T01; parent_gene=GRMZM2G067789 + + + MASHPPPAEP SSKSNKGQSE HEEIHVSSGG VLAYTDDDDC ESRRPLLLRT + PASAECYSVS AAVFPFLFPA LGGLLYGYDI GATSGATISL KSSTFSGTTW + YNLSSVQTGL VVSGSLYGAL IGSVLAYTIA DFLGRRKELI LASISYFIGA + FLTAVAPNFT IMVVGRFLYG IGIGLAMHAA PMYIAETAPS QIRGMLISLK + EFFIVLGMLL GYIAGNLYVE VVSGWRYMYA SSTPLCLIMG VGMCWLPSSP + RWLLLCAIQG KGNLPETKEN ATRCLCRLRG QASPDLVSEQ IDLILEELSY + IDQEKQASFG EIFQGKCLKA MIIGCGLVFF QQVTGQPSVL YYAATIFQSA + GFSGASDATR VSILLGLLKL IMTGVAVLVV DRLGRRPLLI GGVSGITVAL + FLLSSYYTLL KDASYVAVIA LLLYVGCYQL SFGPIGWLMI SEVFPLRLRG + RGLGVAVLVN FASNALVTFA FSPLEDLIGT GALFSGFGVI AVASLAFIFW + IVPETKGLTL EEIEASL + + + + + + + +6.68256 +-0.342695 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +5926 5926 5926 5926 5907 5570 5402 4950 3371 2115 1215 694 320 165 46 16 7 5 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5922 5922 5922 5922 5903 5566 5390 4912 3127 1828 825 290 51 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3086 2403 407 32 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1092 3965 753 112 4 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2586 (charge 2) + +1246.61 +2 + + +152.057 155.081 157.097 159.077 160.853 167.056 167.081 167.094 167.118 169.097 169.133 170.102 171.077 173.092 173.128 175.119 179.093 181.061 183.076 185.092 185.165 186.089 186.123 187.071 195.089 195.113 197.104 197.128 198.124 199.108 +199.181 201.087 209.091 214.118 216.099 218.151 226.155 227.103 234.145 239.095 241.081 244.166 248.383 254.113 259.093 272.125 285.157 292.141 298.14 310.151 313.114 320.135 338.146 343.234 356.145 363.205 367.196 395.194 406.714 418.23 +427.182 455.243 464.25 474.18 476.24 492.245 548.281 573.288 598.507 647.35 684.322 715.361 717.348 807.417 812.415 829.376 831.36 839.944 909.466 + + + + +29 23 12 10 6 12 13 7 10 54 10 7 7 12 12 42 22 7 11 12 8 6 7 10 10 29 68 5 7 29 +12 37 8 58 9 11 41 39 47 42 20 37 6 8 8 11 9 36 26 84 6 39 82 11 30 9 10 56 23 82 +14 10 8 9 6 76 13 56 7 10 21 57 14 8 89 10 9 7 100 + + + + + + +GRMZM5G841727_P01 NP_001169429 hypothetical protein LOC100383299 seq=translation; coord=2:204033977..204034756:1; parent_transcript=GRMZM5G841727_T01; parent_gene=GRMZM5G841727 + + + MSFSPERVRV RGRSPAFTAL AANFESSSNR NLSTPPPVVK KLYPKSVTPD + PSNTASKSPA IAALAGSLDH PSQTPALEFM KGGSESEKPK QEGDGKEGVD + TVATRVESLT INEDVKENEP EDDEGLPIYL YERLKTTAAD PVTEIDVTRR + ETYLSSTEFK EKFGINCSST FLA + + + + + +GRMZM5G841727_P02 NP_001169429 hypothetical protein LOC100383299 seq=translation; coord=2:204033977..204035117:1; parent_transcript=GRMZM5G841727_T02; parent_gene=GRMZM5G841727 + + + MSFSPERVRV RGRSPAFTAL AANFESSSNR NLSTPPPVVK KLYPKSVTPD + PSNTASKSPA IAALAGSLDH PSQTPALEFM KGGSESEKPK QEGDGKEGVD + TVATRVESLT INEDVKENEP EDDEGLPIYL YERLKTTAAD PVTEIDVTRR + ETYLSSTEFK EKFGMTKEAF SKLPKWKQNR LKIALQLF + + + + + + +3.6886 +-0.210777 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 + + + + +5768 5768 4615 4331 3211 2628 1694 1198 777 519 306 211 100 48 24 8 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5794 5794 4641 4297 3058 2297 1358 869 557 268 154 59 28 17 1 0 + + + + + + +0 1 2 3 4 + + + + +3023 2323 409 40 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +995 3706 853 198 24 9 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2590 (charge 2) + +1203.58 +2 + + +152.057 153.102 155.082 157.097 159.078 159.113 160.079 160.116 167.082 169.097 171.022 171.076 171.113 173.092 175.107 175.119 180.061 181.098 185.092 187.072 187.108 188.111 189.088 198.123 199.108 199.181 201.123 203.103 204.612 213.087 +216.045 218.15 226.154 227.103 231.098 234.145 236.104 239.096 243.134 244.129 250.12 252.099 254.113 270.145 272.125 284.123 288.153 296.124 299.137 305.183 315.203 332.15 341.143 352.683 355.16 368.193 372.225 373.225 382.173 397.173 +400.185 406.23 419.182 443.262 453.208 458.721 471.221 478.244 491.255 509.254 514.299 520.27 585.337 607.307 686.386 704.358 706.362 712.358 815.431 819.38 916.449 918.453 1017.49 1034.17 1104.56 1135.14 + + + + +2 1 2 3 2 100 1 7 2 7 1 6 7 6 2 5 1 5 34 2 68 7 2 2 12 8 2 5 1 31 +2 2 14 5 6 7 1 2 2 6 1 2 2 8 1 2 9 3 6 5 19 2 2 11 2 2 26 3 2 2 +3 7 1 14 5 9 7 2 3 1 10 2 9 6 18 60 3 2 10 8 14 2 6 2 2 2 + + + + + + +AC217050.4_FGP006 seq=translation; coord=1:214899491..214901246:-1; parent_transcript=AC217050.4_FGT006; parent_gene=AC217050.4_FG006 + + + MAREENVYMA KLAEQAERYE EMVEYMEKVA KTVDVEELTV EERNLLSVAY + KNVIGARRAS WRIVSSIEQK EESRKNEEHV NLIKEYRAKI EAELSNICDG + ILKLLDSHLV PSSTAAESKV FYLKMKGDYH RYLAEFKTGP ERKESAESTM + MAYKAAQDIA LAELAPTHPI RLGLALNFSV FYYEILNSPD KACNLAKQAF + DEAISQLDTL GEESYKDSTL IMQLLRDNLT LWTSDLTEDG ADEGKEAPKG + EAGDGQ + + + + + + + + +4.91676 +-0.31721 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +1107 1107 1107 1107 1107 983 917 614 517 322 117 63 16 10 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1107 1107 1107 1107 1107 983 912 604 453 284 61 29 2 1 0 + + + + + + +0 1 2 3 4 + + + + +652 408 47 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +309 673 114 10 1 0 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2594 (charge 2) + +1279.52 +2 + + +152.057 155.081 159.076 170.549 171.076 172.071 173.092 173.128 175.119 181.061 183.113 187.071 189.088 199.072 199.108 201.087 217.082 224.103 226.154 234.144 242.115 244.166 252.1 254.115 270.108 288.12 295.08 310.176 327.13 366.115 +381.211 419.236 421.338 432.187 450.169 464.258 515.533 526.196 528.247 573.301 594.185 611.286 615.344 641.314 645.289 648.336 675.296 709.343 712.332 713.344 722.313 735.37 775.362 799.371 803.397 835.912 846.397 863.359 865.39 874.426 +910.397 928.407 999.443 1046.48 + + + + +63 17 34 8 59 13 37 17 33 30 11 8 62 100 17 50 35 59 47 68 9 34 8 9 48 17 9 45 10 10 +16 14 8 11 9 8 9 11 14 9 12 14 12 11 14 31 10 10 32 11 10 67 32 75 36 10 10 32 11 13 +11 14 16 33 + + + + + + +GRMZM2G157329_P01 NP_001145994 hypothetical protein LOC100279524 seq=translation; coord=1:41535916..41540223:-1; parent_transcript=GRMZM2G157329_T01; parent_gene=GRMZM2G157329 + + + MAETLDMTLD DIIKNNKKSN PSSGGARRSR GGSAPGGGSG GVGPTRRSFK + RAGNRQAPYQ PPKAPDAAWQ HDMYPAVAAG GGGGGRVSAL ETGTKLYISN + LDFGVSNDDI KELFSELGDL KRFSIIYDRS GRSKGTAEVV FARRSDAVAA + VKKYNNVQLD GKPMKIEIVG TNTPTASAAL PVSNGGHARN AVRSAPRGAA + PAGVPQRRPH QRGGRRSGGS GGGRRGKERS KPKSAEELDA DLEKYHADAM + QTN + + + + + +GRMZM2G157329_P02 NP_001145994 hypothetical protein LOC100279524 seq=translation; coord=1:41535740..41539719:-1; parent_transcript=GRMZM2G157329_T02; parent_gene=GRMZM2G157329 + + + MAETLDMTLD DIIKNNKKSN PSSGGARRSR GGSAPGGGSG GVGPTRRSFK + RAGNRQAPYQ PPKAPDAAWQ HDMYPAVAAG GGGGGRVSAL ETGTKLYISN + LDFGVSNDDI KELFSELGDL KRFSIIYDRS GRSKGTAEVV FARRSDAVAA + VKKYNNVQLD GKPMKIEIVG TNTPTASAAL PVSNGGHARN AVRSAPRGAA + PAGVPQRRPH QRGGRRSGGS GGGRRGKERS KPKSAEELDA DLEKYHADAM + QTN + + + + + + +5.7343 +-0.294067 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +4927 4927 4927 4767 4514 4246 3779 2276 1833 830 348 157 73 48 23 15 6 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +4929 4929 4929 4769 4516 4230 3726 2151 1368 468 152 42 25 1 0 0 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3110 1628 183 13 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +806 3282 755 74 14 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2597 (charge 2) + +1270.61 +2 + + +152.057 154.05 155.081 157.061 157.097 157.109 158.093 159.077 169.097 171.076 173.056 174.087 175.119 184.072 186.125 195.089 195.112 199.107 202.082 210.087 212.103 217.082 226.155 230.077 235.074 244.165 255.109 258.109 273.12 286.103 +299.658 338.146 343.126 356.156 390.208 413.214 416.14 428.202 430.24 444.223 461.245 467.206 469.278 478.236 499.753 540.415 557.231 567.301 569.274 576.274 598.306 627.803 637.323 643.351 669.339 679.338 696.365 703.345 713.857 725.388 +730.38 740.379 759.379 787.403 830.392 844.419 855.406 865.41 882.427 901.449 981.483 998.501 1000.51 + + + + +18 12 24 3 3 5 11 4 7 18 6 6 34 64 5 4 4 18 31 14 19 13 29 11 3 17 21 5 4 4 +4 4 6 5 16 7 4 4 21 4 18 3 7 5 52 11 4 6 5 6 20 14 15 14 7 5 17 12 4 4 +12 7 4 18 4 26 13 4 12 68 4 100 20 + + + + + + +conta|P13645|K1CJ_HUMAN KERATIN, TYPE I CYTOSKELETAL 10 (CYTOKERATIN 10) (K10) (CK 10) + + + MSVRYSSSKH YSSSRSGGGG GGGGCGGGGG VSSLRISSSK GSLGGGFSSG + GFSGGSFSRG SSGGGCFGGS SGGYGGLGGF GGGSFRGSYG SSSFGGSYGG + SFGGGSFGGG SFGGGSFGGG GFGGGGFGGG FGGGFGGDGG LLSGNEKVTM + QNLNDRLASY LDKVRALEES NYELEGKIKE WYEKHGNSHQ GEPRDYSKYY + KTIDDLKNQI LNLTTDNANI LLQIDNARLA ADDFRLKYEN EVALRQSVEA + DINGLRRVLD ELTLTKADLE MQIESLTEEL AYLKKNHEEE MKDLRNVSTG + DVNVEMNAAP GVDLTQLLNN MRSQYEQLAE QNRKDAEAWF NEKSKELTTE + IDNNIEQISS YKSEITELRR NVQALEIELQ SQLALKQSLE ASLAETEGRY + CVQLSQIQAQ ISALEEQLQQ IRAETECQNT EYQQLLDIKI RLENEIQTYR + SLLEGEGSSG GGGRGGGSFG GGYGGGSSGG GSSGGGYGGG HGGSSGGGYG + GGSSGGGSSG GGYGGGSSSG GHGGGSSSGG HGGSSSGGYG GGSSGGGGGG + YGGGSSGGGS SSGGGYGGGS SSGGHKSSSS GSVGESSSKG PRY + + + + + + +6.64344 +-0.32407 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +6709 6709 6643 6367 6007 5508 4759 4176 3022 2286 1353 737 352 140 72 28 13 4 2 1 1 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +6707 6707 6641 6365 5997 5394 4568 3873 2326 1241 501 76 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2352 2867 1175 276 34 6 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1135 2711 1808 777 236 32 9 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2609 (charge 3) + +1428.69 +3 + + +152.057 153.066 155.082 156.076 157.098 157.109 157.133 158.092 159.077 166.061 167.055 167.081 169.097 169.133 171.077 171.113 173.092 175.119 176.121 181.097 185.092 185.165 187.071 189.087 195.089 195.112 199.071 200.102 201.123 207.087 +209.092 213.087 218.15 221.103 223.063 226.154 227.102 228.632 232.14 235.082 239.094 241.13 244.166 246.155 249.098 252.108 255.145 258.157 267.109 269.105 272.171 276.167 284.171 288.203 295.103 299.06 304.161 315.202 331.685 344.192 +355.202 359.202 364.125 378.142 381.151 392.718 396.153 403.231 414.197 426.239 437.242 450.248 456.258 457.257 462.254 465.748 466.745 475.227 481.583 483.293 487.261 496.604 525.193 527.289 531.326 546.295 567.296 589.27 593.782 611.26 +628.341 662.359 683.388 687.379 729.385 784.428 791.404 804.385 920.443 1049.48 + + + + +3 3 12 3 4 6 2 15 3 3 12 7 14 3 3 5 6 57 2 3 10 8 3 6 3 2 3 15 6 3 +3 3 2 2 3 11 13 9 2 13 13 8 6 5 5 13 11 5 9 13 9 3 2 100 2 11 7 2 2 3 +5 3 3 2 3 9 2 17 2 6 21 3 38 7 2 7 6 3 3 2 7 17 3 8 13 3 6 3 3 7 +6 11 16 11 2 2 7 10 8 7 + + + + + + +GRMZM2G009443_P01 NP_001169540 hypothetical protein LOC100383416 seq=translation; coord=10:35583589..35590383:1; parent_transcript=GRMZM2G009443_T01; parent_gene=GRMZM2G009443 + + + MAGTLLQSVA LGTPFGGRMR THCWRSHGTR RPASMLAVSL SRPVKMSAFV + GLRSVHSFSV TPTVSNSRSA VASYRSSRQT RRSRFVTQAM FERFTEKAIK + VIMLAQEEAR RLGHNFVGTE QILLGLIGEG TGIAAKVLKS MGINLKDARV + EVEKIIGRGN GFVAVEIPFT PRAKRVLELS LEEARQLGHN YIGSEHLLLG + LLREGEGVAA RVLESLGADP SNIRTQVIRM IGETTEAVGA GVGGGSSGNK + MPTLEEYGTN LTKLAEEGKL DPVVGRQPQI ERVVQILGRR TKNNPCLIGE + PGVGKTAIAE GLAQRISTGD VPETIEGKKV ITLDMGLLVA GTKYRGEFEE + RLKKLMEEIK QSDEIILFID EVHTLIGAGA AEGAIDAANI LKPALARGEL + QCIGATTLDE YRKHIEKDPA LERRFQPVKV PEPTVDETIE ILRGLRERYE + IHHKLRYTDE ALIAAAKLSY QYISDRFLPD KAIDLIDEAG SRVRLQHAQV + PEEARELDKE LKQVTKQKNE AVRSQDFEKA GELRDREMEL KAQITALIDK + SKELSKAEEE SGETGPMVNE EDIQHIVSSW TGIPVEKVSS DESDKLLKME + ETLHKRVIGQ DEAVVAISRS IRRARVGLKN PNRPIASFIF AGPTGVGKSE + LAKALAAYYF GSEEAMIRLD MSEFMERHTV SKLIGSPPGY VGYTEGGQLT + EAVRRRPYTV VLFDEIEKAH PDVFNMMLQI LEDGRLTDSK GRTVDFKNTL + LIMTSNVGSS VIEKGGRKIG FDLDSDEKDS SYSRIKSLVI EEMKQYFRPE + FLNRLDEMIV FRQLTKLEVK EIADIMLQEV FDRLKAKDIN LQVTEKFKER + VVDEGYNPSY GARPLRRAIM RLLEDSLAEK MLAGEVKEGD SAIVDVDSEG + KVVVLNGQGG IPELSTPAIT V + + + + + +GRMZM2G123922_P01 seq=translation; coord=10:111239151..111246665:-1; parent_transcript=GRMZM2G123922_T01; parent_gene=GRMZM2G123922 + + + MEGALVQSAI VPAVYRSSSG RFRVRARART NATMVRNTPT RTLTLGGFQG + LRQTNFLDTR SVIKRDFGSI VASQIARPRG SASRGVVRAM FERFTEKAIK + VIMLAQEEAR RLGHNFVGTE QILLGLIGEG TGIAAKVMKS MGINLKDARV + EVEKIIGRGS GFVAVEIPFT PRAKRVLELS LEEARQLGHN YIGSEHLLLG + LLREGEGVAA RVLESLGADP NNIRTQVIRM VGESTEAVGA GVGGGSSGQK + MPTLEEYGTN LTKLAEEGKL DPVVGRQDQI ERVTQILGRR TKNNPCLIGE + PGVGKTAIAE GLAQRISNGD VPETIEGKKV ITLDMGLLVA GTKYRGEFEE + RLKKLMEEIK QNEDIILFID EVHTLIGAGA AEGAIDAANI LKPALARGEL + QCIGATTLDE YRKHIEKDPA LERRFQPVKV PEPTVDETIQ ILRGLRERYE + LHHKLRYTDD ALIAAAQLSY QYISDRFLPD KAIDLIDEAG SRVRLRHAQL + PDEAKELDKE LRQITKQKNE AVRGQDFEKA GELRDREMEL KAQITAIIDK + SKEMIKAETE SGDVGPLVTE ADIQHIVSSW TGIPVEKVSS DESDRLLKME + ETLHTRIIGQ DEAVKAISRA IRRARVGLKN PNRPIASFIF SGPTGVGKSE + LAKALAAYYF GSEEAMIRLD MSEFMERHTV SKLIGSPPGY VGYTEGGQLT + EAVRRRPYTV VLFDEIEKAH PDVFNMMLQI LEDGRLTDSK GRTVDFKNTL + LIMTSNVGSS VIEKGGRKIG FDLDYDEKDT SYNRIKSLVT EELKQYFRPE + FLNRLDEMIV FRQLTKLEVK EIADIMLKEV FDRLKAKEIN LQVTEKFRDR + VVDEGYNPSY GARPLRRAIM RLLEDSLAEK MLAGEVKEGD SAIVDVDSDG + KVIVLNGGSG VAEPLEPALS T + + + + + +GRMZM2G001084_P01 C4J9D9 Putative uncharacterized protein seq=translation; coord=2:63775789..63789530:1; parent_transcript=GRMZM2G001084_T01; parent_gene=GRMZM2G001084 + + + MQAGMNHCTL LSSALDLGTS NPHALDPHTL DLGTSNLRGQ HPTIPTLWIW + ERAISAHLCW FVLHPHAPNI LHQRTYLSPI SAPFHLTWKP KSPPQSAFIV + DSYIRAIPSN METSMPTSIS VHRRVPPSSA HSVPSTLSTS IKTHDHCEGC + RQIPHQTSTL VVCSTPITIA VGFNAFAGHN YVGSEHLLLG LLREGEGTDV + RYDVQVIRMV GESTEAVGAG VGGGSSGQKM PTLEEYGTNL TKLAEESFGR + QDQIERVTQI LGRRTKKQPL PNWRAWCWKR LLLLRGLLSV LPMGMFLKQF + EGKKVITLDM GLLVAGTKYR GEFEERLKKL MEEIKQNEDI ILFIDEVHTL + IGAGAAEGAI DAANILKPAL ARGELQCIGA TTLDEYRKHI EKDPALERRF + QPVKVPEPTV DETIQILRGL RERYELHHKL RYTDDALIAA AQLSYQYISD + RFLPDKAIDL IDEAGSRVRL RHAQLPDEAK ELDKELRQIT KQKNEAVRGQ + DFEKAGELRD REMELKAQIT AIIDKSKEMI KAETESGEVG PLVTEADIQH + IVSSWTGIPV EKVSSDESDR LLKMEETLHT RIIGQDEAVK AISRAIRRAR + VGLKNPNRPI ASFIFSGPTG VGKSELAKAL AAYYFGSEEA MIRLDMSEFM + ERHTVSKLIG SPPGYVGYTE GGQLTEAVRR RPYTVVLFDE IEKAHPDVFN + MMLQILEDGR LTDSKGRTVD FKNTLLIMTS NVGSSVIEKG GRKIGFDLDY + DEKDTSYNRI KSLVTEELKQ YFRPEFLNRL DEMIVFRQLT KLEVKEIADI + MLKEVFDRLK AKDINLQVTE KFRDRVVDEG YNPSYGARPL RRAIMRLLED + SLAEKMLAGE VKEGDSAIVD VDSDGKVIVL NGGSGVAEPL EPALST + + + + + +AC211513.3_FGP003 seq=translation; coord=1:80496139..80497440:-1; parent_transcript=AC211513.3_FGT003; parent_gene=AC211513.3_FG003 + + + MGFLAFWSVS PVGSAAEQVT WTGLLVAGTK YRGEFECTGA TTLDGYRKHI + EKDPALERRF QPVKVPEPTV DETIQILRGL HERYELHHKL RYTDDALIAA + AQLSYQYISD RFLPDKAIDL IDEAGSRVRL RHAQLPDEAK ELDKELRQIS + KQKNKAVRGQ DFEKNL + + + + + +GRMZM5G896496_P04 NP_001136503 hypothetical protein LOC100216618 seq=translation; coord=3:211872506..211878967:1; parent_transcript=GRMZM5G896496_T04; parent_gene=GRMZM5G896496 + + + MPLVCCQASY LQEINGLRPR GLFFLIMCIG ATTLDEYRKH IEKDPALERR + FQPVKVPEPT MDETIQILRG LRERYELHHK LRYTDDALIA AAQLSYQYIS + DRFLPDKAID LIDEAGSRVR LRHAQLPDEA KELDKELRQI SKQKNEAVRG + QDFEKVYCCL AQR + + + + + +GRMZM5G896496_P05 NP_001136503 hypothetical protein LOC100216618 seq=translation; coord=3:211872506..211878967:1; parent_transcript=GRMZM5G896496_T05; parent_gene=GRMZM5G896496 + + + MPLVCCQASY LQEINGLRPR GLFFLIMCIG ATTLDEYRKH IEKDPALERR + FQPVKVPEPT MDETIQILRG LRERYELHHK LRYTDDALIA AAQLSYQYIS + DRFLPDKAID LIDEAGSRVR LRHAQLPDEA KELDKELRQI SKQKNEAVRG + QDFEKVYCCL AQR + + + + + +GRMZM5G896496_P06 NP_001136503 hypothetical protein LOC100216618 seq=translation; coord=3:211872506..211878967:1; parent_transcript=GRMZM5G896496_T06; parent_gene=GRMZM5G896496 + + + MPLVCCQASY LQEINGLRPR GLFFLIMCIG ATTLDEYRKH IEKDPALERR + FQPVKVPEPT MDETIQILRG LRERYELHHK LRYTDDALIA AAQLSYQYIS + DRFLPDKAID LIDEAGSRVR LRHAQLPDEA KELDKELRQI SKQKNEAVRG + QDFEKVYCCL AQR + + + + + + +6.84123 +-0.333718 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +7863 7863 7863 7646 7353 6855 6288 5845 5185 3561 2702 1497 672 246 137 46 25 10 2 1 1 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7866 7866 7866 7638 7326 6746 6089 5527 4861 2956 1827 459 33 6 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2505 3102 1699 496 55 8 25 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1170 3445 2162 860 183 33 37 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2610 (charge 3) + +1207.64 +3 + + +154.061 154.086 155.082 155.118 157.109 157.133 158.092 159.077 165.102 166.061 167.081 169.097 170.101 171.076 172.071 173.092 175.119 176.123 178.134 179 183.076 185.092 185.128 186.121 191 191.082 192.111 195.112 196.061 197.129 +198.124 199.107 199.169 206.129 209.092 213.087 215.139 223.155 224.159 226.119 237.092 240.134 243.134 245.047 248.034 249.159 251.15 254.647 258.092 264.049 266.044 269.125 270.09 272.125 274.187 276.169 282.182 287.135 289.11 293.171 +299.061 303.155 305.165 308.167 312.16 325.169 333.167 337.149 344.171 347.681 355.163 362.182 363.183 366.185 373.172 380.192 382.208 397.215 400.22 411.224 417.245 419.249 468.245 471.257 486.256 488.283 490.29 508.29 512.266 568.309 +569.313 579.322 583.312 585.335 587.341 599.292 605.306 623.318 700.362 727.347 + + + + +3 2 5 1 2 7 13 2 2 2 1 27 3 2 3 5 95 6 17 12 4 7 7 1 1 3 2 2 1 2 +3 6 4 4 5 5 15 100 12 14 3 15 13 26 79 9 63 1 4 3 57 13 6 4 3 7 7 13 7 22 +6 30 3 1 31 3 3 7 3 2 8 36 7 1 9 12 9 6 5 4 60 2 10 3 12 80 3 3 2 8 +2 2 1 87 4 5 10 5 4 4 + + + + + + +GRMZM2G158039_P01 seq=translation; coord=5:192003005..192008209:1; parent_transcript=GRMZM2G158039_T01; parent_gene=GRMZM2G158039 + + + MTCLQLLFED AIDDRILAKE ELGAAADEFL LCLTMRQRAL TREYSRLTNL + KRPSDLSGMT EADRAAEAER LREERLQKAR QLQDQGDMSG ARECEGLARI + IDFDVKQGGR YLNCICYVDD IYTFDQTEEC GATVTRFAGL AGASLPTERR + AAAMVAMAKR EQELEEIRAM TTEQMEEEVV DLRGELFLLR LKRSARQEFK + NSEFSRMRKR IAPMLTVKRE REIEQGINKR LSRKLDRKWK QSIVVRPPPS + LRGNKEE + + + + + +GRMZM2G028216_P01 Q9SWI6 50S ribosomal protein L29, chloroplastic Precursor (CL29) seq=translation; coord=4:180580017..180581711:-1; parent_transcript=GRMZM2G028216_T01; parent_gene=GRMZM2G028216 + + + MATMSLAAAS PLASIPRGIA AQAPCAAFLS IRLGGATATR FAGLAVASQP + AERRAAAMVA MAKREQELEE IRAMTTEQME EEVVDLKGEL FLLRLKRSAR + QEFKNSEFSR MRKRIARMLT VKREREIEQG INKRLSRKLD RKWKQSIVVR + PPPSLRGNKE E + + + + + +GRMZM5G811409_P01 seq=translation; coord=2:227538228..227538693:-1; parent_transcript=GRMZM5G811409_T01; parent_gene=GRMZM5G811409 + + + QLVVPVDRQL KEQKAKTERE IEQGINKRLY RKLDTKWKQS IVVRPPPSLR + ENKEKASRAC ARIGWFSCAV ALFGSYLRHH PCICRIVEM + + + + + + +6.95663 +-0.339348 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7960 7960 7945 7902 7488 7178 6728 6234 5600 4169 3120 1539 796 345 175 62 36 7 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7950 7950 7935 7892 7472 7152 6656 6032 5172 3439 1965 381 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2384 3254 1549 608 135 34 4 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1386 3662 2023 673 199 17 2 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2611 (charge 3) + +1371.73 +3 + + +153.102 155.081 157.108 158.092 166.061 167.056 171.113 172.072 175.119 176.123 181.097 184.072 186.088 193.097 197.128 198.123 199.108 209.09 215.139 226.119 227.102 232.634 235.118 239.094 241.639 244.166 247.611 250.645 254.149 269.124 +286.151 288.983 290.986 294.186 299.061 303.214 313.194 327.177 343.179 349.702 359.15 365.185 369.187 371.24 380.157 383.203 387.198 397.182 398.172 400.23 405.217 415.193 417.257 418.26 421.552 428.225 440.56 446.569 452.246 482.738 +495.248 500.283 503.295 510.266 514.256 528.278 530.34 531.344 532.93 546.288 548.289 550.296 556.293 565.255 570.336 574.337 576.315 582.288 587.363 593.249 611.311 620.31 629.328 637.809 639.31 652.326 657.32 659.331 674.35 675.349 +681.369 685.358 691.349 698.397 715.42 809.428 814.401 825.374 842.395 844.45 + + + + +7 8 5 12 5 8 6 11 100 8 2 7 2 12 6 5 12 8 5 24 11 3 6 10 15 11 10 5 9 16 +19 5 6 8 7 19 5 6 6 14 6 7 4 2 6 11 19 12 7 25 6 47 71 17 4 5 23 2 7 8 +9 24 6 17 6 45 15 5 4 3 8 5 4 5 7 8 5 5 62 6 5 5 21 4 9 4 44 6 10 2 +3 5 4 20 15 8 6 5 16 5 + + + + + + +GRMZM2G158147_P01 NP_001147427 bifunctional 3-phosphoadenosine 5-phosphosulfate synthetase 2 seq=translation; coord=2:112635028..112643280:1; parent_transcript=GRMZM2G158147_T01; parent_gene=GRMZM2G158147 + + + MATTHLLTPP RVHHPSPSAS SSVARVRATA SLAHPLHLCR LRLAAPRSRS + PSPRHGRRAM SVRSSLIDPD GGALVELVAP PDRLPALRAE AEALPRVRLA + PVDLQWAHVL AEGWASPLRG FMREHEYLQS LHFNCVRLPD GGLVNMSLPI + VLAIGDADKE QIGGKPDVAL QGPDGGVVAI LRRVEIYPHN KEERIARTWG + TTAPGLPYVD EAIASAGNWL IGGDLEVLEP IKYNDGLDHY RLSPRQLRKE + FDKRGADAVF AFQLRNPVHN GHALLMNDTR RRLLEMGYKN PILLLHPLGG + YTKADDVPLP VRMEQHSKVL EDGVLDPETT IVSIFPSPMH YAGPTEVQWH + AKARINAGAN FYIVGRDPAG MGHPTEKRDL YNPDHGKKVL SMAPGLEKLN + ILPFKVAAYD TVAKEMAFFD PSRSQDFLFI SGTKMRTYAK TGENPPDGFM + CPGGWKVLVD YYNSLQAEEA TPVPV + + + + + + +5.65598 +-0.275901 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +11758 11758 11556 11358 10709 10140 9313 8454 5968 4382 2519 1466 696 348 221 69 44 28 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +11745 11745 11543 11343 10669 10031 9143 8083 4921 3243 1336 335 38 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3894 4801 2267 654 122 20 0 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2030 5621 2899 1024 171 13 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2612 (charge 3) + +1569.81 +3 + + +150.067 152.057 157.108 158.093 159.077 166.061 167.056 167.093 169.053 169.097 169.134 171.113 175.119 176.123 185.092 195.088 195.114 197.129 199.108 204.076 207.124 209.091 211.119 213.088 222.086 226.155 227.102 229.117 231.098 235.119 +239.114 244.166 252.109 257.139 262.152 269.125 286.148 287.135 299.063 301.06 302.061 304.161 309.203 326.173 331.187 346.972 348.971 355.195 357.225 361.027 368.195 385.219 390.705 406.704 419.032 426.247 433.203 448.242 452.252 455.732 +470.314 474.268 476.214 481.277 498.305 499.306 501.225 518.268 547.247 561.299 571.276 594.373 616.344 625.329 633.372 641.295 644.338 646.336 658.316 661.367 663.373 675.342 677.35 691.424 698.855 758.426 788.477 796.367 809.342 812.402 +814.397 823.378 826.361 837.492 850.45 867.476 892.435 909.446 911.45 1005.58 + + + + +3 2 3 5 2 12 10 15 7 5 3 2 49 2 3 27 2 3 9 5 9 3 6 2 12 24 9 2 2 12 +54 10 2 3 2 5 8 6 9 29 15 100 52 2 2 3 7 2 5 2 2 38 2 12 3 6 9 7 3 6 +13 5 2 6 58 17 2 7 35 18 3 11 6 2 36 2 6 2 17 89 7 49 2 5 2 5 2 2 54 20 +2 2 2 2 2 5 5 12 2 2 + + + + + + +GRMZM2G016457_P01 NP_001131573 hypothetical protein LOC100192917 seq=translation; coord=3:106385610..106413663:-1; parent_transcript=GRMZM2G016457_T01; parent_gene=GRMZM2G016457 + + + MAYAAPPMAS SLTASHPPLS PSHLITHPHR CPARPNPTTG LLRLTPSRRR + GRPPVAVRLA ISASSTSAPP PSADRSEAAS SLERYLSATV TGAVMGTGAA + PPASAPPRAP PAMKGGRKQY SALGAVTLEK AKLDLSQRRK NIMPELATGG + GGGDIGKRIG HGGGDGGDDD GDDDDYFDDF DEGEEEGGLF RRRIVVQELF + NREFVEAVLQ EWYKTMSDLP TGLRQACEMG LVSSAQMVRY LSIFARPTNA + RSFSRALPGW LSRGLVGRTL ADPSFPHKMS LEFIATIASS IWCEMNIRKE + RFKQEWDLVI VNALTAACCN LMVLGLLAPC RSYASTSRFD FQNAIEKLPN + NIFEKSYPLR EFDLAKRISA FFYKAAELSL VGFVAGSVQG GMSIVLSARK + ERRLSVTIPS ISTNALGYGA FLGLYANLRY QLLCGVDQYM VKRFDVLGVA + IFFSTAARLM NIQIGEASRR TWLGEEADPQ YSDRLLRAYK RPVEVDADQS + RWFISKDAIV SGLGLLGIKQ GGPEATFSKS RRKRVIRKKV TSG + + + + + + +6.96293 +-0.376375 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +7416 7416 7416 7308 7027 6771 5745 4833 3439 2037 1141 600 215 73 22 10 5 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7414 7414 7414 7306 7025 6750 5654 4528 2580 998 314 60 7 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2502 3015 1429 403 64 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1348 3236 2043 622 153 14 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2614 (charge 3) + +1271.63 +3 + + +154.05 154.086 155.07 155.082 155.118 157.097 157.108 157.134 158.092 159.077 160.879 166.062 167.093 169.097 169.133 171.077 171.113 173.092 173.129 175.09 175.119 176.122 179.093 181.06 183.113 183.15 185.092 186.124 187.071 187.109 +189.086 194.128 195.089 195.112 197.128 198.088 199.109 199.181 201.124 209.103 213.087 215.139 217.082 226.154 227.102 231.096 238.143 240.134 244.165 245.125 248.16 251.152 254.16 262.152 267.111 272.172 285.135 305.164 309.202 312.175 +322.188 325.234 351.168 353.229 358.18 373.185 390.209 403.178 405.9 411.209 413.168 426.247 427.241 432.233 443.733 449.234 454.278 455.233 459.245 464.26 479.242 482.272 484.621 505.237 516.263 528.266 534.261 553.346 558.783 572.761 +576.274 581.764 669.381 691.3 696.365 709.375 726.401 760.374 1044.25 1162.94 + + + + +7 5 5 16 12 10 18 6 23 25 3 13 5 20 14 21 6 11 12 16 100 4 4 4 17 10 10 6 11 10 +20 16 6 7 14 6 6 11 6 5 6 7 15 31 5 5 6 5 28 11 4 11 18 19 4 7 5 4 11 3 +17 4 4 32 4 11 32 4 5 4 7 5 17 11 4 4 23 6 22 4 7 52 5 28 6 5 4 4 5 5 +25 7 13 16 20 4 27 4 4 4 + + + + + + +GRMZM5G821988_P01 seq=translation; coord=2:204696776..204699559:1; parent_transcript=GRMZM5G821988_T01; parent_gene=GRMZM5G821988 + + + MPSPGTPVQA MHKAERKYVI GKVSDEEEAK QRQLKAILNK LTPQNFEKLF + EQVKEVNIDS VATLTGVISQ IFDKALMEPT FCEMYANFCF HLAGALPDFS + EDNEKITFKR LLLNKCQEEF ERGEREEAEA DKTEEEGEIK QTKEEREEKR + IRARRRMLGN IRLIGELYKK RMLTERIMHE CIKKLFGNHD DPDEENIEAL + CKLMSTIGDM IDHVKAKEHM DAYFSMMQIM STNQKLSSRV RFMLRDSIDL + RRNKWQQRRK VEGPKKIEEV HRDAAQERHA QSSRLGRGPA VSSVPRRAHP + MDYGPRGPSA SASSSSQQGS IRGMPPHSRG SQDIRHDERH QFDNRTVLPQ + RVVKDEAITL GPQGGLARGM SIRGQPPVSN TEIPSVIDHR RIVSSSNGYN + SAADWTSSSG REDSNSRLPD RTSGRIPASS QSAVTSQRPA SQEGRSRSKS + YSEDELREKS VLTIREYYSA KDEKEVVLCI EELNAPNFYP FLVSLWVNDS + FERKDMEREL LAKLLVSLCS GRHNLLSKQQ LSDGLSNVLA SLEDNLSDAP + RATEYLGRLL ARFVEESILL LQEVGKLIQE SGEEPGYLIQ GGIAADILGA + VLDSIKSDKG NSFLDEIKTT SSLKLVDFRP QHLKRSKLDA FM + + + + + +GRMZM5G821988_P02 seq=translation; coord=2:204696776..204699467:1; parent_transcript=GRMZM5G821988_T02; parent_gene=GRMZM5G821988 + + + MPSPGTPVQA MHKAERKYVI GKVSDEEEAK QRQLKAILNK LTPQNFEKLF + EQVKEVNIDS VATLTGVISQ IFDKALMEPT FCEMYANFCF HLAGALPDFS + EDNEKITFKR LLLNKCQEEF ERGEREEAEA DKTEEEGEIK QTKEEREEKR + IRARRRMLGN IRLIGELYKK RMLTERIMHE CIKKLFGNHD DPDEENIEAL + CKLMSTIGDM IDHVKAKEHM DAYFSMMQIM STNQKLSSRV RFMLRDSIDL + RRNKWQQRRK VEGPKKIEEV HRDAAQERHA QSSRLGRGPA VSSVPRRAHP + MDYGPRGPSA SASSSSQQGS IRGMPPHSRG SQDIRHDERH QFDNRTVLPQ + RVVKDEAITL GPQGGLARGM SIRGQPPVSN TEIPSVIDHR RIVSSSNGYN + SAADWTSSSG REDSNSRLPD RTSGRIPASS QSAVTSQRPA SQEGRSRSKS + YSEDELREKS VLTIREYYSA KDEKEVVLCI EELNAPNFYP FLVSLWVNDS + FERKDMEREL LAKLLVSLCS GRHNLLSKQQ LSDGLSNVLA SLEDNLSDAP + RATEYLGRLL ARFVEESILL LQEVGKLIQE SGEEPGYLIQ GGIAADILGA + VLDSIKSDKG NSFLDEIKTT SSLKLVDFRP QHLKRSKLDA FM + + + + + + +5.95893 +-0.361147 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +5589 5589 5589 5589 5589 5522 5422 2683 2332 784 307 167 69 20 5 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5592 5592 5592 5592 5592 5525 5425 2681 2320 722 206 87 26 5 1 0 + + + + + + +0 1 2 3 4 + + + + +4537 950 94 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +588 4850 140 11 1 0 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2618 (charge 2) + +1506.71 +2 + + +155.082 159.076 167.081 175.119 181.062 181.097 185.093 216.099 224.103 226.083 239.617 242.113 247.059 250.118 264.222 267.144 283.319 295.141 347.132 631.7 791.287 862.429 949.47 1003.45 1036.49 1070.61 1107.54 1144.66 1194.57 1217.48 +1352.62 1384.05 1385.87 + + + + +62 14 17 39 15 14 14 11 75 11 12 57 11 13 10 14 12 16 13 12 13 39 24 16 100 17 56 15 76 12 +12 14 12 + + + + + + +GRMZM5G859979_P01 P48183 Photosystem Q(B) protein Precursor (32 kDa thylakoid membrane protein)(Photosystem II protein D1) seq=translation; coord=Pt:75..1150:-1; parent_transcript=GRMZM5G859979_T01; parent_gene=GRMZM5G859979 + + + MTAILERRES TSLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII + AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEAA + SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP + VAAATAVFLI YPIGQGSFSD GMPLGISGTF NFMIVFQAEH NILMHPFHML + GVAGVFGGSL FSAMHGSLVT SSLIRETTEN ESANEGYKFG QEEETYNIVA + AHGYFGRLIF QYASFNNSRS LHFFLAAWPV VGIWFTALGI STMAFNLNGF + NFNQSVVDSQ GRVINTWADI INRANLGMEV MHERNAHNFP LDLAALEVPY + LNG + + + + + +GRMZM2G427369_P01 Q37082 Uncharacterized protein ycf72 (ORF137) seq=translation; coord=5:209970617..209971549:-1; parent_transcript=GRMZM2G427369_T01; parent_gene=GRMZM2G427369 + + + MGREWELSFR LGMRPWIAVA YSAPVAAATA VFLIYPIGQG SFSDGMPLGI + SGTFNFMIVF QAEHNILMHP FHMLGVAGVF GGSLFSAMHG SLVTSSLIRE + TTENESANEG YKFGQEEETY NIVAAHGYFG RLIFQYASFN NSRSLHFFLA + AWPVVGIWFT ALGISTMAFN LNGFIFNQSV VDSQGRVINT WADIINRANL + GMEVMHERNA HNFPLDLAAL EVPYLNG + + + + + +GRMZM2G086723_P01 seq=translation; coord=2:120732844..120733320:1; parent_transcript=GRMZM2G086723_T01; parent_gene=GRMZM2G086723 + + + MHGSLVTSSL IRETTENESA NEGYKFGQEE ETYNIVAAHG YFGRLIFQYA + SFNNSRSLHF FLAAWPVVGI WFTALGISTM AFNLNGFNFN QSVVDSQGRV + INTWADIINR ANLGMEVMHE RNAHNFPLDL AALEVPYLNG + + + + + +GRMZM5G844143_P01 seq=translation; coord=9:36554088..36555027:1; parent_transcript=GRMZM5G844143_T01; parent_gene=GRMZM5G844143 + + + MGREWELSFR LGMRPWIAVA YSAPVAAATA VFLIYPIGQG SFSDGMPLGI + SGTFNFMIVF QAEHNILMHP FHMLGVAGVF GGSLFSAMHG SLVTSSLIRE + TTENESANEG YKFGQEEETY NIVAAHGYFG RLIFQYASFN NSRSLHFFLA + AWPVVGIWFT ALGISTMAFN LNGFNFNQSV VDSQGRVINT WADIINRANL + GMEVMHERNA HNFPLDLAAL EVPYLNG + + + + + +GRMZM2G455413_P01 seq=translation; coord=10:100017747..100018574:1; parent_transcript=GRMZM2G455413_T01; parent_gene=GRMZM2G455413 + + + MGREWELSFR LGMRPWIAVA YSAPVAAATA VFLIYPIGQG SFSDGMPLGI + SGTFNFMIVF QAEHNILMHP FHMLGVAGVF GGSLFSAMHG SLVTSSLIRE + TTENESANEG YKFGQEEETY NIVAAHGYFG RLIFQYASFN NSRSLHFLAA + WPVVGIWFTA LGISTMAFNL NGFNFNQSVV DSQGCVINTW ADIINRANLG + MEVM + + + + + + +6.34107 +-0.362347 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +2418 2418 2418 2418 2388 2337 2209 2054 1799 1373 679 388 199 63 19 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +2442 2442 2442 2442 2412 2361 2215 2043 1771 1305 530 245 93 7 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1034 943 377 78 9 1 0 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +449 1417 434 111 20 2 10 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2619 (charge 3) + +1471.62 +3 + + +152.057 153.066 154.086 155.082 156.077 157.061 157.097 158.082 158.093 159.076 166.061 167.081 168.065 169.061 169.097 169.134 170.045 171.076 171.113 173.092 175.071 175.119 181.061 183.113 185.055 185.092 185.165 186.086 186.124 187.072 +187.108 193.098 194.129 195.075 197.128 198.087 199.072 199.108 199.181 201.123 203.103 209.055 212.102 213.087 216.099 226.082 227.102 231.097 237.135 240.135 244.093 268.13 270.108 278.114 283.101 292.165 296.124 298.103 301.114 310.176 +311.178 314.135 315.202 327.131 338.1 345.139 355.125 367.198 371.241 396.219 407.156 425.167 428.707 443.178 446.205 470.248 472.287 478.23 483.294 496.241 504.187 521.201 529.682 539.21 549.69 561.295 575.239 583.328 591.283 593.257 +610.285 628.341 665.292 675.344 681.32 686.265 719.34 755.346 768.354 891.394 + + + + +13 6 7 22 25 13 14 11 16 38 8 26 8 20 36 13 7 26 19 9 8 78 20 29 13 84 16 28 6 33 +7 33 20 44 8 7 32 20 7 20 58 16 7 73 15 50 26 58 8 7 84 23 8 27 7 18 40 8 39 52 +13 40 36 16 7 25 24 100 14 16 20 8 7 7 14 7 7 37 8 49 12 18 6 8 8 8 16 7 15 35 +81 17 15 13 80 8 7 7 58 6 + + + + + + +GRMZM2G127648_P01 NP_001148331 ras-related protein RIC2 seq=translation; coord=6:159006258..159010274:-1; parent_transcript=GRMZM2G127648_T01; parent_gene=GRMZM2G127648 + + + MAANGGGYRA EDDYDYLFKV VLIGDSGVGK SNLLSRFTKN EFSLESKSTI + GVEFATRSLQ VDGKVIKAQI WDTAGQERYR AITSAYYRGA VGALLVYDVT + RRATFDNVGR WLRELRDHTD QSIVVMLVGN KSDLRHLVAV STDDAKEFAE + AESMYFMETS ALDATNVDSS FSEVLTQIYQ IVSKKTVEAS EEGAAAPGKG + EKINVKDDVS AMKRVGCCSN + + + + + + +4.80369 +-0.259659 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +10467 10467 10407 10189 9464 7781 6113 3979 2413 1409 842 504 279 140 65 23 5 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +10342 10342 10282 10055 9294 7491 5479 3050 1418 705 297 82 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3118 4797 2096 377 80 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2223 5076 2415 604 137 11 6 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2620 (charge 3) + +1630.79 +3 + + +155.082 155.118 157.097 157.133 158.092 159.076 167.081 169.097 169.133 171.113 173.093 173.129 174.132 175.12 181.061 183.076 183.113 185.092 186.123 187.072 189.087 197.128 198.087 199.071 199.107 201.124 209.056 213.087 215.103 217.083 +221.103 225.098 226.155 229.118 230.149 235.119 240.134 241.082 244.165 249.095 252.097 259.093 270.109 271.14 280.092 283.176 288.119 297.12 308.177 311.135 316.114 330.165 333.178 339.129 346.125 354.213 355.197 363.131 369.142 381.141 +385.135 399.15 419.246 429.28 444.25 456.172 461.269 469.244 483.296 487.25 518.291 540.204 543.312 573.287 587.305 597.333 611.309 615.347 621.788 639.307 675.31 686.384 687.387 715.4 727.389 739.371 757.421 788.41 814.419 816.441 +828.45 837.479 841.461 885.482 917.49 978.524 1014.52 1016.52 1067.58 1143.56 + + + + +11 2 5 2 2 6 2 5 4 2 11 100 8 8 7 5 2 6 5 4 5 2 5 8 4 25 1 2 2 14 +2 5 15 4 2 6 4 5 30 2 10 2 8 2 2 21 2 5 8 4 4 4 8 2 5 2 10 1 2 5 +4 2 7 4 2 2 4 7 3 6 5 4 5 2 7 7 2 64 2 1 2 13 4 6 8 2 14 2 2 4 +4 6 2 14 2 2 6 2 7 2 + + + + + + +GRMZM2G008410_P01 NP_001141009 hypothetical protein LOC100273088 seq=translation; coord=4:170332797..170339707:-1; parent_transcript=GRMZM2G008410_T01; parent_gene=GRMZM2G008410 + + + MEAPGSPYAS SPESAPKRAP RSPPQQQQSP SEEGDDKEKP THLRFLVSNT + AAGCIIGKGG STINDFQSQS GARIQLSRSN EFFPGTNDRI IMVSGLFDEV + MKAMELILEK LLAEGEEFNE AEARPKVRLV VPNSSCGGII GKGGATIKSF + IEESHAGIKI SPQDNNYVGL HDRLVTITGT FDNQMNAIDL ILKKLSEDVH + YPPNLSSPFP YAGLTFPSYP GVPVGYMIPQ VPYSNAVNYG PNNGYGGRYQ + NNKPTTPMRS PASNEAQESL TIGIADEHIG AVVGRAGRNI TEIIQASGAR + IKISDRGDYI SGTSDRKVTI TGTPEAIRTA ESMIMQRVSA SSER + + + + + + +5.29636 +-0.271608 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +8048 8048 7951 7559 6927 6201 5069 3915 2799 1729 925 488 248 154 74 32 15 5 1 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8055 8055 7958 7566 6922 6042 4751 3300 1926 812 167 60 19 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2368 3447 1697 433 100 10 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1475 3552 2096 751 141 24 8 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2621 (charge 3) + +1349.66 +3 + + +153.102 155.081 156.077 157.097 157.133 158.092 159.076 164.071 167.056 167.118 169.051 169.097 171.076 171.113 171.149 173.092 173.128 175.09 175.119 176.123 181.061 181.097 182.101 183.113 184.072 184.108 185.092 186.124 187.071 187.108 +193.097 195.04 198.088 198.124 199.108 201.123 203.066 209.092 213.087 215.14 218.15 221.091 226.119 227.122 229.096 232.141 235.12 239.114 241.081 244.166 246.181 248.16 256.092 258.076 272.171 275.103 282.144 290.161 292.129 305.115 +306.16 308.172 313.15 315.202 323.136 340.161 343.18 351.684 361.026 363.025 386.185 387.187 393.188 403.212 406.174 409.695 415.733 434.167 446.254 452.197 458.262 465.212 474.267 504.258 512.75 529.732 565.274 576.777 585.295 589.294 +605.31 637.262 648.243 658.334 684.352 686.341 702.36 704.363 818.369 830.467 + + + + +3 6 3 3 3 11 14 3 3 2 5 6 2 13 6 3 6 6 66 2 7 45 3 3 9 3 6 6 7 6 +34 3 3 3 9 3 3 13 9 2 5 3 28 3 9 2 5 3 5 7 7 3 3 2 7 6 3 3 10 3 +3 3 2 16 18 3 3 3 11 23 18 3 2 32 2 3 3 14 3 2 2 3 10 13 2 8 3 2 3 9 +17 13 3 6 9 3 100 19 3 2 + + + + + + +GRMZM2G302233_P01 NP_001146320 hypothetical protein LOC100279896 seq=translation; coord=2:229667778..229675345:1; parent_transcript=GRMZM2G302233_T01; parent_gene=GRMZM2G302233 + + + MAATSPFSSY PPRLHSKTLK PRHSRPLHHK AAPAASAPRP LLLSFPAPAR + HCGAGLRASA AQKNSADYKF DEDDDDDEEE EYEYDGEEEE WEEEDDEDAM + NVEAMEEEAR GAAADLAKRL ARELHIDDDV REKRRNIRDK TSVSKHIPDN + LLPKVAIIGR PNVGKSALFN RLVGGNRAIV VDEPGVTRDR LYGRSYWGDH + EFMVIDTGGV ITLSKSQAGV MEELAVTTTV GMDGIPLATR EAAIARMPSM + IEKQAVAAVD EASVILFVVD GQAGLVAADI EISDWLRRNY SDKCILLAVN + KCESPRKGQM QALDFWSLGF SPLPISAITG TGTGDLLDLV CSELRKFEVL + DAVEEEKNKV PAIAIVGRPN VGKSSILNAL VGEDRTIVSP VSGTTRDAID + TEFTTADGEK YKLIDTAGIR RRTAVISAGS TTESLSVKRA FRAIRRSDVV + ALVIEAMACV TEQDYKIAER IEKEGKACVI VVNKWDTIPN KNHESTTHYE + QDVREKLRIL DWAPIVYCSA TNGTSVEKII SAAALVEKER SRRLSTSILN + QVIREAIAFK SPPRTRGGKR GRVYYTTQAA VGPPTFVLFV NDAKLFPDTY + RRYMEKKLRS DAGFPGTPIR LLWRSRRRPD KRGKSADSRA QSPGTPSEVA + LAA + + + + + + +6.30891 +-0.382358 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +4000 4000 3924 3756 3386 3090 2750 1680 1175 617 264 89 35 9 5 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3999 3999 3923 3751 3348 2960 2609 1454 801 325 45 9 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1427 1709 735 124 7 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +731 1966 1041 222 38 3 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2624 (charge 3) + +1615.7 +3 + + +155.081 156.077 157.097 157.134 158.093 159.077 165.077 166.061 167.056 167.081 168.055 169.052 169.097 171.076 171.113 175.119 179.093 181.061 183.113 185.092 190.061 195.076 198.087 199.072 199.108 201.123 207.087 213.087 216.097 218.055 +221.105 223.063 226.155 227.102 230.077 235.083 240.097 241.092 244.165 249.097 252.109 257.161 265.119 267.108 274.187 276.19 282.108 283.051 293.111 299.062 301.059 303.056 323.172 338.142 344.977 346.973 359.027 361.027 364.123 376.197 +381.15 395.661 404.173 416.036 417.034 419.034 427.193 437.74 451.159 473.722 477.242 500.246 505.105 510.238 513.277 517.272 522.221 534.199 536.201 538.23 556.229 557.75 564.274 584.316 617.228 623.799 629.301 634.255 644.325 646.316 +661.326 736.408 758.364 764.81 786.38 809.378 811.385 946.437 985.504 1526.27 + + + + +2 1 3 5 8 2 2 2 36 3 10 12 2 3 2 33 1 2 2 7 2 2 2 2 5 2 5 3 2 2 +2 9 12 2 7 26 9 3 5 2 21 6 2 3 91 2 8 3 2 67 100 7 2 2 7 17 7 14 5 2 +8 2 2 9 31 3 2 2 2 6 3 2 2 2 6 9 2 2 2 2 2 2 2 8 2 9 2 5 2 18 +12 2 2 2 5 30 6 5 2 2 + + + + + + +GRMZM2G036609_P01 P23225 Ferredoxin-dependent glutamate synthase, chloroplastic Precursor (EC 1.4.7.1)(Fd-GOGAT) seq=translation; coord=7:170961145..170979959:-1; parent_transcript=GRMZM2G036609_T01; parent_gene=GRMZM2G036609 + + + MATLPRAAPP TPAALLPLPR AAPPLLLAGR AAAARRSRLR ARGPSAAARR + SWVVASAASS SSRAVVGGVA RREAPPAPQK PTQQAADLNH ILSERGACGV + GFVANLKNMS SFDIVRDALM ALGCMEHRGG CGADSDSGDG AGLMSAVPWD + LFDDWASKQG LALFDRRNTG VGMVFLPQDE KSMEEAKAAT EKVFVDEGLE + VLGWRPVPFN VSVVGRNAKE TMPNIQQIFV KVAKEDNADD IERELYISRK + LIERAAKSFS WADELYFCSL SSRTIVYKGM LRSEVLGQFY LDLQNELYKS + PFAIYHRRFS TNTSPRWPLA QPMRLLGHNG EINTIQGNLN WMRSRETTLK + SPVWRGREHE ICPFGDPKAS DSANLDSTAE LLLRSGRSPA EALMILVPEA + YKNHPTLSIK YPEVTDFYDY YKGQMEAWDG PALLLFSDGR TVGATLDRNG + LRPARYWRTS DDFVYVASEV GVIPMDESKV VMKGRLGPGM MITVDLQTGQ + VLENTEVKKT VASASPYGTW LQECTRLIKP VNFLSSTIMD NETVLRHQQA + FGYSSEDVQM VIESMASQGK EPTFCMGDDI PLAVLSQRPH LLYDYFKQRF + AQVTNPAIDP LREGLVMSLE VNIGKRGNIL EVGPENADQV ALSSPVLNEG + ELETLLNDSK LKPKVLSTYF DIRKGLDGSL DKTIQALCEE ADAAVRSGSQ + LLVLSDRSEA PEPTRPAIPI LLAVGAIHQH LIQNGLRMSA SIVADTAQCF + STHHFACLIG YGASAVCPYL ALETCRQWRL SNKTLNLMRN GKMPTVTIEQ + AQRNFIKAVK SGLLKILSKM GISLLSSYCG AQIFEIYGLG QEVVDLAFCG + SVSKIGGLTL DELGRETLSF WVKAFSEDTA KRLENFGFIQ SRPGGEYHAN + NPEMSKLLHK AIREKRDNAY TVYQQHLASR PVNVLRDLLE LKSDRAPIPI + GKVESATSIV ERFCTGGMSL GAISRETHEA IAIAMNRIGG KSNSGEGGED + PIRWNPLTDV VDGYSPTLPH LKGLQNGDTA TSAIKQVASG RFGVTPTFLV + NADQIEIKIA QGAKPGEGGQ LPGKKVSAYI ARLRNSKPGV PLISPPPHHD + IYSIEDLAQL IYDLHQINPK AKVSVKLVSE AGIGTVASGV SKANADIIQI + SGHDGGTGAS PISSIKHAGG PWELGLTETN QTLIQNGLRE RVVLRVDGGF + RSGQDVLIAA AMGADEYGFG SVAMIATGCV MARICHTNNC PVGVASQREE + LRARFPGVPG DLVNYFLFVA EEVRAALAQL GYEKLDDIIG RTDLLKPKHI + SLVKTQHIDL GYLLSNAGLP EWSSSQIRSQ DVHTNGPVLD ETILADPEIA + DAIENEKEVS KAFQIYNVDR AVCGRVAGVI AKKYGDTGFA GQLNITFNGS + AGQSFGCFLT PGMNIRLVGE ANDYVGKGMA GGELVVVPVD KTGFVPEDAT + IVGNTCLYGA TGGQVFVRGK AGERFAVRNS LCQAVVEGTG DHCCEYMTGG + CVVVLGKAGR NVAAGMTGGL AYILDEDDTL VPKVNKEIVK MQRVNAPAGQ + MQLKGLIEAY VDKTGSEKGI AILREWEAYL PLFWQLVPPS EEDSPEACAE + FERVLAKQAT TQLSAK + + + + + +GRMZM2G036609_P02 P23225 Ferredoxin-dependent glutamate synthase, chloroplastic Precursor (EC 1.4.7.1)(Fd-GOGAT) seq=translation; coord=7:170961720..170979959:-1; parent_transcript=GRMZM2G036609_T02; parent_gene=GRMZM2G036609 + + + MATLPRAAPP TPAALLPLPR AAPPLLLAGR AAAARRSRLR ARGPSAAARR + SWVVASAASS SSRAVVGGVA RREAPPAPQK PTQQAADLNH ILSERGACGV + GFVANLKNMS SFDIVRDALM ALGCMEHRGG CGADSDSGDG AGLMSAVPWD + LFDDWASKQG LALFDRRNTG VGMVFLPQDE KSMEEAKAAT EKVFVDEGLE + VLGWRPVPFN VSVVGRNAKE TMPNIQQIFV KVAKEDNADD IERELYISRK + LIERAAKSFS WADELYFCSL SSRTIVYKGM LRSEVLGQFY LDLQNELYKS + PFAIYHRRFS TNTSPRWPLA QPMRLLGHNG EINTIQGNLN WMRSRETTLK + SPVWRGREHE ICPFGDPKAS DSANLDSTAE LLLRSGRSPA EALMILVPEA + YKNHPTLSIK YPEVTDFYDY YKGQMEAWDG PALLLFSDGR TVGATLDRNG + LRPARYWRTS DDFVYVASEV GVIPMDESKV VMKGRLGPGM MITVDLQTGQ + VLENTEVKKT VASASPYGTW LQECTRLIKP VNFLSSTIMD NETVLRHQQA + FGYSSEDVQM VIESMASQGK EPTFCMGDDI PLAVLSQRPH LLYDYFKQRF + AQVTNPAIDP LREGLVMSLE VNIGKRGNIL EVGPENADQV ALSSPVLNEG + ELETLLNDSK LKPKVLSTYF DIRKGLDGSL DKTIQALCEE ADAAVRSGSQ + LLVLSDRSEA PEPTRPAIPI LLAVGAIHQH LIQNGLRMSA SIVADTAQCF + STHHFACLIG YGASAVCPYL ALETCRQWRL SNKTLNLMRN GKMPTVTIEQ + AQRNFIKAVK SGLLKILSKM GISLLSSYCG AQIFEIYGLG QEVVDLAFCG + SVSKIGGLTL DELGRETLSF WVKAFSEDTA KRLENFGFIQ SRPGGEYHAN + NPEMSKLLHK AIREKRDNAY TVYQQHLASR PVNVLRDLLE LKSDRAPIPI + GKVESATSIV ERFCTGGMSL GAISRETHEA IAIAMNRIGG KSNSGEGGED + PIRWNPLTDV VDGYSPTLPH LKGLQNGDTA TSAIKQVASG RFGVTPTFLV + NADQIEIKIA QGAKPGEGGQ LPGKKVSAYI ARLRNSKPGV PLISPPPHHD + IYSIEDLAQL IYDLHQINPK AKVSVKLVSE AGIGTVASGV SKANADIIQI + SGHDGGTGAS PISSIKHAGG PWELGLTETN QTLIQNGLRE RVVLRVDGGF + RSGQDVLIAA AMGADEYGFG SVAMIATGCV MARICHTNNC PVGVASQREE + LRARFPGVPG DLVNYFLFVA EEVRAALAQL GYEKLDDIIG RTDLLKPKHI + SLVKTQHIDL GYLLSNAGLP EWSSSQIRSQ DVHTNGPVLD ETILADPEIA + DAIENEKEVS KAFQIYNVDR AVCGRVAGVI AKKYGDTGFA GQLNITFNGS + AGQSFGCFLT PGMNIRLVGE ANDYVGKGMA GGELVVVPVD KTGFVPEDAT + IVGNTCLYGA TGGQVFVRGK AGERFAVRNS LCQAVVEGTG DHCCEYMTGG + CVVVLGKAGR NVAAGMTGGL AYILDEDDTL VPKVNKEIVK MQRVNAPAGQ + MQLKGLIEAY VDKTGSEKGI AILREWEAYL PLFWQLVPPS EEDSPEACAE + FERVLAKQAT TQLSAK + + + + + + +6.3863 +-0.311527 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +6234 6234 6234 6054 5979 5611 4873 3975 2873 1888 1114 665 317 139 63 22 10 7 5 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6238 6238 6238 6058 5974 5602 4795 3724 2337 1217 611 170 46 21 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1809 2770 1291 293 65 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1310 2801 1562 428 117 12 4 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2631 (charge 3) + +1635.92 +3 + + +152.057 155.082 157.134 158.093 158.137 168.076 169.097 171.076 171.113 173.092 173.129 174.132 175.12 181.061 183.076 185.092 185.128 186.087 186.123 187.071 198.087 199.072 200.139 201.123 209.055 217.082 226.155 227.103 240.098 244.166 +245.169 249.092 252.098 257.124 268.165 270.107 275.208 283.176 293.122 297.118 301.187 315.202 323.179 328.161 332.23 337.185 347.193 355.199 367.207 390.716 408.673 411.271 415.191 419.244 429.283 469.243 478.933 483.294 488.243 503.286 +523.289 526.224 534.301 540.281 542.365 544.314 560.268 587.305 588.306 598.339 611.314 615.347 617.355 622.287 639.312 651.313 662.872 686.379 691.375 715.399 717.893 727.418 761.919 767.4 780.372 782.382 784.472 816.44 837.485 893.415 +913.514 918.501 921.475 970.523 981.481 1005.55 1049.56 1067.59 1069.59 1094.56 + + + + +4 19 58 4 4 7 13 3 9 7 43 8 14 9 9 4 30 14 20 10 3 4 20 9 3 8 26 10 9 45 +8 3 11 36 3 3 8 49 3 3 8 11 3 11 8 4 4 17 10 11 3 7 8 19 100 4 10 12 3 8 +3 15 18 3 14 3 3 12 4 12 21 19 6 9 30 3 11 3 3 3 19 3 11 7 10 4 15 3 17 8 +3 3 10 12 3 8 8 97 22 4 + + + + + + +GRMZM2G318635_P01 seq=translation; coord=5:213291570..213301733:-1; parent_transcript=GRMZM2G318635_T01; parent_gene=GRMZM2G318635 + + + + + + + + +6.4768 +-0.332144 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +5760 5760 5760 5760 5438 5258 4834 4489 2633 2171 955 448 214 88 35 13 10 6 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5762 5762 5762 5762 5440 5257 4828 4431 2537 1760 684 179 87 24 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3653 1917 183 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +812 4116 764 65 4 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2633 (charge 2) + +1158.56 +2 + + +152.057 155.081 157.097 158.092 159.076 167.056 168.055 168.675 169.097 169.134 171.076 171.113 171.37 173.091 173.129 175.119 185.092 187.071 187.145 197.128 199.108 201.087 205.101 209.142 212.104 217.083 221.104 224.361 227.103 228.105 +231.099 235.119 239.094 241.084 244.165 246.181 248.16 267.106 284.124 299.061 301.059 317.218 341.144 344.974 355.07 357.069 359.026 383.192 385.172 440.173 445.277 458.236 475.004 514.214 535.762 544.267 554.306 574.314 662.835 704.365 +729.394 849.383 861.433 885.397 919.458 925.44 972.467 990.471 1124.75 + + + + +7 18 20 21 23 49 5 6 100 20 8 24 5 8 6 71 11 12 8 7 90 7 7 5 8 6 6 4 72 6 +5 5 20 7 9 23 8 7 23 26 8 31 9 7 11 22 9 7 6 7 22 32 7 10 7 36 7 11 8 6 +7 7 59 6 6 8 9 29 7 + + + + + + +GRMZM2G001696_P01 Q9SLZ0 Phosphoenolpyruvate carboxykinase [ATP] (PEP carboxykinase)(PEPCK)(EC 4.1.1.49)(Phosphoenolpyruvate carboxylase) seq=translation; coord=1:35739884..35744291:-1; parent_transcript=GRMZM2G001696_T01; parent_gene=GRMZM2G001696 + + + MATPNGLARI ETTGKKKQDN GVWYDDSSAP VRAQTIDELH SLQRKRSAPS + TPKRSAPTTP IKGGAHSPFA VAISEEERHT QQMQSISASL ASLTRETGPK + VVKGDPAAKG EAAAQGAPST PRAHQQHRHP AAPAIAVSDS SLKFTHVLNN + LSPAELYEQA IKYEKGSFIT STGALATLSG AKTGRSPRDK RVVKDEVTAQ + DLWWGKGSPN IEMDEKTFLI NRERAVDYLN SLEKVFVNDQ YLNWDPENRI + KVRIISARAY HSLFMHNMCI RPTDEELEDF GTPDFTIYNA GQFPCNRYTH + YMTSSTSIDL NLARREMVIM GTQYAGEMKK GLFGVMHYLM PKRGILSLHS + GCNMGKDGDV ALFFGLSGTG KTTLSTDHNR LLIGDDEHCW SDNGVSNIEG + GCYAKCIDLA QEKEPDIWNA IKFGTVLENV VFDEHTREVD YADNSVTENT + RAAYPIEYIP NAKIPCVGPH PKNVILLACD AFGVLPPVSK LNLAQTMYHF + ISGYTALVAG TEDGIKEPQA TFSACFGAAF IMLHPTKYAA MLAEKMQKYG + ATGWLVNTGW SGGRYGVGKR IRLPYTRKII DAIHSGELLT ANYQKTEVFG + LEIPTEINGV PSEILDPINT WTDKAAYKEN LLRLGGLFKK NFEVFASYKI + GDDSSLTDEI LAAGPNF + + + + + +GRMZM2G001696_P02 Q9SLZ0 Phosphoenolpyruvate carboxykinase [ATP] (PEP carboxykinase)(PEPCK)(EC 4.1.1.49)(Phosphoenolpyruvate carboxylase) seq=translation; coord=1:35739885..35744291:-1; parent_transcript=GRMZM2G001696_T02; parent_gene=GRMZM2G001696 + + + MATPNGLARI ETTGKKKQDN GVWYDDSSAP VRAQTIDELH SLQRKRSAPS + TPKRSAPTTP IKGGAHSPFA VAISEEERHT QQMQSISASL ASLTRETGPK + VVKGDPAAKG EAAAQGAPST PRAHQQHRHP AAPAIAVSDS SLKFTHVLNN + LSPAELYEQA IKYEKGSFIT STGALATLSG AKTGRSPRDK RVVKDEVTAQ + DLWWGKGSPN IEMDEKTFLI NRERAVDYLN SLEKVFVNDQ YLNWDPENRI + KVRIISARAY HSLFMHNMCI RPTDEELEDF GTPDFTIYNA GQFPCNRYTH + YMTSSTSIDL NLARREMVIM GTQYAGEMKK GLFGVMHYLM PKRGILSLHS + GCNMGKDGDV ALFFGLSGTG KTTLSTDHNR LLIGDDEHCW SDNGVSNIEG + GCYAKCIDLA QEKEPDIWNA IKFGTVLENV VFDEHTREVD YADNSVTENT + RAAYPIEYIP NAKIPCVGPH PKNVILLACD AFGVLPPVSK LNLAQTMYHF + ISGYTALVAG TEDGIKEPQA TFSACFGAAF IMLHPTKYAA MLAEKMQKYG + ATGWLVNTGW SGGRYGVGKR IRLPYTRKII DAIHSGELLT ANYQKTEVFG + LEIPTEINGV PSEILDPINT WTDKAAYKEN LLRLGGLFKK NFEVFASYKI + GDDSSLTDEI LAAGPNF + + + + + + +5.56699 +-0.27156 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +5051 5051 5051 4881 4642 4483 4072 2606 2042 1071 653 355 219 113 49 23 15 5 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +5024 5024 5024 4854 4615 4449 4011 2426 1762 780 318 136 56 3 2 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2619 1992 390 45 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1160 3286 522 75 8 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2634 (charge 2) + +1212.6 +2 + + +155.082 157.109 157.133 158.092 159.076 167.055 169.097 173.092 175.119 183.076 185.092 185.914 186.088 187.071 187.107 188.074 200.102 201.087 213.087 223.156 225.043 227.102 230.114 239.094 244.166 255.146 258.108 259.11 268.13 272.172 +279.992 284.123 285.128 297.156 299.061 301.15 311.136 325.149 329.144 339.162 355.162 356.161 369.14 372.185 382.174 388.691 400.181 430.229 442.252 541.291 555.791 557.306 584.304 586.336 590.273 597.825 611.335 628.336 655.338 677.301 +685.365 687.367 765.411 796.397 813.425 815.418 867.429 884.455 897.407 955.484 1215.38 + + + + +11 4 4 7 31 15 6 5 32 5 13 3 4 100 3 5 21 12 22 11 27 4 6 30 5 31 99 16 6 32 +3 36 6 6 13 17 5 4 27 3 13 4 4 3 5 3 7 11 3 17 5 81 15 7 14 27 5 15 6 18 +97 6 7 14 44 5 5 41 4 7 4 + + + + + + +GRMZM2G082640_P01 seq=translation; coord=1:200401193..200409521:1; parent_transcript=GRMZM2G082640_T01; parent_gene=GRMZM2G082640 + + + MMLKQENKSA MEAFREVLEK ELSGVNLRSD YEDGYEEEDV NSKGGDNKGT + SKKTSSRKAR KQEGLKQQYN GEEDQNGGSN ATTGGARKKK GGHVRQSSAT + HDAIDKNYSG SSAEGLRNKR QKSAAQSASV GRREGLRQRS DAKQHPDAAE + GSTEPLADVP GSDGAAQGSM QHGTSAPHTE IKAMVRNILF KDIVDKEHDA + EMAYVEEVIN GICNATDSMV GGGGGDASAK GGRGSKQSGS GVEGESSNAT + ERRRDEATEN ALAVKGNTPS RGTMAMTPGQ LSARQNRQNR IMQTLALIPP + SGSPFGRNEE VAASRQKL + + + + + +GRMZM2G082640_P02 seq=translation; coord=1:200401193..200409521:1; parent_transcript=GRMZM2G082640_T02; parent_gene=GRMZM2G082640 + + + MMLKQENKSA MEAFREVLEK ELSGVNLRSD YEDGYEEEDV NSKGGDNKGT + SKKTSSRKAR KQEGLKQQYN GEEDQNGGSN ATTGGARKKK GGHVRQSSAT + HDAIDKNYSG SSAEGLRNKR QKSAAQSASV GRREGLRQRS DAKQHPDAAE + GSTEPLADVP GSDGAAQGSM QHGTSAPHTE IKAMVRNILF KDIVDKEHDA + EMAYVEEVIN GICNATDSMV GGGGGDASAK GGRGSKQSGS GVEGESSNAT + ERRRDEATEN ALAVKGNTPG NNGDDAGAA + + + + + +GRMZM2G082640_P03 seq=translation; coord=1:200401193..200409279:1; parent_transcript=GRMZM2G082640_T03; parent_gene=GRMZM2G082640 + + + MMLKQENKSA MEAFREVLEK ELSGVNLRSD YEDGYEEEDV NSKGGDNKGT + SKKTSSRKAR KQEGLKQQYN GEEDQNGGSN ATTGGARKKK GGHVRQSSAT + HDAIDKNYSG SSAEGLRNKR QKSAAQSASV GRREGLRQRS DAKQHPDAAE + GSTEPLADVP GSDGAAQGSM QHGTSAPHTE IKAMVRNILF KDIVDKEHDA + EMAYVEEVIN GICNATDSMV GGGGGDASAK GGRGSKQSGS GVEGESSNAT + ERRRDEATEN ALAVKGNTPV S + + + + + + +5.47728 +-0.353373 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +2447 2447 2447 2447 2447 2318 2231 1220 952 399 128 64 26 11 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2444 2444 2444 2444 2444 2315 2226 1207 884 335 64 19 1 0 + + + + + + +0 1 2 3 4 + + + + +1826 596 33 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +417 1847 173 9 1 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2636 (charge 2) + +1594.69 +2 + + +157.098 167.958 170.092 171.076 175.119 181.061 184.072 198.088 205.918 231.098 244.128 262.277 305.859 325.115 382.134 400.149 405.214 471.233 506.331 619.249 677.324 764.351 779.833 788.842 893.397 950.411 1061.45 1079.46 1209.46 1235.55 +1379.6 + + + + +9 7 10 9 33 11 9 18 6 9 9 8 8 18 61 21 10 13 10 14 20 48 13 40 16 79 35 100 13 14 +15 + + + + + + +AC155496.2_FGP009 seq=translation; coord=5:4777029..4786789:-1; parent_transcript=AC155496.2_FGT009; parent_gene=AC155496.2_FG009 + + + MSQSYAAAAS KRPFSSPTTS PSPTSSPATP LMKKAKHPAA ASSSSVGTVE + KNGIQLDTVA AAMGGGRTNG EEDADMVLVN QDKLPAPSVP ASAGVAANLF + RKKATLPQPS TSARKPLRIK IGQPKLPKNF EEDTWSILKD AITAIFLKQK + LSCDVEKLYQ AAGDLCLHKL GANLYDRIKK ECGIHIAEKI SALVGQSPDL + VVFLSLVQRT WQDFCDQMLI IRGIALLLDV KYVKNVANIC SVWDMGLQLF + RKHLSLSTEI EHKTVTGLLR LIESERLGEA IDRTLLSHLL KMLTALGMYS + ESFEKPFLEC TSEFYATEGV RYMQQSDIPD YLKHVESRLQ EEHERCILYL + EANTRKPLIA TTEKQLLERH TSAIIEKGFT MLMDANRIND LSRMYNLFQR + VNAVELLKLA LSSYIRATGQ GIIMDEEKDR ELVPFLLDFK ASLDKILEES + FAKNEAFSNT IKDSFEHLIN LRQNRPAELI AKFLDEKLRA GNKGTSEEEL + EGILDKVLVL FRFIQGKDVF EAFYKKDLAK RLLLGKSASI DAEKSMITKL + KTECGSQFTN KLEGMFKDIE LSKEINDSFR QSSQARTKLP SGIEMSVHVL + TTGYWPTYPP MDVKLPHELN VYQDIFKEFY LSKYSGRRLM WQNSLGHCVL + KADFPKGKKE LAVSLFQSVV LMLFNDAQKL SFIDIKDSTG IEDKELRRTL + QSLACGKVRV LQKIPKGRDV EDKDEFVFNE DFSAPLYRIK VNAIQMKETV + EENTSTTERV FQDRQYQVDA AIVRIMKTRK VLSHTLLITE LYQQLKFPVK + PADIKKRIES LIDREYLERD RSNPQIYNYL A + + + + + +AC177936.6_FGP008 seq=translation; coord=1:285647286..285648424:1; parent_transcript=AC177936.6_FGT008; parent_gene=AC177936.6_FG008 + + + SVVLMLFNDA QKLSFLDIKD STGIEDKELR RTLQSLACGK VRVLQKIPKG + RDVEDKDDFV FNEDFSAPLY RIKVNAIQMK ETVEENTSTT ERVFQDRQYQ + VDAAIVRIMK TRKVLSHTLL ITELYQQLKF PVKPADIKKR IESLIDREYL + ERDRSNPQIY NYLA + + + + + + +4.89353 +-0.315712 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +2765 2765 2765 2765 2765 2684 2632 2478 1499 1149 745 227 89 43 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2779 2779 2779 2779 2779 2698 2646 2492 1490 1098 706 175 63 21 1 0 + + + + + + +0 1 2 3 + + + + +1536 1193 50 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +616 2007 128 24 0 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2642 (charge 2) + +1395.62 +2 + + +167.081 169.323 171.076 173.129 175.119 185.092 189.087 194.128 195.077 201.123 203.103 213.087 226.118 229.118 231.098 239.095 241.08 244.131 259.092 266.149 286.139 294.146 299.171 312.155 341.072 372.443 446.706 467.931 518.617 593.288 +626.356 694.338 713.335 733.622 791.352 808.379 920.404 937.413 1066.46 1165.53 + + + + +9 8 9 31 60 38 15 9 37 15 16 100 9 42 48 11 11 8 9 17 13 35 10 29 9 8 8 12 8 47 +9 29 9 10 13 64 12 46 47 16 + + + + + + +GRMZM2G123558_P01 NP_001130834 hypothetical protein LOC100191938 seq=translation; coord=3:1711864..1714237:1; parent_transcript=GRMZM2G123558_T01; parent_gene=GRMZM2G123558 + + + MTSVWKTKVL PGLNKIFDKD GKKAAAAGFL KSFNKEEFDK EIEDKKTELE + PKVVEAYEAS PPEVKALFKD KKPVKVSKKN SAAVTKFLDE LAKIDFPGAK + VVSEAVAKSG TSPLLPAITF ILDKVAPFIP KEEPKEEPAA EATSREVAVE + EKKEEAEPAA ATEAAPAPAE TPSEAAVVEE KKEEEKKEEE DKPAAEEAAP + PAAAAAAAEE K + + + + + +GRMZM2G123558_P02 NP_001130834 hypothetical protein LOC100191938 seq=translation; coord=3:1711861..1714122:1; parent_transcript=GRMZM2G123558_T02; parent_gene=GRMZM2G123558 + + + MYASLCLVSC LFIHHRPAGD FPFIIDLPAS LNFFCCVCWP GAEVATRIYS + EEEIEMTSVW KTKVLPGLNK IFDKDGKKAA AAGFLKSFNK EEFDKEIEDK + KTELEPKVVE AYEASPPEVK ALFKDKKPVK VSKKNSAAVT KFLDELAKID + FPGAKVVSEA VAKSGTSPLL PAITFILDKV APFIPKEEPK EEPAAEATSR + EVAVEEKKEE AEPAAATEAA PAPAETPSEA AVVEEKKEEE KKEEEDKPAA + EEAAPPAAAA AAAEEK + + + + + + +5.14395 +-0.278051 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +8708 8708 8708 8708 8447 8137 7596 7024 5832 4688 3268 1995 999 528 265 99 40 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +8747 8747 8747 8747 8486 8168 7592 6947 5664 3992 2211 837 224 65 28 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3454 3331 1419 411 98 25 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1386 3863 2341 870 195 74 8 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2646 (charge 3) + +1543.72 +3 + + +155.082 158.093 166.061 167.082 169.097 173.092 175.119 183.077 185.093 189.087 195.076 195.113 199.107 201.087 207.125 213.087 217.109 226.155 227.101 231.098 235.119 241.082 245.125 254.149 259.093 262.151 264.133 272.171 282.145 284.124 +291.15 297.193 302.135 312.119 323.187 325.188 330.13 337.187 338.137 346.172 355.198 363.199 373.175 383.156 400.268 409.229 416.228 417.212 434.236 436.235 450.757 456.246 466.234 471.307 473.754 484.244 494.275 500.262 509.269 517.276 +534.303 545.269 553.799 556.259 558.337 563.28 565.282 567.795 577.266 581.294 591.298 595.273 600.305 602.322 611.329 616.31 624.336 626.319 634.317 636.323 645.37 652.332 662.402 689.376 705.354 716.407 724.312 742.318 763.448 802.406 +817.453 892.388 900.509 931.452 946.495 969.52 987.539 1017.54 1060.5 1124.6 + + + + +100 19 15 14 25 66 71 35 5 6 20 5 9 74 13 25 6 62 11 47 66 29 18 18 19 21 6 21 6 17 +11 20 6 25 8 8 7 11 6 10 14 39 5 6 10 14 9 9 99 5 7 8 17 10 7 30 11 8 12 6 +55 20 14 6 17 75 6 8 8 14 7 14 6 23 71 9 6 5 85 6 41 19 17 13 29 31 36 10 26 29 +34 9 28 6 11 10 45 9 13 7 + + + + + + +GRMZM2G140545_P01 NP_001149589 14-3-3-like protein A seq=translation; coord=4:196903412..196904780:1; parent_transcript=GRMZM2G140545_T01; parent_gene=GRMZM2G140545 + + + MAAAAAAAGT REEMVYMAKL AEQAERYEEM VEFMEKVAAA AELTVEERNL + LSVAYKNVIG ARRASWRIVS SIEHKEETRG AAGHAAAARG YRARVEAELS + GICAGILRLL DERLVPAAAA VDARVFYLKM KGDYHRYLAE FKTGAERKDA + ADSTLAAYQA AQDIAVKELP PTHPIRLGLA LNFSVFYYEI LSSPDRACSL + AKQAFDEAIS ELDSLGEESY KDSTLIMQLL RDNLTLWTSD MQEDGGDEMR + DANKPDEEQ + + + + + + +6.08179 +-0.296672 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +7605 7605 7605 7442 7275 6970 6466 5843 4631 3440 2269 1221 605 309 152 72 47 13 4 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7606 7606 7606 7443 7276 6953 6373 5642 4058 2419 806 140 36 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2549 3129 1474 364 82 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1212 2664 2462 933 247 65 23 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2647 (charge 3) + +1427.75 +3 + + +152.057 155.081 155.092 156.077 157.06 157.097 158.092 159.076 159.113 166.062 167.056 167.082 169.098 171.076 171.113 173.092 173.129 175.071 175.119 177.102 181.096 185.165 186.169 187.072 187.107 189.087 195.076 197.104 197.129 199.072 +199.108 201.124 213.16 215.139 217.082 221.104 226.155 227.102 230.114 232.139 237.134 239.095 241.082 244.165 249.099 252.108 256.13 259.14 266.162 270.145 272.173 274.188 276.167 277.168 284.172 288.204 299.062 302.154 312.125 317.193 +368.16 377.193 396.151 400.206 405.207 416.261 436.994 441.179 455.722 464.727 466.244 487.267 496.602 501.301 503.762 521.269 525.194 530.309 534.253 553.317 564.786 567.301 569.231 596.233 599.796 603.302 608.302 645.321 657.83 662.348 +667.308 683.375 695.298 714.341 733.344 799.406 801.413 911.431 928.448 940.435 + + + + +3 10 3 10 3 3 13 6 5 6 10 9 12 6 5 14 16 9 58 22 3 100 13 3 7 6 14 3 3 3 +10 11 18 6 7 10 18 12 5 5 6 13 9 11 15 6 7 3 22 19 3 3 59 8 12 7 8 6 3 3 +3 5 8 34 17 3 16 5 17 10 15 3 10 3 3 9 21 4 38 9 15 5 3 16 9 11 34 6 7 55 +6 8 6 3 3 53 3 6 34 3 + + + + + + +GRMZM2G060947_P01 NP_001130826 hypothetical protein LOC100191930 seq=translation; coord=4:160565693..160569675:-1; parent_transcript=GRMZM2G060947_T01; parent_gene=GRMZM2G060947 + + + MPGITEDGVV AEEVPNGVNF SPQNESLPAP KSTAASTMAG SMQSEALEMH + VEASGAGEPS IEQLYNNVCE MESSSEGGSP SRESFGSDGE ESRIDSELRH + LVAGEMEAMK VIEEEEENGS VANVVPPAPA ENGTPVKEHS SSSSKKSKKA + SKSQLESDAS VGLNGKASTE EGESEVSKPA SRVGRRRKSN ANPQSGTEDA + GLDNPDLGPF LLKHARDLIA SENPRRALKY ALRATKSFEK CAGGKPSLNL + VMSLHVVAAI YCNLGKYEEA VPVLHRSIEI PVIEEGQEHA LAKFSGCMQL + GDTYGMLGQT AHSLQWYASG LEIQKQTLGE QDPRVGETCR YLAEAHVQAL + QLDEAQRLCQ IALDIHREHR ETASLEETAD RRLMGLICDT KGDHEAALEH + LVMASMSMVA NGQETEVASV DCSIGDIYLS LGRYDEAVFA YQKALTVFKT + SKGENHATVA SVFVRLADLY NKTGKLRESK SYCENALKIY QKPIPGTSLE + EIATGLTDVS AIYETMNEHE QALKLLQKAL KMYNNSAGQQ STIAGIEAQM + GVLHYILGNY GESYDSFKSA IAKLRTCGEK KSAFFGIALN QMGLACVQRY + SINEAAELFE EARTVLEQEY GPYHPDTLGV YSNLAGTYDA MGRLDEAIEI + LEYVVGMREE KLGTANPDVD DEKRRLGELL KEAGRVRSRK AKSLENLLET + NPYIATKRNA VAA + + + + + + +6.02607 +-0.267825 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 + + + + +8881 8881 8881 8398 8205 7531 6932 5346 4249 2640 1735 879 498 232 124 66 33 21 10 6 3 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8875 8875 8875 8392 8177 7475 6734 4725 3307 1472 582 148 25 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2894 3663 1724 470 114 22 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1761 3731 2265 809 251 44 11 15 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2649 (charge 3) + +1663.78 +3 + + +155.082 157.097 159.077 161.091 166.061 167.081 168.066 169.061 169.098 171.077 173.092 173.129 175.119 185.092 187.072 189.087 195.076 198.124 199.072 199.108 201.124 203.103 209.092 213.087 217.082 224.103 226.155 228.134 231.098 242.114 +244.166 254.152 256.13 259.092 262.152 270.109 272.171 274.103 282.108 284.102 290.146 298.104 301.13 316.113 323.173 333.188 337.187 367.125 370.215 372.724 379.68 383.193 385.134 413.215 427.144 430.241 437.246 452.258 480.759 482.273 +496.168 512.314 517.308 536.276 545.278 548.305 554.3 556.297 558.339 563.283 564.787 567.3 573.788 627.355 629.308 638.313 645.368 651.256 661.302 678.353 684.825 686.349 694.337 702.833 713.367 744.437 746.443 751.384 753.38 759.365 +790.438 797.391 833.399 852.413 873.476 903.491 943.486 960.512 1129.6 1146.59 + + + + +8 5 19 3 3 3 4 4 8 12 3 4 28 37 19 12 3 3 10 27 4 25 4 22 13 9 91 4 26 14 +14 4 15 4 3 3 9 8 4 8 4 8 12 3 3 8 4 4 3 4 3 10 9 9 3 100 3 14 26 5 +10 3 3 3 5 3 8 4 19 3 3 4 25 3 11 24 70 3 4 5 3 14 4 4 4 29 4 26 3 3 +3 3 3 3 13 9 3 22 4 10 + + + + + + +GRMZM2G083173_P01 NP_001151936 LOC100285573 seq=translation; coord=1:84413344..84417967:1; parent_transcript=GRMZM2G083173_T01; parent_gene=GRMZM2G083173 + + + MGGAVMVAIA ASIGNLLQGW DNATIAGAVL YIKKEFNLQS EPLIEGLIVA + MSLIGATVIT TFSGAAADCV GRRPMLVASA VLYFVSGLVM LWAPSVYILL + LARLIDGFGI GLAVTLVPLY ISETAPTDIR GLLNTLPQFS GSGGMFLSYC + MVFGMSLMPK PDWRLMLGVL SIPSLIYFGL TVFYLPESPR WLVSKGRMAE + AKRVLQRLRG REDVSGEMAL LVEGLGVGKD TRIEEYIIGP DDELADEGLA + PDPEKIKLYG PEEGLSWVAR PVRGQSALGS ALGLISRHGS MAASQGKPLV + DPMVTLFGSV HEKMPEIMGS MRSTLFPNFG SMFSVADQQQ VKADWDAESQ + REGEDYASDH GGDDIEDNLQ SPLISRQATS VEGKEIAAPH GSILGAVGRS + SSLQGGEAVS SMGIGGGWQL AWKWTEREGE DGQKEGGFQR IYLHEEGVQG + NRGSILSLPG GDVPPGGEFI QAAALVSQPA LYSKELLEQR AAGPAMMHPS + EAVTKGPRWA DLFEPGVKHA LFVGIGIQIL QQFAGINGVL YYTPQILEQA + GVGVLLSNLG LNASSASILI SALTTLLMLP SIGIAMRLMD MSGRRFLLLA + TIPVLIVALL VLVVSNIVDV GDVAHAALST ASVIVYFCFF VMGFGPVPNI + LCAEIFPTTV RGVCIAICAL AFWLGDIIVT YTLPVMLNVV GLAGVFGVYA + VVCVLALAFV FVKVPETKGM PLEVITEFFS VGAKQAKEEE EEEAREG + + + + + +GRMZM2G083173_P02 NP_001151936 LOC100285573 seq=translation; coord=1:84413344..84417615:1; parent_transcript=GRMZM2G083173_T02; parent_gene=GRMZM2G083173 + + + MGGAVMVAIA ASIGNLLQGW DNATIAGAVL YIKKEFNLQS EPLIEGLIVA + MSLIGATVIT TFSGAAADCV GRRPMLVASA VLYFVSGLVM LWAPSVYILL + LARLIDGFGI GLAVTLVPLY ISETAPTDIR GLLNTLPQFS GSGGMFLSYC + MVFGMSLMPK PDWRLMLGVL SIPSLIYFGL TVFYLPESPR WLVSKGRMAE + AKRVLQRLRG REDVSGEMAL LVEGLGVGKD TRIEEYIIGP DDELADEGLA + PDPEKIKLYG PEEGLSWVAR PVRGQSALGS ALGLISRHGS MAASQGKPLV + DPMVTLFGSV HEKMPEIMGS MRSTLFPNFG SMFSVADQQQ VKADWDAESQ + REGEDYASDH GGDDIEDNLQ SPLISRQATS VEGKEIAAPH GSILGAVGRS + SSLQGGEAVS SMGIGGGWQL AWKWTEREGE DGQKEGGFQR IYLHEEGVQG + NRGSILSLPG GDVPPGGEFI QAAALVSQPA LYSKELLEQR AAGPAMMHPS + EAVTKGPRWA DLFEPGVKHA LFVGIGIQIL QQFAGINGVL YYTPQILEQA + GVGVLLSNLG LNASSASILI SALTTLLMLP SIGIAMRLMD MSGRRFLLLA + TIPVLIVALL VLVVSNIVDV GDVAHAALST ASVIVYFCFF VMGFGPVPNI + LCAEIFPTTV RGVCIAICAL AFWLGDIIVT YTLPVMLNVV GLAGVFGVYA + VVCVLALAFV FVKVPETKGM PLEVITEFFS VGAKQAKEEE EEEAREG + + + + + +GRMZM2G083173_P03 NP_001151936 LOC100285573 seq=translation; coord=1:84413383..84417967:1; parent_transcript=GRMZM2G083173_T03; parent_gene=GRMZM2G083173 + + + MAASQGKPLV DPMVTLFGSV HEKMPEIMGS MRSTLFPNFG SMFSVADQQQ + VKADWDAESQ REGEDYASDH GGDDIEDNLQ SPLISRQATS VEGKEIAAPH + GSILGAVGRS SSLQGGEAVS SMGIGGGWQL AWKWTEREGE DGQKEGGFQR + IYLHEEGVQG NRGSILSLPG GDVPPGGEFI QAAALVSQPA LYSKELLEQR + AAGPAMMHPS EAVTKGPRWA DLFEPGVKHA LFVGIGIQIL QQFAGINGVL + YYTPQILEQA GVGVLLSNLG LNASSASILI SALTTLLMLP SIGIAMRLMD + MSGRRFLLLA TIPVLIVALL VLVVSNIVDV GDVAHAALST ASVIVYFCFF + VMGFGPVPNI LCAEIFPTTV RGVCIAICAL AFWLGDIIVT YTLPVMLNVV + GLAGVFGVYA VVCVLALAFV FVKVPETKGM PLEVITEFFS VGAKQAKEEE + EEEAREG + + + + + +GRMZM2G083173_P04 NP_001151936 LOC100285573 seq=translation; coord=1:84413404..84417967:1; parent_transcript=GRMZM2G083173_T04; parent_gene=GRMZM2G083173 + + + MGIGGGWQLA WKWTEREGED GQKEGGFQRI YLHEEGVQGN RGSILSLPGG + DVPPGGEFIQ AAALVSQPAL YSKELLEQRA AGPAMMHPSE AVTKGPRWAD + LFEPGVKHAL FVGIGIQILQ QFAGINGVLY YTPQILEQAG VGVLLSNLGL + NASSASILIS ALTTLLMLPS IGIAMRLMDM SGRRFLLLAT IPVLIVALLV + LVVSNIVDVG DVAHAALSTA SVIVYFCFFV MGFGPVPNIL CAEIFPTTVR + GVCIAICALA FWLGDIIVTY TLPVMLNVVG LAGVFGVYAV VCVLALAFVF + VKVPETKGMP LEVITEFFSV GAKQAKEEEE EEAREG + + + + + + +6.43195 +-0.36754 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +4029 4029 4029 3987 3929 3628 3360 2898 2465 1614 1107 530 193 73 27 11 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4041 4041 4041 3999 3941 3639 3348 2783 2339 1339 755 237 18 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1571 1627 701 135 7 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +812 1905 993 261 49 10 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2666 (charge 3) + +1436.64 +3 + + +152.057 154.05 155.082 156.077 157.097 157.133 158.091 159.077 166.062 167.081 169.061 169.097 171.077 172.072 173.092 173.128 175.119 177.102 181.061 185.129 186.088 186.124 187.071 189.087 195.114 197.092 197.129 199.072 199.107 201.123 +203.121 207.124 209.139 212.103 215.103 217.081 222.124 226.155 227.103 235.119 240.134 241.136 244.166 252.099 257.161 258.145 266.16 268.129 270.109 275.125 284.171 286.143 297.157 303.177 305.182 309.158 344.125 346.207 355.161 357.177 +364.124 365.647 381.225 395.119 400.232 402.702 411.217 417.255 424.228 433.678 436.511 443.264 444.264 450.246 468.188 473.19 477.19 480.256 487.17 501.185 503.758 507.269 514.299 534.296 548.294 549.299 562.284 564.289 566.295 601.33 +633.32 638.243 659.329 672.366 675.319 693.331 695.335 743.398 819.407 821.431 + + + + +32 4 15 14 5 13 17 25 4 8 45 19 11 4 26 4 100 8 9 5 9 9 12 16 7 53 5 13 11 5 +23 9 9 9 23 13 8 20 11 18 60 5 13 9 9 21 5 35 11 10 12 25 28 21 21 9 10 4 5 8 +10 8 13 5 12 4 8 12 9 4 4 56 12 11 14 4 5 9 4 10 5 18 4 4 14 8 5 71 9 22 +4 9 10 30 21 57 5 8 8 25 + + + + + + +GRMZM5G836250_P03 NP_001141584 hypothetical protein LOC100273700 seq=translation; coord=3:175707821..175710858:-1; parent_transcript=GRMZM5G836250_T03; parent_gene=GRMZM5G836250 + + + MDHAADAHRT DLMTITRHVL NEQSRNPESR GDFTILLSHI VLGCKFVASA + VNKAGLAQLI GLAGETNVQG EEQKKLDVLS NEVFVKALVS SGRTCVLVSE + EDEEATFVDP KLRGRYCVCF DPLDGSSNID CGVSIGTIFG IYIIKDKDNV + TLEDVLQPGK NMLAAGYCMY GSSCTLVLST GTGVNGFTLD PSLGEFILTH + PDIKIPKKGK IYSVNEGNAK NWDAPVAKFV EKCKYPKDGS PPRSLRYIGS + MVADVHRTLL YGGVFLYPAD EKNPNGKLRI LYEVFPMSFL MEQAGGQSFT + GKERALDLIP TKIHDRSPIF LGSYDDVEEI KALYAEQAKS SSASS + + + + + + +GRMZM5G836250_P02 NP_001141584 hypothetical protein LOC100273700 seq=translation; coord=3:175708055..175710858:-1; parent_transcript=GRMZM5G836250_T02; parent_gene=GRMZM5G836250 + + + MDHAADAHRT DLMTITRHVL NEQSRNPESR GDFTILLSHI VLGCKFVASA + VNKAGLAQLI GLAGETNVQG EEQKKLDVLS NEVFVKALVS SGRTCVLVSE + EDEEATFVDP KLRGRYCVCF DPLDGSSNID CGVSIGTIFG IYIIKDKDNV + TLEDVLQPGK NMLAAGYCMY GSSCTLVLST GTGVNGFTLD PSLGEFILTH + PDIKIPKKGK IYSVNEGNAK NWDAPVAKFV EKCKYPKDGS PPRSLRYIGS + MVADVHRTLL YGGVFLYPAD EKNPNGKLRI LYEVFPMSFL MEQAGGQSFT + GKERVGFTPL HFLYKKKSTS APSS + + + + + + +GRMZM5G836250_P01 NP_001141584 hypothetical protein LOC100273700 seq=translation; coord=3:175708055..175710858:-1; parent_transcript=GRMZM5G836250_T01; parent_gene=GRMZM5G836250 + + + MDHAADAHRT DLMTITRHVL NEQSRNPESR GDFTILLSHI VLGCKFVASA + VNKAGLAQLI GLAGETNVQG EEQKKLDVLS NEVFVKALVS SGRTCVLVSE + EDEEATFVDP KLRGR + + + + + + + +5.12373 +-0.310529 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +2341 2341 2341 2066 1993 1782 1596 1414 1228 739 490 262 90 33 25 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2342 2342 2342 2067 1993 1759 1540 1351 1147 516 330 110 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1351 879 108 3 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +501 1382 382 45 31 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2667 (charge 2) + +1065.45 +2 + + +152.057 155.081 155.093 156.077 157.109 158.092 162.091 164.082 166.061 167.056 167.082 169.097 171.077 172.071 173.055 173.091 174.059 175.119 176.124 179.118 181.095 181.109 183.076 183.113 185.092 189.134 195.089 195.113 197.128 198.124 +199.07 199.108 205.096 207.113 209.105 213.087 226.155 227.102 232.14 235.144 239.095 242.15 244.165 247.086 253.093 258.145 263.136 265.117 268.128 272.171 278.121 284.171 295.149 299.063 312.177 324.126 355.197 361.701 364.204 380.14 +383.216 389.192 395.165 398.147 403.722 408.134 412.73 426.144 434.24 445.566 447.241 452.249 466.207 484.236 493.155 497.18 499.928 518.93 534.304 538.273 549.297 552.253 554.307 569.279 581.29 623.291 625.344 637.337 640.316 642.319 +646.329 659.343 683.246 722.395 727.398 753.265 774.408 777.373 803.353 824.446 + + + + +5 13 3 8 3 16 5 3 3 18 5 14 11 5 3 5 26 100 4 3 3 9 3 3 5 3 4 10 9 9 +3 28 3 10 22 5 60 23 8 11 39 5 21 3 35 5 4 5 3 3 3 3 4 16 9 3 11 10 5 4 +63 19 8 23 4 5 21 29 3 11 4 5 3 9 9 14 4 3 10 3 3 4 14 38 11 4 4 9 54 3 +3 3 3 4 16 4 8 11 3 12 + + + + + + +GRMZM2G405459_P01 seq=translation; coord=5:145524164..145526605:-1; parent_transcript=GRMZM2G405459_T01; parent_gene=GRMZM2G405459 + + + MAPATLLLAR LAVACALALG AMAQLSPTFY DASCPSLQAI VRAGMAAAVQ + QEPRMGASIL RLFFHDCFVQ GCDASVLLDD SPTLTGEKNA GPNANSLRGF + EVIDSIKSQV EAACPGTVSC ADILALAARD GVNLLSGPTW AVQLGRRDTR + TASQSAANSN LPSPSSSAAA LVSAFASKGL DSRDLVALSG AHTIGAARCA + TFRSRVYNDT NISAGFAAKR RQICQAQAGA SDGNLAPLDA MSSVRFDNGY + FRNLVAQFGL LHSDQELFGA GGGAVDFITA QYARNGAAFS RDFVTAVLKM + GSIGPLTGSS GEIRANCRKP N + + + + + + +GRMZM2G405459_P02 seq=translation; coord=5:145524169..145526605:-1; parent_transcript=GRMZM2G405459_T02; parent_gene=GRMZM2G405459 + + + MAPATLLLAR LAVACALALG AMAQLSPTFY DASCPSLQAI VRAGMAAAVQ + QEPRMGASIL RLFFHDCFVQ VSMHVVAPWA CCWSSVCVAP RHPSNTPLLL + LLLPMQGCDA SVLLDDSPTL TGEKNAGPNA NSLRGFEVID SIKSQVEAAC + PGTVSCADIL ALAARDGVNL LSGPTWAVQL GRRDTRTASQ SAANSNLPSP + SSSAAALVSA FASKGLDSRD LVALSGAHTI GAARCATFRS RVYNDTNISA + GFAAKRRQIC QAQAGASDGN LAPLDAMSSV RFDNGYFRNL VAQFGLLHSD + QELFGAGGGA VDFITAQYAR NGAAFSRDFV TAVLKMGSIG PLTGSSGEIR + ANCRKPN + + + + + + + +5.1698 +-0.229769 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +6367 6367 6367 6310 5897 5669 5326 4465 3827 2513 1652 730 479 309 207 112 65 39 18 13 4 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6336 6336 6336 6279 5866 5605 5193 4235 2921 1281 561 260 97 47 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2929 2587 712 134 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1124 3156 1767 249 66 7 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2668 (charge 2) + +1244.61 +2 + + +152.057 155.082 157.098 158.092 159.077 159.092 167.081 169.097 171.076 172.072 173.092 173.129 175.119 181.097 183.075 184.108 185.092 187.108 187.144 188.038 189.087 190.086 191.085 197.104 199.108 201.087 205.065 212.103 214.119 217.082 +219.08 225.123 226.154 228.135 240.134 242.149 244.166 246.156 249.162 252.134 255.145 261.156 266.114 270.144 272.172 274.103 276.101 290.116 298.14 302.118 304.097 313.188 315.133 319.143 320.139 326.182 338.142 345.178 347.138 354.177 +373.155 375.199 383.201 386.162 388.46 390.182 401.215 403.716 418.227 425.214 452.254 492.243 504.234 507.264 515.279 518.257 529.279 591.302 619.267 640.309 657.333 696.321 715.358 756.399 784.362 801.368 804.345 827.435 829.437 872.411 +898.476 900.486 909.466 933.384 969.511 971.52 1004.43 + + + + +8 18 5 6 6 4 7 15 6 4 3 3 41 5 4 4 3 5 5 7 24 4 6 5 14 6 18 21 8 34 +15 4 37 8 6 23 12 5 4 5 30 4 4 4 100 36 68 6 5 27 5 5 4 8 5 13 4 4 28 25 +14 4 6 4 4 7 5 3 6 12 4 7 5 4 4 5 10 5 5 7 37 5 4 54 4 12 6 68 6 7 +48 5 13 6 39 5 20 + + + + + + +GRMZM2G166441_P02 NP_001141289 hypothetical protein LOC100273380 seq=translation; coord=8:170330883..170335331:1; parent_transcript=GRMZM2G166441_T02; parent_gene=GRMZM2G166441 + + + MAASLLHASA AAASLLSSTQ HARAGAAAFH PLACAPSLRL TRSSFSTNRH + LEISLRAISA SRRFAGRGAP RDRRVVAALA GEQTEGSEVG DDRNGEIKPE + EAQEIWKVML EQFKAEALRM QALSMQAYDV YSERTREVLL EASEKLKIQA + DKAQKDLSVV ATEIGQEGQE YLMMAARNSP DSIKDITTTF RALGKLNWPS + EYEDYHVGIP FGTFLTVGGF LNFMLAGSTS ALRFGIILGL ALLALGISSL + RSQRDGGRRP RLLVKGQAAI ASVIFFREFS VLLQNGWFPK IFMVLLSGVV + AGFYFYRIAA GSPKELSSNS DSVN + + + + + +GRMZM2G166441_P03 NP_001141289 hypothetical protein LOC100273380 seq=translation; coord=8:170330883..170335331:1; parent_transcript=GRMZM2G166441_T03; parent_gene=GRMZM2G166441 + + + MAASLLHASA AAASLLSSTQ HARAGAAAFH PLACAPSLRL TRSSFSTNRH + LEISLRAISA SRRFAGRGAP RDRRVVAALA GEQTEGSEVG DDRNGEIKPE + EAQEIWKVML EQFKAEALRM QALSMQAYDV YSERTREVLL EASEKLKIQA + DKAQKDLSVV ATEIGQEGQE YLMMAARNSP DSIKDITTTF RALGKLNWPS + EYEDYHVGIP FGTFLTVGGF LNFMLAGSTS ALRFGIILGL ALLALGISSL + RSQRDGGRRP RLLVKGQAAI ASVIFFREFS VLLQNGWFPK IFMVLLSGVV + AGFYFYRIAA GSPKELSSNS DSVN + + + + + + +5.34147 +-0.288728 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +1351 1351 1351 1351 1215 1173 1087 993 550 479 162 115 58 30 21 4 3 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1346 1346 1346 1346 1210 1168 1080 979 539 401 120 83 4 1 0 + + + + + + +0 1 2 3 4 + + + + +949 374 26 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +280 920 132 15 4 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2671 (charge 2) + +1449.61 +2 + + +175.119 187.071 189.807 212.102 222.088 226.157 230.115 240.098 258.108 262.139 275.134 280.649 290.146 315.129 324.12 341.146 351.73 364.013 450.156 462.195 468.182 470.186 518.857 543.827 561.261 690.3 777.339 834.358 963.407 1064.45 +1175.48 + + + + +69 40 6 11 7 11 9 27 47 7 22 7 100 9 7 7 6 7 7 33 7 6 6 6 23 12 10 87 38 55 +7 + + + + + + +GRMZM2G130062_P01 NP_001146891 2-isopropylmalate synthase B seq=translation; coord=10:1725712..1731899:-1; parent_transcript=GRMZM2G130062_T01; parent_gene=GRMZM2G130062 + + + MASSLLSSPA KPTITTTTKT TPAPRPARSA HVHVLSAARC LRLRLRASSQ + HPPPPPTPRS RRPDYVPNRI DDPNYVRIFD TTLRDGEQSP GATMTSAQKL + VVARQLARLG VDIIEAGFPA SSPDDLDAVR SIAIEVGNPA PGPAGEEDAV + HVPVICGLSR CNRKDIDAAW EAVRHARRPR IHTFIATSDI HMQHKLRKTP + DQVVAIAREM VAYARSLGCT DVEFSPEDAG RSNREFLYHI LGEVIKAGAT + TLNIPDTVGY NLPYEFGKLI ADIKANTPGI EKAIISTHCQ NDLGLATANT + LAGARAGARQ LEVTINGIGE RAGNASLEEV VMAIKCRREL LDGLYTGIDS + RHITLTSKMV QEHSGLHVQP HKAIVGANAF AHESGIHQDG MLKYKGTYEI + ISPDDIGLTR ANEFGIVLGK LSGRHAVRSK LVELGYEIGD KEFEDFFKRY + KEVAEKKKRV TDEDLEALLS DEIFQPKVIW SLADVQATCG TLALSTATVK + LVAPDGEEKI ACSVGTGPVD AAYKAVDKII QIPTVLREYS MTSVTEGIDA + IATTRVVVTG DVSNNAKHAL TGQSFNRSFS GSGASMDIVV SSVRAYLSAL + NKICSFAGAV KASSDVAETA SVPSTE + + + + + + +5.639 +-0.304811 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +7035 7035 7035 6854 6608 6170 5250 4215 2780 1656 948 363 177 91 42 17 3 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7041 7041 7041 6860 6608 6140 5124 3781 2207 842 227 58 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2322 2967 1342 355 54 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1279 3204 1832 566 142 13 7 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2674 (charge 3) + +1297.66 +3 + + +153.103 154.05 154.087 155.081 156.077 157.061 157.098 157.134 158.093 159.077 166.062 167.082 167.118 169.097 169.134 171.077 171.113 172.109 173.092 175.089 175.119 176.123 181.097 183.078 183.113 185.091 186.086 186.124 187.071 187.108 +187.143 189.087 194.129 195.112 197.128 199.071 199.108 201.124 203.086 205.987 208.953 210.95 213.087 215.138 223.998 226.155 235.063 240.08 244.167 246.156 248.035 251.151 255.146 258.145 266.047 268.129 272.172 283.14 287.083 295.148 +304.16 313.198 317.651 320.92 332.169 339.69 344.978 346.977 351.167 362.028 367.245 371.239 373.218 376.477 383.131 385.216 394.19 398.238 414.2 416.007 419.743 422.752 438.198 452.262 455.271 461.183 464.235 468.297 470.272 505.76 +511.25 521.755 537.243 538.985 567.33 634.293 653.377 661.36 732.391 897.409 + + + + +6 4 10 20 3 3 6 4 19 27 3 3 6 6 20 22 13 5 11 18 100 5 12 9 5 4 3 4 13 5 +4 6 5 6 10 5 14 11 4 4 15 21 4 5 6 23 11 4 11 4 12 5 12 6 5 11 24 4 6 4 +28 6 4 3 4 3 6 4 5 12 11 4 4 4 4 4 4 3 4 25 4 10 26 12 3 5 5 6 31 3 +13 5 5 4 30 6 4 4 4 4 + + + + + + +GRMZM2G451224_P01 O65101 Photosystem I reaction center subunit VI, chloroplastic Precursor (PSI-H)(Light-harvesting complex I 11 kDa protein) seq=translation; coord=6:163973641..163974980:-1; parent_transcript=GRMZM2G451224_T01; parent_gene=GRMZM2G451224 + + + + + + + + +5.26332 +-0.284504 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +8705 8705 8662 8396 7853 7229 6143 4896 3155 1896 1115 586 327 175 57 24 6 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8708 8708 8665 8383 7763 7001 5821 3872 1852 542 176 25 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2759 3707 1564 502 140 25 16 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1193 3468 2455 1152 334 94 12 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2677 (charge 3) + +1287.68 +3 + + +152.082 155.082 157.108 158.092 159.077 167.055 167.081 167.118 169.097 172.108 175.119 176.122 181.097 181.133 183.149 184.624 186.123 195.113 198.124 200.139 201.124 206.122 208.953 212.139 213.627 226.119 227.102 230.62 234.159 241.081 +243.145 252.135 255.145 258.109 262.128 266.154 269.161 272.172 274.014 284.009 287.652 296.165 297.155 298.679 300.203 309.191 312.166 319.169 323.171 326.183 329.193 338.134 341.019 343.21 344.976 349.188 352.198 355.16 359.029 361.028 +366.215 368.24 376.201 380.229 392.191 394.209 396.236 409.219 411.236 413.184 423.235 426.246 428.251 438.234 440.265 460.233 467.309 477.246 494.274 497.284 505.239 508.288 512.282 522.267 524.259 531.308 537.278 540.277 542.285 554.305 +609.328 610.335 616.321 620.304 625.344 637.331 639.339 651.359 674.385 751.409 + + + + +2 12 1 6 1 12 1 2 2 2 22 1 5 2 1 2 3 7 2 1 1 2 6 22 10 23 3 2 3 2 +2 2 14 2 3 1 5 6 2 8 2 6 3 2 3 1 11 4 8 2 11 2 1 4 4 4 1 6 29 6 +3 2 2 2 2 6 2 15 8 1 2 100 3 2 3 7 2 2 2 7 3 2 4 13 2 2 12 39 2 2 +4 1 4 3 3 23 2 5 4 2 + + + + + + +GRMZM2G172322_P01 B4FVZ4 Putative uncharacterized protein seq=translation; coord=1:12987102..12993471:1; parent_transcript=GRMZM2G172322_T01; parent_gene=GRMZM2G172322 + + + MAAHATLPFS CSSTLQTLTR TLSSRGAHQL RGGFLRLPSL AALPRLAHPC + RRHVSASAAA APNGASVEGE YDYDLFTIGA GSGGVRASRF ASALYGSRVA + ICEMPFATIA SDELGGLGGT CVLRGCVPKK LLVYASKYSH EFEESRGFGW + TYETDPKHDW STLIANKNTE LQRLVGIYRN ILNNAGVTLI EGRGKIVDPH + TVSVNGKLYT AKHILVSVGG RPSMPDIPGI EHVIDSDAAL DLPSKPEKIA + IVGGGYIALE FAGIFNGLKS EVHVFIRQKK VLRGFDEEVR DFVAEQMSLR + GITFHTEQSP QAITKSNDGL LSLKTNKENF GGFSHVMFAT GRRPNSKNLG + LEAVGVEMDK NGAIVVDEYS RTSVDSIWAV GDVTNRVNLT PVALMEGGAF + AKTVFGNEPT KPDYRAIPSA VFSQPPIGQV GLTEEQAIEE YGDVDVFVAN + FRPLKATLSG LPDRVLMKIL VCATSNKVVG VHMCGDDAPE IIQGIAIAVK + AGLTKQDFDA TIGIHPTSAE EFVTMRSPTR KIRKSSTDQV ESKDEVVSKQ + + + + + + +GRMZM2G172322_P02 B4FVZ4 Putative uncharacterized protein seq=translation; coord=1:12987116..12993471:1; parent_transcript=GRMZM2G172322_T02; parent_gene=GRMZM2G172322 + + + MFVYQIVDPH TVSVNGKLYT AKHILVSVGG RPSMPDIPGI EHVIDSDAAL + DLPSKPEKIA IVGGGYIALE FAGIFNGLKS EVHVFIRQKK VLRGFDEEVR + DFVAEQMSLR GITFHTEQSP QAITKSNDGL LSLKTNKENF GGFSHVMFAT + GRRPNSKNLG LEAVGVEMDK NGAIVVDEYS RTSVDSIWAV GDVTNRVNLT + PVALMEGGAF AKTVFGNEPT KPDYRAIPSA VFSQPPIGQV GLTEEQAIEE + YGDVDVFVAN FRPLKATLSG LPDRVLMKIL VCATSNKVVG VHMCGDDAPE + IIQGIAIAVK AGLTKQDFDA TIGIHPTSAE EFVTMRSPTR KIRKSSTDQV + ESKDEVVSKQ + + + + + + +5.85727 +-0.354986 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +10100 10100 10100 10100 9639 9175 6837 5438 3044 1540 798 314 96 45 11 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +10080 10080 10080 10080 9619 9154 6782 5191 2730 1174 474 174 23 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4588 4292 1072 130 18 0 2 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2224 6179 1537 149 12 1 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2683 (charge 3) + +1893.94 +3 + + +150.925 152.057 155.082 155.367 156.076 159.077 167.093 169.097 171.077 171.113 175.071 175.119 183.113 183.927 188.405 190.052 194.129 195.088 197.107 198.123 199.107 201.123 212.102 216.134 226.153 229.118 242.115 244.165 258.144 275.171 +285.198 297.589 315.17 329.193 344.144 348.069 362.203 452.243 461.272 474.18 519.243 536.269 603.283 612.268 647.305 729.342 746.367 815.412 847.337 875.409 975.445 1616.43 1779.32 1799.78 + + + + +5 52 10 5 7 8 7 5 5 14 7 16 7 6 5 5 16 7 6 28 17 5 10 100 49 7 6 47 11 35 +10 7 8 7 14 9 35 8 8 12 15 8 13 8 15 12 14 11 9 15 9 10 10 9 + + + + + + +GRMZM2G177273_P01 NP_001149262 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDasubunit seq=translation; coord=2:26391864..26395400:-1; parent_transcript=GRMZM2G177273_T01; parent_gene=GRMZM2G177273 + + + MTDHRDVMLP LSLQYIATRA LLLLVIASAV SCSSLPPEDG IRVVSAEKRI + DLTGPIVKVF LTLKVENAPT ASEASRVLLA FTPTEFQHLS IVKATRAEGK + RKKKAFVPLS VQASELATTA PDAPRLYSVL LSTPLKPGDA TTLEVLYMLT + HSLEPFPAEI SQSESQLVYY RDSAVLLSPY HVLEQVTYIK MPSNRIESFT + RVDPTTRAGS EVKYGTYSNQ MPNSYLPVLV HYENNRPFAV VEELVRKVEI + SHWGNIQITE QYKLKHGGAR HKGVFSRLEY QSRPSISGAS SFKNLLARLP + PRVHSVYYRD EIGNISSSHL RTDSHKSDLE IEPRYPLFGG WHCTFTIGYG + LPLQDFVFES VDGRRYINLT FGCPLLDTVV DDLTVKVVLP EGSKNPEHVV + PFVTEKHLET SYSYLDVVGR TTVVLKKKNV VGEHNVPFQV YYEFNPIFML + AEPLMLISAV LLFFVAFIAY LHMDLSIRKS S + + + + + + +3.73383 +-0.201829 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +4919 4919 4919 4813 4489 4252 3842 2479 1945 1041 680 490 305 175 123 55 11 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +4926 4926 4926 4820 4496 4247 3800 2415 1741 868 468 368 130 80 35 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2599 2064 210 54 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +981 3378 461 96 10 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2688 (charge 2) + +1231.59 +2 + + +155.081 155.117 158.092 159.077 165.062 169.097 171.076 171.113 175.119 181.096 183.076 183.111 185.091 186.087 186.123 187.071 195.088 198.087 199.071 199.108 201.123 204.134 209.129 213.087 216.098 219.116 226.155 229.118 233.165 235.119 +241.091 244.165 252.134 256.093 261.158 270.11 272.171 297.122 315.165 327.128 333.187 343.161 385.133 409.704 414.201 474.182 491.99 494.932 543.254 549.258 620.297 662.338 666.281 705.867 717.343 721.346 758.378 818.399 820.404 889.443 +948.308 1003.48 + + + + +6 4 21 5 3 6 5 5 38 12 3 3 4 14 6 5 6 3 6 18 43 7 3 3 15 5 46 54 31 4 +4 41 5 4 4 4 100 3 6 3 7 39 4 16 6 20 4 4 4 6 14 4 5 4 18 19 5 88 5 6 +4 7 + + + + + + +GRMZM2G133314_P01 NP_001146364 hypothetical protein LOC100279942 seq=translation; coord=3:5437230..5447745:-1; parent_transcript=GRMZM2G133314_T01; parent_gene=GRMZM2G133314 + + + MLLRPSRGLS CLQPFSLHQS RAAMSETESA AAAPVAAAES KPRRLRGHKK + GAVTCCVASS ARPGVVASSG EPGWSEAWSV VTPSKSRMYP ECFSSQDGCL + CWFDLRTKDA LLTMEAANKP ISSICFKPGN EDFVYISAGN EILSFDVRMG + TQSKPLETYN YNRDEINQIA VSSKGFLAAA DDSGDVKICS SVQFIPWRPW + TAITGGLDSK LAAWDFSKGR TLFSIDYVAV SEEGILGGLY KVCAVARGDG + AVDVVDLEYE LAPAKSKGPP RAAILTTRSK GAELGDGSCN QSRAKRIHLD + YTMGGHTAAV SCVAFSAFGE KGKFLISGGN DASVKLWDWS KGFYSETNSK + VDLVLDIDVK KKSETLSGCK LLLYPLEQEE EEGSSKLASL PAIAKKVLSY + EEGIYAKLSR KWIEEGLRTV SIGRQEPGGF AAVLWRRREM GGLLLPHHRT + FPNSLQASIP GPLSLHKGDR KNLHYFAPDV HLFCSLRQGF PRSSWSAVIR + SEASGNAVAS PGTVIKRSKE ELITFFRDIQ TSIAECSRKA SKRTRKQPPD + LFQEVRRREE QSHGGGDSGT DDVSEGPRKV KSLEDMNVAG LRELARARRM + RGYSKLKKGE LIDRLRGATT + + + + + + +4.4085 +-0.267182 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +1192 1192 1192 1168 966 787 605 387 248 160 80 30 16 10 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +1193 1193 1193 1169 966 775 558 332 188 117 38 9 1 0 + + + + + + +0 1 2 3 4 + + + + +607 494 89 10 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +337 599 205 43 9 4 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2689 (charge 3) + +2015.82 +3 + + +152.057 152.316 153.587 155.082 159.076 169.097 175.119 189.087 199.071 200.102 213.087 219.131 226.155 227.1 231.096 241.081 253.089 255.145 258.109 262.402 272.172 274.102 289.587 312.166 329.193 332.112 340.159 385.141 446.235 458.236 +511.192 545.268 565.24 573.225 593.234 639.817 644.335 731.857 759.365 764.302 843.395 845.399 874.393 879.317 1121.49 1826.12 + + + + +5 3 3 7 6 4 12 6 6 6 5 4 5 6 9 6 6 5 6 4 6 4 4 10 50 5 5 6 20 9 +6 100 7 5 7 10 46 9 35 7 30 7 43 9 7 8 + + + + + + +GRMZM5G856084_P01 seq=translation; coord=10:82046176..82050508:-1; parent_transcript=GRMZM5G856084_T01; parent_gene=GRMZM5G856084 + + + MALVQFNGAL VPQLGEKPRL LSLSAAIAKA AYSDARFLTP KTGSRGRGKH + LLSPSYSLHS QTSSEQLNHV PSSRFRQKRG SRFIVRAEAD FYSVLGVSRN + ASKSEIKSAY RKLARSYHPD VNKDPGAEQK FKDISNAYEV LSDDEKRSIY + DKYGEAGLKG AGMGTGDYSN PFDLFESLFE GFGGMGGMGG GRAARNRPMQ + GDDESYNLVL NFKEAVFGVE KEIEITRLEG CNTCDGSGAK PGTKATTCKT + CGGQGQVVSS TRTPLGIFQQ VSTCNTCGGT GEFSTPCNTC GGDGRVRRTK + RISLKVPAGV DSGSRLRVRS EGNAGRRGGP PGDLYVFIDV LSDPVLKRDG + TNILYTCKVS YIDAILGTTV KVPTVDGTVD LKIPSGTQPG TTLVMSKKGV + PLLGKSNARG DQLVRVQVEI PKRLSSDEKK LIEELANLNK AQTANSRR + + + + + +GRMZM2G091811_P01 NP_001168577 hypothetical protein LOC100382361 seq=translation; coord=4:34554405..34559141:-1; parent_transcript=GRMZM2G091811_T01; parent_gene=GRMZM2G091811 + + + MALVQFNGAL LPQLGEKPRP LSSPPAVARA TYADARFLAP KTSSRGRGKH + LLSPSYSLHS QTSSEQINHV PSSRSRQKRG SSFVVRAEAD FYNVLGVSRN + ASKSEIKSAY RKLARSYHPD VNKDPGAEQK FKEISNAYEV LSDDEKRSIY + DKYGEAGLKG AGMGTGDYSN PFDLFESLFE GFGGMGGMGG GRAARNRPMQ + GDDESYNLVL NFKDAVFGVE KEIEITRLEG CNTCDGSGAK PGTKATTCKT + CGGQGQVVSS TRTPLGIFQQ VSTCNTCGGT GEFSTPCNTC SGDGRVRRTK + RISLKVPAGV DSGSRLRVRS EGNAGRRGGP PGDLYVFIDV LSDPVLKRDG + TNILYTCKVS YIDAILGTTV KVPTVDGMVD LKIPSGTQPG TTLVMAKKGV + PLLGKSNARG DQLVRVQVEI PKRLSSDEKK LVEELANLNK AQTANSRS + + + + + + +6.68356 +-0.310863 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +9600 9600 9378 9186 8343 7550 6350 4927 3496 2255 1338 717 364 214 96 43 25 3 2 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9604 9604 9382 9187 8329 7480 5943 4103 2201 1010 270 68 13 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2867 3897 1727 885 166 61 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1678 4187 2459 972 241 57 9 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2690 (charge 3) + +1684.79 +3 + + +155.082 167.082 175.119 178.086 181.097 185.092 187.108 198.124 199.107 201.087 209.091 213.087 214.089 223.108 224.111 226.119 230.114 234.135 235.119 240.134 243.145 251.103 258.144 259.148 269.125 275.171 284.127 301.129 307.172 309.156 +312.155 315.166 323.135 327.166 332.135 337.149 341.145 345.212 350.145 355.161 356.164 358.172 370.151 371.154 381.176 386.207 388.161 394.688 403.693 426.197 430.231 438.197 440.214 443.222 449.217 455.227 457.238 466.195 470.191 472.252 +475.252 483.219 487.255 501.229 503.241 507.271 515.292 518.93 532.273 537.267 543.288 554.291 563.796 572.27 584.307 600.242 612.299 613.329 629.325 630.329 634.285 649.323 651.307 653.308 655.337 669.318 671.323 697.363 699.314 726.347 +744.352 788.366 806.384 851.44 872.447 912.463 952.481 980.474 986.484 1013.53 + + + + +16 2 7 5 2 9 4 7 8 4 7 33 2 39 8 45 2 4 14 9 7 2 29 4 2 13 2 7 2 9 +13 19 2 8 8 2 6 8 2 24 5 5 54 11 4 11 49 7 7 9 6 5 4 5 4 2 10 2 4 5 +9 12 2 10 4 4 5 2 22 5 7 6 42 5 9 14 12 12 100 36 4 2 22 2 2 18 7 17 5 2 +8 4 2 8 2 2 7 9 2 2 + + + + + + +GRMZM2G010406_P01 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522742..38534648:1; parent_transcript=GRMZM2G010406_T01; parent_gene=GRMZM2G010406 + + + MASARGPCGI SVRSDFSSAC LIHKAGAPSN SVSGVMAVQV HRHRNKVRNG + QAIRCAMATG KEQGAISTAS SGDQTKGGLR GKLNKVVLAY SGGLDTSVIV + PWLRENYGCE VVCFTADVGQ GAIELEGLEK KAKASGACQL VVKDLKEEFV + SEYIYPCLRA GAVYERKYLL GTSMARPVIA KAMVDVAKEV GADAVAHGCT + GKGNDQVRFE LTFYALNPEL KVVAPWREWD ITGREDAIEY AKKHNVPVPV + SKKSIYSRDR NLWHLSHEGD ILEDPANEPK EDMYMMSIAP ENAPSKPEYL + EIGIIAGVPV SINGRDLSPA SLLAELNEIG GKHGIGRIDM VENRLVGMKS + RGVYETPGGT IMAAAVRELE SLTLDRETMQ WKDIIALKYA ELVYAGRWFD + PLRQSFDAFM EKVTATTTGS VTLKLYKGSV NVASRKSPYS LYREDISSFE + NGEIYNQADA EGFIRLYGLP TRVRAMLEKG I + + + + + +GRMZM2G010406_P03 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522742..38534548:1; parent_transcript=GRMZM2G010406_T03; parent_gene=GRMZM2G010406 + + + MASARGPCAI RCAMATGKEQ GAISTASSGD QTKGGLRGKL NKVVLAYSGG + LDTSVIVPWL RENYGCEVVC FTADVGQGAI ELEGLEKKAK ASGACQLVVK + DLKEEFVSEY IYPCLRAGAV YERKYLLGTS MARPVIAKAM VDVAKEVGAD + AVAHGCTGKG NDQVRFELTF YALNPELKVV APWREWDITG REDAIEYAKK + HNVPVPVSKK SIYSRDRNLW HLSHEGDILE DPANEPKEDM YMMSIAPENA + PSKPEYLEIG IIAGVPVSIN GRDLSPASLL AELNEIGGKH GIGRIDMVEN + RLVGMKSRGV YETPGGTIMA AAVRELESLT LDRETMQWKD IIALKYAELV + YAGRWFDPLR QSFDAFMEKV TATTTGSVTL KLYKGSVNVA SRKSPYSLYR + EDISSFENGE IYNQADAEGF IRLYGLPTRV RAMLEKGI + + + + + +GRMZM2G010406_P04 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522743..38534548:1; parent_transcript=GRMZM2G010406_T04; parent_gene=GRMZM2G010406 + + + MASARGPCGI SVRSDFSSAC LIHKAGAPSN SVSGVMAVQV HRHRNKVRNG + QAIRCAMATG KEQGAISTAS SGDQTKGGLR GKLNKVVLAY SGGLDTSVIV + PWLRENYGCE VVCFTADVGQ AMVDVAKEVG ADAVAHGCTG KGNDQVRFEL + TFYALNPELK VVAPWREWDI TGREDAIEYA KKHNVPVPVS KKSIYSRDRN + LWHLSHEGDI LEDPANEPKE DMYMMSIAPE NAPSKPEYLE IGIIAGVPVS + INGRDLSPAS LLAELNEIGG KHGIGRIDMV ENRLVGMKSR GVYETPGGTI + MAAAVRELES LTLDRETMQW KDIIALKYAE LVYAGRWFDP LRQSFDAFME + KVTATTTGSV TLKLYKGSVN VASRKSPYSL YREDISSFEN GEIYNQADAE + GFIRLYGLPT RVRAMLEKGI + + + + + +GRMZM2G010406_P05 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522743..38534548:1; parent_transcript=GRMZM2G010406_T05; parent_gene=GRMZM2G010406 + + + MASARGPCGI SVRSDFSSAC LIHKAGAPSN SVSGVMAVQV HRHRNKVRNG + QAIRCAMATG KEQGAISTAS SGDQTKGGLR GKLNKVVLAY SGGLDTSVIV + PWLRENYGCE VVCFTADVGQ GAIELEGLEK KAKASGACQL VVKDLKEEFV + SEYIYPCLRA GAVYERKYLL GTSMARPVIA KAMVDVAKEV GADAVAHGCT + GKGNDQGDIL EDPANEPKED MYMMSIAPEN APSKPEYLEI GIIAGVPVSI + NGRDLSPASL LAELNEIGGK HGIGRIDMVE NRLVGMKSRG VYETPGGTIM + AAAVRELESL TLDRETMQWK DIIALKYAEL VYAGRWFDPL RQSFDAFMEK + VTATTTGSVT LKLYKGSVNV ASRKSPYSLY REDISSFENG EIYNQADAEG + FIRLYGLPTR VRAMLEKGI + + + + + +GRMZM2G010406_P06 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522868..38534548:1; parent_transcript=GRMZM2G010406_T06; parent_gene=GRMZM2G010406 + + + MAVQVHRHRN KVRNGQAIRC AMATGKEQGA ISTASSGDQT KGGLRGKLNK + VVLAYSGGLD TSVIVPWLRE NYGCEVVCFT ADVGQGAIEL EGLEKKAKAS + GACQLVVKDL KEEFVSEYIY PCLRAGAVYE RKYLLGTSMA RPVIAKAMVD + VAKEVGADAV AHGCTGKGND QVRFELTFYA LNPELKVVAP WREWDITGRE + DAIEYAKKHN VPVPVSKKSI YSRDRNLWHL SHEGDILEDP ANEPKEDMYM + MSIAPENAPS KPEYLEIGII AGVPVSINGR DLSPASLLAE LNEIGGKHGI + GRIDMVENRL VGMKSRGVYE TPGGTIMAAA VRELESLTLD RETMQWKDII + ALKYAELVYA GRWFDPLRQS FDAFMEKVTA TTTGSVTLKL YKGSVNVASR + KSPYSLYRED ISSFENGEIY NQADAEGFIR LYGLPTRVRA MLEKGI + + + + + +GRMZM2G010406_P02 NP_001141957 hypothetical protein LOC100274106 seq=translation; coord=10:38522743..38534549:1; parent_transcript=GRMZM2G010406_T02; parent_gene=GRMZM2G010406 + + + MASARGPCGI SVRSDFSSAC LIHKAGAPSN SVSGVMAVQV HRHRNKVRNG + QAIRCAMATG KEQGAISTAS SGDQTKGGLR GKLNKVVLAY SGGLDTSVIV + PWLRENYGCE VVCFTADVGQ GAIELEGLEK KAKASGACQL VVKDLKEEFV + SEYIYPCLRA GAVYERKYLL GTSMARPVIA KAMVDVAKEV GADAVAHGCT + GKGNDQVRFE LTFYALNPEL KVVAPWREWD ITGREDAIEY AKKHNVPVPV + SKKSIYSRDR NLWHLSHENL SYQNFTRWLR SNF + + + + + + +5.81339 +-0.352327 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +4691 4691 4579 4324 4191 2765 2266 1229 737 339 205 69 13 4 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4708 4708 4596 4341 4196 2562 1953 961 458 166 98 15 1 0 + + + + + + +0 1 2 3 4 + + + + +2827 1666 191 25 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +828 3004 767 90 3 5 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2691 (charge 2) + +1479.69 +2 + + +152.057 155.081 157.061 157.097 157.134 159.076 167.055 171.077 175.119 186.087 189.087 198.087 201.123 212.104 214.083 216.097 222.086 225.042 230.112 232.14 240.098 241.081 248.16 258.108 260.088 280.093 285.009 297.119 299.061 315.129 +323.136 325.186 329.145 340.162 344.978 347.119 351.131 355.068 359.028 368.157 376.219 384.148 386.167 388.146 415.035 418.158 482.702 491.245 523.301 548.267 551.225 579.252 606.235 635.3 690.853 704.345 709.277 722.331 783.061 793.369 +806.358 894.417 964.42 981.449 983.466 1056.32 1094.52 1222.59 + + + + +2 2 2 2 2 2 22 3 9 4 4 2 7 9 4 2 6 3 3 4 42 10 9 12 2 3 3 100 49 11 +2 2 2 16 8 2 3 3 23 27 12 2 4 2 2 3 3 3 2 11 2 3 2 14 14 2 8 21 2 14 +3 11 7 33 3 2 10 7 + + + + + + +GRMZM2G079668_P01 NP_001146752 hypothetical protein LOC100280354 seq=translation; coord=1:263143605..263149463:1; parent_transcript=GRMZM2G079668_T01; parent_gene=GRMZM2G079668 + + + MATTTFPTST PFFAAHHGPR RSRPSISAAV YARGRRWRPL RVACEKVVGI + DLGTTNSAVA AMEGGKPTIV TNAEGARTTP SVVAYTKSGD RLVGQIAKRQ + AVVNPENTFF SVKRFIGRKM NEVDEESKQV SYLVIRDDNG NVKLDCPAIG + KQFAAEEISA QVLRKLVDDA SKFLNDKVTK AVITVPAYFN DSQRTATKDA + GRIAGLEVLR IINEPTAASL AYGFEKKNNE TILVFDLGGG TFDVSVLEVG + DGVFEVLSTS GDTHLGGDDF DKRIVDWLAG NFKNDEGIDL LKDKQALQRL + TEAAEKAKME LSSLTQTNMS LPFITATADG PKHIETTLTR AKFEELCSDL + LDRLRTPVDN ALRDAKLQFK DIDEVILVGG STRIPAVQEL VKKMTGKDPN + VTVNPDEVVA LGAAVQAGVL SGDVSDIVLL DVTPLSLGLE TLGGVMTKII + PRNTTLPTSK SEVFSTAADG QTSVEINVLQ GEREFVRDNK SIGSFRLDGI + PPAPRGVPQI EVKFDIDANG ILSVSAVDKG TGKKQDITIT GASTLPKDEV + ERMVGEAEKF AKEDKEKRDA IDTKNQAESV IYQTEKQLKE LGDKVPGDVK + GKVESKLQEL KDAVAGGSTQ TMKDAMSALN QEVMQIGQAL YSQQGAPGAG + PGAADASSAG SAGTSEKPGD GGDVIDADFT DSK + + + + + +GRMZM2G079668_P02 NP_001146752 hypothetical protein LOC100280354 seq=translation; coord=1:263143605..263149455:1; parent_transcript=GRMZM2G079668_T02; parent_gene=GRMZM2G079668 + + + MATTTFPTST PFFAAHHGPR RSRPSISAAV YARGRRWRPL RVACEKVVGI + DLGTTNSAVA AMEGGKPTIV TNAEGARTTP SVVAYTKSGD RLVGQIAKRQ + AVVNPENTFF SVKRFIGRKM NEVDEESKQV SYLVIRDDNG NVKLDCPAIG + KQFAAEEISA QVLRKLVDDA SKFLNDKVTK AVITVPAYFN DSQRTATKDA + GRIAGLEVLR IINEPTAASL AYGFEKKNNE TILVFDLGGG TFDVSVLEVG + DGVFEVLSTS GDTHLGGDDF DKRIVDWLAG NFKNDEGIDL LKDKQALQRL + TEAAEKAKME LSSLTQTNMS LPFITATADG PKHIETTLTR AKFEELCSDL + LDRLRTPVDN ALRDAKLQFK DIDEVILVGG STRIPAVQEL VKKMTGKDPN + VTVNPDEVVA LGAAVQAGVL SGDVSDIVLL DVTPLSLGLE TLGGVMTKII + PRNTTLPTSK SEVFSTAADG QTSVEINVLQ GEREFVRDNK SIGSFRLDGI + PPAPRGVPQI EVKFDIDANG ILSVSAVDKG TGKKQDITIT GASTLPKDEV + ERMVGEAEKF AKEDKEKRDA IDTKNQAESV IYQTEKQLKE LGDKVPGDVK + GKVESKLQEL KDAVAGGSTQ TMKDAMSALN QEVMQIGQAL YSQQGAPGAG + PGAADASSAG SAGTSEKPGD GGDVIDADFT DSK + + + + + +GRMZM2G111475_P01 seq=translation; coord=5:12580030..12585678:-1; parent_transcript=GRMZM2G111475_T01; parent_gene=GRMZM2G111475 + + + MATTTFPTST PFFAAHHGPR RSRPSISAAV YSRSRRWRPL RVACEKVVGI + DLGTTNSAVA AMEGGKPTIV TNAEGARTTP SVVAYTKSGD RLVGQIAKRQ + AVVNPENTFF SVKRFIGRKM NEVDEESKQV SYRVIRDDNG NVKLDCPAIG + KQFAAEEISA QVLRKLVDDA SKFLNDKVTK AVITVPAYFN DSQRTATKDA + GRIAGLEVLR IINEPTAASL AYGFEKKNNE TILVFDLGGG TFDVSVLEVG + DGVFEVLSTS GDTHLGGDDF DKRIVDWLAG NFKNDEGIDL LKDKQALQRL + TEAAEKAKME LSSLTQTNIS LPFITATADG PKHIETTLTR AKFEELCSDL + LDRLRTPVDN ALRDAKLQFK DIDEVILVGG STRIPAVQEL VKKMTGKDPN + VTVNPDEVVA LGAAVQAGVL SGDVSDIVLL DVTPLSLGLE TLGGVMTKII + PRNTTLPTSK SEVFSTAADG QTSVEINVLQ GEREFVRDNK SLGSFRLDGI + PPAPRGVPQI EVKFDIDANG ILSVTAVDKG TGKKQDITIT GASTLPKDEV + ERMVDEAEKF AKEDKEKRDA IDTKNQAESV IYQTEKQLKE LGDKVPGDVK + GKVESKLQEL KDAVAGGSTQ TMKDAISALN QEVMQIGQSL YSQQGAPGAG + PGPADASAGS AAGTSEKPGD DGDVIDADFT DSK + + + + + +GRMZM2G111475_P02 seq=translation; coord=5:12580030..12585678:-1; parent_transcript=GRMZM2G111475_T02; parent_gene=GRMZM2G111475 + + + MELSSLTQTN ISLPFITATA DGPKHIETTL TRAKFEELCS DLLDRLRTPV + DNALRDAKLQ FKDIDEVILV GGSTRIPAVQ ELVKKMTGKD PNVTVNPDEV + VALGAAVQAG VLSGDVSDIV LLDVTPLSLG LETLGGVMTK IIPRNTTLPT + SKSEVFSTAA DGQTSVEINV LQGEREFVRD NKSLGSFRLD GIPPAPRGVP + QIEVKFDIDA NGILSVTAVD KGTGKKQDIT ITGASTLPKD EVERMVDEAE + KFAKEDKEKR DAIDTKNQAE SVIYQTEKQL KELGDKVPGD VKGKVESKLQ + ELKDAVAGGS TQTMKDAISA LNQEVMQIGQ SLYSQQGAPG AGPGPADASA + GSAAGTSEKP GDDGDVIDAD FTDSK + + + + + + +4.70284 +-0.241171 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +5419 5419 5160 4764 4552 4238 3101 2566 1640 1081 617 387 250 128 60 27 12 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +5368 5368 5109 4713 4444 4128 2876 2143 1252 576 236 113 55 3 2 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2959 1996 428 51 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1119 3231 914 151 14 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2693 (charge 2) + +1165.55 +2 + + +152.056 153.066 153.102 155.081 157.097 157.108 158.092 159.076 160.079 167.118 169.097 170.046 171.076 171.112 173.092 175.119 181.097 183.112 183.148 184.072 185.092 186.086 186.122 187.071 188.074 195.112 197.13 198.123 199.108 202.082 +204.134 207.112 209.092 212.102 214.352 226.155 230.113 240.134 242.15 244.165 252.097 255.109 258.146 259.143 270.143 272.171 274.186 278.152 283.107 286.14 297.119 323.207 331.16 337.189 341.22 355.197 365.182 379.2 383.193 395.165 +440.256 446.677 452.248 466.273 470.263 483.226 490.234 507.262 514.223 568.247 574.282 585.261 608.307 613.33 652.342 661.325 670.714 677.302 689.32 752.348 791.375 809.382 811.376 819.024 880.415 882.414 896.401 903.475 + + + + +8 2 2 8 4 3 3 55 4 2 9 2 4 17 4 20 4 3 3 3 3 3 2 100 8 4 2 3 36 3 +3 4 3 4 2 60 10 11 7 17 2 2 12 3 4 3 16 3 2 38 2 3 2 2 3 7 2 21 7 2 +6 2 7 2 3 2 8 3 2 2 2 2 9 2 2 3 2 3 2 9 3 32 2 2 32 4 3 3 + + + + + + +GRMZM2G134738_P01 NP_001144681 hypothetical protein LOC100277708 seq=translation; coord=8:142871869..142875661:-1; parent_transcript=GRMZM2G134738_T01; parent_gene=GRMZM2G134738 + + + MWRRLHTLAP ALRRATAAAA GGPAVPASSA ARAAPLSSAA AGFRRTSPLL + SEDKPARVED VMPIATGLER EELEAELQGK KRFDMDSPVG PFGTKEEPAV + IESYYNKRIV GCPGGEGEDE HDVVWFWLKK DEPHECPVCS QYFVLKVIGD + GGDPDGHDDE DDGHH + + + + + +GRMZM2G134738_P02 NP_001144681 hypothetical protein LOC100277708 seq=translation; coord=8:142871873..142875661:-1; parent_transcript=GRMZM2G134738_T02; parent_gene=GRMZM2G134738 + + + MWRRLHTLAP ALRRATAAAA GGPAVPASSA ARAAPLSSAA AGFRRTSPLL + SEDKPARVED VMPIATGLER EELEAELQGK KRFDMDSPVG PFGTKEEPAV + IESYYNKRIV GCPGGEGEDE HDVVWFWLKK DEPHECPVCS QYFLKVIGDG + GDPDGHDDED DGHH + + + + + +GRMZM2G064753_P01 B6SIM0 Cytochrome c oxidase polypeptide Vb seq=translation; coord=3:224922109..224926422:1; parent_transcript=GRMZM2G064753_T01; parent_gene=GRMZM2G064753 + + + MWRRLHTLAP ALRRATAAAA GAPAASASSA ARAAPLSSAA AAFRRTSPLL + SGDKPASVED VMPIATGLER EELEAELKGK KRFDMDPLVG PFGTKEEPSV + VESYYNKRIV GCPGGEGEDE HDVVWFWLKK DEPHECPVCS QYFVLKVIGD + GGDPDGHDDE DDGHH + + + + + + +2.89753 +-0.251959 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +659 659 659 614 439 379 234 154 63 22 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +671 671 671 626 451 381 227 132 67 19 1 0 0 1 0 + + + + + + +0 1 2 3 4 + + + + +360 278 58 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +185 406 87 7 0 0 12 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2695 (charge 3) + +1958.74 +3 + + +152.057 154.127 155.081 156.077 157.081 157.097 158.093 167.056 169.096 172.071 172.107 175.119 184.071 185.091 185.165 186.167 187.107 195.088 199.108 201.098 209.127 213.16 226.155 230.077 239.093 241.092 244.164 246.98 270.109 275.125 +281.087 284.009 286.113 292.104 298.113 310.113 315.12 327.134 329.663 338.109 345.105 350.154 355.07 360.031 361.157 383.193 402.125 425.138 439.163 465.183 522.193 530.898 538.27 576.62 590.297 595.293 604.308 614.297 620.327 633.315 +638.331 645.317 652.645 664.736 669.206 673.235 684.322 710.246 725.427 777.379 784.231 812.882 824.268 881.289 907.31 939.299 978.311 997.338 1190.41 1253.97 1720.51 1921.31 + + + + +2 2 3 80 4 2 5 4 3 7 3 15 13 3 100 16 3 8 15 4 3 18 38 7 4 14 5 3 4 16 +4 3 6 3 3 5 4 4 3 5 4 17 14 5 6 5 5 5 5 16 15 5 5 6 6 7 4 19 13 7 +4 6 46 5 5 20 17 4 7 5 5 6 6 6 4 18 6 6 6 5 5 6 + + + + + + +AC198353.5_FGP001 seq=translation; coord=2:188791940..188794503:1; parent_transcript=AC198353.5_FGT001; parent_gene=AC198353.5_FG001 + + + MVGNNTVASL FYYSLLIICA AAWHADASQA DRLREFIRSR RNSPSEAADK + GTFEVANIGH SVASSLLSTS SYSDSEQSAL KAADKITALP GQPDGGVDFD + QYAGYVTVDE KNGRALFYYL VEAPQDASAK PLLLWLNGGP GCSSLGYGAM + QELGPFRVNS DNKTLSRNKA AWNNVANVIF LESPAGVGFS YSNTSSDYGL + SGDRRTAADA YLFLANWLER FPEYKSRPFY ISGESYAGHY VPELAATILT + QNSYNSRTAI NLRGILVGNP LLDSYMNLKG AVAYYWSHGL MSDEVFDNIT + RHCKYDSSDG VACSGALEAV DPGQIDPYNV YAPICVDAAN GAYYPTGYLP + GYDPCSDYYT YSYLNDPAVQ NAFHARTTSW NLNWTDAPIS MVPTVAGLIE + KKLPVWIFSG DFDSVCPLPA TRFSIHDLNL HVTTPWRPWT VNMEVGGYVQ + QYQGGFTFAS VRGAGHMVPS SQADRALVLL DSFLKGVLPP YVQEQ + + + + + + +5.58645 +-0.30197 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +5527 5527 5527 5220 5039 4604 4066 3530 3067 1942 1418 794 393 160 75 21 9 1 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5522 5522 5522 5215 5024 4542 3937 3322 2841 1560 839 199 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2122 2269 916 175 44 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +814 2494 1503 565 132 15 5 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2696 (charge 3) + +1312.61 +3 + + +151.01 153.066 154.086 155.082 156.076 157.06 157.097 157.108 157.134 158.092 159.076 166.061 166.097 167.081 167.093 169.096 169.133 171.076 171.112 172.107 173.092 173.128 175.119 176.122 178.061 181.061 183.112 185.091 185.129 186.124 +187.071 187.107 189.088 189.134 194.129 195.087 195.113 197.128 199.107 201.087 204.134 211.12 214.13 216.097 218.149 226.154 235.118 240.134 244.166 251.15 253.092 258.144 263.134 267.109 274.187 276.123 290.145 295.151 304.161 310.176 +312.176 323.141 326.125 344.154 346.551 349.194 351.171 361.184 371.239 378.183 405.75 416.198 420.199 423.508 430.256 435.254 439.845 449.252 454.186 468.292 472.212 474.602 480.718 486.274 489.238 500.279 502.288 508.297 517.8 525.262 +536.271 553.255 576.273 646.362 651.364 663.303 683.388 698.376 760.356 771.33 + + + + +3 3 4 15 3 8 11 3 16 26 12 4 4 9 8 13 8 3 8 14 14 4 100 4 3 2 3 10 4 5 +3 3 3 13 18 12 6 10 12 12 4 4 15 4 3 19 5 8 12 3 3 3 11 5 8 3 8 3 3 5 +4 9 7 3 3 2 3 26 5 4 3 3 10 16 4 3 21 5 18 4 16 3 3 3 11 9 3 4 4 11 +4 15 15 3 3 12 3 3 3 3 + + + + + + +GRMZM2G339540_P04 NP_001146031 hypothetical protein LOC100279562 seq=translation; coord=3:224163656..224168718:-1; parent_transcript=GRMZM2G339540_T04; parent_gene=GRMZM2G339540 + + + MAGPSVPAAA LAALLAVAAL TCCAVAEPPP SERSALLAFL TATPHERRLG + WNASTPACGW VGVTCDNANS TVVEVRLPGV GLVGAIPPGT LGRLTNLRVL + SLRSNRVLGT VPDDVLQLAS LKALFLQQNL LSGPIPTGIQ KLGGLERLVL + SHNNLSGSIP FALNKLTALR VLKLDGNHLS GSIPSISIAG LGALNVSDNN + LNGSIPKSLS HFPRESFAGN LQLCGDPLPP CSSSFFPPAP SPGLSPGPAT + GSSKRRKLSG AAIAGIVVGG VVVGLLLLIA VVLCAVSKRR SAGAREGPKA + ATSSAAAAAG SGATRGQPPP ASGEGGGMTS SSKEDLGGGA SGSAAAVAAA + AAGGAAGEQS RLVFVGKGAG YSFDLEDLLR ASAEVLGKGS VGTSYKAVLE + EGTTVVVKRL KDVAVQRREF DAHMEAVGRV EHRNVLPVRA YYFSKDEKLL + VYDYLPNGSL SAMLHGSRGS GRTPLDWEAR MRAALSAARG LAHLHTAHNL + VHGNVKASNV LLRPDADAAA LSDFGLHQLF AASTAARGGG YRAPEAVDAR + RLTYKSDVYS LGVLLLELLT GKSPSHASLE GDGTLDLPRW VQSVVREEWT + AEVFDVELVR LGASAEEEMV ALLQVAMACV ATVPDARPDA PDVVRMVEEI + GAGHGGRTTT EESEGVRATS EEERSGGTPP AAPTP + + + + + +GRMZM2G339540_P05 NP_001146031 hypothetical protein LOC100279562 seq=translation; coord=3:224154533..224168718:-1; parent_transcript=GRMZM2G339540_T05; parent_gene=GRMZM2G339540 + + + MAGPSVPAAA LAALLAVAAL TCCAVAEPPP SERSALLAFL TATPHERRLG + WNASTPACGW VGVTCDNANS TVVEVRLPGV GLVGAIPPGT LGRLTNLRVL + SLRSNRVLGT VPDDVLQLAS LKALFLQQNL LSGPIPTGIQ KLGGLERLVL + SHNNLSGSIP FALNKLTALR VLKLDGNHLS GSIPSISIAG LGALNVSDNN + LNGSIPKSLS HFPRESFAGN LQLCGDPLPP CSSSFFPPAP SPGLSPGPAT + GSSKRRKLSG AAIAGIVVGG VVVGLLLLIA VVLCAVSKRR SAGAREGPKA + ATSSAAAAAG SGATRGQPPP ASGEGGGMTS SSKEDLGGGA SGSAAAVAAA + AAGGAAGEQS RLVFVGKGAG YSFDLEDLLR ASAEVLGKGS VGTSYKAVLE + EGTTVVVKRL KDVAVQRREF DAHMEAVGRV EHRNVLPVRA YYFSKDEKLL + VYDYLPNGSL SAMLHGHDLQ VLIQRNLLNF MKRRTTGYCY CLLTKIKPRQ + FNIKDRMIRT RHLSIHP + + + + + +GRMZM2G339540_P03 NP_001146031 hypothetical protein LOC100279562 seq=translation; coord=3:224163656..224168717:-1; parent_transcript=GRMZM2G339540_T03; parent_gene=GRMZM2G339540 + + + MAGPSVPAAA LAALLAVAAL TCCAIPPGTL GRLTNLRVLS LRSNRVLGTV + PDDVLQLASL KALFLQQNLL SGPIPTGIQK LGGLERLVLS HNNLSGSIPF + ALNKLTALRV LKLDGNHLSG SIPSISIAGL GALNVSDNNL NGSIPKSLSH + FPRESFAGNL QLCGDPLPPC SSSFFPPAPS PGLSPGPATG SSKRRKLSGA + AIAGIVVGGV VVGLLLLIAV VLCAVSKRRS AGAREGPKAA TSSAAAAAGS + GATRGQPPPA SGEGGGMTSS SKEDLGGGAS GSAAAVAAAA AGGAAGEQSR + LVFVGKGAGY SFDLEDLLRA SAEVLGKGSV GTSYKAVLEE GTTVVVKRLK + DVAVQRREFD AHMEAVGRVE HRNVLPVRAY YFSKDEKLLV YDYLPNGSLS + AMLHGSRGSG RTPLDWEARM RAALSAARGL AHLHTAHNLV HGNVKASNVL + LRPDADAAAL SDFGLHQLFA ASTAARGGGY RAPEAVDARR LTYKSDVYSL + GVLLLELLTG KSPSHASLEG DGTLDLPRWV QSVVREEWTA EVFDVELVRL + GASAEEEMVA LLQVAMACVA TVPDARPDAP DVVRMVEEIG AGHGGRTTTE + ESEGVRATSE EERSGGTPPA APTP + + + + + + +5.1906 +-0.314582 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 + + + + +2194 2194 2194 2101 1731 1268 972 623 436 286 103 28 8 6 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2200 2200 2200 2107 1737 1202 929 551 333 181 59 17 12 10 1 0 + + + + + + +0 1 2 3 4 + + + + +867 1182 142 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1155 818 203 18 0 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2698 (charge 2) + +1631.73 +2 + + +152.636 167.056 167.118 169.061 169.097 171.077 185.09 186.087 187.09 189.087 195.112 201.123 211.292 217.081 226.154 228.098 234.144 244.048 266.15 270.154 274.372 278.562 285.009 288.118 299.059 321.177 338.146 355.069 363.202 408.208 +429.134 509.256 626.776 666.301 673.765 675.302 697.318 715.319 723.833 811.365 824.665 952.459 997.424 1084.45 1155.49 1230.6 1252.54 1254.55 1349.6 1446.63 + + + + +2 5 7 4 7 5 3 24 4 3 13 3 3 19 4 4 5 3 3 3 3 3 3 28 12 5 3 14 4 4 +3 4 15 8 4 100 5 5 38 14 6 7 6 24 7 8 42 5 17 6 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + + + + + +GRMZM5G871264_P01 seq=translation; coord=10:136892662..136893603:-1; parent_transcript=GRMZM5G871264_T01; parent_gene=GRMZM5G871264 + + + MASTKAPGPG EKHHSIDAQL RQLVPGKVFE DDKLIEYDAL LVDRFLNILQ + DLHGPSLREF VQECYEVSTD YEGKGDTTKL GELSAKLTGL APADAILVAS + SILHMLNLAN LAEEVQITHC RRNSKLKKGG FADEGSATTE SDIEETLKRL + VSEVGKSPKE VFEALKNQTV DLVFTAHPTQ SSRRSLLQKN ARIRNCLTQL + NARTSLTMTS KSSMRLCREW YVH + + + + + + +4.69657 +-0.253869 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +8287 8287 8236 6675 5863 5057 4032 2910 1894 1192 684 358 180 107 50 21 15 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8290 8290 8239 6674 5630 4745 3261 2162 1164 547 340 116 24 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4261 3295 627 102 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1607 4409 1985 235 41 10 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2700 (charge 2) + +1076.56 +2 + + +152.082 155.081 156.076 156.113 157.108 158.092 159.076 167.055 168.055 169.051 171.076 171.112 172.107 173.092 173.128 175.071 175.096 175.119 176.121 179.093 180.076 185.055 185.092 187.071 193.097 195.075 195.112 197.103 197.128 198.087 +200.103 202.108 207.087 213.087 214.108 221.091 223.063 225.098 227.103 230.104 232.141 239.094 240.097 244.166 247.129 258.098 259.101 271.174 275.125 282.053 283.049 288.203 290.16 299.061 301.059 303.057 314.135 316.15 326.136 345.976 +346.973 360.029 361.025 382.208 387.19 395.203 413.212 416.038 417.034 428.214 430.239 435.195 452.219 461.247 470.252 487.298 489.303 501.275 506.243 515.245 521.266 529.778 561.255 578.268 584.314 590.263 596.279 602.326 634.292 643.32 +715.409 731.362 759.345 784.435 802.44 804.452 812.425 922.479 939.496 941.498 + + + + +2 4 5 4 4 20 6 55 15 13 2 5 2 15 8 4 3 66 5 4 5 2 5 7 2 4 4 7 5 2 +8 37 4 4 7 2 10 29 6 6 5 11 8 6 30 74 10 11 83 5 4 6 4 72 77 2 18 9 4 9 +17 7 13 4 7 4 2 7 23 2 2 4 8 20 21 78 2 4 2 2 9 4 4 5 2 2 24 15 2 2 +23 2 4 7 100 10 10 4 22 2 + + + + + + +GRMZM2G123558_P01 NP_001130834 hypothetical protein LOC100191938 seq=translation; coord=3:1711864..1714237:1; parent_transcript=GRMZM2G123558_T01; parent_gene=GRMZM2G123558 + + + + + + + +GRMZM2G123558_P02 NP_001130834 hypothetical protein LOC100191938 seq=translation; coord=3:1711861..1714122:1; parent_transcript=GRMZM2G123558_T02; parent_gene=GRMZM2G123558 + + + + + + + + +4.7511 +-0.243646 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +6057 6057 6057 5749 5488 5191 3180 2693 1308 605 304 159 117 52 40 34 12 11 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6021 6021 6021 5713 5452 5141 3112 2406 1071 302 92 22 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3834 2034 193 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1093 4353 512 65 34 3 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2702 (charge 2) + +1543.72 +2 + + +155.08 157.5 158.091 164.096 167.082 168.066 169.097 175.119 183.076 201.086 213.087 226.154 231.097 235.118 241.081 259.092 268.129 282.61 297.19 337.186 355.196 387.187 415.181 434.234 466.228 484.239 493.398 531.144 550.625 563.281 +594.796 611.327 634.316 643.324 705.346 743.862 785.373 802.404 804.408 900.506 913.435 931.44 1042.47 1060.49 1062.5 1188.57 1221.63 1285.64 + + + + +5 3 3 4 4 4 4 22 5 4 4 96 11 6 7 6 4 4 5 6 23 4 17 14 6 12 4 4 4 5 +20 6 12 42 5 4 4 100 12 4 7 34 5 44 5 12 6 6 + + + + + + +GRMZM2G015875_P01 seq=translation; coord=4:161070624..161077204:-1; parent_transcript=GRMZM2G015875_T01; parent_gene=GRMZM2G015875 + + + MFTPQGKGWT GWSTPTPANQ RSGGGAPAAS APLGKGKGRV AELEQELHEY + QYNMGLLLIE KKEWAAKFEE ISEVLTQKEE ILKREQAAHL NAISEYERRE + ENMRKALGVE KQCVADLEKA LRDIRAEIAE VKFTSEKKIT DAQSLEASLE + EKSLEIEGKL HAADAKLAEA NRKKSQADRD LEEAEARQRR LEKEKLYFET + ERKAREKQLK EQEESLQEWE KKLKESQNRL NELQRSINER EERANKNDQL + FKIKQDELEE ARRTVEAAKV TLKVKEDDIN KRLNELHLQE KDADSKRSAL + EEQGKKLDER EAKVTNREKE GLQKLLEDHQ VELESKRRDF ELELERERKS + FDQNMTQKQA DLLKREKDVK SLEAKLSKSE QALNDKKKSM ENLQNDLDAK + SKALKSWDES LKNDEKRLLK EKQQMDHERE QLETYKLELE KIKSALEAEK + EKISEEQNNL KLTAQERQEH SLLIAKLKKE IEEYRMRSNS LSEEMEDLRK + QRQKFEEEWE QLDEKRALLV EEDKRLNIER MNLERWRDNE EKRLNDMKLK + MDEEYKQQLE SLERKEKALS DDMKHKQMEN DEFLKGERAD VQRKLQLKRH + ELEMEMEQKQ ATKEKELEEK ENELNKKIDF VENKLRHAIE LNESKIEKLL + LEKREVQMER ELLLEERKKT ETDKADIRRD IESLHSLSKS LKERREAYNR + DRSRLIELFE KYKACKNCGI SIFEGLDSLL LKDSAEIEHP SLAVEGDDHA + LTTDTSGPDT GTLVNSGGRF SLLQKCSRLF KFSPRKKGEQ SSEQPSERNI + SFGARLEEAT QSDGDYVPTP VYEIAHDSFN AEDELPSDGE TRENEESERH + DIADNAQMES SVGVADNSID ILGTKSFDGA NDMAVEATIV SVDQNGEDSV + VPAEAGVEPE TSEQGRRQQN QRGRRKGGMK RTRSVNAVVE DAKMILGEVF + EEKTDDQGDT VKVGATRKRR FAGATISEQD EEGSEAHSES VSLGGQRRKR + RQTAGAVTDA PGERRYNLRH SRAANAGAAT AQADKKKSSK ARNKHTVEAS + ADDTEGTSKV VEEPAPESKR VSESADYDAS QLHEFSQVEV GDAHAVDGEG + AGEEDGDILD GQDALPDVPM TPSGSEFGAE QEDEDDDDSE RRNQSISKKL + WSFFTT + + + + + + +5.6882 +-0.264568 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +7618 7618 7618 7510 7259 6934 6395 5742 5106 3901 2966 1513 913 409 180 97 50 33 28 3 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7627 7627 7627 7519 7268 6916 6288 5488 4856 3177 1872 601 167 27 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2575 3062 1441 418 90 37 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1211 3184 2123 863 204 22 13 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2703 (charge 3) + +1428.72 +3 + + +152.057 154.086 155.081 155.117 157.096 157.108 158.092 159.077 166.061 167.055 169.097 169.134 171.076 171.113 173.056 173.092 173.128 175.119 176.122 177.102 181.097 183.112 185.092 185.164 186.124 187.071 187.107 189.087 192.996 193.097 +195.112 197.128 198.125 199.108 201.123 213.087 217.081 222.626 226.154 227.102 229.621 232.14 239.095 241.083 244.165 248.159 251.148 255.146 258.144 268.141 272.171 276.156 284.125 285.197 295.104 299.063 300.063 315.168 321.167 331.197 +343.19 347.193 361.183 368.229 396.146 404.223 427.181 437.239 441.208 444.246 452.222 458.235 466.238 495.832 511.262 514.273 525.192 529.272 536.279 540.287 557.313 577.286 585.31 587.318 596.228 603.3 644.299 656.382 678.338 684.38 +685.373 698.389 706.35 732.337 741.39 745.344 747.362 777.403 900.451 1000.46 + + + + +5 4 15 4 5 14 20 13 4 20 43 10 15 12 4 11 14 100 5 17 4 6 6 6 4 4 4 11 5 5 +6 5 5 21 9 16 23 6 36 17 22 6 27 4 35 5 4 5 23 4 6 6 16 4 5 20 5 4 5 4 +4 14 16 4 4 5 4 11 20 33 5 71 4 30 4 37 10 68 4 4 63 4 99 5 11 5 23 27 4 27 +5 4 4 5 4 24 4 4 10 4 + + + + + + +GRMZM2G145589_P01 NP_001130788 hypothetical protein LOC100191892 seq=translation; coord=6:129031310..129036927:1; parent_transcript=GRMZM2G145589_T01; parent_gene=GRMZM2G145589 + + + MAPKLPVLRR ARSLPLLFLA NFVVLQLQCS YGLPLQNEPR QIYIIYLGGR + QSDDADLVTA SHHDLLASVV GSKQEAVESI IYSYRHGFSG FAALLTKSQS + TKIAGLPGVV SVTKNRVHHT RTTRSWDFVG LHYNDDQPNG LLAKAAKYGD + DVIVGVIDSG FWPESPSYAD HGYGPPPSRW KGVCQGGDDG SFGPNNCNRK + VIGARWYAAG VSDDKERLKG EYMSPRDAEG HGTHTSSTAA GNVVGNVSFH + GLAAGAARGG APRARLAIYK ACWGAPPLSG SCDDADVMKA MDDAVHDGVD + VLSVSIGGPS ETPGTLHVVA SGVTVVYAAG NDGPVAQMVE NSSPWLFTVA + ATTVDRMFPT AITLGNNQIV HGQSLYVGTQ GREDHFHEVV PLVNSGCDPE + YVNSSDVKGK IVFCITPDSL YPSATVTAVA QLVLDNGGKG FIFTGYNRDN + IVRWEPVTSK MIPFILIDLE VAYHILQYCI STDGTPRAKI SLAQTTFGTG + VPAPKVAVFS SRGPSAVYPG VLKPDIAAPG VNILAAAPQI PYYKEQLGGV + LYHFESGTSM ATPHVSGIVA LLKSLHPDWS PAALKSALMT TALTTDNNGI + PIQADGNPVK IADAFDYGAG FVNPTKADDP GLIYDIQPSD YLRFFDCTGG + LGTNDNCTAP RASVVDLNLP SIAIPSLKAP QTVTRTVTNV GRQTNAVYRA + VLQPPPGVEM SVEPSVLVFD AKRKAQSFKV AFKATRRFQG DYTFGSLAWH + DGGSHWVRIP VAVRIVIQDL YSTVS + + + + + +GRMZM2G012062_P01 B4FDK4 Putative uncharacterized protein seq=translation; coord=10:1891328..1894470:-1; parent_transcript=GRMZM2G012062_T01; parent_gene=GRMZM2G012062 + + + MSPRDAEGHG THTSSTAAGN VVGNVSFHGL AAGAARGGAP RARLAIYKAC + WGAPPLSGSC DDADVMKAMD DAVHDGVDVL SVSIGGPSET PGTLHVVASG + VTVVYAAGND GPVAQMVENS SPWLFTVAAT TVDRMFPTAI TLGNNQIVHG + QSLYVGTQGR EDHFHEVVPL VNSGCDPEYV NSSDVKGKIV FCITPDSLYP + SATVTAVAQL VLDNGGKGFI FTGYNRDNIV RWEPVTSKMI PFILIDLEVA + YHILQYCIST DGTPRAKISL AQTTFGTGVP APKVAVFSSR GPSAVYPGVL + KPDIAAPGVN ILAAAPQIPY YKEQLGGVLY HFESGTSMAT PHVSGIVALL + KSLHPDWSPA ALKSALMTTA LTTDNNGIPI QADGNPVKIA DAFDYGAGFV + NPTKADDPGL IYDIQPSDYL RFFDCTGGLG TNDNCTAPRA SVVDLNLPSI + AIPSLKAPQT VTRTVTNVGR QTNAVYRAVL QPPPGVEMSV EPSVLVFDAK + RKAQSFKVAF KATRRFQGDY TFGSLAWHDG GSHWVRIPVA VRIVIQDLYS + TVS + + + + + + +7.29915 +-0.324407 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +7209 7209 7209 7075 6989 6673 6270 5676 4561 3546 2138 1309 651 333 174 110 47 23 3 2 2 1 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7210 7210 7210 7076 6989 6663 6174 5471 4071 2691 1070 348 162 26 5 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2403 2743 1525 413 122 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +893 2926 2214 944 187 40 6 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2704 (charge 3) + +1408.75 +3 + + +152.057 154.086 155.081 156.076 157.097 157.133 158.092 159.076 159.113 166.061 167.081 169.097 169.133 171.077 171.113 173.092 173.129 175.071 175.119 175.133 181.096 183.149 185.115 185.129 185.165 186.087 186.122 187.071 187.108 189.088 +194.129 195.075 197.128 198.088 198.123 199.107 201.124 204.134 213.16 216.099 218.151 224.103 226.155 237.134 242.113 244.165 246.18 253.093 258.145 263.166 270.107 272.172 275.17 284.125 287.133 295.14 309.203 311.692 319.198 330.177 +343.235 346.207 355.161 360.2 365.198 384.189 391.224 394.73 437.893 444.241 448.242 451.257 455.227 457.252 478.271 483.253 487.297 504.782 520.78 526.295 552.805 558.337 561.298 563.292 569.316 577.803 583.292 597.299 613.323 614.327 +632.334 648.844 719.394 729.39 764.414 883.483 905.468 912.385 922.483 954.513 + + + + +19 3 10 4 3 36 11 13 9 4 9 39 3 3 10 12 3 11 51 3 4 3 100 22 45 7 3 7 3 3 +13 3 8 3 3 13 4 14 10 3 12 8 16 3 10 8 3 10 3 9 20 4 8 3 3 7 7 15 9 3 +13 9 3 27 38 7 10 13 3 6 7 8 6 14 3 9 7 7 10 18 3 8 27 8 13 10 8 6 21 9 +36 12 6 25 13 6 3 3 6 7 + + + + + + +GRMZM2G411536_P01 seq=translation; coord=3:111553578..111570930:1; parent_transcript=GRMZM2G411536_T01; parent_gene=GRMZM2G411536 + + + MAAAAAAHRA SFPLRLQQIL AGSRAVSPAI KVESEPPANV KAFIDQVINI + PLHDIAIPLS GFRWEFNKGN FHHWKPLFIH FDTYFKTYIS SRKDLLLSDD + MTEAEPMPKN AILKILIVMQ IILENCQNRS SFTGLEHLKL LLASSDPEIV + VAALETLVAL VKINPSKLHM NGKLISCGSI NTHLLSLAQG WGSKEEGLGI + YSCVVANEGN QQGGLSLFPV DLESKYQHRL GSTLHFEYNL GSAQYPDQTS + DKGKSSNLCV IHIPDMHLQK EDDLSILKQC VDKFNVPPEH RFALLTRIRY + ARAFNSTRTC SIYSRISLLS FIVLVQSSDA HDELTYFFTN EPEYINELIR + LVRSEDSVPG PIRALAMLAL GAQLAAYASS HERARILSGS SIISAGGNRM + VLLSVLQKAI FSLNSPNDAS SPLIVDALLQ FFLLHVLSSS SSGTTVRGSG + MVPPLLPLLR DNDSSHMHLV CLAVKTLQKL MEYSSPAVSL FKDLGGVDLL + SRRLHVEVQR VIGTADGHNS MVTDAVKSKE DHLYSQKRLI KALLKALGSS + TYSPGIPARS QSSQDNSLPV SLSLIFQNVE KFGGDIYFSA VTVMSEIIHK + DPTCFPALKE LGLPDAFLSS VTAGVIPSCK ALICVPNGLG AICLNNQGLE + AVRETSALRF LVYTFTSRKY LIPLNEGVVL LANAAEELLR HVQSLRSIGV + DIIIEIINKL SSSLKDRNNE TAILEEKTDM ETDVEGRDLV GGMDSSVEGS + NDEQFSHLSI FHVMVLVHRT MENSETCRLF VEKGGLNALL TLLLRPSITL + SSGGMPIALH STMVFKGFTQ HHSTPLARAF CSSLREHLKS ALGELDKVSN + SFEMTKIEKG AIPSLFVVEF LLFLAASKDN RWMNALLSEF GDASREVLED + IGRVHREVLW KISLFEENKI DAEISLSSST SEAQQPDLSA SDIGDSRYTS + FRQYLDPILR RRGSGWNIES QVSDLINMYR DIGSAASDSQ RVGSDRYSSL + GLPSSSQDQS SSSSDANVST RSEEEKKNSE HSSCFDMMRS LSYHINHLFM + ELGKAMLLTS RRENSPVNLS PSVISVANNI ASIMLEHLNF EGHSVSSERE + MTVTTKCQYL GKVAEFIDGI LLDRPESCNP IMVNSFYCCG VIQAILTTFQ + ATSELLFTMS RPPSSPMETD SKTGKDGKDM NSSWIYGPLI SYGAIMDHLV + TSSFILSSST RQLLEQPIFN GSVRFPQDAE RFMKLLQSKV LKTVLPIWAH + PEFPECNIEL ISSVMSIMRH VCSGVEVKNT VGNDGARLTG PPPDESAISL + IVEMGFSRAR AEEALRQVGT NSVEIATDWL FSHPEDELAR ALAMSLGNSD + TPAQEGNGRS NDLELEEVTV QLPPIDEMLH SCFQLLQTKE ALAFPVRDML + VTISSQKDGQ NRVKVLTYLI ENLKQCVVAS EPSNDTALSA LLHVLALILH + GDTAAREVAS KAGIVKVALD LLSSWELELR ESGMIEVPNW VSSCFLSVDQ + MLQLEPKLPD VTELDVLKRD NSNIKTSLVI DESKKKDSES LSSVGLLDME + DQYQLLKICC KCIEKQLPSA SMHAILQLSA TLTKVHAAAI CFLESGGLNA + LLSLPTSSLF SGFNSVASTI IRHILEDPHT LQQAMELEIR HSLVTAANRH + TNPRVTPRNF VQNLAFVIYR DPVIFMKAVQ SVCQIEMVGD RPYVVLLKDR + EKERSKEKDK DKSVDKDKAT GAVAKVVSGD TAAGSPANAQ GKQSDLNSRN + VKSHRKPPQS FVTVIEHLLD LVMSFVPPPR PEDQADVVSG TALSSDMDID + CSSAKGKGKA VSVPPEESKH AIQESTASLA KASFFLKLMT DVLLTYTSSI + QVVLRHDADL SNMHGPNRTN SGLISGGIFN HILQHFLPHA TKQKKERKSD + GDWMYKLATR ANQFLVASSI RSAEARKKVF SEICNILLDF TDSSAAYKAP + VARMNVYVDL LNDILSARSP TGSSLSAESA VTFVEVGLAP SLLKMLQNLD + LDHPDSAKIV TAIVKALELV SKEHVHSADN AKGENSSKIA SDSNNVNSSP + NRFQALDMTS QPTEMITDHR ETFNADQTSQ SSDSVADEMD HDRDMDGGFA + RDGEDDFMHE MAGDGTGNES TMEIRFEISR NRDDMADDDD DDDNTDEDMS + AEDDEEVNED DEDEDEENNN LEEDDAHQMS HPDTDQEDRE MDEEEFDEDL + LEDDDDEDEE GVILRLEEGI NGINVFDHIE VFGGSNNLSG DTLRVMPLDI + FGTRRQGRST SIYNLLGRAS DHGVLDHPLL EEPSSTLNFS HQEQPENLVE + MAFSDRNHEG SSSRLDAIFR SLRSGRNGHR FNMWLDDGPQ RNGSAAPAVP + EGIEELLISH LSRPTQQPGA QTVGGTQEND QPKHGSAAEA REGSPAQQNE + NSENTTNPVD LSESAGPAPP DSDALQRVVS NASIEHATEM QYERSDTITR + DVEAVSQASS GSGATLGESL RSLEVEIGSV EGHDDGDRHG TSGASERLPL + GDIQAAARSR RPSGNAVAVS SRDMSLESVS EVPQNPDQEP DHNASEGNQE + PRGVGADTID PTFLEALPED LRAEVLSSRQ NQVTQTSNDQ PQNDGDIDPE + FLAALPLDIR EEVLAQQRSQ RIQQQSQELE GQPVEMDAVS IIATFPSEIR + EEVLLTSPDT LLATLTPALV AEANMLRERF AHRYHSSSLF GMNSRNRRGE + SSRRDIMAAG LDRNTGDPSR STSKPIEIEG APLVDEDGLK ALIRLLRVVQ + PLYKGQLQRL LVNLCTHRDN RQALVQILVD MLMLDLQGFS KKSVDASEPP + FRLYGCHANI TYSRPQSSNG VPPLVSRRVL ETLTNLARSH PNVAKLLLFL + EFPCPSRCRS EAHDHRHGKA VLEDGEERKA FAVVLLLTLL NQPLYMRSVA + HLEQLLNLLE VVMHNAENEI NQAKLEASSE KPSENAVKDV KDNTSISDSY + GSKSNPEDGS KALAVDNKSN LRAVLRSLPQ SELRLLCSLL AHDGLSDSAY + LLVGEVLKKI VALAPFFCCH FINELARSMQ SLTFCAMKEL RLYENSEKAL + LSSTSANGTA ILRVVQALSS LVSTLQDRKD PEQPAEKDHS DAVSQISEIN + TALDALWLEL SNCISKIESS SEYASNLTPA SASAATLTAG VAPPLPAGTQ + NILPYIESFF VTCEKLRPGQ PDAVQEASTS DMEDASTSSG GQRSYSCQAS + LDEKQNAFVK FSEKHRRLLN AFIHQNPGLL EKSFSLMLKI PRLIDFDNKR + AYFRSKIKHQ YDHHHHNPVR ISVRRSYILE DSYNQLRMRS PQDLKGRLTV + HFQGEEGIDA GGLTREWYQS LSRVIFDKSA LLFTTVGNDL TFQPNPNSVY + QTEHLSYFKF AGRVVGKALF DGQLLDAHFT RSFYKHILGV RVTYHDIEAI + DPAYYKNLKW MLENDISDVL DLTFSMDADE EKLILYEKAE VTDCELIPGG + RNIRVTEENK HQYVDRVAEH RLTTAIRPQI NAFLEGFNEL IPRELISIFN + DKELELLISG LPDIDLDDLK ANTEYSGYSI ASPVIQWFWE IVQGFSKEDK + ARFLQFVTGT SKVPLEGFSA LQGISGPQRF QIHKAYGSTN HLPSAHTCFN + QLDLPEYTSK EQLQERLLLA IHEANEGFGF G + + + + + +GRMZM2G411536_P03 seq=translation; coord=3:111553578..111570905:1; parent_transcript=GRMZM2G411536_T03; parent_gene=GRMZM2G411536 + + + MAAAAAAHRA SFPLRLQQIL AGSRAVSPAI KVESEPPANV KAFIDQVINI + PLHDIAIPLS GFRWEFNKGN FHHWKPLFIH FDTYFKTYIS SRKDLLLSDD + MTEAEPMPKN AILKILIVMQ IILENCQNRS SFTGLEHLKL LLASSDPEIV + VAALETLVAL VKINPSKLHM NGKLISCGSI NTHLLSLAQG WGSKEEGLGI + YSCVVANEGN QQGGLSLFPV DLESKYQHRL GSTLHFEYNL GSAQYPDQTS + DKGKSSNLCV IHIPDMHLQK EDDLSILKQC VDKFNVPPEH RFALLTRIRY + ARAFNSTRTC SIYSRISLLS FIVLVQSSDA HDELTYFFTN EPEYINELIR + LVRSEDSVPG PIRALAMLAL GAQLAAYASS HERARILSGS SIISAGGNRM + VLLSVLQKAI FSLNSPNDAS SPLIVDALLQ FFLLHVLSSS SSGTTVRGSG + MVPPLLPLLR DNDSSHMHLV CLAVKTLQKL MEYSSPAVSL FKDLGGVDLL + SRRLHVEVQR VIGTADGHNS MVTDAVKSKE DHLYSQKRLI KALLKALGSS + TYSPGIPARS QSSQDNSLPV SLSLIFQNVE KFGGDIYFSA VTVMSEIIHK + DPTCFPALKE LGLPDAFLSS VTAGVIPSCK ALICVPNGLG AICLNNQGLE + AVRETSALRF LVYTFTSRKY LIPLNEGVVL LANAAEELLR HVQSLRSIGV + DIIIEIINKL SSSLKDRNNE TAILEEKTDM ETDVEGRDLV GGMDSSVEGS + NDEQFSHLSI FHVMVLVHRT MENSETCRLF VEKGGLNALL TLLLRPSITL + SSGGMPIALH STMVFKGFTQ HHSTPLARAF CSSLREHLKS ALGELDKVSN + SFEMTKIEKG AIPSLFVVEF LLFLAASKDN RWMNALLSEF GDASREVLED + IGRVHREVLW KISLFEENKI DAEISLSSST SEAQQPDLSA SDIGDSRYTS + FRQYLDPILR RRGSGWNIES QVSDLINMYR DIGSAASDSQ RVGSDRYSSL + GLPSSSQDQS SSSSDANVST RSEEEKKNSE HSSCFDMMRS LSYHINHLFM + ELGKAMLLTS RRENSPVNLS PSVISVANNI ASIMLEHLNF EGHSVSSERE + MTVTTKCQYL GKVAEFIDGI LLDRPESCNP IMVNSFYCCG VIQAILTTFQ + ATSELLFTMS RPPSSPMETD SKTGKDGKDM NSSWIYGPLI SYGAIMDHLV + TSSFILSSST RQLLEQPIFN GSVRFPQDAE RFMKLLQSKV LKTVLPIWAH + PEFPECNIEL ISSVMSIMRH VCSGVEVKNT VGNDGARLTG PPPDESAISL + IVEMGFSRAR AEEALRQVGT NSVEIATDWL FSHPEDELAR ALAMSLGNSD + TPAQEGNGRS NDLELEEVTV QLPPIDEMLH SCFQLLQTKE ALAFPVRDML + VTISSQKDGQ NRVKVLTYLI ENLKQCVVAS EPSNDTALSA LLHVLALILH + GDTAAREVAS KAGIVKVALD LLSSWELELR ESGMIEVPNW VSSCFLSVDQ + MLQLEPKLPD VTELDVLKRD NSNIKTSLVI DESKKKDSES LSSVGLLDME + DQYQLLKICC KCIEKQLPSA SMHAILQLSA TLTKVHAAAI CFLESGGLNA + LLSLPTSSLF SGFNSVASTI IRHILEDPHT LQQAMELEIR HSLVTAANRH + TNPRVTPRNF VQNLAFVIYR DPVIFMKAVQ SVCQIEMVGD RPYVVLLKDR + EKERSKEKDK DKSVDKDKAT GAVAKVVSGD TAAGSPANAQ GKQSDLNSRN + VKSHRKPPQS FVTVIEHLLD LVMSFVPPPR PEDQADVVSG TALSSDMDID + CSSAKGKGKA VSVPPEESKH AIQESTASLA KASFFLKLMT DVLLTYTSSI + QVVLRHDADL SNMHGPNRTN SGLISGGIFN HILQHFLPHA TKQKKERKSD + GDWMYKLATR ANQFLVASSI RSAEARKKVF SEICNILLDF TDSSAAYKAP + VARMNVYVDL LNDILSARSP TGSSLSAESA VTFVEVGLAP SLLKMLQNLD + LDHPDSAKIV TAIVKALELV SKEHVHSADN AKGENSSKIA SDSNNVNSSP + NRFQALDMTS QPTEMITDHR ETFNADQTSQ SSDSVADEMD HDRDMDGGFA + RDGEDDFMHE MAGDGTGNES TMEIRFEISR NRDDMADDDD DDDNTDEDMS + AEDDEEVNED DEDEDEENNN LEEDDAHQMS HPDTDQEDRE MDEEEFDEDL + LEDDDDEDEE GVILRLEEGI NGINVFDHIE VFGGSNNLSG DTLRVMPLDI + FGTRRQGRST SIYNLLGRAS DHGVLDHPLL EEPSSTLNFS HQEQPENLVE + MAFSDRNHEG SSSRLDAIFR SLRSGRNGHR FNMWLDDGPQ RNGSAAPAVP + EGIEELLISH LSRPTQQPGA QTVGGTQEND QPKHGSAAEA REGSPAQQNE + NSENTTNPVD LSESAGPAPP DSDALQRVVS NASIEHATEM QYERSDTITR + DVEAVSQASS GSGATLGESL RSLEVEIGSV EGHDDGDRHG TSGASERLPL + GDIQAAARSR RPSGNAVAVS SRDMSLESVS EVPQNPDQEP DHNASEGNQE + PRGVGADTID PTFLEALPED LRAEVLSSRQ NQVTQTSNDQ PQNDGDIDPE + FLAALPLDIR EEVLAQQRSQ RIQQQSQELE GQPVEMDAVS IIATFPSEIR + EEVLLTSPDT LLATLTPALV AEANMLRERF AHRYHSSSLF GMNSRNRRGE + SSRRDIMAAG LDRNTGDPSR STSKPIEIEG APLVDEDGLK ALIRLLRVVQ + PLYKGQLQRL LVNLCTHRDN RQALVQILVD MLMLDLQGFS KKSVDASEPP + FRLYGCHANI TYSRPQSSNG VPPLVSRRVL ETLTNLARSH PNVAKLLLFL + EFPCPSRCRS EAHDHRHGKA VLEDGEERKA FAVVLLLTLL NQPLYMRSVA + HLEQLLNLLE VVMHNAENEI NQAKLEASSE KPSENAVKDV KDNTSISDSY + GSKSNPEDGS KALAVDNKSN LRAVLRSLPQ SELRLLCSLL AHDGLSDSAY + LLVGEVLKKI VALAPFFCCH FINELARSMQ SLTFCAMKEL RLYENSEKAL + LSSTSANGTA ILRVVQALSS LVSTLQDRKD PEQPAEKDHS DAVSQISEIN + TALDALWLEL SNCISKIESS SEYASNLTPA SASAATLTAG VAPPLPAGTQ + NILPYIESFF VTCEKLRPGQ PDAVQEASTS DMEDASTSSG GQRSYSCQAS + LDEKQNAFVK FSEKHRRLLN AFIHQNPGLL EKSFSLMLKI PRLIDFDNKR + AYFRSKIKHQ YDHHHHNPVR ISVRRSYILE DSYNQLRMRS PQDLKGRLTV + HFQGEEGIDA GGLTREWYQS LSRVIFDKSA LLFTTVGNDL TFQPNPNSVY + QTEHLSYFKF AGRVVGKALF DGQLLDAHFT RSFYKHILGV RVTYHDIEAI + DPAYYKNLKW MLENDISDVL DLTFSMDADE EKLILYEKAE VFAVTDCELI + PGGRNIRVTE ENKHQYVDRV AEHRLTTAIR PQINAFLEGF NELIPRELIS + IFNDKELELL ISGLPDIDLD DLKANTEYSG YSIASPVIQW FWEIVQGFSK + EDKARFLQFV TGTSKVPLEG FSALQGISGP QRFQIHKAYG STNHLPSAHT + CFNQLDLPEY TSKEQLQERL LLAIHEANEG FGFG + + + + + + +3.91907 +-0.252843 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6742 6742 6742 6742 6643 3715 3022 1598 1022 673 398 178 50 8 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6741 6741 6741 6741 6642 3714 2968 1503 790 477 300 77 40 1 0 + + + + + + +0 1 2 3 4 + + + + +5250 1345 136 18 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +816 5493 418 17 1 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2706 (charge 2) + +1529.76 +2 + + +152.055 163.053 169.096 171.149 172.152 175.119 187.107 199.107 199.144 226.155 244.164 260.086 305.036 315.164 332.191 353.173 359.149 403.229 414.158 482.232 615.018 668.342 685.358 829.408 831.417 900.451 1072.53 1149.89 1157.59 1223.58 +1331.62 + + + + +6 6 7 100 7 10 8 9 39 31 53 7 9 13 11 7 7 27 8 7 7 9 62 25 9 37 10 8 28 8 +8 + + + + + + +GRMZM2G157758_P01 Q41898 ATP synthase subunit epsilon, mitochondrial (ATPase subunit epsilon) seq=translation; coord=8:142294150..142298116:1; parent_transcript=GRMZM2G157758_T01; parent_gene=GRMZM2G157758 + + + MSATTAAVPF WRAAGMTYIG YSNICAALVR NCLKEPFKSE AASREKVHFS + ISKWTDGKQE KPTVRTESDD + + + + + +GRMZM2G143234_P01 NP_001149572 LOC100283198 seq=translation; coord=3:224457571..224459736:1; parent_transcript=GRMZM2G143234_T01; parent_gene=GRMZM2G143234 + + + MSATTAAVPF WRAAGMTYIG YSNICAALVR NCLKEPFKSE AASREKVHFS + ISKWTDGKQE KPTVRTESDE + + + + + + +6.73674 +-0.313337 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +8493 8493 8493 8261 8173 7393 6869 6100 5060 3640 2175 1442 738 307 96 44 19 11 7 4 1 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8497 8497 8497 8265 8173 7370 6776 5898 4711 2865 1283 231 73 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2437 3789 1754 393 108 20 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1493 3707 2303 761 203 20 6 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2707 (charge 3) + +1444.75 +3 + + +152.056 154.086 155.081 155.117 156.076 157.096 157.108 157.133 158.06 158.092 159.078 159.091 160.095 169.097 169.133 170.06 170.096 171.076 171.112 173.091 173.128 175.119 176.122 181.096 183.113 183.148 185.092 185.127 186.09 186.124 +187.107 189.087 194.129 195.112 197.128 198.123 199.071 199.107 199.18 201.123 204.134 209.09 213.086 215.118 217.081 222.123 225.099 226.154 236.646 240.134 242.128 244.165 254.15 258.108 260.07 271.107 274.185 283.139 288.063 291.166 +295.14 303.211 323.172 326.01 341.181 355.197 359.137 375.233 383.192 387.13 390.232 412.183 420.733 438.236 443.224 445.238 452.252 455.262 470.258 472.287 477.229 487.297 489.278 503.321 515.33 521.801 575.303 579.314 586.369 600.385 +620.837 629.836 644.33 667.856 677.388 687.314 729.423 840.462 857.479 869.493 + + + + +4 8 12 3 3 9 3 8 24 13 4 100 11 13 3 20 4 11 10 9 8 70 10 11 3 3 3 4 8 25 +11 3 16 9 10 4 4 32 8 9 9 6 4 4 7 4 3 68 9 14 3 23 4 4 4 8 5 8 9 20 +3 7 4 4 4 9 10 11 10 8 9 4 8 5 4 3 8 4 3 82 4 3 3 15 3 10 3 8 3 19 +3 10 3 3 8 3 22 4 28 3 + + + + + + +GRMZM2G318635_P01 seq=translation; coord=5:213291570..213301733:-1; parent_transcript=GRMZM2G318635_T01; parent_gene=GRMZM2G318635 + + + + + + + + +5.68517 +-0.344556 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +8203 8203 8203 8203 8203 7960 4528 3510 1297 409 170 79 56 24 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +8211 8211 8211 8211 8211 7968 4532 3282 949 224 103 47 43 11 3 1 0 + + + + + + +0 1 2 3 + + + + +6543 1588 83 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +954 6580 647 19 12 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2713 (charge 2) + +1695.86 +2 + + +152.313 159.076 159.614 175.119 191.693 195.006 201.087 209.127 218.149 226.154 265.059 299.192 305.181 337.186 355.197 450.852 505.257 560.787 572.483 576.294 596.802 622.808 631.816 647.328 671.333 774.386 784.379 904.434 1063.43 1116.51 +1118.52 1342.66 + + + + +5 9 5 16 6 7 10 8 31 100 7 8 53 83 59 8 14 11 11 9 16 14 11 15 10 15 16 17 10 66 +14 35 + + + + + + +GRMZM5G808402_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=Pt:54176..56114:-1; parent_transcript=GRMZM5G808402_T01; parent_gene=GRMZM5G808402 + + + MRTNPTTSRP GISTIEEKSV GRIDQIIGPV LDITFPPGKL PYIYNALIVK + SRDTADKQIN VTCEVQQLLG NNRVRAVAMS ATEGLMRGME VIDTGTPLSV + PVGGATLGRI FNVLGEPIDN LGPVDTSATF PIHRSAPAFI ELDTKLSIFE + TGIKVVDLLA PYRRGGKIGL FGGAGVGKTV LIMELINNIA KAHGGVSVFG + GVGERTREGN DLYMEMKESG VINEKNIEES KVALVYGQMN EPPGARMRVG + LTALTMAEYF RDVNKQDVLL FIDNIFRFVQ AGSEVSALLG RMPSAVGYQP + TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP ADDLTDPAPA TTFAHLDATT + VLSRGLASKG IYPAVDPLDS TSTMLQPRIV GNEHYETAQR VKETLQRYKE + LQDIIAILGL DELSEEDRLT VARARKIERF LSQPFFVAEV FTGSPGKYVG + LAETIRGFQL ILSGELDGLP EQAFYLVGNI DEASTKAINL EEESKLKK + + + + + +GRMZM2G385622_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=2:200098864..200103052:1; parent_transcript=GRMZM2G385622_T01; parent_gene=GRMZM2G385622 + + + MRTNPTTSRP GISTIEEKSV GRIDQIIGPV LDITFPPGKL PYIYNALIVK + SRDTADKQIN VTCEVQQLLG NNRVRAVAMS ATEGLMRGME VIDTGTPLSV + PVGGATLGRI FNVLGEPIDN LGPVDTSATF PIHRSAPAFI ELDTKLSIFE + TGIKVVDLLA PYRRGGKIGL FGGAGVGKTV LIMELINNIA KAHGGVSVFG + GVGERTREGN DLYMEMKESG VINEKNIEES KVALVYGQMN EPPGARMRVG + LTALTMAEYF RDVNKQDVLL FIDNIFRFVQ AGSEVSALLG RMPSAVGYQP + TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP ADDLTDPAPA TTFAHLDATT + VLSRGLASKG IYPAVDPLDS TSTMLQPRIV GNEHYETAQR VKETLQRYKE + LQDIIAILGL DELSEEDRLT VARARKIERF LSQPFFVAEV FTGSPGKYVG + LAETIRGFQL ILSGELDGLP EQAFYLVGNI DEASTKAINL EEESKLKK + + + + + +GRMZM2G062854_P01 Q5SBI2 Putative uncharacterized protein seq=translation; coord=6:160782373..160789444:-1; parent_transcript=GRMZM2G062854_T01; parent_gene=GRMZM2G062854 + + + MRTNPTTSRP GISTIEEKSV GRIDQIIGPV LDITFPPGKL PYIYNALIVK + SRDTADKQIN VTCEVQQLLG NNRVRAVAMS ATEGLMRGME VIDTGTPLSV + PVGGATLGRI FNVLGEPIDN LGPVDTSATF PIHRSAPAFI ELDTKLSIFE + TGIKVVDLLA PYRRGGKIGL FGGAGVGKTV LIMELINNIA KAHGGVSVFG + GVGERTREGN DLYMEMKESG VINEKNIEES KVALVYGQMN EPPGARMRVG + LTALTMAEYF RDVNKQDVLL FIDNIFRFVQ AGSEVSALLG RMPSAVGYQP + TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP ADDLTDPAPA TTFAHLDATT + VLSRGLASKG IYPAVDPLDS TSTMLQPRIV GNEHYETAQR VKETLQRYKE + LQDIIAILG + + + + + +GRMZM2G448142_P02 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203904004..203910810:-1; parent_transcript=GRMZM2G448142_T02; parent_gene=GRMZM2G448142 + + + MSATEGLMRG MEVIDTGTPL SVPVGGATLG RIFNVLGEPI DNLGPVDTSA + TFPIHRSAPA FIELDTKLSI FETGIKVVDL LAPYRRGGKI GLFGGAGVGK + TVLIMELINN IAKAHGGVSV FGGVGERTRE GNDLYMEMKE SGVINEKNIE + ESKVALVYGQ MNEPPGARMR VGLTALTMAE YFRDVNKQDV LLFIDNIFRF + VQAGSEVSAL LGRMPSAVGY QPTLSTEMGS LQERITSTKK GSITSIQAVY + VPADDLTDPA PATTFAHLDA TTVLSRGLAS KGIYPAVDPL DSTSTMLQPR + IVGNEHYETA QRVKETLQRY KELQDIIAIL GLDELSEEDR LTVARARKIE + RFLSQPFFVA EVFTGSPGNG QIGVLPNHAP INTAVDMGPL RIRLLNDQWL + TAVLWSGFAR IVNNEIIILG NDAELGSDID PEEAQQALEI AEADSDLF + + + + + +GRMZM2G448142_P03 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203907697..203910810:-1; parent_transcript=GRMZM2G448142_T03; parent_gene=GRMZM2G448142 + + + MSATEGLMRG MEVIDTGTPL SVPVGGATLG RIFNVLGEPI DNLGPVDTSA + TFPIHRSAPA FIELDTKLSI FETGIKVVDL LAPYRRGGKI GLFGGAGVGK + TVLIMELINN IAKAHGGVSV FGGVGERTRE GNDLYMEMKE SGVINEKNIE + ESKVALVYGQ MNEPPGARMR VGLTALTMAE YFRDVNKQDV LLFIDNIFRF + VQAGSEVSAL LGRMPSAVGY QPTLSTEMGS LQERITSTKK GSITSIQAVY + VPADDLTDPA PATTFAHLDA TTVLSRGLAS KGIYPAVDPL DSTSTMLQPR + IVGNEHYETA QRVKETLQRY KELQDIIAIL GLDELSEEDR LTVARARKIE + RFLSQPFFVA EVFTGSPGNG QIGVLPNHAP INTAVDMGPL RIRLLNDQWL + TAVLWSGFAR IVNNEIIILG NDAELGSDID PEEAQQALEI AEADSDLF + + + + + +GRMZM2G113408_P01 P19023 ATP synthase subunit beta, mitochondrial Precursor (EC 3.6.3.14) seq=translation; coord=6:162937179..162940714:-1; parent_transcript=GRMZM2G113408_T01; parent_gene=GRMZM2G113408 + + + MASRRVVSSL LRSASRLRAA SPAAPRPRAP PHRPSPAGYL FNRAAAYASS + AAAQAAPATP PPATGKTGGG KITDEFTGAG AIGQVCQVIG AVVDVRFDEG + LPPILTALEV LDNNIRLVLE VAQHLGENMV RTIAMDGTEG LVRGQRVLNT + GSPITVPVGR ATLGRIINVI GEPIDEKGDI KTNHFLPIHR EAPAFVEQAT + EQQILVTGIK VVDLLAPYQR GGKIGLFGGA GVGKTVLIME LINNVAKAHG + GFSVFAGVGE RTREGNDLYR EMIESGVIKL DDKQSESKCA LVYGQMNEPP + GARARVGLTG LTVAEHFRDA EGQDVLLFID NIFRFTQANS EVSALLGRIP + SAVGYQPTLA TDLGGLQERI TTTKKGSITS VQAIYVPADD LTDPAPATTF + AHLDATTVLS RQISELGIYP AVDPLDSTSR MLSPHVLGED HYNTARGVQK + VLQNYKNLQD IIAILGMDEL SEDDKLTVAR ARKIQRFLSQ PFHVAEVFTG + APGKYVELKE SVKSFQGVLD GKYDDLPEQS FYMVGGIEEV IAKAEKIAKE + SAS + + + + + +GRMZM2G041275_P01 seq=translation; coord=3:207616747..207621242:-1; parent_transcript=GRMZM2G041275_T01; parent_gene=GRMZM2G041275 + + + MATRRAFSSI LRSASRIRSA SPSPCPRAPL HHRPSPAGFI LNRVAAYASS + ATAQAAPAPP PPSTGKKTGG GKITDEFTGA GAIGQVCQVI GAVVDVRFDE + GLPPILTALE VLDNNIRLVL EVAQHLGENM VRTIAMDGTE GLVRGQRVLN + TGSPITVPVG RATLGRIINV IGEPIDEKGD ITTNHFLPIH REAPAFVEQA + TEQQILVTGI KVVDLLAPYQ RGGKIGLFGG AGVGKTVLIM ELINNVAKAH + GGFSVFAGVG ERTREGNDLY REMIESGVIK LDDKQSESKC ALVYGQMNEP + PGARARVGLT GLTVAEHFRD AEGQDVLLFI DNIFRFTQAN SEVSALLGRI + PSAVGYQPTL ATDLGGLQER ITTTKKGSIT SVQAIYVPAD DLTDPAPATT + FAHLDATTVL SRQISELGIY PAVDPLDSTS RMLSPHVLGE DHYNTARGVQ + KVLQNYKNLQ DIIAILGMDE LSEDDKLTVA RARKIQRFLS QPFHVAEVFT + GAPGKYVELK ESVKSFQGVL DGKYDDLPEQ SFYMVGGIEE VIAKAEKIAK + ESAS + + + + + +GRMZM2G021331_P01 NP_001151807 ATP synthase beta chain seq=translation; coord=8:65969534..65973268:1; parent_transcript=GRMZM2G021331_T01; parent_gene=GRMZM2G021331 + + + MASRRVVSSL LRSASRLRAA SPAAPRPRGA PHRPSPAGYL FNRAAAYASA + AAAQVAPATP PPATGKTGGG KITDEFTGAG AIGQVCQVIG AVVDVRYDEG + LPPILTALEV LDNDIRLVLE VAQHLGENMV RTIAMDGTEG LVRGQRVLNT + GSPITVPVGR ATLGRIINVI GEPIDEKGDI TTNHFLPIHR EAPAFVEQAT + EQQILVTGIK VVDLLAPYQR GGKIGLFGGA GVGKTVLIME LINNVAKAHG + GFSVFAGVGE RTREGNDLYR EMIESGVIKL GDKQSESKCA LVYGQMNEPP + GARARVGLTG LTVAEHFRDA EGQDVLLFID NIFRFTQANS EVSALLGRIP + SAVGYQPTLA TDLGGLQERI TTTKKDSITS VQAIYVPADD LTDPAPATTF + AHLDATTVLS RQISELGIYP AVDPLDSTSR MLSPHVLGED HYNTARGVQK + VLQNYKNLQD IIAILGMDEL SEDDKLTVAR ARKIQRFLSQ PFHVAEVFTG + APGKYVELKE SVKSFQGVLD GKYDDLPEQS FYMVGGIEEV IAKAEKIAKE + SAS + + + + + +GRMZM2G478934_P01 Q5SBI3 Putative uncharacterized protein seq=translation; coord=4:111776910..111780853:1; parent_transcript=GRMZM2G478934_T01; parent_gene=GRMZM2G478934 + + + MELINNIAKA HGGVSVFGRV GERTREGNDL YMEMKESGVI NEKNIEESKV + ALVYGQMNEP PGARMRVGLT ALTMAEAEYF RDVNKQDVLL FIDNIFRFVQ + AGSEVSALLG RMPSAVGYQP TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP + ADDLTDPAPA TTFAHLDATT VLSRGLASKG IYPAVDPLD + + + + + +GRMZM2G113408_P02 P19023 ATP synthase subunit beta, mitochondrial Precursor (EC 3.6.3.14) seq=translation; coord=6:162937243..162940714:-1; parent_transcript=GRMZM2G113408_T02; parent_gene=GRMZM2G113408 + + + MASRRVVSSL LRSASRLRAA SPAAPRPRAP PHRPSPAGYL FNRAAAYASS + AAAQAAPATP PPATGKTGGG KITDEFTGAG AIGQVCQVIG AVVDVRFDEG + LPPILTALEV LDNNIRLVLE VAQHLGENMV RTIAMDGTEG LVRGQRVLNT + GSPITVPVGR ATLGRIINVI GEPIDEKGDI KTNHFLPIHR EAPAFVEQAT + EQQILVTGIK VVDLLAPYQR GGKIGLFGGA GVGKTVLIME LINNVAKAHG + GFSVFAGVGE RTREGNDLYR EMIESGVIKL DDKQSESKCA LVYGQMNEPP + GARARVGLTG LTVAEHFRDA EGQDVLLFID NIFRFTQVSF AGISFA + + + + + +GRMZM2G155238_P01 seq=translation; coord=4:111657121..111661039:1; parent_transcript=GRMZM2G155238_T01; parent_gene=GRMZM2G155238 + + + MELINNIAKA HGGVSVFGGV GERTREGNDL YMEMKESGVI NEKNIEESKV + ALVYGQMNEP PGARMRVGLT ALTMAEAEYF RDVNKQDMLL FIDNIFRFVQ + AGSEVSALLG RMPSAVGYQP TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP + ADDLTDPAPA TTFAHWTLLP YFLED + + + + + +GRMZM2G384988_P01 seq=translation; coord=5:35005734..35007041:1; parent_transcript=GRMZM2G384988_T01; parent_gene=GRMZM2G384988 + + + MELINNIAKA HGGISVFGVV GERTREGNDL YMEMKESRVI NEKNIEESKV + ALVYGQMNEP PGARMRVGLT ALTMAEVEYF RDVNKQDTLY SSIISFILFK + QDLKYPLY + + + + + + +7.32779 +-0.396097 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +3394 3394 3352 3160 2859 2599 2398 1649 1297 681 297 104 45 14 3 2 2 1 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3385 3385 3342 3123 2789 2490 2257 1292 866 302 69 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1667 1415 309 19 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +776 1758 708 143 16 0 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2715 (charge 2) + +1056.49 +2 + + +152.034 152.057 154.061 155.081 157.097 157.108 157.134 158.092 159.076 167.081 169.06 169.097 170.064 171.076 171.112 172.071 173.092 173.128 175.119 176.122 181.06 181.097 183.112 184.071 185.092 186.087 186.123 187.09 193.096 194.128 +195.113 197.128 199.107 201.069 204.134 209.092 213.086 215.139 218.095 224.103 226.154 229.063 232.14 235.119 239.016 244.093 246.09 249.144 252.097 254.149 258.144 270.109 272.171 286.144 293.123 303.175 307.141 317.127 321.117 323.171 +341.181 342.181 357.123 369.124 375.132 383.202 400.228 404.189 414.144 426.245 432.252 437.25 438.253 445.232 452.256 459.246 463.229 470.271 480.257 481.256 497.282 499.289 518.591 537.931 543.284 556.942 565.28 568.335 608.316 615.284 +626.319 644.811 658.834 680.337 723.339 726.373 740.365 854.385 871.405 873.416 + + + + +9 1 1 8 2 2 1 10 5 4 37 4 1 1 7 2 4 1 32 1 1 4 2 2 4 68 2 5 2 2 +1 1 8 3 2 3 4 2 2 5 18 2 4 1 2 6 10 5 2 1 2 2 1 1 1 6 1 1 1 3 +7 2 1 1 4 8 19 2 2 1 2 5 1 4 1 4 2 3 14 2 100 2 2 3 1 3 4 1 4 1 +9 2 1 1 5 1 18 1 12 1 + + + + + + +GRMZM5G856084_P01 seq=translation; coord=10:82046176..82050508:-1; parent_transcript=GRMZM5G856084_T01; parent_gene=GRMZM5G856084 + + + + + + + +GRMZM2G091811_P01 NP_001168577 hypothetical protein LOC100382361 seq=translation; coord=4:34554405..34559141:-1; parent_transcript=GRMZM2G091811_T01; parent_gene=GRMZM2G091811 + + + + + + + + +4.30521 +-0.277755 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + + + + +5728 5728 3993 3913 2354 1726 992 630 359 188 72 35 15 4 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5717 5717 3982 3902 2140 1443 892 448 254 85 23 1 0 0 1 0 + + + + + + +0 1 2 3 4 + + + + +4290 1334 100 14 0 + + + + + + +0 1 2 3 4 5 + + + + +693 4465 533 39 8 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2718 (charge 2) + +1684.79 +2 + + +173.083 175.119 191.104 204.086 205.847 211.089 213.086 223.107 226.117 232.205 235.118 245.767 258.144 275.171 309.156 312.154 344.171 355.16 370.149 386.205 388.16 438.195 447.495 483.218 501.226 554.29 571.758 611.313 629.323 651.305 +669.318 683.004 744.352 806.367 1023.47 1056.46 1238.99 1297.64 1734.07 + + + + +2 2 2 3 2 2 7 5 6 2 4 2 11 5 3 3 5 6 48 3 47 3 3 12 5 5 4 7 100 5 +24 4 5 4 5 11 3 22 4 + + + + + + +GRMZM2G121186_P01 NM_001112124 LOC542588 (si946054f08), mRNA seq=translation; coord=6:161659850..161663090:-1; parent_transcript=GRMZM2G121186_T01; parent_gene=GRMZM2G121186 + + + MSDGKDSLDL SALGAAIPNS AELSAEDKAN LVASIKNTLE GLASRHTDVL + ENLEPKVRKR VEKLREIQGE HDELEAKFFE ERAALEAKYQ KLYEPLYSKR + YEIVNGVVEI EGITKESAAE TPEEQKSGDE TSAEQKEEKG VPAFWLNAMK + NHEILAEEIQ ERDEEALKYL KDIKWYRISE PKGFKLEFHF GTNMFFKNSV + LTKTYHMIDE DEPILEKAIG TEIEWYPGKC LTQKVLKKKP RKGSKNTKPI + TKTEDCESFF NFFSPPQVPD DDEEIDEDTA EQLQNQMEQD YDIGSTIETK + LSHMLSRGSL ERLLKMRTLK LWMARTTTMK TTMMKTTRMK MTMIMIQRRP + RELLEGKGSR VNDLQSASNS EV + + + + + + +6.52983 +-0.373133 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +3525 3525 3525 3525 3481 3188 2732 2219 1512 1001 531 194 78 29 10 8 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3524 3524 3524 3524 3480 3187 2711 2075 1311 691 203 63 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1219 1562 599 121 26 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1437 1569 380 135 4 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2723 (charge 3) + +2637.16 +3 + + +181.06 185.091 189.086 190.736 199.071 199.108 201.086 204.088 205.74 209.347 213.086 217.081 224.102 227.101 231.096 240.133 249.747 252.096 258.104 270.108 272.122 276.154 284.123 288.118 302.135 313.15 341.144 356.144 359.154 361.143 +373.172 384.137 387.189 405.196 416.323 421.178 442.191 470.186 484.202 533.292 571.232 612.296 644.319 661.348 665.3 729.873 763.181 770.823 774.358 816.363 835.936 838.894 851.352 880.409 903.41 911.919 949.461 977.451 1016.46 1025.47 +1050.51 1075.99 1130.99 1162.48 1178.54 1294.59 1350.63 1389.57 1437.65 1530.67 1565.71 2679.66 + + + + +13 8 15 6 48 13 47 7 6 6 15 16 44 40 15 17 8 16 10 85 10 17 11 15 10 41 45 43 17 8 +11 7 16 16 7 9 9 11 39 30 14 36 15 17 9 13 16 10 14 15 10 13 12 20 16 33 17 13 19 100 +18 35 13 12 20 15 38 14 66 12 13 12 + + + + + + +GRMZM2G096962_P01 NP_001151379 50S ribosomal protein L9 seq=translation; coord=5:214377336..214380504:-1; parent_transcript=GRMZM2G096962_T01; parent_gene=GRMZM2G096962 + + + MASLSCASTL PWTPASYPRP SAGRCLTASR RAPSLVIVAQ GKVKKYRQVI + LTDDIEEVGK KGDTLKVRAG FYRNFLLPKG KATLLTPEVL KEMQLEQERI + EAEKKRVKED AQQLARVFET IGAFKLPRKG GKGKQIFGSV TAQDVVDIIK + SQLNRDVDKK LVTVPEIREI GEYVAEIKLH PDVTARVRLN VYAK + + + + + +GRMZM2G096962_P02 NP_001151379 50S ribosomal protein L9 seq=translation; coord=5:214377336..214380502:-1; parent_transcript=GRMZM2G096962_T02; parent_gene=GRMZM2G096962 + + + MASLSCASTL PWTPASYPRP SAGRCLTASR RAPSLVIVAQ GKVKKYRQVI + LTDDIEEVGK KGDTLKVRAG FYRNFLLPKG KATLLTPEVL KEMQLEQERI + EAEKKRVKED AQQLARVFET IGAFKLPRKG GKGKQIFGSV TAQDVVDIIK + SQLNRDVDKK LVTVPEIREI GEYVAEIKLH PDVTARVRLN VYAK + + + + + +GRMZM2G096962_P03 NP_001151379 50S ribosomal protein L9 seq=translation; coord=5:214377336..214380499:-1; parent_transcript=GRMZM2G096962_T03; parent_gene=GRMZM2G096962 + + + MASLSCASTL PWTPASYPRP SAGRCLTASR RAPSLVIVAQ GKVKKYRQVI + LTDDIEEVGK KGDTLKVRAG FYRNFLLPKG KATLLTPEVL KEMQLEQERI + EAEKKRVKED AQQLARVFET IGAFKLPRKG GKGKQIFGRD VDKKLVTVPE + IREIGEYVAE IKLHPDVTAR VRLNVYAK + + + + + + +6.55876 +-0.305059 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +6633 6633 6633 6633 6428 6243 5759 5374 4812 3628 2867 1431 714 292 190 79 35 16 9 2 1 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +6617 6617 6617 6617 6412 6223 5725 5239 4681 2858 1787 378 117 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3238 2805 537 61 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1271 3422 1468 404 64 6 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2725 (charge 2) + +1157.63 +2 + + +152.056 153.102 155.081 157.097 157.133 158.092 159.076 164.41 165.102 166.061 167.055 169.06 169.096 171.076 171.113 173.091 173.128 175.119 184.107 185.091 186.088 186.124 187.071 189.087 195.112 199.107 201.105 209.09 211.144 213.087 +226.155 228.17 232.139 235.118 239.094 244.165 246.155 258.145 268.164 272.169 285.008 287.007 299.061 301.058 309.193 313.187 344.977 356.069 357.068 359.24 383.195 386.735 394.192 416.223 423.222 444.25 448.204 452.252 458.234 464.741 +487.296 521.763 530.284 545.272 551.297 615.354 629.32 639.31 662.833 686.391 715.363 801.415 912.442 930.462 932.472 + + + + +11 9 11 18 9 23 9 5 5 10 56 6 24 8 6 6 6 96 5 20 6 5 6 6 18 39 8 6 7 10 +77 27 6 22 27 25 9 8 10 5 28 6 43 6 6 6 5 30 19 8 7 9 6 8 7 7 24 9 6 5 +8 10 27 6 32 10 8 8 35 55 11 44 10 100 8 + + + + + + +GRMZM2G439339_P01 NP_001132045 hypothetical protein LOC100193455 seq=translation; coord=4:182566741..182604817:1; parent_transcript=GRMZM2G439339_T01; parent_gene=GRMZM2G439339 + + + MESERLQNLL LEKEVDAEMC KRELEMQKAE IANLNQSISE LIENSKGIDL + NTYEAMKNEL QNIKSTLREN SMELESAKIL LSEKEVAIKI LEDKLSLCQS + ELDSKEKKLN DVEASLKSEI DKHKKINLNL KRKHDNLMKE KGEIAKENQS + LVKQMEDLKS TAQKTTSETT LEQAIKEKDF RIQTLERTLE KERDDNKKEK + AKSRRNENTI FGALQKVQQD KKQVEESIDK HKQAVRELIE NYPGLSSEVP + PISALEEQLL SYFRAAKDME ESSSPFRDGA ATQTPVVETA PVDAPTSAGV + AGRPVDTSSR PAKAKMTEER AVPKPSSEVR RPGGRRPLVR PTLERTEEPH + ADTDISAVDA STVQDKGGPP AEQETSGILP VLQPLSRKRL ITSSQTVDSA + SQGEANDVNP PSKKPKEEES SQGTSELKSG QPPLGDVAAQ VNVLPATDDL + DGQQPTEEID TDQAPEPMVE VEATREEDGG DKDDSGDAST DIKGQDADAN + IDANAIPLEE EHVVAKSEAI IESFDDDRKT EDSKEDAQRT TATDVDDDME + EGELAEEPED KSDVDMSEIE GEATAERAAV EPDQSPITQP GAADASPSRT + ADASPAREPS PSPVQAGASS RPQNTSTATE AREPSSNPAQ AGASSEQRNT + STVVEAAETR SRTINLSERA RQNRQTRFQR AQQPGTARGR GQQSVTLRKD + ATGRGSRGRG GRGQS + + + + + +GRMZM2G439339_P02 NP_001132045 hypothetical protein LOC100193455 seq=translation; coord=4:182566741..182604817:1; parent_transcript=GRMZM2G439339_T02; parent_gene=GRMZM2G439339 + + + MESERLQNLL LEKEVDAEMC KRELEMQKAE IANLNQSISE LIENSKGIDL + NTYEAMKNEL QNIKSTLREN SMELESAKIL LSEKEVAIKI LEDKLSLCQS + ELDSKEKKLN DVEASLKSEI DKHKKINLNL KRKHDNLMKE KGEIAKENQS + LVKQMEDLKS TQKTTSETTL EQAIKEKDFR IQTLERTLEK ERDDNKKEKA + KSRRNENTIF GALQKVQQDK KQVEESIDKH KQAVRELIEN YPGLSSEVPP + ISALEEQLLS YFRAAKDMEE SSSPFRDGAA TQTPVVETAP VDAPTSAGVA + GRPVDTSSRP AKAKMTEERA VPKPSSEVRR PGGRRPLVRP TLERTEEPHA + DTDISAVDAS TVQDKGGPPA EQETSGILPV LQPLSRKRLI TSSQTVDSAS + QGEANDVNPP SKKPKEEESS QGTSELKSGQ PPLGDVAAQV NVLPATDDLD + GQQPTEEIDT DQAPEPMVEV EATREEDGGD KDDSGDASTD IKGQDADANI + DANAIPLEEE HVVAKSEAII ESFDDDRKTE DSKEDAQRTT ATDVDDDMEE + GELAEEPEDK SDVDMSEIEG EATAERAAVE PDQSPITQPG AADASPSRTA + DASPAREPSP SPVQAGASSR PQNTSTATEA REPSSNPAQA GASSEQRNTS + TVVEAAETRS RTINLSERAR QNRQTRFQRA QQPGTARGRG QQSVTLRKDA + TGRGSRGRGG RGQS + + + + + +GRMZM2G439339_P03 NP_001132045 hypothetical protein LOC100193455 seq=translation; coord=4:182566741..182604817:1; parent_transcript=GRMZM2G439339_T03; parent_gene=GRMZM2G439339 + + + MESERLQNLL LEKEVDAEMC KRELEMQKAE IANLNQSISE LIENSKGIDL + NTYEAMKNEL QNIKSTLREN SMELESAKIL LSEKEVAIKI LEDKLSLCQS + ELDSKEKKLN DVEASLKSEI DKHKKINLNL KRKHDNLMKE KGEIAKENQS + LVKQMEDLKS TAQKTTSETT LEQAIKEKDF RIQTLERTLE KERDDNKKEK + AKSRRNENTI FGALQKVQQD KKQVEESIDK HKQAVRELIE NYPGLSSEVP + PISALEEQLL SYFRAAKDME ESSSPFRDGA ATQTPVVETA PVDAPTSAGG + RPVDTSSRPA KAKMTEERAV PKPSSEVRRP GGRRPLVRPT LERTEEPHAD + TDISAVDAST VQDKGGPPAE QETSGILPVL QPLSRKRLIT SSQTVDSASQ + GEANDVNPPS KKPKEEESSQ GTSELKSGQP PLGDVAAQVN VLPATDDLDG + QQPTEEIDTD QAPEPMVEVE ATREEDGGDK DDSGDASTDI KGQDADANID + ANAIPLEEEH VVAKSEAIIE SFDDDRKTED SKEDAQRTTA TDVDDDMEEG + ELAEEPEDKS DVDMSEIEGE ATAERAAVEP DQSPITQPGA ADASPSRTAD + ASPAREPSPS PVQAGASSRP QNTSTATEAR EPSSNPAQAG ASSEQRNTST + VVEAAETRSR TINLSERARQ NRQTRFQRAQ QPGTARGRGQ QSVTLRKDAT + GRGSRGRGGR GQS + + + + + +GRMZM2G439339_P04 NP_001132045 hypothetical protein LOC100193455 seq=translation; coord=4:182566741..182604691:1; parent_transcript=GRMZM2G439339_T04; parent_gene=GRMZM2G439339 + + + MPLFISDEEL RLLGGDTAAV AERADAAIRE LRRQVDTVRA EADAAAIAAE + QTCALLEQRY ASLSAEFDRS KAEAAELTAS AERRAAELAS SQAEIHQLRI + QAIAKDGEVE RLKIEISELH KSKCQSLELI EQRDAEIKEK DGIIQSYYNK + IVNLAETSAG KEARIQEVEA KFTHCQAICN RMTQEKELLE KHNVWLDEEL + KAKVKNLAEL RKTNMDEEAR LSASIAELER EISESSSSLR RSKERISELE + QRVSYMEKVK KLAELHQESS EEWSKKAGEL EGVIKALETH LTQVEDEYKE + KLEKETLSRR DLEKEAVNLK QKLEKCEFDL ENTRKSSELS LVPLTSIAAG + SSDVVDTTVQ GLPISDAVNQ NDLMVIPKVP SGVSGTALAA SLLRDGWSLA + KIYEKYQEAT DAFLHERRGR RHAEAVLERV LHEIEEKAEL ILDERAEHER + MVEAYAMMDQ KLQQALLEHD NFENNVRNLK SELKRRERDH SVAQKEIDDL + QKQVAVLLKE CQDIQLRCGS SLPNVGYVAS SSLVNVLSNV EHDIKDNMSF + KDINGLVQQN VQLRNQIHML SADLDKKDME LRESFQIELK KITDAAASRV + EKVMKKSEEQ AIMIESLHRS VAMYRKLCEE QQKARSNVES APTTLQDSSR + TDLMVLFEGS QEVSKKAYEQ VSERARSLDE ELTKLRTELE SLRSERDKAV + LEADFARDRL NGFAAELEHQ RKESNSASLR NAELTRLVVD YERRLREDLD + SKQALEENLR KLSMEVSTLK NAKESLEKSE RRALDEVRDL TERVHRLQAT + IDTIHTTEEV QENARSMERR NHEEHIKRLE RDWAELNKEL QEQRDHVRVL + SLDKKNVFDS CMKQVEDMRK ELNNSWKAVS DAEARAAIAE AKCSDLEAKV + KSRKAISRDG CHEISAASEE NDELFQLKEE LEKYKEEAQA NKNYMVQYKE + IAHSNEVALK QLESAHQDYK AETEVGRKAL EDEIVNLRDK LSEMEKSYVI + KCEEAANAIE SKEKHITSLM NEISVLRTEV SQKLPQLEKL EIELALSKSS + LDEQYKRWRT AQDNYERQVI LQSETIQELT NTSKQLSSLQ HEITVLRQTA + DALKNENECL RSSAEQEKIG LLKEKDDALQ KYNELNDQNR ILHNQLEALH + IRLAEKERNI AGLSSHRTDN SHAEDDLQSV ISYLRRSKEI AETEISLLKQ + EKSRLQIELE SSLKSAKEAQ DLLRSQADSA RALMFKDEEF KSLQIQVREI + NLLRESNIQL REENRHNFEE CQKFREEAQK AKMESERLQN LLLEKEVDAE + MCKRELEMQK AEIANLNQSI SELIENSKGI DLNTYEAMKN ELQNIKSTLR + ENSMELESAK ILLSEKEVAI KILEDKLSLC QSELDSKEKK LNDVEASLKS + EIDKHKKINL NLKRKHDNLM KEKGEIAKEN QSLVKQMEDL KSTQKTTSET + TLEQAIKEKD FRIQTLERTL EKERDDNKKE KAKSRRNENT IFGALQKVQQ + DKKQVEESID KHKQAVRELI ENYPGLSSEV PPISALEEQL LSYFRAAKDM + EESSSPFRDG AATQTPVVET APVDAPTSAG GRPVDTSSRP AKAKMTEERA + VPKPSSEVRR PGGRRPLVRP TLERTEEPHA DTDISAVDAS TVQDKGGPPA + EQETSGILPV LQPLSRKRLI TSSQTVDSAS QGEANDVNPP SKKPKEEESS + QGTSELKSGQ PPLGDVAAQV NVLPATDDLD GQQPTEEIDT DQAPEPMVEV + EATREEDGGD KDDSGDASTD IKGQDADANI DANAIPLEEE HVVAKSEAII + ESFDDDRKTE DSKEDAQRTT ATDVDDDMEE GELAEEPEDK SDVDMSEIEG + EATAERAAVE PDQSPITQPG AADASPSRTA DASPAREPSP SPVQAGASSR + PQNTSTATEA REPSSNPAQA GASSEQRNTS TVVEAAETRS RTINLSERAR + QNRQTRFQRA QQPGTARGRG QQSVTLRVWF LYSCSFQLGA YIQH + + + + + +GRMZM2G439339_P05 NP_001132045 hypothetical protein LOC100193455 seq=translation; coord=4:182566741..182604685:1; parent_transcript=GRMZM2G439339_T05; parent_gene=GRMZM2G439339 + + + MPLFISDEEL RLLGGDTAAV AERADAAIRE LRRQVDTVRA EADAAAIAAE + QTCALLEQRY ASLSAEFDRS KAEAAELTAS AERRAAELAS SQAEIHQLRI + QAIAKDGEVE RLKIEISELH KSKCQSLELI EQRDAEIKEK DGIIQSYYNK + IVNLAETSAG KEARIQEVEA KFTHCQAICN RMTQEKELLE KHNVWLDEEL + KAKVKNLAEL RKTNMDEEAR LSASIAELER EISESSSSLR RSKERISELE + QRVSYMEKVK KLAELHQESS EEWSKKAGEL EGVIKALETH LTQVEDEYKE + KLEKETLSRR DLEKEAVNLK QKLEKCEFDL ENTRKSSELS LVPLTSIAAG + SSDVVDTTVQ GLPISDAVNQ NDLMVIPKVP SGVSGTALAA SLLRDGWSLA + KIYEKYQEAT DAFLHERRGR RHAEAVLERV LHEIEEKAEL ILDERAEHER + MVEAYAMMDQ KLQQALLEHD NFENNVRNLK SELKRRERDH SVAQKEIDDL + QKQVAVLLKE CQDIQLRCGS SLPNVGYVAS SSLVNVLSNV EHDIKDNMSF + KDINGLVQQN VQLRNQIHML SADLDKKDME LRESFQIELK KITDAAASRV + EKVMKKSEEQ AIMIESLHRS VAMYRKLCEE QQKARSNVES APTTLQDSSR + TDLMVLFEGS QEVSKKAYEQ VSERARSLDE ELTKLRTELE SLRSERDKAV + LEADFARDRL NGFAAELEHQ RKESNSASLR NAELTRLVVD YERRLREDLD + SKQALEENLR KLSMEVSTLK NAKESLEKSE RRALDEVRDL TERVHRLQAT + IDTIHTTEEV QENARSMERR NHEEHIKRLE RDWAELNKEL QEQRDHVRVL + SLDKKNVFDS CMKQVEDMRK ELNNSWKAVS DAEARAAIAE AKCSDLEAKV + KSRKAISRDG CHEISAASEE NDELFQLKEE LEKYKEEAQA NKNYMVQYKE + IAHSNEVALK QLESAHQDYK AETEVGRKAL EDEIVNLRDK LSEMEKSYVI + KCEEAANAIE SKEKHITSLM NEISVLRTEV SQKLPQLEKL EIELALSKSS + LDEQYKRWRT AQDNYERQVI LQSETIQELT NTSKQLSSLQ HEITVLRQTA + DALKNENECL RSSAEQEKIG LLKEKDDALQ KYNELNDQNR ILHNQLEALH + IRLAEKERNI AGLSSHRTDN SHAEDDLQSV ISYLRRSKEI AETEISLLKQ + EKSRLQIELE SSLKSAKEAQ DLLRSQADSA RALMFKDEEF KSLQIQVREI + NLLRESNIQL REENRHNFEE CQKFREEAQK AKMESERLQN LLLEKEVDAE + MCKRELEMQK AEIANLNQSI SELIENSKGI DLNTYEAMKN ELQNIKSTLR + ENSMELESAK ILLSEKEVAI KILEDKLSLC QSELDSKEKK LNDVEASLKS + EIDKHKKINL NLKRKHDNLM KEKGEIAKEN QSLVKQMEDL KSTQKTTSET + TLEQAIKEKD FRIQTLERTL EKERDDNKKE KAKSRRNENT IFGALQKVQQ + DKKQVEESID KHKQAVRELI ENYPGLSSEV PPISALEEQL LSYFRAAKDM + EESSSPFRDG AATQTPVVET APVDAPTSAG GRPVDTSSRP AKAKMTEERA + VPKPSSEVRR PGGRRPLVRP TLERTEEPHA DTDISAVDAS TVQDKGGPPA + EQETSGILPV LQPLSRKRLI TSSQTVDSAS QGEANDVNPP SKKPKEEESS + QGTSELKSGQ PPLGDVAAQV NVLPATDDLD GQQPTEEIDT DQAPEPMVEV + EATREEDGGD KDDSGDASTD IKGQDADANI DANAIPLEEE HVVAKSEAII + ESFDDDRKTE DSKEDAQRTT ATDVDDDMEE GELAEEPEDK SDVDMSEIEG + EATAERAAVE PDQSPITQPG AADASPSRTA DASPAREPSP SPVQAGASSR + PQNTSTATEA REPSSNPAQA GASSEQRNTS TVVEAAETRS RTINLSERAR + QNRQTRFQRA QQPGTARGRG QQSVTLRKDA TGRGSRGRGG RGQS + + + + + + +4.84254 +-0.312422 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +3863 3863 3863 3857 3639 3396 1932 1635 820 424 181 80 29 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3866 3866 3866 3860 3642 3397 1922 1489 590 177 61 17 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2895 900 75 5 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +567 2777 478 41 1 2 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2726 (charge 2) + +1615.73 +2 + + +152.057 157.061 169.096 175.071 175.118 184.071 202.082 209.092 226.081 249.085 257.196 268.128 284.708 289.113 297.155 303.177 310.536 347.135 367.127 423.554 434.168 493.93 497.2 516.828 519.254 599.631 606.278 648.996 656.027 662.683 +665.268 707.808 734.343 738.411 759.34 777.751 805.38 809.375 846.381 917.398 933.432 1004.48 1034.97 1084.51 1101.52 1103.53 1215.58 1288.76 1361.56 1471.48 + + + + +5 3 4 4 20 4 4 11 7 5 6 8 4 7 29 21 4 5 4 4 6 8 19 6 8 5 8 6 7 8 +6 11 53 9 5 8 52 20 7 6 28 19 7 7 100 10 7 6 10 7 + + + + + + +GRMZM5G848768_P02 NP_001131193 hypothetical protein LOC100192501 seq=translation; coord=5:215817786..215821620:-1; parent_transcript=GRMZM5G848768_T02; parent_gene=GRMZM5G848768 + + + MEKAIDRQRV LLAHLLPSPS AASSQPQLAA SACAAGDSAA YQRSSSFGDD + VVVVAAYRTP ICKAKRGGFK DTYPEDLLTV VLKAVLDNTR INPADIGDIV + VGTVLGPGSQ RANECRMAAL FAGFPETVPV RTVNRQCSSG LQAVADVAAA + IKAGYYDIGI GAGLESMSIN SIAWEGQVNP KISAFQKAQD CLLPMGITSE + NVAHRYGVTR QEQDQAAAES HRRAAAATAS GKFKDEIVPV PTKIVDPKTG + EEKEVVISVD DGIRPGTTAS GLAKLKPVFK KDGTTTAGNS SQVSDGAGAV + LLMKRSVALK KGLPILGVFR SFAAVGVDPA VMGVGPAVAI PAAVKSAGLE + IGDIDLFELN EAFASQFVYC CNKLGLDRSK VNVNGGAIAL GHPLGATGAR + CVATLLNEMK RRGRDCRFGV VTMCIGSGMG AAAVFERGDA VDGLSNVRDI + QAHNFLSKDA K + + + + + + +GRMZM5G848768_P03 NP_001131193 hypothetical protein LOC100192501 seq=translation; coord=5:215817786..215821620:-1; parent_transcript=GRMZM5G848768_T03; parent_gene=GRMZM5G848768 + + + MEKAIDRQRV LLAHLLPSPS AASSQPQLAA SACAAGDSAA YQRSSSFGDD + VVVVAAYRTP ICKAKRGGFK DTYPEDLLTV VLKAVLDNTR INPADIGDIV + VGTVLGPGSQ RANECRMAAL FAGFPETVPV RTVNRQCSSG LQAVADVAAA + IKAGYYDIGI GAGLESMSIN SIAWEGQVNP KISAFQKAQD CLLPMGITSE + NVAHRYGVTR QEQDQAAAES HRRAAAATAS GKFKDEIVPV PTKIVDPKTG + EEKEVVISVD DGIRPGTTAS GLAKLKPVFK KDGTTTAGNS SQVSDGAGAV + LLMKRSVALK KGLPILGVFR SFAAVGVDPA VMGVGPAVAI PAAVKSAGLE + IGDIDLFELN EAFASQFVYC CNKLGLDPFQ SKCKWRRDCP WTPSGCNRCP + VCGYSSK + + + + + + +GRMZM5G848768_P04 NP_001131193 hypothetical protein LOC100192501 seq=translation; coord=5:215817786..215821620:-1; parent_transcript=GRMZM5G848768_T04; parent_gene=GRMZM5G848768 + + + MEKAIDRQRV LLAHLLPSPS AASSQPQLAA SACAAGDSAA YQRSSSFGDD + VVVVAAYRTP ICKAKRGGFK DTYPEDLLTV VLKAVLDNTR INPADIGDIV + VGTVLGPGSQ RANECRMAAL FAGFPETVPV RTVNRQCSSG LQAVADVAAA + IKAGYYDIGI GAGLESMSIN SIAWEGQVNP KISAFQKAQD CLLPMGITSE + NVAHRYGVTR QEQDQAAAES HRRAAAATAS GKFKDEIVPV PTKIVDPKTG + EEKEVVISVD DGIRPGTTAS GLAKLKPVFK KDGTTTAGNS SQVSDGAGAV + LLMKRSVALK KGLPILGVFR SFAAVGVDPA VMGVGPAVAI PAAVKSAGLE + IGDIDLFELN EVCVDCLDLH PLLSPIYP + + + + + + + +6.52027 +-0.395168 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +2022 2022 2022 2022 1924 1830 1674 1500 1446 819 400 167 68 21 10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2045 2045 2045 2045 1947 1853 1687 1511 1450 713 334 117 34 21 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1366 604 57 0 0 18 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +333 1425 245 24 0 0 0 18 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2730 (charge 2) + +1352.58 +2 + + +155.081 158.091 159.076 171.077 173.092 175.119 185.091 186.123 186.888 193.097 195.075 197.129 198.087 199.108 204.135 213.086 216.098 218.15 221.091 224.103 226.154 230.148 235.118 241.081 244.092 252.144 259.092 266.159 284.009 312.176 +315.202 334.634 351.127 369.141 399.211 426.703 452.25 466.153 475.235 484.165 505.271 518.153 528.25 537.138 599.29 612.223 620.32 670.327 678.346 683.265 741.368 743.384 763.37 852.407 869.421 984.446 1029.49 + + + + +14 6 9 7 8 77 8 27 6 7 11 12 8 32 7 14 10 11 14 8 58 7 14 63 42 7 38 7 11 9 +8 7 9 79 53 10 10 10 7 47 7 7 38 6 57 9 7 100 10 9 79 9 10 21 24 14 7 + + + + + + +GRMZM2G036921_P01 NP_001148437 LOC100282052 seq=translation; coord=9:98777728..98779013:-1; parent_transcript=GRMZM2G036921_T01; parent_gene=GRMZM2G036921 + + + MATSALAALS ATAAAAGKRI LLSRPASSSS LSFASRRLAA GAPLRGFLGA + PIRAVASSAS AAPAAAAKTI AVGDRLPDAT LSYFDTSSPD GELKTVTVRD + LTAGKKVVLF AVPGAFTPTC TQKHLPGFVA KAGELRAKGV DTVACVSVND + AFVMRAWKES LGIGDEVLLL SDGNGELARA MGVELDLSDK PVGLGVRSRR + YALLAEDGVV KVINLEEGGA FTNSSAEDML NAL + + + + + + +5.32859 +-0.247841 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +7163 7163 7151 6920 6701 6292 5915 4417 3019 1972 1205 753 448 262 162 96 49 20 8 5 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7153 7153 7141 6910 6650 6196 5812 3913 2385 1033 612 218 170 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3130 3025 847 140 16 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1266 4192 1444 232 27 2 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2734 (charge 2) + +1243.66 +2 + + +152.057 155.081 157.06 157.097 158.093 159.076 169.097 169.133 171.076 171.112 171.127 172.116 173.091 175.119 183.076 185.092 185.128 186.123 187.072 189.086 191.117 197.128 199.071 199.107 201.087 204.134 210.087 212.102 214.118 217.081 +218.15 220.116 226.154 228.097 230.113 235.083 240.134 242.149 244.164 246.109 252.108 255.144 258.144 272.171 274.102 276.1 281.124 283.176 289.187 299.135 301.149 309.157 311.17 317.147 325.151 327.166 329.18 337.148 345.181 354.213 +355.159 360.225 368.156 370.171 380.191 382.209 386.166 388.18 398.202 442.708 449.24 451.228 453.248 457.204 469.239 479.248 518.251 522.266 528.313 540.275 550.283 599.353 618.314 657.327 670.387 679.33 744.349 747.357 757.42 758.421 +801.373 828.451 829.458 872.399 894.413 898.476 915.473 969.504 1002.52 1073.55 + + + + +2 8 7 9 3 25 16 10 8 100 3 3 2 25 2 8 2 4 3 9 16 8 2 11 2 4 7 12 4 16 +11 4 22 23 7 2 34 29 6 3 4 8 8 15 20 14 4 10 20 18 7 4 38 3 2 10 2 2 4 7 +2 14 7 10 3 23 4 3 9 3 3 2 8 3 4 4 3 3 68 4 3 23 3 7 15 3 4 10 27 16 +8 15 3 3 3 8 8 9 8 3 + + + + + + +GRMZM5G816209_P01 seq=translation; coord=1:230176955..230178674:-1; parent_transcript=GRMZM5G816209_T01; parent_gene=GRMZM5G816209 + + + MQVCLRRGLS LVRQHTSRVL PPLSLHPTRF FLHQSASDPM GEGSVPGKDA + KGKGKAKHPA QASALVARDD SYLEAVTHKR IRLFEEIQAR QAVERLNIGG + EVIKITLPDG AIKEGKKWIT TPMDIAKEIS SGFAASCLIA QVDETLWDMG + RPLEGDCKLQ MFKFDTNEGR DTFWHSSAHI LGESLERAYG CKLCIGPCTT + RGEGFYYDAY YNELTLNEEH FGVIENQAKK AVAEKQPFER IEVSRAEALE + MFAENKFKVE IINELPEDKT + + + + + + +5.55814 +-0.30044 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +4483 4483 4483 4471 4403 4194 3891 3546 3166 2495 1884 1122 550 267 110 42 12 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4485 4485 4485 4473 4405 4196 3852 3444 2967 2106 1218 333 16 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1137 1797 1029 418 105 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +784 1768 1225 560 135 15 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2735 (charge 3) + +1319.75 +3 + + +155.081 155.118 156.076 157.097 157.108 157.133 158.092 159.076 159.113 166.061 167.118 169.097 169.133 171.112 173.091 173.128 175.119 176.122 181.097 183.076 183.112 183.149 185.091 185.128 185.165 186.123 187.071 187.107 194.129 195.113 +197.128 200.102 201.123 212.103 214.118 218.15 222.124 226.154 229.129 231.123 235.119 240.133 244.166 246.156 248.15 251.104 258.145 261.155 268.13 272.171 275.124 284.009 288.143 295.212 299.008 301.186 304.145 311.171 313.224 323.207 +329.185 341.145 345.226 346.224 353.217 372.261 374.251 381.223 385.703 388.118 399.794 414.269 417.258 425.222 426.233 439.842 442.244 458.308 470.268 473.752 480.247 483.29 493.312 511.324 512.327 516.322 523.283 529.348 544.308 565.312 +571.355 608.374 610.388 616.377 642.392 673.35 687.416 705.43 713.425 769.409 + + + + +20 12 8 13 6 9 19 18 7 8 5 29 13 14 19 12 100 4 12 12 8 9 10 5 8 24 10 8 4 9 +13 24 20 9 10 8 4 28 11 17 20 36 37 18 29 4 8 4 5 11 10 18 7 4 17 26 5 12 8 8 +9 9 24 9 5 4 7 10 15 4 4 12 8 5 9 38 5 21 5 5 5 4 9 26 9 8 9 17 9 8 +11 5 10 14 13 19 10 8 8 4 + + + + + + +GRMZM2G087186_P01 Q05327 Pyruvate decarboxylase isozyme 3 Fragment (PDC)(EC 4.1.1.1) seq=translation; coord=1:45512802..45515978:-1; parent_transcript=GRMZM2G087186_T01; parent_gene=GRMZM2G087186 + + + MDTHIGSVNG AASNQTVGCP ASAPGCPMAS TPAQPAATLS AGEASLGRHL + ARRLVQVGVN DVFAVPGDFN LTLLDHLIAE PGLRLVGCCN ELNAGYAADG + YARARGVGAC AVTFTVGGLS VLNAIAGAYS ENLPVICIAG GPNSNDYGTN + RILHHTIGLP DFSQELRCFQ TVTCHQAVVN NLDDAHEQID TAIATALRES + KPVYLSISCN LPGLPHPTFS RDPVPFFLTP RTSNKMGLEA AVEATVEFLN + KAVKPVLVAG PKLRVAKAGK AFVDMVDASG YAYAVMPSAK GLVPETHPHF + IGTYWGAVST AFCAEIVESA DAYLFAGPIF NDYSSVGYSF LLKKEKAIIV + QPERVIVGNG PAFGCVMMKE FLSELAKRVN KNTTAYENYK RIFVPEGQPL + ESEPNEPLRV NVLFKHVQKM LTGDSAVIAE TGDSWFNCQK LKLPEGCGYE + FQMQYGSIGW SVGALLGYAQ GANHKRVIAF IGDGSFQVTA QDVSTMLRCE + QNSIIFLINN GGYTIEVEIH DGPYNVIKNW NYTGFVDAIH NGLGKCWTSK + VKSEEELTAA IETALGEKKD CLCFIEVIAH KDDTSKELLE WGSRVSAANS + RPPNPQ + + + + + +GRMZM2G087186_P02 Q05327 Pyruvate decarboxylase isozyme 3 Fragment (PDC)(EC 4.1.1.1) seq=translation; coord=1:45512802..45515978:-1; parent_transcript=GRMZM2G087186_T02; parent_gene=GRMZM2G087186 + + + MDTHIGSVNG AASNQTVGCP ASAPGCPMAS TPAQPAATLS AGEASLGRHL + ARRLVQVGVN DVFAVPGDFN LTLLDHLIAE PGLRLVGCCN ELNAGYAADG + YARARGVGAC AVTFTVGGLS VLNAIAGAYS ENLPVICIAG GPNSNDYGTN + RILHHTIGLP DFSQELRCFQ TVTCHQAVVN NLDDAHEQID TAIATALRES + KPVYLSISCN LPGLPHPTFS RDPVPFFLTP RSNKMGLEAA VEATVEFLNK + AVKPVLVAGP KLRVAKAGKA FVDMVDASGY AYAVMPSAKG LVPETHPHFI + GTYWGAVSTA FCAEIVESAD AYLFAGPIFN DYSSVGYSFL LKKEKAIIVQ + PERVIVGNGP AFGCVMMKEF LSELAKRVNK NTTAYENYKR IFVPEGQPLE + SEPNEPLRVN VLFKHVQKML TGDSAVIAET GDSWFNCQKL KLPEGCGYEF + QMQYGSIGWS VGALLGYAQG ANHKRVIAFI GDGSFQVTAQ DVSTMLRCEQ + NSIIFLINNG GYTIEVEIHD GPYNVIKNWN YTGFVDAIHN GLGKCWTSKV + KSEEELTAAI ETALGEKKDC LCFIEVIAHK DDTSKELLEW GSRVSAANSR + PPNPQ + + + + + +GRMZM2G038821_P01 Q05326 Pyruvate decarboxylase isozyme 2 Fragment (PDC)(EC 4.1.1.1) seq=translation; coord=8:15548387..15551947:-1; parent_transcript=GRMZM2G038821_T01; parent_gene=GRMZM2G038821 + + + MPRARLPLDS NAPTHPTTIL VYTPSRQPAF PPEPSFHSLA DPPPAPAMDT + AIGSVPAASD AARHPAPSAS APRDATLGRH LARRLAEVGA RDVFTVPGDF + NLTLLDELEA EPGGVRLVGC CNELNAAYAA DGYARARAGG VGACAVTFTV + GGLSAINGVA GAFSENLPVV CIVGGPNSND YGSNRILHHT IGLPDFTQEL + RCFQNVTCYQ AVVNNLEDAH EQIDTAISTA IKESKPVYIS ISCNLPSIPH + PTFSRHPVPF FLSPRLSNQM NLEAAVEAAA AFLNKAVKPV LVGGPKMRVS + KAWEALAELA DACGYPVAVM PSAKGLVPVH HSRFIGTYWG AVSTPFCAEI + VESADAYLFA GPVFNDYSSV GYSLLLKKEK AIIVQPERVV VGHGPAFGCV + LMKDFLHALA TRLKKNTVAY ENYRRIYVPP GEPLSSEPGE PLRVNVLFKH + IQAMLSGDMA VIAETGDSWF NCQKLKLPEG CGYEFQMQYG SIGWSVGATL + GYAQAAKDKR VIACIGDGSF QVTAQEVSTM LRWGQNSIIF LINNGGYTIE + VEIHDGPYNV IKNWNYTGLV EAFHNGEGAC YTAKVRTEEE LTEALEAALG + PKKDCLCFIE VIVHKDDTSK ALLEWGSRVS AANSRPPNPQ + + + + + +AC197705.4_FGP001 seq=translation; coord=8:118165588..118167724:1; parent_transcript=AC197705.4_FGT001; parent_gene=AC197705.4_FG001 + + + METLLAGNPA NGVAKPTCNG VGALPVANSH AIIATPPAAA TLAPAGATLG + RHLARRLVQI GASDVFAVPG DFNLTLLDYL IAEPGLTLVG CCNELNAGYA + ADGYARSRGV GACAVTFTVG GLSVLNAIAG AYSENLPVVC IVGGPNSNDY + GTNRILHHTI GLPDFSQELR CFQTITCYQA IINNLDDAHE QIDTAIATAL + RESKPVYISV SCNLAGLSHP TFSRDPVPMF ISPRLSNKAN LEYAVEAAAD + FLNKAVKPVM VGGPKIRVAK AREAFAAVAD ASGYPFAVMP AAKGLVPEHH + PRFIGTYWGA VSTTFCAEIV ESADAYLFAG PIFNDYSSVG YSLLLKREKA + VIVQPDRMVV GDGPAFGCIL MPEFLRALAK RLRRNTTAYD NYRRIFVPDR + EPPNGKPNEP LRVNVLFKHI KGMLSGDSAV VAETGDSWFN CQKLRLPEGC + GYEFQMQYGS IGWSVGATLG YAQAAKDKRV IACIGDGSFQ VTAQDVSTML + RCGQKSIIFL INNGGYTIEV EIHDGPYNVI KNWDYTGLVN AIHNSEGNCW + TMKVRTEEQL KEAIATATGA KKDCLCFIEV IVHKDDTSKE LLEWGSRVSA + ANSRPPNPQ + + + + + +GRMZM2G434792_P01 seq=translation; coord=7:174746426..174748651:1; parent_transcript=GRMZM2G434792_T01; parent_gene=GRMZM2G434792 + + + MDTSGIVGSV DGHRPAASGA VACPASGVSG FITSTGGGGE PPPRDATLGR + HLARRLVQVG VSDVFAVPGD FNLTLLDHLI AEPGLRVVGC CNELNAGYAA + DGYARARGVG ACVVTFTVGG LSVLNAIAGA YSENLPVVCV VGGPNSNDYG + TNRVLHHTIG LPDFSQELRC FQPVTCHQAV VNNLEDAHEQ IDGAISTALR + ESKPVYMSVS CNLPGLPHPT FATDPVPYLL APRPSNLTGL AAAVEATVSF + LDKAVKPVVV AGPKIRVAKA AAAFVELAEA SGYAVAAMPS AKGLVPETLP + RFLGTYWGAV STAFCAEIVE SADAYLLAGP IFNDYSSVGY SILLRKDKAV + VVQPDRVTVG NGPTFGCVMM RDFLSALAKR VRPNTTAYDN YRRIFVPGGQ + PPECEAGEPL RVNVLFKHIQ RMLSGGSAVI AETGDSWFNC QKLRLPDGCG + YEFQMQYGSI GWSVGALLGY AQGAPDKRVI ACIGDGSFQV TAQDVSTMLR + CEQRSIIFLI NNGGYTIEVE IHDGPYNVIK NWDYTGLVDA IHNGQGRCWT + ARVATEEELT AAIATATGDD RKDCLCFIEV VVHKDDTSKE LLEWGSRVSA + ANSRPPNPQ + + + + + + +5.70436 +-0.292531 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +6914 6914 6914 6551 6257 4561 4280 2469 1768 1095 630 369 180 86 50 10 7 2 1 1 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6927 6927 6927 6564 6268 4548 4041 2138 1289 565 276 110 47 35 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4257 2196 455 9 10 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1021 4589 1089 194 18 6 10 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2739 (charge 2) + +1237.63 +2 + + +152.056 154.087 155.081 157.097 158.092 159.076 159.112 169.097 171.113 175.118 185.091 186.087 187.108 195.112 197.129 199.108 204.134 212.102 221.128 226.155 230.114 232.14 240.133 242.149 244.129 249.121 258.144 265.12 269.124 281.161 +309.154 331.671 353.142 380.162 383.192 398.202 497.278 505.251 552.278 554.284 558.264 615.35 686.357 695.321 708.378 784.388 795.411 809.402 866.44 909.452 911.432 966.51 980.484 982.484 994.495 1052.52 1139.56 + + + + +22 2 5 4 4 24 22 51 4 13 4 4 24 9 4 19 3 4 31 48 10 23 44 3 100 16 15 3 4 4 +15 3 3 4 3 3 3 3 32 3 9 4 6 6 14 3 30 5 3 25 4 9 12 4 13 11 6 + + + + + + +GRMZM2G063592_P01 NP_001146551 hypothetical protein LOC100280147 seq=translation; coord=10:89988812..90000754:-1; parent_transcript=GRMZM2G063592_T01; parent_gene=GRMZM2G063592 + + + MACVAALFAS PALLPFPSTT SSMASCSCRL RPAVVARAPR QQPRGRRALR + RFDEVEGVSK KRRGIGGGGG VGAGGSQPSS SRRDRGLSVD FKEPQVAEFD + DLEEDKFLNA VVKVYCTHIA PDYGLPWQKQ RQHSSSGSAF MIGDGKLLTN + AHCVEHDTQV KVKRRGDDKK YIAKVLARGV ECDLALLSVE NEEFWRGTEA + LHFGRLPCLQ DSVTVVGYPL GGDTISVTKG VVSRIEVTPY AHGTSDLLGI + QIDAAINPGN SGGPAFNDQG ECIGVAFQVY RSDEAENIGY VIPTTVVSHF + LNDYQKNGKY TGFPCLGVLL QKLENPALRE SLKVPSSEGV LVRRVEPTAP + ASSVLRKGDV IVSFDGIAVG CEATVPFRST ERIAFRYLTS QKYAGDIAQL + GIIRDGNSMK VQTILQPRKH LVPFHVEGGQ PSYLIVAGLV FTPLTEPFIE + EECEDTLGLK LLAKARYSLA TFEGEEIVIV SQVLAHEVNI GYEHMGNQQV + MKLNGTTIKN IHHLAHLVDT CKDKFLTFEF EDDFLVVLHR EEADAASSDI + LKEHAIPSIR SSDLSEPYAE ANNNEIQKTS EDFGESPVTN FEMGIDCLLW + A + + + + + + +5.6099 +-0.249329 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +11758 11758 11758 11229 10958 10015 9119 7631 6116 3879 2654 1537 903 501 326 169 84 39 21 13 4 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +11766 11766 11766 11237 10943 9913 8829 7097 4602 2244 897 425 134 31 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3278 4710 2468 893 328 74 12 5 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2125 4804 3197 1269 292 56 16 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2740 (charge 3) + +1700.84 +3 + + +155.081 157.097 157.109 158.092 159.077 166.061 167.081 169.097 171.076 175.119 181.097 182.045 183.113 184.071 185.092 186.087 187.071 195.113 198.087 199.107 209.091 213.087 216.098 218.15 226.154 240.098 244.165 252.17 255.145 256.129 +258.108 267.138 272.171 278.152 284.124 305.181 312.13 322.161 337.186 342.198 349.182 355.197 383.192 384.709 412.257 426.244 434.231 436.215 452.251 470.264 503.259 505.262 510.216 516.243 523.299 533.267 536.596 555.297 561.286 576.299 +584.326 597.303 612.32 614.322 624.343 644.302 648.334 649.338 661.324 666.365 678.357 683.395 707.37 712.364 713.368 740.412 748.36 763.366 768.41 770.413 774.408 783.391 785.379 793.43 805.375 808.423 811.449 834.402 839.448 844.385 +862.398 864.406 868.478 872.436 880.453 904.447 934.427 990.467 1012.52 1118.53 + + + + +8 4 3 8 8 3 4 5 5 36 4 7 3 3 10 5 9 3 4 29 5 12 9 10 80 4 19 4 4 4 +5 9 83 5 5 14 4 3 10 3 4 10 5 9 4 4 5 12 9 4 4 11 3 13 19 100 8 4 3 8 +10 3 66 5 10 5 10 8 9 3 4 35 3 24 8 4 4 8 44 3 5 4 3 4 15 5 11 4 8 4 +38 10 3 3 4 3 4 11 3 12 + + + + + + +GRMZM2G086553_P01 NP_001149978 AT-hook protein 1 seq=translation; coord=10:135576590..135577696:-1; parent_transcript=GRMZM2G086553_T01; parent_gene=GRMZM2G086553 + + + MDVRDLHQQP QQQQAPPRVG SPPQAGAGGV MMQHAAAFGA APPPSGLPQA + SAANVMHGMS LAFNPMASPD ASSPISSMKI VDMPLGSMYR PDSGATGLQQ + QQPGSGGVGA SGGAIVAVSG GDLVKKKRGR PRKYGPDGSI GLGLKTAAAG + VTEATGAQSG GGGSTPNPDG KRRGRPPGSG KKKQLDALGN IACSPAPYLC + LPFMFMSQFF KVCSYLRAKT NKISISLLCF + + + + + +GRMZM2G086553_P02 NP_001149978 AT-hook protein 1 seq=translation; coord=10:135573176..135577696:-1; parent_transcript=GRMZM2G086553_T02; parent_gene=GRMZM2G086553 + + + MDVRDLHQQP QQQQAPPRVG SPPQAGAGGV MMQHAAAFGA APPPSGLPQA + SAANVMHGMS LAFNPMASPD ASSPISSMKI VDMPLGSMYR PDSGATGLQQ + QQPGSGGVGA SGGAIVAVSG GDLVKKKRGR PRKYGPDGSI GLGLKTAAAG + VTEATGAQSG GGGSTPNPDG KRRGRPPGSG KKKQLDALGS SGTSFTPHII + TVKPNEDVAS KIMAFSQQGP RTTCIISANG ALCTATLRQP ATSGGIVTYE + GHFDILSLSG SFLLAEDGDT RSRTGGLSVA LAGSDGRIVG GCVAGMLMAA + TPVQVVVGSF IAEAKKPKEE QPKREPTSVP PHTAVFGAAS TASPPSDGTS + SEHSDDPGSP MGPNGSAFTS AGLPLHSTYA AVGWSLSEDQ SRYDPDLKMM + TD + + + + + +GRMZM2G086553_P03 NP_001149978 AT-hook protein 1 seq=translation; coord=10:135573176..135577696:-1; parent_transcript=GRMZM2G086553_T03; parent_gene=GRMZM2G086553 + + + MDVRDLHQQP QQQQAPPRVG SPPQAGAGGV MMQHAAAFGA APPPSGLPQA + SAANVMHGMS LAFNPMASPD ASSPISSMKI VDMPLGSMYR PDSGATGLQQ + QQPGSGGVGA SGGAIVAVSG GDLVKKKRGR PRKYGPDGSI GLGLKTAAAG + VTEATGAQSG GGGSTPNPDG KRRGRPPGSG KKKQLDALGS SGTSFTPHII + TVKPNEDVAS KIMAFSQQGP RTTCIISANG ALCTATLRQP ATSGGIVTYE + GHFDILSLSG SFLLAEDGDT RSRTGGLSVA LAGSDGRIVG GCVAGMLMAA + TPVQVVVGSF IAEAKKPKEE QPKREPTSVP PHTAVFGAAS TASPPSDGTS + SEHSDDPGSP MGPNGSAFTS AGLPLHSTYA AVGWSLSEDQ SRYDPDLKMM + TD + + + + + + +7.56318 +-0.336141 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +11983 11983 11983 11983 11666 10800 9868 8199 6369 4707 3279 1678 925 489 279 126 58 7 3 2 2 1 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +11970 11970 11970 11970 11653 10779 9772 7903 5669 3671 1856 458 106 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3233 4961 2767 794 182 49 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2292 5419 3289 769 189 24 2 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2741 (charge 3) + +1670.84 +3 + + +155.081 155.118 157.097 158.092 159.076 166.061 167.093 167.116 169.097 171.076 171.113 172.072 173.055 173.092 173.128 175.105 175.119 183.112 185.092 185.115 187.071 188.103 189.087 193.096 195.112 197.128 198.087 198.123 199.071 199.107 +201.123 204.134 209.092 212.103 216.134 219.116 223.107 226.154 228.114 231.124 240.097 241.137 244.165 248.109 255.145 257.123 266.126 272.171 283.14 301.129 312.161 326.179 337.15 341.139 348.167 352.198 354.176 356.977 366.177 369.223 +383.198 394.18 427.182 432.23 436.213 440.261 452.223 456.241 494.234 501.278 504.765 511.26 528.765 551.289 553.304 555.275 559.274 561.27 568.325 596.279 599.277 619.293 622.294 630.321 651.317 679.354 680.344 684.323 686.342 696.375 +702.315 736.34 759.362 802.37 824.439 826.402 848.428 938.478 1293.43 1665.92 + + + + +30 7 9 10 14 8 5 5 34 14 7 5 7 32 14 9 100 7 14 19 6 5 6 5 7 6 9 10 8 27 +27 8 14 11 6 11 5 65 5 39 23 6 22 6 26 23 18 43 7 36 6 6 14 6 25 38 13 8 42 80 +12 12 7 11 40 46 14 6 37 13 46 30 37 11 8 9 12 9 53 10 69 8 70 14 8 13 20 23 11 43 +9 23 24 8 11 35 9 14 8 9 + + + + + + +GRMZM2G116292_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31201315..31206122:-1; parent_transcript=GRMZM2G116292_T01; parent_gene=GRMZM2G116292 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLQALARKYN QDKMICRKCY + ARLHPRAVNC RKKKCGHSNQ LRAKKKIKN + + + + + +GRMZM2G116292_P02 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T02; parent_gene=GRMZM2G116292 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLQALARKYN QDKMICRNSG + + + + + + +GRMZM2G116292_P03 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T03; parent_gene=GRMZM2G116292 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLQALARKYN QDKMICRKCY + ARLHPRAVNC RKKKCGHSNQ LRAKKKIKN + + + + + +GRMZM2G116292_P04 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T04; parent_gene=GRMZM2G116292 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLQALARKYN QDKMICRKVE + VVEGVFAKNT GQRDGCWIQN ELSQFNICTM YTKGDTDAMH GCTLGLSTAA + RRSVVTATS + + + + + +GRMZM2G116292_P05 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31206122:-1; parent_transcript=GRMZM2G116292_T05; parent_gene=GRMZM2G116292 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGIIEPSLQA LARKYNQDKM ICRKCYARLH PRAVNCRKKK CGHSNQLRAK + KKIKN + + + + + + + +GRMZM2G047727_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=2:165103157..165107176:-1; parent_transcript=GRMZM2G047727_T01; parent_gene=GRMZM2G047727 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLQALARKYN QDKMICRKCY + ARLHPRAVNC RKKKCGHSNQ LRAKKKIKN + + + + + +GRMZM2G409726_P01 NP_001105376 polyubiquitin seq=translation; coord=5:82443403..82446794:-1; parent_transcript=GRMZM2G409726_T01; parent_gene=GRMZM2G409726 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVESS + DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV + LRLRGGMQIF VKTLTGKTIT LEVESSDTID NVKAKIQDKE GIPPDQQRLI + FAGKQLEDGR TLADYNIQKE STLHLVLRLR GGQ + + + + + + + + + + + + + + + + + +GRMZM2G409726_P02 NP_001105376 polyubiquitin seq=translation; coord=5:82443815..82446714:-1; parent_transcript=GRMZM2G409726_T02; parent_gene=GRMZM2G409726 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGQ + + + + + + + +GRMZM2G409726_P03 NP_001105376 polyubiquitin seq=translation; coord=5:82443856..82446714:-1; parent_transcript=GRMZM2G409726_T03; parent_gene=GRMZM2G409726 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQKESTL HLVLRLRGGM + QIFVKTLTGK TITLEVESSD TIDNVKAKIQ DKEGIPPDQQ RLIFAGKQLE + DGRTLADYNI QKESTLHLVL RLRGGMQIFV KTLTGKTITL EVESSDTIDN + VKAKIQDKEG IPPDQQRLIF AGKQLEDGRT LADYNIQKES TLHLVLRLRG + GQ + + + + + + + + + + + + + + + +GRMZM2G006293_P01 NP_001150700 40S ribosomal protein S27a seq=translation; coord=1:191263450..191264705:-1; parent_transcript=GRMZM2G006293_T01; parent_gene=GRMZM2G006293 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPKK IKHKHKKVKL + SVLQFYKVDD TTSKVTRLRK ECPNTECGAG VFMANHFDRH YCGKCGLTYV + YNQKA + + + + + +GRMZM2G118637_P01 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236857988..236860949:1; parent_transcript=GRMZM2G118637_T01; parent_gene=GRMZM2G118637 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG Y + + + + + + + + + + + + + +GRMZM2G118637_P02 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859470..236861173:1; parent_transcript=GRMZM2G118637_T02; parent_gene=GRMZM2G118637 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG Y + + + + + + + + + + + + + +GRMZM2G118637_P03 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860675:1; parent_transcript=GRMZM2G118637_T03; parent_gene=GRMZM2G118637 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDI + QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV LRLRGGY + + + + + + + + + + + +GRMZM2G118637_P04 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860669:1; parent_transcript=GRMZM2G118637_T04; parent_gene=GRMZM2G118637 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQKESTLHL VLRLRGGMQI + FVKTLTGKTI TLEVESSDTI DNVKAKIQDK EGIPPDQQRL IFAGKQLEDG + RTLADYNIQK ESTLHLVLRL RGGMQIFVKT LTGKTITLEV ESSDTIDNVK + AKIQDKEGIP PDQQRLIFAG KQLEDGRTLA DYNIQKESTL HLVLRLRGG + + + + + + + + + + + +GRMZM2G118637_P05 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859647..236860633:1; parent_transcript=GRMZM2G118637_T05; parent_gene=GRMZM2G118637 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKE + + + + + + + + + +GRMZM2G419891_P01 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883718:1; parent_transcript=GRMZM2G419891_T01; parent_gene=GRMZM2G419891 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVESS + DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV + LRLRGGMQIF VKTLTGKTIT LEVESSDTID NVKAKIQDKE GIPPDQQRLI + FAGKQLEDGR TLADYNIQKE STLHLVLRLR GGQ + + + + + + + + + + + + + + + + + +GRMZM2G419891_P02 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883699:1; parent_transcript=GRMZM2G419891_T02; parent_gene=GRMZM2G419891 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVESS + DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV + LRLRGGQ + + + + + + + + + + + + + + + +GRMZM2G419891_P03 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883232:1; parent_transcript=GRMZM2G419891_T03; parent_gene=GRMZM2G419891 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQKESTLHL VLRLRGGMQI + FVKTLTGKTI TLEVESSDTI DNVKAKIQDK EGIPPDQQRL IFAGKQLEDG + RTLADYNIQK ESTLHLVLRL RGGMQIFVKT LTGKTITLEV ESSDTIDNVK + AKIQDKEGIP PDQQRLIFAG KQLEDGRTLA DYNIQKESTL HLVLRLRGG + + + + + + + + + + + +GRMZM2G419891_P04 NP_001105376 polyubiquitin seq=translation; coord=4:236879381..236883699:1; parent_transcript=GRMZM2G419891_T04; parent_gene=GRMZM2G419891 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID + NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLADYNIQKE STLHLVLRLR + GGQ + + + + + + + +GRMZM2G419891_P05 NP_001105376 polyubiquitin seq=translation; coord=4:236881289..236883469:1; parent_transcript=GRMZM2G419891_T05; parent_gene=GRMZM2G419891 + + + MQMQIFVKTL TGKTITLEVE SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK + QLEDGRTLAD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT + IDNVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLADYNIQ KESTLHLVLR + LRGGMQIFVK TLTGKTITLE VESSDTIDNV KAKIQDKEGI PPDQQRLIFA + GKQLEDGRTL ADYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVESS + DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN IQKESTLHLV + LRLRGGMQIF VKTLTGKTIT LEVESSDTID NVKAKIQDKE GIPPDQQRLI + FAGKQLEDGR TLADYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE + SSDTIDNVKA KIQDKEGIPP DQQRLIFAGK QLEDGRTLAD YNIQKESTLH + LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT IDNVKAKIQD KEGIPPDQQR + LIFAGKQLED GRTLADYNIQ KESTLHLVLR LRGGQ + + + + + + + + + + + + + + + + + +GRMZM2G431821_P01 P27923 Ubiquitin-40S ribosomal protein S27a Precursor [Contains Ubiquitin;40S ribosomal protein S27a] seq=translation; coord=8:171603815..171604536:-1; parent_transcript=GRMZM2G431821_T01; parent_gene=GRMZM2G431821 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPKK IKHKHKKVKL + AVLQFYKVDD ATGKVTRLRK ECPNTECGAG VFMANHFDRH YCGKCGLTYV + YNQKA + + + + + +GRMZM2G047732_P01 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126474..39127702:1; parent_transcript=GRMZM2G047732_T01; parent_gene=GRMZM2G047732 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPKK IKHKHKKVKL + AVLQFYKVDD ATGKVTRLRK ECPNAECGAG VFMANHFDRH YCGKCGLTYV + YNQQA + + + + + +GRMZM2G047732_P02 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126804..39127596:1; parent_transcript=GRMZM2G047732_T02; parent_gene=GRMZM2G047732 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPKK IKHKHKKVKL + AVLQFYKVDD ATGKVTRLRK ECPNAECGAG VFMANHFDRH YCGKCGLTYV + YNQQA + + + + + +GRMZM2G357296_P01 B6SIL9 40S ribosomal protein S27a seq=translation; coord=6:125241154..125242106:-1; parent_transcript=GRMZM2G357296_T01; parent_gene=GRMZM2G357296 + + + MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGAKKR KKKTYTKPKK IKHKHKKVKL + SVLQFYKVDD ATGKVTRLRK ECPNTECGAG VFMANHFDRH YCGKCGLTYV + YNQKA + + + + + +GRMZM2G116689_P01 NP_001148606 LOC100282222 seq=translation; coord=7:116376688..116380988:1; parent_transcript=GRMZM2G116689_T01; parent_gene=GRMZM2G116689 + + + MQIFVKTLTG KTITLEVESS DTVDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDSID + RIKERVEEKE GIPPVQQRLI YAGKQLADDK TAKDYNIEGG SVLHLVLALR + GGY + + + + + +GRMZM2G116689_P03 NP_001148606 LOC100282222 seq=translation; coord=7:116376702..116380916:1; parent_transcript=GRMZM2G116689_T03; parent_gene=GRMZM2G116689 + + + MQIFVKTLTG KTITLEVESS DTVDNVKAKI QDKEGIPPDQ QRLIFAGKQL + EDGRTLADYN IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDSID + RIKERVEEKE GIPPVQQRLI YAGKQLADDK TAKDYNIEGG SVLHLVLALR + GGY + + + + + +GRMZM2G005461_P01 seq=translation; coord=9:19289416..19290344:-1; parent_transcript=GRMZM2G005461_T01; parent_gene=GRMZM2G005461 + + + MNYDYDDEEE EVRRVGGGSY RFRRSRAWSP ESPRLPNPTA RPRFSSSYYK + SAGSPALWPL NARPPPDVSD LVSLLPSSEI FVHSEMQIFV KTLAGKSITL + EVESSDTVEN VKAKIQDKEG IPPDQQRLIF AGKQLDDGRI LADYNIQKES + TLHLVLRLRG GGGGQ + + + + + +GRMZM2G406643_P01 seq=translation; coord=7:150270916..150273417:1; parent_transcript=GRMZM2G406643_T01; parent_gene=GRMZM2G406643 + + + MQIFVKTLTG KTITLEVESS DTVANDKAKI QDKEGIPPDQ QRLIFAGKQL + EDDRTLADYS IQKDSTLHLV LRLRGGGRGG YPLMSVPWDL INLARKHNED + KMICRKCYAR LPPRSKNCRK KKCGHSNELR SKKKLISKFS M + + + + + + +5.33035 +-0.288127 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +4943 4943 4830 4568 4392 3010 2721 1406 862 383 221 131 73 28 15 6 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4946 4946 4833 4559 4384 2928 2249 964 407 159 93 43 7 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3385 1553 104 16 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +671 2957 1141 158 21 0 0 112 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2746 (charge 2) + +1039.52 +2 + + +150.045 158.092 159.076 167.055 167.118 168.055 169.062 169.133 170.064 175.119 183.149 187.071 187.144 188.074 195.113 199.107 213.086 217.107 223.063 225.042 227.101 232.14 239.094 244.165 254.149 266.999 272.158 281.051 283.025 286.149 +299.061 301.059 303.177 310.139 313.649 322.161 326.967 341.144 342.996 344.976 346.973 359.028 361.026 370.687 380.155 413.22 415.035 417.033 431.235 438.198 469.204 525.275 529.235 546.262 566.255 584.269 626.287 643.314 645.321 680.334 +723.343 724.345 740.367 742.372 803.365 + + + + +1 2 5 56 1 7 13 1 1 10 1 29 4 2 2 3 3 2 6 5 3 3 10 1 6 1 2 5 2 1 +100 19 2 4 1 25 1 2 1 22 5 10 3 56 1 2 6 2 24 2 1 1 2 12 2 3 3 56 3 3 +4 1 39 3 1 + + + + + + +GRMZM2G139296_P01 NP_001143877 hypothetical protein LOC100276678 seq=translation; coord=8:171762195..171768664:1; parent_transcript=GRMZM2G139296_T01; parent_gene=GRMZM2G139296 + + + MATRAAARFL QRRFLSSGGK VLSEEEKAAE NVYIKKVEQE KLEKLARKGP + SSGEQPSSTT GSAASDVKAD AGPTESASAS VSTDKNKNYA VLAGAVAALG + GLGWYLLLKP KKSEEVVD + + + + + + +5.67825 +-0.276988 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 + + + + +9547 9547 9016 8777 7989 6922 5710 4145 2937 1813 1124 590 291 154 73 32 15 5 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +9549 9549 9018 8767 7911 6722 5106 3205 1622 653 232 71 13 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2627 3760 2012 853 248 42 8 6 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1810 4402 2372 738 185 42 3 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2747 (charge 3) + +1977.94 +3 + + +152.057 153.066 155.081 157.097 159.076 167.081 171.076 173.092 175.12 181.061 185.092 187.071 189.087 198.087 199.071 199.107 201.087 203.103 209.092 213.087 224.102 227.102 228.171 230.113 236.103 240.134 242.113 244.165 246.181 254.113 +258.106 270.108 272.124 274.103 287.134 299.133 311.135 313.15 315.04 322.155 329.145 337.148 341.146 345.14 355.162 361.206 373.171 386.182 402.163 432.172 434.712 448.24 451.191 456.212 458.188 469.21 471.181 475.216 489.193 494.235 +514.26 519.277 533.298 540.241 545.246 558.251 568.24 572.235 586.251 590.318 614.289 625.283 627.284 643.304 644.305 661.335 677.347 683.643 691.301 708.337 716.358 734.367 736.357 754.335 755.347 771.361 773.367 790.385 817.394 835.415 +887.436 936.46 938.437 948.465 955.444 1024.49 1025.47 1042.47 1110.52 1207.58 + + + + +2 2 5 18 8 12 8 3 2 2 25 5 5 3 3 9 8 2 2 5 9 9 3 3 8 7 6 2 39 14 +7 7 8 9 3 3 5 7 2 2 8 8 4 6 5 8 3 8 3 2 3 17 2 3 5 6 2 3 6 5 +9 18 3 6 2 2 2 6 7 12 2 5 3 46 16 13 15 3 2 2 7 56 7 20 6 100 13 3 6 28 +2 16 5 6 11 15 9 8 6 5 + + + + + + +GRMZM2G069174_P01 NP_001150471 LOC100284101 seq=translation; coord=2:78022601..78028183:1; parent_transcript=GRMZM2G069174_T01; parent_gene=GRMZM2G069174 + + + MASQPPPPAA AAASGAPPPA QVVGNAFVHQ YYNILHQSPE LVYRFYQEAS + CLGRPAGTGA DGMDTVTTMD AINDKIVSMG IDRAEIKAVD AQESLCGGVS + VLVMGHLTGR NSVSRQFVQS FFLAPQEKGY FVLNDILRYV GEGGGDEGAE + KQPAPEVAAD AETTTSAPIL SARWPSLHLI QRRKF + + + + + +GRMZM2G069174_P02 NP_001150471 LOC100284101 seq=translation; coord=2:78022601..78028183:1; parent_transcript=GRMZM2G069174_T02; parent_gene=GRMZM2G069174 + + + MASQPPPPAA AAASGAPPPA QVVGNAFVHQ YYNILHQSPE LVYRFYQEAS + CLGRPAGTGA DGMDTVTTMD AINDKIVSMG IDRAEIKAVD AQESLCGGVS + VLVMGHLTGR NSVSRQFVQS FFLAPQEKGY FVLNDILRYV GEGGGDEGAE + KQPAPEVAAD AETTTSAPIL ANGTVGGDAT TVPQDASPQP ECQVAEPALN + PKEEVLNGEV CNSLSDVEKP VAEETPVPDV INEVPNNVAV APPISSPPVP + LKEAPKKSYA SIVKVMKEHR PLAPAVPSRP APPITEKQAS PAPTPVTEAP + AFSPNPQSGG FQDPEGII + + + + + +GRMZM2G069174_P03 NP_001150471 LOC100284101 seq=translation; coord=2:78022601..78028183:1; parent_transcript=GRMZM2G069174_T03; parent_gene=GRMZM2G069174 + + + MASQPPPPAA AAASGAPPPA QVVGNAFVHQ YYNILHQSPE LVYRFYQEAS + CLGRPAGTGA DGMDTVTTMD AINDKIVSMG IDRAEIKAVD AQESLCGGVS + VLVMGHLTGR NSVSRQFVQS FFLAPQEKGY FVLNDILRYV GEGGGDEGAE + KQPAPEVAAD AETTTSAPIL ANGTVGGDAT TVPQDASPQP ECQVAEPALN + PKEEVLNGEV CNSLSDVEKP VAEETPVPDV INEVPNNVAV APPISSPPVP + LKEAPKKSYA SIVKVMKEHR PLAPAVPSRP APPITEKQAS PAPTPVTEAP + AFSPNPQSGG FQDPEVDAHA IYVRSLPLNA TPQQLEEEFK RFGTIKHEGI + QVRSNKIQGF CYGFVEFEDA SAVQAAIEAS PVTIGERQCF VEEKRTTGSR + GGSRGGRFPP GRGGNFRGEG IRGRGTYNGG RGYGRGEFSY RSDYGGRGGG + RGGSLHGGDV GYQRVDYSGT SSGRGARAPS AAAAMAK + + + + + +GRMZM2G069174_P04 NP_001150471 LOC100284101 seq=translation; coord=2:78022601..78028183:1; parent_transcript=GRMZM2G069174_T04; parent_gene=GRMZM2G069174 + + + MASQPPPPAA AAASGAPPPA QVVGNAFVHQ YYNILHQSPE LVYRFYQEAS + CLGRPAGTGA DGMDTVTTMD AINDKIVSMG IDRAEIKAVD AQESLCGGVS + VLVMGHLTGR NSVSRQFVQS FFLAPQEKGY FVLNDILRYV GEGGGDEGAE + KQPAPEVAAD AETTTSAPIL ANGTVGGDAT TVPQDASPQP ECQVAEPALN + PKEEVLNGEV CNSLSDVEKP VAEETPVPDV INEVPNNVAV APPISSPPVP + LKEAPKKSYA SIVKVMKEHR PLAPAVPSRP APPITEKQAS PAPTPVTEAP + AFSPNPQSGG FQDPEVDAHA IYVRSLPLNA TPQQLEEEFK RFGTIKHEGI + QVRSNKIQGF CYGFVEFEDA SAVQAAIEAS PVTIGERQCF VEEKRTTGSR + GGGSRGGRFP PGRGGNFRGE GIRGRGTYNG GRGYGRGEFS YRSDYGGRGG + GRGGSLHGGD VGYQRVDYSG TSSGRGARAP SAAAAMAK + + + + + + +5.34234 +-0.344667 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +2167 2167 2167 2031 1887 1788 1099 842 462 211 63 46 9 4 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2175 2175 2175 2039 1886 1784 1074 779 352 140 48 38 1 0 + + + + + + +0 1 2 3 4 + + + + +1164 850 152 10 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +590 1450 120 7 0 0 9 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2748 (charge 2) + +1267.55 +2 + + +152.056 155.081 156.077 157.097 158.092 159.076 159.091 167.081 169.097 171.076 171.112 172.112 173.055 173.092 175.119 184.072 185.165 187.071 195.088 199.108 201.087 204.134 212.103 226.154 230.078 233.164 235.144 237.121 240.132 244.165 +258.145 260.123 263.138 270.147 285.196 313.189 320.16 348.123 404.212 408.671 420.103 433.167 442.155 446.238 470.26 515.244 525.79 533.254 673.231 696.359 705.298 762.326 819.34 832.268 901.45 921.468 998.494 1005.41 + + + + +6 5 14 3 5 12 3 4 4 6 4 13 5 18 18 4 5 15 4 6 15 16 6 33 6 5 100 4 3 29 +5 16 12 4 42 5 5 4 17 3 3 3 4 3 4 4 4 11 4 4 5 5 16 5 4 4 6 21 + + + + + + +GRMZM2G467007_P01 NP_001140281 hypothetical protein LOC100272325 seq=translation; coord=9:154307169..154311241:-1; parent_transcript=GRMZM2G467007_T01; parent_gene=GRMZM2G467007 + + + MWVTSMPQVW DEEGAAKGGA VTPAPAAAML GSLAGWLSRT VQPQPPAPRV + CGTAGGPPVT APRLRLRDGR HLAYCESGVP RDQARFAVVF SHGFTGSRED + SVRASQEVAE ELGVYMVGFD RAGYGQSDPN PNRSVKSAAL DVEELADALG + LGPKFYVIGI SLGCHAVWGA LKYIPDRIAG AAMMAPVVNY WWPGFSPELA + AEVYAKQEVG DQWALRVSHH APGILHWWME QSWLPTSTVV AGTTPLPNER + DAEIRSKMKA DGTFQQKREQ ATQQGIHESY YRDMTVMFGK WEFDPMALPE + PPCPVHLWQG DEDGLVPVVL QRYLAGKIGW INYHELPGTG HFLSSVPGLG + DNVLRTLFSD KQ + + + + + +GRMZM2G467007_P02 NP_001140281 hypothetical protein LOC100272325 seq=translation; coord=9:154307396..154311241:-1; parent_transcript=GRMZM2G467007_T02; parent_gene=GRMZM2G467007 + + + MVGFDRAGYG QSDPNPNRSV KSAALDVEEL ADALGLGPKF YVIGISLGCH + AVWGALKYIP DRIAGAAMMA PVVNYWWPGF SPELAAEVYA KQEVGDQWAL + RVSHHAPGIL HWWMEQSWLP TSTVVAGTTP LPNERDAEIR SKMKADGTFQ + QKREQATQQG IHESYYRDMT VMFGKWEFDP MALPEPPCPV HLWQGDEDGL + VPVVLQRYLA GKIGWINYHE LPGTGHFLSS VPGLGDNVLR TLFSDKQ + + + + + +GRMZM2G467007_P04 NP_001140281 hypothetical protein LOC100272325 seq=translation; coord=9:154307169..154310878:-1; parent_transcript=GRMZM2G467007_T04; parent_gene=GRMZM2G467007 + + + MWVTSMPQVW DEEGAAKGGA VTPAPAAAML GSLAGWLSRT VQPQPPAPRV + CGTAGGPPVT APRLRLRDGR HLAYCESGVP RDQARFAVVF SHGFTGSRED + SVRASQGRWT ATSVYCLSTC NAKLEFGELQ LVSYTGSLPL ARRLSVGCHF + HSQAADGALR RDAVIAASDA DWALIRIGLV VGPLEEQSRH GHADTAGSST + KSLGRPGAGV LALAAMELLA KAPVLGCAGK MQRQRQRGSA LGRWICRAVA + PPRAAPATPP RVRLRDGRHL AYAESGASKE DARFKVVFSH GFTGSRLDTV + RPAPEVAEEL GVYMVGFDRA GYGQSDPNPN RSVKSAALDV EELADALGLG + PKFYVIGISL GCHAVWGALK YIPDRIAGAA MMAPVVNYWW PGFSPELAAE + VYAKQEVGDQ WALRVSHHAP GILHWWMEQS WLPTSTVVAG TTPLPNERDA + EIRSKMKADG TFQQKREQAT QQGIHESYYR DMTVMFGKWE FDPMALPEPP + CPVHLWQGDE DGLVPVVLQR YLAGKIGWIN YHELPGTGHF LSSVPGLGDN + VLRTLFSDKQ + + + + + + +4.73894 +-0.379115 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +2674 2674 2601 2516 2379 2196 988 697 317 70 26 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2677 2677 2604 2513 2372 2179 930 586 213 25 21 1 0 0 1 0 + + + + + + +0 1 2 3 4 + + + + +1930 680 72 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +402 2062 210 3 0 0 13 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2752 (charge 2) + +1275.57 +2 + + +152.057 155.081 169.061 169.096 171.076 171.111 173.092 175.119 181.097 184.07 186.087 187.144 193.097 195.087 197.129 199.109 212.102 216.134 221.092 226.155 234.146 239.15 241.08 244.166 250.118 255.111 264.002 271.14 278.112 292.127 +330.18 349.15 358.927 369.186 371.116 386.215 400.229 432.184 580.282 597.31 599.32 667.367 712.333 799.362 827.45 943.471 967.415 984.446 + + + + +7 2 4 2 3 2 2 17 2 2 16 2 8 2 2 6 8 3 7 9 2 3 2 2 2 2 2 3 2 3 +2 6 2 8 3 17 2 2 4 100 2 4 4 8 3 2 3 12 + + + + + + +GRMZM2G161673_P01 NP_001141335 hypothetical protein LOC100273426 seq=translation; coord=6:65490775..65492414:1; parent_transcript=GRMZM2G161673_T01; parent_gene=GRMZM2G161673 + + + MARAGVSTAP LSRTHLLPPR PSLLHNTQPH SLLLRPQRKA PATTAAALPP + AADFPALSLP AAAAAAAALA AAVSLSDPER RRRSQAEAAG GGDKEAVRAY + FNSTGFERWR KIYGSATEGV NRVQLDIREG HAQTVAAALA MLRDSPLELA + GATVCDAGCG TGSLAIPLAA AGADVLASDI SAAMVSEAQR QAAAQSSSSS + FRMPRFEVRD LESLEGRYDV VVCLDVLIHY PREEARAMIR HLASLADKRL + LISFAPRTLY FDFLKRVGEL FPGPSKATRA YLHAEADIED ALRQAGWRVA + NRGFISTQFY FAKLFDAVPV GSST + + + + + + +6.90973 +-0.394842 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +4343 4343 4343 4343 4231 3934 3764 3450 3196 1803 1302 596 260 77 20 10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +4346 4346 4346 4346 4234 3937 3751 3403 3148 1640 1051 391 40 16 2 1 0 + + + + + + +0 1 2 3 4 + + + + +2220 1805 291 30 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1033 2864 408 34 5 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2757 (charge 2) + +1226.57 +2 + + +152.056 154.097 155.081 157.06 157.108 157.134 158.092 159.076 167.055 169.05 169.097 171.076 171.112 172.108 173.055 173.092 173.128 174.993 175.119 182.092 183.076 183.112 185.091 185.127 185.164 186.123 187.071 189.087 190.052 195.112 +198.087 198.123 199.071 200.103 201.123 204.134 213.086 217.082 226.118 233.165 239.094 241.093 244.093 254.113 255.114 271.138 275.169 283.141 286.009 287.006 297.155 299.062 301.058 305.159 325.15 329.193 356.07 357.067 359.065 365.198 +375.073 392.194 415.701 420.993 421.993 427.234 452.215 483.009 496.253 501.276 508.749 512.207 516.256 549.803 583.283 605.281 624.355 630.317 657.28 670.313 700.361 729.386 757.346 759.355 798.284 830.403 868.375 885.396 956.44 1027.47 +1168.7 + + + + +24 64 74 10 10 20 25 31 10 7 33 8 21 62 8 13 29 7 100 73 31 9 6 8 22 8 7 11 10 6 +9 9 9 75 40 22 9 11 61 21 37 23 11 53 6 58 11 6 21 31 26 22 24 6 27 6 33 78 9 9 +7 8 24 11 8 46 6 7 8 10 6 6 6 28 25 28 6 12 8 49 8 8 93 26 7 12 27 40 34 43 +7 + + + + + + +GRMZM2G081037_P01 NP_001141129 hypothetical protein LOC100273215 seq=translation; coord=4:156953772..156958300:1; parent_transcript=GRMZM2G081037_T01; parent_gene=GRMZM2G081037 + + + + + + + +GRMZM2G081037_P02 NP_001141129 hypothetical protein LOC100273215 seq=translation; coord=4:156953772..156958300:1; parent_transcript=GRMZM2G081037_T02; parent_gene=GRMZM2G081037 + + + + + + + + +8.39552 +-0.508819 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +3361 3361 3361 3352 3210 3163 2928 2143 1629 915 325 207 19 5 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3367 3367 3367 3358 3216 3158 2926 2109 1063 435 91 31 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1867 1230 125 145 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +638 2068 630 26 0 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2758 (charge 2) + +1412.63 +2 + + +155.081 156.076 157.061 158.092 159.076 169.097 171.075 173.091 175.119 186.089 187.071 195.113 198.088 199.072 201.087 204.134 214.119 227.102 228.099 230.114 235.144 240.134 244.128 246.108 251.103 259.472 263.139 283.138 286.14 291.165 +301.149 312.167 317.145 320.129 332.161 348.188 419.226 476.246 517.379 530.893 609.053 620.322 648.296 763.318 795.84 834.353 884.423 905.397 1063.46 1111.5 1150.49 1326.97 + + + + +22 5 6 5 16 16 5 5 31 4 20 4 5 6 7 16 13 17 17 9 100 6 30 6 5 4 32 4 5 18 +15 5 6 5 6 30 6 39 6 5 6 6 40 21 7 39 16 31 6 5 24 5 + + + + + + +GRMZM2G087570_P01 seq=translation; coord=6:44382950..44385913:-1; parent_transcript=GRMZM2G087570_T01; parent_gene=GRMZM2G087570 + + + + + + + + +5.54326 +-0.35763 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + + + + +4672 4672 4672 4672 4596 4295 3952 3731 3569 1637 1471 434 158 46 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4686 4686 4686 4686 4610 4309 3953 3729 3571 1557 1199 191 5 1 0 + + + + + + +0 1 2 3 4 + + + + +2618 1930 133 7 0 + + + + + + +0 1 2 3 4 5 + + + + +590 3615 424 56 3 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2764 (charge 2) + +1418.69 +2 + + +155.081 156.076 167.12 171.873 173.091 175.119 179.818 199.07 199.107 199.18 216.098 227.175 243.135 252.137 303.178 329.154 347.165 360.176 486.244 532.236 587.759 600.09 653.3 702.314 720.871 794.135 1046.46 1132.47 1175.48 1244.56 + + + + + +7 8 6 6 9 100 5 9 8 83 8 30 6 23 12 9 7 6 12 10 10 9 8 13 6 7 12 10 24 28 + + + + + + + +GRMZM2G134668_P02 NP_001150317 calnexin seq=translation; coord=2:61490885..61494711:-1; parent_transcript=GRMZM2G134668_T02; parent_gene=GRMZM2G134668 + + + MGGRALLLLL LVSALVFQIH ASDPLLYEPF DEDFEGRWVV SKKDEYQGVW + RHAKSDGHED YGLLVSEKAR KYAIIKELDE PVTLKDGTVV LQFEVRLQNG + LECGGAYIKY IRPQDAGWDA KEFDNETPYT IMFGPDKCGS TNKVHFILKH + KNPKTGKYVE HHLKFPPSVP YDKLSHVYTA ILKPDNEVKI LVDGEEKKKA + NFLSADDFEP ALIPSKTIPD PDDKKPEDWD ERAKIPDPDA VKPDDWDEDA + PMEIVDDEAT KPEGWLDDEP EEIDDPEAAK PEDWDDEEDG EWEAPKIDNP + KCEEAPGCGE WKRPMKQNPA YKGKWHAPMI DNPNYKGIWK PQEIPNPEYF + ELDKPDFDPI AAIGIEIWTM QDGILFDNIL IADDEKVATS ILEKTWKPKY + DVEKEKEKAE EEAAAGADGL SEFQKKIFDV LYKIADVPFL APYKTKIIDV + IEKGEKQPNI TIGILVSVVV VFVTVLFKIL FGGKKPVAPV KPAAEAKKPK + ATVTDGAGSS GDKDEKEDEK EETAGPRRRT RRET + + + + + + +4.76895 +-0.307674 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +2208 2208 2208 2208 2208 2038 1723 1465 937 539 302 136 54 14 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2219 2219 2219 2219 2219 2049 1732 1474 924 506 262 94 36 6 1 0 + + + + + + +0 1 2 3 4 + + + + +900 1169 132 19 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +995 1082 130 10 2 0 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2765 (charge 3) + +2779.25 +3 + + +201.123 204.087 226.154 254.149 274.102 355.197 400.229 443.941 501.276 539.323 630.319 686.122 738.577 746.357 759.358 764.674 837.025 880.921 887.452 1010.96 1016.5 1073.99 1082.47 1131.51 1137.5 1147.02 1204.52 1254.55 1260.57 1518.71 +1632.71 1834.85 2497.2 2566.23 + + + + +10 11 12 63 15 11 10 10 22 12 51 11 14 14 66 22 16 52 37 22 53 41 64 16 14 100 50 58 19 18 +16 13 15 17 + + + + + + +GRMZM2G019325_P01 P25460 40S ribosomal protein S11 seq=translation; coord=10:142067983..142070677:1; parent_transcript=GRMZM2G019325_T01; parent_gene=GRMZM2G019325 + + + MAEQTEKAFL KQPKVFLSSK KSGKGKKPGK GGNRFWKSIG LGFKTPREAI + EGTYIDKKCP FTGTVSIRGR IIAGTCHSAK MNRTIIVRRN YLHFVKKYQR + YEKRHSNIPA HISPCFRVKE GDHVIIGQCR PLSKTVRFNV VKVIPAGSAA + AGKKAFTAA + + + + + +GRMZM2G044800_P01 P25460 40S ribosomal protein S11 seq=translation; coord=2:10477304..10479869:-1; parent_transcript=GRMZM2G044800_T01; parent_gene=GRMZM2G044800 + + + MAEQTEKAFL KQPKVFLSSK KSGKGKKPGK GGNRFWKSIG LGFKTPREAI + EGTYIDKKCP FTGTVSIRGR IIAGTCHSAK MNRTIIVRRN YLHFVKKYQR + YEKRHSNIPA HISPCFRVKE GDHVIIGQCR PLSKTVRFNV VKVIPAGSAA + AGKKAFTAA + + + + + + +6.18098 +-0.287487 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +2548 2548 2548 2504 2264 2181 1871 1601 1096 700 407 247 127 60 43 14 6 3 2 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2556 2556 2556 2506 2269 2158 1813 1307 669 299 105 95 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +936 1154 418 57 9 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +500 1345 530 161 29 8 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2769 (charge 2) + +941.542 +2 + + +152.057 155.081 157.097 157.133 158.092 159.076 167.081 169.082 169.097 170.1 171.113 173.092 173.129 175.119 176.122 183.149 185.092 185.115 185.129 185.165 186.088 186.122 186.168 187.108 194.128 195.113 197.129 198.087 199.108 201.123 +204.134 213.159 214.119 216.098 226.119 230.114 235.119 238.119 240.135 242.114 244.166 246.157 249.1 258.147 259.142 269.125 272.172 275.171 283.14 285.157 287.135 293.162 295.139 297.157 309.203 312.167 313.149 330.178 340.161 346.208 +356.192 358.17 365.198 372.224 378.7 384.187 391.226 411.197 417.245 427.231 429.208 437.211 452.251 455.223 457.254 461.253 467.754 470.263 489.275 498.265 504.28 505.278 508.252 520.791 526.262 544.294 553.309 561.299 563.306 578.307 +601.305 613.33 632.336 634.343 648.845 659.339 711.382 729.388 731.391 764.419 + + + + +9 6 3 19 3 6 3 2 48 4 5 7 5 24 1 3 3 53 9 100 4 13 12 6 13 2 1 7 7 3 +31 16 3 7 19 2 1 3 5 5 5 2 2 2 2 5 2 30 5 4 12 4 10 3 3 3 12 4 9 17 +6 11 57 7 3 12 4 6 8 8 2 7 1 14 5 3 6 5 4 6 8 2 4 3 6 5 2 55 5 3 +3 5 58 4 3 4 2 27 2 4 + + + + + + +GRMZM5G819807_P01 NP_001140352 hypothetical protein LOC100272400 seq=translation; coord=3:38240385..38253883:-1; parent_transcript=GRMZM5G819807_T01; parent_gene=GRMZM5G819807 + + + MEAAAAAFLS PPRVALDVRT LFSPPRCLPV SPSSQLRLAA RPRALAGAKP + RFLSPHREPA VDGGRGARDV VAMVVPFLRG AAWEQPPPDL ASFLYKNRIV + YLGMCLVPSV TELMLAEFLY LQYDDAEKPI YMYINSTGTT KNGEKLGYET + EALAVYDAMR YVKVPIFTLC VGNAWGEAAL LLAAGAKGNR AALPSSTIMI + KQPIGRFQGQ ATDVDIARKE IRNVKIEMVK LLARHIGKPM EEIARDIRRP + KYFSPSEAVD YGIIDKVIYN EKIQEDGGVV SELKRSNLI + + + + + + +GRMZM5G819807_P02 NP_001140352 hypothetical protein LOC100272400 seq=translation; coord=3:38240385..38255415:-1; parent_transcript=GRMZM5G819807_T02; parent_gene=GRMZM5G819807 + + + MCLVPSVTEL MLAEFLYLQY DDAEKPIYMY INSTGTTKNG EKLGYETEAL + AVYDAMRYVK VPIFTLCVGN AWGEAALLLA AGAKGNRAAL PSSTIMIKQP + IGRFQGQATD VDIARKEIRN VKIEMVKLLA RHIGKPMEEI ARDIRRPKYF + SPSEAVDYGI IDKVIYNEKI QEDGGVVSEL KRSNLI + + + + + + + +5.9626 +-0.290859 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +7168 7168 7168 7168 7057 6400 5867 4770 3621 2542 1698 952 571 283 150 70 26 7 3 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7172 7172 7172 7172 7061 6402 5757 4486 3071 1682 812 265 44 19 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2424 2974 1351 329 81 13 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1345 3000 1798 771 231 20 4 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2770 (charge 3) + +1296.67 +3 + + +153.102 154.086 155.081 157.097 158.092 159.076 161.092 166.061 167.118 169.097 169.133 171.076 171.113 173.092 175.072 175.089 175.119 178.134 181.06 181.097 183.076 185.091 186.123 187.107 189.087 194.129 195.113 197.128 199.107 201.105 +208.953 210.949 214.119 218.149 223.155 226.155 229.099 235.12 240.134 242.113 244.165 246.156 248.034 251.15 255.145 258.157 266.044 272.172 283.163 290.159 291.677 299.18 303.653 311.173 322.154 327.196 329.194 331.857 345.977 347.706 +351.665 359.239 366.214 370.712 383.662 393.859 399.21 404.222 412.229 417.263 421.235 426.234 431.21 452.259 464.239 470.271 474.231 488.284 499.3 500.308 521.758 538.232 541.28 565.318 567.326 580.349 582.346 597.352 605.269 617.325 +634.288 664.371 669.266 694.402 700.363 702.323 764.357 770.383 797.413 861.409 + + + + +37 6 12 6 24 9 9 9 12 25 15 20 36 8 9 9 100 23 5 18 8 7 50 8 8 20 12 12 15 32 +14 18 5 11 87 39 10 17 13 4 22 12 12 35 14 29 7 27 13 7 38 26 11 10 20 21 5 8 8 13 +13 14 8 24 20 11 23 9 8 13 50 16 19 18 10 39 11 24 11 13 9 20 5 14 20 9 13 13 23 28 +11 8 15 9 28 13 8 8 52 13 + + + + + + +GRMZM2G036921_P01 NP_001148437 LOC100282052 seq=translation; coord=9:98777728..98779013:-1; parent_transcript=GRMZM2G036921_T01; parent_gene=GRMZM2G036921 + + + + + + + + +6.36951 +-0.296256 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +8485 8485 8485 8315 8232 7961 7558 6952 6333 4891 3830 2299 1115 636 331 159 76 33 10 4 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8477 8477 8477 8307 8224 7948 7531 6863 6108 4338 2829 981 144 12 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2314 3803 1627 542 157 47 3 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1387 3735 2337 783 215 19 16 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2771 (charge 3) + +1243.66 +3 + + +154.086 155.082 156.076 157.061 157.109 157.133 158.092 159.076 159.091 166.061 167.081 169.097 169.133 171.113 172.117 173.092 173.128 175.071 175.119 176.121 179.127 181.095 181.109 183.076 183.149 184.108 185.092 186.124 197.128 200.139 +201.123 204.134 210.087 212.103 214.118 218.15 221.103 226.119 228.098 230.113 232.141 240.134 242.15 244.129 246.109 249.098 254.114 256.145 257.652 260.197 264.661 267.108 269.123 271.139 281.122 283.176 286.152 287.135 289.187 299.138 +303.177 309.203 311.171 315.128 327.131 329.182 337.187 344.976 350.146 354.214 357.249 360.224 362.164 368.157 370.174 374.214 382.209 386.161 398.204 400.219 416.26 431.263 439.193 444.194 451.232 457.201 485.248 492.717 497.271 503.257 +514.298 528.314 538.264 585.337 599.349 656.372 666.32 670.386 727.41 757.414 + + + + +7 16 7 7 4 7 31 32 13 7 13 47 14 60 4 74 27 4 100 4 6 3 6 10 30 4 7 8 13 9 +10 3 13 17 18 24 4 17 29 9 3 82 12 35 8 7 3 9 20 9 40 13 8 6 4 23 14 4 24 82 +12 22 63 3 7 4 4 10 8 16 11 27 7 9 7 45 37 8 7 10 11 24 8 4 3 7 14 3 11 64 +48 69 4 19 11 61 32 4 7 9 + + + + + + +GRMZM5G858454_P02 NP_001147431 aconitase2 seq=translation; coord=10:96330046..96338713:-1; parent_transcript=GRMZM5G858454_T02; parent_gene=GRMZM5G858454 + + + MANPTATKHA FKRILTSLLK PGGGEYGKFF SLPALNDPRI DKLPYSIRVL + LESAIRHCDN FQVTESDVEK IIDWENTSPK LAEIPFKPAR CILMDNTGVP + AVVDLAAMRD MMPKLGCDPY KINPLIPVDA VIDHAVRVDV AGTYDALDRN + EELEFQRNKE RFAFLKWASN AFHNMQVFPP GSGTVHQVNL EYLARVVFNE + DGILYFDSVV GTDSHTTMIN SLGVAGWGVG GIEAVVAMLG QPMGMVLPGV + VGFKLSGKLR DGVTTTDIVL TMTQMLRKHG AIGKFVEFYG VGVGELSLPA + RATIANMSPE YGATMGFFPV DQVALDYLKL TGRSDETVSM IEAYLRANKM + FVDKHEPETE RVFSSHLELD LSEVEPCVSG PKRPHDRVPL KEMKSDWHAC + LDNEVGFKGY AVPKEQQGKV VKFDFHGRPA EIKHGSVVLA AICSSTNTSN + PSVMIGAGLV AKKACELGLE VKPWVKTSLT PGSVVATEYL KHSGLQDYLN + QQGFHVAAHG CATCVGNSGD LDGSVSAAIT ENDMVAAAVL SANRNFEGRV + NPLTRANYLA SPPLVVAYAL AGTVDIDFEK EPIGVGKGGK EVFLRDIWPS + NQEIDEVVES SVQTHLFKKV YDSIMERNPR WNQLPVPKEA LYPWEDRSTY + IRKPTYLEGM SMTPPAAPPT VTEAYCLLNL GDSITTDHIS YSGKIPEGTP + AAKYLLEYGV EPKNFSSYGG RRGNNEVVMR GAFANMRIVN KLLDGKAGPW + TIHVPTGEKL YVYDAAMKYK SEGHDMVIIA GSEYGSGSSR DSAAKGPMLL + GVKSVIAKSF ERIHRSNLVG MGIIPLCFKA GEDADSLGLT GRERYTIHLP + TSTAELSPGQ DVTVTTHDGR SFTCTLRLDT QLEVTYFNHG GILPYMVRNL + AAQMK + + + + + + +GRMZM2G467338_P01 C4J6M5 Putative uncharacterized protein seq=translation; coord=2:114883820..114891121:-1; parent_transcript=GRMZM2G467338_T01; parent_gene=GRMZM2G467338 + + + MAANSTATKH AFKRILTSLI KPGGGEYGKF FSLPALNDPR IDKLPYSIRV + LLESAIRHCD NFQVTESDVE KIIDWENTSP KLAEIPFKPA RCILMDNTGV + PAVVDLAAMR DMMPKLGCDP YKINPLIPVD AVIDHAVRVD VAGTYDALDR + NEELEFQRNK ERFAFLKWAS NAFHNMQVFP PGSGTVHQVN LEYLARVVFN + EDGILYFDSV VGTDSHTTMI NSLGVAGWGV GGIEAVVAML GQPMGMVLPG + VVGFKLSGKL QDGVTTTDIV LTMTQMLRKH GAIGKFVEFY GVGVGELSLP + ARATIANMSP EYGATMGFFP VDQVALDYLK LTGRSDETVS MIEAYLRANK + MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP LKEMKSDWHA + CLDNEVGFKG YAVPKEQQGK VVKFDFHGRP AEIKHGSVVL AAICSSTNTS + NPSVMIGAGL VAKKACELGL EVKPWVKTSL TPGSVVATEY LKHSGLQDYL + NQQGFHVAAH GCATCVGNSG DLDGSVSAAI TENDIVAAAV LSANRNFEGR + VNPLTRANYL ASPPLVVAYA LAGTVDIGFE EEPIGVGKGG KEIFLRDIWP + SNQEIDEVVE SSVQTHLFKK VYDSIMERNP RWNQLPVPKE ALYPWDDRST + YIRKPTYLEG MSMTPPGPPT VTEAYCLLNL GDSITTDHIS YSGKIPEGTP + AAKYLLEYGV EPKNFSSYGG RRGNNEVVMR GAFANMRIVN KLLNGEAGPW + TIHVPTGEKL YVYDAAMKYK SEGHDMVIIA GSEYGSGSSR DSAAKGPMLL + GVKSVIAKSF ERIHRSNLVG MGIIPLCFQA GEDADSLGLT GRERYTIHLP + TSTAEISPGQ DVTVTTHDGR SFTCTLRLDT QLEVTYFNHG GILPYMVRNL + AAQMK + + + + + + +GRMZM2G467338_P02 C4J6M5 Putative uncharacterized protein seq=translation; coord=2:114883990..114890380:-1; parent_transcript=GRMZM2G467338_T02; parent_gene=GRMZM2G467338 + + + MEQQLLCGGC HTHTPPPPSL PCPCLRRRPR TLSVSSRCHA IHPDQLLRAR + LVPDVTTSAK LQPRDDALHR IRVGVGATKH AFKRILTSLI KPGGGEYGKF + FSLPALNDPR IDKLPYSIRV LLESAIRHCD NFQVTESDVE KIIDWENTSP + KLAEIPFKPA RCILMDNTGV PAVVDLAAMR DMMPKLGCDP YKINPLIPVD + AVIDHAVRVD VAGTYDALDR NEELEFQRNK ERFAFLKWAS NAFHNMQVFP + PGSGTVHQVN LEYLARVVFN EDGILYFDSV VGTDSHTTMI NSLGVAGWGV + GGIEAVVAML GQPMGMVLPG VVGFKLSGKL QDGVTTTDIV LTMTQMLRKH + GAIGKFVEFY GVGVGELSLP ARATIANMSP EYGATMGFFP VDQVALDYLK + LTGRSDETVS MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS + GPKRPHDRVP LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFDFHGRP + AEIKHGSVVL AAICSSTNTS NPSVMIGAGL VAKKACELGL EVKPWVKTSL + TPGSVVATEY LKHSGLQDYL NQQGFHVAAH GCATCVGNSG DLDGSVSAAI + TENDIVAAAV LSANRNFEGR VNPLTRANYL ASPPLVVAYA LAGTVDIGFE + EEPIGVGKGG KEIFLRDIWP SNQEIDEVVE SSVQTHLFKK VYDSIMERNP + RWNQLPVPKE ALYPWDDRST YIRKPTYLEG MSMTPPGPPT VTEAYCLLNL + GDSITTDHIS YSGKIPEGTP AAKYLLEYGV EPKNFSSYGG RRGNNEVVMR + GAFANMRIVN KLLNGEAGPW TIHVPTGEKL YVYDAAMKYK SEGHDMVIIA + GSEYGSGSSR DSAAKGPMLL GVKSVIAKSF ERIHRSNLVG MGIIPLCFQA + GEDADSLGLT GRERYTIHLP TSTAEISPGQ DVTVTTHDGR SFTCTLRLDT + QLEVTYFNHG GILPYMVRNL AAQMK + + + + + + +GRMZM2G364988_P01 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=5:91434867..91439005:-1; parent_transcript=GRMZM2G364988_T01; parent_gene=GRMZM2G364988 + + + MATLPSRPGT SSSFGPVPSA SSGVSAGHLD AVKPVGRVRV ISAPLLQMAK + PYLVVASLPL QTPLSSWSVL PTTRLIRKHG AIGKFVEFYG VGVGELSLPA + RATIANMSPE YGATMGFFLV SMIEAYLRAN KMFVDKHEPE TERVFSSYLE + LDLSEVEPCV SGPKRPHDRV PLKEMKSDWH ACLDNEVGFK VKPWVKTSLT + PGSVVATEYL KHRYRCCCGA VSYYLLNLGD SITTDHISYS GKIPEGTPAA + KYLLEYGVEP KNFSSYGGRR GNNEVVMRGA FANMRIVNKL LNGEAGPWTI + HVPTGEKLYV YDAAMVEKMV LLACGWRYTI TVCDSSNLYT YGWRKYVQLG + HIDFEDDLVP HKLEALKDST ISQVIPFTNI P + + + + + + +GRMZM2G029204_P01 seq=translation; coord=7:110162687..110164873:1; parent_transcript=GRMZM2G029204_T01; parent_gene=GRMZM2G029204 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPRDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFDFHGRP AEIKHGSVVL + AAICSSTNTS NPSVMIGAGL VAKKACELGL EVKPWVKTSL TPGSVVATEY + LKHSGLQDYL NQQGFHVAAH GCATCVGNSG DLDGSISVAI TENDIVAATV + LSANRNFEGR VNPHSG + + + + + + +GRMZM2G364988_P02 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=5:91434878..91439446:-1; parent_transcript=GRMZM2G364988_T02; parent_gene=GRMZM2G364988 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFNFHGRP AEIKHGSVVL + AAICSSTNTS NPSFMIGAGL VEESMRIGP + + + + + + +GRMZM2G364988_P03 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=5:91434878..91438625:-1; parent_transcript=GRMZM2G364988_T03; parent_gene=GRMZM2G364988 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFNFHGRP AEIKHGSVVL + AAICSSTNTS NPSFMIGAGL VEESMRIGP + + + + + + +GRMZM2G036131_P01 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=3:64518828..64524123:-1; parent_transcript=GRMZM2G036131_T01; parent_gene=GRMZM2G036131 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFNFHGRP AEIKHGSVVL + AAICSSTNTS NPSFMIGAGL VEESMRIGP + + + + + + +GRMZM2G036131_P03 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=3:64518825..64523306:-1; parent_transcript=GRMZM2G036131_T03; parent_gene=GRMZM2G036131 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFNFHGRP AEIKHGSVVL + AAICSSTNTS NPSFMIGAGL VEESMRIGP + + + + + + +GRMZM2G036131_P04 NP_001141579 hypothetical protein LOC100273695 seq=translation; coord=3:64518828..64523306:-1; parent_transcript=GRMZM2G036131_T04; parent_gene=GRMZM2G036131 + + + MIEAYLRANK MFVDKHEPET ERVFSSYLEL DLSEVEPCVS GPKRPHDRVP + LKEMKSDWHA CLDNEVGFKG YAVPKEQQGK VVKFNFHGRP AEIKHGSVVL + AAICSSTNTS NPSFMIGAGL VEESMRIGP + + + + + + + +3.99948 +-0.216188 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7417 7417 7417 6698 6407 5583 4671 3620 2315 1542 1048 646 398 206 114 69 53 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7442 7442 7442 6723 6399 5515 4435 3078 1640 902 487 246 150 105 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2528 3058 1418 347 79 11 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1296 3159 1989 769 136 57 13 24 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2772 (charge 3) + +1533.7 +3 + + +152.056 153.102 155.081 156.076 157.061 157.097 157.109 157.133 158.092 159.076 166.062 167.081 169.097 169.134 171.077 171.113 173.092 175.087 175.119 176.121 181.061 181.098 183.149 184.108 185.092 185.165 186.09 186.123 187.072 187.108 +191.613 195.114 198.124 199.072 199.108 199.181 201.123 203.118 209.09 212.139 214.119 217.082 219.15 221.103 226.154 231.124 234.144 239.114 240.134 244.166 249.098 254.149 257.128 267.114 272.172 285.165 295.108 300.664 304.162 307.151 +311.171 312.171 316.155 324.154 331.197 332.2 346.68 354.177 356.196 382.211 388.186 392.205 399.245 405.209 412.184 417.178 420.209 431.196 446.222 449.207 453.254 462.247 482.288 510.281 528.31 534.25 544.237 609.304 614.272 620.301 +631.304 633.315 637.312 673.275 692.34 720.341 742.34 747.367 760.343 897.406 + + + + +11 4 10 7 8 7 4 4 13 9 3 7 21 4 4 11 9 4 56 3 20 9 3 9 12 8 3 3 4 5 +3 7 8 12 25 9 4 24 6 12 11 37 3 3 48 34 8 10 17 61 10 3 7 29 10 12 3 13 5 3 +12 4 13 3 24 4 12 5 3 3 3 3 10 22 3 8 4 4 3 8 3 4 11 17 3 13 3 10 4 4 +100 4 4 3 3 5 10 13 24 13 + + + + + + +GRMZM2G124307_P01 NP_001152548 LOC100286188 seq=translation; coord=1:212054704..212055806:-1; parent_transcript=GRMZM2G124307_T01; parent_gene=GRMZM2G124307 + + + MAMQVVRNLD LERYAGRWYE IACFPSRFQP KTGTNTRATY TLNPDGTVKV + VNETWADGRR GHIEGTAWRA DPASDEAKLK VRFYVPPFLP LIPVTGDYWV + LHIDADYQYA LVGQPSRNYL WILCRQPHMD ESVYKELVER AKEEGYDVSK + LRKTAHPDPP PESEQSPRDG GMWWVKSIFG K + + + + + + +6.28956 +-0.279536 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +8638 8638 8638 8638 8372 8014 7378 6686 5455 4304 2777 1669 940 492 268 157 70 29 13 9 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8638 8638 8638 8638 8372 8003 7262 6491 5112 3374 1642 607 167 15 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3051 3614 1464 394 101 18 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1525 3459 2379 1007 213 42 16 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2773 (charge 3) + +1644.76 +3 + + +155.082 156.077 157.097 158.092 159.076 169.133 171.076 171.113 172.071 175.119 184.072 185.092 187.071 189.087 193.097 195.112 197.128 199.108 199.18 203.121 213.088 216.135 217.082 226.154 227.102 232.139 235.063 239.094 241.081 244.165 +253.093 255.146 258.108 261.619 272.171 299.062 303.177 310.148 328.162 332.136 340.126 359.204 364.712 369.736 386.215 388.117 403.206 413.711 415.228 432.253 436.718 440.773 450.213 452.248 457.226 466.278 467.282 475.735 487.261 492.75 +504.22 507.737 522.232 524.215 532.284 547.931 553.241 559.762 568.773 574.33 580.773 595.256 601.262 611.879 616.301 619.282 636.799 645.304 678.331 685.331 689.357 692.331 699.453 703.337 705.337 709.84 723.385 727.377 743.861 766.376 +770.495 775.369 794.363 814.369 826.415 832.382 851.434 898.55 914.445 929.428 + + + + +22 7 10 21 8 7 10 10 7 63 6 33 8 6 7 7 7 34 48 15 11 6 10 77 34 7 25 22 7 21 +23 23 22 9 29 7 21 41 6 7 6 17 9 7 9 9 8 32 8 6 9 6 7 7 10 99 35 19 36 7 +24 8 66 9 7 6 6 7 45 71 6 6 6 6 7 87 8 21 9 8 100 8 10 66 7 45 7 8 7 6 +43 10 10 20 34 22 29 8 7 53 + + + + + + +GRMZM2G042118_P01 NP_001150149 LOC100283778 seq=translation; coord=8:162236975..162239554:-1; parent_transcript=GRMZM2G042118_T01; parent_gene=GRMZM2G042118 + + + MAAFNKLGGL LRHSALVSGI TGGSSPAVFN AARLMSTKLF IGGLDWGVDD + VKLREAFSSF GEVTEARVIT DRETGRSRGF GFVNYSDSDA AKEAISAMDG + KEIDGRQVRV NMANERPAGN RGGGGYGGGG YGGGGYGGGG GYGGGGYGGG + SQSYDA + + + + + + +4.00476 +-0.216474 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +6454 6454 6373 5859 4578 3620 2292 1630 892 551 288 167 91 56 43 36 28 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6431 6431 6348 5825 4456 3272 1855 923 407 196 56 23 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2553 2518 935 339 73 38 0 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1173 3430 1435 365 37 10 5 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2776 (charge 3) + +1328.65 +3 + + +153.066 155.081 157.108 158.092 167.055 169.061 169.097 169.134 170.092 171.113 175.09 175.119 176.122 186.087 186.124 197.092 201.069 203.085 214.118 216.097 218.095 223.063 225.043 229.064 233.165 244.092 246.09 252.134 255.108 257.64 +269.124 272.136 283.075 290.145 300.101 317.127 324.988 328.133 329.156 335.69 341.017 342.997 346.184 359.028 366.141 383.167 389.191 391.206 400.21 417.221 426.243 429.087 440.21 448.721 450.25 457.233 471.228 478.241 480.217 484.243 +492.752 497.246 498.245 514.273 516.277 521.282 549.758 558.272 563.26 598.272 602.271 606.78 615.293 653.35 699.287 716.309 782.389 792.374 828.394 879.402 896.434 907.41 924.453 941.424 959.435 967.469 1056.46 + + + + +3 1 2 4 29 1 15 2 9 1 6 20 1 3 5 9 1 3 15 1 7 3 8 5 1 3 5 6 1 3 +2 2 2 1 2 3 1 3 1 10 5 7 3 100 1 2 1 1 3 2 1 2 2 3 2 9 2 2 2 2 +19 5 2 29 1 1 3 18 2 1 2 12 21 4 1 1 3 1 1 1 4 1 1 1 1 4 1 + + + + + + +GRMZM2G416388_P01 NP_001150216 CBS domain protein seq=translation; coord=1:273865741..273870770:-1; parent_transcript=GRMZM2G416388_T01; parent_gene=GRMZM2G416388 + + + MQRAVQAVRS HGNVLKYAVL QHISAPKPAM LPAAFSRFMS VSSARLEDRG + FETATVADVL KSKGKSADGS WLWCTTEDSV YDAVKSMTQH NVGALVVVKP + GQNKSIAGIV TERDYLRKII VQGRSSKSTK VGDIMTEENK LITVNPDTKV + LQAMQLMTEN RVRHIPVIDG TGMLGMVSIG DVVRAVVAEH REELNRLNDY + IQGGY + + + + + +GRMZM2G416388_P02 NP_001150216 CBS domain protein seq=translation; coord=1:273865741..273870770:-1; parent_transcript=GRMZM2G416388_T02; parent_gene=GRMZM2G416388 + + + MQRAVQAVRS HGNVLKYAVL QHISAPKPAM LPAAFSRFMS VSSARLEDRG + FETATVADVL KSKGKSADGS WLWCTTEDSV YDAVKSMTQH NVGALVVVKP + GQNKSIAGIV TERDYLRKII VQGRSSKSTK VGDIMTEENK LITVNPDTKV + LQAMQLMTEN RVRHIPVIDG TGMLGMVSIG DVVRAVVAEH REELNRLNDY + IQGGY + + + + + +GRMZM2G416388_P03 NP_001150216 CBS domain protein seq=translation; coord=1:273865741..273868546:-1; parent_transcript=GRMZM2G416388_T03; parent_gene=GRMZM2G416388 + + + MQRAVQAVRS HGNVLKYAVL QHISAPKPAM LPAAFSRFMS VSSARLEDRG + FETATVADVL KSKGKSADGS WLWCTTEDSV YDAVKSMTQH NVGALVVVKP + GQNKSIAGIV TERDYLRKII VQGRSSKSTK VGDIMTEENK LITVNPDTKV + LQAMQLMTEN RVRHIPVIDG TGMLGMVSIG DVVRAVVAEH REELNRLNDY + IQGGY + + + + + +GRMZM2G416388_P06 NP_001150216 CBS domain protein seq=translation; coord=1:273866192..273868141:-1; parent_transcript=GRMZM2G416388_T06; parent_gene=GRMZM2G416388 + + + MQRAVQAVRS HGNVLKYAVL QHISAPKPAM LPAAFSRFMS VSSARLEDRG + FETATVADVL KSKGKSADGS WLWCTTEDSV YDAVKSVCPH FPMIVLTPSE + SMVMHQMIRL PFGTLNFLQM TQHNVGALVV VKPGQNKSIA GIVTERGDEQ + ISVLLASNFW PVAVHHSTFG IKESQLFRAL YSRYNRNCIK LKYTYYLRKI + IVQGRSSKST KVGDIMTEEN KLITVNPDTK VLQAMQLMTE NRVRHIPVID + GTGMLGMVSI GDVVRAVVAE HREELNRLND YIQGGY + + + + + + +6.49862 +-0.302262 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +8007 8007 8007 7907 7479 7125 6403 5764 5082 3743 2833 1487 861 465 276 138 40 18 8 2 1 1 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8016 8016 8016 7916 7488 7093 6290 5484 4638 3061 1929 538 157 99 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2028 3601 1763 495 97 33 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2023 3307 1775 634 189 66 15 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2777 (charge 3) + +1422.74 +3 + + +155.082 157.11 157.133 158.092 158.137 159.076 169.097 171.077 171.113 171.149 172.115 173.056 173.092 175.119 176.123 181.061 185.128 187.071 189.087 194.624 197.128 198.088 199.071 199.108 199.18 209.09 215.139 217.081 221.104 226.119 +227.067 232.14 235.118 244.129 245.076 249.099 252.14 256.091 270.181 272.171 277.142 284.087 285.196 289.162 299.062 302.661 309.119 327.13 360.173 371.214 384.236 388.241 402.247 408.722 414.231 424.699 430.206 448.217 460.223 463.763 +468.736 477.249 480.208 489.217 500.259 512.27 520.787 524.255 531.294 533.252 541.771 546.73 560.268 564.236 568.775 577.289 578.292 587.292 597.26 602.266 604.316 611.279 611.783 618.315 619.318 626.823 642.318 660.333 661.333 668.284 +676.362 702.315 715.409 732.318 790.334 799.405 851.404 936.486 979.455 1078.53 + + + + +8 5 100 13 9 4 6 5 64 11 6 12 7 98 8 15 19 4 5 17 4 4 17 7 14 7 9 14 5 23 +20 5 5 10 10 8 7 5 4 12 5 6 8 4 4 35 5 5 7 10 5 6 12 4 6 6 4 6 8 8 +17 56 7 23 4 5 5 5 9 8 15 19 5 5 13 63 16 8 8 5 7 15 6 15 5 85 5 17 6 8 +7 6 6 6 4 9 6 7 4 5 + + + + + + +GRMZM2G318635_P01 seq=translation; coord=5:213291570..213301733:-1; parent_transcript=GRMZM2G318635_T01; parent_gene=GRMZM2G318635 + + + + + + + + + +3.85748 +-0.285739 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +797 797 797 757 688 517 376 194 122 72 23 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +802 802 802 762 693 517 373 186 114 66 10 7 1 0 + + + + + + +0 1 2 3 4 + + + + +423 351 25 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +262 505 33 1 0 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2781 (charge 2) + +1398.56 +2 + + +155.081 157.097 166.985 171.076 173.128 175.119 181.06 187.072 189.087 194.129 197.128 198.087 198.124 199.108 201.069 209.055 212.103 216.134 219.079 224.116 226.082 228.135 234.145 240.098 244.167 252.109 264.098 281.124 286.14 314.133 +319.178 332.106 340.096 345.177 357.123 363.188 409.116 455.124 460.24 555.211 579.288 587.172 597.297 637.316 711.334 727.383 812.387 894.309 923.961 927.411 1042.43 + + + + +7 16 3 6 5 8 4 4 6 6 5 4 4 14 4 7 5 5 5 3 26 4 58 5 4 7 5 21 7 8 +6 4 6 16 20 4 7 6 100 5 14 4 8 7 5 14 15 4 5 7 7 + + + + + + +GRMZM2G035503_P01 NP_001130324 hypothetical protein LOC100191418 seq=translation; coord=5:208090222..208094428:-1; parent_transcript=GRMZM2G035503_T01; parent_gene=GRMZM2G035503 + + + MEGRARLSLV HAAAALVVLL QLHGGAVVVA SEPPYTCGAG APPNIPFCDA + GLPIDRRVDD LVSRMTVAEK ISQLGDQSPA IPRLGVPAYK WWSEALHGIS + NQGRGIHLDG PLRAATSFPQ VILTAASFNP HLWYRIGQVI GVEARAVYNN + GQAEGLTFWA PNINVFRDPR WGRGQETPGE DPTMTGKYAA VFVRGVQGYG + LAGPVNSTGL EASACCKHFT AYDLENWKGV TRYVFDAKVT AQDLADTYNP + PFKSCVEDGH ASGIMCSYNR VNGVPTCADY NLLSTTARQD WGFYGYITSD + CDAVAIIHDA QGYAKTAEDA VADVLKAGMD VNCGSYVQDH GASALQQGKI + TEQDINRALH NLFAVRMRLG LFNGDPRRNL YGDIGPDQVC TQEHQDLALE + AAQDGIVLLK NDGGAGALPL SKPNVASLAV IGFNANDAIR LRGNYFGPPC + VTVTPLQVLQ GYVKDTSFVA GCNSAACNVT TIPEAVQAAS SADSVVLFMG + LDQDQEREEV DRLDLTLPGQ QQTLIESVAN AAKKPVILVL LCGGPVDVSF + AKTNPKIGAI LWAGYPGEAG GIAIAQVLFG EHNPGGRLPV TWYPQDFTRV + PMTDMRMRAD PATGYPGRTY RFYRGPTVFN FGYGLSYSKY SHRFATKPPP + TSNVAGLKAV EATAGGMASY DVEAIGSETC DRLKFPAVVR VQNHGPMDGK + HSVLVFMRWP NATDGSGRPA SQLIGFQSLH LRATQTAHVE FEVSPCKHFS + RATEDGRKVI DQGSHFVMVG EDEFEMSFMA + + + + + + + +5.39461 +-0.326946 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + + + + +1822 1822 1822 1822 1771 1153 877 615 316 161 71 48 10 5 2 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +1828 1828 1828 1828 1777 1159 881 612 299 143 70 48 9 8 1 0 + + + + + + +0 1 2 3 4 + + + + +1214 583 30 1 0 + + + + + + +0 1 2 3 4 5 + + + + +465 1315 42 0 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2782 (charge 2) + +1463.63 +2 + + +152.034 152.057 155.081 158.092 159.076 169.061 175.118 180.448 181.097 185.091 186.087 199.108 204.133 213.087 226.154 231.098 241.081 244.166 284.124 305.18 315.13 346.141 383.192 399.152 470.26 586.316 650.313 655.997 678.37 704.454 +984.457 1048.47 1213.51 1458.17 + + + + +7 5 6 9 6 55 10 5 6 18 100 10 8 10 62 6 7 18 8 9 26 6 7 35 6 44 47 6 6 5 +42 31 5 5 + + + + + + +GRMZM2G019177_P01 NP_001152706 LOC100286347 seq=translation; coord=4:169006869..169011322:1; parent_transcript=GRMZM2G019177_T01; parent_gene=GRMZM2G019177 + + + MQEVFKRVDG KAAVAAQPSS EEERTKALQA LLSCPTSSIH TEKPPKDILK + VQNMFPLPID DKLLPGVYLC GYNSEDSYGA TSYLVIHPQG NILIDSPRYT + PKLANNIEKL GGARYMFLTH IDDVADHRKW AEQLKCERII HSGDVEEATA + DVEWKLEGNG PWNLGTDFEL ITYARPYPRL SVLVLQTAKG AVHWRPCCKV + RRIRRSEPLS DVQQAVSEPS AGKHQEATGA RVRVAFTWTW LSNQVQRCAC + QECSHGVPPS + + + + + +GRMZM2G019177_P02 NP_001152706 LOC100286347 seq=translation; coord=4:169006869..169011322:1; parent_transcript=GRMZM2G019177_T02; parent_gene=GRMZM2G019177 + + + MALMSLGAAG YTTATAPPRP RRCTLPFRAA ASPAALDRRR RPHNVAGDFF + VDHRCIDCQT CRWMAPEVFK RVDGKAAVAA QPSSEEERTK ALQALLSCPT + SSIHTEKPPK DILKVQNMFP LPIDDKLLPG VYLCGYNSED SYGATSYLVI + HPQGNILIDS PRYTPKLANN IEKLGGARYM FLTHIDDVAD HRKWAEQLKC + ERIIHSGDVE EATADVEWKL EGNGPWNLGT DFELITYARP YPRLSVLVLQ + TAKGAVHWRP CCKVRRIRRS EPLSDVQQAV SEPSAGKHQE ATGARVRVAF + TWTWLSNQVQ RCACQECSHG VPPS + + + + + +GRMZM2G019177_P03 NP_001152706 LOC100286347 seq=translation; coord=4:169006869..169011322:1; parent_transcript=GRMZM2G019177_T03; parent_gene=GRMZM2G019177 + + + MALMSLGAAG YTTATAPPRP RRCTLPFRAA ASPAALDRRR RPHNVAGDFF + VDHRCIDCQT CRWMAPEVFK RVDGKAAVAA QPSSEEERTK ALQALLSCPT + SSIHTEKPPK DILKVQNMFP LPIDDKLLPG VYLCGYNSED SYGATSYLVI + HPQGNILIDS PRYTPKLANN IEKLGGARYM FLTHIDDVAD HRKWAEQLKC + ERIIHSGDVE EATADVEWKL EGNGPWNLGT DFELINTPGH TPGSVCLYFK + PLKVLFTGDH VAKSEESDDL NLFLMYSKQS VSLQLESIRK LLELEFEWLL + PGHGYRIKYK DVRAKNVAME SLLANYTS + + + + + + +4.75817 +-0.288374 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +4790 4790 4697 4430 4233 3957 3711 2169 1658 848 396 203 129 39 31 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4799 4799 4706 4439 4222 3878 3606 1956 1335 458 129 63 13 9 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2676 1776 303 39 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +907 3076 692 99 20 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2786 (charge 2) + +1344.64 +2 + + +152.056 155.081 156.076 157.097 157.108 158.092 159.076 166.062 167.117 169.097 169.133 171.077 171.113 175.119 185.165 195.113 197.129 200.103 214.118 217.082 221.103 227.102 230.113 242.15 249.099 253.089 257.16 267.109 271.14 285.156 +297.156 303.176 313.187 325.15 339.204 342.177 353.181 356.228 361.027 363.024 384.223 400.703 413.213 417.183 424.218 428.26 430.24 433.205 441.718 468.004 472.713 490.245 494.262 498.228 501.639 530.204 538.775 613.328 641.283 656.334 +659.257 680.865 731.847 736.31 744.357 773.34 816.349 833.362 835.368 882.432 944.397 961.416 979.481 1032.47 1076.53 1103.49 + + + + +4 3 5 2 2 2 2 3 2 9 3 3 20 30 10 5 20 10 9 2 3 9 4 49 14 2 2 11 12 18 +3 14 20 3 3 4 3 10 3 4 9 5 5 4 3 2 13 8 4 2 3 23 2 3 3 3 4 3 4 12 +2 3 5 8 2 3 8 100 10 9 13 12 9 20 4 15 + + + + + + +GRMZM2G085019_P01 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T01; parent_gene=GRMZM2G085019 + + + + + + + +GRMZM2G085019_P02 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T02; parent_gene=GRMZM2G085019 + + + + + + + + +4.88291 +-0.250406 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 + + + + +7165 7165 7165 6672 6493 4736 4094 2744 1964 1151 774 487 303 98 50 23 17 13 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7169 7169 7169 6676 6485 4689 3819 2255 1161 565 240 50 31 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4218 2373 489 74 14 0 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1110 4475 1200 333 35 15 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2787 (charge 2) + +1371.72 +2 + + +152.056 155.081 156.076 159.091 165.138 167.055 167.081 175.119 181.096 181.133 183.149 187.071 193.098 198.123 199.107 209.128 211.143 223.107 226.155 227.102 229.156 235.118 239.094 241.093 244.165 249.097 252.134 256.145 260.197 265.166 +267.107 270.144 284.138 299.061 301.06 319.138 336.165 339.238 346.15 356.07 357.249 359.028 361.025 383.191 386.159 394.223 396.15 412.236 417.222 419.993 429.087 431.085 443.717 452.252 468.279 475.201 483.272 486.293 492.719 508.239 +533.209 548.26 556.766 565.288 573.788 604.243 622.318 623.341 637.725 663.366 677.867 731.354 742.383 749.363 752.392 758.34 762.331 790.326 806.393 859.4 869.39 872.421 874.519 887.379 888.379 890.452 903.457 921.501 960.481 962.491 +970.423 987.468 998.442 999.468 1015.47 1037.47 1146.56 1153.63 1225.59 1243.61 + + + + +4 4 5 10 8 18 3 13 5 4 39 4 3 4 22 13 20 10 100 26 4 8 18 9 25 12 4 14 18 10 +25 8 22 8 4 3 8 5 4 16 74 52 31 4 9 8 9 4 4 3 10 5 4 4 13 5 5 4 13 8 +11 4 12 3 9 17 18 10 4 3 3 3 8 10 5 12 3 13 3 3 4 3 4 23 12 9 3 4 14 3 +4 4 4 3 13 3 12 3 3 9 + + + + + + +GRMZM5G844562_P01 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98997371:-1; parent_transcript=GRMZM5G844562_T01; parent_gene=GRMZM5G844562 + + + MGSLASERKV VGWAARDATG HLSPYSYTLR NTGPEDVVVK VLYCGICHTD + IHQAKNHLGA SKYPMVPGHE VVGEVVEVGP EVAKYGVGDV VGVGVIVGCC + RECSPCKANV EQYCNKKIWS YNDVYTDGRP TQGGFASTMV VDQKFVVKIP + AGLAPEQAAP LLCAGVTVYS PLKHFGLTTP GLRGGILGLG GVGHMGVKVA + KAMGHHVTVI SSSSKKRAEA MDHLGADAYL VSSDAAAMAA AADSLDYIID + TVPVHHPLEP YLALLKLDGK LVLLGVIGEP LSFVSPMVML GRKAITGSFI + GSIDETAEVL QFCVDKGLTS QIEVVKMGYV NEALERLERN DVRYRFVVDV + AGSNVEAEAA AADAASN + + + + + +GRMZM5G844562_P03 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98996099:-1; parent_transcript=GRMZM5G844562_T03; parent_gene=GRMZM5G844562 + + + MVLVFGKKKK LTLVSFSYGM CCGGDNRNTG PEDVVVKVLY CGICHTDIHQ + AKNHLGASKY PMVPGHEVVG EVVEVGPEVA KYGVGDVVGV GVIVGCCREC + SPCKANVEQY CNKKIWSYND VYTDGRPTQG GFASTMVVDQ KFVVKIPAGL + APEQAAPLLC AGVTVYSPLK HFGLTTPGLR GGILGLGGVG HMGVKVAKAM + GHHVTVISSS SKKRAEAMDH LGADAYLVSS DAAAMAAAAD SLDYIIDTVP + VHHPLEPYLA LLKLDGKLVL LGVIGEPLSF VSPMVMLGRK AITGSFIGSI + DETAEVLQFC VDKGLTSQIE VVKMGYVNEA LERLERNDVR YRFVVDVAGS + NVEAEAAAAD AASN + + + + + +GRMZM5G844562_P02 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98997371:-1; parent_transcript=GRMZM5G844562_T02; parent_gene=GRMZM5G844562 + + + MVVDQKFVVK IPAGLAPEQA APLLCAGVTV YSPLKHFGLT TPGLRGGILG + LGGVGHMGVK VAKAMGHHVT VISSSSKKRA EAMDHLGADA YLVSSDAAAM + AAAADSLDYI IDTVPVHHPL EPYLALLKLD GKLVLLGVIG EPLSFVSPMV + MLGRKAITGS FIGSIDETAE VLQFCVDKGL TSQIEVVKMG YVNEALERLE + RNDVRYRFVV DVAGSNVEAE AAAADAASN + + + + + + +7.12842 +-0.347728 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +7958 7958 7958 7958 7705 7581 6964 6373 5087 3746 2254 1196 558 282 97 46 21 6 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7971 7971 7971 7971 7718 7588 6946 6252 4701 2992 1370 409 107 28 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2853 3184 1430 404 98 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1091 3643 2331 712 150 32 0 13 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2788 (charge 3) + +1440.73 +3 + + +152.057 154.087 155.081 155.093 156.077 157.061 157.098 157.134 158.093 159.077 166.061 167.093 167.119 169.098 171.077 171.113 173.093 173.128 175.074 175.09 175.119 178.062 181.096 181.134 183.112 183.15 185.056 185.092 185.165 186.124 +187.108 189.087 194.128 195.089 195.113 196.145 197.128 198.124 199.107 201.124 204.135 209.141 212.103 214.155 216.135 224.139 226.155 230.077 232.141 234.144 237.133 240.135 244.164 253.093 258.145 266.634 275.125 286.145 314.135 321.178 +324.128 332.148 356.19 359.174 369.177 377.215 383.195 390.202 397.167 408.206 431.216 438.241 452.253 470.262 477.23 492.243 495.241 506.231 514.25 534.226 556.277 559.269 570.253 572.279 589.293 602.311 608.321 634.317 664.332 678.353 +695.397 707.392 716.333 718.334 734.353 790.422 808.439 814.263 821.408 907.509 + + + + +27 6 16 8 7 8 5 6 17 7 6 13 5 21 12 12 8 25 6 58 71 5 6 6 8 7 15 13 24 18 +8 6 24 24 14 17 36 7 64 30 22 16 8 15 15 7 100 6 6 28 23 22 47 23 7 5 6 6 40 22 +14 20 6 14 19 23 16 7 8 29 8 7 26 15 21 5 60 14 15 19 6 14 6 6 51 7 36 18 5 8 +6 6 17 16 6 5 25 6 7 19 + + + + + + +GRMZM5G821637_P04 NP_001140813 hypothetical protein LOC100272888 seq=translation; coord=1:298687651..298689984:1; parent_transcript=GRMZM5G821637_T04; parent_gene=GRMZM5G821637 + + + MAEQIAKDPA FTEMAEQLQK TVVSPRQQQQ QQARQQQQQL DPQKYVATMQ + QLMQNPQFVA MAERLGSALM QDPAMSAMLG GLTNPAHKEQ LEARVARMKE + DPTLKPILDE IESGGPAAMM KYWNDPEALQ KFGRAMGVGV GPSGEAGGAE + HAEAEDDAGE EGEYEDESIV HHTASVGDVE GLKKALEDGA DKDEEDSEGR + RGLHFACGYG ELQCAQALLE AGAAVDAVDK NKNTALHYAA GYGRKDCVAL + LLESGAAVTL QNLDGKTPID VAKLNNQDDV LKLLEKHAFV + + + + + +GRMZM5G821637_P05 NP_001140813 hypothetical protein LOC100272888 seq=translation; coord=1:298687651..298689984:1; parent_transcript=GRMZM5G821637_T05; parent_gene=GRMZM5G821637 + + + MAAQEEKTAV VVAAAADVAT EEPTPAAEQQ PQPAGAARRA GPSAPGGAPP + NPFDFSTMMN LLNDPSIKEM AEQIAKDPAF TEMAEQLQKT VVSPRQQQQQ + QARQQQQQLD PQKYVATMQQ LMQNPQFVAM AERLGSALMQ DPAMSAMLGG + LTNPAHKEQL EARVARMKED PTLKPILDEI ESGGPAAMMK YWNDPEALQK + FGRAMGVGVG PSGEAGGAEH AEAEDDAGEE GEYEDESIVH HTASVGDVEG + LKKALEDGAD KDEEDSEGRR GLHFACGYGE LQCAQALLEA GAAVDAVDKN + KNTALHYAAG YGRKDCVALL LESGAAVTLQ NLDGKTPIDV AKLNNQDDVL + KLLEKHAFV + + + + + + +5.29454 +-0.286191 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 + + + + +4093 4093 4049 3789 3481 3167 2759 2042 1535 840 461 237 125 76 43 7 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4098 4098 4054 3788 3463 3095 2636 1864 1130 485 140 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1359 1633 756 262 85 0 4 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +904 1977 895 225 74 21 2 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2792 (charge 3) + +1891.83 +3 + + +152.057 155.081 157.134 158.137 159.076 167.118 171.076 171.112 172.11 173.056 173.092 173.129 175.119 176.122 181.06 185.093 185.113 185.129 186.088 186.132 187.072 189.087 194.624 199.071 199.108 201.088 204.133 213.087 215.139 217.081 +226.119 232.14 240.133 243.133 244.092 254.154 256.092 285.195 286.201 302.662 313.025 327.128 341.144 355.125 360.174 371.216 380.07 388.241 424.697 430.202 440.193 445.868 448.216 466.275 474.179 480.212 487.213 489.217 511.229 527.229 +546.729 558.239 563.905 569.281 581.261 587.29 602.258 604.316 610.78 617.241 619.295 668.292 685.315 692.283 702.314 703.811 713.277 719.347 723.314 732.322 733.324 781.33 789.835 798.396 803.311 818.451 830.36 836.346 845.353 854.856 +860.324 942.4 960.401 977.427 1015.42 1075.43 1077.45 + + + + +6 2 100 10 1 1 2 3 1 2 1 3 39 3 2 1 2 30 2 3 2 1 5 6 2 1 2 1 8 3 +10 2 1 5 7 1 2 5 1 29 1 2 2 3 6 6 1 8 3 1 1 3 3 3 2 2 6 29 2 6 +11 2 12 3 2 6 11 15 46 6 3 15 2 2 8 7 7 2 5 51 15 10 25 2 2 2 3 5 19 22 +3 2 3 3 2 7 2 + + + + + + +GRMZM2G058173_P01 NP_001151824 undecaprenyl pyrophosphate synthetase seq=translation; coord=7:144837690..144838974:-1; parent_transcript=GRMZM2G058173_T01; parent_gene=GRMZM2G058173 + + + + + + + + + +8.53699 +-0.517394 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +3178 3178 3178 3178 2965 2696 2565 2359 1049 924 319 72 15 4 2 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3178 3178 3178 3178 2965 2696 2553 2344 1019 847 264 28 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2266 855 55 3 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +618 2428 126 7 0 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2798 (charge 2) + +1442.65 +2 + + +152.057 167.092 171.076 175.119 189.087 192.261 195.088 209.104 226.083 234.144 237.135 241.082 258.432 270.146 275.554 293.452 296.134 310.178 332.147 342.129 360.141 366.682 419.715 429.162 499.936 523.291 530.206 630.322 682.943 701.357 +743.302 838.408 895.439 996.48 1013.48 1083.5 1482.51 + + + + +6 11 22 74 20 5 8 14 6 11 6 27 7 7 5 5 10 6 12 9 7 6 7 13 7 7 7 100 7 56 +7 20 12 12 6 8 9 + + + + + + +GRMZM2G013619_P01 seq=translation; coord=10:128864859..128868237:-1; parent_transcript=GRMZM2G013619_T01; parent_gene=GRMZM2G013619 + + + MSAQVAVVPN GGPGAVPAVV SPGAVGVAQP LPTTSLYVGD LEGAVSDSQL + YELFSQAGQV VSVRVCRDVT SRRSLGYAYV NYSNPLDAAR ALEVLNFAAL + NNKPIRVMYS NRDPSSRRSG SANIFIKNLD KTIDNKTLHE TFSSFGTILS + CKVAVDEAGQ SKGFGFVQYD KEEAAQNAIK SLNGMLINDK PVFVGPFVRK + QERDHSFDKT KFNNVFVKNL SESTTKEDLL KIFGEYGDIT SAVVMIGMDG + KSRCFGFINF ENPDAASHAV QELNGKKIND KEWYVGRAQK KSEREMELKR + RFEQSLKDAA DKYQGLNLYL KNLDDSIGDD QLCELFSNFG KITSYKVMRD + QNGLSKGSGF VAFSTREEAS QALTEMNGKM ISGKPLYVAF AQRKEDRKAM + LQVTVLKPVE FV + + + + + +GRMZM2G352129_P01 NP_001151785 LOC100285420 seq=translation; coord=2:30905783..30911404:-1; parent_transcript=GRMZM2G352129_T01; parent_gene=GRMZM2G352129 + + + MAAQVAAVVV PNGSPGAVPA VVSPGAVGVG LGVAQPLPTT SLYVGDLEGS + VSDSQLYELF SQAGQVVSVR VCRDVTSRRS LGYAYVNFNN PLDAARALEV + LNFAPLNNKP IRVMYSNRDP SSRRSGSANI FIKNLDKMID NKSLHETFSS + FGTILSCKVA MDEGGQSKGF GFVQYEKEEA AQNAIKSLNG MLINDKPVFV + GPFLRKQERD HSFDKTKFNN VFVKNLSEST TKEDLLKIFG EYGNITSAVV + MIGMDGKSRC FGFINFENPD AASRAVQELN GKKINDKEWY VGRAQKKSER + EMELKRRFEQ ILKDAADKYQ GLNLYLKNLD DSIGDDQLRE LFSNFGKITS + CKVMRDQNGL SKGSGFVAFS TREEASQALT EMNGKMISGK PLYVAFAQRK + EDRKAMLQAQ FSQMRPAVPM TPTLAPRLPM YPPMAPQQLF YGQAPPAMIP + PQPGFGFQQQ LVPGMRPGGP HMPNYFVPVV QHQQGQQGPR PGIRRGAGAQ + GQQPVPPFQQ QIVPRGRMYR YPTGRNMPEA PAMPGVAGGM MQAYDMGGFP + VRDAALSPAA QIGTLTSALA NANPEQQRTI LGENLYPLVE QLEPNQAAKV + TGMLLEMDQT EVLHLLESPD ALKSKVAEAM DVLHNVAHQQ NANTPTSQLA + ALSLTEGIIS + + + + + + +6.50317 +-0.351523 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +5705 5705 5619 5337 5101 4612 4221 3661 3018 2219 1215 718 319 175 42 8 3 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5695 5695 5609 5327 5071 4551 4012 3445 2789 1416 650 100 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2044 2381 961 280 50 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +922 2438 1647 527 140 30 2 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2799 (charge 3) + +1311.61 +3 + + +151.01 154.086 155.081 155.092 155.118 156.076 156.102 156.121 157.061 157.097 157.109 157.133 158.091 159.076 162.102 166.061 168.008 169.097 169.133 171.113 173.092 173.127 174.133 175.119 176.12 181.096 181.109 183.113 185.093 185.128 +185.165 186.123 187.071 187.107 189.087 194.128 195.113 197.128 199.108 201.123 203.121 211.106 213.087 215.139 217.081 223.107 226.155 231.117 235.119 240.134 244.092 251.151 260.198 262.15 267.115 272.171 276.165 288.202 309.202 312.178 +316.654 324.129 366.177 379.922 386.205 398.215 410.213 423.256 426.751 429.214 436.231 446.235 452.232 459.723 463.195 466.24 473.21 492.75 500.277 518.299 524.25 526.243 532.251 537.28 539.266 541.252 564.286 600.255 606.775 619.246 +636.271 648.32 671.29 695.33 704.278 767.309 769.309 814.372 901.41 942.598 + + + + +3 7 10 2 89 6 6 9 3 3 3 3 13 9 2 11 2 8 8 15 4 5 2 74 2 3 3 29 7 2 +8 2 9 3 3 14 3 12 8 38 51 3 4 4 3 9 10 8 13 7 11 3 2 4 13 14 3 9 2 10 +4 2 3 2 3 3 2 4 18 8 3 100 2 10 7 3 4 4 2 2 3 2 4 2 3 35 11 3 15 3 +34 2 3 3 2 18 3 3 7 2 + + + + + + +GRMZM2G137329_P01 NP_001148304 LOC100281913 seq=translation; coord=1:3000161..3000884:-1; parent_transcript=GRMZM2G137329_T01; parent_gene=GRMZM2G137329 + + + MAKQQQQGMA AVALVVLVVL ATAAAETASA ASCNAGQLAA CAPAITAGAR + PSASCCSNLK AQQGCFCQFV KNPTYGRYIN SPNARKVVAS CGVSVPRC + + + + + + +5.66113 +-0.343099 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +4113 4113 4078 3781 3451 3084 2755 1742 1149 514 227 81 37 20 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4116 4116 4081 3763 3404 3021 2656 1414 751 156 60 15 13 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2253 1573 267 25 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +790 2456 762 101 6 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2807 (charge 2) + +934.473 +2 + + +152.057 153.102 154.086 155.081 155.117 156.077 157.061 157.097 157.108 158.092 159.076 163.133 164.136 165.102 166.061 167.081 167.093 169.097 169.134 171.076 171.113 173.055 173.092 173.129 174.087 175.119 176.123 181.096 183.113 183.149 +184.108 185.055 185.091 186.087 186.124 187.071 194.128 195.073 195.088 195.113 197.129 199.108 202.082 204.138 209.104 212.103 221.102 226.154 229.131 235.119 238.13 240.134 244.165 246.156 249.16 254.161 266.161 277.154 278.157 283.139 +300.166 301.186 306.943 324.954 343.172 345.682 360.199 368.202 370.172 385.232 388.22 391.198 395.206 397.223 423.199 440.226 446.274 457.252 459.253 485.271 496.26 527.258 544.284 624.277 641.302 642.305 658.326 660.332 669.374 768.427 +771.41 + + + + +2 1 2 2 2 2 3 5 2 9 5 11 2 2 4 3 2 2 2 2 3 2 2 5 3 34 3 7 2 2 +3 2 5 2 2 2 3 1 3 2 3 3 4 4 2 13 2 5 5 8 2 2 4 4 100 5 3 9 1 8 +2 2 3 3 6 2 3 3 2 3 1 2 2 1 3 14 1 23 2 5 3 2 21 2 16 4 77 5 2 4 +8 + + + + + + +GRMZM2G053322_P01 NP_001148807 UDP-sulfoquinovose synthase seq=translation; coord=8:90964173..90967651:-1; parent_transcript=GRMZM2G053322_T01; parent_gene=GRMZM2G053322 + + + MKMAHLITNC SFQTFSSSPN YCRNIGQLQN SKSSNLSLKS CSRRQKKSYV + TCASAAVQGQ TQTPLTGSQQ AYEHSSSKPK KVMVIGGDGY CGWATALHLS + NKGYEVAIVD NLVRRAFDNQ LGLDSLTPIT SIQNRVRRWK SLTAKTIQLF + IGDICDFEFL SEAFKSFEPD AAVHFGEQRS APYSMIDRSR AVYTQHNNVI + GTLNVLFAIK EYSEECHLVK LGTMGEYGTP NIDIEEGFIT ITHNGRTDTL + PYPKQASSFY HLSKVHDSHN IAFTCKAWGI RATDLNQGVV YGVRTDETAM + HEELSNRFDY DGVFGTALNR FCVQAAVGHP LTVYGKGGQT RGYLDIRDTV + QCVELAIANP AKPGEFRVFN QFTEQFSVNE LAKLVTAAGA KLGLEVETKS + IPNPRVEAEE HYYNAKHTKL IELGLVPHLL SDSLLDSLLN FAIQYKDRVD + TAQIMPSVSW KKMGAKPRTV SV + + + + + + + +5.91506 +-0.338004 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +3339 3339 3265 3157 2897 2694 2444 1803 1302 707 360 163 71 25 8 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3341 3341 3267 3159 2897 2666 2369 1495 922 375 85 38 3 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1419 1285 519 85 30 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +642 1486 845 295 58 13 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2808 (charge 3) + +1548.66 +3 + + +153.066 155.082 157.097 158.093 167.081 169.098 171.076 173.056 173.092 173.129 175.119 181.061 185.092 189.087 193.095 195.076 195.113 199.071 199.108 201.087 203.103 213.087 217.082 221.104 226.155 231.097 238.118 240.134 244.165 255.107 +256.128 259.093 262.151 267.109 272.134 284.124 289.162 290.986 299.009 301.187 304.693 308.196 328.112 342.138 346.125 350.146 353.218 359.167 376.194 378.141 396.153 399.15 405.25 408.751 417.265 424.703 434.24 442.715 452.248 462.273 +475.719 480.282 484.232 489.278 493.314 502.232 511.323 519.751 522.23 551.75 561.27 563.28 570.276 577.335 590.368 600.303 602.274 608.376 616.785 618.32 620.327 625.792 635.315 657.791 672.337 683.303 687.417 692.307 705.429 707.439 +724.313 729.351 747.362 749.37 833.527 868.395 884.422 886.428 967.459 1038.48 + + + + +6 13 2 6 3 3 47 6 23 2 29 4 5 32 2 4 7 9 6 9 2 13 48 10 26 6 5 21 11 3 +2 2 2 7 5 7 5 4 4 12 3 2 11 3 7 2 16 5 21 3 3 6 5 3 5 4 7 36 4 9 +8 7 13 25 2 2 20 10 4 5 2 5 9 7 6 6 5 53 4 40 3 13 8 5 4 2 5 6 100 5 +5 8 56 6 6 4 38 4 16 7 + + + + + + +GRMZM2G110567_P01 NP_001151334 protein binding protein seq=translation; coord=10:92536953..92538977:1; parent_transcript=GRMZM2G110567_T01; parent_gene=GRMZM2G110567 + + + MSFSDDEPII PSPNSGPRPT PIVPGRVQLV SKNNNMAPLE ENTQKVLLEL + TGGDSTSDRS GLDLVAVLDV SGSMQGEKIE KMKTAMKFVV KKLSSIDRLS + IVTFLDTANR ICPLRQVTED SQPQLLKLID ALQPGGNTNI SDGLQTGLKV + LADRKLSSGR VVGVMLMSDG QQNRGEPAAN VKIGNVPVYT FGFGADYDPT + VLNAVARNSM GGTFSVVNDV NLLSMAFSQC LAGLLTVVVQ DLTVTVARIE + DESTLQKVAA GNYPQTPDAD AGSVTVAFGD LYSKEVRKVI VDLLLPAIDS + DRGADILEVT YSYKTAGKLF DAPPATVTVR RSGTAFPADD PPVDVQTEEA + RLKTATMIQQ ARTMADGKKL GDARDKLAEA QNALEDVVAQ SDPLLDALRT + ELQELLKLMK SQDVYEKQGR PYAMSSETSH DRQRFAARGD IESNRLFSTP + RMDKYLEQAK KFDEDPAAPL PSADKDEEEE VAANPLAPLV GPITFYIRAA + VEALQAIEKL INKGAN + + + + + + + +GRMZM2G565911_P01 seq=translation; coord=10:35920773..35922350:1; parent_transcript=GRMZM2G565911_T01; parent_gene=GRMZM2G565911 + + + MQGRGRRRSC PERVQLVSKN NNMAPLEENT QKVLLELTGD DSTSDRSGLD + LVAVLDVSSS MQGEKIEKMK TAMKFVVKKL SSIDRLSIVT FLDTANRICP + LRQVTEDSQP QLLKLIDALQ PGGNTNISDG LQTGLKVLAD RKLSSGRVVG + VMLMSDGQQN RGEPAANVKI GNVPVYTFGF GAHYDPTVLN VVARNSMGGT + FSVVNDVNLL SMAFSQCLAG LLTVVVQDLT LTVARIEDES TIQKVAAGNY + LQTPDADAGS VTVAFGDLYS KEVRKVIFDL LLPAIDSDRG ADILEVTYSY + KTAGKLFDAP PATVTVRRSG TAFPADDPPV DVQTEEARLK TATMIQQART + MADGKKLGDA RDKLAEAQNA LENVVAQSDP LLDALRTELQ ELLKLMKSQE + VYEKQGRPYA MSSETSHDRQ RFAARGDIEN NRLFSTPRMD KYLEQAKKFD + EDPAAPLPSA DKDEEEEVAA NPLAPLVGPI TFYIRAAVEA LQAIEKLINK + GAN + + + + + + + + +5.4343 +-0.293746 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +3123 3123 3114 3010 2906 2676 2397 2134 1547 1199 683 394 193 84 34 16 4 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3119 3119 3110 3006 2900 2647 2331 1989 1350 764 250 24 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1528 1067 381 111 35 2 0 4 + + + + + + +0 1 2 3 4 5 6 7 + + + + +471 1307 785 430 108 19 4 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2809 (charge 3) + +1720.73 +3 + + +153.066 153.102 157.061 158.092 169.097 171.076 175.071 175.119 181.097 185.093 185.128 189.086 194.128 199.072 199.108 201.123 212.102 214.106 217.082 226.154 227.102 233.128 235.118 244.165 253.092 257.622 274.187 276.171 279.144 284.124 +290.147 297.166 303.178 308.669 319.173 322.667 325.161 328.661 355.198 357.249 363.661 369.227 399.698 402.175 405.187 410.178 414.728 422.219 427.206 434.206 450.744 452.253 461.258 470.259 514.236 531.264 552.921 557.283 585.278 587.281 +597.273 602.293 615.283 617.297 628.32 635.316 647.311 656.315 658.32 661.289 673.334 679.347 711.36 726.315 728.313 739.349 744.328 757.361 770.377 772.394 798.392 803.347 805.348 814.345 826.391 831.359 862.382 872.408 882.372 885.422 +890.384 895.399 900.385 913.418 918.39 920.395 949.427 966.429 1014.49 1042.45 + + + + +3 3 6 6 3 8 3 64 4 3 3 3 2 3 14 4 3 14 7 38 12 7 7 13 8 7 8 4 14 2 +14 3 3 9 11 29 22 2 2 2 8 4 6 2 8 7 3 11 20 3 2 3 2 3 35 2 3 25 46 3 +6 15 62 3 40 2 3 100 8 3 10 2 13 10 2 10 33 17 27 3 7 15 3 3 7 19 3 7 4 6 +4 6 6 7 22 6 2 2 3 2 + + + + + + +GRMZM2G318635_P01 seq=translation; coord=5:213291570..213301733:-1; parent_transcript=GRMZM2G318635_T01; parent_gene=GRMZM2G318635 + + + + + + + + +6.94617 +-0.338837 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +6547 6547 6547 6547 6400 6317 5856 5498 4976 3774 2774 1492 769 408 204 72 20 8 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6551 6551 6551 6551 6404 6321 5847 5451 4841 3443 2011 562 61 7 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1997 2722 1368 363 83 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1009 2927 1884 534 172 21 2 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2815 (charge 3) + +1449.69 +3 + + +154.049 155.081 155.118 156.077 157.061 157.097 157.133 158.093 159.076 159.092 166.062 167.093 169.097 169.134 171.076 171.113 173.128 175.054 175.071 175.119 178.061 181.061 181.096 183.113 185.129 186.124 187.108 189.087 192.048 193.097 +194.129 195.089 195.112 197.128 199.072 199.108 199.181 201.123 204.134 207.127 212.139 217.083 226.154 227.103 230.077 233.091 235.12 237.135 240.134 244.166 246.157 255.145 266.161 270.145 272.172 276.106 284.17 291.166 303.202 315.203 +329.192 344.126 359.14 373.219 381.097 386.969 394.107 437.159 465.153 473.734 480.165 484.786 488.243 491.258 503.32 538.264 547.264 551.201 553.318 560.272 561.262 573.252 581.767 602.29 604.314 606.269 619.32 638.311 642.358 656.372 +674.344 714.349 730.38 731.376 747.381 773.409 778.289 884.438 909.328 946.457 + + + + +8 13 13 14 7 8 8 22 29 7 7 21 16 6 15 14 60 14 34 100 17 7 8 16 6 22 22 42 8 24 +22 52 14 14 19 17 16 31 79 9 13 34 35 16 8 7 33 6 25 22 8 21 6 14 37 7 17 20 24 12 +16 7 7 51 58 8 6 14 7 14 24 18 16 14 16 19 7 24 7 17 7 11 27 48 14 13 21 6 17 8 +16 16 29 34 6 21 8 7 8 34 + + + + + + +GRMZM2G102760_P01 NP_001105975 lipoxygenase seq=translation; coord=5:12274159..12279067:-1; parent_transcript=GRMZM2G102760_T01; parent_gene=GRMZM2G102760 + + + + + + + +GRMZM2G102760_P03 NP_001105975 lipoxygenase seq=translation; coord=5:12275542..12279067:-1; parent_transcript=GRMZM2G102760_T03; parent_gene=GRMZM2G102760 + + + MFWHGVADRL TGKNKEAWSE GKIRGTVRLV KKEVLDVGDF NASLLDGVHR + ILGWDDGVAF QLVSATAADP SNGGRGKVGK AAHLEEAVVS LKSTADGETV + YRVSFEWDES QGIPGAVLVR NLQHAEFFLK TLTLEGVPGK GTVVFVANSW + VYPHKLYSQE RIFFANDTYL PSKMPAALVP YRQDELKILR GDDNPGPYQE + HDRVYRYDYY NDLGDPDKGE EHARPILGGS QEHPYPRRCR TGRHPTKKDP + NSESRLFLLN LNIYVPRDER FGHLKMSDFL GYSLKTIIEA VLPTLGTFVD + DTPKEFDSFE DILGLYELGP EAPNNPLIAE IRKKIPSEFL RSILPNGSHD + HPLKMPLPNV IKSDVLKKAP EFKFGWRTDE EFARETLAGV NPVIIKRLTE + FPAKSTLDPR QYGDHTSKIT EAHIRHNMGG LSVQNALRNK RLFILDHHDH + FMPYLDEINE LEGNFIYASR TLLFLKDDGT LKPLAIELSL PHPDGQQRGA + VSKVYTPAHT GVEGHVWQLA KAYACVNDSA WHQLISHWYK KCFWCLFLFF + FPFN + + + + + + +4.04742 +-0.261124 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +1537 1537 1537 1537 1463 1348 1199 1029 824 440 281 130 75 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1541 1541 1541 1541 1467 1350 1195 1002 758 357 171 68 3 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +664 691 142 43 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +304 806 305 111 14 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2817 (charge 3) + +1499.62 +3 + + +152.057 155.081 156.076 157.097 157.133 158.092 159.076 159.112 167.081 169.097 169.134 171.076 172.108 173.056 173.092 173.129 175.119 176.122 183.112 185.056 185.092 185.129 185.165 186.122 187.071 187.107 195.04 195.076 199.107 201.123 +204.135 205.1 212.102 221.103 226.118 230.077 233.128 235.071 239.114 240.098 244.166 246.156 249.097 253.092 256.164 257.124 261.123 267.108 270.072 288.082 290.146 303.175 333.187 339.093 357.104 367.17 372.225 389.184 393.499 421.727 +424.187 427.204 442.247 451.266 468.297 472.714 479.769 489.276 492.714 501.54 503.291 512.622 526.309 528.288 545.319 549.751 556.247 557.253 559.284 565.819 568.818 577.33 587.999 601.014 618.316 626.356 646.365 667.274 673.328 684.302 +699.382 706.366 744.361 815.402 817.396 826.366 847.369 886.436 944.419 1001.44 + + + + +9 41 6 15 16 14 14 9 7 15 6 6 10 31 5 7 100 7 22 17 6 20 6 9 6 5 5 5 5 14 +10 8 9 6 17 10 25 11 9 17 9 5 9 6 8 12 8 9 8 9 13 8 7 6 7 9 21 6 11 9 +8 23 16 8 12 31 7 9 5 27 29 34 9 8 8 18 27 10 21 5 8 7 9 9 5 5 10 10 9 33 +9 5 9 21 5 5 30 13 20 22 + + + + + + +GRMZM2G059083_P01 NP_001104851 ferredoxin seq=translation; coord=3:147290518..147292751:-1; parent_transcript=GRMZM2G059083_T01; parent_gene=GRMZM2G059083 + + + MAAVTAAAVS LPSSSSSPAA AKAKASASAS PSSPCGHLQF PRRHGGPRAV + RLRVQVSTTE TAEAEPVKKL EKVSKKQEEG LVTNKYKPKE PYVGRCLLNT + RITGDQAPGE TWHMVFSTEG EVPYREGQSI GVIADGEDKN GKPHKLRLYS + IASSALGDFG DSKTVSLCVK RLVYTNDQGE VVKGVCSNFL CDLKPGAEVK + ITGPVGKEML MPKDPNATII MLATGTGIAP FRSFLWKMFF EEHEDYKYTG + LAWLFLGVPT SDTLLYKEEL EKMKEMAPDN FRLDFAVSRE QTNAAGEKMY + IQTRMAEYKE ELWELLKKDN TYVYMCGLKG MEKGIDDIML DLAAKDGINW + LDYKKQLKKS EQWNVEVY + + + + + +GRMZM2G059083_P03 NP_001104851 ferredoxin seq=translation; coord=3:147290712..147292701:-1; parent_transcript=GRMZM2G059083_T03; parent_gene=GRMZM2G059083 + + + MAAVTAAAVS LPSSSSSPAA AKAKASASAS PSSPCGHLQF PRRHGGPRAV + RLRVQVSTTE TAEAEPVKKL EKVSKKQEEG LVTNKYKPKE PYVGRCLLNT + RITGDQAPGE TWHMVFSTEG EVPYREGQSI GVIADGEDKN GKPHKLRLYS + IASSALGDFG DSKTVSLCVK RLVYTNDQGE VVKGVCSNFL CDLKPGAEVK + ITGPVGKEML MPKDPNATII MLATGTGIAP FRSFLWKMFF EEHEDYKYTG + LAWLFLGVPT SDTLLYKEEL EKMKEMAPDN FRLDFAVSRE QTNAAGEKMY + IQTRMAEYKE ELWELLKKDN TYVYMCGLKG MEKGIDDIML DLAAKDGKLS + VIALVLRFCA RYEQVAS + + + + + +GRMZM2G059083_P04 NP_001104851 ferredoxin seq=translation; coord=3:147286676..147292683:-1; parent_transcript=GRMZM2G059083_T04; parent_gene=GRMZM2G059083 + + + MAAVTAAAVS LPSSSSSPAA AKAKASASAS PSSPCGHLQF PRRHGGPRAV + RLRVQVSTTE TAEAEPVKKL EKVSKKQEEG LVTNKYKPKE PYVGRCLLNT + RITGDQAPGE TWHMVFSTEG EVPYREGQSI GVIADGEDKN GKPHKLRLYS + IASSALGDFG DSKTVSLCVK RLVYTNDQGE VVKGVCSNFL CDLKPGAEVK + ITGPVGKEML MPKDPNATII MLATGTGIAP FRSFLWKMFF EEHEDYKYTG + LAWLFLGVPT SDTLLYKEEL EKMKEMAPDN FRLDFAVSRE QTNAAGEKMY + IQTRMAEYKE ELWELLKKDN TYVYMCGLKG MEKGIDDIML DLAAKDGINW + LDYKKQLKKS EQWNVEVY + + + + + +GRMZM2G059083_P02 NP_001104851 ferredoxin seq=translation; coord=3:147290527..147292751:-1; parent_transcript=GRMZM2G059083_T02; parent_gene=GRMZM2G059083 + + + MAAVTAAAVS LPSSSSSPAA AKAKASASAS PSSPCGHLQF PRRHGGPRAV + RLRVQVSTTE TAEAEPVKKL EKVSKKQEEG LVTNKYKPKE PYVGRCLLNT + RITGDQAPGE TWHMVFSTEG EVPYREGQSI GVIADGEDKN GKPHKLRLYS + IASSALGDFG DSKTVSLCVK RLVYTNDQGE VVKGVCSNFL CDLKPGAEVK + ITGPVGKEML MPKDPNATII MYTGLAWLFL GVPTSDTLLY KEELEKMKEM + APDNFRLDFA VSREQTNAAG EKMYIQTRMA EYKEELWELL KKDNTYVYMC + GLKGMEKGID DIMLDLAAKD GINWLDYKKQ LKKSEQWNVE VY + + + + + + +6.804 +-0.316465 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +6941 6941 6789 6582 6288 5934 5526 5099 3428 2713 1288 583 282 144 77 44 12 6 3 2 1 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6946 6946 6794 6587 6279 5865 5449 4981 3027 1976 482 79 21 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3127 2941 758 100 20 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1396 4240 1106 177 23 1 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2819 (charge 2) + +1175.58 +2 + + +152.057 155.082 157.061 157.097 158.081 158.1 159.077 167.081 169.097 169.134 171.076 171.113 173.056 173.092 173.129 174.087 175.107 175.122 176.111 181.098 183.076 184.072 185.075 185.092 186.094 187.071 187.108 195.075 197.128 199.108 +201.087 203.121 213.086 214.118 216.134 226.154 227.102 231.116 233.165 238.119 240.134 242.114 244.167 246.156 248.16 254.114 258.145 266.114 270.144 273.132 284.124 296.123 298.14 301.13 314.134 315.135 325.223 329.662 343.234 346.182 +353.143 355.159 373.172 395.154 401.165 413.165 418.728 431.18 446.235 454.266 468.208 472.273 474.224 484.199 502.215 520.265 526.285 530.298 540.267 543.313 548.27 561.266 585.299 611.8 654.341 658.314 670.39 672.367 698.385 700.382 +743.392 745.346 832.381 844.44 882.382 929.398 946.424 955.457 973.488 1045.48 + + + + +3 10 4 35 3 35 15 7 7 24 3 3 2 19 2 2 57 17 3 2 3 2 3 75 3 2 3 2 19 7 +21 75 19 2 3 12 10 20 7 8 3 6 6 26 8 2 3 4 6 11 8 3 4 10 15 2 3 7 100 2 +2 2 2 2 2 8 3 2 34 15 3 4 2 7 3 2 2 3 2 20 2 2 15 2 3 34 3 13 13 2 +16 9 11 20 3 3 24 3 16 2 + + + + + + +GRMZM2G053322_P01 NP_001148807 UDP-sulfoquinovose synthase seq=translation; coord=8:90964173..90967651:-1; parent_transcript=GRMZM2G053322_T01; parent_gene=GRMZM2G053322 + + + + + + + + + +5.71305 +-0.368584 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +2186 2186 2186 2178 2043 1858 1033 784 439 195 126 42 4 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2190 2190 2190 2182 2047 1860 1017 705 301 95 43 10 1 0 + + + + + + +0 1 2 3 4 + + + + +1484 641 63 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +468 1432 264 28 1 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2820 (charge 2) + +1548.66 +2 + + +168.065 169.097 171.076 175.119 183.149 189.087 195.113 199.072 201.069 204.087 211.144 213.086 214.731 217.082 226.156 230.113 239.114 253.557 258.144 262.738 266.149 272.136 289.162 346.123 350.144 363.059 376.189 379.232 397.208 429.215 +442.714 447.17 476.23 489.277 491.247 514.298 516.237 534.261 542.301 563.542 565.297 570.272 618.317 644.339 662.352 742.837 747.362 860.83 884.425 891.046 967.463 1039.49 1139.55 1236.18 + + + + +6 3 6 21 22 9 5 3 5 5 18 7 3 43 5 6 4 3 4 4 8 4 10 15 4 4 6 6 8 8 +25 6 4 23 5 7 7 7 15 6 30 9 26 19 100 10 43 5 39 5 31 15 9 5 + + + + + + +GRMZM5G844562_P01 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98997371:-1; parent_transcript=GRMZM5G844562_T01; parent_gene=GRMZM5G844562 + + + + + + + +GRMZM5G844562_P03 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98996099:-1; parent_transcript=GRMZM5G844562_T03; parent_gene=GRMZM5G844562 + + + + + + + +GRMZM5G844562_P02 O24562 Probable cinnamyl alcohol dehydrogenase (CAD)(EC 1.1.1.195)(Brown-midrib 1 protein) seq=translation; coord=5:98993016..98997371:-1; parent_transcript=GRMZM5G844562_T02; parent_gene=GRMZM5G844562 + + + + + + + + +4.77329 +-0.272759 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +5906 5906 5906 5906 5906 5819 3876 3473 2065 1408 745 442 222 109 36 16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5917 5917 5917 5917 5917 5830 3887 3410 1964 1126 516 269 91 21 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3774 1913 209 11 0 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +965 4295 571 72 4 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2823 (charge 2) + +1440.73 +2 + + +150.067 164.082 167.092 169.097 171.075 175.073 175.09 175.119 189.087 195.088 199.107 201.123 204.132 209.14 216.134 226.155 234.145 237.134 244.093 247.13 282.18 314.134 321.174 332.634 369.17 374.194 397.166 408.209 411.246 428.458 +472.817 477.228 495.242 506.229 523.76 534.223 550.332 557.604 568.37 602.312 605.296 608.321 623.423 630.319 633.296 659.4 701.356 714.302 716.325 734.339 776.393 808.44 815.398 833.404 895.438 907.51 931.696 1044.57 1046.52 1083.51 + + + + + +13 47 88 21 14 13 20 90 13 49 16 48 11 55 12 19 73 77 18 14 20 27 91 13 79 15 70 74 13 12 +14 18 92 69 19 70 19 16 16 17 24 49 27 100 22 13 47 19 29 26 15 68 19 53 23 64 15 58 16 16 + + + + + + + +GRMZM2G063800_P01 seq=translation; coord=4:76812503..76816090:-1; parent_transcript=GRMZM2G063800_T01; parent_gene=GRMZM2G063800 + + + MDIFKTFIEL LRQTGNVTKG QGDIDESSPR WLLKQEVPKV VKSINRQLRE + KSIKTKVGAF SVLKELVVVL PDCLADHFGS LVPGIEKALN DKSSTSNLKI + EALVLTRLVM ASHSPSVFHP YIKALSAPIL SVIRDRYYKV TTEALRKTVV + DFEPYIGPIY NAILGRLANQ DQDQCTLIYH ANLCSPKREL PACLPILVDR + MGNEITRLTA VKWMNMPNLL EVIDFKDTFL DANHVQQSFP DYQSRNNMAD + GEPQKEKLIV ETYIPADPGP YPQDKPKQNS VRFTPTQEMY EDASQVAVDA + VGSIRTVASF CAEKIVVAAY RDKCEALRKQ GIRNGVIGGL GYGFSFLMLF + FTYGLCFYVG AQFVRQGKTT FPDVFKVFFA LVLAAIGVSQ ASALASDATK + ARDSAISIFS VLDRESKIDS SSGDGMTLED VSGKIDFRNV SFKYPLCLDV + QIFSDFTLRI PSGKTVALVR ESGSGKSTII ALLERLYDPD SVSQWVKLWF + D + + + + + +GRMZM2G168629_P01 NP_001169972 hypothetical protein LOC100383873 seq=translation; coord=4:236362229..236373144:1; parent_transcript=GRMZM2G168629_T01; parent_gene=GRMZM2G168629 + + + MANLNITNIL EKMTGKDKDY RYMATSDLLS ELNKESFKAD QDLEPKLTIT + VLQQLEDASG DVSGLAVKCL APLVKKVGED RVVEMTNKLC DKLINGKDQH + RDTASIALKT IIAEVTTPSL AEKILLSLAP QLIKGVNTAK SAEIKCECLD + ILADVLHRFG NLITKDHEYM LNALLSQLGS NPASVRKKSI SCIASLAPSL + SDDLLAKATL QVVQLLKNRG AKSEITRTNI QMIGSLSRSV GYRFGPHLAE + TVPLLISYCT SASENDEELR EYSLQALESF MLRCPRDISP YCEGILNLAL + EYVSYDPNFT DSMDEDTDEE AKEEDDDDES ANEYTDDEDA SWKVRRASAK + CLSAIIVSRP EMLSKMFLEA CPKLIERFRE REENVKMDIF NTFIELLRQT + GNVTKGQGDI DESSPRWLLK QEVPKVVKSI NRQLREKSIK TKVGAFSVLK + ELVVVLPDCL ADHFGSLVPG IEKALNDKSS TSNLKIEALV LTRLVMASHS + PSVFHPYIKA LSAPILSAIR DRYYKVTAEA LRVCGELVRV LRPNLETTSV + DFKPYIGPIY NAILGRLANQ DQDQEVKECA ISCMSLVVST FGDGLERELP + ACLPILVDRM GNEITRLTAV KAFSVIANSP LRIDLSCVLD HVVSELTAFL + RKANRALRQA TLGTLNSLVV TYGGQIGSSS YETIIAELST LISDMDLHMT + ALALELCCTI MVDRKSIQNV GLAVRDKVLP QALVLIRSAL LQGQALQALQ + RFFASLVQSA NTSFDALLES LISAAKPSHS GSLAKQALSS IAKCVAVLCL + AAGDQKCAST IEMLKGILKD DSTTNSAKQH MALLCLGEIG RRKDLSNHVQ + IENIVIESFQ SPFEEIKSAA SYALGNIAVG NLSKYLPFIL DQIDNQQKKQ + YLLLHSLKEV IVRQSVDHTG QSELQDSNIE KILALLFNHC ESEEEGVRNV + VAECLGKISL IEPKKLVPAL EVRTSSPAAN TRATVAIAIK YSIVERPEKI + DEIMYSKIST FLMLIKDSDR HVRRAAVLAL STAAHNKPNL IKGLLPEILP + LLYDQTVIKQ ELIRTVDLGP FKHVVDDGLE LRKAAFECVD TLLDSCLDQV + NPSSFIVPFL LSGLGDHYDV KMPCHLILSK LADKCPSAVL AVLDSIVEPI + EKTISHKPKG DAVKQEVDRN EDMIRSALRA ISSLSRISGS DYSIRFKNLM + NKITATPALA EKYNSVRGE + + + + + +GRMZM2G168629_P02 NP_001169972 hypothetical protein LOC100383873 seq=translation; coord=4:236362229..236373143:1; parent_transcript=GRMZM2G168629_T02; parent_gene=GRMZM2G168629 + + + MANLNITNIL EKMTGKDKDY RYMATSDLLS ELNKESFKAD QDLEPKLTIT + VLQQLEDASG DVSGLAVKCL APLVKKVGED RVVEMTNKLC DKLINGKDQH + RDTASIALKT IIAEVTTPSL AEKILLSLAP QLIKGVNTAK SAEIKCECLD + ILADVLHRFG NLITKDHEYM LNALLSQLGS NPASVRKKSI SCIASLAPSL + SDDLLAKATL QVVQLLKNRG AKSEITRTNI QMIGSLSRSV GYRFGPHLAE + TVPLLISYCT SASENDEELR EYSLQALESF MLRCPRDISP YCEGILNLAL + EYVSYDPNFT DSMDEDTDEE AKEEDDDDES ANEYTDDEDA SWKVRRASAK + CLSAIIVSRP EMLSKMFLEA CPKLIERFRE REENVKMDIF NTFIELLRQT + GNVTKGQGDI DESSPRWLLK QEVPKVVKSI NRQLREKSIK TKVGAFSVLK + ELVVVLPDCL ADHFGSLVPG IEKALNDKSS TSNLKIEALV LTRLVMASHS + PSVFHPYIKA LSAPILSAIR DRYYKVTAEA LRVCGELVRV LRPNLETTSV + DFKPYIGPIY NAILGRLANQ DQDQVWQNSL FSLPLLCACS ALSFIMQICV + LPGGKRMRHI LHEFGGLYFW + + + + + +GRMZM2G168629_P03 NP_001169972 hypothetical protein LOC100383873 seq=translation; coord=4:236362229..236373143:1; parent_transcript=GRMZM2G168629_T03; parent_gene=GRMZM2G168629 + + + MANLNITNIL EKMTGKDKDY RYMATSDLLS ELNKESFKAD QDLEPKLTIT + VLQQLEDASG DVSGLAVKCL APLVKKVGED RVVEMTNKLC DKLINGKDQH + RDTASIALKT IIAEVTTPSL AEKILLSLAP QLIKGVNTAK SAEIKCECLD + ILADVLHRFG NLITKDHEYM LNALLSQLGS NPASVRKKSI SCIASLAPSL + SDDLLAKATL QVVQLLKNRG AKSEITRTNI QMIGSLSRSV GYRFGPHLAE + TVPLLISYCT SASENDEELR EYSLQALESF MLRCPRDISP YCEGILNLAL + EYVSYDPNFT DSMDEDTDEE AKEEDDDDES ANEYTDDEDA SWKVRRASAK + CLSAIIVSRP EMLSKMFLEA CPKLIERFRE REENVKMDIF NTFIELLRQT + GNVTKGQGDI DESSPRWLLK QEVPKVVKSI NRQLREKSIK TKVGAFSVLK + ELVVVLPDCL ADHFGSLVPG IEKALNDKSS TSNLKIEALV LTRLVMASHS + PSVFHPYIKA LSAPILSAIR DRYYKVTAEA LRVCGELVRV LRPNLETTSV + DFKPYIGPIY NAILGRLANQ DQDQEVKECA ISCMSLVVST FGDGLERELP + ACLPILVDRM GNEITRLTAV KAFSVIANSP LRIDLSCVLD HVVSELTAFL + RKANRALRQA TLGTLNSLVV TYGGQIGSSS YETIIAELST LISW + + + + + +GRMZM2G168629_P04 NP_001169972 hypothetical protein LOC100383873 seq=translation; coord=4:236362229..236372866:1; parent_transcript=GRMZM2G168629_T04; parent_gene=GRMZM2G168629 + + + MANLNITNIL EKMTGKDKDY RYMATSDLLS ELNKESFKAD QDLEPKLTIT + VLQQLEDASG DVSGLAVKCL APLVKKVGED RVVEMTNKLC DKLINGKDQH + RDTASIALKT IIAEVTTPSL AEKILLSLAP QLIKGVNTAK SAEIKCECLD + ILADVLHRFG NLITKDHEYM LNALLSQLGS NPASVRKKSI SCIASLAPSL + SDDLLAKATL QVVQLLKNRG AKSEITRTNI QMIGSLSRSV GYRFGPHLAE + TVPLLISYCT SASENDEELR EYSLQALESF MLRCPRDISP YCEGILNLAL + EYVSYDPNFT DSMDEDTDEE AKEEDDDDES ANEYTDDEDA SWKVRRASAK + CLSAIIVSRP EMLSKMFLEA CPKLIERFRE REENVKMDIF NTFIELLRQT + GNVTKGQGDI DESSPRWLLK QEVPKVVKSI NRQLREKSIK TKVGAFSVLK + ELVVVLPDCL ADHFGSLVPG IEKALNDKSS TSNLKIEALV LTRLVMASHS + PSVFHPYIKA LSAPILSAIR DRYYKVTAEA LRVCGELVRV LRPNLETTSV + DFKPYIGPIY NAILGRLANQ DQDQEVKECA ISCMSLVVST FGDGLERELP + ACLPILVDRM GNEITRLTAV KAFSVIANSP LRIDLSCVLD HVVSELTAFL + RKANRALRQA TLGTLNSLVV TYGGQIGSSS YETIIAELST LISDMDLHMT + ALALELCCTI MVDRKSIQNV GLAVRDKVLP QALVLIRSAL LQGQALQALQ + RFFASLVQSA NTSFDALLES LISAAKPSHS GSLAKQALSS IAKCVAVLCL + AAGDQKCAST IEMLKGILKD DSTTNSAKQH MALLCLGEIG RRKDLSNHVQ + IENIVIESFQ SPFEEIKSAA SYALGNIAVG NLSKYLPFIL DQIDNQQKKQ + YLLLHSLKEV IVRQSVDHTG QSELQDSNIE KILALLFNHC ESEEEGVRNV + VAECLGKISL IEPKKLVPAL EVRTSSPAAN TRATVAIAIK YSIVERPEKI + DEIMYSKIST FLMLIKDSDR HVRRAAVLAL STAAHNKPNL IKGLLPEILP + LLYDQTVIKQ ELIRTVDLGP FKHVVDDGLE LRKAAFECVD TLLDSCLDQV + NPSSFIVPFL LSGLGDHYDV KMPCHLILSK LADKCPSAVL AVLDSIVEPI + EKTISHKPKG DAVKQEVDRN EDMIRSALRA ISSLSRISGS DYSIRFKNLM + NKITATPALA EKYNSVRGE + + + + + +GRMZM2G168629_P05 NP_001169972 hypothetical protein LOC100383873 seq=translation; coord=4:236362229..236371012:1; parent_transcript=GRMZM2G168629_T05; parent_gene=GRMZM2G168629 + + + MANLNITNIL EKMTGKDKDY RYMATSDLLS ELNKESFKAD QDLEPKLTIT + VLQQLEDASG DVSGLAVKCL APLVKKVGED RVVEMTNKLC DKLINGKDQH + RDTASIALKT IIAEVTTPSL AEKILLSLAP QLIKGVNTAK SAEIKCECLD + ILADVLHRFG NLITKDHEYM LNALLSQLGS NPASVRKKSI SCIASLAPSL + SDDLLAKATL QVVQLLKNRG AKSEITRTNI QMIGSLSRSV GYRFGPHLAE + TVPLLISYCT SASENDEELR EYSLQALESF MLRCPRDISP YCEGILNLAL + EYVSYDPNFT DSMDEDTDEE AKEEDDDDES ANEYTDDEDA SWKVRRASAK + CLSAIIVSRP EMLSKMFLEA CPKLIERFRE REENVKMDIF NTFIELLRQT + GNVTKGQGDI DESSPRWLLK QEVPKVVKSI NRQLREKSIK TKVGAFSVLK + ELVVVLPDCL ADHFGSLVPG IEKALNDKSS TSNLKIEALV LTRLVMASHS + PSVFHPYIKA LSAPILSAIR DRYYKVTAEA LRVCGELVRV LRPNLETTSV + DFKPYIGPIY NAILGRLANQ DQDQEVKECA ISCMSLVVST FGDGLERELP + ACLPILVDRM GNEITRLTAV KAFSVIANSP LRIDLSCVLD HVVSELTAFL + RKANRALRQA TLGTLNSLVV TYGGQIGSSS YETIIAELST LISDMDLHMT + ALALELCCTI MVDRKSIQNV GLAVRDKVLP QALVLIRSAL LQGQALQALQ + RFFASLVQSA NTSFDALLES LISAAKPSHS GSLAKQALSS IAKCVAVLCL + AAGDQKCAST IEMLKGILKD DSTTNSAKQH MALLCLGEIG RRKDLSNHVQ + IENIVIESFQ SPFEEIKSAA SYALGNIAVG NLSKYLPFIL DQIDNQQKKQ + YLLLHSLKEV IVRQSVDHTG QSELQDSNIE KILALLFNHC ESEEEGVRNV + VAECLGKISL IEPKKLVPAL EVRTSSPAAN TRATVAIAIK YSIVERPEKI + DEIMYSKIST FLMLIKDSDR HVRRAAVLAL STAAHNKPNL IKGLLPEILP + LLYDQTVIKV LSQFFELS + + + + + + +5.31329 +-0.272476 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +3528 3528 3528 3338 3262 2832 2643 2491 1721 1499 965 484 279 141 69 35 12 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3526 3526 3526 3336 3258 2823 2575 2406 1567 1048 531 161 33 1 0 + + + + + + +0 1 2 3 4 + + + + +2024 1188 276 50 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +678 1978 767 89 13 3 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2824 (charge 2) + +1160.52 +2 + + +152.034 152.056 155.045 155.081 157.097 157.108 157.134 158.093 159.077 161.092 167.055 167.082 168.076 169.061 169.097 171.077 171.113 172.072 173.092 175.119 176.121 181.061 181.097 183.113 183.149 185.092 185.128 186.087 186.123 187.072 +187.091 187.144 189.087 194.13 197.127 198.087 198.124 199.072 199.107 201.123 204.135 208.615 212.102 214.119 217.081 225.099 226.155 229.117 240.134 242.113 244.165 255.145 258.146 260.124 269.123 272.171 280.868 284.086 285.156 295.103 +300.121 306.072 310.151 313.151 323.098 327.178 341.112 343.161 359.203 369.177 391.161 399.199 401.193 408.192 416.223 417.225 426.196 430.23 446.236 452.256 458.23 534.183 543.255 549.748 557.269 575.279 582.314 626.291 654.316 662.834 +690.306 699.372 704.322 801.371 803.389 881.453 902.404 918.418 975.437 998.487 + + + + +32 3 4 14 4 3 5 21 9 13 15 4 4 95 6 52 3 14 21 69 4 4 4 4 4 15 4 86 3 6 +4 14 18 10 4 9 3 3 28 12 9 12 3 4 5 4 53 3 5 47 11 45 3 10 12 31 4 4 4 4 +6 4 10 4 16 12 19 4 15 10 9 18 13 4 22 6 10 4 54 4 3 3 3 3 13 77 4 13 3 100 +79 18 5 39 37 4 3 17 60 16 + + + + + + +GRMZM2G059083_P01 NP_001104851 ferredoxin seq=translation; coord=3:147290518..147292751:-1; parent_transcript=GRMZM2G059083_T01; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P03 NP_001104851 ferredoxin seq=translation; coord=3:147290712..147292701:-1; parent_transcript=GRMZM2G059083_T03; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P04 NP_001104851 ferredoxin seq=translation; coord=3:147286676..147292683:-1; parent_transcript=GRMZM2G059083_T04; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P02 NP_001104851 ferredoxin seq=translation; coord=3:147290527..147292751:-1; parent_transcript=GRMZM2G059083_T02; parent_gene=GRMZM2G059083 + + + + + + + + +4.89037 +-0.296386 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +6633 6633 6633 6475 6120 4468 3878 2249 1541 893 461 257 92 25 9 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6637 6637 6637 6479 6123 4459 3706 2010 1052 480 153 35 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3169 2691 679 100 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1520 4484 560 69 3 0 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2825 (charge 2) + +1489.77 +2 + + +155.081 157.097 159.077 159.113 169.097 169.134 170.044 171.077 172.108 173.091 175.107 175.12 185.092 187.107 189.087 197.128 199.108 201.088 203.102 213.086 215.287 226.154 228.171 231.098 239.094 252.135 254.113 257.197 270.144 272.123 +275.207 284.126 286.138 296.124 298.14 300.063 302.135 312.118 314.134 316.175 325.223 330.133 332.145 353.18 362.027 371.191 373.17 401.166 413.167 466.186 471.329 473.332 484.201 502.211 532.215 535.775 567.952 573.25 582.357 592.808 +600.371 602.315 619.317 669.406 671.402 774.393 781.57 796.412 800.449 836.473 871.482 972.534 974.518 1083.56 1101.58 1202.62 1303.67 + + + + +3 5 3 21 10 16 2 10 3 5 12 8 25 23 9 16 5 4 18 13 2 19 5 15 2 6 4 11 16 17 +34 5 5 5 5 5 4 3 17 2 38 3 6 5 5 10 5 11 3 3 100 3 5 5 3 3 4 4 6 4 +4 3 4 17 25 5 10 5 19 4 27 44 3 4 21 16 4 + + + + + + +GRMZM2G375984_P01 seq=translation; coord=5:19048283..19055775:1; parent_transcript=GRMZM2G375984_T01; parent_gene=GRMZM2G375984 + + + MEEKAVTNGA AAADVAAPDN KDNTKEEVSK SKEPVANKDA EEQNKGSENG + AEGHSGGDVN MAEAEITEEG GGGDAGAAKQ VDSGDVKTDA DTKEDANART + EEGEDAKMTE ADVGSTEVKD KEEKEDEVEN TNEQDESKEQ EKGASAEQEE + NEGKETDADE NQEEEEAEEK GSADKKDEAE AEGDKKTEEN KETPKNKKAR + SARDRSQGKD KEQDGSKSKE AKSLLNTPSP YGTNRPQRER KIVERLVEVI + DKEPNKNFVV EKGQGTPLKD IPSVAHRISR KKPSDLKFLH SILFGRKGKA + VDFKGHILQF SGFVWHESDE KQRAKAKEKL DKCVKDTLLD LCWTLGIPTP + KANIRKEDIV SKLLDFIAEP HSAAESWGSD DQGSNSKKRK RGGESASKTP + DGTPSRSRKK FVDDGTSSKR QNKALQYDTE EDESMKSDSE ENIDEDSDEA + ADKQEVDYGS GKEKAGKKLS EVKESSGKKK SNTGSGHKSG PPNKIIKNLV + KKVSSKIHEE KESPNGSAKV FSRKKKPTAE KEIKEKKSSG KKVTKGKGES + AEAVLPSKDD LRKTITEILK KVDFNTATFS DILKKLDNHY KMDLTPKKEA + IKVMIQDELT KLSEEDEEGE GDEDAGKKQQ QPQAQEIEA + + + + + +GRMZM2G375984_P02 seq=translation; coord=5:19048283..19055775:1; parent_transcript=GRMZM2G375984_T02; parent_gene=GRMZM2G375984 + + + MEEKAVTNGA AAADVAAPDN KDNTKEEVSK SKEPVANKDA EEQNKGSENG + AEGHSGGDVN MAEAEITEEG GGGDAGAAKQ VDSGDVKTDA DTKEDANART + EEGEDAKMTE ADVGSTEVKD KEEKEDEVEN TNEQDESKEQ EKGASAEQEE + NEGKETDADE NQEEEEAEEK GSADKKDEAE AEGDKKTEEN KETPKNKKAR + SARDRSQGKD KEQDGSKSKE AKSLLNTPSP YGTNRPQRER KIVERLVEVI + DKEPNKNFVV EKGQGTPLKD IPSVAHRISR KKPSDLKFLH SILFGRKGKA + VDFKGHILQF SGFVWHESDE KQRAKAKEKL DKCVKDTLLD LCWTLGIPTP + KANIRKEDIV SKLLDFIAEP HSAAESWGSD DQGSNSKKRK RGGESASKTP + DGTPSRSRKK FVDDGTSSKR QNKALQYDTE EDESMKSDSE ENIDEDSDEA + ADKQEVDYGS GKEKAGKKLS EVKESSGKKK SNTGSGHKSG PPNKIIKNLV + KKVSSKIHEE KESPNGSAKV FSRKKKPTAE KEIKEKKSSG KKVTKGKGES + AEAVLPSKDD LRKTITEILK KVDFNTATFS DILKKLDNHY KMDLTPKKEA + IKVMIQDELT KLSEEDEEGE GDEDAGKKQQ QPQAQEIEA + + + + + + +6.21055 +-0.376397 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +2120 2120 2120 2056 1949 1809 1527 1152 821 417 153 55 21 8 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2116 2116 2116 2052 1945 1801 1515 1109 706 322 79 15 1 0 + + + + + + +0 1 2 3 4 5 + + + + +797 976 312 40 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +615 979 468 52 3 5 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2826 (charge 3) + +1836.76 +3 + + +152.057 154.097 155.081 158.092 159.076 167.055 168.056 169.097 171.077 171.113 172.108 173.092 173.128 175.119 181.061 181.097 182.092 183.076 183.113 185.057 185.092 186.123 187.071 189.087 195.113 198.124 199.071 200.103 201.123 209.092 +212.103 217.082 226.118 227.102 231.098 239.094 241.084 245.076 254.113 257.161 259.092 271.139 275.171 285.009 287.006 289.161 297.155 299.061 301.059 303.02 305.018 325.15 328.113 332.228 337.186 342.178 346.122 352.165 356.07 357.068 +372.224 375.078 376.078 403.267 406.235 417.033 420.993 443.214 454.762 487.211 518.294 532.277 555.796 566.261 583.282 604.778 608.257 614.363 629.325 647.334 652.302 670.318 685.328 697.655 714.42 720.362 757.348 759.359 811.47 819.383 +868.389 885.407 886.41 908.524 948.424 956.449 1005.45 1027.48 1134.5 1210.5 + + + + +13 14 25 4 39 13 3 10 10 6 6 5 25 22 4 3 7 11 11 3 6 13 19 19 3 3 12 19 16 3 +6 38 35 5 10 43 16 28 24 6 11 15 5 31 23 3 12 29 28 4 4 13 4 7 5 3 10 3 62 100 +52 14 4 24 5 12 13 5 11 5 5 4 4 4 12 31 3 32 4 17 6 24 3 3 21 18 60 6 12 32 +13 35 5 18 6 26 30 40 10 5 + + + + + + +GRMZM2G174807_P01 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18133361..18135367:-1; parent_transcript=GRMZM2G174807_T01; parent_gene=GRMZM2G174807 + + + + + + + +GRMZM2G174807_P02 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18134011..18135367:-1; parent_transcript=GRMZM2G174807_T02; parent_gene=GRMZM2G174807 + + + + + + + +GRMZM2G174807_P03 Q41870 Aquaporin PIP1-1 (Plasma membrane intrinsic protein 1-1)(ZmPIP1-1)(ZmPIP1;1)(ZmPIP1a) seq=translation; coord=2:18133344..18135342:-1; parent_transcript=GRMZM2G174807_T03; parent_gene=GRMZM2G174807 + + + + + + + + +7.8775 +-0.384268 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +5579 5579 5579 5579 5486 5191 4915 3767 3300 2097 1293 763 310 129 70 8 3 2 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5592 5592 5592 5592 5499 5203 4906 3747 3048 1516 690 295 60 9 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2866 2326 369 26 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1136 3182 1062 185 21 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2830 (charge 2) + +1301.63 +2 + + +152.056 155.081 157.096 158.092 159.076 167.055 167.081 169.097 171.076 171.112 172.072 173.092 173.128 175.119 180.113 181.062 181.097 183.15 185.092 186.087 186.123 191.084 193.097 197.128 198.087 198.124 199.071 199.107 201.123 208.108 +212.102 215.139 219.08 226.155 227.103 233.384 239.094 241.08 244.165 254.15 258.108 262.14 264.863 269.16 272.165 292.13 294.18 297.121 299.065 301.15 306.047 309.119 314.132 322.175 327.13 355.07 359.028 363.185 377.166 379.198 +397.17 402.157 462.232 478.216 520.204 533.268 535.232 550.3 610.836 619.307 622.305 628.323 642.315 646.265 663.29 707.853 717.352 734.336 749.384 765.313 792.402 805.369 848.402 869.411 892.485 906.418 916.451 945.431 963.437 1014.73 +1022.48 1076.51 1137.5 + + + + +44 17 9 8 26 25 9 9 21 10 6 22 25 41 19 6 45 8 6 7 7 7 6 7 17 6 9 34 10 89 +18 10 7 72 41 5 25 40 24 33 16 76 5 6 8 8 9 5 6 8 6 54 5 11 19 11 100 11 26 9 +7 7 47 8 5 9 57 10 7 7 21 19 40 30 10 6 8 34 9 6 8 49 41 7 6 10 7 11 32 6 +22 11 9 + + + + + + +GRMZM2G004878_P01 NP_001144569 hypothetical protein LOC100277576 seq=translation; coord=4:81250432..81251801:-1; parent_transcript=GRMZM2G004878_T01; parent_gene=GRMZM2G004878 + + + MATEEVAKPS PIPPYPEMIL AAIEDLGDKS GSNKSAISRY IEGKYDGDLP + PAHASLLAAH LARMKESGEL VFVKNNYFRA DAPDAPPKRG RGRPPKARDP + GAPVSPPSGR GRGRPPKPKD PLDAAVKQAT AGMPRARGRP PKKAKTEGGA + SPAPAGDGST PVKRGRGRPP KVRPVVPSET AAA + + + + + + +5.6224 +-0.288328 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 + + + + + +11775 11775 11775 11637 11048 10289 9473 7608 6046 3627 2240 1117 506 278 121 64 36 7 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +11778 11778 11778 11640 11048 10274 9350 7299 4944 2201 942 294 69 18 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4616 4592 1829 608 115 19 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2225 5715 2587 920 254 66 8 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2833 (charge 3) + +1754.87 +3 + + +155.081 157.097 158.081 159.076 168.065 169.097 169.133 171.076 171.113 175.119 183.149 184.071 185.092 186.087 187.071 197.128 198.087 199.108 203.103 212.102 213.087 216.098 226.155 228.098 231.097 232.101 238.118 242.15 244.166 248.16 +251.15 255.108 256.13 270.108 273.119 288.119 289.161 303.213 335.135 337.186 341.146 383.192 398.166 404.227 418.224 423.197 441.208 443.193 452.252 456.256 458.745 461.74 467.19 470.261 482.309 485.197 494.264 499.334 504.25 533.785 +542.791 554.792 557.304 568.267 578.308 586.3 600.387 611.791 619.279 626.834 629.314 650.357 653.285 670.394 678.329 687.408 698.384 706.821 725.376 735.339 744.436 746.444 748.326 763.843 794.348 836.441 859.458 880.477 898.486 903.486 +910.462 916.484 918.483 987.52 1066.56 1084.57 1086.58 1155.61 1252.68 1257.62 + + + + +4 7 6 14 21 39 8 3 8 35 6 3 26 10 7 7 6 18 99 4 6 4 38 6 46 4 8 9 18 13 +3 8 12 9 10 6 4 7 7 3 24 7 10 5 13 9 7 11 8 6 8 10 9 6 7 9 7 31 7 10 +100 8 9 10 8 7 12 5 3 14 7 7 3 14 8 8 42 9 4 10 75 8 10 3 4 6 13 11 6 7 +3 57 6 37 6 72 12 10 14 6 + + + + + + +GRMZM2G162200_P01 Q9ZT00 Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic Precursor (RuBisCO activase)(RA) seq=translation; coord=4:693736..696087:1; parent_transcript=GRMZM2G162200_T01; parent_gene=GRMZM2G162200 + + + MAAAFSSTVG APASTPTRSS FLGKKLNKPQ VSAAVTYHGK SSSSNSRFKA + MAAKEVDETK QTDEDRWKGL AYDISDDQQD ITRGKGLVDN LFQAPMGDGT + HVAVLSSYDY ISQGQKSYNF DNMMDGFYIA KGFMDKLVVH LSKNFMTLPN + IKVPLILGIW GGKGQGKSFQ CELVFAKMGI TPIMMSAGEL ESGNAGEPAK + LIRQRYREAS DLIKKGKMSC LFINDLDAGA GRMGGTTQYT VNNQMVNATL + MNIADNPTNV QLPGMYNKED NPRVPIIVTG NDFSTLYAPL IRDGRMEKFY + WAPTREDRIG VCKGIFRTDG VDEEHVVQLV DTFPGQSIDF FGALRARVYD + DEVRRWVSET GVENIARKLV NSKEGPPTFE QPKITIEKLL EYGHMLVAEQ + ENVKRVQLAD KYLNEAALGE ANEDAMKTGS FFK + + + + + +GRMZM2G162200_P02 Q9ZT00 Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic Precursor (RuBisCO activase)(RA) seq=translation; coord=4:693736..695531:1; parent_transcript=GRMZM2G162200_T02; parent_gene=GRMZM2G162200 + + + MAAAFSSTVG APASTPTRSS FLGKKLNKPQ VSAAVTYHGK SSSSNSRFKA + MAAKEVDETK QTDEDRWKGL AYDISDDQQD ITRGKGLVDN LFQAPMGDGT + HVAVLSSYDY ISQGQKSYNF DNMMDGFYIA KGFMDKLVVH LSKNFMTLPN + IKVPLILGIW GGKGQGKSFQ CELVFAKMGI TPIMMSAGEL ESGNAGEPAK + LIRQRYREAS DLIKKGKMSC LFINDLDAGA GRMGGTTQYT VNNQMVNATL + MNIADNPTNV QLPGMYNKED NPRVPIIVTG NDFSTLYAPL IRDGRMEKFY + WAPTREDRIG VCKGIFRTDG VDEEHVVQLV DTFPGQSIDF FGALRARVYD + DEVRRWVSET GVENIARKLV NSKEGPPTFE QPKITIEKLL EYGHMLVAEQ + ENVKRVQLAD KYLNEAALGE ANEDAMKTGS FFK + + + + + +GRMZM2G162282_P01 NP_001168488 hypothetical protein LOC100382265 seq=translation; coord=4:691410..693139:1; parent_transcript=GRMZM2G162282_T01; parent_gene=GRMZM2G162282 + + + MAAAAAFSST SVVAALAASG FLGKKLVTSI IIRNKKKGYD SLHGATTTIR + VRAMAVNKET EQDRWRGLAL DTSDDQQDIT RGKGRVDPLF QAPMGDGTHV + AVLSSYDYIS QGLRHYSLDN MMDGYYIAPA FMDKLVVHIA KNFMPLPNIK + VPLILGIWGG KGQGKSFQCE LVLAKMGINP IVMSAGELES GNAGEPAKLI + RQRYREAADM IKKGKMCVLF INDLDAGAGR MGGTTQYTVN NQMVNATLMN + IADNPTNVQL PGMYNKEENP RVPIIVTGND FSTLYAPLIR DGRMDKFYWA + PTREDRVGVC KGIFRSDGVP DEDVVRLVDA FPGQSIDFFG ALRARVYDDE + VRRWVAETGV ENIARRLVNS KEGPPTFEQP RMTLDKLMEY GRMLVEEQEN + VKRVQLADKY LSEAALGDAN DDDDLYGKAA QHVRVPVPEG CTDPKAGNFD + PTARSDDGSC VYN + + + + + + +5.03821 +-0.22392 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +6603 6603 6599 6288 6003 5540 4993 4656 4333 2918 2208 1543 703 373 249 171 80 59 37 18 13 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +6618 6618 6614 6303 6005 5512 4870 4464 4089 1902 992 281 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2202 3368 918 122 18 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1252 3215 1539 459 108 35 4 19 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2839 (charge 2) + +1051.52 +2 + + +152.057 155.081 157.108 158.092 159.076 159.113 166.061 169.097 169.134 171.076 171.113 171.149 173.056 175.119 176.123 183.113 184.071 186.123 187.072 191.084 195.076 197.128 199.107 199.144 201.087 204.134 205.137 212.103 215.647 219.079 +226.155 227.102 230.114 232.14 235.144 237.134 239.089 241.639 245.076 249.637 251.102 254.16 258.108 263.138 266.126 271.163 274.187 280.169 281.171 297.166 303.174 309.203 314.674 329.171 331.219 337.682 360.103 363.2 370.255 385.217 +395.196 403.229 413.261 430.289 459.172 468.213 476.727 482.309 492.241 498.268 518.255 519.259 523.167 527.265 542.304 559.331 569.305 579.275 615.263 628.342 633.284 657.332 666.305 674.357 725.394 729.351 747.361 755.336 772.355 773.361 +778.334 789.381 796.353 877.402 892.418 895.414 896.418 918.402 935.423 952.447 + + + + +7 5 7 9 4 3 3 8 3 3 3 8 3 100 5 4 2 6 6 6 1 3 5 4 7 16 3 3 22 3 +12 6 5 5 65 3 6 6 6 3 6 3 14 12 2 10 7 54 3 3 6 30 7 5 3 66 8 13 3 3 +14 5 10 7 3 3 35 3 4 5 8 3 2 17 8 4 8 3 5 12 8 13 2 6 17 7 4 3 23 9 +4 7 3 3 5 10 4 2 13 2 + + + + + + +GRMZM2G077054_P01 seq=translation; coord=8:151204529..151215672:-1; parent_transcript=GRMZM2G077054_T01; parent_gene=GRMZM2G077054 + + + MADSEACCSA MSTAQGTALK SAPIGAGHRA RRGRPVVPPY RSGWQAYGGV + SLEGSGFLGG LQRTEERVAT LAPRAAARDA EVVRPLSKLP NSSIGLYDPS + FERDACGVGF VAELSGDYKR ETVNDAIEML ERMAHRGACG CEKNTGDGAG + IMVALPHDFF KEVTKDAGFE LPPPGDYAVG MFFMPTDEKR REKGKAEFKK + VAESLGHVIL GWRPVPTDNS DLGESALETE PVIEQVFVTK SSRSEAEFEQ + QLYILRRLSI ISVRASLNIK RGGERDFYMC SLSSRTIVYK GQLKPCQLKG + YYYADLGQEN FMSYMALVHS RFSTNTFPSW DRAQPMRVLG HNGEINTLRG + NKNWMTAREG LLEAEKLGLS KEQLARILPI VDATSSDSGA FDNVLELLVR + GGRSLLEAVM MMIPEAWQND GNMDPEKKAL YEFLSALMEP WDGPALISFT + DGRYLGATLD RNGLRPGRFY VTHSGRVIMG SEVGVVDVPP EDVLRKGRLN + PGMMLLVDFE NHTVVDDEAL KAQYSKAHPY GEWLKRQKIY LKDIVESVPE + TDRVAPSISS SLPAKNENKD HVGINGILTP LKAFGYTVEA LDMLLLPMAK + DGVEALGSMG NDTPLAVMSN REKLTFEYFK QMFAQVTNPP IDPIREKIVT + SMECMIGPEG DLLETTEKQC NRLSLKGPLV SIDEMEAIKK MNYRGWRSKV + LDITYPKKSG RKGLEETLNR MCAEAREAIR EGYTILVLSD RGFSSDRVAA + SSLLAVGAVH QHLVANLERT RIGLLVESAE PREVHHFCTL LGFGADAICP + YLAIEAIWCL QNDGKIPPNG DGQPNSKEEL VKKYFYASNY GMMKVLAKMG + ISTLASYKGA QIFEALGLSS EVIGKCFEGT PSRIEGATFE MLARDALRLH + ELAFPSRTPP AGSADAKALP NPGDYHWRKN GEVHLNDPLA MGKLQEAARV + NSRAAYKEYS KRIQELNKAC NLRGMLKFKD ISDKISLDDV EPASEIVKRF + CTGAMSYGSI SLEAHTALAI AMNKLGGKSN TGEGGEQPSR MEPLPDGSMN + PRRSAIKQVA SGRFGVSSYY LTNADELQIK MAQGAKPGEG GELPGHKVIG + DIAVTRHSTA GVGLISPPPH HDIYSIEDLA QLIHDLKNSN PGARISVKLV + SEAGVGVVAS GVVKGHADHV LISGHDGGTG ASRWTGIKNA GLPWELGLAE + THQTLVANGL RGRAVLQTDG QLKTGRDVAV ACLLGAEEFG FSTAPLITLG + CIMMRKCHMN TCPVGIATQD PVLREKFAGE PEHVINFFFM LAEELREIMA + NLGFRTITEM VGRSDMLEVD PEVVKTNEKL ENIDLSLILK PASEIRPGVA + QYCVEKQDHG LDMALDNKLI DLSRTAIEKQ VRVFIETPIQ NTNRAVGTML + SHEVTKRYHI NGLPAGTIHV KFTGSAGQSF GAFLCPGVTL ELEGDSNDYL + GKGLSGGKIV VYPPRNSSFS PEDNIVIGNV ALYGATMGEA YFNGMAAERF + CVRNSGAQAV VEGIGDHGCE YMTGGTVVIL GKTGRNFAAG MSGGIAYVYD + VDGKFSARCN NELVDLYHVE EEDDIITLKM MIEQHRRNTE SVLARDILSD + FDNLLPKFVK VYPRDYKRVL ENMKLEKSVA NHAKEPKMVN GISVTTKKVQ + PDQSASRPTR VANAKKYRGF ITYERESISY RDPKERVKDW KEVAIESTPG + PLLNTQSARC MDCGTPFCHQ ESSGAGCPLG NKIPEFNELV HQNRWREALD + RLLETNNFPE FTGRVCPAPC EGSCVLGIIE NPVSIKSIEC AIIDKGFEEG + WMIPRPPLQR TGRKVAIVGS GPAGLAAADQ LNKMGHFVTV FERADRIGGL + MMYGVPNMKT DKIGIVQRRV NLMAEEGVTF VVNANVGSDP LYSIERLRSE + NDAVILACGA TKPRDLTIPG RELSGVHFAM EFLHANTKSL LDSNLEDGKY + ISARGKKVVV IGGGDTGTDC IGTSIRHGCT SLVNLELLTK PPSNRAADNP + WPQWPRIFRV DYGHQEAATK FGKDPRTYEV LTKRFIGDEN GKVKALELVR + VKWEKVDGRF QLKEIQGSEE IIEADLVLLA MGFLGPEASI AEKLGLEKDN + RSNFKAQFGD FATSVDGVFA AGDCRRGQSL VVWAITEGRQ AAAAVDKYIS + RHDQNVAGDI TPFGAGLVQP VGA + + + + + +GRMZM2G085078_P01 seq=translation; coord=3:208332821..208344531:1; parent_transcript=GRMZM2G085078_T01; parent_gene=GRMZM2G085078 + + + MTGCEACCSA MSTAQGTALR SAPLGAGRWA RRGRPVAAPY RSGWQAYGGV + SLEGSGFLGR VHRTEERVAP RAPHAAARDA EVVRPLSKLP NSSIGLYDSS + FERDACGVGF VAELSGDYKR ETVNDAIEML ERMAHRGACG CEKNTGDGAG + IMVALPHDFF KEVAKDAGFE LPPPGEYAVG MFFMPTDEKR REKGKAEFMK + VAESLGHVIL GWRLVPTDNS DLGESALETE PVIEQVFVTK SSRSEAEFEQ + QLYILRRLSI ISVRASLNIK RGGERDFYMC SLSSRTIVYK GQLKPSQLKG + YYYADLGHEN FMSYMALVHS RFSTNTFPSW DRAQPMRVLG HNGEINTLRG + NKNWMTAREG LLEAEKLGLS KEQLSRILPI VDATSSDSGA FDNVLELLVR + GGRSLPEAVM MMIPEAWQND VNMDPEKKAL YEFLSALMEP WDGPALISFT + DGRYLGATLD RNGLRPGRFY VTHSGRVIMG SEVGVVDVPP EDVLRKGRLN + PGMMLLVDFE NHTVVDDEAL KAQYSKAHPY GEWLKRQKIY LKDIVESVPE + TDRVAPSISS SLSQKNENID HVGISGILTQ LKAFGYTVEA LEMLLLPMAK + DGVEALGSMG NDTPLAVMSN REKLTFEYFK QMFAQVTNPP IDPIREKIVT + SMECMIGPEG DLLETTEKQC NRLALKGPLV SIDEMEAIKK MNYRGWRSKV + LDITYPKKSG RKGLEETLNR ICAEARKAIR EGYTILVLSD RGFSSDRVAA + SSLLAVGAVH QHLVANLERT RIGLLVESAE PREVHHFCTL VGFGADAICP + YLAIEAIWCL QNDGKITPNG DGQPYSKEEL VAKYFYASNY GMMKVLAKMG + ISTLASYKGA QIFEALGLSS EVVGKCFEGT PSRIEGATFE MLARDALRLH + ELAFPSRALP AGSADAKALP NPGDYHWRKN GEIHLNDPLA MGKLQEAARV + NSRAAYKEYS KRIQELNKAC NLRGMLKFKH VSDKISLDEV EPASEIVKRF + CTGAMSYGSI SLEAHTALAI AMNKLGGKSN TGEGGEQPSR MEPLPDGSMN + PRRSAIKQVA SGRFGVSSYY LTNADELQIK MAQGAKPGEG GELPGHKVIG + DIAVTRHSTA GVGLISPPPH HDIYSIEDLA QLIHDLKNSN PGARISVKLV + SEAGVGVVAS GVVKGHADHV LISGHDGGTG ASRWTGIKNA GLPWELGLAE + THQTLVANGL RGRAVLQTDG QLKTGRDVAV ACLLGAEEFG FSTAPLITLG + CIMMRKCHMN TCPVGIATQD PVLREKFAGE PEHVINFFFM LAEELREIMA + NLGFRTITEM VGRSDMLEVD PEVVKSNEKL ENIDLSLILK PASEIRPGVA + QYCVEKQDHG LDMALDNKLI DLSRTAIEKQ VRVFIETPIQ NTNRAVGTML + SHQVTKRYHM NGLPAGTIHV KFTGSAGQSF GAFLCPGITL ELEGDSNDYV + GKGLSGGKIV VYPPRNSSFS PEDNIVIGNV ALYGATMGEA YFNGMAAERF + CVRNSGAQAV VEGIGDHGCE YMTGGTVVIL GKTGRNFAAG MSGGIAYVYD + VDGKFSARCN NELVDLYHVE EEDDIITLKM MIEQHRRNTE SVLARDILSD + FDNLLPKFVK VYPRDYKRVL ESMKVEKAVA KHAKEPKMAN GISVTTKLSL + TTCINFHVQK VQPDQSASRP THVANAKKYR GFITYERESI SYRDPKERVR + DWKEVAIEST PGPLLNTQSA RCMDCGTPFC HQESSGAGCP LGNKIPEFNE + LVHQNRWREA LDRLLETNNF PEFTGRVCPA PCEGSCVLGI IENPVSIKSI + ECAIIDKGFE EGWMIPRPPL QRTGRKVAIV GSGPSGLAAA DQLNKMGHFV + TVFERADRIG GLMMYGVPNM KTDKIGVVQR RVNLMAEEGV TFVVNANVGS + DPLYSIERLR SENDAVILAC GATKPRDLTI PGRELSGVHF AMEFLHANTK + SLLDSNLEDG KYISARGKKV VVIGGGDTGT DCIGTSIRHG CTSLVNLELL + SKPPSTRAAD NPWPQWPRIF RVDYGHQEAA TKFGKDPRTY GVLTKRFIGD + GNGKVKALEV VRVKWEKVDG RFQLKEMEGS EEIIEADLVL LAMGFLGPEA + TIAEKLGLEK DNRSNFKAQF GDFATSVDGV FAAGDCRRGQ SLVVWAITEG + RQAAAAVDKY LSRYDQNAAA TGDSTPSGTG LVQPVAA + + + + + +GRMZM2G085078_P02 seq=translation; coord=3:208332821..208344526:1; parent_transcript=GRMZM2G085078_T02; parent_gene=GRMZM2G085078 + + + MTGCEACCSA MSTAQGTALR SAPLGAGRWA RRGRPVAAPY RSGWQAYGGV + SLEGSGFLGR VHRTEERVAP RAPHAAARDA EVVRPLSKLP NSSIGLYDSS + FERDACGVGF VAELSGDYKR ETVNDAIEML ERMAHRGACG CEKNTGDGAG + IMVALPHDFF KEVAKDAGFE LPPPGEYAVG MFFMPTDEKR REKGKAEFMK + VAESLGHVIL GWRLVPTDNS DLGESALETE PVIEQVFVTK SSRSEAEFEQ + QLYILRRLSI ISVRASLNIK RGGERDFYMC SLSSRTIVYK GQLKPSQLKG + YYYADLGHEN FMSYMALVHS RFSTNTFPSW DRAQPMRVLG HNGEINTLRG + NKNWMTAREG LLEAEKLGLS KEQLSRILPI VDATSSDSGA FDNVLELLVR + GGRSLPEAVM MMIPEAWQND VNMDPEKKAL YEFLSALMEP WDGPALISFT + DGRYLGATLD RNGLRPGRFY VTHSGRVIMG SEVGVVDVPP EDVLRKGRLN + PGMMLLVDFE NHTVVDDEAL KAQYSKAHPY GEWLKRQKIY LKDIVESVPE + TDRVAPSISS SLSQKNENID HVGISGILTQ LKAFGYTVEA LEMLLLPMAK + DGVEALGSMG NDTPLAVMSN REKLTFEYFK QMFAQVTNPP IDPIREKIVT + SMECMIGPEG DLLETTEKQC NRLALKGPLV SIDEMEAIKK MNYRGWRSKV + LDITYPKKSG RKGLEETLNR ICAEARKAIR EGYTILVLSD RGFSSDRVAA + SSLLAVGAVH QHLVANLERT RIGLLVESAE PREVHHFCTL VGFGADAICP + YLAIEAIWCL QNDGKITPNG DGQPYSKEEL VAKYFYASNY GMMKVLAKMG + ISTLASYKGA QIFEALGLSS EVVGKCFEGT PSRIEGATFE MLARDALRLH + ELAFPSRALP AGSADAKALP NPGDYHWRKN GEIHLNDPLA MGKLQEAARV + NSRAAYKEYS KRIQELNKAC NLRGMLKFKH VSDKISLDEV EPASEIVKRF + CTGAMSYGSI SLEAHTALAI AMNKLGGKSN TGEGGEQPSR MEPLPDGSMN + PRRSAIKQVA SGRFGVSSYY LTNADELQIK MAQGAKPGEG GELPGHKVIG + DIAVTRHSTA GVGLISPPPH HDIYSIEDLA QLIHDLKNSN PGARISVKLV + SEAGVGVVAS GVVKGHADHV LISGHDGGTG ASRWTGIKNA GLPWELGLAE + THQTLVANGL RGRAVLQTDG QLKTGRDVAV ACLLGAEEFG FSTAPLITLG + CIMMRKCHMN TCPVGIATQD PVLREKFAGE PEHVINFFFM LAEELREIMA + NLGFRTITEM VGRSDMLEVD PEVVKSNEKL ENIDLSLILK PASEIRPGVA + QYCVEKQDHG LDMALDNKLI DLSRTAIEKQ VRVFIETPIQ NTNRAVGTML + SHQVTKRYHM NGLPAGTIHV KFTGSAGQSF GAFLCPGITL ELEGDSNDYV + GKGLSGGKIV VYPPRNSSFS PEDNIVIGNV ALYGATMGEA YFNGMAAERF + CVRNSGAQAV VEGIGDHGCE YMTGGTVVIL GKTGRNFAAG MSGGIAYVYD + VDGKFSARCN NELVDLYHVE EEDDIITLKM MIEQHRRNTE SVLARDILSD + FDNLLPKFVK VYPRDYKRVL ESMKVEKAVA KHAKEPKMAN GISVTTKKVQ + PDQSASRPTH VANAKKYRGF ITYERESISY RDPKERVRDW KEVAIESTPG + PLLNTQSARC MDCGTPFCHQ ESSGAGCPLG NKIPEFNELV HQNRWREALD + RLLETNNFPE FTGRVCPAPC EGSCVLGIIE NPVSIKSIEC AIIDKGFEEG + WMIPRPPLQR TGRKVAIVGS GPSGLAAADQ LNKMGHFVTV FERADRIGGL + MMYGVPNMKT DKIGVVQRRV NLMAEEGVTF VVNANVGSDP LYSIERLRSE + NDAVILACGA TKPRDLTIPG RELSGVHFAM EFLHANTKSL LDSNLEDGKY + ISARGKKVVV IGGGDTGTDC IGTSIRHGCT SLVNLELLSK PPSTRAADNP + WPQWPRIFRV DYGHQEAATK FGKDPRTYGV LTKRFIGDGN GKVKALEVVR + VKWEKVDGRF QLKEMEGSEE IIEADLVLLA MGFLGPEATI AEKLGLEKDN + RSNFKAQFGD FATSVDGVFA AGDCRRGQSL VVWAITEGRQ AAAAVDKYLS + RYDQNAAATG DSTPSGTGLV QPVAA + + + + + + +5.95035 +-0.290261 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 + + + + +10908 10908 10908 10415 10057 9302 8541 6587 4914 2843 1809 992 434 225 109 53 27 14 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +10913 10913 10913 10420 10047 9243 8340 5995 3855 1554 515 141 27 14 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3945 4242 1858 595 207 53 7 7 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2057 5153 2606 748 299 37 8 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2840 (charge 3) + +1843.88 +3 + + +150.066 155.081 156.076 157.097 158.093 159.076 167.093 172.107 175.119 178.061 185.092 185.165 187.144 195.088 196.09 199.108 201.124 204.135 209.139 213.16 215.139 226.154 233.165 237.134 241.092 242.114 244.164 248.114 253.092 255.148 +259.609 264.109 266.124 306.118 309.142 310.11 315.165 324.129 341.155 346.113 352.161 357.067 365.683 381.151 390.209 395.203 397.147 412.182 423.198 429.197 435.043 440.18 452.25 455.174 458.207 465.243 478.219 483.175 490.21 501.223 +518.208 532.26 536.279 544.279 548.278 557.766 560.264 582.242 587.292 589.282 605.299 610.315 617.278 652.331 666.281 673.336 679.32 687.841 702.375 717.344 720.326 730.368 738.368 822.353 826.395 830.394 840.358 844.44 857.387 914.408 +930.475 965.413 983.432 996.474 1001.44 1003.45 1066.42 1114.52 1129.61 1227.61 + + + + +10 3 3 6 4 6 31 3 28 31 11 3 29 89 6 11 3 4 10 3 5 32 23 5 3 3 12 4 29 3 +6 3 17 11 13 3 3 34 4 5 13 4 10 14 4 5 6 3 16 22 3 3 4 4 3 5 3 4 10 12 +25 3 14 3 11 9 5 4 4 13 100 3 27 3 9 16 3 5 4 4 59 17 13 3 4 9 3 6 6 17 +4 3 4 4 43 8 6 18 4 21 + + + + + + +GRMZM5G868664_P01 NP_001151884 snRK1-interacting protein 1 seq=translation; coord=7:138554824..138557837:1; parent_transcript=GRMZM5G868664_T01; parent_gene=GRMZM5G868664 + + + MEAAAATALP FAAAVPTAWR VRASPRTRRR SVAAKLERGL GKGVPTTNYV + VPLDKATGMT RPLVEILRDL NKRVPDKIID PDTNTVNWYH ANRMLSFYAP + GWCGEVRDVI YSENGTVTVV YRVILKGTDG EAYRDATGTA QLHEGRREDA + VAAAEEAAFC KACARFGFGL YLYHQDDSHY DDHFH + + + + + + +5.92548 +-0.303871 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +5914 5914 5829 5521 5284 4807 4228 3369 2589 1568 906 364 192 103 43 28 5 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5917 5917 5832 5524 5277 4759 4120 3061 1866 737 267 38 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1978 2572 1079 236 35 16 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1041 2625 1396 644 167 40 6 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2841 (charge 3) + +1255.6 +3 + + +155.081 155.092 157.097 157.109 157.134 158.092 159.076 159.112 160.08 166.061 167.081 167.093 169.061 169.097 169.134 171.076 171.113 173.092 173.129 175.119 176.122 183.076 183.113 183.149 184.108 185.092 187.071 187.108 188.075 194.094 +195.088 197.129 198.087 199.071 200.103 201.123 203.048 207.149 212.102 214.118 216.098 220.108 224.103 226.154 229.129 232.14 237.134 239.114 242.113 244.165 249.624 251.15 255.145 260.125 262.05 267.107 270.108 272.171 277.159 284.121 +292.166 301.15 302.681 306.166 311.688 315.672 322.185 323.138 338.115 340.162 343.172 352.197 358.172 361.184 366.189 369.226 377.192 388.194 394.183 405.714 436.226 456.251 467.297 476.742 493.249 498.241 500.247 516.254 533.282 535.293 +553.31 564.281 611.326 613.319 621.315 624.344 630.336 722.363 739.385 810.418 + + + + +6 2 5 2 3 9 100 9 6 5 5 3 3 3 3 6 3 9 5 31 3 3 4 2 4 12 22 4 2 2 +3 3 3 2 13 4 3 3 11 3 3 2 8 6 2 26 4 4 11 10 11 7 4 6 4 6 4 4 5 5 +3 3 6 4 4 6 3 3 5 3 4 4 2 23 2 5 2 5 3 8 4 8 4 2 3 35 3 3 20 4 +19 4 25 3 4 4 12 5 11 10 + + + + + + +GRMZM2G128491_P01 NP_001143558 hypothetical protein LOC100276254 seq=translation; coord=9:120079591..120082284:1; parent_transcript=GRMZM2G128491_T01; parent_gene=GRMZM2G128491 + + + MERAAPVRSS HTSTAGLLAW PHPDGAGSLP ARRPNQPTEE FRNVVFGGQL + TEGADGLNKT KRKTGSSPKG KETTGTGISK AESAVATASR DRQASQITFS + QDGTVPTRKA TSVAGVARQR ELSHTVESEG DSKMKRQVSS TKSKELSGHD + IFADHEDPKP NRSRRSDYGS SAAQSPVKNA NVSSFSFGEA DIDSTVKTAK + KKGSSNLSTD LNGKTMPKKD SASAEKQPPN RARPKGMSGS SNFADGKAST + STTGDHEGRR TRQPPGGDSS ILLG + + + + + + +6.56438 +-0.397841 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +3030 3030 3030 3030 2972 2745 2523 1413 1119 461 231 75 27 6 4 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2982 2982 2982 2982 2924 2697 2460 1264 908 278 43 1 0 0 1 0 + + + + + + +0 1 2 3 4 + + + + +2397 596 31 10 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +368 2241 402 19 1 0 3 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2843 (charge 2) + +1417.65 +2 + + +155.081 157.696 167.094 173.092 175.118 181.06 185.092 197.103 199.071 199.109 215.139 225.098 234.145 239.114 254.021 326.145 406.19 421.219 439.233 449.211 467.22 475.224 538.224 541.645 550.256 565.953 579.262 608.638 622.268 631.327 +751.305 850.381 951.422 1188.85 1405.78 + + + + +10 6 7 11 29 7 10 10 6 13 34 38 100 12 7 9 9 15 7 10 8 7 7 12 11 7 8 10 16 9 +14 15 41 9 9 + + + + + + +GRMZM2G102760_P01 NP_001105975 lipoxygenase seq=translation; coord=5:12274159..12279067:-1; parent_transcript=GRMZM2G102760_T01; parent_gene=GRMZM2G102760 + + + + + + + +GRMZM2G102760_P03 NP_001105975 lipoxygenase seq=translation; coord=5:12275542..12279067:-1; parent_transcript=GRMZM2G102760_T03; parent_gene=GRMZM2G102760 + + + + + + + + +4.07741 +-0.247116 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +1255 1255 1252 1098 1067 931 583 425 233 150 68 33 21 14 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +1256 1256 1253 1099 1059 927 551 357 164 52 16 1 0 + + + + + + +0 1 2 3 4 + + + + +792 413 50 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +267 760 191 25 12 1 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2844 (charge 2) + +1499.62 +2 + + +154.811 155.081 157.097 159.076 163.458 171.076 173.055 175.119 185.055 185.092 190.568 195.075 198.123 199.108 201.123 212.102 220.443 222.087 226.118 230.077 233.128 240.097 241.101 257.124 267.108 275.171 288.082 290.145 303.177 337.186 +351.129 354.213 368.156 369.161 372.224 374.228 380.19 385.181 427.204 462.161 467.228 472.713 479.189 481.236 487.251 492.713 496.217 497.211 501.226 521.26 549.75 556.247 573.196 595.278 600.334 607.249 613.301 624.279 650.276 684.303 +711.374 728.386 751.354 840.424 880.395 924.376 944.421 968.484 984.491 993.474 1001.44 1098.49 1108.52 + + + + +2 10 2 5 2 3 11 21 3 3 2 3 5 3 9 9 2 5 43 4 4 53 5 35 4 4 3 3 4 17 +16 4 33 4 100 4 2 17 11 4 3 9 8 2 5 3 12 3 4 3 16 9 2 3 4 3 3 10 3 3 +3 3 4 3 2 3 21 3 3 3 18 12 12 + + + + + + +GRMZM2G126190_P01 NP_001150248 LOC100283878 seq=translation; coord=4:214239084..214241779:1; parent_transcript=GRMZM2G126190_T01; parent_gene=GRMZM2G126190 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYDQELE NAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KAEYDESGPA IVHRKCF + + + + + +GRMZM2G126190_P02 NP_001150248 LOC100283878 seq=translation; coord=4:214239217..214241699:1; parent_transcript=GRMZM2G126190_T02; parent_gene=GRMZM2G126190 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYDQELE NAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KAEYDESGPA IVHRKCF + + + + + +GRMZM2G126190_P03 NP_001150248 LOC100283878 seq=translation; coord=4:214239219..214241500:1; parent_transcript=GRMZM2G126190_T03; parent_gene=GRMZM2G126190 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYDQELE NAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KAEYDESGPA IVHRKCF + + + + + +GRMZM2G152328_P01 NP_001150462 LOC100284092 seq=translation; coord=5:10223674..10226373:-1; parent_transcript=GRMZM2G152328_T01; parent_gene=GRMZM2G152328 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY + SFTTTAEREI VRDMKEKLAY IALDYDQEME TAKTSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIA KAEYDESGPS IVHRKCF + + + + + +GRMZM2G152328_P02 NP_001150462 LOC100284092 seq=translation; coord=5:10224230..10226373:-1; parent_transcript=GRMZM2G152328_T02; parent_gene=GRMZM2G152328 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY + SFTTTAEREI VRDMKEKLAY IALDYDQEME TAKTSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIA KAEYDESGPS IVHRKCF + + + + + +GRMZM2G047055_P01 NP_001150462 LOC100284092 seq=translation; coord=1:269035042..269037767:1; parent_transcript=GRMZM2G047055_T01; parent_gene=GRMZM2G047055 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY + SFTTTAEREI VRDMKEKLAY IALDYDQEME TAKTSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIA KAEYDESGPS IVHRKCF + + + + + +GRMZM2G047055_P03 NP_001150462 LOC100284092 seq=translation; coord=1:269035096..269037632:1; parent_transcript=GRMZM2G047055_T03; parent_gene=GRMZM2G047055 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY + SFTTTAEREI VRDMKEKLAY IALDYDQEME TAKTSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIA KAEYDESGPS IVHRKCF + + + + + +GRMZM2G047055_P02 NP_001150462 LOC100284092 seq=translation; coord=1:269035042..269037447:1; parent_transcript=GRMZM2G047055_T02; parent_gene=GRMZM2G047055 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY + SFTTTAEREI VRDMKEKLAY IALDYDQEME TAKTSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQVNKR SSGQKIKKTH SDFPKSDLYL LTILLPSADV DCQG + + + + + +GRMZM2G067985_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521573..134531903:1; parent_transcript=GRMZM2G067985_T04; parent_gene=GRMZM2G067985 + + + MASIWPDPWC GVVWVEIHLQ GHGSASHESG SALLRAGEMV HGQQHRCIST + SVEMADGEDI QPLVCDNGTG MVKAGFAGDD APRAVFPSIV GRPRHTGVMV + GMGQKDAYVG DEAQSKRGIL TLKYPIEHGI VSNWDDMEKI WHHTFYNELR + VAPEEHPVLL TEAPLNPKAN REKMTQIMFE TFNVPAMYVA IQAVLSLYAS + GRTTGIVLDS GDGVSHTVPI YEGYALPHAI LRLDLAGRDL TDSLMKILTE + RGYSFTTSAE REIVRDIKEK LAYIALDYEQ ELETAKNSSS VEKSYELPDG + QVITIGAERF RCPEVLFQPS MIGMEAAGIH ETTYNSIMKC DVDIRKDLYG + NIVLSGGSTM FPGIADRMSK EITSLAPSSM KIKVVAPPER KYSVWIGGSI + LASLSTFQQM WISKEEYDES GPAIVHRKCF + + + + + +GRMZM2G067985_P05 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521573..134523825:1; parent_transcript=GRMZM2G067985_T05; parent_gene=GRMZM2G067985 + + + MASIWPDPWC GVVWVEIHLQ GHGSASHESG SALLRAGEMV HGQQHRCIST + SVEMADGEDI QPLVCDNGTG MVKAGFAGDD APRAVFPSIV GRPRHTGVMV + GMGQKDAYVG DEAQSKRGIL TLKYPIEHGI VSNWDDMEKI WHHTFYNELR + VAPEEHPVLL TEAPLNPKAN REKMTQIMFE TFNVPAMYVA IQAVLSLYAS + GRTTGIVLDS GDGVSHTVPI YEGYALPHAI LRLDLAGRDL TDSLMKILTE + RGYSFTTSAE REIVRDIKEK LAYIALDYEQ ELETAKNSSS VEKSYELPDG + QVITIGAERF RCPEVLFQPS MIGMEAAGIH ETTYNSIMKC DVDIRKDLYG + NIVLSGGSTM FPGIADRMSK EITSLAPSSM KIKVVAPPER KYSVWIGGSI + LASLSTFQQM WISKEEYDES GPAIVHRKCF + + + + + +GRMZM2G067985_P06 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521637..134531903:1; parent_transcript=GRMZM2G067985_T06; parent_gene=GRMZM2G067985 + + + MASIWPDPWC GVVWVEIHLQ GHGSASHESG SALLRAGEMV HGQQHRCIST + SVEMADGEDI QPLVCDNGTG MVKAGFAGDD APRAVFPSIV GRPRHTGVMV + GMGQKDAYVG DEAQSKRGIL TLKYPIEHGI VSNWDDMEKI WHHTFYNELR + VAPEEHPVLL TEAPLNPKAN REKMTQIMFE TFNVPAMYVA IQAVLSLYAS + GRTTGIVLDS GDGVSHTVPI YEGYALPHAI LRLDLAGRDL TDSLMKILTE + RGYSFTTSAE REIVRDIKEK LAYIALDYEQ ELETAKNSSS VEKSYELPDG + QVITIGAERF RCPEVLFQPS MIGMEAAGIH ETTYNSIMKC DVDIRKDLYG + NIVLSGGSTM FPGIADRMSK EITSLAPSSM KIKVVAPPER KYSVWIGGSI + LASLSTFQQM WISKEEYDES GPAIVHRKCF + + + + + +GRMZM2G067985_P09 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134526764..134531903:1; parent_transcript=GRMZM2G067985_T09; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G067985_P10 seq=translation; coord=8:134529140..134532339:1; parent_transcript=GRMZM2G067985_T10; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G067985_P12 seq=translation; coord=8:134529314..134532338:1; parent_transcript=GRMZM2G067985_T12; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G067985_P15 seq=translation; coord=8:134529353..134532428:1; parent_transcript=GRMZM2G067985_T15; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G104017_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187787..41190730:-1; parent_transcript=GRMZM2G104017_T02; parent_gene=GRMZM2G104017 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G104017_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187649..41190517:-1; parent_transcript=GRMZM2G104017_T03; parent_gene=GRMZM2G104017 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G104017_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187649..41190516:-1; parent_transcript=GRMZM2G104017_T04; parent_gene=GRMZM2G104017 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G110378_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236360..41239234:-1; parent_transcript=GRMZM2G110378_T01; parent_gene=GRMZM2G110378 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G110378_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236434..41239320:-1; parent_transcript=GRMZM2G110378_T02; parent_gene=GRMZM2G110378 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G110378_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236494..41239316:-1; parent_transcript=GRMZM2G110378_T04; parent_gene=GRMZM2G110378 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G110378_P05 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236752..41239103:-1; parent_transcript=GRMZM2G110378_T05; parent_gene=GRMZM2G110378 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KEEYDESGPA IVHRKCF + + + + + +GRMZM2G006765_P02 NP_001159156 hypothetical protein LOC100304239 seq=translation; coord=2:140057140..140059599:1; parent_transcript=GRMZM2G006765_T02; parent_gene=GRMZM2G006765 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVNN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY VALEYDQELE NAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KAEYDESGPG IVHRKCF + + + + + +GRMZM2G067985_P11 seq=translation; coord=8:134529314..134532428:1; parent_transcript=GRMZM2G067985_T11; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQVCIF YICFSCSTSF LLTLLSPK + + + + + +GRMZM2G067985_P13 seq=translation; coord=8:134529314..134532337:1; parent_transcript=GRMZM2G067985_T13; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQVCIF YICFSCSTSF LLTLLSPK + + + + + +GRMZM2G104017_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187750..41190730:-1; parent_transcript=GRMZM2G104017_T01; parent_gene=GRMZM2G104017 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQVCGC LYLLSAAALH LF + + + + + +GRMZM2G110378_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236442..41239320:-1; parent_transcript=GRMZM2G110378_T03; parent_gene=GRMZM2G110378 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTSAEREI VRDIKEKLAY IALDYEQELE TAKNSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAAGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT SLAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQVWVV YIAFSCCT + + + + + +GRMZM2G030169_P01 NP_001146931 actin-2 seq=translation; coord=5:23016144..23019861:1; parent_transcript=GRMZM2G030169_T01; parent_gene=GRMZM2G030169 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFS VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYEQELE TAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS RAEYEESGPA IVHRKCF + + + + + +GRMZM2G030169_P02 NP_001146931 actin-2 seq=translation; coord=5:23016216..23019859:1; parent_transcript=GRMZM2G030169_T02; parent_gene=GRMZM2G030169 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFS VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYEQELE TAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS RAEYEESGPA IVHRKCF + + + + + +GRMZM2G030169_P03 NP_001146931 actin-2 seq=translation; coord=5:23017613..23019859:1; parent_transcript=GRMZM2G030169_T03; parent_gene=GRMZM2G030169 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFS VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYEQELE TAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSMIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS RAEYEESGPA IVHRKCF + + + + + +GRMZM2G082484_P01 NP_001167929 hypothetical protein LOC100381643 seq=translation; coord=1:224444114..224447387:-1; parent_transcript=GRMZM2G082484_T01; parent_gene=GRMZM2G082484 + + + MADSEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFS VPAMYVAIQA VLSLYASGRT + TGIVLDSGDG VSHTVPIYEG YALPHAILRL DLAGRDLTDS LMKILTERGY + SFTTTAEREI VRDIKEKLAY VALDYEQELE TAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLFQPSFIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGSTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS RAEYEESGPA IVHRKCF + + + + + +GRMZM2G053299_P01 NP_001141313 hypothetical protein LOC100273404 seq=translation; coord=1:296022541..296026398:-1; parent_transcript=GRMZM2G053299_T01; parent_gene=GRMZM2G053299 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVNN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN APAMYVAIQA VLSLYASGRT + TGIVLDSGDG VTHTVPIYEG YALPHAILRL DLAGRDLTDC LMKILTERGY + SFTTTAEREI VRDIKEKLAF VALDYEQELE TAKSSSSVEK SYELPDGQVI + TIGAERFRCP EVLLQPSLIG MEAPGIHETT YNSIMKCDVD IRKDLYGNIV + LSGGTTMFPG IADRMSKEIT ALAPSSMKIK VVAPPERKYS VWIGGSILAS + LSTFQQMWIS KDEYDESGPA IVHRKCF + + + + + +GRMZM2G469900_P01 seq=translation; coord=7:45858534..45867604:1; parent_transcript=GRMZM2G469900_T01; parent_gene=GRMZM2G469900 + + + MEFVPRRGSS SRASPRAASR RTPRAGTSSS SSPPSASATP TASSTATSSP + RISSLTSAAT SRSPTSALSA ANKFTEATLP ADAEKKPQDG KTLPKYGAMI + MEALLELNEP NGSDIAAIFG FIEVSDFGLS AVADKFHPDA LLHTFCGTPS + YVAPKVSSRS LKKAIGFKTH SRRPASSSGP TKRGGLLLGR YELGRLLAHG + TFAKVYHARH DDDTGETIAI KVLDKEKALC NGLVLHIKRE IAILRRVRRP + NIIRLFEVMA TRSKIYFAME FVRGGELFAC VAKGRLKEDT ARRYGAMIME + ALLELNEPNG SDIAAIFGFI EVSDFGLSAV ADKFHPDALL HTFCGTPSYV + APKVSSRSLK KAIGFKTHAA GVKHWPPGAA RQRPTGAPCR WAEAASDNSR + AQHADIVNQG KLVSDEIIIN LLSRRLEEGE EKGELGFILD GFPRTLRQAK + MADAEDIQPL VCDNRTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPILLTEV PLNPKANKEK MTQIMFETFN TPAIGRTTGI VLDSGDGVSH + TVPIYEGYAL PHAILRLDLA GRDLTDCSSA LDCVCSKDII QNLTERFYSL + HNYCIAFFVE YYLLGDGLLL LLAGLRTDGL QSIVGAWYQR GRQGCTCSQS + + + + + + +GRMZM2G478779_P01 seq=translation; coord=1:287300193..287305323:-1; parent_transcript=GRMZM2G478779_T01; parent_gene=GRMZM2G478779 + + + MDHVVGGKFK LGKKIRSGSF GKLYLAVNVQ NGEEVAVKLG GSCRREALAT + GCCTSTANRG HRAGGQKQPA TTVGHRRLEE GEEKGELGFI LDGFPRTMRQ + AHQPRQAGFA GDDAPRAVFP SIVGRPRHTG VMVGMGQKDA YVGDEAQSKR + GILTLKYPIE HGIVSNWDDM EKIWHHTFYN ELRVAPEEHP VLLTEAPLNP + KANREKMTQI MFETFNTPAM YVAIQTVLSL YASGRTTDFR DYLYRNFRYS + VEKTEGLGVF RTHVLTGLAR CILVQ + + + + + +GRMZM2G478779_P02 seq=translation; coord=1:287301564..287305323:-1; parent_transcript=GRMZM2G478779_T02; parent_gene=GRMZM2G478779 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQT VLSLYASGRT + TGELIPFSA + + + + + +GRMZM2G478779_P04 seq=translation; coord=1:287301831..287302499:-1; parent_transcript=GRMZM2G478779_T04; parent_gene=GRMZM2G478779 + + + MADAEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQT VLSLYASGRT + TGELIPFSA + + + + + +GRMZM2G067985_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134532296:1; parent_transcript=GRMZM2G067985_T01; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVL + + + + + +GRMZM2G067985_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134524347:1; parent_transcript=GRMZM2G067985_T02; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVL + + + + + +GRMZM2G067985_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134524303:1; parent_transcript=GRMZM2G067985_T03; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGIVL + + + + + +GRMZM2G067985_P07 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521637..134523822:1; parent_transcript=GRMZM2G067985_T07; parent_gene=GRMZM2G067985 + + + MASIWPDPWC GVVWVEIHLQ GHGSASHESG SALLRAGEMV HGQQHRCIST + SVEMADGEDI QPLVCDNGTG MVKAGFAGDD APRAVFPSIV GRPRHTGVMV + GMGQKDAYVG DEAQSKRGIL TLKYPIEHGI VSNWDDMEKI WHHTFYNELR + VAPEEHPVLL TEAPLNPKAN REKMTQIMFE TFNVPAMYVA IQAVLSLYAS + GRTTGIVL + + + + + +GRMZM2G067985_P14 seq=translation; coord=8:134529314..134530793:1; parent_transcript=GRMZM2G067985_T14; parent_gene=GRMZM2G067985 + + + MADGEDIQPL VCDNGTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPVLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT + TGMT + + + + + +GRMZM2G053284_P01 NP_001141305 hypothetical protein LOC100273396 seq=translation; coord=3:175897257..175900286:-1; parent_transcript=GRMZM2G053284_T01; parent_gene=GRMZM2G053284 + + + MAEEDVQPLV CDNGTGMVKA GFAGDDAPRA VFPSIVGRPR HTGVMVGMGQ + KDAYVGDEAQ SKRGILTLKY PIEHGIVGNW DDMEKIWHHT FYNELRVAPE + EHPILLTEAP LNPKANREKM TQIMFETFSC PAMYVSIQAV LSLYASGRTT + GIVLDSGDGV SHTVPIYEGY TLPHAIIRLD LAGRDLTDNL MKILTERGYS + FTTTAEREIV RDIKEKLAYV ALDYEQELET ARTSSTVEKS YELPDGQVIT + IGAERFRCPE VLFQPSFIGM ESPGIHEATY NSIMKCDVDI RKDLYGNVVL + SGGSTMFPGI GDRMSKEITA LAPSSMKVKV VAPPERKYSV WIGGSILASL + STFQQMWISK EEYDESGPGI VHMKCF + + + + + +GRMZM2G084769_P01 seq=translation; coord=5:165863401..165866226:1; parent_transcript=GRMZM2G084769_T01; parent_gene=GRMZM2G084769 + + + MANGEDIQPL VCDNGTRMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAL + EEHPVLLTKA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYAILNG + TYLYYINSVS LLDF + + + + + +GRMZM2G469900_P02 seq=translation; coord=7:45866261..45867604:1; parent_transcript=GRMZM2G469900_T02; parent_gene=GRMZM2G469900 + + + MADAEDIQPL VCDNRTGMVK AGFAGDDAPR AVFPSIVGRP RHTGVMVGMG + QKDAYVGDEA QSKRGILTLK YPIEHGIVSN WDDMEKIWHH TFYNELRVAP + EEHPILLTEV PLNPKANKEK MTQIMFETFN TPAMYVAI + + + + + +GRMZM2G333399_P01 seq=translation; coord=2:37701545..37702934:1; parent_transcript=GRMZM2G333399_T01; parent_gene=GRMZM2G333399 + + + HADIVNQGKL VSDEIIINLL SRRLEEGEEK GELGFILDGF PRTMRQAKMA + DAEDIQPLVC DNRTGMVKAG FAGDDAPRAV FPSIVGRPRH TGVMVEMGQK + DAYVGDEAQS KRGIRTLKYP IEHGIVSNWD DMEKIWHHTF YNELRVAPEE + HPILLTEAPL NPKANKEKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG + IVLDSGDGVS HTAPIYEGYA LPHAILRLDL AGRDLIDCSS ALDCVCSKDI + IQNLTERFYS LHNYCIAFFV EYYLLGDGLL LLLAGLRTDG LQSIVGAWYQ + RGRQGCTCSQ S + + + + + +GRMZM5G859691_P01 seq=translation; coord=2:79285142..79305370:1; parent_transcript=GRMZM5G859691_T01; parent_gene=GRMZM5G859691 + + + MPLLPAAALA LFAPPDVPLP THTLALLLRR LFTTRSIAAA QGLLHKLHLP + SCSALPARNL RAHPALPSFA QPPHAAKLPL ALISSHACLR TPLDPMPLLP + AVALALFAPP DMPLPTHTLA LLLRRLFTTR SIAAVQGLLH KLLDIGVDAR + PQFLEQQLKK AKGPNLMFGR GDETEGSDNS KSKFKDDEQD GQVSSRSLKK + AIGFKTHVRY CDTLMVLKLW IMSKVPFRSS TGHRVLHVNG QQGHRAGGQK + QPATTVGHSF LSYICMFFKG MYMDLPNTLD FCKQPKILSE KKVENGRCRG + YPAPCLRQWN CMVKAGFAGD DAPRVVFPSI VGRPRHTGVM VGMGQKDAYV + GDEAQSKRGI LTLKYPIEHG IASNWDDMEK IWHHTFYNEL RVAPEEHPVL + LTEAPLNPKA KREKMTQIMF ETFNTPAMYV AIQVVLSLYA SGRTTGIVLD + SGDGVSHTVP IYEGYTLPHA ILHLDLAGRD LTDCSFALDC VCSKDIIQNL + TERFYLLHNY CIALFVEYYL LGDGLLLLLA GLRTDGLQSI VGAWYQRVHL + FTILRSKVLG GEGLDNHQVA NYETITVDEL FRKWRGGSKD ECFNCGDPDH + YIASCPKTKS RAEADKGDHH SGRRKGKQEY TSGEHKSKGT FDKEALKKAY + LHKAKIK + + + + + +GRMZM2G320797_P03 NM_001154731 actin-7 (LOC100281811), mRNA seq=translation; coord=8:166528899..166530154:-1; parent_transcript=GRMZM2G320797_T03; parent_gene=GRMZM2G320797 + + + MVGMGQKDAY VGDEAQSKRG ILTLKYPIEH GIVGNWDDME KIWHHTFYNE + LRVAPEEHPI LLTEAPLNPK ANREKMTQIM FETFNCPAMY VAIQAVLSLY + ASGRTTGIVL DSGDGVSHTV PIYEGYTLPH AILRLDLAGR DLTDNLMKIL + TERGYSFTTT AEREIVRDIK EKLAYVALDY EQELETARTS SSVEKSYELP + DGQVITIGAE RFRCPEVLFQ PSFIGMESAG IHEATYNSIM KCDVDIRKDL + YGNVVLSGGS TMFPGIGDRM SKEITALAPS SMKVKVVAPP ERKYSVWIGG + SILASLSTFQ QMWISKEEYD ESGPGIVHMK CF + + + + + +GRMZM2G465072_P01 seq=translation; coord=6:166831395..166832311:1; parent_transcript=GRMZM2G465072_T01; parent_gene=GRMZM2G465072 + + + PRGSRPREQP YRTITTTALS SFALLCLPEL TAPRLLTVDP PLIRYKMADA + EDIQPLVCDN GTGMVKAGFA GDDAPRAVFP SIVGRPRHTG VMVGMGQKDA + YVGDEAQSKR GILTLKYLSL HIT + + + + + +GRMZM2G437445_P01 seq=translation; coord=2:232893400..232895794:-1; parent_transcript=GRMZM2G437445_T01; parent_gene=GRMZM2G437445 + + + MTYFAEGSLL LGHVLALLEL KVRVEADPHG VQHWDPSNAA GLACEKEQFH + PREDENDGCP ALMSSFMDSP IVHDIDLVSM QVSLVTTHRE LSFLALKTYR + VCHTGVMVGM GQKDAYVGDE AQSKRGILIL KYPIEHGIVG NWDGMEKIWH + HIFYNELRVE PEEHPIPLTE APLNPKENRE KMTQIMFETF NCPAMYVAIQ + AVLSLYASGR TTGIVLDSGD GVSHTVPIYE GYTLPHAILR LDLAGHDLTD + NLMKILTERG YSFTMTVDRE IVSDIKEKLV YVALDYEQEL ETARTSSSVE + KSYEMPDGQV ITIGA + + + + + + +5.28863 +-0.320523 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +5836 5836 5799 5535 5151 4581 4111 3313 2289 1280 582 227 90 52 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5936 5936 5899 5618 5229 4611 4101 3263 2000 975 293 113 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1877 2586 1108 286 65 18 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1508 2870 1121 267 60 10 1 103 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2848 (charge 3) + +1338.63 +3 + + +150.045 151.042 155.081 157.061 157.097 158.092 159.076 160.08 167.055 168.055 169.051 169.097 173.056 173.092 174.059 175.119 176.107 176.122 181.061 183.076 185.055 185.091 186.124 187.071 188.074 190.123 200.102 201.087 203.066 207.113 +209.103 215.648 221.103 223.063 225.042 227.04 228.632 235.144 241.118 245.075 251.142 255.116 263.138 272.123 280.169 283.176 286.186 295.174 302.099 303.214 305.112 311.135 316.113 325.985 337.683 342.018 343.997 344.995 350.69 354.155 +360.029 361.026 372.167 373.132 390.245 395.196 400.161 406.207 412.659 417.207 430.087 436.713 445.719 468.293 476.728 481.23 495.253 501.277 502.279 509.224 518.304 542.304 554.307 565.343 572.317 589.342 591.346 599.278 622.367 657.331 +700.373 709.401 718.383 720.386 772.358 833.412 873.411 890.432 892.437 989.494 + + + + +3 2 4 1 10 4 61 4 41 14 8 1 18 2 1 41 4 2 1 3 2 3 1 18 2 2 2 4 1 7 +2 5 1 9 12 3 1 50 5 6 3 4 5 5 11 3 2 6 9 5 3 2 2 2 10 6 7 7 12 4 +100 78 4 4 21 11 2 2 3 4 2 2 22 3 20 1 6 5 2 3 20 2 1 3 3 26 2 2 3 2 +4 4 18 2 2 6 2 31 4 2 + + + + + + +GRMZM2G077206_P01 NP_001105627 LOC542632 seq=translation; coord=8:136911622..136912881:1; parent_transcript=GRMZM2G077206_T01; parent_gene=GRMZM2G077206 + + + MATAGGGAGH LKLLGAWPSP FVNRVRMALH LKGLEYENVE EDLTNKSDLL + LASNPVHKLV PVLLHGDKPI SESLVIVEYL DDAFPGAGQA VLPADPYERA + VARFWAKYVD GKLHGMMVKA LMGATEEERA TATVDALAAM DTLEGAFAEC + SGGKKFFAGD APGYLDVALG GFIGWLRAWD KVGGVKLLDA GRVPRLATWA + ERFAALDVAK EVIPDPDHIA EFAKVLQARS AAAATSN + + + + + + + +4.85138 +-0.262237 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +3462 3462 3421 3270 2873 2618 2463 1849 1557 913 633 264 190 74 34 18 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3481 3481 3440 3289 2875 2586 2378 1745 1177 544 147 49 3 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1491 1425 457 101 7 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +596 2119 587 162 10 4 1 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2849 (charge 2) + +981.512 +2 + + +150.066 155.082 156.076 157.097 157.108 158.092 159.076 167.093 169.061 169.097 169.133 171.076 172.071 172.108 173.056 173.092 173.128 175.119 176.122 181.097 184.072 185.092 185.165 186.095 187.107 193.097 195.089 197.092 197.129 198.094 +201.086 204.134 215.102 216.106 222.124 226.119 230.114 240.134 251.15 258.144 260.197 266.15 268.129 272.136 286.139 289.161 295.15 308.172 311.208 320.184 323.146 325.15 334.217 343.163 348.694 352.172 354.213 364.163 371.239 380.166 +397.256 409.193 419.238 428.234 437.189 438.191 442.28 447.221 452.227 454.279 465.257 480.23 489.176 493.252 497.286 509.245 514.237 522.278 525.315 532.262 539.33 541.338 543.262 550.273 566.266 571.258 582.336 593.315 621.312 623.29 +639.355 667.426 678.376 680.311 696.378 698.385 706.33 737.327 767.416 796.468 + + + + +3 9 9 4 2 9 3 5 2 14 6 5 4 2 2 20 5 39 3 2 3 34 6 3 3 7 6 59 8 4 +14 2 35 3 4 6 4 47 7 5 6 2 21 3 8 11 2 3 2 3 3 2 3 3 3 3 16 3 9 4 +7 12 2 2 17 4 5 3 3 7 3 4 3 3 3 5 3 10 4 2 100 5 6 12 4 15 7 2 3 3 +11 12 4 3 36 4 5 4 8 4 + + + + + + +GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01; parent_gene=GRMZM5G815453 + + + MSCREGLMSP QTETKASVGF KAGVKDYKLT YYTPEYETKD TDILAAFRVT + PQLGVPPEEA GAAVAAESST GTWTTVWTDG LTSLDRYKGR CYHIEPVPGD + PDQYICYVAY PLDLFEEGSV TNMFTSIVGN VFGFKALRAL RLEDLRIPPA + YSKTFQGPPH GIQVERDKLN KYGRPLLGCT IKPKLGLSAK NYGRACYECL + RGGLDFTKDD ENVNSQPFMR WRDRFVFCAE AIYKAQAETG EIKGHYLNAT + AGTCEEMIKR AVFARELGVP IVMHDYLTGG FTANTTLSHY CRDNGLLLHI + HRAMHAVIDR QKNHGMHFRV LAKALRMSGG DHIHSGTVVG KLEGEREITL + GFVDLLRDDF IEKDRSRGIF FTQDWVSMPG VIPVASGGIH VWHMPALTEI + FGDDSVLQFG GGTLGHPWGN APGAAANRVA LEACVQARNE GRDLAREGNE + IIKAACKWSA ELAAACEIWK EIKFDGFKAM DTI + + + + + +GRMZM2G448344_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=1:203925927..203931405:-1; parent_transcript=GRMZM2G448344_T01; parent_gene=GRMZM2G448344 + + + MSCREGLMSP QTETKASVGF KAGVKDYKLT YYTPEYETKD TDILAAFRVT + PQLGVPPEEA GAAVAAESST GTWTTVWTDG LTSLDRYKGR CYHIEPVPGD + PDQYICYVAY PLDLFEEGSV TNMFTSIVGN VFGFKALRAL RLEDLRIPPA + YSKTFQGPPH GIQVERDKLN KYGRPLLGCT IKPKLGLSAK NYGRACYECL + RGGLDFTKDD ENVNSQPFMR WRDRFVFCAE AIYKAQAETG EIKGHYLNAT + AGTCEEMIKR AVFARELGVP IVMHDYLTGG FTANTTLSHY CRDNGLLLHI + HRAMHAVIDR QKNHGMHFRV LAKALRMSGG DHIHSGTVVG KLEGEREITL + GFVDLLRDDF IEKDRSRGIF FTQDWVSMPG VIPVASGGIH VWHMPALTEI + FGDDSVLQFG GGTLGHPWGN APGAAANRVA LEACVQARNE GRDLAREGNE + IIKAACKWSA ELAAACEIWK EIKFDGFKAM DTI + + + + + +GRMZM2G385635_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=2:200096578..200100853:-1; parent_transcript=GRMZM2G385635_T01; parent_gene=GRMZM2G385635 + + + MSCREGLMSP QTETKASVGF KAGVKDYKLT YYTPEYETKD TDILAAFRVT + PQLGVPPEEA GAAVAAESST GTWTTVWTDG LTSLDRYKGR CYHIEPVPGD + PDQYICYVAY PLDLFEEGSV TNMFTSIVGN VFGFKALRAL RLEDLRIPPA + YSKTFQGPPH GIQVERDKLN KYGRPLLGCT IKPKLGLSAK NYGRACYECL + RGGLDFTKDD ENVNSQPFMR WRDRFVFCAE AIYKAQAETG EIKGHYLNAT + AGTCEEMIKR AVFARELGVP IVMHDYLTGG FTANTTLSHY CRDNGLLLHI + HRAMHAVIDR QKNHGMHFRV LAKALRMSGG DHIHSGTVVG KLEGEREITL + GFVDLLRDDF IEKDRSRGIF FTQDWVSMPG VIPVASGGIH VWHMPALTEI + FGDDSVLQFG GGTLGHPWGN APGAAANRVA LEACVQARNE GRDLAREGNE + IIKAACKWSA ELAAACEIWK EIKFDGFKAM DTI + + + + + +GRMZM2G360821_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=6:160783975..160786062:1; parent_transcript=GRMZM2G360821_T01; parent_gene=GRMZM2G360821 + + + MSCREGLMSP QTETKASVGF KAGVKDYKLT YYTPEYETKD TDILAAFRVT + PQLGVPPEEA GAAVAAESST GTWTTVWTDG LTSLDRYKGR CYHIEPVPGD + PDQYICYVAY PLDLFEEGSV TNMFTSIVGN VFGFKALRAL RLEDLRIPPA + YSKTFQGPPH GIQVERDKLN KYGRPLLGCT IKPKLGLSAK NYGRACYECL + RGGLDFTKDD ENVNSQPFMR WRDRFVFCAE AIYKAQAETG EIKGHYLNAT + AGTCEEMIKR AVFARELGVP IVMHDYLTGG FTANTTLSHY CRDNGLLLHI + HRAMHAVIDR QKNHGMHFRV LAKALRMSGG DHIHSGTVVG KLEGEREITL + GFVDLLRDDF IEKDRSRGIF FTQDWVSMPG VIPVASGGIH VWHMPALTEI + FGDDSVLQFG GGTLGHPWGN APGAAANRVA LEACVQARNE GRDLAREGNE + IIKAACKWSA ELAAACEIWK EIKFDGFKAM DTI + + + + + +GRMZM2G308907_P01 seq=translation; coord=9:32379686..32380603:1; parent_transcript=GRMZM2G308907_T01; parent_gene=GRMZM2G308907 + + + MRWRDRFVFC AEAIYKAQAE TGEIKGHYLN ATAGTCEEMI KRAVFARELG + VPIVMHDYLT GGFTANTTLS HYCRDNGLLL HIHRAMHAVI DRQKNHGMHF + RVLAKALRMS GGDHIHSGTV VGKLEGEREI TLGFVDLLRD DFIEKDRSRG + IFFTQDSVSM PGVIPVASGG IHVWHMPALT EIFGDDSVLQ FGGGTLGHPW + GNAPGAAANR VALEACVQAR NEGRDLAREG NEIIKAACKW SAELAAACEI + WKEIKFDGFK AMDTI + + + + + +GRMZM2G115168_P01 seq=translation; coord=1:131325136..131327527:1; parent_transcript=GRMZM2G115168_T01; parent_gene=GRMZM2G115168 + + + MIKRVVFARE LGVPIVMHDY LTRGFTANTT LSHYCRDNDL LHIHRAMHAV + IDRQKNHGMY FRVLAKALCM SGGDHIHSGT VVGKFEGERE ISLGFVDLLR + NHFIEKDRSC SMFFTQDWVS MPGVIPVASG GIHV + + + + + + +6.00399 +-0.32454 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +7797 7797 7797 7735 7347 6936 5648 4572 3055 1733 918 441 218 108 28 12 2 1 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7801 7801 7801 7739 7351 6920 5560 4099 2238 758 160 54 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2823 3120 1251 479 114 9 5 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1288 3869 1925 585 120 12 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2852 (charge 3) + +1481.72 +3 + + +156.076 157.097 159.076 159.113 166.061 169.097 171.113 173.092 174.058 175.119 186.123 187.108 191.085 197.128 199.108 201.087 204.134 213.033 216.133 219.08 223.155 225.098 227.103 234.145 239.15 244.165 251.15 253.093 256.177 258.145 +291.166 303.202 310.114 327.166 339.14 345.171 365.155 367.135 378.199 402.272 404.23 415.678 418.228 422.688 426.172 428.264 431.692 436.157 452.22 454.167 456.256 461.215 462.905 466.203 467.214 472.221 475.207 480.219 482.235 495.833 +501.74 510.743 517.788 521.247 534.25 539.257 549.242 552.262 557.305 558.83 560.342 563.294 567.25 575.282 581.307 585.298 615.302 617.276 632.326 647.376 670.392 676.332 686.292 698.384 699.388 704.307 705.31 766.424 784.431 786.436 +796.329 844.365 848.36 862.38 897.518 931.402 949.411 961.443 1030.47 1048.48 + + + + +4 6 6 5 4 10 5 6 4 15 29 15 43 7 9 8 100 5 6 13 11 13 5 12 14 4 13 5 7 5 +8 35 6 7 13 8 7 16 12 5 5 7 6 10 17 7 7 7 10 30 16 5 9 30 6 4 15 10 10 22 +7 7 6 4 4 16 5 26 18 5 7 5 20 10 11 41 5 6 7 14 6 13 6 19 4 17 6 6 26 5 +5 7 5 4 6 13 8 4 10 7 + + + + + + +GRMZM2G073351_P04 NP_001167680 protochlorophyllide reductase B seq=translation; coord=5:24860869..24863845:-1; parent_transcript=GRMZM2G073351_T04; parent_gene=GRMZM2G073351 + + + MALQAATSFL PSALSARKER VSRSADIRAQ TAAVSSPSVT PASPSGKKTL + RKGTAVITGA SSGLGLATAK ALAETGKWHV IMACRDFLKA SRAAKAAGMD + KDSFTVVHLD LASLDSVRQF VRNVRQLEMP IDVVVCNAAV YQPTAKEPSY + TADGFEMSVG VNHLGHFLLA RELLSDLQSS DYPSKRLIIV GSITGNTNTL + AGNVPPKANL GDLRGLAGGL NGVGSSVMID GGEFDGAKAY KDSKVCNMLT + MQEFHRRYHE ETGVTFASLY PGCIATTGLF REHIPLFRLL FPPFQKYITK + GYVSEEEAGK RLAQVVSDPS LTKSGVYWSW NKNSASFENQ LSEEASDADK + AKKLWEISEK LVGLA + + + + + +GRMZM2G073351_P02 NP_001167680 protochlorophyllide reductase B seq=translation; coord=5:24860812..24863845:-1; parent_transcript=GRMZM2G073351_T02; parent_gene=GRMZM2G073351 + + + MALQAATSFL PSALSARKEG SVKDSASFLG VRLAADGLKL DTTALGLRTV + RVSRSADIRA QTAAVSSPSV TPASPSGKKT LRKGTAVITG ASSGLGLATA + KALAETGKWH VIMACRDFLK ASRAAKAAGM DKDSFTVVHL DLASLDSVRQ + FVRNVRQLEM PIDVVVCNAA VYQPTAKEPS YTADGFEMSV GVNHLGHFLL + ARELLSDLQS SDYPSKRLII VGSITGNTNT LAGNVPPKAN LGDLRGLAGG + LNGVGSSVMI DGGEFDGAKA YKDSKVCNML TMQEFHRRYH EETGVTFASL + YPGCIATTGL FREHIPLFRL LFPPFQKYIT KGYVSEEEAG KRLAQVVSDP + SLTKSGVYWS WNKNSASFEN QLSEEASDAD KAKKLWEISE KLVGLA + + + + + +GRMZM2G036455_P01 NP_001149903 protochlorophyllide reductase B seq=translation; coord=1:227507580..227510668:-1; parent_transcript=GRMZM2G036455_T01; parent_gene=GRMZM2G036455 + + + MALQAATSFL PSALSARKEG SSVKDSAFLG VHLADDGLKL ETAALGLRTK + RVITSVAIRA QAAAVSSPSV TPASPSGKKT LRKGTAIITG ASSGLGLATA + KALAETGKWH VIMACRDFLK ASRAAKAAGM DKDSFTVVHL DLASLDSVRQ + FVKNVRQLEM PVDVVVCNAA VYQPTAKEPS YTADGFEMSV GVNHLGHFLL + ARELLSDLQS SDYPSKRLII VGSITGNTNT LAGNVPPKAN LGDLRGLAGG + LNGIGGSAMI DGGEFDGAKA YKDSKVCNML TMQEFHRRYH EETGVTFASL + YPGCIATTGL FREHIPLFRL LFPPFQKYIT KGYVSEEEAG KRLSQVVSDP + SLTKSGVYWS WNKNSASFEN QLSEEASDAD KAKKLWEISE KLVGLA + + + + + + +5.49735 +-0.255691 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +7165 7165 7110 6850 6691 6097 5811 4426 3524 2130 1305 798 427 230 124 68 41 25 8 4 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7168 7168 7113 6853 6685 6078 5715 4194 2922 1439 713 225 85 7 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3109 3073 882 97 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1479 4286 1139 227 32 2 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2853 (charge 2) + +1114.58 +2 + + +152.056 154.087 155.081 155.117 156.077 157.097 157.132 158.091 158.102 159.077 159.112 167.081 168.065 169.097 169.134 170.101 171.076 171.113 172.061 173.092 173.129 175.119 181.097 183.113 185.092 186.095 186.124 187.071 187.108 187.143 +188.111 189.087 195.112 197.128 199.071 199.107 201.123 204.134 209.09 212.14 217.082 219.115 224.103 226.155 231.097 236.102 238.118 240.135 242.113 244.165 247.111 252.134 254.113 256.129 260.124 266.149 268.128 270.145 272.124 284.16 +288.153 291.165 311.168 322.174 325.188 335.17 338.183 339.169 343.197 353.182 354.179 357.175 360.14 366.176 370.209 371.191 388.219 410.207 436.213 440.209 454.231 457.24 475.251 476.258 515.248 546.292 564.278 580.778 622.288 625.333 +643.341 645.347 684.374 701.338 726.374 744.392 843.457 928.867 930.482 1068.2 + + + + +2 2 11 9 3 97 2 2 3 3 23 21 3 20 3 3 9 8 2 12 15 33 3 10 93 8 11 4 22 3 +3 3 7 3 3 17 9 23 6 3 5 4 9 25 7 11 3 8 4 10 2 3 76 16 4 15 2 10 38 8 +4 11 2 13 10 14 4 8 11 20 4 3 3 3 16 4 100 3 4 3 3 11 31 4 2 13 15 2 3 10 +83 3 4 4 4 35 8 3 14 3 + + + + + + +GRMZM2G085019_P01 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T01; parent_gene=GRMZM2G085019 + + + + + + + +GRMZM2G085019_P02 P16243 NADP-dependent malic enzyme, chloroplastic Precursor (NADP-ME)(EC 1.1.1.40) seq=translation; coord=3:7275169..7280519:1; parent_transcript=GRMZM2G085019_T02; parent_gene=GRMZM2G085019 + + + + + + + + +5.8477 +-0.316092 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +7473 7473 7473 7272 7148 6777 5696 4772 3112 1951 1123 580 244 89 40 27 4 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7486 7486 7486 7285 7160 6772 5671 4574 2642 1243 447 104 30 17 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3391 2665 1050 295 67 7 5 10 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1146 3903 1729 537 157 7 7 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2855 (charge 3) + +1371.72 +3 + + +155.081 158.094 159.078 159.091 165.138 173.128 175.119 181.095 181.108 181.134 183.149 184.152 199.108 204.134 209.103 211.144 221.104 226.154 229.154 239.115 242.186 249.098 256.144 260.196 267.108 277.092 284.139 295.104 312.178 315.634 +336.167 338.145 346.147 351.153 355.174 357.249 364.163 365.674 367.695 378.139 379.673 386.156 395.182 396.15 415.547 417.219 421.206 424.143 429.721 435.203 444.189 445.731 464.239 466.245 468.281 475.203 477.246 480.747 483.27 486.291 +492.719 494.233 499.729 508.24 524.224 533.207 534.212 548.756 549.263 552.227 556.763 561.202 565.272 574.287 576.253 593.281 604.243 621.274 623.351 630.265 633.285 661.281 701.301 724.373 730.339 734.372 749.373 752.399 758.337 762.341 +773.299 790.328 859.384 887.378 889.458 960.492 962.485 984.428 1015.47 1147.56 + + + + +4 8 3 41 9 3 22 3 10 7 72 13 8 4 14 23 14 20 12 16 9 36 72 29 61 3 73 6 8 9 +18 16 12 3 32 100 8 11 8 3 14 15 10 23 3 8 9 11 17 9 32 7 11 7 22 13 4 10 8 9 +40 9 14 17 10 20 3 4 3 4 8 8 7 12 9 7 30 23 21 6 7 7 18 4 9 6 11 16 19 4 +4 17 12 38 17 26 3 10 4 6 + + + + + + +GRMZM2G119499_P01 NP_001104980 glutathione transferase11 seq=translation; coord=1:7824444..7825878:-1; parent_transcript=GRMZM2G119499_T01; parent_gene=GRMZM2G119499 + + + MAAAHNHTRI ALHSFSSVVC SDSEMASVKV FGSPTSAEVA RVLMCLFEKE + VEFQLIRVDA YRGTKRMPQY LKLQPQGEAL TFEDESLTLS DSRGILRHIS + HKYAKQGNPY LIGTGALERA SIEQWLQTEA QSFDAPSAEM VYSLAFLPPT + LPKQNDNGNG GAFNARDATV GSNADASSGK RGVAGSQPAA SQTKVSAQKE + EEMLKLFEQR KKDLEKLLDI YEQRLEEATF LAGDNFTIAD LSHLPYADHL + VSDPRSRRMF ESRKNVSRWW HDVSGRDTWK YVKTLQRPPS TSTDASAKNG + QLGQQQHLPS STDGHGVKTQ RLVQNERHF + + + + + + +6.38781 +-0.311601 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +11696 11696 11657 11109 9428 7824 5557 3734 2358 1449 754 407 263 91 51 31 3 2 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +11702 11702 11663 11072 9259 7447 4570 2660 1264 564 177 49 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4083 4514 2218 638 213 42 0 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2327 5667 2665 859 133 52 4 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2858 (charge 3) + +1559.8 +3 + + +157.109 159.076 161.092 167.055 168.055 169.063 169.133 171.076 175.119 187.071 187.144 188.147 189.087 197.128 200.139 213.087 215.139 218.15 219.153 223.063 225.043 239.094 242.149 251.114 254.149 256.091 268.14 269.143 281.051 283.03 +285.166 299.061 301.059 305.181 306.185 310.138 322.161 344.976 346.974 357.138 359.027 361.026 370.687 376.218 377.222 398.251 410.211 415.036 417.034 431.235 477.227 485.731 491.247 499.296 529.237 531.259 538.319 546.261 548.286 566.314 +584.267 592.292 609.311 626.289 643.315 645.321 650.342 655.821 664.829 667.352 673.338 679.317 686.297 723.343 729.882 736.37 740.367 742.371 754.381 780.36 842.402 855.43 867.405 953.432 954.432 964.455 970.458 972.464 1041.5 1043.51 +1061.51 1063.52 1083.54 1084.54 1100.53 1110.52 1128.53 1154.55 1171.57 1199.57 + + + + +1 3 1 22 4 4 3 2 5 10 100 10 2 1 3 1 8 13 2 3 2 6 1 2 3 2 16 2 3 1 +13 54 17 12 2 1 11 13 5 2 6 3 40 15 2 2 2 5 3 11 3 3 4 3 1 4 1 6 1 3 +2 5 5 2 32 3 2 2 8 2 17 5 5 3 3 1 28 3 2 2 2 1 2 3 2 2 14 2 3 2 +8 2 4 2 1 2 3 2 4 2 + + + + + + +GRMZM2G126190_P01 NP_001150248 LOC100283878 seq=translation; coord=4:214239084..214241779:1; parent_transcript=GRMZM2G126190_T01; parent_gene=GRMZM2G126190 + + + + + + + +GRMZM2G126190_P02 NP_001150248 LOC100283878 seq=translation; coord=4:214239217..214241699:1; parent_transcript=GRMZM2G126190_T02; parent_gene=GRMZM2G126190 + + + + + + + +GRMZM2G126190_P03 NP_001150248 LOC100283878 seq=translation; coord=4:214239219..214241500:1; parent_transcript=GRMZM2G126190_T03; parent_gene=GRMZM2G126190 + + + + + + + +GRMZM2G152328_P01 NP_001150462 LOC100284092 seq=translation; coord=5:10223674..10226373:-1; parent_transcript=GRMZM2G152328_T01; parent_gene=GRMZM2G152328 + + + + + + + +GRMZM2G152328_P02 NP_001150462 LOC100284092 seq=translation; coord=5:10224230..10226373:-1; parent_transcript=GRMZM2G152328_T02; parent_gene=GRMZM2G152328 + + + + + + + +GRMZM2G047055_P01 NP_001150462 LOC100284092 seq=translation; coord=1:269035042..269037767:1; parent_transcript=GRMZM2G047055_T01; parent_gene=GRMZM2G047055 + + + + + + + +GRMZM2G047055_P03 NP_001150462 LOC100284092 seq=translation; coord=1:269035096..269037632:1; parent_transcript=GRMZM2G047055_T03; parent_gene=GRMZM2G047055 + + + + + + + +GRMZM2G047055_P02 NP_001150462 LOC100284092 seq=translation; coord=1:269035042..269037447:1; parent_transcript=GRMZM2G047055_T02; parent_gene=GRMZM2G047055 + + + + + + + +GRMZM2G067985_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521573..134531903:1; parent_transcript=GRMZM2G067985_T04; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P05 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521573..134523825:1; parent_transcript=GRMZM2G067985_T05; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P06 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521637..134531903:1; parent_transcript=GRMZM2G067985_T06; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P09 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134526764..134531903:1; parent_transcript=GRMZM2G067985_T09; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P10 seq=translation; coord=8:134529140..134532339:1; parent_transcript=GRMZM2G067985_T10; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P12 seq=translation; coord=8:134529314..134532338:1; parent_transcript=GRMZM2G067985_T12; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P15 seq=translation; coord=8:134529353..134532428:1; parent_transcript=GRMZM2G067985_T15; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G104017_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187787..41190730:-1; parent_transcript=GRMZM2G104017_T02; parent_gene=GRMZM2G104017 + + + + + + + +GRMZM2G104017_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187649..41190517:-1; parent_transcript=GRMZM2G104017_T03; parent_gene=GRMZM2G104017 + + + + + + + +GRMZM2G104017_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187649..41190516:-1; parent_transcript=GRMZM2G104017_T04; parent_gene=GRMZM2G104017 + + + + + + + +GRMZM2G110378_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236360..41239234:-1; parent_transcript=GRMZM2G110378_T01; parent_gene=GRMZM2G110378 + + + + + + + +GRMZM2G110378_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236434..41239320:-1; parent_transcript=GRMZM2G110378_T02; parent_gene=GRMZM2G110378 + + + + + + + +GRMZM2G110378_P04 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236494..41239316:-1; parent_transcript=GRMZM2G110378_T04; parent_gene=GRMZM2G110378 + + + + + + + +GRMZM2G110378_P05 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236752..41239103:-1; parent_transcript=GRMZM2G110378_T05; parent_gene=GRMZM2G110378 + + + + + + + +GRMZM2G006765_P02 NP_001159156 hypothetical protein LOC100304239 seq=translation; coord=2:140057140..140059599:1; parent_transcript=GRMZM2G006765_T02; parent_gene=GRMZM2G006765 + + + + + + + +GRMZM2G067985_P11 seq=translation; coord=8:134529314..134532428:1; parent_transcript=GRMZM2G067985_T11; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P13 seq=translation; coord=8:134529314..134532337:1; parent_transcript=GRMZM2G067985_T13; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G104017_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41187750..41190730:-1; parent_transcript=GRMZM2G104017_T01; parent_gene=GRMZM2G104017 + + + + + + + +GRMZM2G110378_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=6:41236442..41239320:-1; parent_transcript=GRMZM2G110378_T03; parent_gene=GRMZM2G110378 + + + + + + + +GRMZM2G030169_P01 NP_001146931 actin-2 seq=translation; coord=5:23016144..23019861:1; parent_transcript=GRMZM2G030169_T01; parent_gene=GRMZM2G030169 + + + + + + + +GRMZM2G030169_P02 NP_001146931 actin-2 seq=translation; coord=5:23016216..23019859:1; parent_transcript=GRMZM2G030169_T02; parent_gene=GRMZM2G030169 + + + + + + + +GRMZM2G030169_P03 NP_001146931 actin-2 seq=translation; coord=5:23017613..23019859:1; parent_transcript=GRMZM2G030169_T03; parent_gene=GRMZM2G030169 + + + + + + + +GRMZM2G082484_P01 NP_001167929 hypothetical protein LOC100381643 seq=translation; coord=1:224444114..224447387:-1; parent_transcript=GRMZM2G082484_T01; parent_gene=GRMZM2G082484 + + + + + + + +GRMZM2G053299_P01 NP_001141313 hypothetical protein LOC100273404 seq=translation; coord=1:296022541..296026398:-1; parent_transcript=GRMZM2G053299_T01; parent_gene=GRMZM2G053299 + + + + + + + +GRMZM2G469900_P01 seq=translation; coord=7:45858534..45867604:1; parent_transcript=GRMZM2G469900_T01; parent_gene=GRMZM2G469900 + + + + + + + +GRMZM2G478779_P01 seq=translation; coord=1:287300193..287305323:-1; parent_transcript=GRMZM2G478779_T01; parent_gene=GRMZM2G478779 + + + + + + + +GRMZM2G478779_P02 seq=translation; coord=1:287301564..287305323:-1; parent_transcript=GRMZM2G478779_T02; parent_gene=GRMZM2G478779 + + + + + + + +GRMZM2G478779_P04 seq=translation; coord=1:287301831..287302499:-1; parent_transcript=GRMZM2G478779_T04; parent_gene=GRMZM2G478779 + + + + + + + +GRMZM2G067985_P01 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134532296:1; parent_transcript=GRMZM2G067985_T01; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P02 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134524347:1; parent_transcript=GRMZM2G067985_T02; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P03 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521536..134524303:1; parent_transcript=GRMZM2G067985_T03; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P07 NP_001130463 hypothetical protein LOC100191561 seq=translation; coord=8:134521637..134523822:1; parent_transcript=GRMZM2G067985_T07; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G067985_P14 seq=translation; coord=8:134529314..134530793:1; parent_transcript=GRMZM2G067985_T14; parent_gene=GRMZM2G067985 + + + + + + + +GRMZM2G053284_P01 NP_001141305 hypothetical protein LOC100273396 seq=translation; coord=3:175897257..175900286:-1; parent_transcript=GRMZM2G053284_T01; parent_gene=GRMZM2G053284 + + + + + + + +GRMZM2G084769_P01 seq=translation; coord=5:165863401..165866226:1; parent_transcript=GRMZM2G084769_T01; parent_gene=GRMZM2G084769 + + + + + + + +GRMZM2G469900_P02 seq=translation; coord=7:45866261..45867604:1; parent_transcript=GRMZM2G469900_T02; parent_gene=GRMZM2G469900 + + + + + + + +GRMZM2G333399_P01 seq=translation; coord=2:37701545..37702934:1; parent_transcript=GRMZM2G333399_T01; parent_gene=GRMZM2G333399 + + + + + + + +GRMZM5G859691_P01 seq=translation; coord=2:79285142..79305370:1; parent_transcript=GRMZM5G859691_T01; parent_gene=GRMZM5G859691 + + + + + + + +GRMZM2G320797_P03 NM_001154731 actin-7 (LOC100281811), mRNA seq=translation; coord=8:166528899..166530154:-1; parent_transcript=GRMZM2G320797_T03; parent_gene=GRMZM2G320797 + + + + + + + +GRMZM2G465072_P01 seq=translation; coord=6:166831395..166832311:1; parent_transcript=GRMZM2G465072_T01; parent_gene=GRMZM2G465072 + + + + + + + +GRMZM2G437445_P01 seq=translation; coord=2:232893400..232895794:-1; parent_transcript=GRMZM2G437445_T01; parent_gene=GRMZM2G437445 + + + + + + + + +5.22552 +-0.298601 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 + + + + +4374 4374 4348 4149 3789 3553 3232 1889 1435 586 272 143 75 47 15 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4508 4508 4482 4281 3905 3648 3293 1829 1364 468 224 123 104 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2403 1754 333 17 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +979 2841 409 132 15 29 0 103 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2859 (charge 2) + +1338.63 +2 + + +152.034 157.097 158.092 159.076 167.055 169.061 173.055 175.119 185.092 186.087 187.071 188.075 201.087 207.112 216.134 225.043 235.144 239.093 242.113 245.076 260.197 263.138 272.123 285.009 302.096 305.113 322.14 332.124 350.134 359.027 +361.026 373.218 390.245 417.208 445.719 495.254 501.278 518.304 572.313 576.786 589.34 648.34 700.376 718.383 720.386 813.349 816.385 833.408 841.86 873.409 874.417 890.431 892.438 972.48 989.5 991.507 1152.56 + + + + +4 3 2 20 7 7 3 30 1 6 26 2 2 4 3 4 28 4 2 1 1 5 3 2 4 15 2 2 40 12 +14 5 9 3 9 8 1 5 2 2 20 1 4 33 3 2 2 12 2 7 2 100 11 3 37 5 4 + + + + + + +GRMZM2G142413_P01 seq=translation; coord=3:9460378..9462549:1; parent_transcript=GRMZM2G142413_T01; parent_gene=GRMZM2G142413 + + + MEIGDLIYSM FYLQMESKLA ENEAALSLMR DNYEKRLLEQ QAAQKKQSMK + FQEQEVSLSG QLASATKTLT SLSEEFRKEK KLAEELRDEI QRLESSITQA + GIDNDVLETK LEEKLGEINF LQEKVSLLNQ EIDDKEKHIR ELSASLSSKE + VDYQKLTAFT NQTKKSLELA NSRVQQLEEE LSTTKNALVS KISSIDSLNA + KLETLNSEKE EADKKINELI QEYTDLKVAS ETRASHDSKL LSERDDLIKQ + LEEKLSVALT DSSKDQETIV ELNKELDATK MMLKNELKSM EALKDSIRSS + EEALKTSRSE VSKLSKELEE ANELNEDLVS QISKLREESN EMQVDLTNKL + GEAESLSKAL SEDLASVNEM VQKGQEELEA TSIELASIAE ARDNLKKELL + DAYKNLESTT HELVEERKIV TALNKELEAL AKQLQVDSEA RKSLESDLEE + ATKSLDEMNN SALLLSKELE STHSRSATLE SEKEMLRKAL AEQTKITTEA + KENTEDAQNL ITRLETEKES FELRCRHLEE ELALAKGEIL RLRRQISTNS + SQKPRARGPP EASETLKEQP VNDYNQKTSG VVAGTPQPVK RTVRRRKGGA + + + + + + + +4.95118 +-0.253906 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +4963 4963 4904 4650 4435 4106 2952 2149 1269 748 508 302 183 140 38 15 8 2 1 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4966 4966 4907 4653 4429 4074 2757 1656 793 384 201 52 14 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2534 1950 431 50 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +933 2944 867 153 65 1 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2861 (charge 2) + +1234.57 +2 + + +152.057 155.081 157.096 159.076 159.113 167.081 169.097 169.133 170.136 173.093 175.119 178.049 181.097 183.076 183.149 184.108 185.092 187.108 187.144 188.147 189.087 195.075 197.128 199.107 201.124 203.103 206.045 209.091 212.103 216.098 +218.15 223.071 226.154 230.077 233.093 240.097 243.108 244.129 249.124 253.092 256.13 258.144 266.148 270.107 275.171 278.112 284.123 285.166 292.128 302.135 305.181 309.119 311.171 320.126 327.129 329.146 337.151 341.144 355.161 372.186 +375.127 380.192 389.214 393.141 398.168 405.155 408.186 426.197 489.238 497.283 535.254 536.252 552.277 561.267 568.306 589.265 635.238 651.263 652.334 667.301 674.344 679.336 686.28 703.306 720.323 744.334 764.32 776.388 781.346 795.403 +831.36 863.414 880.421 887.454 891.382 906.348 929.421 960.469 977.465 994.498 + + + + +2 10 13 8 3 12 11 100 11 2 14 4 7 2 4 3 44 3 47 7 3 16 31 7 4 3 4 3 30 4 +4 20 16 12 3 56 9 11 2 2 8 27 3 3 12 3 3 2 8 3 4 8 16 3 9 6 9 3 15 11 +3 2 30 15 2 4 2 21 11 3 4 2 25 9 2 7 3 2 3 11 3 8 3 3 6 21 9 20 43 3 +3 4 12 4 3 3 3 14 24 2 + + + + + + +GRMZM2G041275_P01 seq=translation; coord=3:207616747..207621242:-1; parent_transcript=GRMZM2G041275_T01; parent_gene=GRMZM2G041275 + + + + + + + + +5.90061 +-0.302595 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +11491 11491 11491 11410 11078 10467 8389 6537 4361 2508 1468 787 411 167 64 28 16 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +11474 11474 11474 11393 11061 10433 8242 6175 3600 1579 602 192 41 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3898 4938 2038 503 75 44 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2475 5841 2466 584 115 11 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2862 (charge 3) + +1834.97 +3 + + +152.057 155.081 159.076 167.056 167.118 169.097 171.113 173.092 175.119 181.061 181.096 183.076 185.092 186.087 186.124 187.072 195.113 200.103 201.087 210.087 212.103 216.097 221.084 224.103 226.154 228.096 239.094 240.095 242.114 252.098 +254.114 260.123 270.107 271.139 283.14 285.01 287.007 295.14 299.061 301.058 303.021 313.15 325.151 327.165 337.15 341.144 344.977 355.069 357.067 373.08 375.079 382.172 384.187 398.203 400.182 406.237 416.038 417.257 419.995 420.993 +433.277 454.762 512.248 514.26 568.309 583.281 586.313 599.276 617.369 625.308 633.33 636.801 648.331 653.295 665.36 670.31 688.325 690.341 696.413 714.416 715.415 720.363 723.342 741.349 757.352 759.364 762.414 793.454 811.467 813.472 +885.401 887.457 889.471 908.519 910.525 933.469 979.557 1076.61 1091.54 1093.56 + + + + +10 24 30 15 9 31 12 12 15 4 8 23 5 4 12 5 15 25 4 15 11 14 6 4 16 21 54 24 6 5 +10 6 28 23 5 28 21 5 29 21 8 10 4 9 4 14 5 90 98 13 12 10 5 5 9 28 4 17 13 21 +4 58 5 4 26 5 4 5 34 4 14 9 10 5 14 17 14 5 8 100 44 31 4 13 5 12 13 5 80 9 +4 40 6 86 11 11 4 24 4 4 + + + + + + +GRMZM2G119499_P01 NP_001104980 glutathione transferase11 seq=translation; coord=1:7824444..7825878:-1; parent_transcript=GRMZM2G119499_T01; parent_gene=GRMZM2G119499 + + + + + + + + +4.52367 +-0.231983 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 + + + + + +10724 10724 10724 10498 8283 7690 5527 4364 2870 1880 1174 641 371 201 108 78 24 9 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +10711 10711 10711 10485 8264 7549 5219 3657 2027 1070 575 154 28 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4362 4518 1512 263 69 0 0 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3267 6387 959 108 3 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2863 (charge 2) + +1559.8 +2 + + +155.08 157.108 159.076 160.385 164.957 167.081 169.099 171.076 175.119 183.076 187.144 188.147 189.086 197.128 200.139 215.139 218.149 219.152 226.118 243.145 250.129 256.092 268.14 273.83 285.167 287.172 300.117 305.181 306.185 329.143 +343.198 358.208 376.219 388.17 471.303 482.273 491.245 499.298 526.28 531.26 593.297 596.352 619.091 673.338 686.304 711.341 742.828 758.386 771.899 781.409 839.398 842.398 868.415 881.479 883.671 912.415 940.519 954.43 964.466 968.515 +970.459 1018.43 1025.5 1043.52 1061.51 1111.52 1112.59 1119.48 1140.57 1184.59 1186.59 1255.62 1314.65 1342.66 1386.7 1387.68 1413.7 + + + + +3 3 4 2 2 3 2 14 7 3 98 3 3 5 14 39 75 5 7 7 4 4 16 3 6 3 10 48 4 3 +3 5 69 5 7 4 4 82 5 7 15 4 4 5 24 12 4 6 22 40 5 7 5 6 4 4 4 11 4 18 +25 6 5 4 33 7 7 4 20 100 12 13 13 21 23 10 17 + + + + + + +GRMZM2G028156_P01 seq=translation; coord=8:4108305..4111250:-1; parent_transcript=GRMZM2G028156_T01; parent_gene=GRMZM2G028156 + + + MAAAMGNPIL TLPAPEGNGT GGGDADQQLQ QAPPKPPPPG AKTDPPATVA + THTRTIGIIH PPPDIRVIIE KTATFVAKNG PEFERRIISL NQGNAKFNFL + QPSDPYHAYY QHRVSEIAAA PPGADGPSGA DTGAAPDESP ASAPADGAAA + APVDGAAADA KADHSAPFRV GPPPKVLVPP KAELYTVRLP EGITGEELDI + IKLTAQFVAR NGKNFLTSLA QRESNNMQFH FIRPTHSMFP FFTALTDAYS + RVLRPAEGVP ALLKELREGS KDLTTVLERC LNRLEWDRSQ EQARQQAEDE + VEQERMQMSM IDWHDFVVVE TIEFADDEYE GLPVPLTLEE LKRQKRMENL + GEEEAMDLTE PSKEVEMEMD EEEMQLVEEG MRAARLEEND GAAQVSLPGD + DEAPMRIVKN YKRPEERIPA ERDPTKFVVS PITGELIPIS EMEEHMRISL + IDPKYKEQKE RMLAKIKETT LAPDDEISRN IVGLARTRPD IFGTTEEEVS + NAVKAEIEKK KDEQPKQVIW DGHSGSIGRT ATHALSQPQG GEEQFDATNV + DGRPVPGPAP LVRPGMPLPR PPQPLPLVNV PRFIAPPAPY SVPPPGSHMP + GVPHMMPHMH LPPQQIPGQP PMVRMPGQMV HMPTSIPPPP GQTQFMPGPP + RTFAMPPSSH MPPMINPIGI PQPPAPPLPP QPPAEEQPPP PDEPEPKRQR + TDDASLIPAE QYLVQHPGPA SISVSVPNLD EGNLRGQILQ IPVQSLSDTV + GSLKEQIAGE LQLPANKQKL SVRTSFLKDN LTLAYYNVGP GVVINLTLRE + RGGRKK + + + + + +GRMZM2G431306_P01 NP_001169587 hypothetical protein LOC100383468 seq=translation; coord=3:39472712..39476212:-1; parent_transcript=GRMZM2G431306_T01; parent_gene=GRMZM2G431306 + + + MPAAMGTPIL TLPAPDGNGT GGGDANQQLL QAPPKPPPPG AKTDPPATVA + THTRTIGIIH PPPDIRVIIE KTATFVAKNG PEFERRIISL NQGNAKFNFL + QPSDPYHAYY QHRVSEIAAT PPSADGLSGA ETDTAPAEAP ASTPADGAAA + VPADGAAVDT KADHSAPFRV VPPPKVLVPP KAELYTVRLP EGITGEELDI + IKLTAQFVAR NGKNFLTSLA QRESNNMQFH FIRPTHSMFP FFTELTDAYS + RVLRPAEGVP ALLKELREGS KDLTTVLERC LNRLEWDRSQ EQARQQAEDE + VEQERMQMSM IDWHDFVVVE TIEFADDEYE GLPVPLTLEE LKRQKRMENL + GEEEAMDLTE PAKEVEMEMD EEEMQLVEEG MRAAQLEEND GGSQVNVAGD + DETPMRIVKN YKRPEERIPA ERDPTKFVVS PITGELIPIS EMEEHMRISL + IDPKYKEQKE RMLAKIKETT LAPDDEISRN IVGLARTRPD IFGTTEEEVS + NAVKAEIEKK KDEQPKQVIW DGHSGSIGRT ATHALSQIQG GEEQFDASNV + DGRPVPGPAP LVRPGMPLPR PPQPLPLVNV PRFIAPPAPY SVPPPGSHMP + GVPQMMPHMH LHPQQIPGQP PMVRMPGQMV HMPTSIPPPP GQTQFMPGPP + PHTFAMPPSS HMPHMINPIG IPQPPAPPLP PQPPAEEQPP PPDEPEPKRQ + RTDDGSLIPA EQFLAQHQGP ASISVSVPNL DEGNLRGQVL QIPVQSLSDT + VGSLKEQIAG ELQLPANKQK LSVRTSFLKD NLTLAYYNVG PGVVINLTLR + ERGGRKK + + + + + +GRMZM2G431306_P02 NP_001169587 hypothetical protein LOC100383468 seq=translation; coord=3:39472712..39476212:-1; parent_transcript=GRMZM2G431306_T02; parent_gene=GRMZM2G431306 + + + MPAAMGTPIL TLPAPDGNGT GGGDANQQLL QAPPKPPPPG AKTDPPATVA + THTRTIGIIH PPPDIRVIIE KTATFVAKNG PEFERRIISL NQGNAKFNFL + QPSDPYHAYY QHRVSEIAAT PPSADGLSGA ETDTAPAEAP ASTPADGAAA + VPADGAAVDT KADHSAPFRV VPPPKVLVPP KAELYTVRLP EGITGEELDI + IKLTAQFVAR NGKNFLTSLA QRESNNMQFH FIRPTHSMFP FFTELTDAYS + RVLRPAEGVP ALLKELREGS KDLTTVLERC LNRLEWDRSQ EQARQQAEDE + VEQERMQMSM IDWHDFVVVE TIEFADDEYE GLPVPLTLEE LKRQKRMENL + GEEEAMDLTE PAKEVEMEMD EEEMQLVEEG MRAAQLEEND GGSQVNVAGD + DETPMRIVKN YKRPEERIPA ERDPTKFVVS PITGELIPIS EMEEHMRISL + IDPKYKEQKE RMLAKIKETT LAPDDEISRN IVGLARTRPD IFGTTEEEVS + NAVKAEIEKK KDEQPKQVIW DGHSGSIGRT ATHALSQIQG GEEQFDASNV + DGRPVPGPAP LVRPGMPLPR PPQPLPLVNV PRFIAPPAPY SVPPPGSHMP + GVPQMMPHMH LHPQQIPGQP PMVRMPGQMV HMPTSIPPPP GQTQFMPGPP + PHTFAMPPSS HMPHMINPIG IPQPPAPPLP PQPPAEEQPP PPDEPEPKRQ + RTDDGSLIPA EQFLAQHQGP ASISVSVPNL DEGNLRGQVL QIPVQSLSDT + VGSLKEQIAG ELQLPANKQK LSVRTSFLKD NLTLAYYNVG PGVVINLTLR + ERGGRKK + + + + + +GRMZM2G431306_P03 NP_001169587 hypothetical protein LOC100383468 seq=translation; coord=3:39473215..39476212:-1; parent_transcript=GRMZM2G431306_T03; parent_gene=GRMZM2G431306 + + + MPAAMGTPIL TLPAPDGNGT GGGDANQQLL QAPPKPPPPG AKTDPPATVA + THTRTIGIIH PPPDIRVIIE KTATFVAKNG PEFERRIISL NQGNAKFNFL + QPSDPYHAYY QHRVSEIAAT PPSADGLSGA ETDTAPAEAP ASTPADGAAA + VPADGAAVDT KADHSAPFRV VPPPKVLVPP KAELYTVRLP EGITGEELDI + IKLTAQFVAR NGKNFLTSLA QRESNNMQFH FIRPTHSMFP FFTELTDAYS + RVLRPAEGVP ALLKELREGS KDLTTVLERC LNRLEWDRSQ EQARQQAEDE + VEQERMQMSM IDWHDFVVVE TIEFADDEYE GLPVPLTLEE LKRQKRMENL + GEEEAMDLTE PAKEVEMEMD EEEMQLVEEG MRAAQLEEND GGSQVNVAGD + DETPMRIVKN YKRPEERIPA ERDPTKFVVS PITGELIPIS EMEEHMRISL + IDPKYKEQKE RMLAKIKETT LAPDDEISRN IVGLARTRPD IFGTTEEEVS + NAVKAEIEKK KDEQPKQVIW DGHSGSIGRT ATHALSQIQG GEEQFDASNV + DGRPVPGPAP LVRPGMPLPR PPQPLPLVNV PRFIAPPAPY SVPPPGSHMP + GVPQMMPHMH LHPQQIPGQP PMVRMPGQMV HMPTSIPPPP GQTQFMPGPP + PHTFAMPPSS HMPHMINPIG IPQPPAPPLP PQPPAEEQPP PPDEPEPKRQ + RTDDGSLIPA EQFLAQHQGP ASISVSVPNL DEGNLRGQVL QIPVQSLSDT + VGSLKEQIAG ELQLPANKQK LSVRTSFLKD NLTLAYYNVG PGVVINLTLR + ERGGRKK + + + + + + +6.81355 +-0.316909 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +7789 7789 7789 7755 7648 7165 6694 6148 5433 3930 2732 1378 663 282 124 74 33 16 6 3 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7795 7795 7795 7761 7654 7166 6684 6008 5128 3367 1869 535 95 7 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2646 3169 1509 388 69 14 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1462 3252 2112 806 135 23 4 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2864 (charge 3) + +1266.64 +3 + + +154.086 155.081 155.118 157.097 157.109 157.134 158.092 159.076 159.09 167.081 167.118 169.097 169.133 171.076 171.113 173.055 173.092 173.128 175.071 175.119 176.122 183.113 183.149 185.092 186.123 187.107 189.087 194.128 195.113 197.128 +199.071 199.108 200.139 201.123 204.134 207.115 210.088 212.103 217.082 218.152 226.154 228.097 232.139 235.118 237.135 240.135 242.149 244.166 252.133 254.153 258.144 266.148 270.144 272.172 276.167 280.169 283.176 293.159 299.133 304.948 +309.198 311.171 313.186 318.51 337.187 346.969 350.148 351.203 358.174 360.223 367.199 380.228 382.209 386.212 395.197 396.198 398.207 400.219 408.227 413.222 416.222 428.737 431.258 468.256 475.223 476.727 479.261 497.266 514.274 525.783 +528.313 585.308 602.233 625.368 680.351 684.378 699.285 785.426 856.46 953.517 + + + + +8 16 10 7 7 12 23 22 5 9 7 63 8 59 43 8 14 28 5 100 5 12 15 17 11 8 40 15 17 10 +5 11 5 11 4 10 11 16 27 6 14 25 4 8 4 32 12 9 15 4 9 16 22 59 17 10 11 9 10 4 +9 36 17 12 17 9 34 17 7 12 9 7 15 32 14 10 11 9 17 21 10 9 10 10 14 20 9 10 22 8 +40 55 38 40 4 24 18 44 24 18 + + + + + + +GRMZM5G834758_P02 P27347 DNA-binding protein MNB1B (HMG1-like protein) seq=translation; coord=5:63800401..63802605:-1; parent_transcript=GRMZM5G834758_T02; parent_gene=GRMZM5G834758 + + + MKGAKSKGAA KADAKLAVKS KGAEKPAKGR KGKAGKDPNK PKRAPSAFFV + FMEEFRKEFK EKNPKNKSVA AVGKAAGDRW KSLSESDKAP YVAKANKLKL + EYNKAIAAYN KGESTAAKKA PAKEEEEEDE EESDKSKSEV NDEDDEEGSE + EDEDDDE + + + + + +GRMZM5G834758_P03 P27347 DNA-binding protein MNB1B (HMG1-like protein) seq=translation; coord=5:63800401..63802605:-1; parent_transcript=GRMZM5G834758_T03; parent_gene=GRMZM5G834758 + + + MKGAKSKGAA KADAKLAVKS KGAEKPAKGR KGKAGKDPNK PKRAPSAFFV + FMEEFRKEFK EKNPKNKSVA AVGKAAGDRW KSLSESDKAP YVAKANKLKL + EYNKAIAAYN KGESTAAKKA PAKEEEEEDE EESDKSKSEV NDEDDEEGSE + EVYKIYSCLL HIFSLDKIPI NPGYIACSCI KQVAKFIFDH NVDLVVLYWI + PSMQNICRFA YATLFCKSSI + + + + + + +5.6249 +-0.288456 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +7383 7383 7383 7042 6813 6082 5678 3812 2987 1475 883 535 367 185 117 24 6 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7339 7339 7339 6998 6757 5978 5519 3437 2385 916 487 255 159 1 0 + + + + + + +0 1 2 3 4 + + + + +3433 3224 670 68 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1798 4490 949 125 23 0 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2867 (charge 2) + +1394.73 +2 + + +152.056 154.61 155.081 157.108 157.133 158.092 158.137 159.076 169.097 171.076 175.119 181.097 185.092 185.128 186.133 187.071 189.087 197.13 200.139 207.112 209.103 212.104 215.139 218.15 226.118 227.102 234.145 243.143 256.165 275.103 +278.114 286.141 289.187 292.128 299.207 302.134 306.143 310.169 327.203 331.161 333.187 335.56 363.198 374.206 375.723 377.953 390.232 411.191 418.203 462.232 473.214 477.268 482.226 488.181 517.235 573.323 606.304 645.318 663.33 687.817 +690.331 696.823 717.321 729.35 734.346 747.358 791.421 857.407 888.442 893.449 905.454 972.44 1068.53 1106.01 1133.51 1139.55 1210.59 + + + + +3 2 4 3 100 4 4 4 3 6 29 13 3 84 3 11 14 5 4 5 12 3 30 23 12 5 4 11 67 3 +4 3 11 3 9 4 6 13 14 3 9 2 4 3 3 3 6 4 5 4 3 17 14 3 3 5 6 9 37 17 +3 47 4 10 5 5 14 5 3 5 13 5 11 3 5 12 10 + + + + + + +GRMZM2G019876_P01 seq=translation; coord=2:18003198..18004791:-1; parent_transcript=GRMZM2G019876_T01; parent_gene=GRMZM2G019876 + + + MAEAANEEDA KRTGLEGTGL PLQGGSHGNL RSAGSDQQLR QMLDSLKSSK + SPAVINYGAS WCRVCSQILP SFCKCSDKFK KLTFIYVDID ECPETTQNIR + YTPTFHFYRD GERVDEMLGA GEERLHDRLW LHS + + + + + + + +5.9158 +-0.319773 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +3614 3614 3614 3555 3422 3181 2862 2672 1720 1022 493 261 115 57 22 11 6 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3619 3619 3619 3560 3427 3162 2841 2589 1301 661 150 69 10 1 0 + + + + + + +0 1 2 3 4 + + + + +2083 1315 202 19 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +679 2075 692 143 23 3 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2868 (charge 2) + +1245.57 +2 + + +152.057 155.081 157.061 157.097 159.076 159.113 167.081 169.096 169.133 171.077 171.112 172.117 173.092 173.128 175.119 181.097 185.092 186.124 187.108 189.087 197.128 199.108 201.086 204.134 212.103 217.082 226.154 228.098 230.113 239.114 +240.135 243.097 244.164 249.098 262.14 264.133 267.109 274.103 286.138 289.189 299.136 306.156 311.172 314.135 324.166 327.167 349.172 366.176 374.251 382.208 398.204 417.256 448.237 489.278 528.314 537.272 557.336 560.544 570.301 572.061 +582.305 590.815 595.563 597.305 599.352 601.562 606.305 608.569 612.828 618.318 619.832 624.337 671.347 699.342 701.33 717.695 720.357 726.416 729.343 732.373 747.363 757.413 770.411 772.389 781.385 786.728 791.408 796.398 798.402 801.405 +832.448 844.376 861.413 869.482 889.468 897.471 915.421 932.446 990.519 1003.48 + + + + +10 14 10 12 35 12 11 9 5 9 48 8 16 4 43 11 11 6 5 5 5 13 17 6 10 13 20 13 6 21 +21 53 10 6 12 5 21 11 5 4 4 13 14 29 22 5 19 4 17 10 4 4 4 4 21 4 11 26 4 4 +4 20 5 12 4 100 4 22 27 11 4 5 9 37 4 4 10 21 5 12 16 5 12 16 12 58 6 5 33 6 +4 10 20 14 10 9 5 19 14 10 + + + + + + +GRMZM5G834758_P02 P27347 DNA-binding protein MNB1B (HMG1-like protein) seq=translation; coord=5:63800401..63802605:-1; parent_transcript=GRMZM5G834758_T02; parent_gene=GRMZM5G834758 + + + + + + + +GRMZM5G834758_P03 P27347 DNA-binding protein MNB1B (HMG1-like protein) seq=translation; coord=5:63800401..63802605:-1; parent_transcript=GRMZM5G834758_T03; parent_gene=GRMZM5G834758 + + + + + + + + +5.78921 +-0.31293 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +8977 8977 8841 8524 8147 7482 6302 4760 2932 1808 1088 604 229 105 43 14 6 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8981 8981 8845 8528 8122 7409 6012 4088 2155 881 393 104 10 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2795 3651 1854 507 147 43 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1685 4512 2036 551 183 14 6 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2871 (charge 3) + +1394.73 +3 + + +155.081 155.118 157.098 157.133 158.092 158.137 159.076 163.133 166.062 167.055 169.097 169.133 170.117 171.076 171.149 173.092 173.128 175.119 176.107 181.11 183.113 185.092 185.128 187.071 189.087 192.077 195.088 197.128 198.13 199.107 +201.123 204.134 207.112 209.105 213.086 215.139 218.15 221.128 226.118 227.102 232.141 234.144 235.118 243.142 245.075 256.166 266.161 270.96 278.115 287.975 290.985 296.134 300.119 304.947 309.669 322.958 328.113 333.188 347.228 360.028 +361.026 363.023 365.154 383.163 389.19 401.212 404.17 417.707 431.086 444.221 453.24 460.211 462.219 473.222 477.267 482.228 485.273 518.239 526.253 531.229 534.767 539.741 566.256 569.306 573.326 575.259 588.282 599.332 601.305 603.263 +606.308 645.321 663.33 704.314 716.328 768.43 782.293 791.426 817.379 905.475 + + + + +3 2 4 100 7 8 9 12 3 3 2 3 3 3 3 4 9 18 7 3 2 4 23 9 2 2 3 31 3 4 +4 4 9 10 4 23 14 3 9 8 3 4 3 4 4 3 3 7 6 6 2 4 3 22 16 18 2 7 3 4 +18 4 5 6 4 2 3 8 3 3 3 3 5 6 8 16 4 2 2 2 3 13 3 3 8 20 2 3 3 3 +4 3 19 2 3 5 4 7 4 5 + + + + + + +GRMZM5G861390_P01 P05494 ATP synthase subunit alpha, mitochondrial seq=translation; coord=Mt:523288..525296:-1; parent_transcript=GRMZM5G861390_T01; parent_gene=GRMZM5G861390 + + + MEFSPRAAEL TTLLESRMIN FYTNLKVDEI GRVVSVGDGI ARVYGLNEIQ + AGEMVEFASG VKGIALNLEN ENVGIVVFGS DTAIKEGDLV KRTGSIVDVP + AGKAMLGRVV DALGVPIDGK GALSDHERRR VEVKAPGIIE RKSVHEPMQT + GLKAVDSLVP IGRGQRELII GDRQTGKTAI AIDTILNQKQ MNSRGTNESE + TLYCVYVAIG QKRSTVAQLV QILSEANALE YSMLVAATAS DPAPLQFLAP + YSGCAMGEYF RDNGMHALII YDDLSKQAVA YRQMSLLLRR PPGREAFPGD + VFYLHSRLLE RAAKRSDQTG AGSLTALPVI ETQAGDVSAY IPTNVISITD + GQICLETELF YRGIRPAINV GLSVSRVGSA AQLKAMKQVC GSSKLELAQY + REVAAFAQFG SDLDAATQAL LNRGARLTEV PKQPQYEPLP IEKQIVVIYA + AVNGFCDRMP LDRISQYEKN ILSTINPELL KSFLEKGGLT NERKMEPDAS + LKESALNL + + + + + + +GRMZM5G829375_P01 P05494 ATP synthase subunit alpha, mitochondrial seq=translation; coord=Mt:454351..456359:-1; parent_transcript=GRMZM5G829375_T01; parent_gene=GRMZM5G829375 + + + MEFSPRAAEL TTLLESRMIN FYTNLKVDEI GRVVSVGDGI ARVYGLNEIQ + AGEMVEFASG VKGIALNLEN ENVGIVVFGS DTAIKEGDLV KRTGSIVDVP + AGKAMLGRVV DALGVPIDGK GALSDHERRR VEVKAPGIIE RKSVHEPMQT + GLKAVDSLVP IGRGQRELII GDRQTGKTAI AIDTILNQKQ MNSRGTNESE + TLYCVYVAIG QKRSTVAQLV QILSEANALE YSMLVAATAS DPAPLQFLAP + YSGCAMGEYF RDNGMHALII YDDLSKQAVA YRQMSLLLRR PPGREAFPGD + VFYLHSRLLE RAAKRSDQTG AGSLTALPVI ETQAGDVSAY IPTNVISITD + GQICLETELF YRGIRPAINV GLSVSRVGSA AQLKAMKQVC GSSKLELAQY + REVAAFAQFG SDLDAATQAL LNRGARLTEV PKQPQYEPLP IEKQIVVIYA + AVNGFCDRMP LDRISQYEKN ILSTINPELL KSFLEKGGLT NERKMEPDAS + LKESALNL + + + + + + +GRMZM5G845063_P01 seq=translation; coord=3:74659634..74660746:1; parent_transcript=GRMZM5G845063_T01; parent_gene=GRMZM5G845063 + + + MEFSPRAAEL TTLLESRMIN FYTNLKVDEI GRVVSVGDGI ARVYGLNEIQ + AGEMVEFASG VKGIALNLEN ENVGIVVFGS DTAIKEGDLV KRTGSIVDVP + AGKAMLGRVV DALGVPIDGK GALSDHEQRR VEVKAPGIIE RKSVHEPMQT + GLKAVDSLVP IGRGQRELII GDRQTGKIAI AIDTILNQKQ MNSRGTNESE + TLYCVYVAIG + + + + + + + +7.9519 +-0.429833 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +7363 7363 7363 7158 6844 6302 5069 3823 2468 1417 694 271 105 40 3 2 2 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +7366 7366 7366 7161 6842 6243 4905 3233 1491 367 79 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2309 3022 1463 503 67 3 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1199 3346 1968 670 173 13 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2872 (charge 3) + +1242.61 +3 + + +153.102 155.081 157.108 157.133 158.092 159.078 159.091 159.113 160.117 166.061 167.082 169.097 171.113 173.092 173.128 175.119 181.097 183.149 184.108 185.091 186.124 187.107 194.093 195.076 197.129 198.124 199.108 201.123 204.134 209.091 +212.103 213.087 221.103 226.119 230.114 232.616 237.135 239.114 242.186 244.166 249.098 252.632 256.145 260.197 267.108 269.126 275.635 284.138 287.136 294.15 299.139 303.154 306.156 309.203 317.217 318.222 320.169 324.166 326.169 346.15 +347.154 349.17 357.25 362.182 364.161 366.178 382.209 394.172 401.217 418.267 425.214 435.198 438.645 447.2 453.21 456.051 464.23 467.456 470.242 488.261 491.226 501.24 505.235 511.289 513.348 515.026 529.299 530.3 532.287 536.786 +546.327 550.262 558.801 570.304 573.053 612.331 629.361 633.299 709.387 726.415 + + + + +3 4 3 3 5 8 4 100 8 5 4 4 5 4 15 19 17 7 3 4 3 13 5 4 4 3 4 3 5 3 +7 3 8 5 4 4 12 21 3 4 18 6 3 12 42 5 10 3 3 3 3 9 15 7 21 4 3 25 6 15 +3 3 5 3 5 5 4 4 3 18 3 11 5 5 20 4 4 3 3 3 6 4 3 5 4 3 17 6 3 6 +5 11 4 3 4 3 3 3 4 8 + + + + + + +GRMZM2G059083_P01 NP_001104851 ferredoxin seq=translation; coord=3:147290518..147292751:-1; parent_transcript=GRMZM2G059083_T01; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P03 NP_001104851 ferredoxin seq=translation; coord=3:147290712..147292701:-1; parent_transcript=GRMZM2G059083_T03; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P04 NP_001104851 ferredoxin seq=translation; coord=3:147286676..147292683:-1; parent_transcript=GRMZM2G059083_T04; parent_gene=GRMZM2G059083 + + + + + + + +GRMZM2G059083_P02 NP_001104851 ferredoxin seq=translation; coord=3:147290527..147292751:-1; parent_transcript=GRMZM2G059083_T02; parent_gene=GRMZM2G059083 + + + + + + + + +6.90563 +-0.354135 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +8743 8743 8743 8743 8185 7668 6583 5068 3567 2126 1068 479 186 69 22 9 6 5 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8750 8750 8750 8750 8192 7675 6538 4813 2888 1450 482 123 23 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3275 3751 1339 336 46 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1400 4586 2051 659 48 3 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2879 (charge 3) + +1489.77 +3 + + +155.082 157.097 158.093 159.077 159.113 161.092 166.061 167.082 169.097 169.134 171.077 171.113 173.092 173.129 175.107 175.119 181.095 183.149 185.092 185.165 186.124 187.108 187.127 189.087 191.085 192.09 193.081 195.112 197.129 199.108 +201.087 204.134 205.138 213.087 219.079 223.155 226.155 227.102 231.098 235.121 240.135 244.165 251.15 253.093 257.198 272.124 275.208 281.672 303.203 305.207 314.133 325.224 331.679 339.14 346.184 352.707 366.18 368.14 400.267 423.692 +426.173 427.173 432.695 453.211 455.175 456.176 466.705 467.207 471.329 476.211 480.215 482.233 495.833 498.267 512.251 540.265 541.267 565.299 568.249 569.259 585.304 594.372 648.381 649.381 671.408 677.339 691.425 699.389 705.312 706.316 +748.362 785.44 786.439 788.471 800.453 871.494 932.406 933.405 972.537 1101.58 + + + + +9 10 7 10 26 7 10 9 18 11 10 7 15 9 7 31 10 7 24 9 28 39 11 7 30 9 16 8 15 8 +16 100 35 18 9 9 19 11 14 8 7 9 11 13 7 14 25 7 29 8 12 19 13 8 11 12 8 9 10 11 +12 12 8 8 14 10 18 23 53 12 7 13 10 46 8 11 10 14 14 9 10 30 10 7 21 10 8 7 11 12 +7 15 14 7 17 13 7 11 17 8 + + + + + + +GRMZM2G314647_P01 NP_001151777 dynamin-related protein 1A seq=translation; coord=8:66662443..66672048:-1; parent_transcript=GRMZM2G314647_T01; parent_gene=GRMZM2G314647 + + + MDNLITLVNK LQRACTALGD HGEESALPTL WDSLPAIAVV GGQSSGKSSV + LESVVGKDFL PRGSGIVTRR PLVLQLHRID GDREYAEFMH LPRKRFTDFA + AVRKEIADET DRETGRSKQI SPVPIHLSIF SPYVVNLTLI DLPGLTKVAV + EGQPENIVQD IENMVRSYIE KPNCIILAVS PANQDLATSD AIKISREVDP + KGERTFGVLT KIDLMDKGTD AVDILEGRSY RLQTPWVGVV NRSQQDINKN + VDMIAARRRE REYFATTPEY KHMASRMGSE YLGKMLSKHL EQVIKSRIPG + IQSLITKTIA ELETELNRLG KPIANDAGGK LYTIMEICRM FDSIYKEHLD + GVRPGGEKVY HVFDNQFPVA IKRLQFDKQL SMENVKKLIT EADGYQPHLI + APEQGYRRLI ESCLISIRGP AEAAVDAVHA ILKDLVRKAI NETHELKQFP + TLRVEVGNAA FESLDRMRDE SKKNTLKLVD MECSYLTVDF FRKLPQDVER + GGNPSHSIFD RYNDSYLRRI GQTVLSYVNM VCSTLRNSIP KSIVYCQVRE + AKRSLLDHFF TELGAREMKQ LSKLLDEDPA VMERRTNLAK RLELYRSAQS + EIDAVAWSK + + + + + +GRMZM2G149717_P01 B8A3F5 Putative uncharacterized protein seq=translation; coord=6:163428972..163435944:-1; parent_transcript=GRMZM2G149717_T01; parent_gene=GRMZM2G149717 + + + MDNLITLVNK LQRACTALGD HGEESALPTL WDSLPAIAVV GGQVPFFPSR + ARFFALVLIG SGAVAPASWV WISRVAGGTA RSSGKSSVLE SVVGKDFLPR + GSGIVTRRPL VLQLHRIDGD REYAEFMHLP RKRFTDFAAV RKEIADETDR + ETGRSKQIST VPIHLSIFSP HGKMQTLEGY IVTVALSHLN CPLPIVNLTL + IDLPGLTKVA VDGQPESIVH DIENMVRSYI EKKCTVVDSG ERTFGVLTKI + DLMDKGTDAV DILEGRSYRL QTPWVGVVNR SQQDINKNVD MIAARRRERE + YFASTPEYKH MASRMGSEYL GKMLSKHLEQ VIKSRIPGIQ SLITKTIAEL + ETELNRLGKP IANDAGGKLY TIMEICRMFD GIYKEHLDGV RPGGEKVYHV + FDNQFPVAIK RLQFDKQLSM ENVRKLITEA DGYQPHLIAP EQGYRRLIES + CLISIRGPAE AAVDAVHAIL KDLVRKAINE THELKQFPTL RVEVGNAAFE + SLDRMRDESK KNTLKLVDME CSYLTVDFFR KLPQDVEKGG NPSHSIFDRY + NDSYLRRIGQ TVLSYVNMVC STLRNSIPKS IVYCQVREAK RSLLDHFFTE + LGAREMKQLS KLLDEDPAVM ERRTNLAKRL ELYRSAQSEI DAVAWSK + + + + + + +5.11407 +-0.276436 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +5205 5205 5205 5080 4844 4536 4106 3502 2752 1871 1115 605 300 122 74 38 15 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5215 5215 5215 5090 4853 4533 4059 3391 2400 1305 641 244 58 19 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1709 2167 1029 266 24 21 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +945 2395 1324 429 105 8 0 11 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2882 (charge 3) + +1391.64 +3 + + +157.098 157.134 158.092 158.137 159.076 159.092 167.056 168.055 169.052 169.134 170.117 171.077 171.149 173.092 173.129 175.119 176.107 177.111 181.061 183.113 185.092 185.129 186.091 187.072 189.087 197.129 198.133 199.071 200.139 201.123 +204.135 207.113 209.089 213.087 215.139 217.082 221.129 223.064 226.119 232.14 237.136 239.114 243.142 245.076 249.123 256.166 270.959 278.113 287.975 290.986 300.166 301.158 304.948 309.67 322.958 329.997 333.188 346.97 360.029 361.026 +363.199 367.183 389.195 401.213 407.216 415.726 417.707 430.091 431.087 444.215 453.24 460.214 462.267 473.223 474.224 477.269 482.229 518.238 531.228 539.742 566.257 569.304 574.283 575.26 599.328 601.308 606.299 663.331 700.377 716.33 +774.369 782.294 789.343 791.431 814.425 817.38 905.479 928.445 946.422 1043.48 + + + + +4 100 16 5 18 4 16 4 3 5 7 8 7 5 4 42 35 3 4 5 10 27 5 19 6 80 9 4 4 5 +7 8 5 4 64 17 16 7 11 8 4 3 4 8 3 4 13 6 12 5 5 4 47 47 40 5 18 7 47 67 +20 5 6 3 3 4 24 9 11 4 4 4 15 18 5 7 57 4 6 36 6 5 5 56 14 7 4 23 7 8 +3 10 3 8 5 9 6 4 3 4 + + + + + + +GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01; parent_gene=GRMZM5G815453 + + + + + + + +GRMZM2G448344_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=1:203925927..203931405:-1; parent_transcript=GRMZM2G448344_T01; parent_gene=GRMZM2G448344 + + + + + + + +GRMZM2G385635_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=2:200096578..200100853:-1; parent_transcript=GRMZM2G385635_T01; parent_gene=GRMZM2G385635 + + + + + + + +GRMZM2G360821_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=6:160783975..160786062:1; parent_transcript=GRMZM2G360821_T01; parent_gene=GRMZM2G360821 + + + + + + + +GRMZM2G308907_P01 seq=translation; coord=9:32379686..32380603:1; parent_transcript=GRMZM2G308907_T01; parent_gene=GRMZM2G308907 + + + + + + + +GRMZM2G115168_P01 seq=translation; coord=1:131325136..131327527:1; parent_transcript=GRMZM2G115168_T01; parent_gene=GRMZM2G115168 + + + + + + + + +5.50872 +-0.297769 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +8796 8796 8796 8548 8162 7512 6872 5345 4173 2241 1222 580 292 151 82 32 19 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +8797 8797 8797 8549 8163 7472 6692 4864 3070 1008 306 74 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2753 3566 1601 667 172 39 4 7 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1644 4082 2246 642 147 35 6 7 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2883 (charge 3) + +1350.68 +3 + + +150.066 155.082 155.118 156.077 157.061 157.097 158.092 159.076 166.062 169.097 171.15 173.128 175.119 177.102 180.076 181.097 183.113 184.072 185.165 186.124 187.108 194.129 199.108 200.103 202.082 204.134 213.16 214.118 223.156 225.098 +228.098 240.134 244.166 246.109 251.15 253.093 258.144 267.134 272.171 292.103 295.145 299.172 303.203 310.115 327.166 329.657 339.138 345.177 347.203 352.659 365.157 367.136 370.197 381.168 383.168 387.167 394.176 402.273 415.681 422.688 +426.172 428.736 431.695 436.157 452.224 454.168 458.222 461.212 464.225 466.206 467.732 475.204 477.244 480.221 482.235 485.757 501.741 503.314 521.245 532.269 539.257 561.263 567.252 581.305 589.287 617.279 647.375 686.295 690.301 702.362 +704.307 766.421 784.431 787.344 803.391 844.371 862.381 931.398 943.432 961.44 + + + + +4 4 5 8 5 5 8 8 6 12 6 10 26 4 4 4 4 5 18 32 14 7 5 4 9 100 6 3 16 13 +10 12 5 8 14 11 6 4 5 8 10 5 38 26 12 5 16 6 4 10 7 19 4 5 5 5 8 6 6 16 +11 3 8 4 13 13 6 4 6 21 4 5 5 14 10 5 4 4 4 4 7 11 8 5 7 8 12 4 15 6 +8 5 14 6 4 6 4 6 6 5 + + + + + + +GRMZM2G050325_P01 NP_001151420 LOC100285053 seq=translation; coord=8:3921705..3924577:1; parent_transcript=GRMZM2G050325_T01; parent_gene=GRMZM2G050325 + + + MGKDGIQYAV VDAFTAEPFK GNPAAVCLLE DAAKAADERW MQSVAAEFNI + SETAFLLREK SSAAGAVPLF QLRWFTPVAE VELCGHATLA SAHFLFTSVL + AEHEKLVEFS TKSGILTAKK VPAPQSTGVS GEGKLFIELD FPTIDLVDCH + PSELPAIPDT LNGASIVSVH KSTTAGDLIV ELSSGKEVAD IIPNIHEIEK + CSGRGIIVTG PAPAGSGYDF FTRFFCPKFG IDEDPVCGSA HCVLAPYWGG + KLGKHKLIAF QASPRSGILY LELEATGRRV RIQGEAVSVM TGTLLA + + + + + +GRMZM2G050325_P02 NP_001151420 LOC100285053 seq=translation; coord=8:3921712..3924577:1; parent_transcript=GRMZM2G050325_T02; parent_gene=GRMZM2G050325 + + + MQSVAAEFNI SETAFLLREK SSAAGAVPLF QLRWFTPVAE VELCGHATLA + SAHFLFTSVL AEHEKLVEFS TKSGILTAKK VPAPQSTGVS GEGKLFIELD + FPTIDLVDCH PSELPAIPDT LNGASIVSVH KSTTAGDLIV ELSSGKEVAD + IIPNIHEIEK CSGRGIIVTG PAPAGSGYDF FTRFFCPKFG IDEDPVCGSA + HCVLAPYWGG KLGKHKLIAF QASPRSGILY LELEATGRRV RIQGEAVSVM + TGTLLA + + + + + +GRMZM2G050325_P03 NP_001151420 LOC100285053 seq=translation; coord=8:3921712..3923926:1; parent_transcript=GRMZM2G050325_T03; parent_gene=GRMZM2G050325 + + + MQSVAAEFNI SETAFLLREK SSAAGAVPLF QLRWFTPVAE VELCGHATLA + SAHFLFTSVL AEHEKLVEFS TKSGILTAKK VPAPQSTGVS GEGKLFIELD + FPTIDLVDCH PSELPAIPDT LNGASIVSVH KSTTAGDLIV ELSSGKEVAD + IIPNIHEIEK CSGRGIIVTG PAPAGSGYDF FTRFFCPKFG IDEDPVCGSA + HCVLAPYWGG KLGKHKLIAF QVRFCTTLGL VRLHLDS + + + + + + +4.85825 +-0.249141 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +7051 7051 7051 6488 6050 5439 4455 3567 2599 1597 1034 613 345 184 79 38 26 22 1 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7055 7055 7055 6492 6037 5364 4261 3104 1908 802 315 132 38 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2269 2820 1371 420 126 55 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1176 3173 1990 558 139 15 3 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2885 (charge 3) + +1441.77 +3 + + +155.081 155.118 157.097 157.134 158.092 159.076 159.092 169.098 171.077 171.113 173.092 173.129 175.09 175.119 181.134 183.15 185.092 185.165 186.095 186.123 187.071 194.13 197.129 198.124 199.072 199.108 199.181 201.087 204.134 209.103 +216.099 218.15 224.103 226.119 228.135 234.145 240.135 244.165 256.129 258.108 266.151 270.108 273.138 288.117 313.153 315.168 327.132 329.183 331.199 333.188 341.218 345.14 347.193 368.265 379.234 385.175 390.199 394.209 396.261 404.215 +416.177 429.221 448.215 457.215 458.219 475.251 477.23 478.234 495.244 506.245 528.301 545.271 546.274 556.285 559.268 562.284 576.297 599.327 600.329 616.309 627.319 633.319 637.311 655.305 670.368 673.315 691.325 698.359 705.44 734.37 +745.347 762.364 768.352 799.413 816.388 821.403 827.403 833.401 853.382 990.443 + + + + +6 3 7 4 5 7 4 10 4 4 16 3 3 20 3 5 100 3 2 6 10 3 4 4 4 5 4 21 19 4 +4 31 3 17 13 5 5 5 26 9 3 7 10 3 4 3 5 5 3 23 3 5 4 3 3 3 7 3 16 23 +3 4 8 16 4 18 17 5 3 4 5 18 7 15 3 66 3 8 3 10 15 10 3 3 7 19 56 10 4 5 +6 33 3 7 4 6 10 10 3 3 + + + + + + +GRMZM2G351125_P01 seq=translation; coord=UNKNOWN:5070241..5074601:-1; parent_transcript=GRMZM2G351125_T01; parent_gene=GRMZM2G351125 + + + MATTSDAAPV APVEEESTSP AAAEEEPPKK VEASMATTDV APVAPAPVED + ENLASAAAEE SPSKKVEAAA AQEEVEEVVE APKKVVAGGG EEEEVRLEGI + DEGFGGPEAE NGQAKGVGGG YDSGDVKEAD AEDKGGNLGP TEAEAETDDG + GEEPASGDGE TPASLAAPMP VVESKSENAE LGDGDPSLVF LDALEGDEMG + ELREEQDEDT GASVEVKVVD KVADDAEPPV TEEEKLEPEV EKGEEVGPRS + GDGGELSNEK EVEVFSLREE AVEPQDMVAH VSEANGELGD EKEASDDVVV + LGVEEAPEEP SNKDTDGDEV LVLGGKEAPE ESTKKDDDVE DEATKPEPMS + EASPVVSQHP QSDLVASSLD VGGDVNNANV TLTQVLNDGS IEELAPASAD + SVLEDSLEKE QNAENLATAS EAVEDVGAEV ENVAAPSVDG ILSRELAPES + INENNGADEI EGATEVVDRE EEVAYNDIIE AVPDDEDGID NEADDDNDGA + NSNTSPARVA ILESSEAAKQ IMKELTEGSS SGNVSRDFTN SMDGQIMLDD + SEDDDDGDEK EFDSAALAAL LKAATGGSSD GNVTVASQDG SRIFTMDRPA + GLGSSAPSLR PTAPRQPARS NLFSPSELAV TADPTEEMTE EEKKLHDKVE + LIRVKFLRLV YRLGATPEET VAAQVLYRLS LAEGIRHGRQ TNRAFSLDNA + RRKALLLEAE GKEDLNFSCN ILVLGKTGVG KSATINSVFG EEKSKTDAFS + SATTNVREII GDVDGVKIRI IDTPGLRPNV MDQGSNRKIL AAVKKYTKKC + PPDIVLYVDR LDSLSRDLND LPLLKTITSV LGSSIWFNAI VALTHAASAP + PEGLNGAPMT YEVLMAQRSH IIQQSIRQAA GDMRLMNPVA LVENHPSCRK + NREGQKVLPN GQSWRHQMLL LCYSSKILSE ANSLLKLQDP NPGKLFGFRF + RSPPLPFLLS SLLQSRAHPK LSAEQGGNEG DSDIELDDYS DVEQDDEEEE + YDQLPPFKPL TKAQLARLTK EQKNAYFDEY DYRVKLLQKK QWKDEIRRLK + EMKKRGKTDL DDYGYANITG EDDQDPPPEN VSVPLPDMVL PPSFDCDNPT + YRYRFLEPTS TVLARPVLDA HGWDHDCGYD GVSVEETLAI LSRFPANVAV + QVTKDKKEFS IHLDSSIAAK HGENTSSLAG FDIQTVGRQL AYILRGETKI + KNIKKNKTTG GFSVTFLGDI VATGLKIEDQ LSLGKRLSLV ASTGAMRAQG + DTAYGANLEA RLKDKDYPIA QSLSTLGLSL MKWRRDLALG ANLQSQFSIG + RGSKMAVRLG LNNKLSGQIT VRTSTSEQVQ IALLGLVPVA ASIYRSFRPS + EPSFAY + + + + + + +5.74025 +-0.294372 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +5601 5601 5570 5326 5081 4630 4298 3985 2860 2153 1231 732 387 208 112 31 12 6 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5588 5588 5557 5313 5064 4583 4207 3743 2177 1439 506 154 38 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2768 2252 499 77 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +920 3158 1069 405 47 3 1 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2886 (charge 2) + +1322.62 +2 + + +152.057 157.061 158.092 159.077 167.082 168.066 169.061 169.098 170.117 171.076 171.113 175.071 175.119 176.122 181.061 185.056 185.092 185.165 187.071 187.144 189.087 195.089 195.112 197.129 199.072 199.108 201.088 203.103 207.113 213.087 +215.139 225.123 227.102 231.098 234.145 240.134 243.134 248.159 256.094 259.102 262.151 266.15 270.108 273.18 280.165 288.119 298.178 308.161 326.171 327.172 332.16 344.184 346.181 361.219 366.213 370.175 391.196 397.209 401.218 409.211 +419.191 429.212 437.204 455.21 468.243 475.264 494.231 495.752 516.244 528.328 532.288 534.257 545.351 565.3 576.236 599.268 603.791 612.34 614.79 616.327 619.317 644.34 652.295 663.352 703.361 706.349 793.38 829.412 832.397 850.402 +852.408 961.437 973.473 979.447 981.452 1036.47 1053.53 1062.48 1080.49 1082.49 + + + + +3 6 6 3 3 5 2 10 3 3 7 9 45 2 2 3 11 2 9 3 2 2 6 29 6 9 3 32 3 14 +96 25 5 29 7 3 31 3 6 3 20 10 7 10 3 9 3 14 26 3 7 6 5 3 16 2 3 9 8 3 +2 13 10 2 3 3 4 8 3 3 17 17 3 21 3 2 12 2 3 6 25 11 3 16 3 42 34 2 11 100 +10 11 3 31 2 3 6 2 28 7 + + + + + + +GRMZM2G030167_P01 NP_001141326 hypothetical protein LOC100273417 seq=translation; coord=8:148264071..148273363:1; parent_transcript=GRMZM2G030167_T01; parent_gene=GRMZM2G030167 + + + MNDADVSKQI QQMVRFIRQE ADEKANEISV SAEEEFNIEK LQLVEAEKKK + IRQEYERKEK QVEVRKKIEY SMQLNASRIK VLQAQDDLVN KMKDDAMKEL + LLVSHNHHEY KNLLKDLIIQ GLLRLKEPAV LLRCRKDDHH HVESVLHSAK + HEYASKADVH EPEIFVDHDV YLPPAPSHHD AHGQFCSGGI VLASRDGKIV + FESTLDARLE VVFRKKLPEI RKLLFGQTAA + + + + + + +6.00466 +-0.387397 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +9735 9735 9581 9034 8025 5893 4182 2100 824 446 162 54 20 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 + + + + +9739 9739 9585 9026 7964 5536 3397 1051 186 53 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3411 4054 1812 364 83 12 1 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2074 4872 2238 471 73 9 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2887 (charge 3) + +1610.77 +3 + + +155.082 156.077 157.134 158.093 159.077 167.056 168.056 169.052 169.098 175.119 185.056 185.092 185.129 185.165 186.087 186.124 199.108 201.124 203.103 207.087 209.14 214.119 218.15 223.063 225.098 227.102 229.118 231.097 234.123 237.135 +239.095 241.093 244.166 247.13 251.15 253.094 258.1 270.109 272.171 275.125 281.052 296.134 299.062 301.06 302.663 305.182 307.626 316.15 321.623 338.182 344.976 346.975 350.109 357.16 359.029 361.027 368.12 394.173 401.215 408.23 +412.184 415.037 417.036 424.23 426.673 435.678 437.251 442.242 461.183 470.19 477.183 479.195 487.17 505.179 508.286 519.722 523.003 529.309 536.295 538.772 553.801 555.326 607.36 614.244 624.229 642.238 644.331 653.325 665.357 671.333 +678.396 741.435 744.365 802.43 815.451 829.419 841.435 870.478 1038.45 1169.55 + + + + +2 3 3 4 2 34 6 2 2 9 3 2 2 2 2 3 2 2 2 2 2 4 5 6 7 3 2 3 2 3 +10 2 2 2 3 2 3 2 2 8 6 2 100 28 2 8 4 2 6 2 13 4 4 3 12 6 8 4 4 2 +2 17 9 3 1 3 2 7 2 5 4 3 2 8 2 3 2 6 11 3 2 5 4 4 2 9 2 2 2 2 +6 5 2 3 2 2 2 4 2 2 + + + + + + +GRMZM2G314647_P01 NP_001151777 dynamin-related protein 1A seq=translation; coord=8:66662443..66672048:-1; parent_transcript=GRMZM2G314647_T01; parent_gene=GRMZM2G314647 + + + + + + + +GRMZM2G149717_P01 B8A3F5 Putative uncharacterized protein seq=translation; coord=6:163428972..163435944:-1; parent_transcript=GRMZM2G149717_T01; parent_gene=GRMZM2G149717 + + + + + + + + +5.86191 +-0.31686 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +4774 4774 4774 4423 4137 3886 3526 3257 2317 1784 925 426 191 87 40 17 6 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +4759 4759 4759 4408 4117 3847 3443 3146 1914 1208 485 91 51 3 2 2 1 0 + + + + + + +0 1 2 3 4 + + + + +2155 2207 401 24 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1070 2621 966 105 17 0 8 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2889 (charge 2) + +1391.64 +2 + + +155.082 157.097 157.108 157.134 158.093 159.077 167.082 167.661 169.098 171.077 175.12 176.108 181.097 183.112 185.092 185.129 187.071 189.087 197.129 199.072 199.107 204.133 213.088 215.139 218.151 221.129 226.119 227.104 232.14 240.099 +243.133 249.123 256.165 257.125 275.102 283.71 292.128 302.134 306.151 309.669 333.188 363.198 408.586 417.706 455.225 460.218 462.223 473.219 482.23 534.77 540.242 599.326 601.309 605.806 618.333 632.306 636.092 663.337 674.311 687.321 +697.328 700.374 716.329 729.353 747.374 807.35 817.388 837.264 857.403 893.454 905.472 921.448 929.447 946.412 972.452 1043.47 1061.46 1082.49 1089.48 1132.48 1144.52 + + + + +6 3 5 48 13 7 3 3 4 7 60 17 16 3 5 35 18 7 20 3 5 3 4 100 12 15 12 4 4 6 +22 4 25 5 3 3 5 6 3 55 20 16 3 20 4 4 6 7 48 5 4 10 4 4 4 11 3 11 11 50 +57 7 5 18 4 4 6 4 6 12 4 13 5 6 5 6 4 5 11 13 7 + + + + + + +GRMZM2G088196_P01 seq=translation; coord=8:136659605..136668296:-1; parent_transcript=GRMZM2G088196_T01; parent_gene=GRMZM2G088196 + + + MPGCGVAGRG GVGVSSAARP TPRRPCLWMP IARGYGRQPE LKYCTSSQSK + SVLLGAGFGR HVTRSNPYLL QNSSSTTMAR LQKSGQFQQL VLDPSRNYLT + KTFYNANMKR RVLSRVECFV SSDPINNGWL KPRRSENFTS LESACVQREY + KLPVRTRADC KAEQYEITGS PLSPSDADAV MIGDTNEISP WWQEFPKRWM + IVLLCFFAFL LCNMDRVNMS IAILPMSSEF SWSPATVGLI QSSFFWGYLL + TQILGGIWAD RFGGKLVLGF GVIWWSIATV LTPLAAKIGL PCLLTMRAFM + GIGEGVAMPA MNNILSKWIP VSERSRSLAL VYSGMYLGSV TGLALSPLLI + SRFGWPSVFY AFGSLGSVWF ALWQSKAHSS PDDDPELSKA EKRHILGGSP + LKEPVTSIPW RLILSKAPVW ALIISHFCHN WGTFILLTWM PTYYNQVLKF + NLTESGLLCV LPWLTMAVFA NIGGWIADTL VQRGISVTNV RKIMQSIGFL + GPALFLTLLS KVRTPAMAVL CMACSQGSDA FSQSGLYSNH QDIGPRYAGV + LLGLSNTAGV LAGVFGTAAT GYILQKGSWD SVFKVSVVLY IVGTVVWNVF + ATGEKVLE + + + + + +GRMZM2G046681_P01 NP_001130577 hypothetical protein LOC100191676 seq=translation; coord=3:226572521..226577418:1; parent_transcript=GRMZM2G046681_T01; parent_gene=GRMZM2G046681 + + + MPGCGVAGRG DVGVSSAARR TPPQGKSRPC LWMTIARGYG RQHELKYCTS + PQSKSLLLEA RFGRHVTRST AYLLQNSRST AMTRLQKSGK FLQPVLDSSR + NYLTSTFYNA SLKRRVLSRV ECFVSSDPIN NGWLKPRRSE NFTSLESACV + QPEYKLPVRT RADCKAEQYE ITGSPLSPSD VPADAVMIGD TNEISPWWQE + FPKRWTVVLL CFFAFLLCNM DRVNMSIAIL PMSSEFSWNP ATVGLIQSSF + FWGYLLTQIL GGIWADRFGG KVVLGFGVVW WSFATVLTPL AAKIGLPCLL + TMRAFMGIGE GVAMPAMNNI LSKWIPVSER SRSLALVYSG MYLGSVTGLS + LSPLLISRFG WPSVFYAFGS LGTVWFALWQ SKAHSSPDDD PELSKAEKRH + ILGGSALKEP VTSIPWRLIL SKAPVWALII SHFCHNWGTF ILLTWMPTYY + NQVLKFNLTE SGLLCVLPWL TMAVFANIGG WIADTLVQRG VSVTNVRKIM + QSIGFLGPAL FLTLLSKVRT PAMAVLCMAC SQGSDAFSQS GLYSNHQDIG + PRYAGVLLGL SNTAGVLAGV FGTAATGYIL QKGSWDSVFK VSVVLYIVGT + VVWNVFSTGE KILE + + + + + +GRMZM2G046681_P02 NP_001130577 hypothetical protein LOC100191676 seq=translation; coord=3:226572535..226577492:1; parent_transcript=GRMZM2G046681_T02; parent_gene=GRMZM2G046681 + + + MPGCGVAGRG DVGVSSAARR TPPQGKSRPC LWMTIARGYG RQHELKYCTS + PQSKSLLLEA RFGRHVTRST AYLLQNSRST AMTRLQKSGK FLQPVLDSSR + NYLTSTFYNA SLKRRVLSRV ECFVSSDPIN NGWLKPRRSE NFTSLESACV + QPEYKLPVRT RADCKAEQYE ITGSPLSPSD VPADAVMIGD TNEISPWWQE + FPKRWTVVLL CFFAFLLCNM DRVNMSIAIL PMSSEFSWNP ATVGLIQSSF + FWGYLLTQIL GGIWADRFGG KVVLGFGVVW WSFATVLTPL AAKIGLPCLL + TMRAFMGIGE GVAMPAMNNI LSKWIPVSER SRSLALVYSG MYLGSVTGLS + LSPLLISRFG WPSVFYAFGS LGTVWFALWQ SKAHSSPDDD PELSKAEKRH + ILGGSALKEP VTSIPWRLIL SKAPVWALII SHFCHNWGTF ILLTWMPTYY + NQVLKFNLTE SGLLCVLPWL TMAVFANIGG WIADTLVQRG VSVTNVRKIM + QSIGFLGPAL FLTLLSKVRT PAMAVLCMAC SQGSDAFSQS GLYSNHQDIG + PRYAGVLLGL SNTAGVLAGV FGTAATGYIL QKGSWDSVFK VSVVLYIVGT + VVWNVFSTGE KILE + + + + + +GRMZM2G046681_P03 NP_001130577 hypothetical protein LOC100191676 seq=translation; coord=3:226572535..226577490:1; parent_transcript=GRMZM2G046681_T03; parent_gene=GRMZM2G046681 + + + MPGCGVAGRG DVGVSSAARR TPPQGKSRPC LWMTIARGYG RQHELKYCTS + PQSKSLLLEA RFGRHVTRST AYLLQNSRST AMTRLQKSGK FLQPVLDSSR + NYLTSTFYNA SLKRRVLSRV ECFVSSDPIN NGWLKPRRSE NFTSLESACV + QPEYKLPVRT RADCKAEQYE ITGSPLSPSD VPADAVMIGD TNEISPWWQE + FPKRWTVVLL CFFAFLLCNM DRVNMSIAIL PMSSEFSWNP ATVGLIQSSF + FWGYLLTQIL GGIWADRFGG KVVLGFGVVW WSFATVLTPL AAKIGLPCLL + TMRAFMGIGE GVAMPAMNNI LSKWIPVSER SRSLALVYSG MYLGSVTGLS + LSPLLISRFG WPSVFYAFGS LGTVWFALWQ SKAHSSPDDD PELSKAEKRH + ILGGSALKEP VTSIPWRLIL SKAPVWALII SHFCHNWGTF ILLTWMPTYY + NQVATMLCCE TFDFPHYLNY IMIAYHAIGC APQILLSRF + + + + + + +4.47441 +-0.271177 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +2745 2745 2719 2597 2417 1522 1029 563 277 147 109 53 28 8 3 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +2745 2745 2719 2594 2401 1449 933 452 178 70 52 25 23 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +1748 920 77 19 0 + + + + + + +0 1 2 3 4 5 6 + + + + +425 1982 322 23 0 12 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2890 (charge 2) + +1397.62 +2 + + +152.057 155.082 156.077 157.098 157.134 164.082 166.061 171.077 173.093 175.119 181.109 182.112 185.092 185.128 189.087 192.077 195.088 199.108 201.123 207.114 209.104 213.087 216.135 225.098 227.102 234.145 240.098 246.098 248.114 256.166 +263.105 266.161 272.172 278.124 286.139 294.12 296.135 300.121 322.114 328.114 338.143 340.187 342.131 347.228 365.159 386.215 427.219 433.637 443.141 458.269 460.261 485.275 530.174 555.311 573.325 585.213 606.308 614.35 630.301 642.805 +663.322 669.24 688.343 697.826 736.253 756.271 768.429 790.271 807.289 825.303 1015.45 1189.5 + + + + +2 8 2 2 20 3 19 2 2 9 31 2 3 11 2 31 2 9 2 1 100 3 3 10 24 17 2 2 2 9 +2 2 8 13 3 3 17 2 7 7 2 13 2 17 8 3 3 2 19 2 2 3 3 3 50 3 2 6 2 2 +2 3 2 2 2 2 6 3 3 9 9 3 + + + + + + +GRMZM2G103430_P01 NP_001130564 hypothetical protein LOC100191663 seq=translation; coord=4:38181649..38185320:-1; parent_transcript=GRMZM2G103430_T01; parent_gene=GRMZM2G103430 + + + MSDRQPSEEP EEQVDLEGDD DGMDDDDAGY RRRGSRDDSE EPEEDDDNDE + RHGDADDDAG MEPEPAGSKG GDDTGKGPDV AGGGPEDEEE RSKWDDMLAL + PPHGSEVFIG GLPRDITEED LRELCEPLGE IYEVRLTKDK DTKENKGFAF + VTFMDKEAAQ RAIEDVQDRE FKGRTLRCSL SQAKHRLFVG NVPKGLSEEE + LTNTIKGKGP GVINIEMFKD QHDPNRNRGF LFVEYYNHAC ADYARQKLSS + PNFKVDGSQL TVSWAEPKGS TDASSAAAQV KTIYVKNLPE NVSKEKIKDL + FDKHGEVTKI VLPPAKAGHK RDFGFVHFAE RSSALKAVKG SEKYEIDGQV + LEVSMAKPLA DKKPDHSHRP GGGPNYPLPP YGGGGYMGDP YGAYGGGGPA + YNQPMIYGRG PAPAGMRMVP MVLPDGRLGY VLQQPGGMPP PPPPRRGSDR + RDSGRGGEGH SRRYRPY + + + + + +GRMZM2G103430_P02 NP_001130564 hypothetical protein LOC100191663 seq=translation; coord=4:38181649..38185316:-1; parent_transcript=GRMZM2G103430_T02; parent_gene=GRMZM2G103430 + + + MSDRQPSEEP EEQVDLEGDD DGMDDDDAGY RRRGSRDDSE EPEEDDDNDE + RHGDADDDAG MEPEPAGSKG GDDTGKGPDV AGGGPEDEEE RSKWDDMLAL + PPHGSEVFIG GLPRDITEED LRELCEPLGE IYEVRLTKDK DTKENKGFAF + VTFMDKEAAQ RAIEDVQDRE FKGRTLRCSL SQAKHRLFVG NVPKGLSEEE + LTNTIKGKGP GVINIEMFKD QHDPNRNRGF LFVEYYNHAC ADYARQKLSS + PNFKVDGSQL TVSWAEPKGS TDASSAAAQV KTIYVKNLPE NVSKEKIKDL + FDKHGEVTKI VLPPAKAGHK RDFGFVHFAE RSSALKAVKG SEKYEIDGQV + LEVSMAKPLA DKKPDHSHRP GGGPNYPLPP YGGGGYMGDP YGAYGGGGPA + YNQPMIYGRG PAPAGMRMVP MVLPDGRLGY VLQQPGGMPP PPPPRRGSDR + RDSGRGGEGH SRRYRPY + + + + + +GRMZM2G103430_P03 NP_001130564 hypothetical protein LOC100191663 seq=translation; coord=4:38181649..38185316:-1; parent_transcript=GRMZM2G103430_T03; parent_gene=GRMZM2G103430 + + + MSDRQPSEEP EEQVDLEGDD DGMDDDDAGY RRRGSRDDSE EPEEDDDNDE + RHGDADDDAG MEPEPAGSKG GDDTGKGPDV AGGGPEDEEE RSKWDDMLAL + PPHGSEVFIG GLPRDITEED LRELCEPLGE IYEVRLTKDK DTKENKGFAF + VTFMDKEAAQ RAIEDVQDRE FKGRTLRCSL SQAKHRLFVG NVPKGLSEEE + LTNTIKGKGP GVINIEMFKD QHDPNRNRGF LFVEYYNHAC ADYARQKLSS + PNFKVDGSQL TVSWAEPKGS TDASSAAAQV KTIYVKNLPE NVSKEKIKDL + FDKHGEVTKI VLPPAKAGHK RDFGFVHFAE RSSALKAVKG SEKYEIDGQV + LEVSMAKPLA DKKPDHSHRP GGGPNYPLPP YGGGGYMGDP YGAYGGGGPA + YNQPMIYGRG PAPAGMRMVP MVLPDGRLGY VLQQPGGMPP PPPPRRGSDR + RDSGRGGEGH SRRYRPY + + + + + +GRMZM2G103430_P04 NP_001130564 hypothetical protein LOC100191663 seq=translation; coord=4:38181649..38185316:-1; parent_transcript=GRMZM2G103430_T04; parent_gene=GRMZM2G103430 + + + MSDRQPSEEP EEQVDLEGDD DGMDDDDAGY RRRGSRDDSE EPEEDDDNDE + RHGDADDDAG MEPEPAGSKG GDDTGKGPDV AGGGPEDEEE RSKWDDMLAL + PPHGSEVFIG GLPRDITEED LRELCEPLGE IYEVRLTKDK DTKENKGFAF + VTFMDKEAAQ RAIEDVQDRE FKGRTLRCSL SQAKHRLFVG NVPKGLSEEE + LTNTIKGKGP GVINIEMFKH DPNRNRGFLF VEYYNHACAD YARQKLSSPN + FKVDGSQLTV SWAEPKGSTD ASSAAAQVKT IYVKNLPENV SKEKIKDLFD + KHGEVTKIVL PPAKAGHKRD FGFVHFAERS SALKAVKGSE KYEIDGQVLE + VSMAKPLADK KPDHSHRPGG GPNYPLPPYG GGGYMGDPYG AYGGGGPAYN + QPMIYGRGPA PAGMRMVPMV LPDGRLGYVL QQPGGMPPPP PPRRGSDRRD + SGRGGEGHSR RYRPY + + + + + +GRMZM2G103430_P05 NP_001130564 hypothetical protein LOC100191663 seq=translation; coord=4:38182016..38185320:-1; parent_transcript=GRMZM2G103430_T05; parent_gene=GRMZM2G103430 + + + MSDRQPSEEP EEQVDLEGDD DGMDDDDAGY RRRGSRDDSE EPEEDDDNDE + RHGDADDDAG MEPEPAGSKG GDDTGKGPDV AGGGPEDEEE RSKWDDMLAL + PPHGSEVFIG GLPRDITEED LRELCEPLGE IYEVRLTKDK DTKENKGFAF + VTFMDKEAAQ RAIEDVQDRE FKGRTLRCSL SQAKHRLFVG NVPKGLSEEE + LTNTIKGKGP GVINIEMFKD QHDPNRNRGF LFVEYYNHAC ADYARQKLSS + PNFKVDGSQL TVSWAEPKGS TDASSAAAQV KTIYVKNLPE NVSKEKIKDL + FDKHGEVTKI VLPPAKAGHK RDFGFVHFAE RSSALKAVKG SEKYEIDGQV + LEVSMAKPLA DKKPDHSHRP GGGPNYPLPP YGGGGYMGDP YGAYGGGGPA + YNQPMIYGRG PAPAGMRMVP MVLPDGRLGY VLQQPGGMPP PPPPRRGSDR + RDSGRGGEGH SRRYRPY + + + + + + +6.76089 +-0.346712 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +6807 6807 6807 6793 6343 6147 5531 4240 3416 2030 1163 550 207 73 46 24 5 3 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6809 6809 6809 6795 6345 6125 5479 4137 2753 1320 333 77 16 3 1 0 + + + + + + +0 1 2 3 4 + + + + +3377 2991 421 22 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1283 3911 1340 237 32 4 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2902 (charge 2) + +1192.58 +2 + + +152.057 153.102 155.081 156.077 157.061 157.097 158.092 159.076 166.062 167.056 167.081 169.052 169.097 171.076 171.113 171.149 173.056 173.092 173.129 175.072 175.119 176.123 181.062 181.096 182.092 183.078 183.113 185.092 186.124 187.072 +189.087 191.085 195.09 198.123 199.071 200.103 201.123 204.134 210.088 212.103 214.119 217.082 221.085 226.155 228.098 230.114 235.118 239.095 241.092 244.165 246.181 252.135 255.117 262.153 270.108 272.17 274.188 285.01 287.007 289.085 +299.063 301.06 302.06 305.018 309.204 311.134 317.145 325.113 339.13 343.123 352.162 356.071 357.069 359.067 362.163 365.697 372.167 374.24 390.2 396.155 400.16 412.662 415.164 420.994 421.995 429.211 445.276 454.167 478.21 482.238 +516.316 523.298 587.348 659.348 674.381 690.342 730.389 761.415 817.41 832.454 + + + + +4 4 15 5 16 5 5 20 6 24 8 6 7 36 4 8 6 6 17 7 41 4 5 4 7 6 14 17 6 13 +19 13 5 4 19 26 19 30 16 7 5 34 4 49 34 13 5 30 7 22 29 5 6 5 17 5 6 51 51 5 +23 27 8 8 100 5 6 8 8 8 5 40 58 7 7 6 6 15 6 7 5 7 5 7 5 4 29 5 5 5 +17 43 19 8 33 7 27 36 13 15 + + + + + + +GRMZM2G156861_P02 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168699190:1; parent_transcript=GRMZM2G156861_T02; parent_gene=GRMZM2G156861 + + + + + + + + +5.02942 +-0.257919 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +7412 7412 7412 7403 6343 5986 4498 3719 2787 1969 1309 756 323 181 83 43 22 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7415 7415 7415 7406 6346 5939 4269 3221 2080 1092 474 184 40 9 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3074 3272 902 151 16 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1411 4252 1419 278 51 2 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2904 (charge 2) + +1173.65 +2 + + +154.087 155.082 155.093 155.118 156.077 157.097 158.093 159.077 159.113 161.092 167.093 169.097 169.134 171.076 171.113 171.149 173.092 175.106 175.119 176.123 181.097 183.077 183.113 185.092 186.124 187.072 187.108 189.087 191.085 194.13 +195.09 195.113 196.145 197.129 199.108 201.088 204.134 211.119 214.155 219.08 224.14 226.155 228.099 231.098 235.119 239.115 242.15 244.166 254.153 256.129 258.145 270.145 272.172 284.125 295.15 303.204 311.172 316.175 323.18 334.188 +346.183 373.706 397.215 405.191 411.247 415.431 436.161 449.255 457.253 466.276 476.236 491.269 493.278 498.121 508.3 543.292 556.802 579.311 585.309 586.309 621.323 645.365 650.362 651.364 657.347 672.358 729.388 741.367 743.391 746.408 +748.407 784.43 800.385 845.463 916.477 932.505 988.509 1008.67 1085.56 1156.56 + + + + +5 23 4 7 4 5 9 8 8 4 5 20 26 7 14 4 50 5 98 5 4 5 6 27 16 5 8 8 23 5 +6 5 39 56 23 37 48 7 48 6 13 46 6 8 5 16 19 19 5 6 14 18 8 6 13 12 19 5 16 5 +5 5 5 4 5 4 5 7 5 6 7 14 6 4 100 14 25 5 14 6 5 31 36 17 7 15 5 4 5 33 +6 5 14 6 7 34 5 5 7 5 + + + + + + +GRMZM2G107089_P01 NP_001149927 prolyl-tRNA synthetase seq=translation; coord=7:7453972..7459323:1; parent_transcript=GRMZM2G107089_T01; parent_gene=GRMZM2G107089 + + + MAIALAFGGT EPPNPGGQSP QATMASLLRL PSLLSPSKPL LRRRLPAARL + AASAASRGQA SATAGAAAPA AAETRGGDRE GQVTPRSADF NAWYTDVIAA + AELADYGPVR GTMVIRPYGY AIWEAIQDYL NVKFKETGHS NMYFPQFIPY + SFIEKEASHV EGFSPELALV TIGGGKELEE KLVVRPTSET IVNHMFTKWI + QSYRDLPLMI NQWANVTRWE MRTKPFIRTL EFLWQEGHTA HATLEEAEKE + AMQMIDVYTK FAFEHAAIPV IPGRKSRVET FAGANRTYTI EAMMGDKKAL + QAGTSHNLGQ NFSRAFGTQF MDENGQIEHV WQTSWAISTR FVGGIIMTHG + DDAGLMLPPR IAPIQVIIVP IWKKGDEKAV VVEAVDSVQK ILKEAGIRVK + VDDSELRTPG WKFNHYEMKG VPVRIEIGPR DVTNKSVVVS RRDVPGKQGK + EFGVSMEPSI LVNHIKGRLD DIQASLLQKA ITFRDSNIVD VSSYGELKEA + ISEGKWARGP WSASDADELK VKEETSATIR CYPFEQPEGT KKCFMTGNPA + EEVAIFAKSY + + + + + + +4.72663 +-0.201133 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +6558 6558 6229 6146 5840 5409 5010 3642 2932 1770 1016 660 338 198 123 80 54 45 22 19 10 5 1 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6560 6560 6231 6148 5792 5276 4924 3202 2300 848 367 74 19 8 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3297 2599 577 80 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1020 3577 1545 340 44 25 8 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2908 (charge 2) + +1228.63 +2 + + +153.066 155.07 155.082 157.097 158.093 159.077 161.092 169.098 170.092 171.076 171.113 172.108 173.093 175.119 181.061 181.097 182.067 185.092 185.165 186.125 187.072 187.144 197.129 198.088 198.123 199.071 200.103 204.135 212.103 214.119 +216.098 226.119 227.102 230.114 233.165 238.119 240.135 243.146 244.128 252.136 256.129 259.14 262.085 271.14 272.171 276.167 283.14 287.008 289.163 297.158 301.151 305.184 309.154 311.172 314.182 323.171 327.167 342.178 344.195 354.177 +357.067 358.191 362.182 372.186 380.195 382.211 386.215 395.194 398.204 399.202 408.719 419.693 425.214 440.214 443.225 459.233 477.209 533.253 547.283 563.289 585.816 618.323 655.335 673.338 698.346 702.389 715.375 717.38 786.412 788.409 +816.435 837.454 857.447 859.45 901.456 903.456 928.481 985.508 987.491 1056.54 + + + + +3 2 48 2 10 3 3 14 7 3 6 3 18 27 20 9 2 8 3 4 3 19 9 3 2 2 28 9 6 3 +3 34 9 12 14 3 18 11 5 4 7 3 8 21 15 33 18 3 6 12 13 2 7 12 8 3 13 6 6 17 +8 8 3 7 2 2 2 2 9 2 2 7 18 2 6 2 3 2 3 2 6 6 2 7 8 6 100 3 35 2 +7 9 36 2 2 2 8 17 2 6 + + + + + + +GRMZM2G034243_P01 NP_001145084 hypothetical protein LOC100278292 seq=translation; coord=9:152858133..152859928:-1; parent_transcript=GRMZM2G034243_T01; parent_gene=GRMZM2G034243 + + + MATSSVLPLH LLSCARRAST STSTAARASA APAVAATTAQ SLEESFGRKG + LRFVADPAGG PLAAELSVRN GSSLHLRLGD GLVTSYRPKV YWKDDGCREV + LHTVAGKGGV GLVLNDATSS SAQPSLVDGA EWAVRDADSD SYDAVQVELG + CTIGKLDISY VVTLYSLSMA TAVIVRNTGS KPVALTGAVL SHIKFDKRGG + TAVEGLRGCP YCSYPPPAAA FSLLSPAEAM KREDPGWFGG AEELRQGVWT + VEEDLYTTLK KKVSRVYAAP PEERKKRVYS TAPSKFTTID QYSGLGFRLV + RMGFDDMYLC SPGGMYDKFG KDYFLCTGMA SMLVPVVVNP GEEWKAAQVI + EHDNL + + + + + + +4.12064 +-0.249736 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +2574 2574 2574 2555 2464 2300 2087 1906 1427 1149 702 454 175 86 27 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +2604 2604 2604 2585 2494 2328 2067 1904 1355 911 457 119 80 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +1182 1159 240 27 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +475 1497 494 129 9 1 1 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2910 (charge 2) + +953.54 +2 + + +154.087 155.082 155.093 155.117 156.086 157.097 157.109 157.134 158.092 159.077 159.092 166.061 166.098 167.055 167.081 169.097 169.134 171.113 171.15 173.093 173.129 175.119 181.097 183.113 183.15 185.056 185.092 185.165 186.096 186.124 +187.071 192.996 193.096 194.093 194.13 195.088 195.113 197.128 199.072 199.108 201.124 204.135 209.09 211.12 215.139 217.082 221.104 223.156 226.155 227.103 229.119 231.097 234.124 239.115 244.166 249.161 251.15 254.151 260.124 269.126 +272.172 275.17 292.176 294.157 297.672 301.186 306.678 329.191 338.187 341.219 352.2 354.215 363.211 374.24 409.223 433.257 436.221 438.272 445.241 448.227 461.252 466.247 468.771 471.745 475.289 496.605 544.291 548.281 558.323 562.296 +580.311 612.347 643.368 661.366 677.321 714.382 725.432 783.364 790.398 796.439 + + + + +4 39 4 6 9 4 4 4 16 13 13 8 18 10 4 22 10 11 15 4 15 73 9 37 3 3 17 13 4 26 +5 4 4 5 4 15 9 10 4 14 100 53 7 11 5 4 10 13 21 5 33 4 10 35 13 38 29 4 4 4 +6 23 5 5 14 5 18 5 8 5 5 5 8 15 9 14 5 9 12 4 11 4 5 4 24 4 4 13 11 11 +4 15 5 3 25 19 5 4 5 14 + + + + + + +GRMZM2G102499_P03 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306867:-1; parent_transcript=GRMZM2G102499_T03; parent_gene=GRMZM2G102499 + + + MASAELSREE NVYMAKLAEQ AERYEEMVEF MEKVAKTVDS EELTVEERNL + LSVAYKNVIG ARRASWRIIS SIEQKEEGRG NEDRVTLIKD YRGKIETELT + KICDGILKLL ETHLVPSSTA PESKVFYLKM KGDYYRYLAE FKTGAERKDA + AENTMVAYKA AQDIALAELA PTHPIRLGLA LNFSVFYYEI LNSPDRACSL + AKQAFDEAIS ELDTLSEESY KDSTLIMQLL RDNLTLWTSD ISEDPAEEIR + EAPKRDSSEG Q + + + + + + +GRMZM2G102499_P04 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306867:-1; parent_transcript=GRMZM2G102499_T04; parent_gene=GRMZM2G102499 + + + MASAELSREE NVYMAKLAEQ AERYEEMVEF MEKVAKTVDS EELTVEERNL + LSVAYKNVIG ARRASWRIIS SIEQKEEGRG NEDRVTLIKD YRGKIETELT + KICDGILKLL ETHLVPSSTA PESKVFYLKM KGDYYRYLAE FKTGAERKDA + AENTMVAYKA AQDIALAELA PTHPIRLGLA LNFSVFYYEI LNSPDRACSL + AKQAFDEAIS ELDTLSEESY KDSTLIMQLL RDNLTLWTSD ISEDPAEEIR + EAPKRDSSEG Q + + + + + + +GRMZM2G078641_P01 Q01526 14-3-3-like protein GF14-12 seq=translation; coord=10:123105640..123109630:1; parent_transcript=GRMZM2G078641_T01; parent_gene=GRMZM2G078641 + + + MASAELSREE NVYMAKLAEQ AERYEEMVEF MEKVAKTVDS EELTVEERNL + LSVAYKNVIG ARRASWRIIS SIEQKEEGRG NEDRVTLIKD YRGKIETELT + KICDGILKLL ESHLVPSSTA PESKVFYLKM KGDYYRYLAE FKTGAERKDA + AENTMVAYKA AQDIALAELA PTHPIRLGLA LNFSVFYYEI LNSPDRACSL + AKQAFDEAIS ELDTLSEESY KDSTLIMQLL RDNLTLWTSD ISEDPAEEIR + EAPKHDSSEG Q + + + + + + +GRMZM2G102499_P02 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306124:-1; parent_transcript=GRMZM2G102499_T02; parent_gene=GRMZM2G102499 + + + MYICRSGVLQ ILKLNCKMAS AELSREENVY MAKLAEQAER YEEMVEFMEK + VAKTVDSEEL TVEERNLLSV AYKNVIGARR ASWRIISSIE QKEEGRGNED + RVTLIKDYRG KIETELTKIC DGILKLLETH LVPSSTAPES KVFYLKMKGD + YYRYLAEFKT GAERKDAAEN TMVAYKAAQD IALAELAPTH PIRLGLALNF + SVFYYEILNS PDRACSLAKQ AFDEAISELD TLSEESYKDS TLIMQLLRDN + LTLWTSDISE DPAEEIREAP KRDSSEGQ + + + + + + +GRMZM2G078641_P02 Q01526 14-3-3-like protein GF14-12 seq=translation; coord=10:123105938..123116261:1; parent_transcript=GRMZM2G078641_T02; parent_gene=GRMZM2G078641 + + + MASAELSREE NVYMAKLAEQ AERYEEMVEF MEKVAKTVDS EELTVEERNL + LSVAYKNVIG ARRASWRIIS SIEQKEEGRG NEDRVTLIKD YRGKIETELT + KICDGILKLL ESHLVPSSTA PESKVFYLKM KGDYYRYYDC MNPIVVIRYL + AEFKTGAERK DAAENTMVAY KAAQDIALAE LAPTHPIRLG LALNFSVFYY + EILNSPDRAC SLAKQAFDEA ISELDTLSEE SYKDSTLIMQ LLRDNLTLWT + SDISSCLYYS LRAERRRPHH HGSASAHPLP PRRDARQSRH RVLRAPPISQ + RRARQTLFPT AVPLSPPTGD HALPPSPQRP PDPAWHTPEI ALFPTESGLA + HTGDHALPPF PTVATGSSMA HARSSMAHPQ RERPEWSSEH PCTHWRPGHS + PPQSPPHPIP PRITPNPHPD PETFIHLPWS LSLFGSNIRE FGSVSGSDGV + TGVASNADAV AMWMVSCRAP CGWCSSPQAT PRLRPRCPPQ HPQHPGGWAA + RDTRSSQSPT SRWVATASAI GIHHKTTQWR ARSSLLERMH VLDEANYLVK + RAASIQAAVP SVNSAPAVTS GGPFKLPNGV GKPAAPLADL LDLSSDDAPV + TISAPTTAPN DFLQDLLGIG LTHSSPIGGA PSISTDILMD LLSIGSSSVQ + NGPPTSNFSL PSIETKSVAV TPQVVDLLDG LSSGTSLSVH PVRLDPASNS + TLPASGNGSV TQSLSVTNNQ HGQISKGFKF NVKGVVVVLD KFSGRSRGLG + FVNFNEKQAM EDAIEATNGL CLDGSNITVD KARPHGPSRD RNGDRYYDRE + LGSRYDHGRN YGGGCALRGG GGDCFKCGNP IILLETTHLG TVGEGTNMVV + GMTCMVVLEV VMVLIVAVTN TLVIVEMAVA IGAATVMALI DQVLPDGLSS + + + + + + + + +6.79005 +-0.315816 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6954 6954 6954 6954 6954 6628 6296 5862 5154 3964 2825 1541 878 361 204 109 55 30 3 2 1 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6965 6965 6965 6965 6965 6639 6289 5727 4921 3428 2023 781 183 16 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2388 2794 1268 388 86 27 2 19 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1171 2886 2028 659 179 47 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2915 (charge 3) + +1356.65 +3 + + +151.063 153.066 155.082 155.118 157.097 157.108 158.093 159.077 167.082 167.118 169.097 171.076 171.113 173.092 173.128 175.119 181.061 181.097 183.113 185.091 185.165 186.124 187.072 187.108 194.129 195.113 197.091 198.087 199.108 201.087 +204.135 207.113 209.09 213.087 214.119 216.098 219.116 226.155 227.103 240.135 244.129 245.097 247.113 249.092 251.151 254.148 258.106 261.156 272.172 274.188 279.162 282.163 293.163 295.148 298.141 303.203 310.177 315.167 318.148 332.193 +343.682 347.207 349.183 356.666 359.195 368.192 369.179 379.202 381.215 384.683 386.205 418.242 424.202 426.196 428.736 433.728 451.756 456.259 459.228 469.236 477.244 480.282 485.758 497.237 515.248 525.226 532.275 541.285 563.325 584.334 +612.322 620.334 627.319 629.29 669.329 677.361 686.351 712.326 740.371 757.396 + + + + +10 11 20 24 12 11 25 59 12 9 46 15 27 22 13 100 8 27 17 15 10 74 51 10 42 14 19 11 24 14 +57 29 13 13 39 10 9 37 30 14 41 14 14 9 11 17 15 11 30 14 31 9 23 11 18 12 93 30 17 13 +9 15 12 13 8 9 8 45 68 11 37 15 11 10 65 14 10 14 13 12 60 48 91 9 30 11 18 35 26 18 +17 11 16 15 19 25 8 12 27 12 + + + + + + +GRMZM2G102499_P03 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306867:-1; parent_transcript=GRMZM2G102499_T03; parent_gene=GRMZM2G102499 + + + + + + + + +GRMZM2G102499_P04 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306867:-1; parent_transcript=GRMZM2G102499_T04; parent_gene=GRMZM2G102499 + + + + + + + + +GRMZM2G078641_P01 Q01526 14-3-3-like protein GF14-12 seq=translation; coord=10:123105640..123109630:1; parent_transcript=GRMZM2G078641_T01; parent_gene=GRMZM2G078641 + + + + + + + + +GRMZM2G102499_P02 P49106 14-3-3-like protein GF14-6 seq=translation; coord=2:41302953..41306124:-1; parent_transcript=GRMZM2G102499_T02; parent_gene=GRMZM2G102499 + + + + + + + + +GRMZM2G078641_P02 Q01526 14-3-3-like protein GF14-12 seq=translation; coord=10:123105938..123116261:1; parent_transcript=GRMZM2G078641_T02; parent_gene=GRMZM2G078641 + + + + + + + + + +4.47482 +-0.241882 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +5315 5315 5315 5279 4879 4759 3132 2569 1710 1063 657 438 213 119 48 20 6 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +5323 5323 5323 5287 4887 4748 3097 2327 1401 731 427 207 80 31 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2836 2000 403 72 4 0 16 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1140 3492 591 88 4 0 16 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2916 (charge 2) + +1356.65 +2 + + +152.057 155.082 155.118 157.062 157.098 159.077 165.102 167.081 169.097 171.113 173.092 175.119 181.097 184.108 185.092 185.13 186.123 187.072 194.129 198.088 200.104 201.087 204.135 207.113 209.092 212.103 214.118 216.098 226.118 227.102 +242.113 244.129 248.161 258.109 259.112 283.141 292.167 297.155 310.177 315.167 317.182 319.197 325.184 329.145 331.196 352.953 356.668 381.213 386.206 400.181 430.186 434.229 439.191 442.602 480.286 487.257 490.423 497.227 515.238 521.064 +563.319 592.239 629.787 633.322 646.828 671.844 680.362 696.325 712.331 728.362 762.362 778.415 813.371 817.884 842.413 877.387 889.411 907.438 912.435 931.411 971.467 978.481 1005.49 1032.46 1047.5 1049.52 1131.51 1164.56 + + + + +6 18 17 6 4 70 3 7 18 6 7 20 4 6 6 4 5 100 28 4 19 8 14 5 13 14 29 6 32 25 +4 29 16 71 5 8 7 6 45 15 20 14 4 23 5 4 6 32 4 5 7 5 5 5 7 4 4 4 5 4 +4 6 8 6 15 4 39 4 5 5 7 7 7 5 6 24 4 6 5 8 5 13 7 7 5 13 5 16 + + + + + + +GRMZM2G090542_P01 seq=translation; coord=1:217021624..217059348:1; parent_transcript=GRMZM2G090542_T01; parent_gene=GRMZM2G090542 + + + MAASPDQFRG HARLPHFAAP LRYDLRLRPD LAACTFTGAA AIAVVVSAPT + RFLVLNAAEL DVDRASIRFQ DLAPTDVAQF DEDEIMVISF DRELPFGEGV + LTMDFTGTLN DQMRGFYRSK YVYNGESRNM AVTQFEAADA RRCFPCWDDP + AFKAKFKLTL EVPSDLVALS NMPVAKETVS GLTKTIYYEE SPLMSTYLVA + IVVGIFDYIE SSTSEGTKVR VYTQVGKTNQ GKFALDVAVK SLDLYKDYFA + TPYPLPKLDM IAIPDFSAGA MENYGLVTYR DTALLYDELL SSASNKQQVA + ITVAHELAHQ WFGNLVTMEW WTHLWLNEGF ASWVSYLAVE SLFPEWNNWT + QFLDETTSGL RLDALAESHP IEVEVNHASE IDAIFDSISY DKGASVIRML + QSYLGAECFQ KALASYIKKY AYSNAKTEDL WVVLEEESGE PVKDLMTTWT + KQQGYPVIYA KINGHDLELE QAQFLSDGSS GPGMWIVPVT ACCGSYDAQK + KFLLKDKMDK INIKEFSDSQ SADGEKNQII WIKLNIDQTG FYRVKYDDEL + AAGLVNAIKA KKLSLMDKIG IVEDSYALSV ACKQTLTSLL RLLNAYNDES + DYTVLSHVTS VCLSISKITV DATPDLNKDI KQLLINLLLP AVIKLGWDPK + DGESHLDVML RSLLLTALVR LGHNETINEG VRRFHIFFED GKTSLLPPDT + RKAAYLAVMR TVSTSSRSGF DALLKIYREA SEPQEKSRVL GSLSSSPDQD + IVLEALNFMF TDEVRNQDSF YILGGISLEG REIAWTWLKE NWDHVLKTWK + SSSLISDFIE SIVPRFTSEE KAVEVTEFFA GQVKPSFERA LKQSLERVRI + SARWIESIRS EPKLGQTVQE LLQADA + + + + + + +4.10015 +-0.264526 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +1401 1401 1401 1329 1275 1184 1073 745 535 376 206 92 34 13 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1406 1406 1406 1334 1279 1167 1037 669 455 224 79 22 7 1 0 + + + + + + +0 1 2 3 4 5 + + + + +645 570 169 22 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +376 781 209 41 0 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2917 (charge 2) + +1299.53 +2 + + +152.057 155.081 155.118 157.061 157.097 158.092 159.076 163.06 167.055 169.097 171.077 171.114 172.072 173.056 173.092 173.127 175.071 175.119 183.113 185.056 185.092 186.091 186.124 187.071 198.087 199.072 199.108 201.087 203.067 205.102 +207.112 212.103 216.098 219.116 226.155 227.157 231.113 235.108 240.134 244.166 249.123 258.145 259.108 267.108 272.088 277.119 283.107 290.098 299.136 302.1 309.119 311.171 313.115 315.167 318.146 326.145 328.13 333.177 346.14 359.029 +371.172 384.151 397.151 400.145 402.173 415.158 418.207 422.219 443.158 448.203 461.17 507.253 519.24 530.189 548.199 581.267 588.264 606.273 608.271 622.21 675.339 678.333 696.374 717.305 734.333 770.415 781.321 791.356 799.342 803.358 +821.367 843.431 855.363 878.385 896.387 936.39 1005.41 1013.49 1023.43 1141.53 + + + + +4 12 8 12 18 4 12 16 4 16 9 3 6 3 14 3 13 27 3 3 4 20 15 11 4 3 10 8 32 4 +3 4 16 14 25 4 96 3 12 22 100 9 30 3 10 10 3 9 3 3 4 4 4 3 3 3 4 72 17 31 +4 3 11 9 3 3 9 4 4 30 4 10 27 3 3 20 8 70 3 3 3 3 3 17 11 5 4 9 3 4 +31 4 4 3 4 11 4 11 29 3 + + + + + + +GRMZM2G110201_P01 NP_001142099 hypothetical protein LOC100274263 seq=translation; coord=5:31131578..31135872:-1; parent_transcript=GRMZM2G110201_T01; parent_gene=GRMZM2G110201 + + + MEKAVDRQRV LLRHLNPAAA GSPAPPAISA SACAAGDSAA YHRRPAFADD + VVIVAAYRTA ICKAKRGGFK DTFAEDLLVP VFKALVDKTK LDPSEVGDIV + VGTVLAPGSQ RAIECRMAAL YAGFPDTVPL KTVNRQCSSG LQAVADVATA + IKAGLYDIGI AAGLESMTVN KVSLDGQANP KVELFSQARD CLLPMGLTSE + NVAHRFGITR LEQDQAAVES HRKAAAAAAA GKFKEEIVPV HTKIVDPKTG + EEKKIVISAD DGIRVDTSLA VLSKLKPAFS KDGSTTAGNA SQVSDGAGAV + LLMRRDVAMK KGLPVLGVFR TFAAVGVDPA VMGIGPAVAI PAAVKAAGLQ + MDDIDLFEIN EAFASQYVYC CKKLKLDPAK VNVNGGAMAL GHPLGATGAR + CVSTLLNEMK RRGKDCRFGV ISMCIGSGMG AAAVFERGDG VDELTNARGI + STHNWLSKDA M + + + + + +GRMZM2G110201_P02 NP_001142099 hypothetical protein LOC100274263 seq=translation; coord=5:31131598..31135872:-1; parent_transcript=GRMZM2G110201_T02; parent_gene=GRMZM2G110201 + + + MTVNKVSLDG QANPKVELFS QARDCLLPMG LTSENVAHRF GITRLEQDQA + AVESHRKAAA AAAAGKFKEE IVPVHTKIVD PKTGEEKKIV ISADDGIRVD + TSLAVLSKLK PAFSKDGSTT AGNASQVSDG AGAVLLMRRD VAMKKGLPVL + GVFRTFAAVG VDPAVMGIGP AVAIPAAVKA AGLQMDDIDL FEINEAFASQ + YVYCCKKLKL DPAKVNVNGG AMALGHPLGA TGARCVSTLL NEMKRRGKDC + RFGVISMCIG SGMGAAAVFE RGDGVDELTN ARGISTHNWL SKDAM + + + + + +GRMZM2G110201_P03 NP_001142099 hypothetical protein LOC100274263 seq=translation; coord=5:31131598..31135872:-1; parent_transcript=GRMZM2G110201_T03; parent_gene=GRMZM2G110201 + + + MAALYAGFPD TVPLKTVNRQ CSSGLQAVAD VATAIKAGLY DIGIAAGLES + MTVNKVSLDG QANPKVELFS QARDCLLPMG LTSENVAHRF GITRLEQDQA + AVESHRKAAA AAAAGKFKEE IVPVHTKIVD PKTGEEKKIV ISADDGIRVD + TSLAVLSKLK PAFSKDGSTT AGNASQVSDG AGAVLLMRRD VAMKKGLPVL + GVFRTFAAVG VDPAVMGIGP AVAIPAAVKA AGLQMDDIDL FEINEAFASQ + YVYCCKKLKL DPAKVNVNGG AMALGHPLGA TGARCVSTLL NEMKRRGKDC + RFGVISMCIG SGMGAAAVFE RGDGVDELTN ARGISTHNWL SKDAM + + + + + + +5.37339 +-0.346671 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +5973 5973 5925 5459 4971 4524 2999 2103 1121 473 193 71 30 7 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5981 5981 5927 5434 4910 4417 2822 1655 635 147 16 2 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2441 2457 900 149 23 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1096 3215 1298 292 70 2 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2920 (charge 3) + +1382.67 +3 + + +155.082 156.077 157.108 158.092 159.077 167.056 167.082 171.059 171.113 175.119 181.061 197.129 198.087 200.105 201.124 212.103 215.139 217.134 223.064 225.043 227.066 233.165 235.119 240.098 244.093 245.129 252.147 255.625 258.109 269.125 +292.615 295.151 299.063 304.162 312.177 314.081 329.193 338.1 341.018 342.997 350.148 355.124 356.127 359.029 369.19 372.151 382.183 386.215 399.21 417.258 423.682 426.163 429.089 445.12 486.222 501.243 503.247 510.243 528.254 554.222 +562.279 602.236 604.235 610.299 627.322 699.28 701.285 769.396 880.416 897.462 1012.49 + + + + +2 1 1 4 1 18 1 1 1 19 1 1 1 1 1 1 10 8 3 5 3 1 1 4 7 3 1 1 1 1 +1 2 1 2 3 3 5 1 4 3 36 8 2 100 1 3 2 29 10 1 3 3 16 1 1 4 2 2 13 1 +1 29 2 1 11 13 2 6 1 2 2 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + + + + + + +6.64811 +-0.282898 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +8406 8406 8406 8406 8301 7854 7182 5754 4660 3596 2101 1260 776 431 287 165 77 36 13 3 2 2 1 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +8366 8366 8366 8366 8261 7813 7118 5594 3733 2149 693 165 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1883 4168 1779 468 90 26 1 3 + + + + + + +0 1 2 3 4 5 6 + + + + +1907 4845 1468 175 21 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2924 (charge 2) + +1260.64 +2 + + +152.057 155.081 155.118 157.061 157.097 157.109 157.134 158.091 159.077 167.082 169.097 171.077 171.112 172.108 173.092 175.072 175.119 183.076 183.112 185.092 185.129 187.144 188.103 194.128 197.128 199.072 200.139 201.088 204.136 214.082 +216.098 218.15 226.155 233.642 240.135 242.113 252.098 258.145 260.088 270.107 272.172 276.156 283.141 311.098 317.22 329.11 347.12 352.201 356.2 369.225 373.171 400.692 408.687 428.177 456.255 466.28 485.248 515.292 525.22 528.313 +537.315 543.291 566.287 572.283 597.257 606.272 614.29 631.825 652.332 672.284 697.361 703.329 714.389 717.341 728.3 734.345 745.33 767.36 782.368 788.373 797.426 800.378 801.381 816.366 818.367 822.361 825.418 833.399 854.407 916.432 +927.392 944.426 945.429 1015.5 1017.49 1043.48 1069.5 1086.53 1114.52 1132.55 + + + + +5 15 10 10 14 9 19 5 10 6 11 16 10 15 5 23 33 14 6 16 17 13 6 14 5 15 26 18 18 11 +21 81 15 10 12 16 11 11 13 20 19 13 11 12 18 5 22 9 5 15 13 14 15 15 22 47 10 15 20 12 +28 40 6 5 6 15 62 11 11 11 16 33 5 12 5 5 69 5 6 22 9 70 33 69 13 10 14 10 17 40 +11 100 48 37 6 15 5 22 12 5 + + + + + + +GRMZM2G427404_P01 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=5:209967831..209970936:1; parent_transcript=GRMZM2G427404_T01; parent_gene=GRMZM2G427404 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYRKKTN PFVARHLLAK IEKVNMKEEK EIIVTWSRAS SILPAMVGHT + IAIHNGKEHI PIYITNPMVG RKLGEFVPTR HFTSYESTRK DTKSRR + + + + + + +GRMZM2G427404_P02 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=5:209968651..209970215:1; parent_transcript=GRMZM2G427404_T02; parent_gene=GRMZM2G427404 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRK + + + + + + +GRMZM2G427404_P03 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=5:209968406..209969950:1; parent_transcript=GRMZM2G427404_T03; parent_gene=GRMZM2G427404 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + + + + + + + +GRMZM2G455420_P01 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=10:100018777..100021282:-1; parent_transcript=GRMZM2G455420_T01; parent_gene=GRMZM2G455420 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + + + + + + + +GRMZM2G405476_P01 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=10:90119267..90121274:-1; parent_transcript=GRMZM2G405476_T01; parent_gene=GRMZM2G405476 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + + + + + + + +GRMZM2G405476_P02 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=10:90119739..90120227:-1; parent_transcript=GRMZM2G405476_T02; parent_gene=GRMZM2G405476 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRR + + + + + + +GRMZM5G813019_P01 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=Pt:82930..84414:-1; parent_transcript=GRMZM5G813019_T01; parent_gene=GRMZM5G813019 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + + + + + + + +GRMZM5G818111_P01 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=Pt:139291..139807:1; parent_transcript=GRMZM5G818111_T01; parent_gene=GRMZM5G818111 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRK + + + + + + +GRMZM5G818111_P02 P17788 50S ribosomal protein L2, chloroplastic seq=translation; coord=Pt:138323..139807:1; parent_transcript=GRMZM5G818111_T02; parent_gene=GRMZM5G818111 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + + + + + + + +GRMZM5G854146_P01 YP_588382 hypothetical protein ZeamMp129 seq=translation; coord=1:234659420..234660776:1; parent_transcript=GRMZM5G854146_T01; parent_gene=GRMZM5G854146 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRKVSKYV TRNMENCIFG ICNNAMGERR ELNPRMVDSQ + STALIHLATS APYPAKGFSL FSIHYYSIYS DLHTSIEIVD IGCHSLK + + + + + + +GRMZM2G343713_P01 seq=translation; coord=2:9501629..9502126:-1; parent_transcript=GRMZM2G343713_T01; parent_gene=GRMZM2G343713 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRK + + + + + + +GRMZM2G309193_P01 YP_588382 hypothetical protein ZeamMp129 seq=translation; coord=2:65002440..65016255:1; parent_transcript=GRMZM2G309193_T01; parent_gene=GRMZM2G309193 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRKVSKYV TRNMENCIFG ICNNAMGERR ELNPRMVDSQ + STALIHLATS APYPAKGFSL FSIHYYSIYS DLHTSIEIVD IGCHSLK + + + + + + +GRMZM2G309193_P02 YP_588382 hypothetical protein ZeamMp129 seq=translation; coord=2:65001638..65016255:1; parent_transcript=GRMZM2G309193_T02; parent_gene=GRMZM2G309193 + + + MGNALPLTDM PLGTAIHNIE ITRGRGGQLA RAAGAVAKLI AKEGKLATLR + LPSGEVRLVS QNCLATVGQV GNVGVNQKSL GRAGSKCWLG KRPVVRGVVM + NPVDHPHGGG EGKAPIGRKK PTTPWGYPAL GRRTRKRKKY SDSFILRRRK + VSKYVTRNME NCIFGICNNA MGERRELNPR MVDSQSTALI HLATSAPYPA + KGFSLFSIHY YSIYSDLHTS IEIVDIGCHS LK + + + + + + +GRMZM2G056170_P01 seq=translation; coord=3:152609586..152610053:1; parent_transcript=GRMZM2G056170_T01; parent_gene=GRMZM2G056170 + + + GRGGQLARAA GAVAKLIAKE GKLATLRLPS GEVRLVSQNC LATVGQVGNV + GVNQKSLGRA GSKCWLGKRP VVRGVVMNPV DHPHGGGEGK APIGRKKPTT + PWGYPALGRR TRKRKKYSDS FILRRRK + + + + + + +GRMZM5G827951_P01 YP_588382 hypothetical protein ZeamMp129 seq=translation; coord=Mt:346145..347501:-1; parent_transcript=GRMZM5G827951_T01; parent_gene=GRMZM5G827951 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + KRKKYSDSFI LRRRKVSKYV TRNMENCIFG ICNNAMGERR ELNPRMVDSQ + STALIHLATS APYPAKGFSL FSIHYYSIYS DLHTSIEIVD IGCHSLK + + + + + + +GRMZM2G430501_P01 seq=translation; coord=4:139905281..139905770:1; parent_transcript=GRMZM2G430501_T01; parent_gene=GRMZM2G430501 + + + MLWKKLVQFG KGFFEKKEES TSTDMPLGTA IHNIEITRGR GGQLARAAGA + VAKLIAKEGK LATLRLPSGE VRLVSQNCLA TVGQVGNVGV NQKSLGRAGS + KCWLGKRPVV RGVVMNPVDH PHGGGEGKAP IGRKKPTTPW GYPALGRRTR + EKEKI + + + + + + + +6.31889 +-0.308238 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +9051 9051 9051 9051 8446 8322 7731 6783 5403 3741 2110 1141 611 324 106 52 25 11 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9073 9073 9073 9073 8468 8336 7712 6667 4990 2794 1028 400 204 58 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3076 3918 1443 487 124 21 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1563 4226 2260 829 159 12 3 24 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2925 (charge 3) + +1702.8 +3 + + +153.066 155.082 157.097 157.134 158.093 159.077 166.062 166.086 169.098 169.134 171.077 171.113 173.092 175.119 181.061 183.113 185.092 185.129 186.124 187.072 187.108 189.087 195.113 197.129 198.087 199.108 199.181 201.124 204.135 207.112 +209.14 211.144 217.064 225.099 226.155 230.084 235.109 237.136 240.134 242.114 244.166 247.111 253.094 256.165 258.145 262.086 272.171 297.156 304.13 312.155 321.155 322.14 326.147 354.167 368.212 376.22 380.157 416.736 421.219 440.262 +447.224 449.213 504.241 535.233 545.258 563.333 569.304 576.295 584.783 592.256 593.784 610.256 613.861 620.352 638.368 641.303 651.3 675.384 692.324 718.381 720.342 735.412 738.353 740.353 743.411 748.417 786.35 814.441 832.468 857.409 +875.424 892.469 901.468 902.484 935.409 961.466 984.435 990.442 998.418 1186.57 + + + + +5 7 41 12 6 15 7 61 6 27 6 7 6 39 6 19 7 6 17 7 7 6 7 7 14 17 14 6 61 48 +7 16 21 21 49 12 24 11 7 6 14 33 25 29 8 23 13 14 14 23 6 7 12 11 48 7 5 20 17 20 +6 12 55 14 7 5 53 7 7 7 61 7 5 12 30 37 19 6 12 6 19 25 100 13 36 6 6 12 71 6 +20 11 20 14 7 6 6 20 7 15 + + + + + + +GRMZM2G018619_P01 NP_001149955 ras-related protein RIC2 seq=translation; coord=9:76755814..76760164:1; parent_transcript=GRMZM2G018619_T01; parent_gene=GRMZM2G018619 + + + MAAGYRAEDD YDYLFKVVLI GDSGVGKSNL LSRFTRNEFS LESKSTIGVE + FATRSLQVDG KVVKAQIWDT AGQERYRAIT SAYYRGAVGA LLVYDVTRHS + TFENVERWLK ELRDHTDPNI VVMLVGNKSD LRHLVAVQTD EGKAFAERES + LYFMETSALE STNVENAFAE VLAQIYRIVD KRAVEAGEDA ASGPGRGEKI + NIKDDVSAVK KGGCCSS + + + + + +GRMZM2G018619_P02 NP_001149955 ras-related protein RIC2 seq=translation; coord=9:76755814..76760102:1; parent_transcript=GRMZM2G018619_T02; parent_gene=GRMZM2G018619 + + + MLVGNKSDLR HLVAVQTDEG KAFAERESLY FMETSALEST NVENAFAEVL + AQIYRIVDKR AVEAGEDAAS GPGRGEKINI KDDVSAVKKG GCCSS + + + + + + +5.17314 +-0.265289 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +4127 4127 4127 4101 3768 3664 3190 2396 1890 1220 731 396 230 125 83 19 10 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +4127 4127 4127 4101 3768 3656 3143 2302 1469 753 310 110 62 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2121 1626 357 30 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +779 2308 868 146 29 1 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2932 (charge 2) + +1286.59 +2 + + +152.057 153.103 155.082 157.097 158.093 159.077 161.092 166.061 167.082 169.097 169.135 170.046 171.077 171.113 173.057 173.092 175.12 181.097 183.077 184.072 185.056 185.092 186.125 187.072 189.087 198.124 199.072 199.107 201.087 204.135 +207.125 210.088 212.103 214.118 217.082 223.071 226.155 231.062 235.119 240.097 244.166 254.15 258.108 260.124 269.161 272.171 275.208 284.09 289.187 300.156 302.099 310.145 312.166 323.172 329.146 348.071 369.185 373.138 377.201 386.215 +421.177 445.276 456.218 469.278 473.246 500.266 506.759 515.213 522.228 544.286 573.283 575.287 585.773 615.323 619.284 632.29 663.336 670.38 689.342 703.33 719.323 730.35 748.404 819.392 859.395 916.411 917.417 929.426 932.426 987.447 +1013.52 1019.46 1032.45 1098.49 1116.5 1118.51 1308.56 + + + + +79 19 18 14 5 20 4 6 8 15 4 4 7 100 5 17 42 15 20 14 6 16 8 31 4 8 8 25 15 7 +4 6 17 4 7 4 55 6 18 19 18 4 23 6 6 6 4 6 13 22 15 7 8 5 8 8 8 8 5 21 +4 5 5 6 41 20 5 4 8 29 5 5 4 65 18 8 4 13 6 6 5 40 15 5 16 64 26 6 7 44 +18 6 15 5 24 5 5 + + + + + + +GRMZM2G155662_P01 NP_001123589 LOC100170235 seq=translation; coord=6:71618436..71621497:-1; parent_transcript=GRMZM2G155662_T01; parent_gene=GRMZM2G155662 + + + MPPPAPLFLS LASTPPPALM PVHHPRAPQS LTLVPPVASS RKAAAVPACP + VASPRHSDYF DPRAPPPPRG DGGYGRPPNG AQDGRVFTSY SIYKGKAALS + FDPRPPLFVP LDSGAYKVAK EGFVLLQFAP AVATRQYDWT RKQVFSLSVW + EIGTLLTLGP TDSCEFFHDP FKGRSEEGKV RKVLKIEPTP DGNGRFFNLS + VQNRLINVDE SIYIPITKGE FAVIVSTFNY IIPHLMGWST FVSSIKPEES + RPYSRPQSTS EYEWRR + + + + + +GRMZM2G155662_P02 NP_001123589 LOC100170235 seq=translation; coord=6:71618445..71621426:-1; parent_transcript=GRMZM2G155662_T02; parent_gene=GRMZM2G155662 + + + MPPPAPLFLS LASTPPPALM PVHHPRAPQS LTLVPPVASS RKAAAVPACP + VASPRHSDYF DPRAPPPPRG DGGYGRPPNG AQDGRVFTSY SIYKGKAALS + FDPRPPLFVP LDSGAYKVAK EGFVLLQFAP AVATRQYDWT RKQVFSLSVW + EIGTLLTLGP TDSCEFFHDP FKGRSEEGKV RKVLKIEPTP DGNGRFFNLK + SAYQR + + + + + +GRMZM2G155662_P03 NP_001123589 LOC100170235 seq=translation; coord=6:71618445..71621426:-1; parent_transcript=GRMZM2G155662_T03; parent_gene=GRMZM2G155662 + + + MPPPAPLFLS LASTPPPALM PVHHPRAPQS LTLVPPVASS RKAAAVPACP + VASPRHSDYF DPRAPPPPRG DGGYGRPPNG AQDGRVFTSY SIYKGKAALS + FDPRPPLFVP LDSGAYKVAK EGFVLLQFAP AVATRQYDWT RKQVFSLSVW + EIGTLLTLGP TDSCEFFHDP FKGRRLI + + + + + +GRMZM2G155662_P04 NP_001123589 LOC100170235 seq=translation; coord=6:71620756..71621431:-1; parent_transcript=GRMZM2G155662_T04; parent_gene=GRMZM2G155662 + + + MPPPAPLFLS LASTPPPALM PVHHPRAPQS LTLVPPVASS RKAAAVPACP + VASPRHSDYF DPRAPPPPRG DGGYGRPPNG AQDGRVFTSY SIYKGKAALS + FDPRPPLFVP LDSGAYKVAK EGFVLLQFAP AVATRQYDWT RKQVCFFIPN + API + + + + + + +4.5128 +-0.273503 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + + + + +4091 4091 4091 4005 3827 2433 2070 1131 546 377 166 87 40 18 12 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4091 4091 4091 4005 3827 2417 2013 1078 469 150 75 30 1 0 + + + + + + +0 1 2 3 4 + + + + +3118 926 42 14 0 + + + + + + +0 1 2 3 4 5 + + + + +538 3100 431 22 9 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2934 (charge 2) + +1573.71 +2 + + +152.057 154.309 158.092 169.197 172.108 175.119 183.179 185.091 201.562 212.952 215.114 219.114 221.698 224.183 232.141 241.092 247.39 287.097 290.185 330.144 409.179 422.167 456.223 603.284 663.284 680.298 701.834 778.354 788.364 800.17 +911.427 971.611 1030.4 1342.57 1543.03 + + + + +4 2 7 2 3 9 3 3 3 4 3 3 3 4 100 5 4 4 4 4 4 6 8 6 19 6 49 6 31 5 +37 5 6 21 6 + + + + + + +GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01; parent_gene=GRMZM5G815453 + + + + + + + +GRMZM2G448344_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=1:203925927..203931405:-1; parent_transcript=GRMZM2G448344_T01; parent_gene=GRMZM2G448344 + + + + + + + +GRMZM2G385635_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=2:200096578..200100853:-1; parent_transcript=GRMZM2G385635_T01; parent_gene=GRMZM2G385635 + + + + + + + +GRMZM2G360821_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=6:160783975..160786062:1; parent_transcript=GRMZM2G360821_T01; parent_gene=GRMZM2G360821 + + + + + + + +GRMZM2G308907_P01 seq=translation; coord=9:32379686..32380603:1; parent_transcript=GRMZM2G308907_T01; parent_gene=GRMZM2G308907 + + + + + + + +GRMZM2G115168_P01 seq=translation; coord=1:131325136..131327527:1; parent_transcript=GRMZM2G115168_T01; parent_gene=GRMZM2G115168 + + + + + + + + +4.93446 +-0.281969 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 + + + + +4578 4578 4480 3859 3294 2362 1880 1239 841 392 216 112 79 17 6 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4599 4599 4501 3876 3216 2220 1657 964 563 174 63 31 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1642 2367 473 88 13 15 0 5 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1874 2149 533 35 7 0 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2936 (charge 2) + +1481.72 +2 + + +156.077 157.097 167.055 169.097 171.149 173.129 186.124 187.108 191.084 196.091 201.123 204.134 219.08 223.155 225.098 228.098 236.067 240.135 246.108 251.15 253.093 258.09 299.062 303.203 317.109 327.165 339.142 345.177 359.029 365.157 +367.135 370.199 383.167 402.272 418.181 422.689 426.172 432.194 448.15 452.224 454.168 464.226 466.204 475.21 481.203 482.237 490.205 518.723 522.719 524.74 526.735 531.725 540.73 553.311 557.213 560.341 563.296 567.266 576.266 581.26 +585.208 587.213 590.263 595.315 632.326 647.372 652.287 670.297 675.843 680.281 698.293 704.307 732.359 766.418 784.432 807.356 817.346 835.353 844.368 862.369 897.523 904.38 922.382 931.403 943.435 949.403 961.426 979.403 1030.46 1034.57 +1036.43 1062.45 1064.44 1080.46 1135.5 1151.54 1161.51 1179.53 1181.51 1278.6 + + + + +3 1 3 3 3 1 22 9 12 2 3 100 9 6 5 4 1 2 4 8 3 3 6 43 5 4 2 3 3 3 +6 2 3 7 2 5 3 1 4 3 4 4 8 6 4 6 9 7 6 1 5 38 21 1 15 7 2 10 8 7 +29 1 6 3 3 13 3 13 6 3 22 4 4 4 21 5 3 12 4 1 7 4 5 5 3 3 3 3 3 2 +3 12 3 8 1 4 6 9 2 4 + + + + + + +GRMZM2G126594_P02 NP_001132615 hypothetical protein LOC100194089 seq=translation; coord=6:131423962..131426896:1; parent_transcript=GRMZM2G126594_T02; parent_gene=GRMZM2G126594 + + + MVKYSTEPSN PTKSAKAMGR DLRVHFKNTR ETAFALRKLS LTKAKSYLED + VIAHKQAIPF RRYCGGVGRT AQAKSRHSNG QGRWPVKSAK FILDLLKNAE + SNAEVKGLDV DTLYVSHIQV NQAQKQRRRT YRAHGRINPY MSSPCHIELI + LSEKEEPVKK EAESQIATRK A + + + + + +GRMZM2G126594_P03 NP_001132615 hypothetical protein LOC100194089 seq=translation; coord=6:131423962..131426896:1; parent_transcript=GRMZM2G126594_T03; parent_gene=GRMZM2G126594 + + + MVKYSTEPSN PTKSAKAMGR DLRVHFKNTR ETAFALRKLS LTKAKSYLED + VIAHKQAIPF RR + + + + + + +5.20856 +-0.297632 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +5662 5662 5662 4777 4710 4090 3478 2752 1691 1049 618 352 132 75 18 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5677 5677 5677 4792 4695 4028 3084 2239 1138 444 152 22 5 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2416 2641 576 44 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1183 3040 1126 290 34 0 3 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2937 (charge 2) + +1123.52 +2 + + +155.081 156.077 157.097 157.134 158.092 159.076 161.092 166.061 167.081 168.066 169.097 169.134 171.076 171.113 173.093 173.128 175.087 175.119 178.086 181.06 181.097 183.076 184.108 185.092 185.128 187.072 187.107 189.087 195.113 197.128 +198.087 199.108 201.087 203.103 205.097 209.091 213.087 216.097 218.15 223.108 226.155 231.097 233.092 240.135 244.094 248.16 251.103 254.113 258.108 265.118 269.125 281.124 282.108 288.134 299.135 300.119 304.162 310.104 316.13 322.175 +327.202 329.147 334.139 345.213 355.163 357.178 363.2 371.154 375.136 386.209 396.189 398.167 404.212 416.18 433.203 434.738 442.228 459.255 497.282 525.782 546.29 563.286 626.308 643.341 645.345 658.36 663.298 725.391 733.314 754.37 +763.365 772.386 773.385 791.355 799.384 830.365 873.431 891.465 931.455 960.457 + + + + +13 3 10 16 7 20 3 3 11 11 10 8 18 12 8 10 4 42 35 8 8 7 3 25 9 20 8 7 9 7 +4 17 10 40 15 4 22 13 42 70 16 21 28 12 7 17 23 8 14 13 4 15 11 3 22 8 12 3 14 16 +11 3 19 70 3 3 3 3 3 4 7 3 11 7 4 3 9 15 9 14 10 15 10 100 3 9 4 3 9 9 +9 9 4 13 4 9 15 3 3 10 + + + + + + +GRMZM2G033641_P01 NP_001131001 hypothetical protein LOC100192106 seq=translation; coord=6:148590842..148593721:1; parent_transcript=GRMZM2G033641_T01; parent_gene=GRMZM2G033641 + + + MADETKQEAA APAAEVVVTE EEKKAEETAP VAEEKAVEAA VEKAAEAEAG + AEEKAAEADS EEEKKAEEAE EAAAGDEAAV IDGTGSFKEE SNLVSELPDP + ERTALAQLKE LVATALANGE FNLPPPPAKE EAKKEEPAKE EAPADKEDEP + KAEEAAAQEP VKEEAKPEEP KTEAPAEAAP EEVKDETPVP EETKTEAPAP + EEPKAEEPAK EELKAEAATE AVAEETKPAE PVPEEEEKTV VVAEEEATKT + VEAIEETVAV AVAAAASEEP EAGEPKEELI WGVPLAGDDE RTDTVLLKFL + RAREFKVKEA MAMLKSAVLW RKRFGIDELL LDADLGLREL EGVVFYRGAD + REGHPVCYNV YGEFQDKELY ERAFGDEEKR ERFLKWRIQL LERGIREQLD + FSPSGICSMV QVTDLKNSPP MLGKHRAVTR QALALLQDNY PEFVAKKVFI + NVPWWYLAAN KVMSPFLTQR TKSKIVFCSP GKSAETLFRY IAPEQVPVQF + GGLYKEDDTE FSTSDAVTEL TVKPSSKETV EIPATENSTV VWELRVLGWE + VSYGAEFTPD AEGGYTVIVQ KTRKVPAHEE PIMKGSFKAT EPGKLVLGVN + NPASRKKKLL CRFKVRSAAA + + + + + + +6.0703 +-0.258311 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +6127 6127 6121 5922 5723 5263 4064 3237 1833 1152 625 384 208 126 68 27 11 5 4 3 3 2 1 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6124 6124 6118 5899 5678 5210 3672 2669 1049 431 184 53 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3020 2485 513 107 17 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +945 3581 1234 329 41 8 2 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2940 (charge 2) + +1173.57 +2 + + +155.082 155.117 156.065 156.085 157.098 158.093 161.092 166.05 167.082 169.097 169.134 171.077 171.113 172.109 173.092 174.096 175.119 181.097 183.077 185.092 187.109 194.13 195.076 197.129 199.108 201.087 203.103 209.092 213.087 215.139 +226.155 228.135 231.098 238.119 241.082 244.166 246.181 252.135 258.145 266.115 268.165 270.145 272.171 276.155 284.124 302.135 306.16 312.119 324.121 330.129 336.683 339.204 342.13 351.203 355.163 367.162 369.215 379.661 387.188 389.174 +395.157 397.209 405.198 413.166 417.192 431.177 435.201 436.204 440.252 452.252 468.247 476.236 478.243 480.245 484.202 498.255 526.251 528.286 544.264 550.229 556.795 575.304 585.3 588.29 650.37 654.352 660.279 672.358 674.362 678.294 +725.38 743.394 775.341 788.324 844.439 902.411 930.419 955.46 973.453 975.443 + + + + +28 2 2 1 1 4 1 9 4 4 23 2 16 3 100 7 15 5 17 5 2 1 5 20 16 71 4 3 14 6 +11 1 7 3 7 3 1 1 13 3 17 3 3 13 7 1 8 3 6 10 9 3 7 3 3 3 5 2 10 2 +3 16 8 7 1 1 15 3 1 3 1 26 1 3 1 3 6 1 3 10 4 6 3 3 5 3 3 49 4 3 +1 12 13 3 7 1 4 1 13 1 + + + + + + +GRMZM2G300408_P01 NP_001159062 transposon protein seq=translation; coord=9:14534848..14536203:1; parent_transcript=GRMZM2G300408_T01; parent_gene=GRMZM2G300408 + + + MATTPTTAIL RLTPAPSPRT ARHPRSATFL QPALSVSLSY SLPDCRNHRL + AAASKDTASS KGQEQDQEPA PSAPQEGGPE KVTEVGAASP GEKSPEAVAA + ELKEVLRARK EAEAAEGRGG WWAGVAQEMT EIEWPAPGKV LGTTGVVLGV + IAGSTVALLS VNALLAELSD TVFAGRGLQD FFSG + + + + + + +4.87086 +-0.216483 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7626 7626 7573 7379 6337 5854 4668 3789 2655 1904 1150 749 431 274 156 73 43 26 22 13 3 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7624 7624 7571 7377 6328 5673 4234 3054 1835 839 389 134 16 5 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3478 3129 820 170 29 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1222 4034 1899 375 84 12 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2941 (charge 2) + +1144.58 +2 + + +153.102 155.082 155.118 157.097 158.092 159.077 166.061 167.081 168.065 169.061 169.098 169.133 171.077 172.108 173.092 173.129 174.132 175.119 181.097 183.113 183.148 184.119 185.056 185.092 186.087 187.071 187.108 195.113 197.129 198.124 +199.108 201.123 203.103 207.125 209.092 211.108 213.087 216.098 226.155 228.05 231.098 232.101 235.119 240.135 242.113 244.166 252.134 256.129 258.145 262.104 268.13 270.11 272.172 276.155 284.124 285.129 287.137 297.156 300.12 302.135 +309.156 312.156 313.157 328.169 330.166 333.177 337.151 339.166 341.145 355.199 369.179 371.155 376.117 394.199 412.22 426.207 430.23 431.234 445.246 469.277 487.293 499.252 513.242 517.262 518.267 588.299 590.283 602.315 638.811 659.34 +687.364 694.422 698.345 716.358 718.365 761.413 815.425 817.431 926.454 944.47 + + + + +6 12 7 7 3 6 6 2 2 6 3 3 11 4 3 40 3 7 4 84 5 8 4 8 9 3 2 3 7 3 +6 45 16 4 7 6 13 3 19 4 25 2 13 8 8 9 2 4 9 4 5 2 4 7 19 4 4 3 3 6 +3 45 9 3 16 9 3 4 4 2 3 7 2 2 8 3 100 20 4 3 2 5 2 25 6 16 4 6 5 8 +2 2 3 43 4 2 14 2 3 8 + + + + + + +GRMZM2G132069_P01 NP_001147976 6-phosphofructokinase 2 seq=translation; coord=3:6801004..6804943:-1; parent_transcript=GRMZM2G132069_T01; parent_gene=GRMZM2G132069 + + + MESFGVPPAP VAAPEKRKKP LDLKDPVPAA AAAAANGGGA TKASPAAKWA + EKKKLVGGDA GYVLEDVPHL TDYLPQLPTY PNPLQDNPAY SVVKQYFVNP + DDTVTQKIVV HKTSARGTHF RRAGPRQRVY FQPDEVNAAI VTCGGLCPGL + NTVIRELVCG LYDMYGVTSV VGIEGGYKGF YSKNTVALTP RSVNGIHKRG + GTVLGTSRGG HDTAKIVDCL QDRGINQVYI IGGDGTQKGA SVIYEEVRRR + GLKCAVVGVP KTIDNDIAVI DKSFGFDTAV EEAQRAINAA HVEAESAENG + IGVVKLMGRN SGFIAMYATL ASRDVDCCLI PESPFYLEGK GGLLEFVERR + LKDNGHMVIV VAEGAGQDLI AKSMNSVDTQ DASGNKLLLD VGLWLSQKIK + DHFKKKPRFP ITLKYIDPTY MIRAVSSNAS DNVYCTLLAH SALHGAMAGY + TGFIVAPVNG RHAYIPFYRI TEKQNKVVIT DRMWARVLCS TNQPCFLSHE + DVENMKHDDD EHHLHNTLLL DSPENSSK + + + + + + +5.40254 +-0.348551 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +2035 2035 2035 2035 1975 1881 1291 988 629 363 119 48 21 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +2035 2035 2035 2035 1975 1881 1289 947 572 266 46 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1110 811 105 13 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +552 1354 119 13 0 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2947 (charge 2) + +1453.62 +2 + + +156.077 157.061 157.097 159.076 169.098 170.092 174.087 175.119 183.112 184.071 185.092 187.071 187.107 191.085 192.089 199.071 199.107 202.082 204.133 209.091 212.103 214.119 219.08 226.155 228.135 230.112 244.092 246.09 261.156 268.317 +283.141 298.141 301.149 318.178 327.131 333.123 370.171 384.236 402.144 405.212 444.247 460.166 474.194 476.246 491.247 591.272 611.03 698.392 702.3 740.245 763.545 820.387 918.388 935.414 937.413 948.339 1034.46 + + + + +8 12 36 12 21 28 22 20 6 29 8 7 9 100 6 7 9 36 7 9 11 23 55 10 7 7 10 10 10 7 +27 6 8 21 7 8 10 6 29 50 7 6 7 45 9 30 6 6 12 8 12 24 9 62 7 6 20 + + + + + + +GRMZM2G004694_P01 seq=translation; coord=7:160808166..160810461:1; parent_transcript=GRMZM2G004694_T01; parent_gene=GRMZM2G004694 + + + MASAPLPAAI EPGKKGNVKF AFACAILASM TSILLGYDIG VMSGASLYIK + KDLKISDVKL EILMGILNVY SLIGSFAAGR TSDWIGRRYT IVFAAVIFFA + GAFLMGFAVN YWMLMFGRFV AGIGVGYALM IAPVYTAEVS PASARGFLTS + FPEVFINFGI LLGYVSNYAF SRLPLRLGWR VMLGIGAAPS VVLALMVLGM + PESPRWLVMK GRLADAKVVL GKTSDTPEEA AERLADIKAA AGIPQELDGD + VVAVPKKRDS EEARVWKELI LSPTPAMRRI LLSGIGIHFF QQASGIDAVV + LYSPRVFKAA GITSDNQLLG TTCAVGVTKT LFILVATFLL DRVGRRPLLL + SSVGGMIFSL VGLAAGLTVI GHYQDEKIPW AIGVAIASTM AYVAFFSIGL + GPITWVYSSE VFPLHVRAMG CALGVASNRL TSGVISMTFI SLSKAITIGG + AFFLYAGVAV LAWVFFFTFL PETRGRTLEA MSKLFGATDD ELKPQDGATK + DKQKLELAAT GTN + + + + + + +6.46214 +-0.349305 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +2320 2320 2320 2320 2312 2119 2033 1840 1688 928 661 302 102 35 17 12 10 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2323 2323 2323 2323 2315 2122 2020 1837 1666 839 515 197 23 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1464 753 97 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +420 1609 256 25 11 0 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2948 (charge 2) + +1205.53 +2 + + +152.057 155.082 157.061 158.057 158.093 161.092 167.082 169.097 171.076 171.113 173.127 175.119 181.06 185.092 185.165 187.071 189.087 191.118 193.098 198.034 198.088 199.108 201.124 204.134 208.072 210.477 212.105 217.082 226.154 241.08 +244.165 249.042 254.151 276.167 286.104 304.114 337.189 341.139 356.147 360.158 386.214 391.194 401.191 443.233 446.235 472.215 517.268 533.688 555.79 575.278 584.302 607.268 704.317 801.375 803.382 842.451 1017.45 1150.91 + + + + +8 15 8 13 14 56 8 14 14 10 8 100 7 24 13 10 44 7 8 8 8 46 9 11 9 7 8 30 82 10 +32 9 8 65 16 26 8 15 8 9 16 10 10 8 14 8 9 8 8 29 9 14 13 68 9 11 11 9 + + + + + + +GRMZM2G055165_P01 Q9TJN6 30S ribosomal protein S17, chloroplastic Precursor seq=translation; coord=8:167665901..167667102:1; parent_transcript=GRMZM2G055165_T01; parent_gene=GRMZM2G055165 + + + MLLLSSPFVS VSPPPPPLSS HGARPALRIE AARQLTGRVV TTKADKTVGV + EVVRLAPHPK YKRRERIKKK YQAHDPDNQF KVGDVVELQP SRPISKTKHF + LAIPLPPRDT RRKSQLLPPL QSDDDQEPSS RE + + + + + +GRMZM2G038013_P01 seq=translation; coord=10:149531451..149532176:1; parent_transcript=GRMZM2G038013_T01; parent_gene=GRMZM2G038013 + + + MLLLSSPFVS VSPPPPPLIS HGARPALRIE AVRQLTRRVV TTKADKTIGV + EVVHLAPHPK YKRRERIKKK YQAHDPDNQF KVGDVVELQP SCPISKTKHF + LAIPLPPRDT RRKSQLLPPL QSDDSQESSL RE + + + + + + +6.23105 +-0.265151 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +6573 6573 6573 6573 6530 6182 5911 5360 4627 3146 2273 1116 605 286 179 85 52 17 13 10 5 2 1 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +6573 6573 6573 6573 6530 6182 5903 5307 4437 2585 1273 252 25 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1719 2832 1448 441 111 17 4 10 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1097 3153 1670 523 93 34 4 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2949 (charge 3) + +1490.7 +3 + + +155.081 157.097 158.092 166.086 167.117 169.097 169.134 172.108 173.13 175.119 176.121 181.097 181.109 183.112 183.149 185.092 185.165 186.124 187.108 195.113 200.103 204.134 209.105 213.087 226.155 227.103 230.078 235.119 240.135 243.109 +247.144 253.093 275.136 276.171 292.154 294.181 300.666 306.151 314.664 320.135 324.13 327.129 331.678 337.159 344.156 358.134 363.664 372.177 374.684 378.71 403.197 405.212 427.195 435.162 438.162 442.157 446.242 452.186 455.189 456.184 +463.268 468.297 472.226 474.233 475.775 478.211 491.263 500.225 501.236 507.624 512.297 518.313 536.286 537.287 544.26 557.24 560.824 565.298 570.217 572.797 580.218 582.666 596.017 601.319 615.251 626.362 628.317 634.28 646.364 651.306 +652.309 658.8 683.389 726.314 731.324 743.343 748.363 750.37 863.391 1071.48 + + + + +13 9 14 11 9 17 14 20 9 77 7 23 22 9 10 19 10 11 16 13 12 19 26 31 12 7 9 8 11 22 +24 59 9 8 42 36 42 18 18 9 36 28 12 9 34 11 24 18 18 7 23 20 7 28 9 9 12 12 41 10 +8 16 15 22 9 9 21 13 12 30 10 14 34 12 10 7 9 18 7 10 8 9 9 18 35 14 9 9 13 28 +10 8 24 9 12 13 100 11 13 7 + + + + + + +GRMZM2G089136_P01 NP_001147628 phosphoglycerate kinase seq=translation; coord=6:156256123..156258890:-1; parent_transcript=GRMZM2G089136_T01; parent_gene=GRMZM2G089136 + + + MASAAAPPTS LSLAARAATR AAAAAAAPLR RGGLATACQP ARSLAFAAGD + ARLAVHVASR CRQAFSGRGT RAMATMAKKS VGELTEADLE GKRVFVRADL + NVPLDENQNI TDDTRIRAAI PTIQYILSKG AKVILSSHLG RPKGFTPKFS + LAPLVGRLSE LLGIQVQKAD DVIGPEVEKL VAALPNGGVL LLENVRFYKE + EEKNDPEFAQ KLASLADLYV NDAFGTAHRA HASTEGVTKF LQPSVAGFLL + QKELDYLVGA VSSPKRPFAA IVGGSKVSSK IGVIESLLEK CDILLLGGGM + IFTFYKAQGL PVGASLVEED KLELATSLLA KAKEKGVSLM LPTDVVIADK + FAPDANSQIV PASAIPDGWM GLDIGPDSVA SFNAALDTTK TVIWNGPMGV + FEFDKFAVGT EAVAKKLAEL SGKGVTTIIG GGDSVAAVEK VGVADVMSHI + STGGGASLEL LEGKELPGVV ALNEAATVTV + + + + + +GRMZM2G089136_P02 NP_001147628 phosphoglycerate kinase seq=translation; coord=6:156255713..156258890:-1; parent_transcript=GRMZM2G089136_T02; parent_gene=GRMZM2G089136 + + + MASAAAPPTS LSLAARAATR AAAAAAAPLR RGGLATACQP ARSLAFAAGD + ARLAVHVASR CRQAFSGRGT RAMATMAKKS VGELTEADLE GKRVFVRADL + NVPLDENQNI TDDTRIRAAI PTIQYILSKG AKVILSSHLG RPKGFTPKFS + LAPLVGRLSE LLGIQVQKAD DVIGPEVEKL VAALPNGGVL LLENVRFYKE + EEKNDPEFAQ KLASLADLYV NDAFGTAHRA HASTEGVTKF LQPSVAGFLL + QKELDYLVGA VSSPKRPFAA IVGGSKVSSK IGVIESLLEK CDILLLGGGM + IFTFYKAQGL PVGASLVEED KLELATSLLA KAKEKGVSLM LPTDVVIADK + FAPDANSQIV PASAIPDGWM GLDIGPDSVA SFNAALDTTK TVIWNGPMGV + FEFDKFAVGT EAVAKKLAEL SGKGVTTIIG GGDSVAAVEK VGVADVMSHI + STGGGASLEL LEGKELPGVV ALNEAATVTR SKL + + + + + +GRMZM2G083016_P01 NP_001151968 metacaspase type II seq=translation; coord=8:120773908..120778906:-1; parent_transcript=GRMZM2G083016_T01; parent_gene=GRMZM2G083016 + + + MASAAAPPTS LSLAARAASR AAAAPLRRGG LAAARQPARS LAFAAGDARL + AVHVASRCRQ ASSARGTRAM ATMAKKSVGD LTEADLKGKR VFVRADLNVP + LDENQNITDD TRIRAAIPTI QYLLGKGAKV ILSSHLGRPK GFTPKFSLAP + LVARLSELLG IQVQKADDVI GPEVEKLVAA LPNGGVLLLE NVRFYKEEEK + NDPEFAQKLA SVADLYVNDA FGTAHRAHAS TEGVTKFLKP SVAGFLLQKE + LDYLVGAVSS PTRPFAAIVG GSKVSSKIGV IESLLEKCDI LLLGGGMIFT + FYKAQGLSVG ASLVEEDKLD LATSLLAKAK EKGVSLMLPT DVVIADKFAP + DANSQIVPAS AIPDGWMGLD IGPDSIAAFN AALETTQTVI WNGPMGVFEY + DKFAIGTEAV AKKLAELSRK GVTTIIGGGD SVAAVEKVGV ADVMSHISTG + GGASLELLEG KELPGVTALD EAATVTV + + + + + + +4.4494 +-0.269661 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + + + + +4945 4945 4945 4945 4807 4632 4383 3521 2864 1871 1137 686 267 132 27 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4942 4942 4942 4942 4804 4623 4332 3438 2559 1315 606 266 15 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1755 1884 1036 244 50 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +894 2324 1305 360 68 10 12 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2950 (charge 3) + +1463.67 +3 + + +152.057 155.081 157.097 158.092 159.076 167.082 168.065 169.097 171.112 173.092 173.129 175.119 183.077 185.092 185.164 186.123 187.071 191.082 191.118 195.076 195.113 196.06 198.124 199.108 200.102 201.122 204.134 208.108 213.087 219.113 +222.124 226.119 227.103 231.096 234.145 240.134 241.082 243.144 247.107 249.123 258.144 259.149 265.118 272.172 275.171 277.119 293.111 295.14 311.171 315.203 323.136 330.145 331.198 337.151 341.145 342.133 346.209 351.181 354.178 358.172 +360.19 374.171 396.108 400.267 418.206 438.247 445.206 452.176 469.204 476.26 480.208 487.211 493.277 498.221 573.263 577.222 584.267 587.286 594.25 596.251 598.247 601.333 604.31 605.307 612.263 613.26 622.322 631.307 649.32 683.353 +684.357 687.404 692.251 709.277 710.265 719.372 727.289 729.295 824.339 953.382 + + + + +8 11 8 7 8 27 7 6 7 10 6 26 13 14 9 7 6 6 22 41 11 7 9 39 31 6 6 16 49 22 +19 16 58 27 13 99 49 6 9 12 100 13 16 8 33 10 7 13 17 6 11 11 35 7 21 7 68 9 9 24 +20 26 7 10 9 6 12 13 17 11 9 14 90 15 9 7 6 6 24 6 7 9 38 16 26 14 30 15 6 16 +9 9 12 18 35 41 98 11 7 7 + + + + + + +GRMZM2G408768_P01 P29306 14-3-3-like protein Fragment seq=translation; coord=2:224904656..224907978:1; parent_transcript=GRMZM2G408768_T01; parent_gene=GRMZM2G408768 + + + MSPSEPTREE SVYMAKLAEQ AERYEEMVEF MERVARSAGG AGGGEELSVE + ERNLLSVAYK NVIGARRASW RIISSIEQKE EGRGNEAHAA SIRAYRSKIE + TELARICDGI LALLDSHLVP SAGGAESKVF YLKMKGDYHR YLAEFKSGAE + RKDAAESTMN AYKAAQDIAL ADLAPTHPIR LGLALNFSVF YYEILNSPDR + ACNLAKQAFD EAISELDSLG EESYKDSTLI MQLLRDNLTL WTSDTNEDGG + DEIKDAAAPK ESAEGQ + + + + + + +GRMZM2G106424_P01 NP_001148842 LOC100282460 seq=translation; coord=4:209797311..209800557:1; parent_transcript=GRMZM2G106424_T01; parent_gene=GRMZM2G106424 + + + MSPSEPTREE SVYMAKLAEQ AERYEEMVEF MERVARYAGG AGGGDELSVE + ERNLLSVAYK NVIGARRASW RIISSIEQKE EGRGNEAHAA SIRAYRSKIE + AELARICDGI LALLDSHLVP SAGGAESKVF YLKMKGDYHR YLAEFKSGAE + RKDAAESTMN AYKAAQDIAL ADLAPTHPIR LGLALNFSVF YYEILNSPDR + ACNLAKQAFD EAISELDSLG EESYKDSTLI MQLLRDNLTL WTSDTNEDAG + DEIKEAAAAP KESAPEGQ + + + + + + +GRMZM2G408768_P02 P29306 14-3-3-like protein Fragment seq=translation; coord=2:224904893..224906863:1; parent_transcript=GRMZM2G408768_T02; parent_gene=GRMZM2G408768 + + + MSPSEPTREE SVYMAKLAEQ AERYEEMVEF MERVARSAGG AGGGEELSVE + ERNLLSVAYK NVIGARRASW RIISSIEQKE EGRGNEAHAA SIRAYRSKIE + TELARICDGI LALLDSHLVP SAGGAESKVF YLKMKGDYHR YLAEFKSGAE + RKDAAESTMN AYKAAQDIAL ADLAPTHPIR LGLALNFSVF YYEILNSPDR + ACNLAKQIVC SFWATD + + + + + + +GRMZM2G408768_P03 P29306 14-3-3-like protein Fragment seq=translation; coord=2:224904656..224906683:1; parent_transcript=GRMZM2G408768_T03; parent_gene=GRMZM2G408768 + + + MSPSEPTREE SVYMAKLAEQ AERYEEMVEF MERVARSAGG AGGGEELSVE + ERNLLSVAYK NVIGARRASW RIISSIEQKE EGRGNEAHAA SIRAYRSKIE + TELARICDGI LALLDSHLVP SAGGAESKVF YLKMKGDYHR YLAEFKSGAE + RKDAAESTMN AYKAAQDIAL ADLAPTHPIR LGLALNFSVF YYEILNSPDR + ACNLAKQVCF FSFYPPFVTC FHFETLCDLF + + + + + + +GRMZM2G305211_P02 seq=translation; coord=7:159911588..159920834:-1; parent_transcript=GRMZM2G305211_T02; parent_gene=GRMZM2G305211 + + + MPRSAPAAAR RGGCAVDPTC RLVAPRASTR GRSNIHFRRL VEYHRRLRMM + RSLRDSLHGR ITARLEAKTV QPMCNRSIKK SRAYSLISSP KSGGGEELSV + EERNLLSVAY KNVIGARRAS WRIISSIEQK EEGRGNEAHA ASIRAYRSKI + ETELARICDG ILALLDSHLV PSAGGAESKV FYLKMKGDYH RYLAEFKSGA + ERKDAAESTM NAYKAAQALS SFSHFFELAV KIMRINMGPP VVSNASVRVA + VQQDVGAASA LPQPLPLHFM VHLQPPCAWR KKETAMRGQR EVFEHEKIKD + WSNVVVAYEP VWAIGTGKVA TPAQAQEVHA SLRDWLKTNV SPEVAESTRI + IYGGSVTVAN CKELAAQPDV DGFLVGGASL KVNSYPTDRG LTEIGTGGDD + FVQTLVVVVE SILQEYLCSV IGDLTIHFCW LWRYYRNITA NTLAVLEAMA + AHNVRTLIYS STCVTYGEPD KMPIAEGTPQ GIRLEKSQAG IFKVSLNCFP + DLFTALKTKH STPKYGSSTM HPQLGRLLKS IMEKTLGLYL QKLLLLSDRM + PLVLMRTTPL VLRVDSRKMC CKPSSVHAQP FALVCLPCPS NRVLAFARLI + DHSESAGYSN LKYLVGAGNL RLEDLICSDA KDSSDRRSLV SIGG + + + + + + +GRMZM2G329740_P01 seq=translation; coord=1:255639238..255646058:1; parent_transcript=GRMZM2G329740_T01; parent_gene=GRMZM2G329740 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VIGARRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY IKMKGDYHRC LIFVGTGHPM GNPYPHGYGY LAEFKSGAER + KDAAESTMNA YKAAQDIALA DLAPTHPIRL GLALNFSVFY YKILNSPDRA + CNLAKQALYK PDADTNDMIS EKLMVQINLN EGIEEDIPPS QYTTRCEEKL + TMTQAAISRE AGPPGYDPGE NFLQVSSMIT SCEQSVIMAP SAIARGVGPP + GYTPGEHQGN GAPWNTSYER RAFTSPATSS REVRPPGYGP EENQGSGISC + NTSREQILFM SPTTISRELG PPGYLPRENQ RSDTSWNTSC LTIQFINIGS + YLSAFKATRV HLDFDYPNSL PLLPLGNGAP WNTSNERRAF TSPATSSREV + RPPGYGPEEN QGSGISCNTS REQILFMSPT TISRELGPPG YLPRENQRSD + TSWNISCLTI QFINIGSYLS AFKATRVHLD FDYPNSLPLL PLAVELIDAE + IAQSFSQQRK KRDGGGPTYH ETFAYAQGPF ARVPEAYVLS LGIYLLPNRE + CTRTLFTCGI PTIKMWEQQV LEISAMVPPP STSADRLGPV LLGCIRDVLW + HGHFLRYLLI LDRTNWKTNM LTALLVPYIF FTLPNVLFSL IRGEVGKWIA + IIAVILRLFF PRHFTDWLEL PGSIILLTAV APSLFAHTFR DDLVGVFICL + AIGCYLLQEH IRASDGLRNA FRKGNGVSNS IGILLLFIYP VWTGVLRIL + + + + + + +GRMZM2G329740_P02 seq=translation; coord=1:255639238..255646058:1; parent_transcript=GRMZM2G329740_T02; parent_gene=GRMZM2G329740 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VIGARRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY IKMKGDYHRY LAEFKSGAER KDAAESTMNA YKAAQDIALA + DLAPTHPIRL GLALNFSVFY YKILNSPDRA CNLAKQALYK PDADTNDMIS + EKLMVQINLN EGIEEDIPPS QYTTRCEEKL TMTQAAISRE AGPPGYDPGE + NFLQVSSMIT SCEQSVIMAP SAIARGVGPP GYTPGEHQGN GAPWNTSYER + RAFTSPATSS REVRPPGYGP EENQGSGISC NTSREQILFM SPTTISRELG + PPGYLPRENQ RSDTSWNTSC LTIQFINIGS YLSAFKATRV HLDFDYPNSL + PLLPLGNGAP WNTSNERRAF TSPATSSREV RPPGYGPEEN QGSGISCNTS + REQILFMSPT TISRELGPPG YLPRENQRSD TSWNISCLTI QFINIGSYLS + AFKATRVHLD FDYPNSLPLL PLAVELIDAE IAQSFSQQRK KRDGGGPTYH + ETFAYAQGPF ARVPEAYVLS LGIYLLPNRE CTRTLFTCGI PTIKMWEQQV + LEISAMVPPP STSADRLGPV LLGCIRDVLW HGHFLRYLLI LDRTNWKTNM + LTALLVPYIF FTLPNVLFSL IRGEVGKWIA IIAVILRLFF PRHFTDWLEL + PGSIILLTAV APSLFAHTFR DDLVGVFICL AIGCYLLQEH IRASDGLRNA + FRKGNGVSNS IGILLLFIYP VWTGVLRIL + + + + + + +GRMZM2G378515_P01 seq=translation; coord=2:236255190..236260495:1; parent_transcript=GRMZM2G378515_T01; parent_gene=GRMZM2G378515 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VISVRRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY IKMKGDYHRG MRLPVKTSSN RVCSVHSTQK VFYKRSMYLA + EFKSGAERKD AAESTMNAYK AAQDIALADL APTHPIRLGL ALNFSVFYYK + ILNSPDRACN LAKQALYKPD ADTNDMISEK LMVQINLNEG IEEDIPPSQY + TTRCEEKLTM TQAAISREAG PPGYDPGENF LQVSSMITSC EQSVIMAPSA + IARGVGPPGY TPGEHQGNGA PWNTSYERRP FTSPATSSRE VRPPGYGPEE + NQGSGISCNT SREQILFMSP TTISRELGPP GYLPRENQRS DTSWNTSCLT + IQFINIGSYL SAFKATRVHL DFDYPNSLPL LPLAVELIDA EIAQSFSQQR + KKRDGGGPTY HETFAYAQGP FARVPEAYVL SLGIYLLPNR ECTRTLFTCG + IPTIKMWEQQ VLEISAMVPP PSTSADRLGP VLLGCIRDVL WHGHFLRYLL + ILDRTNWKTN MLTALLVPYI FFTLPNVLFS LIRGEVGKWI VIIAVILRLF + FPRHFPD + + + + + + +GRMZM2G378515_P02 seq=translation; coord=2:236255190..236260495:1; parent_transcript=GRMZM2G378515_T02; parent_gene=GRMZM2G378515 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VISVRRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY IKMKGDYHRG MRLPVKTSSN RVCSVHSTQK VFYKRSMYLA + EFKSGAERKD AAESTMNAYK AAQDIALADL APTHPIRLGL ALNFSVFYYK + ILNSPDRACN LAKQALYKPD ADTNDMISEK LMVQINLNEG IEEDIPPSQY + TTRCEEKLTM TQAAISREAG PPGYDPGENF LQVSSMITSC EQSVIMAPSA + IARGVGPPGY TPGEHQGNGA PWNTSYERRP FTSPATSSRE VRPPGYGPEE + NQGSGISCNT SREQILFMSP TTISRELGPP GYLPRENQRS DTSWNTSCLT + IQFINIGSYL SAFKATRVHL DFDYPNSLPL LPLAVELIDA EIAQSFSQQR + KKRDGGGPTY HETFAYAQGP FARVPEAYVL SLGIYLLPNR ECTRTLFTCG + IPTIKMWEQQ VLEISAMVPP PSTSADRLGP VLLGCIRDVL WHGHFLRYLL + ILDRTNWKTN MLTALLVPYI FFTLPNVLFS LIRGEVGKWI VIIAVILRLF + FPRHFPAVAP SLFAHTFRDD LVGVFICLAI GCYLLQEHIR ASDGLRNAFR + KGNGVSNSIG ILLLFIYPV + + + + + + +GRMZM2G093944_P01 seq=translation; coord=9:155536907..155542207:-1; parent_transcript=GRMZM2G093944_T01; parent_gene=GRMZM2G093944 + + + MAESPHASKP RGELFVEERN LLSVAYKNVI GARRASWRII SSIEQKEEGR + GNEAHAATIR AYRSKIETEL ARICDGILAL LDSHLVPSAG GAESKVFYLK + MKGDYHRYLA EFKSGAERKD AAESTMNAYK AAQDIALADL APTHPIRLGI + ALNFSVFYYK ILNSPDRACN LAKQALYKPD ADTNDMISEK LMVQINLNEG + IEEDIPPSQY TTRCEEKLTM TQAAISREAG PPGYDPGENF LQVSSMITSC + EQSVIMAPSA IARGVGPPGY TPGEHQGNGA PWNTSYERRP FTSPATSSRE + VRPPGYGPEE NQGSGISCNT SREQILFMSP TTISRELGPP GYFPRENQRS + DTSWNTSCES GLFMSPATTS IEHEIAQSFS QQRKKREGGG PTYHETFAYA + QGPFACVPEA YVLSLGIYLL PNRECTRTLF TCGIPTIKMW EQQVLEISAM + VPPPSTSADR LGPVLLGCIR DVLWHGHFLR YLLILDRTNW KTNMLTTLLV + PYIFFTLPNV LFSLIRGEVG KWIAIIAVIL RLFFPRHFPD WLELPGSIIL + LTAVAPSLFA HTFRDDLVGV FICLAIGCYC FKSTSGRQMD LGTPSGRAMA + CPTPLASSCS SSTLSGPGCC ESCRHCCLRV PVCCRSHFGQ FRLPMM + + + + + + +GRMZM2G097856_P01 seq=translation; coord=7:7070541..7083416:-1; parent_transcript=GRMZM2G097856_T01; parent_gene=GRMZM2G097856 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VIGARRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY LKMKGDYHRY LAEFKSGAER KDAAESTMNA YKAAQDIALA + DLAPTHPIRL GLALNFSVFY YKILNSPDRA CNLAKQALCI EEDIPPSQYT + TRCEEKLTMT QAAISREAGP PGYDPGENFL QVSSMITRCE QSVIMAPSAI + ARGVGPPGYT PGEHQGNGAP WNTSYERRPF TSPATSSREV RPPGYGPEEN + QGSGISCNTS REQILFMSPT TISRELGPPG YLPRENQRSD TSWNTSCESG + LFMSPATTSI EHEIAQSFSQ QRKKREGGGP TYHETFAYAQ GSFARVPEAY + VLSLGIYLLP NRECTRTLST CGIPTIKMWE QQVLEISAMV PPPSTSADRL + GPVLLGCIRD VLWHDHFLRY LLILDRTNWK TNMLTALLVP YIFFTLPNVL + FSLIRGEVGK WIAIIAVILR LFFPRHFPGT TSSVSSYALR SDATCSKSTS + GRQMDLGASD GLRNAFRKGN GVSNSIGILL LFIYPVWTGV LRIL + + + + + + +GRMZM2G097856_P03 seq=translation; coord=7:7070286..7083416:-1; parent_transcript=GRMZM2G097856_T03; parent_gene=GRMZM2G097856 + + + MCNRSIKKSR AYSLISSPKS GGGEELSVEE RNLLSVAYKN VIGARRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLVPS + AGGAESKVFY LKMKGDYHRY LAEFKSGAER KDAAESTMNA YKAAQDIALA + DLAPTHPIRL GLALNFSVFY YKILNSPDRA CNLAKQALCI EEDIPPSQYT + TRCEEKLTMT QAAISREAGP PGYDPGENFL QVSSMITRCE QSVIMAPSAI + ARGVGPPGYT PGEHQGNGAP WNTSYERRPF TSPATSSREV RPPGYGPEEN + QGSGISCNTS REQILFMSPT TISRELGPPG YLPRENQRSD TSWNTSCESG + LFMSPATTSI EHEIAQSFSQ QRKKREGGGP TYHETFAYAQ GSFARVPEAY + VLSLGIYLLP NRECTRTLST CGIPTIKMWE QQVLEISAMV PPPSTSADRL + GPVLLGCIRD VLWHDHFLRY LLILDRTNWK TNMLTALLVP YIFFTLPNVL + FSLIRGEVGK WIAIIAVILR LFFPRHFPDW LELPGSIILL TAVAPSLFAH + TFRDDLVGVF ICLAIGCYLL QEHIRASDGL RGVRWT + + + + + + +GRMZM2G366778_P01 seq=translation; coord=6:164997957..165011468:-1; parent_transcript=GRMZM2G366778_T01; parent_gene=GRMZM2G366778 + + + MCNRSIKKSR AYSLISSPKS GGVEELSVEE RNLLSVAYKN VIGARRASWR + IISSIEQKEE GRGNEAHAAS IRAYRSKIET ELARICDGIL ALLDSHLILS + AGGAESKVFY LKMKGDYHRY LAEFKSGAER KDAAESTMNA YKAAQDIALA + DLAPTHPIRL GLALNFSVFY YEILNSPDRA CNLAKQALYK PDADTNDMIS + EKLMVQINLN EGIEEDIPPS QYTTRCEEKL TMTQAAISRE AGPPGYDPGE + NFLQVSSMIT SCEQSVIMAP SAIARGVGPP GYTPGEHQGN GAPWNTSYER + RPFTSPATSS REVRPPGYGP EENQGSGISC NTSREQILFM SPTTISRELG + LPGYLPRENQ RSDTSWNTSC ESGLFMSPAT TSIEHEIAQS FSQQRKKREG + GGPTYHETFA YAQGSFARVP EAYVLSLGIY LLPNRECTRT LFTCGIPTIK + MWEQQVLEIS AMVPPPSTSA DRLGLVLLGC IRDVLWHGHF LRYLLILDRT + NWKTNMLTAL LVPYIFFTLP NVLFSLIRLV RASRFHHPAH SGRPSLFAHT + FRDDLVGVFI CLAIGCYLLQ EHIRASDGLR NAFRKGNGVS NSIGILLLFI + YPVWTGVLRI L + + + + + + +GRMZM2G305211_P01 seq=translation; coord=7:159919660..159920834:-1; parent_transcript=GRMZM2G305211_T01; parent_gene=GRMZM2G305211 + + + MPRSAPAAAR RGGCAVDPTC RLVAPRASTR GRSNIHFRRL VEYHRRLRMM + RSLRDSLHGR ITARLEAKTV QPMCNRSIKK SRAYSLISSP KSGGGEELSV + EERNLLSVAY KNVIGARRAS WRIISSIEQK EEGRGNEAHA ASIRAYRSKI + ETELARICDG ILALLDSHLV PSAGGAESKV FYLKMKGDYH RYLAEFKSGA + ERKDAAESTM NAYKAAQVGP WCTC + + + + + + + +3.74533 +-0.241634 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +1688 1688 1657 1544 1351 967 787 455 276 162 84 42 22 10 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1711 1711 1679 1545 1346 926 643 372 203 134 75 12 11 1 0 + + + + + + +0 1 2 3 4 5 + + + + +758 829 85 43 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +398 977 270 43 1 0 28 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2953 (charge 2) + +1216.51 +2 + + +152.057 153.066 155.081 155.117 156.076 157.134 158.093 159.076 160.08 167.056 169.061 169.097 170.045 171.077 171.112 171.15 173.092 174.095 175.119 176.121 181.061 183.076 183.113 184.059 185.092 186.087 187.071 188.076 189.087 194.128 +195.113 198.087 199.071 199.108 201.087 203.102 213.086 217.081 218.15 221.085 226.154 227.102 234.145 239.095 241.09 244.165 249.092 253.093 258.108 262.085 266.115 268.977 272.124 277.167 285.009 287.137 299.061 303.02 310.176 333.122 +344.976 349.148 353.152 355.07 363.131 373.081 381.213 387.151 407.178 415.036 418.994 434.169 452.25 457.205 462.224 478.228 495.253 497.717 521.204 523.757 535.248 575.287 578.291 586.253 642.29 661.31 679.343 686.371 730.352 733.355 +743.335 766.377 826.378 830.367 878.403 895.404 960.412 966.448 1031.48 1225.09 + + + + +1 1 6 1 1 1 5 78 2 15 2 1 1 4 1 1 20 1 13 1 1 1 2 1 4 1 100 8 2 7 +4 1 4 5 20 2 11 2 2 5 12 5 5 38 1 1 1 4 22 2 1 2 1 1 24 1 25 7 10 2 +5 1 1 69 2 8 5 1 1 5 10 4 2 2 1 2 8 2 2 1 2 1 5 1 4 1 2 1 1 1 +5 13 1 12 1 7 1 2 1 1 + + + + + + +GRMZM5G845611_P01 B4F8L7 Glyceraldehyde-3-phosphate dehydrogenase BPutative uncharacterized protein ; seq=translation; coord=1:6410461..6413123:1; parent_transcript=GRMZM5G845611_T01; parent_gene=GRMZM5G845611 + + + + + + + +GRMZM2G337113_P02 P09315 Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic Precursor (EC 1.2.1.13)(NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) seq=translation; coord=2:42257261..42259297:-1; parent_transcript=GRMZM2G337113_T02; parent_gene=GRMZM2G337113 + + + + + + + + +4.71533 +-0.269447 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +3739 3739 3563 3262 3057 1870 1475 811 522 267 178 111 39 24 5 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +3732 3732 3556 3246 2992 1711 1242 553 290 105 43 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2000 1451 263 24 2 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +764 2355 535 80 5 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2954 (charge 2) + +1555.68 +2 + + +154.061 158.092 159.077 160.079 175.119 185.092 189.087 195.089 205.1 215.084 223.108 225.099 233.095 239.114 242.114 260.123 268.139 269.125 272.105 274.103 286.15 290.115 296.134 303.177 316.132 326.143 328.132 343.164 346.143 355.144 +363.169 373.154 391.163 438.182 456.189 474.204 475.224 482.218 532.74 539.23 557.238 572.241 576.274 643.252 661.26 664.355 668.284 684.313 694.298 702.325 712.305 730.317 739.338 762.307 809.344 817.346 826.369 828.369 945.406 963.427 +965.43 1046.46 1064.47 1165.52 1266.56 + + + + +1 2 6 1 10 8 3 2 4 3 1 5 6 6 4 2 3 2 9 1 10 2 1 100 3 1 1 1 2 2 +1 4 5 2 4 3 2 6 2 1 3 1 8 3 5 4 1 2 2 3 1 3 12 2 1 2 33 4 2 21 +3 2 14 9 4 + + + + + + +GRMZM5G808402_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=Pt:54176..56114:-1; parent_transcript=GRMZM5G808402_T01; parent_gene=GRMZM5G808402 + + + + + + + +GRMZM2G385622_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=2:200098864..200103052:1; parent_transcript=GRMZM2G385622_T01; parent_gene=GRMZM2G385622 + + + + + + + +GRMZM2G062854_P01 Q5SBI2 Putative uncharacterized protein seq=translation; coord=6:160782373..160789444:-1; parent_transcript=GRMZM2G062854_T01; parent_gene=GRMZM2G062854 + + + + + + + +GRMZM2G448142_P02 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203904004..203910810:-1; parent_transcript=GRMZM2G448142_T02; parent_gene=GRMZM2G448142 + + + + + + + +GRMZM2G448142_P03 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203907697..203910810:-1; parent_transcript=GRMZM2G448142_T03; parent_gene=GRMZM2G448142 + + + + + + + +GRMZM2G113408_P01 P19023 ATP synthase subunit beta, mitochondrial Precursor (EC 3.6.3.14) seq=translation; coord=6:162937179..162940714:-1; parent_transcript=GRMZM2G113408_T01; parent_gene=GRMZM2G113408 + + + + + + + +GRMZM2G041275_P01 seq=translation; coord=3:207616747..207621242:-1; parent_transcript=GRMZM2G041275_T01; parent_gene=GRMZM2G041275 + + + + + + + +GRMZM2G021331_P01 NP_001151807 ATP synthase beta chain seq=translation; coord=8:65969534..65973268:1; parent_transcript=GRMZM2G021331_T01; parent_gene=GRMZM2G021331 + + + + + + + +GRMZM2G478934_P01 Q5SBI3 Putative uncharacterized protein seq=translation; coord=4:111776910..111780853:1; parent_transcript=GRMZM2G478934_T01; parent_gene=GRMZM2G478934 + + + + + + + +GRMZM2G113408_P02 P19023 ATP synthase subunit beta, mitochondrial Precursor (EC 3.6.3.14) seq=translation; coord=6:162937243..162940714:-1; parent_transcript=GRMZM2G113408_T02; parent_gene=GRMZM2G113408 + + + + + + + +GRMZM2G155238_P01 seq=translation; coord=4:111657121..111661039:1; parent_transcript=GRMZM2G155238_T01; parent_gene=GRMZM2G155238 + + + + + + + +GRMZM2G384988_P01 seq=translation; coord=5:35005734..35007041:1; parent_transcript=GRMZM2G384988_T01; parent_gene=GRMZM2G384988 + + + + + + + + +5.29125 +-0.302357 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +4287 4287 4287 4287 4091 3817 3605 3359 3097 2169 1599 818 413 196 67 14 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4250 4250 4250 4250 4054 3770 3533 3237 2932 1701 996 351 43 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2643 1370 264 28 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +653 2443 971 212 16 2 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2956 (charge 2) + +1056.5 +2 + + +155.081 157.061 157.097 157.108 158.092 159.077 159.113 160.076 166.061 167.081 167.119 169.061 169.097 169.133 171.076 171.113 171.149 173.092 175.071 175.119 181.097 183.077 183.113 185.092 185.164 186.087 186.124 187.107 189.102 194.128 +195.088 195.113 196.072 197.128 198.088 199.108 201.087 204.134 212.102 215.139 216.098 221.129 226.155 230.114 232.14 240.134 244.128 246.181 249.122 251.151 255.145 258.146 262.151 269.124 272.125 274.118 283.142 286.152 294.181 297.155 +303.176 308.638 312.191 323.136 341.145 343.233 359.158 372.261 383.201 400.23 404.189 412.188 414.247 422.277 440.287 448.239 454.241 471.267 490.248 497.283 511.322 519.274 525.271 542.304 547.793 554.281 582.359 616.263 621.331 626.324 +629.336 653.393 677.3 700.375 735.334 740.362 787.404 814.369 830.425 871.406 + + + + +21 6 6 5 26 29 18 10 11 11 5 24 35 10 9 49 6 29 11 85 11 100 5 9 18 42 45 22 9 12 +9 12 12 11 5 43 86 44 27 41 11 61 34 13 69 16 22 10 11 5 13 6 5 5 42 10 5 5 13 15 +9 28 14 5 32 14 14 10 10 16 28 5 5 5 74 10 26 47 9 46 5 11 5 14 23 5 13 40 11 5 +58 10 13 24 29 5 43 16 10 10 + + + + + + +GRMZM5G845611_P01 B4F8L7 Glyceraldehyde-3-phosphate dehydrogenase BPutative uncharacterized protein ; seq=translation; coord=1:6410461..6413123:1; parent_transcript=GRMZM5G845611_T01; parent_gene=GRMZM5G845611 + + + + + + + +GRMZM2G337113_P02 P09315 Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic Precursor (EC 1.2.1.13)(NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) seq=translation; coord=2:42257261..42259297:-1; parent_transcript=GRMZM2G337113_T02; parent_gene=GRMZM2G337113 + + + + + + + + +4.40834 +-0.205039 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +4797 4797 4740 4108 3460 2782 2131 1555 981 617 385 238 149 92 63 47 43 7 5 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +4772 4772 4715 4063 3271 2444 1374 801 389 114 69 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1330 1760 1155 429 93 28 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +664 2187 1260 477 139 27 43 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2959 (charge 3) + +1555.68 +3 + + +154.061 156.077 157.097 157.109 158.092 159.076 160.079 167.056 167.093 175.107 175.119 183.059 185.092 187.072 193.109 195.088 196.09 196.108 203.103 205.1 211.119 215.085 221.104 223.108 225.098 233.095 239.114 240.137 244.111 252.096 +268.141 269.124 272.106 274.102 278.125 281.051 286.15 296.135 299.062 303.177 305.182 308.136 316.132 322.156 326.146 340.166 344.976 359.028 370.688 391.167 395.206 409.182 413.214 415.036 417.181 423.201 427.193 431.238 441.216 458.2 +471.197 473.213 475.226 482.217 510.231 523.737 526.245 528.238 532.741 544.255 554.241 559.246 572.248 574.264 576.273 583.265 624.782 633.79 641.268 643.317 659.281 661.256 673.29 691.313 699.312 706.43 722.316 739.337 741.354 744.295 +762.304 808.357 826.369 828.372 836.349 946.406 963.428 965.421 1064.48 1165.53 + + + + +1 1 8 2 3 15 8 13 2 2 9 1 7 2 1 4 1 2 3 8 3 4 1 3 7 5 10 2 3 1 +4 3 5 2 2 2 10 2 39 100 2 2 3 3 3 2 10 5 7 1 1 1 3 4 2 2 1 1 2 1 +1 7 9 11 2 3 2 3 3 2 2 2 2 2 15 2 2 4 1 4 2 5 2 1 1 2 1 18 2 1 +2 4 44 5 2 2 11 2 4 2 + + + + + + +GRMZM2G066460_P01 O24573 60S acidic ribosomal protein P0 seq=translation; coord=6:9203729..9206286:-1; parent_transcript=GRMZM2G066460_T01; parent_gene=GRMZM2G066460 + + + MAIKRTKAEK KIAYDKKLCS LLDEYTKVLI ALADNVGSKQ LQDIRRGLRG + DSVVLMGKNT LIRRCIKVYA EKTGNHTFDP LMDLLVGNVG LIFTKGDLKE + VREEVAKYKV GAPARVGLVA PVDVVVPPGN TGLDPSQTSF FQVLNIPTKI + NKGTVEIITP VELIKKGEKV GSSESALLAK LGIRPFSYGL QVTSVYEDGS + VFSPEVLDLS EEDLIEKFAT GVSMVASLSL AISYPTLAAV PHMFINGYKN + VLAVAVETDY SYPHADKIKE YLKDPSKFAV AAPVAAGDSG AAAAPKEEEK + AAEPEEESDE EMGFSLFDD + + + + + +GRMZM2G179976_P01 NP_001141489 hypothetical protein LOC100273601 seq=translation; coord=4:36122702..36125196:1; parent_transcript=GRMZM2G179976_T01; parent_gene=GRMZM2G179976 + + + MAIKRTKAEK KIAYDKKLCS LLDEYTKVLI ALADNVGSKQ LQDIRRGLRG + DSVVLMGKNT LIRRCIKVYA EKTGNHTFDP LMDLLVGNVG LIFTKGDLKE + VREEVAKYKV GAPARVGLVA PVDVVVPPGN TGLDPSQTSF FQVLNIPTKI + NKGTVEIITP VELIKKGEKV GSSESALLAK LGIRPFSYGL QVTSVYEDGS + VFSPEVLDLS EEDLIEKFAT GVSMVASLSL ALSYPTLAAV PHMFINGYKN + VLAVAVETDY SYPHADKIKE YLKDPSKFAV AAPVAAADSS AAAAPKEEEK + APEPAEESDE EMGFSLFDD + + + + + + +4.33512 +-0.234331 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +4345 4345 4345 4242 4146 3714 3403 2703 1938 1444 819 402 220 129 93 51 26 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4342 4342 4342 4239 4133 3692 2897 2511 1496 887 338 70 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1181 1828 1197 106 41 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1385 2229 606 117 8 0 8 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2961 (charge 2) + +979.511 +2 + + +153.102 155.081 156.077 157.097 158.092 159.077 167.081 168.066 169.097 169.133 171.077 171.113 173.056 173.092 173.129 175.119 181.097 183.077 183.15 185.092 186.091 187.072 191.118 194.129 195.075 195.114 196.08 197.129 198.123 199.108 +202.086 203.103 207.111 209.091 213.087 214.09 217.098 219.114 220.096 222.124 226.119 227.102 231.096 234.145 240.134 242.186 244.129 247.108 249.16 252.108 258.144 259.148 263.103 265.118 273.12 275.171 284.171 293.113 295.178 300.122 +304.162 311.172 313.186 331.197 334.138 339.203 341.147 344.202 346.21 357.214 361.188 374.172 401.175 418.205 419.208 428.212 446.224 447.227 469.204 475.225 493.277 502.228 519.253 574.324 595.249 603.253 605.309 613.284 614.293 623.32 +630.286 631.307 647.311 649.318 687.402 710.273 718.348 720.374 728.288 833.374 + + + + +3 5 8 11 9 8 9 3 3 3 3 4 3 4 10 48 4 7 3 20 3 7 11 4 13 4 3 4 8 24 +8 3 4 5 16 3 19 5 5 6 17 17 7 41 29 13 13 27 5 3 22 6 36 61 7 8 4 16 3 3 +3 4 13 100 4 3 4 3 10 10 4 5 3 19 3 3 14 3 3 3 12 4 28 8 3 3 3 6 3 3 +7 23 9 5 11 4 18 3 7 8 + + + + + + +GRMZM2G089136_P01 NP_001147628 phosphoglycerate kinase seq=translation; coord=6:156256123..156258890:-1; parent_transcript=GRMZM2G089136_T01; parent_gene=GRMZM2G089136 + + + + + + + +GRMZM2G089136_P02 NP_001147628 phosphoglycerate kinase seq=translation; coord=6:156255713..156258890:-1; parent_transcript=GRMZM2G089136_T02; parent_gene=GRMZM2G089136 + + + + + + + +GRMZM2G083016_P01 NP_001151968 metacaspase type II seq=translation; coord=8:120773908..120778906:-1; parent_transcript=GRMZM2G083016_T01; parent_gene=GRMZM2G083016 + + + + + + + + +4.52256 +-0.244463 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +4226 4226 4226 3894 3346 2850 2141 1507 1089 716 482 311 172 70 36 10 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +4240 4240 4240 3908 3357 2718 1818 1128 692 434 266 192 84 18 13 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2104 1690 364 70 5 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +862 2400 799 153 18 1 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2962 (charge 2) + +1463.66 +2 + + +155.081 156.076 159.078 167.082 167.117 169.097 171.077 175.12 183.076 185.091 186.087 187.071 195.076 195.113 198.123 199.108 201.087 204.134 208.108 213.087 219.113 222.123 226.155 227.103 231.097 232.1 236.139 239.15 240.134 242.085 +244.165 258.144 259.092 275.172 295.14 299.17 303.204 306.109 311.171 324.122 329.182 342.128 344.155 346.209 352.115 354.18 358.173 361.183 370.125 372.188 374.172 383.192 388.135 432.219 445.207 452.254 462.237 469.202 476.254 487.219 +493.278 497.235 501.236 515.244 535.812 539.265 561.26 567.234 573.268 584.27 591.276 595.238 604.301 612.26 622.32 630.274 674.275 690.303 702.351 703.346 710.266 719.373 721.373 723.832 727.291 743.366 745.302 768.385 802.36 819.345 +834.398 903.5 914.393 931.414 935.386 948.428 953.386 971.389 1076.54 1206.5 + + + + +8 10 6 16 3 3 3 7 8 3 8 4 21 4 4 18 5 3 9 27 9 10 48 50 58 4 3 12 91 8 +11 72 56 22 4 8 3 3 8 3 4 15 3 44 15 3 10 4 16 3 25 4 9 16 16 6 4 8 3 8 +33 3 3 4 8 4 11 3 10 4 3 9 3 12 3 3 5 14 13 3 11 100 10 8 26 4 13 3 7 15 +9 4 3 5 3 26 10 9 4 3 + + + + + + +AC189750.4_FGP004 seq=translation; coord=7:152351854..152354543:-1; parent_transcript=AC189750.4_FGT004; parent_gene=AC189750.4_FG004 + + + MASATTSISS HPAALRDVKG DMFSLFWMLF PLYNFCSDPT FQLVKCAAPQ + QNSPEFEAHT GLTLLISLPS VRAAARIGGL RQQQASVAPS AAAARGQRAR + AVRSLRAAEP ARQPVAASAA AAAPAAPVAD EAAALAAVDY EALARELEGA + SPLEIMDRAL AMFGSEIAIA FSGAEDVALI EYAKLTGRPF RVFSLDTGRL + NPETYQLFDK VEKHYGIRIE YMFPDASEVQ ELVRTKGLFS FYEDGHQECC + RVRKVRPLRR ALKGLRAWIT GQRKDQSPGT RASIPLVQVD PSFEGLDGGA + GSLVKWNPVA NVDGKDIWTF LRTMDVPVNT LHAQGYVSIG CEPCTRPVLP + GQHEREGRWW WEDAKAKECG LHKGNIDKDA QAAAPRSANG NGSAGAPDIF + ESPAVVSLTR TGIENLLRLE NRAEPWLVVL YAPWCPFCQA MEASYVELAE + KLAGSGVKVA KFRADGEQKP FAQAELQLQS FPTVLLFPGR TARPIKYPSE + KRDVDSLLAF VNSLR + + + + + +GRMZM2G087254_P01 NP_001105805 adenosine 5'-phosphosulfate reductase 2 seq=translation; coord=2:202525441..202528769:-1; parent_transcript=GRMZM2G087254_T01; parent_gene=GRMZM2G087254 + + + MASATTSISS HPAALRDVKA ARIGGALRQV GVAARGQRAR AVPPLRAAEP + ARRPVAASAA AAPPAAPVAD EAAVDYEALA RELEGASPLE IMDRALAMFG + SEIAIAFSGA EDVALIEYAK LTGRPFRVFS LDTGRLNPET YQLFDRVEKH + YGIRIEYMFP DASEVQELVR TKGLFSFYED GHQECCRVRK VRPLRRALRG + LRAWITGQRK DQSPGTRASI PLVQVDPSFE GLDGGAGSLV KWNPVANVDG + KDIWTFLRTM DVPVNALHAQ GYVSIGCEPC TRPVLPGQHE REGRWWWEDA + KAKECGLHKG NIDKDGQAAA AAAAPRTANG NGSAGAPDIF ESPAVVSLTR + AGVENLLRLE SRAEPWLVVL YAPWCPFCQA MEASYVELAE RLAGSGGVKV + ARFRADGEQK PFAQAELQLQ SFPTVLLFPS RTARPIKYPS EKRDVDSLLA + FVNSLR + + + + + + +5.81777 +-0.283794 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6541 6541 6541 6541 6503 6254 5945 5458 4739 3652 2756 1306 645 311 127 76 42 29 2 1 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6541 6541 6541 6541 6503 6254 5935 5405 4567 3355 2011 603 74 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1758 2791 1519 395 73 4 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1475 2781 1687 505 60 32 11 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2963 (charge 3) + +1289.72 +3 + + +152.057 153.102 154.086 155.082 156.077 157.097 157.109 157.134 158.092 159.077 162.103 166.061 167.055 167.081 169.097 169.134 171.113 172.072 173.093 173.129 175.119 176.122 181.097 183.149 184.108 185.092 185.129 187.072 187.144 189.087 +193.096 194.129 195.113 197.129 198.124 199.072 199.108 200.14 201.123 207.126 208.953 211.12 213.086 217.081 226.119 230.623 233.128 235.119 240.133 244.166 252.109 255.145 258.146 265.623 272.171 274.014 276.155 279.134 284.01 289.162 +292.661 296.124 312.167 314.136 329.192 344.976 359.029 360.029 363.187 371.7 393.859 401.748 404.224 406.744 412.166 415.749 426.249 442.23 447.223 453.246 460.24 464.735 487.262 503.295 511.335 513.239 521.756 539.333 556.357 575.315 +584.315 590.281 597.308 623.303 630.3 638.81 667.426 675.339 725.363 746.374 + + + + +8 10 7 40 9 16 10 27 23 34 8 28 27 15 11 10 17 13 21 8 100 8 18 50 9 28 15 21 11 11 +7 10 11 10 7 8 10 11 10 14 17 14 14 9 23 15 9 44 17 19 10 15 29 8 27 11 16 35 40 7 +7 17 8 13 39 15 44 44 37 14 27 8 10 12 8 13 28 10 8 7 58 15 11 19 37 12 26 20 17 11 +22 15 9 9 7 11 31 22 7 16 + + + + + + +GRMZM2G701221_P01 NP_001148935 LOC100282555 seq=translation; coord=6:156819019..156827574:1; parent_transcript=GRMZM2G701221_T01; parent_gene=GRMZM2G701221 + + + MATHPASPTA GAGGDRSPSG PPPVRLSAAQ AVAAIQPTSP RYFFSSLAAA + SAAASSPHRR IGIAVDLSDE SAFAVKWAVQ NYLRPGDAVV LLHVRPTSVL + YGADWGSIPV SVDDDPDVDI AEGAVRAAAA EEEPEEAKKK REEEFDSFTS + TKAQDLAQPL VGAQIPFKIH IVKDHDMKER LCLEAERLGL SAMIMGSRGF + GASRRVGKGR LGSVSDYCVH HCVCPVVVVR YPDDAFGDEL RTVPENEPVY + HAAPEAQKEN + + + + + + + +6.33381 +-0.436815 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +4642 4642 4549 4420 4135 3942 3666 1944 1428 515 152 39 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4650 4650 4557 4428 4141 3900 3615 1808 1210 288 45 5 1 0 + + + + + + +0 1 2 3 4 + + + + +2928 1487 232 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +901 3288 446 18 1 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2968 (charge 2) + +1407.66 +2 + + +151.006 152.057 155.081 157.098 163.06 167.093 169.097 171.076 171.113 175.119 178.462 178.714 181.096 189.087 193.108 199.071 199.108 201.123 211.119 226.156 235.119 239.114 244.166 256.129 259.143 261.212 286.14 288.145 306.156 308.135 +324.166 334.15 352.162 404.185 476.645 532.245 588.279 603.284 714.868 757.352 767.651 783.358 801.386 882.406 888.42 959.447 967.745 1039.48 1040.49 1056.51 1058.52 1133.55 1247.64 + + + + +2 3 8 2 7 3 9 3 2 30 2 2 3 9 3 2 4 2 17 3 13 9 3 11 2 2 10 2 16 3 +28 16 27 2 2 3 9 7 2 2 2 2 21 2 18 15 2 7 2 100 12 2 2 + + + + + + +GRMZM2G140051_P01 NP_001105215 nucleosome/chromatin assembly factor group A seq=translation; coord=9:19393494..19397648:-1; parent_transcript=GRMZM2G140051_T01; parent_gene=GRMZM2G140051 + + + MGGEKETFDT SDLNASLPAA AAALSAEDRA GLVNALKDKL QSLAGQHADV + LETLSPNVRK RVEFLREIQS QHDEIEAKFF EERAALEAKY QKLYEPLYTK + RYGIVNGEVE VDGVCDEPAS ENTVEGKEPD AKGVPDFWLT AMKTNEVLSE + EIQERDEAAL KYLKDIKWSR IEDPKGFKLD FFFDTNPFFK NSVLTKTYHM + VDEDDPILEK AIGTEIEWYP GKNLTQKILK KKPKKGSKNT KPITKTEDCE + SFFNFFNPPQ VPEDDDDIDE DTADELQSQM EHDYDIGTTI RDKIIPHAVS + WFTGEAVQGE DFGELGDDDE DDDDEDDDED DEDEEEDDDE EEDDEEESKP + ARKSGSGRRH KAPQKVSQGN AEQPAECKQQ + + + + + +GRMZM2G140051_P02 NP_001105215 nucleosome/chromatin assembly factor group A seq=translation; coord=9:19393494..19397627:-1; parent_transcript=GRMZM2G140051_T02; parent_gene=GRMZM2G140051 + + + MGGEKETFDT SDLNASLPAA AAALSAEDRA GLVNALKDKL QSLAGQHADV + LETLSPNVRK RVEFLREIQS QHDEIEAKFF EERAALEAKY QKLYEPLYTK + RYGIVNGEVE VDGVCDEPAS ENTVEGKEPD AKGVPDFWLT AMKTNEVLSE + EIQERDEAAL KYLKDIKWSR IEDPKGFKLD FFFDTNPFFK NSVLTKTYHM + VDEDDPILEK AIGTEIEWYP GKNLTQKILK KKPKKGSKNT KPITKTEDCE + SFFNFFNPPQ VPEDDDDIDE DTADELQSQM EHDYDIGTTI RDKIIPHAVS + WFTGEAVQGE DFGELGDDDE DDDDEDDDED DEDEEEDDDE EEDDEEESKP + ARKSGSGRRH KVHDLKFTG + + + + + + +5.75629 +-0.311151 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +6584 6584 6584 6580 6322 6034 5661 4789 3883 2661 1536 809 439 170 78 25 2 1 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +6606 6606 6606 6602 6344 6046 5635 4686 3435 1984 638 212 74 11 5 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2389 2637 1294 248 31 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1119 2909 1736 674 111 56 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2979 (charge 3) + +1426.68 +3 + + +155.082 157.097 158.092 159.077 160.08 166.061 169.097 169.133 170.117 171.076 171.112 173.092 175.119 176.123 181.061 181.095 185.056 185.092 185.165 186.097 186.169 187.071 188.075 197.129 198.087 198.132 199.072 200.14 201.124 204.135 +209.104 213.16 215.139 216.098 218.15 221.104 225.123 230.078 235.119 243.133 245.124 249.098 253.093 256.129 258.108 262.151 263.154 272.159 279.665 300.155 301.158 313.842 328.192 329.182 347.193 354.136 362.203 364.126 382.136 401.73 +421.207 436.194 445.241 460.275 464.187 470.259 479.228 480.233 493.167 495.219 505.78 532.241 541.299 550.266 551.27 558.325 563.28 564.291 579.217 580.218 584.268 589.321 597.226 624.265 641.358 649.334 650.336 655.378 680.264 693.336 +698.387 704.347 708.256 726.412 762.417 763.423 795.438 821.346 841.405 950.389 + + + + +15 10 10 31 7 6 9 11 4 8 5 5 36 4 5 8 6 18 20 5 7 39 11 100 6 11 8 11 24 7 +9 7 42 8 50 8 12 6 5 5 9 8 12 4 4 27 10 7 4 14 9 4 19 15 7 4 11 7 8 7 +13 8 6 5 5 8 14 6 4 5 8 4 6 55 23 25 5 4 12 5 8 5 5 6 4 51 25 15 4 5 +4 12 21 7 14 7 11 7 10 6 + + + + + + +GRMZM2G157018_P01 NP_001150316 ATP synthase D chain, mitochondrial seq=translation; coord=1:200480447..200483616:-1; parent_transcript=GRMZM2G157018_T01; parent_gene=GRMZM2G157018 + + + MSGNGAKKVV DAAVKAGRTI IDWDGMAKLL VTDEARKEFA ALRRAFDDVN + HQLQTKFSQE PQPIDWEYYR KGIGSKVVDM YKEAFESIEI PKYVDTVTPQ + YKPKFDAVIA ELKEAEKEHQ KESERIEKEL AEMEEMRKKI STMTADDYFE + KYPELRKKFD DEIRNDNWGY + + + + + + + + +5.17365 +-0.295637 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +1777 1777 1767 1707 1500 1400 1261 977 820 548 301 168 61 31 8 2 1 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1784 1784 1774 1714 1499 1384 1228 922 633 303 81 16 10 1 0 + + + + + + +0 1 2 3 4 + + + + +802 923 145 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +436 865 362 93 22 103 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2980 (charge 2) + +1169.48 +2 + + +152.056 155.082 155.117 157.097 157.134 158.092 159.076 166.05 167.081 169.097 169.133 170.118 171.076 171.113 172.109 173.092 173.128 175.119 176.122 181.098 183.077 183.112 185.092 187.108 191.118 194.129 195.075 195.112 197.128 200.103 +201.087 203.103 213.087 215.139 219.113 223.155 226.155 227.102 240.134 243.134 249.095 251.15 258.154 265.119 268.165 277.086 284.123 290.147 293.113 296.161 303.178 306.16 322.154 324.12 332.141 341.146 346.208 355.66 364.14 388.171 +400.183 414.171 430.23 432.185 435.203 446.172 451.197 456.248 487.251 493.276 499.268 516.242 527.286 547.243 550.226 555.791 562.227 568.315 572.25 580.241 582.247 599.278 645.267 655.345 661.262 663.273 678.294 681.357 710.304 728.321 +729.322 775.338 792.325 799.358 801.365 811.467 863.36 927.36 973.439 1072.58 + + + + +5 11 8 3 6 7 6 6 6 5 2 7 2 13 2 17 2 41 2 3 18 3 5 2 7 4 13 2 39 17 +27 2 8 100 6 3 16 8 7 22 2 2 12 2 7 5 8 5 4 8 9 8 13 2 7 3 3 2 2 18 +2 5 5 4 17 2 10 7 5 2 6 17 11 2 12 12 4 7 2 17 5 18 3 9 2 20 6 2 6 15 +5 15 11 21 2 2 20 5 14 2 + + + + + + +GRMZM2G434173_P01 NP_001148093 LOC100281701 seq=translation; coord=1:299988513..299993142:-1; parent_transcript=GRMZM2G434173_T01; parent_gene=GRMZM2G434173 + + + MATIPTTDSG LVLSSSALLR RTRRAASSVT ARLPAVARRR PQLLVRASAK + EIAFDQGSRA ALQAGVEKLA AAVGVTLGPR GRNVVLDEFG TPKVVNDGVT + IARAIELADP MENAGASLIR EVASKTNDSA GDGTTTASVL AREIIKLGML + SITSGANPVS VKKGIDKTVQ KLVEELEKKS RPVKGSGDIK AVAAISAGND + EFVGTMIAEA IDKVGPDGVL SIESSSSFET TVEVEEGMEL DRGYISPQFV + TNLEKSIVEF ENARILVTDQ KISSIKEIIP LLEQTTQLRA PLLIIAEDVS + GEALATLVIN KLRGILNVAA IKAPGFGERR KALLQDIAIV TGAEYQSKDL + GLLVEDTTVE QLGIARKVTI SSSSTTIIAD AASKDDIQAR IAQLKRELSQ + TDSTYDSEKL AERIAKLSGG VAVVKVGAST EAELEDRKLR IEDAKNATFA + AIEEGIVPGG GAAYVHLSTF VPAIKETLDD PEERLGADII QKALVAPAAL + IAHNAGVEGE VIVDKIRESE WEFGYNAMAD KHENLVEAGV IDPAKVTRCA + LQNAASVAGM VLTTQAIVVE KPKKAPAAAA AAAP + + + + + + +4.53821 +-0.211079 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +2272 2272 2272 2272 2209 2115 1990 1786 1451 1221 901 641 409 242 166 113 59 33 13 12 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2267 2267 2267 2267 2204 2110 1940 1733 1399 1017 464 164 48 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1020 896 237 119 2 0 0 5 + + + + + + +0 1 2 3 4 5 6 7 + + + + +463 1024 564 159 59 9 1 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2989 (charge 2) + +909.514 +2 + + +155.082 155.118 157.097 157.133 158.092 159.076 161.074 167.081 167.118 169.097 169.134 171.076 172.072 173.128 175.119 181.061 183.113 183.149 185.092 185.104 186.124 187.108 188.111 189.069 193.097 194.129 195.113 197.128 198.087 200.139 +201.123 203.103 212.139 214.118 226.118 228.632 231.097 237.135 240.134 241.137 243.182 254.162 255.655 257.161 272.172 277.656 283.177 285.156 289.159 291.174 297.192 311.172 323.207 326.693 329.191 337.187 342.215 346.183 354.216 356.193 +359.204 362.69 368.228 370.214 382.208 387.201 399.235 408.225 413.253 425.252 427.231 439.273 441.241 442.241 453.246 457.257 479.26 482.308 484.283 487.261 496.292 510.304 513.293 524.284 528.278 536.316 554.3 557.306 581.341 595.317 +606.325 608.307 611.325 624.385 644.336 652.379 695.426 701.36 707.342 724.373 + + + + +12 18 7 7 21 11 33 8 7 40 9 33 10 18 70 7 9 16 9 7 15 100 8 7 7 15 16 8 10 11 +11 35 14 27 14 13 24 26 71 10 10 44 10 14 11 40 14 35 11 42 8 85 8 19 26 11 11 36 14 31 +9 59 7 7 82 12 8 13 15 14 9 16 7 7 81 35 11 7 10 8 11 45 7 58 8 8 30 10 88 15 +8 12 33 11 25 80 11 11 12 48 + + + + + + +GRMZM2G018197_P01 NP_001147047 60S ribosomal protein L4 seq=translation; coord=2:233433323..233435947:-1; parent_transcript=GRMZM2G018197_T01; parent_gene=GRMZM2G018197 + + + MAASSRPLVS VKALEGDMVT DAPGIALPPV FGAPIRPDVV RFTHKLLSCN + KRQPYAVSRR AGHQTSAESW GTGRAVSRIP RVPGGGTHRA GQGAFGNMCR + GGRMFAPTKI WRKWHRRVNV NLRRVAVASA LAATAVPALV QARGHRIETV + PEMPLVISDS AESIEKTSQA LKILKQVGAY ADAEKAKDSV GIRPGKGKMR + NRRYINRKGP LVVYGTEGSK VVKAFRNLPG VDVANVERLN LLDLAPGGHL + GRFVIWTESA FKKLEEVYGS FDAPSQKKKG FVLPRPKMAN ADLGRIINSD + EVQSVVKPLN KEVKRREKRK NPLKNMAAVL KLNPYLGTAR KMATLAEAAR + VKARKEKLDS KRTKLTSEET AKVKAAGKAW YKTMISDSDY TEFENFTKWL + GVTQ + + + + + +GRMZM2G100403_P02 NP_001168309 hypothetical protein LOC100382075 seq=translation; coord=7:10287294..10291100:1; parent_transcript=GRMZM2G100403_T02; parent_gene=GRMZM2G100403 + + + MVAVNRPLVS VKALEGDMVT DAPGIALPPV FGAPIRPDVV RFTHKLLSCN + KRQPYAVSRR AGHQTSAESW GTGRAVSRIP RVPGGGTHRA GQGAFGNMCR + GGRMFAPTKI WRKWHRRVNI NLRRVAVASA LAATAVPALV QARGHRIESV + PEMPLVISDS AESIEKTSQA LKILKQIGAH ADAEKAKDSV GIRPGKGKMR + NRRYINRKGP LIVYGTEGSK VVKAFRNLPG VDVANVERLN LLDLAPGGHL + GRFVIWTQSA FNKLEEVYGS YDAPSQKKKG FVLPRPKMSN ADLGRIINSD + EVQSVVKPLN KEVKRREKRK NPLKNMAAVL KLNPYLGTAR KMATLAEAAR + VKARKAKLDS KRTKLTPETA KVKAAGKAWY KTMVSDSDYT EFENFSKWLG + VTQ + + + + + +GRMZM2G007695_P01 NP_001130508 hypothetical protein LOC100191607 seq=translation; coord=5:4268599..4271215:1; parent_transcript=GRMZM2G007695_T01; parent_gene=GRMZM2G007695 + + + MAASARPLVT VRALEGDMAT DSAGVPLADV LRAPIRPDIV RFVHKLLSCN + SRQPYAVSRR AGHQTSAESW GTGRAVSRIP RVPGGGTHRA GQGAFGNMCR + GGRMFAPTKI WRRWHRRVNI HLRRVAIASA LSATAVPSLV LARGHRVESV + PELPLVVSDS AESIEKTAQA INILKQLGAY ADAEKAKDSV GIRPGKGKMR + NRRYINRKGP LVVYGTEGSK VVKAFRNLPG VDVANVERLN LLDLAPGGHL + GRFVIWTECA FKKLDEVYGT FNAPSAKKKG FVLPRPKMAN ADLSRLINSD + EVQSVVKPIN KDVKRREPRK NPLKNMAAVL KLNPYLGTAR KMAALAEAAR + VKARKQKLDS KRTKLSPEEA SKVKAAGKAW YKTMVSDSDY TEFENFTKWL + GVTQ + + + + + +GRMZM2G068952_P01 NP_001130220 hypothetical protein LOC100191314 seq=translation; coord=1:287818241..287821189:-1; parent_transcript=GRMZM2G068952_T01; parent_gene=GRMZM2G068952 + + + MAAGARPLVS VRALEGDMAT DSVGVPLPDV LRAPIRPDIV RFVHKLLSCN + SRQPYAVSRR AGHQTSAESW GTGRAVSRIP RVPGGGTHRA GQGAFGNMCR + GGRMFAPTKI WRRWHRRVNI HLRRVAIASA LAATAVPSLV LARGHRVEYV + PELPLVVSDS AESIEKTAQA IKVLKQLGAS ADADKAKDSV SIRPGKGKMR + NRRYINRKGP LIVYGAEGSK IVKAFRNLPG VDVANVERLN LLDLAPGGHL + GRFVIWTECA FKKLDEVYGT FDTPSAKKKG FLLPRPKMAN ADLSRLINSD + EVQSVVKPIN KEVKRREPRK NPLKNMAAVL KLNPYLGTAR KMAALAEAAR + VKARKQKLDS KRTKLSPEET SKVKAAGKAW YKTMISDSDY TEFENFTKWL + GVTQ + + + + + +GRMZM2G100403_P01 NP_001168309 hypothetical protein LOC100382075 seq=translation; coord=7:10287328..10288164:1; parent_transcript=GRMZM2G100403_T01; parent_gene=GRMZM2G100403 + + + MVAVNRPLVS VKALEGDMVT DAPGIALPPV FGAPIRPDVV RFTHKLLSCN + KRQPYAVSRR AGHQTSAESW GTGRAVSRIP RVPGGGTHRA GQGAFGNMCR + GGRMFAPTKI WRKWHRRVNI NHRRPGPRPG ARPPHRVCPR DAPCHFRLRG + VH + + + + + + +5.81423 +-0.270429 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 + + + + +9389 9389 9389 9239 8687 8111 7581 6184 4711 3187 1987 1071 620 305 164 84 50 23 9 4 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9406 9406 9406 9256 8704 8110 7458 5613 3495 1555 446 88 52 15 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3291 3519 1738 693 132 12 0 25 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1686 3726 2158 1346 355 87 26 26 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2990 (charge 3) + +1600.76 +3 + + +158.092 159.077 159.092 167.081 169.097 171.077 173.093 175.119 183.124 184.108 185.093 187.088 193.097 197.619 198.058 198.121 199.107 201.087 211.617 215.114 220.13 226.119 227.102 232.141 239.095 242.114 244.166 246.124 258.145 261.648 +266.126 274.119 275.646 280.135 285.167 288.118 299.061 303.175 304.153 308.653 312.17 317.165 326.17 333.188 338.667 343.164 347.175 351.675 355.172 360.68 369.686 372.227 374.186 377.204 387.688 390.21 394.231 396.197 405.203 422.226 +424.234 439.252 468.173 469.72 475.226 506.284 522.293 532.253 535.295 542.329 548.709 550.286 559.265 576.288 604.295 645.315 646.299 663.321 665.335 668.327 677.374 699.411 716.358 734.398 738.366 774.349 781.41 792.364 794.37 809.396 +829.443 856.429 863.401 910.449 932.425 938.455 950.434 952.435 1007.46 1051.48 + + + + +11 10 28 5 4 7 5 25 4 4 4 5 4 36 8 9 5 5 20 7 40 16 5 6 6 6 6 7 7 18 +5 4 51 6 17 4 4 23 8 4 4 24 24 6 8 7 5 23 5 25 14 20 4 6 4 57 36 10 11 100 +4 6 5 5 4 11 5 4 5 7 11 14 7 32 4 4 5 58 4 5 4 5 8 10 4 9 6 28 4 4 +9 5 23 5 4 4 31 5 6 15 + + + + + + +GRMZM2G102075_P01 NP_001148770 40S ribosomal protein S15 seq=translation; coord=7:11335166..11337275:1; parent_transcript=GRMZM2G102075_T01; parent_gene=GRMZM2G102075 + + + MADVDVEPEV AAGAPKKRTF RKYSYRGVDL DALLDMSTDD LVQLFPARAR + RRFQRGLKRK PMALIKKLRK AKKDAPVGEK PEPVKTHLRN MIIVPEMIGS + IVGVYNGKTF NQVEIKPEMI GHYLAEFSIS YKPVKHGRPG IGATHSSRFI + PLK + + + + + + +5.79588 +-0.282726 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +7606 7606 7589 7291 7027 6493 5906 4591 3561 2109 1303 753 404 204 97 48 28 9 7 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7610 7610 7593 7295 6995 6407 5676 4132 2868 1066 398 117 39 32 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2137 2935 1625 719 134 58 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1598 3330 1843 618 159 57 3 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2993 (charge 3) + +1265.67 +3 + + +155.082 155.118 157.097 157.109 157.134 158.091 159.077 160.08 166.062 166.103 167.082 169.061 169.098 169.134 170.137 171.077 171.113 171.15 173.092 173.129 175.119 183.113 183.149 185.056 185.092 187.072 187.108 194.128 195.113 197.129 +199.108 200.14 201.124 203.066 209.092 213.088 216.134 217.135 225.099 227.102 231.062 234.145 238.119 240.135 242.187 244.129 247.108 249.16 254.147 258.146 265.118 272.172 279.15 285.169 286.143 287.665 297.157 313.187 315.166 324.155 +329.193 331.198 337.188 342.622 343.234 346.971 350.148 355.198 357.214 359.204 369.194 383.194 386.215 414.238 417.721 436.681 442.249 446.222 454.27 491.782 496.261 503.245 511.288 541.264 552.776 569.331 574.323 602.235 625.305 631.307 +638.32 640.328 697.424 699.289 724.37 737.386 836.45 883.486 885.499 982.559 + + + + +4 3 10 2 3 7 100 8 3 2 3 3 3 92 10 3 4 3 3 10 29 3 4 9 8 21 8 3 3 29 +8 4 5 5 3 3 6 5 2 15 4 11 3 11 4 5 16 3 6 3 9 5 7 6 3 4 4 4 2 6 +3 29 3 4 39 3 28 10 3 9 3 8 27 3 3 3 16 4 5 11 4 3 4 7 4 30 3 26 4 5 +4 5 7 12 2 8 3 17 3 4 + + + + + + +GRMZM2G343688_P02 NP_001137129 hypothetical protein LOC100217311 seq=translation; coord=1:79707321..79716130:-1; parent_transcript=GRMZM2G343688_T02; parent_gene=GRMZM2G343688 + + + MAETVDDKVS YFQAVTGISN TDLCTEILAA HNWDLQLAVS TITANPSSPS + ASASTSSRDP APSAPLAVDA EYVAPPPPLP LPLPPQQQPG IAWKLVTLPF + HVVSGGVGLV AGTFRLGAWV AGGVLSRSLS LLGLAGQAGS GDRLLELPPS + AAEAADFVAE FEREFGAGRG PRFVAEGFAD ALKRAQREFK LLFVYLHSPD + HPDTPAFCGG CLCAEPVAAF IDENFVAWGG SIRRTEGFKM SNSLNASRFP + FCAVVMASTN QRIVLLQQVE GPKSPEEMIT VLQRVVEECA TSLVAARIEA + EERLNNQRLR EEQDAAYRAA LEADQARERE RLEELKRRER EAAEAEKKRK + EEEEAVARAS QEAAEKEAAL ARRRQEKAMA LGAEPEKGPG VTRVLIRFPT + GERRERRFYS SATVASLYDY VDSLDCMKAE KYTLVSNFPR VTYGPEKQSL + TLEEAGLHLQ ASLFIEIEQ + + + + + +GRMZM2G159538_P01 NP_001149312 fas-associated factor 1-like protein seq=translation; coord=9:155793124..155797446:1; parent_transcript=GRMZM2G159538_T01; parent_gene=GRMZM2G159538 + + + MAETVDDKIS YFQAVTGISD TDLCTEILAA HNWDLQLAVS SITANPSSPS + APVSTSSRDP APSAPLADAE FVAPPPPIPP PPQQQPGIAW KLVTLPFYVV + SGGASLVAGS FRLGAWVAGG VLSRSLSLLG LAGQAGSGDR LLELPPSAAE + AADFVAEFER ECGAGRGPRF VAEGFADALQ RAQREFKLLF VYLHSPDHPD + TPAFCGGCLC AEPVAAFIDE NFVAWGGSIR RTEGFKMSNS LNASRFPFCA + VVMASTNQRI VLLQQVEGPK SPEEMITILQ RVVEECATSL VAARIEAEER + LNNQRLREEQ DAAYRAALEA DQARERERIE EQERREREAV EAEKKRKEEE + EAVARAAQEA AEKEAALARR RQEKAMALGA EPEKGPGVTR VLIRFPTGER + KERRFHSSAT VTSLYDYVDS LDCMKAENYS LVSNFPRVTY GPEKHSLTLE + EAGLHPQASL FIEIEQ + + + + + + +6.54216 +-0.290763 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +7553 7553 7553 7429 7000 6708 5786 5347 4809 3262 2568 1533 682 425 243 152 35 21 8 7 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7567 7567 7567 7443 7012 6704 5720 5108 4595 2540 1494 344 40 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2680 3438 1202 172 65 5 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1786 4077 1398 257 35 3 6 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2995 (charge 2) + +1250.62 +2 + + +152.057 154.086 155.082 155.118 157.097 157.109 158.092 159.076 159.113 167.056 167.081 169.06 169.097 169.134 171.077 173.092 175.119 181.096 183.113 185.091 187.072 187.109 195.076 198.124 200.139 201.124 204.134 206.093 208.144 211.108 +213.087 226.154 228.135 232.112 239.097 240.097 243.08 248.16 253.166 256.128 260.106 267.109 270.195 297.119 300.12 303.177 314.147 321.155 327.167 338.183 339.165 341.146 359.174 369.187 375.172 396.19 409.22 434.26 447.747 453.212 +454.73 474.232 480.257 495.217 528.279 543.046 561.253 568.322 576.286 578.319 595.294 601.81 617.298 624.301 659.308 683.343 710.391 719.333 723.335 740.367 746.349 763.396 765.391 771.36 777.356 826.37 842.396 852.38 874.434 885.435 +891.448 894.495 911.484 913.431 951.867 963.419 981.43 990.519 1048.5 1076.5 + + + + +19 4 21 5 18 6 24 12 7 4 6 5 19 5 17 23 100 3 16 24 7 6 6 4 16 4 5 5 4 5 +6 36 16 4 6 6 21 19 32 4 100 19 4 5 5 21 4 17 7 6 6 4 7 4 3 4 5 7 4 4 +7 5 56 4 12 4 13 29 6 21 5 6 6 4 5 19 7 5 12 14 5 30 4 43 5 5 17 7 23 7 +7 21 13 20 4 6 20 13 7 5 + + + + + + +GRMZM2G018197_P01 NP_001147047 60S ribosomal protein L4 seq=translation; coord=2:233433323..233435947:-1; parent_transcript=GRMZM2G018197_T01; parent_gene=GRMZM2G018197 + + + + + + + +GRMZM2G100403_P02 NP_001168309 hypothetical protein LOC100382075 seq=translation; coord=7:10287294..10291100:1; parent_transcript=GRMZM2G100403_T02; parent_gene=GRMZM2G100403 + + + + + + + +GRMZM2G007695_P01 NP_001130508 hypothetical protein LOC100191607 seq=translation; coord=5:4268599..4271215:1; parent_transcript=GRMZM2G007695_T01; parent_gene=GRMZM2G007695 + + + + + + + +GRMZM2G068952_P01 NP_001130220 hypothetical protein LOC100191314 seq=translation; coord=1:287818241..287821189:-1; parent_transcript=GRMZM2G068952_T01; parent_gene=GRMZM2G068952 + + + + + + + +GRMZM2G100403_P01 NP_001168309 hypothetical protein LOC100382075 seq=translation; coord=7:10287328..10288164:1; parent_transcript=GRMZM2G100403_T01; parent_gene=GRMZM2G100403 + + + + + + + + +6.29303 +-0.381396 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +6763 6763 6763 6489 5811 5436 4901 2838 2142 1065 438 183 51 17 5 1 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +6774 6774 6774 6500 5822 5386 4860 2611 1709 675 130 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4087 2320 284 78 20 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1462 4443 779 83 2 0 20 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 2999 (charge 2) + +1600.76 +2 + + +155.093 157.108 158.092 159.078 159.092 168.065 175.119 183.124 185.005 195.088 211.118 215.114 240.134 258.514 266.125 286.151 303.177 316.159 355.168 369.687 373.186 377.205 389.152 405.198 422.227 427.146 442.164 459.296 463.176 468.17 +469.724 475.229 504.237 513.74 533.258 576.281 588.565 656.247 663.325 664.329 669.25 671.251 675.75 684.27 733.222 770.353 778.865 783.869 792.372 801.883 910.459 921.419 938.447 993.405 1001.92 1008.46 1025.48 1051.48 1094.46 1179.55 +1445.67 + + + + +3 6 15 5 17 3 32 7 3 5 5 7 4 3 13 5 59 5 6 4 4 4 3 4 5 5 4 4 4 4 +5 4 4 5 4 4 5 11 22 5 5 15 6 7 4 8 16 6 100 93 5 5 20 5 4 5 7 15 6 7 +5 + + + + + + +GRMZM2G163437_P01 P55240 Glucose-1-phosphate adenylyltransferase small subunit Fragment (EC 2.7.7.27)(Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase B)(ADP-glucose synthase) seq=translation; coord=1:221648603..221653196:1; parent_transcript=GRMZM2G163437_T01; parent_gene=GRMZM2G163437 + + + MAMAAIASPS SRTLIPPRHH GAAPSPSTSG DSSLRLLCAH PRHGRRGRAM + SVSTPAARSR PFVFSPRAVS DSKSSQTCLD PDASTSVLGI ILGGGAGTRL + YPLTKKRAKP AVPLGANYRL IDIPVSNCLN SNISKIYVLT QFNSASLNRH + LSRAYGNNIG GYKNDGFVEV LAAQQSPDNP NWFQGTADAV RQYLWLFEEH + NVMEFLILAG DHLYRMDYEK FIQAHRETDA DITVAALPMD EKRATAFGLM + KIDEEGRIIE FAEKPKGDQL KAMMVDTTIL GLDDERAKEM PYIASMGIYV + FSKDVMLQLL REQFPGANDF GSEVIPGATS IGKRVQAYLY DGYWEDIGTI + EAFYNANLGI TKKPIPDFSF YDRSAPIYTQ PRHLPPSKVL DADVTDSVIG + EGCVIKNCKI HHSVVGLRSC ISEGAIIEDT LLMGADYYET EADKKLLAEN + GGIPIGIGKN SHIRKAIIDK NARIGDNVKI LNADNVQEAA RETDGYFIKG + GIVTVIKDAL LPSGTVI + + + + + +GRMZM2G163437_P02 P55240 Glucose-1-phosphate adenylyltransferase small subunit Fragment (EC 2.7.7.27)(Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase B)(ADP-glucose synthase) seq=translation; coord=1:221648607..221653113:1; parent_transcript=GRMZM2G163437_T02; parent_gene=GRMZM2G163437 + + + MAMAAIASPS SRTLIPPRHH GAAPSPSTSG DSSLRLLCAH PRHGRRGRAM + SVSTPAARSR PFVFSPRAVS DSKSSQTCLD PDASTSVLGI ILGGGAGTRL + YPLTKKRAKP AVPLGANYRL IDIPVSNCLN SNISKIYVLT QFNSASLNRH + LSRAYGNNIG GYKNDGFVEV LAAQQSPDNP NWFQGTADAV RQYLWLFEEH + NVMEFLILAG DHLYRMDYEK FIQAHRETDA DITVAALPMD EKRATAFGLM + KIDEEGRIIE FAEKPKGDQL KAMMVDTTIL GLDDERAKEM PYIASMGIYV + FSKDVMLQLL REQFPGANDF GSEVIPGATS IGKRVQAYLY DGYWEDIGTI + EAFYNANLGI TKKPIPDFSF YDRSAPIYTQ PRHLPPSKVL DADVTDSVIG + EGCVIKNCKI HHSVVGLRSC ISEGAIIEDT LLMGADYYET EADKKLLAEN + GGIPIGIGKN SHIRKAIIDK NARIGDNVKI LNADNVQEAA RETDGYFIKG + GIVTVIKDAL LPSGTVI + + + + + +GRMZM2G163437_P03 P55240 Glucose-1-phosphate adenylyltransferase small subunit Fragment (EC 2.7.7.27)(Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase B)(ADP-glucose synthase) seq=translation; coord=1:221649581..221653196:1; parent_transcript=GRMZM2G163437_T03; parent_gene=GRMZM2G163437 + + + MEFLILAGDH LYRMDYEKFI QAHRETDADI TVAALPMDEK RATAFGLMKI + DEEGRIIEFA EKPKGDQLKA MMVDTTILGL DDERAKEMPY IASMGIYVFS + KDVMLQLLRE QFPGANDFGS EVIPGATSIG KRVQAYLYDG YWEDIGTIEA + FYNANLGITK KPIPDFSFYD RSAPIYTQPR HLPPSKVLDA DVTDSVIGEG + CVIKNCKIHH SVVGLRSCIS EGAIIEDTLL MGADYYETEA DKKLLAENGG + IPIGIGKNSH IRKAIIDKNA RIGDNVKILN ADNVQEAARE TDGYFIKGGI + VTVIKDALLP SGTVI + + + + + + +5.31986 +-0.259506 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +5210 5210 5210 5053 4784 4220 3714 3113 2342 1560 853 516 269 155 69 39 15 11 2 1 1 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5221 5221 5221 5064 4791 4197 3543 2643 1566 624 175 53 28 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2165 2581 441 35 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1179 2177 1383 371 93 14 1 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3000 (charge 2) + +1017.6 +2 + + +152.056 154.086 155.082 157.097 157.108 157.134 158.092 159.076 159.091 159.113 166.061 167.065 167.081 169.097 169.134 171.076 171.113 173.093 173.129 175.09 175.119 176.122 178.134 181.097 183.113 185.093 185.164 186.087 186.124 187.071 +187.108 189.087 195.088 195.113 197.128 197.165 198.124 199.107 201.123 204.135 207.088 212.103 215.14 218.15 221.103 223.156 225.099 227.102 234.124 235.122 240.135 242.15 244.165 247.131 249.098 251.15 256.128 258.099 267.109 271.176 +275.126 284.126 288.203 290.146 299.172 303.119 306.156 317.182 324.166 327.167 328.197 333.189 343.199 345.224 359.203 370.201 375.225 384.23 388.211 423.233 427.266 435.24 443.756 452.76 461.195 492.283 543.361 574.28 577.276 626.307 +630.394 640.38 666.323 687.358 727.378 749.444 767.453 769.458 775.388 888.473 + + + + +3 3 26 9 3 3 20 11 3 10 100 3 7 10 10 6 18 3 15 8 86 3 18 5 3 13 6 5 10 8 +13 6 8 3 8 7 3 13 9 27 3 7 8 3 3 35 29 10 45 8 6 16 5 6 6 88 3 14 3 6 +20 5 10 3 8 8 3 37 11 4 9 8 3 7 3 11 19 21 8 10 3 6 15 21 8 3 15 11 3 3 +77 3 6 8 3 10 91 7 3 3 + + + + + + +GRMZM2G140051_P01 NP_001105215 nucleosome/chromatin assembly factor group A seq=translation; coord=9:19393494..19397648:-1; parent_transcript=GRMZM2G140051_T01; parent_gene=GRMZM2G140051 + + + + + + + +GRMZM2G140051_P02 NP_001105215 nucleosome/chromatin assembly factor group A seq=translation; coord=9:19393494..19397627:-1; parent_transcript=GRMZM2G140051_T02; parent_gene=GRMZM2G140051 + + + + + + + + +4.43795 +-0.268967 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +5356 5356 5356 5184 5059 4611 4333 2689 2004 976 480 282 146 72 10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5321 5321 5321 5149 5022 4557 4228 2368 1631 665 215 85 67 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3041 2076 208 33 0 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1019 3533 721 76 9 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3003 (charge 2) + +1426.68 +2 + + +151.084 155.081 155.118 159.077 168.872 169.134 171.077 171.113 175.119 181.061 186.088 194.092 197.129 198.087 200.14 201.123 209.102 215.139 218.15 221.104 225.123 230.078 235.12 243.133 249.098 253.094 306.156 326.147 329.182 335.146 +344.118 347.193 353.181 364.125 371.195 382.134 387.157 415.16 460.275 468.183 493.167 495.218 505.781 579.218 584.27 589.32 597.231 624.263 634.323 639.589 646.321 655.339 668.852 675.091 679.345 686.35 690.361 704.357 708.259 710.311 +723.344 725.294 821.346 823.386 838.365 841.398 842.4 949.397 951.383 967.408 1056.49 1062.48 1167.52 1191.55 1409.41 + + + + +3 3 3 3 3 3 11 3 26 3 3 2 37 5 16 4 3 100 64 4 17 5 3 15 3 9 5 5 25 4 +4 10 16 10 11 15 3 4 9 4 6 6 3 10 11 13 18 14 4 4 5 9 3 4 16 5 10 22 13 4 +4 4 14 5 12 23 5 15 4 14 16 4 3 3 3 + + + + + + +GRMZM2G077851_P01 NP_001136667 hypothetical protein LOC100216796 seq=translation; coord=1:151356484..151358622:1; parent_transcript=GRMZM2G077851_T01; parent_gene=GRMZM2G077851 + + + + + + + +GRMZM2G072729_P01 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34222504..34224841:1; parent_transcript=GRMZM2G072729_T01; parent_gene=GRMZM2G072729 + + + + + + + +GRMZM2G072729_P02 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34222942..34224888:1; parent_transcript=GRMZM2G072729_T02; parent_gene=GRMZM2G072729 + + + + + + + +GRMZM2G067456_P01 NP_001131396 hypothetical protein LOC100192723 seq=translation; coord=3:127004080..127006073:-1; parent_transcript=GRMZM2G067456_T01; parent_gene=GRMZM2G067456 + + + + + + + +GRMZM2G077851_P03 NP_001136667 hypothetical protein LOC100216796 seq=translation; coord=1:151356736..151358244:1; parent_transcript=GRMZM2G077851_T03; parent_gene=GRMZM2G077851 + + + + + + + +GRMZM2G072729_P03 NP_001130582 hypothetical protein LOC100191681 seq=translation; coord=7:34223087..34224612:1; parent_transcript=GRMZM2G072729_T03; parent_gene=GRMZM2G072729 + + + + + + + +GRMZM2G067456_P02 NP_001131396 hypothetical protein LOC100192723 seq=translation; coord=3:127004341..127005956:-1; parent_transcript=GRMZM2G067456_T02; parent_gene=GRMZM2G067456 + + + + + + + + +4.78624 +-0.273499 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 + + + + +8093 8093 8093 8005 7327 6351 5283 3883 2834 1654 1056 509 250 103 54 22 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8103 8103 8103 8015 7337 6334 5169 3640 2283 1119 613 257 84 18 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2806 3839 1172 232 54 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2909 3673 1270 210 27 4 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3004 (charge 3) + +2696.29 +3 + + +186.077 195.088 197.128 204.087 205.088 209.092 217.109 221.103 228.135 235.119 246.091 249.098 264.134 267.108 274.188 283.176 293.162 297.156 303.178 317.127 326.17 337.822 342.177 354.168 394.173 423.176 428.198 432.245 435.233 445.218 +463.226 489.769 533.304 543.279 544.791 556.276 629.295 657.292 670.362 727.386 736.361 742.365 755.869 764.88 769.35 785.353 794.354 824.398 832.909 840.474 860.898 872.931 881.436 922.406 936.442 940.962 977.536 979.497 1005.49 1015.48 +1104.03 1105.58 1113.05 1161.05 1169.56 1320.63 1330.39 1470.72 1527.75 1529.77 1761.85 1763.85 + + + + +9 5 7 41 3 7 7 10 83 31 9 9 11 9 5 9 5 11 8 11 29 5 6 23 8 8 8 27 11 7 +16 8 26 6 6 7 7 7 25 97 8 11 8 27 8 11 7 8 45 57 8 40 100 11 9 7 66 7 9 7 +7 24 52 7 22 10 7 10 40 7 21 11 + + + + + + +GRMZM2G415359_P02 Q08062 Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) seq=translation; coord=1:231336278..231341950:-1; parent_transcript=GRMZM2G415359_T02; parent_gene=GRMZM2G415359 + + + MAKEPMRVLV TGAAGQIGYA LVPMIARGVM LGADQPVILH MLDIPPAAEA + LNGVKMELVD AAFPLLKGVV ATTDVVEACT GVNVAVMVGG FPRKEGMERK + DVMSKNVSIY KSQASALEAH AAPNCKVLVV ANPANTNALI LKEFAPSIPE + KNVTCLTRLD HNRALGQISE RLNVQVSDVK NVIIWGNHSS SQYPDVNHAT + VKTSTGEKPV RELVSDDEWL NGEFITTVQQ RGAAIIKARK FSSALSAASS + ACDHIRDWVL GTPEGTFVSM GVYSDGSYGV PSGLIYSFPV TCSGGEWKIV + QGLPIDEFSR KKMDATAQEL TEEKTLAYSC LE + + + + + + +GRMZM2G415359_P03 Q08062 Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) seq=translation; coord=1:231336334..231337977:-1; parent_transcript=GRMZM2G415359_T03; parent_gene=GRMZM2G415359 + + + MGVYSDGSYG VPSGLIYSFP VTCSGGEWKI VQGLPIDEFS RKKMDATAQE + LTEEKTLAYS CLE + + + + + + + +6.72705 +-0.274574 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +12522 12522 12522 12522 12410 12142 11596 10874 8987 7510 5342 3357 2140 1191 666 331 204 99 43 22 7 5 2 1 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +12524 12524 12524 12524 12412 12144 11579 10780 8532 5991 3025 894 208 33 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3188 5183 2708 1130 253 39 21 4 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1965 4780 3371 1634 549 179 38 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3005 (charge 3) + +1637.81 +3 + + +152.057 155.082 155.118 156.077 157.097 158.092 159.077 167.081 169.097 171.077 171.113 173.093 173.129 175.119 183.077 185.092 187.071 189.087 194.129 195.076 195.113 197.129 199.071 200.103 201.087 203.103 212.103 213.087 215.14 217.082 +222.123 226.118 227.102 231.098 232.14 240.134 243.133 244.165 246.156 258.145 276.156 289.162 303.176 308.162 317.174 323.668 326.171 332.179 336.669 344.181 346.179 351.171 354.166 357.25 360.14 369.178 372.69 381.696 387.188 390.206 +405.199 429.713 437.203 446.229 455.211 467.257 488.234 495.767 506.247 514.793 519.256 526.295 547.278 575.28 590.3 601.323 619.331 627.348 632.337 661.327 672.329 674.328 691.346 698.384 730.362 748.374 750.377 760.376 762.381 790.405 +836.449 841.397 847.43 859.402 860.41 877.43 890.439 894.408 912.434 947.479 + + + + +7 17 11 7 11 10 18 7 12 10 11 25 12 46 13 12 7 16 16 7 16 26 18 22 7 7 7 23 24 10 +7 14 19 45 12 42 11 12 17 100 81 12 14 15 13 15 26 14 21 6 12 12 13 6 17 18 15 13 65 21 +30 17 32 13 22 17 12 6 97 12 21 14 18 15 24 12 68 13 12 14 31 13 14 18 31 73 15 7 18 19 +7 14 11 55 27 31 13 10 15 15 + + + + + + +GRMZM2G102075_P01 NP_001148770 40S ribosomal protein S15 seq=translation; coord=7:11335166..11337275:1; parent_transcript=GRMZM2G102075_T01; parent_gene=GRMZM2G102075 + + + + + + + + +5.55094 +-0.246708 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 + + + + +6936 6936 6936 6700 6333 5945 4534 3708 2371 1708 1041 626 354 221 135 80 35 16 8 4 2 1 1 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6946 6946 6946 6710 6342 5929 4278 3066 1524 712 257 106 50 14 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3657 2561 593 123 11 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1118 3713 1600 403 87 15 8 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3006 (charge 2) + +1265.67 +2 + + +152.057 157.097 159.077 161.092 167.093 169.097 169.134 170.137 171.076 171.113 173.092 175.12 183.113 185.092 187.072 195.089 197.129 198.088 199.108 201.087 203.102 211.12 213.087 216.098 226.155 227.103 234.144 239.114 240.135 246.182 +248.16 251.102 254.149 256.128 259.093 265.118 272.172 275.208 279.098 284.124 286.145 293.113 295.637 303.177 311.174 315.166 329.183 331.157 338.181 339.167 343.235 347.229 352.16 355.198 366.674 383.194 384.19 417.724 423.216 433.244 +440.215 442.245 453.258 454.266 456.255 466.278 473.211 482.219 491.783 511.29 512.288 534.292 537.315 540.309 543.29 551.32 562.288 567.311 569.33 576.271 587.266 590.266 602.358 640.327 661.305 682.338 697.432 709.385 737.385 773.324 +781.41 826.351 883.49 885.495 893.476 933.501 963.431 967.465 982.561 1079.6 + + + + +7 3 54 3 6 9 100 11 6 5 5 18 5 11 26 9 39 19 8 8 4 4 3 11 14 12 5 25 20 9 +7 9 8 9 6 5 4 13 4 25 6 5 9 45 4 6 3 6 5 4 51 5 3 13 6 13 3 8 8 7 +5 7 6 6 5 6 3 5 8 13 5 7 5 40 6 3 12 8 36 4 5 6 12 5 5 15 13 5 20 10 +5 16 61 8 3 7 3 5 22 10 + + + + + + +GRMZM5G862331_P02 NP_001132591 hypothetical protein LOC100194063 seq=translation; coord=5:208749279..208751400:-1; parent_transcript=GRMZM5G862331_T02; parent_gene=GRMZM5G862331 + + + MDEEEHEVYG QEIPEDGDMD GADVDMAASG DDAAKLQELD EMKRRLKEME + EEAAALRDMQ AKVAKEMQGG DPSASTAEAK EQVDARSVYV GNVRIYNNLP + LFIVTLHISG NMLCCFEIFI + + + + + +GRMZM5G862331_P03 NP_001132591 hypothetical protein LOC100194063 seq=translation; coord=5:208748919..208751400:-1; parent_transcript=GRMZM5G862331_T03; parent_gene=GRMZM5G862331 + + + MDEEEHEVYG QEIPEDGDMD GADVDMAASG DDAAKLQELD EMKRRLKEME + EEAAALRDMQ AKVAKEMQGG DPSASTAEAK EQVDARSVYV GNG + + + + + +GRMZM5G862331_P04 NP_001132591 hypothetical protein LOC100194063 seq=translation; coord=5:208745686..208751400:-1; parent_transcript=GRMZM5G862331_T04; parent_gene=GRMZM5G862331 + + + MDEEEHEVYG QEIPEDGDMD GADVDMAASG DDAAKLQELD EMKRRLKEME + EEAAALRDMQ AKVAKEMQGG DPSASTAEAK EQVDARSVYV GNVDYACTPE + EVQQHFQACG TVNRVTILTD KFGQPKGFAY VEFLEQEGVQ EALNLNESEL + HGRQIKVAPK RTNVPGMKQR PPRGYNPYHG YPYRSYGAPY FPPYGYGRAP + RFRRPMRYRP YF + + + + + + +5.88425 +-0.287037 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +2597 2597 2591 2399 2324 2206 1731 1418 866 557 358 200 120 69 40 11 3 2 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2619 2619 2613 2421 2343 2220 1675 1172 666 331 136 73 14 2 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1193 1002 363 46 10 19 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +605 1460 452 93 8 0 0 15 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3007 (charge 2) + +1478.64 +2 + + +152.057 155.082 157.097 158.092 159.076 165.103 167.056 167.082 169.061 171.075 173.092 175.12 185.092 186.089 186.124 187.072 191.085 198.087 201.087 204.135 209.371 212.103 215.086 218.15 224.103 227.085 230.079 233.096 238.119 240.098 +243.08 256.13 258.107 260.105 269.125 272.172 295.105 297.121 299.062 302.136 303.204 313.113 325.151 329.182 340.125 343.162 344.977 347.193 358.135 371.138 389.157 392.157 408.187 415.038 418.231 426.203 428.16 431.219 442.192 472.857 +481.202 485.195 497.235 519.275 531.726 540.731 557.212 572.226 585.209 600.778 606.309 616.3 626.279 644.29 661.296 677.347 698.297 712.086 741.366 746.375 764.375 784.437 843.419 861.432 863.433 931.432 976.458 1033.46 1062.44 1090.5 +1179.53 1201.56 1274.96 + + + + +4 4 8 4 9 3 13 75 4 3 4 16 56 11 4 4 3 4 9 24 2 3 21 45 4 7 2 52 15 3 +38 14 3 15 4 38 13 7 33 3 12 3 4 21 31 8 10 11 19 40 4 4 4 4 15 3 5 12 3 2 +3 3 4 20 15 8 3 2 4 5 32 3 5 10 3 18 5 3 5 3 15 5 5 100 8 3 8 3 3 22 +4 4 3 + + + + + + +GRMZM2G130095_P01 NP_001148654 KH domain containing protein seq=translation; coord=1:167864280..167870604:1; parent_transcript=GRMZM2G130095_T01; parent_gene=GRMZM2G130095 + + + MDVPVDDPVE NLTGSPSTLG NEEEATTYAN VQDQSKEEPE KLYEEPKDPM + QDELGNQGHV SMNNEDVGGQ NKVDQATPTE HGEEAGVKQH DATVPDDKKW + PGWPGESVFR ILVPTTKVGA VIGRKGDFIK KMCEESRARI KVLEGPPAVP + ERAVMISAKD EPDTELPPAV DGLLRVHRRI TDGLETETDQ PQRATVNTGP + TRLLVPASQA GSLIGKQGAT IKSIQDASKC VLRIVENVPP VALNDDRVVE + IQGEPHDSHK AVELIASHLR KFLVDRSVLP LFETQIKAHN MHREQPMPPP + QAWGPPPPSP WGHPPPNLPP GGPGYVGNPH YMPPRPQENY YPPPDVPPVE + KQPHYGISSY GRDAPPSAPP GNQNQAHGSS QVTHSMQVPL SYADAVIGAA + GASISYIRRH SGATISIQEG APGEMTVEIT GSASQVQTAQ QLIKNFMAEA + SPQGPPAPGP HGQPVDTGYG SYPPYGGASY GSPPGAPAPA PHNGGSYGAA + PYSSSYGY + + + + + +GRMZM2G130095_P03 NP_001148654 KH domain containing protein seq=translation; coord=1:167864280..167870561:1; parent_transcript=GRMZM2G130095_T03; parent_gene=GRMZM2G130095 + + + MDVPVDDPVE NLTGSPSTLG NEEEATTYAN VQDQSKEEPE KLYEEPKDPM + QDELGNQGHV SMNNEDVGGQ NKVDQATPTE HGEEAGVKQH DATVPDDKKW + PGWPGESVFR ILVPTTKVGA VIGRKGDFIK KMCEESRARI KVLEGPPAVP + ERAVMISAKD EPDTELPPAV DGLLRVHRRI TDGLETETDQ PQRATVNTGP + TRLLVPASQA GSLIGKQGAT IKSIQDASKC VLRIVENVPP VALNDDRVVE + IQGEPHDSHK AVELIASHLR KFLVDRSVLP LFETQIKAHN MHREQPMPPP + QAWGPPPPSP WGHPPPNLPP GGPGYVGNPH YMPPRPQENY YPPPDVPPVE + KQPHYGISSY GRDAPPSAPP GNQNQAHGSS QVTHSMQVPL SYADAVIGAA + GASISYIRRH SGATISIQEG APGEMTVEIT GSASQVQTAQ QLIKGPPAPG + PHGQPVDTGY GSYPPYGGAS YGSPPGAPAP APHNGGSYGA APYSSSYGY + + + + + + +5.09018 +-0.261035 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +9447 9447 9447 9447 8437 7945 6815 5622 4191 2997 1951 1017 535 253 138 61 29 5 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9452 9452 9452 9452 8442 7831 6612 5068 3229 1975 805 250 75 36 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3686 3738 1535 395 76 25 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1585 3940 2429 1206 232 53 5 7 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3009 (charge 3) + +1667.78 +3 + + +155.082 157.097 158.092 159.076 159.113 167.082 169.097 169.133 171.077 171.113 173.092 173.129 175.09 175.119 181.098 183.077 185.092 186.124 187.108 189.087 199.108 201.087 204.135 212.104 215.103 216.099 226.155 227.103 238.119 240.097 +242.113 244.093 246.181 249.098 254.114 256.13 272.125 283.142 298.105 303.176 310.14 315.13 322.174 325.152 335.171 343.161 353.183 357.18 360.196 370.209 372.226 374.241 386.166 388.219 413.707 438.247 439.24 457.242 459.267 475.251 +481.24 498.268 503.282 514.275 525.807 528.753 546.289 558.321 569.302 577.278 580.297 593.265 622.332 626.324 628.307 643.342 680.304 689.341 691.356 697.394 700.364 705.359 726.38 744.388 762.387 782.414 826.404 851.347 863.427 893.433 +908.378 916.394 930.496 955.445 957.463 1007.45 1056.51 1077.54 1135.54 1153.55 + + + + +19 41 6 6 5 7 28 4 12 21 23 5 6 54 7 6 49 5 30 5 23 13 14 7 17 5 32 15 5 14 +5 41 7 4 38 7 17 6 6 15 7 16 5 7 6 6 13 5 11 13 4 13 5 64 20 10 5 6 6 18 +13 34 4 5 39 13 13 100 4 56 13 5 21 48 6 86 6 37 4 19 5 4 12 49 16 20 40 5 13 5 +15 5 21 13 4 6 15 5 4 33 + + + + + + +GRMZM2G127648_P01 NP_001148331 ras-related protein RIC2 seq=translation; coord=6:159006258..159010274:-1; parent_transcript=GRMZM2G127648_T01; parent_gene=GRMZM2G127648 + + + + + + + + +4.29957 +-0.232409 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +5347 5347 5322 5200 4798 4450 2927 2152 1192 629 411 240 123 73 38 32 17 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5349 5349 5324 5195 4739 4350 2407 1545 585 199 147 52 13 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2641 1942 696 51 20 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1005 3014 1129 189 11 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3010 (charge 2) + +1316.63 +2 + + +152.057 154.679 155.081 155.117 157.097 158.093 159.077 160.079 167.082 167.118 169.097 171.078 173.093 173.129 174.132 175.119 181.097 183.076 183.113 185.091 186.087 186.124 187.108 189.088 195.113 198.124 199.072 199.108 200.104 201.124 +204.135 213.087 217.082 226.155 228.104 239.114 241.082 244.166 251.103 254.15 258.145 266.111 270.109 272.171 276.155 284.01 288.119 298.102 301.187 303.178 309.158 311.171 315.04 324.153 330.165 337.187 341.181 355.198 365.184 369.1 +372.225 381.141 383.193 394.127 399.15 434.24 438.235 440.178 443.259 452.255 470.262 474.189 529.267 561.296 571.319 579.788 598.241 600.271 616.254 628.32 633.33 660.357 664.332 677.401 690.35 695.405 700.358 714.385 715.389 762.384 +789.409 800.399 834.426 889.436 903.503 917.432 921.501 987.482 1116.53 1129.59 + + + + +5 1 8 1 2 2 3 2 2 1 3 2 11 100 8 15 2 2 3 2 1 2 2 2 2 5 7 32 2 31 +12 5 6 86 3 2 3 20 2 2 3 1 6 6 5 4 2 2 54 5 2 2 7 2 8 2 3 3 2 2 +11 1 11 4 2 5 3 2 1 15 6 1 2 2 5 6 1 2 2 2 2 9 2 9 2 3 1 6 2 2 +2 5 2 2 9 2 2 2 2 2 + + + + + + +GRMZM2G180625_P01 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T01; parent_gene=GRMZM2G180625 + + + MTYMFKYDTV HGQWKHSDIA LKDSKTLLFG EKPVTVFGIR NPEEIPWGEA + GAEYVVESTG VFTDKDKAAA HLKGGAKKVV ISAPSKDAPM FVVGVNEDKY + TSDVNIVSNA SCTTNCLAPL AKVIHDNFGI IEGLMTTVHA ITATQKTVDG + PSAKDWRGGR AASFNIIPSS TGAAKAVGKV LPELNGKLTG MSFRVPTVDV + SVVDLTVRIE KGASYEEIKK AIKAASEGPL KGIMGYVEED LVSTDFTGDS + RSSIFDAKAG IALNDHFIKL VSWYDNEWGY SNRVVDLIRH MFKTQ + + + + + +GRMZM2G180625_P02 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T02; parent_gene=GRMZM2G180625 + + + MGKIKIGING FGRIGRLVAR VALQSEDVEL VAVNDPFITT DYMTYMFKYD + TVHGQWKHSD IALKDSKTLL FGEKPVTVFG IRNPEEIPWG EAGAEYVVES + TGVFTDKDKA AAHLKGGAKK VVISAPSKDA PMFVVGVNED KYTSDVNIVS + NASCTTNCLA PLAKVIHDNF GIIEGLMTTV HAITATQKTV DGPSAKDWRG + GRAASFNIIP SSTGAAKAVG KVLPELNGKL TGMSFRVPTV DVSVVDLTVR + IEKGASYEEI KKAIKAASEG PLKGIMGYVE EDLVSTDFTG DSRSSIFDAK + AGIALNDHFI KLVSWYDNEW GYSNRVVDLI RHMFKTQ + + + + + +GRMZM2G180625_P03 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903153:-1; parent_transcript=GRMZM2G180625_T03; parent_gene=GRMZM2G180625 + + + MRLLEKGKIK IGINGFGRIG RLVARVALQS EDVELVAVND PFITTDYMTY + MFKYDTVHGQ WKHSDIALKD SKTLLFGEKP VTVFGIRNPE EIPWGEAGAE + YVVESTGVFT DKDKAAAHLK GGAKKVVISA PSKDAPMFVV GVNEDKYTSD + VNIVSNASCT TNCLAPLAKV IHDNFGIIEG LMTTVHAITA TQKTVDGPSA + KDWRGGRAAS FNIIPSSTGA AKAVGKVLPE LNGKLTGMSF RVPTVDVSVV + DLTVRIEKGA SYEEIKKAIK AASEGPLKGI MGYVEEDLVS TDFTGDSRSS + IFDAKAGIAL NDHFIKLVSW YDNEWGYSNR VVDLIRHMFK TQ + + + + + + +5.88616 +-0.301855 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6341 6341 6341 6124 5844 5308 4112 3314 2203 1342 716 323 156 68 30 18 8 2 1 1 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +6363 6363 6363 6146 5856 5279 3918 2822 1418 498 107 15 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2818 2901 581 55 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1483 3271 1223 299 63 11 2 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3012 (charge 2) + +1024.53 +2 + + +152.057 155.082 157.061 157.097 157.109 158.091 159.077 160.077 162.113 167.082 169.098 171.077 171.113 173.056 173.093 173.129 175.072 175.119 176.071 178.087 181.098 183.113 183.15 185.091 186.091 186.125 187.072 187.108 188.072 189.088 +194.13 195.113 197.129 198.087 198.124 199.072 199.108 204.135 205.098 209.092 213.087 216.098 217.082 223.108 226.155 232.14 233.094 235.093 239.115 242.186 244.166 249.123 251.102 254.152 257.197 259.092 265.118 267.109 272.171 275.208 +276.212 286.144 293.113 301.188 303.178 314.687 324.157 326.174 333.155 354.169 362.136 372.178 380.146 383.193 388.292 405.224 416.23 422.156 448.74 452.258 481.195 489.269 491.179 499.327 504.258 509.187 517.335 548.281 620.317 628.368 +646.378 649.334 650.337 678.344 720.403 740.341 748.403 782.375 809.441 896.479 + + + + +4 6 6 9 3 5 11 3 4 5 4 20 4 3 3 3 3 22 3 6 3 15 4 7 3 4 3 3 3 3 +6 6 5 12 4 4 25 5 8 4 5 19 6 100 42 11 4 4 5 20 16 12 27 5 12 31 10 4 8 45 +7 3 17 4 13 3 5 5 6 3 5 6 13 5 18 8 3 20 7 5 3 5 4 5 3 16 16 6 8 8 +29 7 3 3 4 3 3 3 11 12 + + + + + + +GRMZM2G096153_P01 NM_001111509 glutathione transferase10 (gst10), mRNA seq=translation; coord=1:7866607..7868253:-1; parent_transcript=GRMZM2G096153_T01; parent_gene=GRMZM2G096153 + + + + + + + +GRMZM2G096153_P02 NM_001111509 glutathione transferase10 (gst10), mRNA seq=translation; coord=1:7866691..7868236:-1; parent_transcript=GRMZM2G096153_T02; parent_gene=GRMZM2G096153 + + + + + + + + +4.86232 +-0.237186 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +7177 7177 7177 6846 6726 6144 5821 3675 2253 1243 696 385 218 164 79 60 20 17 12 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +7179 7179 7179 6848 6726 6119 5736 3413 1847 725 292 150 91 16 3 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3241 3218 613 94 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1720 4612 727 104 14 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3016 (charge 2) + +1360.69 +2 + + +152.057 155.081 157.097 158.093 161.092 165.916 166.06 167.055 167.117 169.097 171.076 171.113 172.108 173.091 175.12 176.123 181.059 183.077 183.149 185.092 185.129 186.123 187.072 187.108 189.087 194.129 195.113 200.176 203.103 210.16 +213.085 215.139 217.082 226.155 228.171 231.097 237.135 240.132 242.151 254.161 260.107 267.185 285.155 299.139 344.165 362.138 371.139 414.246 439.232 442.242 456.257 490.192 513.291 539.276 557.304 562.272 574.181 586.364 618.285 623.789 +644.338 667.374 672.344 681.852 728.369 754.378 772.395 823.876 868.427 886.402 903.431 905.433 931.427 1032.47 1046.5 1078.46 1089.5 1116.5 1117.51 1133.53 1135.53 1232.59 1234.59 + + + + +4 4 4 3 4 3 3 3 6 12 5 3 4 5 24 3 4 4 45 4 11 3 6 3 4 3 5 6 37 18 +3 4 5 5 20 24 22 3 6 11 4 4 4 4 3 5 3 4 14 4 33 4 3 12 14 4 11 15 4 4 +43 5 4 5 4 6 40 3 3 3 52 6 6 31 4 5 12 7 4 100 20 19 4 + + + + + + +GRMZM2G124307_P01 NP_001152548 LOC100286188 seq=translation; coord=1:212054704..212055806:-1; parent_transcript=GRMZM2G124307_T01; parent_gene=GRMZM2G124307 + + + + + + + + +5.26229 +-0.269861 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +8601 8601 8601 8391 8242 7850 7282 6174 5019 3675 2478 1502 869 448 226 92 32 5 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +8609 8609 8609 8399 8240 7810 7166 5869 4255 2348 1000 310 143 28 10 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2633 3597 1660 549 147 16 4 5 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1291 3368 2480 1049 371 43 4 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3018 (charge 3) + +1644.76 +3 + + +156.102 157.097 158.093 159.077 167.081 169.097 171.077 173.092 173.129 175.119 183.113 185.092 186.123 189.087 195.113 199.071 199.108 199.181 201.124 204.135 211.108 213.087 216.135 217.082 226.155 227.102 229.118 231.098 234.145 239.094 +241.082 245.077 254.163 255.145 259.092 261.619 267.109 272.171 288.201 292.138 299.063 303.178 306.159 310.149 312.155 322.155 324.157 337.187 342.178 346.124 350.143 355.198 358.673 363.166 374.12 379.199 383.194 397.208 427.181 446.237 +452.249 457.161 462.263 470.249 475.165 487.264 504.216 508.241 513.745 516.236 522.231 526.251 550.264 560.314 591.291 598.296 601.277 616.305 619.283 621.29 627.312 637.282 655.293 678.351 703.336 706.347 727.384 750.361 752.306 766.37 +770.321 814.369 832.38 853.357 871.368 894.413 904.488 912.421 929.432 982.445 + + + + +9 9 8 3 4 4 14 3 6 34 79 8 3 20 3 14 25 3 100 3 15 10 9 39 57 30 12 3 40 12 +7 12 6 21 12 8 6 18 3 7 4 13 4 40 14 8 7 7 3 14 6 8 10 6 15 3 7 44 3 3 +9 6 3 7 16 25 15 15 4 4 57 21 13 7 7 3 6 13 83 8 4 22 35 11 41 4 8 6 5 4 +43 9 17 9 54 7 3 9 40 3 + + + + + + +GRMZM2G169384_P01 NP_001149362 DAG protein seq=translation; coord=9:150809669..150813518:1; parent_transcript=GRMZM2G169384_T01; parent_gene=GRMZM2G169384 + + + MASASRALLL SRALQAGASR RVPALLRPVA AAASLLPAVA GPAGAALGAR + VRCFATQPAT SSLRDSSPNW SNRPPKETIL LDGCDFEHWL VIMEPPPGDA + SNPDITRDEI IDSYIKTLAQ VVGSEEEARQ KIYSVSTRHY FGFGALVSEE + LSYKLKEIPK VRWVLPDSYL DVKNKDYGGE PFINGQAVPY DPKYHEEWVR + NNARANDRNR RNDRPRNFDR SRNFDRRREN MQNYQNRDGP PAQGFNGPPP + PPGQNQMPSH HSQGNMSPQP PHAGGGQPNY QPQMQNPQTG YNPGGAPHYQ + QGAAPGYQGG PPGYQGGYQG NPGPAYQGGN TGYQGGNPPP PYQGSNPPPP + YQGGSPPGPP PPYRGGSPPG PPPPYRGGNP NVPPYSGGGN PGYPGGSPGY + QGQGGNSNFQ + + + + + + +5.43358 +-0.293707 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +2304 2304 2304 2245 2163 1875 1670 1516 1034 844 521 294 129 60 28 10 6 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2307 2307 2307 2248 2160 1862 1641 1449 942 621 286 65 17 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1216 902 171 17 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +478 1258 478 80 9 3 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3022 (charge 2) + +1196.51 +2 + + +153.066 155.082 157.061 157.097 157.109 158.093 159.077 166.05 169.097 169.134 170.092 171.077 171.113 173.092 175.119 176.122 181.061 181.097 185.091 194.129 195.114 197.129 198.087 198.124 199.072 199.108 201.123 204.135 209.057 212.103 +216.099 218.096 226.082 227.103 229.065 234.146 236.102 240.135 244.093 245.096 250.12 255.108 260.107 264.098 272.135 278.114 281.125 289.162 292.13 303.178 309.119 312.102 323.137 329.128 337.189 340.095 341.098 344.126 357.123 366.142 +374.148 383.166 389.143 394.179 400.193 402.691 406.171 417.221 420.152 427.206 432.244 438.238 452.255 460.68 485.181 546.233 557.222 559.299 563.258 564.268 569.255 580.284 590.268 660.278 661.273 677.296 694.327 696.335 732.387 788.332 +805.359 806.363 822.386 824.382 833.356 903.489 953.425 955.427 963.408 1078.43 + + + + +6 12 12 8 6 17 4 8 7 3 10 7 18 7 71 3 31 10 3 3 4 3 13 3 37 29 7 6 14 7 +14 3 90 24 6 10 3 8 67 7 13 9 22 35 29 7 32 47 8 8 9 9 3 6 5 31 3 6 33 6 +11 7 10 3 20 7 12 41 3 3 9 3 11 3 3 6 3 3 8 3 3 65 7 8 3 21 100 8 3 9 +35 17 49 3 6 6 27 6 3 8 + + + + + + +GRMZM2G112149_P01 B8A1R8 Putative uncharacterized protein seq=translation; coord=5:15546617..15552849:-1; parent_transcript=GRMZM2G112149_T01; parent_gene=GRMZM2G112149 + + + MASHIVGYPR MGPKRELKFA LESFWDGKSS AEDLEKVATD LRSSIWKQMS + EAGIKYIPSN TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG LSTYFSMARG + NATVPAMEMT KWFDTNYHFI VPELGPSTKF TYASHKAVSE YKEAKALGID + TVPVLVGPVS YLLLSKPAKG VEKSFSLLSL LGSILPIYKE VVAELKAAGA + SWIQLDEPTL VKDLDAHELA AFSSAYAELE SSFSGLNVLI ETYFADIPAE + SYKTLTSLSG VTAYGFDLIR GAKTLDLIRS SFPSGKYLFA GVVDGRNIWA + DDLAASLSTL HSLEAVAGKD KLVVSTSCSL MHTAVDLVNE TKLDDEIKSW + LAFAAQKVVE VNALAKALAG QKDEVYFAAN AAAQASRRSS PRVTNEEVQK + AAAALRGSDH RRSTTVSARL DAQQKKLNLP VLPTTTIGSF PQTVELRRVR + REYKAKKITE DEYISAIKEE ISKVVKIQEE LDIDVLVHGE PERNDMVEYF + GEQLSGFAFT ANGWVQSYGS RCVKPPIIYG DVSRPNPMTV FWSKMAQSMT + PRPMKGMLTG PVTILNWSFV RNDQPRFETC YQIALAIKKE VEDLEAAGIQ + VIQIDEAALR EGLPLRKSEH AFYLDWAVHS FRITNCGVQD TTQIHTHMCY + SNFNDIIHSI IDMDADVITI ENSRSDEKLL SVFREGVKYG AGIGPGVYDI + HSPRIPSTEE IADRVEKMLA VLDTNILWVN PDCGLKTRKY TEVKPALTNM + VSATKLIRTQ LASAK + + + + + +GRMZM2G112149_P03 B8A1R8 Putative uncharacterized protein seq=translation; coord=5:15547422..15552620:-1; parent_transcript=GRMZM2G112149_T03; parent_gene=GRMZM2G112149 + + + MASHIVGYPR MGPKRELKFA LESFWDGKSS AEDLEKVATD LRSSIWKQMS + EAGIKYIPSN TFSYYDQVLD TTAMLGAVPE RYSWTGGEIG LSTYFSMARG + NATVPAMEMT KWFDTNYHFI VPELGPSTKF TYASHKAVSE YKEAKALGID + TVPVLVGPVS YLLLSKPAKG VEKSFSLLSL LGSILPIYKE VVAELKAAGA + SWIQLDEPTL VKDLDAHELA AFSSAYAELE SSFSGLNVLI ETYFADIPAE + SYKTLTSLSG VTAYGFDLIR GAKTLDLIRS SFPSGKYLFA GVVDGRNIWA + DDLAASLSTL HSLEAVAGKD KLVVSTSCSL MHTAVDLVNE TKLDDEIKSW + LAFAAQKVVE VNALAKALAG QKDEVYFAAN AAAQASRRSS PRVTNEEVQK + AAAALRGSDH RRSTTVSARL DAQQKKLNLP VLPTTTIGSF PQTVELRRVR + REYKAKKITE DEYISAIKEE ISKVVKIQEE LDIDVLVHGE PERNDMVEYF + GEQLSGFAFT ANGWVQSYGS RCVKPPIIYG DVSRPNPMTV FWSKMAQSMT + PRPMKGMLTG PVTILNWSFV RNDQPRFETC YQIALAIKKE VEDLEAAGIQ + VIQIDEAALR EGLPLRKSEH AFYLDWAVHS FRITNCGVQD TTQIHTHMCY + SNFNDIIHSI IDMDADVITI ENSRSDEKLL SVFREGVKYG AGIGPGVYDI + HSPRIPSTEE IADRVEKMLA VLDTNILWVN PDCGLKTRKY TEVKPALTNM + VSATKLIRTQ LASAK + + + + + +GRMZM2G112149_P02 B8A1R8 Putative uncharacterized protein seq=translation; coord=5:15547422..15552849:-1; parent_transcript=GRMZM2G112149_T02; parent_gene=GRMZM2G112149 + + + MKPTNPSDFP CSSSPVHHPP PTPSSPRRPR RHHSSSPGAT PPLHGPRMAS + HIVGYPRMGP KRELKFALES FWDGKSSAED LEKVATDLRS SIWKQMSEAG + IKYIPSNTFS YYDQVLDTTA MLGAVPERYS WTGGEIGLST YFSMARGNAT + VPAMEMTKWF DTNYHFIVPE LGPSTKFTYA SHKAVSEYKE AKALGIDTVP + VLVGPVSYLL LSKPAKGVEK SFSLLSLLGS ILPIYKEVVA ELKAAGASWI + QLDEPTLVKD LDAHELAAFS SAYAELESSF SGLNVLIETY FADIPAESYK + TLTSLSGVTA YGFDLIRGAK TLDLIRSSFP SGKYLFAGVV DGRNIWADDL + AASLSTLHSL EAVAGKDKLV VSTSCSLMHT AVDLVNETKL DDEIKSWLAF + AAQKVVEVNA LAKALAGQKD EVYFAANAAA QASRRSSPRV TNEEVQKAAA + ALRGSDHRRS TTVSARLDAQ QKKLNLPVLP TTTIGSFPQT VELRRVRREY + KAKKITEDEY ISAIKEEISK VVKIQEELDI DVLVHGEPER NDMVEYFGEQ + LSGFAFTANG WVQSYGSRCV KPPIIYGDVS RPNPMTVFWS KMAQSMTPRP + MKGMLTGPVT ILNWSFVRND QPRFETCYQI ALAIKKEVED LEAAGIQVIQ + IDEAALREGL PLRKSEHAFY LDWAVHSFRI TNCGVQDTTQ IHTHMCYSNF + NDIIHSIIDM DADVITIENS RSDEKLLSVF REGVKYGAGI GPGVYDIHSP + RIPSTEEIAD RVEKMLAVLD TNILWVNPDC GLKTRKYTEV KPALTNMVSA + TKLIRTQLAS AK + + + + + + +4.45573 +-0.270044 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +2434 2434 2411 2266 2024 1801 1280 1082 519 380 121 80 41 20 10 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 + + + + +2430 2430 2407 2227 1980 1750 1102 632 212 78 1 0 + + + + + + +0 1 2 3 4 + + + + +1327 986 117 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +357 1309 578 161 28 3 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3023 (charge 2) + +921.427 +2 + + +155.082 157.109 157.133 158.064 158.092 159.077 167.056 167.082 169.097 169.134 170.093 171.077 171.113 173.092 173.129 175.09 175.119 176.093 176.122 181.061 181.096 183.077 187.144 191.085 197.129 198.087 200.103 203.085 209.092 212.139 +217.134 219.081 223.064 225.043 227.103 233.095 244.166 246.156 251.15 255.145 269.124 272.172 287.137 303.214 312.167 314.08 324.986 329.193 341.017 342.997 345.225 350.148 356.193 359.028 371.103 373.22 383.2 386.215 400.23 409.229 +418.238 429.089 431.162 486.252 504.261 535.248 547.267 549.282 556.322 562.291 573.278 591.292 593.29 602.234 627.358 633.324 699.287 702.325 703.327 719.351 724.412 773.362 790.388 + + + + +4 1 1 4 4 2 21 1 2 1 1 2 1 2 2 21 18 2 1 1 1 2 1 1 2 2 4 7 1 2 +2 1 3 5 2 1 2 2 1 13 1 11 1 6 2 1 1 3 5 3 2 14 2 100 1 5 1 12 2 1 +1 11 1 2 5 1 1 1 2 1 1 14 2 9 2 2 4 4 2 8 1 1 5 + + + + + + +GRMZM2G027640_P01 B6SLG6 Lil3 protein seq=translation; coord=4:238744350..238745606:1; parent_transcript=GRMZM2G027640_T01; parent_gene=GRMZM2G027640 + + + MAMATSTFSP RPASLRPLRA GGKPVGLLPF PRRLACATAS GEAPPVEQRD + EAEPALAAAS NGAAVKSEAP PPPPAPAPVP AFRDARWVNG TWDLAKFDKG + SGVDWDAVID AEARRRRWLE DYPEATNTDE AVVFATSIIP WWAWMKRFHL + PEAEKLNGRA AMVGFFMAYF VDSLTGAGLV DQMGNFFCKT LLFAAVAGVL + LVRKNEDVES LKKLVDETTF YDRQWQATWQ DDSAGGPNN + + + + + + +6.60308 +-0.33862 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +6145 6145 6145 5825 5715 5311 4868 3846 3082 1871 1044 599 347 133 43 18 6 3 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6137 6137 6137 5817 5682 5259 4761 3705 2564 1296 356 98 38 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2813 2803 500 29 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1205 3622 996 250 70 2 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3027 (charge 2) + +1241.61 +2 + + +152.057 155.082 157.097 157.109 158.092 159.077 161.092 166.061 167.081 169.097 169.134 171.076 171.112 173.092 173.129 175.119 183.076 185.093 185.128 185.164 186.087 186.123 187.071 187.108 189.087 190.053 194.129 195.113 197.129 198.086 +198.126 199.071 199.108 201.087 213.087 214.118 217.082 223.107 226.154 229.117 231.097 240.134 242.113 244.166 256.093 258.109 260.125 266.15 272.171 274.104 276.168 294.182 299.135 303.177 311.17 314.674 327.13 337.15 345.141 363.202 +404.253 423.217 429.182 458.214 467.169 499.21 505.24 516.522 543.609 561.28 569.302 591.816 611.309 619.637 628.344 645.309 651.805 665.354 700.333 708.369 715.376 725.394 727.398 729.374 769.375 773.364 786.406 796.432 799.422 828.911 +857.451 870.421 915.416 919.433 926.486 982.494 985.487 1028.49 1069.52 + + + + +17 13 10 5 5 29 17 4 3 32 4 10 19 60 12 41 3 5 4 4 3 3 19 10 16 10 4 17 4 3 +3 4 12 24 6 4 11 4 23 6 6 23 9 10 4 15 4 18 12 21 3 3 11 33 4 5 10 4 6 41 +4 4 4 4 3 4 4 3 4 4 4 3 4 4 20 4 4 4 4 14 19 100 11 4 3 4 4 32 12 4 +5 4 4 4 4 15 3 3 18 + + + + + + +GRMZM2G033641_P01 NP_001131001 hypothetical protein LOC100192106 seq=translation; coord=6:148590842..148593721:1; parent_transcript=GRMZM2G033641_T01; parent_gene=GRMZM2G033641 + + + + + + + +GRMZM2G429695_P01 seq=translation; coord=8:101897957..101900533:1; parent_transcript=GRMZM2G429695_T01; parent_gene=GRMZM2G429695 + + + MADETKQEVA APAVELVVTE AEKNAEDPAL VAEKKAVEAA EEKAMEAEEN + ATEADSEEEK KAEEAAAGDE AAVIDGTGSF KEESNLVSEL PDPERTVLAQ + LKELVATTLA NGEFNLPPPP PVKEETKKEE PAKEEAPADK EDEPKAEEAP + RSLPKRSSRQ RRRRETKPAE PVLEEKTVVV ADEPAKEELK EEATMEAVVE + ETKPAYPVPE EKTVVVAEEE ATKTVEAIEE TAAAASEPEA EAAPSPAAEP + KEELIWGVPL VGDDERTDTV LLKFLRAREF KVKEAMAMLK SAVLWRKRLG + IDELLGADLG LPDLEKMVFY RGANRKGHPV CYNVTDLKNS PPMLGKHRGV + TRQALALLQD NYPEFVAKKV FINVPWWYFA ANKVMSPFLT QRTKSKIVFC + SPGRYVAPEQ VPVQFGDLYK EDDTEFSASN AVIKLIVKPS SKETVEVPAT + EGSTVVWELR VLGWEVSYDA EFTPDAEGGY TVIVQKTRKV PAHEEPIMKG + SFKAAGPGKV VLAVDNRASK KKMLLYRFRV KSTAAEPAT + + + + + +GRMZM2G352319_P01 seq=translation; coord=2:161032899..161034897:-1; parent_transcript=GRMZM2G352319_T01; parent_gene=GRMZM2G352319 + + + MDASAPRPHP PPHDIISLRD GHNDVVGEAV RVRTVRIARG SVAQRGAGVE + GEAVASTSIQ CEQAREQALR SVGESDAKTS ARISSGQFKV KEAMAMLKSV + VLWRKRFGID ELLGVDLGLP ELEKVVFYRG ADREGHPVCY NVTDLKNSSP + MLGKHQGVTR QALALLQDNY PEFVAKKVFI NVSWWYLATN KVMSPFLTQR + TKSKIVFCSP DRYVALEQVP VRFGGLYKED DTEFSASDVV TELTVKPSSK + ETIELRVLGW EVSYDAEFAP DAEGGYTVIV EKMRKVPAHE EPIMKGSFKA + AGPSKVVLAV DNRASKKKKL LLYRFRVKST AAEPAA + + + + + +GRMZM5G882189_P01 seq=translation; coord=2:164164062..164169326:-1; parent_transcript=GRMZM5G882189_T01; parent_gene=GRMZM5G882189 + + + MDASAPRPHP PPHDIISFCD GHSAVVGEVV RARTVRTARG SVAQRGAGIE + GEAVASTSIQ REQAREQALR SVGESDAKTS ARISSGSNTK DSLEFASARR + VKIRTRVTVA CEDWVVDHNV DAATMADMAY LTHDYFTLPP EDKPPLGPYI + DTAPSPASFI PQLVETEEED EFFHTSPSTC STMVPNRDAT TSMLAMVEAT + WSDEYTLVDL QSVCYYSTSN AKPKLNSLDE VDPKLLKTFI PLTEQKHLSD + VAIDAVINSA SITITHHDAL MAKGVIFCSI PKSICEYPDL VRHYLGSIVL + PGDNYYAALN SAVFSDGSFC FVPKDTVCPM EIWTYFRINK KETNQFESTL + IVADERCTYV LLIELCLQVD GVKVRLPPWP PPVWTFWLPY DARSPKYISL + LNHLRIYLPE LFPNLNKVVF LDDDIVVQRY LSSLWAINLE GKVNEAVETC + RREDHWVMCK RFRTYFNFSH PMMAQRLDPD ECDWAYGEGG HGDAQVGGAV + AQALRHRRAP GRRPRPAGAG EGGVLPRRRP RGPPRLLQRV RRVPGKELYE + KAFRNAGKRE RFLRWRIQLL ERNIREQLDF SPNGICSMVQ VTDLKNSPPM + LGKHHGVTCQ SLALLQDNYP EFVAKKVFIN VPWWYLAANK VMSPFLTQRT + KSKIVFCSPD RSAETLFRNR RGPRQRGLHG GVAVWKLRVL GWEVSYGAEF + APDAEGRYTV IVEKMRKVPA HEEPIMKGSF KAAGPDKVVL AVDNRASKKK + KLLLYRFRVK STATEPAA + + + + + + +7.56164 +-0.387776 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +8084 8084 8084 8084 7911 7702 7063 6202 5300 3594 2432 1107 521 206 82 33 6 2 1 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8104 8104 8104 8104 7931 7721 7066 6086 4984 2928 1560 329 61 36 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2462 3708 1527 311 69 27 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1372 3590 2036 978 103 8 1 16 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3030 (charge 3) + +1278.69 +3 + + +155.081 155.118 156.077 157.097 157.134 158.092 159.077 162.103 166.062 166.086 167.08 167.093 169.061 169.097 169.133 170.06 171.113 173.092 175.119 183.113 183.149 184.153 185.092 185.129 186.124 187.144 191.118 193.097 194.129 197.128 +199.108 201.123 204.134 207.124 209.106 211.144 213.087 215.139 217.064 219.112 225.099 227.102 231.098 235.12 239.114 244.652 247.111 249.098 251.15 253.093 260.143 267.109 278.153 285.653 302.15 306.157 323.174 331.15 342.185 346.184 +354.17 356.145 366.144 378.139 387.691 390.203 391.237 396.153 405.218 435.198 442.221 447.216 467.191 477.74 487.263 488.288 493.205 495.185 504.242 526.263 533.307 536.25 546.232 564.242 570.3 575.315 599.326 606.293 617.335 634.304 +641.333 647.285 661.295 663.314 684.353 728.369 738.349 746.378 774.379 883.432 + + + + +12 8 6 21 6 19 17 6 13 31 10 6 6 15 20 6 6 9 79 11 100 9 5 6 11 6 24 9 6 9 +9 6 23 8 16 42 8 9 8 17 11 11 7 24 8 8 6 14 7 11 10 20 49 12 6 39 5 21 7 6 +6 9 12 9 11 6 6 16 5 28 28 6 6 6 56 30 8 7 11 13 6 21 9 39 14 10 9 9 7 7 +12 8 28 6 7 6 16 18 19 6 + + + + + + +GRMZM2G415359_P02 Q08062 Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) seq=translation; coord=1:231336278..231341950:-1; parent_transcript=GRMZM2G415359_T02; parent_gene=GRMZM2G415359 + + + + + + + + +GRMZM2G415359_P03 Q08062 Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) seq=translation; coord=1:231336334..231337977:-1; parent_transcript=GRMZM2G415359_T03; parent_gene=GRMZM2G415359 + + + + + + + + + +6.15766 +-0.332846 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 + + + + +8167 8167 8167 8167 8148 5615 4906 3463 2356 1653 829 416 186 72 27 7 3 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8170 8170 8170 8170 8151 5618 4893 3406 1973 1227 517 157 28 8 1 0 + + + + + + +0 1 2 3 4 5 + + + + +6064 1928 159 20 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1110 6047 919 89 3 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3035 (charge 2) + +1637.81 +2 + + +155.082 163.06 171.077 175.119 189.107 197.129 204.087 231.098 240.134 246.603 251.098 258.146 270.107 276.155 287.976 292.755 325.113 327.171 369.179 387.187 405.195 437.204 506.246 510.244 619.332 659.299 748.373 755.361 787.91 947.469 +1048.52 1068.56 1119.55 1234.58 1299.64 1317.61 1381.62 + + + + +7 10 9 10 7 11 14 19 23 8 10 78 14 64 10 10 21 11 12 62 15 14 100 22 45 12 41 21 65 20 +43 14 36 49 22 55 14 + + + + + + +GRMZM2G046804_P01 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36880092..36884475:-1; parent_transcript=GRMZM2G046804_T01; parent_gene=GRMZM2G046804 + + + MGKIKIGING FGRIGRLVAR VALQSEDVEL VAVNDPFITT DYMTYMFKYD + TVHGHWKHSD ITLKDSKTLL FGDKPVTVFG IRNPEEIPWG EAGAEYVVES + TGVFTDKDKA AAHLKGGAKK VVISAPSKDA PMFVVGVNED KYTSDVNIVS + NASCTTNCLA PLAKVIHDNF GIVEGLMTTV HAITATQKTV DGPSAKDWRG + GRAASFNIIP SSTGAAKAVG KVLPDLNGKL TGMSFRVPTV DVSVVDLTVR + IEKGASYEDI KKAIKAASEG PLKGIMGYAE EDLVSTDFLG DSRSSIFDAK + AGIALNDHFV KLVSWYDNEW GYSNRVVDLI RHMFKTQ + + + + + +GRMZM2G046804_P02 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881035..36884475:-1; parent_transcript=GRMZM2G046804_T02; parent_gene=GRMZM2G046804 + + + MGNSSLPDSA SGKIKIGING FGRIGRLVAR VALQSEDVEL VAVNDPFITT + DYMTYMFKYD TVHGHWKHSD ITLKDSKTLL FGDKPVTVFG IRNPEEIPWG + EAGAEYVVES TGVFTDKDKA AAHLKGGAKK VVISAPSKDA PMFVVGVNED + KYTSDVNIVS NASCTTNCLA PLAKVIHDNF GIVEGLMTTV HAITATQKTV + DGPSAKDWRG GRAASFNIIP SSTGAAKAVG KVLPDLNGKL TGMSFRVPTV + DVSVVDLTVR IEKGASYEDI KKAIKAASEG PLKGIMGYAE EDLVSTDFLG + DSRSSIFDAK AGIALNDHFV KLVSWYDNEW GYSNRVVDLI RHMFKTQ + + + + + +GRMZM2G046804_P04 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T04; parent_gene=GRMZM2G046804 + + + MGNSSLPDSA SGFSLSLYNY HYLLLPHAPC SNLTKVGSAD CFLCFFGVSR + SSLDAGKIKI GINGFGRIGR LVARVALQSE DVELVAVNDP FITTDYMTYM + FKYDTVHGHW KHSDITLKDS KTLLFGDKPV TVFGIRNPEE IPWGEAGAEY + VVESTGVFTD KDKAAAHLKG GAKKVVISAP SKDAPMFVVG VNEDKYTSDV + NIVSNASCTT NCLAPLAKVI HDNFGIVEGL MTTVHAITAT QKTVDGPSAK + DWRGGRAASF NIIPSSTGAA KAVGKVLPDL NGKLTGMSFR VPTVDVSVVD + LTVRIEKGAS YEDIKKAIKA ASEGPLKGIM GYAEEDLVST DFLGDSRSSI + FDAKAGIALN DHFVKLVSWY DNEWGYSNRV VDLIRHMFKT Q + + + + + +GRMZM2G046804_P05 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T05; parent_gene=GRMZM2G046804 + + + MTYMFKYDTV HGHWKHSDIT LKDSKTLLFG DKPVTVFGIR NPEEIPWGEA + GAEYVVESTG VFTDKDKAAA HLKGGAKKVV ISAPSKDAPM FVVGVNEDKY + TSDVNIVSNA SCTTNCLAPL AKVIHDNFGI VEGLMTTVHA ITATQKTVDG + PSAKDWRGGR AASFNIIPSS TGAAKAVGKV LPDLNGKLTG MSFRVPTVDV + SVVDLTVRIE KGASYEDIKK AIKAASEGPL KGIMGYAEED LVSTDFLGDS + RSSIFDAKAG IALNDHFVKL VSWYDNEWGY SNRVVDLIRH MFKTQ + + + + + +GRMZM2G046804_P06 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T06; parent_gene=GRMZM2G046804 + + + MTYMFKYDTV HGHWKHSDIT LKDSKTLLFG DKPVTVFGIR NPEEIPWGEA + GAEYVVESTG VFTDKDKAAA HLKGGAKKVV ISAPSKDAPM FVVGVNEDKY + TSDVNIVSNA SCTTNCLAPL AKVIHDNFGI VEGLMTTVHA ITATQKTVDG + PSAKDWRGGR AASFNIIPSS TGAAKAVGKV LPDLNGKLTG MSFRVPTVDV + SVVDLTVRIE KGASYEDIKK AIKAASEGPL KGIMGYAEED LVSTDFLGDS + RSSIFDAKAG IALNDHFVKL VSWYDNEWGY SNRVVDLIRH MFKTQ + + + + + +GRMZM2G046804_P07 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881117..36884877:-1; parent_transcript=GRMZM2G046804_T07; parent_gene=GRMZM2G046804 + + + MGNSSLPDSA SGFSLSLYNY HYLLLPHAPC SNLTKVGSAD CFLCFFGVSR + SSLDAGKIKI GINGFGRIGR LVARVALQSE DVELVAVNDP FITTDYMTYM + FKYDTVHGHW KHSDITLKDS KTLLFGDKPV TVFGIRNPEE IPWGEAGAEY + VVESTGVFTD KDKAAAHLKG GAKKVVISAP SKDAPMFVVG VNEDKYTSDV + NIVSNASCTT NCLAPLAKVI HDNFGIVEGL MTTVHAITAT QKTVDGPSAK + DWRGGRAASF NIIPSSTGAA KAVGKVLPDL NGKLTGMSFR VPTVDVSVVD + LTVRIEKGAS YEDIKKAIKA ASEGPLKGIM GYAEEDLVST DFLGDSRSSI + FDAKAGIALN DHFVKLVSWY DNEWGYSNRV VDLIRHMFKT Q + + + + + +GRMZM2G046804_P08 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881357..36884877:-1; parent_transcript=GRMZM2G046804_T08; parent_gene=GRMZM2G046804 + + + MTYMFKYDTV HGHWKHSDIT LKDSKTLLFG DKPVTVFGIR NPEEIPWGEA + GAEYVVESTG VFTDKDKAAA HLKGGAKKVV ISAPSKDAPM FVVGVNEDKY + TSDVNIVSNA SCTTNCLAPL AKVIHDNFGI VEGLMTTVHA ITATQKTVDG + PSAKDWRGGR AASFNIIPSS TGAAKAVGKV LPDLNGKLTG MSFRVPTVDV + SVVDLTVRIE KGASYEDIKK AIKAASEGPL KGIMGYAEED LVSTDFLGDS + RSSIFDAKAG IALNDHFVKL VSWYDNEWGY SNRVVDLIRH MFKTQ + + + + + +GRMZM2G180625_P01 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T01; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G180625_P02 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T02; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G180625_P03 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903153:-1; parent_transcript=GRMZM2G180625_T03; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G046804_P03 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884877:-1; parent_transcript=GRMZM2G046804_T03; parent_gene=GRMZM2G046804 + + + MGNSSLPDSA SGFSLSLYNY HYLLLPHAPC SNLTKVGSAD CFLCFFGVSR + SSLDAGKIKI GINGFGRIGR LVARVALQSE DVELVAVNDP FITTDYMTYM + FKYDTVHGHW KHSDITLKDS KTLLFGDKPV TVFGIRNPEE IPWGEAGAEY + VVESTGVFTD KDKAAAHLKG GAKKVVISAP SKDAPMFVVG VNEDKYTSDV + NIVSNASCTT NCLAPLAKVI HDNFGIVEGL MTTVHAITAT QKTVDGPSAK + DWRGGRAASF NIIPSSTGAA KAVGKVLPDL NGKLTGMSFR VPTVDVSVVD + LTVRIEKGAS YEDIKKAIKA ASEGPLKGIM GYAEEDLVST DFLGDSRYGF + ASII + + + + + +GRMZM2G176307_P01 NP_001105951 cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC4 seq=translation; coord=5:181520274..181524899:1; parent_transcript=GRMZM2G176307_T01; parent_gene=GRMZM2G176307 + + + MAKIKIGING FGRIGRLVAR VALQSDDVEL VAVNDPFIST DYMTYMFKYD + TVHGQWKHHE VKVKDSKTLL FGEKEVAVFG CRNPEEIPWG SVGAEYVVES + TGVFTDQEKA AAHLKGGAKK VVISAPSKDA PMFVVGVNEK EYKSDINIVS + NASCTTNCLA PLAKVINDKF GIVEGLMTTV HAITATQKTV DGPSSKDWRG + GRAASFNIIP SSTGAAKAVG KVLPVLNGKL TGMSFRVPTV DVSVVDLTVR + LEKSATYDEI KAAVKAEAEG SLKGILGYVE EDLVSTDFQG DSRSSIFDAK + AGIALNGNFV KLVSWYDNEW GYSTRVVDLI RHMNSTN + + + + + +GRMZM2G176307_P02 NP_001105951 cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC4 seq=translation; coord=5:181520571..181525066:1; parent_transcript=GRMZM2G176307_T02; parent_gene=GRMZM2G176307 + + + MAKIKIGING FGRIGRLVAR VALQSDDVEL VAVNDPFIST DYMTYMFKYD + TVHGQWKHHE VKVKDSKTLL FGEKEVAVFG CRNPEEIPWG SVGAEYVVES + TGVFTDQEKA AAHLKGGAKK VVISAPSKDA PMFVVGVNEK EYKSDINIVS + NASCTTNCLA PLAKVINDKF GIVEGLMTTV HAITATQKTV DGPSSKDWRG + GRAASFNIIP SSTGAAKAVG KVLPVLNGKL TGMSFRVPTV DVSVVDLTVR + LEKSATYDEI KAAVKAEAEG SLKGILGYVE EDLVSTDFQG DSRSSIFDAK + AGIALNGNFV KLVSWYDNEW GYSTRVVDLI RHMNSTN + + + + + +GRMZM2G071630_P01 Q43247 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12) seq=translation; coord=4:133103720..133107109:1; parent_transcript=GRMZM2G071630_T01; parent_gene=GRMZM2G071630 + + + MAKIKIGING FGRIGRLVAR VALQSDDVEL VAVNDPFIST DYMTYMFKYD + TVHGQWKHHE VKVKDSKTLL FGEKEVAVFG CRNPEEIPWG SVGAEYVVES + TGVFTDQEKA AAHLKGGAKK VVISAPSKDA PMFVVGVNEK EYKSDINIVS + NASCTTNCLA PLAKVINDKF GIVEGLMTTV HAITATQKTV DGPSSKDWRG + GRAASFNIIP SSTGAAKAVG KVLPVLNGKL TGMSFRVPTV DVSVVDLTVR + LEKSATYDEI KAAVKAEAEG SLKGILGYVE EDLVSTDFQG DSRSSIFDAK + AGIALNGNFV KLVSWYDNEW GYSTRVVDLI RHMNSTK + + + + + +GRMZM2G071630_P02 Q43247 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12) seq=translation; coord=4:133104109..133107067:1; parent_transcript=GRMZM2G071630_T02; parent_gene=GRMZM2G071630 + + + MTYMFKYDTV HGQWKHHEVK VKDSKTLLFG EKEVAVFGCR NPEEIPWGSV + GAEYVVESTG VFTDQEKAAA HLKGGAKKVV ISAPSKDAPM FVVGVNEKEY + KSDINIVSNA SCTTNCLAPL AKVINDKFGI VEGLMTTVHA ITATQKTVDG + PSSKDWRGGR AASFNIIPSS TGAAKAVGKV LPVLNGKLTG MSFRVPTVDV + SVVDLTVRLE KSATYDEIKA AVKAEAEGSL KGILGYVEED LVSTDFQGDS + RSSIFDAKAG IALNGNFVKL VSWYDNEWGY STRVVDLIRH MNSTK + + + + + +GRMZM2G104632_P01 NP_001149357 LOC100282981 seq=translation; coord=5:85252669..85257667:1; parent_transcript=GRMZM2G104632_T01; parent_gene=GRMZM2G104632 + + + MAALSAPLRA VAAGSRVAAS DPVKVSCVRS TGSAHFGCAF PYIRASSSAA + RNLEPLRAIA TQAPPAMPQY SSGEKTKIGI NGFGRIGRLV LRIATSRDDI + EVVAVNDPFI DAKYMAYMFK YDSTHGPFKG SIRVVDDSTL EINGKKVTIT + SKRDPAEIPW GNFGAEYVVE SSGVFTTTDK ASAHLKGGAK KVVISAPSAD + APMFVVGVNE NSYDPKMNVV SNASCTTNCL APLAKVVHEE FGIVEGLMTT + VHATTATQKT VDGPSMKDWR GGRGAAQNII PSSTGAAKAV GKVLPELNGK + LTGMAFRVPT PNVSVVDLTC RIEKSASYDD VKAAIKTASE GALKGILGYT + DEDVVSNDFV GDSRSSIFDA KAGIGLSSSF MKLVSWYDNE WGYSNRVLDL + IAHMALVSAK H + + + + + +GRMZM2G051004_P01 NP_001130796 hypothetical protein LOC100191900 seq=translation; coord=4:236083133..236088143:-1; parent_transcript=GRMZM2G051004_T01; parent_gene=GRMZM2G051004 + + + MAALSVPLHA AAGSRAAAAD PVKVPCVRST GSAHFGRAFP SVAVSSLAAR + HIEPMRAIAT QAPPAVPQYL SGEKTKIGIN GFGRIGRLVL RIATSRDDIE + VVAVNDPFVD AKYMAYMFKY DSTHGPFKGS ICVVDDSTLE INGKKVTITS + KRDPAEIPWG NFGAEYVVES SGVFTTTDKA SAHLKGGAKK VVISAPSADA + PMFVVGVNEN SYDSKMNVVS NASCTTNCLA PLAKVVHEEF GIVEGLMTTV + HATTATQKTV DGPSMKDWRG GRGAGQNIIP SSTGAAKAVG KVLPELNGKL + TGMAFRVPTP NVSVVDLTCR IEKNASYDDV KAAIKAASEG ALKGILGYTD + EDVVSNDFVG DSRSSIFDAK AGIGLSSSFM KLVSWYDNEW GYSNRVLDLI + AHMALVSAAA KL + + + + + + +4.88378 +-0.25045 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +3841 3841 3818 3732 3572 3283 2826 2296 1451 957 471 301 200 119 86 15 13 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3870 3870 3847 3761 3595 3288 2783 2043 1066 440 186 161 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1437 1958 402 87 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +853 2133 676 133 82 6 0 13 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3037 (charge 2) + +944.541 +2 + + +155.081 157.097 158.091 159.077 167.081 169.097 171.076 171.113 171.149 173.092 175.119 181.061 183.113 185.092 185.114 185.165 186.097 186.12 187.072 189.087 193.097 194.129 199.071 199.108 199.181 201.087 212.103 216.097 218.15 219.153 +221.103 224.103 227.176 228.133 230.114 237.124 240.135 244.166 246.107 249.099 254.113 256.129 258.108 262.152 270.108 272.124 288.12 289.187 299.134 301.151 315.131 317.146 327.129 329.183 341.145 346.208 347.21 355.162 359.69 368.156 +370.173 386.164 388.181 394.172 398.167 404.217 412.184 414.245 416.177 430.193 442.762 447.257 456.26 465.208 475.254 478.227 483.222 490.256 501.23 516.28 534.289 536.249 544.275 549.261 554.258 562.283 572.266 603.308 621.32 623.326 +631.305 648.33 673.315 691.325 700.359 718.373 720.373 748.346 762.358 833.4 + + + + +4 25 4 11 7 4 3 4 7 11 21 2 2 87 9 5 3 3 14 3 6 3 3 5 100 13 3 3 45 2 +3 3 14 8 6 3 2 4 3 3 7 14 12 4 6 8 2 6 4 3 2 6 4 5 3 13 2 4 31 3 +3 3 3 2 3 10 3 2 2 2 3 9 4 4 7 2 5 3 5 3 21 3 6 7 2 21 4 4 42 2 +3 5 6 12 3 35 4 3 6 2 + + + + + + +GRMZM5G863596_P01 seq=translation; coord=3:202942770..202965565:-1; parent_transcript=GRMZM5G863596_T01; parent_gene=GRMZM5G863596 + + + MRPPGSVAIK DYAIETPLEI LPNSEGQPLY EMQIKFDKDI PIAAVNFVLK + EEETGAWFQH KGRDFRIPLN GSFNDGGKQD IDIWPGDLGH VLKKSEGSSS + QPQNTSPEDT GLSGKHISGF YEEYPILKSE YVQNLVTVTV RRDIEAHKRL + VEFDTDIPGE VIIHWGVCRD NTMTWEIPPE PHPPKTKIFR HKALQTLLQQ + KADGAGNSIS FSLDAEYSCL FFVLKLDEYT WLRNLENGSD FYVPLTRVGQ + YGSTQDPDKA EAQKIEDKSS QADGLISDIR NLVVGLSSRR GQKAKNKVLQ + EDILQEIERL AAEAYSIFRS PTIDSVDESV QLDDTLSAKP ACSGTGSGFE + ILCQGFNWES HKSGKWYVEL GTKAKELSSL GFTIVWSPPP TDSVSPEGYM + PRDLYNLNSR YGSMDELKEL VKIFHEAGIK VLGDAVLNHR CAQFQNNNGV + WNIFGGRMNW DDRAVVADDP HFQGRGNKSS GDNFHAAPNI DHSQEFVRND + LKEWLCWMRK EVGYDGWRLD FVRGFWGGYV KDYLEASEPY FAVGEYWDSL + SYTYGEMDYN QDAHRQRIVD WINATNGTAG AFDVTTKGIL HAALERSEYW + RLSDEKGKPP GVLGWWPSRA VTFIENHDTG STQGHWRFPY GMELQGYAYI + LTHPGTPAVF YDHIFSHLQP EIAKFISIRH RQKIHCRSKI KILKAERSLY + AAEIDEKVTM KIGSEHFEPS GPQNWIVAAE GQDYKIWEAS S + + + + + +GRMZM5G863596_P02 seq=translation; coord=3:202942770..202965565:-1; parent_transcript=GRMZM5G863596_T02; parent_gene=GRMZM5G863596 + + + MRPPGSVAIK DYAIETPLEI LPNSEGQPLY EMQIKFDKDI PIAAVNFVLK + EEETGAWFQH KGRDFRIPLN GSFNDGGKQD IDIWPGDLGH VLKKSEGSSS + QPQNTSPEDT GLSGKHISGF YEEYPILKSE YVQNLVTVTV RRDIEAHKRL + VEFDTDIPGE VIIHWGVCRD NTMTWEIPPE PHPPKTKIFR HKALQTLLQQ + KADGAGNSIS FSLDAEYSCL FFVLKLDEYT WLRNLENGSD FYVPLTRVGQ + YGSTQDPDKA EAQKIEDKSS QADGLISDIR NLVVGLSSRR GQKAKNKVLQ + EDILQEIERL AAEAYSIFRS PTIDSVDESV QLDDTLSAKP ACSGTGSGFE + ILCQGFNWES HKSGKWYVEL GTKAKELSSL GFTIVWSPPP TDSVSPEGYM + PRDLYNLNSR YGSMDELKEL VKIFHEAGIK VLGDAVLNHR CAQFQNNNGV + WNIFGGRMNW DDRAVVADDP HFQGRGNKSS GDNFHAAPNI DHSQEFVRND + LKEWLCWMRK EVGYDGWRLD FVRGFWGGYV KDYLEASEPY FAVGEYWDSL + SYTYGEMDYN QDAHRQRIVD WINATNGTAG AFDVTTKGIL HAALERSEYW + RLSDEKGKPP GVLGWWPSRA VTFIENHDTG STQGHWRFPY GMELQGYAYI + LTHPGTPAVF YDHIFSHLQP EIAKFISIRH RQKIHCRSKI KILKAERSLY + AAEIDEKVTM KIGSEHFEPS GPQNWIVAAE GQDYKIWEAS S + + + + + + +6.57771 +-0.30594 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +10336 10336 10336 10336 10075 9754 8704 7459 5806 4106 2511 1338 766 451 185 83 43 13 5 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +10324 10324 10324 10324 10063 9724 8609 7176 5055 2949 1226 329 150 87 9 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3331 4185 2021 582 202 17 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1740 4741 2799 859 170 26 1 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3040 (charge 3) + +1821.87 +3 + + +153.066 155.082 157.097 157.134 158.092 159.077 167.055 167.082 169.061 171.077 173.092 173.128 174.124 175.119 185.092 186.087 187.072 189.087 195.075 195.113 199.071 200.14 201.087 204.134 213.087 221.091 223.108 226.155 227.102 230.081 +239.095 244.093 247.108 258.108 261.156 272.172 275.102 285.155 299.059 311.171 323.172 327.129 341.18 346.208 349.151 355.069 359.194 401.669 412.219 426.249 432.172 443.737 475.25 478.714 495.252 504.254 521.207 541.263 546.291 549.927 +556.77 572.305 584.304 607.254 608.827 612.297 620.325 642.288 652.262 655.34 670.326 674.385 679.343 687.827 717.376 723.339 729.337 740.354 743.344 748.408 760.403 766.373 769.369 789.398 794.353 817.382 830.372 842.409 869.433 886.463 +888.463 895.421 927.489 956.402 959.419 966.453 984.472 1001.49 1069.54 1112.52 + + + + +5 13 35 13 6 75 6 6 15 14 25 7 15 22 11 45 100 6 6 12 6 14 30 6 23 13 12 38 7 16 +26 17 34 27 11 6 11 35 11 11 13 5 24 29 6 21 5 17 12 40 6 27 14 6 13 6 6 15 23 5 +5 12 6 11 6 24 17 5 6 5 13 22 7 25 11 5 6 27 12 5 5 31 5 14 5 13 30 21 13 94 +11 16 16 9 13 11 5 18 11 6 + + + + + + +GRMZM2G044132_P01 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53846005:1; parent_transcript=GRMZM2G044132_T01; parent_gene=GRMZM2G044132 + + + + + + + + +4.19204 +-0.239545 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +1641 1641 1627 1568 1520 1363 1243 722 576 341 219 108 57 38 16 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +1651 1651 1637 1578 1526 1354 1222 671 491 238 133 46 12 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1005 527 98 17 5 0 + + + + + + +0 1 2 3 4 5 6 + + + + +348 1035 200 63 0 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3042 (charge 2) + +1620.67 +2 + + +153.388 155.082 158.093 159.076 160.078 163.06 173.092 175.119 176.124 185.092 187.071 188.075 199.071 201.087 213.087 226.119 258.108 274.238 280.131 286.151 293.106 298.103 303.178 316.113 325.113 341.144 367.179 387.152 431.706 444.174 +458.246 461.177 475.273 502.179 508.251 524.737 536.249 551.25 560.255 577.269 587.291 600.244 604.311 618.266 665.291 706.28 716.333 718.322 733.367 747.38 753.327 779.848 794.317 802.339 811.842 845.375 874.345 881.393 945.384 976.37 +988.43 1031.44 1078.41 1094.45 1102.48 1217.51 1465.59 + + + + +1 3 2 18 2 35 4 35 2 3 46 2 3 10 8 2 29 2 2 3 2 3 20 17 22 2 3 10 10 3 +9 2 10 5 3 12 4 5 100 5 4 2 7 16 3 22 10 11 3 13 53 3 3 11 25 9 5 3 3 4 +4 16 3 3 4 8 3 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + + + + + + +6.31391 +-0.360795 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +6059 6059 5952 5685 5338 4903 4472 3172 2529 1333 649 280 96 35 11 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6073 6073 5966 5698 5327 4808 4299 2853 1893 575 175 19 6 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2215 2441 1099 251 60 5 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1191 2649 1582 522 104 16 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3043 (charge 3) + +1328.64 +3 + + +153.102 155.081 157.108 158.092 159.076 164.609 167.055 167.081 168.113 169.097 170.092 171.077 171.113 172.118 173.129 174.07 175.119 176.123 178.606 179.107 181.097 183.125 183.148 185.092 185.165 186.123 198.124 199.072 199.108 201.123 +204.621 209.091 211.119 217.081 223.063 226.118 228.145 229.149 237.626 245.172 246.14 254.653 255.653 264.134 269.141 272.171 277.656 289.133 294.664 297.156 299.062 303.178 306.159 311.183 321.168 324.988 328.209 339.177 341.146 342.997 +356.204 359.028 373.136 379.66 388.173 400.165 417.191 429.09 435.202 437.204 442.192 444.242 453.163 470.188 482.282 493.254 510.275 511.275 526.309 527.313 533.202 536.295 545.267 550.229 552.23 554.305 601.228 646.299 658.351 661.261 +662.265 678.287 680.282 715.325 740.302 758.312 775.34 777.343 + + + + +10 2 4 8 1 2 21 1 1 3 2 1 27 2 2 2 27 3 7 2 6 5 2 2 3 1 5 1 5 2 +8 3 6 1 2 10 25 2 2 10 19 42 2 3 4 2 11 5 3 1 1 10 27 3 1 2 26 13 6 5 +100 77 2 3 6 2 3 1 18 1 1 1 1 5 3 1 9 2 11 3 2 5 1 13 2 10 1 1 2 10 +3 13 3 2 3 3 45 6 + + + + + + +GRMZM2G113250_P01 seq=translation; coord=1:296260884..296265865:-1; parent_transcript=GRMZM2G113250_T01; parent_gene=GRMZM2G113250 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDESKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KETDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AYLPVIESFG FSSQLRAATS GQAFPQAVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMIPLSEFE DKL + + + + + + +GRMZM2G040369_P01 NP_001151465 LOC100285098 seq=translation; coord=1:296477860..296482170:1; parent_transcript=GRMZM2G040369_T01; parent_gene=GRMZM2G040369 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDETKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KETDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AFLPVIESFG FSSQLRAATS GQAFPQCVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMTPLSEFE DKL + + + + + + +GRMZM2G040369_P02 NP_001151465 LOC100285098 seq=translation; coord=1:296477860..296482080:1; parent_transcript=GRMZM2G040369_T02; parent_gene=GRMZM2G040369 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDETKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KETDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AFLPVIESFG FSSQLRAATS GQAFPQCVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMTPLSEFE DKL + + + + + + +GRMZM2G095851_P01 NP_001151465 LOC100285098 seq=translation; coord=1:296344357..296348667:1; parent_transcript=GRMZM2G095851_T01; parent_gene=GRMZM2G095851 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDETKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KETDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AFLPVIESFG FSSQLRAATS GQAFPQCVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMTPLSEFE DKL + + + + + + +GRMZM2G095851_P02 NP_001151465 LOC100285098 seq=translation; coord=1:296344357..296348577:1; parent_transcript=GRMZM2G095851_T02; parent_gene=GRMZM2G095851 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDETKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KETDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AFLPVIESFG FSSQLRAATS GQAFPQCVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMTPLSEFE DKL + + + + + + +AC203173.3_FGP004 seq=translation; coord=8:175215853..175219214:-1; parent_transcript=AC203173.3_FGT004; parent_gene=AC203173.3_FG004 + + + MVKFTAEELR AIMDKKNNIR NMSVIAHVDH GKSTLTDSLV AAAGIIAQEV + AGDVRMTDTR ADEAERGITI KSTGISLYYE MTDESLKNYK GERDGNQYLI + NLIDSPGHVD FSSEVTAALR ITDGALVVVD CIEGVCVQTE TVLRQALGER + IRPVLTVNKM DRCFLELQVE GEEAYQTFSR VIENANVIMA TYEDKLLGDV + QVYPEKGTVA FSAGLHGWAF TLTNFAKMYA SKFGVDESKM MERLWGENFF + DPATKKWTTK NTGSPTCKRG FVQFCYEPIK QIIKTCMNDQ KEKLWPMLQK + LNVTMKADEK ELIGKALMKR VMQTWLPAST ALLEMMIFHL PSPAKAQKYR + VENLYEGPLD DVYATAIRNC DPEGPLMLYV SKMIPASDKG RFFAFGRVFS + GKVATGMKVR IMGPNYVPGQ KKDLYVKSVQ RTVIWMGKKQ ESVEDVPCGN + TVAMVGLDQF ITKNATLTNE KEVDACPIRA MKFSVSPVVR VAVQCKVASD + LPKLVEGLKR LAKSDPMVLC TMEESGEHII AGAGELHLEI CLKDLQEDFM + GGAEIIVSPP VVSFRETVLE KSCRTVMSKS PNKHNRLYME ARPLEEGLAE + AIDDGRIGPR DDPKVRSQIL SQEFGWDKDL AKKIWCFGPE TTGPNMVVDM + CKGVQYLNEI KDSVVAGFQW ASKEGALAEE NMRGICFEVC DVVLHADAIH + RGGGQVIPTA RRVIYASQLT AKPRLLEPVY LVEIQAPENA LGGIYGVLNQ + KRGHVFEEMQ RPGTPLYNIK AFLPVIESFG FSSQLRAATS GQAFPQCVFD + HWDMMGSDPL EAGSQAAQLV LDIRKRKGLK EQMTPLSEFE DKL + + + + + + + +5.42335 +-0.293154 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +3286 3286 3281 3155 2992 2800 2606 1743 1389 867 482 262 156 43 20 10 6 1 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3296 3296 3291 3161 2994 2778 2547 1609 1140 542 218 127 64 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1463 1282 492 58 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +766 2033 420 61 7 0 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3044 (charge 2) + +1135.5 +2 + + +155.081 157.061 157.098 157.134 158.092 159.077 166.086 169.061 169.097 169.134 171.077 171.113 172.072 173.092 173.128 175.119 176.122 178.086 181.098 183.113 185.092 185.129 187.071 187.107 188.074 189.087 194.129 195.076 197.129 198.088 +199.108 201.087 203.103 205.098 212.103 213.087 216.098 223.107 226.155 230.113 233.092 240.098 242.15 244.092 248.112 251.102 256.166 258.109 266.114 282.109 284.124 295.141 300.12 309.119 313.152 316.13 322.156 325.187 327.202 329.184 +334.138 343.197 345.213 353.181 355.172 372.198 373.2 397.212 424.225 436.197 442.231 459.254 483.233 501.242 565.239 567.243 603.263 612.271 622.333 630.284 632.296 639.347 657.358 674.303 676.277 684.3 694.282 696.291 701.321 703.324 +738.354 747.309 765.32 767.324 814.405 878.404 885.444 887.446 942.471 974.473 + + + + +4 3 5 29 7 10 5 25 3 2 4 3 1 9 7 31 2 6 3 1 4 18 57 3 4 3 1 2 3 2 +8 14 5 4 33 9 1 16 8 7 7 24 9 3 2 6 4 58 1 1 8 6 2 1 7 3 8 30 3 5 +4 6 17 15 6 19 3 3 2 11 2 4 5 33 20 1 3 8 1 62 4 1 22 3 3 4 24 1 100 8 +2 3 31 5 23 5 4 5 3 1 + + + + + + +GRMZM2G109526_P01 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168483295:1; parent_transcript=GRMZM2G109526_T01; parent_gene=GRMZM2G109526 + + + MQQLLPGPPR PCTPSPLPKV QLISCPVDSF QHALNPKVTG QVHAHTKTCG + ACKCPTHIHG LLVSAGGRRT FLPVSAVGSG QGSSVTEADR KSDLSLENVK + TSVVSRDGEK INVRVQLPGK ATQKVFDEAL TFLARDAPPV PGFRKSKGGK + TSNIPSSILL QMLGKSRVTK FVLQEILSIT IEEFVKKENL KVKPEIQTTQ + SEGEMESAFA PGSAFGFNVV LQLETPDSDD PEEKPGSDDD LQEESGSSE + + + + + +GRMZM2G109526_P02 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168483295:1; parent_transcript=GRMZM2G109526_T02; parent_gene=GRMZM2G109526 + + + MASAATATLP KVQLRPRCNS YFQVTGQVHA HTKTCGACKC PTHIHGLLVS + AGGRRTFLPV SAVGSGQGSS VTEADRKSDL SLENVKTSVV SRDGEKINVR + VQLPGKATQK VFDEALTFLA RDAPPVPGFR KSKGGKTSNI PSSILLQMLG + KSRVTKFVLQ EILSITIEEF VKKENLKVKP EIQTTQSEGE MESAFAPGSA + FGFNVVLQLE TPDSDDPEEK PGSDDDLQEE SGSSE + + + + + +GRMZM2G109526_P03 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168483088:1; parent_transcript=GRMZM2G109526_T03; parent_gene=GRMZM2G109526 + + + MASAATATLP KVQLRPRCNS YFQVTGQVHA HTKTCGACKC PTHIHGLLVS + AGGRRTFLPV SAVGSGQGSS VTEADRKSDL SLENVKTSVV SRDGEKINVR + VQLPGKATQK VFDEALTFLA RDAPPVPGFR KSKGGTDHHK HTATSLSLSL + SLSLSLSISY + + + + + +GRMZM2G109526_P04 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168483088:1; parent_transcript=GRMZM2G109526_T04; parent_gene=GRMZM2G109526 + + + MASAATATLP KVQLRPRCNS YFQVTGQVHA HTKTCGACKC PTHIHGLLVS + AGGRRTFLPV SAVGSGQGSS VTEADRKSDL SLENVKTSVV SRDGEKINVR + VQLPGKATQK VFDEALTFLA RDAPPVPGFR KSKGDTQQHP AADAWQEPGH + QIRSSGNTEH HH + + + + + +GRMZM2G109526_P05 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168482368:1; parent_transcript=GRMZM2G109526_T05; parent_gene=GRMZM2G109526 + + + MQQLLPGPPR PCTPSPLPKV QLISCPVDSF QHALNPKVTG QVHAHTKTCG + ACKCPTHIHG LLVSAGGRRT FLPVSAVGSG QGSSVTEADR KSDLSLENVK + TSVVSRDGEK INVRVQLPGK ATQKVFDEAL TFLARDAPPV PGFRKSKGGK + TSNIPSSILL QMLGKSRVTK FVLQEILSIT IEEFVKKVNA SSDNTWQKKK + PVTGRYDTDL LLINQENLKV KPEIQT + + + + + +GRMZM2G109526_P06 NP_001141889 hypothetical protein LOC100274034 seq=translation; coord=3:168480648..168481862:1; parent_transcript=GRMZM2G109526_T06; parent_gene=GRMZM2G109526 + + + MQQLLPGDRS SPCPHQNMRC LQVSDPYPRV NKLDAAPLSP VIFRFSVFSL + HVCLHRLLVS AGGRRTFLPV SAVGSGQGSS VTEADRKSDL SLENVKTSVV + SRDGEKINVS SNQLSCPDVQ IESFDLIWPC QLFLCMQVRV QLPGKATQKV + FDEALTFLAR DAPPVPGFRK SKGGTDHHKH TATSLSLSLS LSLSLSISY + + + + + + +5.76956 +-0.295875 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 + + + + +4871 4871 4847 4652 4373 4080 3722 3379 2308 1792 922 614 365 171 99 28 8 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4879 4879 4855 4660 4377 4038 3674 3239 2177 1365 519 138 40 8 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2318 2060 436 65 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1051 2823 789 195 15 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3046 (charge 2) + +1420.66 +2 + + +155.081 155.118 157.06 157.097 158.092 159.077 167.082 168.065 169.061 169.098 171.076 171.113 172.117 173.092 175.119 176.122 183.075 183.113 184.072 185.092 186.088 187.107 193.096 195.113 198.087 199.072 199.108 201.099 208.107 213.124 +214.118 216.098 219.109 226.154 228.134 242.114 247.11 251.1 255.108 264.134 270.146 273.12 276.11 290.144 295.104 302.135 312.13 315.167 325.116 327.164 330.141 339.168 344.155 352.123 361.183 369.151 414.198 437.207 441.219 443.736 +455.229 465.211 490.221 492.264 516.239 527.721 539.273 540.786 579.262 591.274 610.606 616.779 631.34 632.341 644.134 690.343 718.377 725.359 754.341 777.373 864.407 886.463 904.41 905.476 921.427 922.427 969.339 983.517 985.523 1032.45 +1049.48 1071.48 1089.46 1106.51 1163.53 1193.54 1221.6 1232.54 1250.56 1386.74 + + + + +5 9 5 4 10 2 36 3 10 4 4 59 4 35 75 5 2 9 12 4 27 4 3 4 2 3 5 9 2 4 +4 2 19 12 20 11 3 3 10 65 14 21 2 5 4 3 9 3 2 3 5 3 5 4 29 3 4 3 3 4 +4 3 17 27 5 3 5 5 3 47 4 5 12 4 4 25 4 3 3 33 31 40 12 2 100 52 3 19 3 5 +11 4 3 26 3 5 5 4 26 3 + + + + + + +GRMZM2G031501_P03 NP_001140638 hypothetical protein LOC100272713 seq=translation; coord=1:261486889..261490473:1; parent_transcript=GRMZM2G031501_T03; parent_gene=GRMZM2G031501 + + + MPRRSSGRSA PRPAPRAASL RNPPQPARQA PPPAPVRDGG GSMFGGIGST + IAQGMAFGTG SAMAHRAVDS VLGPRTIQHE TLATEAPAAA PAAPAMNADA + CSFHSKAFQD CLNNYGSEIS KCQFYLDMLN ECRRGGVSV + + + + + +GRMZM2G031501_P05 NP_001140638 hypothetical protein LOC100272713 seq=translation; coord=1:261486945..261491063:1; parent_transcript=GRMZM2G031501_T05; parent_gene=GRMZM2G031501 + + + MPRRSSGRSA PRPAPRAASL RNPPQPARQA PPPAPVRDGG GSMFGGIGST + IAQGMAFGTG SAMAHRAVDS VLGPRTIQHE TLATEAPAAA PAAPAMNADA + CSFHSKAFQD CLNNYGSEIS KCQFYLDMLN ECRRGGVSV + + + + + +GRMZM2G028379_P01 NP_001150231 p8MTCP1 seq=translation; coord=1:261408681..261412620:1; parent_transcript=GRMZM2G028379_T01; parent_gene=GRMZM2G028379 + + + LREPTRQIFL CRKTGPQTGT NGSRVETSSA FSLIKPNAQG PPCSISLSVV + LSLSIRSPPH PEPAVSLGFR RRRRHASPQL RSAPRPAPRA APVRNPPQPA + RQAPPPAPVR DGGGSMFGGI GSTIAQGMAF GTGSAMAHRA VDAVLGPRTI + QHETVASEAA AAAPAPPVMN ADACSIHSKA FQDCLNNYGS EISKCQFYLD + MLNECRRGGV SA + + + + + +GRMZM2G028379_P02 NP_001150231 p8MTCP1 seq=translation; coord=1:261408681..261412620:1; parent_transcript=GRMZM2G028379_T02; parent_gene=GRMZM2G028379 + + + MPRRSSGRSA PRPAPRAAPV RNPPQPARQA PPPAPVRDGG GSMFGGIGST + IAQGMAFGTG SAMAHRAVDA VLGPRTIQHE TVASEAAAAA PAPPVMNADA + CSIHSKAFQD CLNNYGSEIS KCQFYLDMLN ECRRGGVSA + + + + + +GRMZM2G028379_P04 NP_001150231 p8MTCP1 seq=translation; coord=1:261408716..261411902:1; parent_transcript=GRMZM2G028379_T04; parent_gene=GRMZM2G028379 + + + MPRRSSGRSA PRPAPRAAPV RNPPQPARQA PPPAPVRDGG GSMFGGIGST + IAQGMAFGTG SAMAHRAVDA VLGPRTIQHE TVASEAAAAA PAPPVMNADA + CSIHSKAFQD VCLLATLCSL IFPQFDAVVK VV + + + + + + +5.99854 +-0.279002 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +3114 3114 3114 3114 3089 2951 2810 2511 2208 1730 1332 806 475 244 121 61 21 11 9 2 1 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3124 3124 3124 3124 3099 2961 2799 2484 2124 1336 764 150 20 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1379 1249 437 61 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +525 1454 868 229 38 9 0 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3049 (charge 2) + +932.532 +2 + + +152.057 154.097 155.081 155.118 157.097 157.134 158.092 159.077 163.133 164.137 166.062 167.082 167.118 169.097 169.134 171.113 172.108 173.055 173.092 173.129 175.119 181.061 182.093 183.077 183.113 185.093 185.128 187.107 187.145 189.087 +193.098 194.129 195.077 195.114 197.128 198.087 200.103 201.123 204.135 209.104 212.104 215.14 217.082 218.15 223.108 226.119 227.102 230.15 232.141 235.119 240.134 242.15 244.165 246.157 249.159 252.109 253.094 258.146 262.151 266.153 +270.168 272.172 276.157 280.127 287.977 290.115 294.149 297.156 303.146 304.948 306.941 316.133 318.695 322.959 324.954 354.215 361.028 363.024 367.221 368.704 371.238 377.181 390.238 398.24 410.179 417.221 442.279 462.236 514.235 517.289 +539.33 545.283 627.326 630.372 636.383 658.364 703.336 733.436 759.423 787.416 + + + + +10 50 50 10 11 41 20 7 84 9 10 8 11 20 14 13 38 15 10 10 88 7 42 10 10 8 14 8 8 7 +9 7 8 17 17 8 16 24 10 10 10 13 12 8 8 26 14 11 18 10 16 14 16 15 18 17 9 18 41 9 +30 20 7 16 8 9 10 9 29 12 13 8 100 9 13 13 12 19 28 7 14 11 7 25 7 20 7 23 14 12 +87 35 9 26 53 9 8 44 8 9 + + + + + + +GRMZM5G861390_P01 P05494 ATP synthase subunit alpha, mitochondrial seq=translation; coord=Mt:523288..525296:-1; parent_transcript=GRMZM5G861390_T01; parent_gene=GRMZM5G861390 + + + + + + + +GRMZM5G829375_P01 P05494 ATP synthase subunit alpha, mitochondrial seq=translation; coord=Mt:454351..456359:-1; parent_transcript=GRMZM5G829375_T01; parent_gene=GRMZM5G829375 + + + + + + + +GRMZM5G845063_P01 seq=translation; coord=3:74659634..74660746:1; parent_transcript=GRMZM5G845063_T01; parent_gene=GRMZM5G845063 + + + + + + + + +5.97246 +-0.29134 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +6741 6741 6741 6559 6387 6113 5537 4233 3423 1836 1050 599 323 175 94 40 15 8 7 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6747 6747 6747 6565 6393 6102 5432 3900 2562 923 358 108 33 19 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3474 2638 553 69 9 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +881 3874 1650 278 52 7 0 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3050 (charge 2) + +1354.72 +2 + + +152.056 153.102 155.082 155.118 157.06 157.097 158.092 159.077 161.092 164.118 166.061 171.076 171.113 173.092 175.071 175.119 176.119 183.149 185.092 186.123 187.072 187.108 189.087 198.124 199.072 199.107 201.087 204.133 209.14 213.086 +215.102 216.134 221.14 226.155 230.113 237.136 239.113 244.166 249.098 254.149 260.196 262.153 267.109 270.107 279.181 284.124 287.206 306.155 315.203 317.217 324.167 352.16 357.158 366.176 397.218 402.234 407.241 414.248 416.25 418.265 +424.265 434.252 440.196 452.262 458.202 460.721 472.781 514.275 520.764 529.294 546.327 551.234 553.303 563.29 577.309 581.31 600.317 628.307 630.327 634.336 638.84 713.366 737.334 740.352 757.391 765.364 774.418 776.42 784.391 824.37 +885.442 893.429 894.429 903.461 982.459 989.478 1006.5 1012.4 1040.51 1095.53 + + + + +12 10 20 5 4 4 4 6 23 4 11 11 5 14 6 31 5 10 4 5 7 19 25 12 6 12 4 4 4 6 +5 6 11 16 6 28 17 6 16 52 11 20 50 4 5 4 4 15 6 14 16 5 23 23 4 4 5 41 4 29 +12 5 5 24 4 4 6 23 26 6 4 4 5 6 6 25 11 4 19 35 11 10 6 5 14 5 100 14 4 5 +19 10 5 24 4 4 6 41 20 5 + + + + + + +GRMZM2G141277_P01 NP_001148494 stem 28 kDa glycoprotein seq=translation; coord=8:109218692..109219673:-1; parent_transcript=GRMZM2G141277_T01; parent_gene=GRMZM2G141277 + + + MALEPLRHGL VSLLVLLLLL VHAASAARAR DLHLEMVTTS AATARAVPSC + ASWRLGVETN NIRDWYSIPA ECRGYVRDYM YGDLFRQDCA VVAREAAAYA + EGLELGGDGK EVWVFDVDDT TLSNLPYYAD TGFGAEPYNA TYFDEYVANA + TAPPLPEVLQ LYETLLSLGI KVVFITGRHD YEKEPTIKNL RSAGYHTWDK + LVLKYVNFLI FAYQVG + + + + + + +6.59181 +-0.356314 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +7858 7858 7858 7525 7255 6650 6162 4774 3768 2112 850 434 234 108 47 8 2 1 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +7866 7866 7866 7533 7257 6615 5988 4414 2895 989 185 34 15 5 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2849 3366 1268 308 58 16 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1183 3441 2250 873 88 26 7 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3051 (charge 3) + +1259.63 +3 + + +155.082 156.077 157.097 157.134 158.092 159.077 159.113 164.082 166.061 167.118 168.102 169.096 169.134 171.113 175.119 176.122 181.097 181.109 182.1 183.113 183.149 185.092 185.129 187.144 188.147 193.097 194.129 195.113 197.129 199.108 +201.123 205.098 210.025 212.14 213.124 215.139 222.124 225.098 227.103 229.652 232.141 235.083 235.144 240.134 242.186 244.166 249.16 251.102 253.093 255.145 258.144 260.197 272.172 279.098 294.182 307.679 310.14 312.191 328.146 331.209 +332.211 352.197 361.245 369.225 371.229 379.167 388.163 392.666 395.229 398.146 401.672 403.707 408.14 416.156 437.23 440.29 458.297 466.278 485.759 499.3 517.205 527.187 532.244 545.199 546.203 550.25 553.273 562.227 569.333 575.299 +576.299 581.269 647.268 665.277 667.299 673.294 695.411 709.351 784.321 802.339 + + + + +6 3 3 3 6 3 3 3 3 4 3 4 14 22 28 2 35 10 3 5 3 4 3 19 2 2 3 18 7 31 +6 4 20 3 4 5 5 6 3 16 8 9 12 24 5 5 5 18 100 3 6 29 6 8 13 3 6 5 4 9 +3 4 17 6 8 3 4 10 3 43 13 3 3 34 3 7 32 14 4 10 8 3 3 28 8 4 3 8 8 10 +3 3 6 10 3 5 3 3 7 2 + + + + + + +GRMZM2G076075_P02 seq=translation; coord=2:187379358..187383614:1; parent_transcript=GRMZM2G076075_T02; parent_gene=GRMZM2G076075 + + + MASISGAAAP PSSAVCRLRL RRHLLLRPSH LRLRAPHSIA DLSRSSNSAP + SPARPALGSG PENGSGGVRA VEKDPIKLWE RYVEWLYQHK ELGIFVDVSR + MGFTEEFLRQ MEPRMQQAFV DMRELEKGAI ANPDEGRMVG HYWLRDPALA + PNSFLRNKIE TALDRILAFS QDVVSGKILS PSGRFTSILS IGIGGSALGP + QFVAEALAPD NPPLKIRFID NTDPAGIDHQ IAQLGPELAT TLVIVISKSG + GTPETRNGLL EVQKAFRDAG LQFSKQGVAI TQENSLLDNT ARIEGWLARF + PMFDWVGGRT SEMSAVGLLP AALQGIDIKE MLVGAALMDE ETRNTVVKAN + PAALLALCWY WASEGIGKKD MVVLPYKDSL LLLSRYLQQL VMESLGKEFD + LDGNRVNQGL TVYGNKGSTD QHAYIQQLRE GVQNFFVTFI EVLRDRPAGH + DWELEPGVTC GDYLFGMLQG TRSALYANDR ESISVTVQEV TPRAVGALIA + LYERAVGIYA SLVNINAYHQ PGVEAGKKAA GEVLALQKRV LTVLKEAMYG + TSDLCSFCFS VK + + + + + +GRMZM2G076075_P01 seq=translation; coord=2:187379328..187383441:1; parent_transcript=GRMZM2G076075_T01; parent_gene=GRMZM2G076075 + + + MASISGAAAP PSSAVCRLRL RRHLLLRPSH LRLRAPHSIA DLSRSSNSAP + SPARPALGSG PENGSGGVRA VEKDPIKLWE RYVEWLYQHK ELGIFVDVSR + MGFTEEFLRQ MEPRMQQAFV DMRELEKGAI ANPDEGRMVG HYWLRDPALA + PNSFLRNKIE TALDRILAFS QDVVSGKILS PSGRFTSILS IGIGGSALGP + QFVAEALAPD NPPLKIRFID NTDPAGIDHQ IAQLGPELAT TLVIVISKSG + GTPETRNGLL EVQKAFRDAG LQFSKQGVAI TQENSLLDNT ARIEGWLARF + PMFDWVGGRT SEMSAVGLLP AALQGIDIKE MLVGAALMDE ETRNTVVSHY + + + + + + + +5.91683 +-0.303427 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +2838 2838 2838 2769 2656 2467 2245 2060 1434 1124 627 305 162 71 38 15 6 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2839 2839 2839 2770 2653 2455 2208 2002 1262 785 278 60 11 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1588 1026 211 19 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +490 1579 631 131 8 0 1 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3053 (charge 2) + +999.485 +2 + + +152.057 155.081 157.097 157.108 157.134 158.092 159.077 161.092 167.082 169.061 169.097 169.133 171.077 171.113 171.149 173.093 173.129 175.119 181.061 183.113 183.149 185.055 185.092 185.129 185.165 186.087 186.124 187.108 187.144 189.087 +193.097 195.076 195.113 197.129 198.088 199.072 199.108 201.124 204.135 209.14 212.103 213.087 215.139 218.15 226.155 232.14 233.145 237.135 240.135 242.15 244.166 255.145 268.166 269.124 272.172 285.192 287.136 294.146 297.12 299.171 +301.188 303.203 306.156 308.171 311.173 314.142 325.224 327.13 336.167 342.129 357.7 361.183 362.187 377.231 405.224 409.25 426.246 459.186 470.226 476.209 480.276 546.305 556.241 568.288 573.262 575.271 598.321 630.282 659.372 670.279 +671.28 673.363 687.304 700.874 714.393 727.362 730.419 758.343 760.352 871.422 + + + + +19 13 10 5 25 22 7 20 9 9 15 12 34 15 3 6 11 62 18 9 6 3 10 22 6 20 7 8 3 28 +6 6 3 23 13 3 7 7 7 19 8 21 6 6 14 47 3 17 8 73 8 9 6 18 7 3 19 3 16 7 +3 5 35 3 13 8 5 10 18 12 13 89 15 11 29 3 3 6 3 10 7 12 8 3 100 3 9 5 7 12 +5 16 38 3 21 13 6 60 8 3 + + + + + + +GRMZM2G092021_P01 NP_001140569 hypothetical protein LOC100272635 seq=translation; coord=3:231116120..231118084:1; parent_transcript=GRMZM2G092021_T01; parent_gene=GRMZM2G092021 + + + MEGEAVHMLQ SGHHQWNKGQ PTLQAFPATQ RLNSRLHQIS EETKKMAPKL + VFVLPVVLLA LALQAILRPP PPKLCGSPGG PPLTSPRIKL RDGRYLAYKE + DGVQRDKARY KIITVHAFDS TKDFPSPVSK ELVEGLGIYL LAYDRAGYGE + SDPNPNRHVK SEALDIEELA DQLGLGHKFY VLGASMGGYS VWGCLQYIPH + RLAGAALVVP IINYWWPSFP AELSKQAFNR LIVPEQRTLW IAHNIPSLLY + LWMTQRWFPS SAAAMHHPEI FSKHDMEVLQ KMMAMPRTIE NKSRQQGIYE + SIHRDLLVAF GTWEFDPMNV TNPFPQNEGS VHIWQGREDR LVLVELQRYI + AKKLPWIKYH EVPEGGHMFV MVDGWTDRIL KALLLGEEPL DV + + + + + + +5.29312 +-0.392083 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +2525 2525 2484 2288 2166 1938 1018 656 322 97 29 9 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2529 2529 2488 2279 2157 1888 863 487 145 20 1 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1560 812 153 8 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +480 1680 327 39 4 13 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3054 (charge 2) + +1276.56 +2 + + +152.057 155.081 158.093 159.076 169.097 171.076 171.113 173.092 175.072 175.119 183.076 183.149 185.092 185.128 186.088 187.071 193.097 199.108 199.181 201.087 204.135 212.102 216.098 221.092 226.155 230.113 238.119 244.166 254.15 258.11 +270.108 278.153 292.129 299.161 306.158 309.156 317.182 321.155 326.18 349.151 352.161 360.237 369.188 371.12 386.214 442.221 450.199 452.249 483.233 488.292 500.257 526.264 542.303 564.242 580.285 597.31 599.315 671.334 703.325 712.338 +746.375 762.346 774.376 800.374 801.376 883.44 928.409 967.425 985.432 987.429 1051.52 + + + + +2 3 3 5 2 1 1 1 1 16 1 3 1 1 1 11 12 4 3 3 1 7 1 11 11 1 1 2 5 1 +1 4 2 3 1 1 1 1 3 1 1 1 9 1 14 7 1 1 2 3 3 5 1 4 6 100 6 1 1 3 +3 8 2 8 3 1 4 1 13 2 3 + + + + + + +GRMZM2G169160_P01 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666220..5677820:-1; parent_transcript=GRMZM2G169160_T01; parent_gene=GRMZM2G169160 + + + + + + + +GRMZM2G169160_P03 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666399..5677820:-1; parent_transcript=GRMZM2G169160_T03; parent_gene=GRMZM2G169160 + + + + + + + + +5.69449 +-0.27778 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +8451 8451 8451 8190 7496 5557 4266 2681 1742 1086 545 270 144 71 38 17 10 4 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8448 8448 8448 8187 7493 5510 3869 2188 1082 543 110 58 17 2 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4386 3325 622 117 1 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1450 5646 1196 152 6 1 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3056 (charge 2) + +1533.75 +2 + + +152.057 157.097 157.667 167.081 171.076 175.119 185.091 193.304 199.107 204.133 212.139 214.406 217.083 226.154 230.149 244.129 248.16 264.134 282.145 303.145 320.172 335.193 365.182 383.194 400.189 426.215 436.239 442.232 448.718 457.72 +470.224 504.254 506.753 516.254 563.216 589.284 620.329 651.84 667.372 688.339 699.364 717.377 720.618 727.903 740.346 748.409 758.374 768.385 789.387 817.383 819.376 914.43 956.419 1030.49 1055.49 1112.5 1181.56 1258.59 1359.64 1510.78 + + + + + +3 6 3 4 5 12 14 3 3 5 3 3 3 15 12 4 32 4 11 55 30 20 7 4 4 4 5 5 4 6 +4 6 3 4 4 5 6 3 5 6 13 56 3 4 4 5 11 16 30 100 5 6 14 5 6 13 4 5 5 5 + + + + + + + +GRMZM2G016066_P01 NP_001149700 photosystem I reaction center subunit IV A seq=translation; coord=2:169557301..169558384:-1; parent_transcript=GRMZM2G016066_T01; parent_gene=GRMZM2G016066 + + + MASTNMASAT SRFMLAAGVP TASSGSGRVS FASAPNRLGR RLVVRADEES + PAEPAPTAEG EGAVATKPKA EKPPPIGPKR GAKVKILRRE SYWYNGIGNV + VTVDQDPNTR YPVVVRFNKV NYAGVSTNNY ALDEILEVK + + + + + +GRMZM2G016622_P02 NP_001149459 LOC100283085 seq=translation; coord=7:38025162..38027027:1; parent_transcript=GRMZM2G016622_T02; parent_gene=GRMZM2G016622 + + + MASTNMASAT SRFMLAAGVP TGSSGGRVNF ASAPNRLGRR LVARADNEAA + AAEAAEGEGA VATKPKAEKP PPIGPKRGAK VKILRRESYW YNGIGNVVTV + DQDPNTRYPV VVRFNKVNYA GVSTNNYALD EVSEVK + + + + + +GRMZM2G016066_P02 NP_001149700 photosystem I reaction center subunit IV A seq=translation; coord=2:169557404..169558294:-1; parent_transcript=GRMZM2G016066_T02; parent_gene=GRMZM2G016066 + + + SLSPSAPVQP SQHPRAARSS RPWRAPTWRR PPRGSCWPRA CPPPVAAEGE + GAVATKPKAE KPPPIGPKRG AKVKILRRES YWYNGIGNVV TVDQDPNTRY + PVVVRFNKVN YAGVSTNNYA LDEILEVK + + + + + +GRMZM2G016622_P01 NP_001149459 LOC100283085 seq=translation; coord=7:38025162..38027027:1; parent_transcript=GRMZM2G016622_T01; parent_gene=GRMZM2G016622 + + + MASTNMASAT SRFMLAAGVP TGSSGGRVNF ASAPNRLGRR LVARADNEAA + AAEAAEGEGA VATKPKAEKP PPIGPKRGAK VKILRRESYW YNGIGNVVTV + DQVTSSLSSS + + + + + + +4.8692 +-0.249702 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +3397 3397 3357 2655 2239 1555 1166 753 532 382 265 124 57 30 15 6 3 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3390 3390 3350 2647 2202 1375 899 522 344 203 86 2 1 1 0 + + + + + + +0 1 2 3 4 + + + + +1901 1171 280 60 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +649 2123 541 79 7 1 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3060 (charge 2) + +1033.6 +2 + + +155.081 157.097 159.077 165.138 167.118 173.092 174.096 175.119 181.134 183.149 195.113 198.087 201.087 208.145 211.144 216.096 218.15 222.124 226.155 240.134 244.166 254.15 258.145 262.15 268.131 280.202 283.176 286.142 294.145 299.063 +301.187 304.691 308.196 311.171 329.182 353.218 365.219 377.255 383.231 405.249 408.754 414.269 417.266 424.255 426.237 434.274 448.585 462.271 480.283 493.314 503.274 511.324 514.236 577.335 590.365 608.376 610.382 627.319 632.324 687.419 +705.429 707.432 731.387 833.523 + + + + +16 3 2 3 5 33 3 3 3 4 14 2 11 2 2 1 5 4 7 41 11 2 3 6 3 2 3 2 2 2 +26 7 6 2 3 23 7 6 2 11 2 4 4 2 3 2 3 14 9 3 11 37 3 9 11 80 5 2 4 9 +100 10 5 6 + + + + + + +GRMZM2G172932_P01 NP_001168511 hypothetical protein LOC100382290 seq=translation; coord=8:171328319..171331663:-1; parent_transcript=GRMZM2G172932_T01; parent_gene=GRMZM2G172932 + + + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DTTGRYTGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DDDEEAEYED EEEPADGM + + + + + +GRMZM2G172932_P02 NP_001168511 hypothetical protein LOC100382290 seq=translation; coord=8:171328319..171331663:-1; parent_transcript=GRMZM2G172932_T02; parent_gene=GRMZM2G172932 + + + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DTTGRYTGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DDDEEAEYED EEEPADGM + + + + + +GRMZM2G172932_P03 NP_001168511 hypothetical protein LOC100382290 seq=translation; coord=8:171328488..171331663:-1; parent_transcript=GRMZM2G172932_T03; parent_gene=GRMZM2G172932 + + + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DTTGRYTGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DDDEEAEYED EEEPADGIIP + PSWPIPSIVA VDACVSLFYR TLLLVR + + + + + +GRMZM2G043822_P02 Q41784 Tubulin beta-7 chain (Beta-7-tubulin) seq=translation; coord=6:92813319..92815990:-1; parent_transcript=GRMZM2G043822_T02; parent_gene=GRMZM2G043822 + + + MREILHIQGG QCGNQIGAKF WEVICDEHGI DHTGKYAGDS DLQLERINVY + YNEASGGRFV PRAVLMDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLSTP TFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDSKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + SSVCDIPPIG LKMSSTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EDEEYEEEEE EDPAA + + + + + +GRMZM2G043822_P03 Q41784 Tubulin beta-7 chain (Beta-7-tubulin) seq=translation; coord=6:92813568..92815975:-1; parent_transcript=GRMZM2G043822_T03; parent_gene=GRMZM2G043822 + + + MREILHIQGG QCGNQIGAKF WEVICDEHGI DHTGKYAGDS DLQLERINVY + YNEASGGRFV PRAVLMDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLSTP TFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDSKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + SSVCDIPPIG LKMSSTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EDEEYEEEEE EDPAA + + + + + +GRMZM5G853513_P01 C0PDB9 Putative uncharacterized protein seq=translation; coord=5:5214906..5217855:-1; parent_transcript=GRMZM5G853513_T01; parent_gene=GRMZM5G853513 + + + MREILHIQGG QCGNQIGAKF WEVICDEHGI DATGRYAGDS DLQLERVNVY + YNEASGGRFV PRAVLMDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLSTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LKMAGTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVA EYQQYQDATA DEEYEDEEEE ENVAE + + + + + +AC234515.1_FGP003 seq=translation; coord=5:83557023..83560095:1; parent_transcript=AC234515.1_FGT003; parent_gene=AC234515.1_FG003 + + + MREILHIQGG QCGNQIGAKF WEVICDEHGI DHTGKYAGDS DLQLERINVY + YNEAGGGRFV PRAVLMDLEP GTMDSVRSGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLATP TFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + SSVCDIPPTG LAMASTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EEEEEYKEGD EVAA + + + + + +GRMZM2G066191_P01 Q41782 Tubulin beta-4 chain (Beta-4-tubulin) seq=translation; coord=5:14853348..14857185:-1; parent_transcript=GRMZM2G066191_T01; parent_gene=GRMZM2G066191 + + + MREILHIQGG QCGNQIGAKF WEVICGEHCV DSTGRYSGTS SQQLELERIN + VYYNEAGGGR YVPRAVLMDL EPGTMESIRA GPFGGIFRPD NFVYGQSGAG + NNWAKGHYTE GAELIDSVLD VVRKEAENCD CLQGFQVCHS LGGGTGSGMG + TLLISKIREE YPDRMMLTFS VFPSPKVSDT VVEPYNATLS VHQLVENADE + CMVLDNEALY DICFRTLKLT NPSFGDLNHL ISATMSGVTC CLRFPGQLNS + DLRKLAVNLI PFPRLHFFMV GFAPLTSRGS QQYRALTVPE LTQQMWDAKN + MMCAADPRHG RYLTASAMFR GKMSTKEVDE QMINVQNKNS SYFVEWIPNN + VKSSVCDIPP VGLPMASTFV GNSTSIQEMF RRVSEQFTAM FRRKAFLHWY + TSEGMDEMEF TEAESNMNDL VAEYQQYQDA TAEEYEEEEH DGEEEHA + + + + + +GRMZM2G066191_P03 Q41782 Tubulin beta-4 chain (Beta-4-tubulin) seq=translation; coord=5:14852959..14857053:-1; parent_transcript=GRMZM2G066191_T03; parent_gene=GRMZM2G066191 + + + MREILHIQGG QCGNQIGAKF WEVICGEHCV DSTGRYSGTS SQQLELERIN + VYYNEAGGGR YVPRAVLMDL EPGTMESIRA GPFGGIFRPD NFVYGQSGAG + NNWAKGHYTE GAELIDSVLD VVRKEAENCD CLQGFQVCHS LGGGTGSGMG + TLLISKIREE YPDRMMLTFS VFPSPKVSDT VVEPYNATLS VHQLVENADE + CMVLDNEALY DICFRTLKLT NPSFGDLNHL ISATMSGVTC CLRFPGQLNS + DLRKLAVNLI PFPRLHFFMV GFAPLTSRGS QQYRALTVPE LTQQMWDAKN + MMCAADPRHG RYLTASAMFR GKMSTKEVDE QMINVQNKNS SYFVEWIPNN + VKSSVCDIPP VGLPMASTFV GNSTSIQEMF RRVSEQFTAM FRRKAFLHWY + TSEGMDEMEF TEAESNMNDL VAEYQQYQDA TAEEYEEEEH DGEEEHA + + + + + +GRMZM2G108766_P01 Q43695 Tubulin beta-3 chain (Beta-3-tubulin) seq=translation; coord=1:258551317..258555202:-1; parent_transcript=GRMZM2G108766_T01; parent_gene=GRMZM2G108766 + + + MREILHIQGG QCGNQIGAKF WEVICGEHGV DSTGCYSGVS PQQLERINVY + YNEAGGGRYV PRAVLMDLEP GTMESIRAGP FGGIFRPDNF VYGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTNP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPVG LSMSSTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTS + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EEYDEEEQDG EEEHA + + + + + +GRMZM2G108766_P02 Q43695 Tubulin beta-3 chain (Beta-3-tubulin) seq=translation; coord=1:258551378..258555288:-1; parent_transcript=GRMZM2G108766_T02; parent_gene=GRMZM2G108766 + + + MREILHIQGG QCGNQIGAKF WEVICGEHGV DSTGCYSGVS PQQLERINVY + YNEAGGGRYV PRAVLMDLEP GTMESIRAGP FGGIFRPDNF VYGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTNP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPVG LSMSSTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTS + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EEYDEEEQDG EEEHA + + + + + +GRMZM2G108766_P03 Q43695 Tubulin beta-3 chain (Beta-3-tubulin) seq=translation; coord=1:258551401..258555376:-1; parent_transcript=GRMZM2G108766_T03; parent_gene=GRMZM2G108766 + + + MREILHIQGG QCGNQIGAKF WEVICGEHGV DSTGCYSGVS PQQLERINVY + YNEAGGGRYV PRAVLMDLEP GTMESIRAGP FGGIFRPDNF VYGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTNP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPVG LSMSSTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTS + EGMDEMEFTE AESNMNDLVA EYQQYQDATA EEYDEEEQDG EEEHA + + + + + +GRMZM2G042636_P01 NP_001140291 hypothetical protein LOC100272336 seq=translation; coord=8:1370962..1373972:-1; parent_transcript=GRMZM2G042636_T01; parent_gene=GRMZM2G042636 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VHDE + + + + + +GRMZM2G042636_P02 NP_001140291 hypothetical protein LOC100272336 seq=translation; coord=8:1370993..1374720:-1; parent_transcript=GRMZM2G042636_T02; parent_gene=GRMZM2G042636 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE DLDAADI + + + + + +GRMZM2G042636_P03 NP_001140291 hypothetical protein LOC100272336 seq=translation; coord=8:1371027..1374720:-1; parent_transcript=GRMZM2G042636_T03; parent_gene=GRMZM2G042636 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VHDE + + + + + +GRMZM2G042636_P04 NP_001140291 hypothetical protein LOC100272336 seq=translation; coord=8:1371027..1374637:-1; parent_transcript=GRMZM2G042636_T04; parent_gene=GRMZM2G042636 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VHDE + + + + + +GRMZM2G071790_P01 Q41783 Tubulin beta-6 chain (Beta-6-tubulin) seq=translation; coord=3:187441065..187444892:-1; parent_transcript=GRMZM2G071790_T01; parent_gene=GRMZM2G071790 + + + MLAAATAAYG YFNPALLPTP HSPPASSRLP DLARSAPVAS QFGSSHTSAK + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DPTGRYTGNS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VQADDM + + + + + +GRMZM2G071790_P02 Q41783 Tubulin beta-6 chain (Beta-6-tubulin) seq=translation; coord=3:187441506..187445356:-1; parent_transcript=GRMZM2G071790_T02; parent_gene=GRMZM2G071790 + + + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DPTGRYTGNS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VQADDM + + + + + +GRMZM2G071790_P03 Q41783 Tubulin beta-6 chain (Beta-6-tubulin) seq=translation; coord=3:187441509..187443944:-1; parent_transcript=GRMZM2G071790_T03; parent_gene=GRMZM2G071790 + + + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DPTGRYTGNS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VQADDM + + + + + +GRMZM2G071790_P04 Q41783 Tubulin beta-6 chain (Beta-6-tubulin) seq=translation; coord=3:187441519..187444944:-1; parent_transcript=GRMZM2G071790_T04; parent_gene=GRMZM2G071790 + + + MLAAATAAYG YFNPALLPTP HSPPASSRLP DLARSAPVAS QFGSSHTSAK + MREILHIQGG QCGNQIGAKF WEVVCDEHGI DPTGRYTGNS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEEYEDEEE VQADDM + + + + + +GRMZM2G071790_P05 Q41783 Tubulin beta-6 chain (Beta-6-tubulin) seq=translation; coord=3:187441570..187444557:-1; parent_transcript=GRMZM2G071790_T05; parent_gene=GRMZM2G071790 + + + MRLDPLICHL GMSWPMLVSL SLSFDEGYSI GFVIDSLVCR AKMREILHIQ + GGQCGNQIGA KFWEVVCDEH GIDPTGRYTG NSDLQLERVN VYYNEASCGR + FVPRAVLMDL EPGTMDSVRT GPYGQIFRPD NFVFGQSGAG NNWAKGHYTE + GAELIDSVLD VVRKEAENCD CLQGFQVCHS LGGGTGSGMG TLLISKIREE + YPDRMMLTFS VFPSPKVSDT VVEPYNATLS VHQLVENADE CMVLDNEALY + DICFRTLKLT TPSFGDLNHL ISATMSGVTC CLRFPGQLNS DLRKLAVNLI + PFPRLHFFMV GFAPLTSRGS QQYRALTVPE LTQQMWDAKN MMCAADPRHG + RYLTASAMFR GKMSTKEVDE QMINVQNKNS SYFVEWIPNN VKSSVCDIPP + RGLSMASTFI GNSTSIQEMF RRVSEQFTAM FRRKAFLHWY TGEGMDEMEF + TEAESNMNDL VSEYQQYQDA TADEEEYEDE EEVQADDM + + + + + +GRMZM2G133802_P01 Q43697 Tubulin beta-5 chain (Beta-5-tubulin) seq=translation; coord=3:47736769..47739503:-1; parent_transcript=GRMZM2G133802_T01; parent_gene=GRMZM2G133802 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEAEYEDEE AIQDE + + + + + +GRMZM2G133802_P02 Q43697 Tubulin beta-5 chain (Beta-5-tubulin) seq=translation; coord=3:47736772..47740094:-1; parent_transcript=GRMZM2G133802_T02; parent_gene=GRMZM2G133802 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEAEYEDEE AIQDE + + + + + +GRMZM2G133802_P03 Q43697 Tubulin beta-5 chain (Beta-5-tubulin) seq=translation; coord=3:47736824..47739988:-1; parent_transcript=GRMZM2G133802_T03; parent_gene=GRMZM2G133802 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEAEYEDEE AIQDE + + + + + +GRMZM2G099944_P01 NP_001168917 hypothetical protein LOC100382727 seq=translation; coord=1:276428674..276431930:-1; parent_transcript=GRMZM2G099944_T01; parent_gene=GRMZM2G099944 + + + MREILHIQGG QCGNQIGAKF WEVICDEHGI DATGRYAGDS DLQLERVNVY + YNEASGGRFV PRAVLMDLEP GTMDSLRSGP FGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADQCM + VLDNEALYDI CFRTLKLATP TFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + SSVCDIPPKG LRMSGTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVA EYQQYQDATA DEEYEDEDEE EAVSE + + + + + +GRMZM2G133802_P04 Q43697 Tubulin beta-5 chain (Beta-5-tubulin) seq=translation; coord=3:47737075..47740094:-1; parent_transcript=GRMZM2G133802_T04; parent_gene=GRMZM2G133802 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYVGTS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMASTFIGN STSIQEMRKA FLHWYTGEGM DEMEFTEAES + NMNDLVSEYQ QYQDATADEE AEYEDEE + + + + + +GRMZM2G164696_P01 P18025 Tubulin beta-1 chain (Beta-1-tubulin) seq=translation; coord=1:2038186..2040079:1; parent_transcript=GRMZM2G164696_T01; parent_gene=GRMZM2G164696 + + + MREILHIQGG QCGNQIGAKF WEVVCAEHGI DATGRYGGDS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRSGP YGHIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + STVCDIPPTG LKMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEGEYEDEE EGDLQD + + + + + +GRMZM2G164696_P03 P18025 Tubulin beta-1 chain (Beta-1-tubulin) seq=translation; coord=1:2037790..2039758:1; parent_transcript=GRMZM2G164696_T03; parent_gene=GRMZM2G164696 + + + MREILHIQGG QCGNQIGAKF WEVVCAEHGI DATGRYGGDS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRSGP YGHIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRALTVPELT QQMWDAKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM LNVQNKNSSY FVEWIPNNVK + STVCDIPPTG LKMASTFIGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEGEYEDEE EGDLQD + + + + + +GRMZM2G334899_P01 P18026 Tubulin beta-2 chain (Beta-2-tubulin) seq=translation; coord=8:104770563..104774039:-1; parent_transcript=GRMZM2G334899_T01; parent_gene=GRMZM2G334899 + + + MREILHIQGG QCGNQIGSKF WEVVCDEHGI DPTGRYMGTS DVQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDAVRTGP YGQIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMMTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMVGF APLTSRGSQQ YRSLTVPELT QQMWDSKNMM + CAADPRHGRY LTASAMFRGK MSTKEVDEQM INVQNKNSSY FVEWIPNNVK + SSVCDIPPRG LSMSSTFVGN STSIQEMFRR VSEQFTAMFR RKAFLHWYTG + EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEEADYEEEE AAAE + + + + + +GRMZM2G164696_P02 P18025 Tubulin beta-1 chain (Beta-1-tubulin) seq=translation; coord=1:2038220..2039999:1; parent_transcript=GRMZM2G164696_T02; parent_gene=GRMZM2G164696 + + + MREILHIQGG QCGNQIGAKF WEVVCAEHGI DATGRYGGDS DLQLERVNVY + YNEASCGRFV PRAVLMDLEP GTMDSVRSGP YGHIFRPDNF VFGQSGAGNN + WAKGHYTEGA ELIDSVLDVV RKEAENCDCL QGFQVCHSLG GGTGSGMGTL + LISKIREEYP DRMMLTFSVF PSPKVSDTVV EPYNATLSVH QLVENADECM + VLDNEALYDI CFRTLKLTTP SFGDLNHLIS ATMSGVTCCL RFPGQLNSDL + RKLAVNLIPF PRLHFFMMWD AKNMMCAADP RHGRYLTASA MFRGKMSTKE + VDEQMLNVQN KNSSYFVEWI PNNVKSTVCD IPPTGLKMAS TFIGNSTSIQ + EMFRRVSEQF TAMFRRKAFL HWYTGEGMDE MEFTEAESNM NDLVSEYQQY + QDATADEEGE YEDEEEGDLQ D + + + + + +GRMZM2G043822_P01 Q41784 Tubulin beta-7 chain (Beta-7-tubulin) seq=translation; coord=6:92813290..92815973:-1; parent_transcript=GRMZM2G043822_T01; parent_gene=GRMZM2G043822 + + + MGTLLISKIR EEYPDRMMLT FSVFPSPKVS DTVVEPYNAT LSVHQLVENA + DECMVLDNEA LYDICFRTLK LSTPTFGDLN HLISATMSGV TCCLRFPGQL + NSDLRKLAVN LIPFPRLHFF MVGFAPLTSR GSQQYRALTV PELTQQMWDS + KNMMCAADPR HGRYLTASAM FRGKMSTKEV DEQMLNVQNK NSSYFVEWIP + NNVKSSVCDI PPIGLKMSST FIGNSTSIQE MFRRVSEQFT AMFRRKAFLH + WYTGEGMDEM EFTEAESNMN DLVAEYQQYQ DATAEDEEYE EEEEEDPAA + + + + + +GRMZM2G373040_P01 seq=translation; coord=5:16371197..16373966:-1; parent_transcript=GRMZM2G373040_T01; parent_gene=GRMZM2G373040 + + + MQQQYKLVPI QMKKMSNNVK ELSAANREIC WDAFGHTLLI SKIREEYPDR + MMLTFSVFPS PKVSDTVVEP YNATLGENVG VLYWHLDPKK SESEEELAKI + RRDRGYSYMD LIEICPDKLE NYEEKVKNFF REHMHADEEI RYCLEGSGFF + DVRDKDDKWI RIRIREGDMI ILPAGIYHRL TLDSAKYTKE DHPARQEYVK + NVSASTGFAL VAHFLANTNL PSKPF + + + + + + +5.55133 +-0.258201 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +6961 6961 6918 6697 5946 5225 4220 3568 2977 1823 1439 844 490 284 141 66 50 10 5 2 1 1 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7073 7073 7030 6803 5952 5126 3932 3024 2524 1047 749 126 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2305 3264 1145 235 122 1 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1207 3922 1493 297 71 5 0 79 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3061 (charge 2) + +1077.53 +2 + + +155.081 156.113 157.097 157.109 158.092 159.077 166.061 167.055 169.133 173.092 175.09 175.119 176.123 181.061 183.113 185.091 185.106 185.165 187.071 199.108 201.087 203.085 209.105 211.144 213.087 221.103 223.155 226.119 228.134 230.114 +235.12 241.13 249.098 253.166 259.092 267.109 270.192 273.119 290.146 299.061 301.059 303.177 327.167 332.176 352.162 356.203 370.172 376.151 382.209 387.198 394.169 398.166 417.246 462.267 474.214 482.726 500.282 511.249 524.737 528.277 +530.762 533.237 540.772 550.262 560.252 617.767 661.296 663.346 674.315 679.304 682.287 691.342 693.34 717.809 727.385 790.335 808.346 810.354 831.436 833.428 840.467 846.412 903.421 905.409 921.428 947.421 977.529 + + + + +2 3 9 2 12 9 2 2 4 2 5 100 7 1 1 2 4 2 7 2 2 1 1 3 8 2 1 2 4 4 +3 2 2 27 3 2 7 5 2 5 5 3 3 2 2 2 13 1 4 9 2 3 2 2 5 4 8 5 2 22 +3 2 2 14 5 2 2 8 1 6 2 13 1 2 4 3 13 1 5 1 2 3 16 3 3 6 2 + + + + + + +GRMZM2G113696_P01 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T01; parent_gene=GRMZM2G113696 + + + MSDSEEHHFE SKADAGASKT YPQQAGTVRK NGFIVIKNRP CKVVEVSTSK + TGKHGHAKCH FVAIDIFNGK KLEDIVPSSH NCDIPHVNRT EYQLIDISED + GFVSLLTSDG NTKDDLRLPT DETLVAQIKE GFESGKDLVV TVQSAMGEEQ + ICALKDVGPK + + + + + + +GRMZM2G144030_P01 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=7:163002247..163005888:-1; parent_transcript=GRMZM2G144030_T01; parent_gene=GRMZM2G144030 + + + MSDSEEHHFE SKADAGASKT YPQQAGTVRK NGFIVIKNRP CKVVEVSTSK + TGKHGHAKCH FVAIDIFNGK KLEDIVPSSH NCDIPHVNRT EYQLIDISED + GFVSLLTSDG NTKDDLRLPT DETLVAQIKE GFESGKDLVV TVQSAMGEEQ + ICALKDVGPK + + + + + + +GRMZM2G113696_P02 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T02; parent_gene=GRMZM2G113696 + + + MSDSEEHHFE SKADAGASKT YPQQAGTVRK NGFIVIKNRP CKVVEVSTSK + TGKHGHAKCH FVAIDIFNGK KLEDIVPSSH NCDVS + + + + + + +GRMZM2G113696_P03 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T03; parent_gene=GRMZM2G113696 + + + MSDSEEHHFE SKADAGASKT YPQQAGTVRK NGFIVIKNRP CKVVEVSTSK + TGKREPSYFR WQH + + + + + + +GRMZM2G144030_P02 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=7:163002247..163005888:-1; parent_transcript=GRMZM2G144030_T02; parent_gene=GRMZM2G144030 + + + MSDSEEHHFE SKADAGASKT YPQQAGTVRK NGFIVIKNRP CKVVEVSTSK + TGKHGHAKCH FVAIDIFNGK KLEDIVPSSH NCDVS + + + + + + + +3.89247 +-0.222427 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +1541 1541 1541 1541 1424 1330 1210 955 674 456 233 146 93 49 34 13 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +1550 1550 1550 1550 1433 1323 1176 864 564 243 76 47 12 7 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +531 585 332 72 23 3 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +326 643 409 129 27 9 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3062 (charge 3) + +1373.56 +3 + + +154.049 155.082 156.077 157.061 158.093 159.076 161.074 166.062 167.056 169.097 171.076 171.112 173.129 175.071 175.119 181.061 181.097 185.056 189.087 192.102 194.13 198.124 199.071 199.108 201.123 203.066 216.134 221.104 226.156 227.066 +229.119 232.141 234.145 237.122 239.093 241.082 244.165 247.13 249.098 255.146 257.139 259.093 267.108 272.171 275.125 278.157 285.134 293.65 299.061 314.098 324.163 329.193 341.217 345.177 363.19 378.14 386.157 392.69 396.164 404.173 +414.177 426.245 428.252 448.207 455.186 483.188 487.208 501.209 510.256 512.728 515.201 521.736 533.219 551.237 554.302 555.31 565.247 570.216 580.201 586.292 592.246 598.21 612.331 613.753 620.242 622.763 629.304 647.315 662.265 680.277 +690.257 707.261 717.262 725.377 726.379 735.268 767.307 784.372 896.37 913.417 + + + + +6 6 7 20 5 9 10 4 5 7 18 10 5 35 27 5 7 15 24 8 5 9 17 15 15 17 31 9 7 34 +5 5 100 7 6 4 19 6 12 4 12 5 15 6 20 15 27 6 4 15 6 8 7 25 31 8 9 14 22 14 +14 5 4 8 7 13 5 6 31 7 7 5 8 10 7 10 12 8 5 7 7 12 11 6 8 8 7 31 8 6 +7 5 4 23 7 13 8 13 7 6 + + + + + + +GRMZM2G099657_P01 NP_001149295 40S ribosomal protein SA seq=translation; coord=9:150090384..150093179:-1; parent_transcript=GRMZM2G099657_T01; parent_gene=GRMZM2G099657 + + + MAASAGGGAV RALSQKEQDI QMMLAADVHL GTKNCDFQME RYVFKRRTDG + IYIINLGKTW DKLQLAARVI VAIENPQDII VQSARPYGQR AVLKFAQYTG + AHAIAGRHTP GTFTNQLQTS FSEPRLLILT DPRTDHQPIK ESALGNIPTI + AFCDTDSPMR YVDIGIPANN KGRNSIGCLF WLLARMVLQM RGTILPGHKW + EVMVDLFFYR DPEEAKEQEE EAAAAPEFAA VTDYQGADQW GGDQWTSDVA + APPVAPTGAD WGAAPAPVPT GDGWDQTVAP VPVDGTVPPV VAPTGWESAA + QPTAQGWE + + + + + + +GRMZM2G099657_P02 NP_001149295 40S ribosomal protein SA seq=translation; coord=9:150092448..150093179:-1; parent_transcript=GRMZM2G099657_T02; parent_gene=GRMZM2G099657 + + + MAASAGGGAV RALSQKEQDI QMMLAADVHL GTKNCDFQME RYVFKRRTDG + MFFPPASLPF CLSACESM + + + + + + + +4.41474 +-0.196211 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +3668 3668 3614 3488 3100 2810 2597 2371 1540 1334 878 586 383 229 132 77 58 30 22 14 2 1 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3667 3667 3613 3481 3075 2747 2457 2257 1153 791 295 97 61 4 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +926 1931 619 188 11 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +548 2141 756 188 34 2 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3063 (charge 2) + +858.443 +2 + + +153.102 155.082 157.061 157.097 157.109 158.092 159.076 160.08 166.061 167.056 167.081 169.061 169.097 169.133 171.112 171.149 172.072 173.092 173.129 175.119 176.122 183.113 183.149 184.108 185.056 185.092 185.128 186.087 186.095 186.123 +187.108 187.143 193.097 194.128 195.113 197.129 198.087 199.108 199.144 200.14 201.123 203.067 208.953 212.103 213.087 215.114 218.149 226.154 228.182 231.061 235.119 240.135 243.109 254.113 256.177 260.196 269.124 272.124 274.187 279.145 +284.008 286.151 289.673 297.155 298.679 314.176 316.151 325.151 328.195 342.178 346.087 353.228 356.193 359.028 361.245 370.256 383.71 385.221 402.246 413.705 426.242 432.234 440.729 449.241 459.267 481.325 487.261 499.265 516.289 518.297 +567.303 570.298 584.318 587.326 589.327 596.354 656.347 674.358 684.343 745.396 + + + + +2 6 2 7 9 12 27 2 2 11 7 3 3 8 4 3 5 4 4 58 5 4 3 5 2 65 2 3 4 2 +3 5 2 2 2 5 6 3 3 2 5 2 4 10 2 8 4 11 15 3 3 4 16 74 24 4 2 12 5 2 +3 3 3 7 3 5 2 11 3 5 3 2 4 19 4 5 3 4 9 5 3 3 2 4 21 2 3 5 100 5 +2 2 4 41 2 3 2 19 4 2 + + + + + + +GRMZM2G044074_P01 O81220 Uroporphyrinogen decarboxylase, chloroplastic Precursor (URO-D)(UPD)(EC 4.1.1.37) seq=translation; coord=1:56558248..56562800:1; parent_transcript=GRMZM2G044074_T01; parent_gene=GRMZM2G044074 + + + MATACPPLSL PSTSLFRGRS ARAGPRRRQL TAVRCSAVGE AVVEEASPRT + AEEPLLVSAI RGRKVERPPV WLMRQAGRYM KSYQLLCERY PSFRERSENV + DLVVEISLQP WKVFKPDGVI LFSDILTPLP GMNIPFDIVK GKGPVIYDPL + RTAAAVNEVR EFVPEEWVPY VGQALNILRQ EVKNEAAVLG FVGAPFTLAS + YCVEGGSSKN FTLIKKMAFS EPAILHNLLQ KFTTSMANYI KYQADNGAQA + VQIFDSWATE LSPADFEEFS LPYLKQIVDS VRETHPNLPL ILYASGSGGL + LERLPLTGVD VVSLDWTVDM AEGRKRLGSN TAVQGNVDPG VLFGSKEFIS + RRIYDTVQKA GNVGHVLNLG HGIKVGTPEE NVAHFFEVAK GIRY + + + + + +GRMZM2G044074_P02 O81220 Uroporphyrinogen decarboxylase, chloroplastic Precursor (URO-D)(UPD)(EC 4.1.1.37) seq=translation; coord=1:56558221..56561693:1; parent_transcript=GRMZM2G044074_T02; parent_gene=GRMZM2G044074 + + + MATACPPLSL PSTSLFRGRS ARAGPRRRQL TAVRCSAVGE AVVEEASPRT + AEEPLLVSAI RGRKVERPPV WLMRQAGRYM KSYQLLCERY PSFRERSENV + DLVVEISLQP WKVFKPDGVI LFSDILTPLP GMNIPFDIVK GKGPVIYDPL + RTAAAVNEVR EFVPEEWVPY VGQALNILRQ EVKNEAAVLG FVGAPFTLAS + YCVEGGSSKN FTLIKKMAFS EPAILHNLLQ KFTTSMANYI KYQADNGAQA + VQIFDSWATE LSPADFEEFS LPYLKQIVDS VRETHPNLPL ILYASGSGGL + LERLPLTGVD VVSLDWTVDM AEGRKRLGSN TAVQGNVDPG VLFGSKEFIS + RRIYDTVQKA GNVGHVLNLG HGIKVGTPEE NVAHFFEVAK GIRY + + + + + + +5.11437 +-0.249481 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +6149 6149 6149 6149 5879 5665 4876 4024 3273 2178 1425 931 554 346 174 96 48 14 7 1 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6138 6138 6138 6138 5868 5648 4814 3734 2496 1084 440 93 35 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1764 2689 1244 404 49 0 0 4 + + + + + + +0 1 2 3 4 5 + + + + +1153 3685 1075 204 37 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3065 (charge 2) + +1022.56 +2 + + +155.082 157.061 157.097 157.109 158.093 159.077 166.086 167.081 167.118 171.076 173.129 175.072 175.119 181.097 183.149 185.092 187.071 189.087 195.113 198.087 199.071 199.108 199.18 204.135 205.098 209.092 211.144 213.123 216.098 217.083 +223.108 225.171 226.155 234.145 240.134 242.184 244.166 248.16 251.102 258.144 259.148 261.125 265.12 268.13 270.193 275.208 282.148 286.139 293.113 301.187 303.145 310.666 320.172 333.156 335.192 351.166 359.193 380.146 388.292 422.156 +433.256 436.239 448.741 470.223 476.297 486.246 504.257 505.26 509.188 517.335 523.27 531.256 548.283 589.279 591.22 602.313 605.301 620.325 622.339 628.368 631.319 646.378 649.331 651.34 660.345 670.331 671.333 676.377 688.341 689.35 +704.377 717.379 720.406 748.398 789.391 809.442 817.386 848.463 876.455 896.466 + + + + +12 7 20 10 6 8 7 17 8 19 8 6 20 7 15 28 6 11 13 8 8 6 21 7 6 7 7 7 18 9 +77 15 12 6 30 14 15 9 19 80 12 5 7 13 6 28 5 8 12 36 51 16 27 5 14 6 30 9 11 15 +12 11 7 6 9 14 42 14 14 11 15 15 100 8 7 8 19 59 7 8 27 27 80 6 16 27 12 13 14 7 +14 35 52 37 32 11 19 11 11 12 + + + + + + +conta|P35527|K1CI_HUMAN Keratin, type I cytoskeletal 9 (Cytokeratin 9) (K9) (CK 9) - Homo sapiens (Human). + + + + + + + + +5.625 +-0.25 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 + + + + +1413 1413 1412 1347 1208 962 800 498 319 178 100 62 33 23 18 12 5 4 4 3 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +1440 1440 1439 1373 1230 955 677 400 183 71 19 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +692 571 137 29 8 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +319 745 281 61 5 14 6 11 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3066 (charge 2) + +1791.73 +2 + + +175.119 182.093 184.072 185.093 196.072 202.082 214.082 221.092 223.107 226.082 233.092 241.095 253.093 259.104 262.149 271.103 273.085 274.14 281.087 283.104 289.113 290.114 293.087 298.114 302.112 310.115 316.124 319.172 328.124 338.108 +340.126 347.136 355.136 359.135 365.145 367.135 377.145 385.146 387.13 399.128 404.156 406.204 412.158 416.156 424.158 432.22 434.166 440.217 442.165 456.152 461.177 463.229 473.178 485.179 491.19 503.19 513.175 518.196 520.239 530.2 +538.222 548.209 557.21 560.235 575.219 577.269 587.215 605.232 632.242 644.244 662.254 701.264 719.273 740.334 797.35 819.344 854.377 887.87 911.396 913.397 948.391 980.413 998.428 1055.45 1057.46 1077.44 1112.47 1151.47 1169.5 1171.49 +1191.48 1206.48 1208.5 1226.51 1228.51 1335.52 1389.58 1391.58 1464.58 1476.61 + + + + +12 2 7 2 5 12 3 4 7 2 5 9 7 9 3 10 2 5 4 4 3 8 5 13 5 6 7 8 5 2 +7 5 7 5 2 12 5 19 2 2 5 5 4 6 2 5 9 2 4 5 6 8 6 5 4 7 4 4 13 13 +4 8 2 5 5 36 6 6 6 4 3 3 4 13 16 2 21 7 32 2 4 3 24 23 2 5 32 4 41 5 +2 3 8 100 12 4 26 5 4 8 + + + + + + +GRMZM2G044132_P01 B6UCP6 Putative uncharacterized protein seq=translation; coord=2:53844493..53846005:1; parent_transcript=GRMZM2G044132_T01; parent_gene=GRMZM2G044132 + + + + + + + + +4.76924 +-0.272528 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +2387 2387 2340 2246 1816 1536 1223 832 556 392 214 122 50 26 6 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2388 2388 2341 2247 1810 1501 1150 662 396 244 71 30 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1009 926 366 92 7 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +381 1374 471 116 33 18 4 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3067 (charge 3) + +1620.67 +3 + + +155.081 157.097 157.109 158.092 159.077 160.08 169.134 173.092 175.092 175.119 176.123 177.102 185.165 187.071 187.107 188.075 197.128 201.087 203.085 212.103 213.087 217.137 221.103 228.134 235.12 238.14 241.082 245.077 247.108 249.098 +253.166 254.169 258.108 265.118 267.108 270.192 272.171 298.104 302.662 316.114 326.171 355.124 367.183 370.172 382.208 387.198 395.184 399.234 431.705 458.248 462.268 474.713 483.227 496.227 500.285 511.25 524.735 528.277 531.26 533.305 +539.772 550.262 552.262 560.255 587.293 604.313 609.256 617.769 663.349 670.361 673.278 679.308 682.29 683.292 688.287 692.344 693.347 708.376 717.808 718.309 727.384 733.358 764.884 790.34 791.336 802.373 809.35 810.356 832.442 833.424 +837.423 840.473 845.373 904.424 905.423 922.435 948.422 949.426 977.535 1031.44 + + + + +3 9 2 7 57 4 7 9 6 70 8 2 3 54 2 4 3 10 2 4 7 3 3 5 6 3 4 4 2 4 +15 5 9 4 3 4 2 4 3 9 2 2 5 9 2 7 4 2 8 6 3 4 3 3 5 3 12 14 4 4 +100 10 3 45 5 3 3 21 4 2 8 5 14 4 3 13 5 2 19 15 11 2 3 3 4 3 13 3 5 2 +3 5 6 21 10 4 6 2 4 4 + + + + + + +GRMZM2G156673_P01 NP_001132138 hypothetical protein LOC100193556 seq=translation; coord=8:6590983..6592937:1; parent_transcript=GRMZM2G156673_T01; parent_gene=GRMZM2G156673 + + + MAEVEQQQDT PKLFNRWTFD DVQVNDISLN DYLAVNATKH AMYLPHTAGR + YSKKRFRKAQ CPIVERLTNS LMMHGRNNGK KVMAVRIIKH TLEIIHLLTD + ANPIQVVVDA IINSGPREDA TRIGSAGVVR RQAVDISPLR RVNQAIYLLT + TGARESAFRN IKTIAECLAD ELINAAKGSS NSYAIKKKDE IERVAKANR + + + + + + +GRMZM2G156673_P03 NP_001132138 hypothetical protein LOC100193556 seq=translation; coord=8:6591025..6592937:1; parent_transcript=GRMZM2G156673_T03; parent_gene=GRMZM2G156673 + + + MAEVEQQQDT PKLFNRWTFD DVQVNDISLN DYLAVNATKH AMYLPHTAGR + YSKKRFRKAQ CPIVERLTNS LMMHGRNNGK KVMAVRIIKH TLEIIHLLTD + ANPIQVVVDA IINRYSLNLG + + + + + + + +6.35223 +-0.309865 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +6781 6781 6781 6773 6486 6228 5933 5598 4437 3352 2056 1142 602 313 126 50 24 15 4 1 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6791 6791 6791 6783 6496 6235 5929 5477 4114 2661 1189 375 107 26 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1762 2865 1464 534 156 9 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1236 3018 1719 600 175 28 5 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3068 (charge 3) + +1269.62 +3 + + +152.071 155.082 155.118 157.097 158.092 159.077 159.113 161.093 164.082 166.061 167.046 169.097 169.134 170.137 171.076 171.113 172.108 173.092 173.129 174.132 175.119 180.105 181.109 183.112 185.056 185.09 186.059 187.073 187.108 188.111 +189.088 197.129 201.124 203.066 207.124 209.104 212.104 215.103 219.08 221.104 229.117 231.061 235.119 239.114 247.107 248.635 262.14 267.109 271.146 274.129 283.11 286.153 292.14 298.14 301.188 303.178 310.666 313.156 316.149 318.146 +319.672 338.129 341.193 342.176 346.088 350.147 356.138 359.204 362.691 366.177 382.142 386.215 404.225 413.213 442.245 455.203 467.224 491.207 496.262 519.203 523.27 525.318 541.285 542.289 568.289 588.293 602.229 604.299 607.297 608.291 +620.327 625.305 632.281 638.337 640.337 653.41 699.283 724.374 754.459 825.424 + + + + +5 8 5 5 19 45 9 9 4 12 8 6 35 4 11 4 4 8 80 8 61 4 24 7 100 6 7 6 65 6 +5 10 32 50 16 44 4 12 19 10 5 45 45 12 7 24 18 13 14 22 5 5 8 12 4 21 11 10 6 9 +15 10 7 15 16 8 17 86 10 7 6 23 59 11 4 8 5 12 51 25 10 5 27 8 11 6 10 5 7 4 +12 46 8 56 6 18 5 21 6 20 + + + + + + +GRMZM2G116292_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31201315..31206122:-1; parent_transcript=GRMZM2G116292_T01; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P02 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T02; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P03 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T03; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P04 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T04; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P05 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31206122:-1; parent_transcript=GRMZM2G116292_T05; parent_gene=GRMZM2G116292 + + + + + + + + + +GRMZM2G047727_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=2:165103157..165107176:-1; parent_transcript=GRMZM2G047727_T01; parent_gene=GRMZM2G047727 + + + + + + + +GRMZM2G409726_P01 NP_001105376 polyubiquitin seq=translation; coord=5:82443403..82446794:-1; parent_transcript=GRMZM2G409726_T01; parent_gene=GRMZM2G409726 + + + + + + + + + + + + + + + + + + + +GRMZM2G409726_P02 NP_001105376 polyubiquitin seq=translation; coord=5:82443815..82446714:-1; parent_transcript=GRMZM2G409726_T02; parent_gene=GRMZM2G409726 + + + + + + + + + +GRMZM2G409726_P03 NP_001105376 polyubiquitin seq=translation; coord=5:82443856..82446714:-1; parent_transcript=GRMZM2G409726_T03; parent_gene=GRMZM2G409726 + + + + + + + + + + + + + + + + + +GRMZM2G006293_P01 NP_001150700 40S ribosomal protein S27a seq=translation; coord=1:191263450..191264705:-1; parent_transcript=GRMZM2G006293_T01; parent_gene=GRMZM2G006293 + + + + + + + +GRMZM2G118637_P01 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236857988..236860949:1; parent_transcript=GRMZM2G118637_T01; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + + + +GRMZM2G118637_P02 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859470..236861173:1; parent_transcript=GRMZM2G118637_T02; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + + + +GRMZM2G118637_P03 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860675:1; parent_transcript=GRMZM2G118637_T03; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + +GRMZM2G118637_P04 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860669:1; parent_transcript=GRMZM2G118637_T04; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + +GRMZM2G118637_P05 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859647..236860633:1; parent_transcript=GRMZM2G118637_T05; parent_gene=GRMZM2G118637 + + + + + + + + + + + +GRMZM2G419891_P01 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883718:1; parent_transcript=GRMZM2G419891_T01; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + + + +GRMZM2G419891_P02 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883699:1; parent_transcript=GRMZM2G419891_T02; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + +GRMZM2G419891_P03 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883232:1; parent_transcript=GRMZM2G419891_T03; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + +GRMZM2G419891_P04 NP_001105376 polyubiquitin seq=translation; coord=4:236879381..236883699:1; parent_transcript=GRMZM2G419891_T04; parent_gene=GRMZM2G419891 + + + + + + + + + +GRMZM2G419891_P05 NP_001105376 polyubiquitin seq=translation; coord=4:236881289..236883469:1; parent_transcript=GRMZM2G419891_T05; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + + + +GRMZM2G431821_P01 P27923 Ubiquitin-40S ribosomal protein S27a Precursor [Contains Ubiquitin;40S ribosomal protein S27a] seq=translation; coord=8:171603815..171604536:-1; parent_transcript=GRMZM2G431821_T01; parent_gene=GRMZM2G431821 + + + + + + + +GRMZM2G047732_P01 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126474..39127702:1; parent_transcript=GRMZM2G047732_T01; parent_gene=GRMZM2G047732 + + + + + + + +GRMZM2G047732_P02 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126804..39127596:1; parent_transcript=GRMZM2G047732_T02; parent_gene=GRMZM2G047732 + + + + + + + +GRMZM2G357296_P01 B6SIL9 40S ribosomal protein S27a seq=translation; coord=6:125241154..125242106:-1; parent_transcript=GRMZM2G357296_T01; parent_gene=GRMZM2G357296 + + + + + + + +GRMZM2G116689_P01 NP_001148606 LOC100282222 seq=translation; coord=7:116376688..116380988:1; parent_transcript=GRMZM2G116689_T01; parent_gene=GRMZM2G116689 + + + + + + + +GRMZM2G116689_P03 NP_001148606 LOC100282222 seq=translation; coord=7:116376702..116380916:1; parent_transcript=GRMZM2G116689_T03; parent_gene=GRMZM2G116689 + + + + + + + +GRMZM2G005461_P01 seq=translation; coord=9:19289416..19290344:-1; parent_transcript=GRMZM2G005461_T01; parent_gene=GRMZM2G005461 + + + + + + + +GRMZM2G406643_P01 seq=translation; coord=7:150270916..150273417:1; parent_transcript=GRMZM2G406643_T01; parent_gene=GRMZM2G406643 + + + + + + + + +6.57992 +-0.306043 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +13645 13645 13645 13410 13003 12426 11353 10049 7691 5268 3255 1828 891 454 210 104 42 17 8 2 1 1 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +13648 13648 13648 13413 13006 12379 11106 9326 5962 2782 523 73 16 3 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3933 5179 2990 1110 585 62 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2150 5422 3764 1594 601 88 24 227 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3070 (charge 3) + +1523.78 +3 + + +155.082 157.097 157.134 158.092 166.061 167.081 169.097 171.112 173.129 175.119 181.097 183.113 185.092 185.128 186.124 187.072 187.108 191.084 195.113 199.107 201.124 204.134 213.087 218.15 223.155 226.119 227.102 233.092 240.133 242.15 +244.093 246.156 250.118 251.15 253.093 255.146 258.145 261.088 269.125 272.171 274.187 278.113 286.151 292.13 303.205 310.142 317.183 322.161 333.188 337.15 341.147 355.16 357.178 367.133 370.688 371.189 396.153 400.258 414.208 431.237 +432.24 445.236 447.232 454.166 466.203 475.207 500.757 507.268 509.757 515.284 539.259 541.227 543.278 546.264 558.257 567.252 575.29 583.286 596.304 626.307 627.304 643.317 645.321 654.309 662.327 671.335 689.345 704.304 723.352 733.365 +738.352 740.369 741.372 756.431 768.386 784.431 818.376 835.373 852.396 863.367 + + + + +7 4 12 10 4 4 5 4 9 43 6 6 7 4 10 4 6 11 4 5 7 23 7 5 4 8 5 19 4 16 +6 4 7 5 5 4 4 10 6 4 6 15 6 5 8 4 8 22 7 4 6 5 5 4 47 19 4 4 4 39 +9 8 17 6 9 5 3 4 25 11 4 5 4 20 8 5 16 5 5 15 4 100 8 4 5 13 6 3 10 7 +27 47 19 4 4 8 8 5 12 4 + + + + + + +GRMZM5G800734_P02 B6TNC0 Ankyrin repeat domain-containing protein 2Putative uncharacterized protein ; seq=translation; coord=7:138591141..138594806:1; parent_transcript=GRMZM5G800734_T02; parent_gene=GRMZM5G800734 + + + MASDESKNSK PEKPSSAAGA GLPNPFDFSS MSNLLNDPSI REMAEQIASD + PVFNQMAEQL QKSAQGAGEQ GIPALDPQQY METMQQVMQN PQFVSMAERL + GNALMQDPAM SSMLENLTSP AHKEQLEERM ARIKEDPSLK PILDEIENGG + PSAMVKYWND PEVLQKIGQA MGVNLPGDSS VSTVLSGPEE TEEEGGDDDE + SIVHHTASVG DEEGLKKALE GGADKDEEDA EGRRALHFAC GYGELKCAEI + LLEAGAAVDA LDKNKNTPLH YAAGYGRKEC VDLLLKYGAA VTLQNLDGKT + PIEVAKLNSQ DEVLKLLEKD AFL + + + + + + +6.44358 +-0.286381 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +6425 6425 6397 6233 5793 5364 4762 3783 2967 1810 1086 569 312 178 93 39 13 11 3 2 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6429 6429 6401 6237 5797 5347 4667 3564 2278 1112 263 56 16 11 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2086 2605 1234 397 97 8 2 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1581 2794 1375 437 163 65 10 7 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3071 (charge 3) + +1817.83 +3 + + +155.082 157.097 157.134 158.093 158.137 159.077 167.056 169.061 173.093 175.119 185.093 185.129 186.087 187.072 194.625 198.087 199.109 201.124 209.09 215.139 217.081 226.119 227.102 232.141 239.095 244.128 258.145 269.126 272.171 285.157 +294.665 297.12 301.114 310.072 323.173 352.177 355.07 359.193 371.216 388.242 401.668 412.142 416.701 420.133 426.246 432.221 466.103 472.214 481.221 483.218 500.258 502.227 504.255 529.272 539.235 544.238 546.292 571.294 572.3 577.744 +584.306 588.322 594.273 598.249 602.782 608.377 617.242 620.328 651.782 655.269 660.292 670.331 673.268 677.232 680.371 686.327 687.831 696.316 703.34 717.382 724.323 740.354 744.323 748.411 752.834 788.268 800.341 802.324 808.35 815.371 +817.36 886.477 903.451 917.353 943.431 961.436 1028.39 1059.43 1082.44 1459.6 + + + + +4 4 100 4 8 2 2 7 5 40 4 32 8 4 6 4 4 4 3 9 4 18 6 2 6 9 3 5 3 5 +22 4 3 5 3 4 5 8 6 11 17 3 4 4 28 8 5 4 20 5 4 8 5 7 20 5 4 9 5 5 +5 18 7 6 43 5 4 6 5 6 10 2 8 4 4 5 5 4 6 7 8 3 12 9 39 6 5 3 16 2 +31 10 6 4 2 5 3 4 4 4 + + + + + + +GRMZM2G113696_P01 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T01; parent_gene=GRMZM2G113696 + + + + + + + + +GRMZM2G144030_P01 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=7:163002247..163005888:-1; parent_transcript=GRMZM2G144030_T01; parent_gene=GRMZM2G144030 + + + + + + + + +GRMZM2G113696_P02 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T02; parent_gene=GRMZM2G113696 + + + + + + + + +GRMZM2G113696_P03 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=2:209289645..209292956:-1; parent_transcript=GRMZM2G113696_T03; parent_gene=GRMZM2G113696 + + + + + + + + +GRMZM2G144030_P02 P80639 Eukaryotic translation initiation factor 5A (eIF-5A)(eIF-4D) seq=translation; coord=7:163002247..163005888:-1; parent_transcript=GRMZM2G144030_T02; parent_gene=GRMZM2G144030 + + + + + + + + + +3.77488 +-0.215707 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +1391 1391 1391 1385 1260 1129 793 569 383 229 133 87 51 29 15 9 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +1364 1364 1364 1358 1233 1101 732 497 262 107 22 5 3 2 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +682 570 119 23 0 0 0 12 + + + + + + +0 1 2 3 4 5 6 7 + + + + +402 806 165 21 0 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3072 (charge 2) + +1373.56 +2 + + +153.102 155.081 156.077 157.061 157.097 157.134 158.093 159.077 167.056 171.076 171.113 175.071 175.119 181.097 185.056 185.092 186.087 189.087 198.124 199.071 199.108 203.066 216.134 221.104 225.043 227.066 234.145 239.095 240.096 242.113 +245.077 247.129 249.099 257.139 259.093 267.109 275.125 277.118 285.134 296.087 304.113 314.098 332.107 345.177 360.028 361.026 363.187 378.14 386.157 392.689 396.164 404.176 414.178 443.142 455.192 457.207 461.154 469.278 483.189 501.209 +510.256 515.201 533.219 551.234 565.75 570.3 582.301 589.803 592.248 620.245 629.297 633.646 647.315 673.367 680.28 699.259 709.243 727.256 732.354 735.269 740.34 767.314 770.415 784.377 796.875 816.898 836.319 844.899 860.9 864.309 +895.403 901.432 904.417 913.41 950.461 965.47 983.383 993.373 1011.38 1140.42 + + + + +7 9 5 8 8 6 6 3 3 14 10 9 22 5 18 7 5 7 10 18 12 9 29 8 5 57 100 6 3 9 +11 7 5 12 6 13 23 8 27 9 12 35 13 25 9 15 16 5 9 3 22 15 14 17 5 6 11 6 10 6 +34 5 7 13 7 7 14 18 8 10 8 9 47 5 8 8 8 29 7 6 5 8 27 16 31 6 13 6 8 25 +6 15 9 7 9 6 6 4 10 6 + + + + + + +GRMZM2G700208_P01 NP_001130085 hypothetical protein LOC100191178 seq=translation; coord=10:33349087..33352992:-1; parent_transcript=GRMZM2G700208_T01; parent_gene=GRMZM2G700208 + + + MGTNDRAVIS LVLLVCIASR SSLGAAETDV EQKRLSVPLM FVFGDSLVDV + GNNNFLPPPA PRAASPYGID FHAGTAGAVS GRFTNGYNLA DLVARRLGFK + MSPPAYLSLT PVSKFDLFTC RIGANYASGG SGILNTTGNG TLTLQKQITL + FSKTQARMSW ARCKLRSMVS RSLFLVSAGG NDFSAFSEMG MGEQDAPAYI + SSMVSTYVQH IDALYKLGAR RLGILDVPAI GCTPGSRVPM ANGGCNDAAN + SMAQNFNRLL RLEVAKAVAS SMPGMKYSIA STYNFVTDLM NSHLVAGLRV + VDRACCGSGK LNAAVMCAQP NTTYCSDRDD YMFWDMLHPT QATNERGVVA + IFYGPQEYAD PINFAQLAAA TANDDDDINT AMTAGVYAAI + + + + + + + +4.29316 +-0.209422 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +3354 3354 2818 2780 2431 2027 1723 1264 828 609 335 226 127 78 38 21 19 11 9 1 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3305 3305 2769 2731 2336 1884 1463 841 441 252 102 11 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1734 1244 314 56 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +543 1894 750 147 20 1 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3075 (charge 2) + +994.47 +2 + + +155.082 157.061 157.097 157.133 158.092 159.077 166.061 167.081 167.118 169.061 169.097 169.134 171.113 172.117 173.092 173.129 175.072 175.089 175.119 176.122 177.102 181.096 183.113 183.149 185.092 186.088 186.124 187.071 187.108 191.084 +191.118 195.088 195.113 197.103 197.128 198.125 199.108 201.124 204.134 209.103 211.144 213.087 215.14 217.137 225.099 228.098 230.15 235.119 238.118 240.135 242.15 244.165 246.108 249.098 256.13 267.109 272.172 274.187 287.17 294.148 +296.133 302.118 313.151 315.202 320.129 331.157 341.144 351.169 356.686 361.197 366.215 375.172 384.224 430.214 432.272 446.189 448.223 450.222 453.21 460.268 503.308 515.268 524.246 525.248 531.299 557.22 565.297 579.261 602.299 615.317 +666.3 689.33 712.36 733.36 742.346 748.338 753.33 760.366 802.385 824.359 + + + + +14 5 8 6 6 17 5 4 4 2 13 5 100 18 8 5 2 2 49 4 2 8 2 6 6 2 2 4 7 2 +6 6 6 6 9 2 7 9 5 5 2 2 8 22 14 11 8 7 8 7 9 5 4 2 6 5 5 12 4 8 +5 11 2 19 4 8 2 6 10 8 2 2 77 6 7 4 61 4 5 8 6 7 11 4 6 2 6 6 8 7 +2 11 5 8 2 7 6 22 2 10 + + + + + + +GRMZM2G141277_P01 NP_001148494 stem 28 kDa glycoprotein seq=translation; coord=8:109218692..109219673:-1; parent_transcript=GRMZM2G141277_T01; parent_gene=GRMZM2G141277 + + + + + + + + +5.78774 +-0.296807 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +7343 7343 7265 6821 6706 6162 4821 3938 2324 1344 514 320 168 97 37 17 9 4 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +7345 7345 7267 6823 6697 6131 4660 3410 1781 486 135 36 7 4 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3094 3501 676 66 7 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1523 4460 1146 183 28 4 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3076 (charge 2) + +1259.63 +2 + + +152.057 155.082 157.061 157.097 158.093 159.077 164.082 167.081 169.097 169.134 171.077 171.113 173.093 175.072 175.12 181.094 181.111 183.076 183.112 185.092 187.071 187.145 189.087 194.129 195.113 197.127 198.087 199.072 199.107 201.124 +207.113 209.093 212.104 214.084 216.097 218.15 222.123 225.098 226.155 235.082 240.134 242.114 244.165 251.102 253.093 258.145 260.197 268.13 270.108 272.171 276.155 279.099 283.141 294.181 297.158 311.099 312.19 315.129 343.235 347.12 +358.143 361.245 369.176 371.23 382.212 398.146 401.673 408.141 416.158 421.208 440.286 458.297 487.224 491.715 501.222 525.231 532.239 534.261 537.321 543.27 545.199 550.249 562.227 567.326 569.33 587.341 631.333 647.265 665.282 673.29 +703.321 715.431 784.326 785.342 800.378 802.336 844.471 915.401 1007.54 1122.56 + + + + +10 9 7 2 4 8 4 3 11 3 8 15 4 9 22 16 22 3 2 3 3 9 6 3 7 3 3 2 25 7 +6 9 3 4 12 3 3 7 14 10 20 7 9 12 100 10 19 2 4 8 4 3 3 13 2 4 3 3 4 3 +3 9 2 8 3 26 3 3 15 2 12 56 2 3 3 9 3 4 3 8 25 3 8 12 12 8 8 8 9 9 +13 8 23 11 21 8 9 2 9 11 + + + + + + +GRMZM5G803275_P01 NP_001147154 RNA-binding protein 8A seq=translation; coord=10:88191606..88197105:1; parent_transcript=GRMZM5G803275_T01; parent_gene=GRMZM5G803275 + + + MAAVMNADVE VVDFDLDDDD LMDEDAGPDP APAPTSRLRS TIAGDDAPRR + TKGRGFREDP NSSAPRDSRF GAGGRADLDS LGGPGPIQSI EGWIVLVTGV + HEEAQEDDLQ NAFQEFGQVK NLHLNLDRRT GFVKGYALIE YEKFEEAQAA + IKELDGAELY EQKMSVDWAF SSGPAKRRFT RKRSPPRARS RTPPRRRH + + + + + +GRMZM5G817255_P03 NP_001150298 LOC100283928 seq=translation; coord=8:128698509..128701507:1; parent_transcript=GRMZM5G817255_T03; parent_gene=GRMZM5G817255 + + + MAAAATNADV EVVDFDLDDD DLMDEDAGPD PAPPPASRLR STIAGDDAPR + RTKGRGFRED PNSSATRDSR FGAGGRADLD SLGGPGPIQS IEGWIVLVTG + VHEEAQEDDL QNAFQEFGQV KNLHLNLDRR TGFVKGYALI EYEKFEEAQA + AIKELDGAEL YKQRMSVDWA FSSGPAKRRN TRKRSPPRAR SRTPPRRRH + + + + + +GRMZM5G817255_P02 NP_001150298 LOC100283928 seq=translation; coord=8:128698509..128701507:1; parent_transcript=GRMZM5G817255_T02; parent_gene=GRMZM5G817255 + + + MAAAATNADV EVVDFDLDDD DLMDEDAGPD PAPPPASRLR STIAGDDAPR + RTKGRGFRED PNSSATRDSR FGAGGRADLD SLGGPGPIQS IEGWIVLVTG + VHEEAQEDDL QNAFQEFGQV KNLHLNLDRR TGFVKVTTKS SFKDPTQEKA + LMFPQHVLNY LLCVTESKKS GDSKYYLGVC GSPDFDGGY + + + + + + +5.42989 +-0.241329 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +5026 5026 5026 4895 4854 4467 4272 3849 3602 2637 1882 1088 611 334 163 95 67 45 15 13 4 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5005 5005 5005 4874 4832 4430 4198 3757 3444 2093 1250 488 91 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2435 2257 298 44 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1074 2454 1142 275 74 7 1 9 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3077 (charge 2) + +1002.48 +2 + + +154.086 155.081 157.061 157.097 157.109 157.134 158.092 158.128 159.076 159.113 161.092 167.055 167.082 169.061 169.097 169.134 171.077 173.092 173.129 175.119 176.123 181.061 181.097 183.113 183.149 185.093 185.129 186.089 186.124 187.108 +187.144 189.087 193.098 194.129 195.077 195.113 197.092 197.128 198.088 199.072 199.108 201.124 209.14 212.14 213.086 215.14 217.082 226.155 229.118 231.098 232.14 237.135 240.135 242.15 244.165 255.145 256.167 259.093 268.167 269.125 +272.172 284.16 288.083 297.121 299.062 302.171 306.158 326.182 336.173 343.208 355.2 361.184 362.187 377.231 383.195 400.701 415.036 431.273 453.214 458.235 470.263 543.326 556.237 560.318 573.262 575.27 630.284 632.3 659.377 687.307 +689.36 701.32 703.331 714.393 730.414 758.338 800.399 814.409 818.402 905.431 + + + + +3 15 3 8 3 29 19 6 12 16 44 23 7 4 29 10 41 13 9 100 3 7 6 9 7 9 22 8 9 13 +15 61 8 4 8 8 3 16 7 9 19 11 9 11 12 11 12 35 6 6 18 8 10 22 41 60 8 3 3 8 +27 41 7 3 41 4 9 9 6 73 3 19 3 3 3 7 4 15 12 43 3 3 3 12 29 3 60 3 4 10 +17 83 8 8 3 16 3 23 14 17 + + + + + + +GRMZM2G000280_P01 NP_001131404 hypothetical protein LOC100192732 seq=translation; coord=5:204209307..204287307:-1; parent_transcript=GRMZM2G000280_T01; parent_gene=GRMZM2G000280 + + + MASPTAGDAP LASPSPSPAA DATDAALAAA AAVPDPDISF GFLRPELGKE + KLVGTVGFHE RHVFLCYKGP EVWPSHVEAA HSDRLPRLLA AAIKARKPNL + KKTIKFTICE GEDGTESSNG DVLIFPDMIR YKGLTHFDVD NFVEEVFVKD + IDWLPGSPEP ISGSYVFVCS HQRRDIRCGI CGPALIKRFK EEINGLGLDG + QVAVSACSHV GGHKYAGNVI IFSSDAKGEV VGHWYGYVVP DDVPVLLHKH + IGQGEVVDRL WRGQMGLSEE QQKQALELRS MTNGGKESLE ETETDGASCN + PAATGGCCQG NGGFTRALEQ QKQALELRSM TNGGKESLEE TETDGASCNP + AATGGCCQGN GSFTCCHPDL PKEKRDKSIA IEQNPKSCEE NGKEGGGAGS + KKGNSKTCPM PTWFETWERA DTYAALAVVA AAAAVFISFR IYKNLN + + + + + + +7.42758 +-0.401491 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +6438 6438 6262 6107 5854 5395 4978 4516 4109 2216 1434 575 297 86 50 7 2 1 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6449 6449 6273 6114 5835 5318 4809 4282 3952 1410 1035 48 9 1 0 + + + + + + +0 1 2 3 4 + + + + +3186 2740 495 29 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +982 3900 1359 189 18 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3079 (charge 2) + +1109.57 +2 + + +152.057 153.065 154.05 155.081 155.118 156.077 157.061 157.097 157.108 158.092 159.077 166.06 169.06 169.097 169.134 171.076 171.113 173.092 175.072 175.119 176.122 178.134 181.061 181.097 183.113 185.055 185.092 185.165 186.088 186.123 +187.072 187.108 187.144 189.087 194.129 195.113 197.128 198.124 199.071 199.107 199.181 201.123 203.066 206.129 212.103 216.135 217.081 219.08 221.103 223.155 226.154 227.1 234.145 240.134 241.081 244.165 246.181 251.15 258.146 267.109 +273.119 275.125 285.133 290.146 303.176 308.17 314.098 323.171 345.177 378.14 386.16 389.215 392.69 396.162 404.169 408.187 414.273 426.198 448.211 455.188 477.243 482.283 488.282 498.267 510.263 517.265 526.308 565.751 598.208 626.32 +647.314 668.355 674.348 727.354 822.43 842.402 859.427 861.436 896.361 972.505 + + + + +3 2 2 8 3 3 10 10 2 11 8 3 3 6 3 9 8 12 14 80 3 19 3 5 3 3 8 3 6 3 +6 7 2 6 3 3 6 3 8 9 3 6 7 3 6 11 8 5 2 100 12 4 31 7 3 10 2 32 2 7 +6 6 9 2 2 2 3 2 8 3 2 2 6 2 2 2 3 2 2 2 3 2 6 3 8 2 6 3 2 2 +9 2 3 2 3 2 47 2 2 14 + + + + + + +GRMZM2G010196_P01 NP_001131876 hypothetical protein LOC100193255 seq=translation; coord=1:54598727..54601782:1; parent_transcript=GRMZM2G010196_T01; parent_gene=GRMZM2G010196 + + + MVTPATFSLR PSAPPAPPRA GLPRARACFA PAIRTSPSVA FSYQPRRFSG + IRRAVAVDSE QGSPESPEQE KKPKTYYFLV ANAKFMLDEE EHFQEQLAEK + LRNYAERDKE QDFWLVVEPK FLDRFPNITK RLKRPAVALV STDGNWITFM + KLRLDRVLQD QFDAESVEEA LASNPVELKF EKPEKWTAPY PKYGFGWWEP + FLPPKFSNGT A + + + + + + +5.5569 +-0.271068 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 + + + + +11421 11421 11163 10103 9183 7180 5546 4049 2775 1833 1237 729 456 250 91 47 22 3 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +11421 11421 11163 10103 9087 6990 5002 3230 1910 1151 771 351 250 23 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3741 4929 2086 583 71 16 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2441 5745 2524 592 90 27 4 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3080 (charge 3) + +2240.11 +3 + + +155.082 157.097 159.077 167.083 169.061 169.097 171.077 171.113 172.117 175.071 175.12 183.15 185.056 186.087 187.109 189.087 197.128 199.071 199.108 203.066 215.103 217.083 223.072 226.155 240.098 242.15 244.166 251.15 255.109 257.196 +268.131 273.12 275.125 286.14 296.124 314.134 327.13 332.11 345.143 355.162 357.249 372.262 384.145 386.24 394.176 416.205 425.262 460.168 484.205 492.279 500.357 511.254 517.191 535.796 539.272 553.224 571.239 612.295 618.026 638.347 +640.344 644.684 648.845 650.35 653.668 668.297 677.345 683.347 692.376 699.336 712.347 716.34 719.364 721.37 740.402 746.401 748.415 776.391 797.318 827.428 893.438 925.429 942.444 950.452 983.563 985.55 1036.52 1053.52 1055.53 1070.59 +1160.57 1199.61 1296.68 1298.69 1383.71 1441.72 1541.69 1659.44 + + + + +2 2 2 2 2 2 3 100 6 2 3 4 2 4 2 2 9 4 3 5 4 5 2 24 12 57 49 10 3 5 +2 3 5 18 5 16 3 2 3 11 13 18 3 3 5 3 3 4 12 6 9 3 3 6 5 3 5 11 3 5 +4 13 25 18 4 3 10 4 10 4 3 4 4 6 18 4 43 12 4 10 9 13 5 14 24 5 12 22 4 19 +4 4 44 10 9 13 4 3 + + + + + + +GRMZM2G116292_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31201315..31206122:-1; parent_transcript=GRMZM2G116292_T01; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P02 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T02; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P03 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T03; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P04 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31074889:-1; parent_transcript=GRMZM2G116292_T04; parent_gene=GRMZM2G116292 + + + + + + + +GRMZM2G116292_P05 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=1:31068644..31206122:-1; parent_transcript=GRMZM2G116292_T05; parent_gene=GRMZM2G116292 + + + + + + + + + +GRMZM2G047727_P01 B6SHW9 Putative uncharacterized proteinUbiquitin fusion protein ; seq=translation; coord=2:165103157..165107176:-1; parent_transcript=GRMZM2G047727_T01; parent_gene=GRMZM2G047727 + + + + + + + +GRMZM2G409726_P01 NP_001105376 polyubiquitin seq=translation; coord=5:82443403..82446794:-1; parent_transcript=GRMZM2G409726_T01; parent_gene=GRMZM2G409726 + + + + + + + + + + + + + + + + + + + +GRMZM2G409726_P02 NP_001105376 polyubiquitin seq=translation; coord=5:82443815..82446714:-1; parent_transcript=GRMZM2G409726_T02; parent_gene=GRMZM2G409726 + + + + + + + + + +GRMZM2G409726_P03 NP_001105376 polyubiquitin seq=translation; coord=5:82443856..82446714:-1; parent_transcript=GRMZM2G409726_T03; parent_gene=GRMZM2G409726 + + + + + + + + + + + + + + + + + +GRMZM2G006293_P01 NP_001150700 40S ribosomal protein S27a seq=translation; coord=1:191263450..191264705:-1; parent_transcript=GRMZM2G006293_T01; parent_gene=GRMZM2G006293 + + + + + + + +GRMZM2G118637_P01 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236857988..236860949:1; parent_transcript=GRMZM2G118637_T01; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + + + +GRMZM2G118637_P02 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859470..236861173:1; parent_transcript=GRMZM2G118637_T02; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + + + +GRMZM2G118637_P03 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860675:1; parent_transcript=GRMZM2G118637_T03; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + +GRMZM2G118637_P04 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859530..236860669:1; parent_transcript=GRMZM2G118637_T04; parent_gene=GRMZM2G118637 + + + + + + + + + + + + + +GRMZM2G118637_P05 NP_001148453 polyubiquitin containing 7 ubiquitin monomers seq=translation; coord=4:236859647..236860633:1; parent_transcript=GRMZM2G118637_T05; parent_gene=GRMZM2G118637 + + + + + + + + + + + +GRMZM2G419891_P01 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883718:1; parent_transcript=GRMZM2G419891_T01; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + + + +GRMZM2G419891_P02 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883699:1; parent_transcript=GRMZM2G419891_T02; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + +GRMZM2G419891_P03 NP_001105376 polyubiquitin seq=translation; coord=4:236879357..236883232:1; parent_transcript=GRMZM2G419891_T03; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + +GRMZM2G419891_P04 NP_001105376 polyubiquitin seq=translation; coord=4:236879381..236883699:1; parent_transcript=GRMZM2G419891_T04; parent_gene=GRMZM2G419891 + + + + + + + + + +GRMZM2G419891_P05 NP_001105376 polyubiquitin seq=translation; coord=4:236881289..236883469:1; parent_transcript=GRMZM2G419891_T05; parent_gene=GRMZM2G419891 + + + + + + + + + + + + + + + + + + + +GRMZM2G431821_P01 P27923 Ubiquitin-40S ribosomal protein S27a Precursor [Contains Ubiquitin;40S ribosomal protein S27a] seq=translation; coord=8:171603815..171604536:-1; parent_transcript=GRMZM2G431821_T01; parent_gene=GRMZM2G431821 + + + + + + + +GRMZM2G047732_P01 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126474..39127702:1; parent_transcript=GRMZM2G047732_T01; parent_gene=GRMZM2G047732 + + + + + + + +GRMZM2G047732_P02 NP_001105472 40S ribosomal protein S27a seq=translation; coord=8:39126804..39127596:1; parent_transcript=GRMZM2G047732_T02; parent_gene=GRMZM2G047732 + + + + + + + +GRMZM2G357296_P01 B6SIL9 40S ribosomal protein S27a seq=translation; coord=6:125241154..125242106:-1; parent_transcript=GRMZM2G357296_T01; parent_gene=GRMZM2G357296 + + + + + + + +GRMZM2G116689_P01 NP_001148606 LOC100282222 seq=translation; coord=7:116376688..116380988:1; parent_transcript=GRMZM2G116689_T01; parent_gene=GRMZM2G116689 + + + + + + + +GRMZM2G116689_P03 NP_001148606 LOC100282222 seq=translation; coord=7:116376702..116380916:1; parent_transcript=GRMZM2G116689_T03; parent_gene=GRMZM2G116689 + + + + + + + +GRMZM2G005461_P01 seq=translation; coord=9:19289416..19290344:-1; parent_transcript=GRMZM2G005461_T01; parent_gene=GRMZM2G005461 + + + + + + + +GRMZM2G406643_P01 seq=translation; coord=7:150270916..150273417:1; parent_transcript=GRMZM2G406643_T01; parent_gene=GRMZM2G406643 + + + + + + + + +5.36986 +-0.275378 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 + + + + +9619 9619 9538 8891 8188 5697 4598 2374 1324 605 373 216 105 47 26 12 7 6 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +9609 9609 9528 8847 8008 5455 3742 1543 468 123 25 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +4866 3636 967 138 12 224 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1858 6070 1472 186 30 0 4 223 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3082 (charge 2) + +1523.79 +2 + + +157.133 158.093 159.077 168.066 169.097 175.119 185.129 187.071 187.108 197.129 199.108 204.136 209.092 216.1 218.15 226.118 227.103 230.115 240.135 242.15 244.129 251.149 254.151 256.13 258.145 301.128 310.139 337.151 341.146 355.163 +357.178 369.254 373.175 413.222 428.252 431.236 438.194 453.702 456.249 459.259 462.269 466.198 483.22 515.281 525.262 532.22 539.269 541.225 543.277 546.264 566.26 584.273 588.257 596.305 614.317 626.316 636.301 643.318 653.326 661.784 +667.377 671.335 680.341 682.352 723.345 724.344 740.369 742.373 757.425 784.419 853.453 910.472 912.483 986.435 1021.5 1039.52 1089.48 1167.61 1282.64 + + + + +8 2 1 1 1 13 4 1 1 1 2 2 2 1 2 11 2 1 2 12 9 1 2 1 2 2 2 4 2 6 +7 1 2 2 4 34 1 1 1 1 1 1 2 4 1 1 2 2 5 5 4 4 1 5 7 2 2 8 4 1 +2 8 7 1 14 4 100 6 4 5 7 25 2 1 2 14 1 4 6 + + + + + + +GRMZM2G001327_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695861:-1; parent_transcript=GRMZM2G001327_T01; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G001327_P03 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695738:-1; parent_transcript=GRMZM2G001327_T03; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G154218_P01 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515921..136519080:-1; parent_transcript=GRMZM2G154218_T01; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G154218_P02 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515968..136519018:-1; parent_transcript=GRMZM2G154218_T02; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G149768_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136568621..136572271:-1; parent_transcript=GRMZM2G149768_T01; parent_gene=GRMZM2G149768 + + + + + + + +GRMZM2G110509_P01 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T01; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P02 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T02; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P03 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607316..84610225:1; parent_transcript=GRMZM2G110509_T03; parent_gene=GRMZM2G110509 + + + + + + + + +4.26897 +-0.230755 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 + + + + +6965 6965 6965 6463 6158 4255 3479 2316 1407 899 564 290 195 102 63 26 4 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6983 6983 6983 6480 6135 4025 2877 1646 585 267 43 11 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3452 2737 671 111 23 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1081 4091 1384 350 49 10 0 29 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3084 (charge 2) + +1335.65 +2 + + +152.056 155.082 157.097 159.077 167.056 167.081 168.056 169.097 171.076 171.113 172.108 173.092 175.119 177.102 178.106 185.092 187.107 189.087 198.124 199.108 201.086 205.097 213.088 216.134 218.15 225.043 227.102 239.095 242.112 244.166 +259.144 272.124 281.125 283.14 285.01 297.192 299.062 301.187 304.165 305.168 315.203 324.987 341.019 342.994 355.069 359.029 361.026 375.204 382.171 399.15 414.238 416.261 418.994 428.179 430.23 446.188 481.231 508.088 511.285 514.221 +516.754 518.263 532.234 545.257 560.232 568.309 569.316 579.619 603.27 608.378 618.316 647.266 655.341 666.821 673.353 701.279 705.428 718.301 733.348 752.397 753.402 760.389 809.413 811.413 817.362 834.398 848.401 874.43 892.412 920.44 +944.439 949.425 961.456 1015.47 1021.46 1032.49 1034.5 1092.54 1131.56 1179.58 + + + + +3 13 3 7 32 3 4 10 1 6 1 5 9 45 6 3 1 1 4 1 3 50 2 4 11 20 1 20 5 6 +10 3 4 3 13 1 12 3 19 4 44 1 4 6 13 100 20 3 1 1 5 4 6 3 7 4 1 2 9 1 +3 1 3 5 4 6 3 2 3 1 4 11 1 5 3 2 4 13 3 6 6 6 12 4 6 2 2 5 3 3 +2 2 12 3 4 14 4 1 3 2 + + + + + + +GRMZM2G018484_P01 NP_001168313 hypothetical protein LOC100382079 seq=translation; coord=5:213279291..213281471:1; parent_transcript=GRMZM2G018484_T01; parent_gene=GRMZM2G018484 + + + MTTPSTAPAP LASLLRVSAA AVPVARRRPK SPAAAAAARW EGGGGRRRCR + AAVVEEAGVL LPKEGEGEGE GEEAPDAAAG RYDWREEWYP LYLAKEVPDD + AALPLTVFDR QLVLWRDAHG VLRCHEDRCP HRLAKLSEGQ IVDGKLECLY + HGWQFDGDGK CVKIPQLPEG AKIPRSACAR NYEVRDSQGV VWVWMSDANP + PDEGKLPWFE PYARAGFTDL STVHELPYDH SILLENLMDP AHVPISHDRT + DWTAKREDAQ PLFFDVTERT PRGFAGYWGR TGTPHLRNLL RFEAPCVLTN + TLEFADKDGR EQCFSAHFLC RPAGQGKSML LVRFGSTLRS PLAKVLPSWY + FHQNACKVFE QDMGFLSSQN EVLLREKLPT RELYLNLRSS DTWVAEYRKW + MDRAGHGMPY YFGHSTLSPP PVPAVVEQAP AGAVAGISAS FPAKGGVGMV + HAPNPTNRYF RHVVHCKGCR ATVKKYTSLK TVFAALAAAA LSAAILAATR + QWKAVLVAAS AVLAAASYAC DAVLSLITTN FIRTHRRL + + + + + + +5.6775 +-0.306892 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +2502 2502 2497 2258 2190 2056 1815 1675 1184 814 357 183 114 60 24 7 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2492 2492 2487 2248 2175 2031 1782 1619 896 576 159 52 26 1 0 + + + + + + +0 1 2 3 4 + + + + +1098 1140 232 33 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +680 1371 379 66 4 2 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3086 (charge 2) + +1358.58 +2 + + +152.034 152.057 155.081 156.077 157.061 157.109 158.092 159.076 161.092 167.081 169.061 169.098 170.045 171.076 171.113 172.107 173.092 175.071 175.119 181.061 184.072 185.092 186.088 187.072 187.089 188.075 189.087 195.089 198.087 199.109 +201.087 213.087 216.098 217.082 224.102 226.119 229.131 230.114 232.141 241.082 244.093 256.13 257.124 259.092 267.11 270.108 272.171 284.124 286.15 288.119 298.103 300.166 303.177 306.16 309.119 311.171 316.114 319.172 329.17 337.115 +341.147 355.124 374.214 398.202 414.246 438.159 445.252 484.171 491.255 560.277 613.214 634.331 640.312 657.332 659.344 664.298 671.31 682.292 728.369 730.382 737.343 775.426 810.338 827.363 839.406 857.412 859.419 861.398 893.372 895.378 +924.453 930.446 948.429 968.435 986.448 1001.5 1012.41 1035.46 1043.47 1115.55 + + + + +4 9 9 2 8 3 11 26 11 3 39 4 9 2 18 3 3 10 47 9 3 4 20 97 3 3 4 7 4 2 +12 12 4 3 3 8 4 3 13 14 15 3 9 7 8 16 3 11 3 3 35 3 15 8 4 3 24 7 7 7 +3 19 11 3 10 3 71 3 2 11 2 4 7 100 28 4 4 3 48 17 3 2 2 4 4 33 11 2 2 3 +2 10 4 2 8 3 14 10 21 3 + + + + + + +GRMZM2G156861_P02 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168699190:1; parent_transcript=GRMZM2G156861_T02; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G156861_P03 NP_001105003 lipoxygenase seq=translation; coord=3:168695539..168839001:1; parent_transcript=GRMZM2G156861_T03; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G156861_P01 NP_001105003 lipoxygenase seq=translation; coord=3:168835321..168839001:1; parent_transcript=GRMZM2G156861_T01; parent_gene=GRMZM2G156861 + + + + + + + +GRMZM2G109130_P01 NP_001105515 lipoxygenase seq=translation; coord=1:264200949..264205758:1; parent_transcript=GRMZM2G109130_T01; parent_gene=GRMZM2G109130 + + + + + + + +GRMZM2G109130_P02 NP_001105515 lipoxygenase seq=translation; coord=1:264202964..264205732:1; parent_transcript=GRMZM2G109130_T02; parent_gene=GRMZM2G109130 + + + + + + + + +6.92845 +-0.337973 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +5299 5299 5299 5299 5000 4822 4347 3907 3432 2110 1435 761 436 184 104 34 20 3 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5322 5322 5322 5322 5023 4837 4331 3836 3297 1755 930 276 50 29 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2189 2079 708 258 56 12 0 20 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1162 2461 1220 344 90 23 0 22 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3087 (charge 3) + +1927.86 +3 + + +152.057 155.082 157.085 157.097 157.133 158.093 175.119 181.061 183.113 185.079 199.072 200.139 201.125 208.109 212.104 214.106 218.15 226.155 228.134 233.128 235.12 240.098 244.092 258.109 260.197 267.109 268.093 286.103 290.147 314.16 +329.182 344.672 361.245 384.235 391.676 400.188 410.177 418.204 421.727 427.206 434.72 443.235 445.237 470.254 472.715 483.243 491.757 499.772 540.285 546.262 556.251 572.238 596.348 599.327 612.268 625.363 645.31 654.289 667.283 668.287 +671.311 674.355 684.308 688.338 711.373 717.373 724.373 726.389 745.376 765.384 771.371 791.372 795.395 799.37 808.404 816.399 826.403 842.453 847.365 868.43 885.457 899.427 909.439 923.47 927.421 929.464 939.505 944.427 946.431 956.456 +965.48 967.433 982.506 984.448 1001.44 1003.46 1024.51 1026.53 1111.6 1161.57 + + + + +19 11 5 5 5 6 81 19 5 6 20 21 5 6 5 6 18 17 6 20 20 15 6 14 11 6 16 28 20 4 +9 14 4 5 5 6 5 13 27 25 10 22 10 83 14 22 55 5 11 18 33 4 5 4 10 11 29 10 25 5 +100 5 40 22 13 10 18 15 12 10 14 5 5 39 5 6 20 40 39 24 33 17 6 6 20 15 39 38 10 10 +24 14 30 33 52 10 5 5 5 4 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + + + + + + +5.14939 +-0.239507 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +5707 5707 5576 5345 5073 4717 4350 4061 2646 2332 1259 834 478 308 173 116 32 23 14 9 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5713 5713 5582 5351 5052 4664 4276 3885 2412 1616 598 108 20 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1843 2709 954 180 28 1 1 4 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1021 3546 940 176 20 5 8 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3089 (charge 2) + +1328.64 +2 + + +157.108 158.092 159.076 167.081 168.113 169.098 171.113 174.07 175.119 176.123 181.097 183.124 185.092 198.124 200.151 208.107 211.119 226.119 228.146 244.165 245.077 258.145 277.656 289.133 297.156 306.159 308.158 311.183 324.119 328.209 +339.177 341.146 342.148 356.204 388.172 400.166 417.192 435.202 437.202 442.196 453.161 470.189 493.25 510.276 511.279 515.191 519.269 526.309 533.201 537.281 538.279 542.25 550.228 554.305 634.293 642.809 647.8 656.31 665.824 715.307 +734.393 741.297 751.419 758.315 762.383 775.34 777.338 779.42 792.364 797.433 805.431 822.46 833.394 850.417 860.385 873.429 877.413 878.415 894.442 896.448 929.414 956.409 973.441 975.448 979.467 995.494 1006.46 1023.49 1025.5 1084.48 +1085.47 1101.5 1126.53 1128.53 1138.5 1154.53 1156.52 1172.54 1174.54 1269.59 + + + + +18 21 2 3 6 5 5 7 68 4 4 30 2 3 4 4 28 12 12 3 6 2 3 15 5 100 2 7 4 8 +13 20 3 20 4 4 5 66 3 3 3 7 3 9 2 2 2 11 4 7 3 3 3 32 6 18 3 55 77 3 +2 3 4 6 3 19 3 9 2 3 4 8 4 5 5 2 19 10 64 7 5 3 24 5 4 10 7 28 4 7 +3 2 7 3 2 5 2 14 3 4 + + + + + + +GRMZM2G079538_P01 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110621503..110626726:1; parent_transcript=GRMZM2G079538_T01; parent_gene=GRMZM2G079538 + + + MHMSEATTVN FQVVTLTSPV FSILFQLLTI IHVFFSALVS ATSECSNLPR + CYYLPNPSPY QVWSRSFASD NGDKFEAVVP FMGESVTDGT LANFLKKPGD + RVEADEPIAQ IETDKVTIDV ASPEAGVIEK LIASEGDTVT PGTKVAIISK + SAQPAETHVA PSEEATSKES SPPKVEDKPK VEEKAPKVDP PKMQAPKPTA + PSKTSPSEPQ LPPKERERRV PMPRLRKRIA NRLKDSQNTF AMLSTFNEVD + MTNLMKLRSD YKDEFVTKHG VKLGLMSCFV KAAVSALQNQ PIVNAVIDGD + DIIYRDYVDI SVAVGTSKGL VVPVIRDADT MNFADIEKGI NNLAKKATEG + ALSIDDMAGG TFTISNGGVY GSLLSTPIIN PPQSSILGMH SIVQRPVVVN + GDILARPMMY LALTYDHRLI DGREAVFFLR RIKDVVEDPR RLLLDI + + + + + +GRMZM2G079538_P02 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110620918..110626719:1; parent_transcript=GRMZM2G079538_T02; parent_gene=GRMZM2G079538 + + + MASRVASGLL RRRAGATLGL LRSYAHVRSY NSQLSALVSA TSECSNLPRR + CYYLPNPSPY QVWSRSFASD NGDKFEAVVP FMGESVTDGT LANFLKKPGD + RVEADEPIAQ IETDKVTIDV ASPEAGVIEK LIASEGDTVT PGTKVAIISK + SAQPAETHVA PSEEATSKES SPPKVEDKPK VEEKAPKVDP PKMQAPKPTA + PSKTSPSEPQ LPPKERERRV PMPRLRKRIA NRLKDSQNTF AMLSTFNEVD + MTNLMKLRSD YKDEFVTKHG VKLGLMSCFV KAAVSALQNQ PIVNAVIDGD + DIIYRDYVDI SVAVGTSKGL VVPVIRDADT MNFADIEKGI NNLAKKATEG + ALSIDDMAGG TFTISNGGVY GSLLSTPIIN PPQSSILGMH SIVQRPVVVN + GDILARPMMY LALTYDHRLI DGREAVFFLR RIKDVVEDPR RLLLDI + + + + + +GRMZM2G079538_P03 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110621503..110626716:1; parent_transcript=GRMZM2G079538_T03; parent_gene=GRMZM2G079538 + + + MASRVASGLL RRRAGATLGL LRSYAHVRSY NSQLSALVSA TSECSNLPRC + YYLPNPSPYQ VWSRSFASDN GDKFEAVVPF MGESVTDGTL ANFLKKPGDR + VEADEPIAQI ETDKVTIDVA SPEAGVIEKL IASEGDTVTP GTKVAIISKS + AQPAETHVAP SEEATSKESS PPKVEDKPKV EEKAPKVDPP KMQAPKPTAP + SKTSPSEPQL PPKERERRVP MPRLRKRIAN RLKDSQNTFA MLSTFNEVDM + TNLMKLRSDY KDEFVTKHGV KLGLMSCFVK AAVSALQNQP IVNAVIDGDD + IIYRDYVDIS VAVGTSKGLV VPVIRDADTM NFADIEKGIN NLAKKATEGA + LSIDDMAGGT FTISNGGVYG SLLSTPIINP PQSSILGMHS IVQRPVVVNG + DILARPMMYL ALTYDHRLID GREAVFFLRR IKDVVEDPRR LLLDI + + + + + +GRMZM5G807639_P03 NP_001150636 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=2:66624116..66641809:-1; parent_transcript=GRMZM5G807639_T03; parent_gene=GRMZM5G807639 + + + MASRVASGLL RRRAVATLGL LRSHTHVRNY SSQLSALIPA TSQCSNLTRR + RYYLPNPSLY QVWSRSFASD SGDKFEAVVP FMGESVTDGT LANFLKKPGD + RVEADEPIAQ IETDKVTIDV ASPEAGVIEK LIASEGDTVT PGTKVAIISK + SAQPAETHVA PSEEATSKGS SPPKVEEKSR VEEKAPKVEP PKMQAPKPTA + PLKTSPSEPQ LPPKERERRV PMPRLRKRIA NRLKDSQNTF AMLSTFNEVD + MTNLMKLRSD YKDEFVTKHG VKLGLMSCFV KAAVSALQNQ PIVNAVIDGD + DIIYRDYVDV SVAVGTSKGL VVPVIRDADT MNFADIEKGI NNLAKKANEG + ALSIDDMAGG TFTISNGGVY GSLLSTPIIN PPQSSILGMH SIVQRPVVVN + GDILARPMMF LALTYDHRLI DGREAVFFLR RIKDVVEDPR RLLLDI + + + + + +GRMZM5G807639_P02 NP_001150636 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=2:66624116..66641809:-1; parent_transcript=GRMZM5G807639_T02; parent_gene=GRMZM5G807639 + + + MASRVASGLL RRRAVATLGL LRSHTHVRNY SSQLSALIPA TSQCSNLTRR + YYLPNPSLYQ VWSRSFASDS GDKFEAVVPF MGESVTDGTL ANFLKKPGDR + VEADEPIAQI ETDKVTIDVA SPEAGVIEKL IASEGDTVTP GTKVAIISKS + AQPAETHVAP SEEATSKGSS PPKVEEKSRV EEKAPKVEPP KMQAPKPTAP + LKTSPSEPQL PPKERERRVP MPRLRKRIAN RLKDSQNTFA MLSTFNEVDM + TNLMKLRSDY KDEFVTKHGV KLGLMSCFVR LLFLHFKTSQ LLMLSLMAMT + SYTETT + + + + + + +4.70186 +-0.229359 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 67 + + + + +8390 8390 8378 6522 5798 4687 3956 3023 2081 1255 688 392 227 127 68 31 18 14 8 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8391 8391 8379 6523 5698 4422 3288 2216 1297 484 188 55 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4958 2627 719 75 11 0 0 10 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1355 4856 1767 370 30 11 1 10 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3090 (charge 2) + +1839.87 +2 + + +159.076 163.061 169.097 171.076 173.093 175.119 176.103 185.093 189.087 200.102 204.087 206.718 216.135 224.534 226.118 234.145 237.133 239.113 242.113 284.123 287.135 290.16 294.372 296.123 298.139 302.135 308.172 314.134 325.112 335.192 +338.182 367.162 371.198 381.178 384.186 388.219 399.186 406.229 409.22 443.177 444.768 453.662 455.222 490.243 508.251 514.217 518.235 536.247 538.264 557.255 566.255 574.763 578.292 585.256 597.246 607.318 615.265 635.312 664.311 668.289 +681.56 685.313 686.307 688.336 706.35 719.184 722.345 746.348 751.347 759.349 768.875 777.375 794.379 804.363 817.386 822.372 824.393 830.39 833.396 848.4 850.409 877.414 883.422 893.449 901.423 903.426 911.44 919.437 922.434 964.469 +992.484 1018.51 1155.56 1257.61 1302.6 1385.64 1401.72 1456.69 1505.67 1554.75 + + + + +34 3 21 3 2 3 10 3 2 6 3 2 14 2 2 47 4 14 2 5 19 5 2 5 36 2 3 6 14 36 +20 4 3 16 3 3 16 32 6 18 3 3 3 4 15 23 4 31 6 4 5 4 4 5 4 11 4 29 4 6 +11 4 5 5 34 5 4 5 11 4 3 34 6 13 10 15 6 19 15 88 5 4 4 6 11 6 4 100 12 4 +22 41 28 16 4 10 11 5 4 31 + + + + + + +GRMZM2G129513_P01 P15719 Malate dehydrogenase [NADP], chloroplastic Precursor (EC 1.1.1.82)(NADP-MDH) seq=translation; coord=1:203170067..203174226:-1; parent_transcript=GRMZM2G129513_T01; parent_gene=GRMZM2G129513 + + + MGLSTVYSPA GPRLVPAPLG RCRSAQPRRP RRAPLATVRC SVDATKQAQD + GVATAVATEA PASRKECFGV FCTTYDLKAE DKTKSWKKLV NVAVSGAAGM + ISNHLLFKLA SGEVFGQDQP IALKLLGSER SFQALEGVAM ELEDSLYPLL + REVSIGIDPY VVFQDVDWAL LIGAKPRGPG MERAALLDIN GQIFADQGKA + LNAVASRNAK VLVVGNPCNT NALICLKNAP NIPAKNFHAL TRLDENRAKC + QLALKAGVFY DKVSNVTIWG NHSTTQVPDF LNAKIDGRPV KEVIKDTKWL + EEEFTLTVQK RGGVLIQKWG RSSAASTAVS IVDAIRSLVT PTPEGDWFST + GVYTTGNPYG IAEDIVFSMP CRSKGDGDYE LASDVLMDDF LWERIKKSEA + ELLAEKKCVA HLTGEGNAFC DLPEDTMLPG EV + + + + + + +4.61059 +-0.236441 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +2593 2593 2577 2438 2338 2154 2011 1403 1020 672 422 225 124 77 49 23 10 3 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2596 2596 2580 2436 2331 2081 1734 1208 690 218 84 43 9 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1170 973 426 23 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +486 1204 690 176 34 5 2 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3091 (charge 2) + +824.462 +2 + + +155.081 155.118 157.109 157.134 158.093 158.136 159.079 159.095 166.062 167.081 169.061 169.097 169.134 170.101 171.077 171.113 172.108 173.093 173.129 175.119 176.121 181.096 181.11 183.077 183.113 183.149 184.108 185.129 185.166 186.087 +187.09 187.108 194.129 195.113 197.128 200.14 201.124 204.135 209.104 212.103 213.106 215.139 218.15 219.113 221.091 224.103 226.154 228.135 238.119 240.135 244.166 249.087 254.152 255.145 258.147 269.163 272.172 280.166 283.111 290.145 +293.125 297.192 301.187 304.693 308.16 311.681 315.203 317.208 320.195 323.207 325.187 329.192 341.219 365.22 368.232 375.766 378.215 387.2 396.224 404.223 414.271 422.237 426.235 428.287 473.247 493.284 500.282 515.292 517.323 525.304 +528.277 542.331 586.332 608.376 628.377 639.382 657.367 680.358 690.36 720.404 + + + + +8 2 3 12 100 2 3 8 2 3 2 25 2 2 2 3 2 6 11 33 2 2 1 3 6 3 4 3 2 19 +2 8 1 3 6 7 4 3 2 56 6 5 13 3 6 2 5 3 2 2 24 2 2 5 2 2 4 3 3 1 +3 8 15 4 3 2 80 2 14 2 13 3 21 2 2 3 2 6 1 3 19 2 2 9 2 1 2 2 3 3 +2 6 3 2 2 12 5 2 5 3 + + + + + + +GRMZM2G046804_P01 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36880092..36884475:-1; parent_transcript=GRMZM2G046804_T01; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P02 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881035..36884475:-1; parent_transcript=GRMZM2G046804_T02; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P04 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T04; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P05 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T05; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P06 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T06; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P07 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881117..36884877:-1; parent_transcript=GRMZM2G046804_T07; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P08 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881357..36884877:-1; parent_transcript=GRMZM2G046804_T08; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P03 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884877:-1; parent_transcript=GRMZM2G046804_T03; parent_gene=GRMZM2G046804 + + + + + + + + +5.73728 +-0.29422 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6377 6377 6377 6262 5951 5530 5129 4591 2827 1911 823 364 193 88 52 33 13 5 1 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +6407 6407 6407 6292 5981 5527 5069 4410 2177 1359 234 7 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3300 2707 360 38 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1122 3840 1148 229 35 8 6 21 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3092 (charge 2) + +1010.52 +2 + + +153.066 153.103 154.05 155.081 156.077 157.097 158.092 159.077 159.113 167.055 169.097 169.133 171.076 171.112 173.093 173.129 175.119 176.071 178.086 181.061 181.097 185.092 186.124 187.108 188.071 188.103 189.087 193.097 194.101 194.129 +197.128 198.087 199.071 199.108 200.14 201.123 205.098 209.092 213.087 216.098 217.082 221.091 223.108 226.155 227.103 231.115 233.092 241.081 242.186 245.077 249.123 251.102 255.145 257.197 272.173 275.208 284.171 293.113 299.063 301.058 +312.698 316.13 333.189 336.177 345.182 351.166 358.162 360.235 366.202 377.221 380.149 388.292 398.216 400.701 408.14 418.995 431.273 441.732 448.221 453.22 466.245 468.295 477.163 493.23 495.172 497.262 503.318 535.242 560.314 614.355 +632.362 636.298 689.359 712.361 737.347 740.371 795.423 818.406 882.453 906.437 + + + + +4 4 4 8 4 6 9 10 9 9 5 6 26 6 4 4 47 5 6 4 4 5 7 7 4 4 17 69 11 3 +5 13 5 5 4 8 8 3 5 21 12 14 100 12 6 6 5 10 16 15 9 29 12 10 10 40 4 8 5 6 +8 4 8 4 3 5 4 6 4 11 5 21 11 4 24 14 11 7 5 7 4 16 4 5 20 5 17 7 8 7 +29 5 9 6 6 4 13 4 15 4 + + + + + + +GRMZM2G169160_P01 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666220..5677820:-1; parent_transcript=GRMZM2G169160_T01; parent_gene=GRMZM2G169160 + + + + + + + +GRMZM2G169160_P03 B6TBG7 Seryl-tRNA synthetase seq=translation; coord=4:5666399..5677820:-1; parent_transcript=GRMZM2G169160_T03; parent_gene=GRMZM2G169160 + + + + + + + + +7.34576 +-0.326478 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +11977 11977 11977 11806 11332 10769 9295 7566 5644 3726 2179 1290 711 345 172 91 40 8 3 2 2 1 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +11984 11984 11984 11813 11339 10739 9159 7166 4613 2131 659 231 60 12 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +4460 4605 2198 569 123 29 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1768 5148 3375 1220 355 92 21 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3093 (charge 3) + +1533.76 +3 + + +152.034 155.082 157.061 157.097 158.092 159.077 167.082 167.118 169.061 169.097 171.076 171.113 173.092 175.072 175.119 181.061 181.097 183.149 185.092 186.087 189.087 195.112 197.129 198.087 199.072 199.108 199.181 204.135 209.091 211.143 +216.098 217.082 223.108 225.172 226.155 230.149 234.145 238.635 240.135 244.166 248.161 251.103 258.144 268.165 275.207 283.177 286.143 287.162 296.124 301.187 303.145 310.666 320.172 335.194 355.16 359.193 398.208 414.271 418.237 424.256 +436.239 470.219 476.259 486.246 493.314 504.258 505.262 510.257 513.333 523.273 548.283 565.239 575.314 589.284 602.318 605.304 620.325 622.333 631.321 646.384 649.331 660.345 663.346 670.331 676.37 688.342 689.351 717.378 720.401 726.412 +748.4 789.39 791.407 814.426 817.385 819.39 828.411 848.461 876.454 896.467 + + + + +4 17 5 14 5 5 11 4 8 5 8 4 6 5 23 6 6 22 16 5 8 4 4 3 7 9 6 4 6 6 +5 9 10 4 20 5 14 4 9 34 7 4 17 10 4 8 5 4 4 100 30 12 20 9 4 29 5 16 5 11 +6 5 7 10 7 34 14 4 5 15 22 5 4 10 5 4 56 5 6 6 18 11 12 25 9 15 5 38 12 4 +12 30 4 5 24 5 4 3 7 4 + + + + + + +GRMZM2G023591_P01 NP_001150253 ribonucleoprotein seq=translation; coord=1:182100287..182102156:-1; parent_transcript=GRMZM2G023591_T01; parent_gene=GRMZM2G023591 + + + MALALPLARL VPACQCQPWP HLRFRKRHVS FAAHASSRAA FAACAAAPAL + QVQAPEAEAE AETVEQVGPK TRLVAQNIPW DCTADEMRAL FESHGSVVGV + ELSMYSANKN RGLAFVTMGS EEEALAALTH LNSTILNDRK IKVDFARPRK + KQPKQPAVVS DDTEKYVVFV GNLTWRVRNR HLRELFASAP GVVSAEVIFH + TTTPRRSAGY AFVSFSSKES AGAAISAFNG KILMGRPINV MFKDENGEKN + EPSSVPKKAE VEPSDDQSDK LSMNC + + + + + +GRMZM2G023591_P02 NP_001150253 ribonucleoprotein seq=translation; coord=1:182100190..182102107:-1; parent_transcript=GRMZM2G023591_T02; parent_gene=GRMZM2G023591 + + + MALALPLARL VPACQCQPWP HLRFRKRHVS FAAHASSRAA FAACAAAPAL + QVQAPEAEAE AETVEQVGPK TRLVAQNIPW DCTADEMRAL FESHGSVVGV + ELSMYSANKN RGLAFVTMGS EEEALAALTH LNSTILNDRK IKVDFARPRK + KQPKQPAVVS DDTEKCGIS + + + + + + +5.07798 +-0.307756 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +5662 5662 5662 5596 5402 5088 4733 3162 2507 1434 687 292 119 55 10 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5658 5658 5658 5592 5396 5080 4671 3047 2066 719 121 12 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2700 2722 226 11 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1419 3048 982 209 6 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3094 (charge 2) + +1188.57 +2 + + +155.081 157.061 157.097 158.092 159.076 159.113 161.092 167.056 168.055 169.097 171.077 171.113 171.149 173.092 175.072 175.119 180.113 181.061 181.097 183.076 185.092 186.088 186.123 187.072 187.107 189.087 195.09 197.104 197.128 198.088 +198.125 199.071 199.108 200.103 201.123 203.066 208.108 212.103 217.081 221.085 226.154 227.103 232.14 239.095 241.094 244.165 252.134 255.146 258.144 268.978 272.171 276.155 280.13 282.053 285.01 286.01 299.062 301.06 303.02 305.019 +309.204 314.1 317.181 344.977 346.974 351.202 356.07 357.068 374.081 375.078 377.203 379.197 401.131 417.034 419.996 420.993 430.238 470.262 474.224 477.284 492.226 501.277 510.233 530.171 554.322 564.307 572.313 585.786 586.787 607.256 +629.245 631.768 673.297 676.275 679.348 694.288 793.358 795.365 877.401 963.469 + + + + +12 8 7 8 7 6 5 38 9 17 12 18 7 6 3 34 16 8 23 5 6 3 3 7 11 5 2 3 3 2 +7 10 11 8 6 6 46 3 5 8 19 8 33 68 14 7 20 8 22 12 9 11 8 2 100 57 53 19 23 11 +75 3 9 8 3 38 85 58 11 5 24 12 6 3 18 15 6 5 5 3 11 5 2 3 7 11 6 18 6 6 +3 3 3 2 10 34 33 10 3 10 + + + + + + +GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01; parent_gene=GRMZM5G815453 + + + + + + + +GRMZM2G448344_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=1:203925927..203931405:-1; parent_transcript=GRMZM2G448344_T01; parent_gene=GRMZM2G448344 + + + + + + + +GRMZM2G385635_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=2:200096578..200100853:-1; parent_transcript=GRMZM2G385635_T01; parent_gene=GRMZM2G385635 + + + + + + + +GRMZM2G360821_P01 P00874 Ribulose bisphosphate carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) seq=translation; coord=6:160783975..160786062:1; parent_transcript=GRMZM2G360821_T01; parent_gene=GRMZM2G360821 + + + + + + + +GRMZM2G308907_P01 seq=translation; coord=9:32379686..32380603:1; parent_transcript=GRMZM2G308907_T01; parent_gene=GRMZM2G308907 + + + + + + + +GRMZM2G115168_P01 seq=translation; coord=1:131325136..131327527:1; parent_transcript=GRMZM2G115168_T01; parent_gene=GRMZM2G115168 + + + + + + + + +8.14446 +-0.397291 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +7819 7819 7819 7819 7410 7062 6469 5268 3852 2252 1092 523 230 81 13 4 3 3 2 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7832 7832 7832 7832 7423 7020 6382 5058 3324 1387 256 61 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2818 3025 1385 459 132 12 1 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1473 3921 1945 401 79 11 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3098 (charge 3) + +1481.72 +3 + + +155.081 156.077 157.097 157.133 158.092 159.077 166.062 169.097 169.134 171.076 171.113 171.15 173.092 173.128 175.119 181.096 183.15 185.092 186.124 187.108 191.085 199.108 201.123 204.134 205.137 208.108 215.139 219.08 223.156 225.098 +228.098 235.119 240.135 244.166 249.161 251.15 253.093 258.145 267.109 282.187 301.187 303.203 327.167 331.678 339.139 345.176 365.155 367.135 415.679 422.69 426.173 436.158 452.219 454.167 457.196 461.207 464.218 466.203 475.208 480.22 +482.237 486.292 495.835 501.741 510.748 515.74 517.791 521.248 524.743 527.293 539.259 549.247 555.323 560.347 563.295 565.3 567.254 581.305 617.276 632.325 647.377 676.336 704.307 718.312 766.416 784.431 791.342 844.366 847.353 862.385 +897.518 905.461 931.401 933.429 949.417 984.409 1020.48 1030.48 1048.49 1081.46 + + + + +10 5 5 5 9 7 8 13 12 5 6 7 17 9 39 7 6 4 28 13 43 6 14 100 8 5 5 14 10 15 +7 9 12 7 8 12 6 8 5 5 11 34 7 5 9 5 6 15 5 11 18 8 10 31 8 6 6 32 20 10 +13 6 17 8 10 6 6 5 5 5 17 5 5 6 6 7 22 11 6 7 13 12 15 10 5 27 6 8 10 5 +7 5 15 5 10 5 5 8 7 5 + + + + + + +GRMZM5G838129_P01 seq=translation; coord=5:205580677..205582732:-1; parent_transcript=GRMZM5G838129_T01; parent_gene=GRMZM5G838129 + + + MAKEPSRLCV EEVHRVLLDI VNAAANATPG LGRYPPFKRE VIAIASNALD + AFKSDAKKMV VALVDMERAF VPPQHFIRLV QRRMERQRRE DELKNNRSSK + KGQDAELSKM NRASSPQTGS DEAGGNLKSM KDKSNKQDND TKEGPNLQVA + GPGGEITAGY LLKKSAKNNE WSKR + + + + + + +5.34953 +-0.305687 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +6158 6158 6158 6151 4587 4176 2730 2097 1304 769 476 324 88 23 10 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6160 6160 6160 6153 4589 3989 2593 1664 881 454 306 195 19 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3741 2087 321 11 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1225 3893 923 114 2 2 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3099 (charge 2) + +1518.7 +2 + + +150.13 155.081 157.061 157.097 159.076 166.63 167.055 167.081 171.113 172.345 175.119 181.097 183.078 185.092 187.742 195.076 198.123 199.108 209.093 212.104 216.134 226.119 228.098 229.093 239.094 242.113 244.13 246.156 252.099 260.196 +270.107 283.137 295.141 299.062 309.156 313.152 316.116 323.136 325.151 327.167 345.139 352.162 355.071 357.211 359.028 361.028 374.239 431.262 453.203 488.284 559.32 579.775 582.218 586.251 628.792 637.307 688.366 705.42 764.346 803.384 +890.416 902.385 947.441 952.432 1030.49 1048.49 1159.52 1176.54 1274.59 + + + + +4 4 5 20 8 4 15 5 4 4 6 4 4 22 3 5 31 9 6 6 8 100 20 6 7 5 5 6 4 18 +4 5 24 35 9 8 5 4 6 18 6 5 7 6 21 5 6 7 5 38 42 8 5 7 20 20 28 6 9 16 +20 5 50 5 12 81 19 5 7 + + + + + + +GRMZM5G821637_P04 NP_001140813 hypothetical protein LOC100272888 seq=translation; coord=1:298687651..298689984:1; parent_transcript=GRMZM5G821637_T04; parent_gene=GRMZM5G821637 + + + + + + + +GRMZM5G821637_P05 NP_001140813 hypothetical protein LOC100272888 seq=translation; coord=1:298687651..298689984:1; parent_transcript=GRMZM5G821637_T05; parent_gene=GRMZM5G821637 + + + + + + + + +5.00965 +-0.270792 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 + + + + +1492 1492 1492 1492 1426 1297 937 768 368 214 126 66 31 13 12 5 4 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +1493 1493 1493 1493 1427 1294 922 737 290 96 34 4 1 0 + + + + + + +0 1 2 3 4 + + + + +897 526 68 9 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +425 838 193 27 8 1 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3100 (charge 2) + +1735.72 +2 + + +152.057 157.134 158.092 171.077 175.119 183.148 185.128 215.115 226.118 232.141 234.146 236.89 240.134 244.093 248.383 272.124 275.103 291.166 311.17 343.161 350.135 407.155 420.227 448.215 461.21 474.267 488.168 518.23 528.316 563.24 +595.304 605.265 606.841 654.288 662.833 699.378 711.785 742.318 748.862 776.309 813.361 821.333 823.324 827.878 870.441 936.36 1056.45 1064.45 1179.47 1201.52 1307.54 1402.8 1422.57 + + + + +4 44 6 3 23 3 30 4 7 65 6 4 8 5 4 24 11 11 22 10 24 20 5 43 6 33 8 7 34 11 +8 21 5 7 100 9 11 20 21 6 9 27 8 19 44 36 10 9 25 8 10 7 24 + + + + + + +GRMZM2G109448_P01 B6T101 Histone H2A seq=translation; coord=7:143296604..143298282:-1; parent_transcript=GRMZM2G109448_T01; parent_gene=GRMZM2G109448 + + + MDASGAGSKA KKGAAGRKAG GPRKKSVSRS VKAGLQFPVG RIGRYLKKGR + YAQRVGTGAP VYLAAVLEYL AAEVLELAGN AAKDNKKTRI VPRHVLLAIR + NDVELGKLLA GVTIAHGGVL PNINPVLLPK KVAEKASSGG SKESKSPKKA + AKSPKKAAKS PKKA + + + + + + + +5.12891 +-0.29308 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + + + + +1794 1794 1794 1695 1590 1439 1299 1042 871 380 239 123 56 25 10 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +1801 1801 1801 1702 1597 1429 1256 995 555 227 61 14 1 0 + + + + + + +0 1 2 3 4 5 + + + + +983 731 88 8 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +331 909 451 91 21 2 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3103 (charge 2) + +865.372 +2 + + +153.102 155.081 157.097 157.109 157.134 158.092 159.077 166.061 167.081 169.097 171.076 171.113 172.108 173.091 173.129 174.058 175.061 175.119 181.097 185.092 185.165 186.095 187.072 190.061 191.084 193.098 194.649 195.076 198.087 199.072 +199.108 201.123 207.089 212.139 213.087 216.134 218.056 223.108 224.114 226.119 228.134 232.141 234.145 235.146 237.637 240.135 244.166 251.103 255.145 257.653 267.109 272.173 273.121 275.208 279.098 288.203 289.207 291.166 306.167 312.167 +331.687 342.141 345.225 347.099 362.204 364.123 369.189 377.214 381.151 387.201 393.86 403.23 413.174 419.226 426.211 443.236 454.238 460.256 464.244 474.267 476.139 488.247 493.17 506.258 510.196 514.274 531.331 577.295 589.293 594.302 +605.184 611.326 632.365 639.236 645.333 662.36 674.31 682.361 692.32 732.365 + + + + +4 7 8 3 3 14 21 5 3 14 4 3 2 4 5 52 3 42 3 100 5 5 10 2 8 3 2 3 5 3 +5 8 6 5 4 5 4 22 5 8 5 4 15 3 3 7 3 33 8 3 5 4 3 5 4 71 6 21 16 6 +4 4 15 3 8 4 3 3 5 4 3 20 3 13 4 19 4 4 4 23 3 3 3 22 4 22 8 8 3 4 +3 47 4 2 5 3 3 3 12 4 + + + + + + +GRMZM2G135498_P01 NP_001149639 3-oxoacyl-synthase I seq=translation; coord=6:107821435..107825807:-1; parent_transcript=GRMZM2G135498_T01; parent_gene=GRMZM2G135498 + + + MQSLLLPTAA VAPVAPPCGR RNLPGRLSVR ASATVVAAPR RETDPKKRVV + ITGMGLVSVF GNDVDAYYDR LLVGESGIGP IDRFDASKFP TRFAGQIRGF + SSEGYIDGKN DRRLDDCLRY CIVSGKKALE ASGIAHGSKP MEKIDKTRAG + VLVGTGMGGL TVFSDGVQNL IEKGYRKITP FFIPYAITNM GSALLGMDIG + FMGPNYSIST ACATSNYCFY AAANHIRRGE ADIMIAGGTE AAIIPIGVGG + FVACRALSQR NDDPKTASRP WDKDRDGFVM GEGAGVLVME SLEHAMKRDA + PIIAEYLGGA VNCDAYHMTD PRSDGLGVSS CIKQSLKDAG VAPEEVNYIN + AHATSTLAGD LAEVNAIKQV FKDPSGIKIN ATKSMIGHCL GAAGGLEAIA + TIKAITTGWV HPSINQFNPE EAVEFDTVPN VKKQHEVNVG ISNSFGFGGH + NSVVVFAPFK P + + + + + + + +5.96891 +-0.277624 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +11946 11946 11946 11820 11495 10905 10196 8675 7151 4826 3038 1728 888 521 303 166 81 35 8 4 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +11931 11931 11931 11805 11480 10835 10030 8215 6038 3012 897 350 35 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3507 4975 2315 868 248 24 9 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1981 4857 3179 1409 337 154 28 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3104 (charge 3) + +1641.83 +3 + + +155.082 157.098 157.134 158.093 158.137 159.077 166.061 171.077 171.113 173.092 175.119 176.123 181.096 183.077 185.092 185.129 185.165 187.108 195.089 195.113 197.129 198.087 199.072 199.108 199.181 209.105 213.087 215.139 223.108 226.155 +235.119 240.134 243.133 244.166 258.145 262.15 266.124 270.108 272.172 274.13 276.156 301.187 309.119 311.172 314.172 327.129 329.182 345.141 359.198 375.229 392.196 410.215 412.219 433.231 438.239 452.252 456.245 465.23 468.748 478.774 +481.251 500.748 520.241 522.237 531.318 538.3 564.31 582.319 597.321 602.306 620.313 621.321 629.312 632.834 664.833 673.375 688.855 697.857 701.378 702.381 719.387 728.393 729.393 731.429 737.335 738.341 772.447 792.394 800.433 801.449 +840.468 849.36 859.491 865.378 866.362 868.382 929.452 936.496 956.542 1000.49 + + + + +17 11 100 6 10 6 5 3 5 10 33 5 5 6 6 36 3 5 9 3 3 5 3 12 35 10 6 11 19 23 +47 12 9 8 40 3 7 6 10 12 18 7 7 3 6 11 5 6 5 13 5 6 10 9 8 7 22 12 8 8 +6 10 24 12 9 12 6 3 8 9 14 5 8 8 5 6 5 7 16 10 11 20 10 3 13 3 6 20 8 3 +3 8 12 10 24 5 15 13 10 6 + + + + + + +GRMZM5G876898_P01 NP_001145825 hypothetical protein LOC100279332 seq=translation; coord=2:8906086..8909067:-1; parent_transcript=GRMZM5G876898_T01; parent_gene=GRMZM5G876898 + + + MRGLLACATL ARRAAASSAP ARVRHLAGAA EAAEAELKRT ALYDFHVAHG + GKMVPFAGWS MPIQYRDSIM DSTVNCRANG SLFDVAHMCG LSLKGRGAIP + FLESLVVADV AALRDGTGTL TVFTNEQGGA IDDSVIAKVT DHHIYLVVNA + GCRDKDLAHI EAHMEAFNKK GGDVKWHIHD DRSLLALQGP LAAPTLQLLT + KEDLSKMYFS DFKMIDINGY ACFLTRTGYT GEDGFEISVP SENAVDLAEA + ILERSEGKVR LTGLGARDSL RLEAGLCLYG NDMEQHITPV EAGLSWAIGK + RRRAEGGFLG ADVILKQLQE GPKIRRVGMV TQGPPARSHS ELVSGSGERI + GEVTSGGFSP CLKKNIAMGY VKSGMHKAGT ELKVVVRGKS YDAVVTKMPF + VPTKYYKPS + + + + + + +GRMZM5G876898_P02 NP_001145825 hypothetical protein LOC100279332 seq=translation; coord=2:8906080..8909067:-1; parent_transcript=GRMZM5G876898_T02; parent_gene=GRMZM5G876898 + + + MRGLLACATL ARRAAASSAP ARVRHLAGAA EAAEAELKRT ALYDFHVAHG + GKMVPFAGWS MPIQYRDSIM DSTVNCRANG SLFDVAHMCG LSLKGRGAIP + FLESLVVADV AALRDGTGTL TVFTNEQGGA IDDSVIAKVT DHHIYLVVNA + GCRDKDLAHI EAHMEAFNKK GGDVKWHIHD DRSLLALQGP LAAPTLQLLT + KEDLSKMYFS DFKMIDINGY ACFLTRTGYH FDSLSPLFEQ YCKDCLISYF + SYTGEDGFEI SVPSENAVDL AEAILERSEG KVRLTGLGAR DSLRLEAGLC + LYGNDMEQHI TPVEAGLSWA IGKRRRAEGG FLGADVILKQ LQEGPKIRRV + GMVTQGPPAR SHSELVSGSG ERIGEVTSGG FSPCLKKNIA MGYVKSGMHK + AGTELKVVVR GKSYDAVVTK MPFVPTKYYK PS + + + + + + + +6.6667 +-0.310079 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +7070 7070 7070 6988 6832 6506 6230 5612 4491 3800 2426 1533 844 512 231 120 51 14 6 2 1 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7070 7070 7070 6988 6832 6488 6181 5476 4208 3089 1510 457 121 12 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +3232 2872 819 127 25 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1164 4017 1457 396 35 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3105 (charge 2) + +1128.58 +2 + + +152.057 154.086 155.082 155.118 157.097 157.108 157.133 158.093 159.076 166.062 167.082 169.097 169.134 171.113 173.092 173.128 175.119 176.123 181.097 183.113 185.091 186.088 187.071 187.108 188.037 194.129 195.075 195.113 198.124 199.108 +199.125 199.181 201.123 205.064 209.092 211.107 213.088 216.134 218.15 219.117 226.155 227.102 229.118 234.145 240.134 242.15 244.166 248.161 254.15 258.108 270.107 272.172 284.16 287.137 304.133 311.208 324.155 327.129 332.16 341.184 +343.208 355.197 375.206 383.195 387.168 391.197 394.692 397.209 402.211 419.192 422.211 440.261 446.232 450.222 452.247 468.251 470.26 480.256 497.283 517.276 547.28 563.781 566.301 608.314 625.342 628.329 629.332 631.34 682.36 705.427 +709.366 726.39 728.392 746.372 789.382 808.439 825.457 827.462 900.437 965.508 + + + + +4 8 25 15 29 6 8 13 11 4 7 77 7 4 13 7 70 4 10 41 13 9 8 11 17 4 4 8 10 47 +4 8 71 34 10 16 16 9 17 25 100 35 27 28 29 8 27 11 4 8 17 17 4 8 58 8 7 8 22 5 +8 11 8 14 4 4 9 22 14 9 14 39 14 4 11 17 4 10 64 9 12 8 4 17 42 8 4 14 8 4 +9 82 9 17 8 4 35 4 4 12 + + + + + + +GRMZM5G859592_P01 seq=translation; coord=1:248587698..248589524:-1; parent_transcript=GRMZM5G859592_T01; parent_gene=GRMZM5G859592 + + + + + + + + +4.02328 +-0.243835 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +1729 1729 1729 1729 1423 1293 1163 887 764 494 366 220 88 26 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1735 1735 1735 1735 1429 1297 1094 878 691 467 235 149 21 1 0 + + + + + + +0 1 2 3 4 + + + + +825 694 204 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +535 974 210 12 1 0 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3108 (charge 2) + +1565.65 +2 + + +152.057 171.077 173.128 175.118 183.113 185.091 187.072 189.087 199.071 201.124 203.103 208.526 213.087 217.082 227.067 229.118 231.098 241.082 245.077 258.144 274.102 276.156 284.122 300.155 302.098 312.156 328.113 338.099 346.125 356.109 +374.119 377.204 457.158 461.15 492.23 531.717 549.252 556.222 620.288 674.208 677.309 740.377 757.701 761.028 775.373 784.428 790.43 806.36 863.377 974.412 992.416 1107.44 + + + + +11 10 38 5 53 6 14 33 28 38 36 5 8 56 10 6 13 49 42 28 9 12 6 82 9 40 10 6 12 37 +7 52 6 9 11 7 58 7 12 9 100 8 9 7 8 9 7 13 79 11 14 27 + + + + + + +GRMZM2G025227_P02 NM_001175054 hypothetical protein LOC100382305 (LOC100382305), mRNA seq=translation; coord=5:1457568..1462915:1; parent_transcript=GRMZM2G025227_T02; parent_gene=GRMZM2G025227 + + + MAEATDTAAA TPPPAPAMAT LSPPPKSGIP PRYNLDAKWD ACLDLSIRRV + AYSSLAGALA GLLLFRSPTT RWASVTLGAG VGIGAAYTEC SYLFSGGPPN + WSPKVSTIPS AHSEGEDK + + + + + + +8.46865 +-0.376384 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +6509 6509 6509 6509 6509 6384 6123 5785 5000 3932 2962 1719 946 495 214 93 41 7 3 2 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +6527 6527 6527 6527 6527 6402 6141 5757 4933 3628 2273 772 227 75 22 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2067 2766 1227 314 132 19 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1323 2717 1662 657 143 14 8 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3113 (charge 3) + +1456.69 +3 + + +155.082 157.098 157.133 158.092 159.077 159.113 161.092 167.081 169.097 169.134 171.076 171.113 171.149 173.092 173.128 175.119 181.109 183.077 183.113 183.149 185.092 185.165 187.071 187.108 187.144 188.147 189.087 194.129 197.129 199.107 +200.103 201.124 209.104 211.144 213.086 216.133 217.082 223.107 226.119 227.102 230.113 232.14 234.145 238.154 240.134 244.167 252.135 256.128 258.109 262.14 270.145 272.173 283.139 296.134 298.176 304.162 306.119 324.13 328.167 365.191 +371.683 383.697 389.195 393.188 401.173 444.282 448.204 480.213 515.323 518.271 520.228 528.733 542.301 577.247 591.246 604.334 609.254 614.306 635.245 643.381 649.333 664.276 666.286 669.337 714.414 732.428 742.36 749.353 758.408 766.389 +782.313 795.325 801.336 837.432 850.431 872.367 910.35 959.402 1056.46 1058.47 + + + + +30 32 12 21 58 70 11 23 42 28 33 21 42 30 14 83 57 14 11 31 28 31 96 35 98 10 24 11 20 12 +18 17 77 19 15 18 14 16 33 12 15 12 44 21 18 17 23 16 63 49 38 16 13 11 19 12 10 11 20 24 +20 14 10 18 23 100 19 24 18 24 13 66 12 16 13 15 17 36 39 61 15 66 11 23 26 24 21 11 22 83 +33 20 37 15 12 24 19 28 63 12 + + + + + + +GRMZM2G039396_P01 NP_001105564 protoporphyrinogen IX oxidase seq=translation; coord=8:876212..882478:-1; parent_transcript=GRMZM2G039396_T01; parent_gene=GRMZM2G039396 + + + MVAATATATA MATAASPLLN GTRIPARLRH RGLSVRCAAV AGGAAEAPAS + TGARLSADCV VVGGGISGLC TAQALATRHG VGDVLVTEAR ARPGGNITTV + ERPEEGYLWE EGPNSFQPSD PVLTMAVDSG LKDDLVFGDP NAPRFVLWEG + KLRPVPSKPA DLPFFDLMSI PGKLRAGLGA LGIRPPPPGR EESVEEFVRR + NLGAEVFERL IEPFCSGVYA GDPSKLSMKA AFGKVWRLEE TGGSIIGGTI + KTIQERSKNP KPPRDARLPK PKGQTVASFR KGLAMLPNAI TSSLGSKVKL + SWKLTSITKS DDKGYVLEYE TPEGVVSVQA KSVIMTIPSY VASNILRPLS + SDAADALSRF YYPPVAAVTV SYPKEAIRKE CLIDGELQGF GQLHPRSQGV + ETLGTIYSSS LFPNRAPDGR VLLLNYIGGA TNTGIVSKTE SELVEAVDRD + LRKMLINSTA VDPLVLGVRV WPQAIPQFLV GHLDLLEAAK AALDRGGYDG + LFLGGNYVAG VALGRCVEGA YESASQISDF LTKYAYK + + + + + + +5.32059 +-0.259541 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 + + + + +6568 6568 6520 6239 5954 5675 5311 3882 3234 1807 1108 675 375 232 121 47 22 11 7 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6569 6569 6521 6240 5950 5631 5189 3559 2611 1151 492 167 47 12 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2725 2840 867 118 22 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1534 3791 1010 202 28 6 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3114 (charge 2) + +1356.69 +2 + + +152.057 155.082 157.097 158.092 159.077 161.092 167.081 169.061 169.097 169.134 171.076 171.113 172.116 173.092 175.119 183.113 183.149 185.093 186.087 187.072 187.09 187.107 189.087 197.092 197.129 199.072 200.104 201.087 212.103 224.103 +227.103 229.13 232.141 239.151 240.135 242.15 244.093 252.097 254.15 257.125 259.093 268.165 270.109 272.125 283.14 286.151 298.104 300.166 303.178 306.159 309.118 311.171 316.113 328.161 330.178 337.115 341.147 343.163 355.125 368.156 +371.202 374.215 382.21 386.167 399.197 404.225 412.182 414.247 427.23 438.272 445.252 457.201 474.231 491.257 528.24 562.293 599.315 634.33 642.323 657.331 659.347 661.349 713.349 728.366 730.384 732.388 841.421 857.411 859.428 861.428 +912.444 930.465 932.472 986.452 1001.51 1012.39 1043.47 1058.52 1115.54 1186.58 + + + + +7 8 3 12 9 7 5 13 11 5 3 60 2 8 35 4 2 5 34 34 2 9 5 2 8 2 7 13 10 2 +8 26 6 2 5 10 2 3 3 41 3 5 5 13 14 5 13 14 7 2 4 9 7 33 5 3 5 3 8 10 +2 3 11 3 6 3 7 5 8 5 28 9 2 3 3 5 3 5 8 42 100 5 5 20 62 4 4 19 40 6 +3 48 4 3 12 2 7 13 22 17 + + + + + + +GRMZM2G079538_P01 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110621503..110626726:1; parent_transcript=GRMZM2G079538_T01; parent_gene=GRMZM2G079538 + + + + + + + +GRMZM2G079538_P02 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110620918..110626719:1; parent_transcript=GRMZM2G079538_T02; parent_gene=GRMZM2G079538 + + + + + + + +GRMZM2G079538_P03 NP_001147014 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=10:110621503..110626716:1; parent_transcript=GRMZM2G079538_T03; parent_gene=GRMZM2G079538 + + + + + + + +GRMZM5G807639_P03 NP_001150636 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=2:66624116..66641809:-1; parent_transcript=GRMZM5G807639_T03; parent_gene=GRMZM5G807639 + + + + + + + +GRMZM5G807639_P02 NP_001150636 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex seq=translation; coord=2:66624116..66641809:-1; parent_transcript=GRMZM5G807639_T02; parent_gene=GRMZM5G807639 + + + + + + + + +5.97758 +-0.254365 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +9980 9980 9980 9980 9689 9003 7961 6511 4855 3549 2160 1323 765 465 190 102 60 38 16 12 5 3 1 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +9969 9969 9969 9969 9678 8985 7828 5741 3481 1639 639 97 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2558 3922 2368 801 287 50 4 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1788 4042 2704 1021 335 71 15 15 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3119 (charge 3) + +1839.87 +3 + + +157.097 159.076 162.103 169.097 175.119 176.103 181.097 183.076 185.092 190.097 193.095 200.103 201.087 209.092 216.134 221.092 234.145 237.134 239.114 242.15 268.627 284.124 287.135 290.161 296.125 298.14 309.653 314.134 318.16 323.651 +335.193 338.182 350.146 368.156 373.182 381.178 388.218 399.189 406.229 409.22 411.198 424.702 439.187 443.177 467.232 486.219 490.24 492.219 508.251 510.259 514.214 518.235 536.246 537.248 559.295 574.762 578.287 585.247 597.25 607.321 +609.3 615.26 617.308 619.284 629.264 635.314 647.281 648.285 664.315 678.357 684.312 687.356 688.349 706.352 718.354 729.352 746.348 747.352 751.346 752.349 777.375 786.425 817.385 818.393 830.387 833.401 848.398 850.404 857.465 901.424 +905.433 906.435 919.436 921.442 985.518 1018.5 1020.5 1155.57 1219.57 1256.62 + + + + +5 76 9 29 8 16 7 7 7 7 9 15 10 9 13 5 46 12 24 9 6 6 15 8 8 23 12 13 6 15 +35 25 8 10 5 13 8 16 32 9 5 15 8 20 6 6 7 6 30 9 22 14 57 16 6 8 11 8 12 16 +8 6 7 8 7 41 26 8 11 8 6 19 12 39 9 7 22 7 23 8 30 11 23 17 14 11 100 11 10 10 +11 6 90 12 11 39 8 14 6 6 + + + + + + +GRMZM2G087570_P01 seq=translation; coord=6:44382950..44385913:-1; parent_transcript=GRMZM2G087570_T01; parent_gene=GRMZM2G087570 + + + + + + + +GRMZM2G076544_P01 NP_001149265 peptidyl-prolyl cis-trans isomerase seq=translation; coord=8:135138380..135140767:-1; parent_transcript=GRMZM2G076544_T01; parent_gene=GRMZM2G076544 + + + + + + + + +6.48184 +-0.35037 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +5965 5965 5915 5783 5476 5048 4868 2505 1816 694 397 139 61 20 19 4 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5968 5968 5918 5783 5450 4969 4758 2285 1553 439 55 27 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3528 2115 289 39 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1090 4112 656 100 10 0 0 5 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3120 (charge 2) + +1090.54 +2 + + +157.109 158.092 171.076 175.119 176.123 181.061 187.144 189.087 195.076 197.128 198.087 199.072 199.18 213.087 215.139 217.081 227.175 228.178 231.097 241.081 243.133 258.109 273.119 275.207 290.146 309.119 315.646 327.129 342.132 345.139 +374.164 391.193 456.17 474.184 502.225 520.237 574.263 631.267 648.293 718.308 735.326 737.329 820.344 846.357 848.355 864.368 866.374 977.453 + + + + +1 5 3 34 3 1 5 2 1 2 2 4 100 2 12 2 20 3 2 3 7 2 2 3 3 4 1 4 1 2 +2 10 2 1 2 8 1 4 4 2 24 2 1 9 1 38 4 4 + + + + + + +GRMZM2G001327_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695861:-1; parent_transcript=GRMZM2G001327_T01; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G001327_P03 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695738:-1; parent_transcript=GRMZM2G001327_T03; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G154218_P01 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515921..136519080:-1; parent_transcript=GRMZM2G154218_T01; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G154218_P02 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515968..136519018:-1; parent_transcript=GRMZM2G154218_T02; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G149768_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136568621..136572271:-1; parent_transcript=GRMZM2G149768_T01; parent_gene=GRMZM2G149768 + + + + + + + +GRMZM2G110509_P01 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T01; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P02 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T02; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P03 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607316..84610225:1; parent_transcript=GRMZM2G110509_T03; parent_gene=GRMZM2G110509 + + + + + + + + +6.25024 +-0.337851 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +7690 7690 7600 7120 5924 4835 3445 2224 1275 622 357 170 84 19 11 3 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7664 7664 7568 7056 5761 4342 2551 1061 448 142 59 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2387 3027 1597 540 124 19 6 6 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1560 3443 1989 566 93 40 3 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3121 (charge 3) + +1335.65 +3 + + +155.081 157.061 157.097 158.093 159.076 166.061 167.055 168.056 169.052 169.097 171.076 171.113 174.088 175.119 177.102 178.106 181.109 183.113 185.056 187.107 192.076 195.113 198.123 200.139 202.082 205.097 209.104 216.134 218.15 223.063 +225.043 228.134 232.14 237.135 240.135 244.165 253.093 255.145 258.144 272.171 289.115 297.192 304.165 313.15 315.202 317.208 324.986 338.148 341.017 342.996 344.995 347.168 356.203 359.028 361.026 366.655 382.171 400.179 424.169 430.23 +437.713 456.258 467.191 473.212 481.232 517.254 532.234 545.257 560.232 585.26 603.273 615.325 630.237 647.261 659.37 673.357 701.276 718.3 737.315 760.381 815.347 817.367 857.397 874.422 886.385 961.459 1032.49 + + + + +1 3 1 1 5 2 37 5 2 8 1 13 2 5 95 10 3 1 1 3 2 1 2 3 5 18 5 4 13 5 +11 2 5 1 2 1 2 1 2 1 1 2 2 2 48 1 2 1 6 7 2 1 1 100 20 2 1 1 1 4 +2 3 1 1 4 3 2 4 4 1 2 1 2 8 1 3 1 10 1 6 1 3 1 3 1 5 1 + + + + + + +GRMZM5G849087_P01 seq=translation; coord=6:167749462..167750447:-1; parent_transcript=GRMZM5G849087_T01; parent_gene=GRMZM5G849087 + + + MAGSAADAEQ EQKRAAAAAY DYEGDARWAE YWSNVLVPPN LASRPDVVDH + LKRKFYQRYI DRNFNLVYYR KREKSLNFGE SQPKFVTLVR ILILL + + + + + + + +5.3598 +-0.274861 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 + + + + +5347 5347 5337 5283 5052 4698 4458 3120 2335 1312 726 384 210 104 61 28 10 5 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5287 5287 5277 5221 4982 4568 4238 2789 1606 653 158 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2723 2124 437 69 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +839 3274 943 253 38 3 0 17 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3123 (charge 2) + +1402.66 +2 + + +153.066 155.082 157.061 158.092 159.077 166.05 169.097 169.134 170.093 171.076 172.108 173.092 175.119 183.076 183.113 185.092 187.071 187.108 194.128 195.076 197.128 198.087 200.103 201.106 212.103 213.087 216.098 218.149 226.119 230.113 +240.098 242.112 244.131 258.108 269.16 283.14 287.135 297.155 299.171 301.151 303.213 311.135 312.138 315.202 316.205 323.134 325.187 329.145 333.188 345.141 368.193 372.224 373.228 384.148 386.205 394.171 400.185 402.163 416.25 431.272 +443.26 445.229 478.267 497.198 502.245 514.301 529.246 537.762 545.263 560.318 573.273 585.337 616.8 626.266 636.298 645.306 671.352 686.384 688.374 703.349 799.403 815.431 817.415 871.433 872.432 888.452 890.453 916.474 986.448 987.457 +997.528 1003.48 1005.47 1017.52 1057.5 1074.52 1076.51 1104.55 1145.55 1203.62 + + + + +6 13 2 2 10 9 3 4 2 26 6 7 36 30 2 6 7 8 4 2 3 19 97 9 8 4 8 2 10 24 +100 2 3 46 2 9 2 4 8 3 8 59 10 14 2 7 2 36 4 4 2 24 4 2 2 8 5 6 2 13 +18 2 2 4 7 12 2 7 4 12 5 8 2 2 2 4 8 9 23 19 4 7 22 4 2 41 3 10 5 2 +2 43 4 6 5 34 2 13 14 6 + + + + + + +GRMZM2G180399_P01 NP_001131336 hypothetical protein LOC100192652 seq=translation; coord=8:161837476..161841019:1; parent_transcript=GRMZM2G180399_T01; parent_gene=GRMZM2G180399 + + + MALRLHDVAL CLSPPLAARR RSGGSFVAVA SMTSAAVSTR VENKKPFAPP + REVHVQVTHS MPSHKIEIFK SLDDWARDNI LTHLKPVEKC WQPQDFLPDP + ASEGFHDEVK ELRERAKEIP DDYFVCLVGD MITEEALPTY QTMLNTLDGV + RDETGASPTA WAVWTRAWTA EENRHGDLLN KYMYLTGRVD MRQIEKTIQY + LIGSGMDPRT ENNPYLGFIY TSFQERATFI SHGNTARHAK DFGDLKLAQI + CGIIASDEKR HETAYTKIVE KLFEIDPDGT VVALADMMKK KISMPAHLMF + DGQDDKLFEH FSMVAQRLGV YTARDYADIL EFLVDRWKVA DLTGLSGEGN + KAQDYLCTLA SRIRRLDERA QSRAKKAGTL PFSWVYGREV QL + + + + + +GRMZM5G852502_P01 NP_001130573 hypothetical protein LOC100191672 seq=translation; coord=3:160666715..160671398:1; parent_transcript=GRMZM5G852502_T01; parent_gene=GRMZM5G852502 + + + MALRLNDVAL CLSPPLAARR RRSRSRSSGR FVAVASMTSA VSTKVENKKP + FAPPREVHVQ VTHSMPPHKI EIFKSLDDWA RDNILTHLKP VEKCWQPQDF + LPDPASEGFH DEVKELRERA KEIPDDYFVC LVGDMITEEA LPTYQTMLNT + LDGVRDETGA SPTAWAVWTR AWTAEENRHG DLLNKYMYLT GRVDMRQIEK + TIQYLIGSGM DPRTENNPYL GFIYTSFQER ATFISHGNTA RHAKDFGDLK + LAQICGIIAS DEKRHETAYT KIVEKLFEID PDGTVVALAD MMRKKISMPA + HLMFDGQDDK LFEHFSMVAQ RLGVYTARDY ADILEFLVDR WKVVNLTGLS + GEGNKAQDYL CTLASRIRRL EERAQSRAKK AGTLPFSWVY GRDVQL + + + + + +GRMZM2G027673_P01 NP_001140670 hypothetical protein LOC100272745 seq=translation; coord=4:102090319..102092193:-1; parent_transcript=GRMZM2G027673_T01; parent_gene=GRMZM2G027673 + + + MATVTSLSFS GSCRHGPRYT ARPAASSRSS QLLNDQLARA SRRLQVAAGM + AVAAFPSCGA FAPPCLVSTR RAFSSVVAMA SAAPVRAPSR KPFAPPREVH + RPVAHSLPPQ KREIFESLES WAADNILVLL KPVERSWQPQ DYLPDAASES + FDDEVRELRE RAREIPDDYF VCFVGDMVTE EALPTYQTML NTLDGGVRDE + TGASSTSWAV WTRAWAAEEN RHGDLMNKYL FLTGRVDMRQ IEKTVQYLIA + SGMDPKTETN PYMGFVYTSF QERATFISHG NTARHARRYG DTKLAQICGT + IAADEKRHES AYERIVEKLF EVDPDYTVRA FADTMRKKVA MPAHLMYDGQ + DDGLFARFSA VAQRIGVYTA RDYVDILEFL VRRWGVQELT GLSGEGRRAQ + EFVCELGPRF RRLEERAHDN KAKDPEFAPF SWIHGRQVQL + + + + + +GRMZM2G027673_P02 NP_001140670 hypothetical protein LOC100272745 seq=translation; coord=4:102090150..102092144:-1; parent_transcript=GRMZM2G027673_T02; parent_gene=GRMZM2G027673 + + + MAVAAFPSCG AFAPPCLVST RRAFSSVVAM ASAAPRKPFA PPREVHRPVA + HSLPPQKREI FESLESWAAD NILVLLKPVE RSWQPQDYLP DAASESFDDE + VRELRERARE IPDDYFVCFV GDMVTEEALP TYQTMLNTLD GGVRDETGAS + STSWAVWTRA WAAEENRHGD LMNKYLFLTG RVDMRQIEKT VQYLIASGMD + PKTETNPYMG FVYTSFQERA TFISHGNTAR HARRYGDTKL AQICGTIAAD + EKRHESAYER IVEKLFEVDP DYTVRAFADT MRKKVAMPAH LMYDGQDDGL + FARFSAVAQR IGVYTARDYV DILEFLVRRW GVQELTGLSG EGRRAQEFVC + ELGPRFRRLE ERAHDNKAKD PEFAPFSWIH GRQVQL + + + + + +GRMZM2G027673_P03 NP_001140670 hypothetical protein LOC100272745 seq=translation; coord=4:102090437..102092144:-1; parent_transcript=GRMZM2G027673_T03; parent_gene=GRMZM2G027673 + + + MAVAAFPSCG AFAPPCLVST RRAFSSVVAM ASAAPVRAPS RKPFAPPREV + HRPVAHSLPP QKREIFESLE SWAADNILVL LKPVERSWQP QDYLPDAASE + SFDDEVRELR ERAREIPDDY FVCFVGDMVT EEALPTYQTM LNTLDGGVRD + ETGASSTSWA VWTRAWAAEE NRHGDLMNKY LFLTGRVDMR QIEKTVQYLI + ASGMDPKTET NPYMGFVYTS FQERATFISH GNTARHARRY GDTKLAQICG + TIAADEKRHE SAYERIVEKL FEVDPDYTVR AFADTMRKKV AMPAHLMYDG + QDDGLFARFS AVAQRIGVYT ARDYVDILEF LVRRWGVQEL TGLSGEGRRA + QEFVCELGPR FRRLEERAHD NKAKDPEFAP FSWIHGRQVQ L + + + + + +GRMZM2G027673_P04 NP_001140670 hypothetical protein LOC100272745 seq=translation; coord=4:102090235..102091953:-1; parent_transcript=GRMZM2G027673_T04; parent_gene=GRMZM2G027673 + + + MVTEEALPTY QTMLNTLDGG VRDETGASST SWAVWTRAWA AEENRHGDLM + NKYLFLTGRV DMRQIEKTVQ YLIASGMDPK TETNPYMGFV YTSFQERATF + ISHGNTARHA RRYGDTKLAQ ICGTIAADEK RHESAYERIV EKLFEVDPDY + TVRAFADTMR KKVAMPAHLM YDGQDDGLFA RFSAVAQRIG VYTARDYVDI + LEFLVRRWGV QELTGLSGEG RRAQEFVCEL GPRFRRLEER AHDNKAKDPE + FAPFSWIHGR QVQL + + + + + + +6.55404 +-0.319709 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 + + + + +7889 7889 7689 7518 7073 6787 6203 5688 4108 3253 1524 978 354 149 68 40 20 6 2 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7905 7905 7705 7534 7073 6705 6063 5527 3694 2233 684 121 20 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3849 3409 573 80 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1338 4637 1580 294 38 13 0 16 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3124 (charge 2) + +1174.6 +2 + + +155.081 157.061 157.097 158.092 159.112 169.097 169.134 171.113 173.092 173.128 175.119 181.061 181.097 183.076 183.112 183.149 184.107 185.056 185.092 187.107 191.084 194.129 195.088 197.103 197.129 198.087 199.071 199.108 201.124 208.072 +212.139 216.098 218.15 221.128 225.099 226.153 229.129 233.165 240.135 242.149 244.166 246.156 249.122 254.078 257.128 261.16 269.161 272.087 274.155 276.137 282.118 291.165 295.104 302.15 309.132 313.115 315.202 318.149 320.16 326.148 +328.167 331.126 343.234 345.161 354.166 362.677 366.178 367.162 371.683 389.182 428.226 444.22 461.246 483.296 485.239 503.247 504.247 515.323 518.268 552.281 555.837 568.246 574.281 595.29 609.797 638.305 655.327 674.358 707.327 725.339 +729.426 731.437 742.359 744.367 753.395 761.345 802.419 855.443 965.482 1002.51 + + + + +18 8 2 15 5 9 4 16 28 26 70 5 3 2 3 5 2 7 5 6 3 5 5 6 3 5 6 7 16 7 +11 6 5 18 27 13 4 29 6 2 11 7 11 7 5 7 4 10 6 3 2 12 6 76 2 7 13 2 12 2 +40 2 2 2 6 4 5 5 23 5 9 3 6 5 4 17 5 3 65 2 7 2 8 2 7 6 44 2 2 7 +44 4 100 10 2 5 5 27 5 12 + + + + + + +GRMZM2G013342_P01 NP_001130880 hypothetical protein LOC100191984 seq=translation; coord=1:290448166..290449263:1; parent_transcript=GRMZM2G013342_T01; parent_gene=GRMZM2G013342 + + + MAMATQASAA TRHLLAAAWA PAAKPRQLSS QLALPSSSSR GPAPLRASTE + EAVEAPKGFV APQLDPSTPS PIFGGSTGGL LRKAQVEEFY VITWTSPKEQ + VFEMPTGGAA IMREGPNLLK LARKEQCLAL GTRLRSKYKI TYQFYRVFPN + GEVQYLHPKD GVYPEKVNPG REGVGQNFRS IGKNVNPIDV KFTGKATFD + + + + + + +6.85483 +-0.334382 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +6122 6122 6094 5871 5701 5485 5099 4766 3475 2194 1463 735 394 172 78 38 10 3 2 1 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6090 6090 6062 5839 5660 5428 4995 4653 2920 1668 522 154 46 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2817 2696 505 102 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1264 3289 1317 225 26 1 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3126 (charge 2) + +1060.52 +2 + + +152.057 153.102 155.081 155.154 156.077 157.061 157.097 157.108 158.092 159.076 159.092 161.092 166.061 167.081 169.097 169.133 171.076 171.113 172.081 173.092 173.128 175.071 175.119 181.097 183.113 183.149 185.056 185.091 186.123 187.071 +189.087 193.097 194.129 195.076 195.113 197.128 198.124 199.071 199.108 201.087 203.103 211.144 213.087 216.134 217.081 221.128 226.155 227.102 229.117 231.097 234.145 241.081 244.165 246.154 249.123 251.103 254.163 256.13 259.092 272.173 +283.152 284.126 288.202 293.16 300.156 312.119 315.202 330.132 331.679 345.177 369.225 383.192 389.195 397.209 398.21 411.19 419.192 429.205 437.204 444.242 453.688 468.245 486.268 497.323 516.245 521.269 534.258 543.315 547.283 565.298 +584.353 591.813 614.347 662.351 725.377 735.336 743.396 744.394 763.356 872.429 + + + + +6 3 10 3 5 6 4 2 8 8 7 49 3 3 36 2 49 14 2 11 7 4 44 6 3 45 2 4 5 4 +32 3 20 6 6 6 5 6 14 16 10 21 11 7 5 24 40 13 8 9 27 14 83 2 4 6 9 4 8 7 +15 5 7 6 14 9 30 9 100 3 5 6 5 16 2 5 8 7 2 12 3 11 8 15 2 5 7 12 6 84 +5 10 16 30 3 8 12 5 3 9 + + + + + + +conta|P13645|K1CJ_HUMAN KERATIN, TYPE I CYTOSKELETAL 10 (CYTOKERATIN 10) (K10) (CK 10) + + + + + + + + +5.43585 +-0.29383 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +3627 3627 3488 3379 3098 2843 2555 2330 1366 834 499 348 146 71 28 12 4 1 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3629 3629 3490 3377 3079 2785 2434 2223 1080 588 133 48 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1917 1450 220 43 0 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +663 2160 648 128 28 1 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3129 (charge 2) + +1300.59 +2 + + +152.057 155.082 156.113 157.097 157.108 158.092 159.076 166.061 167.055 169.097 169.134 171.076 171.112 173.056 173.092 175.119 179.092 181.097 185.092 187.108 190.061 193.097 197.092 197.128 199.071 199.108 201.087 207.089 209.091 212.103 +214.118 218.056 224.115 226.154 230.077 235.083 239.115 240.134 244.166 249.097 252.109 256.129 258.107 267.109 271.175 272.173 283.14 285.155 288.203 310.14 311.172 326.173 354.176 359.028 364.122 367.197 372.187 381.151 388.136 397.208 +443.226 446.236 452.254 454.731 488.246 510.199 517.272 536.257 540.234 553.297 584.261 592.782 599.269 633.776 642.294 646.313 656.403 660.303 662.359 717.348 719.354 744.284 773.391 776.37 788.384 791.409 833.394 851.41 859.431 876.401 +890.421 903.45 907.442 920.45 922.456 930.444 932.406 1032.47 1049.49 1051.48 + + + + +11 7 2 4 2 7 5 6 2 13 2 5 2 5 8 43 5 2 5 20 2 6 5 2 2 9 5 10 2 7 +11 5 7 17 11 48 4 5 6 5 43 4 2 7 5 4 8 2 100 2 2 2 6 17 7 2 2 9 2 2 +2 5 4 2 2 2 7 2 2 4 2 21 2 4 5 5 2 2 7 7 2 2 2 2 6 8 5 2 7 2 +7 2 2 18 2 2 4 6 23 5 + + + + + + +GRMZM2G028834_P01 seq=translation; coord=2:233905742..233910753:1; parent_transcript=GRMZM2G028834_T01; parent_gene=GRMZM2G028834 + + + MRPILMKGHE RPLTFLRYNR DGDLLFSCAK DHTPTVWYAD NGDRLGTYRG + HNGAVWTCDV SRDSARLITG SADQTAKLWE VSTGKELFSF RFDAPARSVE + FAIGDALAVV TTDNFMDHVP TVQVKRIAED IDDQTEESAL VITGIKGRIN + RAVWGPLNRT IITAGEDATI RIWDSETGQL LKESDKESGH QKTISSLSKS + LDWSHFITGS LDKSAKLWDT RTLTLIKTYV TERPVNAVDI SPTHDTVVLG + GGQDAMNVTM TDRRAGKFEA KFYHKILQEE IGGVKGHFGP INALAFNPDG + RSFSSGGEDG YVRLHHFDSD YFSIKM + + + + + +GRMZM2G028834_P02 seq=translation; coord=2:233905762..233910628:1; parent_transcript=GRMZM2G028834_T02; parent_gene=GRMZM2G028834 + + + MRPILMKGHE RPLTFLRYNR DGDLLFSCAK DHTPTVWYAD NGDRLGTYRG + HNGAVWTCDV SRDSARLITG SADQTAKLWE VSTGKELFSF RFDAPARSVE + FAIGDALAVV TTDNFMDHVP TVQVKRIAED IDDQTEESAL VITGIKGRIN + RAVWGPLNRT IITAGEDATI RIWDSETGQL LKESDKESGH QKTISSLSKS + LDWSHFITGS LDKSAKLWDT RTLTLIKTYV TERPVNAVDI SPTHDTVVLG + GGQDAMNVTM TDRRAGKFEA KFYHKILQEE IGGVKGHFGP INALAFNPDG + RSFSSGGEDG YVRLHHFDSD YFSIKM + + + + + +GRMZM2G028834_P03 seq=translation; coord=2:233905762..233910320:1; parent_transcript=GRMZM2G028834_T03; parent_gene=GRMZM2G028834 + + + MRPILMKGHE RPLTFLRYNR DGDLLFSCAK DHTPTVWYAD NGDRLGTYRG + HNGAVWTCDV SRDSARLITG SADQTAKLWE VSTGKELFSF RFDAPARSVE + FAIGDALAVV TTDNFMDHVP TVQVKRIAED IDDQTEESAL VITGIKGRIN + RAVWGPLNRT IITAGEDATI RIWDSETGQL LKESDKESGH QKTISSLSKS + LDWSHFITGS LDKSAKLWDT RTLTLIKTYV TERPVNAVDI SPTHDTVVLG + GGQDAMNVTM TDRRAGKFEA KFYHKILQEE IGGVKGHFGP INALAFNPDG + RSFSSGGEDG YVRLHHFDSD YFSIKM + + + + + +GRMZM2G143330_P01 NP_001147501 eukaryotic translation initiation factor 3 subunit 2 seq=translation; coord=7:7507005..7510800:-1; parent_transcript=GRMZM2G143330_T01; parent_gene=GRMZM2G143330 + + + MRPILMKGHE RPLTFLRYNR DGDLLFSCAK DHTPTVWYAD NGDRLGTYRG + HNGAVWTCDV SRDSARLITG SADQTAKLWD VSTGKELFSF RFDAPARSVE + FAIGDALAVV TTDNFMDHVP TVQVKRIAED IDDQTEESAL VITGIKGRIN + RAVWGPLNRT IITAGEDATV RIWDSETGQL LKESDKESGH QKTISSLSKS + LDWSHFITGS LDKSAKLWDT RTLTLIKTYV TERPVNAVDI SPTHDTVVLG + GGQDAMNVTM TDRRAGKFEA KFYHKILQEE IGGVKGHFGP INALAFNPDG + RSFSSGGEDG YVRLHHFDSD YFSIKM + + + + + + +5.09527 +-0.308804 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 + + + + +8214 8214 8108 7857 7438 6571 4517 3610 1775 1006 412 215 77 39 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8262 8262 8156 7905 7470 6552 4250 2893 872 271 124 24 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +4456 3227 550 28 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1376 5214 1239 372 55 3 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3130 (charge 2) + +1104.59 +2 + + +155.081 156.077 157.061 157.097 158.092 159.076 167.082 168.077 169.098 171.076 172.071 173.128 174.087 175.072 175.119 183.15 184.072 185.056 185.091 185.165 186.087 186.123 187.071 187.144 189.086 193.097 197.128 198.087 198.124 199.071 +199.108 199.18 202.082 203.066 207.089 212.103 215.139 218.15 226.155 227.175 230.114 234.145 240.096 244.092 246.181 258.107 267.109 275.126 276.112 285.133 297.155 299.135 315.165 319.198 327.129 331.125 346.656 363.183 382.705 392.691 +395.182 398.165 403.207 413.17 414.172 423.242 430.23 432.171 447.256 449.198 496.265 510.256 518.262 544.302 546.771 554.299 562.283 565.247 575.28 595.25 628.305 633.323 643.27 647.314 656.807 667.355 685.321 692.301 720.353 725.357 +764.404 777.372 784.375 789.355 821.427 845.474 860.413 878.42 880.417 888.406 + + + + +3 2 7 4 7 11 2 2 3 4 4 2 3 6 21 4 4 5 3 11 2 2 2 3 3 3 3 3 2 3 +4 100 29 3 2 4 9 6 4 19 3 14 3 5 4 2 2 3 2 3 2 3 3 9 3 2 6 8 3 2 +10 2 2 2 4 3 8 3 8 2 4 4 2 2 2 3 6 3 11 3 8 5 2 4 3 5 2 7 6 11 +3 11 2 4 5 2 3 20 2 2 + + + + + + +GRMZM2G117707_P02 NP_001150866 phospho-2-dehydro-3-deoxyheptonate aldolase 1 seq=translation; coord=7:166462601..166467163:-1; parent_transcript=GRMZM2G117707_T02; parent_gene=GRMZM2G117707 + + + MALATNSAAA AAAAVSGGAA SQPHRAATFL PLKRRTISAI HAADPSKNNG + PAVPAAAAAK SSASAVATPE KNPAAPVKWA VDSWKSKKAL QLPEYPNQEE + LDTVLKTIET FPPVVFAGEA RHLEERMAEA AMGRAFILQG GDCAESFKEF + HANNIRDTFR ILLQMGAVLM FGGQVPVVKV GRMAGQFAKP RSEPLEERDG + VKLPSYRGDN VNGDDFTEKS RVPDPQRMIR AYSQSVATLN LLRALATGGY + AAMQRVTQWN LDFMDHSEQG DRYRELAHRV DEALGFMTAA GLTVDHPIMT + TTDFWTSHEC LLLPYEQSLT RKDSTSGLFY DCSAHMLWVG ERTRQLDGAH + VEFLRGVANP LGIKVSDKMN PSDLVKLIEI LNPSNKPGRI TIITRMGAEN + MRVKLPHLIR AVRNAGLIVT WITDPMHGNT IKAPCGLKTR PFDSILAEVR + AFFDVHDQEG SHPGGIHLEM TGQNVTECIG GSRTVTFDDL SDRYHTHCDP + RLNASQSLEL AFIIAERLRK RRMRSGLNNS LPLPPLAF + + + + + +GRMZM2G365160_P01 C4J284 Putative uncharacterized protein seq=translation; coord=2:212180089..212183936:-1; parent_transcript=GRMZM2G365160_T01; parent_gene=GRMZM2G365160 + + + MALATNSAAA AAAVSGGVAS QPRRAAVFLP LKRRTISAIH AADPSKNNGP + AVPAAAGANS SASAVATPEK KPAAHGKWAV YSWRSKKALQ LPEYPNAEEL + DAVLKTIETF PPVVFAGEAR RLEERMAEAA MGRAFVLQGG DCAESFKEFH + ANNIRDTFRV LLQMGVVLMF GGQMPVVKVG RMAGQFAKPR SEPFEEKDGV + KLPSYRGDNV NGDDFTEKSR VPDPQRMIRA YAQSVATLNL LRAFATGGYA + AMQRVTQWNL DFMDHNEQGD RYRELAHRVD DALGFMTASG LTVDHPIMTT + TDFWTSHECL LLPYEQALTR EDSTSGLFYD CSAHMLWVGE RTRQLDGAHV + EFLRGVANPL GIKVSDKMNP SELVKLIDIL NPSNKPGRIT IITRMGAENM + RVKLPHLIRA VRNAGLIVTW ITDPMHGNTI KAPCGLKTRP FDSILAEVRA + FFDVHDQEGS HPGGVHLEMT GQNVTECIGG SRTVTFDDLS DRYHTHCDPR + LNASQSLELA FIIAERLRKR RMRSGLNSSL PLPPLAF + + + + + +GRMZM2G117707_P01 NP_001150866 phospho-2-dehydro-3-deoxyheptonate aldolase 1 seq=translation; coord=7:166462601..166467163:-1; parent_transcript=GRMZM2G117707_T01; parent_gene=GRMZM2G117707 + + + MALATNSAAA AAAAVSGGAA SQPHRAATFL PLKRRTISAI HAADPSKNNG + PAVPAAAAAK SSASAVATPE KNPAAPVKWA VDSWKSKKAL QLPEYPNQEE + LDTVLKTIET FPPVVFAGEA RHLEERMAEA AMGRAFILQG GDCAESFKEF + HANNIRDTFR ILLQMGAVLM FGGQVPVVKV GRMAGQFAKP RSEPLEERDG + VKLPSYRGDN VNGDDFTEKS RVPDPQRMIR AYSQSVATLN LLRALATGGY + AAMQRVTQWN LDFMDHSEQG DRYRELAHRV DEALGFMTAA GLTVDHPIMT + TTDFWTSHEC LLLPYEQSLT RKDSKDYACL FVDAWCGGLV GALGTSYMLG + SYRRVPVALW KTVASIMCCN CMPSFHVLGA + + + + + +GRMZM2G145692_P01 seq=translation; coord=5:197981348..197982126:1; parent_transcript=GRMZM2G145692_T01; parent_gene=GRMZM2G145692 + + + MALATNSAAA AAAVSGGAAS QSRRAVAFLP LKRRTISAIH AADPSKNNGP + VVPAAAGAKS SSSAVATPEK KPAALGNWAV DSWRSKKALQ LPEYSNAEEL + DAVLKTIETF PPVVFAGEAR HLEERMAEAA MGRAFVLQGS DCAESFKEFH + ANNICDTFRI LLQMGVVLMF GGQVPVVKVP TDTSNPPPNS GHQVCRFARS + DPTLLCVVGG EDGWPVRQVK + + + + + + +5.31389 +-0.272507 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 + + + + +2219 2219 2111 2046 1912 1752 1608 1394 1258 898 573 332 175 83 45 20 9 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2226 2226 2118 2053 1914 1746 1534 1265 1123 557 279 85 15 1 0 + + + + + + +0 1 2 3 4 + + + + +1190 841 176 21 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +288 1200 516 195 20 1 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3131 (charge 2) + +836.375 +2 + + +154.087 155.081 155.118 157.097 157.109 157.133 158.064 158.092 159.077 159.093 159.113 165.138 166.061 167.118 169.097 169.134 170.138 171.076 171.112 172.108 173.092 173.127 174.056 175.09 175.119 176.093 176.122 177.086 181.097 181.134 +183.076 183.113 183.149 185.091 187.072 187.108 187.144 189.07 194.129 195.113 197.129 198.086 201.087 203.085 206.094 211.144 213.087 215.114 218.15 226.154 229.1 232.14 235.119 240.134 244.166 248.15 250.152 254.113 256.13 258.146 +262.05 268.165 272.124 274.124 278.184 286.151 301.187 304.692 309.156 311.172 313.188 323.208 332.128 341.185 343.161 346.154 353.217 363.181 399.18 414.272 417.193 426.235 434.218 436.223 466.277 487.291 499.299 505.255 507.254 511.324 +519.776 608.377 610.387 616.287 634.297 636.304 681.372 695.423 705.331 707.336 + + + + +2 19 1 3 4 5 12 20 4 3 6 2 2 3 3 26 3 1 4 6 23 4 1 100 54 9 4 3 1 3 +3 2 5 4 2 2 11 2 4 5 9 2 25 40 1 1 2 18 2 6 1 18 3 8 9 6 6 4 2 1 +4 1 21 2 2 3 14 2 5 1 3 4 6 1 6 11 5 12 1 3 4 5 20 2 2 3 22 41 4 8 +3 10 1 7 30 3 2 2 23 3 + + + + + + +GRMZM2G146951_P01 NP_001130383 hypothetical protein LOC100191479 seq=translation; coord=10:47749003..47752985:1; parent_transcript=GRMZM2G146951_T01; parent_gene=GRMZM2G146951 + + + MEPSAWAVAF AALCIVALAP PASGFYLPGV APNDFEKKDP LPVKVNKLTS + IKTQLPYSYY SLPFCKPDTI VDSAENLGEV LRGDRIENSP YTFEMREPQM + CQVVCKISVG EKEAKLLKEK IEDEYRVNMI LDNLPLVVPI QRVDQEGAYF + YQHGFHVGAK GKYSGSKDEK YFIHNHLSFT VKYHRDEQRD VSRIVAFEVK + PYSVKHEYEG QWNDKKTRLT TCDPHAQRII TSSESPQEVE VGKDIIFTYD + VDFKESDIKW ASRWDSYLLM TDDQIHWFSI VNSLMIVLFL SGMVAMIMLR + TLYRDISKYN QLETQEEAQE ETGWKLVHGD VFRPPSNSDW LCVYVGTGVQ + FFGMLLVTMV FAVLGFLSPS NRGGLMTAML LLWVFMGLLA GYSSSRLYKL + FKGSEWKNIA LRTAFTFPGS VFAIFFFLNA LIWGQKSSGA VPFTTMFALV + LLWFGISVPL VFVGSFLGFK KPTIEDPVKT NKIPRQIPEQ AWYMNPIFSI + LIGGILPFGA VFIELFFILT SIWLHQFYYI FGFLFLVFLI LIVTCAEISI + VLCYFQLCSE DYLWWWRSYL TSGSSALYLF LYATFYFFTK LEITKFVSAV + MYFGYMLIAS YAFFALTGTI GFYACFLFTR LIYSSVKIE + + + + + + +4.81764 +-0.275294 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +4390 4390 4390 4390 4009 3782 3174 2442 1696 1101 649 318 152 63 33 3 1 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4383 4383 4383 4383 4002 3773 3117 2349 1480 695 272 58 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1327 1994 836 211 18 12 0 + + + + + + +0 1 2 3 4 5 + + + + +939 2312 829 288 30 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3133 (charge 3) + +1433.65 +3 + + +152.056 155.081 155.118 157.097 157.134 158.06 158.092 159.076 159.092 160.095 169.061 169.097 169.134 170.06 171.112 173.092 173.129 175.087 175.119 176.082 181.061 183.113 183.148 185.092 185.165 186.087 186.123 187.073 187.087 187.107 +191.118 193.097 194.092 195.076 197.129 199.071 199.107 200.139 203.119 209.092 212.103 213.087 216.098 221.103 226.119 227.102 230.078 234.145 239.115 240.097 244.129 246.158 249.098 253.093 257.196 265.118 267.109 270.124 272.171 275.208 +277.639 284.102 293.112 305.686 323.136 341.144 358.172 375.199 390.235 401.196 412.16 430.171 431.173 443.578 457.243 470.758 487.254 492.765 504.286 513.314 542.297 555.294 559.214 575.274 590.823 598.226 601.321 610.369 616.233 626.339 +633.258 655.324 673.331 682.595 686.314 690.357 697.4 703.339 744.291 790.367 + + + + +13 14 8 23 7 6 16 26 100 10 10 13 15 13 10 9 6 7 74 6 7 10 7 24 8 11 6 13 7 17 +6 9 8 6 17 9 10 12 11 8 9 7 7 14 27 6 7 7 30 18 17 13 22 13 12 18 85 12 24 42 +8 6 7 14 11 6 7 11 14 6 57 46 16 14 15 10 15 18 18 19 9 10 22 22 12 7 10 36 15 7 +20 6 6 7 7 19 27 10 14 15 + + + + + + +GRMZM2G035520_P01 C4J9I5 Putative uncharacterized protein seq=translation; coord=3:93414907..93420917:1; parent_transcript=GRMZM2G035520_T01; parent_gene=GRMZM2G035520 + + + MAEKEGNLEA VLKEAVDLEN IPLEEVFENL RCSREGLSTE QAQQRLEIFG + PNKLEEKEES KFLKFLGFMW NPLSWVMEAA AIMAIALANG GGKPPDWQDF + VGIITLLVIN STISFIEENN AGNAAAALMA RLAPKAKVLR DGRWTEEDAA + ILVPGDIVSI KLGDIIPADA RLLEGDPLKI DQSALTGESL PVTKGPGDGV + YSGSTVKQGE IEAVVIATGV HTFFGKAAHL VDSTNQVGHF QKVLTAIGNF + CICSIAVGMF VEIIVMYPIQ HRAYRPGIDN LLVLLIGGIP IAMPTVLSVT + MAIGSHRLSQ QGAITKRMTA IEEMAGMDVL CSDKTGTLTL NKLTVDRNLV + EVFERGTTQD QVILMAARAS RTENQDAIDT AIVGMLADPK EARAGIQEVH + FLPFNPTDKR TALTYIDGDG KMYRVSKGAP EQILHLAHNK SDIERRVHAM + IDKFAERGLR SLAVAYQEVP EGRKESPGGP WHFVGLMPLF DPPRHDSAET + IRRALNLGVN VKMITGDQLA IGKETGRRLG MGTNMYPSSA LLGQNKDESI + AALPVDDLIE KADGFAGVFP EHKYEIVKRL QARKHICGMT GDGVNDAPAL + KKADIGIAVA DATDAARSAS DIVLTEPGLS VIISAVLTSR AIFQRMKNYT + IYAVSITIRI VLGFMLLALI WKFDFPPFMV LIIAILNDGT IMTISKDRVK + PSPLPDSWKL AEIFTTGVVL GGYQAMMTVI FFWAAYKTNF FPKIFHVESL + EKTAQDDFQK LASAVYLQVS TISQALIFVT RSRSWSFVER PGFLLVFAFL + VAQLIATLIA VYADWAFTSI KGIGWGWAGI VWLYNIIFYF PLDIIKFLIR + YALSGKAWDL VIEQRIAFTR KKDFGREERE LKWAHAQRTL HGLQAPDAKM + FPEKAGYNEL NQMAEEAKRR AEIARLRELH TLKGHVESVV KLKGLDIETI + QQSYTV + + + + + +GRMZM2G035520_P02 C4J9I5 Putative uncharacterized protein seq=translation; coord=3:93414907..93420917:1; parent_transcript=GRMZM2G035520_T02; parent_gene=GRMZM2G035520 + + + MAEKEGNLEA VLKEAVDLEN IPLEEVFENL RCSREGLSTE QAQQRLEIFG + PNKLEEKEES KFLKFLGFMW NPLSWVMEAA AIMAIALANG GGKPPDWQDF + VGIITLLVIN STISFIEENN AGNAAAALMA RLAPKAKVLR DGRWTEEDAA + ILVPGDIVSI KLGDIIPADA RLLEGDPLKI DQSALTGESL PVTKGPGDGV + YSGSTVKQGE IEAVVIATGV HTFFGKAAHL VDSTNQVGHF QKVLTAIGNF + CICSIAVGMF VEIIVMYPIQ HRAYRPGIDN LLVLLIGGIP IAMPTVLSVT + MAIGSHRLSQ QGAITKRMTA IEEMAGMDVL CSDKTGTLTL NKLTVDRNLV + EVFERGTTQD QVILMAARAS RTENQDAIDT AIVGMLADPK EARAGIQEVH + FLPFNPTDKR TALTYIDGDG KMYRVSKGAP EQILHLAHNK SDIERRVHAM + IDKFAERGLR SLAVAYQEVP EGRKESPGGP WHFVGLMPLF DPPRHDSAET + IRRALNLGVN VKMITGDQLA IGKETGRRLG MGTNMYPSSA LLGQNKDESI + AALPVDDLIE KADGFAGVFP EHKYEIVKRL QARKHICGMT GDGVNDAPAL + KKADIGIAVA DATDAARSAS DIVLTEPGLS VIISAVLTSR AIFQRMKNYT + IYAVSITIRI VLGFMLLALI WKFDFPPFMV LIIAILNDGT IMTISKDRVK + PSPLPDSWKL AEIFTTGVVL GGYQAMMTVI FFWAAYKTNF FPKIFHVESL + EKTAQDDFQK LASAVYLQVS TISQALIFVT RSRSWSFVER PGFLLVFAFL + VAQLVSSYSL SL + + + + + + +5.21562 +-0.242587 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 + + + + +5915 5915 5827 5692 5358 5172 4853 4531 3473 2873 1679 1099 690 395 212 116 59 26 16 5 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + + + + +5861 5861 5773 5638 5302 5102 4714 4312 3175 2023 886 273 62 3 2 2 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2640 2379 736 155 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1201 3068 1295 301 46 7 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3134 (charge 2) + +1246.6 +2 + + +152.057 153.066 155.082 155.118 157.097 157.109 158.093 159.076 161.092 167.081 169.061 169.097 170.063 171.076 171.113 173.092 173.129 175.119 176.122 181.061 183.113 183.149 185.092 187.071 188.075 189.087 194.129 195.112 197.128 199.071 +200.103 201.123 203.103 207.113 213.086 216.098 225.099 227.102 231.098 239.094 240.098 244.165 254.149 258.145 262.151 269.125 272.163 274.103 282.145 286.151 297.147 300.155 303.177 311.136 323.172 328.161 337.151 341.182 351.166 359.155 +369.177 371.19 380.156 383.193 397.182 410.165 413.223 414.212 424.218 431.237 432.24 434.204 439.198 446.188 447.708 452.213 456.219 485.246 502.273 581.26 613.307 614.31 625.318 630.331 632.34 678.344 698.358 724.336 741.365 759.375 +761.375 816.391 843.397 860.422 862.42 911.432 930.434 931.43 947.454 949.456 + + + + +14 28 7 5 6 3 14 19 8 3 44 6 4 30 13 7 16 74 5 2 12 2 8 100 10 12 3 2 2 2 +11 16 10 6 10 7 13 7 13 9 17 3 30 10 2 7 6 3 19 22 6 12 31 13 3 9 3 8 15 3 +15 2 3 3 7 2 3 12 2 35 7 14 6 3 5 3 6 7 74 3 23 7 5 75 6 2 5 6 13 69 +6 3 3 65 6 16 7 3 71 7 + + + + + + +GRMZM2G015419_P04 NP_001105980 lipoxygenase seq=translation; coord=4:233625700..233629448:1; parent_transcript=GRMZM2G015419_T04; parent_gene=GRMZM2G015419 + + + + + + + + + +GRMZM2G015419_P02 NP_001105980 lipoxygenase seq=translation; coord=4:233625689..233629426:1; parent_transcript=GRMZM2G015419_T02; parent_gene=GRMZM2G015419 + + + + + + + + + +GRMZM2G015419_P05 NP_001105980 lipoxygenase seq=translation; coord=4:233625821..233629381:1; parent_transcript=GRMZM2G015419_T05; parent_gene=GRMZM2G015419 + + + + + + + + + + +4.34422 +-0.248241 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 + + + + +1198 1198 1134 1044 856 667 510 376 222 147 78 34 19 8 5 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +1202 1202 1138 1034 844 620 465 287 146 93 49 8 5 1 0 + + + + + + +0 1 2 3 4 5 + + + + +428 626 136 14 3 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +468 565 149 11 8 0 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3138 (charge 2) + +1664.68 +2 + + +153.066 155.081 164.034 169.133 170.092 170.137 171.076 171.096 172.107 173.091 181.06 182.068 196.071 197.128 198.087 213.086 217.117 229.117 239.096 245.059 259.093 262.085 276.155 278.111 280.164 284.123 295.139 298.1 299.061 308.158 +311.171 326.171 327.172 341.146 344.164 359.192 372.224 380.157 394.208 396.158 399.171 413.168 418.18 423.189 430.211 455.214 458.207 470.226 488.233 496.202 503.612 509.197 523.25 527.205 529.302 534.222 552.235 569.249 617.279 628.25 +638.242 670.297 674.295 702.299 739.29 753.34 767.294 771.351 785.293 817.367 828.37 835.349 836.352 852.372 867.384 885.392 892.37 949.391 981.411 996.429 1014.43 1057.43 1060.43 1071.5 1078.43 1107.47 1115.54 1125.47 1143.48 1145.49 +1189.47 1207.48 1242.55 1306.53 1322.59 1339.6 1341.61 1385.57 1403.6 1405.62 + + + + +8 3 8 43 37 3 1 1 1 2 100 25 2 24 12 1 2 3 2 20 3 67 3 1 1 11 7 2 2 1 +2 17 3 2 2 6 5 2 2 2 2 8 2 12 3 10 2 2 9 2 2 7 2 2 2 2 10 3 2 2 +2 5 2 3 2 5 2 27 2 2 12 20 8 6 2 30 15 35 3 7 17 2 6 2 17 3 2 13 23 3 +8 17 5 5 5 39 8 2 21 3 + + + + + + +GRMZM2G069095_P01 NP_001105380 vacuolar proton pump homolog1 seq=translation; coord=5:95903606..95910954:-1; parent_transcript=GRMZM2G069095_T01; parent_gene=GRMZM2G069095 + + + MAAAAILPEL ATQVLIPVAA AVGIAFAVVQ WVLVSKVRVT PERRADGGAV + KSGPSDYLIE EEEGLNDHNV VVKCAEIQTA ISEGATSFLF TEYKYVGLFM + GIFAILIFLF LGSVEGFSTK SQPCHYIKDQ TCKPALANAI FSTIAFVLGA + VTSLVSGFLG MKIATYANAR TTLEARKGVG KAFITAFRAG AVMGFLLAAS + GLLVLYIAIN LFGIYYGDDW EGLFEAITGY GLGGSSMALF GRVGGGIYTK + AADVGADLVG KVERNIPEDD PRNPAVIADN VGDNVGDIAG MGSDLFGSYA + ESSCAALVVA SISSFGINHE FTPMVYPLLV SSVGIIACLI TTLFATDFFE + IKAVDEIEPA LKKQLIISTI VMTIGIALIS WLGLPYTFTI FNFGVQKTVQ + SWQLFLCVAV GLWAGLVIGF VTEYYTSNAY SPVQDVADSC RTGAATNVIF + GLALGYKSVI IPIFAIAFSI FLSFSLAAMY GVAVAALGML STIATGLAID + AYGPISDNAG GIAEMAGMSH RIRERTDALD AAGNTTAAIG KGFAIGSAAL + VSLALFGAFV SRAAISTVDV LTPKVFIGLI VGAMLPYWFS AMTMKSVGSA + ALKMVEEVRR QFNNIPGLME GTTKPDYATC VKISTDASIK EMIPPGALVM + LTPLIVGILF GVETLSGVLA GALVSGVQIA ISASNTGGAW DNAKKYIEAG + VSEHARTLGP KGSDPHKAAV IGDTIGDPLK DTSGPSLNIL IKLMAVESLV + FAPFFAAHGG ILFKWL + + + + + +GRMZM2G069095_P02 NP_001105380 vacuolar proton pump homolog1 seq=translation; coord=5:95903606..95910785:-1; parent_transcript=GRMZM2G069095_T02; parent_gene=GRMZM2G069095 + + + MVYPLLVSSV GIIACLITTL FATDFFEIKA VDEIEPALKK QLIISTIVMT + IGIALISWLG LPYTFTIFNF GVQKTVQSWQ LFLCVAVGLW AGLVIGFVTE + YYTSNAYSPV QDVADSCRTG AATNVIFGLA LGYKSVIIPI FAIAFSIFLS + FSLAAMYGVA VAALGMLSTI ATGLAIDAYG PISDNAGGIA EMAGMSHRIR + ERTDALDAAG NTTAAIGKGF AIGSAALVSL ALFGAFVSRA AISTVDVLTP + KVFIGLIVGA MLPYWFSAMT MKSVGSAALK MVEEVRRQFN NIPGLMEGTT + KPDYATCVKI STDASIKEMI PPGALVMLTP LIVGILFGVE TLSGVLAGAL + VSGVQIAISA SNTGGAWDNA KKYIEAGVSE HARTLGPKGS DPHKAAVIGD + TIGDPLKDTS GPSLNILIKL MAVESLVFAP FFAAHGGILF KWL + + + + + + +5.7193 +-0.27899 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + + + + +8993 8993 8993 8993 8640 8313 7714 7103 6372 4909 3703 2470 1283 744 336 161 66 36 6 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9006 9006 9006 9006 8653 8309 7668 6870 5924 4347 2487 709 117 32 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2456 3660 1876 717 231 60 4 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1655 3538 2585 905 287 28 5 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3140 (charge 3) + +1359.7 +3 + + +155.081 155.117 157.097 157.108 157.133 158.093 159.076 166.061 169.097 169.133 171.077 171.112 173.092 173.128 175.119 176.123 177.102 183.076 183.113 186.123 187.073 187.107 189.086 192.111 195.113 197.129 199.071 199.108 201.087 203.121 +209.104 212.102 215.139 218.15 221.104 226.117 231.116 239.162 240.134 243.134 244.164 246.156 249.159 250.163 255.145 258.107 264.17 267.108 272.171 275.138 277.154 288.202 292.166 300.147 311.171 329.181 336.13 339.167 341.229 343.233 +354.139 366.187 371.193 378.194 383.215 384.217 387.194 400.23 406.196 413.712 446.278 453.205 457.258 462.27 489.276 494.244 508.299 512.257 513.258 534.299 535.249 561.294 573.305 575.263 581.276 582.267 599.289 601.3 627.322 644.341 +655.357 662.352 674.314 698.358 700.341 755.38 809.39 826.415 937.443 955.459 + + + + +17 7 6 5 14 12 16 5 11 7 6 9 14 13 100 7 13 11 7 6 7 7 12 24 5 5 5 5 13 21 +12 7 24 8 6 12 7 10 8 20 10 35 60 7 6 8 5 10 66 7 13 7 6 14 9 6 6 6 10 5 +12 13 5 6 52 9 7 6 5 6 9 10 6 5 5 7 9 19 8 7 7 7 8 5 8 9 82 7 5 6 +5 10 5 6 6 29 5 34 6 25 + + + + + + +GRMZM2G059191_P01 NP_001149023 ferredoxin--NADP reductase, leaf isozyme seq=translation; coord=8:157455159..157458787:-1; parent_transcript=GRMZM2G059191_T01; parent_gene=GRMZM2G059191 + + + + + + + + +5.44241 +-0.294184 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 + + + + +7531 7531 7400 7005 6608 6151 4397 2918 2049 1329 910 338 150 53 30 11 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7533 7533 7402 6990 6569 6060 3950 2377 1258 691 439 31 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3584 3037 727 147 39 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1541 4669 1075 229 16 1 0 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3141 (charge 2) + +1402.72 +2 + + +153.065 155.081 159.077 166.05 169.097 171.076 172.108 173.092 175.119 183.076 183.112 184.079 185.092 187.072 187.108 189.087 194.129 198.087 200.103 201.106 212.102 216.098 218.149 226.119 228.134 230.113 240.098 242.114 244.129 252.134 +254.115 258.108 270.145 272.124 283.139 287.135 297.156 299.17 301.151 303.213 311.135 312.138 315.202 316.206 323.134 329.145 333.188 351.166 354.214 368.193 372.224 384.152 394.172 397.212 400.183 402.162 416.248 431.273 443.261 497.199 +502.236 514.298 527.247 537.757 545.264 560.317 573.271 585.336 626.277 671.349 686.382 688.376 703.353 799.41 815.422 817.419 871.418 888.451 916.471 986.458 1003.48 1005.48 1017.52 1057.5 1068.53 1074.52 1076.52 1086.53 1104.55 1106.55 +1145.55 1203.62 + + + + +2 9 4 9 4 11 5 5 13 35 3 3 3 3 6 2 5 7 100 10 3 3 3 8 1 7 32 1 2 2 +2 17 3 2 4 2 4 10 2 3 23 5 16 2 2 12 3 2 2 2 31 1 2 2 2 2 3 6 19 2 +2 12 2 3 4 5 2 8 2 2 11 9 6 2 6 7 2 14 9 2 14 2 7 2 2 13 2 2 14 3 +5 8 + + + + + + +GRMZM2G122871_P01 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104071298:1; parent_transcript=GRMZM2G122871_T01; parent_gene=GRMZM2G122871 + + + MALVLHSGAG NKNAFKALIA AEYSGIKVEL TKDFEMGVSN KTPEFLKMNP + LGKVPVLETP DGPVFESNAI ARYVARLKDD NPLFGSSRIE QAHVEQWMDF + AATEVDPGVA WYLYPRLGYL PYVSTTEETA ISSLKRSLGA LNTHLASNTY + LVGHAVTLAD IVMTCNLYHG IARILTKTFT SDFPHVERYF WTMVNQPNFK + KVIGEVKQAE SAPPIPKKAA PSKEPKAKDV KKEAPKEAPK PKVVEAPAEE + EAPKPKPKNP LDLLPPSKMV LDDWKRLYSN TKTNFREVAI KGFWDMYDPE + GYSLWFCDYK YNDENTVSFV TLNKVGGFLQ RMDLCRKYAF GKMLVIGSEP + PFKLKGLWLF RGQDVPKFVM DEVYDMELYE WTKVDISDEA QKERVNAMIE + DQEPFEGEAL LDAKCFK + + + + + +GRMZM2G122871_P04 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104068352..104071134:1; parent_transcript=GRMZM2G122871_T04; parent_gene=GRMZM2G122871 + + + MGVSNKTPEF LKMNPLGKVP VLETPDGPVF ESNAIARYVA RLKDDNPLFG + SSRIEQAHVE QWMDFAATEV DPGVAWYLYP RLGYLPYVST TEETAISSLK + RSLGALNTHL ASNTYLVGHA VTLADIVMTC NLYHGIARIL TKTFTSDFPH + VERYFWTMVN QPNFKKVIGE VKQAESAPPI PKKAAPSKEP KAKDVKKEAP + KEAPKPKVVE APAEEEAPKP KPKNPLDLLP PSKMVLDDWK RLYSNTKTNF + REVAIKGFWD MYDPEGYSLW FCDYKYNDEN TVSFVTLNKV GGFLQRMDLC + RKYAFGKMLV IGSEPPFKLK GLWLFRGQDV PKFVMDEVYD MELYEWTKVD + ISDEAQKERV NAMIEDQEPF EGEALLDAKC FK + + + + + +GRMZM2G122871_P02 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104071298:1; parent_transcript=GRMZM2G122871_T02; parent_gene=GRMZM2G122871 + + + MALVLHSGAG NKNAFKALIA AEYSGIKVEL TKDFEMGVSN KTPEFLKMNP + LGKVPVLETP DGPVFESNAI ARYVARLKDD NPLFGSSRIE QAHVEQWMDF + AATEVDPGVA WYLYPKVVEA PAEEEAPKPK PKNPLDLLPP SKMVLDDWKR + LYSNTKTNFR EVAIKGFWDM YDPEGYSLWF CDYKYNDENT VSFVTLNKVG + GFLQRMDLCR KYAFGKMLVI GSEPPFKLKG LWLFRGQDVP KFVMDEVYDM + ELYEWTKVDI SDEAQKERVN AMIEDQEPFE GEALLDAKCF K + + + + + +GRMZM2G122871_P03 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104070943:1; parent_transcript=GRMZM2G122871_T03; parent_gene=GRMZM2G122871 + + + MALVLHSGAG NKNAFKALIA AEYSGIKVEL TKDFEMGVSN KTPEFLKMNP + LGKVPVLETP DGPVFESNAI ARYVARLKDD NPLFGSSRIE QAHVEQWMDF + AATEVDPGVA WYLYPRLGYL PYVSTTEETA ISSLKRSLGA LNTHLASNTY + LVGHAVTLAD IVMTCNLYHG IARILTKTFT SDFPHVERYF WTMVNQPNFK + KVIGEVKQAE SAPPIPKKAA PSKEPKAKDV KKEAPKEAPK PKVVEAPAEE + EAPKPKPKNP LDLLPPSKMV LDDWKRLYSN TKTNFREVAI KADGPVPQVR + LWEDARDRL + + + + + + +6.26599 +-0.338702 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 + + + + +8711 8711 8610 8387 7893 7317 5947 4662 3043 1768 962 481 238 93 21 10 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +8694 8694 8593 8370 7873 7251 5770 4191 2414 1192 446 201 88 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2779 3925 1674 298 36 9 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1995 4448 1786 382 95 5 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3144 (charge 3) + +1718.93 +3 + + +153.102 155.081 158.092 159.076 169.097 171.076 171.149 172.153 173.092 173.129 175.119 181.061 181.097 183.076 183.113 186.124 187.071 197.128 198.088 198.124 199.108 199.144 201.087 212.103 226.155 227.159 229.118 235.119 240.134 244.165 +259.093 270.145 280.129 298.14 299.141 303.177 315.201 328.186 330.129 341.182 351.166 358.207 369.177 372.261 399.191 416.225 427.181 440.91 451.305 469.317 523.079 532.484 538.283 541.294 543.283 547.29 550.293 555.491 557.227 561.098 +564.305 567.814 576.817 597.407 599.26 601.31 610.847 612.835 627.257 628.263 630.321 632.332 651.855 654.831 655.839 660.861 662.833 672.1 678.591 682.849 694.461 696.883 699.383 704.343 712.853 731.427 759.37 760.901 765.499 797.365 +876.526 887.438 894.54 909.468 998.494 1023.59 1077.56 1152.61 1223.66 1320.73 + + + + +2 10 2 6 34 5 95 9 12 5 20 6 6 4 2 4 4 2 2 4 11 47 15 4 100 12 14 4 7 61 +8 6 9 28 5 4 3 12 5 4 6 6 2 4 4 6 15 5 10 24 6 4 2 5 4 5 4 26 2 2 +8 2 5 3 3 5 8 7 13 4 2 4 7 4 5 29 33 4 5 14 34 5 7 5 5 2 4 2 17 5 +2 4 11 4 5 14 8 13 12 6 + + + + + + +GRMZM2G064518_P01 NP_001145761 hypothetical protein LOC100279268 seq=translation; coord=6:104269642..104276065:-1; parent_transcript=GRMZM2G064518_T01; parent_gene=GRMZM2G064518 + + + MAGYGEENQN TMSGYEEEEE EEVEEVEEVY EEEEEEEVEE EEEDGEGEAD + EGAVASEPAA MAAETRSVVG GRGLAKAVGN VDTGGEDGRD ADSSGGDASG + KIFVGGVAWE TTEETFTKHF QKYGAITDSV IMKDKHTRMP RGFGFVTFSD + PSVLDRVLED EHVIDGRTVE VKRTVPKEEM SSKDGPKTKK IFVGGIPPSL + TEDKLKEHFS SYGKVVEHQI MLDHSTGRSR GFGFVTFESE DAVERVMSEG + RMHDLGGKQV EIKKAEPKKP GVGDSSSNGR HSRGGGHRDS YRGSGGNGFS + GNSSGGGYGY SGGYRSTAAA HYGSTAYGAY GRGYGYGGTA GYGLGYGSAY + GGSMYGGPYG AYAAYGGAYG GGAYGAPGGY GAGGYGSYGG AGGMGGGGSA + GGRGSSRYHP YGK + + + + + + +4.21614 +-0.240922 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 + + + + +2568 2568 2568 2568 2452 1892 1514 1175 908 650 384 210 114 59 13 8 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2569 2569 2569 2569 2453 1891 1448 1124 806 481 269 120 38 6 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1030 1115 317 94 17 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +617 1380 471 87 14 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3145 (charge 3) + +2293.98 +3 + + +159.076 169.097 171.113 172.072 172.117 175.118 186.124 187.107 197.165 198.086 199.071 199.108 204.134 212.102 214.117 217.081 223.107 226.118 228.134 237.432 241.082 244.165 256.093 259.092 271.14 273.155 291.166 297.155 313.151 325.149 +337.151 342.176 344.193 355.197 359.119 362.203 369.14 388.141 396.225 413.25 424.219 432.234 441.247 443.497 454.293 477.225 515.22 540.237 555.237 591.275 613.245 640.277 650.288 659.331 670.294 678.305 714.286 730.376 742.372 745.323 +764.379 766.855 788.31 791.805 801.408 819.338 860.851 869.859 874.35 902.454 918.357 927.357 929.445 931.447 974.377 976.892 1053.94 1062.43 1089.41 1276.47 1279.55 1359.53 1377.52 1493.53 1563.6 1762.66 + + + + +9 8 69 72 4 8 37 6 6 5 7 5 84 5 5 8 8 52 11 5 36 99 6 22 39 5 100 57 5 21 +7 30 9 21 6 79 8 7 12 7 8 8 9 5 6 7 10 6 6 31 6 33 7 13 6 11 8 26 8 9 +10 60 9 8 44 55 9 76 7 70 41 54 8 7 28 17 8 36 20 10 10 8 21 21 8 8 + + + + + + +GRMZM2G030784_P01 P12863 Triosephosphate isomerase, cytosolic (TIM)(Triose-phosphate isomerase)(EC 5.3.1.1) seq=translation; coord=3:17824258..17828243:1; parent_transcript=GRMZM2G030784_T01; parent_gene=GRMZM2G030784 + + + MGRKFFVGGN WKCNGTTDQV EKIVKTLNEG QVPPSDVVEV VVSPPYVFLP + VVKSQLRQEF HVAAQNCWVK KGGAFTGEVS AEMLVNLGVP WVILGHSERR + ALLGESNEFV GDKVAYALSQ GLKVIACVGE TLEQREAGST MDVVAAQTKA + IAEKIKDWSN VVVAYEPVWA IGTGKVATPA QAQEVHASLR DWLKTNASPE + VAESTRIIYG GSVTAANCKE LAAQPDVDGF LVGGASLKPE FIDIINAATV + KSA + + + + + +GRMZM2G030784_P02 P12863 Triosephosphate isomerase, cytosolic (TIM)(Triose-phosphate isomerase)(EC 5.3.1.1) seq=translation; coord=3:17823962..17827573:1; parent_transcript=GRMZM2G030784_T02; parent_gene=GRMZM2G030784 + + + MQLCNASMQT RPSVRHPCRD APAADSPPPP VPRSTATART FAVRSSAPQS + NRHLTEMGRK FFVGGNWKCN GTTDQVEKIV KTLNEGQVPP SDVVEVVVSP + PYVFLPVVKS QLRQEFHVAA QNCWVKKGGA FTGEVSAEML VNLGVPWVIL + GHSERRALLG ESNEFVGDKV AYALSQGLKV IACVGETLEQ REAGSTMDVV + AAQTKAIAEK IKDWSNVVVA YEPVWAIGTG KVATPAQAQE VHASLRDWLK + TNASPEVAES TRIIYGGSVT AANCKELAAQ PDVDGFLVGG ASLKPEFIDI + INAATVKSA + + + + + + +6.04006 +-0.294637 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 + + + + +5920 5920 5809 5706 5233 5017 4546 3241 2580 1385 800 274 147 59 26 13 10 8 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5923 5923 5812 5709 5227 4922 4438 2879 1929 820 359 53 10 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2600 2654 595 74 5 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1238 3588 936 144 14 4 1 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3146 (charge 2) + +1261.6 +2 + + +152.057 155.082 155.118 157.097 158.092 159.076 166.05 167.081 169.061 169.097 171.077 171.113 172.072 172.108 173.092 173.128 175.071 175.119 181.061 183.076 183.111 185.092 186.087 186.123 187.143 188.103 198.087 199.072 199.107 201.123 +204.134 212.103 213.087 216.098 224.104 226.154 227.102 229.118 241.081 242.113 244.165 252.098 256.092 259.14 270.107 272.171 276.165 284.126 287.135 288.14 296.124 301.115 311.134 314.135 326.172 329.145 339.13 346.174 357.141 358.142 +363.198 374.167 376.155 397.21 428.179 444.725 454.763 466.275 492.24 526.25 537.306 543.286 563.276 601.376 632.357 656.345 662.346 672.412 684.313 703.325 773.38 785.387 791.391 800.372 803.45 825.407 852.419 854.398 870.425 884.449 +888.441 890.446 908.498 932.491 967.487 975.473 977.487 1044.52 1046.51 1061.53 + + + + +11 6 2 6 11 10 2 4 2 9 12 6 6 2 4 2 4 36 8 11 3 6 7 2 3 7 7 12 14 9 +4 2 4 100 2 9 26 2 4 6 5 4 4 6 7 10 2 5 41 2 2 2 7 5 11 14 7 5 6 9 +19 6 2 4 2 12 4 6 5 2 5 2 22 5 6 6 26 7 2 2 2 7 13 4 7 2 2 2 4 4 +94 11 2 2 2 23 2 2 22 7 + + + + + + +GRMZM2G430266_P01 seq=translation; coord=3:220854440..220857597:1; parent_transcript=GRMZM2G430266_T01; parent_gene=GRMZM2G430266 + + + MMAPAAPPPP PPPPRRRRRS VEKLPTSEEL EQEIVVEEVR NPPMPPPSLA + MFPPGTPPPP PPPLPPPSTV SRSKKKRSGS VGGAKELASA IATFYQKKRK + SITMKAKRRP HAHHHHHSDG QYYSSPSSDA SASPDSTART TTAPPRPPPP + PPPPPPPSSI FSNLFRNKKG GSKNRRIHSV APPQPPPPPP PARRSKKPPP + PPSRPAPPAP PPPPQPVRTR PQRAHVHAST QQPPLYPRRV YYTYYPLPPP + SPPLPPPPPP PPPLVPEGED DSPSVTASPA PAYCASPDVN TKADRFIESF + REGLKLEKLN SYREKWQRQI QENAAVEIGE EEEGEFMVIG SLFGDDDEED + EDGISLPQTP ATAVAVGF + + + + + + +6.64294 +-0.308974 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +5711 5711 5711 5689 5484 5088 4484 3382 2339 1564 905 436 227 95 48 18 11 3 2 2 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5717 5717 5717 5695 5490 5078 4407 3132 1921 902 252 70 9 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1584 2540 1124 381 73 12 2 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +954 2478 1658 502 94 29 1 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3147 (charge 3) + +1261.72 +3 + + +155.081 155.118 156.077 157.097 157.109 157.134 158.092 159.076 166.049 166.061 167.081 167.118 169.097 169.133 171.113 172.108 173.092 173.128 175.091 175.119 176.123 181.095 183.076 183.113 183.149 185.091 185.129 185.165 186.124 187.071 +187.144 190.624 194.129 195.074 195.113 197.128 200.103 201.124 203.085 204.621 210.025 213.086 218.15 226.154 227.103 231.097 233.095 235.119 239.15 241.081 244.164 251.102 253.147 255.146 259.092 272.172 282.168 287.676 292.679 299.17 +301.673 303.214 309.198 311.181 312.179 331.143 336.709 341.219 350.199 352.197 357.222 361.242 369.224 372.121 374.251 398.143 402.231 408.235 416.156 422.26 447.253 449.247 458.296 462.74 466.276 473.321 500.293 505.294 518.295 522.269 +545.199 563.33 569.328 584.354 601.377 618.285 655.385 660.386 672.414 803.456 + + + + +14 7 4 6 7 6 18 13 16 4 12 5 8 11 11 5 8 9 10 100 8 12 29 13 7 11 4 5 6 5 +9 16 8 9 14 10 29 9 5 17 77 13 4 6 4 16 6 5 77 20 8 8 64 10 15 13 4 20 6 5 +43 7 6 8 4 5 7 6 8 9 5 5 16 9 30 11 6 9 5 4 5 5 6 9 37 26 6 8 4 5 +5 29 5 9 20 5 5 7 30 15 + + + + + + +GRMZM5G838396_P01 P06586 30S ribosomal protein S3, chloroplastic seq=translation; coord=Pt:81113..82518:-1; parent_transcript=GRMZM5G838396_T01; parent_gene=GRMZM5G838396 + + + MGQKINPLGF RLGTTQNHHS FWFAQPKNYS EGLQEDKKIR NCIKNYIQKN + RKKGSNRKME SDSSSEVITH IEIQKEIDTI HVIIHIGFPN LLKKKGAIEE + LEKDLQKEVN SVNQRLNIAI EKVKEPYRQP NILAEYIAFQ LKNRVSFRKA + MKKAIELTKK ADIKGIKIQI AGRLAGKEIA RAECIKKGRL PLQTIRAKID + YCCYPIRTIY GVLGVKIWIF VEEE + + + + + +GRMZM2G448151_P01 P06586 30S ribosomal protein S3, chloroplastic seq=translation; coord=1:203905970..203907361:1; parent_transcript=GRMZM2G448151_T01; parent_gene=GRMZM2G448151 + + + MGQKINPLGF RLGTTQNHHS FWFAQPKNYS EGLQEDKKIR NCIKNYIQKN + RKKGSNRKME SDSSSEVITH IEIQKEIDTI HVIIHIGFPN LLKKKGAIEE + LEKDLQKEVN SVNQRLNIAI EKVKEPYRQP NILAEYIAFQ LKNRVSFRKA + MKKAIELTKK ADIKGIKIQI AGRLAGKEIA RAECIKKGRL PLQTIRAKID + YCCYPIRTIY GVLGVKIWIF VEEE + + + + + + +5.4876 +-0.296627 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 + + + + +5643 5643 5614 5441 5055 3909 3114 2109 1384 676 365 195 81 33 18 8 2 1 1 0 0 0 0 0 0 0 0 0 0 0 +1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +5648 5648 5619 5436 5035 3746 2716 1435 665 159 65 20 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2507 2380 624 126 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1418 2975 1007 217 24 6 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3149 (charge 2) + +1310.63 +2 + + +155.081 155.117 157.096 159.076 169.097 171.076 171.113 173.092 175.119 181.06 182.127 183.148 185.091 187.072 187.107 188.071 189.086 191.081 195.112 198.087 199.071 199.107 201.123 205.097 209.092 213.122 217.082 223.107 226.118 227.102 +233.092 234.095 240.134 242.149 244.128 250.118 256.093 258.144 261.086 275.207 276.155 278.113 282.146 286.141 299.171 309.119 311.17 327.13 330.111 337.187 347.133 355.123 359.193 362.133 365.144 369.174 373.208 375.222 382.207 387.188 +390.233 397.704 408.223 410.238 430.227 446.257 458.223 479.266 483.216 501.277 515.246 519.275 603.787 612.306 622.808 626.303 630.311 632.319 647.335 685.387 687.394 726.387 727.387 760.415 783.407 794.398 817.44 819.43 853.475 858.415 +865.434 870.441 924.509 928.464 936.469 946.483 967.493 1016.51 1033.52 1035.52 + + + + +4 5 4 2 10 4 6 2 10 2 2 2 4 6 2 4 5 10 4 2 4 4 2 4 2 4 7 4 12 10 +29 6 18 4 7 100 3 16 14 23 6 26 2 2 4 7 12 5 2 5 8 2 4 2 4 4 12 2 2 6 +11 2 3 5 2 5 5 8 2 7 2 8 3 1 5 1 7 4 8 12 1 6 3 3 4 4 19 6 15 9 +2 3 4 4 5 10 2 3 28 7 + + + + + + +GRMZM2G001327_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695861:-1; parent_transcript=GRMZM2G001327_T01; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G001327_P03 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136692489..136695738:-1; parent_transcript=GRMZM2G001327_T03; parent_gene=GRMZM2G001327 + + + + + + + +GRMZM2G154218_P01 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515921..136519080:-1; parent_transcript=GRMZM2G154218_T01; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G154218_P02 NP_001105935 elongation factor 1 alpha seq=translation; coord=6:136515968..136519018:-1; parent_transcript=GRMZM2G154218_T02; parent_gene=GRMZM2G154218 + + + + + + + +GRMZM2G149768_P01 NP_001105933 elongation factor alpha2 seq=translation; coord=6:136568621..136572271:-1; parent_transcript=GRMZM2G149768_T01; parent_gene=GRMZM2G149768 + + + + + + + +GRMZM2G110509_P01 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T01; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P02 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607094..84610318:1; parent_transcript=GRMZM2G110509_T02; parent_gene=GRMZM2G110509 + + + + + + + +GRMZM2G110509_P03 NP_001104939 elongation factor alpha6 seq=translation; coord=8:84607316..84610225:1; parent_transcript=GRMZM2G110509_T03; parent_gene=GRMZM2G110509 + + + + + + + + +5.86588 +-0.300815 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 + + + + +10846 10846 10846 10562 10125 9305 7962 6470 4438 2759 1412 704 356 147 68 36 15 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +10846 10846 10846 10562 10122 9256 7740 5820 3360 1435 515 141 28 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3057 4776 2195 617 119 72 14 3 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2369 4571 2798 982 111 8 11 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3151 (charge 3) + +1621.87 +3 + + +153.102 156.077 157.097 158.093 159.076 166.061 167.081 169.097 169.134 171.113 173.092 173.129 175.119 177.102 178.106 181.096 185.092 185.164 187.071 187.107 188.111 199.107 202.082 204.134 205.097 207.125 209.14 213.087 215.102 218.149 +223.107 226.155 227.101 229.099 235.119 237.135 240.134 244.165 251.102 258.145 272.171 279.097 297.192 301.059 303.177 304.16 313.15 315.202 323.169 341.218 360.15 430.234 437.714 446.185 454.214 459.208 481.234 493.724 502.738 505.247 +508.239 513.307 516.751 532.238 539.771 545.255 548.279 560.234 566.284 570.321 603.268 617.28 620.274 627.325 645.331 647.258 655.337 667.388 673.356 701.287 718.297 727.386 739.368 746.38 752.359 760.376 770.36 799.355 803.373 815.354 +817.369 840.468 845.443 874.424 886.388 907.419 961.455 1004.47 1032.49 1164.54 + + + + +4 2 6 5 14 4 2 12 4 16 3 3 17 100 11 5 8 9 4 46 4 11 4 4 28 3 4 5 12 14 +5 6 9 2 14 4 3 3 2 4 5 4 3 5 4 6 4 73 8 3 3 6 3 5 16 5 9 11 17 4 +3 3 21 2 5 8 6 7 6 3 4 3 5 3 33 14 12 3 6 3 22 5 3 10 3 12 20 2 4 2 +15 3 4 7 3 4 12 5 3 3 + + + + + + +GRMZM2G061928_P01 O48556 Soluble inorganic pyrophosphatase (EC 3.6.1.1)(Pyrophosphate phospho-hydrolase)(PPase) seq=translation; coord=2:24608141..24615659:1; parent_transcript=GRMZM2G061928_T01; parent_gene=GRMZM2G061928 + + + MSEEDKTAAS AEQPKRAPKL NERILSSLSR RSVAAHPWHD LEIGPDAPAV + FNVVVEITKG SKVKYELDKK TGLIKVDRVL YSSVVYPHNY GFVPRTLCED + NDPMDVLVLM QEPVVPGSFL RARAIGLMPM IDQGEKDDKI IAVCADDPEY + RHYNDISELS PHRLQEIKRF FEDYKKNENK EVAVDAFLPA TTAREAIQYS + MDLYAQYILQ SLRQ + + + + + + +GRMZM2G061928_P02 O48556 Soluble inorganic pyrophosphatase (EC 3.6.1.1)(Pyrophosphate phospho-hydrolase)(PPase) seq=translation; coord=2:24608141..24615659:1; parent_transcript=GRMZM2G061928_T02; parent_gene=GRMZM2G061928 + + + MSEEDKTAAS AEQPKRAPKL NERILSSLSR RSVAAHPWHD LEIGPDAPAV + FNVVVEITKG SKVKYELDKK TGLIKVDRVL YSSVVYPHNY GFVPRTLCED + NDPMDVLVLM QEPVVPGSFL RARAIGLMPM IDQGEKDDKI IAVCADDPEY + RHYNDISELS PHRLQEIKRF FEDYKKNENK EVAVDAFLPA TTAREAIQYS + MDLYAQYILQ SLRQ + + + + + + +GRMZM2G061928_P03 O48556 Soluble inorganic pyrophosphatase (EC 3.6.1.1)(Pyrophosphate phospho-hydrolase)(PPase) seq=translation; coord=2:24608141..24615659:1; parent_transcript=GRMZM2G061928_T03; parent_gene=GRMZM2G061928 + + + MSEEDKTAAS AEQPKRAPKL NERILSSLSR RSVAAHPWHD LEIGPDAPAV + FNVVVEITKG SKVKYELDKK TGLIKVDRVL YSSVVYPHNY GFVPRTLCED + NDPMDVLVLM QEPVVPGSFL RARAIGLMPM IDQGEKDDKI IAVCADDPEY + RHYNDISELS PHRLQEIKRF FEDYKKNENK EVAVDAFLPA TTAREAIQYS + MDLYAQYILQ SLRQ + + + + + + +GRMZM2G061928_P04 O48556 Soluble inorganic pyrophosphatase (EC 3.6.1.1)(Pyrophosphate phospho-hydrolase)(PPase) seq=translation; coord=2:24608141..24615457:1; parent_transcript=GRMZM2G061928_T04; parent_gene=GRMZM2G061928 + + + MSEEDKTAAS AEQPKRAPKL NERILSSLSR RSVAAHPWHD LEIGPDAPAV + FNVVVEITKG SKVKYELDKK TGLIKVDRVL YSSVVYPHNY GFVPRTLCED + NDPMDVLVLM QEPVVPGSFL RARAIGLMPM IDQGEKDDKI IAVCADDPEY + RHYNDISELS PHRLQEIKRF FEDYKKNENK EVAVDAFLPA TTAREAIQYS + M + + + + + + + +4.30765 +-0.220905 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +5887 5887 5838 4493 3593 2923 2134 1558 1008 745 478 386 166 86 47 17 12 6 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5882 5882 5833 4450 3445 2664 1685 1060 637 452 354 295 42 33 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2553 2499 672 145 16 2 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1232 3901 676 76 2 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3152 (charge 2) + +1532.71 +2 + + +155.081 157.097 159.076 169.096 171.075 171.112 172.071 173.092 175.119 181.096 185.091 186.124 189.087 199.071 199.106 201.087 204.134 209.092 212.102 217.081 223.107 226.154 228.133 230.112 241.081 242.084 244.165 248.16 259.092 271.139 +283.14 288.119 291.165 297.155 301.149 310.176 313.15 325.15 327.164 329.144 331.161 337.15 342.176 355.196 356.201 359.155 362.203 366.18 369.142 372.225 374.119 384.187 388.132 412.18 416.175 441.245 456.21 467.138 485.153 495.213 +501.267 503.161 513.231 515.78 531.241 558.251 572.3 591.278 613.251 631.25 638.273 641.275 642.292 659.336 670.263 696.277 714.294 717.372 730.371 732.302 758.336 765.332 774.355 785.33 787.392 801.411 817.376 869.849 874.357 885.428 +902.454 904.453 918.359 927.869 943.379 996.42 1030.55 1146.57 1225.21 1493.55 + + + + +2 1 4 2 2 15 13 5 2 2 2 8 2 9 1 5 14 6 5 2 2 28 2 2 50 5 100 1 16 6 +4 1 9 5 4 6 4 2 2 4 1 6 4 25 4 5 6 2 2 8 6 2 7 2 2 2 1 2 5 2 +6 4 4 2 4 3 5 2 2 2 1 4 2 12 6 2 9 2 15 7 2 2 2 5 2 18 5 2 2 4 +29 4 2 2 3 2 4 2 1 1 + + + + + + +GRMZM2G352415_P01 NP_001130539 hypothetical protein LOC100191638 seq=translation; coord=1:297016125..297019051:-1; parent_transcript=GRMZM2G352415_T01; parent_gene=GRMZM2G352415 + + + MSSSAENDPT VTVTERGGKD KHEDGGDKEQ GGGGFIDKVK DFIHDIGEKI + EEVVGFGKPT ADVCGIHIPH ISLHRADLVV DVLIKNPNPV PIPLVDIDYL + IDSDGRKLVS GLIPDAGTIH AHGQETVKIP VSLVFDDIKS TYKDIQPGSI + IPYLVRVVLL VDVPIIGRVK IPIQKDGEIP IPYKPDVDVE KIKFHHFSFE + ETTATLHLKL ENKNDFDLGL NLLEYEMWLG DDSIASAELT QTAKIEKQGI + TRMQVPFSFR PKDFGSAVWD MIRGRGTGYT IKGKIDVDTP FGNMKLPISK + EGGTTRLKKE EEEDDDDDN + + + + + +GRMZM2G352415_P02 NP_001130539 hypothetical protein LOC100191638 seq=translation; coord=1:297016125..297018853:-1; parent_transcript=GRMZM2G352415_T02; parent_gene=GRMZM2G352415 + + + MSSSAENDPT VTVTERGGKD KHEDGGDKEQ GGGGFIDKVK DFIHDIGEKI + EEVVGFGKPT ADVCGIHIPH ISLHRADLVV DVLIKNPNPV PIPLVDIDYL + IDSDGRKLVS GLIPDAGTIH AHGQETVKIP VSLVFDDIKS TYKDIQPGSI + IPYLVRVVLL VDVPIIGRVK IPIQKDGEIP IPYKPDVDVE KIKFHHFSFE + ETTATLHLKL ENKNDFDLGL NLLEYEMWLG DDSIASAELT QTAKIEKQGI + TRMQVPFSFR PKDFGSAVWD MIRGRGTGYT IKGKIDVDTP FGNMKLPISK + EGGTTRLKKE EEEDDDDDN + + + + + +GRMZM2G352415_P03 NP_001130539 hypothetical protein LOC100191638 seq=translation; coord=1:297016039..297018846:-1; parent_transcript=GRMZM2G352415_T03; parent_gene=GRMZM2G352415 + + + MSSSAENDPT VTVTERGGKD KHEDGGDKEQ GGGGFIDKVK DFIHDIGEKI + EEVVGFGKPT ADVCGIHIPH ISLHRADLVV DVLIKNPNPV PIPLVDIDYL + IDSDGRKLVS GLIPDAGTIH AHGQETVKIP VSLVFDDIKS TYKDIQPGSI + IPYLVRVVLL VDVPIIGRVK IPIQKDGEIP IPYKPDVDVE KIKFHHFSFE + ETTATLHLKL ENKNDFDLGL NLLEYEMWLG DDSIASAELT QTAKIEKQGI + TRMQVPFSFR PKDFGSAVWD MIRGRGTGYT IKGKIDVDTP FGNMKLPISK + EGGTTRLKKE EEEDDDDDN + + + + + + +6.0145 +-0.29339 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +5791 5791 5791 5492 5319 4945 4123 3422 2288 1594 975 567 293 123 55 34 10 4 3 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5797 5797 5797 5498 5323 4915 3996 3061 1654 737 284 71 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2150 2354 859 351 65 14 6 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1013 2471 1554 555 176 15 13 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3153 (charge 3) + +1988.89 +3 + + +152.057 155.081 158.092 167.081 173.092 175.119 184.108 185.092 185.165 186.087 195.112 198.123 199.107 209.091 226.118 231.124 234.144 239.113 240.134 244.129 249.097 262.139 267.108 270.145 283.103 285.12 291.145 295.104 306.16 327.165 +340.126 348.165 363.177 375.225 382.134 401.217 425.67 429.21 430.714 435.198 459.198 461.25 468.183 487.2 492.217 498.714 510.229 522.292 534.252 554.299 565.297 579.316 582.927 597.263 602.24 611.2 615.28 625.256 628.225 636.333 +642.39 644.339 656.306 660.319 662.35 664.821 672.282 683.321 693.356 703.274 713.274 715.327 721.284 731.289 734.316 739.299 750.378 752.383 754.328 775.336 792.357 796.349 805.363 836.317 850.328 854.329 860.406 861.409 871.35 873.38 +878.433 879.434 894.441 906.437 973.435 990.453 991.447 1007.48 1023.48 1172.5 + + + + +3 3 3 3 4 16 7 3 3 3 10 4 7 16 51 52 3 9 6 20 10 58 25 8 3 3 6 3 14 3 +15 12 23 16 12 3 10 8 6 9 7 4 3 10 3 3 10 3 7 4 7 3 7 3 3 21 4 13 3 10 +6 4 20 9 42 100 7 3 14 3 10 3 3 3 3 10 44 4 3 4 7 4 4 3 7 14 7 21 3 7 +9 3 15 4 8 3 6 12 11 3 + + + + + + +GRMZM2G010960_P01 seq=translation; coord=6:114177100..114187293:-1; parent_transcript=GRMZM2G010960_T01; parent_gene=GRMZM2G010960 + + + MSGAWGGTTQ KCASCGRRVY PVEELAADGR VYHRPCFRCH HCKSTLQFSN + YSSVEGVLYC KPHYDQILKS TGSLEKSFEG VARSAKSEKS NGHKGQQSSR + FSNMFVGTQE KCVVCNKTVY PLEKVALNGN SYHKSCFRCT HGGCTLSPSN + HITHEGKLYC KTHHSQLFMV KGNFSQFEDN SGNAKVTIEK LPETEEATKN + PDQGDEATRK PVENEPTDEK TSKNNVAAEK QLQSGVDVTK PSESTTAENE + RGTEGESKSN VVNKKPSESI VEKPLQNSVV DVKPSGNSAA MRKPWQRSMQ + TDKPFLSSTS TVNPSSSSDT TEKLSSSNGV DMKQSESSTL VKTTCKQNSP + TENPPQSVLP SDKPSATSVD DAKPSESSKV IKKPWQRNMA AEKQLQNSAP + SQKSVATDKP SPTTGMKSLD NTTEVKSPWG RRMFNNKSLK RSVDTEKSSE + TSVVDVRPGE TSTVAPVPQQ QTENVEKPSA TSADDAKSAD DTKSADDVKP + SVASPDAKST DDVKSSENNA AVVRKPWQRN IGTGKQPLTT VVGPKTTETS + GTVKRLWQRS AATASKSGTA VVTPLQSSVV VSKPFQSNVA VKKTWQRSVT + PENQLESNMS SNKPLPSKVV VESLLQSNTV EKVFQSTVPT EEPQKGIMAT + ENQSQTIKVT KKSNETSMEL SVTSETTKPP PLAATVLQSD VSTEQPSQTD + MPTMAPSQIP EPTEKPSESD FNAEKLSESV VKAEKSSTTD TAAEKPLPSM + ITEKVESVAG TLKPSQSDTA LQEILERNMA TEEILQTAMA VEDAPPTNLI + TEKSLMKDAS EEPVQTNEPS EQPLKTEEIE KPQQSEKIAT DTRGSEVSTE + EMLELESNAT KLNKDQSELE GLSSGRNPPN FQSNPNAGQR SESKGIVAEK + AADHIMEAED DVDAEHSSES QSVAPAEVRK EQPSEHQKDV DMEQLLEPQN + QDHPWNPLDP VSDTAAKDSS EPKSDIATEK PAESQNNAEQ SVEQQSEPQS + DKSTERPEVH QSNTSNDELS RLQNDAGTDK LSVQSSDPES NASVSKPSES + QTDVATMEAL EPQIDAPPDK ATDQPVKPQD DASAKNPMGT ESDAVCDKPS + ESSSDTETLL VCHQNSSITT DEPVQGGISY DTPHQRSAPI ETTPGSETVV + DDCIHHEDTS SKPSEENKAI EEPEEVSAKL PDDHVTSEKS SEEDKENAEA + SVDSAPLGNP LEVNEESSNP SGDTVTPEKP LEEDKTSAEP SESDASFGKI + LEADEVSANP SEDIATPEKP LEEGVGSVEP SEDNSVLDKP LEEEEVDAKP + VKDVVTPEKP LEEGSTTAEP LEDNAAHEEA KEEDEVIAKP LSSVALEKSL + EGSEASVEPS EDNAALEKPS EDDEANAKSS EDSVYVEKPQ QEEDDNGVKA + LEEGVSPEKS AAGKPLEEDP VHEKPADAVA EPSSQDDTAT EKPSATTDTA + ETA + + + + + + +5.53561 +-0.27003 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 + + + + +7493 7493 7490 7239 6825 6549 5824 4711 3661 2330 1298 641 304 190 82 40 27 19 4 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7495 7495 7492 7241 6825 6530 5764 4369 2967 1511 375 155 32 13 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2959 3129 1150 194 38 24 0 2 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1382 3141 1869 852 216 31 1 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3157 (charge 3) + +2186.01 +3 + + +152.057 155.093 158.092 159.076 161.092 171.076 175.119 183.15 187.107 189.086 197.092 199.107 202.083 209.092 215.102 227.102 237.135 240.135 245.124 246.155 249.098 262.149 266.124 269.125 272.171 286.461 294.118 306.158 310.14 326.169 +330.788 375.233 397.206 446.262 454.732 468.73 474.232 477.244 486.262 504.279 512.642 518.76 532.759 567.271 576.273 619.304 624.291 633.289 642.277 656.401 672.333 700.323 702.323 716.314 717.994 723.669 728.379 731.31 733.348 768.384 +771.396 799.393 801.401 820.381 833.874 842.375 908.453 921.425 936.455 938.45 985.423 1018.46 1035.48 1105.48 1122.5 1124.49 1233.55 1250.56 1383.42 1440.77 + + + + +2 3 7 4 4 7 31 3 23 4 4 5 3 3 7 13 5 3 4 3 4 6 7 4 5 3 3 14 3 3 +3 14 4 5 30 25 15 27 3 38 4 5 28 5 14 15 5 7 4 7 17 100 7 5 5 16 19 32 13 4 +17 94 15 42 5 5 24 20 62 6 4 7 27 12 55 6 13 13 4 5 + + + + + + +GRMZM2G157061_P01 seq=translation; coord=2:32257322..32262715:1; parent_transcript=GRMZM2G157061_T01; parent_gene=GRMZM2G157061 + + + MQPDQPVISL RPGGGGGPRA GRLFSPAFAT SVSGDFLRPH GGGASGISKI + GDSHFEPRER VRYTRDQLLE LREIVDVSEE ILRIKQEIDV ELHGEDQSWV + RNDSTVQGQA QAQTQAQNRY AETDSRDWRA RSAQLTPTNE EKSWDNIREA + KEAYASSGRQ QEQANRQDQL SSQFASKAQV GPTPALIKAE VPWSARRGNL + SEKERVLKTV KGILNKLTPE KFDLLKGQLM EAGITTADIL KDVISLIFEK + AVFEPTFCPM YAQLCSDLNE KLPTFPSEEP GGKEITFKRV ILNNCQEAFE + GASNLRAEIS KLTGPDQGME RRDKERLVKL RTLGNIRLIG ELLKQKMVPE + KIVHHIVMEL LGSGTDKKPC PEEEDVEAIC HFFNTIGKQL DENTKSRRIN + DTYFIQMKEL TMNPQLAPRL RFMVRDVIDL RSNNWVPRRE EIKAKTISEI + HSEAEKNLGL RPGAASVIRN GRSSPGGPLS PGGGFPMNRP GTGGMMPGMP + GSRKMPGMPG LDNDNWEVPR SKSMPRGDSI RNQGLLLNKP STVHKTSSIN + TRLLPQGSGA ALIGKSALLG TGVSASRPLS FTPGPTPAQT TPKPIRAAPA + VVPAPDKQAS APKGNTAELQ KKTIALLEEY FGIRILDEAH QCIVELQSPD + YYPEIVKEAV NLALDKGTNF VDPLVRLLEH LYTKKIFKTQ DLESGCLLYG + TLLDDIGIDL PKAPAQFGEI IARLTLLGAL RFEALEVILK KMEDTYNRKA + VSNAFMKTLE ANPSGQAILG SPAAAAVIDA CNSLLE + + + + + + +5.8112 +-0.314119 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6350 6350 6224 6141 5584 5247 3832 2929 1709 943 579 267 133 53 26 8 3 1 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6325 6325 6199 6109 5542 5137 3365 2353 936 394 145 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2856 2727 674 81 14 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1115 3735 1281 210 9 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3164 (charge 2) + +1217.6 +2 + + +155.081 155.118 157.097 158.092 159.076 167.055 167.081 169.097 169.133 171.077 171.112 173.092 173.128 175.119 176.103 181.097 183.076 183.113 185.091 185.128 186.123 187.071 187.144 193.107 195.112 196.144 197.128 200.102 201.086 212.103 +214.154 216.097 218.15 221.083 226.154 227.101 239.094 240.097 242.149 244.092 256.129 258.145 262.139 264.134 266.161 269.124 276.154 281.05 285.009 287.134 295.139 297.119 299.061 303.02 310.173 313.151 325.186 327.129 344.975 355.069 +359.172 373.079 375.23 387.186 400.215 405.201 412.266 415.036 418.993 442.193 454.23 474.183 483.263 487.286 502.208 512.752 514.266 519.24 521.259 543.237 571.233 602.273 616.329 620.291 627.322 666.309 675.397 699.328 703.361 705.344 +717.339 719.351 774.361 777.334 785.435 818.386 820.386 905.416 914.455 931.473 + + + + +4 2 2 3 38 20 2 2 2 3 34 11 2 14 7 5 7 5 8 2 5 2 2 5 2 5 13 12 9 3 +11 5 2 6 10 4 50 8 9 8 5 13 2 2 8 6 10 2 32 31 5 2 35 8 6 7 6 2 7 100 +6 13 2 7 4 4 5 9 19 11 5 2 5 2 4 2 2 11 4 5 8 2 2 12 8 11 2 6 2 2 +43 4 4 2 2 20 2 4 6 7 + + + + + + +GRMZM2G112165_P01 seq=translation; coord=2:189443283..189447454:1; parent_transcript=GRMZM2G112165_T01; parent_gene=GRMZM2G112165 + + + MASETETFAF QAEINQLLSL IINTFYSNKE IFLRELISNS SDALDKIRFE + SLTDKSKLDA QPELFIHLVP DKATNTLSII DSGIGMTKSD LVNNLGTIAR + SGTKEFMEAL AAGADVSMIG QFGVGFYSAY LVADRVVVTT KHNDDEQYVW + ESQAGGSFTV TRDTSGEQLG RGTKITLFLK DDQLEYLEER RLKDLVKKHS + EFISYPISLW TEKTTEKEIS DDEDEEEKKD AEEGKVEDVD EKEEKEKKKK + KIKEVSHEWS LVNKQKPIWM RKPEEITKEE YAAFYKSLTN DWEEHLAVKH + FSVEGQLEFK AVLFVPKRAP FDLFDTKKKQ NNIKLYVRRV FIMDNCEELI + PEWLSFVKGI VDSEDLPLNI SRETLQQNKI LKVIRKNLVK KCVELFFEIA + ENKEDYNKFY EAFSKNLKLG IHEDSQNRTK IAELLRYHST KSGDELTSLK + DYVTRMKEGQ NDIYYITGES KKAVENSPFL EKLKKRGYEV LYMVDAIDEY + AVGQLKEFEG KKLVSATKEG LKLDETEDEK KRKEELKEKF EGLCKVIKEV + LGDKVEKVVV SDRVVDSPCC LVTGEYGWTA NMERIMKAQA LRDSSMAGYM + SSKKTMEINP ENPIMDELRK RAEADKNDKS VKDLVMLLFE TALLTSGFSL + DDPNTFGNRI HRMLKLGLSI DEDEPVEAEA EMPQLEDDAG ESKMEEVD + + + + + + + +GRMZM2G112165_P02 seq=translation; coord=2:189443283..189447454:1; parent_transcript=GRMZM2G112165_T02; parent_gene=GRMZM2G112165 + + + MASETETFAF QAEINQLLSL IINTFYSNKE IFLRELISNS SDQQNKILKV + IRKNLVKKCV ELFFEIAENK EDYNKFYEAF SKNLKLGIHE DSQNRTKIAE + LLRYHSTKSG DELTSLKDYV TRMKEGQNDI YYITGESKKA VENSPFLEKL + KKRGYEVLYM VDAIDEYAVG QLKEFEGKKL VSATKEGLKL DETEDEKKRK + EELKEKFEGL CKVIKEVLGD KVEKVVVSDR VVDSPCCLVT GEYGWTANME + RIMKAQALRD SSMAGYMSSK KTMEINPENP IMDELRKRAE ADKNDKSVKD + LVMLLFETAL LTSGFSLDDP NTFGNRIHRM LKLGLSIDED EPVEAEAEMP + QLEDDAGESK MEEVD + + + + + + + + +4.00441 +-0.258349 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +736 736 736 727 683 622 527 458 306 215 141 67 28 2 1 1 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +776 776 776 767 723 657 556 475 300 226 150 36 6 1 0 + + + + + + +0 1 2 3 4 + + + + +333 350 93 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +273 372 88 10 2 0 12 20 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3165 (charge 2) + +1195.46 +2 + + +153.066 154.05 155.081 157.061 157.133 158.092 159.076 165.103 169.096 171.076 173.092 173.128 174.095 175.071 175.119 176.075 181.061 181.096 183.076 183.112 185.055 185.091 187.071 189.087 191.084 193.097 195.113 198.087 198.123 199.071 +199.107 201.087 203.066 213.087 214.085 216.133 219.08 221.091 222.087 226.154 230.113 234.145 240.097 244.092 254.077 268.165 272.087 273.09 278.152 287.006 290.094 296.159 299.134 304.161 308.123 314.171 317.146 321.176 327.129 337.116 +354.14 357.067 365.184 372.15 383.193 404.214 417.244 439.164 452.215 468.21 476.217 488.198 493.239 564.282 577.264 587.318 594.29 624.296 631.276 651.314 672.302 681.32 688.295 693.32 711.33 716.354 738.347 741.32 759.333 775.327 +780.345 795.364 803.388 842.371 867.381 882.394 884.394 906.361 929.4 932.427 + + + + +15 23 57 41 8 6 9 11 6 28 94 20 6 81 46 4 6 5 64 8 54 3 8 15 25 6 6 3 5 21 +18 100 29 7 10 13 17 6 7 42 7 43 12 22 43 14 80 9 7 6 14 8 6 8 25 3 6 69 7 7 +6 6 30 6 12 17 9 3 24 9 9 6 12 5 6 20 9 16 6 15 14 8 15 3 39 8 13 9 40 27 +6 33 19 16 5 51 6 8 9 8 + + + + + + +GRMZM2G179941_P01 seq=translation; coord=9:98884455..98895674:1; parent_transcript=GRMZM2G179941_T01; parent_gene=GRMZM2G179941 + + + MASAPFPPVA ASAASAPPRL APRHPFAAAA AARRSSLSFR PAARRPVLPL + RSSAVAANTL RCTHRRAVSS RSRRRAQELG AAPALAASTW GVGEEKGGCL + SCFPKSRRGR SGLARFAPCA LPHASGLSFR SRLSGSKVKP SHILHAAGPD + EPHVASPTWS DTSLDTRDMD HAISKEELED VLNTPLPEHP KLIRGQLKNG + LRYLILPNKV PANRFEAHME VHVGSIDEEE DEQGIAHMIE HVAFLGSKKR + EKLLGTGARS NAYTDFHHTV FHIHSPTKTK EYGEDLLPSV LDALNEIAFH + PKFSSSRVEK ERRAILSELQ MMNTIEYRVD CQLLQHLHSE NKLSNRFPIG + LEEQIQKWDP EKIRRFHERW YYPANATLYL VGEIDDIPRA VREIEAVFEH + TLSENEGNPV PSTSPFGAMA SLFAPKLPSG FTTNLTGEKS PATDKIKPVK + RERQAVRPPV EHKWSLPEVA QDAKPPAIFQ HELIQSFSIN MFCKIPVSKV + QTYKDLRSVL MKRIFLSALH FRINTRYKSS NPPFTSVELD HSDSGREGCT + VTTLTVTAEP QNWRSAIKVA VHEVRRLKEF GVTMGEMTRY MDALIKDSEQ + LAMMIDSVPS VDNLDFIMES DALGHTVMDQ LQGHESLLAV AETVTLEEVN + TVGAEVLEFI SDFGKPNAPL PAAIVACVPK KVHVDDIGET EFEIYPEEIT + EAIKAGLEEP IYPEPELEVP KELITQSKLD ELKLQHNPSF VPLTKEENAV + KVFDSETGIS QRRLSNGISI NYKITQNEAR VGVMRLIVGG GRATEDSESK + GSVIVGVRSL SEGGCVGNFS REQVELFCVN NLINCSLESN EEFIFMEFRF + ALRDNGMRAA FQLLHMVLEH NVWLEDAFDR AIQLYLSYYR SIPKSLERST + AHKLMLAMLN HDERFVEPSP HSLQKLTLQS VKDAVMNQFV GSNMEVSIVG + DFTEEEVESC VLDYLGTVRA SSSPTIEERI EKISFRPFPS DVHFQQVYIK + DTDERACAYI AGPAPNRWGF ATEGNDLFNV IQRSDADAEI SEPVSLDLTG + KRHINVRSHP LFFGITLSLL AEIINSRLFT TVRDSMGLTY DVSFELNLFD + KLDLGWYVIA VTSTPSKVHK AVDACKGVLR GLHSSRIVER ELDRAKRTLL + MKHEAETKTN AYWLGLLAHL QSSSVPRKDV SCIKELTTLY ENATIEDLYI + AYEHLKVDDS SLFACIGIAG AESGEDTNGN KLLMLIQL + + + + + + +6.73693 +-0.345484 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +6799 6799 6799 6605 6352 6016 5700 5341 4867 3010 2165 1466 468 211 102 33 15 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6808 6808 6808 6614 6342 5997 5653 5281 4773 2591 1677 464 22 1 0 + + + + + + +0 1 2 3 4 + + + + +3680 2791 319 24 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1234 3875 1457 207 33 6 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3166 (charge 2) + +1076.52 +2 + + +152.057 153.102 154.086 155.081 157.061 157.097 157.108 157.133 158.092 159.076 166.086 167.055 167.081 168.055 169.051 169.097 169.133 171.076 171.112 173.091 173.128 175.072 175.119 176.122 181.096 183.077 183.113 183.149 185.092 185.164 +187.108 187.144 194.128 195.113 197.128 198.087 199.071 199.107 201.087 204.134 208.108 210.087 213.159 215.139 217.081 223.063 226.154 228.097 235.119 236.103 239.095 241.09 244.165 252.096 254.113 259.091 269.124 272.17 275.126 281.051 +287.135 288.202 294.18 297.12 299.061 301.059 304.16 305.164 315.129 345.977 346.973 355.161 360.029 361.025 370.173 372.697 382.207 398.166 407.208 416.037 417.033 433.202 441.236 505.232 528.276 540.275 546.286 550.263 620.263 647.334 +649.335 657.318 691.338 727.375 744.387 746.396 802.361 831.417 903.413 918.451 + + + + +8 6 3 13 29 19 4 5 23 64 3 69 6 18 18 9 2 3 21 9 9 12 100 8 15 11 5 5 11 23 +3 6 3 2 9 5 3 32 6 3 6 29 10 5 3 12 13 31 6 5 15 6 13 3 7 2 11 6 3 6 +9 5 6 9 91 88 51 3 9 11 18 5 8 15 5 48 3 6 10 7 25 24 3 7 7 3 33 3 3 44 +5 7 5 10 85 9 9 21 7 20 + + + + + + +GRMZM2G344911_P01 NM_001157408 estradiol 17-beta-dehydrogenase 8 (LOC100284513), mRNA seq=translation; coord=7:88915398..88917303:-1; parent_transcript=GRMZM2G344911_T01; parent_gene=GRMZM2G344911 + + + MGVGAGEAVG AERAPMGARR PSAGAYGGGS RWRGGKRRDG RLLGLEVTSF + ISTRQTVHTF EPHMAEPKSN NGGADATASM MLHGRVAIVT GGAGGIGSAV + SKHLSSLGAR VVVGYIGDPA PALTLVAAIN SSEHPGESQQ PRAIAVEADV + SDAAAVKALF DAAAAAFGGE LHILVTLAAV LDYSYPPLAE TSEATFDAAF + SVNTRGTFLC CREAARRLVR DGRGRIVTFS SSGVGSLRPG YSAYAASKAA + VEVMTKILAR ELRGTGITAN VVAPGSTGTP MMYTGKTEDD MERYIAEAPL + GRLGMPEDIA PLVSFLASDA GHWVNAQVLR CNGGTI + + + + + + +5.73807 +-0.255025 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +5052 5052 5052 4970 4800 4535 4217 3998 3674 2566 1857 1212 643 375 249 141 87 36 17 6 2 1 1 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +5044 5044 5044 4962 4792 4462 4150 3833 3486 1773 1003 246 34 2 1 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2513 1887 537 90 26 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +601 2407 1553 431 55 5 0 1 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3168 (charge 2) + +946.478 +2 + + +154.086 155.081 155.118 157.061 157.097 157.108 158.092 159.076 159.112 160.08 160.116 166.061 167.081 169.061 169.097 171.076 171.113 173.092 173.128 175.119 176.122 181.096 183.112 185.092 185.164 186.088 186.123 187.071 187.107 188.074 +189.087 190.122 194.129 197.129 198.124 199.071 199.108 199.18 201.086 204.134 209.091 214.118 215.139 218.149 223.107 226.118 227.175 230.113 235.143 237.122 240.134 242.113 244.166 246.181 248.104 256.127 258.109 262.149 270.107 272.172 +274.102 276.155 284.124 286.14 288.202 299.136 302.134 317.218 327.127 329.145 335.174 345.157 355.161 371.156 388.255 398.164 404.215 416.176 444.205 446.208 456.258 459.291 475.25 515.243 528.278 546.287 549.264 562.282 574.32 621.321 +634.321 646.287 648.331 661.349 675.33 684.293 691.32 760.414 762.357 818.404 + + + + +4 13 5 4 11 4 25 98 100 4 6 4 6 5 17 6 11 15 8 83 5 6 5 50 17 4 6 64 38 5 +12 4 8 5 4 9 8 40 13 7 7 12 6 21 4 21 11 4 47 9 14 4 9 20 8 8 18 4 7 10 +16 4 5 5 21 4 4 13 8 11 4 31 5 4 5 9 8 23 4 6 11 12 8 7 5 19 6 13 9 5 +7 9 4 27 8 28 8 5 27 7 + + + + + + +GRMZM2G154169_P01 NP_001106031 putative GRF-interacting factor 2 seq=translation; coord=4:5375612..5380694:1; parent_transcript=GRMZM2G154169_T01; parent_gene=GRMZM2G154169 + + + MQQQMPMPPA PAAAAAAAPP AAGITTEQIQ KYLDENKQLI LAILENQNLG + KLAECAQYQA QLQKNLLYLA AIADAQPQPP QNPAGRPQMM QPGIVPGAGH + YMSQVPMFPP RTPLTPQQMQ EQQQQQQFQQ QQQQVQALTF PGQMVMRPGT + INGMQQQQPM QADPARAAAE LQQAAPIPAD GRGSKQDTAG GASSEPSANE + SHKSATGADT EAGGDVAEKS + + + + + +GRMZM2G154169_P02 NP_001106031 putative GRF-interacting factor 2 seq=translation; coord=4:5375620..5379628:1; parent_transcript=GRMZM2G154169_T02; parent_gene=GRMZM2G154169 + + + MMQPGIVPGA GHYMSQVPMF PPRTPLTPQQ MQEQQQQQQF QQQQQQVQAL + TFPGQMVMRP GTINGMQQQQ PMQADPARAA AELQQAAPIP ADGRGSKQDT + AGGASSEPSA NESHKSATGA DTEAGGDVAE KS + + + + + + +5.72307 +-0.327033 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +4418 4418 4418 4418 4240 3341 2902 1804 1252 889 573 292 146 40 6 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +4426 4426 4426 4426 4248 3344 2661 1634 1020 659 336 107 69 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2278 1747 357 29 15 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1022 2722 588 82 4 0 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3172 (charge 2) + +1565.69 +2 + + +152.057 155.081 157.097 159.076 160.08 171.076 171.113 173.092 173.128 175.118 183.076 185.092 187.071 187.107 195.075 198.736 199.071 201.087 212.103 215.102 217.081 226.155 228.098 230.112 232.128 234.144 240.133 242.113 244.165 256.128 +260.123 270.108 272.123 281.123 283.139 299.134 301.114 311.135 317.145 325.152 327.129 340.15 342.177 345.14 355.196 357.139 363.185 370.173 372.187 382.208 400.181 403.143 410.206 412.147 417.158 428.174 434.224 446.188 466.199 471.221 +485.199 503.211 513.194 529.223 533.288 557.22 572.26 589.802 595.242 600.266 656.4 716.995 745.296 762.36 784.393 798.35 833.397 962.437 983.46 1063.48 1178.52 1196.82 1307.58 1582.47 + + + + +7 4 4 100 5 7 10 22 4 9 4 12 7 26 4 4 5 9 8 22 12 10 4 30 6 52 58 20 51 5 +10 7 7 18 5 46 26 56 9 6 10 7 9 38 18 7 19 12 8 21 20 8 10 20 6 9 44 7 6 6 +6 5 7 11 26 6 7 8 6 6 7 8 8 37 23 6 49 24 7 22 26 7 9 8 + + + + + + +GRMZM2G315088_P01 seq=translation; coord=4:49407189..49408154:-1; parent_transcript=GRMZM2G315088_T01; parent_gene=GRMZM2G315088 + + + MKRNPRVTSS RRKCRKAHFT APSSVRRVLM SAGLSTELRH KYNMRSIPIR + KDDEVQVVRG TFKGREGKVV QVYRRCWIIH VERITREKVN GSTVNVGIHP + SKVIVTKLKL DKDHKALLDR KAGAAPPTKL RASLLPTTSP RPPLAPPPPA + PLSRRSTRLF TVI + + + + + +GRMZM2G327564_P01 O82579 Ribosomal protein L26 Fragment seq=translation; coord=3:19669523..19670484:-1; parent_transcript=GRMZM2G327564_T01; parent_gene=GRMZM2G327564 + + + MKRNPRVTSS RRKCRKAHFT APSSVRRVLM SAGLSTELRH KYNVRSIPIR + KDDEVQVVRG TYKGREGKVV QVYRRRWVIH VERITREKVN GSTVNVGIHP + SKVIVTKLKL DKDRKALLDR KARGRAADKA KGKFTADDVA AAAAGGAATG + ASLQEID + + + + + +GRMZM2G041238_P01 NP_001151634 LOC100285268 seq=translation; coord=8:13554391..13555376:1; parent_transcript=GRMZM2G041238_T01; parent_gene=GRMZM2G041238 + + + MKRNPRVTSS RRKCRKAHFT APSSVRRVLM SAALSTELRH KYNVRSIPIR + KDDEVQVVRG TYKGREGKVV QVYRRRWVIH VERITREKVN GSTVNVGIHP + SKVMVTKLKL DKDRKALLDR KARGRAADKA KGKFTADDVA AAAGGAAATG + ASLQEID + + + + + +GRMZM2G470608_P01 seq=translation; coord=2:180794699..180795223:-1; parent_transcript=GRMZM2G470608_T01; parent_gene=GRMZM2G470608 + + + MKCNPRATSS CRKCRKAHFT APSSVRRVLM SVGLSTELHH KYNVLSIPIR + KDDEVQVVRG TYKGREGKVV QVYRRRWVIH IERITREKVN GSTVNVGIHP + SKVIVTKLKL DKDRKALLDR KAQNN + + + + + +GRMZM2G463887_P01 seq=translation; coord=4:236012675..236013130:1; parent_transcript=GRMZM2G463887_T01; parent_gene=GRMZM2G463887 + + + APRQLGAVES IPGRQSHSTE RSILPPATST RSPTQKTLAA ATEAASQVSR + SAHPAAAMKR NPRITSSRRK CSKAHFTAPS SVRCVLMSDG LSTELHPDPQ + GRRGAGRARH LQGP + + + + + + +7.34586 +-0.341668 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +8582 8582 8582 8582 8457 8164 7850 7273 6644 5272 4107 2455 1283 615 245 132 71 25 6 2 1 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +8608 8608 8608 8608 8483 8174 7724 7046 6270 4530 2684 765 136 21 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1972 3347 2342 714 183 51 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1363 3172 2606 1088 271 76 10 27 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3173 (charge 3) + +1200.65 +3 + + +155.081 155.118 157.097 157.108 158.092 159.076 159.092 159.112 165.069 166.061 166.086 167.081 169.097 169.134 171.113 173.092 173.129 175.119 176.121 181.133 183.113 183.149 185.091 185.116 185.164 186.09 186.123 187.107 187.144 192.076 +197.128 200.139 201.123 204.134 209.104 211.143 215.138 226.154 228.17 231.113 244.165 246.181 254.112 255.143 257.162 260.07 261.645 272.123 273.155 275.641 283.14 285.132 286.151 293.161 297.163 301.187 304.161 305.676 308.196 320.169 +325.221 333.214 337.197 341.131 343.204 350.162 357.248 361.219 363.214 368.172 378.198 384.164 396.266 402.198 404.251 431.223 439.202 448.251 450.734 458.231 478.275 482.308 484.268 493.278 500.245 505.242 527.294 541.27 545.304 547.309 +557.338 567.308 607.248 616.341 618.331 626.382 715.339 732.368 803.404 900.462 + + + + +12 13 17 6 24 5 7 12 7 6 7 8 24 5 9 6 6 100 6 11 13 23 13 7 6 5 6 11 8 7 +8 10 7 5 28 12 11 22 11 7 21 9 12 9 9 5 10 7 32 22 31 17 6 8 9 8 16 5 5 17 +9 5 24 5 7 5 16 26 7 5 7 6 7 8 6 7 8 89 5 6 5 5 5 10 15 37 13 6 93 7 +7 6 5 13 8 12 6 7 7 7 + + + + + + +conta|P35908|K22E_HUMAN Keratin, type II cytoskeletal 2 epidermal (Cytokeratin 2e) (K2e) (CK 2e) - Homo sapiens (Human). + + + MSCQISCKSR GRGGGGGGFR GFSSGSAVVS GGSRRSTSSF SCLSRHGGGG + GGFGGGGFGS RSLVGLGGTK SISISVAGGG GGFGAAGGFG GRGGGFGGGS + GFGGGSGFGG GSGFSGGGFG GGGFGGGRFG GFGGPGGVGG LGGPGGFGPG + GYPGGIHEVS VNQSLLQPLN VKVDPEIQNV KAQEREQIKT LNNKFASFID + KVRFLEQQNQ VLQTKWELLQ QMNVGTRPIN LEPIFQGYID SLKRYLDGLT + AERTSQNSEL NNMQDLVEDY KKKYEDEINK RTAAENDFVT LKKDVDNAYM + IKVELQSKVD LLNQEIEFLK VLYDAEISQI HQSVTDTNVI LSMDNSRNLD + LDSIIAEVKA QYEEIAQRSK EEAEALYHSK YEELQVTVGR HGDSLKEIKI + EISELNRVIQ RLQGEIAHVK KQCKNVQDAI ADAEQRGEHA LKDARNKLND + LEEALQQAKE DLARLLRDYQ ELMNVKLALD VEIATYRKLL EGEECRMSGD + LSSNVTVSVT SSTISSNVAS KAAFGGSGGR GSSSGGGYSS GSSSYGSGGR + QSGSRGGSGG GGSISGGGYG SGGGSGGRYG SGGGSKGGSI SGGGYGSGGG + KHSSGGGSRG GSSSGGGYGS GGGGSSSVKG SSGEAFGSSV TFSFR + + + + + + +4.11893 +-0.211227 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 + + + + +1248 1248 1224 1136 1084 807 633 395 239 132 80 47 27 17 14 8 5 2 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 + + + + +1255 1255 1231 1143 1066 752 525 292 123 39 8 1 0 + + + + + + +0 1 2 3 4 5 + + + + +611 485 131 20 11 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +276 691 222 46 13 5 2 3 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3174 (charge 2) + +1740.71 +2 + + +157.061 158.092 167.046 169.061 171.076 172.069 175.071 175.119 184.071 187.072 190.645 193.097 196.071 202.082 214.081 221.091 223.107 226.082 232.14 233.091 241.093 244.093 246.386 248.064 251.101 253.093 256.092 259.104 263.101 271.103 +283.103 289.161 295.102 301.114 307.138 311.097 313.114 320.126 323.1 328.125 340.124 352.126 359.134 368.122 370.136 376.194 380.119 388.141 394.171 397.148 415.157 419.157 422.164 427.159 433.215 446.166 454.166 456.156 458.166 461.178 +464.174 473.178 491.184 533.199 551.215 596.277 599.219 608.235 635.242 662.833 683.309 758.367 770.343 857.377 869.376 872.448 896.392 914.395 983.414 1001.43 1003.43 1034.42 1052.43 1070.45 1088.46 1090.45 1251.51 1253.51 1290.54 1299.56 +1308.54 1365.56 1422.6 + + + + +10 3 1 2 3 1 3 13 3 2 2 4 11 3 17 3 1 3 8 2 3 2 2 2 2 2 4 9 3 4 +11 11 2 13 8 3 2 3 3 3 7 2 2 2 4 12 4 2 4 2 2 2 3 2 34 8 8 2 2 2 +2 4 4 3 2 19 3 2 6 9 23 7 25 16 3 3 2 50 4 57 7 2 4 9 100 13 17 3 3 3 +22 22 22 + + + + + + +GRMZM2G145968_P01 NP_001105108 nucleosome/chromatin assembly factor D seq=translation; coord=2:17348097..17355999:-1; parent_transcript=GRMZM2G145968_T01; parent_gene=GRMZM2G145968 + + + MKDTSFKATG AKRKKVGGAK RGLTPFFAFL AEFRPQYLEK HPELKGVKEV + SKAAGEKWRS MSDEEKAKYG GSKKQDGKAS KKENTSSKKA KADVREGDEA + EGSNKSKSEV EDDEQDGNED EDE + + + + + +GRMZM2G145968_P02 NP_001105108 nucleosome/chromatin assembly factor D seq=translation; coord=2:17348097..17355999:-1; parent_transcript=GRMZM2G145968_T02; parent_gene=GRMZM2G145968 + + + MSDEEKAKYG GSKKQDGKAS KKENTSSKKA KADVREGDEA EGSNKSKSEV + EDDEQDGNED EDE + + + + + + +3.62567 +-0.219738 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +455 455 455 383 329 303 229 179 118 90 34 22 16 7 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + + + + +461 461 461 389 335 302 226 175 108 69 33 24 12 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +206 218 28 3 0 0 0 8 + + + + + + +0 1 2 3 4 + + + + +192 230 40 1 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3179 (charge 2) + +2068.76 +2 + + +162.501 164.446 171.112 172.071 179.079 181.06 182.044 183.113 185.055 195.114 198.123 199.071 203.066 209.055 217.081 218.085 227.066 229.118 231.062 240.098 245.076 246.079 258.108 263.086 268.13 285.156 287.097 301.115 303.165 310.103 +316.15 327.165 338.098 342.092 353.108 356.107 360.103 361.108 365.916 374.119 379.451 381.101 392.127 399.114 407.117 414.198 416.139 432.207 435.115 444.247 453.124 471.136 472.24 489.143 496.13 503.278 511.14 513.266 527.174 531.277 +545.183 570.199 586.17 588.218 607.159 625.17 642.2 657.236 660.318 732.232 775.346 890.37 1019.41 1147.47 1262.5 1433.56 1986.4 + + + + +3 3 5 6 4 10 4 3 22 3 10 21 6 3 53 3 61 16 6 5 100 7 4 59 4 7 8 7 9 5 +24 9 22 25 4 21 37 6 4 10 4 8 5 10 7 17 20 20 8 6 24 26 5 18 7 15 5 9 19 28 +6 6 5 6 7 18 9 6 25 6 17 20 9 21 8 6 6 + + + + + + +GRMZM2G099626_P01 NP_001150951 cell envelope integrity inner membrane protein TolA seq=translation; coord=6:167515353..167516623:-1; parent_transcript=GRMZM2G099626_T01; parent_gene=GRMZM2G099626 + + + MATAGSKQGG GSSKPPAAAG QELDPRYEWE ENASSFILRI HLSGFRKQDF + RVQVDGAGRL TVRGQRSDAA AANANARHSR FNKVFQLPST SNLDDIAGRF + DLGVLTLTVP KRLPAPAKED QQQAKKPEDA DADAAAATKQ VAGAKGAKSE + PEQQHKEAAA KEDKPKAAAA AAAPAPAADT TAKEDKPKAA AAAPAPAADT + KKQPETQANA ESKATDPTES LAERRTEEER ANANAAAAAE HQRKACRGFK + ERVAEELQGL AGSEWAEGLV ETVKRNREVI AVAVAAFSLG VFVSSRLFSR + SSRN + + + + + +GRMZM2G099626_P02 NP_001150951 cell envelope integrity inner membrane protein TolA seq=translation; coord=6:167515353..167516623:-1; parent_transcript=GRMZM2G099626_T02; parent_gene=GRMZM2G099626 + + + MATAGSKQGG GSSKPPAAAG QELDPRYEWE ENASSFILRI HLSEGFRKQD + FRVQVDGAGR LTVRGQRSDA AAANANARHS RFNKVFQLPS TSNLDDIAGR + FDLGVLTLTV PKRLPAPAKE DQQQAKKPED ADADAAAATK QVAGAKGAKS + EPEQQHKEAA AKEDKPKAAA AAAAPAPAAD TTAKEDKPKA AAAAPAPAAD + TKKQPETQAN AESKATDPTE SLAERRTEEE RANANAAAAA EHQRKACRGF + KERVAEELQG LAGSEWAEGL VETVKRNREV IAVAVAAFSL GVFVSSRLFS + RSSRN + + + + + + +5.31919 +-0.259473 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 + + + + +6458 6458 6458 6052 5922 4453 3846 2450 1732 1116 635 328 211 136 69 35 15 3 2 1 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6461 6461 6461 6055 5924 4421 3444 2118 1127 760 323 152 86 4 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3453 2498 430 59 26 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1157 4126 972 185 19 1 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3180 (charge 2) + +1439.75 +2 + + +152.056 155.081 157.097 167.081 169.097 173.092 173.128 173.225 175.119 181.11 183.112 183.149 185.091 187.071 197.128 198.089 199.107 201.123 209.105 211.144 214.118 218.149 222.124 226.154 229.118 240.134 242.113 244.167 254.15 257.16 +262.149 266.149 270.108 281.16 283.175 285.155 295.14 311.171 313.15 328.197 337.186 341.906 356.193 357.194 382.208 387.703 399.237 408.224 420.244 427.229 429.293 438.197 453.248 456.209 488.238 497.247 521.238 523.248 528.765 535.27 +539.246 548.788 557.263 566.181 570.67 606.302 611.299 624.301 643.625 663.324 680.338 689.333 756.389 774.399 785.452 796.384 845.438 896.482 942.489 944.485 1013.51 1084.55 1274.45 1339.6 + + + + +3 3 3 3 59 9 3 3 11 3 5 9 3 3 3 3 3 9 4 4 100 18 4 14 11 60 9 3 3 20 +3 5 3 2 8 81 3 71 5 26 4 3 69 10 44 9 18 4 20 58 4 5 10 4 3 3 3 13 5 13 +5 4 3 8 3 13 3 4 4 3 3 4 5 55 5 3 4 3 72 4 14 4 3 3 + + + + + + +GRMZM2G140667_P01 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589206..218592127:-1; parent_transcript=GRMZM2G140667_T01; parent_gene=GRMZM2G140667 + + + + + + + + +GRMZM2G140667_P02 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589352..218592127:-1; parent_transcript=GRMZM2G140667_T02; parent_gene=GRMZM2G140667 + + + + + + + + +GRMZM2G140667_P04 NP_001105500 ascorbate peroxidase2 seq=translation; coord=2:218589294..218592021:-1; parent_transcript=GRMZM2G140667_T04; parent_gene=GRMZM2G140667 + + + + + + + + + +5.54597 +-0.270535 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +7053 7053 6949 6819 6303 5748 4253 3371 2219 1321 725 369 200 98 48 28 15 8 3 1 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7057 7057 6953 6823 6296 5671 4013 2839 1474 480 111 28 3 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3467 2897 594 110 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1430 3955 1341 290 35 5 1 16 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3185 (charge 2) + +1233.6 +2 + + +155.081 158.092 159.076 167.117 169.096 171.076 171.113 173.092 175.119 178.049 181.06 181.096 185.092 186.087 186.123 187.071 187.107 191.084 195.076 195.112 198.087 199.071 199.107 200.102 202.118 205.063 209.091 212.103 216.098 218.15 +219.153 227.102 230.113 232.14 240.133 243.109 244.092 258.108 260.196 267.06 270.108 278.148 284.122 295.103 310.101 313.113 315.129 324.154 326.673 329.181 331.123 337.149 341.144 345.14 347.191 355.159 364.174 381.177 387.193 398.202 +421.21 424.145 426.198 442.156 445.239 446.261 452.21 458.235 460.166 466.192 495.255 523.211 538.261 541.224 545.328 553.261 555.289 559.23 581.256 582.259 592.306 635.321 645.354 652.34 654.346 674.365 722.396 727.337 728.345 762.339 +779.416 781.383 791.329 850.452 878.437 889.457 918.422 925.431 1004.49 1115.52 + + + + +11 7 13 4 5 7 10 8 19 5 4 6 4 8 2 10 2 6 27 12 6 4 18 7 6 2 9 11 5 29 +4 28 32 25 6 4 9 5 2 4 4 7 5 4 4 6 4 6 25 20 2 13 4 9 15 5 2 4 4 5 +2 7 4 13 5 19 9 12 8 4 4 4 4 8 10 8 23 7 10 4 4 7 7 100 8 5 8 11 2 15 +12 4 4 8 16 8 5 8 12 4 + + + + + + +GRMZM2G161295_P01 NP_001142140 hypothetical protein LOC100274305 seq=translation; coord=3:155960410..155963163:-1; parent_transcript=GRMZM2G161295_T01; parent_gene=GRMZM2G161295 + + + MPQHDSSATP PVEYHDSSAT FETKKGTGKD SGKILDGRCP TPAHHYPLAF + LSLGRNVKCS SSQQRGLEHS PVTTQQRSQH RGEIMSSLSS GISASPSAAP + STARRRHDAA PQQLRVKAAA RPQLLHAGRR RSSVGRRPGG GAVVVRAGPG + PLSEIEPDLE EDAIDVYRTN GISPEDFEYG KYDGHHTYFE GQDKKGFWED + VSEWYQEAEP PQGFQALISW AFPPAIILGM AFNVPGEYLY IGAAVFIVVF + CVIEMGKPDK PHNFEPEIYM MERSARDKLI ADYNSMDIWD FNEKYGELWD + FTVNTRDDIV KST + + + + + + +6.62594 +-0.339792 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +5465 5465 5465 5465 5369 5056 4681 4189 2918 1973 1018 421 183 93 41 17 6 4 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5467 5467 5467 5467 5371 5058 4666 4080 2648 1411 439 56 11 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1535 2425 1140 298 59 11 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1262 2693 1183 261 49 18 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3188 (charge 3) + +1724.77 +3 + + +155.081 157.097 159.077 167.092 169.061 169.097 171.076 171.149 172.152 173.091 173.128 175.119 181.06 183.112 185.092 186.088 186.124 187.071 195.089 198.086 199.108 199.144 201.086 207.112 209.092 213.086 226.154 227.158 229.117 233.092 +237.123 239.114 244.165 246.09 249.123 251.102 257.196 275.207 277.118 279.096 285.009 292.101 297.118 299.141 301.115 304.159 310.114 314.135 333.141 334.136 337.15 342.147 355.07 383.194 390.235 402.173 406.16 414.675 416.223 419.179 +423.677 427.178 445.181 447.173 452.246 456.148 470.316 473.178 497.216 501.271 530.209 532.272 548.22 576.323 582.24 587.276 610.239 618.297 627.278 644.305 654.836 661.863 665.271 683.284 686.343 688.327 693.27 696.463 704.357 706.336 +711.28 815.382 851.425 852.426 856.337 1014.49 1079.57 1115.53 1226.66 1252.57 + + + + +15 15 17 11 5 30 10 57 14 11 5 44 6 5 9 15 12 16 15 9 17 25 12 12 15 11 100 24 9 24 +15 19 55 5 12 24 12 56 12 18 11 16 19 10 12 9 24 23 5 8 10 10 35 5 18 10 5 15 9 10 +11 11 12 11 10 5 11 14 5 4 9 11 12 18 14 21 13 9 5 10 12 16 5 5 13 18 20 12 23 12 +16 5 29 14 10 19 5 11 5 9 + + + + + + +GRMZM2G056462_P01 NP_001148481 eukaryotic translation initiation factor 2 beta subunit seq=translation; coord=1:55442662..55452658:1; parent_transcript=GRMZM2G056462_T01; parent_gene=GRMZM2G056462 + + + MADDEQAEKK EEVPELAPFD PTKKKKKKKV VIQEPSDEVD NLAEKTESLT + VTESSEPSFA GMKKKKKKHV ELDSSLTETG DVDDTGDDQV REDEEGEGIV + LAGAAATRYP WEGTDRDYKY EELLGRVFNI LRENNPDLAG DRRRTVMRPP + QVLREGTKKT VFVNFMDLCK TMHRQPEHVM MFLLAEMGTS GSLDGQQRLV + IKGRFAPKNF EAILRRYINE YVICNGCKSP DTILSKENRL FFLRCEQCGS + SRSVAPIKAG FVAQVGRRKA GS + + + + + +GRMZM2G030646_P01 NP_001132460 hypothetical protein LOC100193916 seq=translation; coord=2:217093149..217097528:-1; parent_transcript=GRMZM2G030646_T01; parent_gene=GRMZM2G030646 + + + MADEEHPERR EEASELAPFD PTKKKKKKKV VIQEPSDEVD KLAEKTESLA + VAEPAELNFT GMKKKKKKQV DLDSSIDDLG DGEDTQGDQV VEEQGDGIVL + GGGPTYPWEG TDRDYKYEEL LDRVFNILRE NNPDLAGDRR RTVMRPPQVL + REGTKKTVFV NFMDLCKTMH RQPEHVMMFL LAEMGTSGSL DGQQRLVIKG + RFAPKNFEAI LRRYINEYVI CNGCKSPDTI LSKENRLFFL RCEQCGSSRS + VAPIKAGFVA QVGRRKA + + + + + +GRMZM2G030646_P02 NP_001132460 hypothetical protein LOC100193916 seq=translation; coord=2:217093149..217097090:-1; parent_transcript=GRMZM2G030646_T02; parent_gene=GRMZM2G030646 + + + MKKKKKKQVD LDSSIDDLGD GEDTQGDQVV EEQGDGIVLG GGPTYPWEGT + DRDYKYEELL DRVFNILREN NPDLAGDRRR TVMRPPQVLR EGTKKTVFVN + FMDLCKTMHR QPEHVMMFLL AEMGTSGSLD GQQRLVIKGR FAPKNFEAIL + RRYINEYVIC NGCKSPDTIL SKENRLFFLR CEQCGSSRSV APIKAGFVAQ + VGRRKA + + + + + +GRMZM2G080048_P01 B6TI18 Eukaryotic translation initiation factor 2 beta subunitPutative uncharacterized protein ; seq=translation; coord=7:173275632..173279449:-1; parent_transcript=GRMZM2G080048_T01; parent_gene=GRMZM2G080048 + + + MADEEHSERR EEASELAPFD PTKKKKKKKV VIQEPSDEVD KLAEKTETLA + VAEPAELNFT GMKKKKKKPV DLDSTLDELG DGEDTQDDQA VEEQGEGIVL + GSVPTYPWEG TDRDYKYEEL LDRVFNILRE NNPDLAGDRR RTVMRPPQVL + REGTKKTVFV NFMDLCKTMH RQPEHVMMFL LAEMGTSGSL DGQQRLVIKG + RFAPKNFEAI LRRYINEYVI CNGCKSPDTI LSKENRLFFL RCEQCGSSRS + VAPIKAGFVA QVGRRKA + + + + + +GRMZM2G080048_P02 B6TI18 Eukaryotic translation initiation factor 2 beta subunitPutative uncharacterized protein ; seq=translation; coord=7:173275646..173279449:-1; parent_transcript=GRMZM2G080048_T02; parent_gene=GRMZM2G080048 + + + MADEEHSERR EEASELAPFD PTKKKKKKKV VIQEPSDEVD KLAEKTETLA + VAEPAELNFT GMKKKKKKPV DLDSTLDELG DGEDTQDDQA VEEQGEGIVL + GSVPTYPWEG TDRDYKYEEL LDRVFNILRE NNPDLAGDRR RTVMRPPQVL + REGTKKTVFV NFMDLCKTMH RQPEHVMMFL LAEMGTSGSL DGQQRLVIKG + RFAPKNFEAI LRRYINEYVI CNGCKSPDTI LSKENRLFFL RCEQCGSSRS + VAPIKAGFVA QVGRRKA + + + + + + +6.48613 +-0.332622 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 + + + + +2955 2955 2955 2885 2728 2590 2419 2195 1938 1140 856 475 247 99 48 21 5 2 1 1 0 0 0 0 0 0 0 0 0 0 +0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +2960 2960 2960 2890 2733 2587 2397 2116 1812 920 521 199 16 1 0 + + + + + + +0 1 2 3 4 + + + + +1425 1254 275 21 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +634 1627 549 139 6 2 2 16 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3190 (charge 2) + +1100.5 +2 + + +152.057 155.082 155.117 156.076 157.061 157.097 157.109 157.133 158.092 159.076 166.05 167.081 169.097 171.076 171.113 173.092 173.128 175.119 176.123 181.06 181.096 183.076 183.113 184.072 185.055 185.092 185.129 185.165 186.086 187.071 +187.108 189.086 192.111 194.129 195.075 198.087 199.072 199.107 202.082 204.134 208.072 213.087 215.139 216.098 219.116 226.082 227.066 229.092 235.144 239.095 240.097 243.132 244.092 246.155 249.159 255.108 258.108 270.108 272.171 278.076 +288.204 293.077 295.104 300.149 303.213 309.654 312.129 323.099 326.172 330.139 340.123 347.166 363.182 372.188 383.214 392.213 395.18 412.182 418.203 466.206 517.273 531.288 535.178 554.308 575.273 599.29 618.303 628.304 641.333 646.315 +656.299 685.32 692.303 725.357 743.366 744.373 755.385 789.358 826.413 857.411 + + + + +7 12 6 3 11 6 5 12 21 15 7 12 11 7 9 8 5 100 3 11 6 14 11 7 4 17 14 27 6 6 +22 6 4 6 3 8 18 11 30 3 16 30 9 9 7 35 10 8 14 18 7 5 29 6 16 7 3 3 12 5 +3 6 12 6 11 3 7 18 8 8 6 27 8 13 8 9 13 26 40 3 18 56 6 13 24 15 8 14 12 28 +3 3 9 17 53 24 6 4 16 8 + + + + + + +GRMZM2G164538_P01 NP_001130932 hypothetical protein LOC100192037 seq=translation; coord=10:95345548..95351279:1; parent_transcript=GRMZM2G164538_T01; parent_gene=GRMZM2G164538 + + + MMESQPLQAP TATAPAPGSA EPAGAPPAVT PGKEFTRTCK GLVVVLIGGY + VLLQLLPSSL NYLAIIPSKT IPYVWTVFTA GYIEQVLPGA IGSSLGLLFC + GKDIEPAWGR KEFLKFIILI NSICGILAFC FAIGLYYVTG KESFLVTPLS + GFHGCLAGFL VALKQLLPNL ELPMCFFWKI KAKWMPFFVV CFSSIMAFIV + PDSINFLPTL VSGMYVSWLY LRYFQRNPLT GLKGDPSDDF SFPSLFPAAM + RPVTDPVANL FDRLLCARSR PLEVALPISD PTKASRRRER GERVLEERLA + ADNAGDTEAS PRGHGTAED + + + + + + +5.29664 +-0.271623 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 + + + + +4550 4550 4546 4328 4192 3750 3522 2072 1625 700 440 232 160 75 31 17 8 2 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4553 4553 4549 4331 4179 3704 3445 1887 1285 470 157 87 31 7 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2100 1958 450 37 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1047 2862 554 79 9 0 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3191 (charge 2) + +1387.64 +2 + + +152.057 155.081 155.118 157.061 157.097 157.133 158.092 158.137 159.076 159.113 159.942 169.097 171.076 171.113 173.092 175.118 183.112 183.148 185.092 185.128 186.087 186.132 187.071 187.107 191.084 195.112 197.128 198.121 199.106 202.084 +205.096 211.144 213.087 215.137 219.078 223.108 226.154 228.133 230.077 234.145 237.123 242.113 244.164 247.107 255.145 256.165 258.107 265.117 272.171 274.101 283.103 293.112 301.114 309.119 325.185 327.129 342.175 354.139 359.204 369.175 +372.15 398.166 408.155 426.158 430.24 440.212 443.191 468.207 485.235 511.248 548.63 559.283 590.301 598.299 616.296 642.318 660.329 664.86 741.357 775.357 804.87 814.365 832.377 834.381 903.415 905.414 913.397 1000.42 1017.46 1019.45 +1115.47 1132.48 1143.42 1186.48 1203.52 + + + + +3 10 4 2 7 73 9 2 13 3 2 3 4 4 3 26 15 7 2 89 4 4 13 3 3 2 3 2 4 3 +2 12 8 2 3 3 10 3 11 3 4 4 3 3 33 8 9 12 29 3 3 3 26 3 3 9 9 3 16 3 +10 9 2 3 35 15 4 12 2 3 2 17 3 4 3 4 72 9 3 21 3 8 100 13 40 3 3 9 25 3 +3 18 3 3 15 + + + + + + +GRMZM2G122871_P01 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104071298:1; parent_transcript=GRMZM2G122871_T01; parent_gene=GRMZM2G122871 + + + + + + + +GRMZM2G122871_P04 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104068352..104071134:1; parent_transcript=GRMZM2G122871_T04; parent_gene=GRMZM2G122871 + + + + + + + +GRMZM2G122871_P02 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104071298:1; parent_transcript=GRMZM2G122871_T02; parent_gene=GRMZM2G122871 + + + + + + + +GRMZM2G122871_P03 NP_001131533 hypothetical protein LOC100192872 seq=translation; coord=6:104066600..104070943:1; parent_transcript=GRMZM2G122871_T03; parent_gene=GRMZM2G122871 + + + + + + + + +4.67055 +-0.252462 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 + + + + +5704 5704 5704 5689 5607 3703 3131 1663 1062 673 446 315 201 71 42 9 2 1 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +5705 5705 5705 5690 5608 3704 3097 1553 962 571 329 225 113 2 1 0 + + + + + + +0 1 2 3 4 + + + + +3971 1545 182 18 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +941 4393 316 53 1 0 0 12 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3194 (charge 2) + +1718.93 +2 + + +162.619 168.065 169.097 169.783 171.076 171.149 175.118 181.06 188 199.144 201.086 226.155 229.118 240.135 244.165 259.103 270.466 298.138 300.155 328.186 331.554 351.166 395.162 399.224 427.181 451.3 469.312 543.297 553.68 556.221 +597.286 627.261 649.962 651.852 660.862 694.458 696.88 765.499 768.349 843.402 858.44 861.447 894.533 933.847 1023.58 1088.05 1152.61 1320.71 1322.72 1521.76 + + + + +4 4 21 4 3 89 9 3 4 86 6 77 8 5 42 4 3 25 9 59 4 4 4 7 16 8 38 5 5 9 +5 23 4 15 55 48 8 17 5 6 69 28 16 5 9 5 18 100 20 6 + + + + + + +GRMZM5G808402_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=Pt:54176..56114:-1; parent_transcript=GRMZM5G808402_T01; parent_gene=GRMZM5G808402 + + + + + + + +GRMZM2G385622_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=2:200098864..200103052:1; parent_transcript=GRMZM2G385622_T01; parent_gene=GRMZM2G385622 + + + + + + + +GRMZM2G062854_P01 Q5SBI2 Putative uncharacterized protein seq=translation; coord=6:160782373..160789444:-1; parent_transcript=GRMZM2G062854_T01; parent_gene=GRMZM2G062854 + + + + + + + +GRMZM2G448389_P01 Q5SBI4 Putative uncharacterized protein seq=translation; coord=1:203928301..203930456:1; parent_transcript=GRMZM2G448389_T01; parent_gene=GRMZM2G448389 + + + MRTNPTTSRP GISTIEEKSV GRIDQIIGPV LDITFPPGKL PYIYNALIVK + SRDTADKQIN VTCEVQQLLG NNRVRAVAMS ATEGLMRGME VIDTGTPLSV + PVGGATLGRI FNVLGEPIDN LGPVDTSATF PIHRSAPAFI ELDTKLSIFE + TGIKVVDLLA PYRRGGKIGL FGGAGVGKTV LIMELINNIA KAHGGVSVFG + GVGERTREGN DLYMEMKESG VINEKNIEES KVALVYGQMN EPPGVRMRVG + LTALTMAEYF RDVNKQDVLL FIDNIFRFVQ AGSEVSALLG RMPSAVGYQP + TLSTEMGSLQ ERITSTKKGS ITSIQAVYVP ADDLTDPAPA TTFAHLDATT + VLSRGLASKG IYPAVDPLDS TSTMLQPRIV GNEHYETAQR VKETLQRYKE + LQDIIAILGL DELSEEDRLT VARARKIERF LSQPFFVAEV FTGSPGKYVG + LAETIRGFQL ILSGELDGLP EQAFYLVGNI DEASTKAINL EEESKLKK + + + + + +GRMZM2G448142_P02 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203904004..203910810:-1; parent_transcript=GRMZM2G448142_T02; parent_gene=GRMZM2G448142 + + + + + + + +GRMZM2G448142_P03 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203907697..203910810:-1; parent_transcript=GRMZM2G448142_T03; parent_gene=GRMZM2G448142 + + + + + + + + +5.60204 +-0.26056 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +7756 7756 7640 7375 7020 6502 5842 5144 3519 2472 1125 629 359 197 113 55 24 15 13 2 1 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7745 7745 7629 7364 6991 6429 5610 4820 2773 1310 263 47 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2378 3099 1646 485 125 26 5 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1340 3598 2071 510 168 61 8 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3196 (charge 3) + +1416.69 +3 + + +150.066 155.045 156.076 157.097 158.092 159.076 159.112 164.118 166.061 171.112 172.071 173.092 175.119 176.122 185.091 185.164 186.168 187.071 187.107 200.102 213.159 216.097 218.149 221.103 226.118 235.142 239.113 244.092 246.179 249.098 +258.107 261.119 265.117 267.108 269.122 271.141 273.134 284.087 286.15 293.113 301.128 303.177 317.217 329.148 340.16 345.137 347.095 355.16 357.187 364.122 374.214 381.15 393.151 394.157 410.177 412.158 416.174 421.145 430.17 438.172 +443.71 447.185 452.716 458.24 459.292 475.261 492.219 509.245 510.247 515.244 517.237 537.239 548.227 557.231 562.282 573.242 579.743 585.247 586.294 594.259 601.232 602.769 604.303 606.31 634.323 652.304 661.35 672.306 684.294 730.282 +750.344 760.419 767.366 769.372 777.352 818.407 887.4 904.425 906.431 1033.46 + + + + +4 10 3 5 9 7 21 4 2 2 22 3 42 3 6 88 10 7 8 4 12 2 2 13 7 2 4 5 4 18 +3 3 3 15 6 6 10 5 10 4 10 6 3 2 4 3 2 2 4 3 12 4 14 5 13 6 6 4 4 15 +3 2 28 3 3 39 4 8 2 2 3 5 2 3 3 6 2 3 9 5 5 16 55 4 4 7 12 2 3 3 +6 3 100 11 4 6 3 29 5 6 + + + + + + +GRMZM2G435373_P01 NP_001151199 LOC100284832 seq=translation; coord=8:103922075..103930908:-1; parent_transcript=GRMZM2G435373_T01; parent_gene=GRMZM2G435373 + + + MDEEYDVIVL GTGLKECILS GLLSVDGLKV LHMDRNDYYG GDSTSLNLNQ + LWKRFRGEDK PPAHLGASRD YNVDMVPKFM MANGTLVRTL IHTDVTKYLS + FKAVDGSYVF SKGKIYKVPA TDMEALKSPL MGLFEKRRAR NFFIYVQDYN + EADPRTHQGL DLTRVTTREL IAKYGLSDDT VDFIGHALAL HRDDRYLDEP + ALDTVKRMKL YSESLARFQG GSPYIYPLYG LGELPQGFAR LSAVYGGTYM + LNKPECKVEF DMEGKVCGVT SEGETAKCKK VVCDPSYLPN KVRKIGRVVR + AIAIMSHPIP NTNESHSVQI ILPQKQLGRR SDMYVFCCSY THNVAPRGKF + IAFVSAEAET DNPQSELKPG IDLLGSVDEI LYDIYDRYEP VNEPSLDNCF + VTTSYDATTH FETTVTDVLN MYTMITGKTV DLSVDLSAAS AAEEY + + + + + +GRMZM2G435373_P02 NP_001151199 LOC100284832 seq=translation; coord=8:103922075..104021247:-1; parent_transcript=GRMZM2G435373_T02; parent_gene=GRMZM2G435373 + + + MDEEYDVIVL GTGLKECILS GLLSVDGLKV LHMDRNDYYG GDSTSLNLNQ + LWKRFRGEDK PPAHLGASRD YNVDMVPKFM MANGTLVRTL IHTDVTKYLS + FKAVDGSYVF SKGKIYKVPA TDMEALKSPL MGLFEKRRAR NFFIYVQDYN + EADPRTHQGL DLTRVTTREL IAKYGLSDDT VDFIGHALAL HRDDRYLDEP + ALDTVKRMKL YSESLARFQG GSPYIYPLYG LGELPQGFAR LSAVYGGTYM + LNKPECKVEF DMEGKVCGVT SEGETAKCKK VVCDPSYLPN KVRKIGRVVR + AIAIMSHPIP NTNESHSVQI ILPQKQLGRR SDMYVFCCSY THNVAPRGKF + IAFVSAEAET DNPQSELKPG IDLLGSVDEI LYDIYDRYEP VNEPSLDNCF + VTTSYDATTH FETTVTDVLN MYTMITGKTV DLSVDLSAAS AAEEY + + + + + +GRMZM2G117507_P01 seq=translation; coord=6:147337293..147347544:-1; parent_transcript=GRMZM2G117507_T01; parent_gene=GRMZM2G117507 + + + MDEEYDVIVL GTGLKECILS GLLSVDGLKV LHMDRNDYYG GDSTSLNLNQ + LWKRFRGEDK PPAHLGASRD YNVDMVPKFM MANGTLVRTL IHTDVTKYLS + FKAVDGSYVF SKGKIYKVPA TDMEALKSPL MGLFEKRRAR NFFIYVQDYN + EADPRTHQGL DLTRVTTREL IAKYGLSDDT VDFVGHALAL HRDDRYLDEP + ALDTVKRMKL YADSLARFQG GSPYIYPLYG LGELPQGFAR LSAVYGGTYM + LNKPDCKVEF DMEGKVCGVT SEGETAKCKK VVCDPSYLQN KVRKIGRVVR + AIAIMSHPIP NTNESHSVQI ILPQKQLGRR SDMYVFCCSY THNVAPRGKF + IAFVSAEAET DNPQSELKPG IDLLGSVDEI FYDIYDRYEP VNEPSLDNCF + VSTSYDATTH FETTVTDVLN MYTMITGKTV DLSVDLSAAS AAEEY + + + + + + +7.82337 +-0.332909 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 + + + + +12509 12509 12509 12509 12173 11732 10720 9806 8695 6440 4525 2495 1367 686 317 155 86 24 12 3 2 2 1 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +12518 12518 12518 12518 12182 11727 10662 9626 8374 5043 2972 746 135 15 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3101 5375 2989 843 181 20 0 10 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2553 5570 2892 1129 285 74 8 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3197 (charge 3) + +1637.85 +3 + + +152.057 155.081 157.097 158.092 159.076 162.091 165.102 171.076 171.113 175.119 181.133 185.091 185.165 189.086 195.113 198.087 199.071 199.107 199.18 201.123 203.102 207.112 213.159 215.139 217.097 223.155 226.118 227.175 229.117 234.144 +240.134 243.134 245.126 251.15 258.144 262.151 278.153 284.125 287.15 303.177 306.155 309.118 320.68 327.131 345.213 347.168 379.205 390.209 401.713 404.725 415.711 453.251 460.204 462.243 487.226 488.229 490.235 499.756 503.293 507.264 +517.293 520.227 533.283 542.269 547.289 551.221 554.291 568.286 575.273 576.275 605.266 618.31 622.294 640.354 648.296 672.333 691.326 711.392 713.359 715.358 733.362 735.326 736.326 739.336 751.398 776.348 792.337 808.442 814.407 818.393 +826.369 830.411 846.35 864.367 866.363 870.335 880.456 905.501 970.508 977.452 + + + + +6 8 6 14 8 6 10 8 6 84 8 9 34 7 8 6 7 11 100 25 6 21 10 8 8 15 19 22 14 11 +7 6 13 12 7 13 7 7 23 19 8 7 21 11 18 7 7 58 7 22 18 36 6 7 25 9 14 6 60 6 +6 12 13 6 24 22 19 16 8 6 90 16 21 35 8 6 6 26 15 6 44 51 20 6 7 9 12 63 6 8 +8 6 16 85 10 7 12 15 9 9 + + + + + + +GRMZM5G808402_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=Pt:54176..56114:-1; parent_transcript=GRMZM5G808402_T01; parent_gene=GRMZM5G808402 + + + + + + + +GRMZM2G385622_P01 P00827 ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)(F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) seq=translation; coord=2:200098864..200103052:1; parent_transcript=GRMZM2G385622_T01; parent_gene=GRMZM2G385622 + + + + + + + +GRMZM2G062854_P01 Q5SBI2 Putative uncharacterized protein seq=translation; coord=6:160782373..160789444:-1; parent_transcript=GRMZM2G062854_T01; parent_gene=GRMZM2G062854 + + + + + + + +GRMZM2G448389_P01 Q5SBI4 Putative uncharacterized protein seq=translation; coord=1:203928301..203930456:1; parent_transcript=GRMZM2G448389_T01; parent_gene=GRMZM2G448389 + + + + + + + +GRMZM2G448142_P02 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203904004..203910810:-1; parent_transcript=GRMZM2G448142_T02; parent_gene=GRMZM2G448142 + + + + + + + +GRMZM2G448142_P03 P06670 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 1.6.5.-)(NAD(P)H dehydrogenase subunit K)(NADH-plastoquinone oxidoreductase subunit K) seq=translation; coord=1:203907697..203910810:-1; parent_transcript=GRMZM2G448142_T03; parent_gene=GRMZM2G448142 + + + + + + + + +5.98971 +-0.234891 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 67 68 69 + + + + +6412 6412 6412 6154 5840 5409 5015 4620 2958 2356 1209 590 323 210 138 65 39 28 12 7 5 3 2 2 1 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6422 6422 6422 6164 5846 5344 4902 4415 2378 1474 379 77 32 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3209 2517 569 110 16 0 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1265 3547 1236 266 85 20 2 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3198 (charge 2) + +1416.69 +2 + + +155.045 155.081 157.097 158.092 159.112 171.076 172.071 175.119 176.121 178.134 181.108 185.165 186.168 187.107 200.103 209.104 213.159 221.104 226.118 244.093 249.098 267.108 270.181 271.139 273.135 284.087 286.15 293.113 301.121 303.178 +339.201 347.097 357.186 363.141 372.187 374.215 381.15 384.223 393.15 400.183 410.176 412.159 421.148 430.171 438.172 452.716 458.233 468.248 475.261 492.215 508.233 513.264 517.237 520.218 522.227 537.24 548.224 557.23 565.744 574.258 +579.741 586.294 587.289 594.259 601.235 602.77 604.304 606.306 608.258 622.33 634.312 643.791 650.324 652.303 700.319 710.359 730.284 750.346 767.366 769.372 777.352 813.38 818.402 844.4 868.425 887.397 904.426 906.427 914.406 1015.45 +1030.42 1033.47 1130.51 1147.5 1187.5 1188.52 1204.53 1206.54 1263.6 1304.58 + + + + +6 9 5 6 5 2 17 53 3 5 4 96 11 3 3 7 33 6 6 6 12 12 7 9 7 6 11 3 8 10 +3 4 4 3 4 17 4 3 5 6 8 7 4 5 15 33 4 3 42 3 9 3 5 3 4 7 5 6 3 7 +3 9 4 9 7 32 56 4 4 7 4 9 7 22 7 4 8 5 100 9 8 5 5 3 5 5 59 5 4 5 +3 14 3 3 6 6 41 9 6 3 + + + + + + +AC195340.3_FGP002 seq=translation; coord=5:5423706..5426538:1; parent_transcript=AC195340.3_FGT002; parent_gene=AC195340.3_FG002 + + + MASLLARQAA QALRARQTAQ LGPAASAMQG HLRTYMNAGI PKRFKEDEEK + EQLAKDLAKD WNAVFERSIN TLFLTEMVRG LMLTLKYFFD RNVTINYPFE + KGPLSPRFRG EHALRRYESG EERCIACKLC EAICPAQAIT IEAEEREDGS + RRTTRYDIDM TKCIYCGFCQ EACPVDAIVE GPNFEFATET HEELLYDKEK + LLENGDRWET EIAENLRSES LYR + + + + + + +7.07186 +-0.344969 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 + + + + +9194 9194 9194 9194 9194 9063 8740 8208 7462 5933 4477 2574 1521 558 238 115 52 18 6 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +9202 9202 9202 9202 9202 9071 8747 8156 7295 5371 3035 1310 423 18 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2557 3909 1834 710 163 24 0 6 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1460 3873 2826 835 174 30 3 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3200 (charge 3) + +1493.75 +3 + + +152.056 155.081 155.117 157.061 157.097 157.134 158.092 159.076 166.05 167.081 167.117 169.061 169.097 169.133 171.113 172.071 173.128 175.119 177.102 181.06 183.076 183.149 185.092 186.087 186.123 187.071 195.113 197.128 199.071 200.102 +201.123 204.134 211.144 213.123 218.15 219.15 223.155 224.102 226.118 231.124 240.134 242.113 245.076 251.149 258.108 262.139 267.108 274.187 276.171 286.139 308.158 329.191 331.236 351.165 353.182 356.684 363.178 369.178 371.194 374.119 +405.211 439.184 442.27 459.292 461.234 480.293 501.278 502.282 536.234 543.274 544.283 570.327 588.336 589.34 599.817 610.303 615.309 620.324 625.216 631.249 639.838 648.345 649.355 673.843 684.329 697.401 712.362 716.431 742.285 748.347 +750.369 754.421 785.388 809.416 841.452 845.481 861.427 870.353 884.411 885.414 + + + + +12 55 13 10 13 11 27 36 19 13 12 11 14 22 20 13 19 100 22 15 32 44 12 15 14 12 35 16 20 27 +18 18 11 14 73 21 21 16 36 23 48 15 26 16 21 26 11 88 26 11 24 15 21 11 15 70 11 17 12 13 +37 22 16 15 12 15 66 19 15 69 11 19 36 12 51 11 51 19 12 13 12 95 25 16 12 31 69 23 19 23 +12 29 25 18 35 11 14 13 27 11 + + + + + + +GRMZM2G058173_P01 NP_001151824 undecaprenyl pyrophosphate synthetase seq=translation; coord=7:144837690..144838974:-1; parent_transcript=GRMZM2G058173_T01; parent_gene=GRMZM2G058173 + + + + + + + + + +4.73357 +-0.230906 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 +60 61 62 63 64 65 66 67 68 69 70 71 72 73 + + + + +7646 7646 7545 7259 6536 5971 5142 4579 2959 1568 1093 620 338 184 122 81 37 23 21 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +7650 7650 7549 7223 6479 5760 4857 4267 1978 788 191 42 4 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3892 2876 723 134 14 10 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1745 3983 1436 407 64 14 0 2 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3201 (charge 2) + +1584.73 +2 + + +155.081 158.092 167.093 169.096 171.076 173.092 175.119 185.092 186.095 189.087 195.087 199.071 209.103 212.102 217.082 226.118 240.134 244.092 258.145 266.123 268.128 270.107 273.118 286.139 288.118 290.142 296.134 300.119 318.127 344.155 +347.151 355.166 361.182 367.171 369.138 371.156 383.156 389.166 401.166 419.711 438.202 440.175 445.203 448.22 454.202 456.212 462.23 466.193 473.235 484.208 490.739 498.746 502.212 527.253 533.262 542.262 553.222 555.248 571.236 592.783 +613.296 630.32 632.321 641.308 654.268 672.28 684.326 701.357 729.297 743.329 771.326 775.346 784.354 794.342 838.415 856.379 884.375 895.435 897.441 955.411 996.479 1006.51 1010.46 1083.51 1184.57 1186.56 1299.59 1400.65 + + + + +7 2 4 2 5 7 42 38 1 2 7 2 8 1 10 2 8 2 5 6 10 16 3 15 10 2 5 3 5 2 +1 3 6 2 2 2 19 3 9 7 2 2 2 2 3 10 5 2 2 9 2 5 12 1 8 5 4 3 10 9 +7 100 5 2 3 5 3 47 2 2 5 2 2 2 23 9 12 31 2 6 21 2 2 27 13 2 12 2 + + + + + + +GRMZM2G036609_P01 P23225 Ferredoxin-dependent glutamate synthase, chloroplastic Precursor (EC 1.4.7.1)(Fd-GOGAT) seq=translation; coord=7:170961145..170979959:-1; parent_transcript=GRMZM2G036609_T01; parent_gene=GRMZM2G036609 + + + + + + + +GRMZM2G036609_P02 P23225 Ferredoxin-dependent glutamate synthase, chloroplastic Precursor (EC 1.4.7.1)(Fd-GOGAT) seq=translation; coord=7:170961720..170979959:-1; parent_transcript=GRMZM2G036609_T02; parent_gene=GRMZM2G036609 + + + + + + + + +7.24661 +-0.322071 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 + + + + +4237 4237 4237 4237 4237 4235 3943 3780 3420 2596 1910 1163 712 393 256 178 36 8 6 4 2 1 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4232 4232 4232 4232 4232 4230 3938 3758 3324 2356 1388 509 101 31 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1562 1530 801 203 54 87 0 1 + + + + + + +0 1 2 3 4 5 6 7 + + + + +681 1865 1156 358 112 62 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3202 (charge 3) + +1530.66 +3 + + +155.081 157.097 158.092 159.076 167.081 171.076 171.113 173.092 173.128 175.119 184.072 185.091 186.086 186.123 187.072 187.144 195.075 197.128 199.071 199.108 204.134 209.105 212.103 213.087 216.134 225.124 227.102 228.106 234.145 241.08 +244.166 248.16 254.15 258.144 276.154 282.146 289.161 295.138 299.138 301.128 307.14 313.15 321.137 324.126 331.207 335.661 341.145 342.142 347.194 358.142 365.185 371.186 395.168 399.692 413.676 418.242 431.238 437.187 460.239 462.248 +470.698 476.215 490.241 504.204 511.746 514.234 516.219 519.228 524.208 533.257 544.212 561.28 587.251 591.28 592.286 610.241 615.252 641.266 644.323 645.322 670.321 676.305 690.297 695.399 712.294 714.793 729.298 741.372 742.384 747.341 +794.331 798.364 819.364 826.33 843.338 876.383 890.404 923.367 940.385 1069.43 + + + + +63 19 18 52 20 19 25 20 16 80 22 23 14 14 26 14 15 46 15 58 31 32 52 23 37 21 100 15 92 21 +45 36 13 25 14 23 14 20 15 24 63 19 39 20 14 38 69 22 36 20 57 19 16 19 29 20 15 14 51 41 +60 42 70 30 49 19 28 14 20 44 23 26 16 77 22 15 22 22 35 29 29 94 14 16 14 23 21 17 17 51 +18 16 18 21 41 28 32 14 29 15 + + + + + + +GRMZM2G064877_P02 seq=translation; coord=3:3692326..3694505:-1; parent_transcript=GRMZM2G064877_T02; parent_gene=GRMZM2G064877 + + + MGLLAGSTVF LLTLLWGTCV VVGKCDLGPN REAVDVTDTK GFSLTGTGIT + TDVQTSYAAR IMGLSVIPFI IAQFPKMLKT HHGQRLAMLL ALIVSFLLVL + SYCLYQVFQP WIQRRKLAYA KHKHVISGIL RHAQMQSLGR LLNDDGTPND + DVIRKLFRKI DMDQSESLSR AELHALIVGI NFEEVDFDRT DAVDKVMDDF + DTSRNDVVEQ EEFVQGMKKW LNEAKRSVPV GGAFSTKFIN EYHERTRQEH + NELVDRSDEA VESVENPGWC IAKAVALLLL GAAIAAAFAD PLVDAVHNFS + NATHIPSFFI SFIALPLATN SSEAVSAIIF ASRKKQRTCS LTFSEVYGGV + TMNNTLCLGV FLALIYFRNL TWDFSSEVLI ILLVCVVMAL FTSFRTTFPL + WTCLVAYMLY PFSLVLVYIL DYVFGWS + + + + + + + +5.68055 +-0.29131 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 + + + + +6756 6756 6756 6756 6676 6447 6090 5603 4922 3719 2807 1772 804 439 192 79 43 15 1 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +6706 6706 6706 6706 6626 6397 6011 5461 4680 3170 1864 513 2 1 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2527 2598 1208 357 57 16 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1104 2798 1886 770 169 30 6 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3205 (charge 3) + +1424.67 +3 + + +152.056 155.081 156.077 157.097 157.133 158.027 158.092 159.076 159.113 160.116 167.055 169.097 171.076 171.112 172.07 173.091 173.128 175.119 176.123 181.061 181.096 185.092 185.129 185.165 186.124 186.168 187.071 187.107 188.074 189.087 +197.128 198.087 199.071 199.108 199.18 201.123 204.134 209.092 215.139 217.081 221.103 226.118 239.094 242.15 244.094 245.124 249.098 255.145 258.144 262.151 267.109 270.105 272.171 288.203 309.119 312.677 341.19 343.209 345.161 357.215 +375.234 416.177 440.252 454.217 456.258 462.266 476.734 491.774 504.253 527.291 535.297 546.29 555.283 573.302 574.305 591.308 592.318 601.332 605.306 606.31 619.274 624.346 634.318 636.3 637.303 646.283 649.334 661.35 662.354 678.342 +679.346 684.385 692.301 762.354 768.373 770.375 771.381 819.411 820.409 906.427 + + + + +6 15 8 10 19 16 29 54 87 12 7 11 19 21 8 14 31 100 9 11 13 18 6 38 7 12 37 24 9 12 +7 7 25 12 27 20 12 10 7 14 7 21 11 7 10 21 7 7 9 39 8 8 26 19 11 11 7 7 25 12 +17 8 9 8 6 75 15 8 8 27 7 11 11 20 12 20 8 23 8 8 13 20 12 17 7 9 9 10 21 27 +7 16 7 15 17 19 13 16 8 7 + + + + + + +GRMZM2G046804_P01 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36880092..36884475:-1; parent_transcript=GRMZM2G046804_T01; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P02 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881035..36884475:-1; parent_transcript=GRMZM2G046804_T02; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P04 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T04; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P05 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T05; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P06 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884475:-1; parent_transcript=GRMZM2G046804_T06; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P07 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881117..36884877:-1; parent_transcript=GRMZM2G046804_T07; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G046804_P08 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881357..36884877:-1; parent_transcript=GRMZM2G046804_T08; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G180625_P01 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T01; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G180625_P02 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903246:-1; parent_transcript=GRMZM2G180625_T02; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G180625_P03 Q09054 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12) seq=translation; coord=6:6898695..6903153:-1; parent_transcript=GRMZM2G180625_T03; parent_gene=GRMZM2G180625 + + + + + + + +GRMZM2G046804_P03 P08735 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12) seq=translation; coord=4:36881090..36884877:-1; parent_transcript=GRMZM2G046804_T03; parent_gene=GRMZM2G046804 + + + + + + + +GRMZM2G176307_P01 NP_001105951 cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC4 seq=translation; coord=5:181520274..181524899:1; parent_transcript=GRMZM2G176307_T01; parent_gene=GRMZM2G176307 + + + + + + + +GRMZM2G176307_P02 NP_001105951 cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC4 seq=translation; coord=5:181520571..181525066:1; parent_transcript=GRMZM2G176307_T02; parent_gene=GRMZM2G176307 + + + + + + + +GRMZM2G071630_P01 Q43247 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12) seq=translation; coord=4:133103720..133107109:1; parent_transcript=GRMZM2G071630_T01; parent_gene=GRMZM2G071630 + + + + + + + +GRMZM2G071630_P02 Q43247 Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12) seq=translation; coord=4:133104109..133107067:1; parent_transcript=GRMZM2G071630_T02; parent_gene=GRMZM2G071630 + + + + + + + + +5.40678 +-0.263745 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +1897 1897 1897 1862 1818 1748 1642 1461 1165 802 542 337 217 139 57 37 23 4 2 1 1 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +1885 1885 1885 1850 1806 1730 1596 1303 876 357 101 16 1 0 + + + + + + +0 1 2 3 4 5 + + + + +562 882 429 64 4 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +278 893 486 199 39 2 0 44 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3211 (charge 2) + +928.583 +2 + + +155.081 157.097 157.133 158.092 159.076 163.133 167.055 169.053 169.097 171.076 171.112 171.149 173.092 175.119 176.107 178.133 183.076 183.114 183.149 184.153 185.091 185.128 185.165 186.124 187.071 187.127 189.087 194.129 197.128 197.165 +199.108 199.144 199.181 201.123 203.103 210.16 211.144 214.118 215.139 218.15 223.155 226.119 228.17 234.145 240.098 242.151 244.164 247.107 251.15 255.145 257.125 258.145 260.196 272.171 273.174 276.156 282.181 285.156 287.975 290.987 +299.173 304.947 310.149 311.135 313.186 322.958 328.161 331.197 332.954 339.203 346.969 349.152 353.219 359.029 361.026 370.207 375.223 382.206 389.197 402.234 409.22 410.204 431.088 446.263 456.285 489.267 490.272 501.268 557.291 574.319 +587.376 598.394 602.353 644.43 669.393 685.353 701.42 715.47 782.297 800.484 + + + + +8 7 17 7 13 12 13 4 18 4 8 6 7 35 4 5 4 7 37 4 12 5 17 45 8 3 5 4 9 4 +5 10 50 8 3 8 12 11 11 4 18 9 9 17 11 4 5 6 10 7 9 15 12 50 6 10 7 3 12 4 +4 40 5 15 14 30 6 100 16 4 4 4 7 12 53 4 8 6 4 16 6 5 6 7 5 22 6 4 5 4 +3 4 15 4 7 10 24 24 4 7 + + + + + + +GRMZM2G110289_P01 seq=translation; coord=9:2332757..2339255:1; parent_transcript=GRMZM2G110289_T01; parent_gene=GRMZM2G110289 + + + MESSLLLSTP RPLKPFHPHH FPTARRRDAS FRGKPPPPPP LPPLGRGSRR + LGRAVPRASS EAFGDGFRSQ DRPPGVSSGG VRRRTYREAQ GEAAVPPVAA + AARAVAPYVA PVGAVLMLSF VIWKVVQNMI PGKKKDHGSG KHAPSGIMWS + FAAGSNLATS TLSAEKESRK NLNKFYKELR TLKTVNMAGR QFGDEGLFFL + AESLAYDKSA EEVDFSGNGI TAVGIEAFDG VLQINTTLKT LNLSGNDIGD + EGAKCLSDIL VENVGIQKLL LNSINIGDEG AKALSNMLKK NKSIRILQFS + NNAIEYSGFA SIAEALLENN TIRSLYLNGN YGGPLGACSL AQGILGNKSL + REIHLHGNGI GNEGIRELMS ALSAHKGKIT VVDIGNNNIS PEGLHPVAEF + LKRTKSLQWF SLYMNDISDE GAEKVAEALK DNKTISTIDL GGNNIHSKAV + SAVAETLKDN AVLTTLDLSY NPIGSDGVKA LCDVLKFHGK IQTLKLGWCQ + IGMEGAECIA DCLKYNTTLS TLDLRANGLG NDGAICLARS FKIINESLTS + LDLGFNEIRD DGAFALAQAL KANEDLAVTS LNLANNFFTK FGQVALSEAR + DHVYEMTERE IDIYF + + + + + + +6.36801 +-0.326565 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 + + + + +7354 7354 7354 7354 7336 6930 6637 5980 5235 3944 2816 1535 697 331 145 67 21 14 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +7286 7286 7286 7286 7268 6862 6562 5817 4896 3467 1897 398 1 0 + + + + + + +0 1 2 3 4 5 6 + + + + +2381 3083 1327 443 109 18 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1528 3129 1865 634 172 26 3 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3212 (charge 3) + +1398.71 +3 + + +155.081 157.097 157.109 157.133 158.092 159.076 159.112 163.133 169.061 169.097 171.113 173.092 173.128 175.072 175.119 176.122 180.094 181.061 183.149 185.129 185.165 186.087 186.123 187.072 194.129 199.071 199.107 199.182 201.125 213.087 +216.098 218.15 223.155 226.154 227.1 231.097 240.135 242.149 244.165 247.107 250.118 252.137 255.109 258.145 261.155 272.171 273.177 278.113 306.942 324.953 327.166 331.199 333.671 337.15 359.182 363.024 375.234 383.161 388.229 401.214 +412.21 424.218 437.736 456.748 463.2 467.837 475.26 476.28 481.22 487.226 510.254 513.257 530.26 531.268 534.8 539.33 544.294 562.295 574.293 592.314 609.299 628.342 634.294 636.385 647.828 657.323 666.342 676.411 692.338 694.332 +702.417 710.357 719.36 721.328 728.363 738.353 809.427 815.439 826.403 912.49 + + + + +15 9 8 32 26 13 10 42 13 12 13 12 20 8 100 8 8 15 9 9 39 21 13 8 21 9 13 9 13 11 +18 12 15 19 12 9 11 14 16 11 8 7 32 21 13 26 8 9 9 8 7 20 10 11 25 8 9 9 34 22 +10 9 25 10 8 9 42 42 8 15 18 10 8 13 19 12 8 64 10 26 13 21 8 8 18 8 8 13 8 12 +7 14 12 9 9 32 12 8 8 22 + + + + + + +GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841 + + + + + + + + + +4.87163 +-0.314299 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +5808 5808 5808 5586 5310 5098 3698 3068 1811 1025 597 208 79 36 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +5831 5831 5831 5609 5333 5099 3618 2725 1433 640 254 58 13 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2771 2535 473 50 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1272 3683 797 68 1 0 12 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3213 (charge 2) + +1499.72 +2 + + +151.086 153.414 157.097 159.077 165.227 168.113 169.097 171.077 175.119 181.061 183.113 185.092 186.124 187.072 187.107 187.126 193.097 195.077 195.113 197.129 198.124 201.086 204.134 205.097 212.102 216.098 219.116 222.123 226.118 228.133 +230.114 239.113 240.097 244.166 247.111 255.146 257.124 262.118 268.13 272.171 279.145 283.139 285.156 291.166 293.164 296.172 301.15 304.13 314.181 331.211 339.166 340.167 346.18 348.123 356.197 358.142 368.156 372.223 388.182 395.206 +406.193 422.201 425.213 440.189 442.241 475.213 486.199 493.225 513.314 524.283 543.637 563.634 598.06 617.296 624.348 634.391 649.694 656.29 695.293 710.34 713.308 715.319 741.364 792.221 810.381 812.377 895.42 897.412 959.406 994.489 +1040.48 1058.48 1105.52 1123.53 1233.56 + + + + +6 3 4 5 3 7 29 7 22 4 4 5 100 4 4 4 7 5 19 4 3 4 55 23 17 5 6 29 15 4 +6 17 40 4 15 11 31 6 5 20 6 5 5 100 4 32 4 4 42 5 24 3 4 3 5 6 5 16 3 3 +37 6 18 4 7 6 22 62 6 7 4 3 22 16 6 5 10 21 13 3 86 5 5 4 4 43 52 4 22 33 +5 17 11 5 5 + + + + + + +GRMZM2G064877_P02 seq=translation; coord=3:3692326..3694505:-1; parent_transcript=GRMZM2G064877_T02; parent_gene=GRMZM2G064877 + + + + + + + + + +6.04182 +-0.366171 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 + + + + + +4496 4496 4496 4496 4438 4111 4003 3724 2330 2041 785 365 154 35 14 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +4484 4484 4484 4484 4426 4099 3982 3688 2242 1551 458 54 1 0 + + + + + + +0 1 2 3 4 + + + + +3307 1067 126 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +518 3171 689 111 9 0 0 4 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3216 (charge 2) + +1424.67 +2 + + +152.056 155.081 156.077 158.092 159.112 168.077 171.077 175.119 176.122 185.165 186.088 186.124 187.108 190.718 197.165 198.087 199.107 214.192 224.176 226.154 240.136 242.186 245.125 248.107 262.151 277.155 357.212 361.19 375.234 440.253 +452.254 462.266 470.495 517.262 637.33 678.347 680.837 733.336 737.678 789.379 806.401 808.417 921.422 1004.46 1101.49 1119.49 1184.49 1232.57 + + + + +7 7 9 35 7 6 7 69 6 7 13 7 10 5 60 6 32 13 9 75 5 24 7 34 9 26 13 30 7 7 +6 29 6 10 9 38 48 10 8 11 63 7 39 39 9 100 11 32 + + + + + + +GRMZM2G017730_P01 seq=translation; coord=5:50726678..50756498:1; parent_transcript=GRMZM2G017730_T01; parent_gene=GRMZM2G017730 + + + MGKTRALLLA LRQICFPLMV RVFKIDPPTN SPLINTCGHQ RSNCVRRRTV + AKVVDTNLFS VPYERRIQQQ NRSVLSCRFQ YAKAMFERNQ KYRLAKYVPD + SHAEGFKDGK KVQGLCTFMS PFSFKIKLNL SCQLSFAAQN NSVFSLIINT + FSQSRASILG VIERKMEDRL EKMSREKSSV EEDDLLGWAL KQSNLSKEQI + LDLLLSLLFA GHETSSMVLA LAIFFLEGCP KAVQELRMWI SRAEYEESGP + AIVHRKDSLT QAVEEVNIVI KFNSLLTTLS KHPEADNFAR GLGPISLAGE + DDHDRRADDL KILYKAYATE VLSDGIVDDK KEVLYMFWKE IYRQKLQQFV + ADGELSKEEV EALMAFQVRL CIPQETVDAA HIEICGQLFE KVVKFFNQYL + WATVRKDNVE AVVFWYVLVY FSILFIRFRA GIVTREMLAL PKPQFMLIGL + LEALGAASGM AAAVYTIYCL CMYLLHAFGS FYDCLKVCSS LFSFERHNNF + LSRSNEIIPQ RAAAQCILLT DLKLLFRFDG VVPEPRKGIR SGHVPGSKCV + PFPQVLDSSQ KLLPRDELRK RFEQEVTTHA AI + + + + + +GRMZM2G017730_P03 seq=translation; coord=5:50728628..50756498:1; parent_transcript=GRMZM2G017730_T03; parent_gene=GRMZM2G017730 + + + MSPFSFKIKL NLSCQLSFAA QNNSVFSLII NTFSQSRASI LGVIERKMED + RLEKMSREKS SVEEDDLLGW ALKQSNLSKE QILDLLLSLL FAGHETSSMV + LALAIFFLEG CPKAVQELRM WISRAEYEES GPAIVHRKDS LTQAVEEVNI + VIKFNSLLTT LSKHPEADNF ARGLGPISLA GEDDHDRRAD DLKILYKAYA + TEVLSDGIVD DKKEVLYMFW KEIYRQKLQQ FVADGELSKE EVEALMAFQV + RLCIPQETVD AAHIEICGQL FEKVVKFFNQ YLWATVRKDN VEAVVFWYVL + VYFSILFIRF RAGIVTREML ALPKPQFMLI GLLEALGAAS GMAAAVYTIY + CLCMYLLHAF GSFYDCLKVC SSLFSFERHN NFLSRSNEII PQRAAAQCIL + LTDLKLLFRF DGVVPEPRKG IRSGHVPGSK CVPFPQVLDS SQKLLPRDEL + RKRFEQEVTT HAAI + + + + + +GRMZM2G467212_P01 seq=translation; coord=10:75216816..75222519:-1; parent_transcript=GRMZM2G467212_T01; parent_gene=GRMZM2G467212 + + + MADSEDIQPL VCDNGTGMVK FGFAGDDAPR VVFRIMFETF SVLAMYVAIQ + ADLSLYASGC TTDIVLDSVE KSYELPDGQV ITIGTERFRC PEVLFQPSFI + GMKAPGIHET TYNSIMKCDV DIRKNLYGNI VFSGGSTMFP GITDRMSKEI + TTLTPSSMKI KMWISRAEYE ESGPAIVHRK DSLTQAVEEV NIVIKFNSLL + TTLSKHPEAD NFARGLGPIS LEIYRQKLQQ FVADGELSKE EVEALMAFQV + RLCIPQETVD AAHTEICGQL FKKVGPTTFE AKLQPHLLWS LDQVKENIKT + QTHQLIDARS KPRLHAFGSF YDCLKVCSSL FSFERHNNFL SRCNEIIPQC + AAAQCILFDG AVPEPRKGIR SGHVPGSKCV PFPQVKTLYF SILLSVLFCI + WMFLPMFAVD GNGYLSDKVP SWISNFNI + + + + + + +5.78622 +-0.269126 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 + + + + +3825 3825 3802 3672 3366 3091 2814 2552 2330 1550 1112 739 322 178 115 75 24 12 7 3 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +3823 3823 3800 3669 3333 2999 2692 2462 2205 1114 688 175 30 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1747 1636 404 46 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +711 1991 867 209 46 2 0 8 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3218 (charge 2) + +1056.49 +2 + + +155.082 157.097 157.109 158.092 159.076 162.102 166.061 167.082 169.061 169.097 171.077 171.113 172.072 173.038 173.092 173.129 175.119 176.123 183.077 185.165 186.088 186.124 186.167 187.072 187.108 193.097 194.129 197.074 199.108 201.124 +204.135 207.124 212.104 217.11 219.113 221.129 226.118 227.102 229.13 235.119 236.121 240.135 246.156 262.119 288.201 298.14 301.114 308.106 328.141 341.151 343.209 346.151 376.196 389.197 393.224 413.169 414.168 417.667 420.191 430.178 +448.184 453.184 453.683 460.213 473.214 475.264 482.189 490.241 497.282 500.226 507.268 510.187 518.239 519.74 527.207 532.214 559.218 575.317 604.298 605.287 622.293 629.257 646.265 664.27 674.275 681.3 693.331 695.336 765.33 767.365 +782.295 793.328 804.366 822.374 824.376 853.331 864.366 902.404 919.426 921.425 + + + + +6 3 4 27 3 2 4 2 3 4 4 5 2 2 3 3 100 7 2 11 6 5 2 2 4 4 2 5 50 2 +5 2 4 7 2 2 6 33 14 71 8 3 9 5 6 9 7 4 5 3 2 65 6 12 9 11 2 23 4 2 +2 33 18 10 2 2 4 10 8 2 76 5 16 38 3 9 2 2 5 2 11 3 8 4 3 11 66 5 4 6 +17 4 8 49 5 11 4 4 61 10 + + + + + + +GRMZM2G161295_P01 NP_001142140 hypothetical protein LOC100274305 seq=translation; coord=3:155960410..155963163:-1; parent_transcript=GRMZM2G161295_T01; parent_gene=GRMZM2G161295 + + + + + + + + +6.0521 +-0.345834 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 + + + + +4312 4312 4312 4312 4312 4157 2900 2272 1587 916 501 204 75 23 11 2 1 1 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +4316 4316 4316 4316 4316 4161 2903 2206 1441 660 324 54 9 7 1 0 + + + + + + +0 1 2 3 4 5 + + + + +2346 1675 251 41 3 0 + + + + + + +0 1 2 3 4 5 6 + + + + +1017 2950 316 25 4 4 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3219 (charge 2) + +1724.77 +2 + + +157.097 167.093 169.098 171.063 171.076 172.33 173.056 175.119 186.087 187.072 187.108 195.088 204.134 209.092 226.118 228.114 235.136 239.114 242.113 244.092 248.161 251.102 257.197 265.118 268.129 275.208 279.396 297.118 301.114 311.14 +314.135 315.129 337.149 355.161 369.174 372.148 397.206 402.236 408.178 412.188 422.22 434.211 445.183 459.257 473.178 549.238 576.288 582.243 610.235 617.803 628.343 711.287 797.415 809.71 824.853 851.419 861.46 864.414 884.446 941.453 +1014.48 1054.52 1113.24 1115.53 1235.58 1252.59 1304.65 1322.64 1450.61 + + + + +39 21 10 12 100 6 12 21 15 9 39 15 14 15 49 29 7 17 21 38 15 10 9 10 8 82 9 8 11 13 +34 9 17 12 10 15 15 9 10 16 9 9 89 20 22 11 65 56 21 18 11 16 48 17 15 18 21 18 14 15 +34 33 11 20 15 41 15 12 15 + + + + + + +GRMZM2G326066_P01 NP_001131879 hypothetical protein LOC100193258 seq=translation; coord=10:143162642..143163490:1; parent_transcript=GRMZM2G326066_T01; parent_gene=GRMZM2G326066 + + + MVKFLKPGKA VILLQGRFAG RKAVIVRVFE EGTRDRPYGH CLVAGLAKYP + KKVIRKDSAK KTAKKSRVKC FIKLVNFTHL MPTRYTLDVD FKDVASGGPD + ALSTRDKKVE ACKAAKARLE ERFKTGKNRW FFTKLRF + + + + + +GRMZM2G302712_P01 NP_001131879 hypothetical protein LOC100193258 seq=translation; coord=2:8814586..8815407:-1; parent_transcript=GRMZM2G302712_T01; parent_gene=GRMZM2G302712 + + + MLVSLALSAP ISSTSQTLPA AQQHHNHRPK MVKFLKPGKA VILLQGRFAG + RKAVIVRVFE EGTRDRPYGH CLVAGLAKYP KKVIRKDSAK KTAKKSRVKC + FIKLVNFTHL MPTRYTLDVD FKDVASGGPD ALSTRDKKVE ACKAAKARLE + ERFKTGKNRW FFTKLRF + + + + + +GRMZM2G366077_P01 NP_001150228 60S ribosomal protein L27 seq=translation; coord=5:41196776..41198106:1; parent_transcript=GRMZM2G366077_T01; parent_gene=GRMZM2G366077 + + + MRPVLSCRAG AHEGMLGWNL DWPTGSFSVR QRKATVVLML GLGPLTTSLT + SDPELLHPAP PEARARQHRP ILDPTAETHP PGNPSAATLY NLLSSPCSDL + THLPNPTLPA AAAAAQQRQQ HPKMVKFLKP GKAVILLQGR FAGRKAVIVR + VFEEGTRDRP YGHCLVAGLA KYPKKVIRKD SAKKTAKKSR VKCFIKLVNF + THLMPTRYTL DVDFKDVATG GPDALSTHDK KVAACKTAKA RLEERFKTGK + NRWFFTKLRF + + + + + +GRMZM2G016250_P01 NP_001146947 60S ribosomal protein L27 seq=translation; coord=6:90530607..90532293:-1; parent_transcript=GRMZM2G016250_T01; parent_gene=GRMZM2G016250 + + + MVKFLKPGKA VILLQGRFAG RKAVIVRVFE EGTRDRPYGH CLVAGLAKYP + KKVVRRDSAK KTAKKSRVKC FIKLVNFTHL MPTRYTLDVD FKDVATGGPD + ALSTRDKKVA ACKAAKARLE ERFKTGKNRW FFTKLRF + + + + + + +4.76804 +-0.257732 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + + + + +3080 3080 3019 2783 2616 2405 2249 2088 1594 1197 807 386 217 112 62 27 4 1 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 + + + + +3093 3093 3029 2785 2537 2344 2201 2010 1258 779 294 60 1 0 + + + + + + +0 1 2 3 4 5 + + + + +1312 1529 238 12 2 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +446 1491 813 273 53 5 12 0 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3222 (charge 2) + +837.41 +2 + + +155.082 155.118 157.061 157.097 157.108 157.134 158.092 159.077 159.095 159.113 166.062 167.081 167.094 169.097 169.133 171.113 173.075 173.092 173.128 174.057 175.072 175.119 176.122 181.098 183.113 183.15 184.109 185.092 186.09 187.072 +187.109 187.144 188.148 193.097 194.13 195.075 197.129 199.107 201.124 203.067 213.087 215.139 219.149 224.103 231.097 235.12 241.082 243.134 245.077 247.144 249.123 252.108 254.125 259.14 262.14 264.149 269.124 277.118 278.124 288.201 +296.089 298.151 305.158 307.141 310.177 316.161 317.165 330.189 333.188 342.216 358.183 367.198 373.209 381.141 399.153 404.224 409.181 424.217 427.187 441.284 444.222 462.231 475.263 481.239 484.243 487.285 491.269 512.255 519.775 527.297 +548.258 556.236 573.262 575.261 584.313 591.273 593.281 681.374 738.34 740.345 + + + + +6 4 1 2 3 1 30 8 3 2 1 1 1 3 5 2 1 1 6 3 3 52 4 2 3 1 1 2 1 1 +1 39 5 1 1 1 4 5 3 2 4 12 100 3 2 1 5 4 1 17 19 3 4 8 1 1 2 12 3 2 +1 6 1 3 3 12 1 2 44 1 3 1 4 3 3 3 1 2 3 1 6 43 5 8 3 1 1 2 12 1 +1 3 18 1 3 78 4 6 39 4 + + + + + + +GRMZM2G140150_P01 NP_001150259 pyruvate dehydrogenase E1 component alpha subunit seq=translation; coord=5:205777032..205781614:-1; parent_transcript=GRMZM2G140150_T01; parent_gene=GRMZM2G140150 + + + MAAAALLRRI PAARAPATAF MAARPVSDST AALTIETSVP FTSHLVDPPS + RDVTTTPAEL VTFFRDMSLM RRMEIAADSL YKAKLIRGFC HLYDGQEAVA + VGMEAAITRS DSIITAYRDH CTYLARGGDL VSAFSELMGR EAGCSRGKGG + SMHFYKKDAN FYGGHGIVGA QVPLGCGLAF AQKYKKEETA TFALYGDGAA + NQGQLFEALN ISALWKLPAI LVCENNHYGM GTAEWRAAKS PAYYKRGDYV + PGLKVDGMDV LAVKQACKFA KDHAVANGPI VLEMDTYRYH GHSMSDPGST + YRTRDEISGV RQERDPIERV RKLLLAHDLA TAAELKDMEK EIRKQVDDAI + AKAKESSMPD TSELFTNVYK KGFNVESFGP DRKELRATLP + + + + + +GRMZM2G361693_P01 B4FGJ4 Putative uncharacterized protein seq=translation; coord=4:182736035..182740799:1; parent_transcript=GRMZM2G361693_T01; parent_gene=GRMZM2G361693 + + + MAAAALIRRL PAARAQAPAF MAARPISDST AAFTIETSVP FTSHLVDPPS + RDVTTTPAEL VTFFRDMSLM RRMEIAADSL YKAKLIRGFC HLYDGQEAVA + VGMEAAITRS DSIITAYRDH CTYLARGGDL VSAFSELMGR EAGCSRGKGG + SMHFYKKDAN FYGGHGIVGA QVPLGCGLAF AQKYKKEDTA TFALYGDGAA + NQGQLFEALN ISALWKLPAI LVCENNHYGM GTAEWRAAKS PAYYKRGDYV + PGLKVDGMDV LAVKQACKFA KDHAVANGPI VLEMDTYRYH GHSMSDPGST + YRTRDEISGV RQERDPIERV RKLLLTHDLA NAAELKNMEK EIRKQVDDAI + AKAKESSMPD TSELFTNVYK KGFGVESFGP DRKEMRASLP + + + + + +GRMZM2G027627_P01 NP_001140222 hypothetical protein LOC100272256 seq=translation; coord=9:1443455..1448097:1; parent_transcript=GRMZM2G027627_T01; parent_gene=GRMZM2G027627 + + + MAAAILRRLV PTAASQLVAP LPLLARGVSD SADAVTVDTS VPFKSHIVDP + PPREATTSAR ELLSFFRDMS LMRRFEIAAD SLYKAKLIRG FCHLYDGQEA + VAVGMEAAAT RADAIITAYR DHCAYLARGG DPVAAFAELM GRRDGCSRGK + GGSMHFYKRD ANFFGGHGIV GAQVPLGCGI AFAQRYRKEG TVTFDLYGDG + AANQGQLFEA LNMAALWKLP VILVCENNHY GMGTAEWRAS KSPAYYKRGD + YVPGLKVDGM DVLAVKQACK FAKEHALENG PIILEMDTYR YHGHSMSDPG + STYRTRDEIA GIRQERDPIE RVRKLMLVHE FATAQELKDM EKEIRKQVDA + AIAKAKECPL PDPSELFTNV YVNDCGLESF GVDRKEVRTV LP + + + + + + +5.92736 +-0.303967 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 + + + + +2626 2626 2626 2602 2424 2245 2057 1508 1143 696 363 188 71 37 14 6 5 3 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +2600 2600 2600 2576 2398 2211 1985 1349 902 363 88 1 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +963 1043 464 123 27 6 17 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +480 1171 677 241 55 3 1 15 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3223 (charge 3) + +1594.67 +3 + + +155.081 157.097 158.092 159.076 161.092 166.061 167.093 169.097 171.077 171.113 175.119 181.095 183.149 187.072 189.087 191.085 194.129 195.088 199.072 199.108 201.086 203.066 205.1 211.144 215.139 217.082 226.155 227.102 229.118 233.096 +239.093 242.113 244.165 245.076 248.108 254.151 258.144 260.197 264.109 273.135 275.172 277.627 282.12 284.103 286.143 291.624 301.129 303.177 310.176 314.136 319.148 321.155 324.155 331.679 338.181 340.671 355.198 358.152 376.643 383.195 +401.166 415.144 419.182 439.228 442.229 452.252 467.217 470.262 473.271 495.21 497.319 526.262 539.283 547.206 558.202 565.298 566.303 583.284 584.286 597.204 615.218 635.279 641.275 662.345 678.345 680.336 682.341 695.407 734.37 739.338 +742.321 752.284 820.403 826.37 849.384 873.357 903.496 915.338 921.505 949.447 + + + + +10 5 6 4 8 8 6 6 7 10 28 4 17 7 19 6 6 23 8 19 6 4 6 7 20 7 44 17 6 5 +5 4 22 6 7 4 10 5 7 7 7 5 10 10 4 12 24 25 8 9 7 8 7 25 7 22 4 9 7 8 +5 7 5 10 5 9 9 7 5 12 5 21 4 5 4 28 9 67 22 5 8 4 5 14 6 100 6 7 6 4 +10 5 9 7 7 4 6 5 7 8 + + + + + + +GRMZM2G124455_P01 P41980 Superoxide dismutase [Mn] 3.4, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=8:91831315..91844753:1; parent_transcript=GRMZM2G124455_T01; parent_gene=GRMZM2G124455 + + + + + + + +GRMZM2G059991_P01 P09233 Superoxide dismutase [Mn] 3.1, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=6:135883373..135887597:1; parent_transcript=GRMZM2G059991_T01; parent_gene=GRMZM2G059991 + + + + + + + +GRMZM2G124455_P02 P41980 Superoxide dismutase [Mn] 3.4, mitochondrial Precursor (EC 1.15.1.1) seq=translation; coord=8:91831315..91844753:1; parent_transcript=GRMZM2G124455_T02; parent_gene=GRMZM2G124455 + + + + + + + + +5.48061 +-0.267347 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 + + + + +12039 12039 12039 11737 11120 10102 8452 6654 4829 3069 2011 1058 586 345 155 50 30 21 12 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +12045 12045 12045 11743 11125 9939 7923 5474 2845 1222 468 118 33 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +3228 4812 2727 967 275 36 8 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +2235 4696 3198 1465 352 81 15 11 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3224 (charge 3) + +1616.84 +3 + + +155.082 155.118 157.097 158.092 159.076 166.061 167.056 169.133 170.045 171.113 172.071 173.092 173.128 175.09 175.119 181.097 183.113 183.149 185.165 187.071 189.087 191.084 195.089 199.072 200.139 201.123 204.134 207.124 210.088 211.144 +213.098 217.082 221.103 226.155 228.134 235.12 238.082 244.092 246.155 249.098 252.171 267.107 268.153 272.172 280.165 294.18 299.061 301.06 304.159 321.227 323.181 332.169 339.204 341.193 346.973 351.174 372.698 389.195 407.203 409.206 +418.205 420.236 421.236 425.249 427.221 433.205 438.246 484.24 517.291 533.297 535.299 537.307 546.288 555.316 566.367 604.302 632.281 635.392 646.338 647.333 653.409 661.287 670.36 721.361 727.389 728.393 744.392 767.373 778.384 831.419 +835.405 837.412 840.465 855.42 861.399 918.453 946.435 948.432 977.527 1051.48 + + + + +4 8 12 4 10 5 7 4 3 4 5 4 5 5 22 4 13 26 6 14 5 3 8 6 42 6 14 4 4 11 +5 8 3 8 19 19 3 8 5 4 6 4 17 4 6 8 13 22 10 4 5 4 5 30 4 6 6 5 18 3 +8 11 3 3 5 3 24 4 11 4 100 8 4 5 7 4 5 4 4 8 4 7 4 4 15 5 14 4 8 5 +16 4 6 3 6 5 3 8 4 7 + + + + + + +GRMZM2G315088_P01 seq=translation; coord=4:49407189..49408154:-1; parent_transcript=GRMZM2G315088_T01; parent_gene=GRMZM2G315088 + + + + + + + +GRMZM2G327564_P01 O82579 Ribosomal protein L26 Fragment seq=translation; coord=3:19669523..19670484:-1; parent_transcript=GRMZM2G327564_T01; parent_gene=GRMZM2G327564 + + + + + + + +GRMZM2G041238_P01 NP_001151634 LOC100285268 seq=translation; coord=8:13554391..13555376:1; parent_transcript=GRMZM2G041238_T01; parent_gene=GRMZM2G041238 + + + + + + + +GRMZM2G470608_P01 seq=translation; coord=2:180794699..180795223:-1; parent_transcript=GRMZM2G470608_T01; parent_gene=GRMZM2G470608 + + + + + + + +GRMZM2G463887_P01 seq=translation; coord=4:236012675..236013130:1; parent_transcript=GRMZM2G463887_T01; parent_gene=GRMZM2G463887 + + + + + + + + +5.71939 +-0.278995 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 + + + + +7519 7519 7519 7488 7186 7017 6558 6138 5086 4179 2058 1290 597 314 167 70 48 27 6 1 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +7539 7539 7539 7508 7206 7035 6551 6063 4798 3093 1083 248 79 17 1 0 + + + + + + +0 1 2 3 4 5 + + + + +3019 3469 917 127 12 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +1371 4249 1509 325 64 3 0 23 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3225 (charge 2) + +1200.65 +2 + + +150.055 151.062 155.082 155.093 155.118 157.097 158.092 159.076 159.113 166.061 167.081 168.066 169.061 169.097 171.077 171.112 171.15 173.093 175.119 176.121 181.108 182.129 183.076 183.113 183.148 185.092 186.123 187.108 189.087 192.077 +195.113 199.071 200.139 201.123 204.134 209.104 212.102 214.119 219.087 221.139 226.154 229.117 235.119 237.134 240.134 244.166 249.096 252.097 255.145 257.139 258.144 267.108 272.123 285.134 286.139 300.119 302.098 312.168 315.167 319.188 +324.147 333.174 337.197 353.181 356.173 366.177 384.164 386.18 396.224 448.24 456.273 466.252 470.238 485.268 492.257 501.262 528.277 529.277 545.304 586.369 598.334 599.328 616.34 647.827 673.366 680.332 695.389 699.376 700.372 717.388 +719.392 733.851 790.875 797.406 846.442 864.457 866.461 994.496 1001.5 1072.56 + + + + +7 7 27 4 8 7 13 6 6 14 7 4 7 13 16 10 3 12 68 7 8 13 7 7 3 10 9 15 17 12 +4 6 13 9 16 50 6 26 3 16 18 4 24 10 8 12 3 6 6 42 16 10 7 63 9 4 7 4 7 29 +9 7 18 7 17 11 4 4 7 7 4 6 10 6 9 33 16 8 44 7 11 11 38 19 6 8 19 14 4 100 +7 8 7 8 8 96 14 7 10 5 + + + + + + +GRMZM2G377797_P01 NP_001149616 40S ribosomal protein S16 seq=translation; coord=2:149785316..149786131:1; parent_transcript=GRMZM2G377797_T01; parent_gene=GRMZM2G377797 + + + MTVLSRPTPG TAQCFGRKKT AVAVAYTKPG RGLIKVNGVP IELIRPEMLR + LKAFEPILLA GRSRFKDIDM RIRVRGGGKT SQIYAIRQAV AKGLVAYYQK + YVDEAAKKEI KDIFTRYDRT LLVADPRRCE PKKFGGRGAR ARFQKSYR + + + + + +GRMZM2G353103_P01 B6SNQ7 40S ribosomal protein S16Putative uncharacterized protein ; seq=translation; coord=3:230441023..230443000:1; parent_transcript=GRMZM2G353103_T01; parent_gene=GRMZM2G353103 + + + MSTVLQRPTP GTVQCFGRKK TAVAVAYTKP GRGLIKVNGV PIELIRPEML + RLKAFEPILL AGRSRFKDID MRIRVRGGGK TSQIYAIRQA VAKGLVAYYQ + KYVDEAAKKE VKDIFTRYDR TLLVADPRRC EPKKFGGRGA RARFQKSYR + + + + + +GRMZM2G427014_P01 NP_001150980 40S ribosomal protein S16 seq=translation; coord=10:2656675..2657137:1; parent_transcript=GRMZM2G427014_T01; parent_gene=GRMZM2G427014 + + + MGPVLKRPTP GTVQCFGRKK TAVAVAYTKP GRGMIKVNGV PIELLRPEML + RLKAMEPVLL AGRSRFKDID MRIRVRGGGK TSQIYAIRQA VAKGLVAYYQ + KYVDEAAKKE IKDIFMRYER TLLVADPRRC EPKKFGGRGA RARFQKSYR + + + + + + +5.79848 +-0.269697 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 31 32 33 34 35 36 37 38 39 40 41 42 43 + + + + +3298 3298 3298 3298 3220 3114 2983 2725 2453 2061 1508 882 464 248 118 65 34 20 12 9 1 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + + + + +3303 3303 3303 3303 3225 3118 2985 2697 2365 1856 1170 419 86 2 1 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +730 1223 914 308 95 35 7 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +675 1410 900 222 67 17 7 14 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3228 (charge 3) + +1361.79 +3 + + +151.087 155.082 155.118 157.097 157.134 158.092 159.076 159.092 165.102 166.061 167.081 169.097 169.133 171.076 171.113 172.108 173.092 173.128 175.119 176.122 181.097 183.077 183.112 183.149 185.092 185.128 185.165 186.124 187.108 192.114 +194.129 195.113 197.129 199.108 201.123 204.134 207.112 209.14 212.139 213.124 215.139 217.081 226.119 227.102 230.15 233.164 235.109 237.135 239.163 242.15 244.128 246.156 247.143 249.16 254.149 258.145 261.157 265.12 268.13 269.16 +272.16 300.15 312.167 325.188 329.193 339.168 341.219 343.198 354.143 361.204 366.186 372.19 383.217 396.722 414.205 446.255 457.289 471.294 480.22 497.32 511.254 512.259 535.247 539.261 558.336 570.362 599.288 636.313 641.4 646.319 +663.305 710.421 721.401 755.383 775.411 792.436 826.417 891.507 955.457 962.539 + + + + +8 23 9 9 9 21 12 6 6 7 6 15 10 9 62 6 55 25 100 6 8 6 9 12 6 9 22 6 7 9 +10 10 11 13 20 10 12 11 12 7 15 6 20 14 21 20 6 7 21 37 15 11 9 22 13 7 10 7 11 9 +28 6 26 12 85 6 7 20 8 8 6 6 19 12 8 9 30 22 6 6 9 9 15 6 52 8 28 7 7 10 +11 6 34 10 6 58 12 19 8 20 + + + + + + +GRMZM2G060470_P01 NP_001130656 hypothetical protein LOC100191757 seq=translation; coord=4:184857223..184861548:1; parent_transcript=GRMZM2G060470_T01; parent_gene=GRMZM2G060470 + + + MAATAAALRC CFPGSSGVGS GFVKPNSSRR GWCAAAVAAP SREAEPVSSL + GHRTRVDFPI LHQEFDDAKL VYFDNGATSQ KPCSVMKTLD EYYRSYNSNV + HRGIHALSAK ATHAYEDARR KVANFVNAAD SREIVFTRNA TEAINLVAYS + WGLSNLKEGD EKTGATLKYV GLTKENVPDI EQLKGFLSNK TKIVVVHHVS + NVLGSMLPIE EIVTWSNRVG AKVLVDACQS VPHMPVDVQK LGADFLVASS + HKMCGPTGVG FLHGKFEILS SMEPFLGGGE MIADVFEDKS TYAEPPSRFE + AGTPAIGEAI GLGAAIDYLS CIGMEQIHEY EKELGTYLYE SLLSVPNVQI + YGPAPSQTVH RAPLCSFNIE NVHPTDIAEI LDLQHSVAIR SGHHCAQILH + RTLGINASAR ASLHFYNTKD EVDTFVDALK ATVDFLTDRY + + + + + +GRMZM2G060470_P02 NP_001130656 hypothetical protein LOC100191757 seq=translation; coord=4:184857414..184861548:1; parent_transcript=GRMZM2G060470_T02; parent_gene=GRMZM2G060470 + + + MAATAAALRC CFPGSSGVGS GFVKPNSSRR GWCAAAVAAP SREAEPVSSL + GHRTRVDFPI LHQEFDDAKL VYFDNGATSQ KPCSVMKTLD EYYRSYNSNV + HRGIHALSAK ATHAYEDARR KVANFVNAAD SREIVFTRNA TEAINLVAYS + WGLSNLKEGD EIVLTVAEHH SAIVPWQFVS QKTGATLKYV GLTKENVPDI + EQLKGFLSNK TKIVVVHHVS NVLGSMLPIE EIVTWSNRVG AKVLVDACQS + VPHMPVDVQK LGADFLVASS HKMCGPTGVG FLHGKFEILS SMEPFLGGGE + MIADVFEDKS TYAEPPSRFE AGTPAIGEAI GLGAAIDYLS CIGMEQIHEY + EKELGTYLYE SLLSVPNVQI YGPAPSQTVH RAPLCSFNIE NVHPTDIAEI + LDLQHSVAIR SGHHCAQILH RTLGINASAR ASLHFYNTKD EVDTFVDALK + ATVDFLTDRY + + + + + +GRMZM2G060470_P03 NP_001130656 hypothetical protein LOC100191757 seq=translation; coord=4:184857414..184861548:1; parent_transcript=GRMZM2G060470_T03; parent_gene=GRMZM2G060470 + + + MLPIEEIVTW SNRVGAKVLV DACQSVPHMP VDVQKLGADF LVASSHKMCG + PTGVGFLHGK FEILSSMEPF LGGGEMIADV FEDKSTYAEP PSRFEAGTPA + IGEAIGLGAA IDYLSCIGME QIHEYEKELG TYLYESLLSV PNVQIYGPAP + SQTVHRAPLC SFNIENVHPT DIAEILDLQH SVAIRSGHHC AQILHRTLGI + NASARASLHF YNTKDEVDTF VDALKATVDF LTDRY + + + + + + +5.97883 +-0.32318 + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +30 + + + + +6286 6286 6263 5746 5089 4672 3170 2262 1159 501 260 105 46 23 9 6 2 1 0 0 0 0 0 0 0 0 0 0 0 1 +0 + + + + + + +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 + + + + +6290 6290 6263 5713 4971 4370 2664 1618 445 60 31 7 2 1 0 + + + + + + +0 1 2 3 4 + + + + +4001 2011 270 13 0 + + + + + + +0 1 2 3 4 5 6 7 + + + + +589 3801 1561 294 42 2 0 6 + + + + + + +20120906_balliau_extract_1_A12_teal-3.mzXML scan 3232 (charge 2) + +1007.48 +2 + + +155.082 155.118 157.097 157.109 158.092 159.077 161.092 162.093 167.02 167.056 169.097 171.076 173.092 173.129 175.119 181.061 181.097 183.034 183.113 185.092 185.165 186.124 187.144 189.087 190.089 191.085 195.113 199.071 199.107 201.087 +204.134 207.113 209.091 213.087 217.082 219.113 227.101 228.632 235.107 237.123 240.134 241.082 244.167 247.108 256.129 258.145 262.152 265.119 272.172 276.158 282.145 289.119 299.171 301.06 303.203 306.144 324.162 334.14 336.154 342.178 +352.151 355.161 359.204 364.15 396.224 418.995 422.204 439.23 440.234 456.256 458.262 507.266 543.323 567.289 585.299 604.305 622.291 638.325 656.336 658.34 693.322 767.365 819.4 821.406 + + + + +1 1 2 1 3 1 19 2 2 5 1 8 2 1 17 1 3 1 1 3 3 2 4 15 1 2 2 2 2 5 +6 18 4 1 1 1 3 6 17 7 2 1 1 2 1 2 3 3 4 1 1 1 5 1 1 3 1 15 2 5 +4 1 8 2 6 2 1 14 3 100 3 2 1 4 10 1 1 1 21 2 1 2 11 1 + + + + + + + + + + /tmp/xtpcpp-HDpOXY/QExactive_analysis_FDR.xml + /tmp/xtpcpp.YBMdtF + 30 + yes + 0.1 + 0.01 + yes + yes + /gorgone/pappso/data_extraction_pappso/tandem_output/20120906_balliau_extract_1_A12_teal-3.xml + no + yes + yes + valid + yes + spectrum + yes + tandem-style.xsl + 0.0 + 0.0 + +17.00305 + +1.00794 + no + [RK]|{P} + + yes + yes + yes + usedefined + yes + yes + 0.01 + 57.02146@C + + no + + +42.01056@[ + 15.99491@M + + + + yes + no + yes + 57.02146@C + + 15.99491@M + + no + yes + no + yes + yes + 1 + 4 + no + yes + no + 100.0 + monoisotopic + 0.02 + Daltons + 4 + 150.0 + 500.0 + 15 + 18.01057 + 0.02 + 10 + 10 + ppm + yes + /gorgone/pappso/data_extraction_pappso/mzXML/20120906_balliau_extract_1_A12_teal-3.mzXML + 1000 + 4 + 100 + no + yes + + + yes + 3 + + + + + + + + + no + + yes + + + /gorgone/pappso/formation/2018novembre/shotgun/database/contaminants_standards.fasta + /gorgone/pappso/formation/2018novembre/shotgun/database/Genome_Z_mays_5a.fasta + no description + no description + 6487 + 19735 + 31 + 6 + 127745223 + 273656 + 6985 + 11574 + 5701 + 2021:05:11:09:31:20 + X! Tandem Alanine (2017.2.1.4) + 227 453 397 377 370 389 418 394 390 361 327 358 325 314 251 277 251 205 219 182 + 4536 + 5665 + 3629 + 0 + 0 + 119 + 0 + 115.45 + 0.0100 + 0.50 + 0.0189 + + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/tandem_run_params.xml libpappsomspp-0.8.58/tests/data/tandem/tandem_run_params.xml --- libpappsomspp-0.8.15/tests/data/tandem/tandem_run_params.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/tandem_run_params.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,12 @@ + + + Paths + /gorgone/pappso/tmp/xtpcpp.AjyZGg/Lumos_trypsin_rev_camC_oxM_10ppm_HCDOT_12102017CH.xml + /gorgone/pappso/tmp/xtpcpp.AjyZGg/database.xml + /gorgone/pappso/jouy/raw/2021_Lumos/20210729_02_Clouet/20210729_18_blc.mzXML + Protein general + usedefined + Output + /gorgone/pappso/jouy/users/Lydie/2021/2021_lumos/20210729_02_Clouet/xtpcpp/20210729_18_blc.xml + + diff -Nru libpappsomspp-0.8.15/tests/data/tandem/wrapper/wrapped_tandem_input.xml libpappsomspp-0.8.58/tests/data/tandem/wrapper/wrapped_tandem_input.xml --- libpappsomspp-0.8.15/tests/data/tandem/wrapper/wrapped_tandem_input.xml 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/tandem/wrapper/wrapped_tandem_input.xml 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,11 @@ + + + Paths + /gorgone/pappso/tmp/xtpcpp.AjyZGg/Lumos_trypsin_rev_camC_oxM_10ppm_HCDOT_12102017CH.xml + /gorgone/pappso/tmp/xtpcpp.AjyZGg/database.xml + mzdata_source.mzXML + Protein general + usedefined + Output + wrapped_tandem_output.xml + diff -Nru libpappsomspp-0.8.15/tests/data/xic/PXD014777_xic.tsv libpappsomspp-0.8.58/tests/data/xic/PXD014777_xic.tsv --- libpappsomspp-0.8.15/tests/data/xic/PXD014777_xic.tsv 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/data/xic/PXD014777_xic.tsv 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,12029 @@ +rt intensity +1.72895269925 56.3953312722 +2.53687997823 229.609563037 +3.71247680563 182.277767148 +4.88697482957 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/srv/release.debian.org/tmp/SxIFRls3td/libpappsomspp-0.8.58/tests/data/xic/real_xic.ods differ Binary files /srv/release.debian.org/tmp/wp6jDaiuvp/libpappsomspp-0.8.15/tests/data/xic/xic.ods and /srv/release.debian.org/tmp/SxIFRls3td/libpappsomspp-0.8.58/tests/data/xic/xic.ods differ diff -Nru libpappsomspp-0.8.15/tests/memory/test_tandemwrapperrun.cpp libpappsomspp-0.8.58/tests/memory/test_tandemwrapperrun.cpp --- libpappsomspp-0.8.15/tests/memory/test_tandemwrapperrun.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/memory/test_tandemwrapperrun.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,67 @@ + +// File: test_tandemwrapperrun.cpp +// Created by: Olivier Langella +// Created on: 11/2/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [TandemWrapperRun] -s + +// valgrind --leak-check=yes ./tests/catch2-only-tests [TandemWrapperRun] -s + + +#include + +#include + +#include +#include +#include "../config.h" + + +using namespace pappso; + +TEST_CASE("running X!Tandem on tims raw data.", "[TandemWrapperRun]") +{ + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); +#if USEPAPPSOTREE == 1 + + QTextStream outputStream(stdout, QIODevice::WriteOnly); + UiMonitorText monitor(outputStream); + + TandemWrapperRun run_tandem("/usr/bin/tandem", "/tmp"); + + for(int i = 0; i < 5; i++) + { + INFO(QString("run %1").arg(i).toStdString()); + run_tandem.run(monitor, + QString("%1/tests/data/tandem/tandem_run_params.xml") + .arg(CMAKE_SOURCE_DIR)); + } +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} diff -Nru libpappsomspp-0.8.15/tests/memory/test_timsdata_reader_memory.cpp libpappsomspp-0.8.58/tests/memory/test_timsdata_reader_memory.cpp --- libpappsomspp-0.8.15/tests/memory/test_timsdata_reader_memory.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/memory/test_timsdata_reader_memory.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,259 @@ + +// File: test_timsdata_reader_memory.cpp +// Created by: Olivier Langella +// Created on: 12/2/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [MemTimsData] -s +// ./tests/catch2-only-tests [MonothreadTimsData] -s + + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include "../config.h" + + +using namespace pappso; + +TEST_CASE("Check memory usage of tandemrun wrapper.", "[MemTandemWrapper]") +{ + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); +#if USEPAPPSOTREE == 1 + + + QTextStream errorStream(stderr, QIODevice::WriteOnly); + QTextStream outputStream(stdout, QIODevice::WriteOnly); + + TandemWrapperRun run_tandem("/usr/bin/tandem", "/tmp"); + UiMonitorText monitor(outputStream); + for(int i = 0; i < 5; i++) + { + INFO(QString("run %1").arg(i).toStdString()); + run_tandem.run(monitor, + QString("%1/tests/data/tandem/tandem_run_params.xml") + .arg(CMAKE_SOURCE_DIR)); + } +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} + +TEST_CASE("Check memory usage of timsdata reader.", "[MemTimsData]") +{ + // VIRT 484Mo => 666Mo scan num="23944" + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); +#if USEPAPPSOTREE == 1 + INFO("Test case start"); + + /* + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/" + "PXD014777_maxquant_timstof/" + "20180809_120min_200ms_WEHI25_brute20k_timsON_100ng_HYE124A_Slot1-7_1_890." + "d", + ""); +*/ + + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/example_data/" + "200ngHeLaPASEF_2min_compressed.d", + ""); + + /* + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/home/langella/data1/bruker/5-18-2021_1_robert_28_mic02-std_1354.d", + ""); +*/ + INFO(QString("number of runIds = %1") + .arg(file_access_A01.getMsRunIds().size()) + .toStdString()); + pappso::MsRunReaderSPtr msrunA01 = + file_access_A01.getMsRunReaderSPtrByRunId("", "runa01"); + file_access_A01.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + file_access_A01.getMsRunIds(); + + QTextStream outputStream(stdout, QIODevice::WriteOnly); + UiMonitorText monitor(outputStream); + + + pappso::MsRunReaderSPtr p_reader; + p_reader = + file_access_A01.msRunReaderSp(file_access_A01.getMsRunIds().front()); + + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_reader.get()); + REQUIRE(tims2_reader != nullptr); + if(tims2_reader != nullptr) + { + qDebug(); + tims2_reader->setMs2BuiltinCentroid(true); + + std::shared_ptr ms2filter; + QString filters_str = + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"; + ms2filter = std::make_shared(filters_str); + + monitor.setStatus(QString("timsTOF MS2 filters : %1").arg(filters_str)); + + tims2_reader->setMs2FilterCstSPtr(ms2filter); + + qDebug(); + } + + + // 517760 + // REQUIRE(p_reader.get()->spectrumListSize() == 517760); + + + QFile output_file("/tmp/test.xml"); + // qDebug() << " TsvDirectoryWriter::writeSheet " << + // QFileInfo(*_p_ofile).absoluteFilePath(); + REQUIRE(output_file.open(QIODevice::WriteOnly)); + pappso::UiMonitorVoid monitor_null; + + pappso::MzxmlOutput mzxml_ouput(monitor_null, + QTextStream(&output_file).device()); + + mzxml_ouput.setReadAhead(true); + mzxml_ouput.maskMs1(true); + QThreadPool::globalInstance()->setMaxThreadCount(10); + mzxml_ouput.write(p_reader.get()); + + mzxml_ouput.close(); +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} + + +TEST_CASE("Check monothread usage of timsdata reader.", "[MonothreadTimsData]") +{ + // VIRT 484Mo => 666Mo scan num="23944" + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); +#if USEPAPPSOTREE == 1 + INFO("Test case start"); + + /* + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/" + "PXD014777_maxquant_timstof/" + "20180809_120min_200ms_WEHI25_brute20k_timsON_100ng_HYE124A_Slot1-7_1_890." + "d", + ""); +*/ + + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/example_data/" + "200ngHeLaPASEF_2min_compressed.d", + ""); + + /* + pappso::MsFileAccessor file_access_A01( + // "/gorgone/pappso/data_extraction_pappso/mzXML/" + "/home/langella/data1/bruker/5-18-2021_1_robert_28_mic02-std_1354.d", + ""); +*/ + INFO(QString("number of runIds = %1") + .arg(file_access_A01.getMsRunIds().size()) + .toStdString()); + pappso::MsRunReaderSPtr msrunA01 = + file_access_A01.getMsRunReaderSPtrByRunId("", "runa01"); + file_access_A01.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + file_access_A01.getMsRunIds(); + + QTextStream outputStream(stdout, QIODevice::WriteOnly); + UiMonitorText monitor(outputStream); + + + pappso::MsRunReaderSPtr p_reader; + p_reader = + file_access_A01.msRunReaderSp(file_access_A01.getMsRunIds().front()); + + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_reader.get()); + REQUIRE(tims2_reader != nullptr); + if(tims2_reader != nullptr) + { + qDebug(); + tims2_reader->setMs2BuiltinCentroid(true); + + std::shared_ptr ms2filter; + QString filters_str = + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"; + ms2filter = std::make_shared(filters_str); + + monitor.setStatus(QString("timsTOF MS2 filters : %1").arg(filters_str)); + + tims2_reader->setMs2FilterCstSPtr(ms2filter); + + qDebug(); + } + + + // 517760 + // REQUIRE(p_reader.get()->spectrumListSize() == 517760); + p_reader.get()->setMonoThread(true); + + QFile output_file("/tmp/test.xml"); + // qDebug() << " TsvDirectoryWriter::writeSheet " << + // QFileInfo(*_p_ofile).absoluteFilePath(); + REQUIRE(output_file.open(QIODevice::WriteOnly)); + pappso::UiMonitorVoid monitor_null; + + pappso::MzxmlOutput mzxml_ouput(monitor_null, + QTextStream(&output_file).device()); + + mzxml_ouput.setReadAhead(true); + mzxml_ouput.maskMs1(true); + QThreadPool::globalInstance()->setMaxThreadCount(10); + mzxml_ouput.write(p_reader.get()); + + mzxml_ouput.close(); +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} diff -Nru libpappsomspp-0.8.15/tests/test_aa.cpp libpappsomspp-0.8.58/tests/test_aa.cpp --- libpappsomspp-0.8.15/tests/test_aa.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_aa.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,9 +26,12 @@ *implementation ******************************************************************************/ -// make test ARGS="-V -I 5,5" -#define CATCH_CONFIG_MAIN +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [Aa] -s + + #include #include #include @@ -52,15 +55,16 @@ SECTION("..:: AA init ::..", "[Aa]") { - // cout << endl << "..:: AA init ::.." << endl; + // cout << std::endl << "..:: AA init ::.." << std::endl; // OboPsiMod test; Aa leucine('L'); MzRange mz_range(leucine.getMass(), PrecisionFactory::getPpmInstance(1)); cout << "leucine: " - << QString::number(leucine.getMass(), 'g', 10).toStdString() << endl; + << QString::number(leucine.getMass(), 'g', 10).toStdString() + << std::endl; cout << "leucine number of N15 : " - << leucine.getNumberOfIsotope(Isotope::N15) << endl; - cout << mz_range.toString().toStdString() << endl; + << leucine.getNumberOfIsotope(Isotope::N15) << std::endl; + cout << mz_range.toString().toStdString() << std::endl; /* if(!mz_range.contains(pappso_double(131.094635) - MASSH2O)) { @@ -99,20 +103,20 @@ OboPsiMod psimod(filter_label); - cout << "term_list.size= " << term_list.size() << endl; + cout << "term_list.size= " << term_list.size() << std::endl; REQUIRE(term_list.size() == 12); MzRange range(pappso_double(57.02), PrecisionFactory::getDaltonInstance(pappso_double(0.02))); - cout << range.getMz() << endl; + cout << range.getMz() << std::endl; cout << "choses " << MzRange(pappso_double(57.02), PrecisionFactory::getDaltonInstance(pappso_double(0.02))) .toString() .toStdString() - << endl; + << std::endl; FilterOboPsiModSink term_listb; FilterOboPsiModTermDiffMono filter_labelb( term_listb, @@ -124,15 +128,24 @@ for(auto term : term_listb.getOboPsiModTermList()) { // cout << term._accession.toStdString() << " " << mz(term._diff_mono) - // << endl; + // << std::endl; } - cout << "term_listb.size= " << term_listb.size() << endl; - REQUIRE(term_listb.size() == 9); + cout << "term_listb.size= " << term_listb.size() << std::endl; + REQUIRE(term_listb.size() == 8); Aa alaninebis('A'); + REQUIRE(alaninebis.getNumberOfAtom(AtomIsotopeSurvey::C) == 3); + REQUIRE(alaninebis.getNumberOfAtom(AtomIsotopeSurvey::H) == 5); + + // xref: DiffFormula: "C 2 H 3 N 1 O 1" alaninebis.addAaModification(AaModification::getInstance("MOD:00397")); + REQUIRE(alaninebis.getNumberOfAtom(AtomIsotopeSurvey::C) == 5); + REQUIRE(alaninebis.getNumberOfAtom(AtomIsotopeSurvey::H) == 8); + + REQUIRE(alaninebis.toAbsoluteString().toStdString() == "A(MOD:00397)"); + alaninebis.addAaModification( AaModification::getInstanceCustomizedMod(18.022316354654)); // SUCCESS @@ -155,33 +168,33 @@ { AaModificationP mod = AaModification::getInstance("MOD:00397"); cout << " MOD:00397 mass=" - << QString::number(mod->getMass(), 'g', 15).toStdString() << endl; + << QString::number(mod->getMass(), 'g', 15).toStdString() << std::endl; // 57.021464 // MOD:00429 mod = AaModification::getInstance("MOD:00429"); cout << " MOD:00429 mass=" - << QString::number(mod->getMass(), 'g', 15).toStdString() << endl; + << QString::number(mod->getMass(), 'g', 15).toStdString() << std::endl; // 28.0313 // MOD:00382 mod = AaModification::getInstance("MOD:00382"); cout << " MOD:00382 mass=" - << QString::number(mod->getMass(), 'g', 15).toStdString() << endl; + << QString::number(mod->getMass(), 'g', 15).toStdString() << std::endl; //-20.026215 REQUIRE(mod->getMass() == Approx(-20.026215)); // MOD:00234 mod = AaModification::getInstance("MOD:00234"); cout << " MOD:00234 mass=" - << QString::number(mod->getMass(), 'g', 15).toStdString() << endl; + << QString::number(mod->getMass(), 'g', 15).toStdString() << std::endl; // 305.068156 // MOD:00838 mod = AaModification::getInstance("MOD:00838"); cout << " MOD:00838 mass=" - << QString::number(mod->getMass(), 'g', 15).toStdString() << endl; + << QString::number(mod->getMass(), 'g', 15).toStdString() << std::endl; for(auto amino_acid : pappso::Aa::getAminoAcidCharList()) @@ -189,7 +202,7 @@ pappso::Aa aa_enumi(amino_acid); cout << " " << (char)amino_acid << " " << QString::number(aa_enumi.getMass(), 'g', 15).toStdString() - << endl; + << std::endl; } /* * A 71.037113785565 @@ -222,6 +235,7 @@ REQUIRE(pappso::Aa('D').getMass() == Approx(115.026943024685)); // AaModification::getInstance("MOD:00397_wrong"); + REQUIRE_THROWS_AS(AaModification::getInstance("MOD:00397_wrong"), pappso::ExceptionNotFound); } diff -Nru libpappsomspp-0.8.15/tests/test_big_hyperscore.cpp libpappsomspp-0.8.58/tests/test_big_hyperscore.cpp --- libpappsomspp-0.8.15/tests/test_big_hyperscore.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_big_hyperscore.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -52,12 +52,12 @@ main() { // return 1; - cout << endl + cout << std::endl << "..:: test all identified peptides in an XML tandem result file ::.." - << endl; + << std::endl; PrecisionPtr precision = PrecisionFactory::getDaltonInstance(0.02); - bool refine_spectrum_synthesis = false; + //bool refine_spectrum_synthesis = false; QFileInfo fileinfo( "/gorgone/pappso/formation/Janvier2014/TD/xml_tandem/" "20120906_balliau_extract_1_A01_urnb-1.xml"); diff -Nru libpappsomspp-0.8.15/tests/test_fasta_reader.cpp libpappsomspp-0.8.58/tests/test_fasta_reader.cpp --- libpappsomspp-0.8.15/tests/test_fasta_reader.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_fasta_reader.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -58,9 +58,9 @@ setSequence(const QString &description_in, const QString &sequence_in) override { - cout << endl << "begin description=" << description_in.toStdString(); - cout << endl << "sequence=" << sequence_in.toStdString(); - cout << endl << "end" << endl; + cout << std::endl << "begin description=" << description_in.toStdString(); + cout << std::endl << "sequence=" << sequence_in.toStdString(); + cout << std::endl << "end" << std::endl; description = description_in; sequence = sequence_in; }; @@ -89,13 +89,13 @@ /* Spectrum spectrum_low_masses(spectrum_parent.applyCutOff(150)); if (! spectrum_low_masses.equals(sremove_low_masses, precision)) { - cerr << "spectrum_low_masses() != tandem"<< endl; + cerr << "spectrum_low_masses() != tandem"<< std::endl; return 1; }*/ } SECTION("..:: Test Fasta file indexer ::..", "[FastaIndexer]") { - cout << endl << "..:: Test Fasta file indexer ::.." << endl; + cout << std::endl << "..:: Test Fasta file indexer ::.." << std::endl; QFileInfo file(QString(CMAKE_SOURCE_DIR) .append("/tests/data/asr1_digested_peptides.txt")); @@ -134,7 +134,7 @@ "LLLEYLEEKYEEHLYER LTQSMAIIRYIADK KFELGLEFPNLPYYIDGDVK " "ERAEISMLEGAVLDIR"); - cout << endl << " getSequenceByIndex(seq, 12) is OK " << endl; + cout << std::endl << " getSequenceByIndex(seq, 12) is OK " << std::endl; } catch(pappso::ExceptionOutOfRange &error) { @@ -151,12 +151,12 @@ SECTION("..:: Test Fasta big file indexer ::..", "[FastaBigIndexer]") { FastaSeq seq; - cout << endl << "..:: Test Fasta big file indexer ::.." << endl; + cout << std::endl << "..:: Test Fasta big file indexer ::.." << std::endl; QFileInfo file2("/gorgone/pappso/moulon/database/Genome_Z_mays_5a.fasta"); pappso::FastaFileIndexer big_fasta_file_indexer(file2); big_fasta_file_indexer.getSequenceByIndex(seq, 12); - cout << endl << seq.getDescription().toStdString() << endl; + cout << std::endl << seq.getDescription().toStdString() << std::endl; // GRMZM2G147579_P01 // GRMZM2G147579_P01 NP_001159186 hypothetical protein LOC100304271 @@ -189,7 +189,7 @@ REQUIRE(seq.getDescription() == "YGR254W "); // YGR254W fuzzy_fasta_file_indexer.getSequenceByIndex(seq, 2); - cout << endl << seq.getDescription().toStdString() << endl; + cout << std::endl << seq.getDescription().toStdString() << std::endl; // GRMZM2G147579_P01 // GRMZM2G147579_P01 NP_001159186 hypothetical protein LOC100304271 @@ -203,8 +203,8 @@ pappso::FastaFileIndexer fuzzy_macos_fasta_file_indexer(fuzzy_macos_file); fuzzy_macos_fasta_file_indexer.getSequenceByIndex(seq, 0); - cout << endl << "sequence0: " << seq.getDescription().toStdString() << - endl; + cout << std::endl << "sequence0: " << seq.getDescription().toStdString() << + std::endl; // GRMZM2G147579_P01 // GRMZM2G147579_P01 NP_001159186 hypothetical protein LOC100304271 @@ -216,13 +216,13 @@ cerr << "sequence 0 in fuzzy_macos.fasta is not OK seq.getDescription() != " "YGR254W " - << seq.getDescription().toStdString() << endl; + << seq.getDescription().toStdString() << std::std::std::std::endl; return 1; } fuzzy_macos_fasta_file_indexer.getSequenceByIndex(seq, 2); - cout << endl << "sequence2: "<< seq.getDescription().toStdString() << - endl; + cout << std::endl << "sequence2: "<< seq.getDescription().toStdString() << + std::endl; // GRMZM2G147579_P01 // GRMZM2G147579_P01 NP_001159186 hypothetical protein LOC100304271 @@ -234,7 +234,7 @@ cerr << "sequence 2 in fuzzy_macos.fasta is not OK seq.getDescription() != " "YGR254Wb " - << seq.getDescription().toStdString() << endl; + << seq.getDescription().toStdString() << std::endl; return 1; }*/ } diff -Nru libpappsomspp-0.8.15/tests/test_fragmentationcid.cpp libpappsomspp-0.8.58/tests/test_fragmentationcid.cpp --- libpappsomspp-0.8.15/tests/test_fragmentationcid.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_fragmentationcid.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -41,97 +41,96 @@ int main() { - - cout << endl << "..:: test ion direction ::.." << endl; + cout << std::endl << "..:: test ion direction ::.." << std::endl; if(getPeptideIonDirection(PeptideIon::b) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::b) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::bstar) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::bstar) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::bo) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::bo) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::a) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::a) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::astar) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::astar) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::ao) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::ao) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::bp) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::bp) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::c) != PeptideDirection::Nter) { cerr << "getPeptideIonDirection(PeptideIon::c) != PeptideDirection::Nter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::y) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::y) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::ystar) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::ystar) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::yo) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::yo) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::z) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::z) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::yp) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::yp) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } if(getPeptideIonDirection(PeptideIon::x) != PeptideDirection::Cter) { cerr << "getPeptideIonDirection(PeptideIon::x) != PeptideDirection::Cter" - << endl; + << std::endl; return 1; } - cout << endl << "..:: peptide fragment init ::.." << endl; + cout << std::endl << "..:: peptide fragment init ::.." << std::endl; // http://proteus.moulon.inra.fr/w2dpage/proticdb/angular/#/peptide_hits/10053478 Peptide peptide("DSTIPDKQITASSFYK"); list cid_ion = PeptideFragmentIonListBase::getCIDionList(); @@ -141,12 +140,12 @@ while(it != frag_cid.end()) { - unsigned int size = it->get()->size(); - QString name = it->get()->getPeptideIonName(); + // unsigned int size = it->get()->size(); + QString name = it->get()->getPeptideIonName(); cout << it->get()->getSequence().toStdString() << " " << it->get()->getPeptideIonName().toStdString() << " " << it->get()->getMz(1) << " " - << it->get()->getFormula(1).toStdString() << endl; + << it->get()->getFormula(1).toStdString() << std::endl; it++; } diff -Nru libpappsomspp-0.8.15/tests/test_hyperscore.cpp libpappsomspp-0.8.58/tests/test_hyperscore.cpp --- libpappsomspp-0.8.15/tests/test_hyperscore.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_hyperscore.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -60,7 +60,7 @@ SECTION("..:: readMgf ::..", "[hyperscore]") { - cout << endl << "..:: readMgf ::.." << endl; + cout << std::endl << "..:: readMgf ::.." << std::endl; bool refine_spectrum_synthesis = false; MassSpectrum spectrum_simple = @@ -76,7 +76,7 @@ std::list ion_list; ion_list.push_back(PeptideIon::y); ion_list.push_back(PeptideIon::b); - cout << "spectrum_simple size " << spectrum_simple.size() << endl; + cout << "spectrum_simple size " << spectrum_simple.size() << std::endl; qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; XtandemHyperscore hyperscore_withxtspectrum(spectrum_simple, @@ -88,7 +88,7 @@ qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; cout << "spectrum_simple " << peptide.getSequence().toStdString() - << " hyperscore=" << hyperscore_withxtspectrum.getHyperscore() << endl; + << " hyperscore=" << hyperscore_withxtspectrum.getHyperscore() << std::endl; float test_tandem = std::round(10 * hyperscore_withxtspectrum.getHyperscore()) / 10; REQUIRE(test_tandem == (float)33.5); @@ -105,7 +105,7 @@ refine_spectrum_synthesis); cout << "spectrum_simple with spectrum model " << peptide.getSequence().toStdString() - << " hyperscore=" << hyperscore_model.getHyperscore() << endl; + << " hyperscore=" << hyperscore_model.getHyperscore() << std::endl; // hyperscore="35.4" test_tandem = round(10 * hyperscore_model.getHyperscore()) / 10; REQUIRE(test_tandem == (float)35.4); @@ -138,7 +138,7 @@ // spectrum.applyCutOff(150); // spectrum_temp.takeNmostIntense(50,spectrum); - cout << "spectrum size " << spectrum.size() << endl; + cout << "spectrum size " << spectrum.size() << std::endl; refine_spectrum_synthesis = false; @@ -151,7 +151,7 @@ qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; cout << "peptide " << peptide.getSequence().toStdString() - << " hyperscore=" << hyperscore.getHyperscore() << endl; + << " hyperscore=" << hyperscore.getHyperscore() << std::endl; // SUCCESS qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; @@ -183,7 +183,7 @@ qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; cout << "peptide " << pep.getSequence().toStdString() - << " hyperscore=" << hyperscoreb.getHyperscore() << endl; + << " hyperscore=" << hyperscoreb.getHyperscore() << std::endl; qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; // match ion ED b 245.077, pi=15 for X!Tandem @@ -218,10 +218,10 @@ ion_list, refine_spectrum_synthesis); cout << "peptide " << pep15968.getSequence().toStdString() - << " hyperscore15968=" << hyperscore15968.getHyperscore() << endl; + << " hyperscore15968=" << hyperscore15968.getHyperscore() << std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; std::vector ion_vec; ion_vec.push_back(PeptideIon::y); @@ -233,11 +233,11 @@ cout << "XtandemHyperscoreBis peptide " << pep15968.getSequence().toStdString() << " hyperscore15968bis=" << hyperscore15968bis.getHyperscore() - << endl; + << std::endl; cout << "XtandemHyperscoreBis peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; } // FISLQLGQPPAMGSHM(MOD:00719)TDSNSR diff -Nru libpappsomspp-0.8.15/tests/test_isotope_with_spectrum.cpp libpappsomspp-0.8.58/tests/test_isotope_with_spectrum.cpp --- libpappsomspp-0.8.15/tests/test_isotope_with_spectrum.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_isotope_with_spectrum.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -58,7 +58,7 @@ MassSpectrum spectrum = readMgf( QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf")); - cout << "spectrum size:" << spectrum.size() << endl; + cout << "spectrum size:" << spectrum.size() << std::endl; Peptide peptide("AIADGSLLDLLR"); @@ -84,14 +84,14 @@ PrecisionFactory::getPpmInstance(100)) .contains(peak.x)) { - cout << endl + cout << std::endl << isotope.get()->getIsotopeNumber() << "..:: " << isotope.get()->getFormula(1).toStdString() << " mz1=" << isotope.get()->getMz(1) << " ratio=" << isotope.get()->getIntensityRatio(1) - << " ::.." << endl; + << " ::.." << std::endl; cout << " real mz=" << peak.x << " real intensity" << peak.y - << endl; + << std::endl; } } } @@ -99,10 +99,10 @@ map_isotope_number = isotopeListFrag.getIntensityRatioPerIsotopeNumber(); - cout << "isotope levels" << endl; + cout << "isotope levels" << std::endl; for(unsigned int i = 0; i < map_isotope_number.size(); i++) { - cout << "frag isotope " << i << " " << map_isotope_number[i] << endl; + cout << "frag isotope " << i << " " << map_isotope_number[i] << std::endl; } /* 0..:: C39H70O11N11S0 C13(0) H2(0) O17(0) O18(0) N15(0) S34(0) mz1=886.536 diff -Nru libpappsomspp-0.8.15/tests/test_massrange.cpp libpappsomspp-0.8.58/tests/test_massrange.cpp --- libpappsomspp-0.8.15/tests/test_massrange.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_massrange.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -29,6 +29,8 @@ // make test ARGS="-V -I 4,4" #include +#include + #include #include #include @@ -38,17 +40,6 @@ using namespace std; -long long int -roundDecimal(pappso::pappso_double input) -{ - pappso::pappso_double test_decimal = 100000000000; - if(sizeof(int *) == 4) - { // 32bits - test_decimal = 100000000; - } - return (floor(input * test_decimal)); -} - int main() { @@ -58,7 +49,7 @@ { cerr << "precision == precisionb ERROR " << precision->toString().toStdString() << " " - << precisionb->toString().toStdString() << endl; + << precisionb->toString().toStdString() << std::endl; return 1; } precisionb = PrecisionFactory::getPpmInstance(10); @@ -66,11 +57,11 @@ { cerr << "precision != precisionb ERROR " << precision->toString().toStdString() << " " - << precisionb->toString().toStdString() << endl; + << precisionb->toString().toStdString() << std::endl; return 1; } - cout << endl << "..:: Mass Ranges ::.." << endl; + cout << std::endl << "..:: Mass Ranges ::.." << std::endl; MzRange mz_range1(pappso_double(1200.001), PrecisionFactory::getDaltonInstance(6.0)); MzRange mz_range2(pappso_double(1200.001), @@ -78,49 +69,49 @@ MzRange mz_range3(pappso_double(1200.001), PrecisionFactory::getPpmInstance(10), PrecisionFactory::getPpmInstance(30)); - cout << "mz_range1: " << mz_range1.toString().toStdString() << endl; - cout << "mz_range2: " << mz_range2.toString().toStdString() << endl; - cout << "mz_range3: " << mz_range3.toString().toStdString() << endl; + cout << "mz_range1: " << mz_range1.toString().toStdString() << std::endl; + cout << "mz_range2: " << mz_range2.toString().toStdString() << std::endl; + cout << "mz_range3: " << mz_range3.toString().toStdString() << std::endl; - cout << endl << "..:: Contains ::.." << endl; - cout << mz_range1.toString().toStdString() << endl; + cout << std::endl << "..:: Contains ::.." << std::endl; + cout << mz_range1.toString().toStdString() << std::endl; if(mz_range1.contains(pappso_double(600))) { - cerr << "mz_range1.contains(pappso_double(600)) ERROR" << endl; + cerr << "mz_range1.contains(pappso_double(600)) ERROR" << std::endl; return 1; } - cout << mz_range1.toString().toStdString() << endl; + cout << mz_range1.toString().toStdString() << std::endl; if(!mz_range1.contains(pappso_double(1200))) { - cerr << "!mz_range1.contains(pappso_double(1200)) ERROR" << endl; + cerr << "!mz_range1.contains(pappso_double(1200)) ERROR" << std::endl; return 1; } - cout << mz_range2.toString().toStdString() << endl; + cout << mz_range2.toString().toStdString() << std::endl; if(mz_range2.contains(pappso_double(600))) { - cerr << "mz_range2.contains(pappso_double(600)) ERROR" << endl; + cerr << "mz_range2.contains(pappso_double(600)) ERROR" << std::endl; return 1; } - cout << mz_range2.toString().toStdString() << endl; + cout << mz_range2.toString().toStdString() << std::endl; if(!mz_range2.contains(pappso_double(1200))) { - cerr << "!mz_range2.contains(pappso_double(1200)) ERROR" << endl; + cerr << "!mz_range2.contains(pappso_double(1200)) ERROR" << std::endl; return 1; } - cout << mz_range2.toString().toStdString() << endl; + cout << mz_range2.toString().toStdString() << std::endl; if(!mz_range2.contains(pappso_double(1200.00001))) { - cerr << "!mz_range2.contains(pappso_double(1200.00001)) ERROR" << endl; + cerr << "!mz_range2.contains(pappso_double(1200.00001)) ERROR" << std::endl; return 1; } - cout << mz_range2.toString().toStdString() << endl; + cout << mz_range2.toString().toStdString() << std::endl; if(mz_range2.contains(pappso_double(1200.1))) { - cerr << "mz_range2.contains(pappso_double(1200.1)) ERROR" << endl; + cerr << "mz_range2.contains(pappso_double(1200.1)) ERROR" << std::endl; return 1; } @@ -129,23 +120,23 @@ MzRange mz_range_test_ref(pappso_double(633.29706487392), PrecisionFactory::getPpmInstance(10)); cerr.precision(17); - if(roundDecimal(mz_range_test_ref.getMz()) != roundDecimal(633.29706487392)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test_ref.getMz()) != Utils::roundToDecimal32bitsAsLongLongInt(633.29706487392)) { cerr << "mz_range_test_ref.getMz() != 633.29706487392 ERROR " - << roundDecimal(mz_range_test_ref.getMz()) - << " != " << roundDecimal(633.29706487392) << endl; + << Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test_ref.getMz()) + << " != " << Utils::roundToDecimal32bitsAsLongLongInt(633.29706487392) << std::endl; return 1; } - if(roundDecimal(mz_range_test_ref.lower()) != roundDecimal(633.290731903271)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test_ref.lower()) != Utils::roundToDecimal32bitsAsLongLongInt(633.290731903271)) { cerr << "mz_range_test_ref.lower() != 633.290731903271 ERROR " - << mz_range_test_ref.lower() << endl; + << mz_range_test_ref.lower() << std::endl; return 1; } - if(roundDecimal(mz_range_test_ref.upper()) != roundDecimal(633.303397844569)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test_ref.upper()) != Utils::roundToDecimal32bitsAsLongLongInt(633.303397844569)) { cerr << "mz_range_test_ref.upper() != 633.303397844569 ERROR" - << mz_range_test_ref.upper() << endl; + << mz_range_test_ref.upper() << std::endl; return 1; } @@ -154,22 +145,22 @@ PrecisionFactory::getPpmInstance(10), PrecisionFactory::getPpmInstance(10)); cerr.precision(17); - if(roundDecimal(mz_range_test.getMz()) != roundDecimal(633.29706487392)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test.getMz()) != Utils::roundToDecimal32bitsAsLongLongInt(633.29706487392)) { cerr << "mz_range_test.getMz() != 633.29706487392 ERROR " - << mz_range_test.getMz() << endl; + << mz_range_test.getMz() << std::endl; return 1; } - if(roundDecimal(mz_range_test.lower()) != roundDecimal(633.290731903271)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test.lower()) != Utils::roundToDecimal32bitsAsLongLongInt(633.290731903271)) { cerr << "mz_range_test.lower() != 633.290731903271 ERROR " - << mz_range_test.lower() << endl; + << mz_range_test.lower() << std::endl; return 1; } - if(roundDecimal(mz_range_test.upper()) != roundDecimal(633.303397844569)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_test.upper()) != Utils::roundToDecimal32bitsAsLongLongInt(633.303397844569)) { cerr << "mz_range_test.upper() != 633.303397844569 ERROR" - << mz_range_test.upper() << endl; + << mz_range_test.upper() << std::endl; return 1; } @@ -178,25 +169,25 @@ PrecisionFactory::getDaltonInstance(1)); cerr.precision(17); - if(roundDecimal(mz_range_lower_upper_test.getMz()) != - roundDecimal(633.79389838859572)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_lower_upper_test.getMz()) != + Utils::roundToDecimal32bitsAsLongLongInt(633.79389838859572)) { cerr << "mz_range_lower_upper_test.getMz() != 633.79389838859572 ERROR " - << mz_range_lower_upper_test.getMz() << endl; + << mz_range_lower_upper_test.getMz() << std::endl; return 1; } - if(roundDecimal(mz_range_lower_upper_test.lower()) != - roundDecimal(633.290731903271)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_lower_upper_test.lower()) != + Utils::roundToDecimal32bitsAsLongLongInt(633.290731903271)) { cerr << "mz_range_lower_upper_test.lower() != 633.290731903271 ERROR " - << mz_range_lower_upper_test.lower() << endl; + << mz_range_lower_upper_test.lower() << std::endl; return 1; } - if(roundDecimal(mz_range_lower_upper_test.upper()) != - roundDecimal(634.29706487392)) + if(Utils::roundToDecimal32bitsAsLongLongInt(mz_range_lower_upper_test.upper()) != + Utils::roundToDecimal32bitsAsLongLongInt(634.29706487392)) { cerr << "mz_range_lower_upper_test.upper() != 633.303397844569 ERROR" - << mz_range_lower_upper_test.upper() << endl; + << mz_range_lower_upper_test.upper() << std::endl; return 1; } // SUCCESS diff -Nru libpappsomspp-0.8.15/tests/test_massspectrumcombiner.cpp libpappsomspp-0.8.58/tests/test_massspectrumcombiner.cpp --- libpappsomspp-0.8.15/tests/test_massspectrumcombiner.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_massspectrumcombiner.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -1,7 +1,11 @@ +#include +#include + #include #include +#include #include #include #include @@ -56,6 +60,11 @@ } } + +#if !defined (__i386__) + + // This test unbelievable does not pass on i386... + TEST_CASE("Performing combinations with MassSpectrumPlusCombiner", "[MassSpectrumPlusCombiner][combinations]") { @@ -166,6 +175,10 @@ mass_spectrum_combiner.combine(map_trace, mass_spectrum1); + //std::cout << std::setprecision(10) + //<< "First map item x: " << map_trace.begin()->first + //<< " y: " << map_trace.begin()->second << std::endl; + REQUIRE(map_trace.size() == 20); REQUIRE(map_trace[610.02000] == 12963.5715942383); REQUIRE(map_trace[610.27000] == 54459.4762458801); @@ -286,4 +299,6 @@ } } +#endif + } // namespace pappso diff -Nru libpappsomspp-0.8.15/tests/test_msrunalignment.cpp libpappsomspp-0.8.58/tests/test_msrunalignment.cpp --- libpappsomspp-0.8.15/tests/test_msrunalignment.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_msrunalignment.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -20,15 +20,18 @@ ******************************************************************************/ -// make test ARGS="-V -I 20,20" -// cmake .. -DCMAKE_BUILD_TYPE=Debug -DMAKE_TEST=1 -DUSEPAPPSOTREE=1 +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [alignment] -s +// cmake .. -DCMAKE_BUILD_TYPE=Debug -DMAKE_TEST=1 -DUSEPAPPSOTREE=1 +#include #include //#include #include #include -#include +#include #include #include @@ -37,7 +40,7 @@ #include #include #include "config.h" -//#include "common.h" +#include "common.h" using namespace std; @@ -46,10 +49,10 @@ writeTrace(const QString &filename, const pappso::Trace &trace) { QFile file(filename); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " - << QFileInfo(filename).absoluteFilePath(); - // file.open(QIODevice::WriteOnly); - OdsDocWriter writer(&file); + qDebug() << QFileInfo(filename).absoluteFilePath(); + file.open(QIODevice::WriteOnly); + QTextStream textstream(&file); + TsvOutputStream writer(textstream); for(auto &data_point : trace) { @@ -60,29 +63,34 @@ writer.close(); } -class CustomHandler : public OdsDocHandlerInterface +class PeptideTableHandler : public OdsDocHandlerInterface { public: - CustomHandler(pappso::MsRunRetentionTime &rt1, - pappso::MsRunRetentionTime &rt2) + PeptideTableHandler(pappso::MsRunRetentionTime &rt1, + pappso::MsRunRetentionTime &rt2) : m_rt1(rt1), m_rt2(rt2) { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "; + qDebug(); } /** * callback that indicates the begining of a data sheet. Override it in * order to retrieve information about the current data sheet. * */ - virtual void startSheet(const QString &sheet_name - [[maybe_unused]]) override{}; + virtual void + startSheet(const QString &sheet_name [[maybe_unused]]) override + { + qDebug(); + }; /** * callback that indicates the end of the current data sheet. Override it if * needed */ - virtual void endSheet() override{ - // qDebug() << "endSheet"; + virtual void + endSheet() override + { + qDebug() << "endSheet"; }; /** @@ -93,7 +101,7 @@ startLine() override { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "; + qDebug() << m_sample; if(m_sample == "20120906_balliau_extract_1_A01_urnb-1") { m_rt1.addPeptideAsSeamark(m_peptideId, m_scan - 1); @@ -108,7 +116,7 @@ m_scan = 0; m_sequenceLi = ""; - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "; + qDebug(); }; /** @@ -118,15 +126,13 @@ virtual void endLine() override { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ - << "() _is_title=" << _is_title; + qDebug() << "() _is_title=" << _is_title; m_col = 0; if(!_is_title) { } _is_title = false; - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ - << "() _is_title=" << _is_title; + qDebug() << " _is_title = " << _is_title; }; /** @@ -137,7 +143,7 @@ setCell(const OdsCell &cell) override { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " << m_col; + qDebug() << m_col; if(_is_title) return; m_col++; @@ -150,18 +156,24 @@ } if(m_col == 2) { + if(!cell.isString()) + return; m_sample = cell.getStringValue(); } if(m_col == 3) { + if(!cell.isDouble()) + return; m_scan = (std::size_t)cell.getDoubleValue(); } if(m_col == 4) { + if(!cell.isString()) + return; m_sequenceLi = cell.getStringValue(); } - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "; + qDebug(); }; /** @@ -169,9 +181,9 @@ * to know that reading is finished. */ virtual void - endDocument() + endDocument() override { - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "; + qDebug(); }; private: @@ -187,129 +199,117 @@ }; -int -main([[maybe_unused]] int argc, [[maybe_unused]] char *argv[]) +TEST_CASE("MSrun alignment test suite.", "[alignment]") { - // QCoreApplication a(argc, argv); + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + SECTION("..:: Test MSrun alignment ::..", "[alignment]") + { - qDebug() << "init test MSrun alignment"; - cout << endl << "..:: Test MSrun alignment ::.." << endl; - QTime timer; + QTime timer; #if USEPAPPSOTREE == 1 - cout << endl << "..:: Test MSrun alignment starts ::.." << endl; - pappso::MsFileAccessor file_access_A01( - "/gorgone/pappso/data_extraction_pappso/mzXML/" - //"/home/langella/data1/mzxml/" - "20120906_balliau_extract_1_A01_urnb-1.mzXML", - "runa1"); + cout << std::endl << "..:: Test MSrun alignment starts ::.." << std::endl; + pappso::MsFileAccessor file_access_A01( + "/gorgone/pappso/data_extraction_pappso/mzXML/" + //"/home/langella/data1/mzxml/" + "20120906_balliau_extract_1_A01_urnb-1.mzXML", + "runa1"); - pappso::MsRunReaderSPtr msrunA01 = - file_access_A01.getMsRunReaderSPtrByRunId("", "runa01"); + pappso::MsRunReaderSPtr msrunA01 = + file_access_A01.getMsRunReaderSPtrByRunId("", "runa01"); + WARN("reading 20120906_balliau_extract_1_A01_urnb ::.."); + pappso::MsRunRetentionTime rt_msrunA01(msrunA01); - cout << endl - << "..:: reading 20120906_balliau_extract_1_A01_urnb ::.." << endl; - pappso::MsRunRetentionTime rt_msrunA01(msrunA01); + pappso::MsFileAccessor file_access_A02( + "/gorgone/pappso/data_extraction_pappso/mzXML/" + //"/home/langella/data1/mzxml/" + "20120906_balliau_extract_1_A02_urzb-1.mzXML", + "runa1"); - pappso::MsFileAccessor file_access_A02( - "/gorgone/pappso/data_extraction_pappso/mzXML/" - //"/home/langella/data1/mzxml/" - "20120906_balliau_extract_1_A02_urzb-1.mzXML", - "runa1"); + pappso::MsRunReaderSPtr msrunA02 = + file_access_A02.getMsRunReaderSPtrByRunId("", "runa02"); - pappso::MsRunReaderSPtr msrunA02 = - file_access_A02.getMsRunReaderSPtrByRunId("", "runa02"); + WARN("..:: reading 20120906_balliau_extract_1_A02_urzb ::.."); + pappso::MsRunRetentionTime rt_msrunA02(msrunA02); + rt_msrunA02.setMs2MedianFilter(pappso::FilterMorphoMedian(10)); + rt_msrunA02.setMs2MeanFilter(pappso::FilterMorphoMean(15)); + rt_msrunA02.setMs1MeanFilter(pappso::FilterMorphoMean(1)); - cout << endl - << "..:: reading 20120906_balliau_extract_1_A02_urzb ::.." << endl; - pappso::MsRunRetentionTime rt_msrunA02(msrunA02); - rt_msrunA02.setMs2MedianFilter(pappso::FilterMorphoMedian(10)); - rt_msrunA02.setMs2MeanFilter(pappso::FilterMorphoMean(15)); - rt_msrunA02.setMs1MeanFilter(pappso::FilterMorphoMean(1)); + QFile realfile(QString(CMAKE_SOURCE_DIR) + .append("/tests/data/alignment/peptide_table.ods")); + PeptideTableHandler handler_rt(rt_msrunA01, rt_msrunA02); + OdsDocReader realreader_prm(handler_rt); + // realreader_prm.setSeparator(TsvSeparator::tab); - cout << endl << "..:: reading peptide table ::.." << endl; + WARN("..:: reading peptide table ::.."); + REQUIRE_NOTHROW(realreader_prm.parse(&realfile)); - QFile realfile( - QString(CMAKE_SOURCE_DIR).append("/test/data/alignment/peptide_table.ods")); - CustomHandler handler_rt(rt_msrunA01, rt_msrunA02); - OdsDocReader realreader_prm(handler_rt); - // realreader_prm.setSeparator(TsvSeparator::tab); - try - { - realreader_prm.parse(&realfile); - } - catch(OdsException &error) - { - cerr << endl << "ERROR: " << error.qwhat().toStdString() << endl; - } - realfile.close(); + realfile.close(); - rt_msrunA01.computePeptideRetentionTimes(); + rt_msrunA01.computeSeamarks(); - cout << endl - << "rt_msrunA01 seamarks " << rt_msrunA01.getSeamarks().size() << endl; + REQUIRE(rt_msrunA01.getSeamarks().size() == 5227); - rt_msrunA02.computePeptideRetentionTimes(); + rt_msrunA02.computeSeamarks(); - cout << endl - << "rt_msrunA02 seamarks " << rt_msrunA02.getSeamarks().size() << endl; + REQUIRE(rt_msrunA02.getSeamarks().size() == 5343); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " - << rt_msrunA01.getSeamarks()[0].entityHash << " " - << rt_msrunA01.getSeamarks()[0].retentionTime << " | " - << rt_msrunA02.getSeamarks()[0].entityHash << " " - << rt_msrunA02.getSeamarks()[0].retentionTime; + qDebug() << rt_msrunA01.getSeamarks()[0].entityHash << " " + << rt_msrunA01.getSeamarks()[0].retentionTime << " | " + << rt_msrunA02.getSeamarks()[0].entityHash << " " + << rt_msrunA02.getSeamarks()[0].retentionTime; - pappso::Trace rt_align; - try - { - rt_align = rt_msrunA02.align(rt_msrunA01); - } - catch(pappso::PappsoException &error) - { - cerr << endl << "ERROR: " << error.qwhat().toStdString() << endl; - } + pappso::Trace rt_align; + REQUIRE_NOTHROW(rt_align = rt_msrunA02.align(rt_msrunA01)); - pappso::Trace common_delta_rt = - rt_msrunA02.getCommonDeltaRt(rt_msrunA01.getSeamarks()); + pappso::Trace common_delta_rt = + rt_msrunA02.getCommonDeltaRt(rt_msrunA01.getSeamarks()); - writeTrace("delta_rt.ods", common_delta_rt); - writeTrace("rt_align.ods", rt_align); - cout << endl - << "rt_msrunA02 seamarks in common with rt_msrunA01 " - << common_delta_rt.size() << endl; - if(common_delta_rt.size() != 4251) - { - cerr << "common_delta_rt.size() " << common_delta_rt.size() << " != 4251" - << endl; + writeTrace("delta_rt.tsv", common_delta_rt); + writeTrace("rt_align.tsv", rt_align); + cout << std::endl + << "rt_msrunA02 seamarks in common with rt_msrunA01 " + << common_delta_rt.size() << std::endl; - // the same as in MassChroQ 2.2.15 - return 1; - } + REQUIRE(common_delta_rt.size() == 4251); + /* + for(auto rt : rt_align) + { + // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " + << + // rt.x + // << " " << rt.y; + } + */ + qDebug() << " first=" << rt_msrunA01.getMs1RetentionTimeVector().front() + << " last=" << rt_msrunA01.getMs1RetentionTimeVector().back(); + cerr << "corrected values " << rt_msrunA02.getNumberOfCorrectedValues() + << " " << std::endl; - for(auto rt : rt_align) - { - // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " << - // rt.x - // << " " << rt.y; - } - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() first=" - << rt_msrunA01.getMs1RetentionTimeVector().front().retentionTime - << " last=" - << rt_msrunA01.getMs1RetentionTimeVector().back().retentionTime; - cerr << "corrected values " << rt_msrunA02.getNumberOfCorrectedValues() << " " - << endl; + REQUIRE( + compareTextFiles("rt_align.tsv", + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/alignment/result_rt_align.tsv"))); + + + double aligned = rt_msrunA02.translateOriginal2AlignedRetentionTime(1200); + + REQUIRE(rt_msrunA02.translateAligned2OriginalRetentionTime(aligned) == + 1200); + #endif - return 0; + } } diff -Nru libpappsomspp-0.8.15/tests/test_msrunoutput.cpp libpappsomspp-0.8.58/tests/test_msrunoutput.cpp --- libpappsomspp-0.8.15/tests/test_msrunoutput.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_msrunoutput.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -51,8 +51,8 @@ SECTION("..:: Test Qexception transferred accross threads ::..") { // QCoreApplication a(argc, argv); - cout << endl - << "..:: Test Qexception transferred accross threads ::.." << endl; + cout << std::endl + << "..:: Test Qexception transferred accross threads ::.." << std::endl; QFuture future = QtConcurrent::run([=]() { throw pappso::ExceptionNotPossible( QObject::tr("Not possible, but possible to catch it accross threads")); @@ -62,7 +62,7 @@ } // return 0; qDebug() << "init test MSrun output"; - cout << endl << "..:: Test MSrun output ::.." << endl; + cout << std::endl << "..:: Test MSrun output ::.." << std::endl; QTime timer; #if USEPAPPSOTREE == 1 @@ -76,7 +76,7 @@ "20120906_balliau_extract_1_A01_urnb-1.mzXML", ""); cout << "number of runIds = " << file_access_A01.getMsRunIds().size() - << endl; + << std::endl; pappso::MsRunReaderSPtr msrunA01 = file_access_A01.getMsRunReaderSPtrByRunId("", "runa01"); diff -Nru libpappsomspp-0.8.15/tests/test_mzintegrationparams.cpp libpappsomspp-0.8.58/tests/test_mzintegrationparams.cpp --- libpappsomspp-0.8.15/tests/test_mzintegrationparams.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_mzintegrationparams.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -2,7 +2,9 @@ #include +#include #include +#include using namespace pappso; @@ -88,41 +90,99 @@ removeZeroValDataPoints); } - SECTION("Construct a MzIntegrationParams with the Savitzky-Golay params", - "[MzIntegrationParams]") +} + + +TEST_CASE("Create bins with Da-based bin size", "[MzIntegrationParams]") +{ + double smallestMz = 1800.373856; + double greatestMz = 1800.373856; + BinningType binningType = BinningType::ARBITRARY; + int decimalPlaces = 3; + PrecisionPtr precision_p = pappso::PrecisionFactory::getDaltonInstance(0.05); + bool applyMzShift = false; + double mzShift = 0; + bool removeZeroValDataPoints = true; + + MzIntegrationParams mz_integration_params(smallestMz, + greatestMz, + binningType, + decimalPlaces, + precision_p, + applyMzShift, + mzShift, + removeZeroValDataPoints); + + SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]") + { + + std::vector bins = mz_integration_params.createBins(); + + // Do not forget that we round to 3 decimal places: + REQUIRE(bins.front() == 1800.374); + + // We create two bins: the first mz value (1800.374) and a new one that is + // that mz value incremented by the delta (that is the size of the bin that + // is created using an increment of 0.05). + + REQUIRE(bins.back() == 1800.374 + precision_p->delta(1800.374)); + } +} + + +TEST_CASE("Create bins with ppm-based bin sizes", "[MzIntegrationParams]") +{ + double smallestMz = 1800.373856; + double greatestMz = 1800.373856; + BinningType binningType = BinningType::ARBITRARY; + int decimalPlaces = 3; + PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20); + bool applyMzShift = false; + double mzShift = 0; + bool removeZeroValDataPoints = true; + + MzIntegrationParams mz_integration_params(smallestMz, + greatestMz, + binningType, + decimalPlaces, + precision_p, + applyMzShift, + mzShift, + removeZeroValDataPoints); + + SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]") { - SavGolParams savgol_params1; - REQUIRE(savgol_params1.nL == 15); - REQUIRE(savgol_params1.nR == 15); - REQUIRE(savgol_params1.m == 4); - REQUIRE(savgol_params1.lD == 0); - REQUIRE(savgol_params1.convolveWithNr == false); - - MzIntegrationParams mz_integration_params(savgol_params1); - - REQUIRE(mz_integration_params.getBinningType() == BinningType::NONE); - REQUIRE(mz_integration_params.getPrecision() == - PrecisionFactory::getPpmInstance(20)); - - SavGolParams savgol_params2 = mz_integration_params.getSavGolParams(); - - REQUIRE(savgol_params2.nL == 15); - REQUIRE(savgol_params2.nR == 15); - REQUIRE(savgol_params2.m == 4); - REQUIRE(savgol_params2.lD == 0); - REQUIRE(savgol_params2.convolveWithNr == false); + std::vector bins = mz_integration_params.createBins(); + + // Do not forget that we round to 3 decimal places: + REQUIRE(bins.front() == 1800.374); + + // Check that the precision delta is computed correctly: + double precision_delta = 1800.374 * 20 / 1000000; + REQUIRE(pappso::Utils::almostEqual( + precision_p->delta(1800.374), precision_delta, /*decimal_places*/ 15)); + + double rounded_precision_delta = + ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) / + pow(10, decimalPlaces); + + // We create two bins: the first mz value (1800.374) and a new one that is + // that mz value incremented by the delta (that is the size of the bin that + // is created using relative proportion of 20 ppm). + + REQUIRE(bins.back() == 1800.374 + rounded_precision_delta); } } -TEST_CASE("Create bins", "[MzIntegrationParams]") + +TEST_CASE("Create bins with res-based bin sizes", "[MzIntegrationParams]") { double smallestMz = 1800.373856; - double greatestMz = 2600.956480; + double greatestMz = 1800.373856; BinningType binningType = BinningType::ARBITRARY; int decimalPlaces = 3; - //PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20); - PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(2000); + PrecisionPtr precision_p = pappso::PrecisionFactory::getResInstance(20000); bool applyMzShift = false; double mzShift = 0; bool removeZeroValDataPoints = true; @@ -143,6 +203,21 @@ // Do not forget that we round to 3 decimal places: REQUIRE(bins.front() == 1800.374); - REQUIRE(bins.back() == 2605.505); + + // Check that the precision delta is computed correctly: + double precision_delta = 1800.374 / 20000; + REQUIRE(pappso::Utils::almostEqual( + precision_p->delta(1800.374), precision_delta, /*decimal_places*/ 15)); + + double rounded_precision_delta = + ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) / + pow(10, decimalPlaces); + + // We create two bins: the first mz value (1800.374) and a new one that is + // that mz value incremented by the delta (that is the size of the bin that + // is created using relative proportion of 20 ppm). + + REQUIRE(bins.back() == 1800.374 + rounded_precision_delta); } } + diff -Nru libpappsomspp-0.8.15/tests/test_natural_isotope_average.cpp libpappsomspp-0.8.58/tests/test_natural_isotope_average.cpp --- libpappsomspp-0.8.15/tests/test_natural_isotope_average.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_natural_isotope_average.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -40,7 +40,7 @@ main() { - cout << endl << "..:: Test natural isotope average ::.." << endl; + cout << std::endl << "..:: Test natural isotope average ::.." << std::endl; Peptide peptide("ALLDEMAVVATEEYR"); peptide.addAaModification(AaModification::getInstance("MOD:00397"), 0); @@ -50,7 +50,7 @@ if(!test_mass.contains(peptide.getMass() - MASSH2O)) { cerr << " peptide.getMass()-MASSH2O != check_mass " << peptide.getMass() - << " " << check_mass << endl; + << " " << check_mass << std::endl; return 1; } @@ -66,7 +66,7 @@ cerr << " MassRange(peptide.getMz(1), " "DaltonPrecision(0.01)).contains(isotopeAverageMono.getMz() " << (check_mass + MHPLUS) << " " << peptide.getMz(1) << " " - << isotopeAverageMono.getMz() << endl; + << isotopeAverageMono.getMz() << std::endl; return 1; } @@ -76,12 +76,12 @@ cout << "monosiotope mz=" << peptide.getMz(charge) - << "average mz=" << isotopeAverage.getMz() << endl; - cout << "intensity ratio =" << isotopeAverage.getIntensityRatio() << endl; + << "average mz=" << isotopeAverage.getMz() << std::endl; + cout << "intensity ratio =" << isotopeAverage.getIntensityRatio() << std::endl; - cout << "z=" << isotopeAverage.getCharge() << endl; + cout << "z=" << isotopeAverage.getCharge() << std::endl; - cout << "sum of :" << endl; + cout << "sum of :" << std::endl; unsigned int rank = 1; for(auto &&peptideNaturalIsotope : isotopeAverage.getComponents()) { @@ -90,13 +90,13 @@ << peptideNaturalIsotope.get()->getIntensityRatio(charge) << " formula=" << peptideNaturalIsotope.get()->getFormula(charge).toStdString() - << endl; + << std::endl; rank++; } if(isotopeAverage.getComponents().size() != 8) { cerr << "isotopeAverage.getComponents().size() " - << isotopeAverage.getComponents().size() << " != 8 " << endl; + << isotopeAverage.getComponents().size() << " != 8 " << std::endl; return 1; } @@ -105,11 +105,11 @@ peptide.makePeptideSp(), 1, isotopeLevel, charge, precision2); cout << "monosiotope mz=" << peptide.getMz(charge) - << "average mz=" << isotopeAverage2.getMz() << endl; - cout << "intensity ratio =" << isotopeAverage2.getIntensityRatio() << endl; - cout << "z=" << isotopeAverage2.getCharge() << endl; + << "average mz=" << isotopeAverage2.getMz() << std::endl; + cout << "intensity ratio =" << isotopeAverage2.getIntensityRatio() << std::endl; + cout << "z=" << isotopeAverage2.getCharge() << std::endl; - cout << "sum of :" << endl; + cout << "sum of :" << std::endl; rank = 1; for(auto &&peptideNaturalIsotope : isotopeAverage2.getComponents()) { @@ -119,42 +119,42 @@ << peptideNaturalIsotope.get()->getIntensityRatio(charge) << " formula=" << peptideNaturalIsotope.get()->getFormula(charge).toStdString() - << endl; + << std::endl; rank++; } if(isotopeAverage2.getComponents().size() != 11) { cerr << " isotopeAverage2.getComponents().size() " - << isotopeAverage2.getComponents().size() << " != 11" << endl; + << isotopeAverage2.getComponents().size() << " != 11" << std::endl; return 1; } /* Spectrum spectrum_low_masses(spectrum_parent.applyCutOff(150)); if (! spectrum_low_masses.equals(sremove_low_masses, precision)) { - cerr << "spectrum_low_masses() != tandem"<< endl; + cerr << "spectrum_low_masses() != tandem"<< std::endl; return 1; }*/ - cout << endl - << "..:: Test natural isotope average on labelled peptide ::.." << endl; + cout << std::endl + << "..:: Test natural isotope average on labelled peptide ::.." << std::endl; peptide.addAaModification(AaModification::getInstance("MOD:00587"), 14); - cout << endl - << "labelled formula " << peptide.getFormula(1).toStdString() << endl; + cout << std::endl + << "labelled formula " << peptide.getFormula(1).toStdString() << std::endl; PeptideNaturalIsotopeAverage isotopeAverage_labeled( peptide.makePeptideSp(), askedIsotopeRank, isotopeLevel, charge, precision); cout << "labeled monosiotope mz=" << peptide.getMz(charge) - << "average mz=" << isotopeAverage_labeled.getMz() << endl; + << "average mz=" << isotopeAverage_labeled.getMz() << std::endl; cout << "intensity ratio =" << isotopeAverage_labeled.getIntensityRatio() - << endl; - cout << "z=" << isotopeAverage_labeled.getCharge() << endl; + << std::endl; + cout << "z=" << isotopeAverage_labeled.getCharge() << std::endl; - cout << "sum of :" << endl; + cout << "sum of :" << std::endl; rank = 1; for(auto &&peptideNaturalIsotope : isotopeAverage_labeled.getComponents()) { @@ -164,7 +164,7 @@ << peptideNaturalIsotope.get()->getIntensityRatio(charge) << " formula=" << peptideNaturalIsotope.get()->getFormula(charge).toStdString() - << endl; + << std::endl; rank++; } return 0; diff -Nru libpappsomspp-0.8.15/tests/test_peptide.cpp libpappsomspp-0.8.58/tests/test_peptide.cpp --- libpappsomspp-0.8.15/tests/test_peptide.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_peptide.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -27,7 +27,9 @@ ******************************************************************************/ // make test ARGS="-V -I 6,6" +// ./tests/catch2-only-tests [Peptide] -s +#include #include #include #include @@ -39,210 +41,130 @@ using namespace pappso; using namespace std; -int -main() +TEST_CASE("Test Peptide", "[Peptide]") { + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); - cout << endl << "..:: peptide init ::.." << endl; - Peptide peptide("LA"); - cout << endl << "..:: peptide LI ::.." << endl; - cout << peptide.getSequence().toStdString() << " " - << peptide.getSequenceLi().toStdString() << endl; - MzRange mz_range(peptide.getMass(), PrecisionFactory::getPpmInstance(10)); - if(!mz_range.contains(Aa('L').getMass() + Aa('A').getMass() + MASSH2O)) - { - cerr << "!mz_range.contains(Aa('L').getMass()+Aa('A').getMass()" << endl; - return 1; - } - // 202.13179 - // http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet?sequence=LA&massType=monoRB&charge=1&bCB=1&yCB=1&nterm=0.0&cterm=0.0&addModifType=&addModifVal= - MzRange mz_range_very_precise(peptide.getMass(), - PrecisionFactory::getPpmInstance(0.5)); - if(!mz_range_very_precise.contains(202.13179)) - { - cerr << QString::number(peptide.getMass(), 'g', 10).toStdString() - << " LA mass != 202.13179" << endl; - return 1; - } - - Peptide peptide2("CCAADDKEACFAVEGPK"); - // 1756.73395 - MzRange mz_range_very_preciseb(peptide2.getMz(1), - PrecisionFactory::getPpmInstance(0.5)); - if(!mz_range_very_preciseb.contains(1756.73395)) - { - cerr << QString::number(peptide2.getMz(1), 'g', 10).toStdString() - << " CCAADDKEACFAVEGPK mass != 1756.73395" << endl; - return 1; - } - /* - - - - - */ - - pappso::AaModificationP aaModcarba = AaModification::getInstance("MOD:00397"); - pappso::AaModificationP aaModcarbab = - AaModification::getInstance("MOD:00397"); - AaModificationP met_oxy = AaModification::getInstance("MOD:00719"); - peptide2.addAaModification(aaModcarba, 0); - peptide2.addAaModification(aaModcarba, 1); - peptide2.addAaModification(aaModcarba, 9); - peptide2.addAaModification(AaModification::getInstance("MOD:01160"), 0); - - cerr << peptide2.getFormula(1).toStdString().c_str() << endl; - - MzRange mz_range2(peptide2.getMz(1), PrecisionFactory::getPpmInstance(10)); - if(!mz_range2.contains(1910.7722)) - { - cerr << peptide2.getMz(1) << "!=" - << "1910.7722" << endl; - return 1; - } - - - PeptideSp peptide_from_str = PeptideStrParser::parseString( - "C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK"); - if(peptide_from_str.get()->getMass() != peptide2.getMass()) - { - cerr << "peptide_from_str.get()->getMass() != peptide2.getMass()" - << peptide_from_str.get()->getMass() << "!=" << peptide2.getMass() - << endl; - return 1; - } - PeptideSp peptide_from_str2 = PeptideStrParser::parseString( - "C(Carbamidomethyl+MOD:01160)C(MOD:00397)AADDKEAC(57.021464)FAVEGPK"); - PeptideSp peptide_from_str3 = PeptideStrParser::parseString( - "C(Carbamidomethyl+MOD:01160)C(397)AADDKEAC(57.021464)FAVEGPK"); - - if(peptide_from_str2.get()->getMass() != peptide_from_str3.get()->getMass()) - { - cerr << "peptide_from_str2.get()->getMass() != " - "peptide_from_str3.get()->getMass()" - << peptide_from_str2.get()->getMass() - << "!=" << peptide_from_str3.get()->getMass() << endl; - return 1; - } - // SUCCESS - Peptide copy_str2(*peptide_from_str2.get()); - copy_str2.rotate(); - cerr << copy_str2.toAbsoluteString().toStdString() << endl; - if(peptide_from_str2.get()->getMass() != copy_str2.getMass()) - { - cerr << "peptide_from_str2.get()->getMass() != copy_str2.getMass()" - << peptide_from_str2.get()->getMass() << "!=" << copy_str2.getMass() - << endl; - return 1; - } - - - // testing isotope labels - //[Term] - // id: MOD:00582 - // name: 6x(13)C,2x(15)N labeled L-lysine - cout << endl << "..:: Test peptide isotope labels::.." << endl; - PeptideSp peptide_normal = - PeptideStrParser::parseString("CCAALDDKEACFAVEGPK"); - PeptideSp peptide_lys_label = - PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK"); - if(peptide_normal.get()->getNumberOfAtom(AtomIsotopeSurvey::C) != - peptide_lys_label.get()->getNumberOfAtom(AtomIsotopeSurvey::C)) - { - cerr << "peptide_normal.get()->getNumberOfAtom(AtomIsotopeSurvey::C) " - << peptide_normal.get()->getNumberOfAtom(AtomIsotopeSurvey::C) - << "!= " - << peptide_lys_label.get()->getNumberOfAtom(AtomIsotopeSurvey::C) - << " peptide_lys_label.get()->getNumberOfAtom(AtomIsotopeSurvey::C)" - << endl; - return 1; - } - if(peptide_normal.get()->getNumberOfIsotope(Isotope::C13) != 0) - { - cerr << "peptide_normal.get()->getNumberOfIsotope(Isotope::C13) != 0 " - << endl; - return 1; - } - if(peptide_lys_label.get()->getNumberOfIsotope(Isotope::C13) != 6) - { - cerr << "peptide_lys_label.get()->getNumberOfIsotope(Isotope::C13) != 6 " - << endl; - return 1; - } - // xref: DiffMono: "8.014199" - MzRange mz_range_lys(8.014199, PrecisionFactory::getPpmInstance(10)); - if(!mz_range_lys.contains(peptide_lys_label.get()->getMz(1) - - peptide_normal.get()->getMz(1))) - { - cerr << "mz_range_lys - peptide_normal != 8.014199" << endl; - return 1; - } - - if(*peptide_normal.get() == *peptide_lys_label.get()) - { - cerr << "(*peptide_normal.get() == *peptide_lys_label.get()) ERROR" - << endl; - return 1; - } - if(!(*peptide_normal.get() < *peptide_lys_label.get())) - { - cerr << "!(*peptide_normal.get() < *peptide_lys_label.get()) ERROR" - << endl; - return 1; - } - - PeptideSp peptide_lys_label_bis = - PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK"); - - if(!(*peptide_lys_label_bis.get() == *peptide_lys_label.get())) - { - cerr - << "!(*peptide_lys_label_bis.get() == *peptide_lys_label.get()) ERROR" - << endl; - return 1; - } - - - cout << endl << "..:: peptide palindrome ::.." << endl; - Peptide peptide_pal_a("ALA"); - - if(!peptide_pal_a.isPalindrome()) - { - cerr << "!peptide_pal_a.isPalindrome() ERROR" << endl; - return 1; - } - - if(peptide_normal.get()->isPalindrome()) - { - cerr << "peptide_normal.isPalindrome() ERROR " - << peptide_normal.get()->getSequence().toStdString() << " " - << peptide_normal.get()->isPalindrome() << endl; - return 1; - } - - - cout << endl << "..:: peptide dimethyl ::.." << endl; - //"Q(internal:Nter_hydrolytic_cleavage_H,MOD:00429)SLPSLSS(MOD:00696)FLNR(internal:Cter_hydrolytic_cleavage_HO)" - Peptide peptide_dimethyl("QSLPSLSSFLNR"); - pappso::AaModificationP aaModDimethyl = - AaModification::getInstance("MOD:00429"); - pappso::AaModificationP aaModDimethyl2 = - AaModification::getInstance("MOD:00696"); - peptide_dimethyl.addAaModification(aaModDimethyl, 0); - peptide_dimethyl.addAaModification(aaModDimethyl2, 7); - cout << "Before " << peptide_dimethyl.toAbsoluteString().toStdString(); - cout << endl << "remove AaModif" << endl; - peptide_dimethyl.removeAaModification(aaModDimethyl); - if(peptide_dimethyl.toAbsoluteString() != - "Q(internal:Nter_hydrolytic_cleavage_H)SLPSLSS(MOD:00696)FLNR(internal:" - "Cter_hydrolytic_cleavage_HO)") - { - cerr << "peptide_dimethyl.removeAaModification(aaModDimethyl) ERROR " - << peptide_dimethyl.toAbsoluteString().toStdString() << " " - << aaModDimethyl->getName().toStdString(); - return 1; - } - cout << "Finish " << peptide_dimethyl.toAbsoluteString().toStdString(); + SECTION("..:: Test Peptide ::..", "[Peptide]") + { - return 0; + cout << std::endl << "..:: peptide init ::.." << std::endl; + Peptide peptide("LA"); + cout << std::endl << "..:: peptide LI ::.." << std::endl; + cout << peptide.getSequence().toStdString() << " " + << peptide.getSequenceLi().toStdString() << std::endl; + MzRange mz_range(peptide.getMass(), PrecisionFactory::getPpmInstance(10)); + REQUIRE(mz_range.contains(Aa('L').getMass() + Aa('A').getMass() + MASSH2O)); + // 202.13179 + // http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet?sequence=LA&massType=monoRB&charge=1&bCB=1&yCB=1&nterm=0.0&cterm=0.0&addModifType=&addModifVal= + MzRange mz_range_very_precise(peptide.getMass(), + PrecisionFactory::getPpmInstance(0.5)); + REQUIRE(mz_range_very_precise.contains(202.13179)); + + + Peptide peptide2("CCAADDKEACFAVEGPK"); + // 1756.73395 + MzRange mz_range_very_preciseb(peptide2.getMz(1), + PrecisionFactory::getPpmInstance(0.5)); + REQUIRE(mz_range_very_preciseb.contains(1756.73395)); + /* + + + + + */ + + pappso::AaModificationP aaModcarba = + AaModification::getInstance("MOD:00397"); + /* + pappso::AaModificationP aaModcarbab = + AaModification::getInstance("MOD:00397"); + AaModificationP met_oxy = AaModification::getInstance("MOD:00719");*/ + peptide2.addAaModification(aaModcarba, 0); + peptide2.addAaModification(aaModcarba, 1); + peptide2.addAaModification(aaModcarba, 9); + peptide2.addAaModification(AaModification::getInstance("MOD:01160"), 0); + + cerr << peptide2.getFormula(1).toStdString().c_str() << std::endl; + + MzRange mz_range2(peptide2.getMz(1), PrecisionFactory::getPpmInstance(10)); + REQUIRE(mz_range2.contains(1910.7722)); + + + PeptideSp peptide_from_str = PeptideStrParser::parseString( + "C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK"); + REQUIRE(peptide_from_str.get()->getMass() == peptide2.getMass()); + + PeptideSp peptide_from_str2 = PeptideStrParser::parseString( + "C(Carbamidomethyl+MOD:01160)C(MOD:00397)AADDKEAC(57.021464)FAVEGPK"); + PeptideSp peptide_from_str3 = PeptideStrParser::parseString( + "C(Carbamidomethyl+MOD:01160)C(397)AADDKEAC(57.021464)FAVEGPK"); + + REQUIRE(peptide_from_str2.get()->getMass() == + peptide_from_str3.get()->getMass()); + + // SUCCESS + Peptide copy_str2(*peptide_from_str2.get()); + copy_str2.rotate(); + cerr << copy_str2.toAbsoluteString().toStdString() << std::endl; + REQUIRE(peptide_from_str2.get()->getMass() == copy_str2.getMass()); + + + // testing isotope labels + //[Term] + // id: MOD:00582 + // name: 6x(13)C,2x(15)N labeled L-lysine + cout << std::endl << "..:: Test peptide isotope labels::.." << std::endl; + PeptideSp peptide_normal = + PeptideStrParser::parseString("CCAALDDKEACFAVEGPK"); + PeptideSp peptide_lys_label = + PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK"); + REQUIRE(peptide_normal.get()->getNumberOfAtom(AtomIsotopeSurvey::C) == + peptide_lys_label.get()->getNumberOfAtom(AtomIsotopeSurvey::C)); + + REQUIRE(peptide_normal.get()->getNumberOfIsotope(Isotope::C13) == 0); + REQUIRE(peptide_lys_label.get()->getNumberOfIsotope(Isotope::C13) == 6); + // xref: DiffMono: "8.014199" + MzRange mz_range_lys(8.014199, PrecisionFactory::getPpmInstance(10)); + REQUIRE(mz_range_lys.contains(peptide_lys_label.get()->getMz(1) - + peptide_normal.get()->getMz(1))); + + REQUIRE_FALSE(peptide_normal.get()->toString().toStdString() == + peptide_lys_label.get()->toString().toStdString()); + REQUIRE_FALSE(peptide_normal.get()->toString().toStdString() < + peptide_lys_label.get()->toString().toStdString()); + + PeptideSp peptide_lys_label_bis = + PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK"); + + REQUIRE(peptide_lys_label_bis.get()->toString().toStdString() == + peptide_lys_label.get()->toString().toStdString()); + + cout << std::endl << "..:: peptide palindrome ::.." << std::endl; + Peptide peptide_pal_a("ALA"); + + REQUIRE(peptide_pal_a.isPalindrome()); + + REQUIRE_FALSE(peptide_normal.get()->isPalindrome()); + + + cout << std::endl << "..:: peptide dimethyl ::.." << std::endl; + //"Q(internal:Nter_hydrolytic_cleavage_H,MOD:00429)SLPSLSS(MOD:00696)FLNR(internal:Cter_hydrolytic_cleavage_HO)" + Peptide peptide_dimethyl("QSLPSLSSFLNR"); + pappso::AaModificationP aaModDimethyl = + AaModification::getInstance("MOD:00429"); + pappso::AaModificationP aaModDimethyl2 = + AaModification::getInstance("MOD:00696"); + peptide_dimethyl.addAaModification(aaModDimethyl, 0); + peptide_dimethyl.addAaModification(aaModDimethyl2, 7); + cout << "Before " << peptide_dimethyl.toAbsoluteString().toStdString(); + cout << std::endl << "remove AaModif" << std::endl; + peptide_dimethyl.removeAaModification(aaModDimethyl); + REQUIRE( + peptide_dimethyl.toAbsoluteString().toStdString() == + "Q(internal:Nter_hydrolytic_cleavage_H)SLPSLSS(MOD:00696)FLNR(internal:" + "Cter_hydrolytic_cleavage_HO)"); + cout << "Finish " << peptide_dimethyl.toAbsoluteString().toStdString(); + } } diff -Nru libpappsomspp-0.8.15/tests/test_peptidefragment.cpp libpappsomspp-0.8.58/tests/test_peptidefragment.cpp --- libpappsomspp-0.8.15/tests/test_peptidefragment.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_peptidefragment.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -44,7 +44,7 @@ { - cout << endl << "..:: peptide fragment init ::.." << endl; + cout << std::endl << "..:: peptide fragment init ::.." << std::endl; PeptideFragment pep_fragment( std::make_shared("PEPTIDE"), PeptideDirection::Cter, 4); @@ -57,7 +57,7 @@ cout << "pep_fragmentr" << pep_fragmentr.getMass() << " z=1 " - << pep_fragmentr.getMz(1) << " z=2 " << pep_fragmentr.getMz(2) << endl; + << pep_fragmentr.getMz(1) << " z=2 " << pep_fragmentr.getMz(2) << std::endl; try { @@ -68,8 +68,8 @@ } catch(const PappsoException &error) { - cerr << "Oops! an error occurred. Dont Panic :" << endl; - cerr << error.qwhat().toStdString() << endl; + cerr << "Oops! an error occurred. Dont Panic :" << std::endl; + cerr << error.qwhat().toStdString() << std::endl; return 1; } @@ -82,13 +82,13 @@ } catch(const pappso::PappsoException &error) { - cout << "ok, y ion is not Nter" << endl; - cout << error.qwhat().toStdString() << endl; + cout << "ok, y ion is not Nter" << std::endl; + cout << error.qwhat().toStdString() << std::endl; } catch(const std::exception &error) { - cout << "ok, y ion is not Nter" << endl; - cout << error.what() << endl; + cout << "ok, y ion is not Nter" << std::endl; + cout << error.what() << std::endl; } // cout << pep_fragmentr.getMz(0); return 0; diff -Nru libpappsomspp-0.8.15/tests/test_peptidenaturalisotopelist.cpp libpappsomspp-0.8.58/tests/test_peptidenaturalisotopelist.cpp --- libpappsomspp-0.8.15/tests/test_peptidenaturalisotopelist.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_peptidenaturalisotopelist.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -45,18 +45,18 @@ main() { - cout << endl << "..:: peptide natural isotope list init ::.." << endl; + cout << std::endl << "..:: peptide natural isotope list init ::.." << std::endl; Peptide peptide("LA"); PeptideNaturalIsotopeList isotopeList(peptide.makePeptideSp()); - cout << endl << "isotope list OK" << isotopeList.size() << endl; + cout << std::endl << "isotope list OK" << isotopeList.size() << std::endl; PeptideNaturalIsotopeList::const_iterator it(isotopeList.begin()); while(it != isotopeList.end()) { // qDebug() << it->getIntensityRatio(); - cout << endl << it->get()->getSequence().toStdString(); + cout << std::endl << it->get()->getSequence().toStdString(); cout.flush(); cout << "..:: " << it->get()->getFormula(1).toStdString(); cout.flush(); @@ -67,10 +67,10 @@ cout << " mz(2)=" << it->get()->getMz(2); cout.flush(); - cout << " ratio=" << it->get()->getIntensityRatio(1) << " ::.." << endl; + cout << " ratio=" << it->get()->getIntensityRatio(1) << " ::.." << std::endl; it++; } - cout << endl << "print isotope list OK" << endl; + cout << std::endl << "print isotope list OK" << std::endl; // MassRange mz_range(peptide.getMass(), ppm_precision(10)); // if (!mz_range.contains(Aa('L').getMass()+Aa('A').getMass())) // return 1; @@ -98,7 +98,7 @@ { if(it->get()->getMass() != mass_before) { - cerr << "it->get()->getMass() != mass_before FAILED" << endl; + cerr << "it->get()->getMass() != mass_before FAILED" << std::endl; return 1; } } @@ -108,50 +108,50 @@ if(it->get()->getNumberOfAtom(AtomIsotopeSurvey::C) != 57) { cerr << "it->getNumberOfAtom(AtomIsotopeSurvey::C) != 57 FAILED" - << endl; + << std::endl; return 1; } if(it->get()->getNumberOfAtom(AtomIsotopeSurvey::H) != 100) { cerr << "it->getNumberOfAtom(AtomIsotopeSurvey::H) != 100 FAILED" - << endl; + << std::endl; return 1; } if(it->get()->getNumberOfAtom(AtomIsotopeSurvey::N) != 16) { cerr << "it->getNumberOfAtom(AtomIsotopeSurvey::N) != 16 FAILED" - << endl; + << std::endl; return 1; } if(it->get()->getNumberOfAtom(AtomIsotopeSurvey::O) != 19) { cerr << "it->getNumberOfAtom(AtomIsotopeSurvey::O) != 19 FAILED" - << endl; + << std::endl; return 1; } // qDebug() << it->getIntensityRatio(); - cout << endl + cout << std::endl << it->get()->getSequence().toStdString() << "..:: " << it->get()->getFormula(1).toStdString() << " C13=" << it->get()->getNumberOfIsotope(Isotope::C13) << " mass=" << it->get()->getMz(1) << " mz(2)=" << it->get()->getMz(2) - << " ratio=" << it->get()->getIntensityRatio(1) << " ::.." << endl; + << " ratio=" << it->get()->getIntensityRatio(1) << " ::.." << std::endl; it++; } std::map map_isotope_number = isotopeListb.getIntensityRatioPerIsotopeNumber(); - cout << "isotope levels" << endl; + cout << "isotope levels" << std::endl; for(unsigned int i = 0; i < map_isotope_number.size(); i++) { - cout << "isotope " << i << " " << map_isotope_number[i] << endl; + cout << "isotope " << i << " " << map_isotope_number[i] << std::endl; } - cout << endl + cout << std::endl << "..:: peptide natural isotope list init test on fragment ::.." - << endl; + << std::endl; list cid_ion = PeptideFragmentIonListBase::getCIDionList(); PeptideFragmentIonListBase fragmentation_cid(peptideSp, cid_ion); @@ -160,10 +160,10 @@ PeptideNaturalIsotopeList isotopeListFrag(pepfrag_sp); map_isotope_number = isotopeListFrag.getIntensityRatioPerIsotopeNumber(); - cout << "isotope levels" << endl; + cout << "isotope levels" << std::endl; for(unsigned int i = 0; i < map_isotope_number.size(); i++) { - cout << "frag isotope " << i << " " << map_isotope_number[i] << endl; + cout << "frag isotope " << i << " " << map_isotope_number[i] << std::endl; } std::vector naturalIsotopeAverageList = @@ -175,12 +175,12 @@ { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } // SUCCESS - cout << "test with a big peptide at 10ppm" << endl; + cout << "test with a big peptide at 10ppm" << std::endl; PeptideSp peptide_from_str = PeptideStrParser::parseString( "M(internal:Nter_hydrolytic_cleavage_H,0.00163028)" "GGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNK(internal:Cter_hydrolytic_cleavage_" @@ -194,73 +194,73 @@ { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << "test with a big peptide at 5ppm" << endl; + cout << "test with a big peptide at 5ppm" << std::endl; for(PeptideNaturalIsotopeAverageSp isotopeAverageSp : isotopeListBig.getByIntensityRatio( 3, PrecisionFactory::getPpmInstance(5), 0.6)) { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << "test with a big peptide at 3ppm" << endl; + cout << "test with a big peptide at 3ppm" << std::endl; for(PeptideNaturalIsotopeAverageSp isotopeAverageSp : isotopeListBig.getByIntensityRatio( 3, PrecisionFactory::getPpmInstance(3), 0.6)) { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << "test with a big peptide at 2ppm" << endl; + cout << "test with a big peptide at 2ppm" << std::endl; for(PeptideNaturalIsotopeAverageSp isotopeAverageSp : isotopeListBig.getByIntensityRatio( 3, PrecisionFactory::getPpmInstance(2), 0.6)) { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << "test with a big peptide at 1ppm" << endl; + cout << "test with a big peptide at 1ppm" << std::endl; for(PeptideNaturalIsotopeAverageSp isotopeAverageSp : isotopeListBig.getByIntensityRatio( 3, PrecisionFactory::getPpmInstance(1), 0.6)) { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << endl - << "..:: peptide natural isotope list from labeled peptide ::.." << endl; + cout << std::endl + << "..:: peptide natural isotope list from labeled peptide ::.." << std::endl; PeptideSp peptide_lys_label = PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK"); PeptideNaturalIsotopeList isotopeList_lys(peptide_lys_label); - cout << endl << "isotope list OK" << isotopeList_lys.size() << endl; + cout << std::endl << "isotope list OK" << isotopeList_lys.size() << std::endl; map_isotope_number = isotopeList_lys.getIntensityRatioPerIsotopeNumber(); - cout << "isotope levels" << endl; + cout << "isotope levels" << std::endl; for(unsigned int i = 0; i < map_isotope_number.size(); i++) { - cout << "frag isotope " << i << " " << map_isotope_number[i] << endl; + cout << "frag isotope " << i << " " << map_isotope_number[i] << std::endl; } - cout << endl + cout << std::endl << "..:: get 80 % intensity of natural isotope average PPM = 2 ::.." - << endl; + << std::endl; naturalIsotopeAverageList = isotopeList_lys.getByIntensityRatio( 1, PrecisionFactory::getPpmInstance(2), 0.8); @@ -269,15 +269,15 @@ { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } - cout << endl << "print lys isotope list OK" << endl; + cout << std::endl << "print lys isotope list OK" << std::endl; - cout << endl + cout << std::endl << "..:: get 10 % intensity of small peptide natural isotope average " "dalton = 0.2 ::.." - << endl; + << std::endl; naturalIsotopeAverageList = isotopeList_lys.getByIntensityRatio( 1, PrecisionFactory::getDaltonInstance(0.2), 0.1); @@ -286,26 +286,26 @@ { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } if(naturalIsotopeAverageList.size() != 1) { cerr << "naturalIsotopeAverageList.size() " - << naturalIsotopeAverageList.size() << " != 1 ERROR" << endl; + << naturalIsotopeAverageList.size() << " != 1 ERROR" << std::endl; return 1; } if(naturalIsotopeAverageList.at(0).get()->getIsotopeNumber() != 0) { cerr << "naturalIsotopeAverageList.at(0).get()->getIsotopeNumber() !=0 ERROR" - << endl; + << std::endl; return 1; } - cout << endl + cout << std::endl << "..:: get 10 % intensity of big peptide natural isotope average " "dalton = 0.2 ::.." - << endl; + << std::endl; naturalIsotopeAverageList = isotopeListBig.getByIntensityRatio( 1, PrecisionFactory::getDaltonInstance(0.2), 0.1); @@ -314,23 +314,23 @@ { cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; } if(naturalIsotopeAverageList.size() != 1) { - cerr << "naturalIsotopeAverageList.size() != 1 ERROR" << endl; + cerr << "naturalIsotopeAverageList.size() != 1 ERROR" << std::endl; return 1; } if(naturalIsotopeAverageList.at(0).get()->getIsotopeNumber() != 2) { cerr << "naturalIsotopeAverageList.at(0).get()->getIsotopeNumber() !=2 ERROR" - << endl; + << std::endl; return 1; } - cout << endl << "..:: peptide rank test ::.." << endl; + cout << std::endl << "..:: peptide rank test ::.." << std::endl; PeptideSp peptide_ratio_test = PeptideStrParser::parseString("DPTLAVVAYR"); PeptideNaturalIsotopeList isotopeListRatioTest(peptide_ratio_test, 0.001); @@ -344,13 +344,13 @@ cout << "average isotope " << isotopeAverageSp.get()->getIntensityRatio() << " average mz=" << isotopeAverageSp.get()->getMz() << " number=" << isotopeAverageSp.get()->getIsotopeNumber() - << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << endl; + << " rank=" << isotopeAverageSp.get()->getIsotopeRank() << std::endl; /* if(isotopeAverageSp.get()->getIsotopeRank() == 3) { cerr << "isotopeAverageSp.get()->getIsotopeRank()== 3 ERROR, not " "possible with 10ppm" - << endl; + << std::endl; return 1; } */ diff -Nru libpappsomspp-0.8.15/tests/test_protein.cpp libpappsomspp-0.8.58/tests/test_protein.cpp --- libpappsomspp-0.8.15/tests/test_protein.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_protein.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -26,8 +26,10 @@ *implementation ******************************************************************************/ -// make test ARGS="-V -I 2,2" +// make test ARGS="-V -I 3,3" +// ./tests/catch2-only-tests [Protein] -s +#include #include #include @@ -80,6 +82,12 @@ _peptide_list.clear(); } + std::size_t + size() const + { + return _peptide_list.size(); + }; + private: QStringList _peptide_list; }; @@ -131,352 +139,352 @@ using namespace pappso; -int -main([[maybe_unused]] int argc, [[maybe_unused]] char *argv[]) + +TEST_CASE("Test Protein", "[Protein]") { - // QCoreApplication a(argc, argv); + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + SECTION("..:: Test Protein ::..", "[Protein]") + { - qDebug() << "init test protein"; - cout << endl << "..:: Test Protein ::.." << endl; + qDebug() << "init test protein"; + cout << std::endl << "..:: Test Protein ::.." << std::endl; - Protein cry1Ac( - "cry1Ac", - "MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWD" - "AFLVQIEQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIPLF" - "AVQNYQVPLLSVYVQAANLHLSVLRDVSVFGQRWGFDAATINSRYNDLTRLIGNYTDYAVRWYNTGLERVWGPD" - "SRDWVRYNQFRRELTLTVLDIVALFPNYDSRRYPIRTVSQLTREIYTNPVLENFDGSFRGSAQGIERSIRSPHL" - "MDILNSITIYTDAHRGYYYWSGHQIMASPVGFSGPEFTFPLYGTMGNAAPQQRIVAQLGQGVYRTLSSTLYRRP" - "FNIGINNQQLSVLDGTEFAYGTSSNLPSAVYRKSGTVDSLDEIPPQNNNVPPRQGFSHRLSHVSMFRSGFSNSS" - "VSIIRAPMFSWIHRSAEFNNIIASDSITQIPAVKGNFLFNGSVISGPGFTGGDLVRLNSSGNNIQNRGYIEVPI" - "HFPSTSTRYRVRVRYASVTPIHLNVNWGNSSIFSNTVPATATSLDNLQSSDFGYFESANAFTSSLGNIVGVRNF" - "SGTAGVIIDRFEFIPVTATLEAEYNLERAQKAVNALFTSTNQLGLKTNVTDYHIDQVSNLVTYLSDEFCLDEKR" - "ELSEKVKHAKRLSDERNLLQDSNFKDINRQPERGWGGSTGITIQGGDDVFKENYVTLSGTFDECYPTYLYQKID" - "ESKLKAFTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRCAPHLEWNPDLDC" - "SCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKRAEKKWR" - "DKREKLEWETNIVYKEAKESVDALFVNSQYDQLQADTNIAMIHAADKRVHSIREAYLPELSVIPGVNAAIFEEL" - "EGRIFTAFSLYDARNVIKNGDFNNGLSCWNVKGHVDVEEQNNQRSVLVVPEWEAEVSQEVRVCPGRGYILRVTA" - "YKEGYGEGCVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASV" - "YEEKSYTDGRRENPCEFNRGYRDYTPLPVGYVTKELEYFPETDKVWIEIGETEGTFIVDSVELLLMEE"); - - cout << endl << "cry1Ac Mass = " << cry1Ac.getMass() << endl; - MzRange cry1Ac_mass(133248.068195739, PrecisionFactory::getPpmInstance(0.5)); - if(!cry1Ac_mass.contains(cry1Ac.getMass())) - { - cerr << "ERROR cry1Ac Mass =" << cry1Ac.getMass() - << " is not expected 133248.068195739 " << endl; - return 1; - } - - // BSA - qDebug() << "init bsa"; - Protein bsa( - "BSA", - "MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFA" - "KTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCD" - "EFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLR" - "CASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISS" - "KLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLL" - "RLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTP" - "TLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDE" - "TYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFA" - "VEGPKLVVSTQTALA"); - qDebug() << "init bsa sp"; - ProteinSp protein_sp = bsa.makeProteinSp(); - qDebug() << "init kinase"; - Enzyme kinase; - qDebug() << "kinase.setMiscleavage(2)"; - kinase.setMiscleavage(2); - DigestionHandler digestion; - qDebug() << "kinase.eat(protein_sp,digestion)"; - kinase.eat(0, protein_sp, false, digestion); - - PeptideSizeFilter peptide_size(7, 35); - peptide_size.setSink(&digestion); - - qDebug() << " kinase.eat(protein_sp,peptide_size);"; - kinase.eat(0, protein_sp, false, peptide_size); - - qDebug() << " modification_sink"; - - PeptideModHandler modification_sink; - - - qDebug() << " fixed_mod_builder"; - PeptideBuilder fixed_mod_builder; - fixed_mod_builder.setSink(&modification_sink); - - // QChar aa =QChar('C'); - // carbamido : - QString acc = "MOD:00397"; - - qDebug() << " carbamido"; - AaModificationP carbamido = AaModification::getInstance("MOD:00397"); - - fixed_mod_builder.addFixedAaModification('C', carbamido); - - PeptideSizeFilter peptide_size2mod(7, 35); - peptide_size2mod.setSink(&fixed_mod_builder); - - kinase.setMiscleavage(0); - - - qDebug() << " kinase.eat(protein_sp,peptide_size2mod);"; - - kinase.eat(0, protein_sp, false, peptide_size2mod); - - qDebug() << " kinase.eat(protein_sp,peptide_size2mod) ; end"; - - // - // unsigned int i = 0; - // do { - // i++; - // } - // while (i < 100000000000000); - - // variable modifications : - // MOD:00719 - // acc = "MOD:00719"; - AaModificationP met_oxy = AaModification::getInstance("MOD:00719"); - - PeptideVariableModificationBuilder var_mod_builder(met_oxy); - var_mod_builder.addAa('M'); - var_mod_builder.setSink(&modification_sink); - - // QString accMo = "MOD:00719"; - cout << endl << "..:: chose ::.." << endl; - - PeptideBuilder fixed_mod_builder2; - fixed_mod_builder2.setSink(&var_mod_builder); - fixed_mod_builder2.addFixedAaModification('C', carbamido); - - PeptideSizeFilter peptide_size2varmod(7, 35); - peptide_size2varmod.setSink(&fixed_mod_builder2); - - - kinase.setMiscleavage(0); - - qDebug() << " kinase.eat(protein_sp,peptide_size2varmod);"; - - ProteinSp fake = - Protein("fakeBSA", "MVVKKVVVMAMEEKWVTFISLLLLFTKVHKECCVVSTQTALA") - .makeProteinSp(); - kinase.eat(0, fake, false, peptide_size2varmod); - - digestion.clear(); - cout << endl << "..:: Test trypsin peptides on fake prot ::.." << endl; - kinase.eat(0, fake, false, digestion); - - if(!digestion.contain("K")) - { - cerr << "ERROR digestion for " << fake.get()->getAccession().toStdString() - << " K NOT FOUND" << endl; - return 1; - } - - - if(!digestion.contain("ECCVVSTQTALA")) - { - cerr << "ERROR digestion for " << fake.get()->getAccession().toStdString() - << " ECCVVSTQTALA NOT FOUND" << endl; - return 1; - } - - if(!digestion.contain("VVVMAMEEK")) - { - cerr << "ERROR digestion for " << fake.get()->getAccession().toStdString() - << " VVVMAMEEK NOT FOUND" << endl; - return 1; - } - - // BSA - cout << endl << "..:: Test semi tryptic peptides on BSA ::.." << endl; - kinase.setMiscleavage(0); - PeptideSemiEnzyme semi_tryptic; - semi_tryptic.setSink(&digestion); - qDebug() << "kinase.eat(protein_sp,semi_tryptic)"; - kinase.eat(0, protein_sp, false, semi_tryptic); - - - qDebug() << endl << "..:: Test enzyme motif ::.." << endl; - Enzyme motif_digest("(MAMEE[KR])([^P])"); - motif_digest.eat(0, fake, false, digestion); - - - // potential Nter mod +42.01056@[ - // fixed mod mass 57.02146@C - // 15.99491@M,79.96633@Y - // 79.96633:-97.9769@[ST!] - PeptideModificatorPipeline pmp; - peptide_size2varmod.setSink(&pmp); - PeptideVariableModificationReplacement mod_replace( - AaModification::getInstance("MOD:00397"), - AaModification::getInstance("MOD:00419")); - QString pattern_str("^E(C)"); - mod_replace.setModificationPattern(pattern_str); - - pmp.setSink(&mod_replace); - mod_replace.setSink(&modification_sink); - - pmp.addFixedModificationString("MOD:00397@C"); - // fixed: MOD:00397@C,MOD:00696@[YST] - pmp.addPotentialModificationString( - "MOD:00719@M,MOD:00696(0-1)@[YST],MOD:00719(1)@M,MOD:00696(1)@[YST]"); - // var: MOD:00719@M - // MOD:00429@^K - pmp.addLabeledModificationString("MOD:00429@(^.|K)"); - // MOD:00552@^K - pmp.addLabeledModificationString("MOD:00552@(^.|K)"); - // MOD:00638@^K - pmp.addLabeledModificationString("MOD:00638@(^.|K)"); - kinase.eat(0, fake, false, peptide_size2varmod); - - // reverse protein : - cout << endl - << "reverse :" - << Protein(*fake.get()).reverse().getSequence().toStdString(); - - PeptideSp peptide_test = PeptideStrParser::parseString( - "E(MOD:00429)C(MOD:00419)C(MOD:00397)VVSTQT(MOD:00696,MOD:00696)ALA"); - if(!modification_sink.contain(peptide_test)) - { - cerr << "ERROR modification_sink for " - << peptide_test.get()->toString().toStdString() << " NOT FOUND" - << endl; - return 1; - } - cout << peptide_test.get()->toString().toStdString() << " is present" << endl; - - - peptide_test = - PeptideStrParser::parseString("V(MOD:00552)VVMAMEEK(MOD:00429)"); - if(modification_sink.contain(peptide_test)) - { - cerr << "ERROR modification_sink for " - << peptide_test.get()->toString().toStdString() << " FOUND" << endl; - return 1; - } - cout << peptide_test.get()->toString().toStdString() << " is absent" << endl; - - peptide_test = - PeptideStrParser::parseString("V(MOD:00552)VVMAMEEK(MOD:00552)"); - if(!modification_sink.contain(peptide_test)) - { - cerr << "ERROR modification_sink for " - << peptide_test.get()->toString().toStdString() << " NOT FOUND" - << endl; - return 1; - } - cout << peptide_test.get()->toString().toStdString() << " is present" << endl; - - - peptide_test = PeptideStrParser::parseString( - "E(MOD:00429)C(MOD:00397)C(MOD:00397)VVSTQT(MOD:00696,MOD:00696)ALA"); - if(!modification_sink.contain(peptide_test)) - { - cerr << "ERROR modification_sink for " - << peptide_test.get()->toString().toStdString() << " NOT FOUND" - << endl; - return 1; - } - cout << peptide_test.get()->toString().toStdString() << " is present" << endl; - - cout << endl << "..:: test modification motifs ::.." << endl; - - ProteinSp prot_test_motif = - Protein("prot_test_motif", "MVVVVVMAMEEWVTFISLLLLFTVHECCVVSTQTALA") - .makeProteinSp(); - modification_sink.clear(); - PeptideBuilder pep_builder; - PeptideFixedModificationBuilder fixed_mod_motif( - AaModification::getInstance("MOD:00397")); - pattern_str = "V(V)"; - fixed_mod_motif.setModificationPattern(pattern_str); - pep_builder.setSink(&fixed_mod_motif); - fixed_mod_motif.setSink(&modification_sink); - kinase.eat(0, prot_test_motif, false, pep_builder); - - peptide_test = PeptideStrParser::parseString( - "MVV(MOD:00397)V(MOD:00397)V(MOD:00397)V(MOD:00397)" - "MAMEEWVTFISLLLLFTVHECCVV(MOD:00397)STQTALA"); - if(!modification_sink.contain(peptide_test)) - { - cerr << "ERROR modification_sink for " - << peptide_test.get()->toString().toStdString() << " NOT FOUND" - << endl; - return 1; - } - if(modification_sink.size() != 1) - { - cerr << "ERROR modification_sink.size() != 1 " << modification_sink.size() - << endl; - return 1; - } - cout << peptide_test.get()->toString().toStdString() << " is present" << endl; - - - qDebug() << "init test protein"; - cout << endl << "..:: Test Protein with B and Z wildcard ::.." << endl; - - // BSA - qDebug() << "init bsa with B and Z wildcard"; - Protein bsa_bz( - "BSA", - "MXXXKBWVTFISLLLLFSSAYSRGVFRRDTHKSBEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNE" - "LTEFAKTCVADEBSHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPD" - "PNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASS" - "ARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDN" - "QDTISSKLKECCDKPLLEZKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPE" - "YAVSVLLRLAKEYZEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTR" - "KVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPC" - "FSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAA" - "DDKEACFAVEGPKLVVSTQTALA"); - qDebug() << "init bsa_bz sp"; - ProteinSp protein_bsa_bz_sp = bsa_bz.makeProteinSp(); - qDebug() << "init kinase"; - DigestionHandler digestion_bz; - qDebug() << "kinase.eat(protein_sp,digestion) B Z"; - kinase.eat(0, protein_bsa_bz_sp, false, digestion_bz); - if(digestion_bz.contain("MXXXK")) - { - cerr << endl - << "ERROR digestion_bz for " - << protein_bsa_bz_sp.get()->getAccession().toStdString() - << " MXXXK FOUND" << endl; - return 1; - } - if(digestion_bz.contain("MAXXK")) - { - cerr << endl - << "ERROR digestion_bz for " - << protein_bsa_bz_sp.get()->getAccession().toStdString() - << " MAXXK FOUND" << endl; - return 1; - } - if(!digestion_bz.contain("MAAAK")) - { - cerr << endl - << "ERROR digestion_bz for " - << protein_bsa_bz_sp.get()->getAccession().toStdString() - << " MAAAK NOT FOUND" << endl; - return 1; - } - if(!digestion_bz.contain("SNEIAHR")) - { - cerr << endl - << "ERROR digestion_bz for " - << protein_bsa_bz_sp.get()->getAccession().toStdString() - << " SNEIAHR NOT FOUND" << endl; - return 1; - } - cout << endl << " SNEIAHRFK FOUND " << endl; - if(!digestion_bz.contain("SDEIAHR")) - { - cerr << endl - << "ERROR digestion_bz for " - << protein_bsa_bz_sp.get()->getAccession().toStdString() - << " SDEIAHR NOT FOUND" << endl; - return 1; - } - cout << endl << " SDEIAHRFK FOUND " << endl; - return 0; + Protein cry1Ac( + "cry1Ac", + "MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQ" + "WD" + "AFLVQIEQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIP" + "LF" + "AVQNYQVPLLSVYVQAANLHLSVLRDVSVFGQRWGFDAATINSRYNDLTRLIGNYTDYAVRWYNTGLERVWG" + "PD" + "SRDWVRYNQFRRELTLTVLDIVALFPNYDSRRYPIRTVSQLTREIYTNPVLENFDGSFRGSAQGIERSIRSP" + "HL" + "MDILNSITIYTDAHRGYYYWSGHQIMASPVGFSGPEFTFPLYGTMGNAAPQQRIVAQLGQGVYRTLSSTLYR" + "RP" + "FNIGINNQQLSVLDGTEFAYGTSSNLPSAVYRKSGTVDSLDEIPPQNNNVPPRQGFSHRLSHVSMFRSGFSN" + "SS" + "VSIIRAPMFSWIHRSAEFNNIIASDSITQIPAVKGNFLFNGSVISGPGFTGGDLVRLNSSGNNIQNRGYIEV" + "PI" + "HFPSTSTRYRVRVRYASVTPIHLNVNWGNSSIFSNTVPATATSLDNLQSSDFGYFESANAFTSSLGNIVGVR" + "NF" + "SGTAGVIIDRFEFIPVTATLEAEYNLERAQKAVNALFTSTNQLGLKTNVTDYHIDQVSNLVTYLSDEFCLDE" + "KR" + "ELSEKVKHAKRLSDERNLLQDSNFKDINRQPERGWGGSTGITIQGGDDVFKENYVTLSGTFDECYPTYLYQK" + "ID" + "ESKLKAFTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRCAPHLEWNPDL" + "DC" + "SCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKRAEKK" + "WR" + "DKREKLEWETNIVYKEAKESVDALFVNSQYDQLQADTNIAMIHAADKRVHSIREAYLPELSVIPGVNAAIFE" + "EL" + "EGRIFTAFSLYDARNVIKNGDFNNGLSCWNVKGHVDVEEQNNQRSVLVVPEWEAEVSQEVRVCPGRGYILRV" + "TA" + "YKEGYGEGCVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYA" + "SV" + "YEEKSYTDGRRENPCEFNRGYRDYTPLPVGYVTKELEYFPETDKVWIEIGETEGTFIVDSVELLLMEE"); + + cout << std::endl << "cry1Ac Mass = " << cry1Ac.getMass() << std::endl; + MzRange cry1Ac_mass(133248.068195739, + PrecisionFactory::getPpmInstance(0.5)); + REQUIRE(cry1Ac_mass.contains(cry1Ac.getMass())); + + // BSA + qDebug() << "init bsa"; + Protein bsa("BSA", + "MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDE" + "HVKLVNELTEFA" + "KTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDL" + "PKLKPDPNTLCD" + "EFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMRE" + "KVLASSARQRLR" + "CASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLA" + "KYICDNQDTISS" + "KLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYS" + "RRHPEYAVSVLL" + "RLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIV" + "RYTRKVPQVSTP" + "TLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVN" + "RRPCFSALTPDE" + "TYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDK" + "CCAADDKEACFA" + "VEGPKLVVSTQTALA"); + qDebug() << "init bsa sp"; + ProteinSp protein_sp = bsa.makeProteinSp(); + qDebug() << "init kinase"; + Enzyme kinase; + qDebug() << "kinase.setMiscleavage(2)"; + kinase.setMiscleavage(2); + DigestionHandler digestion; + qDebug() << "kinase.eat(protein_sp,digestion)"; + kinase.eat(0, protein_sp, false, digestion); + + + REQUIRE (digestion.size() == 243); + + PeptideSizeFilter peptide_size(7, 35); + peptide_size.setSink(&digestion); + + qDebug() << " kinase.eat(protein_sp,peptide_size);"; + digestion.clear(); + kinase.eat(0, protein_sp, false, peptide_size); + + REQUIRE (digestion.size() == 191); + + qDebug() << " modification_sink"; + + PeptideModHandler modification_sink; + + + qDebug() << " fixed_mod_builder"; + PeptideBuilder fixed_mod_builder; + fixed_mod_builder.setSink(&modification_sink); + + // QChar aa =QChar('C'); + // carbamido : + QString acc = "MOD:00397"; + + qDebug() << " carbamido"; + AaModificationP carbamido = AaModification::getInstance("MOD:00397"); + + fixed_mod_builder.addFixedAaModification('C', carbamido); + + PeptideSizeFilter peptide_size2mod(7, 35); + peptide_size2mod.setSink(&fixed_mod_builder); + + kinase.setMiscleavage(0); + + + qDebug() << " kinase.eat(protein_sp,peptide_size2mod);"; + + digestion.clear(); + kinase.eat(0, protein_sp, false, peptide_size2mod); + REQUIRE (digestion.size() == 0); + + qDebug() << " kinase.eat(protein_sp,peptide_size2mod) ; end"; + + // + // unsigned int i = 0; + // do { + // i++; + // } + // while (i < 100000000000000); + + // variable modifications : + // MOD:00719 + // acc = "MOD:00719"; + AaModificationP met_oxy = AaModification::getInstance("MOD:00719"); + + PeptideVariableModificationBuilder var_mod_builder(met_oxy); + var_mod_builder.addAa('M'); + var_mod_builder.setSink(&modification_sink); + + // QString accMo = "MOD:00719"; + cout << std::endl << "..:: chose ::.." << std::endl; + + PeptideBuilder fixed_mod_builder2; + fixed_mod_builder2.setSink(&var_mod_builder); + fixed_mod_builder2.addFixedAaModification('C', carbamido); + + PeptideSizeFilter peptide_size2varmod(7, 35); + peptide_size2varmod.setSink(&fixed_mod_builder2); + + + kinase.setMiscleavage(0); + + qDebug() << " kinase.eat(protein_sp,peptide_size2varmod);"; + + ProteinSp fake = + Protein("fakeBSA", "MVVKKVVVMAMEEKWVTFISLLLLFTKVHKECCVVSTQTALA") + .makeProteinSp(); + kinase.eat(0, fake, false, peptide_size2varmod); + + digestion.clear(); + cout << std::endl + << "..:: Test trypsin peptides on fake prot ::.." << std::endl; + kinase.eat(0, fake, false, digestion); + + REQUIRE(digestion.contain("K")); + + + REQUIRE(digestion.contain("ECCVVSTQTALA")); + + REQUIRE(digestion.contain("VVVMAMEEK")); + + REQUIRE(digestion.size() == 6); + + // BSA + cout << std::endl + << "..:: Test semi tryptic peptides on BSA ::.." << std::endl; + kinase.setMiscleavage(0); + PeptideSemiEnzyme semi_tryptic; + semi_tryptic.setSink(&digestion); + qDebug() << "kinase.eat(protein_sp,semi_tryptic)"; + digestion.clear(); + kinase.eat(0, protein_sp, false, semi_tryptic); + + + REQUIRE(digestion.size() == 1132); + + + + qDebug() << Qt::endl << "..:: Test enzyme motif ::.." << Qt::endl; + Enzyme motif_digest("(MAMEE[KR])([^P])"); + digestion.clear(); + motif_digest.eat(0, fake, false, digestion); + REQUIRE(digestion.size() == 2); + REQUIRE(digestion.contain("MVVKKVVVMAMEEK")); + REQUIRE(digestion.contain("WVTFISLLLLFTKVHKECCVVSTQTALA")); + + + // potential Nter mod +42.01056@[ + // fixed mod mass 57.02146@C + // 15.99491@M,79.96633@Y + // 79.96633:-97.9769@[ST!] + PeptideModificatorPipeline pmp; + peptide_size2varmod.setSink(&pmp); + PeptideVariableModificationReplacement mod_replace( + AaModification::getInstance("MOD:00397"), + AaModification::getInstance("MOD:00419")); + QString pattern_str("^E(C)"); + mod_replace.setModificationPattern(pattern_str); + + pmp.setSink(&mod_replace); + mod_replace.setSink(&modification_sink); + + pmp.addFixedModificationString("MOD:00397@C"); + // fixed: MOD:00397@C,MOD:00696@[YST] + pmp.addPotentialModificationString( + "MOD:00719@M,MOD:00696(0-1)@[YST],MOD:00719(1)@M,MOD:00696(1)@[YST]"); + // var: MOD:00719@M + // MOD:00429@^K + pmp.addLabeledModificationString("MOD:00429@(^.|K)"); + // MOD:00552@^K + pmp.addLabeledModificationString("MOD:00552@(^.|K)"); + // MOD:00638@^K + pmp.addLabeledModificationString("MOD:00638@(^.|K)"); + kinase.eat(0, fake, false, peptide_size2varmod); + + // reverse protein : + cout << std::endl + << "reverse :" + << Protein(*fake.get()).reverse().getSequence().toStdString(); + + PeptideSp peptide_test = PeptideStrParser::parseString( + "E(MOD:00429)C(MOD:00419)C(MOD:00397)VVSTQT(MOD:00696,MOD:00696)ALA"); + REQUIRE( + peptide_test.get()->toString().toStdString() == + "E(MOD:00429)C(MOD:00419)C(MOD:00397)VVSTQT(MOD:00696,MOD:00696)ALA"); + REQUIRE(modification_sink.contain(peptide_test)); + cout << peptide_test.get()->toString().toStdString() << " is present" + << std::endl; + + + peptide_test = + PeptideStrParser::parseString("V(MOD:00552)VVMAMEEK(MOD:00429)"); + REQUIRE_FALSE(modification_sink.contain(peptide_test)); + cout << peptide_test.get()->toString().toStdString() << " is absent" + << std::endl; + + peptide_test = + PeptideStrParser::parseString("V(MOD:00552)VVMAMEEK(MOD:00552)"); + REQUIRE(modification_sink.contain(peptide_test)); + cout << peptide_test.get()->toString().toStdString() << " is present" + << std::endl; + + + peptide_test = PeptideStrParser::parseString( + "E(MOD:00429)C(MOD:00397)C(MOD:00397)VVSTQT(MOD:00696,MOD:00696)ALA"); + REQUIRE(modification_sink.contain(peptide_test)); + cout << peptide_test.get()->toString().toStdString() << " is present" + << std::endl; + + cout << std::endl << "..:: test modification motifs ::.." << std::endl; + + ProteinSp prot_test_motif = + Protein("prot_test_motif", "MVVVVVMAMEEWVTFISLLLLFTVHECCVVSTQTALA") + .makeProteinSp(); + modification_sink.clear(); + PeptideBuilder pep_builder; + PeptideFixedModificationBuilder fixed_mod_motif( + AaModification::getInstance("MOD:00397")); + pattern_str = "V(V)"; + fixed_mod_motif.setModificationPattern(pattern_str); + pep_builder.setSink(&fixed_mod_motif); + fixed_mod_motif.setSink(&modification_sink); + kinase.eat(0, prot_test_motif, false, pep_builder); + + peptide_test = PeptideStrParser::parseString( + "MVV(MOD:00397)V(MOD:00397)V(MOD:00397)V(MOD:00397)" + "MAMEEWVTFISLLLLFTVHECCVV(MOD:00397)STQTALA"); + REQUIRE(modification_sink.contain(peptide_test)); + REQUIRE(modification_sink.size() == 1); + cout << peptide_test.get()->toString().toStdString() << " is present" + << std::endl; + + + qDebug() << "init test protein"; + cout << std::endl + << "..:: Test Protein with B and Z wildcard ::.." << std::endl; + + // BSA + qDebug() << "init bsa with B and Z wildcard"; + Protein bsa_bz("BSA", + "MXXXKBWVTFISLLLLFSSAYSRGVFRRDTHKSBEIAHRFKDLGEEHFKGLVLIAFSQY" + "LQQCPFDEHVKLVNE" + "LTEFAKTCVADEBSHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFL" + "SHKDDSPDLPKLKPD" + "PNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACL" + "LPKIETMREKVLASS" + "ARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLE" + "CADDRADLAKYICDN" + "QDTISSKLKECCDKPLLEZKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDA" + "FLGSFLYEYSRRHPE" + "YAVSVLLRLAKEYZEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKL" + "GEYGFQNALIVRYTR" + "KVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEK" + "VTKCCTESLVNRRPC" + "FSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKT" + "VMENFVAFVDKCCAA" + "DDKEACFAVEGPKLVVSTQTALA"); + qDebug() << "init bsa_bz sp"; + ProteinSp protein_bsa_bz_sp = bsa_bz.makeProteinSp(); + qDebug() << "init kinase"; + DigestionHandler digestion_bz; + qDebug() << "kinase.eat(protein_sp,digestion) B Z"; + kinase.eat(0, protein_bsa_bz_sp, false, digestion_bz); + REQUIRE_FALSE(digestion_bz.contain("MXXXK")); + REQUIRE_FALSE(digestion_bz.contain("MAXXK")); + REQUIRE(digestion_bz.contain("MAAAK")); + REQUIRE(digestion_bz.contain("SNEIAHR")); + cout << std::endl << " SNEIAHRFK FOUND " << std::endl; + REQUIRE(digestion_bz.contain("SDEIAHR")); + cout << std::endl << " SDEIAHRFK FOUND " << std::endl; + } + + + SECTION("..:: Test digestion pipeline ::..", "[DigestionPipeline]") + { + + // potential Nter mod +42.01056@[ + // fixed mod mass 57.02146@C + // 15.99491@M,79.96633@Y + // 79.96633:-97.9769@[ST!] + PeptideModHandler modification_sink; + PeptideSizeFilter peptide_size2varmod(7, 35); + PeptideModificatorPipeline pmp; + peptide_size2varmod.setSink(&pmp); + + pmp.setSink(&modification_sink); + + ProteinSp fake = + Protein("fakeBSA", "MVVKKVVVMAMEEKWVTFISLLLLFTKVHKECCVVSTQTALA") + .makeProteinSp(); + Enzyme kinase; + kinase.eat(0, fake, false, peptide_size2varmod); + + PeptideSp peptide_test = PeptideStrParser::parseString("VVVMAMEEK"); + REQUIRE(modification_sink.contain(peptide_test)); + } } diff -Nru libpappsomspp-0.8.15/tests/test_psm.cpp libpappsomspp-0.8.58/tests/test_psm.cpp --- libpappsomspp-0.8.15/tests/test_psm.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_psm.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -27,11 +27,14 @@ ******************************************************************************/ // make test ARGS="-V -I 18,18" +// ./tests/catch2-only-tests [psm] -s +// ./tests/catch2-only-tests [psmfeature] -s +#include -#define CATCH_CONFIG_MAIN #include #include #include +#include #include #include #include @@ -52,7 +55,7 @@ SECTION("..:: readMgf ::..", "[psm]") { - cout << endl << "..:: readMgf ::.." << endl; + cout << std::endl << "..:: readMgf ::.." << std::endl; // bool refine_spectrum_synthesis = false; MassSpectrum spectrum_simple = @@ -70,7 +73,7 @@ std::list ion_list; ion_list.push_back(PeptideIon::y); ion_list.push_back(PeptideIon::b); - cout << "spectrum_simple size " << spectrum_simple.size() << endl; + cout << "spectrum_simple size " << spectrum_simple.size() << std::endl; PeptideSpectrumMatch psm( spectrum_simple, peptide_sp, 2, precision, ion_list); @@ -83,5 +86,242 @@ spectrum_simple, peptide_sp, 2, precision, ion_list); test_count = psmb.countTotalMatchedIons(); REQUIRE(test_count == 0); + + + precision = PrecisionFactory::getDaltonInstance(0.02); + PeptideIsotopeSpectrumMatch psm_iso( + spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0); + + std::list peak_ion_isotope_match_list = + psm_iso.getPeakIonIsotopeMatchList(); + + for(auto peak : peak_ion_isotope_match_list) + { + qDebug() << peak.toString() << " " + << peak.getPeptideNaturalIsotopeAverageSp().get(); + } + REQUIRE(peak_ion_isotope_match_list.size() == 19); + + psm_iso.dropPeaksLackingMonoisotope(); + peak_ion_isotope_match_list = psm_iso.getPeakIonIsotopeMatchList(); + for(auto peak : peak_ion_isotope_match_list) + { + qDebug() << peak.toString() << " " + << peak.getPeptideNaturalIsotopeAverageSp().get(); + } + REQUIRE(peak_ion_isotope_match_list.size() == 19); + + qDebug() << peak_ion_isotope_match_list.size(); + peak_ion_isotope_match_list.sort( + [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { + qDebug() << a.getPeak().y << " > "; + qDebug() << b.getPeak().y << " . "; + return (a.getPeak().y > b.getPeak().y); + }); + + + spectrum_simple = readMgf( + QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf")); + + peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp(); + + + precision = PrecisionFactory::getDaltonInstance(0.02); + qDebug(); + PeptideIsotopeSpectrumMatch psm_iso_check( + spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0); + + qDebug(); + peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList(); + + REQUIRE(peak_ion_isotope_match_list.size() == 39); + qDebug(); + + for(auto &peak : peak_ion_isotope_match_list) + { + qDebug() << peak.toString() << " " + << peak.getPeptideNaturalIsotopeAverageSp().get(); + } + + + peak_ion_isotope_match_list.sort( + [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) { + if(a.getPeptideIonType() < b.getPeptideIonType()) + return true; + if(a.getPeptideFragmentIonSp().get()->size() < + b.getPeptideFragmentIonSp().get()->size()) + return true; + if(a.getCharge() < b.getCharge()) + return true; + if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() < + b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber()) + return true; + return false; + }); + + + auto it = peak_ion_isotope_match_list.begin(); + REQUIRE(it->toString().toStdString() == "b2+isotope0r1mz185.128"); + it++; + REQUIRE(it->toString().toStdString() == "b3+isotope0r1mz256.165"); + + for(auto peak : peak_ion_isotope_match_list) + { + qDebug() << peak.toString() << " " + << peak.getPeptideNaturalIsotopeAverageSp().get(); + } + + psm_iso_check.dropPeaksLackingMonoisotope(); + peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList(); + + for(auto peak : peak_ion_isotope_match_list) + { + qDebug() << peak.toString() << " " + << peak.getPeptideNaturalIsotopeAverageSp().get(); + } + REQUIRE(peak_ion_isotope_match_list.size() == 39); + } +} + + +TEST_CASE("psm features test suite.", "[psmfeature]") +{ + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + SECTION("..:: readMgf ::..", "[psm]") + { + cout << std::endl << "..:: readMgf ::.." << std::endl; + // bool refine_spectrum_synthesis = false; + + MassSpectrum spectrum_simple = + readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_2016.mgf")); + //.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100); + + + Peptide peptide("EDKPQPPPEGR"); + PeptideSp peptide_sp(peptide.makePeptideSp()); + // peptide_sp.get()->addAaModification(AaModification::getInstance("MOD:00397"), + // 0); + + PsmFeatures features(PrecisionFactory::getDaltonInstance(0.02), 150); + + features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 3); + + REQUIRE(features.getTotalIntensity() == Approx(248641.8659667977)); + REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) == + Approx(1751.5864257813).epsilon(0.001)); + REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) == + Approx(57112.2947998047).epsilon(0.001)); + + + REQUIRE(features.countMatchedIonComplementPairs() == 0); + + + /* + + GRMZM5G815453_P01 P00874 Ribulose bisphosphate + carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39) + seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01; + parent_gene=GRMZM5G815453 + + + */ + spectrum_simple = + readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_15968.mgf")); + + + peptide_sp = Peptide("EITLGFVDLLR").makePeptideSp(); + + features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2); + + + REQUIRE( + features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() == + Approx(-0.0036778069).epsilon(0.00001)); + REQUIRE(features.countMatchedIonComplementPairs() == 3); + + REQUIRE(features.getPeakIonPairs().size() == 3); + + REQUIRE(features.getPeakIonPairs()[0].first.toString().toStdString() == + "b2+isotope0r1mz243.134"); + REQUIRE(features.getPeakIonPairs()[0].second.toString().toStdString() == + "y9+isotope0r1mz1033.61"); + + REQUIRE(features.getPeakIonPairs()[1].first.toString().toStdString() == + "b6+isotope0r1mz661.367"); + REQUIRE(features.getPeakIonPairs()[1].second.toString().toStdString() == + "y5+isotope0r1mz615.383"); + + REQUIRE(features.getPeakIonPairs()[2].first.toString().toStdString() == + "b7+isotope0r1mz760.435"); + REQUIRE(features.getPeakIonPairs()[2].second.toString().toStdString() == + "y4+isotope0r1mz516.315"); + + + REQUIRE( + features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[0]) == + Approx(-0.0036778069).epsilon(0.001)); + REQUIRE( + features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[1]) == + Approx(-0.0118262069).epsilon(0.001)); + REQUIRE( + features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[2]) == + Approx(-0.0114600069).epsilon(0.001)); + + + REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 9); + REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 2); + REQUIRE(features.getMaxConsecutiveIon(PeptideIon::a) == 0); + + + spectrum_simple = readMgf( + QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf")); + + peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp(); + + features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2); + REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 10); + REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 3); + REQUIRE(features.getAaSequenceCoverage(PeptideIon::y) == 10); + REQUIRE(features.getAaSequenceCoverage(PeptideIon::b) == 5); + + + REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) == + Approx(863068.6967769999)); + REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::y) == + Approx(114514.0625)); + + REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) == + Approx(254791.342651)); + REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::b) == + Approx(161016.984375)); + + + // SeqCoverComplementPeaks + REQUIRE(features.getComplementPairsAaSequenceCoverage() == 5); + REQUIRE(((double)features.getComplementPairsAaSequenceCoverage() / + (double)peptide_sp.get()->size()) == Approx(5.0 / 12.0)); + REQUIRE(((double)0 / (double)peptide_sp.get()->size()) == Approx(0)); + + + REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() / + features.getTotalIntensity()) == Approx(0.1727291768)); + + REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() < + features.getTotalIntensity())); + + REQUIRE( + features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() == + Approx(0.0008592852).epsilon(0.00001)); } } diff -Nru libpappsomspp-0.8.15/tests/test_rawmasslist.cpp libpappsomspp-0.8.58/tests/test_rawmasslist.cpp --- libpappsomspp-0.8.15/tests/test_rawmasslist.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_rawmasslist.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -45,7 +45,7 @@ main() { - cout << endl << "..:: Raw mass list ::.." << endl; + cout << std::endl << "..:: Raw mass list ::.." << std::endl; PeptideSp peptide_sp(Peptide("SAMPLER").makePeptideSp()); std::list ion_type_list; ion_type_list.push_back(PeptideIon::y); diff -Nru libpappsomspp-0.8.15/tests/test_scan_15968.cpp libpappsomspp-0.8.58/tests/test_scan_15968.cpp --- libpappsomspp-0.8.15/tests/test_scan_15968.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_scan_15968.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -50,7 +50,7 @@ using namespace std; // using namespace pwiz::msdata; -// make test ARGS="-V -I 17,17" +// make test ARGS="-V -I 15,15" TEST_CASE("scan 15968 test suite.", "[scan15968]") { @@ -59,7 +59,7 @@ SECTION("..:: Test scan 15968 ::..", "[scan15968]") { - cout << endl << "..:: Test scan 15968 ::.." << endl; + cout << std::endl << "..:: Test scan 15968 ::.." << std::endl; PrecisionPtr precision = PrecisionFactory::getDaltonInstance(0.02); std::list ion_list; ion_list.push_back(PeptideIon::y); @@ -686,9 +686,9 @@ MassSpectrum spectrum_clean_isotopes(spectrum_neutral.massSpectrumFilter( pappso::FilterTandemDeisotope(1.5, 200))); - cout << spectrum_neutral.size() << endl; - cout << sclean_isotopes.size() << endl; - cout << spectrum_clean_isotopes.size() << endl; + cout << spectrum_neutral.size() << std::endl; + cout << sclean_isotopes.size() << std::endl; + cout << spectrum_clean_isotopes.size() << std::endl; REQUIRE(spectrum_clean_isotopes.equals(sclean_isotopes, precision)); MassSpectrum spectrum_most_intense(spectrum_clean_isotopes); @@ -706,10 +706,10 @@ ion_list, refine_spectrum_synthesis); cout << "peptide " << pep15968.getSequence().toStdString() - << " hyperscore15968=" << hyperscore15968.getHyperscore() << endl; + << " hyperscore15968=" << hyperscore15968.getHyperscore() << std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; // Spectrum::getHyperscore "b" itmap->second 1 1 // Spectrum::getHyperscore "y" itmap->second 9 362880 diff -Nru libpappsomspp-0.8.15/tests/test_tandem_run_wrapper.cpp libpappsomspp-0.8.58/tests/test_tandem_run_wrapper.cpp --- libpappsomspp-0.8.15/tests/test_tandem_run_wrapper.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_tandem_run_wrapper.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,164 @@ +// +// File: test_tandem_run_wrapper.cpp +// Created by: Olivier Langella +// Created on: 12/11/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella . + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [xtrunwrapper] -s + +// ./tests/catch2-only-tests [xtrunwrapper] -s -a + +#include +#include +#include +#include +#include +#include +#include +#include + +#include "config.h" +#include "common.h" + +using namespace pappso; +using namespace std; + + +TEST_CASE("test xtandem run wrapper", "[xtrunwrapper]") +{ + + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + INFO("..:: test X!Tandem run wrapper begin ::.."); + SECTION("test XtandemInputSaxHandler") + { + WrapTandemResults wrap_results("wrapped_tandem_output.xml", + "original_mzdata_source.mzXML"); + + wrap_results.setInputParameters("output, spectrum index", "true"); + REQUIRE(wrap_results.readFile( + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/tandem_result_file.xml"))); + + + QFile fnew("wrapped_tandem_output.xml"); + REQUIRE(fnew.open(QFile::ReadOnly | QFile::Text)); + // REQUIRE(fnew.errorString().toStdString() == ""); + QTextStream infnew(&fnew); + + QString alltandem = infnew.readAll(); + + + REQUIRE(alltandem.contains( + "/tmp/xtpcpp-HDpOXY/QExactive_analysis_FDR.xml")); + REQUIRE(alltandem.contains( + QString("%1") + .arg(QFileInfo("original_mzdata_source.mzXML").absoluteFilePath()))); + REQUIRE(alltandem.contains( + QString("%1") + .arg(QFileInfo("wrapped_tandem_output.xml").absoluteFilePath()))); + + REQUIRE(alltandem.contains( + "true")); + } + + SECTION("test XtandemInputSaxHandler") + { + WrapTandemInput wrap_input("mzdata_source.mzXML", + "wrapped_tandem_input.xml", + "wrapped_tandem_output.xml"); + + + REQUIRE(wrap_input.readFile( + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/tandem_run_params.xml"))); + + REQUIRE(wrap_input.getOriginalTandemPresetFileName().toStdString() == + "/gorgone/pappso/tmp/xtpcpp.AjyZGg/" + "Lumos_trypsin_rev_camC_oxM_10ppm_HCDOT_12102017CH.xml"); + + REQUIRE(wrap_input.getOriginalMsDataFileName().toStdString() == + "/gorgone/pappso/jouy/raw/2021_Lumos/20210729_02_Clouet/" + "20210729_18_blc.mzXML"); + + REQUIRE(wrap_input.getOriginalTandemOutputFileName().toStdString() == + "/gorgone/pappso/jouy/users/Lydie/2021/2021_lumos/" + "20210729_02_Clouet/xtpcpp/20210729_18_blc.xml"); + + REQUIRE(compareTextFiles( + "wrapped_tandem_input.xml", + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/wrapper/wrapped_tandem_input.xml"))); + } + + SECTION("test XtandemPresetReader") + { + XtandemPresetReader preset_reader; + + + REQUIRE_FALSE(preset_reader.readFile( + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/settings/timstofmgf_wrong.xml"))); + + REQUIRE(!preset_reader.errorString().isEmpty()); + + REQUIRE(preset_reader.readFile( + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/settings/timstofmgf.xml"))); + + qDebug() << preset_reader.getMs2FiltersOptions(); + REQUIRE(preset_reader.getNumberOfThreads() == 5); + REQUIRE(preset_reader.getMs2FiltersOptions().toStdString() == + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"); + + REQUIRE_FALSE(preset_reader.readFile("nofile")); + + REQUIRE(!preset_reader.errorString().isEmpty()); + + + REQUIRE(preset_reader.readFile( + QString(CMAKE_SOURCE_DIR) + .append( + "/tests/data/tandem/settings/QExactive_analysis_FDR_nosemi.xml"))); + + qDebug() << preset_reader.getMs2FiltersOptions(); + REQUIRE(preset_reader.getNumberOfThreads() == 1); + REQUIRE(preset_reader.getMs2FiltersOptions().toStdString() == + "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton"); + + REQUIRE_FALSE(preset_reader.readFile( + QString(CMAKE_SOURCE_DIR).append("/tests/data/tandem/database.xml"))); + + REQUIRE(preset_reader.getCountNote() == 0); + + REQUIRE_FALSE(preset_reader.readFile( + QString(CMAKE_SOURCE_DIR) + .append("/tests/data/tandem/tandem_run_params.xml"))); + REQUIRE(preset_reader.getCountNote() == 8); + } +} diff -Nru libpappsomspp-0.8.15/tests/test_tims_data_xic_chromatogram.cpp libpappsomspp-0.8.58/tests/test_tims_data_xic_chromatogram.cpp --- libpappsomspp-0.8.15/tests/test_tims_data_xic_chromatogram.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_tims_data_xic_chromatogram.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,136 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "config.h" + +using namespace pappso; +using namespace std; + + +TEST_CASE("Test tims XIC data extraction right form the SQLite db", "[timsXicDataSqliteDb]") +{ + +#if USEPAPPSOTREE == 1 + + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + QString file_path_name = ""; + + //file_path_name = + //"/gorgone/pappso/jouy/raw/2021_Tims_TOF/20211124_HeLa/" + //"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + file_path_name = + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/" + "example_data/200ngHeLaPASEF_2min_compressed.d/" + "analysis.tdf"; + + // file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/20210126_HeLa.d/" + //"1-26-2021_1_QC_HeLa10ng_826.d/analysis.tdf"; + + //file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/2021_Tims_TOF/20211124_HeLa/" + //"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + qDebug() << "The file to use as a test base is: " << file_path_name; + // When not in debug mode. + std::cout << __FILE__ << ":" << __LINE__ + << " The file to use as a test base is: " + << file_path_name.toStdString(); + + SECTION("Test TIMS TIC chromatogram extractor") + { + INFO("Test the extraction from the SQLite database's Frames table"); + + pappso::MsFileAccessor accessor(file_path_name, "a1"); + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims); + + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims); + + pappso::TimsMsRunReader *tims_reader = + dynamic_cast(p_msreader.get()); + + REQUIRE(tims_reader != nullptr); + + if(tims_reader != nullptr) + { + Trace tic_chromatogram = tims_reader->getTicChromatogram(); + + REQUIRE(tic_chromatogram.size() != 0); + + qDebug().noquote() << "The TIC chromatogram has " + << tic_chromatogram.size() << " points " + << "and has the following points:\n" + << tic_chromatogram.toString(); + // When not in debug mode. + std::cout << __FILE__ << ":" << __LINE__ << "The TIC chromatogram has " + << tic_chromatogram.size() + << " points and has the following points:\n" + << tic_chromatogram.toString().toStdString(); + } + } + + SECTION("Test TIMS MS2 TIC chromatogram extractor") + { + INFO("Test the extraction from the SQLite database's Frames table"); + + pappso::MsFileAccessor accessor(file_path_name, "a1"); + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims_ms2); + + pappso::TimsMsRunReaderMs2 *tims_reader = + dynamic_cast(p_msreader.get()); + + REQUIRE(tims_reader != nullptr); + + if(tims_reader != nullptr) + { + Trace tic_chromatogram = tims_reader->getTicChromatogram(); + + REQUIRE(tic_chromatogram.size() != 0); + + qDebug().noquote() << "The TIC chromatogram has " + << tic_chromatogram.size() << " points " + << "and has the following points:\n" + << tic_chromatogram.toString(); + // When not in debug mode. + std::cout << __FILE__ << ":" << __LINE__ << "The TIC chromatogram has " + << tic_chromatogram.size() + << " points and has the following points:\n" + << tic_chromatogram.toString().toStdString(); + } + } + +#elif USEPAPPSOTREE == 1 + + cout << std::endl + << "..:: NO test TIMS TIC chromatogram extraction ::.." << std::endl; + +#endif +} diff -Nru libpappsomspp-0.8.15/tests/test_timsframe.cpp libpappsomspp-0.8.58/tests/test_timsframe.cpp --- libpappsomspp-0.8.15/tests/test_timsframe.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_timsframe.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -23,10 +23,12 @@ * ******************************************************************************/ -// make test ARGS="-V -I 22,22" +// make test ARGS="-V -I 1,1" +// ./tests/catch2-only-tests [timsframe] -s + +// ./tests/catch2-only-tests [timsframe] -s -a -#define CATCH_CONFIG_MAIN #include #include #include @@ -35,27 +37,30 @@ #include #include #include +#include #include +#include #include #include "config.h" using namespace pappso; using namespace std; -TEST_CASE("test tims frames", "[timsframe]") + +TEST_CASE("Test tims frames", "[timsframe]") { // Set the debugging message formatting pattern. qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); - cout << endl << "..:: test TIMS frame init begin ::.." << endl; + INFO("..:: Test TIMS frame init begin ::.."); // OboPsiMod test; TimsFrameBase frame(1, 671); MzRange mz_range(1200.0001, PrecisionFactory::getPpmInstance(10)); - SECTION("test 1") + SECTION("Test 1") { double temperature_correction = 77.0 * (25.4933665127396 - 25.59978165276) + @@ -119,12 +124,13 @@ std::size_t scan_num = frame.getScanNumFromOneOverK0(one_over_k0); REQUIRE(scan_num == 400); - cout << endl << "..:: test 1 OK ::.." << endl; + cout << std::endl << "..:: Test 1 OK ::.." << std::endl; } - SECTION("test 2") + SECTION("Test 2") { - cout << endl << "..:: second test, new calibration parameters ::.." << endl; + cout << std::endl + << "..:: second test, new calibration parameters ::.." << std::endl; frame.setMzCalibration(25.3072302808429, @@ -199,65 +205,250 @@ REQUIRE_FALSE(mz < 50.0); - cout << endl << "..:: test 2 OK ::.." << endl; + cout << std::endl << "..:: Test 2 OK ::.." << std::endl; } + #if USEPAPPSOTREE == 1 - cout << endl << "..:: test TIMS TDF parsing ::.." << endl; - /* + SECTION("Test TIMS TDF parsing issue #61") + { + INFO("Test case ERROR reading TIMS frame 58581"); + pappso::MsFileAccessor accessor( - "/gorgone/pappso/jouy/raw/2020_Tims_TOF/20201102_HeLa/" - "11-2-2020_1_QC_HeLa10ng_219.d/analysis.tdf", + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/" + "example_data/200ngHeLaPASEF_2min_compressed.d/" + "analysis.tdf", "a1"); - */ - /* - pappso::MsFileAccessor accessor( - "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/example_data/" - "200ngHeLaPASEF_2min_compressed.d/analysis.tdf", - "a1"); + + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + + + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims_ms2); + + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_msreader.get()); + REQUIRE(tims2_reader != nullptr); + if(tims2_reader != nullptr) + { + tims2_reader->setMs2BuiltinCentroid(true); + tims2_reader->setMs2FilterCstSPtr(std::make_shared( + FilterSuiteString("chargeDeconvolution|0.02dalton"))); + } + pappso::QualifiedMassSpectrum mass_spectrum; + REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(5001)); + + + /* + * 23: ..:: Test TIMS frame init begin ::.. +23: Test case ERROR reading TIMS frame 58581 +23: ERROR reading TIMS frame 60575 TIMS binary file +/home/langella/data1/bruker/ 23: +5-18-2021_1_robert_28_mic02-std_1354.d/analysis.tdf_bin: decompressed_size2 23: +== ZSTD_CONTENTSIZE_ERROR, frame_length=265254592 + +*/ + REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6001)); + REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6003)); + REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6005)); + REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6007)); + REQUIRE_THROWS_AS(mass_spectrum = + tims2_reader->qualifiedMassSpectrum(35460), + pappso::ExceptionNotFound); + } + + + SECTION("Test TIMS TDF parsing") + { + INFO("Test case pappso::FileReaderType::tims_ms2 start"); + + pappso::MsFileAccessor accessor( + "/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/" + "PXD014777_maxquant_timstof/" + "20180809_120min_200ms_WEHI25_brute20k_timsON_100ng_HYE124B_Slot1-8_1_" + "894.d/analysis.tdf", + "a1"); + /* + pappso::MsFileAccessor accessor( + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/" + "example_data/200ngHeLaPASEF_2min_compressed.d/" + "analysis.tdf", + "a1"); +*/ + /* + pappso::MsFileAccessor accessor( + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/" + "example_data/" + "200ngHeLaPASEF_2min_compressed.d/analysis.tdf", + "a1"); */ - pappso::MsFileAccessor accessor( - "/home/langella/developpement/git/bruker/" - "200ngHeLaPASEF_2min_compressed.d/" - "analysis.tdf", - "a1"); - accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, - pappso::FileReaderType::tims_ms2); - - pappso::MsRunReaderSPtr p_msreader = - accessor.msRunReaderSp(accessor.getMsRunIds().front()); - - pappso::TimsMsRunReaderMs2 *tims2_reader = - dynamic_cast(p_msreader.get()); - if(tims2_reader != nullptr) + /* + pappso::MsFileAccessor accessor( + "/data/test_tdf_quality/2-3-2021_1_HeLa10ng_871.d/analysis.tdf", + "a1"); + */ + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims); + + + pappso::MsRunReaderSPtr p_msreader_tims_ms1 = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + pappso::TimsMsRunReader *tims1_reader = + dynamic_cast(p_msreader_tims_ms1.get()); + + REQUIRE_FALSE(p_msreader_tims_ms1.get() == nullptr); + REQUIRE_FALSE(tims1_reader == nullptr); + + pappso::TimsDataSp timsdata_sp = tims1_reader->getTimsDataSPtr(); + + REQUIRE_NOTHROW(timsdata_sp.get()->getRawMsBySpectrumIndex(0)); + REQUIRE_NOTHROW(timsdata_sp.get()->getRawMsBySpectrumIndex(1)); + REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(0)); + // REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(1000)); + + for(std::size_t i = 0; i < 1000; i++) + { + qDebug() + << " size(" << (i) << ")=" + << p_msreader_tims_ms1.get()->massSpectrumCstSPtr(i).get()->size(); + } + p_msreader_tims_ms1.get()->massSpectrumCstSPtr(53); + p_msreader_tims_ms1.get()->massSpectrumCstSPtr(5000); + // timsdata_sp.get()->getRawMsBySpectrumIndex(8207); + + REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(8207)); + + // 8206, frameId=9 scanNum=910 ERROR in + // MzCalibrationModel1::getMzFromTofIndex m[0].y!= 0 + REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(8206)); + + // scan_num=899 spectrum_index=899 + REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(899)); + + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + + + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims_ms2); + + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_msreader.get()); + REQUIRE(tims2_reader != nullptr); + if(tims2_reader != nullptr) + { + tims2_reader->setMs2BuiltinCentroid(true); + tims2_reader->setMs2FilterCstSPtr(std::make_shared( + FilterSuiteString("chargeDeconvolution|0.02dalton"))); + } + + pappso::QualifiedMassSpectrum mass_spectrum = + tims2_reader->qualifiedMassSpectrum(7001); + + INFO("mass_spectrum.getMsLevel()=" << mass_spectrum.getMsLevel()); + INFO("mass_spectrum.getPrecursorMz()=" << mass_spectrum.getPrecursorMz()); + INFO("mass_spectrum.getMassSpectrumId().getSpectrumIndex()=" + << mass_spectrum.getMassSpectrumId().getSpectrumIndex()); + + INFO(mass_spectrum.getMassSpectrumSPtr()->xValues().at(0)); + REQUIRE_FALSE(mass_spectrum.getMassSpectrumCstSPtr().get()->back().x < + 40.0); + + + INFO("Test case pappso::FileReaderType::tims start"); + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims); + + + class SpectrumCollectionHandler : public SpectrumCollectionHandlerInterface { - tims2_reader->setMs2BuiltinCentroid(true); - tims2_reader->setMs2FilterCstSPtr(std::make_shared( - FilterSuiteString("chargeDeconvolution|0.02dalton"))); - } - - pappso::QualifiedMassSpectrum mass_spectrum = - tims2_reader->qualifiedMassSpectrum(7); - - - cout << endl - << "mass_spectrum.getMsLevel()=" << mass_spectrum.getMsLevel() << endl; - - cout << endl - << "mass_spectrum.getPrecursorMz()=" << mass_spectrum.getPrecursorMz() - << endl; - cout << endl - << "mass_spectrum.getMassSpectrumId().getSpectrumIndex()=" - << mass_spectrum.getMassSpectrumId().getSpectrumIndex() << endl; - - /* - cout << endl - << mass_spectrum.getMassSpectrumCstSPtr() - .get() - ->toString() - .toStdString() - .c_str() - << endl; + public: + virtual ~SpectrumCollectionHandler(){}; + virtual void + setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override + { + m_count++; + if((m_count % 1000) == 0) + { + WARN("count " + << m_count << " " + << spectrum.getMassSpectrumId().getNativeId().toStdString() + << " MSlevel=" << spectrum.getMsLevel()); + + if(spectrum.getMsLevel() == 1) + { + REQUIRE_FALSE(spectrum.getMassSpectrumCstSPtr() == nullptr); + } + if(spectrum.getMassSpectrumCstSPtr() != nullptr) + { + WARN(" size=" << spectrum.size()); + } + //<< " size=" << spectrum.toString().toStdString()); + } + }; + virtual bool + needPeakList() const override + { + return false; + }; + + std::size_t m_count = 0; + }; + + SpectrumCollectionHandler dummy_handler; + + Catch::Timer t; + t.start(); + + WARN("reading all spectrum collection of file " + << accessor.getFileName().toStdString()); + dummy_handler.setNeedMsLevelPeakList(1, false); + dummy_handler.setNeedMsLevelPeakList(2, false); + // tims1_reader->readSpectrumCollectionByMsLevel(dummy_handler, 1); + + auto s = t.getElapsedSeconds(); + + WARN("reading time in second : " << s); + + + // git hash 597d6a68062a45d5e3ccaaa8398598a62dc69043 reading time in second + // : 1447.15 + + // git hash 7dc0806a4ca1fd0e92da97dcc44ac9b44c381d9f reading time in second + // : 1445.65 + // if we disable binary data reading : reading time in second : 1220.77 => + // there is somehow room for performance enhancements + + // git hash 26c8053d4fcfae15b98c75b715d79cd615bf42e0 reading time in second + // : 1440.25 + + + // git hash 2d0d2a4edcfcef583bc60bd5b14e6b0df1505a02 reading time in second + // : 1447.3 + // => avoiding sql query is not really efficient + } + /* +cout << std::endl + << mass_spectrum.getMassSpectrumCstSPtr() + .get() + ->toString() + .toStdString() + .c_str() + << std::endl; */ /* * @@ -301,10 +492,11 @@ */ - REQUIRE_FALSE(mass_spectrum.getMassSpectrumCstSPtr().get()->back().x < 40.0); + #elif USEPAPPSOTREE == 1 - cout << endl << "..:: NO test TIMS TDF parsing ::.." << endl; + cout << std::endl + << "..:: NO test TIMS TIC chromatogram extraction ::.." << std::endl; #endif } diff -Nru libpappsomspp-0.8.15/tests/test_timsxicextractor.cpp libpappsomspp-0.8.58/tests/test_timsxicextractor.cpp --- libpappsomspp-0.8.15/tests/test_timsxicextractor.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_timsxicextractor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,178 @@ + +// File: test_timsxicextractor.cpp +// Created by: Olivier Langella +// Created on: 3/2/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [TimsXicExtractor] -s + + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include "config.h" +#include "common.h" +#include + + +using namespace pappso; + +TEST_CASE("Extracting XIC from timsdata", "[TimsXicExtractor]") +{ + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + +#if USEPAPPSOTREE == 1 + + + QString file_path_name; + /* + file_path_name = + "/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/" + "example_data/" + "200ngHeLaPASEF_2min_compressed.d/analysis.tdf"; + */ + + // file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/20210126_HeLa.d/" + //"1-26-2021_1_QC_HeLa10ng_826.d/analysis.tdf"; + + + file_path_name = + "/gorgone/pappso/jouy/raw/2021_Tims_TOF/20211124_HeLa/" + "11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + /* + + file_path_name = + "/backup2/" + "11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; +*/ + // file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/2021_Tims_TOF/20211124_HeLa/" + //"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + qDebug() << "The file to use as a test base is: " << file_path_name; + // When not in debug mode. + std::cout << __FILE__ << ":" << __LINE__ + << " The file to use as a test base is: " + << file_path_name.toStdString(); + + pappso::MsFileAccessor accessor(file_path_name, "a1"); + + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + WARN("get reader"); + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + WARN("get reader OK"); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims_ms2); + + pappso::TimsMsRunReaderMs2 *tims2_reader = + dynamic_cast(p_msreader.get()); + REQUIRE(tims2_reader != nullptr); + + + pappso::TimsDataSp tims_data = tims2_reader->getTimsDataSPtr(); + + std::vector precursor_list = {2159}; + std::vector mz_list = { + 466.738, 467.239, 420, 421, 422, 423, 424, 425, 426}; + + std::vector xic_list; + std::vector xic_struct_list; + + clock_t start = clock(); + for(auto precursor_id : precursor_list) + { + xic_list.push_back( + tims_data.get() + ->getXicCoordTimsFromPrecursorId( + precursor_id, PrecisionFactory::getPpmInstance(30.0)) + .initializeAndClone()); + } + + for(pappso::pappso_double mz : mz_list) + { + pappso::XicCoordSPtr new_xic_struct = + xic_list[0].get()->initializeAndClone(); + new_xic_struct.get()->mzRange = + pappso::MzRange(mz, PrecisionFactory::getPpmInstance(30.0)); + xic_struct_list.push_back(new_xic_struct); + } + WARN("buildMsRunXicExtractorSp"); + MsRunXicExtractorInterfaceSp xic_extractor = + MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp( + p_msreader); + + WARN("buildMsRunXicExtractorSp OK"); + xic_extractor.get()->setXicExtractMethod(pappso::XicExtractMethod::sum); + + QTextStream outputStream(stdout, QIODevice::WriteOnly); + UiMonitorTextPercent monitor(outputStream); + WARN("monitor.setStatus"); + monitor.setStatus("Actually starting the XIC extraction."); + WARN("extractXicCoordSPtrList start"); + xic_extractor.get()->extractXicCoordSPtrListParallelized(monitor, + xic_struct_list); + WARN("extractXicCoordSPtrList stop"); + + qInfo() << QString("Time taken: %1\n") + .arg((double)(clock() - start) / CLOCKS_PER_SEC); + for(auto &&xic_struct : xic_struct_list) + { + REQUIRE(xic_struct.get() != nullptr); + QFile fileods(QString("%1/tims_xic_%2.ods") + .arg(CMAKE_BINARY_DIR) + .arg(xic_struct.get()->mzRange.getMz())); + OdsDocWriter writer(&fileods); + writer.writeLine(); + writer.writeCell("rtTarget"); + writer.writeCell(xic_struct.get()->rtTarget); + writer.writeLine(); + XicOdsWriter xic_writer(writer); + xic_writer.write(*xic_struct.get()->xicSptr.get()); + writer.close(); + fileods.close(); + } + +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} diff -Nru libpappsomspp-0.8.15/tests/test_timsxicextractor_based_masspec.cpp libpappsomspp-0.8.58/tests/test_timsxicextractor_based_masspec.cpp --- libpappsomspp-0.8.15/tests/test_timsxicextractor_based_masspec.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_timsxicextractor_based_masspec.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,199 @@ + +// File: test_timsxicextractor.cpp +// Created by: Olivier Langella +// Created on: 3/2/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +// Run using this command line: +// tests/catch2-only-tests "Creating mass spectrum via TIMS XIC extraction from +// timsdata" -s + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include "config.h" +#include "common.h" +#include + + +using namespace pappso; + +TEST_CASE("Creating mass spectrum via TIMS XIC extraction from timsdata", + "[massSpecTimsXicExtractor]") +{ + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + +#if USEPAPPSOTREE == 1 + + QString file_path_name; + + // file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/20210126_HeLa.d/" + //"1-26-2021_1_QC_HeLa10ng_826.d/analysis.tdf"; + + file_path_name = + "/gorgone/pappso/jouy/raw/2021_Tims_TOF/20211124_HeLa/" + "11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + // file_path_name = + //"/home/rusconi/devel/dataForMzml/bruker/2021_Tims_TOF/20211124_HeLa/" + //"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf"; + + qDebug() << "The file to use as a test base is: " << file_path_name; + // When not in debug mode. + std::cout << __FILE__ << ":" << __LINE__ + << " The file to use as a test base is: " + << file_path_name.toStdString() << std::endl; + + pappso::MsFileAccessor accessor(file_path_name, "a1"); + + qDebug() << "Setting the preferred file reader type to tims2."; + + accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims, + pappso::FileReaderType::tims_ms2); + + pappso::MsRunReaderSPtr p_msreader = + accessor.msRunReaderSp(accessor.getMsRunIds().front()); + + REQUIRE(p_msreader != nullptr); + + REQUIRE(accessor.getFileReaderType() == pappso::FileReaderType::tims_ms2); + + pappso::TimsMsRunReaderMs2 *tims_reader = + dynamic_cast(p_msreader.get()); + REQUIRE(tims_reader != nullptr); + + pappso::TimsDataSp tims_data = tims_reader->getTimsDataSPtr(); + + // std::vector precursor_list = {132929}; + std::vector precursor_list = {31693}; + + // Now craft the mz list. We have an acquisition m/z range from 100 to 1700. + std::vector mz_list; + + // Seed the lower m/z value of the m/z range and push it back to the mz_list. + double mz = 100; + mz_list.push_back(mz); + + // We'll need a precision. + PrecisionPtr precision_p = PrecisionFactory::getPpmInstance(30); + + // Compute the last mz value accounting for the delta (we do not want to + // over-trip the 1700 hard limit. + double last_mz = 1700; + last_mz -= 2 * precision_p->delta(last_mz); + + while(mz < last_mz) + { + mz += 2 * precision_p->delta(mz); + mz_list.push_back(mz); + } + + qDebug() << "The mz_list now has " << mz_list.size() << " m/z values."; + std::cout << "The mz_list now has " << mz_list.size() << " m/z values."; + + std::vector xic_list; + std::vector xic_coord_list; + + clock_t start = clock(); + + for(auto precursor_id : precursor_list) + { + XicCoordSPtr xic_coord_tims_struct_sp = + tims_data.get() + ->getXicCoordTimsFromPrecursorId(precursor_id, + PrecisionFactory::getPpmInstance(30)) + .initializeAndClone(); + + xic_list.push_back(xic_coord_tims_struct_sp); + } + + + for(pappso::pappso_double mz : mz_list) + { + pappso::XicCoordSPtr new_xic_coord = + xic_list[0].get()->initializeAndClone(); + new_xic_coord.get()->mzRange = + pappso::MzRange(mz, PrecisionFactory::getPpmInstance(30.0)); + xic_coord_list.push_back(new_xic_coord); + } + + MsRunXicExtractorInterfaceSp xic_extractor = + MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp( + p_msreader); + xic_extractor.get()->setXicExtractMethod(pappso::XicExtractMethod::sum); + + QTextStream outputStream(stdout, QIODevice::WriteOnly); + UiMonitorText monitor(outputStream); + INFO("monitor.setStatus"); + monitor.setStatus("Now starting the actual XIC extraction"); + + INFO("extractXicCoordSPtrList start"); + + // DO THE EXTRACTION!! + xic_extractor.get()->extractXicCoordSPtrList(monitor, xic_coord_list); + + INFO("extractXicCoordSPtrList stop"); + + qInfo() << QString("Time taken: %1\n") + .arg((double)(clock() - start) / CLOCKS_PER_SEC); + + // At this point we have tens of thousands of XICs performed each time over + // the whole set of frames of the acquisition. + + // A XIC is a total ion current chromatogram for a given m/z value over the + // whole rt range. The XIC is a Trace, with x:rt y:int. And there is such a + // Trace for each m/z value in the mz_list above. + + // If we want a full mass spectral integration over the whole acquisiion, all + // we need to do is iterate in the xic_coord_list, get the m/z value for each + // item in this list and sum all the y values of the XIC Trace. + + Trace full_mass_spectrum_trace; + + for(auto xic_coord : xic_coord_list) + { + double mz = xic_coord->mzRange.getMz(); + double sum_y = xic_coord.get()->xicSptr.get()->sumY(); + + full_mass_spectrum_trace.push_back(DataPoint(mz, sum_y)); + } + + std::cout << "The full mass spectrum for the acquisition:\n" + << full_mass_spectrum_trace.toString().toStdString(); + +#elif USEPAPPSOTREE == 1 + + cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl; + +#endif +} diff -Nru libpappsomspp-0.8.15/tests/test_trace.cpp libpappsomspp-0.8.58/tests/test_trace.cpp --- libpappsomspp-0.8.15/tests/test_trace.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_trace.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -2,6 +2,7 @@ #include +#include #include #include #include @@ -246,10 +247,15 @@ // The returned data point is not valid, then x=-1. REQUIRE(datapoint.x == -1); +#if !defined(__i386__) + + // This test unbelievable does not pass on i386... precision_p = pappso::PrecisionFactory::getDaltonInstance(0.00009); datapoint = trace.containsX(1233.5678, precision_p); REQUIRE(datapoint.isValid() == true); REQUIRE(datapoint.x == 1233.56789); + +#endif } SECTION("Get DataPoint having min y value of all.", "[Trace]") @@ -612,8 +618,8 @@ Trace trace(data_point_vector); std::vector::const_iterator const_iterator = - // I (FR) find the test ill-conceived because if the user passes trace.end() as - // the start iterator, then it does not work. + // I (FR) find the test ill-conceived because if the user passes + // trace.end() as the start iterator, then it does not work. moveLowerYLeftDataPoint(trace, std::prev(trace.end())); REQUIRE(const_iterator->x == 610.11000); diff -Nru libpappsomspp-0.8.15/tests/test_trace_filters.cpp libpappsomspp-0.8.58/tests/test_trace_filters.cpp --- libpappsomspp-0.8.15/tests/test_trace_filters.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_trace_filters.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -23,10 +23,12 @@ * ******************************************************************************/ -// make test ARGS="-V -I 20,20" +// make test ARGS="-V -I 1,1" -#define CATCH_CONFIG_MAIN +// ./tests/catch2-only-tests [filters] -s + +//#define CATCH_CONFIG_MAIN #include #include #include @@ -64,7 +66,7 @@ readMgf(QString(CMAKE_SOURCE_DIR) .append("/tests/data/peaklist_15046_simple_xt.mgf")); //.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100); - cout << endl << "..:: FilterGreatestY ::.." << endl; + cout << std::endl << "..:: FilterGreatestY ::.." << std::endl; qDebug(); MassSpectrum most_intense(spectrum_simple); @@ -72,7 +74,7 @@ REQUIRE(most_intense.size() == 10); - qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"; + qDebug(); most_intense = spectrum_simple; most_intense.massSpectrumFilter( pappso::MassSpectrumFilterGreatestItensities(10)); @@ -90,7 +92,7 @@ REQUIRE(most_intense.size() == 100); qDebug(); // 3.018830 - cout << endl << "..:: resample filters ::.." << endl; + cout << std::endl << "..:: resample filters ::.." << std::endl; Trace deca_suite({DataPoint(0, 1), DataPoint(1, 2), DataPoint(2, 3), @@ -147,7 +149,7 @@ deca = deca_suite; deca.filter(FilterResampleKeepGreater(9)); REQUIRE(deca == deca_greater); - cout << endl << "..:: morpho filters ::.." << endl; + cout << std::endl << "..:: morpho filters ::.." << std::endl; deca = deca_suite; deca.filter(FilterMorphoMedian(1)); @@ -165,10 +167,10 @@ DataPoint(11, 5), DataPoint(12, 6)}); REQUIRE(deca.size() == deca_median.size()); - cout << "deca.size() == deca_median.size() " << deca.size() << endl; + cout << "deca.size() == deca_median.size() " << deca.size() << std::endl; REQUIRE(deca == deca_median); - cout << endl << "..:: FilterTandemDeisotope ::.." << endl; + cout << std::endl << "..:: FilterTandemDeisotope ::.." << std::endl; qDebug(); MassSpectrum remove_tandem_deisotope = MassSpectrum(spectrum_simple) @@ -205,7 +207,7 @@ ion_list.push_back(PeptideIon::b); qDebug(); - cout << endl << "..:: FilterRemoveC13 ::.." << endl; + cout << std::endl << "..:: FilterRemoveC13 ::.." << std::endl; qDebug(); MassSpectrum remove_c13 = MassSpectrum(spectrum_simple) @@ -238,10 +240,10 @@ ion_list, true); cout << "peptide " << pep15968.getSequence().toStdString() - << " hyperscore15968=" << hyperscore15968.getHyperscore() << endl; + << " hyperscore15968=" << hyperscore15968.getHyperscore() << std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; XtandemHyperscore hyperscore15968_remove_c13( *spectrum_removed_c13.getMassSpectrumSPtr().get(), @@ -252,13 +254,14 @@ true); cout << "peptide " << pep15968.getSequence().toStdString() << " hyperscore15968_remove_c13=" - << hyperscore15968_remove_c13.getHyperscore() << endl; + << hyperscore15968_remove_c13.getHyperscore() << std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; - cout << endl << "..:: FilterMassSpectrumComplementIonEnhancer ::.." << endl; + cout << std::endl + << "..:: FilterMassSpectrumComplementIonEnhancer ::.." << std::endl; qDebug(); QualifiedMassSpectrum spectrum_complement_ion = @@ -286,13 +289,14 @@ true); cout << "peptide " << pep15968.getSequence().toStdString() << " hyperscore15968_complement_ion_enhancer=" - << hyperscore15968_complement_ion_enhancer.getHyperscore() << endl; + << hyperscore15968_complement_ion_enhancer.getHyperscore() + << std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) - << endl; + << std::endl; - cout << endl << "..:: FilterGreatestYperWindow ::.." << endl; + cout << std::endl << "..:: FilterGreatestYperWindow ::.." << std::endl; FilterGreatestYperWindow filter_per_window(40, 2); qDebug(); QualifiedMassSpectrum spectrum_greatest_y_per_window = @@ -312,8 +316,9 @@ qDebug(); - cout << endl - << "..:: FilterGreatestYperWindow on scan_PXD001468.mgf ::.." << endl; + cout << std::endl + << "..:: FilterGreatestYperWindow on scan_PXD001468.mgf ::.." + << std::endl; QualifiedMassSpectrum spectrum_scan_PXD001468 = readQualifiedMassSpectrumMgf( QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_PXD001468.mgf")); @@ -352,27 +357,27 @@ true); cout << "peptide " << pep15968.getSequence().toStdString() << " hyperscore15968_greatest_y_per_window=" - << hyperscore15968_greatest_y_per_window.getHyperscore() << endl; - cout << "peptide " << pep15968.getSequence().toStdString() + << hyperscore15968_greatest_y_per_window.getHyperscore() << + std::endl; cout << "peptide " << pep15968.getSequence().toStdString() << " mz1=" << pep15968.getMz(1) << " mz2=" << pep15968.getMz(2) << endl; */ - cout << endl << "..:: FilterSuiteString ::.." << endl; + cout << std::endl << "..:: FilterSuiteString ::.." << std::endl; std::shared_ptr filter_suite_str = std::make_shared( "chargeDeconvolution|0.02dalton"); - cout << endl + cout << std::endl << "filter_suite_str = " - << filter_suite_str.get()->toString().toStdString() << endl; + << filter_suite_str.get()->toString().toStdString() << std::endl; - cout << endl + cout << std::endl << "..:: FilterChargeDeconvolution from FilterSuiteString ::.." - << endl; + << std::endl; std::shared_ptr filter_charge_deconvolution = @@ -401,14 +406,14 @@ DataPoint(24, 220), // Third DataPoint(62 - MHPLUS, 35)}); - cout << "Transform Trace data" << endl; + cout << "Transform Trace data" << std::endl; filter_charge_deconvolution->filter(loaded_trace); if(loaded_trace != theorical_trace) { cerr << "transformed Trace are different from theorical trace :" - << endl; + << std::endl; if(loaded_trace.xValues().size() == theorical_trace.xValues().size()) { @@ -418,14 +423,14 @@ cerr << "(" << loaded_trace.xValues()[i] << ", " << loaded_trace.yValues()[i] << ") "; } - cerr << endl; + cerr << std::endl; cerr << "theorical trace : \t"; for(std::size_t i = 0; i < theorical_trace.xValues().size(); i++) { cerr << "(" << theorical_trace.xValues()[i] << ", " << theorical_trace.yValues()[i] << ") "; } - cerr << endl; + cerr << std::endl; } else { @@ -436,8 +441,10 @@ } REQUIRE(loaded_trace == theorical_trace); - - cout << endl << "..:: FilterMorphoAntiSpike filters ::.." << endl; + } + SECTION("..:: test FilterMorphoAntiSpike ::..", "[filters]") + { + // MESSAGE("..:: FilterMorphoAntiSpike filters ::.."); Trace anti_spike_trace({DataPoint(0, 0), DataPoint(1, 1), DataPoint(2, 3), @@ -456,6 +463,63 @@ REQUIRE(anti_spike_trace[9].y == 0); REQUIRE(anti_spike_trace[2].y == 3); - cout << endl << anti_spike_trace.toString().toStdString() << endl; + // cout << std::endl << anti_spike_trace.toString().toStdString() << + // std::endl; + + INFO("filter_anti_spike_too_big"); + FilterMorphoAntiSpike filter_anti_spike_too_big(7); + filter_anti_spike_too_big.filter(anti_spike_trace); + } + + SECTION("..:: check empty trace ::..", "[filters]") + { + // MESSAGE("..:: FilterMorphoAntiSpike filters ::.."); + Trace empty_trace; + FilterMorphoMean m_smooth(3); + + REQUIRE_NOTHROW(m_smooth.filter(empty_trace)); + + + FilterMorphoMinMax m_minMax(5); + REQUIRE_NOTHROW(m_minMax.filter(empty_trace)); + + FilterMorphoMaxMin m_maxMin(5); + REQUIRE_NOTHROW(m_maxMin.filter(empty_trace)); + + Trace xic; + xic.push_back(DataPoint(1434.7806210000, 85.9931205504)); + xic.push_back(DataPoint(1586.4034760000, 162.9869610431)); + xic.push_back(DataPoint(1643.5517360000, 84.9932005440)); + xic.push_back(DataPoint(1645.8830080000, 98.9920806335)); + + FilterMorphoMaxMin m_maxMin2(2); + REQUIRE_NOTHROW(m_maxMin2.filter(xic)); + } + + SECTION("..:: check FilterQuantileBasedRemoveY ::..", "[filters]") + { + + Trace xic_PXD0014777 = + *(readQualifiedMassSpectrumMgf( + QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/PXD014777_xic.tsv")) + .getMassSpectrumSPtr() + .get()); + + REQUIRE(Approx(62.43).epsilon(0.01) == + quantileYTrace(xic_PXD0014777.begin(), xic_PXD0014777.end(), 0.1)); + REQUIRE(Approx(250.75).epsilon(0.01) == + quantileYTrace(xic_PXD0014777.begin(), xic_PXD0014777.end(), 0.5)); + REQUIRE(Approx(136.96).epsilon(0.01) == + quantileYTrace(xic_PXD0014777.begin(), xic_PXD0014777.end(), 0.3)); + + + FilterQuantileBasedRemoveY quantile(0.1); + xic_PXD0014777 = quantile.filter(xic_PXD0014777); + + + QFile fnew("quantile_trace.tsv"); + fnew.open(QFile::WriteOnly | QFile::Text); + QTextStream out(&fnew); + out << xic_PXD0014777.toString(); } } diff -Nru libpappsomspp-0.8.15/tests/test_uimonitor.cpp libpappsomspp-0.8.58/tests/test_uimonitor.cpp --- libpappsomspp-0.8.15/tests/test_uimonitor.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_uimonitor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,72 @@ +// +// File: test_uimonitor.cpp +// Created by: Olivier Langella +// Created on: 25/9/2021 +// +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + + +// make test ARGS="-V -I 1,1" + +// ./tests/catch2-only-tests [uimonitor] -s + + +#include +#include +#include +#include + +using namespace pappso; +using namespace std; + + +TEST_CASE("UiMonitor test suite.", "[uimonitor]") +{ + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + SECTION("..:: UiMonitorTextPercent ::..", "[uimonitor]") + { + QTextStream output(stdout, QIODevice::WriteOnly); + UiMonitorTextPercent monitor(output); + + monitor.setTotalSteps(20); + for(int i = 0; i < 20; i++) + { + monitor.count(); + } + + monitor.setTotalSteps(0); + for(int i = 0; i < 20; i++) + { + monitor.count(); + } + + + monitor.setTotalSteps(100); + for(int i = 0; i < 20; i++) + { + monitor.count(); + } + monitor.setTotalSteps(0); + } +} diff -Nru libpappsomspp-0.8.15/tests/test_xic.cpp libpappsomspp-0.8.58/tests/test_xic.cpp --- libpappsomspp-0.8.15/tests/test_xic.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_xic.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -22,10 +22,14 @@ *implementation ******************************************************************************/ -// make test ARGS="-V -I 4,4" +// make test ARGS="-V -I 1,1" -#define CATCH_CONFIG_MAIN +// ./tests/catch2-only-tests [XIC] -s +// ./tests/catch2-only-tests [tracepeaklist] -s + + +//#define CATCH_CONFIG_MAIN #include #include #include @@ -35,7 +39,9 @@ #include #include #include +#include #include +#include #include #include #include @@ -101,7 +107,7 @@ virtual void setCell(const OdsCell &cell) override { - // qDebug() << "CustomHandler::setCell " << cell.toString(); + qDebug() << "CustomHandler::setCell " << cell.toString(); if(cell.isDouble()) { if(_xic_element.x < 0) @@ -121,7 +127,7 @@ * callback that report the end of the ODS document. Override it if you need * to know that reading is finished. */ - virtual void endDocument(){}; + virtual void endDocument() override{}; private: bool _is_title = true; @@ -255,9 +261,9 @@ SECTION("..:: Test XIC ::..", "[XIC]") { qDebug() << "init test XIC"; - cout << endl << "..:: Test XIC ::.." << endl; + cout << std::endl << "..:: Test XIC ::.." << std::endl; // BSA - cout << endl << "..:: read XIC xic.ods ::.." << endl; + cout << std::endl << "..:: read XIC xic.ods ::.." << std::endl; Xic xic_test; try { @@ -270,7 +276,7 @@ throw error; } - cout << endl << "..:: Test smooth filter ::.." << endl; + cout << std::endl << "..:: Test smooth filter ::.." << std::endl; FilterMorphoMean smooth(3); Xic xic_smooth(xic_test); smooth.filter(xic_smooth); @@ -291,7 +297,7 @@ } */ - cout << endl << "..:: spike filter ::.." << endl; + cout << std::endl << "..:: spike filter ::.." << std::endl; qDebug() << "spike filter"; FilterMorphoAntiSpike spike(3); Xic xic_spike(xic_test); @@ -300,7 +306,7 @@ QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/xic_spike.ods"), xic_spike); - cout << endl << "..:: peak detection ::.." << endl; + cout << std::endl << "..:: peak detection ::.." << std::endl; INFO("peak detection"); Xic xicprm_test; readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/prm_xic.ods"), @@ -383,32 +389,32 @@ realfilemoulondetectods.close(); - cout << endl << "..:: Test MinMax on onexicpeak ::.." << endl; + cout << std::endl << "..:: Test MinMax on onexicpeak ::.." << std::endl; Xic onexicpeak; readOdsXic( QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/onexicpeak.ods"), onexicpeak); - cout << endl << "..:: xic distance ::.." << endl; + cout << std::endl << "..:: xic distance ::.." << std::endl; - cout << endl + cout << std::endl << "distance 3757, 3758 : " - << onexicpeak.getMsPointDistance(3757.0, 3758.0) << endl; + << onexicpeak.getMsPointDistance(3757.0, 3758.0) << std::endl; REQUIRE(onexicpeak.getMsPointDistance(3757.0, 3758.0) == 2); - cout << endl + cout << std::endl << "distance 3757, 3757.14 : " - << onexicpeak.getMsPointDistance(3757.0, 3757.14) << endl; + << onexicpeak.getMsPointDistance(3757.0, 3757.14) << std::endl; REQUIRE(onexicpeak.getMsPointDistance(3757.0, 3757.14) == 0); - cout << endl + cout << std::endl << "distance 3758.26, 3759.61: " - << onexicpeak.getMsPointDistance(3758.26, 3759.61) << endl; + << onexicpeak.getMsPointDistance(3758.26, 3759.61) << std::endl; REQUIRE(onexicpeak.getMsPointDistance(3758.26, 3759.61) == 1); - cout << endl + cout << std::endl << "distance 3758.26, -1: " - << onexicpeak.getMsPointDistance(3758.26, -1) << endl; + << onexicpeak.getMsPointDistance(3758.26, -1) << std::endl; FilterMorphoMinMax minmax(4); Xic xic_minmax(onexicpeak); //"close" courbe du haut @@ -434,3 +440,132 @@ // onexicpeak); } } + +TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]") +{ + + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + SECTION("detection on empty XIC", "[tracepeaklist]") + { + + INFO("peak detection"); + Xic empty_xic; + TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000); + TracePeakList peak_list; + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + + empty_xic.resize(2); + fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1)); + + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + + empty_xic.resize(3); + fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1)); + + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + + empty_xic.resize(4); + fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1)); + + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + + + empty_xic.resize(5); + fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1)); + std::size_t i = 0; + for(auto &dp : empty_xic) + { + dp.x = i; + i++; + } + + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + + + empty_xic.resize(6); + fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1)); + i = 0; + for(auto &dp : empty_xic) + { + dp.x = i; + i++; + } + + _zivy.detect(empty_xic, peak_list); + REQUIRE(peak_list.size() == 0); + } + SECTION("test for masschroq issue#15", "[tracepeaklist]") + { + Xic xic; + xic.push_back(DataPoint(1434.7806210000, 85.9931205504)); + xic.push_back(DataPoint(1586.4034760000, 162.9869610431)); + xic.push_back(DataPoint(1643.5517360000, 84.9932005440)); + xic.push_back(DataPoint(1645.8830080000, 98.9920806335)); + INFO("MassChroQ issue #15"); + + TraceDetectionZivy zivy15(2, 4, 3, 5000, 3000); + TracePeakList peak_list; + qDebug(); + zivy15.detect(xic, peak_list); + qDebug(); + REQUIRE(peak_list.size() == 0); + } + SECTION("test operations on tracepeaklist", "[tracepeaklist]") + { + + INFO("peak detection"); + TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000); + TracePeakList peak_list; + + + Xic xicprm_test; + readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic.ods"), + xicprm_test); + + INFO("readOdsXic OK"); + REQUIRE_NOTHROW(_zivy.detect(xicprm_test, peak_list)); + + REQUIRE(peak_list.size() == 64); + + REQUIRE(findTracePeakGivenRt(peak_list.begin(), peak_list.end(), 2300) == + peak_list.end()); + + REQUIRE(findTracePeakGivenRt(peak_list.begin(), peak_list.end(), 2380) + ->getArea() == Approx(453563.50999997)); + + + REQUIRE(findTracePeakGivenRt(peak_list.begin(), peak_list.end(), 4754) == + peak_list.end()); + + REQUIRE(findTracePeakGivenRt(peak_list.begin(), peak_list.end(), 5460) == + peak_list.end()); + std::size_t nb_match; + REQUIRE(findBestTracePeakGivenRtList( + peak_list.begin(), peak_list.end(), {4754, 4760, 4761}, nb_match) + ->getArea() == Approx(3698171.81499959)); + REQUIRE(nb_match == 1); + REQUIRE( + findBestTracePeakGivenRtList( + peak_list.begin(), peak_list.end(), {4754, 4760, 4761, 5000}, nb_match) + ->getArea() == Approx(5664123.33000009)); + REQUIRE(nb_match == 2); + REQUIRE(findBestTracePeakGivenRtList( + peak_list.begin(), peak_list.end(), {4754, 5460}, nb_match) == + peak_list.end()); + REQUIRE(nb_match == 0); + + + TracePeakList empty_peak_list; + REQUIRE(findBestTracePeakGivenRtList(empty_peak_list.begin(), + empty_peak_list.end(), + {4754, 5460}, + nb_match) == empty_peak_list.end()); + REQUIRE(nb_match == 0); + } +} diff -Nru libpappsomspp-0.8.15/tests/test_xicextractor.cpp libpappsomspp-0.8.58/tests/test_xicextractor.cpp --- libpappsomspp-0.8.15/tests/test_xicextractor.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_xicextractor.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -30,13 +30,16 @@ #include #include #include +#include +#include #include +#include #include #include #include "config.h" //#include "common.h" -// make test ARGS="-V -I 18,18" +// make test ARGS="-V -I 19,19" using namespace std; @@ -47,13 +50,13 @@ // QCoreApplication a(argc, argv); qDebug() << "init test XIC extractor"; - cout << endl << "..:: Test XIC ::.." << endl; - QTime timer; + cout << std::endl << "..:: Test XIC ::.." << std::endl; + QElapsedTimer timer; #if USEPAPPSOTREE == 1 pappso::MsFileAccessor file_access( //"/gorgone/pappso/data_extraction_pappso/mzXML/" - "/espace/bio/mzxml/" + "/home/langella/data1/mzxml/" "20120906_balliau_extract_1_A01_urnb-1.mzXML", "file"); pappso::MsRunReaderSPtr msrun = @@ -62,6 +65,15 @@ pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp"); pappso::MzRange mass_range(600, pappso::PrecisionFactory::getPpmInstance(10)); + + pappso::XicCoordSPtr xic_coord = + msrun.get()->newXicCoordSPtrFromSpectrumIndex( + 3000, pappso::PrecisionFactory::getPpmInstance(10)); + + xic_coord.get()->mzRange = mass_range; + + std::vector xic_coord_list; + xic_coord_list.push_back(xic_coord.get()->initializeAndClone()); // MassRange mass_range_b(600.2, Precision::getPpmInstance(10)); pappso::MsRunXicExtractorInterfaceSp extractor_pwiz = @@ -70,63 +82,84 @@ extractor_pwiz->setXicExtractMethod(pappso::XicExtractMethod::max); - pappso::XicCstSPtr xic_pwiz = extractor_pwiz.get()->getXicCstSPtr(mass_range); - cout << endl << "..:: XIC extractor pwiz is OK ::.." << endl; + QTextStream outputStream(stdout, QIODevice::WriteOnly); + pappso::UiMonitorText monitor(outputStream); + extractor_pwiz.get()->extractXicCoordSPtrList(monitor, xic_coord_list); + pappso::XicCstSPtr xic_pwiz = xic_coord_list[0].get()->xicSptr; + + cout << std::endl << "..:: XIC extractor pwiz is OK ::.." << std::endl; - cout << endl << "building XicExtractorDiskSp .." << endl; + cout << std::endl << "building XicExtractorDiskSp .." << std::endl; timer.start(); + pappso::MsRunXicExtractorFactory::getInstance() + .setMsRunXicExtractorFactoryType( + pappso::MsRunXicExtractorFactoryType::disk); pappso::MsRunXicExtractorInterfaceSp extractor_disk = - pappso::MsRunXicExtractorFactory::getInstance() - .buildMsRunXicExtractorDiskSp(msrun); - cout << endl + pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp( + msrun); + cout << std::endl << "XicExtractorDiskSp built " << timer.elapsed() / 1000 << " seconds" - << endl; + << std::endl; + - pappso::XicCstSPtr xic_disk = extractor_disk.get()->getXicCstSPtr(mass_range); + xic_coord_list.clear(); + xic_coord_list.push_back(xic_coord.get()->initializeAndClone()); + extractor_disk.get()->extractXicCoordSPtrList(monitor, xic_coord_list); + + pappso::XicCstSPtr xic_disk = xic_coord_list[0].get()->xicSptr; if(*xic_pwiz != *xic_disk) { - cerr << "*xic_pwiz != *xic_disk ERROR" << endl; + cerr << "*xic_pwiz != *xic_disk ERROR" << std::endl; for(std::size_t i = 0; i < xic_pwiz->size(); i++) { cerr << "i=" << i << " x=" << (*xic_pwiz)[i].x << " y=" << (*xic_pwiz)[i].y << " x=" << (*xic_disk)[i].x - << " y=" << (*xic_disk)[i].y << endl; + << " y=" << (*xic_disk)[i].y << std::endl; } return 1; } - cout << endl << "..:: XIC extractor on disk is OK ::.." << endl; + cout << std::endl << "..:: XIC extractor on disk is OK ::.." << std::endl; // return 0; - cout << endl << "building XicExtractorDiskBufferSp .." << endl; + cout << std::endl << "building XicExtractorDiskBufferSp .." << std::endl; timer.restart(); + + pappso::MsRunXicExtractorFactory::getInstance() + .setMsRunXicExtractorFactoryType( + pappso::MsRunXicExtractorFactoryType::diskbuffer); pappso::MsRunXicExtractorInterfaceSp extractor_buffer = - pappso::MsRunXicExtractorFactory::getInstance() - .buildMsRunXicExtractorDiskBufferSp(msrun); - cout << endl + pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp( + msrun); + cout << std::endl << "XicExtractorDiskBufferSp built " << timer.elapsed() / 1000 - << " seconds" << endl; + << " seconds" << std::endl; + + + xic_coord_list.clear(); + xic_coord_list.push_back(xic_coord.get()->initializeAndClone()); + extractor_buffer.get()->extractXicCoordSPtrList(monitor, xic_coord_list); + + pappso::XicCstSPtr xic_buffer = xic_coord_list[0].get()->xicSptr; - pappso::XicCstSPtr xic_buffer = - extractor_buffer.get()->getXicCstSPtr(mass_range); if(*xic_pwiz != *xic_buffer) { - cerr << "*xic_pwiz != *xic_buffer ERROR" << endl; + cerr << "*xic_pwiz != *xic_buffer ERROR" << std::endl; /* for(std::size_t i = 0; i < xic_pwiz->size(); i++) { cerr << "i=" << i << " " << (*xic_pwiz)[i].y << " " - << (*xic_buffer)[i].y << endl; + << (*xic_buffer)[i].y << std::endl; } */ return 1; } - cout << endl << "..:: XIC extractor buffered on disk is OK ::.." << endl; + cout << std::endl << "..:: XIC extractor buffered on disk is OK ::.." << std::endl; #endif return 0; } diff -Nru libpappsomspp-0.8.15/tests/test_xtandem_spectrum.cpp libpappsomspp-0.8.58/tests/test_xtandem_spectrum.cpp --- libpappsomspp-0.8.15/tests/test_xtandem_spectrum.cpp 2020-12-22 01:35:32.000000000 +0000 +++ libpappsomspp-0.8.58/tests/test_xtandem_spectrum.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -56,13 +56,13 @@ SECTION("..:: readMgf ::..", "[xtandemspectrum]") { - cout << endl - << "..:: readMgf ::.." << QDir::currentPath().toStdString() << endl; + cout << std::endl + << "..:: readMgf ::.." << QDir::currentPath().toStdString() << std::endl; MassSpectrum spectrum = readMgf( QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf")); - cout << spectrum.toString().toStdString() << endl; + cout << spectrum.toString().toStdString() << std::endl; MassSpectrum spectrum_orig(spectrum); REQUIRE(spectrum.equals(spectrum_orig, PrecisionFactory::getDaltonInstance(0.00002))); diff -Nru libpappsomspp-0.8.15/tests/widget/CMakeLists.txt libpappsomspp-0.8.58/tests/widget/CMakeLists.txt --- libpappsomspp-0.8.15/tests/widget/CMakeLists.txt 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/widget/CMakeLists.txt 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,39 @@ + +# Find includes in corresponding build directories +set(CMAKE_INCLUDE_CURRENT_DIR ON) +# Instruct CMake to run moc automatically when needed. +set(CMAKE_AUTOMOC ON) + + + +find_package( Qt5 COMPONENTS Core Gui Widgets REQUIRED ) + +# File list +set(CPP_FILES +) + +#################################### +# GUI +######################################### +set(TESTWIDGET_GUI_SRCS + testwidgetgui.cpp + main.cpp +) + +set (GUI_UIS + uitestwidgetgui.ui +) + + +# this will run uic on .ui files: +qt5_wrap_ui( GUI_UI_HDRS ${GUI_UIS} ) +#qt5_add_resources(deepprot_RCC_SRCS deepprot.qrc) +add_executable(testwidgetgui ${TESTWIDGET_GUI_SRCS} ${GUI_UI_HDRS}) + +target_link_libraries(testwidgetgui + pappsomspp-shared + pappsomspp-widget-shared + Qt5::Core + Qt5::Gui + Qt5::Widgets +) diff -Nru libpappsomspp-0.8.15/tests/widget/main.cpp libpappsomspp-0.8.58/tests/widget/main.cpp --- libpappsomspp-0.8.15/tests/widget/main.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/widget/main.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,70 @@ +/** + * \file pappsomspp/tests/widget/main.cpp + * \date 17/04/2021 + * \author Olivier Langella + * \brief launch minimalist GUI to test widgets + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include +#include +#include "testwidgetgui.h" + +using namespace std; + +int +main(int argc, char *argv[]) +{ + // Set the debugging message formatting pattern. + qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}")); + + QTextStream errorStream(stderr, QIODevice::WriteOnly); + QApplication app(argc, argv); + + try + { + QCoreApplication::setOrganizationName("PAPPSO"); + QCoreApplication::setOrganizationDomain("pappso.inrae.fr"); + QCoreApplication::setApplicationName("test Widget"); + TestWidgetGui window; + window.show(); + + return app.exec(); + } + catch(pappso::PappsoException &error) + { + errorStream << "Oops! an error occurred in Test Widget. Dont Panic :" + << Qt::endl; + errorStream << error.qwhat() << Qt::endl; + app.exit(1); + } + + catch(std::exception &error) + { + errorStream << "Oops! an error occurred in Test Widget. Dont Panic :" + << Qt::endl; + errorStream << error.what() << Qt::endl; + app.exit(1); + } +} diff -Nru libpappsomspp-0.8.15/tests/widget/testwidgetgui.cpp libpappsomspp-0.8.58/tests/widget/testwidgetgui.cpp --- libpappsomspp-0.8.15/tests/widget/testwidgetgui.cpp 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/widget/testwidgetgui.cpp 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,48 @@ +/** + * \file pappsomspp/tests/widget/testwidgetgui.cpp + * \date 17/04/2021 + * \author Olivier Langella + * \brief minimalist main window to test widgets + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#include "testwidgetgui.h" +#include "ui_uitestwidgetgui.h" +#include + +TestWidgetGui::TestWidgetGui(QWidget *parent) + : QMainWindow(parent), ui(new Ui::TestWidgetMainWindow) +{ + qDebug(); + ui->setupUi(this); + /* + ui->oboChooserWidget->setMzTarget(100); + ui->oboChooserWidget->setPrecision( + pappso::PrecisionFactory::getDaltonInstance(0.02)); + */ +} + +TestWidgetGui::~TestWidgetGui() +{ +} diff -Nru libpappsomspp-0.8.15/tests/widget/testwidgetgui.h libpappsomspp-0.8.58/tests/widget/testwidgetgui.h --- libpappsomspp-0.8.15/tests/widget/testwidgetgui.h 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/widget/testwidgetgui.h 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,55 @@ +/** + * \file pappsomspp/tests/widget/testwidgetgui.h + * \date 17/04/2021 + * \author Olivier Langella + * \brief minimalist main window to test widgets + */ + + +/******************************************************************************* + * Copyright (c) 2021 Olivier Langella + *. + * + * This file is part of the PAPPSOms++ library. + * + * PAPPSOms++ is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * PAPPSOms++ is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with PAPPSOms++. If not, see . + * + ******************************************************************************/ + +#pragma once + +#include + + +namespace Ui +{ +class TestWidgetMainWindow; +} + + +/** + * @todo write docs + */ +class TestWidgetGui : public QMainWindow +{ + Q_OBJECT + + public: + explicit TestWidgetGui(QWidget *parent = 0); + ~TestWidgetGui(); + + + private: + Ui::TestWidgetMainWindow *ui; +}; diff -Nru libpappsomspp-0.8.15/tests/widget/uitestwidgetgui.ui libpappsomspp-0.8.58/tests/widget/uitestwidgetgui.ui --- libpappsomspp-0.8.15/tests/widget/uitestwidgetgui.ui 1970-01-01 00:00:00.000000000 +0000 +++ libpappsomspp-0.8.58/tests/widget/uitestwidgetgui.ui 2022-10-27 09:16:15.000000000 +0000 @@ -0,0 +1,52 @@ + + + TestWidgetMainWindow + + + + 0 + 0 + 800 + 600 + + + + MainWindow + + + + + + + Obo term list + + + + + + + + + + + + 0 + 0 + 800 + 24 + + + + + + + + pappso::OboChooserWidget + QWidget +
pappsomspp/widget/obo/obochooserwidget/obochooserwidget.h
+ 1 + + + + +