System OS: Windows 11, Architecture: AMD64
Java Info: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
.NET Core Info: 6.0.36


Version info:
FragPipe version 20.0
MSFragger version 3.8
IonQuant version 1.9.8
Philosopher version 5.0.0


LCMS files:
  Experiment/Group: 210803ko03IgG_IP_Slot1_01_1_16316
  - J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d	DDA
  Experiment/Group: 210803ko05Rad21_IP_Slot1_01_1_16318
  - J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d	DDA
  Experiment/Group: 210803ko07Stag3_IP_Slot1_01_1_16320
  - J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d	DDA


41 commands to execute:
CheckCentroid
java -Xmx49G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d 15
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\94ee91ae-c0cb-45f0-8eca-6a5afed1c896
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\c96d6df7-e905-4646-ab10-c2443a3640d7
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\4cabbefc-a72a-453e-aadb-ccee77c336f8
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\2659f332-a5af-4446-9bb5-599b33014ce4
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx49G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318.pin
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320.pepXML
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv --decoy-results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko07Stag3_IP_Slot1-01_1_16320.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv --decoy-results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko05Rad21_IP_Slot1-01_1_16318.pin
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv --decoy-results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko03IgG_IP_Slot1-01_1_16316.pin
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko07Stag3_IP_Slot1-01_1_16320.pin 210803ko07Stag3_IP_Slot1-01_1_16320 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv interact-210803ko07Stag3_IP_Slot1-01_1_16320 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko05Rad21_IP_Slot1-01_1_16318.pin 210803ko05Rad21_IP_Slot1-01_1_16318 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv interact-210803ko05Rad21_IP_Slot1-01_1_16318 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko03IgG_IP_Slot1-01_1_16316.pin 210803ko03IgG_IP_Slot1-01_1_16316 210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv 210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv interact-210803ko03IgG_IP_Slot1-01_1_16316 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316_uncalibrated.mzML
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas --prefix rev_
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --razor
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --razor
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
java -Xmx49G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [CheckCentroid], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
    Cmd: [WorkspaceCleanInit], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
    Cmd: [MSFragger], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [Percolator], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [ProteinProphet], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [PhilosopherDbAnnotate], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [PhilosopherFilter], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [PhilosopherReport], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
    Cmd: [WorkspaceClean], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
    Cmd: [IonQuant], Work dir: [J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]

~~~~~~~~~~~~~~~~~~~~~~

~~~~~~Sample of D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas~~~~~~~
>rev_sp|A0A087WPF7|AUTS2_MOUSE Autism susceptibility gene 2 protein homolog OS=Mus musculus OX=10090 GN=Auts2 PE=1 SV=2
>rev_sp|O88998|NOE1_MOUSE Noelin OS=Mus musculus OX=10090 GN=Olfm1 PE=1 SV=1
>rev_sp|P43267|SOX15_MOUSE Protein SOX-15 OS=Mus musculus OX=10090 GN=Sox15 PE=1 SV=3
>rev_sp|Q08ED0|B2L15_MOUSE Bcl-2-like protein 15 OS=Mus musculus OX=10090 GN=Bcl2l15 PE=2 SV=2
>rev_sp|Q60898|SLAP1_MOUSE Src-like-adapter OS=Mus musculus OX=10090 GN=Sla PE=1 SV=3
>rev_sp|Q7TNS2|MIC10_MOUSE MICOS complex subunit Mic10 OS=Mus musculus OX=10090 GN=Micos10 PE=1 SV=1
>rev_sp|Q8BY79|S35G1_MOUSE Solute carrier family 35 member G1 OS=Mus musculus OX=10090 GN=Slc35g1 PE=2 SV=1
>rev_sp|Q8R4U1|MYPOP_MOUSE Myb-related transcription factor, partner of profilin OS=Mus musculus OX=10090 GN=Mypop PE=1 SV=1
>rev_sp|Q9CQ60|6PGL_MOUSE 6-phosphogluconolactonase OS=Mus musculus OX=10090 GN=Pgls PE=1 SV=1
>rev_sp|Q9EQ20|MMSA_MOUSE Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Mus musculus OX=10090 GN=Aldh6a1 PE=1 SV=1
>rev_sp|T1NXB5|VSTM4_MOUSE V-set and transmembrane domain-containing protein 4 OS=Mus musculus OX=10090 GN=Vstm4 PE=1 SV=1
>sp|O88990|ACTN3_MOUSE Alpha-actinin-3 OS=Mus musculus OX=10090 GN=Actn3 PE=2 SV=1
>sp|P43241|CDX2_MOUSE Homeobox protein CDX-2 OS=Mus musculus OX=10090 GN=Cdx2 PE=1 SV=1
>sp|Q08AU9|CQ058_MOUSE UPF0450 protein C17orf58 homolog OS=Mus musculus OX=10090 PE=3 SV=1
>sp|Q60893|OL151_MOUSE Olfactory receptor 151 OS=Mus musculus OX=10090 GN=Olfr151 PE=2 SV=2
>sp|Q7TNP2|2AAB_MOUSE Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform OS=Mus musculus OX=10090 GN=Ppp2r1b PE=1 SV=2
>sp|Q8BY35|FGD2_MOUSE FYVE, RhoGEF and PH domain-containing protein 2 OS=Mus musculus OX=10090 GN=Fgd2 PE=1 SV=1
>sp|Q8R4T1|CYS1_MOUSE Cystin-1 OS=Mus musculus OX=10090 GN=Cys1 PE=1 SV=1
>sp|Q9CQ54|NDUC2_MOUSE NADH dehydrogenase [ubiquinone] 1 subunit C2 OS=Mus musculus OX=10090 GN=Ndufc2 PE=1 SV=1
>sp|Q9EQ14|IL23A_MOUSE Interleukin-23 subunit alpha OS=Mus musculus OX=10090 GN=Il23a PE=1 SV=1
>sp|Q9Z351|KCNQ2_MOUSE Potassium voltage-gated channel subfamily KQT member 2 OS=Mus musculus OX=10090 GN=Kcnq2 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v20.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Users\\gt5oc\\Proteomics_Data\\Uniprot_data\\MSFragger\\UniprotMouse\\2021-07-15-decoys-reviewed-contam-UP000000589.fas

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=304.207146
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=D\:\\Applications\\FragPipe-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=D\:\\Applications\\FragPipe-20.0\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\gt5oc\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=0
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=trypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=stricttrypsin
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.021465,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 1.0 --ion 1.0 --pep 1.0
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=J\:\\MSFragger_process\\Saitou-lab\\Revision\\210803ko-timsTOF\\MSFragger_iBAQ
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=15

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx49G -cp "D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d 15
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:00:35] Executing Workspace  v5.0.0                  
INFO[15:00:35] Removing workspace                           
WARN[15:00:35] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:00:35] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\94ee91ae-c0cb-45f0-8eca-6a5afed1c896
INFO[15:00:36] Executing Workspace  v5.0.0                  
INFO[15:00:36] Creating workspace                           
INFO[15:00:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:00:36] Executing Workspace  v5.0.0                  
INFO[15:00:36] Removing workspace                           
WARN[15:00:36] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:00:36] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\c96d6df7-e905-4646-ab10-c2443a3640d7
INFO[15:00:37] Executing Workspace  v5.0.0                  
INFO[15:00:37] Creating workspace                           
INFO[15:00:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:00:37] Executing Workspace  v5.0.0                  
INFO[15:00:37] Removing workspace                           
WARN[15:00:37] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:00:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\4cabbefc-a72a-453e-aadb-ccee77c336f8
INFO[15:00:37] Executing Workspace  v5.0.0                  
INFO[15:00:37] Creating workspace                           
INFO[15:00:37] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:00:38] Executing Workspace  v5.0.0                  
INFO[15:00:38] Removing workspace                           
WARN[15:00:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:00:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gt5oc\AppData\Local\Temp\2659f332-a5af-4446-9bb5-599b33014ce4
INFO[15:00:38] Executing Workspace  v5.0.0                  
INFO[15:00:38] Creating workspace                           
INFO[15:00:38] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
java -jar -Dfile.encoding=UTF-8 -Xmx49G D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\fragger.params J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d
MSFragger version MSFragger-3.8
Batmass-IO version 1.28.12
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 11, Architecture: AMD64
Java Info: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 49 GB memory
Checking database...
Checking spectral files...
J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d: Scans = 53935
J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d: Scans = 50111
J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d: Scans = 51876
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d converted with timsdata-2-7-0. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d converted with timsdata-2-7-0. Will use this mzBIN file.
There is a mzBIN file from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d converted with timsdata-2-7-0. Will use this mzBIN file.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
group_variable = 0
require_precursor = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
280170470 fragments to be searched in 1 slices (4.17 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.69 s
	001. 210803ko03IgG_IP_Slot1-01_1_16316.mzBIN 13.0 s | deisotoping 1.2 s
		[progress: 53195/53195 (100%) - 25525 spectra/s] 2.1s | postprocessing 0.3 s
	002. 210803ko05Rad21_IP_Slot1-01_1_16318.mzBIN 9.8 s | deisotoping 0.3 s
		[progress: 55950/55950 (100%) - 63507 spectra/s] 0.9s | postprocessing 0.2 s
	003. 210803ko07Stag3_IP_Slot1-01_1_16320.mzBIN 8.7 s | deisotoping 0.3 s
		[progress: 54045/54045 (100%) - 60930 spectra/s] 0.9s | postprocessing 0.2 s
***************************FIRST SEARCH DONE IN 0.724 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -1.88   4.18 |  -0.08   4.19 |  -3.26   7.58 |  -0.31   7.82  
 002 |  -1.85   3.90 |   0.21   3.94 |  -3.54   7.10 |  -0.55   7.21  
 003 |  -2.33   4.30 |   0.17   4.31 |  -3.58   7.31 |  -0.54   7.46  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  |   3802|   3643| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |   3617|   3701|   3774|   3802|   3789| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   3900
-------|-------
-------|-------
 Rm P. |    1  
-------|-------
 Count |   4115
-------|-------
New fragment_mass_tolerance = 15 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
New intensity_transform = 1
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.747 MIN*********

************************************MAIN SEARCH************************************
output_format = pepXML_pin but report_alternative_proteins = 0. Change report_alternative_proteins to 1.
Checking database...
Parameters:
num_threads = 15
database_name = D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
decoy_prefix = rev_
precursor_mass_lower = -50.0
precursor_mass_upper = 50.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 15.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 1
activation_types = all
group_variable = 0
require_precursor = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.021465
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.08 Da.
280170470 fragments to be searched in 1 slices (4.17 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.98 s
	001. 210803ko03IgG_IP_Slot1-01_1_16316.mzBIN_calibrated 1.0 s
		[progress: 52309/52309 (100%) - 47040 spectra/s] 1.1s | remapping alternative proteins and postprocessing 2.4 s
	002. 210803ko05Rad21_IP_Slot1-01_1_16318.mzBIN_calibrated 0.9 s
		[progress: 54940/54940 (100%) - 45218 spectra/s] 1.2s | remapping alternative proteins and postprocessing 1.2 s
	003. 210803ko07Stag3_IP_Slot1-01_1_16320.mzBIN_calibrated 0.8 s
		[progress: 53039/53039 (100%) - 45178 spectra/s] 1.2s | remapping alternative proteins and postprocessing 1.2 s
***************************MAIN SEARCH DONE IN 0.241 MIN***************************

*******************************TOTAL TIME 1.711 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.pepXML J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/Applications/FragPipe-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.pin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320.pin
Process 'MSFragger move pin' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv --decoy-results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko07Stag3_IP_Slot1-01_1_16320.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv --decoy-results-psms 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko07Stag3_IP_Slot1-01_1_16320.pin
Started Thu Jan 16 15:02:23 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 210803ko07Stag3_IP_Slot1-01_1_16320.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 10070 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7571 positives and 2499 negatives, size ratio=3.02961 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 2715 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 2656 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 2632 training set positives with q<0.01 in that direction.
Found 4002 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.1160 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 4456 PSMs with q<0.01
Iteration 2:	Estimated 4558 PSMs with q<0.01
Iteration 3:	Estimated 4572 PSMs with q<0.01
Iteration 4:	Estimated 4582 PSMs with q<0.01
Iteration 5:	Estimated 4586 PSMs with q<0.01
Iteration 6:	Estimated 4594 PSMs with q<0.01
Iteration 7:	Estimated 4603 PSMs with q<0.01
Iteration 8:	Estimated 4594 PSMs with q<0.01
Iteration 9:	Estimated 4596 PSMs with q<0.01
Iteration 10:	Estimated 4595 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-1.0432	-0.9300	-1.4560	abs_ppm
-0.5015	-0.4160	-0.4124	isotope_errors
-1.4336	-0.9955	-1.9087	log10_evalue
-0.8295	 0.1573	-0.6895	hyperscore
 1.0250	 0.6741	 0.9593	delta_hyperscore
 3.6471	 1.5774	 2.7952	matched_ion_num
-1.0760	-0.7920	-1.1059	complementary_ions
-0.2614	 0.0739	 0.0788	ion_series
-0.4324	-0.3467	-0.4669	weighted_average_abs_fragment_ppm
-0.3233	-0.3353	-0.2560	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.4634	-0.4646	-0.5303	nmc
-0.0993	-0.1163	-0.0409	charge_1
 0.0803	-0.0190	 0.0800	charge_2
 0.0734	 0.0586	 0.0687	charge_3
-0.2921	-0.0663	-0.3643	charge_4
 0.0680	 0.0480	 0.2077	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.0894	-0.0283	-0.0262	15.9949M
 0.5205	-0.1336	 0.0442	m0
Found 4522 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7571 target PSMs and 2499 decoy PSMs.
Calculating q values.
Final list yields 4529 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.3050 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv --decoy-results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko05Rad21_IP_Slot1-01_1_16318.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv --decoy-results-psms 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko05Rad21_IP_Slot1-01_1_16318.pin
Started Thu Jan 16 15:02:26 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 210803ko05Rad21_IP_Slot1-01_1_16318.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 10721 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7879 positives and 2842 negatives, size ratio=2.77234 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 2446 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 2421 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 2553 training set positives with q<0.01 in that direction.
Found 3687 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.1180 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 4273 PSMs with q<0.01
Iteration 2:	Estimated 4324 PSMs with q<0.01
Iteration 3:	Estimated 4321 PSMs with q<0.01
Iteration 4:	Estimated 4344 PSMs with q<0.01
Iteration 5:	Estimated 4336 PSMs with q<0.01
Iteration 6:	Estimated 4332 PSMs with q<0.01
Iteration 7:	Estimated 4339 PSMs with q<0.01
Iteration 8:	Estimated 4340 PSMs with q<0.01
Iteration 9:	Estimated 4337 PSMs with q<0.01
Iteration 10:	Estimated 4346 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.7607	-0.4931	-0.5769	abs_ppm
-0.2534	-0.2057	-0.2956	isotope_errors
-1.3846	-1.0158	-1.3332	log10_evalue
 0.3943	 0.3389	-0.3918	hyperscore
 0.6278	 0.7656	 0.7843	delta_hyperscore
 1.5289	 1.4379	 2.4762	matched_ion_num
-0.6496	-0.6518	-0.7302	complementary_ions
 0.3184	 0.2451	 0.2456	ion_series
-0.4029	-0.2744	-0.3243	weighted_average_abs_fragment_ppm
 0.0131	 0.0238	 0.0275	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.6875	-0.7180	-0.8055	nmc
-0.0072	-0.0525	-0.0662	charge_1
 0.0343	-0.0215	-0.0503	charge_2
-0.0654	 0.0204	 0.0759	charge_3
-0.0168	-0.0062	-0.0424	charge_4
 0.1610	 0.0524	 0.0407	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.1201	 0.0862	 0.1058	15.9949M
 0.1703	-0.5089	-0.0729	m0
Found 4268 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7879 target PSMs and 2842 decoy PSMs.
Calculating q values.
Final list yields 4282 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.4840 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv --decoy-results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko03IgG_IP_Slot1-01_1_16316.pin
Protein decoy-preix used is rev_sp|
All files have been read
Percolator version 3.06.0, Build Date May 11 2022 12:43:39
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Applications\FragPipe-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 15 --results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv --decoy-results-psms 210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 210803ko03IgG_IP_Slot1-01_1_16316.pin
Started Thu Jan 16 15:02:29 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 210803ko03IgG_IP_Slot1-01_1_16316.pin
Features:
rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 
Found 10438 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7252 positives and 3186 negatives, size ratio=2.27621 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 4 as initial direction. Could separate 1923 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 4 as initial direction. Could separate 2041 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 4 as initial direction. Could separate 1860 training set positives with q<0.01 in that direction.
Found 2881 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.1180 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 3362 PSMs with q<0.01
Iteration 2:	Estimated 3474 PSMs with q<0.01
Iteration 3:	Estimated 3523 PSMs with q<0.01
Iteration 4:	Estimated 3527 PSMs with q<0.01
Iteration 5:	Estimated 3530 PSMs with q<0.01
Iteration 6:	Estimated 3536 PSMs with q<0.01
Iteration 7:	Estimated 3533 PSMs with q<0.01
Iteration 8:	Estimated 3531 PSMs with q<0.01
Iteration 9:	Estimated 3531 PSMs with q<0.01
Iteration 10:	Estimated 3530 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.8408	-1.0001	-1.0147	abs_ppm
-0.3925	-0.5550	-0.5580	isotope_errors
-1.2899	-1.7256	-1.9789	log10_evalue
 0.5614	-0.3282	-0.5713	hyperscore
 0.4690	 0.8244	 0.4170	delta_hyperscore
 1.3206	 2.7942	 2.3803	matched_ion_num
-0.7108	-0.7961	-0.8982	complementary_ions
 0.4630	 0.4790	 0.4732	ion_series
-0.3820	-0.6413	-0.4228	weighted_average_abs_fragment_ppm
 0.0863	-0.1683	-0.1465	peptide_length
 0.0000	 0.0000	 0.0000	ntt
-0.5602	-0.4058	-0.4762	nmc
-0.0706	-0.1266	 0.0598	charge_1
 0.0749	 0.0202	-0.0237	charge_2
-0.0290	 0.0585	-0.0046	charge_3
-0.0704	-0.0925	 0.0555	charge_4
-0.0109	-0.0521	-0.0309	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.1187	 0.0282	-0.0607	15.9949M
-0.6766	-0.2435	-0.8528	m0
Found 3427 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7252 target PSMs and 3186 decoy PSMs.
Calculating q values.
Final list yields 3437 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.2980 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko07Stag3_IP_Slot1-01_1_16320.pin 210803ko07Stag3_IP_Slot1-01_1_16320 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv 210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv interact-210803ko07Stag3_IP_Slot1-01_1_16320 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\210803ko07Stag3_IP_Slot1-01_1_16320_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko05Rad21_IP_Slot1-01_1_16318.pin 210803ko05Rad21_IP_Slot1-01_1_16318 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv 210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv interact-210803ko05Rad21_IP_Slot1-01_1_16318 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\210803ko05Rad21_IP_Slot1-01_1_16318_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 210803ko03IgG_IP_Slot1-01_1_16316.pin 210803ko03IgG_IP_Slot1-01_1_16316 210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv 210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv interact-210803ko03IgG_IP_Slot1-01_1_16316 DDA 0.5 J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Applications\FragPipe-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\210803ko03IgG_IP_Slot1-01_1_16316_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\filelist_proteinprophet.txt
INFO[15:02:36] Executing ProteinProphet  v5.0.0             
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\interact-210803ko03IgG_IP_Slot1-01_1_16316.pep.xml...
...read in 9 1+, 2958 2+, 1128 3+, 72 4+, 12 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\interact-210803ko05Rad21_IP_Slot1-01_1_16318.pep.xml...
...read in 12 1+, 3478 2+, 1551 3+, 168 4+, 46 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\interact-210803ko07Stag3_IP_Slot1-01_1_16320.pep.xml...
...read in 2 1+, 3675 2+, 1401 3+, 89 4+, 26 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 3740 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.....WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9JMH6|TRXR1_MOUSE : U
 
....:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q80TA1|EPT1_MOUSE : U
MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKVFPTWLAPNLITFSGFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYNTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMVGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL
.26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:........  Total: 34386
Computing degenerate peptides for 1800 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 1854 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1854 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1854 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1854 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1854 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.18254e-05, db_size=38845583
Computing MU for 1854 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[15:02:38] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate D:\Users\gt5oc\Proteomics_Data\Uniprot_data\MSFragger\UniprotMouse\2021-07-15-decoys-reviewed-contam-UP000000589.fas --prefix rev_
INFO[15:02:38] Executing Database  v5.0.0                   
INFO[15:02:38] Annotating the database                      
INFO[15:02:38] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --razor
INFO[15:02:38] Executing Filter  v5.0.0                     
INFO[15:02:38] Processing peptide identification files      
INFO[15:02:38] Parsing J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\interact-210803ko03IgG_IP_Slot1-01_1_16316.pep.xml 
INFO[15:02:39] 1+ Charge profile                             decoy=6 target=3
INFO[15:02:39] 2+ Charge profile                             decoy=153 target=2805
INFO[15:02:39] 3+ Charge profile                             decoy=48 target=1080
INFO[15:02:39] 4+ Charge profile                             decoy=8 target=64
INFO[15:02:39] 5+ Charge profile                             decoy=1 target=11
INFO[15:02:39] 6+ Charge profile                             decoy=0 target=0
INFO[15:02:39] Database search results                       ions=1771 peptides=1591 psms=4179
INFO[15:02:39] Converged to 0.99 % FDR with 3439 PSMs        decoy=34 threshold=0.830427 total=3473
INFO[15:02:39] Converged to 14.46 % FDR with 1390 Peptides   decoy=201 threshold=0.500089 total=1591
INFO[15:02:39] Converged to 12.87 % FDR with 1569 Ions       decoy=202 threshold=0.500089 total=1771
INFO[15:02:39] Protein inference results                     decoy=586 target=1091
INFO[15:02:39] Converged to 57.58 % FDR with 1016 Proteins   decoy=585 threshold=0.4996 total=1601
INFO[15:02:39] Applying sequential FDR estimation            ions=1339 peptides=1180 psms=3473
INFO[15:02:39] Converged to 0.99 % FDR with 3439 PSMs        decoy=34 threshold=0.830427 total=3473
INFO[15:02:39] Converged to 2.88 % FDR with 1147 Peptides    decoy=33 threshold=0.830684 total=1180
INFO[15:02:39] Converged to 2.53 % FDR with 1306 Ions        decoy=33 threshold=0.830684 total=1339
INFO[15:02:39] Post processing identifications              
INFO[15:02:39] Assigning protein identifications to layers  
INFO[15:02:39] Processing protein inference                 
INFO[15:02:39] Synchronizing PSMs and proteins              
INFO[15:02:39] Final report numbers after FDR filtering, and post-processing  ions=1306 peptides=1147 proteins=342 psms=3439
INFO[15:02:39] Saving                                       
INFO[15:02:39] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --razor
INFO[15:02:39] Executing Filter  v5.0.0                     
INFO[15:02:39] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 
INFO[15:02:39] Processing peptide identification files      
INFO[15:02:39] Parsing J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\interact-210803ko05Rad21_IP_Slot1-01_1_16318.pep.xml 
INFO[15:02:39] 1+ Charge profile                             decoy=5 target=7
INFO[15:02:39] 2+ Charge profile                             decoy=173 target=3305
INFO[15:02:39] 3+ Charge profile                             decoy=70 target=1481
INFO[15:02:39] 4+ Charge profile                             decoy=19 target=149
INFO[15:02:39] 5+ Charge profile                             decoy=8 target=38
INFO[15:02:39] 6+ Charge profile                             decoy=0 target=0
INFO[15:02:39] Database search results                       ions=1288 peptides=1139 psms=5255
INFO[15:02:39] Converged to 0.98 % FDR with 4286 PSMs        decoy=42 threshold=0.849918 total=4328
INFO[15:02:39] Converged to 29.58 % FDR with 879 Peptides    decoy=260 threshold=0.500699 total=1139
INFO[15:02:39] Converged to 25.29 % FDR with 1028 Ions       decoy=260 threshold=0.500699 total=1288
INFO[15:02:39] Protein inference results                     decoy=586 target=1091
INFO[15:02:40] Converged to 57.58 % FDR with 1016 Proteins   decoy=585 threshold=0.4996 total=1601
INFO[15:02:40] Applying sequential FDR estimation            ions=774 peptides=642 psms=4328
INFO[15:02:40] Converged to 0.98 % FDR with 4286 PSMs        decoy=42 threshold=0.849918 total=4328
INFO[15:02:40] Converged to 6.12 % FDR with 605 Peptides     decoy=37 threshold=0.850316 total=642
INFO[15:02:40] Converged to 5.02 % FDR with 737 Ions         decoy=37 threshold=0.850316 total=774
INFO[15:02:40] Post processing identifications              
INFO[15:02:40] Assigning protein identifications to layers  
INFO[15:02:40] Processing protein inference                 
INFO[15:02:40] Synchronizing PSMs and proteins              
INFO[15:02:40] Final report numbers after FDR filtering, and post-processing  ions=737 peptides=605 proteins=142 psms=4286
INFO[15:02:40] Saving                                       
INFO[15:02:40] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --prot 1.0 --ion 1.0 --pep 1.0 --tag rev_ --pepxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320 --protxml J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\combined.prot.xml --probin J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 --razor
INFO[15:02:40] Executing Filter  v5.0.0                     
INFO[15:02:40] Fetching protein inference from J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316 
INFO[15:02:40] Processing peptide identification files      
INFO[15:02:40] Parsing J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\interact-210803ko07Stag3_IP_Slot1-01_1_16320.pep.xml 
INFO[15:02:41] 1+ Charge profile                             decoy=1 target=1
INFO[15:02:41] 2+ Charge profile                             decoy=131 target=3544
INFO[15:02:41] 3+ Charge profile                             decoy=55 target=1346
INFO[15:02:41] 4+ Charge profile                             decoy=4 target=85
INFO[15:02:41] 5+ Charge profile                             decoy=3 target=23
INFO[15:02:41] 6+ Charge profile                             decoy=0 target=0
INFO[15:02:41] Database search results                       ions=2048 peptides=1848 psms=5193
INFO[15:02:41] Converged to 0.99 % FDR with 4548 PSMs        decoy=45 threshold=0.827584 total=4593
INFO[15:02:41] Converged to 10.33 % FDR with 1675 Peptides   decoy=173 threshold=0.501647 total=1848
INFO[15:02:41] Converged to 9.23 % FDR with 1875 Ions        decoy=173 threshold=0.501647 total=2048
INFO[15:02:41] Protein inference results                     decoy=586 target=1091
INFO[15:02:41] Converged to 57.58 % FDR with 1016 Proteins   decoy=585 threshold=0.4996 total=1601
INFO[15:02:41] Applying sequential FDR estimation            ions=1667 peptides=1487 psms=4593
INFO[15:02:41] Converged to 0.99 % FDR with 4548 PSMs        decoy=45 threshold=0.827584 total=4593
INFO[15:02:41] Converged to 2.91 % FDR with 1445 Peptides    decoy=42 threshold=0.827584 total=1487
INFO[15:02:41] Converged to 2.58 % FDR with 1625 Ions        decoy=42 threshold=0.827584 total=1667
INFO[15:02:41] Post processing identifications              
INFO[15:02:41] Assigning protein identifications to layers  
INFO[15:02:41] Processing protein inference                 
INFO[15:02:41] Synchronizing PSMs and proteins              
INFO[15:02:41] Final report numbers after FDR filtering, and post-processing  ions=1625 peptides=1445 proteins=349 psms=4548
INFO[15:02:41] Saving                                       
INFO[15:02:41] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[15:02:42] Executing Report  v5.0.0                     
INFO[15:02:42] Creating reports                             
INFO[15:02:42] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[15:02:42] Executing Report  v5.0.0                     
INFO[15:02:42] Creating reports                             
INFO[15:02:42] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[15:02:42] Executing Report  v5.0.0                     
INFO[15:02:42] Creating reports                             
INFO[15:02:42] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:02:42] Executing Workspace  v5.0.0                  
INFO[15:02:42] Removing workspace                           
INFO[15:02:42] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:02:43] Executing Workspace  v5.0.0                  
INFO[15:02:43] Removing workspace                           
INFO[15:02:43] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:02:43] Executing Workspace  v5.0.0                  
INFO[15:02:43] Removing workspace                           
INFO[15:02:43] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318]
D:\Applications\FragPipe-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[15:02:44] Executing Workspace  v5.0.0                  
INFO[15:02:44] Removing workspace                           
INFO[15:02:44] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ]
java -Xmx49G -Dlibs.bruker.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\bruker" -Dlibs.thermo.dir="D:\Applications\FragPipe-20.0\fragpipe\tools\MSFragger-3.8\ext\thermo" -cp "D:\Applications\FragPipe-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\Applications\FragPipe-20.0\fragpipe\tools\IonQuant-1.9.8.jar" ionquant.IonQuant --threads 15 --ionmobility 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\filelist_ionquant.txt --modlist J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\modmasses_ionquant.txt
IonQuant version IonQuant-1.9.8
Batmass-IO version 1.28.12
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 11, Architecture: AMD64
Java Info: 21.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 49 GB memory
2025-01-16 15:02:44 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-01-16 15:02:44 [INFO] - Loading and indexing all psm.tsv files...
2025-01-16 15:02:46 [INFO] - Parameters:
2025-01-16 15:02:46 [INFO] - threads = 15
2025-01-16 15:02:46 [INFO] - mztol = 10.0
2025-01-16 15:02:46 [INFO] - rttol = 0.4
2025-01-16 15:02:46 [INFO] - imtol = 0.05
2025-01-16 15:02:46 [INFO] - minisotopes = 2
2025-01-16 15:02:46 [INFO] - minscans = 3
2025-01-16 15:02:46 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko03IgG_IP_Slot1_01_1_16316\psm.tsv
2025-01-16 15:02:46 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko05Rad21_IP_Slot1_01_1_16318\psm.tsv
2025-01-16 15:02:46 [INFO] - psm = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\210803ko07Stag3_IP_Slot1_01_1_16320\psm.tsv
2025-01-16 15:02:46 [INFO] - multidir = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\.\
2025-01-16 15:02:46 [INFO] - excludemods = 
2025-01-16 15:02:46 [INFO] - minions = 2
2025-01-16 15:02:46 [INFO] - maxlfq = 1
2025-01-16 15:02:46 [INFO] - ibaq = 0
2025-01-16 15:02:46 [INFO] - normalization = 0
2025-01-16 15:02:46 [INFO] - minexps = 1
2025-01-16 15:02:46 [INFO] - minfreq = 0.0
2025-01-16 15:02:46 [INFO] - tp = 0
2025-01-16 15:02:46 [INFO] - mbr = 1
2025-01-16 15:02:46 [INFO] - mbrrttol = 1.0
2025-01-16 15:02:46 [INFO] - mbrimtol = 0.05
2025-01-16 15:02:46 [INFO] - mbrtoprun = 100
2025-01-16 15:02:46 [INFO] - mbrmincorr = 0.0
2025-01-16 15:02:46 [INFO] - ionmobility = 1
2025-01-16 15:02:46 [INFO] - ionfdr = 0.01
2025-01-16 15:02:46 [INFO] - peptidefdr = 1.0
2025-01-16 15:02:46 [INFO] - proteinfdr = 1.0
2025-01-16 15:02:46 [INFO] - light = 
2025-01-16 15:02:46 [INFO] - medium = 
2025-01-16 15:02:46 [INFO] - heavy = 
2025-01-16 15:02:46 [INFO] - requantify = 0
2025-01-16 15:02:46 [INFO] - writeindex = 0
2025-01-16 15:02:46 [INFO] - locprob = 0.75
2025-01-16 15:02:46 [INFO] - uniqueness = 0
2025-01-16 15:02:46 [INFO] - filelist = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\filelist_ionquant.txt
2025-01-16 15:02:46 [INFO] - specdir = J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3
2025-01-16 15:02:46 [INFO] - modlist = J:\MSFragger_process\Saitou-lab\Revision\210803ko-timsTOF\MSFragger_iBAQ\modmasses_ionquant.txt
2025-01-16 15:02:46 [INFO] - mod masses:
2025-01-16 15:02:46 [INFO] - 15.9949
2025-01-16 15:02:46 [INFO] - 42.0106
2025-01-16 15:02:46 [INFO] - 57.021465
2025-01-16 15:02:46 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d...
2025-01-16 15:02:46 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d...
2025-01-16 15:02:46 [INFO] - Checking J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d...
2025-01-16 15:02:47 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.d...
2025-01-16 15:02:47 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 15:05:25 [INFO] - Building index...
2025-01-16 15:06:07 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.quantindex
2025-01-16 15:06:16 [INFO] - Loading 210803ko03IgG_IP_Slot1-01_1_16316....
2025-01-16 15:06:16 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 15:06:16 [INFO] - Quantifying...
2025-01-16 15:06:17 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.d...
2025-01-16 15:06:17 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 15:08:35 [INFO] - Building index...
2025-01-16 15:09:13 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.quantindex
2025-01-16 15:09:20 [INFO] - Loading 210803ko05Rad21_IP_Slot1-01_1_16318....
2025-01-16 15:09:20 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 15:09:20 [INFO] - Quantifying...
2025-01-16 15:09:21 [INFO] - Loading J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.d...
2025-01-16 15:09:21 [INFO] - ...20%...40%...60%...80%...100%
2025-01-16 15:11:55 [INFO] - Building index...
2025-01-16 15:12:27 [INFO] - Writing index to J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.quantindex
2025-01-16 15:12:34 [INFO] - Loading 210803ko07Stag3_IP_Slot1-01_1_16320....
2025-01-16 15:12:34 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-01-16 15:12:34 [INFO] - Quantifying...
2025-01-16 15:12:34 [INFO] - Updating Philosopher's tables...
2025-01-16 15:12:35 [INFO] - Matching-between-runs: 210803ko03IgG_IP_Slot1-01_1_16316...
2025-01-16 15:12:35 [INFO] - Calculating correlations between all other runs...
2025-01-16 15:12:35 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko03IgG_IP_Slot1-01_1_16316.quantindex
2025-01-16 15:12:42 [INFO] - Transferring 210803ko05Rad21_IP_Slot1-01_1_16318...
2025-01-16 15:12:43 [INFO] - Transferring 210803ko07Stag3_IP_Slot1-01_1_16320...
2025-01-16 15:12:43 [INFO] - Training LDA models for all matched features.
2025-01-16 15:12:43 [INFO] - #{+1} = 271, #{-1} = 12, #{+2} = 499, #{-2} = 13
2025-01-16 15:12:43 [INFO] - Standardized coefficients:
2025-01-16 15:12:43 [INFO] - log10(intensity): 0.8872048025343466
2025-01-16 15:12:43 [INFO] - log10(KL): 0.1382111752027858
2025-01-16 15:12:43 [INFO] - abs(ppm): -0.24024335413476425
2025-01-16 15:12:43 [INFO] - IM diff: -0.21943034949025605
2025-01-16 15:12:43 [INFO] - RT diff: -0.29647725363966454
2025-01-16 15:12:43 [INFO] - Fitting a mixture model...
2025-01-16 15:12:44 [INFO] - Matching-between-runs: 210803ko05Rad21_IP_Slot1-01_1_16318...
2025-01-16 15:12:44 [INFO] - Calculating correlations between all other runs...
2025-01-16 15:12:44 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko05Rad21_IP_Slot1-01_1_16318.quantindex
2025-01-16 15:12:50 [INFO] - Transferring 210803ko03IgG_IP_Slot1-01_1_16316...
2025-01-16 15:12:50 [INFO] - Transferring 210803ko07Stag3_IP_Slot1-01_1_16320...
2025-01-16 15:12:50 [INFO] - Training LDA models for all matched features.
2025-01-16 15:12:50 [INFO] - #{+1} = 255, #{-1} = 12, #{+2} = 317, #{-2} = 21
2025-01-16 15:12:50 [INFO] - Standardized coefficients:
2025-01-16 15:12:50 [INFO] - log10(intensity): 0.9807751710463404
2025-01-16 15:12:50 [INFO] - log10(KL): -0.1338148668639186
2025-01-16 15:12:50 [INFO] - abs(ppm): -0.10563447409159438
2025-01-16 15:12:50 [INFO] - IM diff: -0.08792790989957198
2025-01-16 15:12:50 [INFO] - RT diff: -0.03582856136238891
2025-01-16 15:12:50 [INFO] - Fitting a mixture model...
2025-01-16 15:12:50 [INFO] - Matching-between-runs: 210803ko07Stag3_IP_Slot1-01_1_16320...
2025-01-16 15:12:50 [INFO] - Calculating correlations between all other runs...
2025-01-16 15:12:50 [INFO] - Reading index from J:\MSFragger_process\Saitou-lab\Revision\210803ko-Stag3\210803ko07Stag3_IP_Slot1-01_1_16320.quantindex
2025-01-16 15:12:58 [INFO] - Transferring 210803ko03IgG_IP_Slot1-01_1_16316...
2025-01-16 15:12:58 [INFO] - Transferring 210803ko05Rad21_IP_Slot1-01_1_16318...
2025-01-16 15:12:58 [INFO] - Training LDA models for all matched features.
2025-01-16 15:12:58 [INFO] - #{+1} = 313, #{-1} = 8, #{+2} = 571, #{-2} = 13
2025-01-16 15:12:58 [INFO] - Standardized coefficients:
2025-01-16 15:12:58 [INFO] - log10(intensity): 0.8000802353675265
2025-01-16 15:12:58 [INFO] - log10(KL): 0.007876116647713798
2025-01-16 15:12:58 [INFO] - abs(ppm): -0.4323816025967041
2025-01-16 15:12:58 [INFO] - IM diff: -0.4102933006460902
2025-01-16 15:12:58 [INFO] - RT diff: -0.06719479847159228
2025-01-16 15:12:58 [INFO] - Fitting a mixture model...
2025-01-16 15:12:58 [WARNING] - There are not enough data points to fix a mixture model (decoy = 8, target = 313, id = 571). Will estimate the probability using a simplified approach.
2025-01-16 15:12:58 [INFO] - Estimating match-between-runs FDR...
2025-01-16 15:12:58 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.961500
2025-01-16 15:12:58 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2025-01-16 15:12:58 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2025-01-16 15:12:58 [INFO] - Updating Philosopher's tables...
2025-01-16 15:12:58 [INFO] - Combining experiments and estimating protein intensity...
2025-01-16 15:12:59 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003)
(FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021)
(Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

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