System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A


Version info:
FragPipe version 19.1
MSFragger version 3.7
IonQuant version 1.8.10
Philosopher version 4.8.1


LCMS files:
  Experiment/Group: 
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML	DDA
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML	DDA
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML	DDA
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML	DDA
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML	DDA
  - D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML	DDA


49 commands to execute:
CheckCentroid
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML 33
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\90edec0d-c39c-4b11-8d87-cc3910ee1dcc
MSFragger [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx209G D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\MSFragger-3.7.jar D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\fragger.params D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pepXML
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin
MSBooster [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\msbooster-1.1.11.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\msbooster_params.txt
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv --decoy-results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv --decoy-results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv --decoy-results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv --decoy-results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv --decoy-results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_edited.pin
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv --decoy-results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_edited.pin
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin 230327HN02AdipositeKRNpepGlobalTMT6plexFr1 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv interact-230327HN02AdipositeKRNpepGlobalTMT6plexFr1 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin 230327HN04AdipositeKRNpepGlobalTMT6plexFr3 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv interact-230327HN04AdipositeKRNpepGlobalTMT6plexFr3 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin 230327HN06AdipositeKRNpepGlobalTMT6plexFr5 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv interact-230327HN06AdipositeKRNpepGlobalTMT6plexFr5 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin 230327HN07AdipositeKRNpepGlobalTMT6plexFr6 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv interact-230327HN07AdipositeKRNpepGlobalTMT6plexFr6 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin 230327HN03AdipositeKRNpepGlobalTMT6plexFr2 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv interact-230327HN03AdipositeKRNpepGlobalTMT6plexFr2 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin 230327HN05AdipositeKRNpepGlobalTMT6plexFr4 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv interact-230327HN05AdipositeKRNpepGlobalTMT6plexFr4 DDA 0.5
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result --protxml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\combined.prot.xml --razor
FreeQuant [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT
Quant (Isobaric) [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe labelquant --tol 20 --level 2 --minprob 0.900 --purity 0.500 --removelow 0.050 --plex 10 --annot D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\AdipocyteTMT_annotation.txt --brand tmt --dir D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
TmtIntegrator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\tmt-integrator-4.0.4.jar" TMTIntegrator D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\tmt-integrator-conf.yml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\psm.tsv
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [CheckCentroid], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [MSFragger], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [MSBooster], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [Percolator], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [ProteinProphet], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [PhilosopherFilter], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [FreeQuant], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [Quant (Isobaric)], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [PhilosopherReport], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [WorkspaceClean], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
    Cmd: [TmtIntegrator], Work dir: [D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]

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

~~~~~~Sample of D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas~~~~~~~
>rev_sp|A0A087WPF7-2|AUTS2_MOUSE Isoform 2 of Autism susceptibility gene 2 protein homolog OS=Mus musculus OX=10090 GN=Auts2
>rev_sp|Q5UKY4-4|MO2R3_MOUSE Isoform 4 of Cell surface glycoprotein CD200 receptor 3 OS=Mus musculus OX=10090 GN=Cd200r3
>rev_sp|Q91YK0|LRC49_MOUSE Leucine-rich repeat-containing protein 49 OS=Mus musculus OX=10090 GN=Lrrc49 PE=1 SV=1
>rev_tr|A0A0G2JFU4|A0A0G2JFU4_MOUSE Checkpoint with forkhead and ring finger domains OS=Mus musculus OX=10090 GN=Chfr PE=1 SV=1
>rev_tr|A0A3B2W3L2|A0A3B2W3L2_MOUSE Vomeronasal 2, receptor 79 OS=Mus musculus OX=10090 GN=Vmn2r79 PE=4 SV=1
>rev_tr|C0IQA7|C0IQA7_MOUSE Testis specific expressed protein 5 OS=Mus musculus OX=10090 GN=4930544G11Rik PE=2 SV=1
>rev_tr|F6U8V3|F6U8V3_MOUSE Histocompatibility 2, M region locus 11 (Fragment) OS=Mus musculus OX=10090 GN=H2-M11 PE=3 SV=1
>rev_tr|Q3TCL6|Q3TCL6_MOUSE Anthrax toxin receptor OS=Mus musculus OX=10090 GN=Antxr2 PE=1 SV=1
>rev_tr|Q548K2|Q548K2_MOUSE Alcohol dehydrogenase class 4 OS=Mus musculus OX=10090 GN=Adh7 PE=2 SV=1
>rev_tr|Q8C980|Q8C980_MOUSE Uncharacterized protein OS=Mus musculus OX=10090 GN=Gm10006 PE=2 SV=1
>rev_tr|Z4YN74|Z4YN74_MOUSE Transmembrane protein 11 (Fragment) OS=Mus musculus OX=10090 GN=Tmem11 PE=1 SV=1
>sp|Q5U901|CBPA6_MOUSE Carboxypeptidase A6 OS=Mus musculus OX=10090 GN=Cpa6 PE=2 SV=1
>sp|Q91YI4-2|ARRB2_MOUSE Isoform 2 of Beta-arrestin-2 OS=Mus musculus OX=10090 GN=Arrb2
>tr|A0A0G2JFT4|A0A0G2JFT4_MOUSE Microtubule-associated protein (Fragment) OS=Mus musculus OX=10090 GN=Map4 PE=1 SV=1
>tr|A0A3B2W3G7|A0A3B2W3G7_MOUSE Peroxisomal, testis specific 1 OS=Mus musculus OX=10090 GN=Pxt1 PE=4 SV=1
>tr|C0H5Y0|C0H5Y0_MOUSE Asb7 protein OS=Mus musculus OX=10090 GN=Asb7 PE=2 SV=1
>tr|F6U786|F6U786_MOUSE Rho guanine nucleotide exchange factor (GEF) 38 OS=Mus musculus OX=10090 GN=Arhgef38 PE=4 SV=1
>tr|Q3TCI1|Q3TCI1_MOUSE EF-hand domain-containing protein (Fragment) OS=Mus musculus OX=10090 GN=Nucb1 PE=2 SV=1
>tr|Q547S9|Q547S9_MOUSE cAMP response element binding protein OS=Mus musculus OX=10090 GN=Creb1 PE=2 SV=1
>tr|Q8C961|Q8C961_MOUSE Uncharacterized protein (Fragment) OS=Mus musculus OX=10090 GN=Ncoa2 PE=2 SV=1
>tr|Z4YN17|Z4YN17_MOUSE XIAP associated factor 1 (Fragment) OS=Mus musculus OX=10090 GN=Xaf1 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~annotation files~~~~~~~
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\AdipocyteTMT_annotation.txt:
126 P1
127N NA
127C P2
128N NA
128C P3
129N NA
129C C1
130N NA
130C C2
131N C3
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v19.1ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Personal\\Nishida\\Adiposite\\230413_AdipositeTMT\\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas

Table.editor=[^
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=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
fragpipe-config.bin-ionquant=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\IonQuant-1.8.10.jar
fragpipe-config.bin-msfragger=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\MSFragger-3.7\\MSFragger-3.7.jar
fragpipe-config.bin-philosopher=D\:\\Personal\\Nishida\\FragPipe-jre-19.1\\fragpipe\\tools\\philosopher_v4.8.1_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\massUser\\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=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
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=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
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.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.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=-1/0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
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=131.5
msfragger.misc.fragger.clear-mz-lo=125.5
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown-1=lysn_promisc
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.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=-18.01056 79.96633
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=lysn_promisc
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=N
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; 57.02146,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; 229.16293,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; 229.16293,n^,true,1; 229.16293,S,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 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_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.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.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 --picked --prot 0.01
phi-report.pep-level-summary=false
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 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=true
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=false
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_minIons=25
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=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
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.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=3
saintexpress.run-saint-express=true
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=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tmtintegrator.add_Ref=1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0.9
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=1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\Personal\\Nishida\\Adiposite\\230817_Re\\Global_TMT\\Result
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=33

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML 33
Done in 2143 ms.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[13:18:25] Executing Workspace  v4.8.1                  
INFO[13:18:25] Removing workspace                           
WARN[13:18:25] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[13:18:25] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\massUser\AppData\Local\Temp\90edec0d-c39c-4b11-8d87-cc3910ee1dcc
INFO[13:18:26] Executing Workspace  v4.8.1                  
INFO[13:18:26] Creating workspace                           
INFO[13:18:26] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx209G D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\MSFragger-3.7\MSFragger-3.7.jar D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\fragger.params D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML
MSFragger version MSFragger-3.7
Batmass-IO version 1.28.9
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 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 209 GB memory
Checking database...
Checking spectral files...
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML: Scans = 23157
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML: Scans = 23356
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML: Scans = 22772
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML: Scans = 23554
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML: Scans = 24612
D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML: Scans = 23778
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 33
database_name = D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.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 = false
write_calibrated_mzml = 0
write_uncalibrated_mgf = false
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = lysn_promisc
search_enzyme_sense_1 = N
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
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 = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = true
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
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 125.5
clear_mz_range_high = 131.5
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_06 = 229.16293 n^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
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 = 229.16293
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.
828370976 fragments to be searched in 1 slices (12.34 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 4.63 s
	001. 230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML 1.7 s | deisotoping 0.8 s
		[progress: 23663/23663 (100%) - 16410 spectra/s] 1.4s | postprocessing 0.2 s
	002. 230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML 1.0 s | deisotoping 0.1 s
		[progress: 22878/22878 (100%) - 103054 spectra/s] 0.2s | postprocessing 0.1 s
	003. 230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML 1.0 s | deisotoping 0.0 s
		[progress: 22326/22326 (100%) - 100568 spectra/s] 0.2s | postprocessing 0.1 s
	004. 230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML 1.1 s | deisotoping 0.3 s
		[progress: 22098/22098 (100%) - 99541 spectra/s] 0.2s | postprocessing 0.1 s
	005. 230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML 1.3 s | deisotoping 0.0 s
		[progress: 21625/21625 (100%) - 97851 spectra/s] 0.2s | postprocessing 0.1 s
	006. 230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML 1.1 s | deisotoping 0.0 s
		[progress: 22549/22549 (100%) - 69811 spectra/s] 0.3s | postprocessing 0.1 s
***************************FIRST SEARCH DONE IN 0.450 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   2.46   0.43 |  -0.01   0.40 |   2.49   2.86 |   0.41   2.57  
 002 |   2.58   0.48 |  -0.01   0.38 |   2.52   2.99 |   0.32   2.64  
 003 |   2.49   0.45 |  -0.02   0.43 |   2.49   2.96 |   0.35   2.61  
 004 |   2.51   0.47 |   0.02   0.40 |   2.45   2.87 |   0.35   2.56  
 005 |   2.42   0.51 |   0.04   0.37 |   2.42   3.09 |   0.44   2.75  
 006 |   2.52   0.46 |  -0.07   0.37 |   2.53   3.09 |   0.41   2.77  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  |   5550|   5617|   5568| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |   5719|   5723|   5720| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   5670
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |   5600
-------|-------
New fragment_mass_tolerance = 10 PPM
New use_topN_peaks = 200
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.321 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 33
database_name = D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.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 = 10.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mzml = 0
write_uncalibrated_mgf = false
isotope_error = -1/0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = lysn_promisc
search_enzyme_sense_1 = N
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
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 = true
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = true
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 = 200
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 0
activation_types = all
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 125.5
clear_mz_range_high = 131.5
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_06 = 229.16293 n^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
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 = 229.16293
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 0.05 Da.
828370976 fragments to be searched in 1 slices (12.34 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 4.29 s
	001. 230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzBIN_calibrated 0.4 s
		[progress: 23184/23184 (100%) - 42153 spectra/s] 0.6s | remapping alternative proteins and postprocessing 5.6 s
	002. 230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzBIN_calibrated 0.4 s
		[progress: 22176/22176 (100%) - 49946 spectra/s] 0.4s | remapping alternative proteins and postprocessing 5.0 s
	003. 230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzBIN_calibrated 0.4 s
		[progress: 21439/21439 (100%) - 48178 spectra/s] 0.4s | remapping alternative proteins and postprocessing 5.0 s
	004. 230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzBIN_calibrated 0.4 s
		[progress: 20948/20948 (100%) - 63287 spectra/s] 0.3s | remapping alternative proteins and postprocessing 5.0 s
	005. 230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzBIN_calibrated 0.4 s
		[progress: 20030/20030 (100%) - 60150 spectra/s] 0.3s | remapping alternative proteins and postprocessing 7.1 s
	006. 230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzBIN_calibrated 0.5 s
		[progress: 21578/21578 (100%) - 39162 spectra/s] 0.6s | remapping alternative proteins and postprocessing 4.7 s
***************************MAIN SEARCH DONE IN 0.796 MIN***************************

*******************************TOTAL TIME 2.567 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pepXML D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar;/D:/Personal/Nishida/FragPipe-jre-19.1/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\msbooster-1.1.11.jar;D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\batmass-io-1.28.9.jar" Features.MainClass --paramsList D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\msbooster_params.txt
MSBooster v1.1.11
Using 33 threads
Generating input file for DIA-NN
46919 unique peptides from 58508 PSMs
Writing DIA-NN input file
Diann input file generation took 707 milliseconds
Input file at  D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\spectraRT.tsv
46919 unique peptides from 58508 PSMs
createFull input file generation took 406 milliseconds
Input file at  D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\spectraRT_full.tsv
Generating DIA-NN predictions
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\spectraRT.tsv --predict --threads 33 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Sun Sep  3 13:21:09 2023
CPU: GenuineIntel Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 36
Predicted spectra will be saved in a binary format
Thread number set to 33
DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search
Deep learning predictor will predict 100 fragments
Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed
[0:00] Loading spectral library D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\spectraRT.tsv
[0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 46919 precursors in 41286 elution groups.
[0:00] Encoding peptides for spectra and RTs prediction
WARNING: unrecognised amino acid or an incorrectly processed modification name: WARNING: unrecognised amino acid or an incorrectly processed modification name: WARNING: unrecognised amino acid or an incorrectly processed modification name: WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)<(UniMod:1)(TMT)
<(UniMod:1)(TMT)WARNING: unrecognised amino acid or an incorrectly processed modification name: 
<(UniMod:1)(TMT)
<(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)WARNING: unrecognised amino acid or an incorrectly processed modification name: 
<(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)


WARNING: unrecognised amino acid or an incorrectly processed modification name: <(UniMod:1)(TMT)
WARNING: skipping 19 precursors, unrecognised modifications? If these precursors are important, consider forcing prediction of spectra/RTs/IMs for these precursors anyway, using the --strip-unknown-mods option
[0:00] Predicting spectra and IMs
[0:06] Predicting RTs
[0:08] Decoding predicted spectra and IMs
[0:08] Decoding RTs
[0:08] Saving the list of predictions to D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\spectraRT.predicted.bin
Finished
Done generating DIA-NN predictions
Model running took 9384 milliseconds
Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS]
Loading predicted spectra
Processing 230327HN02AdipositeKRNpepGlobalTMT6plexFr1.mzML
RT regression using 2701 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1_edited.pin
Processing 230327HN03AdipositeKRNpepGlobalTMT6plexFr2.mzML
RT regression using 2628 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2_edited.pin
Processing 230327HN04AdipositeKRNpepGlobalTMT6plexFr3.mzML
RT regression using 2026 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3_edited.pin
Processing 230327HN05AdipositeKRNpepGlobalTMT6plexFr4.mzML
RT regression using 1683 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4_edited.pin
Processing 230327HN06AdipositeKRNpepGlobalTMT6plexFr5.mzML
RT regression using 1224 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5_edited.pin
Processing 230327HN07AdipositeKRNpepGlobalTMT6plexFr6.mzML
RT regression using 1937 PSMs
Edited pin file at D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6_edited.pin
Done in 11392 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv --decoy-results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv --decoy-results-psms 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_edited.pin
Started Sun Sep  3 13:21:29 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 11948 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 9265 positives and 2683 negatives, size ratio=3.45322 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 24 as initial direction. Could separate 3959 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 5 as initial direction. Could separate 3875 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 3966 training set positives with q<0.01 in that direction.
Found 5594 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.242 cpu seconds or 1 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 6583 PSMs with q<0.01
Iteration 2:	Estimated 6693 PSMs with q<0.01
Iteration 3:	Estimated 6716 PSMs with q<0.01
Iteration 4:	Estimated 6721 PSMs with q<0.01
Iteration 5:	Estimated 6727 PSMs with q<0.01
Iteration 6:	Estimated 6732 PSMs with q<0.01
Iteration 7:	Estimated 6733 PSMs with q<0.01
Iteration 8:	Estimated 6736 PSMs with q<0.01
Iteration 9:	Estimated 6737 PSMs with q<0.01
Iteration 10:	Estimated 6737 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.1117	 0.0885	 0.2482	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.1915	-0.3661	-0.2970	abs_ppm
-0.1795	-0.0935	-0.1408	isotope_errors
-1.4894	-3.0888	-2.1769	log10_evalue
-0.2003	-0.7321	-0.3590	hyperscore
 1.0405	 1.3008	 1.3244	delta_hyperscore
 1.3860	 1.0312	 1.5801	matched_ion_num
-1.1701	-1.2359	-1.2573	complementary_ions
-0.1691	-0.0163	-0.4304	ion_series
-0.1026	-0.0640	-0.1915	weighted_average_abs_fragment_ppm
 0.0529	 0.1015	-0.1665	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.3215	 0.4509	 0.3305	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0180	-0.0290	-0.1390	charge_2
-0.0773	-0.1101	-0.2185	charge_3
 0.1245	 0.0678	 0.1557	charge_4
-0.0964	 0.0497	 0.2070	charge_5
 0.0116	 0.0743	 0.1478	charge_6
 0.0460	 0.0878	 0.1393	charge_7_or_more
 0.0860	 0.0272	-0.0062	15.9949M
 0.1979	 0.2856	 0.4065	229.16293n^
 1.3948	 1.7463	 1.6732	unweighted_spectral_entropy
-2.9526	-2.1494	-2.2694	delta_RT_loess
 0.1517	 1.2126	 0.8091	m0
Found 6698 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 9265 target PSMs and 2683 decoy PSMs.
Calculating q values.
Final list yields 6699 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.319 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv --decoy-results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv --decoy-results-psms 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_edited.pin
Started Sun Sep  3 13:21:32 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 9642 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7819 positives and 1823 negatives, size ratio=4.28908 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 24 as initial direction. Could separate 3491 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 24 as initial direction. Could separate 3601 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 5 as initial direction. Could separate 3502 training set positives with q<0.01 in that direction.
Found 5022 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.216 cpu seconds or 1 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 5885 PSMs with q<0.01
Iteration 2:	Estimated 5958 PSMs with q<0.01
Iteration 3:	Estimated 5966 PSMs with q<0.01
Iteration 4:	Estimated 5969 PSMs with q<0.01
Iteration 5:	Estimated 5966 PSMs with q<0.01
Iteration 6:	Estimated 5973 PSMs with q<0.01
Iteration 7:	Estimated 5977 PSMs with q<0.01
Iteration 8:	Estimated 5980 PSMs with q<0.01
Iteration 9:	Estimated 5981 PSMs with q<0.01
Iteration 10:	Estimated 5979 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.1109	 0.1095	 0.1189	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.2615	-0.3454	-0.5654	abs_ppm
-0.1585	-0.1498	-0.2926	isotope_errors
-0.3339	-0.2169	-0.6082	log10_evalue
 0.3040	 0.1970	 0.2610	hyperscore
 1.1596	 0.9579	 0.9417	delta_hyperscore
 0.7739	 0.9179	 0.9146	matched_ion_num
-0.3019	-0.4722	-0.5183	complementary_ions
 0.2157	 0.0897	-0.0402	ion_series
-0.0419	-0.1532	-0.0492	weighted_average_abs_fragment_ppm
 0.5565	 0.5321	 0.5066	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.1410	 0.1328	 0.2078	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0081	 0.0542	 0.0595	charge_2
 0.0864	 0.1316	 0.1243	charge_3
 0.0444	 0.1279	 0.1313	charge_4
-0.0425	-0.2194	-0.2144	charge_5
-0.1664	-0.2043	-0.2255	charge_6
-0.1153	-0.2091	-0.1855	charge_7_or_more
 0.1258	 0.0551	 0.0961	15.9949M
 0.3860	 0.2781	 0.2623	229.16293n^
 1.0798	 1.4336	 1.6368	unweighted_spectral_entropy
-1.3798	-0.5118	-0.2747	delta_RT_loess
 0.9269	 1.0062	 0.9915	m0
Found 5904 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7819 target PSMs and 1823 decoy PSMs.
Calculating q values.
Final list yields 5929 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.258 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv --decoy-results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv --decoy-results-psms 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_edited.pin
Started Sun Sep  3 13:21:35 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 7431 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 6034 positives and 1397 negatives, size ratio=4.31926 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 2511 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 24 as initial direction. Could separate 2574 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 2632 training set positives with q<0.01 in that direction.
Found 3551 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.167 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 4575 PSMs with q<0.01
Iteration 2:	Estimated 4645 PSMs with q<0.01
Iteration 3:	Estimated 4651 PSMs with q<0.01
Iteration 4:	Estimated 4660 PSMs with q<0.01
Iteration 5:	Estimated 4660 PSMs with q<0.01
Iteration 6:	Estimated 4663 PSMs with q<0.01
Iteration 7:	Estimated 4664 PSMs with q<0.01
Iteration 8:	Estimated 4665 PSMs with q<0.01
Iteration 9:	Estimated 4666 PSMs with q<0.01
Iteration 10:	Estimated 4664 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0185	 0.1204	 0.0635	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.6168	-0.3200	-0.3352	abs_ppm
-0.1442	-0.2692	-0.3693	isotope_errors
-0.7355	-0.7932	-1.4780	log10_evalue
-0.0203	-0.2139	-0.1010	hyperscore
 0.8678	 1.2876	 1.4968	delta_hyperscore
 0.8046	 1.5265	 1.7576	matched_ion_num
-0.5133	-0.9180	-1.2766	complementary_ions
 0.1831	 0.0613	 0.1071	ion_series
-0.0072	-0.1915	-0.1965	weighted_average_abs_fragment_ppm
 0.9227	 0.5077	 0.6795	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.1562	 0.3417	 0.3739	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0387	 0.0556	 0.0941	charge_2
 0.0017	-0.0811	 0.0339	charge_3
 0.0551	 0.0119	 0.1450	charge_4
-0.1538	-0.0766	-0.3885	charge_5
-0.0966	 0.0294	-0.1403	charge_6
 0.1792	 0.2795	 0.1083	charge_7_or_more
 0.1149	 0.3705	 0.0780	15.9949M
 0.2775	 0.0008	 0.4649	229.16293n^
 1.2256	 1.3991	 1.7022	unweighted_spectral_entropy
-1.4883	-1.7163	-1.0591	delta_RT_loess
 0.7474	 1.3388	 2.0505	m0
Found 4614 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 6034 target PSMs and 1397 decoy PSMs.
Calculating q values.
Final list yields 4616 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.894 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv --decoy-results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv --decoy-results-psms 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_edited.pin
Started Sun Sep  3 13:21:37 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 9392 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7480 positives and 1912 negatives, size ratio=3.91213 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 24 as initial direction. Could separate 3220 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 24 as initial direction. Could separate 3142 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 3221 training set positives with q<0.01 in that direction.
Found 4729 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.177 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 5439 PSMs with q<0.01
Iteration 2:	Estimated 5483 PSMs with q<0.01
Iteration 3:	Estimated 5491 PSMs with q<0.01
Iteration 4:	Estimated 5496 PSMs with q<0.01
Iteration 5:	Estimated 5499 PSMs with q<0.01
Iteration 6:	Estimated 5503 PSMs with q<0.01
Iteration 7:	Estimated 5499 PSMs with q<0.01
Iteration 8:	Estimated 5500 PSMs with q<0.01
Iteration 9:	Estimated 5504 PSMs with q<0.01
Iteration 10:	Estimated 5503 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0354	 0.0983	 0.0965	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.3507	-0.3728	-0.4020	abs_ppm
-0.1827	-0.0022	-0.0421	isotope_errors
-0.5104	-0.3455	-0.6198	log10_evalue
-0.6104	-0.1558	 0.0845	hyperscore
 1.2105	 0.9820	 0.9860	delta_hyperscore
 1.8801	 0.9326	 0.7892	matched_ion_num
-0.7797	-0.3353	-0.3835	complementary_ions
 0.1748	 0.3184	 0.0027	ion_series
-0.0105	-0.0206	-0.1004	weighted_average_abs_fragment_ppm
 0.9604	 0.5361	 0.3844	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.3938	 0.2583	 0.1920	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.1956	 0.0803	 0.0275	charge_2
 0.2159	 0.0819	 0.0697	charge_3
-0.0573	 0.0747	 0.1259	charge_4
-0.2021	-0.1597	-0.2187	charge_5
-0.3502	-0.1916	-0.0733	charge_6
-0.1196	-0.0780	-0.0925	charge_7_or_more
 0.1373	 0.0413	 0.0781	15.9949M
 0.2415	 0.2963	 0.2789	229.16293n^
 1.7134	 1.3622	 1.3197	unweighted_spectral_entropy
-1.1058	-0.5516	-0.5706	delta_RT_loess
 1.2347	 0.9212	 0.9030	m0
Found 5449 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7480 target PSMs and 1912 decoy PSMs.
Calculating q values.
Final list yields 5449 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.137 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv --decoy-results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv --decoy-results-psms 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_edited.pin
Started Sun Sep  3 13:21:40 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 11351 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 9060 positives and 2291 negatives, size ratio=3.9546 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 24 as initial direction. Could separate 3916 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 24 as initial direction. Could separate 3997 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 3989 training set positives with q<0.01 in that direction.
Found 5846 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.202 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 6700 PSMs with q<0.01
Iteration 2:	Estimated 6761 PSMs with q<0.01
Iteration 3:	Estimated 6786 PSMs with q<0.01
Iteration 4:	Estimated 6790 PSMs with q<0.01
Iteration 5:	Estimated 6794 PSMs with q<0.01
Iteration 6:	Estimated 6799 PSMs with q<0.01
Iteration 7:	Estimated 6804 PSMs with q<0.01
Iteration 8:	Estimated 6803 PSMs with q<0.01
Iteration 9:	Estimated 6806 PSMs with q<0.01
Iteration 10:	Estimated 6806 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0287	 0.0756	 0.1095	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.3818	-0.3367	-0.3925	abs_ppm
 0.1381	-0.0075	-0.0750	isotope_errors
-1.3312	-0.1957	-0.3922	log10_evalue
-0.4812	 0.0042	-0.5233	hyperscore
 0.8269	 0.8901	 1.4144	delta_hyperscore
 2.8088	 1.0840	 2.1872	matched_ion_num
-1.0917	-0.5115	-0.9114	complementary_ions
-0.4753	-0.1983	-0.5461	ion_series
-0.2933	-0.2535	-0.3426	weighted_average_abs_fragment_ppm
 0.9480	 0.5288	 0.3184	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.2108	 0.1285	 0.2586	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0158	 0.0806	 0.0362	charge_2
 0.0667	 0.0861	 0.0368	charge_3
 0.2611	 0.0699	 0.0721	charge_4
-0.2287	-0.1462	-0.0239	charge_5
-0.3089	-0.2357	-0.3090	charge_6
-0.0509	-0.0278	 0.0922	charge_7_or_more
 0.2100	 0.0578	 0.0880	15.9949M
 0.3482	 0.2382	 0.3645	229.16293n^
 2.0109	 1.3369	 1.7555	unweighted_spectral_entropy
-1.7961	-0.8687	-0.8127	delta_RT_loess
 1.0184	 0.5691	 1.0149	m0
Found 6762 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 9060 target PSMs and 2291 decoy PSMs.
Calculating q values.
Final list yields 6770 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.357 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv --decoy-results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
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:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 33 --results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv --decoy-results-psms 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_edited.pin
Started Sun Sep  3 13:21:43 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_edited.pin
Features:
retentiontime 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 15.9949M 229.16293n^ unweighted_spectral_entropy delta_RT_loess 
Found 8744 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7158 positives and 1586 negatives, size ratio=4.51324 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 5 as initial direction. Could separate 3117 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 24 as initial direction. Could separate 3079 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 24 as initial direction. Could separate 3245 training set positives with q<0.01 in that direction.
Found 4651 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.189 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 5457 PSMs with q<0.01
Iteration 2:	Estimated 5529 PSMs with q<0.01
Iteration 3:	Estimated 5554 PSMs with q<0.01
Iteration 4:	Estimated 5556 PSMs with q<0.01
Iteration 5:	Estimated 5555 PSMs with q<0.01
Iteration 6:	Estimated 5553 PSMs with q<0.01
Iteration 7:	Estimated 5554 PSMs with q<0.01
Iteration 8:	Estimated 5548 PSMs with q<0.01
Iteration 9:	Estimated 5551 PSMs with q<0.01
Iteration 10:	Estimated 5551 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0769	 0.0308	-0.0540	retentiontime
 0.0000	 0.0000	 0.0000	rank
-0.5047	-0.7666	-0.3668	abs_ppm
-0.0112	 0.0856	-0.1609	isotope_errors
-0.9409	-1.6125	-0.5649	log10_evalue
 0.1030	-0.8071	-0.0031	hyperscore
 0.7450	 1.3850	 1.1784	delta_hyperscore
 1.0167	 1.8625	 0.5195	matched_ion_num
-0.6712	-0.8866	-0.5753	complementary_ions
-0.0583	-0.3647	 0.1033	ion_series
 0.0456	-0.0174	-0.0632	weighted_average_abs_fragment_ppm
 0.5063	 0.7379	 0.4859	peptide_length
 0.0000	 0.0000	 0.0000	ntt
 0.1084	 0.1545	 0.2358	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0789	-0.1905	 0.0252	charge_2
 0.0524	 0.0386	 0.0652	charge_3
 0.1859	 0.3723	 0.1464	charge_4
-0.0458	-0.2929	-0.2019	charge_5
-0.1328	-0.1242	-0.1413	charge_6
-0.2814	 0.1342	-0.1431	charge_7_or_more
 0.2529	 0.7319	 0.1541	15.9949M
 0.3089	 0.3820	 0.2566	229.16293n^
 1.1826	 2.2074	 1.6541	unweighted_spectral_entropy
-1.0204	-1.7482	-0.5743	delta_RT_loess
 1.0010	 1.5488	 0.9319	m0
Found 5503 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 7158 target PSMs and 1586 decoy PSMs.
Calculating q values.
Final list yields 5509 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.139 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pin 230327HN02AdipositeKRNpepGlobalTMT6plexFr1 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv 230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv interact-230327HN02AdipositeKRNpepGlobalTMT6plexFr1 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN02AdipositeKRNpepGlobalTMT6plexFr1_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pin 230327HN04AdipositeKRNpepGlobalTMT6plexFr3 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv 230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv interact-230327HN04AdipositeKRNpepGlobalTMT6plexFr3 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN04AdipositeKRNpepGlobalTMT6plexFr3_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pin 230327HN06AdipositeKRNpepGlobalTMT6plexFr5 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv 230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv interact-230327HN06AdipositeKRNpepGlobalTMT6plexFr5 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN06AdipositeKRNpepGlobalTMT6plexFr5_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pin 230327HN07AdipositeKRNpepGlobalTMT6plexFr6 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv 230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv interact-230327HN07AdipositeKRNpepGlobalTMT6plexFr6 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN07AdipositeKRNpepGlobalTMT6plexFr6_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pin 230327HN03AdipositeKRNpepGlobalTMT6plexFr2 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv 230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv interact-230327HN03AdipositeKRNpepGlobalTMT6plexFr2 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN03AdipositeKRNpepGlobalTMT6plexFr2_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pin 230327HN05AdipositeKRNpepGlobalTMT6plexFr4 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv 230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv interact-230327HN05AdipositeKRNpepGlobalTMT6plexFr4 DDA 0.5
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -cp D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\lib\fragpipe-19.1.jar com.github.chhh.utils.FileDelete D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\230327HN05AdipositeKRNpepGlobalTMT6plexFr4_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\filelist_proteinprophet.txt
INFO[13:21:59] Executing ProteinProphet  v4.8.1             
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 D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pep.xml...
...read in 0 1+, 1689 2+, 2987 3+, 1604 4+, 509 5+, 136 6+, 29 7+ spectra with min prob 0.5

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pep.xml...
...read in 0 1+, 1368 2+, 2912 3+, 1851 4+, 714 5+, 171 6+, 32 7+ spectra with min prob 0.5

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pep.xml...
...read in 0 1+, 1104 2+, 2601 3+, 1710 4+, 552 5+, 173 6+, 36 7+ spectra with min prob 0.5

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pep.xml...
...read in 0 1+, 1167 2+, 2547 3+, 1476 4+, 461 5+, 153 6+, 41 7+ spectra with min prob 0.5

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pep.xml...
...read in 0 1+, 1065 2+, 2189 3+, 1170 4+, 312 5+, 106 6+, 46 7+ spectra with min prob 0.5

Reading in D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pep.xml...
...read in 0 1+, 1116 2+, 2436 3+, 1555 4+, 445 5+, 119 6+, 39 7+ spectra with min prob 0.5

Initializing 26896 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000
.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P11352|GPX1_MOUSE : U
MCAARLSAAAQSTVYAFSARPLTGGEPVSLGSLRGKVLLIENVASLUGTTIRDYTEMNDLQKRLGPRGLVVLGFPCNQFGHQENGKNEEILNSLKYVRPGGGFEPNFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVGPDGVPVRRYSRRFRTIDIEPDIETLLSQQSGNS
..:.........:.........:.........:.........:.........:.........101000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000
.WARNING: Found the following zero-mass residues in protein entry sp|Q80TA1|EPT1_MOUSE : U
MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKVFPTWLAPNLITFSGFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYNTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMVGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL
........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000
.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q99MD6|TRXR3_MOUSE : U
MEKPPSPPPPPRAQTSPGLGKVGVLPNRRLGAVRGGLMSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTRVKELFSSLGVVYNILELDQVDDGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQAHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAKEAANLGKKVMVLDFVVPSPQGTTWGLGGTCVNVGCIPKKLMHQAALLGHALQDAKKYGWEYNQQVKHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIKATNKKGQETFYTASKFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGCTLVVGASYVGLECAGFLAGLGLDVTVMVRSVLLRGFDQEMAEKVGSYLEQQGVKFQRKFTPILVQQLEKGLPGKLKVVAKSTEGPETVEGIYNTVLLAIGRDSCTRKIGLEKIGVKINEKNGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLARRLFGVSLEKCDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLEVYHTLFWPLEWTVAGRDNNTCYAKIICNKFDNERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG
.........:.........:.........:.........:.........:.........:.........118000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000
.........:.........:.........:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|Q9DBC0|SELO_MOUSE : U
MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLALAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS
....:.........:.........:.........120000
.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q9ERR7|SEP15_MOUSE : U
MAAGQGGWLRPALGLRLLLATAFQAVSALGAEFASEACRELGFSSNLLCSSCDLLGQFNLLPLDPVCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
.........:.........:.........:.........:.........:.........:.........:.........121000
..WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6-2|TRXR1_MOUSE : U
MNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG
WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U
MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG
.......:.........:.........:.........:.........:.........:.........:.........:.........:.........122000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........129000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........130000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........131000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........132000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........133000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........134000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........135000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........136000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........137000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........138000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........139000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........140000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........141000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........142000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........143000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........144000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........145000
.........:.........:........WARNING: Found the following zero-mass residues in protein entry tr|B9EJ24|B9EJ24_MOUSE : U
MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLAAAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS
.:.........:.........:.........:.........:.........:.........:.........146000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........147000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........148000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........149000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........150000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........151000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........152000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........153000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........154000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........155000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........156000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........157000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........158000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........159000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........160000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........161000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........162000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........163000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........164000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........165000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........166000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........167000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........168000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........169000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........170000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........171000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........172000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........173000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........174000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........175000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........176000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........177000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........178000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........179000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........180000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........181000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........182000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........183000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........184000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........185000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........186000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........187000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........188000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........189000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........190000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........191000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........192000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........193000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.......  Total: 193978
Computing degenerate peptides for 23055 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28181 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=6.136e-06, db_size=162072768
Computing MU for 28181 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[13:22:17] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe database --annotate D:\Personal\Nishida\Adiposite\230413_AdipositeTMT\2023-04-13-decoys-contam-MouseSPisoTrembl230409.fasta.fas --prefix rev_
INFO[13:22:17] Executing Database  v4.8.1                   
INFO[13:22:17] Annotating the database                      
INFO[13:22:39] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result --protxml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\combined.prot.xml --razor
INFO[13:22:39] Executing Filter  v4.8.1                     
INFO[13:22:39] Processing peptide identification files      
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN02AdipositeKRNpepGlobalTMT6plexFr1.pep.xml 
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN05AdipositeKRNpepGlobalTMT6plexFr4.pep.xml 
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN07AdipositeKRNpepGlobalTMT6plexFr6.pep.xml 
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN04AdipositeKRNpepGlobalTMT6plexFr3.pep.xml 
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN03AdipositeKRNpepGlobalTMT6plexFr2.pep.xml 
INFO[13:22:39] Parsing D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\interact-230327HN06AdipositeKRNpepGlobalTMT6plexFr5.pep.xml 
INFO[13:22:41] 1+ Charge profile                             decoy=0 target=0
INFO[13:22:41] 2+ Charge profile                             decoy=326 target=7183
INFO[13:22:41] 3+ Charge profile                             decoy=295 target=15377
INFO[13:22:41] 4+ Charge profile                             decoy=113 target=9253
INFO[13:22:41] 5+ Charge profile                             decoy=54 target=2939
INFO[13:22:41] 6+ Charge profile                             decoy=20 target=838
INFO[13:22:41] Database search results                       ions=26784 peptides=20100 psms=36621
INFO[13:22:41] Converged to 1.00 % FDR with 35005 PSMs       decoy=350 threshold=0.741273 total=35355
INFO[13:22:41] Converged to 1.00 % FDR with 18633 Peptides   decoy=186 threshold=0.820986 total=18819
INFO[13:22:41] Converged to 1.00 % FDR with 25295 Ions       decoy=252 threshold=0.786556 total=25547
INFO[13:22:47] Protein inference results                     decoy=736 target=9212
INFO[13:22:48] Converged to 1.00 % FDR with 4500 Proteins    decoy=45 threshold=0.9192 total=4545
INFO[13:22:50] Applying sequential FDR estimation            ions=25231 peptides=18656 psms=34794
INFO[13:22:50] Converged to 0.20 % FDR with 34724 PSMs       decoy=70 threshold=0.741362 total=34794
INFO[13:22:50] Converged to 0.25 % FDR with 18609 Peptides   decoy=47 threshold=0.741362 total=18656
INFO[13:22:50] Converged to 0.21 % FDR with 25178 Ions       decoy=53 threshold=0.741362 total=25231
INFO[13:22:51] Post processing identifications              
INFO[13:22:55] Assigning protein identifications to layers  
INFO[13:22:57] Processing protein inference                 
INFO[13:23:59] Synchronizing PSMs and proteins              
INFO[13:23:59] Final report numbers after FDR filtering, and post-processing  ions=25176 peptides=18608 proteins=4499 psms=34721
INFO[13:23:59] Saving                                       
INFO[13:24:00] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
FreeQuant [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT
INFO[13:24:00] Executing Label-free quantification  v4.8.1  
INFO[13:24:03] Indexing PSM information                     
INFO[13:24:03] Reading spectra and tracing peaks            
INFO[13:24:03] Processing 230327HN02AdipositeKRNpepGlobalTMT6plexFr1 
INFO[13:24:17] Processing 230327HN03AdipositeKRNpepGlobalTMT6plexFr2 
INFO[13:24:30] Processing 230327HN04AdipositeKRNpepGlobalTMT6plexFr3 
INFO[13:24:44] Processing 230327HN05AdipositeKRNpepGlobalTMT6plexFr4 
INFO[13:24:57] Processing 230327HN06AdipositeKRNpepGlobalTMT6plexFr5 
INFO[13:25:09] Processing 230327HN07AdipositeKRNpepGlobalTMT6plexFr6 
INFO[13:25:22] Assigning intensities to data layers         
INFO[13:25:23] Done                                         
Process 'FreeQuant' finished, exit code: 0
Quant (Isobaric) [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe labelquant --tol 20 --level 2 --minprob 0.900 --purity 0.500 --removelow 0.050 --plex 10 --annot D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\AdipocyteTMT_annotation.txt --brand tmt --dir D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT
INFO[13:25:23] Executing Isobaric-label quantification  v4.8.1 
INFO[13:25:26] Calculating intensities and ion interference 
INFO[13:25:26] Processing 230327HN02AdipositeKRNpepGlobalTMT6plexFr1 
INFO[13:25:40] Processing 230327HN03AdipositeKRNpepGlobalTMT6plexFr2 
INFO[13:25:54] Processing 230327HN04AdipositeKRNpepGlobalTMT6plexFr3 
INFO[13:26:07] Processing 230327HN05AdipositeKRNpepGlobalTMT6plexFr4 
INFO[13:26:20] Processing 230327HN06AdipositeKRNpepGlobalTMT6plexFr5 
INFO[13:26:33] Processing 230327HN07AdipositeKRNpepGlobalTMT6plexFr6 
INFO[13:26:47] Filtering spectra for label quantification   
INFO[13:26:47] Removing 1740 PSMs from isobaric quantification 
INFO[13:26:47] Saving                                       
INFO[13:26:49] Done                                         
Process 'Quant (Isobaric)' finished, exit code: 0
PhilosopherReport [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe report
INFO[13:26:49] Executing Report  v4.8.1                     
INFO[13:26:49] Creating reports                             
INFO[13:26:55] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\philosopher_v4.8.1_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[13:26:56] Executing Workspace  v4.8.1                  
INFO[13:26:56] Removing workspace                           
INFO[13:26:56] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
TmtIntegrator [Work dir: D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result]
D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\jre\bin\java.exe -Xmx209G -cp "D:\Personal\Nishida\FragPipe-jre-19.1\fragpipe\tools\tmt-integrator-4.0.4.jar" TMTIntegrator D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\tmt-integrator-conf.yml D:\Personal\Nishida\Adiposite\230817_Re\Global_TMT\Result\psm.tsv
TMT-Integrator v4.0.4
Load parameters and check PSMs--- 0.00900 min.
Load fasta--- 7.08748 min.
UpdateColumns--- 0.03465 min.
LoadPsms--- 0.00923 min.
Take log and normalize--- 0.00557 min.
PSM normalization--- 0.00000 min.
outlierRemoval--- 0.01007 min.
Collapse--- 0.00337 min.
protNorm--- 0.00010 min.
Report--- 0.00207 min.
Total run time--- 7.16260 min.
Finish!!!
Process 'TmtIntegrator' 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)
(Isobaric-labeling quantification) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020)
(Visualization with FP-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

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