System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A


Version info:
FragPipe version 24.0
DIA-Umpire version 2.3.3
diaTracer version 2.2.1
MSFragger version 4.4
Crystal-C version 1.5.10
MSBooster version 1.4.14
Percolator version 3.7.1
PTMProphet version 6.3.2
Metaproteomics version 1.0.1
Philosopher version 5.1.3-RC9
PTM-Shepherd version 3.0.11
IonQuant version 1.11.18
TMT-Integrator version 6.1.3
FragPipe-SpecLib version 0.1.58
DIA-NN version 1.8.2 beta 8
Skyline version N/A
Pandas version 2.3.3
Numpy version 1.26.4


LCMS files:
  Experiment/Group: NPS_4
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML	DDA
  Experiment/Group: NPS_5
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML	DDA
  Experiment/Group: NPS_6
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML	DDA
  Experiment/Group: OCBS_10
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML	DDA
  Experiment/Group: OCBS_11
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML	DDA
  Experiment/Group: OCBS_12
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML	DDA


75 commands to execute:
CheckCentroid
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar org.nesvilab.fragpipe.util.CheckCentroid F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML 23
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\c93eb04b-db29-41a5-b71c-c8dc2bcfa92e
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\1cbc1642-dec1-4069-937f-9ba4509efb1a
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\d347b4e3-f4a4-40d3-b5f0-0c8c2a6b69fd
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\f93761e9-3873-4dfd-b7e8-6eb31c7c5626
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\14da9b93-97a5-4af3-ba5c-4c35e5f00f3b
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\dfcf201a-8b42-45da-9f60-5329d1e89f96
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\949b7d8b-cb7a-4151-beab-109554e7d1ce
MSFragger [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx112G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\fragger.params F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pin
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pin
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pin
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pin
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pin
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pepXML
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pin
MSBooster [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -cp C:\FragPipe\FragPipe-24.0\tools\MSBooster-1.4.14.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar mainsteps.MainClass --paramsList F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\msbooster_params.txt
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505616_percolator_target_psms.tsv --decoy-results-psms 202505616_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505616_edited.pin
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505617_percolator_target_psms.tsv --decoy-results-psms 202505617_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505617_edited.pin
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505618_percolator_target_psms.tsv --decoy-results-psms 202505618_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505618_edited.pin
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505622_percolator_target_psms.tsv --decoy-results-psms 202505622_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505622_edited.pin
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505623_percolator_target_psms.tsv --decoy-results-psms 202505623_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505623_edited.pin
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505624_percolator_target_psms.tsv --decoy-results-psms 202505624_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505624_edited.pin
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505616.pin 202505616 202505616_percolator_target_psms.tsv 202505616_percolator_decoy_psms.tsv interact-202505616 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505617.pin 202505617 202505617_percolator_target_psms.tsv 202505617_percolator_decoy_psms.tsv interact-202505617 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505618.pin 202505618 202505618_percolator_target_psms.tsv 202505618_percolator_decoy_psms.tsv interact-202505618 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505622.pin 202505622 202505622_percolator_target_psms.tsv 202505622_percolator_decoy_psms.tsv interact-202505622 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505623.pin 202505623 202505623_percolator_target_psms.tsv 202505623_percolator_decoy_psms.tsv interact-202505623 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505624.pin 202505624 202505624_percolator_target_psms.tsv 202505624_percolator_decoy_psms.tsv interact-202505624 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_percolator_target_psms.tsv
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_percolator_decoy_psms.tsv
ProteinProphet [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe database --annotate F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas --prefix rev_
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --razor
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
IonQuant [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\thermo -cp C:\FragPipe\FragPipe-24.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-24.0\tools\IonQuant-1.11.18.jar ionquant.IonQuant --threads 23 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --intensitymode 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\filelist_ionquant.txt --modlist F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [CheckCentroid], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
    Cmd: [MSFragger], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [MSBooster], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [Percolator], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [ProteinProphet], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [PhilosopherDbAnnotate], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [PhilosopherFilter], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [PhilosopherReport], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
    Cmd: [IonQuant], Work dir: [F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]

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

~~~~~~Sample of F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas~~~~~~~
>XP_013583243.1 PREDICTED: agamous-like MADS-box protein AGL93 [Brassica oleracea var. oleracea]
>XP_013588923.1 PREDICTED: uncharacterized protein LOC106297186 isoform X2 [Brassica oleracea var. oleracea]
>XP_013594603.1 PREDICTED: uncharacterized protein At2g34160-like [Brassica oleracea var. oleracea]
>XP_013600283.1 PREDICTED: uncharacterized protein LOC106307778 [Brassica oleracea var. oleracea]
>XP_013605963.1 PREDICTED: glucose-6-phosphate/phosphate translocator 1, chloroplastic [Brassica oleracea var. oleracea]
>XP_013611643.1 PREDICTED: magnesium transporter MRS2-11, chloroplastic [Brassica oleracea var. oleracea]
>XP_013617323.1 PREDICTED: uncharacterized protein LOC106323800 [Brassica oleracea var. oleracea]
>XP_013623003.1 PREDICTED: CMP-sialic acid transporter 5 [Brassica oleracea var. oleracea]
>XP_013628683.1 PREDICTED: uncharacterized protein LOC106334852 [Brassica oleracea var. oleracea]
>XP_013634363.1 PREDICTED: tropinone reductase homolog At2g30670-like isoform X2 [Brassica oleracea var. oleracea]
>contam_sp|Q29463|TRY2_BOVIN Anionic trypsin OS=Bos taurus OX=9913 PE=2 SV=1
>rev_XP_013588918.1 PREDICTED: beclin-1-like protein isoform X2 [Brassica oleracea var. oleracea]
>rev_XP_013594598.1 PREDICTED: uncharacterized protein LOC106302685 [Brassica oleracea var. oleracea]
>rev_XP_013600278.1 PREDICTED: protein OSB1, mitochondrial isoform X1 [Brassica oleracea var. oleracea]
>rev_XP_013605958.1 PREDICTED: glucan endo-1,3-beta-glucosidase 8 [Brassica oleracea var. oleracea]
>rev_XP_013611638.1 PREDICTED: divinyl chlorophyllide a 8-vinyl-reductase, chloroplastic [Brassica oleracea var. oleracea]
>rev_XP_013617318.1 PREDICTED: uncharacterized protein LOC106323793 [Brassica oleracea var. oleracea]
>rev_XP_013622998.1 PREDICTED: SPX domain-containing protein 2 [Brassica oleracea var. oleracea]
>rev_XP_013628678.1 PREDICTED: uncharacterized protein LOC106334845 [Brassica oleracea var. oleracea]
>rev_XP_013634358.1 PREDICTED: uncharacterized protein LOC106340033 [Brassica oleracea var. oleracea]
>rev_contam_sp|Q14525|KT33B_HUMAN Keratin, type I cuticular Ha3-II OS=Homo sapiens OX=9606 GN=KRT33B PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v24.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=F\:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.channel-normalization-strategy=0
diann.cmd-opts=
diann.gene-level-report=false
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.mbr=false
diann.medium=
diann.min-site-prob=0.75
diann.mod-tag=
diann.modified-peptide-level-report=true
diann.peptide-level-report=true
diann.protein-level-report=false
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=2
diann.redo-protein-inference=false
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.site-level-report=false
diann.unrelated-runs=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=false
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.coadaptr.fpop.fpop_masses=
fpop.coadaptr.fpop.run-fpop-coadaptr=false
fpop.fragpipe.fpop.fpop-tmt=false
fpop.fragpipe.fpop.label_control=
fpop.fragpipe.fpop.label_fpop=
fpop.fragpipe.fpop.region_size=1
fpop.fragpipe.fpop.run-fpop=false
fpop.fragpipe.fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\FragPipe\\FragPipe-24.0\\tools\\diann\\1.8.2_beta_8\\windows\\DiaNN.exe
fragpipe-config.bin-python=C\:\\FragPipe\\FragPipe-24.0\\python\\python.exe
fragpipe-config.tools-folder=C\:\\FragPipe\\FragPipe-24.0\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.formula=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.intensitymode=2
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
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
mbg.allow_chimeric=false
mbg.expand_db=1
mbg.fdr=0.010
mbg.max_glycan_q=0.01
mbg.max_skips=0
mbg.min_glycans=2
mbg.min_psms=5
mbg.residues_to_add=HexNAc(1),Hex(1),Fuc(1),NeuAc(1),NH4(1),Na(1),Fe(1)
mbg.run-mbg=false
metaproteomics.cmd-line-opts=
metaproteomics.delta-hyperscore=0.0
metaproteomics.host-name=Homo sapiens
metaproteomics.iterations=3
metaproteomics.min-pept-cnt-per-prot=1
metaproteomics.min-uniq-pept-cnt=3
metaproteomics.min-uniq-pept-cnt-per-prot=1
metaproteomics.qvalue=0.01
metaproteomics.run-metaproteomics=false
msbooster.find-best-im-model=false
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.fragmentation-type=0
msbooster.im-model=DIA-NN
msbooster.koina-url=
msbooster.predict-im=true
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msbooster.spectral-library-path=
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
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-only=false
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_fragment_ion_series=b,y
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.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=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,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; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.allowed_sites=
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01 --picked
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.prot-level-summary=false
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.override-defaults=false
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotate_assigned_mods=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_lda=false
ptmshepherd.glyco_lda_features=yscore,oxo,mass
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.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.print_full_glyco_params=false
ptmshepherd.prob_mass=0.5
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.shuffle_decoy_intensities=false
ptmshepherd.spectra_condPeaks=150
ptmshepherd.spectra_condRatio=0.0001
ptmshepherd.spectra_maxPrecursorCharge=4
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.use_glycan_fragment_probs=false
ptmshepherd.use_msfragger_localization=false
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
skyline.fdr=1
skyline.generate-skyline-quant-report=false
skyline.min-site-prob=0.75
skyline.mod-tag=
skyline.run-skyline=false
skyline.skyline=false
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=true
skyline.skyline-fragment-tolerance=10
skyline.skyline-library-product-ions=12
skyline.skyline-mods-mode=Default
skyline.skyline-precursor-tolerance=10
skyline.skyline-rt-tolerance=2
skyline.use-existing-skyline-document=false
speclibgen.convert-pepxml=true
speclibgen.convert-psm=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
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.labile_mode=Regular (not glyco)
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_temp_files=true
tab-run.export_matched_fragments=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=-1
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_resolution=0
tmtintegrator.min_site_prob=-1
tmtintegrator.min_snr=0
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_d_tag=Pool
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
transfer-learning.credential=
transfer-learning.instrument=Astral
transfer-learning.keep-decoys=false
transfer-learning.max-charge=3
transfer-learning.min-charge=2
transfer-learning.model-path=
transfer-learning.nce=30
transfer-learning.output-format=tsv
transfer-learning.peptides-to-predict=Whole FASTA file
transfer-learning.perform-transfer-learning=true
transfer-learning.predict-im=true
transfer-learning.predict-ms2=true
transfer-learning.predict-rt=true
transfer-learning.predict-spectral-library=true
transfer-learning.run-transfer-learning=false
transfer-learning.spectral-library-path=
workdir=F\:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.misc.sdrf-type=Default
workflow.ram=0
workflow.threads=23

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar org.nesvilab.fragpipe.util.CheckCentroid F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML 23
Done in 0.7 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:21" level=info msg="Executing Workspace  v5.1.3"
time="07:48:21" level=info msg="Removing workspace"
time="07:48:21" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\c93eb04b-db29-41a5-b71c-c8dc2bcfa92e
time="07:48:21" level=info msg="Executing Workspace  v5.1.3"
time="07:48:21" level=info msg="Creating workspace"
time="07:48:21" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:21" level=info msg="Executing Workspace  v5.1.3"
time="07:48:21" level=info msg="Removing workspace"
time="07:48:21" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\1cbc1642-dec1-4069-937f-9ba4509efb1a
time="07:48:21" level=info msg="Executing Workspace  v5.1.3"
time="07:48:21" level=info msg="Creating workspace"
time="07:48:21" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:21" level=info msg="Executing Workspace  v5.1.3"
time="07:48:21" level=info msg="Removing workspace"
time="07:48:21" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\d347b4e3-f4a4-40d3-b5f0-0c8c2a6b69fd
time="07:48:22" level=info msg="Executing Workspace  v5.1.3"
time="07:48:22" level=info msg="Creating workspace"
time="07:48:22" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:22" level=info msg="Executing Workspace  v5.1.3"
time="07:48:22" level=info msg="Removing workspace"
time="07:48:22" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\f93761e9-3873-4dfd-b7e8-6eb31c7c5626
time="07:48:22" level=info msg="Executing Workspace  v5.1.3"
time="07:48:22" level=info msg="Creating workspace"
time="07:48:22" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:22" level=info msg="Executing Workspace  v5.1.3"
time="07:48:22" level=info msg="Removing workspace"
time="07:48:22" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\14da9b93-97a5-4af3-ba5c-4c35e5f00f3b
time="07:48:22" level=info msg="Executing Workspace  v5.1.3"
time="07:48:22" level=info msg="Creating workspace"
time="07:48:22" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:23" level=info msg="Executing Workspace  v5.1.3"
time="07:48:23" level=info msg="Removing workspace"
time="07:48:23" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\dfcf201a-8b42-45da-9f60-5329d1e89f96
time="07:48:23" level=info msg="Executing Workspace  v5.1.3"
time="07:48:23" level=info msg="Creating workspace"
time="07:48:23" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:48:23" level=info msg="Executing Workspace  v5.1.3"
time="07:48:23" level=info msg="Removing workspace"
time="07:48:23" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\949b7d8b-cb7a-4151-beab-109554e7d1ce
time="07:48:23" level=info msg="Executing Workspace  v5.1.3"
time="07:48:23" level=info msg="Creating workspace"
time="07:48:23" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx112G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\fragger.params F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML
MSFragger version MSFragger-4.4
Batmass-IO version 1.36.5
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 112 GB memory
Checking database...
Checking spectral files...
202505616.mzML: Scans = 11274; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
202505622.mzML: Scans = 11422; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
202505618.mzML: Scans = 11241; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
202505623.mzML: Scans = 11361; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
202505617.mzML: Scans = 11281; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
202505624.mzML: Scans = 11420; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = Agilent instrument model
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 23
database_name = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas
decoy_prefix = rev_
keep_decoys = 1
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mzml = 1
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
use_detailed_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 2
precursor_charge_high = 3
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
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 = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
546661536 fragments to be searched in 1 slices (5.09 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.58 s
	001. 202505616.mzML 2.7 s | deisotoping 0.1 s
		[progress: 11274/11274 (100%) - 20204 spectra/s] 0.6s
	002. 202505617.mzML 2.3 s | deisotoping 0.0 s
		[progress: 11281/11281 (100%) - 26606 spectra/s] 0.4s
	003. 202505618.mzML 2.6 s | deisotoping 0.0 s
		[progress: 11241/11241 (100%) - 35349 spectra/s] 0.3s
	004. 202505622.mzML 3.1 s | deisotoping 0.1 s
		[progress: 11422/11422 (100%) - 101080 spectra/s] 0.1s
	005. 202505623.mzML 3.2 s | deisotoping 0.0 s
		[progress: 11361/11361 (100%) - 102351 spectra/s] 0.1s
	006. 202505624.mzML 3.1 s | deisotoping 0.0 s
		[progress: 11420/11420 (100%) - 106729 spectra/s] 0.1s
postprocessing 202505616.mzML 0.0 s
postprocessing 202505617.mzML 0.0 s
postprocessing 202505618.mzML 0.0 s
postprocessing 202505622.mzML 0.0 s
postprocessing 202505623.mzML 0.0 s
postprocessing 202505624.mzML 0.0 s
***************************FIRST SEARCH DONE IN 0.391 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -9.20   1.23 |   0.07   3.40 |  -4.82   9.57 |  -2.23   9.62  
 002 |  -9.75   1.56 |   0.38   2.32 |  -3.57   9.20 |  -0.79   9.50  
 003 |  -9.07   1.34 |  -0.06   1.72 |  -3.59   8.97 |  -0.99   9.27  
 004 |  -8.58   1.32 |   0.23   2.41 |  -2.89   8.99 |  -0.23   8.89  
 005 |  -8.29   2.09 |   0.39   2.51 |  -2.93   8.69 |  -0.36   8.92  
 006 |  -8.85   1.38 |   0.16   2.12 |  -2.79   9.08 |  -0.28   8.99  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  | skip  |   2375|   2439|   2436| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |   2477|   2461| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   2382
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |   2262
-------|-------
New fragment_mass_tolerance = 25.000000 PPM
New use_topN_peaks = 300
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.636 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 23
database_name = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas
decoy_prefix = rev_
keep_decoys = 1
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 = 25.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mzml = 1
write_mzbin_all = 0
isotope_error = 0/1/2
mass_offsets = 0.0
use_detailed_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
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 = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.13 Da.
546661536 fragments to be searched in 1 slices (5.09 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.34 s
	001. 202505616.mzBIN_calibrated 0.2 s
		[progress: 11274/11274 (100%) - 106358 spectra/s] 0.1s
	002. 202505617.mzBIN_calibrated 0.2 s
		[progress: 11281/11281 (100%) - 106425 spectra/s] 0.1s
	003. 202505618.mzBIN_calibrated 0.2 s
		[progress: 11241/11241 (100%) - 104083 spectra/s] 0.1s
	004. 202505622.mzBIN_calibrated 0.2 s
		[progress: 11422/11422 (100%) - 99322 spectra/s] 0.1s
	005. 202505623.mzBIN_calibrated 0.2 s
		[progress: 11361/11361 (100%) - 107179 spectra/s] 0.1s
	006. 202505624.mzBIN_calibrated 0.2 s
		[progress: 11420/11420 (100%) - 105741 spectra/s] 0.1s
postprocessing 202505616.mzBIN_calibrated 1.2 s
postprocessing 202505617.mzBIN_calibrated 0.9 s
postprocessing 202505618.mzBIN_calibrated 0.8 s
postprocessing 202505622.mzBIN_calibrated 0.8 s
postprocessing 202505623.mzBIN_calibrated 0.8 s
postprocessing 202505624.mzBIN_calibrated 0.8 s
***************************MAIN SEARCH DONE IN 0.165 MIN***************************

*******************************TOTAL TIME 1.192 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.pepXML F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -cp C:\FragPipe\FragPipe-24.0\tools\MSBooster-1.4.14.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar mainsteps.MainClass --paramsList F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\msbooster_params.txt
2026-07-20 07:49:38 [INFO] - MSBooster v1.4.14
2026-07-20 07:49:39 [INFO] - Creating output folder at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster
2026-07-20 07:49:39 [INFO] - Using 23 threads
2026-07-20 07:49:39 [INFO] - Instrument detected: TIMSTOF
2026-07-20 07:49:39 [INFO] - mzml file does not contain filter string. Setting to default.
2026-07-20 07:49:39 [INFO] - NCE and fragmentation type detected: {HCD=25}
2026-07-20 07:49:39 [INFO] - Creating input file for createFull
2026-07-20 07:49:39 [INFO] - 2130 PSMs for prediction
2026-07-20 07:49:39 [INFO] - createFull input file generation took 71 milliseconds
2026-07-20 07:49:39 [INFO] - Input file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT_full.tsv
2026-07-20 07:49:39 [INFO] - Generating input file for DIA-NN
2026-07-20 07:49:39 [INFO] - Creating input file for Diann
2026-07-20 07:49:39 [INFO] - 2130 PSMs for prediction
2026-07-20 07:49:39 [INFO] - Writing DIA-NN input file
2026-07-20 07:49:39 [INFO] - Diann input file generation took 45 milliseconds
2026-07-20 07:49:39 [INFO] - Input file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.tsv
2026-07-20 07:49:39 [INFO] - Generating DIA-NN predictions
2026-07-20 07:49:39 [INFO] - C:\FragPipe\FragPipe-24.0\tools\diann\1.8.2_beta_8\windows\DiaNN.exe --lib F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.tsv --predict --threads 23 --strip-unknown-mods --predict-n-frag 100
2026-07-20 07:49:39 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
2026-07-20 07:49:39 [INFO] - Compiled on Sep 15 2022 18:28:57
2026-07-20 07:49:39 [INFO] - Current date and time: Mon Jul 20 07:49:39 2026
2026-07-20 07:49:39 [INFO] - CPU: AuthenticAMD AMD Ryzen 9 9900X 12-Core Processor
2026-07-20 07:49:39 [INFO] - SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 SSE4a 
2026-07-20 07:49:39 [INFO] - Logical CPU cores: 24
2026-07-20 07:49:39 [INFO] - Predicted spectra will be saved in a binary format
2026-07-20 07:49:39 [INFO] - Thread number set to 23
2026-07-20 07:49:39 [INFO] - 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
2026-07-20 07:49:39 [INFO] - Deep learning predictor will predict 100 fragments
2026-07-20 07:49:39 [INFO] - 
2026-07-20 07:49:39 [INFO] - 0 files will be processed
2026-07-20 07:49:39 [INFO] - [0:00] Loading spectral library F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.tsv
2026-07-20 07:49:39 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
2026-07-20 07:49:39 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 2130 precursors in 1991 elution groups.
2026-07-20 07:49:39 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction
2026-07-20 07:49:39 [INFO] - [0:00] Predicting spectra and IMs
2026-07-20 07:49:40 [INFO] - [0:00] Predicting RTs
2026-07-20 07:49:40 [INFO] - [0:00] Decoding predicted spectra and IMs
2026-07-20 07:49:40 [INFO] - [0:00] Decoding RTs
2026-07-20 07:49:40 [INFO] - [0:00] Saving the list of predictions to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.predicted.bin
2026-07-20 07:49:40 [INFO] - Finished
2026-07-20 07:49:40 [INFO] - Done generating DIA-NN predictions
2026-07-20 07:49:40 [INFO] - Model running took 771 milliseconds
2026-07-20 07:49:40 [INFO] - Generating edited pin with following features: [unweightedSpectralEntropy, weightedSpectralEntropy, hypergeometricProbability, intersection, top6matchedIntensity, deltaRTLOESS, deltaRTLOESSreal]
2026-07-20 07:49:40 [INFO] - Loading predicted spectra: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.predicted.bin
2026-07-20 07:49:40 [INFO] - Loading predicted retention times: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.predicted.bin
2026-07-20 07:49:40 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pin has 1144 PSMs
2026-07-20 07:49:40 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pin
2026-07-20 07:49:40 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:41 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:41 [INFO] - RT regression using 94 PSMs
2026-07-20 07:49:41 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:41 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:41 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_edited.pin
2026-07-20 07:49:42 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pin has 1160 PSMs
2026-07-20 07:49:42 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pin
2026-07-20 07:49:42 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - RT regression using 93 PSMs
2026-07-20 07:49:42 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_edited.pin
2026-07-20 07:49:42 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pin has 1152 PSMs
2026-07-20 07:49:42 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pin
2026-07-20 07:49:42 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:42 [INFO] - RT regression using 103 PSMs
Iteration 1...2...3...4...5...
2026-07-20 07:49:42 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 1.0
2026-07-20 07:49:43 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_edited.pin
2026-07-20 07:49:43 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pin has 1700 PSMs
2026-07-20 07:49:43 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pin
2026-07-20 07:49:43 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - RT regression using 107 PSMs
Iteration 1...2...3...4...5...
2026-07-20 07:49:43 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 1.0
2026-07-20 07:49:43 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_edited.pin
2026-07-20 07:49:43 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pin has 1435 PSMs
2026-07-20 07:49:43 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pin
2026-07-20 07:49:43 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:43 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - RT regression using 107 PSMs
Iteration 1...2...3...4...5...
2026-07-20 07:49:44 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 1.0
2026-07-20 07:49:44 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_edited.pin
2026-07-20 07:49:44 [INFO] - F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pin has 1419 PSMs
2026-07-20 07:49:44 [INFO] - Processing pin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pin
2026-07-20 07:49:44 [INFO] - Processing F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - RT regression using 118 PSMs
Iteration 1...2...3...4...5...
2026-07-20 07:49:44 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 1.0
2026-07-20 07:49:44 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-20 07:49:44 [INFO] - Edited pin file at F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_edited.pin
2026-07-20 07:49:44 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 4130 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505616_percolator_target_psms.tsv --decoy-results-psms 202505616_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505616_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505616_percolator_target_psms.tsv --decoy-results-psms 202505616_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505616_edited.pin
Started Mon Jul 20 07:49:44 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505616_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1144 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 944 positives and 200 negatives, size ratio=4.72 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 448 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 422 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 425 training set positives with q<0.01 in that direction.
Found 613 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0240 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 727 PSMs with q<0.01
Iteration 2:	Estimated 737 PSMs with q<0.01
Iteration 3:	Estimated 742 PSMs with q<0.01
Iteration 4:	Estimated 743 PSMs with q<0.01
Iteration 5:	Estimated 743 PSMs with q<0.01
Iteration 6:	Estimated 743 PSMs with q<0.01
Iteration 7:	Estimated 744 PSMs with q<0.01
Iteration 8:	Estimated 744 PSMs with q<0.01
Iteration 9:	Estimated 744 PSMs with q<0.01
Iteration 10:	Estimated 744 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.6011	-0.7337	-0.6034	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.5227	 0.4523	 0.3063	isotope_error_0
-0.0719	-0.0295	 0.1396	isotope_error_1
-0.6544	-0.6008	-0.5755	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-2.8161	-0.0927	-0.7935	log10_evalue
 0.2699	 3.1667	 1.0109	hyperscore
-0.3231	-0.2654	 0.7230	delta_hyperscore
 2.6615	 2.0828	 0.6870	matched_ion_num
-1.1447	-0.9557	-1.0831	complementary_ions
-0.3028	-0.7952	 0.0659	ion_series
 0.1849	 0.3790	-0.1875	weighted_average_abs_fragment_ppm
-0.0738	-0.2206	-0.2294	length_7
-0.1906	-0.0335	 0.3342	length_8
 0.2068	 0.2252	-0.0474	length_9_30
-0.0348	-0.1743	-0.1669	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.8604	-1.2573	-0.7591	nmc
-0.5710	-0.5713	-0.3179	charge_1
-0.1110	-0.0629	-0.1633	charge_2
 0.6478	 0.3515	 0.2682	charge_3
-0.1050	 0.4486	 0.4468	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.1361	-0.0929	-0.3997	15.9949M
 0.1417	-0.6268	 0.3366	unweighted_spectral_entropy
 0.3996	 0.6069	-0.0113	weighted_spectral_entropy
-0.2223	-0.1598	 0.5784	hypergeometric_probability
 0.0594	 0.1487	 1.2179	intersection
 0.4217	 1.2833	 0.2281	top6_matched_intensity
-0.2899	-2.0640	-1.0942	delta_RT_loess
 0.2029	 1.7544	 0.4126	delta_RT_loess_real
 2.4193	 2.2210	 2.1277	m0
Found 678 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 944 target PSMs and 200 decoy PSMs.
Calculating q values.
Final list yields 679 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.4740 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505617_percolator_target_psms.tsv --decoy-results-psms 202505617_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505617_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505617_percolator_target_psms.tsv --decoy-results-psms 202505617_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505617_edited.pin
Started Mon Jul 20 07:49:46 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505617_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1160 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 969 positives and 191 negatives, size ratio=5.0733 and pi0=1
Warning : the number of negative samples read is too small to perform a correct classification.

Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 9 as initial direction. Could separate 428 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 35 as initial direction. Could separate 423 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 9 as initial direction. Could separate 427 training set positives with q<0.01 in that direction.
Found 585 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0170 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 760 PSMs with q<0.01
Iteration 2:	Estimated 774 PSMs with q<0.01
Iteration 3:	Estimated 784 PSMs with q<0.01
Iteration 4:	Estimated 784 PSMs with q<0.01
Iteration 5:	Estimated 786 PSMs with q<0.01
Iteration 6:	Estimated 786 PSMs with q<0.01
Iteration 7:	Estimated 786 PSMs with q<0.01
Iteration 8:	Estimated 786 PSMs with q<0.01
Iteration 9:	Estimated 786 PSMs with q<0.01
Iteration 10:	Estimated 786 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.8753	-1.2779	-3.0736	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.3621	 0.0295	-0.0348	isotope_error_0
-0.0809	-0.3644	 1.1968	isotope_error_1
-0.4649	 0.4203	-1.4781	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
 0.1244	-0.9354	-2.4891	log10_evalue
 2.9606	 1.2334	 8.0765	hyperscore
 2.0352	 0.6681	 0.1762	delta_hyperscore
 0.8189	 0.3246	 1.7261	matched_ion_num
-0.1776	-0.4579	-1.0624	complementary_ions
-0.8172	 0.1262	-1.6145	ion_series
 0.1014	-0.0918	 0.4837	weighted_average_abs_fragment_ppm
-0.4709	-0.5741	-0.4255	length_7
 0.7828	 0.4930	 0.8105	length_8
-0.1993	 0.0320	-0.1740	length_9_30
-0.1808	 0.1362	-0.5750	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.8734	-0.5368	-0.7443	nmc
-0.1162	-0.1166	-0.3427	charge_1
-0.6041	-0.1181	-0.4906	charge_2
 0.3817	 0.1311	 0.6253	charge_3
 0.9735	 0.2321	 0.5484	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.3152	-0.5335	-0.8939	15.9949M
 0.8521	 0.5086	 1.0721	unweighted_spectral_entropy
 0.9773	 0.3183	 1.8792	weighted_spectral_entropy
-0.6237	 0.1889	-3.1587	hypergeometric_probability
-1.0138	 0.1570	 1.0560	intersection
 1.3001	 0.9053	 0.6394	top6_matched_intensity
-1.2314	-0.5598	-2.6510	delta_RT_loess
 0.5681	-0.1338	-0.6356	delta_RT_loess_real
 2.0450	 2.4625	 6.5022	m0
Found 681 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 969 target PSMs and 191 decoy PSMs.
Calculating q values.
Final list yields 686 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.2800 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505618_percolator_target_psms.tsv --decoy-results-psms 202505618_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505618_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505618_percolator_target_psms.tsv --decoy-results-psms 202505618_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505618_edited.pin
Started Mon Jul 20 07:49:48 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505618_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1152 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 978 positives and 174 negatives, size ratio=5.62069 and pi0=1
Warning : the number of negative samples read is too small to perform a correct classification.

Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 485 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 455 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 457 training set positives with q<0.01 in that direction.
Found 622 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0170 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 794 PSMs with q<0.01
Iteration 2:	Estimated 808 PSMs with q<0.01
Iteration 3:	Estimated 810 PSMs with q<0.01
Iteration 4:	Estimated 811 PSMs with q<0.01
Iteration 5:	Estimated 811 PSMs with q<0.01
Iteration 6:	Estimated 812 PSMs with q<0.01
Iteration 7:	Estimated 812 PSMs with q<0.01
Iteration 8:	Estimated 812 PSMs with q<0.01
Iteration 9:	Estimated 812 PSMs with q<0.01
Iteration 10:	Estimated 812 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.6469	-0.4464	-0.5605	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.9857	 0.4137	 0.2584	isotope_error_0
 0.2228	-0.0423	-0.1638	isotope_error_1
-1.8595	-0.6045	-0.1996	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-5.0006	-0.6728	-0.3567	log10_evalue
 5.5769	 2.5250	 0.7766	hyperscore
 1.5526	 0.5514	 0.1073	delta_hyperscore
-0.7141	 1.4979	 0.3826	matched_ion_num
-2.4145	-1.3145	-0.7453	complementary_ions
 1.1802	-0.0662	 0.2569	ion_series
 0.4456	-0.1228	 0.4097	weighted_average_abs_fragment_ppm
-1.2020	-0.3975	-0.2560	length_7
 1.0800	 0.6071	 0.2599	length_8
 0.1441	-0.1455	 0.0005	length_9_30
-0.5508	-0.1790	-0.0646	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.2010	-0.2487	-0.1953	nmc
-0.2864	-0.2954	-0.1134	charge_1
 0.3110	-0.0039	-0.0865	charge_2
-0.2025	 0.2559	 0.1548	charge_3
 0.1268	 0.0084	 0.1180	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.2046	-0.1990	 0.1187	15.9949M
 3.5693	 0.4967	 0.2031	unweighted_spectral_entropy
-2.5455	 0.6615	 0.2020	weighted_spectral_entropy
-0.1477	 0.0350	 0.3069	hypergeometric_probability
 2.6794	 0.1205	 0.1096	intersection
-0.4550	-0.0735	 0.1928	top6_matched_intensity
-4.1806	-2.0115	-0.4570	delta_RT_loess
 2.7355	 1.8364	 0.1906	delta_RT_loess_real
 9.3314	 3.0333	 1.0018	m0
Found 769 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 978 target PSMs and 174 decoy PSMs.
Calculating q values.
Final list yields 770 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.0470 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505622_percolator_target_psms.tsv --decoy-results-psms 202505622_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505622_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505622_percolator_target_psms.tsv --decoy-results-psms 202505622_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505622_edited.pin
Started Mon Jul 20 07:49:50 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505622_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1700 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 1366 positives and 334 negatives, size ratio=4.08982 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 35 as initial direction. Could separate 584 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 35 as initial direction. Could separate 582 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 588 training set positives with q<0.01 in that direction.
Found 743 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0210 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 1008 PSMs with q<0.01
Iteration 2:	Estimated 1023 PSMs with q<0.01
Iteration 3:	Estimated 1023 PSMs with q<0.01
Iteration 4:	Estimated 1026 PSMs with q<0.01
Iteration 5:	Estimated 1028 PSMs with q<0.01
Iteration 6:	Estimated 1027 PSMs with q<0.01
Iteration 7:	Estimated 1027 PSMs with q<0.01
Iteration 8:	Estimated 1027 PSMs with q<0.01
Iteration 9:	Estimated 1027 PSMs with q<0.01
Iteration 10:	Estimated 1027 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.3511	-0.3979	-0.6115	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0626	 0.5227	 0.3993	isotope_error_0
-0.0908	-0.1376	 0.0695	isotope_error_1
 0.0103	-0.5993	-0.6508	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.3553	-0.1967	-1.6575	log10_evalue
 2.2564	 0.4566	 2.0712	hyperscore
 1.1115	 0.7450	 0.4429	delta_hyperscore
 0.9573	 1.3317	 1.3731	matched_ion_num
-1.2638	-1.3526	-0.3121	complementary_ions
-1.2192	 1.1013	-0.3956	ion_series
-0.2506	-0.1805	-0.1772	weighted_average_abs_fragment_ppm
 0.0523	 0.0741	 0.0082	length_7
 0.1256	-0.0310	 0.0047	length_8
-0.1175	-0.0180	 0.0074	length_9_30
-0.1494	-0.1302	-0.1414	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.4856	-1.2054	-1.2023	nmc
-0.0624	-0.7439	-0.3664	charge_1
-0.0827	-0.0530	-0.1483	charge_2
 0.1431	 0.5967	 0.4099	charge_3
 0.0201	 0.1790	 0.1736	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.0490	-0.4061	-0.0240	15.9949M
 1.1742	 0.4824	 1.0598	unweighted_spectral_entropy
-1.1747	 1.3025	-0.8201	weighted_spectral_entropy
 1.8966	 0.9948	 0.5252	hypergeometric_probability
-0.1130	 0.0800	-0.1173	intersection
 1.3643	 0.9444	 1.6447	top6_matched_intensity
-0.0238	 0.6562	 0.4001	delta_RT_loess
-0.1964	-0.3654	-0.5542	delta_RT_loess_real
 2.7510	 2.3974	 2.6031	m0
Found 946 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1366 target PSMs and 334 decoy PSMs.
Calculating q values.
Final list yields 954 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.2230 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505623_percolator_target_psms.tsv --decoy-results-psms 202505623_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505623_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505623_percolator_target_psms.tsv --decoy-results-psms 202505623_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505623_edited.pin
Started Mon Jul 20 07:49:51 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505623_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1435 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 1162 positives and 273 negatives, size ratio=4.25641 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 543 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 548 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 541 training set positives with q<0.01 in that direction.
Found 747 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0190 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 909 PSMs with q<0.01
Iteration 2:	Estimated 918 PSMs with q<0.01
Iteration 3:	Estimated 922 PSMs with q<0.01
Iteration 4:	Estimated 923 PSMs with q<0.01
Iteration 5:	Estimated 920 PSMs with q<0.01
Iteration 6:	Estimated 920 PSMs with q<0.01
Iteration 7:	Estimated 920 PSMs with q<0.01
Iteration 8:	Estimated 920 PSMs with q<0.01
Iteration 9:	Estimated 920 PSMs with q<0.01
Iteration 10:	Estimated 920 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.2756	-0.3851	-0.3207	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.3120	 0.3337	 0.2496	isotope_error_0
-0.1082	-0.2385	-0.1297	isotope_error_1
-0.3309	-0.2158	-0.2162	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.6294	-0.5294	-0.6241	log10_evalue
 0.8104	 0.3706	 1.1801	hyperscore
 0.0730	 0.2423	 0.0358	delta_hyperscore
 0.5029	 0.3780	 0.3052	matched_ion_num
-0.8132	-0.6988	-0.7760	complementary_ions
 0.0011	 0.3241	-0.0089	ion_series
 0.1016	-0.0414	 0.0371	weighted_average_abs_fragment_ppm
-0.0106	-0.3198	-0.0766	length_7
 0.0451	 0.3215	 0.0739	length_8
-0.0323	 0.0163	-0.0066	length_9_30
 0.0362	-0.0688	 0.0574	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.3025	-0.4847	-0.2545	nmc
-0.1961	-0.1003	-0.0424	charge_1
-0.0801	-0.0352	-0.1895	charge_2
 0.0561	-0.0319	 0.1371	charge_3
 0.4656	 0.3534	 0.2988	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.1043	 0.1221	 0.0683	15.9949M
 0.2497	 0.2128	 0.3546	unweighted_spectral_entropy
 0.3138	 0.2995	 0.2806	weighted_spectral_entropy
 0.1657	 0.6386	-0.2008	hypergeometric_probability
-0.2391	-0.1773	 0.0176	intersection
 0.7153	 0.4114	 0.5417	top6_matched_intensity
 0.1185	-0.2942	-0.0755	delta_RT_loess
-0.2149	 0.1088	-0.0782	delta_RT_loess_real
 0.4926	 0.8656	 0.5042	m0
Found 860 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1162 target PSMs and 273 decoy PSMs.
Calculating q values.
Final list yields 867 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.0200 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505624_percolator_target_psms.tsv --decoy-results-psms 202505624_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505624_edited.pin
Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08
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:
C:\FragPipe\FragPipe-24.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 202505624_percolator_target_psms.tsv --decoy-results-psms 202505624_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 202505624_edited.pin
Started Mon Jul 20 07:49:53 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 202505624_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection top6_matched_intensity delta_RT_loess delta_RT_loess_real 
Found 1419 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 1137 positives and 282 negatives, size ratio=4.03191 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 536 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 35 as initial direction. Could separate 535 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 531 training set positives with q<0.01 in that direction.
Found 705 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0190 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 865 PSMs with q<0.01
Iteration 2:	Estimated 883 PSMs with q<0.01
Iteration 3:	Estimated 884 PSMs with q<0.01
Iteration 4:	Estimated 889 PSMs with q<0.01
Iteration 5:	Estimated 890 PSMs with q<0.01
Iteration 6:	Estimated 890 PSMs with q<0.01
Iteration 7:	Estimated 891 PSMs with q<0.01
Iteration 8:	Estimated 892 PSMs with q<0.01
Iteration 9:	Estimated 892 PSMs with q<0.01
Iteration 10:	Estimated 892 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.0849	-1.0724	-0.2071	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 2.1701	 0.2749	 0.0971	isotope_error_0
-1.6277	-0.1237	 0.2582	isotope_error_1
-1.3123	-0.2655	-0.4573	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.4438	-0.7522	-0.9309	log10_evalue
 10.5421	 1.5070	 1.5100	hyperscore
 1.5524	 0.0884	 1.1308	delta_hyperscore
 0.6587	 0.8093	 1.1479	matched_ion_num
-2.8568	-1.6766	-0.3672	complementary_ions
-1.3597	 0.4116	-1.0133	ion_series
 0.0211	-0.0998	 0.0294	weighted_average_abs_fragment_ppm
 0.1240	-0.4563	-0.2260	length_7
 0.5849	 0.1213	 0.3053	length_8
-0.4901	 0.2626	-0.0412	length_9_30
-0.3214	-0.0354	-0.1120	length_31
 0.0000	 0.0000	 0.0000	ntt
-2.0857	-1.3174	-0.6178	nmc
-0.7513	 0.2835	-0.1014	charge_1
-0.4527	-0.4029	-0.2135	charge_2
 0.6800	 0.1995	 0.3522	charge_3
 1.3175	 0.1382	 0.0103	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.3498	 0.1869	-0.0507	15.9949M
 0.2365	 1.2899	 0.6702	unweighted_spectral_entropy
 0.6592	 0.4968	-0.1453	weighted_spectral_entropy
 3.7296	 1.1285	 0.6195	hypergeometric_probability
-2.2803	-1.0141	-0.7101	intersection
 1.5373	 1.7388	 0.8993	top6_matched_intensity
-4.2939	-1.8250	-2.8667	delta_RT_loess
 2.3638	 0.9513	 2.0981	delta_RT_loess_real
 5.4048	 1.0935	 1.8832	m0
Found 836 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 1137 target PSMs and 282 decoy PSMs.
Calculating q values.
Final list yields 839 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.2760 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505616.pin 202505616 202505616_percolator_target_psms.tsv 202505616_percolator_decoy_psms.tsv interact-202505616 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505617.pin 202505617 202505617_percolator_target_psms.tsv 202505617_percolator_decoy_psms.tsv interact-202505617 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505618.pin 202505618 202505618_percolator_target_psms.tsv 202505618_percolator_decoy_psms.tsv interact-202505618 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505622.pin 202505622 202505622_percolator_target_psms.tsv 202505622_percolator_decoy_psms.tsv interact-202505622 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505623.pin 202505623 202505623_percolator_target_psms.tsv 202505623_percolator_decoy_psms.tsv interact-202505623 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 202505624.pin 202505624 202505624_percolator_target_psms.tsv 202505624_percolator_decoy_psms.tsv interact-202505624 DDA 0.5 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_percolator_target_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator delete temp
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
ProteinProphet [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\filelist_proteinprophet.txt
time="07:49:59" level=info msg="Executing ProteinProphet  v5.1.3"
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 F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\interact-202505616.pep.xml...
...read in 56 1+, 599 2+, 137 3+, 27 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\interact-202505617.pep.xml...
...read in 66 1+, 617 2+, 145 3+, 31 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\interact-202505618.pep.xml...
...read in 59 1+, 604 2+, 120 3+, 24 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\interact-202505622.pep.xml...
...read in 92 1+, 810 2+, 196 3+, 21 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\interact-202505623.pep.xml...
...read in 81 1+, 707 2+, 155 3+, 37 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\interact-202505624.pep.xml...
...read in 81 1+, 680 2+, 161 3+, 27 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 766 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas
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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000
.........:.........:.........:.........:.........:.........:.  Total: 113610
Computing degenerate peptides for 1288 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 1544 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1544 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1544 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.26482e-06, db_size=94128175
Computing MU for 1544 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="07:50:01" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe database --annotate F:\Research\PXD069532-Broccoli-Agilent-QqTOF\2026-07-17-decoys-contam-GCF_000695525.1_BOL_protein.fas --prefix rev_
time="07:50:01" level=info msg="Executing Database  v5.1.3"
time="07:50:01" level=info msg="Annotating the database"
time="07:50:01" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --razor
time="07:50:01" level=info msg="Executing Filter  v5.1.3"
time="07:50:01" level=info msg="Processing peptide identification files"
time="07:50:01" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4\\interact-202505616.pep.xml"
time="07:50:01" level=info msg="1+ Charge profile" decoy=7 target=49
time="07:50:01" level=info msg="2+ Charge profile" decoy=28 target=571
time="07:50:01" level=info msg="3+ Charge profile" decoy=9 target=128
time="07:50:01" level=info msg="4+ Charge profile" decoy=0 target=27
time="07:50:01" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:01" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:01" level=info msg="Database search results" ions=360 peptides=314 psms=819
time="07:50:01" level=info msg="Converged to 0.88 % FDR with 684 PSMs" decoy=6 threshold=0.841686 total=690
time="07:50:01" level=info msg="Converged to 0.93 % FDR with 215 Peptides" decoy=2 threshold=0.879058 total=217
time="07:50:01" level=info msg="Converged to 0.78 % FDR with 257 Ions" decoy=2 threshold=0.879058 total=259
time="07:50:01" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:01" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:01" level=info msg="Applying sequential FDR estimation" ions=255 peptides=212 psms=672
time="07:50:01" level=info msg="671 PSMs" decoy=0 threshold=0.844492 total=671
time="07:50:01" level=info msg="208 Peptides" decoy=0 threshold=0.881186 total=208
time="07:50:01" level=info msg="250 Ions" decoy=0 threshold=0.881186 total=250
time="07:50:01" level=info msg="Post processing identifications"
time="07:50:01" level=info msg="Assigning protein identifications to layers"
time="07:50:01" level=info msg="Processing protein inference"
time="07:50:01" level=info msg="Synchronizing PSMs and proteins"
time="07:50:01" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=250 peptides=208 proteins=99 psms=671
time="07:50:01" level=info msg=Saving
time="07:50:01" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
time="07:50:01" level=info msg="Executing Filter  v5.1.3"
time="07:50:01" level=info msg="Fetching protein inference from F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4"
time="07:50:01" level=info msg="Processing peptide identification files"
time="07:50:01" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_5\\interact-202505617.pep.xml"
time="07:50:01" level=info msg="1+ Charge profile" decoy=6 target=60
time="07:50:01" level=info msg="2+ Charge profile" decoy=31 target=586
time="07:50:01" level=info msg="3+ Charge profile" decoy=6 target=139
time="07:50:01" level=info msg="4+ Charge profile" decoy=2 target=29
time="07:50:01" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:01" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:01" level=info msg="Database search results" ions=355 peptides=312 psms=859
time="07:50:01" level=info msg="Converged to 0.99 % FDR with 706 PSMs" decoy=7 threshold=0.879906 total=713
time="07:50:01" level=info msg="Converged to 0.97 % FDR with 206 Peptides" decoy=2 threshold=0.912356 total=208
time="07:50:01" level=info msg="Converged to 0.83 % FDR with 241 Ions" decoy=2 threshold=0.912356 total=243
time="07:50:01" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:01" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:01" level=info msg="Applying sequential FDR estimation" ions=242 peptides=205 psms=690
time="07:50:01" level=info msg="689 PSMs" decoy=0 threshold=0.8816 total=689
time="07:50:01" level=info msg="199 Peptides" decoy=0 threshold=0.912356 total=199
time="07:50:01" level=info msg="234 Ions" decoy=0 threshold=0.912356 total=234
time="07:50:01" level=info msg="Post processing identifications"
time="07:50:01" level=info msg="Assigning protein identifications to layers"
time="07:50:02" level=info msg="Processing protein inference"
time="07:50:02" level=info msg="Synchronizing PSMs and proteins"
time="07:50:02" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=234 peptides=199 proteins=96 psms=689
time="07:50:02" level=info msg=Saving
time="07:50:02" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
time="07:50:02" level=info msg="Executing Filter  v5.1.3"
time="07:50:02" level=info msg="Fetching protein inference from F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4"
time="07:50:02" level=info msg="Processing peptide identification files"
time="07:50:02" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_6\\interact-202505618.pep.xml"
time="07:50:02" level=info msg="1+ Charge profile" decoy=1 target=58
time="07:50:02" level=info msg="2+ Charge profile" decoy=14 target=590
time="07:50:02" level=info msg="3+ Charge profile" decoy=2 target=118
time="07:50:02" level=info msg="4+ Charge profile" decoy=0 target=24
time="07:50:02" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:02" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:02" level=info msg="Database search results" ions=320 peptides=276 psms=807
time="07:50:02" level=info msg="Converged to 0.91 % FDR with 773 PSMs" decoy=7 threshold=0.736105 total=780
time="07:50:02" level=info msg="Converged to 0.80 % FDR with 251 Peptides" decoy=2 threshold=0.826288 total=253
time="07:50:02" level=info msg="Converged to 0.68 % FDR with 294 Ions" decoy=2 threshold=0.826288 total=296
time="07:50:02" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:02" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:02" level=info msg="Applying sequential FDR estimation" ions=286 peptides=242 psms=757
time="07:50:02" level=info msg="756 PSMs" decoy=0 threshold=0.739475 total=756
time="07:50:02" level=info msg="239 Peptides" decoy=0 threshold=0.829442 total=239
time="07:50:02" level=info msg="282 Ions" decoy=0 threshold=0.829442 total=282
time="07:50:02" level=info msg="Post processing identifications"
time="07:50:02" level=info msg="Assigning protein identifications to layers"
time="07:50:02" level=info msg="Processing protein inference"
time="07:50:02" level=info msg="Synchronizing PSMs and proteins"
time="07:50:02" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=282 peptides=239 proteins=119 psms=756
time="07:50:02" level=info msg=Saving
time="07:50:02" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
time="07:50:02" level=info msg="Executing Filter  v5.1.3"
time="07:50:02" level=info msg="Fetching protein inference from F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4"
time="07:50:02" level=info msg="Processing peptide identification files"
time="07:50:02" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\OCBS_10\\interact-202505622.pep.xml"
time="07:50:02" level=info msg="1+ Charge profile" decoy=10 target=82
time="07:50:02" level=info msg="2+ Charge profile" decoy=32 target=778
time="07:50:02" level=info msg="3+ Charge profile" decoy=10 target=186
time="07:50:02" level=info msg="4+ Charge profile" decoy=0 target=21
time="07:50:02" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:02" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:02" level=info msg="Database search results" ions=382 peptides=325 psms=1119
time="07:50:02" level=info msg="Converged to 0.94 % FDR with 955 PSMs" decoy=9 threshold=0.823081 total=964
time="07:50:02" level=info msg="Converged to 0.88 % FDR with 226 Peptides" decoy=2 threshold=0.921478 total=228
time="07:50:02" level=info msg="Converged to 0.73 % FDR with 273 Ions" decoy=2 threshold=0.911734 total=275
time="07:50:02" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:02" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:02" level=info msg="Applying sequential FDR estimation" ions=271 peptides=221 psms=926
time="07:50:02" level=info msg="924 PSMs" decoy=1 threshold=0.825957 total=925
time="07:50:02" level=info msg="213 Peptides" decoy=1 threshold=0.928486 total=214
time="07:50:02" level=info msg="260 Ions" decoy=1 threshold=0.911734 total=261
time="07:50:02" level=info msg="Post processing identifications"
time="07:50:02" level=info msg="Assigning protein identifications to layers"
time="07:50:02" level=info msg="Processing protein inference"
time="07:50:02" level=info msg="Synchronizing PSMs and proteins"
time="07:50:02" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=260 peptides=213 proteins=111 psms=924
time="07:50:02" level=info msg=Saving
time="07:50:02" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
time="07:50:03" level=info msg="Executing Filter  v5.1.3"
time="07:50:03" level=info msg="Fetching protein inference from F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4"
time="07:50:03" level=info msg="Processing peptide identification files"
time="07:50:03" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\OCBS_11\\interact-202505623.pep.xml"
time="07:50:03" level=info msg="1+ Charge profile" decoy=6 target=75
time="07:50:03" level=info msg="2+ Charge profile" decoy=25 target=682
time="07:50:03" level=info msg="3+ Charge profile" decoy=4 target=151
time="07:50:03" level=info msg="4+ Charge profile" decoy=1 target=36
time="07:50:03" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:03" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:03" level=info msg="Database search results" ions=348 peptides=294 psms=980
time="07:50:03" level=info msg="Converged to 0.92 % FDR with 871 PSMs" decoy=8 threshold=0.84442 total=879
time="07:50:03" level=info msg="Converged to 0.88 % FDR with 227 Peptides" decoy=2 threshold=0.899633 total=229
time="07:50:03" level=info msg="Converged to 0.72 % FDR with 278 Ions" decoy=2 threshold=0.899633 total=280
time="07:50:03" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:03" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:03" level=info msg="Applying sequential FDR estimation" ions=270 peptides=219 psms=855
time="07:50:03" level=info msg="853 PSMs" decoy=1 threshold=0.852981 total=854
time="07:50:03" level=info msg="217 Peptides" decoy=1 threshold=0.908555 total=218
time="07:50:03" level=info msg="268 Ions" decoy=1 threshold=0.908555 total=269
time="07:50:03" level=info msg="Post processing identifications"
time="07:50:03" level=info msg="Assigning protein identifications to layers"
time="07:50:03" level=info msg="Processing protein inference"
time="07:50:03" level=info msg="Synchronizing PSMs and proteins"
time="07:50:03" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=268 peptides=217 proteins=110 psms=853
time="07:50:03" level=info msg=Saving
time="07:50:03" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12 --dbbin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --protxml F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\combined.prot.xml --probin F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4 --razor
time="07:50:03" level=info msg="Executing Filter  v5.1.3"
time="07:50:03" level=info msg="Fetching protein inference from F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\NPS_4"
time="07:50:03" level=info msg="Processing peptide identification files"
time="07:50:03" level=info msg="Parsing F:\\Research\\PXD069532-Broccoli-Agilent-QqTOF\\20260720-FragPipe-LFQ-MBR3\\OCBS_12\\interact-202505624.pep.xml"
time="07:50:03" level=info msg="1+ Charge profile" decoy=7 target=74
time="07:50:03" level=info msg="2+ Charge profile" decoy=26 target=654
time="07:50:03" level=info msg="3+ Charge profile" decoy=9 target=152
time="07:50:03" level=info msg="4+ Charge profile" decoy=1 target=26
time="07:50:03" level=info msg="5+ Charge profile" decoy=0 target=0
time="07:50:03" level=info msg="6+ Charge profile" decoy=0 target=0
time="07:50:03" level=info msg="Database search results" ions=333 peptides=281 psms=949
time="07:50:03" level=info msg="Converged to 0.95 % FDR with 841 PSMs" decoy=8 threshold=0.782941 total=849
time="07:50:03" level=info msg="Converged to 0.93 % FDR with 214 Peptides" decoy=2 threshold=0.831126 total=216
time="07:50:03" level=info msg="Converged to 0.76 % FDR with 262 Ions" decoy=2 threshold=0.831126 total=264
time="07:50:03" level=info msg="Protein inference results" decoy=140 target=405
time="07:50:03" level=info msg="Converged to 0.69 % FDR with 145 Proteins" decoy=1 threshold=0.9807 total=146
time="07:50:03" level=info msg="Applying sequential FDR estimation" ions=256 peptides=207 psms=827
time="07:50:03" level=info msg="825 PSMs" decoy=1 threshold=0.807099 total=826
time="07:50:03" level=info msg="205 Peptides" decoy=1 threshold=0.831126 total=206
time="07:50:03" level=info msg="253 Ions" decoy=1 threshold=0.831126 total=254
time="07:50:03" level=info msg="Post processing identifications"
time="07:50:03" level=info msg="Assigning protein identifications to layers"
time="07:50:03" level=info msg="Processing protein inference"
time="07:50:03" level=info msg="Synchronizing PSMs and proteins"
time="07:50:03" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=253 peptides=205 proteins=99 psms=825
time="07:50:03" level=info msg=Saving
time="07:50:03" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:03" level=info msg="Executing Report  v5.1.3"
time="07:50:03" level=info msg="Creating reports"
time="07:50:03" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:04" level=info msg="Executing Report  v5.1.3"
time="07:50:04" level=info msg="Creating reports"
time="07:50:04" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:04" level=info msg="Executing Report  v5.1.3"
time="07:50:04" level=info msg="Creating reports"
time="07:50:04" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:04" level=info msg="Executing Report  v5.1.3"
time="07:50:04" level=info msg="Creating reports"
time="07:50:04" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:04" level=info msg="Executing Report  v5.1.3"
time="07:50:04" level=info msg="Creating reports"
time="07:50:04" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="07:50:04" level=info msg="Executing Report  v5.1.3"
time="07:50:04" level=info msg="Creating reports"
time="07:50:05" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:05" level=info msg="Executing Workspace  v5.1.3"
time="07:50:05" level=info msg="Removing workspace"
time="07:50:05" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:05" level=info msg="Executing Workspace  v5.1.3"
time="07:50:05" level=info msg="Removing workspace"
time="07:50:05" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:05" level=info msg="Executing Workspace  v5.1.3"
time="07:50:05" level=info msg="Removing workspace"
time="07:50:05" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:05" level=info msg="Executing Workspace  v5.1.3"
time="07:50:05" level=info msg="Removing workspace"
time="07:50:05" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:06" level=info msg="Executing Workspace  v5.1.3"
time="07:50:06" level=info msg="Removing workspace"
time="07:50:06" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:06" level=info msg="Executing Workspace  v5.1.3"
time="07:50:06" level=info msg="Removing workspace"
time="07:50:06" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="07:50:06" level=info msg="Executing Workspace  v5.1.3"
time="07:50:06" level=info msg="Removing workspace"
time="07:50:06" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx112G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\thermo -cp C:\FragPipe\FragPipe-24.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-24.0\tools\IonQuant-1.11.18.jar ionquant.IonQuant --threads 23 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --intensitymode 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\filelist_ionquant.txt --modlist F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\modmasses_ionquant.txt
IonQuant version IonQuant-1.11.18
Batmass-IO version 1.36.5
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 112 GB memory
2026-07-20 07:50:06 [INFO] - Collecting variable modifications from all psm.tsv files...
2026-07-20 07:50:07 [INFO] - Loading and indexing all psm.tsv files...
2026-07-20 07:50:07 [INFO] - Indexing experiments...
2026-07-20 07:50:07 [INFO] - Indexing runs...
2026-07-20 07:50:07 [INFO] - Collecting all compensation voltages if applicable...
2026-07-20 07:50:07 [INFO] - 202505616 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2026-07-20 07:50:07 [INFO] - There is no FAIMS in the dataset.
2026-07-20 07:50:07 [INFO] - Indexing proteins...
2026-07-20 07:50:07 [INFO] - Indexing sequences...
2026-07-20 07:50:07 [INFO] - Indexing peptides...
2026-07-20 07:50:07 [INFO] - Indexing ions...
2026-07-20 07:50:07 [INFO] - Indexing PSMs...
2026-07-20 07:50:08 [INFO] - Parameters:
2026-07-20 07:50:08 [INFO] - perform-ms1quant = 1
2026-07-20 07:50:08 [INFO] - perform-isoquant = 0
2026-07-20 07:50:08 [INFO] - isotol = 20.0
2026-07-20 07:50:08 [INFO] - isolevel = 2
2026-07-20 07:50:08 [INFO] - isotype = tmt10
2026-07-20 07:50:08 [INFO] - site-reports = 1
2026-07-20 07:50:08 [INFO] - msstats = 1
2026-07-20 07:50:08 [INFO] - threads = 23
2026-07-20 07:50:08 [INFO] - mztol = 10.0
2026-07-20 07:50:08 [INFO] - rttol = 0.4
2026-07-20 07:50:08 [INFO] - imtol = 0.05
2026-07-20 07:50:08 [INFO] - minisotopes = 2
2026-07-20 07:50:08 [INFO] - minscans = 3
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\psm.tsv
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\psm.tsv
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\psm.tsv
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\psm.tsv
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\psm.tsv
2026-07-20 07:50:08 [INFO] - psm = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\psm.tsv
2026-07-20 07:50:08 [INFO] - multidir = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\
2026-07-20 07:50:08 [INFO] - excludemods = 
2026-07-20 07:50:08 [INFO] - minions = 1
2026-07-20 07:50:08 [INFO] - maxlfq = 1
2026-07-20 07:50:08 [INFO] - ibaq = 0
2026-07-20 07:50:08 [INFO] - normalization = 1
2026-07-20 07:50:08 [INFO] - minexps = 1
2026-07-20 07:50:08 [INFO] - minfreq = 0.0
2026-07-20 07:50:08 [INFO] - tp = 0
2026-07-20 07:50:08 [INFO] - mbr = 1
2026-07-20 07:50:08 [INFO] - mbrrttol = 1.0
2026-07-20 07:50:08 [INFO] - mbrimtol = 0.05
2026-07-20 07:50:08 [INFO] - mbrtoprun = 10
2026-07-20 07:50:08 [INFO] - mbrmincorr = 0.0
2026-07-20 07:50:08 [INFO] - ionmobility = 0
2026-07-20 07:50:08 [INFO] - ionfdr = 0.01
2026-07-20 07:50:08 [INFO] - peptidefdr = 1.0
2026-07-20 07:50:08 [INFO] - proteinfdr = 1.0
2026-07-20 07:50:08 [INFO] - light = 
2026-07-20 07:50:08 [INFO] - medium = 
2026-07-20 07:50:08 [INFO] - heavy = 
2026-07-20 07:50:08 [INFO] - requantify = 0
2026-07-20 07:50:08 [INFO] - writeindex = 0
2026-07-20 07:50:08 [INFO] - locprob = 0.75
2026-07-20 07:50:08 [INFO] - uniqueness = 0
2026-07-20 07:50:08 [INFO] - intensitymode = 2
2026-07-20 07:50:08 [INFO] - totalintensitymode = 1
2026-07-20 07:50:08 [INFO] - formula = 
2026-07-20 07:50:08 [INFO] - filelist = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\filelist_ionquant.txt
2026-07-20 07:50:08 [INFO] - specdir = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard
2026-07-20 07:50:08 [INFO] - modlist = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\modmasses_ionquant.txt
2026-07-20 07:50:08 [INFO] - mod masses:
2026-07-20 07:50:08 [INFO] - 15.9949
2026-07-20 07:50:08 [INFO] - 42.0106
2026-07-20 07:50:08 [INFO] - 57.02146
2026-07-20 07:50:08 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2026-07-20 07:50:08 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.mzML...
2026-07-20 07:50:09 [INFO] - Building index...
2026-07-20 07:50:09 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.quantindex
2026-07-20 07:50:09 [INFO] - Quantifying...
2026-07-20 07:50:09 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.mzML...
2026-07-20 07:50:10 [INFO] - Building index...
2026-07-20 07:50:10 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.quantindex
2026-07-20 07:50:10 [INFO] - Quantifying...
2026-07-20 07:50:10 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.mzML...
2026-07-20 07:50:11 [INFO] - Building index...
2026-07-20 07:50:11 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.quantindex
2026-07-20 07:50:11 [INFO] - Quantifying...
2026-07-20 07:50:11 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.mzML...
2026-07-20 07:50:12 [INFO] - Building index...
2026-07-20 07:50:12 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.quantindex
2026-07-20 07:50:12 [INFO] - Quantifying...
2026-07-20 07:50:12 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.mzML...
2026-07-20 07:50:13 [INFO] - Building index...
2026-07-20 07:50:13 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.quantindex
2026-07-20 07:50:13 [INFO] - Quantifying...
2026-07-20 07:50:13 [INFO] - Loading F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.mzML...
2026-07-20 07:50:14 [INFO] - Building index...
2026-07-20 07:50:14 [INFO] - Writing index to F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.quantindex
2026-07-20 07:50:14 [INFO] - Quantifying...
2026-07-20 07:50:14 [INFO] - Updating Philosopher's tables...
2026-07-20 07:50:14 [INFO] - Matching-between-runs: 202505616...
2026-07-20 07:50:14 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:14 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505616.quantindex
2026-07-20 07:50:14 [INFO] - Transferring 202505617...
2026-07-20 07:50:15 [INFO] - Transferring 202505618...
2026-07-20 07:50:15 [INFO] - Transferring 202505622...
2026-07-20 07:50:15 [INFO] - Transferring 202505623...
2026-07-20 07:50:15 [INFO] - Transferring 202505624...
2026-07-20 07:50:15 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:15 [INFO] - #{+1} = 124, #{-1} = 51, #{+2} = 115, #{-2} = 49
2026-07-20 07:50:15 [INFO] - Standardized coefficients:
2026-07-20 07:50:15 [INFO] - log10(intensity): 0.9936221491166174
2026-07-20 07:50:15 [INFO] - log10(KL): -0.05672773277880653
2026-07-20 07:50:15 [INFO] - abs(ppm): -0.032573316345372645
2026-07-20 07:50:15 [INFO] - RT diff: -0.09184752680891926
2026-07-20 07:50:15 [INFO] - Fitting a mixture model...
2026-07-20 07:50:15 [INFO] - Matching-between-runs: 202505617...
2026-07-20 07:50:15 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:15 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505617.quantindex
2026-07-20 07:50:15 [INFO] - Transferring 202505616...
2026-07-20 07:50:15 [INFO] - Transferring 202505618...
2026-07-20 07:50:15 [INFO] - Transferring 202505622...
2026-07-20 07:50:15 [INFO] - Transferring 202505623...
2026-07-20 07:50:15 [INFO] - Transferring 202505624...
2026-07-20 07:50:15 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:15 [INFO] - #{+1} = 104, #{-1} = 45, #{+2} = 115, #{-2} = 49
2026-07-20 07:50:15 [INFO] - Standardized coefficients:
2026-07-20 07:50:15 [INFO] - log10(intensity): 0.9569938062849125
2026-07-20 07:50:15 [INFO] - log10(KL): -0.17299017170862568
2026-07-20 07:50:15 [INFO] - abs(ppm): 0.022957778419421752
2026-07-20 07:50:15 [INFO] - RT diff: -0.23175460218640784
2026-07-20 07:50:15 [INFO] - Fitting a mixture model...
2026-07-20 07:50:15 [INFO] - Matching-between-runs: 202505618...
2026-07-20 07:50:15 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:15 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505618.quantindex
2026-07-20 07:50:15 [INFO] - Transferring 202505616...
2026-07-20 07:50:15 [INFO] - Transferring 202505617...
2026-07-20 07:50:15 [INFO] - Transferring 202505622...
2026-07-20 07:50:15 [INFO] - Transferring 202505623...
2026-07-20 07:50:15 [INFO] - Transferring 202505624...
2026-07-20 07:50:15 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:15 [INFO] - #{+1} = 83, #{-1} = 34, #{+2} = 126, #{-2} = 56
2026-07-20 07:50:15 [INFO] - Standardized coefficients:
2026-07-20 07:50:15 [INFO] - log10(intensity): 0.9925161468100415
2026-07-20 07:50:15 [INFO] - log10(KL): -0.0032157298220356397
2026-07-20 07:50:15 [INFO] - abs(ppm): -0.016556123516409463
2026-07-20 07:50:15 [INFO] - RT diff: -0.12094317747260158
2026-07-20 07:50:15 [INFO] - Fitting a mixture model...
2026-07-20 07:50:16 [INFO] - Matching-between-runs: 202505622...
2026-07-20 07:50:16 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:16 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505622.quantindex
2026-07-20 07:50:16 [INFO] - Transferring 202505616...
2026-07-20 07:50:16 [INFO] - Transferring 202505617...
2026-07-20 07:50:16 [INFO] - Transferring 202505618...
2026-07-20 07:50:16 [INFO] - Transferring 202505623...
2026-07-20 07:50:16 [INFO] - Transferring 202505624...
2026-07-20 07:50:16 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:16 [INFO] - #{+1} = 70, #{-1} = 28, #{+2} = 119, #{-2} = 60
2026-07-20 07:50:16 [INFO] - Standardized coefficients:
2026-07-20 07:50:16 [INFO] - log10(intensity): 0.970173355581312
2026-07-20 07:50:16 [INFO] - log10(KL): -0.13707645625272208
2026-07-20 07:50:16 [INFO] - abs(ppm): -0.06236448897713248
2026-07-20 07:50:16 [INFO] - RT diff: -0.18995887917102958
2026-07-20 07:50:16 [INFO] - Fitting a mixture model...
2026-07-20 07:50:16 [INFO] - Matching-between-runs: 202505623...
2026-07-20 07:50:16 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:16 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505623.quantindex
2026-07-20 07:50:16 [INFO] - Transferring 202505616...
2026-07-20 07:50:16 [INFO] - Transferring 202505617...
2026-07-20 07:50:16 [INFO] - Transferring 202505618...
2026-07-20 07:50:16 [INFO] - Transferring 202505622...
2026-07-20 07:50:16 [INFO] - Transferring 202505624...
2026-07-20 07:50:16 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:16 [INFO] - #{+1} = 97, #{-1} = 41, #{+2} = 139, #{-2} = 67
2026-07-20 07:50:16 [INFO] - Standardized coefficients:
2026-07-20 07:50:16 [INFO] - log10(intensity): 0.9887432497342543
2026-07-20 07:50:16 [INFO] - log10(KL): -0.13684619977197512
2026-07-20 07:50:16 [INFO] - abs(ppm): 0.013334693783223737
2026-07-20 07:50:16 [INFO] - RT diff: -0.05900923363866238
2026-07-20 07:50:16 [INFO] - Fitting a mixture model...
2026-07-20 07:50:16 [INFO] - Matching-between-runs: 202505624...
2026-07-20 07:50:16 [INFO] - Calculating correlations between all other runs...
2026-07-20 07:50:16 [INFO] - Reading index from F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard\202505624.quantindex
2026-07-20 07:50:16 [INFO] - Transferring 202505616...
2026-07-20 07:50:16 [INFO] - Transferring 202505617...
2026-07-20 07:50:16 [INFO] - Transferring 202505618...
2026-07-20 07:50:16 [INFO] - Transferring 202505622...
2026-07-20 07:50:16 [INFO] - Transferring 202505623...
2026-07-20 07:50:16 [INFO] - Training LDA models for all matched features.
2026-07-20 07:50:16 [INFO] - #{+1} = 113, #{-1} = 42, #{+2} = 122, #{-2} = 61
2026-07-20 07:50:16 [INFO] - Standardized coefficients:
2026-07-20 07:50:16 [INFO] - log10(intensity): 0.9269323344356989
2026-07-20 07:50:16 [INFO] - log10(KL): -0.2876730521631982
2026-07-20 07:50:16 [INFO] - abs(ppm): 0.12518936852033014
2026-07-20 07:50:16 [INFO] - RT diff: -0.2058355762402997
2026-07-20 07:50:16 [INFO] - Fitting a mixture model...
2026-07-20 07:50:16 [INFO] - Estimating match-between-runs FDR...
2026-07-20 07:50:16 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.552400
2026-07-20 07:50:16 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2026-07-20 07:50:16 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2026-07-20 07:50:16 [INFO] - Updating Philosopher's tables...
2026-07-20 07:50:16 [INFO] - Combining experiments and estimating protein intensity...
2026-07-20 07:50:16 [INFO] - Generating modification reports...
2026-07-20 07:50:17 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

Delete temp files
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_4\202505616_edited.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_5\202505617_edited.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\NPS_6\202505618_edited.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_10\202505622_edited.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_11\202505623_edited.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pepXML
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624.pin
Delete F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\OCBS_12\202505624_edited.pin

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)
(timsTOF ddaPASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics. 19:1575 (2020)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods. 17:1125 (2020)
(Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics. 22:100538 (2023)
(DDA+ search) MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search. Nat Commun. 16:3329 (2025)
(MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 4:923 (2007)
(Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 75:4646 (2003)
(FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 17:869 (2020)
(Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics. 20:100077 (2021)
(Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

Task Runtimes:
  CheckCentroid: 0.01 minutes
  WorkspaceCleanInit: 0.05 minutes
  MSFragger: 1.20 minutes
  MSFragger move pepxml: 0.02 minutes
  MSFragger move pin: 0.02 minutes
  MSBooster: 0.10 minutes
  Percolator: 0.16 minutes
  Percolator: Convert to pepxml: 0.04 minutes
  Percolator delete temp: 0.04 minutes
  ProteinProphet: 0.03 minutes
  PhilosopherDbAnnotate: 0.00 minutes
  PhilosopherFilter: 0.04 minutes
  PhilosopherReport: 0.02 minutes
  WorkspaceClean: 0.02 minutes
  IonQuant: 0.18 minutes
  Finalizer Task: 0.00 minutes

=============================================================ALL JOBS DONE IN 2.0 MINUTES=============================================================
