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: C_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML	DDA
  Experiment/Group: C_2
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.mzML	DDA
  Experiment/Group: C_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.mzML	DDA
  Experiment/Group: C_4
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.mzML	DDA
  Experiment/Group: CdSi_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.mzML	DDA
  Experiment/Group: CdSi_2
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.mzML	DDA
  Experiment/Group: CdSi_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.mzML	DDA
  Experiment/Group: CdSi_4
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.mzML	DDA


97 commands to execute:
CheckCentroid
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML 23
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\b5c4d9b1-8c17-4332-a5b6-45da271f947c
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\a6d9be38-da46-44a8-8269-f718ca980b72
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\b16d965d-3a8d-4c53-8412-5464b77c66fa
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\3bcfb092-1d36-4cf5-a787-fb8a808c65d0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\217b2c9a-154d-43b5-b1c0-2ba068bb69d4
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\0218e2ce-fa64-4e79-963f-e3dff43cdb58
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\f05dc805-32a1-4c2d-ba02-41ed511b5e2a
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\de80520e-9fbc-4997-a3fc-c5da29adf51c
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\7e76bc27-0955-43a5-b00d-e03fe5901e8f
MSFragger [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx105G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\fragger.params F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pin
MSBooster [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\msbooster_params.txt
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
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 Hemphi_Ca_CdSi1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi1_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
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 Hemphi_Ca_C1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C1_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_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 Hemphi_Ca_C4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C4_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_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 Hemphi_Ca_CdSi4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi4_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
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 Hemphi_Ca_C3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C3_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
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 Hemphi_Ca_CdSi2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi2_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
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 Hemphi_Ca_CdSi3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi3_edited.pin
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
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 Hemphi_Ca_C2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C2_edited.pin
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi1.pin Hemphi_Ca_CdSi1 Hemphi_Ca_CdSi1_percolator_target_psms.tsv Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi1 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C1.pin Hemphi_Ca_C1 Hemphi_Ca_C1_percolator_target_psms.tsv Hemphi_Ca_C1_percolator_decoy_psms.tsv interact-Hemphi_Ca_C1 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C4.pin Hemphi_Ca_C4 Hemphi_Ca_C4_percolator_target_psms.tsv Hemphi_Ca_C4_percolator_decoy_psms.tsv interact-Hemphi_Ca_C4 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi4.pin Hemphi_Ca_CdSi4 Hemphi_Ca_CdSi4_percolator_target_psms.tsv Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi4 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C3.pin Hemphi_Ca_C3 Hemphi_Ca_C3_percolator_target_psms.tsv Hemphi_Ca_C3_percolator_decoy_psms.tsv interact-Hemphi_Ca_C3 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi2.pin Hemphi_Ca_CdSi2 Hemphi_Ca_CdSi2_percolator_target_psms.tsv Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi2 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi3.pin Hemphi_Ca_CdSi3 Hemphi_Ca_CdSi3_percolator_target_psms.tsv Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi3 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C2.pin Hemphi_Ca_C2 Hemphi_Ca_C2_percolator_target_psms.tsv Hemphi_Ca_C2_percolator_decoy_psms.tsv interact-Hemphi_Ca_C2 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe database --annotate F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_protein.fas --prefix rev_
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
IonQuant [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\filelist_ionquant.txt --modlist F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [CheckCentroid], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
    Cmd: [WorkspaceCleanInit], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
    Cmd: [MSFragger], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [MSBooster], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [Percolator], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [ProteinProphet], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [PhilosopherDbAnnotate], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [PhilosopherFilter], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [PhilosopherReport], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
    Cmd: [WorkspaceClean], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
    Cmd: [IonQuant], Work dir: [F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]

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

~~~~~~Sample of F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_protein.fas~~~~~~~
>NP_001384864.1 cannabidiolic acid synthase-like 2 precursor [Cannabis sativa]
>XP_030483179.2 endo-1,3;1,4-beta-D-glucanase [Cannabis sativa]
>XP_030489512.1 eukaryotic translation initiation factor 3 subunit F [Cannabis sativa]
>XP_030495580.2 uncharacterized protein LOC115711390 [Cannabis sativa]
>XP_030501362.2 probable transcriptional regulator SLK2 isoform X2 [Cannabis sativa]
>XP_030507787.2 uncharacterized protein LOC115722664 [Cannabis sativa]
>XP_060959237.1 uncharacterized protein LOC133030495 [Cannabis sativa]
>XP_060963244.1 protein PHOX1 [Cannabis sativa]
>XP_060967251.1 uncharacterized protein LOC133035394 [Cannabis sativa]
>XP_060971258.1 uncharacterized protein LOC115716205 isoform X2 [Cannabis sativa]
>contam_sp|Q15323|K1H1_HUMAN Keratin, type I cuticular Ha1 OS=Homo sapiens OX=9606 GN=KRT31 PE=1 SV=3
>rev_XP_030483171.1 sucrose transport protein SUC3 isoform X1 [Cannabis sativa]
>rev_XP_030489503.2 myosin-15 isoform X1 [Cannabis sativa]
>rev_XP_030495571.2 ubiquitin carboxyl-terminal hydrolase 24 [Cannabis sativa]
>rev_XP_030501354.1 ubiquitin-ribosomal protein eS31 fusion protein [Cannabis sativa]
>rev_XP_030507777.2 zinc finger protein 4 [Cannabis sativa]
>rev_XP_060959230.1 uncharacterized protein LOC133030491 [Cannabis sativa]
>rev_XP_060963237.1 outer envelope pore protein 21A, chloroplastic [Cannabis sativa]
>rev_XP_060967244.1 decapping 5-like protein isoform X3 [Cannabis sativa]
>rev_XP_060971251.1 V-type proton ATPase subunit H [Cannabis sativa]
>rev_contam_sp|P99999|CYC_HUMAN Cytochrome c OS=Homo sapiens OX=9606 GN=CYCS PE=1 SV=2
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ 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\\PXD060911-Cannabis-sativa-TripleTOF\\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_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\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR
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 -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML 23
Done in 1.8 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:57" level=info msg="Executing Workspace  v5.1.3"
time="11:19:57" level=info msg="Removing workspace"
time="11:19:57" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\b5c4d9b1-8c17-4332-a5b6-45da271f947c
time="11:19:57" level=info msg="Executing Workspace  v5.1.3"
time="11:19:57" level=info msg="Creating workspace"
time="11:19:57" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:58" level=info msg="Executing Workspace  v5.1.3"
time="11:19:58" level=info msg="Removing workspace"
time="11:19:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\a6d9be38-da46-44a8-8269-f718ca980b72
time="11:19:58" level=info msg="Executing Workspace  v5.1.3"
time="11:19:58" level=info msg="Creating workspace"
time="11:19:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:58" level=info msg="Executing Workspace  v5.1.3"
time="11:19:58" level=info msg="Removing workspace"
time="11:19:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\b16d965d-3a8d-4c53-8412-5464b77c66fa
time="11:19:58" level=info msg="Executing Workspace  v5.1.3"
time="11:19:58" level=info msg="Creating workspace"
time="11:19:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:58" level=info msg="Executing Workspace  v5.1.3"
time="11:19:58" level=info msg="Removing workspace"
time="11:19:58" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\3bcfb092-1d36-4cf5-a787-fb8a808c65d0
time="11:19:59" level=info msg="Executing Workspace  v5.1.3"
time="11:19:59" level=info msg="Creating workspace"
time="11:19:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:59" level=info msg="Executing Workspace  v5.1.3"
time="11:19:59" level=info msg="Removing workspace"
time="11:19:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\217b2c9a-154d-43b5-b1c0-2ba068bb69d4
time="11:19:59" level=info msg="Executing Workspace  v5.1.3"
time="11:19:59" level=info msg="Creating workspace"
time="11:19:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:19:59" level=info msg="Executing Workspace  v5.1.3"
time="11:19:59" level=info msg="Removing workspace"
time="11:19:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\0218e2ce-fa64-4e79-963f-e3dff43cdb58
time="11:20:00" level=info msg="Executing Workspace  v5.1.3"
time="11:20:00" level=info msg="Creating workspace"
time="11:20:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:20:00" level=info msg="Executing Workspace  v5.1.3"
time="11:20:00" level=info msg="Removing workspace"
time="11:20:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\f05dc805-32a1-4c2d-ba02-41ed511b5e2a
time="11:20:00" level=info msg="Executing Workspace  v5.1.3"
time="11:20:00" level=info msg="Creating workspace"
time="11:20:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:20:00" level=info msg="Executing Workspace  v5.1.3"
time="11:20:00" level=info msg="Removing workspace"
time="11:20:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\de80520e-9fbc-4997-a3fc-c5da29adf51c
time="11:20:00" level=info msg="Executing Workspace  v5.1.3"
time="11:20:00" level=info msg="Creating workspace"
time="11:20:00" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:20:01" level=info msg="Executing Workspace  v5.1.3"
time="11:20:01" level=info msg="Removing workspace"
time="11:20:01" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\dtabb\AppData\Local\Temp\7e76bc27-0955-43a5-b00d-e03fe5901e8f
time="11:20:01" level=info msg="Executing Workspace  v5.1.3"
time="11:20:01" level=info msg="Creating workspace"
time="11:20:01" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx105G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\fragger.params F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.mzML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.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 105 GB memory
Checking database...
Checking spectral files...
Hemphi_Ca_C4.mzML: Scans = 50745; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_CdSi3.mzML: Scans = 63461; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_CdSi2.mzML: Scans = 63005; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_C2.mzML: Scans = 62482; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_C3.mzML: Scans = 63437; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_CdSi1.mzML: Scans = 67377; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_CdSi4.mzML: Scans = 66706; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
Hemphi_Ca_C1.mzML: Scans = 66709; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = []; Instrument = TripleTOF 6600
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 23
database_name = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_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
Number of unique peptides
	of length 7: 279443
	of length 8: 277570
	of length 9: 266245
	of length 10: 257158
	of length 11: 254173
	of length 12: 244294
	of length 13: 231192
	of length 14: 223763
	of length 15: 212457
	of length 16: 200741
	of length 17: 190792
	of length 18: 182239
	of length 19: 173441
	of length 20: 167218
	of length 21: 156265
	of length 22: 146009
	of length 23: 139055
	of length 24: 132463
	of length 25: 123273
	of length 26: 117770
	of length 27: 112358
	of length 28: 103613
	of length 29: 98636
	of length 30: 90784
	of length 31: 85097
	of length 32: 79417
	of length 33: 74794
	of length 34: 70871
	of length 35: 65680
	of length 36: 61297
	of length 37: 56228
	of length 38: 52906
	of length 39: 48769
	of length 40: 44087
	of length 41: 40869
	of length 42: 36832
	of length 43: 31650
	of length 44: 25041
	of length 45: 18153
	of length 46: 10933
	of length 47: 6148
	of length 48: 3050
	of length 49: 1350
	of length 50: 550
In total 5194674 peptides.
Generated 8808579 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
368596744 fragments to be searched in 1 slices (3.43 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.37 s
	001. Hemphi_Ca_C1.mzML 3.3 s | deisotoping 0.6 s
		[progress: 66662/66662 (100%) - 30905 spectra/s] 2.2s
	002. Hemphi_Ca_C2.mzML 2.0 s | deisotoping 0.0 s
		[progress: 62397/62397 (100%) - 96440 spectra/s] 0.6s
	003. Hemphi_Ca_C3.mzML 2.1 s | deisotoping 0.0 s
		[progress: 63359/63359 (100%) - 98844 spectra/s] 0.6s
	004. Hemphi_Ca_C4.mzML 1.8 s | deisotoping 0.1 s
		[progress: 50693/50693 (100%) - 120698 spectra/s] 0.4s
	005. Hemphi_Ca_CdSi1.mzML 2.0 s | deisotoping 0.0 s
		[progress: 67357/67357 (100%) - 78050 spectra/s] 0.9s
	006. Hemphi_Ca_CdSi2.mzML 1.9 s | deisotoping 0.0 s
		[progress: 62922/62922 (100%) - 99403 spectra/s] 0.6s
	007. Hemphi_Ca_CdSi3.mzML 1.9 s | deisotoping 0.0 s
		[progress: 63425/63425 (100%) - 97878 spectra/s] 0.6s
	008. Hemphi_Ca_CdSi4.mzML 2.2 s | deisotoping 0.0 s
		[progress: 66655/66655 (100%) - 48406 spectra/s] 1.4s
postprocessing Hemphi_Ca_C1.mzML 0.3 s
postprocessing Hemphi_Ca_C2.mzML 0.1 s
postprocessing Hemphi_Ca_C3.mzML 0.1 s
postprocessing Hemphi_Ca_C4.mzML 0.1 s
postprocessing Hemphi_Ca_CdSi1.mzML 0.2 s
postprocessing Hemphi_Ca_CdSi2.mzML 0.1 s
postprocessing Hemphi_Ca_CdSi3.mzML 0.1 s
postprocessing Hemphi_Ca_CdSi4.mzML 0.2 s
***************************FIRST SEARCH DONE IN 0.611 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   4.65   3.63 |   0.30   2.53 |  -0.40   8.56 |  -0.27   8.51  
 002 |   6.52   3.33 |   0.45   1.88 |  -1.26   8.67 |  -0.55   8.65  
 003 |   6.13   3.25 |   0.27   1.77 |   1.51   8.68 |   0.57   8.62  
 004 |   5.88   2.91 |   0.21   1.98 |  -0.18   9.02 |   0.03   8.85  
 005 |   7.45   3.24 |   0.54   2.30 |   1.73   8.82 |   0.64   8.81  
 006 |   6.43   3.76 |   0.83   1.97 |  -0.75   8.77 |  -0.27   8.78  
 007 |   1.29   3.37 |   0.04   2.00 |   2.39   8.39 |   0.88   8.35  
 008 |   4.86   3.27 |   0.14   2.10 |  -2.09   8.39 |  -0.84   8.32  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count | skip  | skip  | skip  | skip  |   4258|   4571|   4767|   4304
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |   4730|   4737|   4738|   4767|   4611| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   3345
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |   4199
-------|-------
New fragment_mass_tolerance = 30.000000 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.959 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 23
database_name = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_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 = 30.0
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 = 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
Number of unique peptides
	of length 7: 279443
	of length 8: 277570
	of length 9: 266245
	of length 10: 257158
	of length 11: 254173
	of length 12: 244294
	of length 13: 231192
	of length 14: 223763
	of length 15: 212457
	of length 16: 200741
	of length 17: 190792
	of length 18: 182239
	of length 19: 173441
	of length 20: 167218
	of length 21: 156265
	of length 22: 146009
	of length 23: 139055
	of length 24: 132463
	of length 25: 123273
	of length 26: 117770
	of length 27: 112358
	of length 28: 103613
	of length 29: 98636
	of length 30: 90784
	of length 31: 85097
	of length 32: 79417
	of length 33: 74794
	of length 34: 70871
	of length 35: 65680
	of length 36: 61297
	of length 37: 56228
	of length 38: 52906
	of length 39: 48769
	of length 40: 44087
	of length 41: 40869
	of length 42: 36832
	of length 43: 31650
	of length 44: 25041
	of length 45: 18153
	of length 46: 10933
	of length 47: 6148
	of length 48: 3050
	of length 49: 1350
	of length 50: 550
In total 5194674 peptides.
Generated 8808579 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.15 Da.
368596744 fragments to be searched in 1 slices (3.43 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 1.14 s
	001. Hemphi_Ca_C1.mzBIN_calibrated 0.1 s
		[progress: 66662/66662 (100%) - 22258 spectra/s] 3.0s
	002. Hemphi_Ca_C2.mzBIN_calibrated 0.1 s
		[progress: 62397/62397 (100%) - 47270 spectra/s] 1.3s
	003. Hemphi_Ca_C3.mzBIN_calibrated 0.1 s
		[progress: 63359/63359 (100%) - 52363 spectra/s] 1.2s
	004. Hemphi_Ca_C4.mzBIN_calibrated 0.1 s
		[progress: 50693/50693 (100%) - 76001 spectra/s] 0.7s
	005. Hemphi_Ca_CdSi1.mzBIN_calibrated 0.1 s
		[progress: 67357/67357 (100%) - 35885 spectra/s] 1.9s
	006. Hemphi_Ca_CdSi2.mzBIN_calibrated 0.1 s
		[progress: 62922/62922 (100%) - 48327 spectra/s] 1.3s
	007. Hemphi_Ca_CdSi3.mzBIN_calibrated 0.1 s
		[progress: 63425/63425 (100%) - 53254 spectra/s] 1.2s
	008. Hemphi_Ca_CdSi4.mzBIN_calibrated 0.1 s
		[progress: 66655/66655 (100%) - 21571 spectra/s] 3.1s
postprocessing Hemphi_Ca_C1.mzBIN_calibrated 3.6 s
postprocessing Hemphi_Ca_C2.mzBIN_calibrated 1.3 s
postprocessing Hemphi_Ca_C3.mzBIN_calibrated 1.2 s
postprocessing Hemphi_Ca_C4.mzBIN_calibrated 0.9 s
postprocessing Hemphi_Ca_CdSi1.mzBIN_calibrated 1.7 s
postprocessing Hemphi_Ca_CdSi2.mzBIN_calibrated 1.1 s
postprocessing Hemphi_Ca_CdSi3.mzBIN_calibrated 1.1 s
postprocessing Hemphi_Ca_CdSi4.mzBIN_calibrated 2.7 s
***************************MAIN SEARCH DONE IN 0.559 MIN***************************

*******************************TOTAL TIME 2.129 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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.pepXML F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.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\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\msbooster_params.txt
2026-07-17 11:22:15 [INFO] - MSBooster v1.4.14
2026-07-17 11:22:15 [INFO] - Creating output folder at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster
2026-07-17 11:22:15 [INFO] - Using 23 threads
2026-07-17 11:22:17 [INFO] - Instrument detected: SCIEXTOF
2026-07-17 11:22:17 [INFO] - mzml file does not contain filter string. Setting to default.
2026-07-17 11:22:17 [INFO] - NCE and fragmentation type detected: {HCD=25}
2026-07-17 11:22:17 [INFO] - Creating input file for createFull
2026-07-17 11:22:17 [INFO] - 140227 PSMs for prediction
2026-07-17 11:22:17 [INFO] - createFull input file generation took 281 milliseconds
2026-07-17 11:22:17 [INFO] - Input file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT_full.tsv
2026-07-17 11:22:17 [INFO] - Generating input file for DIA-NN
2026-07-17 11:22:17 [INFO] - Creating input file for Diann
2026-07-17 11:22:17 [INFO] - 140227 PSMs for prediction
2026-07-17 11:22:17 [INFO] - Writing DIA-NN input file
2026-07-17 11:22:18 [INFO] - Diann input file generation took 404 milliseconds
2026-07-17 11:22:18 [INFO] - Input file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.tsv
2026-07-17 11:22:18 [INFO] - Generating DIA-NN predictions
2026-07-17 11:22:18 [INFO] - C:\FragPipe\FragPipe-24.0\tools\diann\1.8.2_beta_8\windows\DiaNN.exe --lib F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.tsv --predict --threads 23 --strip-unknown-mods --predict-n-frag 100
2026-07-17 11:22:18 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
2026-07-17 11:22:18 [INFO] - Compiled on Sep 15 2022 18:28:57
2026-07-17 11:22:18 [INFO] - Current date and time: Fri Jul 17 11:22:18 2026
2026-07-17 11:22:18 [INFO] - CPU: AuthenticAMD AMD Ryzen 9 9900X 12-Core Processor
2026-07-17 11:22:18 [INFO] - SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 SSE4a 
2026-07-17 11:22:18 [INFO] - Logical CPU cores: 24
2026-07-17 11:22:18 [INFO] - Predicted spectra will be saved in a binary format
2026-07-17 11:22:18 [INFO] - Thread number set to 23
2026-07-17 11:22:18 [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
2026-07-17 11:22:18 [INFO] - Deep learning predictor will predict 100 fragments
2026-07-17 11:22:18 [INFO] - 
2026-07-17 11:22:18 [INFO] - 0 files will be processed
2026-07-17 11:22:18 [INFO] - [0:00] Loading spectral library F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.tsv
2026-07-17 11:22:18 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
2026-07-17 11:22:18 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 140227 precursors in 135604 elution groups.
2026-07-17 11:22:18 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction
2026-07-17 11:22:18 [INFO] - [0:00] Predicting spectra and IMs
2026-07-17 11:22:41 [INFO] - [0:23] Predicting RTs
2026-07-17 11:22:47 [INFO] - [0:29] Decoding predicted spectra and IMs
2026-07-17 11:22:49 [INFO] - [0:31] Decoding RTs
2026-07-17 11:22:49 [INFO] - [0:31] Saving the list of predictions to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.predicted.bin
2026-07-17 11:22:50 [INFO] - Finished
2026-07-17 11:22:50 [INFO] - Done generating DIA-NN predictions
2026-07-17 11:22:50 [INFO] - Model running took 32078 milliseconds
2026-07-17 11:22:50 [INFO] - Generating edited pin with following features: [unweightedSpectralEntropy, weightedSpectralEntropy, hypergeometricProbability, intersection, top6matchedIntensity, deltaRTLOESS, deltaRTLOESSreal]
2026-07-17 11:22:50 [INFO] - Loading predicted spectra: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.predicted.bin
2026-07-17 11:22:51 [INFO] - Loading predicted retention times: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\MSBooster\spectraRT.predicted.bin
2026-07-17 11:22:51 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.pin has 41732 PSMs
2026-07-17 11:22:51 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.pin
2026-07-17 11:22:51 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:53 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:53 [INFO] - RT regression using 653 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:22:54 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.17
2026-07-17 11:22:54 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:55 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:56 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_edited.pin
2026-07-17 11:22:58 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.pin has 19055 PSMs
2026-07-17 11:22:58 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.pin
2026-07-17 11:22:58 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:59 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:22:59 [INFO] - RT regression using 308 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:22:59 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.17
2026-07-17 11:22:59 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:00 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:00 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_edited.pin
2026-07-17 11:23:00 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.pin has 19207 PSMs
2026-07-17 11:23:00 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.pin
2026-07-17 11:23:00 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:01 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:02 [INFO] - RT regression using 371 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:02 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.1
2026-07-17 11:23:02 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:02 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:02 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_edited.pin
2026-07-17 11:23:02 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.pin has 8343 PSMs
2026-07-17 11:23:02 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.pin
2026-07-17 11:23:02 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:03 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:03 [INFO] - RT regression using 193 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:03 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.17
2026-07-17 11:23:04 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:04 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:04 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_edited.pin
2026-07-17 11:23:04 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.pin has 29526 PSMs
2026-07-17 11:23:04 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.pin
2026-07-17 11:23:04 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:05 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:06 [INFO] - RT regression using 676 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:06 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.11
2026-07-17 11:23:06 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:06 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:06 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_edited.pin
2026-07-17 11:23:07 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.pin has 16602 PSMs
2026-07-17 11:23:07 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.pin
2026-07-17 11:23:07 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:08 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:08 [INFO] - RT regression using 236 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:08 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.17
2026-07-17 11:23:08 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:08 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:09 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_edited.pin
2026-07-17 11:23:09 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.pin has 13250 PSMs
2026-07-17 11:23:09 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.pin
2026-07-17 11:23:09 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:10 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:10 [INFO] - RT regression using 266 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:10 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.14
2026-07-17 11:23:10 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:11 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:11 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_edited.pin
2026-07-17 11:23:11 [INFO] - F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pin has 44926 PSMs
2026-07-17 11:23:11 [INFO] - Processing pin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pin
2026-07-17 11:23:11 [INFO] - Processing F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:12 [INFO] - Setting pin entries
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:12 [INFO] - RT regression using 1186 PSMs
Iteration 1...2...3...4...5...
2026-07-17 11:23:13 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.082
2026-07-17 11:23:13 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:14 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2026-07-17 11:23:14 [INFO] - Edited pin file at F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_edited.pin
2026-07-17 11:23:14 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 24676 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
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 Hemphi_Ca_CdSi1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi1_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 Hemphi_Ca_CdSi1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi1_edited.pin
Started Fri Jul 17 11:23:15 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_CdSi1_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 29526 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 17222 positives and 12304 negatives, size ratio=1.39971 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 2145 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 2357 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 2353 training set positives with q<0.01 in that direction.
Found 3349 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3170 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 4426 PSMs with q<0.01
Iteration 2:	Estimated 4581 PSMs with q<0.01
Iteration 3:	Estimated 4623 PSMs with q<0.01
Iteration 4:	Estimated 4625 PSMs with q<0.01
Iteration 5:	Estimated 4638 PSMs with q<0.01
Iteration 6:	Estimated 4643 PSMs with q<0.01
Iteration 7:	Estimated 4651 PSMs with q<0.01
Iteration 8:	Estimated 4653 PSMs with q<0.01
Iteration 9:	Estimated 4651 PSMs with q<0.01
Iteration 10:	Estimated 4650 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
-0.0393	-0.1368	-0.0684	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0971	 0.1211	 0.1135	isotope_error_0
 0.0196	-0.0523	-0.0379	isotope_error_1
-0.1345	-0.0879	-0.0940	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.2665	-0.5682	-0.5018	log10_evalue
 0.0637	 0.4615	 0.2529	hyperscore
 0.2473	 0.4997	 0.1617	delta_hyperscore
 0.4288	 0.0476	 0.0432	matched_ion_num
-0.3062	-0.2169	-0.2439	complementary_ions
 0.0280	 0.0170	-0.0028	ion_series
 0.0637	 0.0419	 0.1809	weighted_average_abs_fragment_ppm
-0.0831	-0.0651	-0.0494	length_7
-0.0015	-0.0568	-0.0338	length_8
 0.0254	 0.0485	 0.0322	length_9_30
 0.0880	 0.1031	 0.0721	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.4711	-0.6833	-0.4790	nmc
 0.2624	 0.2281	 0.2125	charge_1
-0.0295	-0.0822	-0.0725	charge_2
 0.0371	 0.0765	 0.0506	charge_3
-0.0376	-0.0203	-0.0014	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
-0.0274	 0.0378	 0.0687	15.9949M
 0.7353	 1.2067	 1.1180	unweighted_spectral_entropy
 0.3003	 0.2817	 0.0750	weighted_spectral_entropy
 0.2117	 0.0663	 0.1753	hypergeometric_probability
 0.0073	 0.2881	 0.1447	intersection
 0.2042	 0.3825	 0.2712	top6_matched_intensity
-1.4112	-2.1730	-2.2423	delta_RT_loess
-0.8204	-2.8069	-2.3414	delta_RT_loess_real
-4.2397	-7.4390	-6.7302	m0
Found 4518 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17222 target PSMs and 12304 decoy PSMs.
Calculating q values.
Final list yields 4543 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.3020 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
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 Hemphi_Ca_C1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C1_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 Hemphi_Ca_C1_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C1_edited.pin
Started Fri Jul 17 11:23:17 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_C1_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 41732 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 23378 positives and 18354 negatives, size ratio=1.27373 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 2412 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 2415 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 2415 training set positives with q<0.01 in that direction.
Found 3572 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4860 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 4408 PSMs with q<0.01
Iteration 2:	Estimated 4470 PSMs with q<0.01
Iteration 3:	Estimated 4513 PSMs with q<0.01
Iteration 4:	Estimated 4547 PSMs with q<0.01
Iteration 5:	Estimated 4563 PSMs with q<0.01
Iteration 6:	Estimated 4571 PSMs with q<0.01
Iteration 7:	Estimated 4576 PSMs with q<0.01
Iteration 8:	Estimated 4581 PSMs with q<0.01
Iteration 9:	Estimated 4585 PSMs with q<0.01
Iteration 10:	Estimated 4588 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
-0.3121	-0.1939	 0.0034	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0478	 0.2078	 0.0848	isotope_error_0
 0.1466	 0.1825	 0.1880	isotope_error_1
-0.2051	-0.4236	-0.2895	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.4131	-0.5783	-1.1592	log10_evalue
 1.0082	 1.0870	 0.8939	hyperscore
 0.2775	 0.1367	 0.1700	delta_hyperscore
-0.6623	-0.4027	-0.6745	matched_ion_num
-0.3185	-0.5386	-0.3072	complementary_ions
 0.3702	 0.3890	 0.4805	ion_series
-0.0176	-0.1043	 0.1186	weighted_average_abs_fragment_ppm
-0.0536	-0.1032	 0.0089	length_7
-0.0513	-0.0949	-0.0542	length_8
 0.0866	 0.0739	 0.0639	length_9_30
-0.0390	 0.1255	-0.0693	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.4385	-0.3223	-0.4923	nmc
 0.2761	 0.4452	 0.5028	charge_1
-0.1310	-0.0050	-0.1458	charge_2
 0.1672	 0.1673	 0.2169	charge_3
-0.0770	-0.2230	-0.1415	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
-0.0622	-0.2781	-0.3046	15.9949M
 0.9773	 1.1088	 0.3370	unweighted_spectral_entropy
 0.3561	 0.5037	 1.6013	weighted_spectral_entropy
 0.4686	 0.5248	 0.7980	hypergeometric_probability
 0.1259	 0.2434	 0.0291	intersection
 0.1114	 0.1436	 0.1730	top6_matched_intensity
-2.3560	-1.7988	-2.8307	delta_RT_loess
-0.9051	-2.6966	-2.2887	delta_RT_loess_real
-6.1821	-7.8132	-8.8580	m0
Found 4496 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 23378 target PSMs and 18354 decoy PSMs.
Calculating q values.
Final list yields 4512 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.7330 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_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 Hemphi_Ca_C4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C4_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 Hemphi_Ca_C4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C4_edited.pin
Started Fri Jul 17 11:23:21 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_C4_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 8343 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 5152 positives and 3191 negatives, size ratio=1.61454 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 922 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 1001 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 952 training set positives with q<0.01 in that direction.
Found 1408 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.0810 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 1889 PSMs with q<0.01
Iteration 2:	Estimated 1923 PSMs with q<0.01
Iteration 3:	Estimated 1942 PSMs with q<0.01
Iteration 4:	Estimated 1946 PSMs with q<0.01
Iteration 5:	Estimated 1946 PSMs with q<0.01
Iteration 6:	Estimated 1951 PSMs with q<0.01
Iteration 7:	Estimated 1951 PSMs with q<0.01
Iteration 8:	Estimated 1951 PSMs with q<0.01
Iteration 9:	Estimated 1951 PSMs with q<0.01
Iteration 10:	Estimated 1951 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
-0.1698	-0.4222	-0.5340	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1782	 0.2288	 0.4501	isotope_error_0
 0.0644	-0.0177	-0.1020	isotope_error_1
-0.2824	-0.2591	-0.4406	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.5715	 0.4560	-0.2905	log10_evalue
-0.0034	 0.5256	-0.2240	hyperscore
 0.6030	 0.5652	 0.3729	delta_hyperscore
 1.3537	 0.7392	 2.1161	matched_ion_num
-0.5036	-0.3123	-0.3615	complementary_ions
 0.1686	 0.3402	 0.1714	ion_series
 0.1842	-0.1306	 0.0662	weighted_average_abs_fragment_ppm
 0.1261	-0.1759	-0.1257	length_7
-0.0488	 0.0514	-0.0936	length_8
-0.1798	-0.1289	 0.0310	length_9_30
 0.3311	 0.4883	 0.2818	length_31
 0.0000	 0.0000	 0.0000	ntt
-1.3643	-1.0397	-1.9344	nmc
 0.4559	 0.1849	 0.2913	charge_1
-0.1793	 0.0142	-0.3051	charge_2
 0.4157	 0.1712	 0.4252	charge_3
-0.2971	-0.2156	-0.1578	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
-0.1951	-0.1085	 0.5311	15.9949M
 0.3323	-0.0418	 1.0635	unweighted_spectral_entropy
 2.2194	 2.0441	 2.3147	weighted_spectral_entropy
 0.8365	 0.2519	 0.3527	hypergeometric_probability
-0.1165	-0.1503	-0.4243	intersection
-0.0175	 0.0946	 0.2937	top6_matched_intensity
-5.1695	-1.7871	-6.1548	delta_RT_loess
 0.7802	 0.1957	 3.4644	delta_RT_loess_real
-6.2787	-3.8917	-6.4361	m0
Found 1865 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5152 target PSMs and 3191 decoy PSMs.
Calculating q values.
Final list yields 1865 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.6400 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_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 Hemphi_Ca_CdSi4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi4_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 Hemphi_Ca_CdSi4_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi4_edited.pin
Started Fri Jul 17 11:23:23 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_CdSi4_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 44926 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 26487 positives and 18439 negatives, size ratio=1.43647 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 4073 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 4029 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 4223 training set positives with q<0.01 in that direction.
Found 6208 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5030 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 7533 PSMs with q<0.01
Iteration 2:	Estimated 7687 PSMs with q<0.01
Iteration 3:	Estimated 7726 PSMs with q<0.01
Iteration 4:	Estimated 7745 PSMs with q<0.01
Iteration 5:	Estimated 7742 PSMs with q<0.01
Iteration 6:	Estimated 7756 PSMs with q<0.01
Iteration 7:	Estimated 7761 PSMs with q<0.01
Iteration 8:	Estimated 7768 PSMs with q<0.01
Iteration 9:	Estimated 7767 PSMs with q<0.01
Iteration 10:	Estimated 7768 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
-0.3417	-0.2087	-0.1865	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0837	 0.0827	 0.0410	isotope_error_0
 0.0260	 0.0645	 0.0065	isotope_error_1
-0.1257	-0.1647	-0.0551	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.5124	-0.4609	-0.2543	log10_evalue
 0.5544	 0.3444	 0.2402	hyperscore
 0.3251	 0.3447	 0.3814	delta_hyperscore
-0.2066	 0.6142	 0.4429	matched_ion_num
-0.2662	-0.5019	-0.1970	complementary_ions
 0.2280	 0.0330	 0.2467	ion_series
 0.0852	 0.1458	 0.0276	weighted_average_abs_fragment_ppm
-0.0712	-0.0856	-0.0368	length_7
-0.0495	-0.0391	-0.0475	length_8
 0.0345	 0.0430	 0.0442	length_9_30
 0.1692	 0.1458	 0.0529	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.5647	-0.5761	-0.4130	nmc
 0.1416	 0.1931	 0.2277	charge_1
-0.0139	 0.0169	-0.0296	charge_2
 0.0390	 0.0664	-0.0227	charge_3
-0.0402	-0.1058	 0.0331	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
-0.1531	-0.0737	-0.0338	15.9949M
 0.1966	 0.6903	 0.4105	unweighted_spectral_entropy
 1.6401	 1.7212	 0.7902	weighted_spectral_entropy
 0.2090	 0.3977	 0.2655	hypergeometric_probability
 0.1311	-0.0395	 0.0343	intersection
 0.3268	 0.4034	 0.2625	top6_matched_intensity
-2.2272	-2.7431	-1.3293	delta_RT_loess
-0.6345	-0.7318	-0.6688	delta_RT_loess_real
-5.4584	-6.4148	-4.0235	m0
Found 7685 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 26487 target PSMs and 18439 decoy PSMs.
Calculating q values.
Final list yields 7691 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.0380 cpu seconds or 3 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
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 Hemphi_Ca_C3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C3_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 Hemphi_Ca_C3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C3_edited.pin
Started Fri Jul 17 11:23:27 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_C3_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 19207 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 11343 positives and 7864 negatives, size ratio=1.4424 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 1410 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 1448 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 1462 training set positives with q<0.01 in that direction.
Found 2104 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2090 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 2887 PSMs with q<0.01
Iteration 2:	Estimated 3000 PSMs with q<0.01
Iteration 3:	Estimated 3038 PSMs with q<0.01
Iteration 4:	Estimated 3053 PSMs with q<0.01
Iteration 5:	Estimated 3050 PSMs with q<0.01
Iteration 6:	Estimated 3055 PSMs with q<0.01
Iteration 7:	Estimated 3060 PSMs with q<0.01
Iteration 8:	Estimated 3060 PSMs with q<0.01
Iteration 9:	Estimated 3063 PSMs with q<0.01
Iteration 10:	Estimated 3063 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
-0.2517	-0.3823	-0.4270	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1324	 0.1259	 0.1600	isotope_error_0
 0.0578	 0.1075	 0.0562	isotope_error_1
-0.2140	-0.2573	-0.2446	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.2982	-0.1858	-0.5818	log10_evalue
 0.3853	 0.7172	 0.2703	hyperscore
 0.3977	 0.3504	 0.5807	delta_hyperscore
 0.2335	-0.1129	 0.6324	matched_ion_num
-0.1762	-0.1762	-0.4455	complementary_ions
 0.1790	 0.2559	 0.4361	ion_series
 0.1423	-0.0875	 0.3207	weighted_average_abs_fragment_ppm
-0.0992	-0.1508	-0.0610	length_7
-0.0056	-0.0011	-0.0548	length_8
 0.0541	 0.0790	 0.0575	length_9_30
 0.0311	 0.0419	 0.0512	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.7029	-0.7385	-0.8338	nmc
 0.1786	 0.1801	 0.1972	charge_1
-0.1340	-0.0643	-0.0535	charge_2
 0.0563	 0.0493	 0.0192	charge_3
 0.0604	-0.0033	 0.0161	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
-0.2371	-0.1053	-0.4426	15.9949M
 0.7841	 0.7353	 0.4380	unweighted_spectral_entropy
 0.3512	 0.1569	 0.8448	weighted_spectral_entropy
 0.1686	 0.2061	 0.1257	hypergeometric_probability
 0.0077	 0.0060	-0.0127	intersection
 0.2988	 0.2372	 0.3010	top6_matched_intensity
-1.5627	-2.1150	-1.3033	delta_RT_loess
-0.8262	 0.0306	-1.3089	delta_RT_loess_real
-4.2418	-4.2758	-4.6822	m0
Found 2980 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 11343 target PSMs and 7864 decoy PSMs.
Calculating q values.
Final list yields 2985 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.9950 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
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 Hemphi_Ca_CdSi2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi2_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 Hemphi_Ca_CdSi2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi2_edited.pin
Started Fri Jul 17 11:23:29 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_CdSi2_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 16602 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 9607 positives and 6995 negatives, size ratio=1.37341 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 1053 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 1170 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 1228 training set positives with q<0.01 in that direction.
Found 1665 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.1620 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 2311 PSMs with q<0.01
Iteration 2:	Estimated 2409 PSMs with q<0.01
Iteration 3:	Estimated 2424 PSMs with q<0.01
Iteration 4:	Estimated 2445 PSMs with q<0.01
Iteration 5:	Estimated 2440 PSMs with q<0.01
Iteration 6:	Estimated 2445 PSMs with q<0.01
Iteration 7:	Estimated 2448 PSMs with q<0.01
Iteration 8:	Estimated 2446 PSMs with q<0.01
Iteration 9:	Estimated 2450 PSMs with q<0.01
Iteration 10:	Estimated 2448 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
-0.2145	-0.2183	-0.1022	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1280	 0.4637	 0.3303	isotope_error_0
-0.0063	-0.3778	-0.1466	isotope_error_1
-0.1430	-0.1520	-0.2346	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.5196	-1.3093	-0.9267	log10_evalue
 0.3785	 0.1863	 0.2899	hyperscore
 0.1082	 0.4686	 0.1942	delta_hyperscore
-0.1808	-0.1111	-0.2161	matched_ion_num
-0.1807	-0.2580	-0.3706	complementary_ions
 0.0927	 0.1395	 0.3684	ion_series
 0.1361	 0.1556	-0.0363	weighted_average_abs_fragment_ppm
-0.0767	-0.1436	-0.0330	length_7
-0.0363	-0.0764	-0.0928	length_8
 0.0311	 0.0798	 0.0322	length_9_30
 0.1443	 0.2216	 0.1881	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.3638	-0.4715	-0.2881	nmc
 0.1564	 0.3258	 0.2929	charge_1
 0.0192	 0.1863	 0.1711	charge_2
 0.0538	 0.1028	 0.1338	charge_3
-0.0895	-0.3255	-0.3394	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
-0.1202	 0.1348	-0.1685	15.9949M
 0.5060	 0.2233	 0.5260	unweighted_spectral_entropy
 0.1843	 1.7881	 0.4568	weighted_spectral_entropy
 0.0196	 0.5637	 0.4012	hypergeometric_probability
 0.0781	-0.0302	-0.0699	intersection
 0.2242	 0.1792	 0.2951	top6_matched_intensity
-1.3326	-1.0169	-3.5745	delta_RT_loess
-0.7429	-3.8154	-1.4334	delta_RT_loess_real
-3.7380	-7.7879	-7.0013	m0
Found 2367 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 9607 target PSMs and 6995 decoy PSMs.
Calculating q values.
Final list yields 2372 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.8040 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
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 Hemphi_Ca_CdSi3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi3_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 Hemphi_Ca_CdSi3_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_CdSi3_edited.pin
Started Fri Jul 17 11:23:31 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_CdSi3_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 
ERROR: Reached strange feature with val=nan col=36 for PSM with id Hemphi_Ca_CdSi3.51320.51320.4_1
No-terminate flag set: setting value to 0 and ignoring the error.
Found 13250 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 7773 positives and 5477 negatives, size ratio=1.41921 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 1101 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 1050 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 974 training set positives with q<0.01 in that direction.
Found 1577 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.1560 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 2094 PSMs with q<0.01
Iteration 2:	Estimated 2159 PSMs with q<0.01
Iteration 3:	Estimated 2185 PSMs with q<0.01
Iteration 4:	Estimated 2197 PSMs with q<0.01
Iteration 5:	Estimated 2200 PSMs with q<0.01
Iteration 6:	Estimated 2205 PSMs with q<0.01
Iteration 7:	Estimated 2207 PSMs with q<0.01
Iteration 8:	Estimated 2206 PSMs with q<0.01
Iteration 9:	Estimated 2206 PSMs with q<0.01
Iteration 10:	Estimated 2209 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
-0.1842	-0.2307	-0.2303	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1286	 0.1239	 0.2229	isotope_error_0
 0.0567	 0.0661	 0.2462	isotope_error_1
-0.2113	-0.2155	-0.5198	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.3221	-0.3412	-1.6004	log10_evalue
-0.0461	 0.2208	-0.1089	hyperscore
 0.3703	 0.3917	 0.2547	delta_hyperscore
 0.7150	 0.6599	 0.6612	matched_ion_num
-0.4945	-0.5615	-0.6606	complementary_ions
 0.2594	 0.2132	 0.2051	ion_series
 0.2237	 0.1562	 0.2628	weighted_average_abs_fragment_ppm
-0.0976	-0.0930	-0.1376	length_7
 0.0552	-0.0649	-0.0467	length_8
-0.0136	 0.0742	-0.0257	length_9_30
 0.1072	 0.1069	 0.4616	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.5373	-0.6329	-0.8023	nmc
 0.3225	 0.1760	 0.3029	charge_1
-0.0590	 0.0999	 0.1020	charge_2
 0.0283	 0.0710	 0.1688	charge_3
 0.0022	-0.1935	-0.3093	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
 0.1184	 0.0464	 0.1727	15.9949M
 0.9205	 0.9751	 0.4194	unweighted_spectral_entropy
 0.1922	 0.4630	 1.0117	weighted_spectral_entropy
 0.1260	 0.5869	 0.2356	hypergeometric_probability
 0.0881	-0.0958	-0.1885	intersection
 0.4697	 0.2765	 0.6518	top6_matched_intensity
-1.8177	-1.0427	-3.4932	delta_RT_loess
-1.3441	-1.0247	-1.6345	delta_RT_loess_real
-4.7448	-4.2202	-7.2639	m0
Found 2098 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 7773 target PSMs and 5477 decoy PSMs.
Calculating q values.
Final list yields 2105 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 1.8250 cpu seconds or 1 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
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 Hemphi_Ca_C2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C2_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 Hemphi_Ca_C2_percolator_target_psms.tsv --decoy-results-psms Hemphi_Ca_C2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Hemphi_Ca_C2_edited.pin
Started Fri Jul 17 11:23:33 2026
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Hemphi_Ca_C2_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 19055 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 10788 positives and 8267 negatives, size ratio=1.30495 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 34 as initial direction. Could separate 1165 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 34 as initial direction. Could separate 1302 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 34 as initial direction. Could separate 1238 training set positives with q<0.01 in that direction.
Found 1679 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2050 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 2318 PSMs with q<0.01
Iteration 2:	Estimated 2358 PSMs with q<0.01
Iteration 3:	Estimated 2361 PSMs with q<0.01
Iteration 4:	Estimated 2359 PSMs with q<0.01
Iteration 5:	Estimated 2366 PSMs with q<0.01
Iteration 6:	Estimated 2359 PSMs with q<0.01
Iteration 7:	Estimated 2366 PSMs with q<0.01
Iteration 8:	Estimated 2353 PSMs with q<0.01
Iteration 9:	Estimated 2360 PSMs with q<0.01
Iteration 10:	Estimated 2354 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
-0.3802	-0.4316	-0.4181	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0188	 0.0131	-0.0634	isotope_error_0
-0.0390	-0.0612	 0.0165	isotope_error_1
 0.0186	 0.0482	 0.0566	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.8753	-0.7908	-0.4751	log10_evalue
 0.8841	 0.4679	 0.7012	hyperscore
 0.5293	 0.5438	 0.5696	delta_hyperscore
-0.0229	 0.0954	 0.0308	matched_ion_num
-0.5162	-0.2574	-0.3127	complementary_ions
 0.0771	 0.0749	 0.2885	ion_series
 0.1973	-0.0330	-0.0033	weighted_average_abs_fragment_ppm
-0.1351	-0.1914	-0.1943	length_7
 0.0276	 0.0421	 0.0044	length_8
 0.0125	 0.0232	 0.0651	length_9_30
 0.1321	 0.1671	 0.1348	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.5314	-0.6235	-0.9216	nmc
 0.1997	 0.2107	 0.1858	charge_1
-0.0328	 0.0299	 0.1206	charge_2
 0.0296	 0.0383	-0.0065	charge_3
-0.0171	-0.0894	-0.1304	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
-0.3266	 0.0707	-0.3866	15.9949M
 0.9421	 0.8138	 0.0876	unweighted_spectral_entropy
 0.7579	 0.8036	 1.6132	weighted_spectral_entropy
 0.4171	 0.3819	 0.4032	hypergeometric_probability
-0.0642	-0.0219	-0.0069	intersection
 0.2684	 0.1458	 0.2795	top6_matched_intensity
-0.9558	-1.7320	-1.5038	delta_RT_loess
-0.5284	-0.3229	 0.0274	delta_RT_loess_real
-4.7611	-4.7779	-4.6666	m0
Found 2249 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 10788 target PSMs and 8267 decoy PSMs.
Calculating q values.
Final list yields 2252 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 2.1350 cpu seconds or 2 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi1.pin Hemphi_Ca_CdSi1 Hemphi_Ca_CdSi1_percolator_target_psms.tsv Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi1 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C1.pin Hemphi_Ca_C1 Hemphi_Ca_C1_percolator_target_psms.tsv Hemphi_Ca_C1_percolator_decoy_psms.tsv interact-Hemphi_Ca_C1 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C4.pin Hemphi_Ca_C4 Hemphi_Ca_C4_percolator_target_psms.tsv Hemphi_Ca_C4_percolator_decoy_psms.tsv interact-Hemphi_Ca_C4 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi4.pin Hemphi_Ca_CdSi4 Hemphi_Ca_CdSi4_percolator_target_psms.tsv Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi4 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C3.pin Hemphi_Ca_C3 Hemphi_Ca_C3_percolator_target_psms.tsv Hemphi_Ca_C3_percolator_decoy_psms.tsv interact-Hemphi_Ca_C3 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi2.pin Hemphi_Ca_CdSi2 Hemphi_Ca_CdSi2_percolator_target_psms.tsv Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi2 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_CdSi3.pin Hemphi_Ca_CdSi3 Hemphi_Ca_CdSi3_percolator_target_psms.tsv Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv interact-Hemphi_Ca_CdSi3 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML Hemphi_Ca_C2.pin Hemphi_Ca_C2 Hemphi_Ca_C2_percolator_target_psms.tsv Hemphi_Ca_C2_percolator_decoy_psms.tsv interact-Hemphi_Ca_C2 DDA 0.5 F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_percolator_decoy_psms.tsv
Process 'Percolator delete temp' finished, exit code: 0
ProteinProphet [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\filelist_proteinprophet.txt
time="11:23:45" 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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\interact-Hemphi_Ca_C1.pep.xml...
...read in 4 1+, 2666 2+, 2138 3+, 559 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\interact-Hemphi_Ca_C2.pep.xml...
...read in 3 1+, 1429 2+, 1032 3+, 292 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\interact-Hemphi_Ca_C3.pep.xml...
...read in 0 1+, 1768 2+, 1400 3+, 377 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\interact-Hemphi_Ca_C4.pep.xml...
...read in 4 1+, 1173 2+, 754 3+, 222 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\interact-Hemphi_Ca_CdSi1.pep.xml...
...read in 10 1+, 3019 2+, 1808 3+, 476 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\interact-Hemphi_Ca_CdSi2.pep.xml...
...read in 1 1+, 1559 2+, 987 3+, 280 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\interact-Hemphi_Ca_CdSi3.pep.xml...
...read in 1 1+, 1322 2+, 888 3+, 310 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\interact-Hemphi_Ca_CdSi4.pep.xml...
...read in 3 1+, 4790 2+, 3208 3+, 658 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 7617 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_protein.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.....  Total: 80154
Computing degenerate peptides for 6257 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 7395 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7395 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7395 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 7395 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.63577e-05, db_size=74322823
Computing MU for 7395 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="11:23:48" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe database --annotate F:\Research\PXD060911-Cannabis-sativa-TripleTOF\2026-07-16-decoys-contam-GCF_029168945.1_ASM2916894v1_protein.fas --prefix rev_
time="11:23:48" level=info msg="Executing Database  v5.1.3"
time="11:23:48" level=info msg="Annotating the database"
time="11:23:48" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --razor
time="11:23:48" level=info msg="Executing Filter  v5.1.3"
time="11:23:48" level=info msg="Processing peptide identification files"
time="11:23:48" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1\\interact-Hemphi_Ca_C1.pep.xml"
time="11:23:48" level=info msg="1+ Charge profile" decoy=1 target=3
time="11:23:48" level=info msg="2+ Charge profile" decoy=120 target=2546
time="11:23:48" level=info msg="3+ Charge profile" decoy=137 target=2001
time="11:23:48" level=info msg="4+ Charge profile" decoy=50 target=509
time="11:23:48" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:48" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:48" level=info msg="Database search results" ions=2776 peptides=2467 psms=5367
time="11:23:48" level=info msg="Converged to 1.00 % FDR with 4519 PSMs" decoy=45 threshold=0.788747 total=4564
time="11:23:48" level=info msg="Converged to 0.99 % FDR with 1718 Peptides" decoy=17 threshold=0.868878 total=1735
time="11:23:48" level=info msg="Converged to 0.96 % FDR with 1982 Ions" decoy=19 threshold=0.863287 total=2001
time="11:23:48" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:49" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:49" level=info msg="Applying sequential FDR estimation" ions=2031 peptides=1760 psms=4419
time="11:23:49" level=info msg="4416 PSMs" decoy=2 threshold=0.788881 total=4418
time="11:23:49" level=info msg="1675 Peptides" decoy=1 threshold=0.868878 total=1676
time="11:23:49" level=info msg="1939 Ions" decoy=1 threshold=0.863287 total=1940
time="11:23:49" level=info msg="Post processing identifications"
time="11:23:49" level=info msg="Assigning protein identifications to layers"
time="11:23:49" level=info msg="Processing protein inference"
time="11:23:49" level=info msg="Synchronizing PSMs and proteins"
time="11:23:49" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1939 peptides=1675 proteins=551 psms=4416
time="11:23:49" level=info msg=Saving
time="11:23:49" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:49" level=info msg="Executing Filter  v5.1.3"
time="11:23:49" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:49" level=info msg="Processing peptide identification files"
time="11:23:49" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_2\\interact-Hemphi_Ca_C2.pep.xml"
time="11:23:49" level=info msg="1+ Charge profile" decoy=1 target=2
time="11:23:49" level=info msg="2+ Charge profile" decoy=77 target=1352
time="11:23:49" level=info msg="3+ Charge profile" decoy=53 target=979
time="11:23:49" level=info msg="4+ Charge profile" decoy=36 target=256
time="11:23:49" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:49" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:49" level=info msg="Database search results" ions=1397 peptides=1285 psms=2756
time="11:23:49" level=info msg="Converged to 0.98 % FDR with 2252 PSMs" decoy=22 threshold=0.806728 total=2274
time="11:23:49" level=info msg="Converged to 0.89 % FDR with 894 Peptides" decoy=8 threshold=0.843352 total=902
time="11:23:49" level=info msg="Converged to 0.90 % FDR with 995 Ions" decoy=9 threshold=0.843068 total=1004
time="11:23:49" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:49" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:49" level=info msg="Applying sequential FDR estimation" ions=999 peptides=893 psms=2204
time="11:23:49" level=info msg="2203 PSMs" decoy=0 threshold=0.81236 total=2203
time="11:23:49" level=info msg="871 Peptides" decoy=0 threshold=0.843352 total=871
time="11:23:49" level=info msg="972 Ions" decoy=0 threshold=0.843068 total=972
time="11:23:49" level=info msg="Post processing identifications"
time="11:23:49" level=info msg="Assigning protein identifications to layers"
time="11:23:50" level=info msg="Processing protein inference"
time="11:23:50" level=info msg="Synchronizing PSMs and proteins"
time="11:23:50" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=972 peptides=871 proteins=370 psms=2203
time="11:23:50" level=info msg=Saving
time="11:23:50" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:50" level=info msg="Executing Filter  v5.1.3"
time="11:23:50" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:50" level=info msg="Processing peptide identification files"
time="11:23:50" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_3\\interact-Hemphi_Ca_C3.pep.xml"
time="11:23:50" level=info msg="1+ Charge profile" decoy=0 target=0
time="11:23:50" level=info msg="2+ Charge profile" decoy=88 target=1680
time="11:23:50" level=info msg="3+ Charge profile" decoy=79 target=1321
time="11:23:50" level=info msg="4+ Charge profile" decoy=44 target=333
time="11:23:50" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:50" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:50" level=info msg="Database search results" ions=1750 peptides=1586 psms=3545
time="11:23:50" level=info msg="Converged to 0.97 % FDR with 2993 PSMs" decoy=29 threshold=0.791282 total=3022
time="11:23:50" level=info msg="Converged to 0.98 % FDR with 1119 Peptides" decoy=11 threshold=0.867723 total=1130
time="11:23:50" level=info msg="Converged to 0.95 % FDR with 1261 Ions" decoy=12 threshold=0.863843 total=1273
time="11:23:50" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:50" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:50" level=info msg="Applying sequential FDR estimation" ions=1292 peptides=1149 psms=2931
time="11:23:50" level=info msg="2928 PSMs" decoy=2 threshold=0.792024 total=2930
time="11:23:50" level=info msg="1090 Peptides" decoy=2 threshold=0.867723 total=1092
time="11:23:50" level=info msg="1231 Ions" decoy=2 threshold=0.863843 total=1233
time="11:23:50" level=info msg="Post processing identifications"
time="11:23:50" level=info msg="Assigning protein identifications to layers"
time="11:23:50" level=info msg="Processing protein inference"
time="11:23:51" level=info msg="Synchronizing PSMs and proteins"
time="11:23:51" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1231 peptides=1090 proteins=455 psms=2928
time="11:23:51" level=info msg=Saving
time="11:23:51" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:51" level=info msg="Executing Filter  v5.1.3"
time="11:23:51" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:51" level=info msg="Processing peptide identification files"
time="11:23:51" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_4\\interact-Hemphi_Ca_C4.pep.xml"
time="11:23:51" level=info msg="1+ Charge profile" decoy=0 target=4
time="11:23:51" level=info msg="2+ Charge profile" decoy=44 target=1129
time="11:23:51" level=info msg="3+ Charge profile" decoy=43 target=711
time="11:23:51" level=info msg="4+ Charge profile" decoy=21 target=201
time="11:23:51" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:51" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:51" level=info msg="Database search results" ions=1033 peptides=960 psms=2153
time="11:23:51" level=info msg="Converged to 0.97 % FDR with 1865 PSMs" decoy=18 threshold=0.812781 total=1883
time="11:23:51" level=info msg="Converged to 0.95 % FDR with 739 Peptides" decoy=7 threshold=0.868426 total=746
time="11:23:51" level=info msg="Converged to 0.97 % FDR with 826 Ions" decoy=8 threshold=0.849067 total=834
time="11:23:51" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:51" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:51" level=info msg="Applying sequential FDR estimation" ions=813 peptides=745 psms=1827
time="11:23:51" level=info msg="1825 PSMs" decoy=1 threshold=0.816664 total=1826
time="11:23:51" level=info msg="720 Peptides" decoy=0 threshold=0.868455 total=720
time="11:23:51" level=info msg="802 Ions" decoy=0 threshold=0.853308 total=802
time="11:23:51" level=info msg="Post processing identifications"
time="11:23:51" level=info msg="Assigning protein identifications to layers"
time="11:23:51" level=info msg="Processing protein inference"
time="11:23:51" level=info msg="Synchronizing PSMs and proteins"
time="11:23:51" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=802 peptides=720 proteins=342 psms=1825
time="11:23:51" level=info msg=Saving
time="11:23:51" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:51" level=info msg="Executing Filter  v5.1.3"
time="11:23:51" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:52" level=info msg="Processing peptide identification files"
time="11:23:52" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\CdSi_1\\interact-Hemphi_Ca_CdSi1.pep.xml"
time="11:23:52" level=info msg="1+ Charge profile" decoy=7 target=3
time="11:23:52" level=info msg="2+ Charge profile" decoy=112 target=2907
time="11:23:52" level=info msg="3+ Charge profile" decoy=106 target=1702
time="11:23:52" level=info msg="4+ Charge profile" decoy=58 target=418
time="11:23:52" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:52" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:52" level=info msg="Database search results" ions=2945 peptides=2653 psms=5313
time="11:23:52" level=info msg="Converged to 0.99 % FDR with 4555 PSMs" decoy=45 threshold=0.810119 total=4600
time="11:23:52" level=info msg="Converged to 0.98 % FDR with 1938 Peptides" decoy=19 threshold=0.883373 total=1957
time="11:23:52" level=info msg="Converged to 0.99 % FDR with 2215 Ions" decoy=22 threshold=0.872619 total=2237
time="11:23:52" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:52" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:52" level=info msg="Applying sequential FDR estimation" ions=2216 peptides=1949 psms=4407
time="11:23:52" level=info msg="4403 PSMs" decoy=3 threshold=0.810204 total=4406
time="11:23:52" level=info msg="1858 Peptides" decoy=3 threshold=0.883373 total=1861
time="11:23:52" level=info msg="2127 Ions" decoy=3 threshold=0.872794 total=2130
time="11:23:52" level=info msg="Post processing identifications"
time="11:23:52" level=info msg="Assigning protein identifications to layers"
time="11:23:52" level=info msg="Processing protein inference"
time="11:23:52" level=info msg="Synchronizing PSMs and proteins"
time="11:23:52" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=2127 peptides=1858 proteins=631 psms=4403
time="11:23:52" level=info msg=Saving
time="11:23:52" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:52" level=info msg="Executing Filter  v5.1.3"
time="11:23:52" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:53" level=info msg="Processing peptide identification files"
time="11:23:53" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\CdSi_2\\interact-Hemphi_Ca_CdSi2.pep.xml"
time="11:23:53" level=info msg="1+ Charge profile" decoy=0 target=1
time="11:23:53" level=info msg="2+ Charge profile" decoy=71 target=1488
time="11:23:53" level=info msg="3+ Charge profile" decoy=58 target=929
time="11:23:53" level=info msg="4+ Charge profile" decoy=29 target=251
time="11:23:53" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:53" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:53" level=info msg="Database search results" ions=1517 peptides=1402 psms=2827
time="11:23:53" level=info msg="Converged to 0.97 % FDR with 2375 PSMs" decoy=23 threshold=0.807682 total=2398
time="11:23:53" level=info msg="Converged to 0.98 % FDR with 1024 Peptides" decoy=10 threshold=0.86259 total=1034
time="11:23:53" level=info msg="Converged to 0.98 % FDR with 1122 Ions" decoy=11 threshold=0.85974 total=1133
time="11:23:53" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:53" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:53" level=info msg="Applying sequential FDR estimation" ions=1129 peptides=1029 psms=2315
time="11:23:53" level=info msg="2313 PSMs" decoy=1 threshold=0.808076 total=2314
time="11:23:53" level=info msg="991 Peptides" decoy=1 threshold=0.86259 total=992
time="11:23:53" level=info msg="1089 Ions" decoy=1 threshold=0.85974 total=1090
time="11:23:53" level=info msg="Post processing identifications"
time="11:23:53" level=info msg="Assigning protein identifications to layers"
time="11:23:53" level=info msg="Processing protein inference"
time="11:23:53" level=info msg="Synchronizing PSMs and proteins"
time="11:23:53" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1089 peptides=991 proteins=455 psms=2313
time="11:23:53" level=info msg=Saving
time="11:23:53" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:53" level=info msg="Executing Filter  v5.1.3"
time="11:23:53" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:53" level=info msg="Processing peptide identification files"
time="11:23:53" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\CdSi_3\\interact-Hemphi_Ca_CdSi3.pep.xml"
time="11:23:54" level=info msg="1+ Charge profile" decoy=1 target=0
time="11:23:54" level=info msg="2+ Charge profile" decoy=64 target=1258
time="11:23:54" level=info msg="3+ Charge profile" decoy=59 target=829
time="11:23:54" level=info msg="4+ Charge profile" decoy=30 target=280
time="11:23:54" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:54" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:54" level=info msg="Database search results" ions=1285 peptides=1148 psms=2521
time="11:23:54" level=info msg="Converged to 1.00 % FDR with 2105 PSMs" decoy=21 threshold=0.800906 total=2126
time="11:23:54" level=info msg="Converged to 0.98 % FDR with 815 Peptides" decoy=8 threshold=0.853614 total=823
time="11:23:54" level=info msg="Converged to 0.95 % FDR with 944 Ions" decoy=9 threshold=0.852451 total=953
time="11:23:54" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:54" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:54" level=info msg="Applying sequential FDR estimation" ions=960 peptides=830 psms=2067
time="11:23:54" level=info msg="2064 PSMs" decoy=2 threshold=0.802894 total=2066
time="11:23:54" level=info msg="791 Peptides" decoy=1 threshold=0.853614 total=792
time="11:23:54" level=info msg="920 Ions" decoy=1 threshold=0.852451 total=921
time="11:23:54" level=info msg="Post processing identifications"
time="11:23:54" level=info msg="Assigning protein identifications to layers"
time="11:23:54" level=info msg="Processing protein inference"
time="11:23:54" level=info msg="Synchronizing PSMs and proteins"
time="11:23:54" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=920 peptides=791 proteins=399 psms=2064
time="11:23:54" level=info msg=Saving
time="11:23:54" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4 --dbbin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --protxml F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\combined.prot.xml --probin F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1 --razor
time="11:23:54" level=info msg="Executing Filter  v5.1.3"
time="11:23:54" level=info msg="Fetching protein inference from F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\C_1"
time="11:23:54" level=info msg="Processing peptide identification files"
time="11:23:54" level=info msg="Parsing F:\\Research\\PXD060911-Cannabis-sativa-TripleTOF\\20260717-FragPipe-LFQ-MBR\\CdSi_4\\interact-Hemphi_Ca_CdSi4.pep.xml"
time="11:23:55" level=info msg="1+ Charge profile" decoy=1 target=2
time="11:23:55" level=info msg="2+ Charge profile" decoy=176 target=4614
time="11:23:55" level=info msg="3+ Charge profile" decoy=122 target=3086
time="11:23:55" level=info msg="4+ Charge profile" decoy=47 target=611
time="11:23:55" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:23:55" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:23:55" level=info msg="Database search results" ions=4257 peptides=3703 psms=8659
time="11:23:55" level=info msg="Converged to 0.99 % FDR with 7691 PSMs" decoy=76 threshold=0.803953 total=7767
time="11:23:55" level=info msg="Converged to 0.97 % FDR with 2874 Peptides" decoy=28 threshold=0.871962 total=2902
time="11:23:55" level=info msg="Converged to 0.97 % FDR with 3385 Ions" decoy=33 threshold=0.866083 total=3418
time="11:23:55" level=info msg="Protein inference results" decoy=1225 target=2481
time="11:23:55" level=info msg="Converged to 0.94 % FDR with 849 Proteins" decoy=8 threshold=0.9707 total=857
time="11:23:55" level=info msg="Applying sequential FDR estimation" ions=3352 peptides=2838 psms=7482
time="11:23:55" level=info msg="7472 PSMs" decoy=9 threshold=0.804041 total=7481
time="11:23:55" level=info msg="2755 Peptides" decoy=6 threshold=0.872007 total=2761
time="11:23:55" level=info msg="3258 Ions" decoy=7 threshold=0.866083 total=3265
time="11:23:55" level=info msg="Post processing identifications"
time="11:23:55" level=info msg="Assigning protein identifications to layers"
time="11:23:55" level=info msg="Processing protein inference"
time="11:23:55" level=info msg="Synchronizing PSMs and proteins"
time="11:23:55" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=3257 peptides=2754 proteins=748 psms=7471
time="11:23:55" level=info msg=Saving
time="11:23:55" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:56" level=info msg="Executing Report  v5.1.3"
time="11:23:56" level=info msg="Creating reports"
time="11:23:56" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:56" level=info msg="Executing Report  v5.1.3"
time="11:23:56" level=info msg="Creating reports"
time="11:23:56" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:56" level=info msg="Executing Report  v5.1.3"
time="11:23:56" level=info msg="Creating reports"
time="11:23:56" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:56" level=info msg="Executing Report  v5.1.3"
time="11:23:56" level=info msg="Creating reports"
time="11:23:56" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:56" level=info msg="Executing Report  v5.1.3"
time="11:23:56" level=info msg="Creating reports"
time="11:23:56" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:57" level=info msg="Executing Report  v5.1.3"
time="11:23:57" level=info msg="Creating reports"
time="11:23:57" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:57" level=info msg="Executing Report  v5.1.3"
time="11:23:57" level=info msg="Creating reports"
time="11:23:57" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report
time="11:23:57" level=info msg="Executing Report  v5.1.3"
time="11:23:57" level=info msg="Creating reports"
time="11:23:57" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:57" level=info msg="Executing Workspace  v5.1.3"
time="11:23:57" level=info msg="Removing workspace"
time="11:23:57" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:57" level=info msg="Executing Workspace  v5.1.3"
time="11:23:57" level=info msg="Removing workspace"
time="11:23:57" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:58" level=info msg="Executing Workspace  v5.1.3"
time="11:23:58" level=info msg="Removing workspace"
time="11:23:58" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:58" level=info msg="Executing Workspace  v5.1.3"
time="11:23:58" level=info msg="Removing workspace"
time="11:23:58" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:58" level=info msg="Executing Workspace  v5.1.3"
time="11:23:58" level=info msg="Removing workspace"
time="11:23:58" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:58" level=info msg="Executing Workspace  v5.1.3"
time="11:23:58" level=info msg="Removing workspace"
time="11:23:58" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:58" level=info msg="Executing Workspace  v5.1.3"
time="11:23:58" level=info msg="Removing workspace"
time="11:23:59" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:59" level=info msg="Executing Workspace  v5.1.3"
time="11:23:59" level=info msg="Removing workspace"
time="11:23:59" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4]
C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck
time="11:23:59" level=info msg="Executing Workspace  v5.1.3"
time="11:23:59" level=info msg="Removing workspace"
time="11:23:59" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR]
C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx105G -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\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\filelist_ionquant.txt --modlist F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\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 105 GB memory
2026-07-17 11:23:59 [INFO] - Collecting variable modifications from all psm.tsv files...
2026-07-17 11:24:00 [INFO] - Loading and indexing all psm.tsv files...
2026-07-17 11:24:00 [INFO] - Indexing experiments...
2026-07-17 11:24:00 [INFO] - Indexing runs...
2026-07-17 11:24:00 [INFO] - Collecting all compensation voltages if applicable...
2026-07-17 11:24:02 [INFO] - Hemphi_Ca_C1 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2026-07-17 11:24:02 [INFO] - There is no FAIMS in the dataset.
2026-07-17 11:24:02 [INFO] - Indexing proteins...
2026-07-17 11:24:02 [INFO] - Indexing sequences...
2026-07-17 11:24:02 [INFO] - Indexing peptides...
2026-07-17 11:24:02 [INFO] - Indexing ions...
2026-07-17 11:24:02 [INFO] - Indexing PSMs...
2026-07-17 11:24:03 [INFO] - Parameters:
2026-07-17 11:24:03 [INFO] - perform-ms1quant = 1
2026-07-17 11:24:03 [INFO] - perform-isoquant = 0
2026-07-17 11:24:03 [INFO] - isotol = 20.0
2026-07-17 11:24:03 [INFO] - isolevel = 2
2026-07-17 11:24:03 [INFO] - isotype = tmt10
2026-07-17 11:24:03 [INFO] - site-reports = 1
2026-07-17 11:24:03 [INFO] - msstats = 1
2026-07-17 11:24:03 [INFO] - threads = 23
2026-07-17 11:24:03 [INFO] - mztol = 10.0
2026-07-17 11:24:03 [INFO] - rttol = 0.4
2026-07-17 11:24:03 [INFO] - imtol = 0.05
2026-07-17 11:24:03 [INFO] - minisotopes = 2
2026-07-17 11:24:03 [INFO] - minscans = 3
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\psm.tsv
2026-07-17 11:24:03 [INFO] - psm = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\psm.tsv
2026-07-17 11:24:03 [INFO] - multidir = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\
2026-07-17 11:24:03 [INFO] - excludemods = 
2026-07-17 11:24:03 [INFO] - minions = 1
2026-07-17 11:24:03 [INFO] - maxlfq = 1
2026-07-17 11:24:03 [INFO] - ibaq = 0
2026-07-17 11:24:03 [INFO] - normalization = 1
2026-07-17 11:24:03 [INFO] - minexps = 1
2026-07-17 11:24:03 [INFO] - minfreq = 0.0
2026-07-17 11:24:03 [INFO] - tp = 0
2026-07-17 11:24:03 [INFO] - mbr = 1
2026-07-17 11:24:03 [INFO] - mbrrttol = 1.0
2026-07-17 11:24:03 [INFO] - mbrimtol = 0.05
2026-07-17 11:24:03 [INFO] - mbrtoprun = 10
2026-07-17 11:24:03 [INFO] - mbrmincorr = 0.0
2026-07-17 11:24:03 [INFO] - ionmobility = 0
2026-07-17 11:24:03 [INFO] - ionfdr = 0.01
2026-07-17 11:24:03 [INFO] - peptidefdr = 1.0
2026-07-17 11:24:03 [INFO] - proteinfdr = 1.0
2026-07-17 11:24:03 [INFO] - light = 
2026-07-17 11:24:03 [INFO] - medium = 
2026-07-17 11:24:03 [INFO] - heavy = 
2026-07-17 11:24:03 [INFO] - requantify = 0
2026-07-17 11:24:03 [INFO] - writeindex = 0
2026-07-17 11:24:03 [INFO] - locprob = 0.75
2026-07-17 11:24:03 [INFO] - uniqueness = 0
2026-07-17 11:24:03 [INFO] - intensitymode = 2
2026-07-17 11:24:03 [INFO] - totalintensitymode = 1
2026-07-17 11:24:03 [INFO] - formula = 
2026-07-17 11:24:03 [INFO] - filelist = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\filelist_ionquant.txt
2026-07-17 11:24:03 [INFO] - specdir = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX
2026-07-17 11:24:03 [INFO] - modlist = F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\modmasses_ionquant.txt
2026-07-17 11:24:03 [INFO] - mod masses:
2026-07-17 11:24:03 [INFO] - 15.9949
2026-07-17 11:24:03 [INFO] - 42.0106
2026-07-17 11:24:03 [INFO] - 57.02146
2026-07-17 11:24:03 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2026-07-17 11:24:03 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.mzML...
2026-07-17 11:24:08 [INFO] - Building index...
2026-07-17 11:24:08 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.quantindex
2026-07-17 11:24:08 [INFO] - Quantifying...
2026-07-17 11:24:09 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.mzML...
2026-07-17 11:24:13 [INFO] - Building index...
2026-07-17 11:24:13 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.quantindex
2026-07-17 11:24:13 [INFO] - Quantifying...
2026-07-17 11:24:13 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.mzML...
2026-07-17 11:24:17 [INFO] - Building index...
2026-07-17 11:24:17 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.quantindex
2026-07-17 11:24:17 [INFO] - Quantifying...
2026-07-17 11:24:17 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.mzML...
2026-07-17 11:24:22 [INFO] - Building index...
2026-07-17 11:24:22 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.quantindex
2026-07-17 11:24:22 [INFO] - Quantifying...
2026-07-17 11:24:22 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.mzML...
2026-07-17 11:24:26 [INFO] - Building index...
2026-07-17 11:24:26 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.quantindex
2026-07-17 11:24:26 [INFO] - Quantifying...
2026-07-17 11:24:26 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.mzML...
2026-07-17 11:24:30 [INFO] - Building index...
2026-07-17 11:24:31 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.quantindex
2026-07-17 11:24:31 [INFO] - Quantifying...
2026-07-17 11:24:31 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.mzML...
2026-07-17 11:24:35 [INFO] - Building index...
2026-07-17 11:24:35 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.quantindex
2026-07-17 11:24:35 [INFO] - Quantifying...
2026-07-17 11:24:35 [INFO] - Loading F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.mzML...
2026-07-17 11:24:39 [INFO] - Building index...
2026-07-17 11:24:39 [INFO] - Writing index to F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.quantindex
2026-07-17 11:24:39 [INFO] - Quantifying...
2026-07-17 11:24:39 [INFO] - Updating Philosopher's tables...
2026-07-17 11:24:40 [INFO] - Matching-between-runs: Hemphi_Ca_C1...
2026-07-17 11:24:40 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:40 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C1.quantindex
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:41 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:41 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:41 [INFO] - #{+1} = 1242, #{-1} = 876, #{+2} = 1224, #{-2} = 738
2026-07-17 11:24:41 [INFO] - Standardized coefficients:
2026-07-17 11:24:41 [INFO] - log10(intensity): 0.9347245616434628
2026-07-17 11:24:41 [INFO] - log10(KL): -0.2558785381504403
2026-07-17 11:24:41 [INFO] - abs(ppm): -0.20982814562198157
2026-07-17 11:24:41 [INFO] - RT diff: -0.12956973751331924
2026-07-17 11:24:41 [INFO] - Fitting a mixture model...
2026-07-17 11:24:42 [INFO] - Matching-between-runs: Hemphi_Ca_C2...
2026-07-17 11:24:42 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:42 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C2.quantindex
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:42 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:42 [INFO] - #{+1} = 1780, #{-1} = 1332, #{+2} = 718, #{-2} = 484
2026-07-17 11:24:42 [INFO] - Standardized coefficients:
2026-07-17 11:24:42 [INFO] - log10(intensity): 0.8819686921984307
2026-07-17 11:24:42 [INFO] - log10(KL): -0.35380449410253606
2026-07-17 11:24:42 [INFO] - abs(ppm): -0.24156214260212677
2026-07-17 11:24:42 [INFO] - RT diff: -0.19647223008890588
2026-07-17 11:24:42 [INFO] - Fitting a mixture model...
2026-07-17 11:24:42 [INFO] - Matching-between-runs: Hemphi_Ca_C3...
2026-07-17 11:24:42 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:42 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C3.quantindex
2026-07-17 11:24:42 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:43 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:43 [INFO] - #{+1} = 1611, #{-1} = 1210, #{+2} = 896, #{-2} = 589
2026-07-17 11:24:43 [INFO] - Standardized coefficients:
2026-07-17 11:24:43 [INFO] - log10(intensity): 0.9350216811069544
2026-07-17 11:24:43 [INFO] - log10(KL): -0.2871978914582354
2026-07-17 11:24:43 [INFO] - abs(ppm): -0.1711379257231186
2026-07-17 11:24:43 [INFO] - RT diff: -0.11816783564514027
2026-07-17 11:24:43 [INFO] - Fitting a mixture model...
2026-07-17 11:24:43 [INFO] - Matching-between-runs: Hemphi_Ca_C4...
2026-07-17 11:24:43 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:43 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_C4.quantindex
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:43 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:43 [INFO] - #{+1} = 1893, #{-1} = 1438, #{+2} = 592, #{-2} = 395
2026-07-17 11:24:43 [INFO] - Standardized coefficients:
2026-07-17 11:24:43 [INFO] - log10(intensity): 0.9194436815532931
2026-07-17 11:24:43 [INFO] - log10(KL): -0.26757169098540523
2026-07-17 11:24:43 [INFO] - abs(ppm): -0.23416262780753652
2026-07-17 11:24:43 [INFO] - RT diff: -0.16791834436179529
2026-07-17 11:24:43 [INFO] - Fitting a mixture model...
2026-07-17 11:24:43 [INFO] - Matching-between-runs: Hemphi_Ca_CdSi1...
2026-07-17 11:24:43 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:43 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi1.quantindex
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:43 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:44 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:44 [INFO] - #{+1} = 1182, #{-1} = 811, #{+2} = 1280, #{-2} = 795
2026-07-17 11:24:44 [INFO] - Standardized coefficients:
2026-07-17 11:24:44 [INFO] - log10(intensity): 0.9230415678777576
2026-07-17 11:24:44 [INFO] - log10(KL): -0.3480673651773737
2026-07-17 11:24:44 [INFO] - abs(ppm): -0.13663045496731588
2026-07-17 11:24:44 [INFO] - RT diff: -0.0904184275669301
2026-07-17 11:24:44 [INFO] - Fitting a mixture model...
2026-07-17 11:24:44 [INFO] - Matching-between-runs: Hemphi_Ca_CdSi2...
2026-07-17 11:24:44 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:44 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi2.quantindex
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:44 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:44 [INFO] - #{+1} = 1634, #{-1} = 1209, #{+2} = 756, #{-2} = 481
2026-07-17 11:24:44 [INFO] - Standardized coefficients:
2026-07-17 11:24:44 [INFO] - log10(intensity): 0.9164965247048554
2026-07-17 11:24:44 [INFO] - log10(KL): -0.3632596661916714
2026-07-17 11:24:44 [INFO] - abs(ppm): -0.13994064141092238
2026-07-17 11:24:44 [INFO] - RT diff: -0.09215829861568386
2026-07-17 11:24:44 [INFO] - Fitting a mixture model...
2026-07-17 11:24:44 [INFO] - Matching-between-runs: Hemphi_Ca_CdSi3...
2026-07-17 11:24:44 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:44 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi3.quantindex
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:44 [INFO] - Transferring Hemphi_Ca_CdSi4...
2026-07-17 11:24:44 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:44 [INFO] - #{+1} = 1622, #{-1} = 1264, #{+2} = 657, #{-2} = 453
2026-07-17 11:24:44 [INFO] - Standardized coefficients:
2026-07-17 11:24:44 [INFO] - log10(intensity): 0.9547766859625444
2026-07-17 11:24:44 [INFO] - log10(KL): -0.24587366759850116
2026-07-17 11:24:44 [INFO] - abs(ppm): -0.12316536961193858
2026-07-17 11:24:44 [INFO] - RT diff: -0.11303942344331594
2026-07-17 11:24:44 [INFO] - Fitting a mixture model...
2026-07-17 11:24:44 [INFO] - Matching-between-runs: Hemphi_Ca_CdSi4...
2026-07-17 11:24:44 [INFO] - Calculating correlations between all other runs...
2026-07-17 11:24:44 [INFO] - Reading index from F:\Research\PXD060911-Cannabis-sativa-TripleTOF\mzMLs-SCIEX\Hemphi_Ca_CdSi4.quantindex
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_C1...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_C2...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_C3...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_C4...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_CdSi1...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_CdSi2...
2026-07-17 11:24:45 [INFO] - Transferring Hemphi_Ca_CdSi3...
2026-07-17 11:24:45 [INFO] - Training LDA models for all matched features.
2026-07-17 11:24:45 [INFO] - #{+1} = 555, #{-1} = 416, #{+2} = 1442, #{-2} = 813
2026-07-17 11:24:45 [INFO] - Standardized coefficients:
2026-07-17 11:24:45 [INFO] - log10(intensity): 0.9126870229143788
2026-07-17 11:24:45 [INFO] - log10(KL): -0.3666049094802022
2026-07-17 11:24:45 [INFO] - abs(ppm): -0.16839647368067978
2026-07-17 11:24:45 [INFO] - RT diff: -0.06516031154478148
2026-07-17 11:24:45 [INFO] - Fitting a mixture model...
2026-07-17 11:24:45 [INFO] - Estimating match-between-runs FDR...
2026-07-17 11:24:45 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.986400
2026-07-17 11:24:45 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2026-07-17 11:24:45 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2026-07-17 11:24:45 [INFO] - Updating Philosopher's tables...
2026-07-17 11:24:46 [INFO] - Combining experiments and estimating protein intensity...
2026-07-17 11:24:46 [INFO] - Generating modification reports...
2026-07-17 11:24:46 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

Delete temp files
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_1\Hemphi_Ca_CdSi1_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_2\Hemphi_Ca_CdSi2_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_3\Hemphi_Ca_CdSi3_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\CdSi_4\Hemphi_Ca_CdSi4_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_1\Hemphi_Ca_C1_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_2\Hemphi_Ca_C2_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_3\Hemphi_Ca_C3_edited.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.pepXML
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4.pin
Delete F:\Research\PXD060911-Cannabis-sativa-TripleTOF\20260717-FragPipe-LFQ-MBR\C_4\Hemphi_Ca_C4_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: 0.03 minutes
  WorkspaceCleanInit: 0.06 minutes
  MSFragger: 2.14 minutes
  MSFragger move pepxml: 0.06 minutes
  MSFragger move pin: 0.03 minutes
  MSBooster: 1.00 minutes
  Percolator: 0.36 minutes
  Percolator: Convert to pepxml: 0.09 minutes
  Percolator delete temp: 0.06 minutes
  ProteinProphet: 0.06 minutes
  PhilosopherDbAnnotate: 0.00 minutes
  PhilosopherFilter: 0.12 minutes
  PhilosopherReport: 0.03 minutes
  WorkspaceClean: 0.03 minutes
  IonQuant: 0.80 minutes
  Finalizer Task: 0.01 minutes

=============================================================ALL JOBS DONE IN 4.9 MINUTES=============================================================
