System OS: Windows 10, Architecture: AMD64
Java Info: 22.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
.NET Core Info: N/A


Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1


LCMS files:
  Experiment/Group: 2_ME
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw	DDA
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw	DDA
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw	DDA
  Experiment/Group: IAA
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.raw	DDA
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.raw	DDA
  - Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.raw	DDA


55 commands to execute:
CheckCentroid
java -Xmx213G -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw 32
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\d8235041-b2c3-4d2b-b93c-59acd01e2c7a
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\98714af7-c4cc-4ea1-a60b-eb45cc326dad
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\a46eb887-1ea8-4885-8971-a25b02e122ef
MSFragger [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -jar -Dfile.encoding=UTF-8 -Xmx213G C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\fragger.params Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.raw
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pin
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pin
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pepXML
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pin
MSBooster [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -Xmx213G -cp C:\FragPipe-22.0\fragpipe\tools\MSBooster-1.2.31.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\msbooster_params.txt
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m002_s002_tML_IAA_2uL_T30_edited.pin
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m002_s002_ML_IAA_2uL_T30_edited.pin
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m002_s002_tML_IAA_2uL_T30_edited.pin
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m009_s009_ML_2ME_300mM_2uL_T30_edited.pin
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto232_m002_s002_tML_IAA_2uL_T30.pin Asto232_m002_s002_tML_IAA_2uL_T30 Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto232_m002_s002_tML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin Asto232_m009_s009_tML_2ME_300mM_2uL_T30 Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto232_m009_s009_tML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin Asto233_m009_s009_tML_2ME_300mM_2uL_T30 Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto233_m009_s009_tML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto224_m002_s002_ML_IAA_2uL_T30.pin Asto224_m002_s002_ML_IAA_2uL_T30 Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto224_m002_s002_ML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto233_m002_s002_tML_IAA_2uL_T30.pin Asto233_m002_s002_tML_IAA_2uL_T30 Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto233_m002_s002_tML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin Asto224_m009_s009_ML_2ME_300mM_2uL_T30 Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto224_m009_s009_ML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_uncalibrated.mzML
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
ProteinProphet [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --protxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\combined.prot.xml --razor
PhilosopherFilter [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA --dbbin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --protxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\combined.prot.xml --probin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --razor
PhilosopherReport [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PhilosopherReport [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
IonQuant [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -Xmx213G -Dlibs.bruker.dir=C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe-22.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe-22.0\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 32 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 0 --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 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\filelist_ionquant.txt --modlist Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\modmasses_ionquant.txt
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [CheckCentroid], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [WorkspaceCleanInit], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
    Cmd: [WorkspaceCleanInit], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
    Cmd: [WorkspaceCleanInit], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [MSFragger], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [MSBooster], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [Percolator], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [ProteinProphet], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [PhilosopherDbAnnotate], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [PhilosopherFilter], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [PhilosopherReport], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [WorkspaceClean], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
    Cmd: [WorkspaceClean], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
    Cmd: [WorkspaceClean], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
    Cmd: [IonQuant], Work dir: [Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]

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

~~~~~~Sample of Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas~~~~~~~
>rev_sp|A0A087WPF7|AUTS2_MOUSE Autism susceptibility gene 2 protein homolog OS=Mus musculus OX=10090 GN=Auts2 PE=1 SV=2
>rev_sp|P07759|SPA3K_MOUSE Serine protease inhibitor A3K OS=Mus musculus OX=10090 GN=Serpina3k PE=1 SV=2
>rev_sp|P68372|TBB4B_MOUSE Tubulin beta-4B chain OS=Mus musculus OX=10090 GN=Tubb4b PE=1 SV=1
>rev_sp|Q5RL51|GSTCD_MOUSE Glutathione S-transferase C-terminal domain-containing protein OS=Mus musculus OX=10090 GN=Gstcd PE=2 SV=1
>rev_sp|Q7TT50|MRCKB_MOUSE Serine/threonine-protein kinase MRCK beta OS=Mus musculus OX=10090 GN=Cdc42bpb PE=1 SV=2
>rev_sp|Q8CEF8|RN222_MOUSE RING finger protein 222 OS=Mus musculus OX=10090 GN=Rnf222 PE=2 SV=2
>rev_sp|Q922J9|FACR1_MOUSE Fatty acyl-CoA reductase 1 OS=Mus musculus OX=10090 GN=Far1 PE=1 SV=1
>rev_sp|Q9DBR4|APBB2_MOUSE Amyloid beta precursor protein binding family B member 2 OS=Mus musculus OX=10090 GN=Apbb2 PE=1 SV=2
>rev_tr|A0A087WSB9|A0A087WSB9_MOUSE Membrane-spanning 4-domains, subfamily A, member 12 OS=Mus musculus OX=10090 GN=Ms4a12 PE=1 SV=1
>rev_tr|J3QK55|J3QK55_MOUSE RIKEN cDNA 2010315B03 gene OS=Mus musculus OX=10090 GN=2010315B03Rik PE=4 SV=2
>rev_tr|W4VSP4|W4VSP4_MOUSE Serine (or cysteine) peptidase inhibitor, clade B, member 6c OS=Mus musculus OX=10090 GN=Serpinb6c PE=1 SV=1
>sp|P07742|RIR1_MOUSE Ribonucleoside-diphosphate reductase large subunit OS=Mus musculus OX=10090 GN=Rrm1 PE=1 SV=2
>sp|P68134|ACTS_MOUSE Actin, alpha skeletal muscle OS=Mus musculus OX=10090 GN=Acta1 PE=1 SV=1
>sp|Q5RJI5|BRSK1_MOUSE Serine/threonine-protein kinase BRSK1 OS=Mus musculus OX=10090 GN=Brsk1 PE=1 SV=1
>sp|Q7TT28|REXO1_MOUSE RNA exonuclease 1 homolog OS=Mus musculus OX=10090 GN=Rexo1 PE=1 SV=1
>sp|Q8CEC6|PPWD1_MOUSE Peptidylprolyl isomerase domain and WD repeat-containing protein 1 OS=Mus musculus OX=10090 GN=Ppwd1 PE=1 SV=2
>sp|Q922H7|RSLBB_MOUSE Ras-like protein family member 11B OS=Mus musculus OX=10090 GN=Rasl11b PE=2 SV=1
>sp|Q9DBQ9|SWT1_MOUSE Transcriptional protein SWT1 OS=Mus musculus OX=10090 GN=Swt1 PE=2 SV=3
>tr|A0A087WS16|A0A087WS16_MOUSE von Willebrand factor A domain-containing protein 1 OS=Mus musculus OX=10090 GN=Col6a3 PE=1 SV=1
>tr|J3QK00|J3QK00_MOUSE Predicted gene, 21761 OS=Mus musculus OX=10090 GN=Tcstv2b PE=4 SV=1
>tr|W4VSN8|W4VSN8_MOUSE Predicted gene 5114 OS=Mus musculus OX=10090 GN=Gm5114 PE=4 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=Z\:\\Database\\2025\\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas

Table.editor=CYSDTHEKMn
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=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.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\DIA-NN\\2.2.0\\diann.exe
fragpipe-config.bin-python=C\:\\Users\\KUS_DPCtr\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\FragPipe-22.0\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=0
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
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_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.02
msfragger.fragment_mass_units=0
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=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=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
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; 0.0,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,2; 42.0106,[^,false,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; 57.02146,C,true,2; 75.9977,C,true,2; 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.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 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 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.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_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.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=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.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
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.ignore_unannotated=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_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.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_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=Z\:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=32

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx213G -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw 32
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:32:13" level=info msg="Executing Workspace  v5.1.1"
time="11:32:13" level=info msg="Removing workspace"
time="11:32:13" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\d8235041-b2c3-4d2b-b93c-59acd01e2c7a
time="11:32:13" level=info msg="Executing Workspace  v5.1.1"
time="11:32:13" level=info msg="Creating workspace"
time="11:32:13" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:32:13" level=info msg="Executing Workspace  v5.1.1"
time="11:32:13" level=info msg="Removing workspace"
time="11:32:13" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\98714af7-c4cc-4ea1-a60b-eb45cc326dad
time="11:32:14" level=info msg="Executing Workspace  v5.1.1"
time="11:32:14" level=info msg="Creating workspace"
time="11:32:14" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:32:14" level=info msg="Executing Workspace  v5.1.1"
time="11:32:14" level=info msg="Removing workspace"
time="11:32:14" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\KUS_DP~1\AppData\Local\Temp\a46eb887-1ea8-4885-8971-a25b02e122ef
time="11:32:15" level=info msg="Executing Workspace  v5.1.1"
time="11:32:15" level=info msg="Creating workspace"
time="11:32:15" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -jar -Dfile.encoding=UTF-8 -Xmx213G C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\fragger.params Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.raw Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.raw
MSFragger version MSFragger-4.1
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 22.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 213 GB memory
Checking database...
Checking spectral files...
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.raw: Scans = 30804; ITMS: false; FTMS: true; Isolation sizes = [2.0]
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.raw: Scans = 30531; ITMS: false; FTMS: true; Isolation sizes = [2.0]
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.raw: Scans = 31596; ITMS: false; FTMS: true; Isolation sizes = [2.0]
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw: Scans = 30789; ITMS: false; FTMS: true; Isolation sizes = [2.0]
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw: Scans = 30925; ITMS: false; FTMS: true; Isolation sizes = [2.0]
Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw: Scans = 30408; ITMS: false; FTMS: true; Isolation sizes = [2.0]
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 32
database_name = Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 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 2
variable_mod_10 = 57.02146 C 2
variable_mod_11 = 75.9977 C 2
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 0.0
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: 288575
	of length 8: 280913
	of length 9: 279373
	of length 10: 262300
	of length 11: 249829
	of length 12: 238857
	of length 13: 232514
	of length 14: 217884
	of length 15: 207472
	of length 16: 194221
	of length 17: 180990
	of length 18: 173695
	of length 19: 169228
	of length 20: 153154
	of length 21: 148154
	of length 22: 137780
	of length 23: 128975
	of length 24: 123068
	of length 25: 116156
	of length 26: 109815
	of length 27: 103706
	of length 28: 97427
	of length 29: 89470
	of length 30: 86202
	of length 31: 80426
	of length 32: 77698
	of length 33: 72330
	of length 34: 68866
	of length 35: 62053
	of length 36: 59627
	of length 37: 54805
	of length 38: 51149
	of length 39: 46370
	of length 40: 44069
	of length 41: 41282
	of length 42: 38764
	of length 43: 33259
	of length 44: 25502
	of length 45: 19164
	of length 46: 12379
	of length 47: 7465
	of length 48: 4191
	of length 49: 2378
	of length 50: 1267
In total 5072802 peptides.
Generated 28280595 modified peptides.
Number of peptides with more than 5000 modification patterns: 65
Selected fragment index width 0.10 Da.
1542568524 fragments to be searched in 1 slices (22.99 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 7.22 s
	001. Asto224_m002_s002_ML_IAA_2uL_T30.raw 13.6 s | deisotoping 1.4 s
		[progress: 27835/27835 (100%) - 15594 spectra/s] 1.8s | postprocessing 0.3 s
	002. Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw 12.2 s | deisotoping 0.1 s
		[progress: 28147/28147 (100%) - 50443 spectra/s] 0.6s | postprocessing 0.2 s
	003. Asto232_m002_s002_tML_IAA_2uL_T30.raw 11.7 s | deisotoping 0.1 s
		[progress: 28072/28072 (100%) - 63945 spectra/s] 0.4s | postprocessing 0.2 s
	004. Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw 11.7 s | deisotoping 0.1 s
		[progress: 28138/28138 (100%) - 51160 spectra/s] 0.6s | postprocessing 0.2 s
	005. Asto233_m002_s002_tML_IAA_2uL_T30.raw 12.5 s | deisotoping 0.1 s
		[progress: 29064/29064 (100%) - 52086 spectra/s] 0.6s | postprocessing 0.2 s
	006. Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw 11.1 s | deisotoping 0.1 s
		[progress: 27701/27701 (100%) - 61833 spectra/s] 0.4s | postprocessing 0.2 s
***************************FIRST SEARCH DONE IN 1.716 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   1.20   1.18 |  -0.05   0.86 |   0.76   2.16 |  -0.21   2.13  
 002 |   1.24   1.18 |  -0.09   0.87 |   0.88   2.08 |  -0.19   2.03  
 003 |   0.88   1.18 |  -0.02   0.81 |   0.46   2.01 |  -0.23   1.99  
 004 |   1.24   1.24 |  -0.05   0.90 |   0.73   2.03 |  -0.19   1.98  
 005 |   1.18   1.33 |  -0.07   0.93 |   0.60   1.99 |  -0.21   1.95  
 006 |   1.29   1.27 |  -0.06   0.85 |   0.72   2.10 |  -0.20   2.07  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count |  14597|  14787|  14936|  15036|  14872| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  15150|  15127| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  15301
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |  15331
-------|-------
New fragment_mass_tolerance = 15.000000 PPM
New use_topN_peaks = 300
New minimum_ratio = 0.000000
New intensity_transform = 1
New remove_precursor_peak = 0
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.193 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 32
database_name = Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -10.0
precursor_mass_upper = 10.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 15.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 2
variable_mod_10 = 57.02146 C 2
variable_mod_11 = 75.9977 C 2
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 0.0
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: 288575
	of length 8: 280913
	of length 9: 279373
	of length 10: 262300
	of length 11: 249829
	of length 12: 238857
	of length 13: 232514
	of length 14: 217884
	of length 15: 207472
	of length 16: 194221
	of length 17: 180990
	of length 18: 173695
	of length 19: 169228
	of length 20: 153154
	of length 21: 148154
	of length 22: 137780
	of length 23: 128975
	of length 24: 123068
	of length 25: 116156
	of length 26: 109815
	of length 27: 103706
	of length 28: 97427
	of length 29: 89470
	of length 30: 86202
	of length 31: 80426
	of length 32: 77698
	of length 33: 72330
	of length 34: 68866
	of length 35: 62053
	of length 36: 59627
	of length 37: 54805
	of length 38: 51149
	of length 39: 46370
	of length 40: 44069
	of length 41: 41282
	of length 42: 38764
	of length 43: 33259
	of length 44: 25502
	of length 45: 19164
	of length 46: 12379
	of length 47: 7465
	of length 48: 4191
	of length 49: 2378
	of length 50: 1267
In total 5072802 peptides.
Generated 28280595 modified peptides.
Number of peptides with more than 5000 modification patterns: 65
Selected fragment index width 0.08 Da.
1542568524 fragments to be searched in 1 slices (22.99 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 6.70 s
	001. Asto224_m002_s002_ML_IAA_2uL_T30.mzBIN_calibrated 0.7 s
		[progress: 27835/27835 (100%) - 36149 spectra/s] 0.8s | remapping alternative proteins and postprocessing 3.9 s
	002. Asto224_m009_s009_ML_2ME_300mM_2uL_T30.mzBIN_calibrated 0.9 s
		[progress: 28147/28147 (100%) - 28091 spectra/s] 1.0s | remapping alternative proteins and postprocessing 3.4 s
	003. Asto232_m002_s002_tML_IAA_2uL_T30.mzBIN_calibrated 0.7 s
		[progress: 28072/28072 (100%) - 41899 spectra/s] 0.7s | remapping alternative proteins and postprocessing 3.0 s
	004. Asto232_m009_s009_tML_2ME_300mM_2uL_T30.mzBIN_calibrated 0.7 s
		[progress: 28138/28138 (100%) - 31545 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.2 s
	005. Asto233_m002_s002_tML_IAA_2uL_T30.mzBIN_calibrated 0.9 s
		[progress: 29064/29064 (100%) - 32952 spectra/s] 0.9s | remapping alternative proteins and postprocessing 3.1 s
	006. Asto233_m009_s009_tML_2ME_300mM_2uL_T30.mzBIN_calibrated 1.1 s
		[progress: 27701/27701 (100%) - 35288 spectra/s] 0.8s | remapping alternative proteins and postprocessing 3.3 s
***************************MAIN SEARCH DONE IN 0.748 MIN***************************

*******************************TOTAL TIME 4.657 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.pepXML Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -Xmx213G -cp C:\FragPipe-22.0\fragpipe\tools\MSBooster-1.2.31.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\msbooster_params.txt
2025-10-30 11:36:58 [INFO] - MSBooster v1.2.31
2025-10-30 11:36:58 [INFO] - Using 32 threads
2025-10-30 11:36:58 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:01 [INFO] - Instrument detected: QE
2025-10-30 11:37:01 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:03 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:05 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:07 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:09 [INFO] - Initializing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
2025-10-30 11:37:11 [INFO] - Fragmentation type detected: HCD
2025-10-30 11:37:11 [INFO] - NCE detected: 30.0
2025-10-30 11:37:11 [INFO] - Creating input file for createFull
2025-10-30 11:37:12 [INFO] - 58731 PSMs for prediction
2025-10-30 11:37:12 [INFO] - createFull input file generation took 941 milliseconds
2025-10-30 11:37:12 [INFO] - Input file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\spectraRT_full.tsv
2025-10-30 11:37:12 [INFO] - Generating input file for DIA-NN
2025-10-30 11:37:12 [INFO] - Creating input file for Diann
2025-10-30 11:37:12 [INFO] - 58474 PSMs for prediction
2025-10-30 11:37:12 [INFO] - Writing DIA-NN input file
2025-10-30 11:37:13 [INFO] - Diann input file generation took 567 milliseconds
2025-10-30 11:37:13 [INFO] - Input file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\spectraRT.tsv
2025-10-30 11:37:13 [INFO] - Generating DIA-NN predictions
2025-10-30 11:37:13 [INFO] - C:\DIA-NN\2.2.0\diann.exe --lib Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\spectraRT.tsv --predict --threads 32 --strip-unknown-mods --predict-n-frag 100
2025-10-30 11:37:13 [INFO] - 
2025-10-30 11:37:13 [INFO] - DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
2025-10-30 11:37:13 [INFO] - Compiled on May 29 2025 21:29:29
2025-10-30 11:37:13 [INFO] - Current date and time: Thu Oct 30 11:37:13 2025
2025-10-30 11:37:13 [INFO] - CPU: GenuineIntel Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
2025-10-30 11:37:13 [INFO] - SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
2025-10-30 11:37:13 [INFO] - Logical CPU cores: 36
2025-10-30 11:37:13 [INFO] - Predicted spectra will be exported in a binary format for third-party tool integration
2025-10-30 11:37:13 [INFO] - Thread number set to 32
2025-10-30 11:37:13 [INFO] - WARNING: unrecognised option [--strip-unknown-mods]
2025-10-30 11:37:13 [INFO] - Deep learning predictor will predict up to 100 fragments
2025-10-30 11:37:13 [INFO] - WARNING: protein inference is enabled but no FASTA provided - is this intended?
2025-10-30 11:37:13 [INFO] - 
2025-10-30 11:37:13 [INFO] - 0 files will be processed
2025-10-30 11:37:13 [INFO] - [0:00] Loading spectral library Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\spectraRT.tsv
2025-10-30 11:37:13 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
2025-10-30 11:37:13 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 58474 precursors in 55076 elution groups.
2025-10-30 11:37:13 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction
2025-10-30 11:37:13 [INFO] - [0:00] Predicting spectra and IMs
2025-10-30 11:37:18 [INFO] - [0:05] Predicting RTs
2025-10-30 11:37:19 [INFO] - [0:06] Decoding predicted spectra and IMs
2025-10-30 11:37:19 [INFO] - [0:06] Decoding RTs
2025-10-30 11:37:20 [INFO] - [0:06] Saving in silico predictions to Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\spectraRT.predicted.bin
2025-10-30 11:37:20 [INFO] - 
2025-10-30 11:37:20 [INFO] - The following warnings or errors (in alphabetic order) were detected at least the indicated number of times:
2025-10-30 11:37:20 [INFO] - WARNING: protein inference is enabled but no FASTA provided - is this intended? : 1
2025-10-30 11:37:20 [INFO] - WARNING: unrecognised option [--strip-unknown-mods] : 1
2025-10-30 11:37:20 [INFO] - Finished
2025-10-30 11:37:20 [INFO] - 
2025-10-30 11:37:20 [INFO] - 
2025-10-30 11:37:20 [INFO] - How to cite:
2025-10-30 11:37:20 [INFO] - using DIA-NN: Demichev et al, Nature Methods, 2020, https://www.nature.com/articles/s41592-019-0638-x
2025-10-30 11:37:20 [INFO] - analysing Scanning SWATH: Messner et al, Nature Biotechnology, 2021, https://www.nature.com/articles/s41587-021-00860-4
2025-10-30 11:37:20 [INFO] - analysing PTMs: Steger et al, Nature Communications, 2021, https://www.nature.com/articles/s41467-021-25454-1
2025-10-30 11:37:20 [INFO] - analysing dia-PASEF: Demichev et al, Nature Communications, 2022, https://www.nature.com/articles/s41467-022-31492-0
2025-10-30 11:37:20 [INFO] - analysing Slice-PASEF: Szyrwiel et al, biorxiv, 2022, https://doi.org/10.1101/2022.10.31.514544
2025-10-30 11:37:20 [INFO] - plexDIA / multiplexed DIA: Derks et al, Nature Biotechnology, 2023, https://www.nature.com/articles/s41587-022-01389-w
2025-10-30 11:37:20 [INFO] - CysQuant: Huang et al, Redox Biology, 2023, https://doi.org/10.1016/j.redox.2023.102908
2025-10-30 11:37:20 [INFO] - using QuantUMS: Kistner at al, biorxiv, 2023, https://doi.org/10.1101/2023.06.20.545604
2025-10-30 11:37:21 [INFO] - Done generating DIA-NN predictions
2025-10-30 11:37:21 [INFO] - Model running took 8110 milliseconds
2025-10-30 11:37:21 [INFO] - Generating edited pin with following features: [predRTrealUnits, unweightedSpectralEntropy, deltaRTLOESS]
2025-10-30 11:37:21 [INFO] - Loading predicted library
2025-10-30 11:37:22 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin
2025-10-30 11:37:22 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin has 24244 PSMs
2025-10-30 11:37:22 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:25 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:37:29 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.01
2025-10-30 11:37:30 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:30 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:31 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_edited.pin
2025-10-30 11:37:32 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin
2025-10-30 11:37:32 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin has 23629 PSMs
2025-10-30 11:37:32 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:34 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:37:38 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.01
2025-10-30 11:37:39 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:39 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:40 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
2025-10-30 11:37:40 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin
2025-10-30 11:37:40 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin has 23421 PSMs
2025-10-30 11:37:40 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:43 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:37:47 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.01
2025-10-30 11:37:47 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:48 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:49 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
2025-10-30 11:37:49 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pin
2025-10-30 11:37:49 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pin has 22732 PSMs
2025-10-30 11:37:49 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:52 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:37:56 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.026
2025-10-30 11:37:57 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:57 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:37:58 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30_edited.pin
2025-10-30 11:37:58 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pin
2025-10-30 11:37:58 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pin has 22371 PSMs
2025-10-30 11:37:58 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:00 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:38:05 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.026
2025-10-30 11:38:05 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:06 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:07 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30_edited.pin
2025-10-30 11:38:07 [INFO] - Processing pin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pin
2025-10-30 11:38:07 [INFO] - Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pin has 23594 PSMs
2025-10-30 11:38:07 [INFO] - Processing Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:10 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-10-30 11:38:14 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.044
2025-10-30 11:38:15 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:15 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-10-30 11:38:16 [INFO] - Edited pin file at Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30_edited.pin
2025-10-30 11:38:16 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 55646 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m002_s002_tML_IAA_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m002_s002_tML_IAA_2uL_T30_edited.pin
Started Thu Oct 30 11:38:17 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto232_m002_s002_tML_IAA_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 22371 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 17785 positives and 4586 negatives, size ratio=3.87811 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 8048 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 8095 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 8129 training set positives with q<0.01 in that direction.
Found 12093 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3810 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 12834 PSMs with q<0.01
Iteration 2:	Estimated 12973 PSMs with q<0.01
Iteration 3:	Estimated 13010 PSMs with q<0.01
Iteration 4:	Estimated 13015 PSMs with q<0.01
Iteration 5:	Estimated 13027 PSMs with q<0.01
Iteration 6:	Estimated 13028 PSMs with q<0.01
Iteration 7:	Estimated 13026 PSMs with q<0.01
Iteration 8:	Estimated 13023 PSMs with q<0.01
Iteration 9:	Estimated 13028 PSMs with q<0.01
Iteration 10:	Estimated 13027 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
-0.1762	-0.1372	-0.1564	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0481	 0.0916	 0.0562	isotope_error_0
 0.0043	-0.0231	 0.0222	isotope_error_1
-0.0704	-0.1009	-0.1007	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-0.8303	-0.9939	-0.9421	log10_evalue
 1.5478	 0.5811	 1.2470	hyperscore
 1.5318	 1.4258	 1.2232	delta_hyperscore
-0.1575	 0.1391	-0.0946	matched_ion_num
-0.3501	-0.0439	-0.2365	complementary_ions
 0.4608	 0.4706	 0.3105	ion_series
-0.0719	-0.1434	-0.1232	weighted_average_abs_fragment_ppm
 0.0072	 0.0137	 0.0050	length_7
-0.0284	-0.0040	-0.0221	length_8
 0.0173	-0.0038	 0.0141	length_9_30
-0.0252	-0.0410	-0.0205	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.0563	-0.0534	-0.0352	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0248	-0.0529	 0.0154	charge_2
-0.0382	 0.0898	 0.0754	charge_3
 0.0292	-0.0819	-0.2159	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
-0.0638	-0.0182	-0.0431	15.9949M
-0.0755	-0.0241	-0.0129	57.02146C
-0.3751	-0.1167	-0.1892	75.9977C
-0.0047	 0.0266	 0.0399	pred_RT_real_units
-0.0441	 0.0023	 0.0494	unweighted_spectral_entropy
-3.2633	-2.1812	-2.4395	delta_RT_loess
 0.5616	 0.9122	 0.4569	m0
Found 13009 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17785 target PSMs and 4586 decoy PSMs.
Calculating q values.
Final list yields 13011 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 7.9690 cpu seconds or 8 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto232_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Started Thu Oct 30 11:38:28 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto232_m009_s009_tML_2ME_300mM_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 23629 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 19685 positives and 3944 negatives, size ratio=4.99113 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 9919 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 9859 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 9815 training set positives with q<0.01 in that direction.
Found 14773 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4120 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 15401 PSMs with q<0.01
Iteration 2:	Estimated 15532 PSMs with q<0.01
Iteration 3:	Estimated 15574 PSMs with q<0.01
Iteration 4:	Estimated 15597 PSMs with q<0.01
Iteration 5:	Estimated 15596 PSMs with q<0.01
Iteration 6:	Estimated 15600 PSMs with q<0.01
Iteration 7:	Estimated 15605 PSMs with q<0.01
Iteration 8:	Estimated 15598 PSMs with q<0.01
Iteration 9:	Estimated 15604 PSMs with q<0.01
Iteration 10:	Estimated 15604 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
-0.0511	-0.2151	-0.1096	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1074	 0.1260	 0.1199	isotope_error_0
-0.0424	-0.0067	-0.0303	isotope_error_1
-0.1047	-0.1697	-0.1353	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.4307	-1.0106	-1.1609	log10_evalue
 0.6458	 0.5263	 0.7538	hyperscore
 1.6192	 1.2280	 1.4916	delta_hyperscore
-0.1567	 0.3411	 0.0957	matched_ion_num
 0.0593	-0.0168	-0.1616	complementary_ions
 0.5518	 0.4936	 0.5888	ion_series
-0.1018	-0.0162	-0.0518	weighted_average_abs_fragment_ppm
 0.0217	-0.0131	 0.0045	length_7
 0.0432	 0.0218	 0.0377	length_8
-0.0576	-0.0173	-0.0175	length_9_30
 0.0562	 0.0720	-0.0715	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.0632	-0.0984	-0.1415	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1203	-0.0965	-0.1220	charge_2
 0.1388	 0.1216	 0.1511	charge_3
-0.0284	-0.0444	-0.0506	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
-0.0192	-0.0291	-0.0410	15.9949M
-0.3980	-0.1835	-0.2830	57.02146C
 0.1562	 0.1282	 0.1372	75.9977C
-0.0119	-0.0102	-0.0366	pred_RT_real_units
 0.0429	 0.0249	 0.0379	unweighted_spectral_entropy
-1.5043	-1.7634	-1.3624	delta_RT_loess
 1.8055	 1.7022	 2.0696	m0
Found 15485 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 19685 target PSMs and 3944 decoy PSMs.
Calculating q values.
Final list yields 15486 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.8780 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m009_s009_tML_2ME_300mM_2uL_T30_edited.pin
Started Thu Oct 30 11:38:37 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto233_m009_s009_tML_2ME_300mM_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 23421 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 19513 positives and 3908 negatives, size ratio=4.99309 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 9817 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 9778 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 9725 training set positives with q<0.01 in that direction.
Found 14631 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4040 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 15249 PSMs with q<0.01
Iteration 2:	Estimated 15359 PSMs with q<0.01
Iteration 3:	Estimated 15378 PSMs with q<0.01
Iteration 4:	Estimated 15385 PSMs with q<0.01
Iteration 5:	Estimated 15394 PSMs with q<0.01
Iteration 6:	Estimated 15393 PSMs with q<0.01
Iteration 7:	Estimated 15402 PSMs with q<0.01
Iteration 8:	Estimated 15403 PSMs with q<0.01
Iteration 9:	Estimated 15409 PSMs with q<0.01
Iteration 10:	Estimated 15406 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
-0.0934	-0.1584	-0.0904	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0844	 0.0764	 0.1329	isotope_error_0
-0.0624	 0.0030	-0.0281	isotope_error_1
-0.0505	-0.1107	-0.1562	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.1293	-1.1294	-1.6320	log10_evalue
 0.7526	 1.1181	 1.4054	hyperscore
 1.1883	 1.5972	 1.3806	delta_hyperscore
 0.5979	 0.6341	 0.2765	matched_ion_num
-0.2728	-0.5549	-0.5967	complementary_ions
 0.4880	 0.4432	 0.3458	ion_series
-0.1529	-0.1581	-0.1847	weighted_average_abs_fragment_ppm
-0.0261	-0.0179	 0.0343	length_7
 0.0504	 0.0601	 0.0837	length_8
-0.0242	-0.0399	-0.0570	length_9_30
 0.0552	 0.0690	-0.1720	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.0690	-0.1432	-0.1514	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0745	-0.1063	-0.1196	charge_2
 0.0672	 0.0732	 0.1141	charge_3
 0.0223	 0.0793	 0.0227	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
 0.0064	-0.0143	 0.0537	15.9949M
-0.0695	-0.0703	-0.0936	57.02146C
 0.1199	 0.1047	 0.1468	75.9977C
 0.0688	 0.0416	 0.0186	pred_RT_real_units
 0.0069	-0.0015	 0.0846	unweighted_spectral_entropy
-1.6073	-1.6796	-1.8048	delta_RT_loess
 2.0961	 2.4365	 2.3118	m0
Found 15349 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 19513 target PSMs and 3908 decoy PSMs.
Calculating q values.
Final list yields 15353 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.9070 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m002_s002_ML_IAA_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m002_s002_ML_IAA_2uL_T30_edited.pin
Started Thu Oct 30 11:38:45 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto224_m002_s002_ML_IAA_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 22732 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 18063 positives and 4669 negatives, size ratio=3.86871 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 8174 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 8111 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 8138 training set positives with q<0.01 in that direction.
Found 12201 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4000 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 12860 PSMs with q<0.01
Iteration 2:	Estimated 13031 PSMs with q<0.01
Iteration 3:	Estimated 13065 PSMs with q<0.01
Iteration 4:	Estimated 13084 PSMs with q<0.01
Iteration 5:	Estimated 13085 PSMs with q<0.01
Iteration 6:	Estimated 13093 PSMs with q<0.01
Iteration 7:	Estimated 13093 PSMs with q<0.01
Iteration 8:	Estimated 13092 PSMs with q<0.01
Iteration 9:	Estimated 13092 PSMs with q<0.01
Iteration 10:	Estimated 13091 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
-0.1393	-0.1414	-0.1197	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0787	 0.0785	 0.1282	isotope_error_0
-0.0889	-0.0682	-0.0989	isotope_error_1
-0.0131	-0.0349	-0.0703	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.3731	-1.3083	-1.3429	log10_evalue
 1.1369	 0.6492	 0.6062	hyperscore
 0.9229	 0.9516	 0.8970	delta_hyperscore
-0.2177	-0.0007	 0.2626	matched_ion_num
-0.2997	-0.1205	-0.2331	complementary_ions
 0.3877	 0.6277	 0.5204	ion_series
-0.0361	-0.0996	-0.1019	weighted_average_abs_fragment_ppm
 0.0008	-0.0087	-0.0085	length_7
-0.0145	-0.0117	-0.0089	length_8
-0.0008	 0.0058	 0.0101	length_9_30
 0.0746	 0.0672	 0.0214	length_31
 0.0000	 0.0000	 0.0000	ntt
 0.0157	-0.0274	-0.0509	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0144	 0.0230	 0.0051	charge_2
 0.0421	 0.0558	 0.0930	charge_3
-0.0607	-0.1793	-0.2208	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
-0.0922	-0.0612	-0.0929	15.9949M
-0.0427	 0.0240	-0.0213	57.02146C
-0.1368	-0.2496	-0.2026	75.9977C
 0.0188	 0.1070	 0.0901	pred_RT_real_units
 0.0782	 0.0423	 0.0591	unweighted_spectral_entropy
-2.3999	-2.1673	-2.2090	delta_RT_loess
 0.4426	 0.7603	 0.7920	m0
Found 13045 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 18063 target PSMs and 4669 decoy PSMs.
Calculating q values.
Final list yields 13046 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.0640 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m002_s002_tML_IAA_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto233_m002_s002_tML_IAA_2uL_T30_edited.pin
Started Thu Oct 30 11:38:53 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto233_m002_s002_tML_IAA_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 23594 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 18512 positives and 5082 negatives, size ratio=3.64266 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 8276 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 8258 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 8233 training set positives with q<0.01 in that direction.
Found 12357 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4150 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 13047 PSMs with q<0.01
Iteration 2:	Estimated 13146 PSMs with q<0.01
Iteration 3:	Estimated 13198 PSMs with q<0.01
Iteration 4:	Estimated 13235 PSMs with q<0.01
Iteration 5:	Estimated 13243 PSMs with q<0.01
Iteration 6:	Estimated 13240 PSMs with q<0.01
Iteration 7:	Estimated 13243 PSMs with q<0.01
Iteration 8:	Estimated 13237 PSMs with q<0.01
Iteration 9:	Estimated 13237 PSMs with q<0.01
Iteration 10:	Estimated 13243 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
-0.1341	-0.1119	-0.2240	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.1182	 0.1041	 0.1103	isotope_error_0
-0.0548	-0.0349	-0.0298	isotope_error_1
-0.1026	-0.1043	-0.1180	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.5114	-1.2152	-1.5588	log10_evalue
 0.9312	 0.7215	 1.6201	hyperscore
 1.4711	 1.3971	 1.2182	delta_hyperscore
-0.1971	 0.1728	-0.8375	matched_ion_num
-0.2604	-0.1400	-0.4383	complementary_ions
 0.6490	 0.4899	 0.6504	ion_series
-0.1652	-0.1276	-0.0526	weighted_average_abs_fragment_ppm
 0.0090	-0.0016	 0.0070	length_7
 0.0482	 0.0293	-0.0220	length_8
-0.0513	-0.0104	 0.0075	length_9_30
 0.0696	-0.0614	 0.0156	length_31
 0.0000	 0.0000	 0.0000	ntt
 0.0010	-0.1382	-0.1705	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.0018	-0.0491	 0.0083	charge_2
-0.0383	 0.0686	 0.0724	charge_3
 0.0936	-0.0408	-0.1885	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
 0.0728	-0.0654	 0.0257	15.9949M
-0.0912	 0.0437	-0.0367	57.02146C
-0.0981	-0.1253	-0.0530	75.9977C
 0.1586	-0.0285	-0.0536	pred_RT_real_units
 0.0809	 0.0530	 0.1062	unweighted_spectral_entropy
-2.5332	-2.1176	-2.4661	delta_RT_loess
 0.9776	 0.9653	 0.4262	m0
Found 13121 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 18512 target PSMs and 5082 decoy PSMs.
Calculating q values.
Final list yields 13131 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 4.4020 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m009_s009_ML_2ME_300mM_2uL_T30_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
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-22.0\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 32 --results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv --decoy-results-psms Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Asto224_m009_s009_ML_2ME_300mM_2uL_T30_edited.pin
Started Thu Oct 30 11:39:01 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile Asto224_m009_s009_ML_2ME_300mM_2uL_T30_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 57.02146C 75.9977C pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 24244 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 20111 positives and 4133 negatives, size ratio=4.86596 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 10159 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 10015 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 10116 training set positives with q<0.01 in that direction.
Found 15138 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.4050 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 15737 PSMs with q<0.01
Iteration 2:	Estimated 15838 PSMs with q<0.01
Iteration 3:	Estimated 15853 PSMs with q<0.01
Iteration 4:	Estimated 15847 PSMs with q<0.01
Iteration 5:	Estimated 15847 PSMs with q<0.01
Iteration 6:	Estimated 15848 PSMs with q<0.01
Iteration 7:	Estimated 15854 PSMs with q<0.01
Iteration 8:	Estimated 15850 PSMs with q<0.01
Iteration 9:	Estimated 15852 PSMs with q<0.01
Iteration 10:	Estimated 15855 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
-0.1287	-0.1099	-0.1094	abs_ppm
 0.0000	 0.0000	 0.0000	isotope_error_negative
 0.0882	 0.0935	 0.1178	isotope_error_0
-0.0643	 0.0027	 0.0030	isotope_error_1
-0.0536	-0.1343	-0.1688	isotope_error_2
 0.0000	 0.0000	 0.0000	isotope_error_3_more
-1.2983	-1.5773	-1.4438	log10_evalue
 0.0712	 0.5948	 0.3725	hyperscore
 1.2469	 1.5380	 2.0721	delta_hyperscore
 0.3875	-0.1211	 0.1240	matched_ion_num
 0.0882	 0.0961	-0.1112	complementary_ions
 0.5793	 0.7786	 0.6577	ion_series
-0.1017	-0.1253	-0.1813	weighted_average_abs_fragment_ppm
-0.0027	-0.0104	-0.0105	length_7
 0.0238	 0.0168	 0.0460	length_8
-0.0154	-0.0015	-0.0346	length_9_30
 0.0037	-0.0082	 0.0450	length_31
 0.0000	 0.0000	 0.0000	ntt
-0.2502	-0.1032	-0.2078	nmc
 0.0000	 0.0000	 0.0000	charge_1
-0.1179	-0.1356	-0.1318	charge_2
 0.0821	 0.1028	 0.1058	charge_3
 0.0824	 0.0779	 0.0643	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
-0.0045	-0.0407	-0.0291	15.9949M
-0.3759	-0.5553	-0.5444	57.02146C
 0.1940	 0.1565	 0.1103	75.9977C
 0.0897	 0.0851	 0.0622	pred_RT_real_units
 0.1707	 0.2856	 0.0279	unweighted_spectral_entropy
-1.9583	-1.3264	-1.4331	delta_RT_loess
 1.6748	 2.4739	 2.4251	m0
Found 15780 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20111 target PSMs and 4133 decoy PSMs.
Calculating q values.
Final list yields 15785 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 5.3550 cpu seconds or 5 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto232_m002_s002_tML_IAA_2uL_T30.pin Asto232_m002_s002_tML_IAA_2uL_T30 Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto232_m002_s002_tML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto232_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin Asto232_m009_s009_tML_2ME_300mM_2uL_T30 Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto232_m009_s009_tML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin Asto233_m009_s009_tML_2ME_300mM_2uL_T30 Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto233_m009_s009_tML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto224_m002_s002_ML_IAA_2uL_T30.pin Asto224_m002_s002_ML_IAA_2uL_T30 Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto224_m002_s002_ML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto224_m002_s002_ML_IAA_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto233_m002_s002_tML_IAA_2uL_T30.pin Asto233_m002_s002_tML_IAA_2uL_T30 Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv interact-Asto233_m002_s002_tML_IAA_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\Asto233_m002_s002_tML_IAA_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
java -cp C:\FragPipe-22.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin Asto224_m009_s009_ML_2ME_300mM_2uL_T30 Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv interact-Asto224_m009_s009_ML_2ME_300mM_2uL_T30 DDA 0.5 Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp C:\FragPipe-22.0\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\filelist_proteinprophet.txt
time="11:39:32" level=info msg="Executing ProteinProphet  v5.1.1"
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\interact-Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pep.xml...
...read in 0 1+, 10544 2+, 5015 3+, 784 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\interact-Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pep.xml...
...read in 0 1+, 10618 2+, 4773 3+, 641 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\interact-Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pep.xml...
...read in 0 1+, 10516 2+, 4748 3+, 672 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\interact-Asto224_m002_s002_ML_IAA_2uL_T30.pep.xml...
...read in 0 1+, 9875 2+, 3585 3+, 386 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\interact-Asto232_m002_s002_tML_IAA_2uL_T30.pep.xml...
...read in 0 1+, 9918 2+, 3262 3+, 339 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\interact-Asto233_m002_s002_tML_IAA_2uL_T30.pep.xml...
...read in 0 1+, 10019 2+, 3482 3+, 365 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 22762 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|Q99MD6|TRXR3_MOUSE : U
MGUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTIEGANPGLLHFGVVRENDFKNCIIKAYCTNNDRGAVTWELPWFLTHYVELNEKKYMEIAKEESLGCCGYELPTFVTTPINIYDCKELSVGFLRRALLKGAQIAVPTLEPKGDLIDGIAYVHPVNTQEVDNVPIKGNKENIKVGIKELGIKRTCSDRGIALLVTNYIGEVTEPGETSKAVVKLKGPLGKELQQVLIPTFKRQFKVGQQELYSGVKEAMEQDFGRLLVSRVMVTVDLGLGALFGACELGVYSAGVVLTCGPCYPLSFLDDSTICYEKDGQIGLYRPREGTAIVFKSATYFTEQGKKNTAKIKHLDVFEGFSNVYTVGKERLTVRYGWNLSGIHSQIAETMAEWNHKVQQNYEWGYKKADQLAHGLLAAQHMLKKPICGVNVCTGGLGWTTGQPSPVVFDLVMVKKGLNAAEKACSLGGSGGGIIILDYDHASDDQLLKQLLGNQHAQFTRDCGGVHVKNVFINPVTKQNSIETLVEQVSAGDDVQDLELINYVVGLSSFLEKVRTSHPCYSKSFIMVRNGEILDRLRRRLEERAESSPRSTGPSALRARRGPPSSMLGGRVAGLRRNPLVGVKGLGPSTQARPPPPPSPPKE
.....:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|O70325|GPX4_MOUSE : U
MSWGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL
..:.........:.........:.........:.........:.........:.........:.........24000
.........:.....WARNING: Found the following zero-mass residues in protein entry sp|P11352|GPX1_MOUSE : U
MCAARLSAAAQSTVYAFSARPLTGGEPVSLGSLRGKVLLIENVASLUGTTIRDYTEMNDLQKRLGPRGLVVLGFPCNQFGHQENGKNEEILNSLKYVRPGGGFEPNFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVGPDGVPVRRYSRRFRTIDIEPDIETLLSQQSGNS
....:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|P97364|SPS2_MOUSE : U
MAEAAAAGASGETMAALVAAEGSLGPAGWSAGRSFSNYRPFEPQTLGFSPSWRLTSFSGMKGUGCKVPQETLLKLLEGLTRPALQPPLTSGLVGGQEETVQEGGLSTRPGPGSAFPSLSIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEKEREKVTPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQQNEFIMPDSAVVGDVLVLTKPLGTQVAANAHQWLDNPEKWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQKNEVSFVIHNLPIIAKMAAISKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGASAAAAAAPDNSNAASEPSS
.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9DBC0|SELO_MOUSE : U
MASVRAAVGASLAVARTRPRCVGLALPSSAPRSAWAAAMEPTPRWLAGLRFDNRALRELPVETPPPGPEDSLATPRPVPGACFSRARPAPLRRPRLVALSEPALALLGLEASEEAEVEAEAALFFSGNALLPGTEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVMRDVFYDGNPKYEKCTVVLRIAPTFIRFGSFEIFKPPDEHTGRAGPSVGRDDIRVQLLDYVISSFYPEIQAAHTCDTDNIQRNAAFFREVTQRTARMVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDRYDPDHICNASDNAGRYTYSKQPQVCKWNLQKLAEALEPELPLALAEAILKEEFDTEFQRHYLQKMRKKLGLIRVEKEEDGTLVAKLLETMHLTGADFTNTFCVLSSFPADLSDSAEFLSRLTSQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALIGTQANVTKELERVEHQSRLEQLSPSDLQRKNRDHWEAWLQEYRDRLDKEKEGVGDTAAWQAERVRVMRANNPKYVLRNYIAQKAIEAAENGDFSEVRRVLKLLESPYHSEEEATGPEAVARSTEEQSSYSNRPPLWAAELCVTUSS
......37000
.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q9ERR7|SEP15_MOUSE : U
MAAGQGGWLRPALGLRLLLATAFQAVSALGAEFASEACRELGFSSNLLCSSCDLLGQFNLLPLDPVCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
.......:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q9JLC3|MSRB1_MOUSE : U
MSFCSFFGGEVFQNHFEPGVYVCAKCSYELFSSHSKYAHSSPWPAFTETIHPDSVTKCPEKNRPEALKVSCGKCGNGLGHEFLNDGPKRGQSRFUIFSSSLKFVPKGKEAAASQGH
.:.WARNING: Found the following zero-mass residues in protein entry sp|Q9JLT4|TRXR2_MOUSE : U
MVAAMVAALRGPSRRFRPRTRALTRGTRGAASAAGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTGCUG
......WARNING: Found the following zero-mass residues in protein entry sp|Q9JMH6|TRXR1_MOUSE : U
MPVDDCWLYFPASRGRTFVQTVWVAPTCPNCCWFPGFLPPVPRPPHVPRVLLRGPRGAVLPASRPSKTLPSSSQTPCPTDPCICPPPSTPDSRQEKNTQSELPNKKGQLQKLPTMNGSKDPPGSYDFDLIIIGGGSGGLAAAKEAAKFDKKVLVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKVEDTVKHDWEKMTESVQSHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIVATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLRVTAQSTNSEETIEGEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKIICNLKDDERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCUG
..:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.  Total: 43510
Computing degenerate peptides for 4653 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 4830 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=1.95197e-05, db_size=47043005
Computing MU for 4830 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="11:39:44" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate Z:\Database\2025\2025-04-07-decoys-250318_Mouse_UP000000589_E21755.fasta.fas --prefix rev_
time="11:39:44" level=info msg="Executing Database  v5.1.1"
time="11:39:44" level=info msg="Annotating the database"
time="11:39:45" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --protxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\combined.prot.xml --razor
time="11:39:45" level=info msg="Executing Filter  v5.1.1"
time="11:39:45" level=info msg="Processing peptide identification files"
time="11:39:45" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\2_ME\\interact-Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pep.xml"
time="11:39:45" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\2_ME\\interact-Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pep.xml"
time="11:39:45" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\2_ME\\interact-Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pep.xml"
time="11:39:47" level=info msg="1+ Charge profile" decoy=0 target=0
time="11:39:47" level=info msg="2+ Charge profile" decoy=651 target=31027
time="11:39:47" level=info msg="3+ Charge profile" decoy=145 target=14391
time="11:39:47" level=info msg="4+ Charge profile" decoy=20 target=2077
time="11:39:47" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:39:47" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:39:47" level=info msg="Database search results" ions=17932 peptides=15214 psms=48311
time="11:39:47" level=info msg="Converged to 1.00 % FDR with 46623 PSMs" decoy=466 threshold=0.683817 total=47089
time="11:39:47" level=info msg="Converged to 1.00 % FDR with 13839 Peptides" decoy=138 threshold=0.852563 total=13977
time="11:39:47" level=info msg="Converged to 1.00 % FDR with 16566 Ions" decoy=165 threshold=0.825689 total=16731
time="11:39:47" level=info msg="Protein inference results" decoy=1046 target=3280
time="11:39:47" level=info msg="Converged to 0.97 % FDR with 1748 Proteins" decoy=17 threshold=0.9915 total=1765
time="11:39:48" level=info msg="Applying sequential FDR estimation" ions=16533 peptides=13851 psms=46109
time="11:39:48" level=info msg="Converged to 0.08 % FDR with 46073 PSMs" decoy=36 threshold=0.68382 total=46109
time="11:39:48" level=info msg="Converged to 0.09 % FDR with 13838 Peptides" decoy=13 threshold=0.683981 total=13851
time="11:39:48" level=info msg="Converged to 0.09 % FDR with 16518 Ions" decoy=15 threshold=0.683981 total=16533
time="11:39:48" level=info msg="Post processing identifications"
time="11:39:48" level=info msg="Assigning protein identifications to layers"
time="11:39:53" level=info msg="Processing protein inference"
time="11:39:53" level=info msg="Synchronizing PSMs and proteins"
time="11:39:53" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=16518 peptides=13838 proteins=1642 psms=46073
time="11:39:53" level=info msg=Saving
time="11:39:56" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA --dbbin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --protxml Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\combined.prot.xml --probin Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME --razor
time="11:39:56" level=info msg="Executing Filter  v5.1.1"
time="11:39:56" level=info msg="Fetching protein inference from Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\2_ME"
time="11:39:56" level=info msg="Processing peptide identification files"
time="11:39:56" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\IAA\\interact-Asto233_m002_s002_tML_IAA_2uL_T30.pep.xml"
time="11:39:56" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\IAA\\interact-Asto224_m002_s002_ML_IAA_2uL_T30.pep.xml"
time="11:39:56" level=info msg="Parsing Z:\\FragPipe\\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\\IAA\\interact-Asto232_m002_s002_tML_IAA_2uL_T30.pep.xml"
time="11:39:58" level=info msg="1+ Charge profile" decoy=0 target=0
time="11:39:58" level=info msg="2+ Charge profile" decoy=750 target=29062
time="11:39:58" level=info msg="3+ Charge profile" decoy=118 target=10211
time="11:39:58" level=info msg="4+ Charge profile" decoy=12 target=1078
time="11:39:58" level=info msg="5+ Charge profile" decoy=0 target=0
time="11:39:58" level=info msg="6+ Charge profile" decoy=0 target=0
time="11:39:58" level=info msg="Database search results" ions=15643 peptides=13553 psms=41231
time="11:39:58" level=info msg="Converged to 1.00 % FDR with 39217 PSMs" decoy=392 threshold=0.725854 total=39609
time="11:39:58" level=info msg="Converged to 1.00 % FDR with 12007 Peptides" decoy=120 threshold=0.866841 total=12127
time="11:39:58" level=info msg="Converged to 1.00 % FDR with 14116 Ions" decoy=141 threshold=0.842128 total=14257
time="11:39:58" level=info msg="Protein inference results" decoy=1046 target=3280
time="11:39:58" level=info msg="Converged to 0.97 % FDR with 1748 Proteins" decoy=17 threshold=0.9915 total=1765
time="11:39:58" level=info msg="Applying sequential FDR estimation" ions=14021 peptides=11980 psms=38699
time="11:39:58" level=info msg="Converged to 0.09 % FDR with 38663 PSMs" decoy=36 threshold=0.725958 total=38699
time="11:39:58" level=info msg="Converged to 0.10 % FDR with 11968 Peptides" decoy=12 threshold=0.726014 total=11980
time="11:39:58" level=info msg="Converged to 0.10 % FDR with 14007 Ions" decoy=14 threshold=0.726014 total=14021
time="11:39:58" level=info msg="Post processing identifications"
time="11:39:59" level=info msg="Assigning protein identifications to layers"
time="11:40:03" level=info msg="Processing protein inference"
time="11:40:03" level=info msg="Synchronizing PSMs and proteins"
time="11:40:03" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=14007 peptides=11968 proteins=1619 psms=38663
time="11:40:03" level=info msg=Saving
time="11:40:05" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="11:40:06" level=info msg="Executing Report  v5.1.1"
time="11:40:06" level=info msg="Creating reports"
time="11:40:07" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="11:40:07" level=info msg="Executing Report  v5.1.1"
time="11:40:07" level=info msg="Creating reports"
time="11:40:08" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:40:08" level=info msg="Executing Workspace  v5.1.1"
time="11:40:08" level=info msg="Removing workspace"
time="11:40:08" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:40:09" level=info msg="Executing Workspace  v5.1.1"
time="11:40:09" level=info msg="Removing workspace"
time="11:40:09" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
C:\FragPipe-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:40:09" level=info msg="Executing Workspace  v5.1.1"
time="11:40:09" level=info msg="Removing workspace"
time="11:40:09" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3]
java -Xmx213G -Dlibs.bruker.dir=C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe-22.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe-22.0\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 32 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 0 --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 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\filelist_ionquant.txt --modlist Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\modmasses_ionquant.txt
IonQuant version IonQuant-1.10.27
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 10, Architecture: AMD64
Java Info: 22.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 213 GB memory
2025-10-30 11:40:10 [WARNING] - There are only 2 experiments. Will not calculate MaxLFQ intensity.
2025-10-30 11:40:10 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-10-30 11:40:10 [INFO] - Loading and indexing all psm.tsv files...
2025-10-30 11:40:11 [INFO] - Collecting all compensation voltages if applicable...
2025-10-30 11:40:14 [INFO] - Asto224_m002_s002_ML_IAA_2uL_T30 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2025-10-30 11:40:14 [INFO] - There is no FAIMS in the dataset.
2025-10-30 11:40:17 [INFO] - Parameters:
2025-10-30 11:40:17 [INFO] - perform-ms1quant = 1
2025-10-30 11:40:17 [INFO] - perform-isoquant = 0
2025-10-30 11:40:17 [INFO] - isotol = 20.0
2025-10-30 11:40:17 [INFO] - isolevel = 2
2025-10-30 11:40:17 [INFO] - isotype = tmt10
2025-10-30 11:40:17 [INFO] - site-reports = 1
2025-10-30 11:40:17 [INFO] - msstats = 1
2025-10-30 11:40:17 [INFO] - threads = 32
2025-10-30 11:40:17 [INFO] - mztol = 10.0
2025-10-30 11:40:17 [INFO] - rttol = 0.4
2025-10-30 11:40:17 [INFO] - imtol = 0.05
2025-10-30 11:40:17 [INFO] - minisotopes = 2
2025-10-30 11:40:17 [INFO] - minscans = 3
2025-10-30 11:40:17 [INFO] - psm = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\2_ME\psm.tsv
2025-10-30 11:40:17 [INFO] - psm = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\IAA\psm.tsv
2025-10-30 11:40:17 [INFO] - multidir = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\.\
2025-10-30 11:40:17 [INFO] - excludemods = 
2025-10-30 11:40:17 [INFO] - minions = 1
2025-10-30 11:40:17 [INFO] - maxlfq = 0
2025-10-30 11:40:17 [INFO] - ibaq = 0
2025-10-30 11:40:17 [INFO] - normalization = 0
2025-10-30 11:40:17 [INFO] - minexps = 1
2025-10-30 11:40:17 [INFO] - minfreq = 0.0
2025-10-30 11:40:17 [INFO] - tp = 0
2025-10-30 11:40:17 [INFO] - mbr = 0
2025-10-30 11:40:17 [INFO] - mbrrttol = 1.0
2025-10-30 11:40:17 [INFO] - mbrimtol = 0.05
2025-10-30 11:40:17 [INFO] - mbrtoprun = 10
2025-10-30 11:40:17 [INFO] - mbrmincorr = 0.0
2025-10-30 11:40:17 [INFO] - ionmobility = 0
2025-10-30 11:40:17 [INFO] - ionfdr = 0.01
2025-10-30 11:40:17 [INFO] - peptidefdr = 1.0
2025-10-30 11:40:17 [INFO] - proteinfdr = 1.0
2025-10-30 11:40:17 [INFO] - light = 
2025-10-30 11:40:17 [INFO] - medium = 
2025-10-30 11:40:17 [INFO] - heavy = 
2025-10-30 11:40:17 [INFO] - requantify = 0
2025-10-30 11:40:17 [INFO] - writeindex = 0
2025-10-30 11:40:17 [INFO] - locprob = 0.75
2025-10-30 11:40:17 [INFO] - uniqueness = 0
2025-10-30 11:40:17 [INFO] - filelist = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\filelist_ionquant.txt
2025-10-30 11:40:17 [INFO] - specdir = Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe
2025-10-30 11:40:17 [INFO] - modlist = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\modmasses_ionquant.txt
2025-10-30 11:40:17 [INFO] - mod masses:
2025-10-30 11:40:17 [INFO] - 15.9949
2025-10-30 11:40:17 [INFO] - 57.02146
2025-10-30 11:40:17 [INFO] - 75.9977
2025-10-30 11:40:17 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-10-30 11:40:17 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m002_s002_ML_IAA_2uL_T30.raw...
2025-10-30 11:40:23 [INFO] - Building index...
2025-10-30 11:40:23 [INFO] - Quantifying...
2025-10-30 11:40:23 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.raw...
2025-10-30 11:40:30 [INFO] - Building index...
2025-10-30 11:40:30 [INFO] - Quantifying...
2025-10-30 11:40:30 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m002_s002_tML_IAA_2uL_T30.raw...
2025-10-30 11:40:37 [INFO] - Building index...
2025-10-30 11:40:37 [INFO] - Quantifying...
2025-10-30 11:40:37 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.raw...
2025-10-30 11:40:44 [INFO] - Building index...
2025-10-30 11:40:44 [INFO] - Quantifying...
2025-10-30 11:40:44 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m002_s002_tML_IAA_2uL_T30.raw...
2025-10-30 11:40:50 [INFO] - Building index...
2025-10-30 11:40:50 [INFO] - Quantifying...
2025-10-30 11:40:50 [INFO] - Loading Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.raw...
2025-10-30 11:40:56 [INFO] - Building index...
2025-10-30 11:40:56 [INFO] - Quantifying...
2025-10-30 11:40:56 [INFO] - Updating Philosopher's tables...
2025-10-30 11:41:01 [INFO] - Combining experiments and estimating protein intensity...
2025-10-30 11:41:05 [INFO] - Generating modification reports...
2025-10-30 11:41:05 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(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)
(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)
(Visualization with Skyline) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 26(7):966 (2010)

=============================================================ALL JOBS DONE IN 8.9 MINUTES=============================================================
