System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.25 Version info: FragPipe version 21.0 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: 2023Dec_37_01 (if "spectral library generation" is enabled, all files will be analyzed together) - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8.raw DDA Experiment/Group: 2023Dec_37_02 (if "spectral library generation" is enabled, all files will be analyzed together) - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621.raw DDA Experiment/Group: 2023Dec_37_03 (if "spectral library generation" is enabled, all files will be analyzed together) - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C.raw DDA - E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C.raw DDA 121 commands to execute: CheckCentroid E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw 31 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\4a2c04bd-4409-4b31-945f-ea8ec386b17b WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\471e3b13-94ae-4dfa-8796-5228254005b4 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\3786747b-6f88-4742-b6eb-13a0dbdb924a WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\63e7087c-136e-4777-af45-2150cf1e4216 MSFragger [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx106G E:\Science\fragpipe21\tools\MSFragger-4.0\MSFragger-4.0.jar E:\Data\Peter\TPCA\fragger.params E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C.raw Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_20231217215108_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_20231217215108.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_20231217093831_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_20231217093831.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_20231217123213_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_20231217123213.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_20231217160346_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_20231217160346.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_20231217064450_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_20231217064450.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_20231218012240_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_20231218012240.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_C.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_20231218041621_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_20231218041621.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2.pin Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_20231217185728_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_20231217185728.pin Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6_20231217215108.pin 2023Dec_37_F6_20231217215108 2023Dec_37_F6_20231217215108_percolator_target_psms.tsv 2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv interact-2023Dec_37_F6_20231217215108 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6_C.pin 2023Dec_37_F6_C 2023Dec_37_F6_C_percolator_target_psms.tsv 2023Dec_37_F6_C_percolator_decoy_psms.tsv interact-2023Dec_37_F6_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5.pin 2023Dec_37_F5 2023Dec_37_F5_percolator_target_psms.tsv 2023Dec_37_F5_percolator_decoy_psms.tsv interact-2023Dec_37_F5 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2_C.pin 2023Dec_37_F2_C 2023Dec_37_F2_C_percolator_target_psms.tsv 2023Dec_37_F2_C_percolator_decoy_psms.tsv interact-2023Dec_37_F2_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2_20231217093831.pin 2023Dec_37_F2_20231217093831 2023Dec_37_F2_20231217093831_percolator_target_psms.tsv 2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv interact-2023Dec_37_F2_20231217093831 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1.pin 2023Dec_37_F1 2023Dec_37_F1_percolator_target_psms.tsv 2023Dec_37_F1_percolator_decoy_psms.tsv interact-2023Dec_37_F1 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3_20231217123213.pin 2023Dec_37_F3_20231217123213 2023Dec_37_F3_20231217123213_percolator_target_psms.tsv 2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv interact-2023Dec_37_F3_20231217123213 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7_C.pin 2023Dec_37_F7_C 2023Dec_37_F7_C_percolator_target_psms.tsv 2023Dec_37_F7_C_percolator_decoy_psms.tsv interact-2023Dec_37_F7_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8.pin 2023Dec_37_F8 2023Dec_37_F8_percolator_target_psms.tsv 2023Dec_37_F8_percolator_decoy_psms.tsv interact-2023Dec_37_F8 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3_C.pin 2023Dec_37_F3_C 2023Dec_37_F3_C_percolator_target_psms.tsv 2023Dec_37_F3_C_percolator_decoy_psms.tsv interact-2023Dec_37_F3_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4.pin 2023Dec_37_F4 2023Dec_37_F4_percolator_target_psms.tsv 2023Dec_37_F4_percolator_decoy_psms.tsv interact-2023Dec_37_F4 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8_C.pin 2023Dec_37_F8_C 2023Dec_37_F8_C_percolator_target_psms.tsv 2023Dec_37_F8_C_percolator_decoy_psms.tsv interact-2023Dec_37_F8_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7.pin 2023Dec_37_F7 2023Dec_37_F7_percolator_target_psms.tsv 2023Dec_37_F7_percolator_decoy_psms.tsv interact-2023Dec_37_F7 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4_20231217160346.pin 2023Dec_37_F4_20231217160346 2023Dec_37_F4_20231217160346_percolator_target_psms.tsv 2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv interact-2023Dec_37_F4_20231217160346 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4_C.pin 2023Dec_37_F4_C 2023Dec_37_F4_C_percolator_target_psms.tsv 2023Dec_37_F4_C_percolator_decoy_psms.tsv interact-2023Dec_37_F4_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1_20231217064450.pin 2023Dec_37_F1_20231217064450 2023Dec_37_F1_20231217064450_percolator_target_psms.tsv 2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv interact-2023Dec_37_F1_20231217064450 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7_20231218012240.pin 2023Dec_37_F7_20231218012240 2023Dec_37_F7_20231218012240_percolator_target_psms.tsv 2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv interact-2023Dec_37_F7_20231218012240 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3.pin 2023Dec_37_F3 2023Dec_37_F3_percolator_target_psms.tsv 2023Dec_37_F3_percolator_decoy_psms.tsv interact-2023Dec_37_F3 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5_C.pin 2023Dec_37_F5_C 2023Dec_37_F5_C_percolator_target_psms.tsv 2023Dec_37_F5_C_percolator_decoy_psms.tsv interact-2023Dec_37_F5_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1_C.pin 2023Dec_37_F1_C 2023Dec_37_F1_C_percolator_target_psms.tsv 2023Dec_37_F1_C_percolator_decoy_psms.tsv interact-2023Dec_37_F1_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6.pin 2023Dec_37_F6 2023Dec_37_F6_percolator_target_psms.tsv 2023Dec_37_F6_percolator_decoy_psms.tsv interact-2023Dec_37_F6 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8_20231218041621.pin 2023Dec_37_F8_20231218041621 2023Dec_37_F8_20231218041621_percolator_target_psms.tsv 2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv interact-2023Dec_37_F8_20231218041621 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2.pin 2023Dec_37_F2 2023Dec_37_F2_percolator_target_psms.tsv 2023Dec_37_F2_percolator_decoy_psms.tsv interact-2023Dec_37_F2 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5_20231217185728.pin 2023Dec_37_F5_20231217185728 2023Dec_37_F5_20231217185728_percolator_target_psms.tsv 2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv interact-2023Dec_37_F5_20231217185728 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_uncalibrated.mzML Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_percolator_target_psms.tsv Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv ProteinProphet [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\Data\Peter\TPCA\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --razor PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_02 --dbbin E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --probin E:\Data\Peter\TPCA\2023Dec_37_01 --razor PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_03 --dbbin E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --probin E:\Data\Peter\TPCA\2023Dec_37_01 --razor PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -Dlibs.bruker.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\thermo -cp E:\Science\fragpipe21\tools\jfreechart-1.5.3.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar;E:\Science\fragpipe21\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 31 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist E:\Data\Peter\TPCA\filelist_ionquant.txt --modlist E:\Data\Peter\TPCA\modmasses_ionquant.txt IonQuant [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -Dlibs.bruker.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\thermo -cp E:\Science\fragpipe21\tools\jfreechart-1.5.3.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar;E:\Science\fragpipe21\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 31 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --annotation E:\Data\Peter\TPCA\2023Dec_37_01\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_01\Rep_01_annotation.txt --annotation E:\Data\Peter\TPCA\2023Dec_37_02\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_02\Rep02_annotation.txt --annotation E:\Data\Peter\TPCA\2023Dec_37_03\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_03\Rep03_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist E:\Data\Peter\TPCA\filelist_ionquant.txt --modlist E:\Data\Peter\TPCA\modmasses_ionquant.txt TmtIntegrator [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -cp E:\Science\fragpipe21\tools\tmt-integrator-5.0.6.jar TMTIntegrator E:\Data\Peter\TPCA\tmt-integrator-conf.yml E:\Data\Peter\TPCA\2023Dec_37_01\psm.tsv E:\Data\Peter\TPCA\2023Dec_37_02\psm.tsv E:\Data\Peter\TPCA\2023Dec_37_03\psm.tsv ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [E:\Data\Peter\TPCA] Cmd: [CheckCentroid], Work dir: [E:\Data\Peter\TPCA] Cmd: [WorkspaceCleanInit], Work dir: [E:\Data\Peter\TPCA] Cmd: [WorkspaceCleanInit], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_02] Cmd: [WorkspaceCleanInit], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_03] Cmd: [WorkspaceCleanInit], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_01] Cmd: [MSFragger], Work dir: [E:\Data\Peter\TPCA] Cmd: [Percolator], Work dir: [E:\Data\Peter\TPCA] Cmd: [ProteinProphet], Work dir: [E:\Data\Peter\TPCA] Cmd: [PhilosopherDbAnnotate], Work dir: [E:\Data\Peter\TPCA] Cmd: [PhilosopherFilter], Work dir: [E:\Data\Peter\TPCA] Cmd: [PhilosopherReport], Work dir: [E:\Data\Peter\TPCA] Cmd: [WorkspaceClean], Work dir: [E:\Data\Peter\TPCA] Cmd: [WorkspaceClean], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_02] Cmd: [WorkspaceClean], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_03] Cmd: [WorkspaceClean], Work dir: [E:\Data\Peter\TPCA\2023Dec_37_01] Cmd: [IonQuant], Work dir: [E:\Data\Peter\TPCA] Cmd: [IonQuant], Work dir: [E:\Data\Peter\TPCA] Cmd: [TmtIntegrator], Work dir: [E:\Data\Peter\TPCA] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.fasta.fas~~~~~~~ >contam_sp|CON_A6NCN2|KT81L_HUMAN Keratin-81-like protein OS=Homo sapiens PE=2 SV=3 >rev_sp|O15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 OS=Homo sapiens OX=9606 GN=PDPK1 PE=1 SV=1 >rev_sp|P0CG33|GOG6D_HUMAN Golgin subfamily A member 6D OS=Homo sapiens OX=9606 GN=GOLGA6D PE=3 SV=1 >rev_sp|P48960|AGRE5_HUMAN Adhesion G protein-coupled receptor E5 OS=Homo sapiens OX=9606 GN=ADGRE5 PE=1 SV=4 >rev_sp|Q14147|DHX34_HUMAN Probable ATP-dependent RNA helicase DHX34 OS=Homo sapiens OX=9606 GN=DHX34 PE=1 SV=2 >rev_sp|Q69YZ2|T200B_HUMAN Transmembrane protein 200B OS=Homo sapiens OX=9606 GN=TMEM200B PE=2 SV=1 >rev_sp|Q8IX21|SLF2_HUMAN SMC5-SMC6 complex localization factor protein 2 OS=Homo sapiens OX=9606 GN=SLF2 PE=1 SV=2 >rev_sp|Q8WWZ7|ABCA5_HUMAN Cholesterol transporter ABCA5 OS=Homo sapiens OX=9606 GN=ABCA5 PE=1 SV=2 >rev_sp|Q9BTA0|F167B_HUMAN Protein FAM167B OS=Homo sapiens OX=9606 GN=FAM167B PE=2 SV=2 >rev_sp|Q9NX08|COMD8_HUMAN COMM domain-containing protein 8 OS=Homo sapiens OX=9606 GN=COMMD8 PE=1 SV=1 >rev_tr|A0A1B0GTQ1|A0A1B0GTQ1_HUMAN Uncharacterized protein OS=Homo sapiens OX=9606 PE=3 SV=3 >sp|O43513|MED7_HUMAN Mediator of RNA polymerase II transcription subunit 7 OS=Homo sapiens OX=9606 GN=MED7 PE=1 SV=1 >sp|P0DO97|CC192_HUMAN Coiled-coil domain-containing protein 192 OS=Homo sapiens OX=9606 GN=CCDC192 PE=4 SV=1 >sp|P50219|MNX1_HUMAN Motor neuron and pancreas homeobox protein 1 OS=Homo sapiens OX=9606 GN=MNX1 PE=1 SV=3 >sp|Q14643|ITPR1_HUMAN Inositol 1,4,5-trisphosphate receptor type 1 OS=Homo sapiens OX=9606 GN=ITPR1 PE=1 SV=3 >sp|Q6IQ16|SPOPL_HUMAN Speckle-type POZ protein-like OS=Homo sapiens OX=9606 GN=SPOPL PE=1 SV=1 >sp|Q8IYT1|GAR4_HUMAN Golgi-associated RAB2 interactor protein 4 OS=Homo sapiens OX=9606 GN=GARIN4 PE=1 SV=2 >sp|Q92504|S39A7_HUMAN Zinc transporter SLC39A7 OS=Homo sapiens OX=9606 GN=SLC39A7 PE=1 SV=2 >sp|Q9BVL2|NUP58_HUMAN Nucleoporin p58/p45 OS=Homo sapiens OX=9606 GN=NUP58 PE=1 SV=1 >sp|Q9NYQ3|HAOX2_HUMAN 2-Hydroxyacid oxidase 2 OS=Homo sapiens OX=9606 GN=HAO2 PE=1 SV=1 >tr|Q9H3A6|Q9H3A6_HUMAN PRO2179 OS=Homo sapiens OX=9606 PE=2 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~annotation files~~~~~~~ E:\Data\Peter\TPCA\2023Dec_37_01\Rep_01_annotation.txt: 126 sample-01 127N sample-02 127C sample-03 128N sample-04 128C sample-05 129N sample-06 129C sample-07 130N sample-08 130C sample-09 131N sample-10 131C sample-11 132N sample-12 132C sample-13 133N sample-14 133C sample-15 134N sample-16 E:\Data\Peter\TPCA\2023Dec_37_02\Rep02_annotation.txt: 126 sample-01 127N sample-02 127C sample-03 128N sample-04 128C sample-05 129N sample-06 129C sample-07 130N sample-08 130C sample-09 131N sample-10 131C sample-11 132N sample-12 132C sample-13 133N sample-14 133C sample-15 134N sample-16 E:\Data\Peter\TPCA\2023Dec_37_03\Rep03_annotation.txt: 126 sample-01 127N sample-02 127C sample-03 128N sample-04 128C sample-05 129N sample-06 129C sample-07 130N sample-08 130C sample-09 131N sample-10 131C sample-11 132N sample-12 132C sample-13 133N sample-14 133C sample-15 134N sample-16 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=E\:\\Data\\_FASTA\\2023-11-08-decoys-2023_11_08_UP000005640_CON.fasta.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=true diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=E\:\\Science\\DIA-NN_b27\\DIANN.exe fragpipe-config.bin-ionquant=E\:\\Science\\fragpipe21\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=E\:\\Science\\fragpipe21\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=E\:\\Science\\fragpipe21\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\enoni\\anaconda3\\python.exe freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=false msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.add_topN_complementary=0 msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.enable_offset_file=false msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=-1/0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offset_file= 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=134.5 msfragger.misc.fragger.clear-mz-lo=125.5 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=200 msfragger.misc.fragger.enzyme-dropdown-1=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.output_report_topN_dia2=3 msfragger.output_report_topN_wwa=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses=-18.01056 79.96633 msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 304.20715,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 304.20715,n^,true,1; 229.16293,S,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_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 --picked --prot 0.01 phi-report.group_fdr_variable=0 phi-report.pep-level-summary=false phi-report.philosoher-msstats=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 --minprob 0.5 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagextract_mode=false ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=false ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_mode=false ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.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=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true saintexpress.virtual-controls=100 speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false sub_mzml_prob_threshold=0 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.abn_type=1 tmtintegrator.add_Ref=1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=false tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-16 tmtintegrator.dont-run-fq-lq=false tmtintegrator.extraction-method=IonQuant tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=false tmtintegrator.max_pep_prob_thres=0.9 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=true tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=-1 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=true tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false tpp.run-tpp=false tpp.twodtpp=false workdir=E\:\\Data\\Peter\\TPCA workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw 31 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:11:36] Executing Workspace v5.1.0 INFO[10:11:36] Removing workspace INFO[10:11:36] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\4a2c04bd-4409-4b31-945f-ea8ec386b17b INFO[10:11:36] Executing Workspace v5.1.0 INFO[10:11:36] Creating workspace INFO[10:11:36] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:11:37] Executing Workspace v5.1.0 INFO[10:11:37] Removing workspace INFO[10:11:37] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\471e3b13-94ae-4dfa-8796-5228254005b4 INFO[10:11:37] Executing Workspace v5.1.0 INFO[10:11:37] Creating workspace INFO[10:11:37] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:11:37] Executing Workspace v5.1.0 INFO[10:11:37] Removing workspace INFO[10:11:37] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\3786747b-6f88-4742-b6eb-13a0dbdb924a INFO[10:11:37] Executing Workspace v5.1.0 INFO[10:11:37] Creating workspace INFO[10:11:37] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:11:38] Executing Workspace v5.1.0 INFO[10:11:38] Removing workspace INFO[10:11:38] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\enoni\AppData\Local\Temp\63e7087c-136e-4777-af45-2150cf1e4216 INFO[10:11:38] Executing Workspace v5.1.0 INFO[10:11:38] Creating workspace INFO[10:11:38] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx106G E:\Science\fragpipe21\tools\MSFragger-4.0\MSFragger-4.0.jar E:\Data\Peter\TPCA\fragger.params E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7.raw E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240.raw E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C.raw E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C.raw MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 106 GB memory Checking database... Checking spectral files... E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7.raw: Scans = 25821; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621.raw: Scans = 27313; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw: Scans = 36074; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831.raw: Scans = 39119; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728.raw: Scans = 37499; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C.raw: Scans = 38750; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C.raw: Scans = 37725; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4.raw: Scans = 38245; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8.raw: Scans = 18992; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C.raw: Scans = 20129; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108.raw: Scans = 21065; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C.raw: Scans = 33268; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5.raw: Scans = 36968; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C.raw: Scans = 38689; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2.raw: Scans = 38163; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213.raw: Scans = 38753; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C.raw: Scans = 34494; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C.raw: Scans = 14352; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450.raw: Scans = 37989; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240.raw: Scans = 29334; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6.raw: Scans = 16851; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3.raw: Scans = 38126; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346.raw: Scans = 38795; Isolation sizes = [0.8] E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C.raw: Scans = 39115; Isolation sizes = [0.8] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 31 database_name = E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.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 = 200.0 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 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 = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 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: 290817 of length 8: 281913 of length 9: 281073 of length 10: 265295 of length 11: 251847 of length 12: 241147 of length 13: 234931 of length 14: 220315 of length 15: 208871 of length 16: 195140 of length 17: 182715 of length 18: 175372 of length 19: 172193 of length 20: 154182 of length 21: 147477 of length 22: 138415 of length 23: 129165 of length 24: 122427 of length 25: 115093 of length 26: 107266 of length 27: 102098 of length 28: 97568 of length 29: 88733 of length 30: 84201 of length 31: 78878 of length 32: 74699 of length 33: 69943 of length 34: 65561 of length 35: 59339 of length 36: 57797 of length 37: 52478 of length 38: 49381 of length 39: 44567 of length 40: 42392 of length 41: 39441 of length 42: 36505 of length 43: 30600 of length 44: 24787 of length 45: 19022 of length 46: 12448 of length 47: 7864 of length 48: 4506 of length 49: 2445 of length 50: 1496 In total 5062403 peptides. Generated 15276509 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 619758398 fragments to be searched in 1 slices (9.24 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.53 s 001. 2023Dec_37_F1.raw 8.1 s | deisotoping 0.2 s [progress: 36074/36074 (100%) - 9883 spectra/s] 3.7s | postprocessing 0.1 s 002. 2023Dec_37_F2.raw 7.9 s | deisotoping 0.1 s [progress: 38163/38163 (100%) - 57735 spectra/s] 0.7s | postprocessing 0.1 s 003. 2023Dec_37_F3.raw 12.4 s | deisotoping 0.1 s [progress: 38126/38126 (100%) - 70604 spectra/s] 0.5s | postprocessing 0.1 s 004. 2023Dec_37_F4.raw 13.6 s | deisotoping 0.1 s [progress: 38245/38245 (100%) - 56997 spectra/s] 0.7s | postprocessing 0.1 s 005. 2023Dec_37_F5.raw 10.9 s | deisotoping 0.1 s [progress: 36968/36968 (100%) - 47093 spectra/s] 0.8s | postprocessing 0.1 s 006. 2023Dec_37_F6.raw 8.7 s | deisotoping 0.0 s [progress: 16851/16851 (100%) - 75905 spectra/s] 0.2s | postprocessing 0.0 s 007. 2023Dec_37_F7.raw 9.1 s | deisotoping 0.0 s [progress: 25821/25821 (100%) - 117904 spectra/s] 0.2s | postprocessing 0.0 s 008. 2023Dec_37_F8.raw 10.9 s | deisotoping 0.0 s [progress: 18992/18992 (100%) - 44898 spectra/s] 0.4s | postprocessing 0.0 s 009. 2023Dec_37_F1_20231217064450.raw 9.1 s | deisotoping 0.1 s [progress: 37989/37989 (100%) - 49724 spectra/s] 0.8s | postprocessing 0.1 s 010. 2023Dec_37_F2_20231217093831.raw 13.9 s | deisotoping 0.2 s [progress: 39119/39119 (100%) - 60744 spectra/s] 0.6s | postprocessing 0.1 s 011. 2023Dec_37_F3_20231217123213.raw 13.4 s | deisotoping 0.1 s [progress: 38753/38753 (100%) - 70460 spectra/s] 0.6s | postprocessing 0.1 s 012. 2023Dec_37_F4_20231217160346.raw 13.7 s | deisotoping 0.1 s [progress: 38795/38795 (100%) - 71183 spectra/s] 0.5s | postprocessing 0.1 s 013. 2023Dec_37_F5_20231217185728.raw 11.8 s | deisotoping 0.1 s [progress: 37499/37499 (100%) - 68554 spectra/s] 0.5s | postprocessing 0.1 s 014. 2023Dec_37_F6_20231217215108.raw 9.4 s | deisotoping 0.0 s [progress: 21065/21065 (100%) - 97074 spectra/s] 0.2s | postprocessing 0.0 s 015. 2023Dec_37_F7_20231218012240.raw 9.3 s | deisotoping 0.0 s [progress: 29334/29334 (100%) - 91669 spectra/s] 0.3s | postprocessing 0.1 s 016. 2023Dec_37_F8_20231218041621.raw 11.1 s | deisotoping 0.0 s [progress: 27313/27313 (100%) - 81531 spectra/s] 0.3s | postprocessing 0.0 s 017. 2023Dec_37_F1_C.raw 10.8 s | deisotoping 0.0 s [progress: 20129/20129 (100%) - 94948 spectra/s] 0.2s | postprocessing 0.1 s 018. 2023Dec_37_F2_C.raw 12.1 s | deisotoping 0.0 s [progress: 34494/34494 (100%) - 77865 spectra/s] 0.4s | postprocessing 0.1 s 019. 2023Dec_37_F3_C.raw 13.4 s | deisotoping 0.1 s [progress: 37725/37725 (100%) - 70121 spectra/s] 0.5s | postprocessing 0.1 s 020. 2023Dec_37_F4_C.raw 13.0 s | deisotoping 0.1 s [progress: 38689/38689 (100%) - 70729 spectra/s] 0.5s | postprocessing 0.1 s 021. 2023Dec_37_F5_C.raw 13.7 s | deisotoping 0.1 s [progress: 39115/39115 (100%) - 61309 spectra/s] 0.6s | postprocessing 0.1 s 022. 2023Dec_37_F6_C.raw 12.7 s | deisotoping 0.1 s [progress: 38750/38750 (100%) - 70199 spectra/s] 0.6s | postprocessing 0.1 s 023. 2023Dec_37_F7_C.raw 10.7 s | deisotoping 0.0 s [progress: 33268/33268 (100%) - 100205 spectra/s] 0.3s | postprocessing 0.1 s 024. 2023Dec_37_F8_C.raw 9.9 s | deisotoping 0.0 s [progress: 14352/14352 (100%) - 65835 spectra/s] 0.2s | postprocessing 0.0 s ***************************FIRST SEARCH DONE IN 5.194 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 4.78 1.04 | -0.02 0.78 | 2.14 0.71 | 0.06 0.55 002 | 4.49 0.95 | 0.00 0.75 | 1.95 0.67 | 0.07 0.49 003 | 4.68 1.00 | -0.06 0.78 | 2.03 0.69 | 0.07 0.50 004 | 4.73 1.07 | -0.02 0.77 | 2.03 0.70 | 0.07 0.50 005 | 4.73 1.16 | 0.02 0.80 | 2.07 0.70 | 0.07 0.56 006 | 4.94 0.96 | -0.00 0.68 | 2.22 0.75 | 0.07 0.60 007 | 4.99 1.12 | 0.03 0.89 | 1.91 0.81 | 0.05 0.73 008 | 5.42 1.09 | 0.12 0.83 | 2.24 0.84 | 0.05 0.76 009 | 2.54 1.05 | -0.06 0.77 | 0.02 0.63 | 0.06 0.49 010 | 2.61 1.02 | -0.05 0.78 | 0.11 0.63 | 0.07 0.49 011 | 2.99 1.10 | -0.04 0.76 | 0.41 0.68 | 0.07 0.50 012 | 2.93 1.10 | -0.06 0.82 | 0.24 0.64 | 0.06 0.50 013 | 2.65 1.18 | 0.01 0.79 | 0.03 0.67 | 0.05 0.54 014 | 2.60 0.89 | -0.05 0.66 | -0.02 0.73 | 0.05 0.64 015 | 2.88 1.23 | 0.03 0.87 | -0.18 0.77 | 0.04 0.70 016 | 3.01 1.22 | 0.05 0.85 | -0.30 0.80 | 0.02 0.72 017 | 3.28 1.19 | 0.04 0.93 | 0.08 0.76 | 0.03 0.70 018 | 3.24 1.16 | 0.06 0.83 | 0.50 0.69 | 0.05 0.56 019 | 3.18 1.06 | -0.04 0.78 | 0.67 0.66 | 0.06 0.51 020 | 3.35 1.02 | -0.03 0.77 | 0.75 0.66 | 0.07 0.48 021 | 3.67 1.08 | -0.02 0.78 | 1.02 0.67 | 0.07 0.50 022 | 3.71 1.11 | -0.04 0.78 | 0.99 0.67 | 0.08 0.51 023 | 2.92 0.94 | -0.09 0.68 | 0.66 0.72 | 0.05 0.61 024 | 3.87 0.99 | -0.10 0.68 | 1.09 0.73 | 0.05 0.60 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | 23799| 23735| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 23831| 23860| 23858| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 23919 -------|------- -------|------- Rm P. | 0 -------|------- Count | 23934 -------|------- New fragment_mass_tolerance = 5.000000 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.404 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.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 = 5.0 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 = -1/0/1/2/3 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 = 200.0 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 = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_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 = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 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: 290817 of length 8: 281913 of length 9: 281073 of length 10: 265295 of length 11: 251847 of length 12: 241147 of length 13: 234931 of length 14: 220315 of length 15: 208871 of length 16: 195140 of length 17: 182715 of length 18: 175372 of length 19: 172193 of length 20: 154182 of length 21: 147477 of length 22: 138415 of length 23: 129165 of length 24: 122427 of length 25: 115093 of length 26: 107266 of length 27: 102098 of length 28: 97568 of length 29: 88733 of length 30: 84201 of length 31: 78878 of length 32: 74699 of length 33: 69943 of length 34: 65561 of length 35: 59339 of length 36: 57797 of length 37: 52478 of length 38: 49381 of length 39: 44567 of length 40: 42392 of length 41: 39441 of length 42: 36505 of length 43: 30600 of length 44: 24787 of length 45: 19022 of length 46: 12448 of length 47: 7864 of length 48: 4506 of length 49: 2445 of length 50: 1496 In total 5062403 peptides. Generated 15276509 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.02 Da. 619758398 fragments to be searched in 1 slices (9.24 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.19 s 001. 2023Dec_37_F1.mzBIN_calibrated 0.2 s [progress: 36004/36004 (100%) - 41242 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.3 s 002. 2023Dec_37_F2.mzBIN_calibrated 0.3 s [progress: 38117/38117 (100%) - 38232 spectra/s] 1.0s | remapping alternative proteins and postprocessing 2.3 s 003. 2023Dec_37_F3.mzBIN_calibrated 0.3 s [progress: 38082/38082 (100%) - 41620 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.3 s 004. 2023Dec_37_F4.mzBIN_calibrated 0.3 s [progress: 38186/38186 (100%) - 42148 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.2 s 005. 2023Dec_37_F5.mzBIN_calibrated 0.2 s [progress: 36932/36932 (100%) - 56906 spectra/s] 0.6s | remapping alternative proteins and postprocessing 1.9 s 006. 2023Dec_37_F6.mzBIN_calibrated 0.1 s [progress: 16843/16843 (100%) - 77977 spectra/s] 0.2s | remapping alternative proteins and postprocessing 1.0 s 007. 2023Dec_37_F7.mzBIN_calibrated 0.2 s [progress: 25808/25808 (100%) - 77970 spectra/s] 0.3s | remapping alternative proteins and postprocessing 1.1 s 008. 2023Dec_37_F8.mzBIN_calibrated 0.1 s [progress: 18895/18895 (100%) - 86279 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.8 s 009. 2023Dec_37_F1_20231217064450.mzBIN_calibrated 0.3 s [progress: 37936/37936 (100%) - 38514 spectra/s] 1.0s | remapping alternative proteins and postprocessing 1.9 s 010. 2023Dec_37_F2_20231217093831.mzBIN_calibrated 0.3 s [progress: 39065/39065 (100%) - 43746 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.5 s 011. 2023Dec_37_F3_20231217123213.mzBIN_calibrated 0.3 s [progress: 38706/38706 (100%) - 43884 spectra/s] 0.9s | remapping alternative proteins and postprocessing 1.9 s 012. 2023Dec_37_F4_20231217160346.mzBIN_calibrated 0.3 s [progress: 38748/38748 (100%) - 44744 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.0 s 013. 2023Dec_37_F5_20231217185728.mzBIN_calibrated 0.2 s [progress: 37462/37462 (100%) - 48401 spectra/s] 0.8s | remapping alternative proteins and postprocessing 2.3 s 014. 2023Dec_37_F6_20231217215108.mzBIN_calibrated 0.1 s [progress: 21050/21050 (100%) - 65781 spectra/s] 0.3s | remapping alternative proteins and postprocessing 0.9 s 015. 2023Dec_37_F7_20231218012240.mzBIN_calibrated 0.1 s [progress: 29326/29326 (100%) - 90793 spectra/s] 0.3s | remapping alternative proteins and postprocessing 1.3 s 016. 2023Dec_37_F8_20231218041621.mzBIN_calibrated 0.1 s [progress: 27298/27298 (100%) - 83736 spectra/s] 0.3s | remapping alternative proteins and postprocessing 1.2 s 017. 2023Dec_37_F1_C.mzBIN_calibrated 0.1 s [progress: 20068/20068 (100%) - 90805 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.9 s 018. 2023Dec_37_F2_C.mzBIN_calibrated 0.2 s [progress: 34447/34447 (100%) - 52591 spectra/s] 0.7s | remapping alternative proteins and postprocessing 1.6 s 019. 2023Dec_37_F3_C.mzBIN_calibrated 0.3 s [progress: 37682/37682 (100%) - 43016 spectra/s] 0.9s | remapping alternative proteins and postprocessing 1.9 s 020. 2023Dec_37_F4_C.mzBIN_calibrated 0.3 s [progress: 38638/38638 (100%) - 44057 spectra/s] 0.9s | remapping alternative proteins and postprocessing 2.0 s 021. 2023Dec_37_F5_C.mzBIN_calibrated 0.3 s [progress: 39068/39068 (100%) - 40823 spectra/s] 1.0s | remapping alternative proteins and postprocessing 2.3 s 022. 2023Dec_37_F6_C.mzBIN_calibrated 0.3 s [progress: 38711/38711 (100%) - 44856 spectra/s] 0.9s | remapping alternative proteins and postprocessing 1.9 s 023. 2023Dec_37_F7_C.mzBIN_calibrated 0.2 s [progress: 33238/33238 (100%) - 76585 spectra/s] 0.4s | remapping alternative proteins and postprocessing 1.3 s 024. 2023Dec_37_F8_C.mzBIN_calibrated 0.1 s [progress: 14339/14339 (100%) - 67637 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.8 s ***************************MAIN SEARCH DONE IN 1.144 MIN*************************** *******************************TOTAL TIME 8.741 MIN******************************** Process 'MSFragger' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_20231217215108_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_20231217215108.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_20231217215108_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_20231217215108.pin Started Wed Dec 20 10:20:24 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F6_20231217215108.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 14352 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 11504 positives and 2848 negatives, size ratio=4.03933 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 4869 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 4827 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 4739 training set positives with q<0.01 in that direction. Found 7162 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1280 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 7932 PSMs with q<0.01 Iteration 2: Estimated 7987 PSMs with q<0.01 Iteration 3: Estimated 8072 PSMs with q<0.01 Iteration 4: Estimated 8078 PSMs with q<0.01 Iteration 5: Estimated 8077 PSMs with q<0.01 Iteration 6: Estimated 8101 PSMs with q<0.01 Iteration 7: Estimated 8102 PSMs with q<0.01 Iteration 8: Estimated 8085 PSMs with q<0.01 Iteration 9: Estimated 8092 PSMs with q<0.01 Iteration 10: Estimated 8110 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 -0.7598 -0.7735 -0.7996 abs_ppm -0.2309 -0.2214 -0.2242 isotope_errors -0.9797 -0.8897 -1.0677 log10_evalue 1.1537 1.3754 1.0868 hyperscore 0.5563 0.6411 0.7066 delta_hyperscore 1.6318 1.4991 1.5560 matched_ion_num -1.1418 -1.0526 -0.8569 complementary_ions 0.2680 0.3589 0.4178 ion_series -0.0103 0.0838 0.0846 weighted_average_abs_fragment_ppm -0.0379 -0.0274 -0.0880 length_7 0.0472 0.0011 0.0353 length_8 0.0031 0.0075 0.0226 length_9_30 -0.0304 0.0803 0.1415 length_31 0.0000 0.0000 0.0000 ntt -0.0715 -0.0472 0.0086 nmc 0.0000 0.0000 0.0000 charge_1 0.0551 0.0272 -0.0322 charge_2 0.0032 0.0198 0.0839 charge_3 -0.1039 -0.0617 -0.0792 charge_4 -0.0187 -0.0778 -0.0372 charge_5 -0.0494 -0.0464 -0.0629 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 0.0962 0.1521 0.1100 15.9949M 0.3803 0.3586 0.5098 304.20715n^ 1.2334 1.1587 1.5706 m0 Found 8020 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 11504 target PSMs and 2848 decoy PSMs. Calculating q values. Final list yields 8024 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.4570 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6_C.pin Started Wed Dec 20 10:20:26 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F6_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35763 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29810 positives and 5953 negatives, size ratio=5.00756 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 15822 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 15636 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 15713 training set positives with q<0.01 in that direction. Found 23565 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2810 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 23905 PSMs with q<0.01 Iteration 2: Estimated 23911 PSMs with q<0.01 Iteration 3: Estimated 23910 PSMs with q<0.01 Iteration 4: Estimated 23905 PSMs with q<0.01 Iteration 5: Estimated 23900 PSMs with q<0.01 Iteration 6: Estimated 23901 PSMs with q<0.01 Iteration 7: Estimated 23898 PSMs with q<0.01 Iteration 8: Estimated 23900 PSMs with q<0.01 Iteration 9: Estimated 23897 PSMs with q<0.01 Iteration 10: Estimated 23901 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 -0.3397 -0.2945 -0.2933 abs_ppm -0.0305 -0.0945 -0.0867 isotope_errors -1.6381 -1.4772 -1.5062 log10_evalue 0.6485 0.9379 0.8998 hyperscore 0.6110 1.0179 0.6645 delta_hyperscore 1.3486 1.2864 1.2464 matched_ion_num -0.7164 -0.8685 -0.6579 complementary_ions 0.9170 0.8867 0.9340 ion_series 0.0149 0.0259 0.0082 weighted_average_abs_fragment_ppm 0.0856 0.1312 0.0787 length_7 0.1177 0.0812 0.0948 length_8 -0.0570 -0.0248 -0.0358 length_9_30 -0.1848 -0.2764 -0.1863 length_31 0.0000 0.0000 0.0000 ntt 0.0073 -0.0398 0.0261 nmc 0.0000 0.0000 0.0000 charge_1 -0.1114 -0.1398 -0.1236 charge_2 0.0802 0.0516 0.0970 charge_3 0.0569 0.0714 0.0839 charge_4 -0.0342 0.0455 -0.0855 charge_5 -0.0156 0.0285 -0.0315 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 0.1347 0.1191 0.1201 15.9949M 0.1242 0.1624 0.2098 304.20715n^ 3.1558 3.0456 3.1722 m0 Found 23901 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29810 target PSMs and 5953 decoy PSMs. Calculating q values. Final list yields 23905 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.3220 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5.pin Started Wed Dec 20 10:20:29 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F5.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 33745 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 27794 positives and 5951 negatives, size ratio=4.67048 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 14244 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 14130 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 14263 training set positives with q<0.01 in that direction. Found 21289 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2690 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 21812 PSMs with q<0.01 Iteration 2: Estimated 21835 PSMs with q<0.01 Iteration 3: Estimated 21837 PSMs with q<0.01 Iteration 4: Estimated 21832 PSMs with q<0.01 Iteration 5: Estimated 21832 PSMs with q<0.01 Iteration 6: Estimated 21834 PSMs with q<0.01 Iteration 7: Estimated 21833 PSMs with q<0.01 Iteration 8: Estimated 21833 PSMs with q<0.01 Iteration 9: Estimated 21832 PSMs with q<0.01 Iteration 10: Estimated 21833 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 -0.4046 -0.4056 -0.3676 abs_ppm -0.0996 -0.1092 -0.1498 isotope_errors -1.3425 -1.3917 -1.6964 log10_evalue 1.7316 0.7512 1.6581 hyperscore 0.9795 0.8502 0.9972 delta_hyperscore 2.2487 2.7997 1.9118 matched_ion_num -1.5238 -1.4436 -1.5371 complementary_ions 0.4402 0.3642 0.5369 ion_series 0.0251 -0.0225 0.0024 weighted_average_abs_fragment_ppm 0.1544 0.1365 0.1134 length_7 -0.0046 0.0649 0.0751 length_8 -0.0737 -0.1170 -0.1343 length_9_30 -0.1106 -0.0878 -0.0169 length_31 0.0000 0.0000 0.0000 ntt 0.0151 0.0219 0.0495 nmc 0.0000 0.0000 0.0000 charge_1 -0.0230 -0.0900 -0.0459 charge_2 0.1513 0.0953 0.1230 charge_3 -0.0029 0.0502 0.0123 charge_4 -0.2063 -0.0046 -0.1018 charge_5 -0.2955 -0.2620 -0.2968 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 0.1877 0.1784 0.1622 15.9949M 0.3343 0.2726 0.3242 304.20715n^ 3.5132 3.2420 3.6071 m0 Found 21817 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 27794 target PSMs and 5951 decoy PSMs. Calculating q values. Final list yields 21821 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.1390 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_C.pin Started Wed Dec 20 10:20:32 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F2_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 30694 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 24280 positives and 6414 negatives, size ratio=3.78547 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 11706 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 11664 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 11611 training set positives with q<0.01 in that direction. Found 17455 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2460 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 17662 PSMs with q<0.01 Iteration 2: Estimated 17674 PSMs with q<0.01 Iteration 3: Estimated 17678 PSMs with q<0.01 Iteration 4: Estimated 17679 PSMs with q<0.01 Iteration 5: Estimated 17680 PSMs with q<0.01 Iteration 6: Estimated 17677 PSMs with q<0.01 Iteration 7: Estimated 17677 PSMs with q<0.01 Iteration 8: Estimated 17677 PSMs with q<0.01 Iteration 9: Estimated 17677 PSMs with q<0.01 Iteration 10: Estimated 17674 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 -0.2562 -0.1785 -0.2521 abs_ppm -0.0569 -0.0988 -0.0650 isotope_errors -1.3727 -1.5207 -1.0648 log10_evalue 1.3452 2.3900 0.9963 hyperscore 0.7539 1.2085 0.8809 delta_hyperscore 1.0865 0.6840 1.6097 matched_ion_num -0.5290 -0.7191 -0.6974 complementary_ions 0.6843 0.8330 0.7680 ion_series -0.0268 -0.0316 0.0048 weighted_average_abs_fragment_ppm -0.0089 -0.0401 -0.0133 length_7 0.0219 0.0199 0.0408 length_8 -0.0010 0.0030 -0.0396 length_9_30 -0.0170 0.0258 0.0474 length_31 0.0000 0.0000 0.0000 ntt -0.3532 -0.3322 -0.3336 nmc 0.0000 0.0000 0.0000 charge_1 -0.0268 -0.0387 -0.0422 charge_2 -0.0216 0.0245 0.0398 charge_3 0.0622 0.0058 0.0046 charge_4 0.0373 0.0659 -0.0149 charge_5 0.0163 -0.0488 0.0263 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 0.0492 0.0905 0.0449 15.9949M 0.0882 0.0489 0.0453 304.20715n^ 2.8314 3.4501 2.8086 m0 Found 17618 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 24280 target PSMs and 6414 decoy PSMs. Calculating q values. Final list yields 17631 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.0430 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_20231217093831_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_20231217093831.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_20231217093831_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2_20231217093831.pin Started Wed Dec 20 10:20:35 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F2_20231217093831.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 36383 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 30955 positives and 5428 negatives, size ratio=5.70284 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 16876 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 16829 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 16630 training set positives with q<0.01 in that direction. Found 25127 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2890 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 25406 PSMs with q<0.01 Iteration 2: Estimated 25438 PSMs with q<0.01 Iteration 3: Estimated 25447 PSMs with q<0.01 Iteration 4: Estimated 25443 PSMs with q<0.01 Iteration 5: Estimated 25451 PSMs with q<0.01 Iteration 6: Estimated 25455 PSMs with q<0.01 Iteration 7: Estimated 25455 PSMs with q<0.01 Iteration 8: Estimated 25456 PSMs with q<0.01 Iteration 9: Estimated 25457 PSMs with q<0.01 Iteration 10: Estimated 25456 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 -0.1107 -0.1242 -0.1617 abs_ppm -0.0917 -0.1395 -0.1307 isotope_errors -1.2470 -1.6607 -2.0723 log10_evalue 0.2497 -0.4229 -1.0652 hyperscore 1.0453 1.2830 1.1841 delta_hyperscore 1.3261 2.6679 3.2082 matched_ion_num -0.3542 -0.7991 -0.8395 complementary_ions 0.7886 0.7005 1.0851 ion_series -0.0211 -0.0157 0.0199 weighted_average_abs_fragment_ppm 0.0452 0.1013 0.1289 length_7 0.0459 0.0279 0.0335 length_8 -0.0578 -0.0513 -0.0696 length_9_30 -0.0145 -0.0991 -0.1130 length_31 0.0000 0.0000 0.0000 ntt -0.0594 -0.1314 -0.1749 nmc 0.0000 0.0000 0.0000 charge_1 -0.1579 -0.1765 -0.2165 charge_2 0.1067 0.1218 0.0569 charge_3 0.0624 0.0690 0.1919 charge_4 0.0056 -0.0217 0.0162 charge_5 0.0035 0.0501 0.0837 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 0.0352 0.0286 0.1086 15.9949M 0.1282 0.0855 0.0527 304.20715n^ 3.3834 4.2070 4.6042 m0 Found 25397 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 30955 target PSMs and 5428 decoy PSMs. Calculating q values. Final list yields 25398 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.8330 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1.pin Started Wed Dec 20 10:20:38 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F1.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 33053 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 27459 positives and 5594 negatives, size ratio=4.90865 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 14490 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 14410 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 14384 training set positives with q<0.01 in that direction. Found 21643 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2610 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 21852 PSMs with q<0.01 Iteration 2: Estimated 21865 PSMs with q<0.01 Iteration 3: Estimated 21877 PSMs with q<0.01 Iteration 4: Estimated 21878 PSMs with q<0.01 Iteration 5: Estimated 21885 PSMs with q<0.01 Iteration 6: Estimated 21876 PSMs with q<0.01 Iteration 7: Estimated 21880 PSMs with q<0.01 Iteration 8: Estimated 21880 PSMs with q<0.01 Iteration 9: Estimated 21880 PSMs with q<0.01 Iteration 10: Estimated 21881 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 -0.2133 -0.2971 -0.1703 abs_ppm -0.0889 -0.0638 -0.0879 isotope_errors -1.5178 -1.5447 -1.3484 log10_evalue 0.2094 0.5799 0.5768 hyperscore 1.1756 1.1498 1.0175 delta_hyperscore 2.4753 3.1758 1.8901 matched_ion_num -0.9551 -1.4175 -0.8548 complementary_ions 0.4937 0.4832 0.4817 ion_series -0.0165 0.0349 0.0379 weighted_average_abs_fragment_ppm 0.0473 0.1047 0.0648 length_7 0.0415 0.0667 0.0482 length_8 -0.0289 -0.0468 -0.0312 length_9_30 -0.0761 -0.1691 -0.1101 length_31 0.0000 0.0000 0.0000 ntt -0.1199 -0.1878 -0.1109 nmc 0.0000 0.0000 0.0000 charge_1 -0.1122 -0.0782 -0.0903 charge_2 0.0714 0.0977 0.1045 charge_3 0.0723 -0.0002 -0.0012 charge_4 -0.0185 -0.1091 -0.0579 charge_5 -0.0473 0.0357 -0.0289 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 0.0074 0.0875 0.0389 15.9949M 0.1002 0.1306 0.1159 304.20715n^ 3.6389 4.4556 3.1447 m0 Found 21833 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 27459 target PSMs and 5594 decoy PSMs. Calculating q values. Final list yields 21835 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.0890 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_20231217123213_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_20231217123213.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_20231217123213_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_20231217123213.pin Started Wed Dec 20 10:20:41 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F3_20231217123213.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35418 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29896 positives and 5522 negatives, size ratio=5.41398 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 16130 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 15982 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 15915 training set positives with q<0.01 in that direction. Found 23950 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2870 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 24180 PSMs with q<0.01 Iteration 2: Estimated 24182 PSMs with q<0.01 Iteration 3: Estimated 24186 PSMs with q<0.01 Iteration 4: Estimated 24190 PSMs with q<0.01 Iteration 5: Estimated 24187 PSMs with q<0.01 Iteration 6: Estimated 24186 PSMs with q<0.01 Iteration 7: Estimated 24187 PSMs with q<0.01 Iteration 8: Estimated 24183 PSMs with q<0.01 Iteration 9: Estimated 24185 PSMs with q<0.01 Iteration 10: Estimated 24185 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 -0.3033 -0.3620 -0.3425 abs_ppm -0.0876 -0.1213 -0.0840 isotope_errors -2.4138 -1.8832 -2.2139 log10_evalue -0.5360 1.0943 0.6881 hyperscore 0.8129 0.7157 0.7977 delta_hyperscore 3.0050 2.0045 1.9613 matched_ion_num -1.0810 -1.0935 -1.0104 complementary_ions 0.7752 0.4487 0.7066 ion_series 0.0692 -0.0084 0.0416 weighted_average_abs_fragment_ppm 0.1410 0.0989 0.1300 length_7 0.0167 0.0315 0.0276 length_8 -0.0652 -0.0947 -0.0275 length_9_30 -0.1245 -0.0052 -0.2076 length_31 0.0000 0.0000 0.0000 ntt 0.0218 -0.0255 0.0069 nmc 0.0000 0.0000 0.0000 charge_1 -0.1198 -0.1348 -0.1112 charge_2 0.1508 0.1378 0.1111 charge_3 0.0127 0.0375 0.0193 charge_4 -0.0992 -0.0858 -0.0772 charge_5 -0.0678 -0.0364 0.0514 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 0.0554 0.0893 0.0815 15.9949M 0.1592 0.1080 0.1428 304.20715n^ 4.2130 3.9229 4.1504 m0 Found 24147 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29896 target PSMs and 5522 decoy PSMs. Calculating q values. Final list yields 24149 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.3100 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_C.pin Started Wed Dec 20 10:20:44 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F7_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 25229 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 19846 positives and 5383 negatives, size ratio=3.68679 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 8384 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 8053 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 8249 training set positives with q<0.01 in that direction. Found 12298 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2010 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 13933 PSMs with q<0.01 Iteration 2: Estimated 14007 PSMs with q<0.01 Iteration 3: Estimated 14039 PSMs with q<0.01 Iteration 4: Estimated 14037 PSMs with q<0.01 Iteration 5: Estimated 14041 PSMs with q<0.01 Iteration 6: Estimated 14042 PSMs with q<0.01 Iteration 7: Estimated 14038 PSMs with q<0.01 Iteration 8: Estimated 14044 PSMs with q<0.01 Iteration 9: Estimated 14048 PSMs with q<0.01 Iteration 10: Estimated 14039 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 -0.6311 -0.7234 -0.6879 abs_ppm -0.3130 -0.2539 -0.2412 isotope_errors -1.7170 -1.2270 -1.3426 log10_evalue 1.4508 1.6963 1.6114 hyperscore 0.9050 1.1053 1.0560 delta_hyperscore 2.6019 2.1417 2.5559 matched_ion_num -1.9611 -1.9152 -2.1808 complementary_ions 0.2933 0.4936 0.2318 ion_series 0.2066 0.0801 0.1487 weighted_average_abs_fragment_ppm 0.0328 -0.0069 0.1214 length_7 0.0711 0.0558 -0.0433 length_8 -0.0665 -0.0253 -0.0638 length_9_30 -0.1312 -0.0813 -0.0935 length_31 0.0000 0.0000 0.0000 ntt -0.2801 -0.2142 -0.1301 nmc 0.0000 0.0000 0.0000 charge_1 -0.0785 -0.0638 -0.0563 charge_2 0.0520 0.0448 0.0545 charge_3 0.1229 0.0752 0.0368 charge_4 -0.1203 -0.0297 -0.0453 charge_5 -0.0876 -0.0780 -0.0783 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 0.2751 0.2395 0.2348 15.9949M 0.2327 0.3365 0.3948 304.20715n^ 2.1194 1.8869 1.8950 m0 Found 13972 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 19846 target PSMs and 5383 decoy PSMs. Calculating q values. Final list yields 13975 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.2010 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8.pin Started Wed Dec 20 10:20:46 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F8.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 13998 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 11802 positives and 2196 negatives, size ratio=5.37432 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 5792 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 5844 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 5811 training set positives with q<0.01 in that direction. Found 8664 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1250 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 9317 PSMs with q<0.01 Iteration 2: Estimated 9368 PSMs with q<0.01 Iteration 3: Estimated 9370 PSMs with q<0.01 Iteration 4: Estimated 9377 PSMs with q<0.01 Iteration 5: Estimated 9372 PSMs with q<0.01 Iteration 6: Estimated 9373 PSMs with q<0.01 Iteration 7: Estimated 9369 PSMs with q<0.01 Iteration 8: Estimated 9364 PSMs with q<0.01 Iteration 9: Estimated 9370 PSMs with q<0.01 Iteration 10: Estimated 9368 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 -0.9048 -1.2331 -1.2100 abs_ppm -0.3401 -0.4269 -0.3415 isotope_errors -0.7006 -0.4438 -0.5441 log10_evalue 1.9084 3.8191 3.9119 hyperscore 0.7437 1.0654 0.7378 delta_hyperscore 1.5837 2.9017 1.0514 matched_ion_num -0.9018 -2.0121 -1.3984 complementary_ions 0.2755 -0.1716 -0.1523 ion_series -0.0334 -0.0364 0.0157 weighted_average_abs_fragment_ppm -0.0813 0.0448 0.0195 length_7 0.1304 0.0669 0.1836 length_8 -0.0547 -0.0597 -0.0255 length_9_30 0.0724 -0.0733 -0.3839 length_31 0.0000 0.0000 0.0000 ntt 0.0428 0.2167 -0.0087 nmc 0.0000 0.0000 0.0000 charge_1 0.0721 0.1782 0.0319 charge_2 0.0110 -0.1264 -0.0163 charge_3 -0.0501 -0.0979 0.0265 charge_4 -0.0833 0.0643 -0.0702 charge_5 -0.1532 0.0419 -0.0926 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 0.1274 0.2572 0.1483 15.9949M 0.3102 0.3772 0.2214 304.20715n^ 2.2093 3.9357 2.7924 m0 Found 9273 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 11802 target PSMs and 2196 decoy PSMs. Calculating q values. Final list yields 9283 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 1.8550 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_C.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3_C.pin Started Wed Dec 20 10:20:49 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F3_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35053 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29051 positives and 6002 negatives, size ratio=4.84022 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 15142 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 15060 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 15038 training set positives with q<0.01 in that direction. Found 22601 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2740 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 22857 PSMs with q<0.01 Iteration 2: Estimated 22856 PSMs with q<0.01 Iteration 3: Estimated 22854 PSMs with q<0.01 Iteration 4: Estimated 22858 PSMs with q<0.01 Iteration 5: Estimated 22857 PSMs with q<0.01 Iteration 6: Estimated 22856 PSMs with q<0.01 Iteration 7: Estimated 22856 PSMs with q<0.01 Iteration 8: Estimated 22854 PSMs with q<0.01 Iteration 9: Estimated 22858 PSMs with q<0.01 Iteration 10: Estimated 22858 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 -0.2021 -0.1936 -0.1799 abs_ppm -0.1077 -0.1123 -0.1195 isotope_errors -0.8030 -0.7903 -1.0184 log10_evalue 1.0105 0.7394 0.9323 hyperscore 1.4653 0.8996 0.8376 delta_hyperscore 2.4020 1.9765 1.8650 matched_ion_num -1.1513 -0.9575 -0.9241 complementary_ions 0.8922 0.7361 0.7041 ion_series 0.0224 -0.0205 -0.0584 weighted_average_abs_fragment_ppm 0.0840 0.0718 0.0809 length_7 0.1284 0.0922 0.1036 length_8 -0.0381 -0.0436 -0.0376 length_9_30 -0.2368 -0.1525 -0.1970 length_31 0.0000 0.0000 0.0000 ntt -0.2153 -0.1335 -0.1540 nmc 0.0000 0.0000 0.0000 charge_1 -0.1247 -0.0773 -0.0883 charge_2 0.0746 0.0735 0.0690 charge_3 0.0563 -0.0109 0.0114 charge_4 0.0211 -0.0026 0.0305 charge_5 0.0121 0.0797 -0.0012 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 0.0603 0.0108 0.0427 15.9949M 0.1852 0.1178 0.1449 304.20715n^ 3.9930 3.0655 3.2059 m0 Found 22855 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29051 target PSMs and 6002 decoy PSMs. Calculating q values. Final list yields 22856 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.4230 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4.pin Started Wed Dec 20 10:20:54 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F4.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35239 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29472 positives and 5767 negatives, size ratio=5.11046 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 15554 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 15617 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 15558 training set positives with q<0.01 in that direction. Found 23360 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2770 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 23733 PSMs with q<0.01 Iteration 2: Estimated 23731 PSMs with q<0.01 Iteration 3: Estimated 23730 PSMs with q<0.01 Iteration 4: Estimated 23727 PSMs with q<0.01 Iteration 5: Estimated 23726 PSMs with q<0.01 Iteration 6: Estimated 23729 PSMs with q<0.01 Iteration 7: Estimated 23731 PSMs with q<0.01 Iteration 8: Estimated 23730 PSMs with q<0.01 Iteration 9: Estimated 23731 PSMs with q<0.01 Iteration 10: Estimated 23732 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 -0.3337 -0.3207 -0.2813 abs_ppm -0.0751 -0.0985 -0.0766 isotope_errors -1.8673 -1.2423 -1.5596 log10_evalue 1.0850 0.8061 0.8813 hyperscore 1.0400 0.8431 0.7322 delta_hyperscore 2.0113 1.3500 1.2264 matched_ion_num -1.2154 -0.7574 -0.7759 complementary_ions 0.5732 0.8020 0.6935 ion_series 0.0461 0.0326 0.0015 weighted_average_abs_fragment_ppm 0.1714 0.0754 0.0811 length_7 0.1379 0.0651 0.0613 length_8 -0.1024 -0.0513 -0.0623 length_9_30 -0.2801 -0.1157 -0.0949 length_31 0.0000 0.0000 0.0000 ntt 0.0111 0.0227 -0.0022 nmc 0.0000 0.0000 0.0000 charge_1 -0.1716 -0.1097 -0.0796 charge_2 0.1118 0.1151 0.0945 charge_3 0.0582 0.0272 0.0357 charge_4 0.0831 -0.0079 -0.0548 charge_5 -0.1225 -0.1399 -0.1186 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 0.1480 0.1325 0.1407 15.9949M 0.1829 0.2277 0.2062 304.20715n^ 3.9110 3.0312 3.1111 m0 Found 23711 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29472 target PSMs and 5767 decoy PSMs. Calculating q values. Final list yields 23713 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.3590 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_C.pin Started Wed Dec 20 10:20:56 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F8_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 10721 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 8822 positives and 1899 negatives, size ratio=4.6456 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 3990 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 4026 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 4055 training set positives with q<0.01 in that direction. Found 6014 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1000 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 6507 PSMs with q<0.01 Iteration 2: Estimated 6549 PSMs with q<0.01 Iteration 3: Estimated 6575 PSMs with q<0.01 Iteration 4: Estimated 6578 PSMs with q<0.01 Iteration 5: Estimated 6576 PSMs with q<0.01 Iteration 6: Estimated 6587 PSMs with q<0.01 Iteration 7: Estimated 6586 PSMs with q<0.01 Iteration 8: Estimated 6584 PSMs with q<0.01 Iteration 9: Estimated 6587 PSMs with q<0.01 Iteration 10: Estimated 6585 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 -0.7254 -0.5082 -0.4890 abs_ppm -0.2933 -0.2921 -0.1620 isotope_errors -1.8054 -1.9772 -1.2443 log10_evalue 1.9037 1.8785 1.1012 hyperscore 1.3218 0.9526 0.6696 delta_hyperscore 2.2778 1.6688 1.2903 matched_ion_num -1.9227 -1.6566 -0.9174 complementary_ions 0.3760 0.4455 0.4090 ion_series 0.0545 0.0424 0.0286 weighted_average_abs_fragment_ppm -0.0096 0.0148 -0.0283 length_7 0.1609 0.0830 0.1085 length_8 -0.0924 -0.0470 -0.0320 length_9_30 -0.0662 -0.0973 -0.0870 length_31 0.0000 0.0000 0.0000 ntt -0.1674 -0.1712 -0.1756 nmc 0.0000 0.0000 0.0000 charge_1 -0.0165 -0.0515 -0.0631 charge_2 -0.0093 0.0324 0.0449 charge_3 0.1065 0.1252 0.0465 charge_4 -0.0264 -0.1263 0.0519 charge_5 -0.2012 -0.1589 -0.1298 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 0.1251 0.1081 0.1164 15.9949M 0.3943 0.1243 0.1306 304.20715n^ 3.3298 2.6305 2.1476 m0 Found 6511 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 8822 target PSMs and 1899 decoy PSMs. Calculating q values. Final list yields 6513 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 1.7150 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7.pin Started Wed Dec 20 10:20:58 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F7.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 20656 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 17111 positives and 3545 negatives, size ratio=4.8268 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 8333 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 8288 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 8155 training set positives with q<0.01 in that direction. Found 12285 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1710 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 13256 PSMs with q<0.01 Iteration 2: Estimated 13331 PSMs with q<0.01 Iteration 3: Estimated 13338 PSMs with q<0.01 Iteration 4: Estimated 13340 PSMs with q<0.01 Iteration 5: Estimated 13353 PSMs with q<0.01 Iteration 6: Estimated 13354 PSMs with q<0.01 Iteration 7: Estimated 13352 PSMs with q<0.01 Iteration 8: Estimated 13349 PSMs with q<0.01 Iteration 9: Estimated 13349 PSMs with q<0.01 Iteration 10: Estimated 13349 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -1.0293 -0.9880 -1.2285 abs_ppm -0.2723 -0.2380 -0.2653 isotope_errors -1.4863 -1.1246 -1.2403 log10_evalue 1.2800 1.2246 0.4528 hyperscore 0.7091 0.8141 0.7281 delta_hyperscore 2.7837 2.9967 3.6364 matched_ion_num -1.4239 -1.3891 -1.6573 complementary_ions -0.1304 -0.0840 -0.0322 ion_series 0.0531 0.0152 0.0094 weighted_average_abs_fragment_ppm 0.0707 0.0688 0.0339 length_7 0.0460 0.0503 0.0980 length_8 -0.0191 -0.0471 -0.0496 length_9_30 -0.2990 -0.1880 -0.2063 length_31 0.0000 0.0000 0.0000 ntt 0.0249 0.0479 0.0577 nmc 0.0000 0.0000 0.0000 charge_1 0.1127 0.1526 0.1160 charge_2 0.0736 0.0115 0.0175 charge_3 -0.1580 -0.1224 -0.1646 charge_4 -0.1471 -0.1713 0.0329 charge_5 -0.1803 -0.1297 -0.1425 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 0.2770 0.2561 0.2273 15.9949M 0.3453 0.2787 0.2424 304.20715n^ 2.6956 2.7143 2.5827 m0 Found 13266 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 17111 target PSMs and 3545 decoy PSMs. Calculating q values. Final list yields 13268 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.5170 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_20231217160346_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_20231217160346.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_20231217160346_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_20231217160346.pin Started Wed Dec 20 10:21:03 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F4_20231217160346.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35803 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29610 positives and 6193 negatives, size ratio=4.7812 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 15720 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 15393 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 15464 training set positives with q<0.01 in that direction. Found 23329 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2810 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 23536 PSMs with q<0.01 Iteration 2: Estimated 23550 PSMs with q<0.01 Iteration 3: Estimated 23553 PSMs with q<0.01 Iteration 4: Estimated 23554 PSMs with q<0.01 Iteration 5: Estimated 23556 PSMs with q<0.01 Iteration 6: Estimated 23554 PSMs with q<0.01 Iteration 7: Estimated 23555 PSMs with q<0.01 Iteration 8: Estimated 23553 PSMs with q<0.01 Iteration 9: Estimated 23552 PSMs with q<0.01 Iteration 10: Estimated 23553 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 -0.2372 -0.2549 -0.2623 abs_ppm -0.0667 -0.0947 -0.0638 isotope_errors -1.5399 -1.5782 -1.4187 log10_evalue 0.7835 1.2377 0.8589 hyperscore 1.2297 1.2176 0.9154 delta_hyperscore 2.1485 1.1083 1.2720 matched_ion_num -0.9148 -0.7733 -0.7000 complementary_ions 0.7717 0.6721 0.8676 ion_series 0.0057 0.0010 0.0037 weighted_average_abs_fragment_ppm 0.1049 0.1077 0.0951 length_7 0.0994 0.0206 0.0624 length_8 -0.0563 -0.0271 -0.0645 length_9_30 -0.1655 -0.1283 -0.0901 length_31 0.0000 0.0000 0.0000 ntt -0.0420 -0.0209 -0.0789 nmc 0.0000 0.0000 0.0000 charge_1 -0.1561 -0.1357 -0.1759 charge_2 0.0850 0.0908 0.1220 charge_3 0.0344 0.0090 0.0344 charge_4 0.0664 0.0455 0.0144 charge_5 0.0204 0.0358 0.0382 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 0.1110 0.1608 0.1149 15.9949M 0.1533 0.2529 0.1903 304.20715n^ 3.9788 3.2438 3.1975 m0 Found 23515 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29610 target PSMs and 6193 decoy PSMs. Calculating q values. Final list yields 23517 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.5680 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F4_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F4_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F4_C.pin Started Wed Dec 20 10:21:06 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F4_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 36212 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 30860 positives and 5352 negatives, size ratio=5.76607 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 16694 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 16666 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 16698 training set positives with q<0.01 in that direction. Found 24976 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2830 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 25267 PSMs with q<0.01 Iteration 2: Estimated 25275 PSMs with q<0.01 Iteration 3: Estimated 25282 PSMs with q<0.01 Iteration 4: Estimated 25289 PSMs with q<0.01 Iteration 5: Estimated 25295 PSMs with q<0.01 Iteration 6: Estimated 25298 PSMs with q<0.01 Iteration 7: Estimated 25298 PSMs with q<0.01 Iteration 8: Estimated 25297 PSMs with q<0.01 Iteration 9: Estimated 25300 PSMs with q<0.01 Iteration 10: Estimated 25300 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 -0.1277 -0.1431 -0.2133 abs_ppm -0.1382 -0.0774 -0.1342 isotope_errors -1.2765 -1.7290 -1.3631 log10_evalue -0.5491 -1.0772 -0.2033 hyperscore 1.4218 1.3690 1.0665 delta_hyperscore 2.9779 2.5707 2.7416 matched_ion_num -0.9106 -0.7117 -0.9504 complementary_ions 0.8157 1.0712 0.7257 ion_series -0.1128 -0.0451 -0.0719 weighted_average_abs_fragment_ppm 0.0967 0.0670 0.1292 length_7 0.0774 0.0409 0.0996 length_8 -0.0143 -0.0368 -0.0254 length_9_30 -0.2377 -0.0873 -0.2982 length_31 0.0000 0.0000 0.0000 ntt -0.1067 -0.0778 -0.0245 nmc 0.0000 0.0000 0.0000 charge_1 -0.1381 -0.1567 -0.1183 charge_2 0.0715 0.0744 0.1149 charge_3 0.0461 0.1257 0.0376 charge_4 0.0805 -0.0687 -0.0825 charge_5 0.0029 0.0468 -0.0081 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 0.0158 -0.0265 -0.0448 15.9949M 0.1742 0.2043 0.1766 304.20715n^ 4.0623 4.0509 3.8513 m0 Found 25247 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 30860 target PSMs and 5352 decoy PSMs. Calculating q values. Final list yields 25250 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.2710 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_20231217064450_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_20231217064450.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_20231217064450_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_20231217064450.pin Started Wed Dec 20 10:21:09 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F1_20231217064450.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35275 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 29105 positives and 6170 negatives, size ratio=4.71718 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 15311 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 15121 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 15129 training set positives with q<0.01 in that direction. Found 22740 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2800 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 22990 PSMs with q<0.01 Iteration 2: Estimated 23008 PSMs with q<0.01 Iteration 3: Estimated 23014 PSMs with q<0.01 Iteration 4: Estimated 23016 PSMs with q<0.01 Iteration 5: Estimated 23014 PSMs with q<0.01 Iteration 6: Estimated 23011 PSMs with q<0.01 Iteration 7: Estimated 23013 PSMs with q<0.01 Iteration 8: Estimated 23014 PSMs with q<0.01 Iteration 9: Estimated 23013 PSMs with q<0.01 Iteration 10: Estimated 23013 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 -0.2017 -0.1265 -0.1328 abs_ppm -0.1416 -0.1043 -0.0954 isotope_errors -2.0839 -1.2064 -1.3437 log10_evalue 0.8309 0.4369 0.5142 hyperscore 1.2382 0.9350 0.7452 delta_hyperscore 2.5562 1.6512 1.4520 matched_ion_num -1.3543 -0.8092 -0.7389 complementary_ions 0.7931 0.9830 1.0024 ion_series -0.1273 -0.0660 -0.0618 weighted_average_abs_fragment_ppm 0.1029 0.0696 0.0669 length_7 0.1095 0.0831 0.0647 length_8 -0.0027 0.0041 -0.0104 length_9_30 -0.3117 -0.2366 -0.1745 length_31 0.0000 0.0000 0.0000 ntt -0.1677 -0.2062 -0.2022 nmc 0.0000 0.0000 0.0000 charge_1 -0.1170 -0.1038 -0.1078 charge_2 0.1462 0.0641 0.0854 charge_3 -0.0368 0.0547 0.0303 charge_4 0.0373 0.0229 0.0223 charge_5 -0.1529 -0.0341 -0.0455 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 0.0737 0.0763 0.0591 15.9949M 0.2376 0.1027 0.1092 304.20715n^ 4.7903 3.1998 3.1227 m0 Found 22993 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 29105 target PSMs and 6170 decoy PSMs. Calculating q values. Final list yields 22994 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.7880 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_20231218012240_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_20231218012240.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F7_20231218012240_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F7_20231218012240.pin Started Wed Dec 20 10:21:17 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F7_20231218012240.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 24514 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 20036 positives and 4478 negatives, size ratio=4.47432 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 9624 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 9564 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 9633 training set positives with q<0.01 in that direction. Found 14395 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2020 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 15267 PSMs with q<0.01 Iteration 2: Estimated 15318 PSMs with q<0.01 Iteration 3: Estimated 15335 PSMs with q<0.01 Iteration 4: Estimated 15321 PSMs with q<0.01 Iteration 5: Estimated 15327 PSMs with q<0.01 Iteration 6: Estimated 15328 PSMs with q<0.01 Iteration 7: Estimated 15330 PSMs with q<0.01 Iteration 8: Estimated 15328 PSMs with q<0.01 Iteration 9: Estimated 15329 PSMs with q<0.01 Iteration 10: Estimated 15330 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 -0.8238 -0.7917 -0.7960 abs_ppm -0.2929 -0.3123 -0.2540 isotope_errors -1.0298 -1.2145 -1.0550 log10_evalue 1.5819 1.5542 1.6407 hyperscore 0.6000 0.6145 0.7019 delta_hyperscore 2.1609 2.0037 1.9982 matched_ion_num -1.1315 -1.1781 -1.1510 complementary_ions -0.0065 0.0372 -0.0004 ion_series 0.0226 0.0086 0.0093 weighted_average_abs_fragment_ppm 0.0407 0.0715 0.0567 length_7 0.0778 0.0638 0.0676 length_8 -0.0255 -0.0685 -0.0415 length_9_30 -0.1713 -0.0883 -0.1402 length_31 0.0000 0.0000 0.0000 ntt -0.0392 -0.0341 0.0066 nmc 0.0000 0.0000 0.0000 charge_1 0.0936 0.1018 0.0738 charge_2 0.0748 0.0547 0.0732 charge_3 -0.1425 -0.1204 -0.1193 charge_4 -0.1012 -0.1069 -0.0973 charge_5 -0.0503 -0.0620 -0.0509 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 0.3040 0.2805 0.3181 15.9949M 0.1680 0.0758 0.1048 304.20715n^ 2.4421 2.4251 2.4191 m0 Found 15285 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20036 target PSMs and 4478 decoy PSMs. Calculating q values. Final list yields 15287 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.1420 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F3_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F3.pin Started Wed Dec 20 10:21:19 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F3.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35494 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 30070 positives and 5424 negatives, size ratio=5.54388 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 16217 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 16231 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 16019 training set positives with q<0.01 in that direction. Found 24146 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2800 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 24461 PSMs with q<0.01 Iteration 2: Estimated 24470 PSMs with q<0.01 Iteration 3: Estimated 24472 PSMs with q<0.01 Iteration 4: Estimated 24472 PSMs with q<0.01 Iteration 5: Estimated 24466 PSMs with q<0.01 Iteration 6: Estimated 24470 PSMs with q<0.01 Iteration 7: Estimated 24468 PSMs with q<0.01 Iteration 8: Estimated 24472 PSMs with q<0.01 Iteration 9: Estimated 24471 PSMs with q<0.01 Iteration 10: Estimated 24470 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 -0.2806 -0.1919 -0.2828 abs_ppm -0.0725 -0.0807 -0.1764 isotope_errors -1.4066 -1.8274 -1.7928 log10_evalue -0.0656 1.2209 -0.2482 hyperscore 1.6296 1.4884 1.6268 delta_hyperscore 3.4702 2.9570 2.7274 matched_ion_num -1.2035 -1.5805 -0.8747 complementary_ions 0.3694 0.3331 0.7609 ion_series -0.0651 0.0067 0.0322 weighted_average_abs_fragment_ppm 0.1315 0.1958 0.1312 length_7 -0.0326 0.0442 0.0033 length_8 -0.1002 -0.1840 -0.0901 length_9_30 0.0493 0.0086 -0.0320 length_31 0.0000 0.0000 0.0000 ntt -0.0749 -0.0009 -0.0430 nmc 0.0000 0.0000 0.0000 charge_1 -0.1121 -0.1051 -0.1754 charge_2 0.1421 0.1834 0.2279 charge_3 -0.0374 -0.0609 -0.0538 charge_4 -0.0064 -0.1166 -0.0840 charge_5 -0.0368 0.0053 0.0506 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 0.0802 -0.0190 0.1226 15.9949M 0.1141 0.0855 0.1507 304.20715n^ 4.4161 4.9403 4.4320 m0 Found 24439 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 30070 target PSMs and 5424 decoy PSMs. Calculating q values. Final list yields 24440 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.0300 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_C.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_C.pin Started Wed Dec 20 10:21:23 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F5_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 36512 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 31072 positives and 5440 negatives, size ratio=5.71176 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 16800 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 16775 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 16720 training set positives with q<0.01 in that direction. Found 25108 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2850 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 25395 PSMs with q<0.01 Iteration 2: Estimated 25411 PSMs with q<0.01 Iteration 3: Estimated 25423 PSMs with q<0.01 Iteration 4: Estimated 25419 PSMs with q<0.01 Iteration 5: Estimated 25418 PSMs with q<0.01 Iteration 6: Estimated 25421 PSMs with q<0.01 Iteration 7: Estimated 25422 PSMs with q<0.01 Iteration 8: Estimated 25422 PSMs with q<0.01 Iteration 9: Estimated 25421 PSMs with q<0.01 Iteration 10: Estimated 25421 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 -0.2558 -0.2340 -0.2378 abs_ppm -0.1060 -0.1228 -0.1225 isotope_errors -1.6287 -1.6076 -1.5077 log10_evalue 0.8133 0.6439 0.8852 hyperscore 0.7957 0.6167 0.8057 delta_hyperscore 1.1014 1.0440 1.1336 matched_ion_num -0.6549 -0.6022 -0.6500 complementary_ions 0.7106 0.9207 0.6815 ion_series -0.0584 -0.0805 -0.0801 weighted_average_abs_fragment_ppm 0.1244 0.0921 0.1024 length_7 0.0196 0.0226 0.0255 length_8 0.0024 0.0086 0.0183 length_9_30 -0.2465 -0.2095 -0.2531 length_31 0.0000 0.0000 0.0000 ntt 0.0808 0.0059 0.0587 nmc 0.0000 0.0000 0.0000 charge_1 -0.1042 -0.1321 -0.0793 charge_2 0.1405 0.1017 0.0997 charge_3 0.0188 0.0866 0.0102 charge_4 -0.1349 -0.0982 -0.0700 charge_5 -0.0222 -0.0195 -0.0282 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 0.0502 0.0293 0.0579 15.9949M 0.0977 0.1006 0.1347 304.20715n^ 3.3436 3.0132 3.3577 m0 Found 25403 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 31072 target PSMs and 5440 decoy PSMs. Calculating q values. Final list yields 25410 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.9770 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_C.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F1_C_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F1_C_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F1_C.pin Started Wed Dec 20 10:21:26 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F1_C.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 16906 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 14188 positives and 2718 negatives, size ratio=5.22001 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 7325 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 7343 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 7353 training set positives with q<0.01 in that direction. Found 10954 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1470 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 11264 PSMs with q<0.01 Iteration 2: Estimated 11271 PSMs with q<0.01 Iteration 3: Estimated 11265 PSMs with q<0.01 Iteration 4: Estimated 11262 PSMs with q<0.01 Iteration 5: Estimated 11266 PSMs with q<0.01 Iteration 6: Estimated 11263 PSMs with q<0.01 Iteration 7: Estimated 11261 PSMs with q<0.01 Iteration 8: Estimated 11262 PSMs with q<0.01 Iteration 9: Estimated 11261 PSMs with q<0.01 Iteration 10: Estimated 11267 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 -0.4636 -0.4800 -0.5728 abs_ppm -0.2128 -0.1708 -0.1379 isotope_errors -1.5474 -1.0219 -0.7123 log10_evalue 0.1618 0.1494 0.7359 hyperscore 0.5087 0.8092 0.8570 delta_hyperscore 3.2407 3.6895 3.3893 matched_ion_num -1.4568 -1.5537 -1.5215 complementary_ions 0.0958 0.0565 0.2447 ion_series 0.0196 0.0426 -0.0138 weighted_average_abs_fragment_ppm -0.0126 -0.0039 -0.0425 length_7 0.0042 0.0269 0.0333 length_8 -0.0103 -0.0545 -0.0475 length_9_30 0.0491 0.1129 0.1614 length_31 0.0000 0.0000 0.0000 ntt -0.1345 -0.1694 -0.1139 nmc 0.0000 0.0000 0.0000 charge_1 0.0734 0.0815 0.1321 charge_2 0.0550 -0.0251 -0.0102 charge_3 -0.2737 -0.1074 -0.2210 charge_4 0.0481 -0.0055 -0.0395 charge_5 -0.0108 -0.0219 -0.0479 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 -0.0460 0.0136 0.0344 15.9949M 0.2559 0.2953 0.2642 304.20715n^ 3.2811 3.3237 3.3822 m0 Found 11227 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 14188 target PSMs and 2718 decoy PSMs. Calculating q values. Final list yields 11232 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 1.4170 cpu seconds or 1 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6.pin Protein decoy-prefix used is _ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F6_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F6_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F6.pin Started Wed Dec 20 10:21:28 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F6.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 11659 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 9261 positives and 2398 negatives, size ratio=3.86197 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 3938 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 3962 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 3927 training set positives with q<0.01 in that direction. Found 5883 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1070 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 6497 PSMs with q<0.01 Iteration 2: Estimated 6570 PSMs with q<0.01 Iteration 3: Estimated 6576 PSMs with q<0.01 Iteration 4: Estimated 6600 PSMs with q<0.01 Iteration 5: Estimated 6605 PSMs with q<0.01 Iteration 6: Estimated 6608 PSMs with q<0.01 Iteration 7: Estimated 6617 PSMs with q<0.01 Iteration 8: Estimated 6620 PSMs with q<0.01 Iteration 9: Estimated 6618 PSMs with q<0.01 Iteration 10: Estimated 6614 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -1.0251 -0.9437 -0.6602 abs_ppm -0.2039 -0.2995 -0.2891 isotope_errors -1.5500 -1.1368 -1.7443 log10_evalue 0.7946 1.1651 1.0743 hyperscore 0.8894 0.9430 0.7364 delta_hyperscore 3.3459 3.0377 2.6586 matched_ion_num -1.9018 -1.8484 -1.7427 complementary_ions 0.3459 0.2541 0.4030 ion_series 0.1038 0.1117 0.1584 weighted_average_abs_fragment_ppm 0.0200 0.0783 0.0260 length_7 -0.0897 -0.1177 0.0469 length_8 0.0642 -0.0243 -0.0183 length_9_30 -0.0710 0.2411 -0.2155 length_31 0.0000 0.0000 0.0000 ntt 0.0349 0.0368 -0.0149 nmc 0.0000 0.0000 0.0000 charge_1 0.1071 0.0570 0.0522 charge_2 -0.0062 0.0340 0.0318 charge_3 -0.1451 -0.0989 -0.1064 charge_4 -0.1619 -0.2030 -0.1633 charge_5 -0.0876 -0.1490 -0.0951 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 0.1114 0.1530 0.1423 15.9949M 0.9276 0.8096 0.3069 304.20715n^ 2.1139 2.0796 2.2936 m0 Found 6485 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 9261 target PSMs and 2398 decoy PSMs. Calculating q values. Final list yields 6486 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 1.3040 cpu seconds or 2 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_20231218041621_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_20231218041621.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F8_20231218041621_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F8_20231218041621.pin Started Wed Dec 20 10:21:30 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F8_20231218041621.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 22751 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 19160 positives and 3591 negatives, size ratio=5.33556 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 9671 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 9782 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 9610 training set positives with q<0.01 in that direction. Found 14403 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.1880 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 15170 PSMs with q<0.01 Iteration 2: Estimated 15243 PSMs with q<0.01 Iteration 3: Estimated 15265 PSMs with q<0.01 Iteration 4: Estimated 15272 PSMs with q<0.01 Iteration 5: Estimated 15281 PSMs with q<0.01 Iteration 6: Estimated 15275 PSMs with q<0.01 Iteration 7: Estimated 15273 PSMs with q<0.01 Iteration 8: Estimated 15270 PSMs with q<0.01 Iteration 9: Estimated 15274 PSMs with q<0.01 Iteration 10: Estimated 15275 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 -0.9882 -0.7928 -0.9784 abs_ppm -0.2712 -0.2473 -0.2936 isotope_errors -0.8126 -1.3207 -0.9064 log10_evalue 2.1515 1.4265 1.7892 hyperscore 0.9094 0.7937 0.7911 delta_hyperscore 2.3488 1.8576 1.8001 matched_ion_num -1.2938 -0.9350 -0.9534 complementary_ions -0.1696 0.0054 -0.0363 ion_series -0.0246 -0.0001 0.0083 weighted_average_abs_fragment_ppm 0.0774 0.0653 0.0311 length_7 0.0715 0.0334 0.0482 length_8 -0.0387 -0.0193 -0.0674 length_9_30 -0.1163 -0.0895 0.0276 length_31 0.0000 0.0000 0.0000 ntt 0.1105 0.0113 0.0717 nmc 0.0000 0.0000 0.0000 charge_1 0.0575 0.0036 0.0670 charge_2 0.1237 0.0932 0.0954 charge_3 0.0219 0.0393 0.0359 charge_4 -0.2543 -0.1517 -0.2460 charge_5 -0.2119 -0.1784 -0.1981 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 0.1733 0.1355 0.1647 15.9949M 0.1215 0.0755 0.0960 304.20715n^ 3.2737 3.0143 2.7535 m0 Found 15236 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 19160 target PSMs and 3591 decoy PSMs. Calculating q values. Final list yields 15236 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 4.0160 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F2_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F2.pin Started Wed Dec 20 10:21:34 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F2.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 35636 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 30219 positives and 5417 negatives, size ratio=5.57855 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 16393 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 16365 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 16280 training set positives with q<0.01 in that direction. Found 24443 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2780 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 24748 PSMs with q<0.01 Iteration 2: Estimated 24759 PSMs with q<0.01 Iteration 3: Estimated 24754 PSMs with q<0.01 Iteration 4: Estimated 24756 PSMs with q<0.01 Iteration 5: Estimated 24756 PSMs with q<0.01 Iteration 6: Estimated 24760 PSMs with q<0.01 Iteration 7: Estimated 24762 PSMs with q<0.01 Iteration 8: Estimated 24763 PSMs with q<0.01 Iteration 9: Estimated 24764 PSMs with q<0.01 Iteration 10: Estimated 24764 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 -0.2299 -0.2286 -0.1979 abs_ppm -0.0786 -0.0937 -0.1173 isotope_errors -1.4014 -1.6022 -1.5607 log10_evalue 0.4137 0.4303 0.4438 hyperscore 0.7890 1.3808 0.6505 delta_hyperscore 1.5560 2.6939 1.4204 matched_ion_num -0.7403 -1.2844 -0.6423 complementary_ions 0.8006 0.5094 0.8201 ion_series -0.0118 -0.0422 -0.0299 weighted_average_abs_fragment_ppm 0.0847 0.1321 0.0695 length_7 0.0589 0.0568 0.1076 length_8 -0.0334 -0.0956 -0.0520 length_9_30 -0.1732 -0.1049 -0.1788 length_31 0.0000 0.0000 0.0000 ntt -0.0351 -0.0258 0.0279 nmc 0.0000 0.0000 0.0000 charge_1 -0.0417 -0.0731 -0.0986 charge_2 0.0845 0.1105 0.0653 charge_3 0.0085 0.0077 0.0310 charge_4 -0.1756 -0.1591 0.0265 charge_5 0.0174 0.0186 0.0061 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 0.0228 0.0317 0.0303 15.9949M 0.1220 0.1422 0.1102 304.20715n^ 3.3553 4.3702 3.3444 m0 Found 24738 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 30219 target PSMs and 5417 decoy PSMs. Calculating q values. Final list yields 24739 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 5.6950 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_20231217185728_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_20231217185728.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 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: E:\Science\fragpipe21\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 2023Dec_37_F5_20231217185728_percolator_target_psms.tsv --decoy-results-psms 2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 2023Dec_37_F5_20231217185728.pin Started Wed Dec 20 10:21:41 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 2023Dec_37_F5_20231217185728.pin Features: rank abs_ppm isotope_errors 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 304.20715n^ Found 34276 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 28208 positives and 6068 negatives, size ratio=4.64865 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 14511 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 14503 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 14185 training set positives with q<0.01 in that direction. Found 21472 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2760 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 22001 PSMs with q<0.01 Iteration 2: Estimated 21995 PSMs with q<0.01 Iteration 3: Estimated 21999 PSMs with q<0.01 Iteration 4: Estimated 22001 PSMs with q<0.01 Iteration 5: Estimated 22001 PSMs with q<0.01 Iteration 6: Estimated 21996 PSMs with q<0.01 Iteration 7: Estimated 22004 PSMs with q<0.01 Iteration 8: Estimated 21996 PSMs with q<0.01 Iteration 9: Estimated 21998 PSMs with q<0.01 Iteration 10: Estimated 22000 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 -0.2845 -0.3489 -0.3508 abs_ppm -0.1650 -0.1494 -0.1668 isotope_errors -1.0702 -1.5207 -1.6399 log10_evalue 1.1092 0.9470 1.4859 hyperscore 0.9748 1.2881 1.0503 delta_hyperscore 1.9386 3.0903 2.0367 matched_ion_num -1.0861 -1.6310 -1.4332 complementary_ions 0.5287 0.3240 0.5592 ion_series 0.0068 0.0703 -0.0242 weighted_average_abs_fragment_ppm 0.1194 0.1687 0.1703 length_7 0.0179 0.0609 0.0515 length_8 -0.0742 -0.1033 -0.1165 length_9_30 -0.0634 -0.1454 -0.1055 length_31 0.0000 0.0000 0.0000 ntt 0.0790 -0.0249 0.0988 nmc 0.0000 0.0000 0.0000 charge_1 -0.0521 -0.0479 -0.0442 charge_2 0.1627 0.1455 0.1557 charge_3 -0.0165 0.0327 0.0653 charge_4 -0.1851 -0.2861 -0.2839 charge_5 -0.1355 -0.0400 -0.2469 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 0.1641 0.1690 0.1778 15.9949M 0.1669 0.2764 0.2175 304.20715n^ 2.9570 3.8328 3.5523 m0 Found 21963 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 28208 target PSMs and 6068 decoy PSMs. Calculating q values. Final list yields 21963 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.8930 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6_20231217215108.pin 2023Dec_37_F6_20231217215108 2023Dec_37_F6_20231217215108_percolator_target_psms.tsv 2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv interact-2023Dec_37_F6_20231217215108 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6_C.pin 2023Dec_37_F6_C 2023Dec_37_F6_C_percolator_target_psms.tsv 2023Dec_37_F6_C_percolator_decoy_psms.tsv interact-2023Dec_37_F6_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5.pin 2023Dec_37_F5 2023Dec_37_F5_percolator_target_psms.tsv 2023Dec_37_F5_percolator_decoy_psms.tsv interact-2023Dec_37_F5 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2_C.pin 2023Dec_37_F2_C 2023Dec_37_F2_C_percolator_target_psms.tsv 2023Dec_37_F2_C_percolator_decoy_psms.tsv interact-2023Dec_37_F2_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2_20231217093831.pin 2023Dec_37_F2_20231217093831 2023Dec_37_F2_20231217093831_percolator_target_psms.tsv 2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv interact-2023Dec_37_F2_20231217093831 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1.pin 2023Dec_37_F1 2023Dec_37_F1_percolator_target_psms.tsv 2023Dec_37_F1_percolator_decoy_psms.tsv interact-2023Dec_37_F1 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3_20231217123213.pin 2023Dec_37_F3_20231217123213 2023Dec_37_F3_20231217123213_percolator_target_psms.tsv 2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv interact-2023Dec_37_F3_20231217123213 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7_C.pin 2023Dec_37_F7_C 2023Dec_37_F7_C_percolator_target_psms.tsv 2023Dec_37_F7_C_percolator_decoy_psms.tsv interact-2023Dec_37_F7_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8.pin 2023Dec_37_F8 2023Dec_37_F8_percolator_target_psms.tsv 2023Dec_37_F8_percolator_decoy_psms.tsv interact-2023Dec_37_F8 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3_C.pin 2023Dec_37_F3_C 2023Dec_37_F3_C_percolator_target_psms.tsv 2023Dec_37_F3_C_percolator_decoy_psms.tsv interact-2023Dec_37_F3_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4.pin 2023Dec_37_F4 2023Dec_37_F4_percolator_target_psms.tsv 2023Dec_37_F4_percolator_decoy_psms.tsv interact-2023Dec_37_F4 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8_C.pin 2023Dec_37_F8_C 2023Dec_37_F8_C_percolator_target_psms.tsv 2023Dec_37_F8_C_percolator_decoy_psms.tsv interact-2023Dec_37_F8_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7.pin 2023Dec_37_F7 2023Dec_37_F7_percolator_target_psms.tsv 2023Dec_37_F7_percolator_decoy_psms.tsv interact-2023Dec_37_F7 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4_20231217160346.pin 2023Dec_37_F4_20231217160346 2023Dec_37_F4_20231217160346_percolator_target_psms.tsv 2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv interact-2023Dec_37_F4_20231217160346 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F4_C.pin 2023Dec_37_F4_C 2023Dec_37_F4_C_percolator_target_psms.tsv 2023Dec_37_F4_C_percolator_decoy_psms.tsv interact-2023Dec_37_F4_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1_20231217064450.pin 2023Dec_37_F1_20231217064450 2023Dec_37_F1_20231217064450_percolator_target_psms.tsv 2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv interact-2023Dec_37_F1_20231217064450 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F7_20231218012240.pin 2023Dec_37_F7_20231218012240 2023Dec_37_F7_20231218012240_percolator_target_psms.tsv 2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv interact-2023Dec_37_F7_20231218012240 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F3.pin 2023Dec_37_F3 2023Dec_37_F3_percolator_target_psms.tsv 2023Dec_37_F3_percolator_decoy_psms.tsv interact-2023Dec_37_F3 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5_C.pin 2023Dec_37_F5_C 2023Dec_37_F5_C_percolator_target_psms.tsv 2023Dec_37_F5_C_percolator_decoy_psms.tsv interact-2023Dec_37_F5_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F1_C.pin 2023Dec_37_F1_C 2023Dec_37_F1_C_percolator_target_psms.tsv 2023Dec_37_F1_C_percolator_decoy_psms.tsv interact-2023Dec_37_F1_C DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F6.pin 2023Dec_37_F6 2023Dec_37_F6_percolator_target_psms.tsv 2023Dec_37_F6_percolator_decoy_psms.tsv interact-2023Dec_37_F6 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F8_20231218041621.pin 2023Dec_37_F8_20231218041621 2023Dec_37_F8_20231218041621_percolator_target_psms.tsv 2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv interact-2023Dec_37_F8_20231218041621 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F2.pin 2023Dec_37_F2 2023Dec_37_F2_percolator_target_psms.tsv 2023Dec_37_F2_percolator_decoy_psms.tsv interact-2023Dec_37_F2 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 2023Dec_37_F5_20231217185728.pin 2023Dec_37_F5_20231217185728 2023Dec_37_F5_20231217185728_percolator_target_psms.tsv 2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv interact-2023Dec_37_F5_20231217185728 DDA 0.5 E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp E:\Science\fragpipe21\jre\bin\java.exe -cp E:\Science\fragpipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\Data\Peter\TPCA\filelist_proteinprophet.txt INFO[10:22:31] Executing ProteinProphet v5.1.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F1.pep.xml... ...read in 0 1+, 7577 2+, 11417 3+, 2617 4+, 276 5+, 41 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F2.pep.xml... ...read in 0 1+, 8224 2+, 12416 3+, 3522 4+, 518 5+, 65 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F3.pep.xml... ...read in 0 1+, 7586 2+, 12493 3+, 3754 4+, 603 5+, 82 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F4.pep.xml... ...read in 0 1+, 7172 2+, 12053 3+, 3744 4+, 676 5+, 131 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F5.pep.xml... ...read in 0 1+, 6662 2+, 11528 3+, 3192 4+, 594 5+, 89 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F6.pep.xml... ...read in 0 1+, 3745 2+, 3015 3+, 457 4+, 51 5+, 5 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F7.pep.xml... ...read in 0 1+, 4602 2+, 7397 3+, 1618 4+, 197 5+, 26 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F8.pep.xml... ...read in 0 1+, 3549 2+, 5064 3+, 1090 4+, 148 5+, 19 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F1_20231217064450.pep.xml... ...read in 0 1+, 8096 2+, 11640 3+, 2850 4+, 387 5+, 52 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F2_20231217093831.pep.xml... ...read in 0 1+, 8304 2+, 12684 3+, 3764 4+, 553 5+, 80 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F3_20231217123213.pep.xml... ...read in 0 1+, 7507 2+, 12394 3+, 3636 4+, 533 5+, 77 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F4_20231217160346.pep.xml... ...read in 0 1+, 6569 2+, 12053 3+, 3954 4+, 795 5+, 166 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F5_20231217185728.pep.xml... ...read in 0 1+, 6120 2+, 11899 3+, 3498 4+, 587 5+, 86 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F6_20231217215108.pep.xml... ...read in 0 1+, 4945 2+, 3697 3+, 538 4+, 55 5+, 5 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F7_20231218012240.pep.xml... ...read in 0 1+, 4694 2+, 8475 3+, 2276 4+, 365 5+, 58 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F8_20231218041621.pep.xml... ...read in 0 1+, 3906 2+, 7868 3+, 3257 4+, 640 5+, 96 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F1_C.pep.xml... ...read in 0 1+, 4957 2+, 5520 3+, 811 4+, 109 5+, 31 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F2_C.pep.xml... ...read in 0 1+, 6318 2+, 9075 3+, 2091 4+, 246 5+, 39 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F3_C.pep.xml... ...read in 0 1+, 7471 2+, 11722 3+, 3209 4+, 457 5+, 68 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F4_C.pep.xml... ...read in 0 1+, 7903 2+, 12587 3+, 3993 4+, 635 5+, 105 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F5_C.pep.xml... ...read in 0 1+, 7462 2+, 12729 3+, 4376 4+, 729 5+, 124 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F6_C.pep.xml... ...read in 0 1+, 6917 2+, 11975 3+, 4064 4+, 843 5+, 190 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F7_C.pep.xml... ...read in 0 1+, 7979 2+, 6169 3+, 698 4+, 53 5+, 7 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F8_C.pep.xml... ...read in 0 1+, 3607 2+, 3000 3+, 559 4+, 82 5+, 17 6+, 0 7+ spectra with min prob 0.5 Initializing 140649 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q16881|TRXR1_HUMAN : U MGUCGAQLISAGSRKTVSLTTFVEACVPHIGITSDLQKKTLGCKLAAAFGQTVEGANPGLVHFGVVRENDKTNCIIKAYCKNNDRSPITWELPWFYSHYVEINEEGFKEVAKEESLGCAGYELPTFVTTPVNEYDCKVTSGAYLRQALLRGAQIAVPTLEVKDELIDGIAYIYPVNTQEEDTVPIKGTKENIKVGVTELGIKRTCADRGIALMVTNYEGEIIEESNTSQAVVRLRGPTGAEIQEVKIPVFQRIFKIGHEEMHEGIKNAMDQDFGRLLISRVMVTVDLGIGALFGACELAVYSAGVVLTKGPCYPLSFLDDSSICEYKDGPIGLYRPREGTAILFREASYIKEKGKNNTAKIRHPGIFQGYANEYVVKKERLAVRYGWNLSGIHNQVAEIMRDWDHKVTEEVKWGYNRSDQLAQGLLAAQHMLKKPICGVNVCTGGLGWRTGLPTPTVFDLVMVKKGYQAAEKAAALGGSGGGIIILDYDYSKPLDEPGNMKLLKQLRGEQYAKLTPGHGGIKRQKVFVVPLDTEAALESLTGELARGDETQDLELVFYPVCLSKFLKKVETCRTCTSRSFIVVSHGDIYAQLLARSDATATSTFGAPNEPLTKGPHHDKASRRRGDGNKGKTQLETPAAAAVAKGEACG ...9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U MGUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTVEGANPGLIHFGIVRDHDFKNCIIKAYCTNNERGAVTWELPWFLTHYIELNEKKYVEIAKEESLGCCGYELPTFVTTPVNIYDCKELSAGFLRQALLKGSQIAVPTLEPKDELIDGVAYVYPVNTQEVDNVPIKGSKENIKVGIKELGIKRTCSDRGIALLVTNYVGEITETGETSKALVKLKGPSGKELQQVMVPIFKRLFKVGHQEMYSGVKEAMEQDFGRLLISRVMVTVDLGFGALFGACELAVYSAGVVLTKGPCYPLSFLDDSITCYEKDGQIGLYRPREGTAIVFQAATYYTEQGKKNTAKIKHHEVFEGYSNVYAVAKERLSLRYGWNLSSIHNQIAKTMTEWNHRVQQNYEWGFKRSDCLAQGLLAAQHMLKKPICGVNVCTGGLGWSTGQPSPVVFDLVMVKKGLIAAEKACSLGGSGGGIIILDYDYALDEQLLKQLLGSQYAQFTQDCGGVHVKNVFINPVTKQNTIESLVEQVRAGDDVQDLELVNCEVGLSSFLEKVRTSHPCYSKSFIVVRSREILGVLHRRLEERAESSRSPGPSSLRARRGPPSLVRAGRVHGSRRNPADGAKGPGPSQPPSRE ........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry rev_sp|Q8WWX9|SELM_HUMAN : U MLDAHDSTEEPPKAPAWVYEPPVQADPAAKRYFGLEQVLANIEERTMESLPIRELEEYRRGLLVLEPDAGPLKHMVLNHYFPIDQTVFAKVEKLRNLQUGGCTEVRARTLGSLRNWDPRYATAATAPAVLAALLLLLALPPLLLS .........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q92813|IOD2_HUMAN : UU MGALRTKKURKSFNKELWHRVEQLNYSFPGKGGLYAIKQRQVICVREFAVGYAINANNDMRDAVVRCQPPLSFRELLQQAAACRDEQNQHKKVEFSLSSDGPIAWGDSPHAEDIYVLLFDAVSSFEEVLKRFAPLQTSFPPUTASGFNVVLPREPSAFDLLHCTAGEAIKEQTGNGSNDGGETSSVHVVSSNPADEGLKVQKYADLLFSKWVCRLGESTLMRRWEGRTSKSRSLLLVVHKLLIVSDYLALFLCNSFFVPLIQLTILLDVSLIG ..:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U MSSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTLNVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVA ........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 ......WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI ...:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA .........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF .........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P62341|SELT_HUMAN : U MRLLLLLLVAASAMVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS :........WARNING: Found the following zero-mass residues in protein entry sp|P63302|SELW_HUMAN : U MALAVRVVYCGAUGYKSKYLQLKKKLEDEFPGRLDICGEGTPQATGFFEVMVAGKLIHSKKKGDGYVDTESKFLKLVAAIKAALAQG .:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U MERSPPQSPGPGKAGDAPNRRSGHVRGARVLSPPGRRARLSSPGPSRSSEAREELRRHLVGLIERSRVVIFSKSYCPHSTRVKELFSSLGVECNVLELDQVDDGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQAYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAKEAAILGKKVMVLDFVVPSPQGTSWGLGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIKATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMVQQLEKGSPGKLKVLAKSTEGTETIEGVYNTVLLAIGRDSCTRKIGLEKIGVKINEKSGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLEIYHTLFWPLEWTVAGRENNTCYAKIICNKFDHDRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG ........:.........:.........:.........33000 .........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS .....:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:WARNING: Found the following zero-mass residues in protein entry sp|Q8WWX9|SELM_HUMAN : U MSLLLPPLALLLLLAALVAPATAATAYRPDWNRLSGLTRARVETCGGUQLNRLKEVKAFVTQDIPFYHNLVMKHLPGADPELVLLGRRYEELERIPLSEMTREEINALVQELGFYRKAAPDAQVPPEYVWAPAKPPEETSDHADL .........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q99611|SPS2_HUMAN : U MAEASATGACGEAMAAAEGSSGPAGLTLGRSFSNYRPFEPQALGLSPSWRLTGFSGMKGUGCKVPQEALLKLLAGLTRPDVRPPLGRGLVGGQEEASQEAGLPAGAGPSPTFPALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATAAVLAPDSSNASSEPSS ......:.........37000 .WARNING: Found the following zero-mass residues in protein entry sp|Q9BQE4|SELS_HUMAN : U MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGUG ........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS ........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL .......:.........:.........38000 .........:.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG .:.........:.........:.........39000 .........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP ........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6D0|SELK_HUMAN : U MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR .........:.........:.........:...... Total: 41464 Computing degenerate peptides for 13146 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 13483 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=6.14537e-05, db_size=45923674 Computing MU for 13483 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[10:23:01] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate E:\Data\_FASTA\2023-11-08-decoys-2023_11_08_UP000005640_CON.fasta.fas --prefix rev_ INFO[10:23:02] Executing Database v5.1.0 INFO[10:23:02] Annotating the database INFO[10:23:02] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --razor INFO[10:23:02] Executing Filter v5.1.0 INFO[10:23:02] Processing peptide identification files INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F1.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F8.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F2.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F5.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F6.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F7.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F3.pep.xml INFO[10:23:02] Parsing E:\Data\Peter\TPCA\2023Dec_37_01\interact-2023Dec_37_F4.pep.xml INFO[10:23:04] 1+ Charge profile decoy=0 target=0 INFO[10:23:04] 2+ Charge profile decoy=689 target=48428 INFO[10:23:04] 3+ Charge profile decoy=751 target=74632 INFO[10:23:04] 4+ Charge profile decoy=140 target=19854 INFO[10:23:04] 5+ Charge profile decoy=25 target=3038 INFO[10:23:04] 6+ Charge profile decoy=7 target=451 INFO[10:23:04] Database search results ions=87771 peptides=53734 psms=148015 INFO[10:23:04] Converged to 1.00 % FDR with 146066 PSMs decoy=1460 threshold=0.534014 total=147526 INFO[10:23:04] Converged to 1.00 % FDR with 51166 Peptides decoy=511 threshold=0.78049 total=51677 INFO[10:23:04] Converged to 1.00 % FDR with 85381 Ions decoy=853 threshold=0.667835 total=86234 INFO[10:23:04] Protein inference results decoy=2943 target=9633 INFO[10:23:04] Converged to 0.99 % FDR with 7284 Proteins decoy=72 threshold=0.9844 total=7356 INFO[10:23:05] Applying sequential FDR estimation ions=85486 peptides=51596 psms=145372 INFO[10:23:05] Converged to 0.07 % FDR with 145266 PSMs decoy=106 threshold=0.534149 total=145372 INFO[10:23:05] Converged to 0.11 % FDR with 51539 Peptides decoy=57 threshold=0.535497 total=51596 INFO[10:23:05] Converged to 0.08 % FDR with 85414 Ions decoy=72 threshold=0.534753 total=85486 INFO[10:23:05] Post processing identifications INFO[10:23:06] Assigning protein identifications to layers INFO[10:23:17] Processing protein inference INFO[10:23:17] Synchronizing PSMs and proteins INFO[10:23:18] Final report numbers after FDR filtering, and post-processing ions=85411 peptides=51537 proteins=6493 psms=145263 INFO[10:23:18] Saving INFO[10:23:18] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_02 --dbbin E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --probin E:\Data\Peter\TPCA\2023Dec_37_01 --razor INFO[10:23:18] Executing Filter v5.1.0 INFO[10:23:18] Fetching protein inference from E:\Data\Peter\TPCA\2023Dec_37_01 INFO[10:23:18] Processing peptide identification files INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F8_20231218041621.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F1_20231217064450.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F3_20231217123213.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F5_20231217185728.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F7_20231218012240.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F6_20231217215108.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F4_20231217160346.pep.xml INFO[10:23:18] Parsing E:\Data\Peter\TPCA\2023Dec_37_02\interact-2023Dec_37_F2_20231217093831.pep.xml INFO[10:23:21] 1+ Charge profile decoy=0 target=0 INFO[10:23:21] 2+ Charge profile decoy=739 target=49402 INFO[10:23:21] 3+ Charge profile decoy=753 target=79957 INFO[10:23:21] 4+ Charge profile decoy=201 target=23572 INFO[10:23:21] 5+ Charge profile decoy=18 target=3897 INFO[10:23:21] 6+ Charge profile decoy=8 target=612 INFO[10:23:21] Database search results ions=94359 peptides=59036 psms=159159 INFO[10:23:21] Converged to 1.00 % FDR with 157157 PSMs decoy=1571 threshold=0.5291 total=158728 INFO[10:23:21] Converged to 1.00 % FDR with 56396 Peptides decoy=563 threshold=0.785874 total=56959 INFO[10:23:21] Converged to 1.00 % FDR with 91925 Ions decoy=919 threshold=0.665668 total=92844 INFO[10:23:21] Protein inference results decoy=2943 target=9633 INFO[10:23:21] Converged to 0.99 % FDR with 7284 Proteins decoy=72 threshold=0.9844 total=7356 INFO[10:23:21] Applying sequential FDR estimation ions=91956 peptides=56783 psms=156374 INFO[10:23:21] Converged to 0.07 % FDR with 156259 PSMs decoy=115 threshold=0.5291 total=156374 INFO[10:23:21] Converged to 0.12 % FDR with 56717 Peptides decoy=66 threshold=0.529304 total=56783 INFO[10:23:21] Converged to 0.09 % FDR with 91877 Ions decoy=79 threshold=0.529304 total=91956 INFO[10:23:21] Post processing identifications INFO[10:23:22] Assigning protein identifications to layers INFO[10:23:34] Processing protein inference INFO[10:23:35] Synchronizing PSMs and proteins INFO[10:23:35] Final report numbers after FDR filtering, and post-processing ions=91873 peptides=56714 proteins=6685 psms=156254 INFO[10:23:35] Saving INFO[10:23:36] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\Data\Peter\TPCA\2023Dec_37_03 --dbbin E:\Data\Peter\TPCA\2023Dec_37_01 --protxml E:\Data\Peter\TPCA\combined.prot.xml --probin E:\Data\Peter\TPCA\2023Dec_37_01 --razor INFO[10:23:36] Executing Filter v5.1.0 INFO[10:23:36] Fetching protein inference from E:\Data\Peter\TPCA\2023Dec_37_01 INFO[10:23:36] Processing peptide identification files INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F8_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F1_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F3_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F2_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F4_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F6_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F5_C.pep.xml INFO[10:23:36] Parsing E:\Data\Peter\TPCA\2023Dec_37_03\interact-2023Dec_37_F7_C.pep.xml INFO[10:23:38] 1+ Charge profile decoy=0 target=0 INFO[10:23:38] 2+ Charge profile decoy=715 target=51899 INFO[10:23:38] 3+ Charge profile decoy=705 target=72072 INFO[10:23:38] 4+ Charge profile decoy=128 target=19673 INFO[10:23:38] 5+ Charge profile decoy=13 target=3141 INFO[10:23:38] 6+ Charge profile decoy=7 target=574 INFO[10:23:38] Database search results ions=90074 peptides=55280 psms=148927 INFO[10:23:38] Converged to 1.00 % FDR with 147163 PSMs decoy=1471 threshold=0.51858 total=148634 INFO[10:23:38] Converged to 1.00 % FDR with 53030 Peptides decoy=530 threshold=0.744963 total=53560 INFO[10:23:38] Converged to 1.00 % FDR with 87935 Ions decoy=879 threshold=0.639046 total=88814 INFO[10:23:38] Protein inference results decoy=2943 target=9633 INFO[10:23:38] Converged to 0.99 % FDR with 7284 Proteins decoy=72 threshold=0.9844 total=7356 INFO[10:23:39] Applying sequential FDR estimation ions=87958 peptides=53322 psms=146473 INFO[10:23:39] Converged to 0.07 % FDR with 146373 PSMs decoy=100 threshold=0.518614 total=146473 INFO[10:23:39] Converged to 0.10 % FDR with 53267 Peptides decoy=55 threshold=0.518614 total=53322 INFO[10:23:39] Converged to 0.08 % FDR with 87889 Ions decoy=69 threshold=0.518614 total=87958 INFO[10:23:39] Post processing identifications INFO[10:23:40] Assigning protein identifications to layers INFO[10:23:51] Processing protein inference INFO[10:23:52] Synchronizing PSMs and proteins INFO[10:23:52] Final report numbers after FDR filtering, and post-processing ions=87887 peptides=53266 proteins=6518 psms=146366 INFO[10:23:52] Saving INFO[10:23:53] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[10:23:53] Executing Report v5.1.0 INFO[10:23:53] Creating reports INFO[10:23:54] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[10:23:54] Executing Report v5.1.0 INFO[10:23:54] Creating reports INFO[10:23:55] Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report INFO[10:23:55] Executing Report v5.1.0 INFO[10:23:55] Creating reports INFO[10:23:57] Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:23:57] Executing Workspace v5.1.0 INFO[10:23:57] Removing workspace INFO[10:23:57] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_02] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:23:57] Executing Workspace v5.1.0 INFO[10:23:57] Removing workspace INFO[10:23:57] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_03] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:23:57] Executing Workspace v5.1.0 INFO[10:23:57] Removing workspace INFO[10:23:57] Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: E:\Data\Peter\TPCA\2023Dec_37_01] E:\Science\fragpipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[10:23:57] Executing Workspace v5.1.0 INFO[10:23:57] Removing workspace INFO[10:23:57] Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -Dlibs.bruker.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\thermo -cp E:\Science\fragpipe21\tools\jfreechart-1.5.3.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar;E:\Science\fragpipe21\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 31 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist E:\Data\Peter\TPCA\filelist_ionquant.txt --modlist E:\Data\Peter\TPCA\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 106 GB memory 2023-12-20 10:23:58 [INFO] - Collecting variable modifications from all psm.tsv files... 2023-12-20 10:23:58 [INFO] - Loading and indexing all psm.tsv files... 2023-12-20 10:23:59 [INFO] - Collecting all compensation voltages if applicable... 2023-12-20 10:24:07 [INFO] - Parameters: 2023-12-20 10:24:07 [INFO] - perform-ms1quant = 1 2023-12-20 10:24:07 [INFO] - perform-isoquant = 0 2023-12-20 10:24:07 [INFO] - isotol = 20.0 2023-12-20 10:24:07 [INFO] - isolevel = 2 2023-12-20 10:24:07 [INFO] - isotype = tmt10 2023-12-20 10:24:07 [INFO] - site-reports = 0 2023-12-20 10:24:07 [INFO] - threads = 31 2023-12-20 10:24:07 [INFO] - mztol = 10.0 2023-12-20 10:24:07 [INFO] - rttol = 1.0 2023-12-20 10:24:07 [INFO] - imtol = 0.05 2023-12-20 10:24:07 [INFO] - minisotopes = 1 2023-12-20 10:24:07 [INFO] - minscans = 1 2023-12-20 10:24:07 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_01\psm.tsv 2023-12-20 10:24:07 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_02\psm.tsv 2023-12-20 10:24:07 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_03\psm.tsv 2023-12-20 10:24:07 [INFO] - multidir = E:\Data\Peter\TPCA\.\ 2023-12-20 10:24:07 [INFO] - excludemods = 2023-12-20 10:24:07 [INFO] - minions = 1 2023-12-20 10:24:07 [INFO] - maxlfq = 0 2023-12-20 10:24:07 [INFO] - ibaq = 0 2023-12-20 10:24:07 [INFO] - normalization = 0 2023-12-20 10:24:07 [INFO] - minexps = 1 2023-12-20 10:24:07 [INFO] - minfreq = 0.0 2023-12-20 10:24:07 [INFO] - tp = 0 2023-12-20 10:24:07 [INFO] - mbr = 0 2023-12-20 10:24:07 [INFO] - mbrrttol = 1.0 2023-12-20 10:24:07 [INFO] - mbrimtol = 0.05 2023-12-20 10:24:07 [INFO] - mbrtoprun = 10 2023-12-20 10:24:07 [INFO] - mbrmincorr = 0.0 2023-12-20 10:24:07 [INFO] - ionmobility = 0 2023-12-20 10:24:07 [INFO] - ionfdr = 0.01 2023-12-20 10:24:07 [INFO] - peptidefdr = 1.0 2023-12-20 10:24:07 [INFO] - proteinfdr = 1.0 2023-12-20 10:24:07 [INFO] - light = 2023-12-20 10:24:07 [INFO] - medium = 2023-12-20 10:24:07 [INFO] - heavy = 2023-12-20 10:24:07 [INFO] - requantify = 0 2023-12-20 10:24:07 [INFO] - writeindex = 0 2023-12-20 10:24:07 [INFO] - locprob = 0.0 2023-12-20 10:24:07 [INFO] - uniqueness = 0 2023-12-20 10:24:07 [INFO] - filelist = E:\Data\Peter\TPCA\filelist_ionquant.txt 2023-12-20 10:24:07 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_01 2023-12-20 10:24:07 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_02 2023-12-20 10:24:07 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_03 2023-12-20 10:24:07 [INFO] - modlist = E:\Data\Peter\TPCA\modmasses_ionquant.txt 2023-12-20 10:24:07 [INFO] - mod masses: 2023-12-20 10:24:07 [INFO] - 15.9949 2023-12-20 10:24:07 [INFO] - 42.0106 2023-12-20 10:24:07 [INFO] - 57.02146 2023-12-20 10:24:07 [INFO] - 304.20715 2023-12-20 10:24:07 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2023-12-20 10:24:07 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw... 2023-12-20 10:24:13 [INFO] - Building index... 2023-12-20 10:24:13 [INFO] - Quantifying... 2023-12-20 10:24:13 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F1_20231217064450.raw... 2023-12-20 10:24:18 [INFO] - Building index... 2023-12-20 10:24:19 [INFO] - Quantifying... 2023-12-20 10:24:19 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F1_C.raw... 2023-12-20 10:24:25 [INFO] - Building index... 2023-12-20 10:24:25 [INFO] - Quantifying... 2023-12-20 10:24:25 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F2.raw... 2023-12-20 10:24:30 [INFO] - Building index... 2023-12-20 10:24:30 [INFO] - Quantifying... 2023-12-20 10:24:30 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F2_20231217093831.raw... 2023-12-20 10:24:35 [INFO] - Building index... 2023-12-20 10:24:35 [INFO] - Quantifying... 2023-12-20 10:24:35 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F2_C.raw... 2023-12-20 10:24:41 [INFO] - Building index... 2023-12-20 10:24:41 [INFO] - Quantifying... 2023-12-20 10:24:41 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F3.raw... 2023-12-20 10:24:46 [INFO] - Building index... 2023-12-20 10:24:46 [INFO] - Quantifying... 2023-12-20 10:24:46 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F3_20231217123213.raw... 2023-12-20 10:24:51 [INFO] - Building index... 2023-12-20 10:24:51 [INFO] - Quantifying... 2023-12-20 10:24:51 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F3_C.raw... 2023-12-20 10:24:56 [INFO] - Building index... 2023-12-20 10:24:56 [INFO] - Quantifying... 2023-12-20 10:24:56 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F4.raw... 2023-12-20 10:25:01 [INFO] - Building index... 2023-12-20 10:25:01 [INFO] - Quantifying... 2023-12-20 10:25:01 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F4_20231217160346.raw... 2023-12-20 10:25:06 [INFO] - Building index... 2023-12-20 10:25:06 [INFO] - Quantifying... 2023-12-20 10:25:06 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F4_C.raw... 2023-12-20 10:25:11 [INFO] - Building index... 2023-12-20 10:25:11 [INFO] - Quantifying... 2023-12-20 10:25:11 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F5.raw... 2023-12-20 10:25:16 [INFO] - Building index... 2023-12-20 10:25:16 [INFO] - Quantifying... 2023-12-20 10:25:16 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F5_20231217185728.raw... 2023-12-20 10:25:21 [INFO] - Building index... 2023-12-20 10:25:21 [INFO] - Quantifying... 2023-12-20 10:25:21 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F5_C.raw... 2023-12-20 10:25:26 [INFO] - Building index... 2023-12-20 10:25:26 [INFO] - Quantifying... 2023-12-20 10:25:26 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F6.raw... 2023-12-20 10:25:31 [INFO] - Building index... 2023-12-20 10:25:31 [INFO] - Quantifying... 2023-12-20 10:25:31 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F6_20231217215108.raw... 2023-12-20 10:25:36 [INFO] - Building index... 2023-12-20 10:25:36 [INFO] - Quantifying... 2023-12-20 10:25:36 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F6_C.raw... 2023-12-20 10:25:41 [INFO] - Building index... 2023-12-20 10:25:42 [INFO] - Quantifying... 2023-12-20 10:25:42 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F7.raw... 2023-12-20 10:25:47 [INFO] - Building index... 2023-12-20 10:25:47 [INFO] - Quantifying... 2023-12-20 10:25:47 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F7_20231218012240.raw... 2023-12-20 10:25:52 [INFO] - Building index... 2023-12-20 10:25:52 [INFO] - Quantifying... 2023-12-20 10:25:52 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F7_C.raw... 2023-12-20 10:25:57 [INFO] - Building index... 2023-12-20 10:25:57 [INFO] - Quantifying... 2023-12-20 10:25:57 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F8.raw... 2023-12-20 10:26:03 [INFO] - Building index... 2023-12-20 10:26:03 [INFO] - Quantifying... 2023-12-20 10:26:03 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_02\2023Dec_37_F8_20231218041621.raw... 2023-12-20 10:26:09 [INFO] - Building index... 2023-12-20 10:26:09 [INFO] - Quantifying... 2023-12-20 10:26:09 [INFO] - Loading E:\Data\Peter\TPCA\2023Dec_37_03\2023Dec_37_F8_C.raw... 2023-12-20 10:26:15 [INFO] - Building index... 2023-12-20 10:26:15 [INFO] - Quantifying... 2023-12-20 10:26:15 [INFO] - Updating Philosopher's tables... 2023-12-20 10:26:20 [INFO] - Combining experiments and estimating protein intensity... 2023-12-20 10:26:26 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 IonQuant [Work dir: E:\Data\Peter\TPCA] E:\Science\fragpipe21\jre\bin\java.exe -Xmx106G -Dlibs.bruker.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=E:\Science\fragpipe21\tools\MSFragger-4.0\ext\thermo -cp E:\Science\fragpipe21\tools\jfreechart-1.5.3.jar;E:\Science\fragpipe21\tools\batmass-io-1.30.0.jar;E:\Science\fragpipe21\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 31 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --annotation E:\Data\Peter\TPCA\2023Dec_37_01\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_01\Rep_01_annotation.txt --annotation E:\Data\Peter\TPCA\2023Dec_37_02\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_02\Rep02_annotation.txt --annotation E:\Data\Peter\TPCA\2023Dec_37_03\psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_03\Rep03_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --multidir . --filelist E:\Data\Peter\TPCA\filelist_ionquant.txt --modlist E:\Data\Peter\TPCA\modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 106 GB memory 2023-12-20 10:26:26 [INFO] - Collecting variable modifications from all psm.tsv files... 2023-12-20 10:26:27 [INFO] - Loading and indexing all psm.tsv files... 2023-12-20 10:26:28 [INFO] - Collecting all compensation voltages if applicable... 2023-12-20 10:26:35 [INFO] - Parameters: 2023-12-20 10:26:35 [INFO] - perform-ms1quant = 0 2023-12-20 10:26:35 [INFO] - perform-isoquant = 1 2023-12-20 10:26:35 [INFO] - isotol = 20.0 2023-12-20 10:26:35 [INFO] - isolevel = 2 2023-12-20 10:26:35 [INFO] - isotype = tmt-16 2023-12-20 10:26:35 [INFO] - annotation = 2023Dec_37_02/psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_02\Rep02_annotation.txt 2023-12-20 10:26:35 [INFO] - annotation = 2023Dec_37_01/psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_01\Rep_01_annotation.txt 2023-12-20 10:26:35 [INFO] - annotation = 2023Dec_37_03/psm.tsv=E:\Data\Peter\TPCA\2023Dec_37_03\Rep03_annotation.txt 2023-12-20 10:26:35 [INFO] - site-reports = 0 2023-12-20 10:26:35 [INFO] - threads = 31 2023-12-20 10:26:35 [INFO] - mztol = 10.0 2023-12-20 10:26:35 [INFO] - rttol = 1.0 2023-12-20 10:26:35 [INFO] - imtol = 0.05 2023-12-20 10:26:35 [INFO] - minisotopes = 1 2023-12-20 10:26:35 [INFO] - minscans = 1 2023-12-20 10:26:35 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_01\psm.tsv 2023-12-20 10:26:35 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_02\psm.tsv 2023-12-20 10:26:35 [INFO] - psm = E:\Data\Peter\TPCA\2023Dec_37_03\psm.tsv 2023-12-20 10:26:35 [INFO] - multidir = E:\Data\Peter\TPCA\.\ 2023-12-20 10:26:35 [INFO] - excludemods = 2023-12-20 10:26:35 [INFO] - minions = 1 2023-12-20 10:26:35 [INFO] - maxlfq = 0 2023-12-20 10:26:35 [INFO] - ibaq = 0 2023-12-20 10:26:35 [INFO] - normalization = 0 2023-12-20 10:26:35 [INFO] - minexps = 1 2023-12-20 10:26:35 [INFO] - minfreq = 0.0 2023-12-20 10:26:35 [INFO] - tp = 0 2023-12-20 10:26:35 [INFO] - mbr = 0 2023-12-20 10:26:35 [INFO] - mbrrttol = 1.0 2023-12-20 10:26:35 [INFO] - mbrimtol = 0.05 2023-12-20 10:26:35 [INFO] - mbrtoprun = 10 2023-12-20 10:26:35 [INFO] - mbrmincorr = 0.0 2023-12-20 10:26:35 [INFO] - ionmobility = 0 2023-12-20 10:26:35 [INFO] - ionfdr = 0.01 2023-12-20 10:26:35 [INFO] - peptidefdr = 1.0 2023-12-20 10:26:35 [INFO] - proteinfdr = 1.0 2023-12-20 10:26:35 [INFO] - light = 2023-12-20 10:26:35 [INFO] - medium = 2023-12-20 10:26:35 [INFO] - heavy = 2023-12-20 10:26:35 [INFO] - requantify = 0 2023-12-20 10:26:35 [INFO] - writeindex = 0 2023-12-20 10:26:35 [INFO] - locprob = 0.0 2023-12-20 10:26:35 [INFO] - uniqueness = 0 2023-12-20 10:26:35 [INFO] - filelist = E:\Data\Peter\TPCA\filelist_ionquant.txt 2023-12-20 10:26:35 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_01 2023-12-20 10:26:35 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_02 2023-12-20 10:26:35 [INFO] - specdir = E:\Data\Peter\TPCA\2023Dec_37_03 2023-12-20 10:26:35 [INFO] - modlist = E:\Data\Peter\TPCA\modmasses_ionquant.txt 2023-12-20 10:26:35 [INFO] - mod masses: 2023-12-20 10:26:35 [INFO] - 15.9949 2023-12-20 10:26:35 [INFO] - 42.0106 2023-12-20 10:26:35 [INFO] - 57.02146 2023-12-20 10:26:35 [INFO] - 304.20715 2023-12-20 10:26:35 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2023-12-20 10:26:35 [INFO] - Loading and quantifying E:\Data\Peter\TPCA\2023Dec_37_01\2023Dec_37_F1.raw... java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 42724 at m.(Unknown Source) at p.(Unknown Source) at ionquant.IonQuant.main(Unknown Source) 2023-12-20 10:26:39 [ERROR] - Index -1 out of bounds for length 42724 Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 2 remaining tasks