System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.4.0 LCMS files: Experiment/Group: - D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d DDA - D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.d DDA - D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.d DDA 28 commands to execute: CheckCentroid C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d 19 WorkspaceCleanInit [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Analysis\AppData\Local\Temp\ee480c31-c33f-4876-a863-eb5a83ff013a MSFragger [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\fragger.params D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.d D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.d MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pepXML MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pepXML MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pepXML MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin MSBooster [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\msbooster-1.1.4.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\smile-core-2.6.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\smile-math-2.6.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" Features.MainClass --paramsList D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\msbooster_params.txt Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2499_edited.pin Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2498_edited.pin Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv --decoy-results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv A220811_mtb_synt_peptides_BG_3ul_17min_2497_edited.pin Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin A220817_mtb_synt_peptides_BG_3ul_17min_2499 A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv interact-A220817_mtb_synt_peptides_BG_3ul_17min_2499 DDA 0.5 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin A220817_mtb_synt_peptides_BG_3ul_17min_2498 A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv interact-A220817_mtb_synt_peptides_BG_3ul_17min_2498 DDA 0.5 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin A220811_mtb_synt_peptides_BG_3ul_17min_2497 A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv interact-A220811_mtb_synt_peptides_BG_3ul_17min_2497 DDA 0.5 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif --protxml D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\combined.prot.xml --razor PhilosopherReport [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [CheckCentroid], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [WorkspaceCleanInit], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [MSFragger], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [MSBooster], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [Percolator], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [ProteinProphet], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [PhilosopherDbAnnotate], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [PhilosopherFilter], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [PhilosopherReport], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] Cmd: [WorkspaceClean], Work dir: [D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas~~~~~~~ >entry_1 >entry_112620 >entry_125244 >entry_137869 >entry_24248 >entry_36872 >entry_49496 >entry_62118 >entry_74742 >entry_87366 >entry_99990 >rev_entry_112611 >rev_entry_125235 >rev_entry_13786 >rev_entry_24239 >rev_entry_36863 >rev_entry_49487 >rev_entry_62109 >rev_entry_74733 >rev_entry_87357 >rev_entry_99981 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v18.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=D\:\\fasta\\2022-08-24-decoys-MTB_140K.fasta.fas AdjustFragIntensity=true BoostComplementaryIon=false CorrThreshold=0 DeltaApex=0.2 ExportPrecursorPeak=false RFmax=500 RPmax=25 RTOverlap=0.3 SE.EstimateBG=false SE.IsoPattern=0.3 SE.MS1PPM=10 SE.MS2PPM=20 SE.MS2SN=1.1 SE.MassDefectFilter=true SE.MassDefectOffset=0.1 SE.NoMissedScan=1 SE.SN=1.1 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.library= diann.q-value=0.01 diann.quantification-strategy=3 diann.run-dia-nn=false diann.run-specific-protein-q-value=0.01 diann.unrelated-runs=false diann.use-predicted-spectra=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fragpipe-config.bin-ionquant=C\:\\User_apps\\Fragpipe\\FragPipe-jre-18.0\\fragpipe\\tools\\IonQuant-1.8.0.jar fragpipe-config.bin-msfragger=C\:\\User_apps\\Fragpipe\\FragPipe-jre-18.0\\fragpipe\\tools\\MSFragger-3.5\\MSFragger-3.5.jar fragpipe-config.bin-philosopher=C\:\\User_apps\\Fragpipe\\FragPipe-jre-18.0\\fragpipe\\tools\\philosopher_v4.4.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\Analysis\\anaconda3.9.12\\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=1 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=100000 ionquant.medium= ionquant.minexps=1 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.proteinquant=2 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=true msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.add_topN_complementary=0 msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.data_type=0 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=27 msfragger.digest_min_length=5 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=1 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=1 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=0 msfragger.report_alternative_proteins=true msfragger.restrict_deltamass_to=all msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name=stricttrypsin msfragger.search_enzyme_name_1=lysn_promisc msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=N msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1 msfragger.table.var-mods=15.994900,M,false,3; 42.010600,[^,false,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,true,1; 10.008269,R,true,1; 6.013809,P,true,1; 3.003745,G,true,1; 57.021400,C,false,2; -17.026500,C,false,2; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=true phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 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.assign_glycans=true ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagextract_mode=false ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIons=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_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=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true 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= ptmshepherd.prob_dhexY= ptmshepherd.prob_neuacOx= ptmshepherd.prob_neugcOx= ptmshepherd.prob_phosphoOx= ptmshepherd.prob_regY= ptmshepherd.prob_sulfoOx= ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-diaumpire=false run-psm-validation=true run-validation-tab=true speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.rt-cal=ciRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false speclibgen.use-easypqp=true speclibgen.use-spectrast=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=6 tmtintegrator.dont-run-fq-lq=false tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=D\:\\220728_mtb_synth_peptides_test_dda\\0_MTB_out\\97-99_140k_Db_max_1_modif workflow.input.data-type.im-ms=true workflow.input.data-type.regular-ms=false workflow.ram=0 workflow.threads=19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d 19 Process 'CheckCentroid' finished, exit code: 0 Done in 0 ms. WorkspaceCleanInit [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[13:08:28] Executing Workspace v4.4.0 INFO[13:08:28] Removing workspace WARN[13:08:28] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[13:08:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Analysis\AppData\Local\Temp\ee480c31-c33f-4876-a863-eb5a83ff013a INFO[13:08:28] Executing Workspace v4.4.0 INFO[13:08:28] Creating workspace INFO[13:08:28] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\fragger.params D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.d D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.d MSFragger version MSFragger-3.5 Batmass-IO version 1.25.5 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 116 GB memory Checking database... Checking spectral files... D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d: Scans = 10537 D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.d: Scans = 10481 D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.d: Scans = 10482 There is a mzBIN file from D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.d converted with timsdata-2-8-7-1. Will use this mzBIN file. ***********************************FIRST SEARCH************************************ Parameters: num_threads = 19 database_name = D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = lysn_promisc search_enzyme_sense_1 = N search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 5 digest_max_length = 27 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_08 = 8.014199 K 1 variable_mod_09 = 10.008269 R 1 variable_mod_10 = 6.013809 P 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 5: 111901 of length 6: 246936 of length 7: 294623 of length 8: 285418 of length 9: 264699 of length 10: 246332 of length 11: 224253 of length 12: 205903 of length 13: 188266 of length 14: 173311 of length 15: 157120 of length 16: 142384 of length 17: 129991 of length 18: 120350 of length 19: 108314 of length 20: 97865 of length 21: 87783 of length 22: 80086 of length 23: 71945 of length 24: 65170 of length 25: 59512 of length 26: 54113 of length 27: 47355 In total 3463630 peptides. Generated 24354955 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 676533124 fragments to be searched in 1 slices (10.08 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.59 s 001. A220811_mtb_synt_peptides_BG_3ul_17min_2497.mzBIN 10.7 s | deisotoping 1.3 s [progress: 51359/51359 (100%) - 15620 spectra/s] 3.3s | postprocessing 0.2 s 002. A220817_mtb_synt_peptides_BG_3ul_17min_2498.mzBIN 6.0 s | deisotoping 0.9 s [progress: 51471/51471 (100%) - 21847 spectra/s] 2.4s | postprocessing 0.2 s 003. A220817_mtb_synt_peptides_BG_3ul_17min_2499.mzBIN 6.2 s | deisotoping 1.0 s [progress: 53528/53528 (100%) - 16425 spectra/s] 3.3s | postprocessing 0.1 s ***************************FIRST SEARCH DONE IN 0.812 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 4.59 4.09 | 0.62 4.09 | 3.21 4.26 | 0.63 4.31 002 | 2.34 3.15 | 1.64 3.15 | 0.42 4.39 | 0.68 4.38 003 | 2.20 3.69 | 1.03 3.69 | 0.28 4.59 | -0.17 4.48 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | 357| 376| 214| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 443| 446| 443| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 514 -------|------- -------|------- Rm P. | 1 -------|------- Count | 518 -------|------- New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.488 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 19 database_name = D:\fasta\2022-08-24-decoys-MTB_140K.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 = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = lysn_promisc search_enzyme_sense_1 = N search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 1 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 1 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 5 digest_max_length = 27 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_08 = 8.014199 K 1 variable_mod_09 = 10.008269 R 1 variable_mod_10 = 6.013809 P 1 variable_mod_11 = 3.003745 G 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 5: 799302 of length 6: 2160651 of length 7: 2890521 of length 8: 2947549 of length 9: 2807184 of length 10: 2636746 of length 11: 2470250 of length 12: 2303467 of length 13: 2142209 of length 14: 1986623 of length 15: 1839134 of length 16: 1700626 of length 17: 1570000 of length 18: 1446032 of length 19: 1328787 of length 20: 1220861 of length 21: 1123400 of length 22: 1032011 of length 23: 949731 of length 24: 874558 of length 25: 805658 of length 26: 741711 of length 27: 683472 In total 38460483 peptides. Generated 194537222 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 5544068164 fragments to be searched in 1 slices (82.61 GB total) Operating on slice 1 of 1: Fragment index slice generated in 40.00 s 001. A220811_mtb_synt_peptides_BG_3ul_17min_2497.mzBIN_calibrated 0.6 s [progress: 50123/50123 (100%) - 2854 spectra/s] 17.6s | ramaping alternative proteins and postprocessing 4.9 s 002. A220817_mtb_synt_peptides_BG_3ul_17min_2498.mzBIN_calibrated 0.6 s [progress: 50137/50137 (100%) - 2773 spectra/s] 18.1s | ramaping alternative proteins and postprocessing 4.0 s 003. A220817_mtb_synt_peptides_BG_3ul_17min_2499.mzBIN_calibrated 0.6 s [progress: 51714/51714 (100%) - 2759 spectra/s] 18.7s | ramaping alternative proteins and postprocessing 4.0 s ***************************MAIN SEARCH DONE IN 2.596 MIN*************************** *******************************TOTAL TIME 5.896 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pepXML D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/User_apps/Fragpipe/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\220728_mtb_synth_peptides_test_dda\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\msbooster-1.1.4.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\smile-core-2.6.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\smile-math-2.6.0.jar;C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" Features.MainClass --paramsList D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\msbooster_params.txt MSBooster v1.1.4 Using 19 threads Generating input file for DIA-NN 109710 unique peptides from 140795 PSMs Writing DIA-NN input file Diann input file generation took 662 milliseconds Input file at D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.tsv 111373 unique peptides from 140795 PSMs createFull input file generation took 461 milliseconds Input file at D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT_full.tsv Generating DIA-NN predictions C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\diann\1.8.1\win\DiaNN.exe --lib D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.tsv --predict --threads 19 --strip-unknown-mods DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Mon Sep 5 13:14:25 2022 CPU: GenuineIntel Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 20 Predicted spectra will be saved in a binary format Thread number set to 19 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option 0 files will be processed [0:00] Loading spectral library D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.tsv [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 109710 precursors in 108444 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:27] Predicting RTs [0:33] Decoding predicted spectra and IMs [0:34] Decoding RTs [0:34] Saving the list of predictions to D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 34386 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing A220811_mtb_synt_peptides_BG_3ul_17min_2497_uncalibrated.mgf RT regression using 5000 PSMs Edited pin file at D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497_edited.pin Processing A220817_mtb_synt_peptides_BG_3ul_17min_2498_uncalibrated.mgf RT regression using 5000 PSMs Edited pin file at D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498_edited.pin Processing A220817_mtb_synt_peptides_BG_3ul_17min_2499_uncalibrated.mgf RT regression using 5000 PSMs Edited pin file at D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499_edited.pin Final parameters used for feature annotation: fragger = D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\fragger.params pinPepXMLDirectory = A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin mzmlDirectory = D:\220728_mtb_synth_peptides_test_dda outputDirectory = D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif editedPin = edited renamePin = 1 spectraRTPredInput = D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.tsv detectPredInput = D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\detect.tsv spectraRTPredFile = D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\spectraRT.predicted.bin detectPredFile = null deletePreds = true predictionTimeLimit = 120 fasta = D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas decoyPrefix = >rev_ cutAfter = KR butNotAfter = P digestMinLength = 5 digestMaxLength = 27 digestMinMass = 500.0 digestMaxMass = 5000.0 numThreads = 19 DiaNN = C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\diann\1.8.1\win\DiaNN.exe spectraRTPredModel = DIA-NN ppmTolerance = 20.0 lowResppmTolerance = 300.0 highResppmTolerance = 20.0 matchWithDaltons = false DaTolerance = 0.05 useSpectra = true useTopFragments = true topFragments = 20 removeRankPeaks = true useBasePeak = true percentBasePeak = 1.0 useRT = true RTregressionSize = 5000 uniformPriorPercentile = 10.0 RTescoreCutoff = 3.1622776E-4 RTbinMultiplier = 1 RTIQR = 50.0 noRTscores = false bandwidth = 0.05 robustIters = 2 useDetect = false useIM = null IMregressionSize = 5000 IMescoreCutoff = 3.1622776E-4 IMbinMultiplier = 100 FragmentationType = HCD NCE = 30 createPredFileOnly = false ignoredFragmentIonTypes = onlyFragmentIonTypes = fragmentIonHierarchy = [immonium, y, b, a, y-NL, b-NL, a-NL, internal, internal-NL, unknown] useMatchedIntensities = false usePredIntensities = false usePeakCounts = false useIndividualSpectralSimilarities = false useIntensitiesDifference = false useIntensityDistributionSimilarity = false features = unweightedSpectralEntropy,deltaRTLOESS useMultipleCorrelatedFeatures = false Done in 11433 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2499_edited.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2499_edited.pin Started Mon Sep 5 13:15:11 2022 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile A220817_mtb_synt_peptides_BG_3ul_17min_2499_edited.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc 10.008269R 3.003745G 6.013809P 8.014199K unweighted_spectral_entropy delta_RT_loess Found 48332 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 26453 positives and 21879 negatives, size ratio=1.20906 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 1179 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 1188 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 1212 training set positives with q<0.01 in that direction. Found 1763 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.6 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 2046 PSMs with q<0.01 Iteration 2: Estimated 2164 PSMs with q<0.01 Iteration 3: Estimated 2198 PSMs with q<0.01 Iteration 4: Estimated 2234 PSMs with q<0.01 Iteration 5: Estimated 2247 PSMs with q<0.01 Iteration 6: Estimated 2255 PSMs with q<0.01 Iteration 7: Estimated 2259 PSMs with q<0.01 Iteration 8: Estimated 2253 PSMs with q<0.01 Iteration 9: Estimated 2259 PSMs with q<0.01 Iteration 10: Estimated 2261 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0064 -0.0738 -0.1189 retentiontime 0.0000 0.0000 0.0000 rank -0.5408 -0.5506 -0.1469 abs_ppm 0.3353 0.1958 0.0523 isotope_errors -2.0589 -2.6043 -2.0134 log10_evalue 4.3320 1.2725 1.6980 hyperscore 0.2927 0.3378 0.4491 delta_hyperscore -4.2602 -1.9216 -2.0810 matched_ion_num -0.4298 -0.9307 -0.4818 complementary_ions 0.0284 0.2689 0.2210 ion_series -0.4048 -0.4525 -0.4272 weighted_average_abs_fragment_ppm 0.4956 0.5631 0.3070 peptide_length 0.5383 0.2977 0.2033 ntt 0.4544 0.1970 0.4712 nmc -0.2900 -0.2065 -0.4840 10.008269R -0.2376 -0.5227 -0.5216 3.003745G -0.9815 -1.1889 -1.0808 6.013809P -0.1262 -0.0951 -0.1883 8.014199K 3.1989 3.1152 2.0858 unweighted_spectral_entropy -0.4597 -0.4480 -0.0954 delta_RT_loess -9.2152 -8.5974 -6.3898 m0 Found 2159 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 26453 target PSMs and 21879 decoy PSMs. Calculating q values. Final list yields 2161 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.334 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2498_edited.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv --decoy-results-psms A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2498_edited.pin Started Mon Sep 5 13:15:16 2022 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile A220817_mtb_synt_peptides_BG_3ul_17min_2498_edited.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc 10.008269R 3.003745G 6.013809P 8.014199K unweighted_spectral_entropy delta_RT_loess Found 46267 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 25442 positives and 20825 negatives, size ratio=1.2217 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 1122 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 1090 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 1118 training set positives with q<0.01 in that direction. Found 1631 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.53 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 1895 PSMs with q<0.01 Iteration 2: Estimated 1997 PSMs with q<0.01 Iteration 3: Estimated 2023 PSMs with q<0.01 Iteration 4: Estimated 2035 PSMs with q<0.01 Iteration 5: Estimated 2034 PSMs with q<0.01 Iteration 6: Estimated 2035 PSMs with q<0.01 Iteration 7: Estimated 2039 PSMs with q<0.01 Iteration 8: Estimated 2038 PSMs with q<0.01 Iteration 9: Estimated 2037 PSMs with q<0.01 Iteration 10: Estimated 2040 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.3317 -0.0399 -0.0333 retentiontime 0.0000 0.0000 0.0000 rank -0.1024 -0.1372 -0.0582 abs_ppm 0.0629 0.0678 0.0360 isotope_errors -1.0663 -0.7850 -0.8131 log10_evalue 0.6911 0.1259 0.2138 hyperscore 0.1147 0.0593 0.2315 delta_hyperscore -0.6167 -0.4443 -0.4466 matched_ion_num -0.3216 -0.0388 -0.0992 complementary_ions 0.0855 0.2056 0.1715 ion_series -0.3556 -0.1452 -0.1455 weighted_average_abs_fragment_ppm 0.4811 0.1967 0.1457 peptide_length 0.1575 0.1533 0.0938 ntt 0.1591 0.0890 0.1690 nmc -0.1164 -0.0718 -0.1161 10.008269R -0.2571 -0.1296 -0.1239 3.003745G -0.3838 -0.2007 -0.2843 6.013809P -0.0290 -0.0651 -0.0024 8.014199K 1.8770 1.0750 0.6871 unweighted_spectral_entropy 0.0669 -0.0412 -0.0422 delta_RT_loess -5.1721 -3.4762 -2.6466 m0 Found 1939 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 25442 target PSMs and 20825 decoy PSMs. Calculating q values. Final list yields 1946 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.008 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv --decoy-results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv A220811_mtb_synt_peptides_BG_3ul_17min_2497_edited.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 19 --results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv --decoy-results-psms A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv A220811_mtb_synt_peptides_BG_3ul_17min_2497_edited.pin Started Mon Sep 5 13:15:20 2022 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile A220811_mtb_synt_peptides_BG_3ul_17min_2497_edited.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc 10.008269R 3.003745G 6.013809P 8.014199K unweighted_spectral_entropy delta_RT_loess Found 46196 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 25460 positives and 20736 negatives, size ratio=1.22782 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 1025 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 1016 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 1019 training set positives with q<0.01 in that direction. Found 1471 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.522 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 1772 PSMs with q<0.01 Iteration 2: Estimated 1835 PSMs with q<0.01 Iteration 3: Estimated 1883 PSMs with q<0.01 Iteration 4: Estimated 1889 PSMs with q<0.01 Iteration 5: Estimated 1899 PSMs with q<0.01 Iteration 6: Estimated 1912 PSMs with q<0.01 Iteration 7: Estimated 1913 PSMs with q<0.01 Iteration 8: Estimated 1921 PSMs with q<0.01 Iteration 9: Estimated 1936 PSMs with q<0.01 Iteration 10: Estimated 1935 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0962 -0.2002 -0.0412 retentiontime 0.0000 0.0000 0.0000 rank 0.2642 0.1751 -0.0631 abs_ppm 0.8755 0.7566 0.1784 isotope_errors -2.5902 -2.7829 -0.7668 log10_evalue -0.9099 -0.9839 0.0603 hyperscore -0.5166 -0.4631 0.1005 delta_hyperscore 0.0692 0.3741 -0.0494 matched_ion_num 0.1218 -0.0255 -0.1666 complementary_ions 0.4356 0.3456 0.1098 ion_series -0.8631 -0.6064 -0.1820 weighted_average_abs_fragment_ppm 1.2007 0.6107 0.2018 peptide_length 0.0878 0.1562 0.0133 ntt 0.5685 0.7249 0.2179 nmc -0.5598 -0.0182 -0.1281 10.008269R -0.6504 -1.0144 -0.1648 3.003745G -0.9194 -0.5801 -0.2273 6.013809P -0.2512 -0.0924 -0.0209 8.014199K 4.1940 3.5786 0.8432 unweighted_spectral_entropy -0.1107 0.4379 -0.0031 delta_RT_loess -10.6349 -9.4552 -2.8468 m0 Found 1834 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 25460 target PSMs and 20736 decoy PSMs. Calculating q values. Final list yields 1834 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 3.066 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220817_mtb_synt_peptides_BG_3ul_17min_2499.pin A220817_mtb_synt_peptides_BG_3ul_17min_2499 A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv interact-A220817_mtb_synt_peptides_BG_3ul_17min_2499 DDA 0.5 Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2499_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220817_mtb_synt_peptides_BG_3ul_17min_2498.pin A220817_mtb_synt_peptides_BG_3ul_17min_2498 A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv interact-A220817_mtb_synt_peptides_BG_3ul_17min_2498 DDA 0.5 Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220817_mtb_synt_peptides_BG_3ul_17min_2498_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML A220811_mtb_synt_peptides_BG_3ul_17min_2497.pin A220811_mtb_synt_peptides_BG_3ul_17min_2497 A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv interact-A220811_mtb_synt_peptides_BG_3ul_17min_2497 DDA 0.5 Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\A220811_mtb_synt_peptides_BG_3ul_17min_2497_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\filelist_proteinprophet.txt INFO[13:15:29] Executing ProteinProphet v4.4.0 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 D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220811_mtb_synt_peptides_BG_3ul_17min_2497.pep.xml... ...read in 56 1+, 2016 2+, 512 3+, 18 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220817_mtb_synt_peptides_BG_3ul_17min_2498.pep.xml... ...read in 78 1+, 1982 2+, 570 3+, 21 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220817_mtb_synt_peptides_BG_3ul_17min_2499.pep.xml... ...read in 79 1+, 2109 2+, 678 3+, 29 4+, 1 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 2256 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........271000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........272000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........273000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........274000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........275000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........276000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........277000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........278000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........279000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........280000 .........:.........:.........:.........:.........:.... Total: 280540 Computing degenerate peptides for 2936 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 3465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=1.20079e-05, db_size=42726070 Computing MU for 3465 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[13:15:32] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate D:\fasta\2022-08-24-decoys-MTB_140K.fasta.fas --prefix rev_ INFO[13:15:32] Executing Database v4.4.0 INFO[13:15:32] Annotating the database INFO[13:15:33] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif --protxml D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\combined.prot.xml --razor INFO[13:15:34] Executing Filter v4.4.0 INFO[13:15:34] Processing peptide identification files INFO[13:15:34] Parsing D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220817_mtb_synt_peptides_BG_3ul_17min_2499.pep.xml INFO[13:15:34] Parsing D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220817_mtb_synt_peptides_BG_3ul_17min_2498.pep.xml INFO[13:15:34] Parsing D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif\interact-A220811_mtb_synt_peptides_BG_3ul_17min_2497.pep.xml INFO[13:15:34] 1+ Charge profile decoy=50 target=163 INFO[13:15:34] 2+ Charge profile decoy=484 target=5623 INFO[13:15:34] 3+ Charge profile decoy=132 target=1628 INFO[13:15:34] 4+ Charge profile decoy=14 target=54 INFO[13:15:34] 5+ Charge profile decoy=0 target=2 INFO[13:15:34] 6+ Charge profile decoy=0 target=0 INFO[13:15:34] Database search results ions=2245 peptides=2075 psms=8150 INFO[13:15:34] Converged to 1.00 % FDR with 5963 PSMs decoy=60 threshold=0.8084 total=6023 INFO[13:15:34] Converged to 0.96 % FDR with 929 Peptides decoy=9 threshold=0.886487 total=938 INFO[13:15:34] Converged to 0.94 % FDR with 1061 Ions decoy=10 threshold=0.879977 total=1071 INFO[13:15:34] Protein inference results decoy=418 target=1089 INFO[13:15:34] Converged to 1.06 % FDR with 473 Proteins decoy=5 threshold=0.9073 total=478 INFO[13:15:34] Applying sequential FDR estimation ions=1104 peptides=973 psms=5894 INFO[13:15:34] Converged to 0.28 % FDR with 5877 PSMs decoy=17 threshold=0.8084 total=5894 INFO[13:15:34] Converged to 0.93 % FDR with 964 Peptides decoy=9 threshold=0.811369 total=973 INFO[13:15:34] Converged to 0.82 % FDR with 1095 Ions decoy=9 threshold=0.811369 total=1104 INFO[13:15:34] Post processing identifications INFO[13:15:35] Assigning protein identifications to layers INFO[13:15:36] Processing protein inference Process 'PhilosopherFilter' finished, exit code: 0 INFO[13:15:39] Synchronizing PSMs and proteins INFO[13:15:39] Total report numbers after FDR filtering, and post-processing ions=938 peptides=822 proteins=411 psms=5238 INFO[13:15:39] Saving INFO[13:15:39] Done PhilosopherReport [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report INFO[13:15:39] Executing Report v4.4.0 INFO[13:15:39] Creating reports INFO[13:15:40] Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: D:\220728_mtb_synth_peptides_test_dda\0_MTB_out\97-99_140k_Db_max_1_modif] C:\User_apps\Fragpipe\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck Process 'WorkspaceClean' finished, exit code: 0 INFO[13:15:40] Executing Workspace v4.4.0 INFO[13:15:40] Removing workspace INFO[13:15:40] Done Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020) (Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Mol Cell Proteomics 20:100018 (2020) (Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007) (Label-free quantification/SILAC) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021) (PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020) (DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015) (DIA-NN) High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe. bioRxiv doi:10.1101/2021.03.08.434385 (2021) =============================================================ALL JOBS DONE IN 7.2 MINUTES=============================================================