System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: N/A Version info: FragPipe version 22.0 MSFragger version 4.1 IonQuant version 1.10.27 diaTracer version 1.1.5 Philosopher version 5.1.1 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML DIA 25 commands to execute: CheckCentroid C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx15G -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML 21 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\4ab410d1-0518-411a-9ee8-56a72e7e8696 MSFragger [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\fragger_dia.params C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pepXML MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pepXML MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pepXML MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pepXML MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pepXML MSFragger move pin C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin MSBooster [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx15G -cp C:\Research_Software\fragpipe_v22\tools\MSBooster-1.2.39.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\msbooster_params.txt Percolator [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 21 --results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv --decoy-results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CSP-0030_S01_HSS-C18-1mm-DIA-1_edited.pin Percolator: Convert to pepxml [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CSP-0030_S01_HSS-C18-1mm-DIA-1.pin CSP-0030_S01_HSS-C18-1mm-DIA-1 CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv interact-CSP-0030_S01_HSS-C18-1mm-DIA-1 DIA 0.7 C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv ProteinProphet [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --minPepLen 8 --tag rev_ --pepxml C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 --protxml C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\combined.prot.xml --razor PhilosopherReport [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe report WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck SpecLibGen [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Users\morga\AppData\Local\Programs\Python\Python39\python.exe -u C:\Research_Software\fragpipe_v22\tools\speclib\gen_con_spec_lib.py C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 unused C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 True unused use_easypqp noiRT;noIM 21 "--unimod C:/Research_Software/fragpipe_v22/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_speclibgen.txt DIA-NN [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 21 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_diann.txt DIA-NN [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf DIA-NN: Propagate information [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\diann-output] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar;C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\diann-output] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\commons-io-2.15.1.jar;C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\psm.tsv 0.01 1 0.01 0.01 C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\fragpipe-files.fp-manifest ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [CheckCentroid], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [WorkspaceCleanInit], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [MSFragger], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [MSBooster], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [Percolator], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [ProteinProphet], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [PhilosopherDbAnnotate], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [PhilosopherFilter], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [PhilosopherReport], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [WorkspaceClean], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [SpecLibGen], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] Cmd: [DIA-NN], Work dir: [C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas~~~~~~~ >PIERCE_88320 >rev_sp|O43818|U3IP2_HUMAN U3 small nucleolar RNA-interacting protein 2 OS=Homo sapiens OX=9606 GN=RRP9 PE=1 SV=1 >rev_sp|P0DPA2|VSIG8_HUMAN V-set and immunoglobulin domain-containing protein 8 OS=Homo sapiens OX=9606 GN=VSIG8 PE=2 SV=1 >rev_sp|P49915|GUAA_HUMAN GMP synthase [glutamine-hydrolyzing] OS=Homo sapiens OX=9606 GN=GMPS PE=1 SV=1 >rev_sp|Q14296|FASTK_HUMAN Fas-activated serine/threonine kinase OS=Homo sapiens OX=9606 GN=FASTK PE=1 SV=1 >rev_sp|Q6B9Z1|IGFL4_HUMAN Insulin growth factor-like family member 4 OS=Homo sapiens OX=9606 GN=IGFL4 PE=2 SV=1 >rev_sp|Q8IWZ5|TRI42_HUMAN Tripartite motif-containing protein 42 OS=Homo sapiens OX=9606 GN=TRIM42 PE=1 SV=2 >rev_sp|Q8WWB7|GLMP_HUMAN Glycosylated lysosomal membrane protein OS=Homo sapiens OX=9606 GN=GLMP PE=1 SV=1 >rev_sp|Q9BRX2|PELO_HUMAN Protein pelota homolog OS=Homo sapiens OX=9606 GN=PELO PE=1 SV=2 >rev_sp|Q9NVE7|PANK4_HUMAN 4'-phosphopantetheine phosphatase OS=Homo sapiens OX=9606 GN=PANK4 PE=1 SV=1 >rev_sp|Q9Y6Z4|KIAS1_HUMAN Putative uncharacterized protein KIF25-AS1 OS=Homo sapiens OX=9606 GN=KIF25-AS1 PE=5 SV=2 >sp|O43790|KRT86_HUMAN Keratin, type II cuticular Hb6 OS=Homo sapiens OX=9606 GN=KRT86 PE=1 SV=1 >sp|P0DP42|T225B_HUMAN Transmembrane protein 225B OS=Homo sapiens OX=9606 GN=TMEM225B PE=1 SV=1 >sp|P49888|ST1E1_HUMAN Sulfotransferase 1E1 OS=Homo sapiens OX=9606 GN=SULT1E1 PE=1 SV=1 >sp|Q14244|MAP7_HUMAN Ensconsin OS=Homo sapiens OX=9606 GN=MAP7 PE=1 SV=1 >sp|Q6AWC2|WWC2_HUMAN Protein WWC2 OS=Homo sapiens OX=9606 GN=WWC2 PE=1 SV=2 >sp|Q8IWW8|HOT_HUMAN Hydroxyacid-oxoacid transhydrogenase, mitochondrial OS=Homo sapiens OX=9606 GN=ADHFE1 PE=1 SV=1 >sp|Q8WW38|FOG2_HUMAN Zinc finger protein ZFPM2 OS=Homo sapiens OX=9606 GN=ZFPM2 PE=1 SV=3 >sp|Q9BRT2|UQCC2_HUMAN Ubiquinol-cytochrome-c reductase complex assembly factor 2 OS=Homo sapiens OX=9606 GN=UQCC2 PE=1 SV=1 >sp|Q9NVA1|UQCC1_HUMAN Ubiquinol-cytochrome-c reductase complex assembly factor 1 OS=Homo sapiens OX=9606 GN=UQCC1 PE=1 SV=3 >sp|Q9Y6X5|ENPP4_HUMAN Bis(5'-adenosyl)-triphosphatase ENPP4 OS=Homo sapiens OX=9606 GN=ENPP4 PE=1 SV=3 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v22.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=C\:\\MSData_WorkDirectory\\fasta\\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas Table.editor=166.10938 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=true diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\Research_Software\\fragpipe_v22\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-python=C\:\\Users\\morga\\AppData\\Local\\Programs\\Python\\Python39\\python.exe fragpipe-config.tools-folder=C\:\\Research_Software\\fragpipe_v22\\lib\\..\\tools freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=1 ionquant.minisotopes=1 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.find-best-rt-model=false msbooster.find-best-spectra-model=false msbooster.koina-url= msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=true msbooster.spectra-model=DIA-NN msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=1 msfragger.allowed_missed_cleavage_2=1 msfragger.analyzer_types=all msfragger.calibrate_mass=2 msfragger.check_spectral_files=false msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 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=custom msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=2 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KRBJ msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=nonspecific msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 136.10916,B ,true,-1; 166.10938,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,1; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 0.0,site_06,false,1; 0.0,site_07,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=500 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=--no-terminate --post-processing-tdc --subset-max-train 500000 percolator.keep-tsv-files=false percolator.min-prob=0.7 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--picked --prot 0.01 --minPepLen 8 phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=true 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.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=25 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=12.5 ptmshepherd.diagmine_fragMinSpecDiff=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true ptmshepherd.iterloc_maxEpoch=100 ptmshepherd.iterloc_mode=false ptmshepherd.localization_allowed_res= ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.print_full_glyco_params=false ptmshepherd.prob_mass=0.5 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 skyline.run-skyline=false skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-mode=0 skyline.skyline-mods-mode=Default speclibgen.convert-pepxml=true speclibgen.convert-psm=false speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.ignore_unannotated=true speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=true tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.philosopher-msstats=false tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=C\:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx15G -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML 21 Done in 2.9 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="15:18:18" level=info msg="Executing Workspace v5.1.1" time="15:18:18" level=info msg="Removing workspace" time="15:18:18" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\4ab410d1-0518-411a-9ee8-56a72e7e8696 time="15:18:18" level=info msg="Executing Workspace v5.1.1" time="15:18:18" level=info msg="Creating workspace" time="15:18:18" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\fragger_dia.params C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 15 GB memory Checking database... ***********************************FIRST SEARCH************************************ Parameters: num_threads = 21 database_name = C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 10.0 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 = nonspecific search_enzyme_sense_1 = C search_enzyme_cut_1 = KRBJ search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 1 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 500 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 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 = 0 variable_mod_01 = 15.9949 M 1 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 136.10916 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 = 166.10938 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 145264900 fragments to be searched in 1 slices (2.16 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.42 s 001. CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML 6.5 s | deisotoping 10.8 s [progress: 37924/37924 (100%) - 10698 spectra/s] 3.5s | postprocessing 0.3 s ***************************FIRST SEARCH DONE IN 0.417 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 2.99 1.88 | 0.11 1.43 | -0.32 1.35 | -0.12 1.22 -----|---------------|---------------|---------------|--------------- New fragment_mass_tolerance = 5.000000 PPM New precursor_true_tolerance = 6.000000 PPM ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.155 MIN********* ************************************MAIN SEARCH************************************ Checking database... data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Parameters: num_threads = 21 database_name = C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas decoy_prefix = rev_ precursor_mass_lower = isolation window lower precursor_mass_upper = isolation window upper precursor_mass_units = isolation window data_type = 1 precursor_true_tolerance = 6.0 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 = 0 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 = nonspecific search_enzyme_sense_1 = C search_enzyme_cut_1 = KRBJ search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 1 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 = 5 output_max_expect = 1.7976931348623157E308 report_alternative_proteins = 1 override_charge = 1 precursor_charge_low = 2 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 500 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = isolation window 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 = 0 variable_mod_01 = 15.9949 M 1 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 136.10916 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 = 166.10938 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.02 Da. 145264900 fragments to be searched in 1 slices (2.16 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.05 s 001. CSP-0030_S01_HSS-C18-1mm-DIA-1.mzBIN_calibrated 0.7 s [progress: 37924/37924 (100%) - 1647 spectra/s] 23.0s Building spectral index for the mzBIN_calibrated file 9.4 s Rescoring with peak tracing 11.1 s Picking top PSMs for each precursor 0.8 s Rescoring 2.3 s Writing results 2.9 s ***************************MAIN SEARCH DONE IN 1.146 MIN*************************** *******************************TOTAL TIME 1.718 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pepXML C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx15G -cp C:\Research_Software\fragpipe_v22\tools\MSBooster-1.2.39.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\msbooster_params.txt 2024-07-24 15:20:05 [INFO] - MSBooster v1.2.39 2024-07-24 15:20:05 [INFO] - Using 21 threads 2024-07-24 15:20:05 [INFO] - Initializing C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML 2024-07-24 15:20:07 [INFO] - Instrument detected: QE 2024-07-24 15:20:07 [INFO] - Fragmentation type detected: HCD 2024-07-24 15:20:07 [INFO] - NCE detected: 27.0 2024-07-24 15:20:07 [INFO] - Creating input file for createFull 2024-07-24 15:20:08 [INFO] - 79976 PSMs for prediction 2024-07-24 15:20:08 [INFO] - createFull input file generation took 886 milliseconds 2024-07-24 15:20:08 [INFO] - Input file at C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\spectraRT_full.tsv 2024-07-24 15:20:08 [INFO] - Generating input file for DIA-NN 2024-07-24 15:20:08 [INFO] - Creating input file for Diann 2024-07-24 15:20:08 [INFO] - 79976 PSMs for prediction 2024-07-24 15:20:08 [INFO] - Writing DIA-NN input file 2024-07-24 15:20:08 [INFO] - Diann input file generation took 309 milliseconds 2024-07-24 15:20:08 [INFO] - Input file at C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\spectraRT.tsv 2024-07-24 15:20:08 [INFO] - Generating DIA-NN predictions 2024-07-24 15:20:08 [INFO] - C:\Research_Software\fragpipe_v22\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\spectraRT.tsv --predict --threads 21 --strip-unknown-mods --predict-n-frag 100 2024-07-24 15:20:09 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) 2024-07-24 15:20:09 [INFO] - Compiled on Sep 15 2022 18:28:57 2024-07-24 15:20:09 [INFO] - Current date and time: Wed Jul 24 15:20:09 2024 2024-07-24 15:20:09 [INFO] - CPU: GenuineIntel Intel(R) Core(TM) Ultra 9 185H 2024-07-24 15:20:09 [INFO] - SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 2024-07-24 15:20:09 [INFO] - Logical CPU cores: 22 2024-07-24 15:20:09 [INFO] - Predicted spectra will be saved in a binary format 2024-07-24 15:20:09 [INFO] - Thread number set to 21 2024-07-24 15:20:09 [INFO] - DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option 2024-07-24 15:20:09 [INFO] - Deep learning predictor will predict 100 fragments 2024-07-24 15:20:09 [INFO] - 2024-07-24 15:20:09 [INFO] - 0 files will be processed 2024-07-24 15:20:09 [INFO] - [0:00] Loading spectral library C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\spectraRT.tsv 2024-07-24 15:20:09 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2024-07-24 15:20:09 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 79976 precursors in 76366 elution groups. 2024-07-24 15:20:09 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction 2024-07-24 15:20:09 [INFO] - [0:00] Predicting spectra and IMs 2024-07-24 15:20:26 [INFO] - [0:17] Predicting RTs 2024-07-24 15:20:32 [INFO] - [0:23] Decoding predicted spectra and IMs 2024-07-24 15:20:34 [INFO] - [0:24] Decoding RTs 2024-07-24 15:20:34 [INFO] - [0:24] Saving the list of predictions to C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\spectraRT.predicted.bin 2024-07-24 15:20:34 [INFO] - Finished 2024-07-24 15:20:34 [INFO] - Done generating DIA-NN predictions 2024-07-24 15:20:34 [INFO] - Model running took 25555 milliseconds 2024-07-24 15:20:34 [INFO] - Generating edited pin with following features: [predRTrealUnits, unweightedSpectralEntropy, deltaRTLOESS] 2024-07-24 15:20:34 [INFO] - Loading predicted spectra 2024-07-24 15:20:36 [INFO] - Merging libraries 2024-07-24 15:20:36 [INFO] - Processing pin C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin 2024-07-24 15:20:36 [INFO] - C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.pin has 86574 PSMs 2024-07-24 15:20:36 [INFO] - Processing C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-24 15:20:41 [INFO] - RT regression using 2446 PSMs Iteration 1...2...3...4...5... 2024-07-24 15:20:43 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.082 2024-07-24 15:20:44 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-24 15:20:45 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-24 15:20:46 [INFO] - Edited pin file at C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_edited.pin 2024-07-24 15:20:48 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 13806 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 21 --results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv --decoy-results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CSP-0030_S01_HSS-C18-1mm-DIA-1_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:07:48 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 21 --results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv --decoy-results-peptides CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CSP-0030_S01_HSS-C18-1mm-DIA-1_edited.pin Started Wed Jul 24 15:20:48 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CSP-0030_S01_HSS-C18-1mm-DIA-1_edited.pin Features: rank precursor_detected abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more isotopes log10_kl hyperscore matched_ion_num 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 86574 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 50915 positives and 35659 negatives, size ratio=1.42783 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 38 as initial direction. Could separate 4423 training set positives with q<0.01 in that direction. Split 2: Selected feature 38 as initial direction. Could separate 4581 training set positives with q<0.01 in that direction. Split 3: Selected feature 38 as initial direction. Could separate 4702 training set positives with q<0.01 in that direction. Found 6863 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.0830 cpu seconds or 2 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 11832 PSMs with q<0.01 Iteration 2: Estimated 13228 PSMs with q<0.01 Iteration 3: Estimated 13618 PSMs with q<0.01 Iteration 4: Estimated 13738 PSMs with q<0.01 Iteration 5: Estimated 13757 PSMs with q<0.01 Iteration 6: Estimated 13769 PSMs with q<0.01 Iteration 7: Estimated 13776 PSMs with q<0.01 Iteration 8: Estimated 13772 PSMs with q<0.01 Iteration 9: Estimated 13776 PSMs with q<0.01 Iteration 10: Estimated 13776 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.1278 -0.0779 -0.0737 rank 0.0000 0.0000 0.0000 precursor_detected -0.4703 -0.4425 -0.2398 abs_ppm -0.0256 -0.0725 -0.0449 abs_rt_diff -0.2802 -0.3470 -0.1143 complementary_ions -0.2854 -0.3617 -0.2111 ion_series 0.0307 0.0652 0.0303 weighted_average_abs_fragment_ppm -0.1187 -0.1058 -0.1458 weighted_average_fragment_rt_deviation -0.1644 -0.1191 -0.0913 precursor_rt_deviation 0.0000 0.0000 0.0000 isotope_error_negative 0.1175 0.1194 0.0759 isotope_error_0 -0.1175 -0.1194 -0.0759 isotope_error_1 0.0000 0.0000 0.0000 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more 0.3733 0.5078 0.3823 isotopes -0.1811 -0.1482 -0.1549 log10_kl 0.8909 0.6554 0.6871 hyperscore -0.2233 0.0588 -0.2649 matched_ion_num -0.1120 -0.0831 -0.1152 length_7 -0.1237 -0.1243 -0.1210 length_8 0.0848 0.0661 0.0930 length_9_30 0.1080 0.1177 0.0920 length_31 0.0000 0.0000 0.0000 ntt -0.2792 -0.2538 -0.1896 nmc 0.0000 0.0000 0.0000 charge_1 0.1040 0.1162 0.0217 charge_2 -0.0798 -0.1057 -0.1029 charge_3 -0.0279 -0.0134 0.0861 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.0362 -0.0736 -0.0471 15.9949M 0.1370 0.1844 0.0768 pred_RT_real_units 1.8028 2.1297 1.4980 unweighted_spectral_entropy -3.4662 -3.9791 -2.2808 delta_RT_loess -5.7131 -6.6170 -4.6433 m0 Found 13620 test set PSMs with q<0.01. Scoring full list of PSMs with trained SVMs. Features: rank precursor_detected abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more isotopes log10_kl hyperscore matched_ion_num 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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 86574 PSMs Evaluated set contained 50915 positives and 35659 negatives. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 50915 target PSMs and 35659 decoy PSMs. Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. Calculating q values. Final list yields 13441 target peptides with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 9.3340 cpu seconds or 10 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CSP-0030_S01_HSS-C18-1mm-DIA-1.pin CSP-0030_S01_HSS-C18-1mm-DIA-1 CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv interact-CSP-0030_S01_HSS-C18-1mm-DIA-1 DIA 0.7 C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_proteinprophet.txt time="15:21:05" level=info msg="Executing ProteinProphet v5.1.1" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml... ...read in 0 1+, 5863 2+, 3121 3+, 443 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pep.xml... ...read in 0 1+, 1808 2+, 845 3+, 111 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pep.xml... ...read in 0 1+, 692 2+, 310 3+, 56 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pep.xml... ...read in 0 1+, 375 2+, 166 3+, 30 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Reading in C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pep.xml... ...read in 0 1+, 199 2+, 108 3+, 17 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5 Initializing 14144 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas WARNING: Found the following zero-mass residues in protein entry PIERCE_88320 : JJJJJJ SSAAPPPPPJGISNEGQNASIBHVLTSIGEBDIPVPBPBIGDYAGIBTASEFDSAIAQDBSAAGAFGPELSJELGQSGVDTYLQTBGLILVGGYGTJGILFVGSGVSGGEEGAJSFANQPLEVVYSBLTILEELJNGFILDGFPJELASGLSFPVGFBLSSEAPALFQFDLB .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 ......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:...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 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.. Total: 40920 Computing degenerate peptides for 3167 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 3275 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3275 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3275 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3275 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=8.16234e-06, db_size=45657242 Computing MU for 3275 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="15:21:10" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas --prefix rev_ time="15:21:10" level=info msg="Executing Database v5.1.1" time="15:21:10" level=info msg="Annotating the database" time="15:21:10" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --minPepLen 8 --tag rev_ --pepxml C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 --protxml C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\combined.prot.xml --razor time="15:21:10" level=info msg="Executing Filter v5.1.1" time="15:21:10" level=info msg="Processing peptide identification files" time="15:21:10" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pep.xml" time="15:21:10" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pep.xml" time="15:21:10" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml" time="15:21:10" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pep.xml" time="15:21:10" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pep.xml" time="15:21:11" level=info msg="1+ Charge profile" decoy=0 target=0 time="15:21:11" level=info msg="2+ Charge profile" decoy=152 target=8785 time="15:21:11" level=info msg="3+ Charge profile" decoy=87 target=4463 time="15:21:11" level=info msg="4+ Charge profile" decoy=27 target=630 time="15:21:11" level=info msg="5+ Charge profile" decoy=0 target=0 time="15:21:11" level=info msg="6+ Charge profile" decoy=0 target=0 time="15:21:11" level=info msg="Database search results" ions=14139 peptides=12870 psms=14144 time="15:21:11" level=info msg="Converged to 1.00 % FDR with 13441 PSMs" decoy=134 threshold=0.821414 total=13575 time="15:21:11" level=info msg="Converged to 0.99 % FDR with 12167 Peptides" decoy=121 threshold=0.83266 total=12288 time="15:21:11" level=info msg="Converged to 1.00 % FDR with 13436 Ions" decoy=134 threshold=0.821414 total=13570 time="15:21:11" level=info msg="Protein inference results" decoy=273 target=2668 time="15:21:11" level=info msg="Converged to 0.98 % FDR with 1940 Proteins" decoy=19 threshold=0.9555 total=1959 time="15:21:11" level=info msg="2D FDR estimation: Protein mirror image" decoy=1940 target=1940 time="15:21:11" level=info msg="Second filtering results" ions=13425 peptides=12157 psms=13430 time="15:21:11" level=info msg="Converged to 0.31 % FDR with 13388 PSMs" decoy=42 threshold=0.700196 total=13430 time="15:21:11" level=info msg="Converged to 0.35 % FDR with 12115 Peptides" decoy=42 threshold=0.700564 total=12157 time="15:21:11" level=info msg="Converged to 0.31 % FDR with 13383 Ions" decoy=42 threshold=0.700196 total=13425 time="15:21:11" level=info msg="Post processing identifications" time="15:21:12" level=info msg="Assigning protein identifications to layers" time="15:21:13" level=info msg="Processing protein inference" time="15:21:14" level=info msg="Synchronizing PSMs and proteins" time="15:21:14" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=13382 peptides=12114 proteins=1940 psms=13387 time="15:21:14" level=info msg=Saving time="15:21:14" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe report time="15:21:14" level=info msg="Executing Report v5.1.1" time="15:21:14" level=info msg="Creating reports" time="15:21:14" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="15:21:15" level=info msg="Executing Workspace v5.1.1" time="15:21:15" level=info msg="Removing workspace" time="15:21:15" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 SpecLibGen [Work dir: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3] C:\Users\morga\AppData\Local\Programs\Python\Python39\python.exe -u C:\Research_Software\fragpipe_v22\tools\speclib\gen_con_spec_lib.py C:\MSData_WorkDirectory\fasta\2024-07-24-decoys-contam-uniprotkb_proteome_up000005640_AND_revi_2023_10_11_PRTC-C18.fasta.fas C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 unused C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3 True unused use_easypqp noiRT;noIM 21 "--unimod C:/Research_Software/fragpipe_v22/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_speclibgen.txt File list provided Spectral library building Commands to execute: 'C:\Users\morga\AppData\Local\Programs\Python\Python39\Scripts\easypqp.exe' convert --unimod C:/Research_Software/fragpipe_v22/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml'"'"', '"'"'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pep.xml'"'"', '"'"'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pep.xml'"'"', '"'"'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pep.xml'"'"', '"'"'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pep.xml'"'"']' --spectra 'C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\mzml\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML' --exclude-range -1.5,3.5 --psms CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl --peaks CSP-0030_S01_HSS-C18-1mm-DIA-1.peakpkl 'C:\Users\morga\AppData\Local\Programs\Python\Python39\Scripts\easypqp.exe' library --psmtsv 'C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\psm.tsv' --peptidetsv 'C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\peptide.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 'C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\filelist_easypqp_library.txt' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ easypqp, version 0.1.48 Executing ['C:\\Users\\morga\\AppData\\Local\\Programs\\Python\\Python39\\Scripts\\easypqp.exe', 'convert', '--unimod', 'C:/Research_Software/fragpipe_v22/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['C:\\\\MSData_WorkDirectory\\\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\\\fragpipe\\\\DSQ_PRTC_test3\\\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml', 'C:\\\\MSData_WorkDirectory\\\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\\\fragpipe\\\\DSQ_PRTC_test3\\\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pep.xml', 'C:\\\\MSData_WorkDirectory\\\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\\\fragpipe\\\\DSQ_PRTC_test3\\\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pep.xml', 'C:\\\\MSData_WorkDirectory\\\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\\\fragpipe\\\\DSQ_PRTC_test3\\\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pep.xml', 'C:\\\\MSData_WorkDirectory\\\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\\\fragpipe\\\\DSQ_PRTC_test3\\\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pep.xml']", '--spectra', 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\mzml\\CSP-0030_S01_HSS-C18-1mm-DIA-1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl', '--peaks', 'CSP-0030_S01_HSS-C18-1mm-DIA-1.peakpkl'] 2024-07-24 15:21:26 - Info: Converting ['C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml', 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank2.pep.xml', 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank3.pep.xml', 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank4.pep.xml', 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank5.pep.xml']. 2024-07-24 15:21:26 - Info: Parsing run CSP-0030_S01_HSS-C18-1mm-DIA-1. 2024-07-24 15:21:26 - Info: Parsing pepXML: C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\interact-CSP-0030_S01_HSS-C18-1mm-DIA-1_rank1.pep.xml Traceback (most recent call last): File "C:\Users\morga\AppData\Local\Programs\Python\Python39\Scripts\easypqp-script.py", line 33, in sys.exit(load_entry_point('easypqp==0.1.48', 'console_scripts', 'easypqp')()) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1719, in invoke rv.append(sub_ctx.command.invoke(sub_ctx)) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\main.py", line 90, in convert psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 1039, in conversion psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 956, in parse_pepxmls px = pepxml(pepxmlfile, um, base_name, exclude_range, enable_unannotated, enable_massdiff) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 302, in __init__ self.match_unimod(unimod) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 393, in match_unimod self.psms['modified_peptide'] = self.psms[['peptide_sequence','modifications','nterm_modification','cterm_modification','massdiff']].apply(lambda x: match_modifications(unimod, x), axis=1) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\core\frame.py", line 10374, in apply return op.apply().__finalize__(self, method="apply") File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\core\apply.py", line 916, in apply return self.apply_standard() File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\core\apply.py", line 1063, in apply_standard results, res_index = self.apply_series_generator() File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\core\apply.py", line 1081, in apply_series_generator results[i] = self.func(v, *self.args, **self.kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 393, in self.psms['modified_peptide'] = self.psms[['peptide_sequence','modifications','nterm_modification','cterm_modification','massdiff']].apply(lambda x: match_modifications(unimod, x), axis=1) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 345, in match_modifications record_id0 = um.get_id(peptide_sequence[site - 1], positions, modifications[site]) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\convert.py", line 623, in get_id ptms_site = self.ptms[site] KeyError: 'B' Traceback (most recent call last): File "C:\Users\morga\AppData\Local\Programs\Python\Python39\Scripts\easypqp-script.py", line 33, in sys.exit(load_entry_point('easypqp==0.1.48', 'console_scripts', 'easypqp')()) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1719, in invoke rv.append(sub_ctx.command.invoke(sub_ctx)) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\main.py", line 201, in library generate(infiles, outfile, psmtsv, peptidetsv, perform_rt_calibration, rt_referencefile, rt_reference_run_path, rt_filter, perform_im_calibration, im_referencefile, im_reference_run_path, im_filter, psm_fdr_threshold, peptide_fdr_threshold, protein_fdr_threshold, rt_lowess_fraction, rt_psm_fdr_threshold, im_lowess_fraction, im_psm_fdr_threshold, pi0_lambda, peptide_plot_path, protein_plot_path, min_peptides, proteotypic, consensus, nofdr) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\library.py", line 345, in generate psm_tab = pd.read_pickle(psm_file) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\io\pickle.py", line 185, in read_pickle with get_handle( File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\io\common.py", line 882, in get_handle handle = open(handle, ioargs.mode) FileNotFoundError: [Errno 2] No such file or directory: 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl' 2024-07-24 15:21:32 - Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic. 2024-07-24 15:21:32 - Info: Reading file C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl. Not enough peptides could be found for alignment. Using ciRT for alignment Traceback (most recent call last): File "C:\Users\morga\AppData\Local\Programs\Python\Python39\Scripts\easypqp-script.py", line 33, in sys.exit(load_entry_point('easypqp==0.1.48', 'console_scripts', 'easypqp')()) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1719, in invoke rv.append(sub_ctx.command.invoke(sub_ctx)) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\main.py", line 201, in library generate(infiles, outfile, psmtsv, peptidetsv, perform_rt_calibration, rt_referencefile, rt_reference_run_path, rt_filter, perform_im_calibration, im_referencefile, im_reference_run_path, im_filter, psm_fdr_threshold, peptide_fdr_threshold, protein_fdr_threshold, rt_lowess_fraction, rt_psm_fdr_threshold, im_lowess_fraction, im_psm_fdr_threshold, pi0_lambda, peptide_plot_path, protein_plot_path, min_peptides, proteotypic, consensus, nofdr) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\easypqp\library.py", line 345, in generate psm_tab = pd.read_pickle(psm_file) File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\io\pickle.py", line 185, in read_pickle with get_handle( File "C:\Users\morga\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas\io\common.py", line 882, in get_handle handle = open(handle, ioargs.mode) FileNotFoundError: [Errno 2] No such file or directory: 'C:\\MSData_WorkDirectory\\20240716-MWM_CSP-0029_CSP-0030_WashOpt\\fragpipe\\DSQ_PRTC_test3\\CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl' 2024-07-24 15:21:36 - Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic. 2024-07-24 15:21:36 - Info: Reading file C:\MSData_WorkDirectory\20240716-MWM_CSP-0029_CSP-0030_WashOpt\fragpipe\DSQ_PRTC_test3\CSP-0030_S01_HSS-C18-1mm-DIA-1.psmpkl. Library not generated, not enough peptides could be found for alignment. Library not generated, not enough peptides could be found for alignment. Please try using other options for alignment (e.g. ciRT if used other options) Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 5 remaining tasks