System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: 6.0.408 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) - E:\temp\T23090604_cell-DIA\23090604_ABC_K1.raw DIA - E:\temp\T23090604_cell-DIA\23090604_ABC_S1.raw DIA 36 commands to execute: CheckCentroid D:\software\FragPipe\v22.0\jre\bin\java.exe -Xmx17G -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid E:\temp\T23090604_cell-DIA\23090604_ABC_K1.raw 2 WorkspaceCleanInit [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\hqq\AppData\Local\Temp\d973b483-a7c8-48a0-b88a-7829729f266b MSFragger [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx17G D:\software\FragPipe\v22.0\tools\MSFragger-4.1\MSFragger-4.1.jar E:\temp\T23090604_cell-DIA\FP22-K1S1\fragger_dia.params E:\temp\T23090604_cell-DIA\23090604_ABC_K1.raw E:\temp\T23090604_cell-DIA\23090604_ABC_S1.raw MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank1.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank1.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank2.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank2.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank3.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank3.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank4.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank4.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank5.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank5.pepXML MSFragger move pin D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1.pin E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1.pin MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank1.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank1.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank2.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank2.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank3.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank3.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank4.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank4.pepXML MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank5.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank5.pepXML MSFragger move pin D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1.pin E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1.pin MSBooster [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -Xmx17G -cp D:\software\FragPipe\v22.0\tools\MSBooster-1.2.31.jar;D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList E:\temp\T23090604_cell-DIA\FP22-K1S1\msbooster_params.txt Percolator [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\percolator_3_6_5\windows\percolator.exe --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 2 --results-peptides 23090604_ABC_K1_percolator_target_psms.tsv --decoy-results-peptides 23090604_ABC_K1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 23090604_ABC_K1_edited.pin Percolator [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\percolator_3_6_5\windows\percolator.exe --no-terminate --post-processing-tdc --subset-max-train 500000 --num-threads 2 --results-peptides 23090604_ABC_S1_percolator_target_psms.tsv --decoy-results-peptides 23090604_ABC_S1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 23090604_ABC_S1_edited.pin Percolator: Convert to pepxml [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23090604_ABC_K1.pin 23090604_ABC_K1 23090604_ABC_K1_percolator_target_psms.tsv 23090604_ABC_K1_percolator_decoy_psms.tsv interact-23090604_ABC_K1 DIA 0.7 E:\temp\T23090604_cell-DIA\23090604_ABC_K1_uncalibrated.mzML Percolator: Delete temp D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23090604_ABC_S1.pin 23090604_ABC_S1 23090604_ABC_S1_percolator_target_psms.tsv 23090604_ABC_S1_percolator_decoy_psms.tsv interact-23090604_ABC_S1 DIA 0.7 E:\temp\T23090604_cell-DIA\23090604_ABC_S1_uncalibrated.mzML Percolator: Delete temp D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_percolator_decoy_psms.tsv ProteinProphet [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\temp\T23090604_cell-DIA\FP22-K1S1\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe database --annotate E:\database\fasta\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --minPepLen 8 --tag rev_ --pepxml E:\temp\T23090604_cell-DIA\FP22-K1S1 --protxml E:\temp\T23090604_cell-DIA\FP22-K1S1\combined.prot.xml --razor PhilosopherReport [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe report WorkspaceClean [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck SpecLibGen [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\Python\Python39\python -u D:\software\FragPipe\v22.0\tools\speclib\gen_con_spec_lib.py E:\database\fasta\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.fasta.fas E:\temp\T23090604_cell-DIA\FP22-K1S1 unused E:\temp\T23090604_cell-DIA\FP22-K1S1 True unused use_easypqp noiRT;noIM 2 "--unimod D:/software/FragPipe/v22.0/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 E:\temp\T23090604_cell-DIA\FP22-K1S1\filelist_speclibgen.txt DIA-NN [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\MS\DIA-NN\1.9.2\DiaNN.exe --lib library.tsv --threads 2 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --cfg E:\temp\T23090604_cell-DIA\FP22-K1S1\filelist_diann.txt DIA-NN [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\MS\DIA-NN\1.9.2\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf DIA-NN move speclib for skyline D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\FP22-K1S1\library.tsv.speclib E:\temp\T23090604_cell-DIA\FP22-K1S1\diann-output\report.tsv.speclib DIA-NN: Propagate information [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1\diann-output] D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar;D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation E:\temp\T23090604_cell-DIA\FP22-K1S1 Skyline [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -Xmx17G -cp D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar;D:\software\FragPipe\v22.0\lib\commons-lang3-3.14.0.jar;D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;D:\software\FragPipe\v22.0\lib\maven-artifact-3.9.6.jar;D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.skyline.Skyline D:\software\FragPipe\v22.0\tools\SkylineRunner.exe E:\temp\T23090604_cell-DIA\FP22-K1S1 23.1.0.455 0 0 ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [CheckCentroid], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [WorkspaceCleanInit], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [MSFragger], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [MSBooster], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [Percolator], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [ProteinProphet], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [PhilosopherDbAnnotate], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [PhilosopherFilter], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [PhilosopherReport], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [WorkspaceClean], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [SpecLibGen], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [DIA-NN], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] Cmd: [Skyline], Work dir: [E:\temp\T23090604_cell-DIA\FP22-K1S1] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of E:\database\fasta\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.fasta.fas~~~~~~~ >rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1 >rev_sp|O43825|B3GT2_HUMAN Beta-1,3-galactosyltransferase 2 OS=Homo sapiens OX=9606 GN=B3GALT2 PE=1 SV=1 >rev_sp|P0DPK5|H3Y2_HUMAN Histone H3.X OS=Homo sapiens OX=9606 GN=H3Y2 PE=5 SV=1 >rev_sp|P50440|GATM_HUMAN Glycine amidinotransferase, mitochondrial OS=Homo sapiens OX=9606 GN=GATM PE=1 SV=1 >rev_sp|Q14451|GRB7_HUMAN Growth factor receptor-bound protein 7 OS=Homo sapiens OX=9606 GN=GRB7 PE=1 SV=2 >rev_sp|Q6DRA6|H2B2D_HUMAN Putative histone H2B type 2-D OS=Homo sapiens OX=9606 GN=H2BC19P PE=5 SV=3 >rev_sp|Q8IXB1|DJC10_HUMAN DnaJ homolog subfamily C member 10 OS=Homo sapiens OX=9606 GN=DNAJC10 PE=1 SV=2 >rev_sp|Q8WWM7|ATX2L_HUMAN Ataxin-2-like protein OS=Homo sapiens OX=9606 GN=ATXN2L PE=1 SV=2 >rev_sp|Q9BS92|NPS3B_HUMAN Protein NipSnap homolog 3B OS=Homo sapiens OX=9606 GN=NIPSNAP3B PE=2 SV=1 >rev_sp|Q9NVK5|FGOP2_HUMAN FGFR1 oncogene partner 2 OS=Homo sapiens OX=9606 GN=FGFR1OP2 PE=1 SV=1 >rev_sp|W6CW81|PYDC5_HUMAN Pyrin domain-containing protein 5 OS=Homo sapiens OX=9606 GN=PYDC5 PE=1 SV=1 >sp|O43822|CF410_HUMAN Cilia- and flagella-associated protein 410 OS=Homo sapiens OX=9606 GN=CFAP410 PE=1 SV=1 >sp|P0DPK2|H3Y1_HUMAN Histone H3.Y OS=Homo sapiens OX=9606 GN=H3Y1 PE=1 SV=1 >sp|P50402|EMD_HUMAN Emerin OS=Homo sapiens OX=9606 GN=EMD PE=1 SV=1 >sp|Q14442|PIGH_HUMAN Phosphatidylinositol N-acetylglucosaminyltransferase subunit H OS=Homo sapiens OX=9606 GN=PIGH PE=1 SV=1 >sp|Q6DN14|MCTP1_HUMAN Multiple C2 and transmembrane domain-containing protein 1 OS=Homo sapiens OX=9606 GN=MCTP1 PE=2 SV=2 >sp|Q8IX94|CTGE4_HUMAN cTAGE family member 4 OS=Homo sapiens OX=9606 GN=CTAGE4 PE=2 SV=3 >sp|Q8WWL2|SPIR2_HUMAN Protein spire homolog 2 OS=Homo sapiens OX=9606 GN=SPIRE2 PE=1 SV=3 >sp|Q9BS40|LXN_HUMAN Latexin OS=Homo sapiens OX=9606 GN=LXN PE=1 SV=2 >sp|Q9NVI1|FANCI_HUMAN Fanconi anemia group I protein OS=Homo sapiens OX=9606 GN=FANCI PE=1 SV=4 >sp|S4R3Y5|HMN11_HUMAN Humanin-like 11 OS=Homo sapiens OX=9606 GN=MTRNR2L11 PE=3 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v22.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=E\:\\database\\fasta\\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.fasta.fas Table.editor=304.20535 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=false diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high precision) 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=D\:\\software\\MS\\DIA-NN\\1.9.2\\DiaNN.exe fragpipe-config.bin-ionquant=D\:\\software\\FragPipe\\v21.1\\tools\\IonQuant-1.10.12\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=D\:\\software\\FragPipe\\v21.1\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=D\:\\software\\FragPipe\\v21.1\\tools\\philosopher-5.1.0\\philosopher.exe fragpipe-config.bin-python=D\:\\software\\Python\\Python39\\python fragpipe-config.tools-folder=D\:\\software\\FragPipe\\v22.0\\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 msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.add_topN_complementary=0 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=stricttrypsin 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.output_report_topN_dia2=3 msfragger.override_charge=false msfragger.precursor_mass_lower=-10 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=10 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,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_mgf=false 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.philosoher-msstats=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.diagextract_mode=false 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_minIons=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=true ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 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.iterloc_maxEpoch=100 ptmshepherd.iterloc_mode=false ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.print_full_glyco_params=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_mass=0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 skyline.run-skyline=true skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-mode=0 skyline.skyline-mods-mode=Default speclibgen.convert-pepxml=true speclibgen.convert-psm=false speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.ignore_unannotated=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=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.dont-run-fq-lq=false 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=E\:\\temp\\T23090604_cell-DIA\\FP22-K1S1 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid D:\software\FragPipe\v22.0\jre\bin\java.exe -Xmx17G -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid E:\temp\T23090604_cell-DIA\23090604_ABC_K1.raw 2 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="12:50:37" level=info msg="Executing Workspace v5.1.1" time="12:50:37" level=info msg="Removing workspace" time="12:50:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\hqq\AppData\Local\Temp\d973b483-a7c8-48a0-b88a-7829729f266b time="12:50:37" level=info msg="Executing Workspace v5.1.1" time="12:50:37" level=info msg="Creating workspace" time="12:50:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx17G D:\software\FragPipe\v22.0\tools\MSFragger-4.1\MSFragger-4.1.jar E:\temp\T23090604_cell-DIA\FP22-K1S1\fragger_dia.params E:\temp\T23090604_cell-DIA\23090604_ABC_K1.raw E:\temp\T23090604_cell-DIA\23090604_ABC_S1.raw MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 17 GB memory Checking database... ***********************************FIRST SEARCH************************************ Parameters: num_threads = 2 database_name = E:\database\fasta\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.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 = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR 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 = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 238642 of length 8: 221781 of length 9: 214408 of length 10: 193596 of length 11: 177440 of length 12: 163463 of length 13: 153544 of length 14: 138542 of length 15: 127191 of length 16: 115921 of length 17: 105743 of length 18: 97545 of length 19: 91873 of length 20: 82388 of length 21: 76824 of length 22: 69781 of length 23: 64890 of length 24: 60200 of length 25: 55792 of length 26: 50996 of length 27: 48227 of length 28: 43889 of length 29: 40861 of length 30: 38093 of length 31: 34504 of length 32: 32145 of length 33: 29536 of length 34: 27030 of length 35: 24540 of length 36: 23171 of length 37: 20447 of length 38: 19235 of length 39: 16975 of length 40: 16214 of length 41: 15066 of length 42: 13463 of length 43: 11394 of length 44: 9390 of length 45: 7412 of length 46: 4946 of length 47: 3203 of length 48: 1943 of length 49: 1116 of length 50: 693 In total 2984053 peptides. Generated 4174549 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 145112472 fragments to be searched in 1 slices (2.16 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.43 s 001. 23090604_ABC_K1.raw 30.0 s | deisotoping 3.9 s [progress: 43860/43860 (100%) - 2104 spectra/s] 20.8s | postprocessing 0.2 s 002. 23090604_ABC_S1.raw 32.1 s | deisotoping 4.6 s [progress: 44124/44124 (100%) - 2092 spectra/s] 21.1s | postprocessing 0.1 s ***************************FIRST SEARCH DONE IN 2.013 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 3.59 0.79 | 0.04 0.63 | 3.62 1.48 | -0.06 1.20 002 | 3.15 0.65 | 0.03 0.59 | 3.15 1.42 | -0.06 1.13 -----|---------------|---------------|---------------|--------------- New fragment_mass_tolerance = 5.000000 PPM New precursor_true_tolerance = 3.000000 PPM ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.468 MIN********* ************************************MAIN SEARCH************************************ Checking database... data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Parameters: num_threads = 2 database_name = E:\database\fasta\2023-07-24-decoys-Uniprot.Swissprot.Human.20230619.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 = 3.0 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 = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR 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 = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 238642 of length 8: 221781 of length 9: 214408 of length 10: 193596 of length 11: 177440 of length 12: 163463 of length 13: 153544 of length 14: 138542 of length 15: 127191 of length 16: 115921 of length 17: 105743 of length 18: 97545 of length 19: 91873 of length 20: 82388 of length 21: 76824 of length 22: 69781 of length 23: 64890 of length 24: 60200 of length 25: 55792 of length 26: 50996 of length 27: 48227 of length 28: 43889 of length 29: 40861 of length 30: 38093 of length 31: 34504 of length 32: 32145 of length 33: 29536 of length 34: 27030 of length 35: 24540 of length 36: 23171 of length 37: 20447 of length 38: 19235 of length 39: 16975 of length 40: 16214 of length 41: 15066 of length 42: 13463 of length 43: 11394 of length 44: 9390 of length 45: 7412 of length 46: 4946 of length 47: 3203 of length 48: 1943 of length 49: 1116 of length 50: 693 In total 2984053 peptides. Generated 4174549 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.02 Da. 145112472 fragments to be searched in 1 slices (2.16 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.88 s 001. 23090604_ABC_K1.mzBIN_calibrated 0.7 s [progress: 43860/43860 (100%) - 173 spectra/s] 253.5s Building spectral index for the mzBIN_calibrated file 2.0 s Rescoring with peak tracing 25.7 s Picking top PSMs for each precursor 0.7 s Rescoring 11.7 s Writing results 2.1 s 002. 23090604_ABC_S1.mzBIN_calibrated 0.4 s [progress: 44124/44124 (100%) - 163 spectra/s] 270.2s Building spectral index for the mzBIN_calibrated file 2.1 s Rescoring with peak tracing 26.3 s Picking top PSMs for each precursor 0.6 s Rescoring 12.2 s Writing results 1.5 s ***************************MAIN SEARCH DONE IN 10.879 MIN*************************** *******************************TOTAL TIME 13.361 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank1.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank2.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank3.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank4.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1_rank5.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1_rank5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_K1.pin E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_K1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank1.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank2.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank3.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank4.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1_rank5.pepXML E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1_rank5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe\v22.0\jre\bin\java.exe -cp D:\software\FragPipe\v22.0\lib\fragpipe-22.0.jar;/D:/software/FragPipe/v22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\temp\T23090604_cell-DIA\23090604_ABC_S1.pin E:\temp\T23090604_cell-DIA\FP22-K1S1\23090604_ABC_S1.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: E:\temp\T23090604_cell-DIA\FP22-K1S1] D:\software\FragPipe\v22.0\jre\bin\java.exe -Xmx17G -cp D:\software\FragPipe\v22.0\tools\MSBooster-1.2.31.jar;D:\software\FragPipe\v22.0\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList E:\temp\T23090604_cell-DIA\FP22-K1S1\msbooster_params.txt 2024-10-30 13:04:04 [INFO] - MSBooster v1.2.31 2024-10-30 13:04:04 [INFO] - Using 2 threads 2024-10-30 13:04:04 [INFO] - Initializing E:\temp\T23090604_cell-DIA\23090604_ABC_K1_uncalibrated.mzML 2024-10-30 13:04:09 [INFO] - Could not detect instrument type. Setting to Lumos. If a different instrument was used, specify using '--instrument' via the command line or 'instrument=' in the param file. 2024-10-30 13:04:09 [INFO] - Initializing E:\temp\T23090604_cell-DIA\23090604_ABC_S1_uncalibrated.mzML 2024-10-30 13:04:11 [INFO] - Fragmentation type detected: HCD 2024-10-30 13:04:11 [INFO] - NCE detected: 28.0 2024-10-30 13:04:11 [INFO] - Creating input file for createFull 2024-10-30 13:04:11 [INFO] - 156494 PSMs for prediction 2024-10-30 13:04:11 [INFO] - createFull input file generation took 550 milliseconds 2024-10-30 13:04:11 [INFO] - Input file at E:\temp\T23090604_cell-DIA\FP22-K1S1\spectraRT_full.tsv 2024-10-30 13:04:11 [INFO] - Generating input file for DIA-NN 2024-10-30 13:04:11 [INFO] - Creating input file for Diann 2024-10-30 13:04:12 [INFO] - 156494 PSMs for prediction 2024-10-30 13:04:12 [INFO] - Writing DIA-NN input file 2024-10-30 13:04:12 [INFO] - Diann input file generation took 270 milliseconds 2024-10-30 13:04:12 [INFO] - Input file at E:\temp\T23090604_cell-DIA\FP22-K1S1\spectraRT.tsv 2024-10-30 13:04:12 [INFO] - Generating DIA-NN predictions 2024-10-30 13:04:12 [INFO] - D:\software\MS\DIA-NN\1.9.2\DiaNN.exe --lib E:\temp\T23090604_cell-DIA\FP22-K1S1\spectraRT.tsv --predict --threads 2 --strip-unknown-mods --predict-n-frag 100 2024-10-30 13:04:12 [INFO] - DIA-NN 1.9.2 (Data-Independent Acquisition by Neural Networks) 2024-10-30 13:04:12 [INFO] - Compiled on Oct 17 2024 21:58:43 2024-10-30 13:04:12 [INFO] - Current date and time: Wed Oct 30 13:04:12 2024 2024-10-30 13:04:12 [INFO] - CPU: GenuineIntel 12th Gen Intel(R) Core(TM) i3-12100 2024-10-30 13:04:12 [INFO] - SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 2024-10-30 13:04:12 [INFO] - Logical CPU cores: 8 2024-10-30 13:04:12 [INFO] - Predicted spectra will be saved in a binary format 2024-10-30 13:04:12 [INFO] - Thread number set to 2 2024-10-30 13:04:12 [INFO] - WARNING: unrecognised option [--strip-unknown-mods] 2024-10-30 13:04:12 [INFO] - Deep learning predictor will predict 100 fragments 2024-10-30 13:04:12 [INFO] - WARNING: protein inference is enabled but no FASTA provided - is this intended? 2024-10-30 13:04:12 [INFO] - 2024-10-30 13:04:12 [INFO] - 0 files will be processed 2024-10-30 13:04:12 [INFO] - [0:00] Loading spectral library E:\temp\T23090604_cell-DIA\FP22-K1S1\spectraRT.tsv 2024-10-30 13:04:12 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2024-10-30 13:04:12 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 156494 precursors in 143911 elution groups. 2024-10-30 13:04:12 [INFO] - ERROR: library contains fragments with invalid/unspecified charges 2024-10-30 13:04:13 [ERROR] - Abnormal DIANN termination: -1, please run the following command from the command line for more information D:\software\MS\DIA-NN\1.9.2\DiaNN.exe --lib E:\temp\T23090604_cell-DIA\FP22-K1S1\spectraRT.tsv --predict --threads 2 --strip-unknown-mods --predict-n-frag 100 Process 'MSBooster' finished, exit code: -1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 20 remaining tasks