System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: N/A Version info: FragPipe version 23.0 DIA-Umpire version 2.3.2 diaTracer version 1.3.3 MSFragger version 4.3 Crystal-C version 1.5.8 MSBooster version 1.3.9 Percolator version 3.7.1 Philosopher version 5.1.1 PTM-Shepherd version 3.0.1 IonQuant version 1.11.11 TMT-Integrator version 6.1.1 EasyPQP version 0.1.52 DIA-NN version 1.8.2 beta 8 Skyline version 24.1.0.414 Pandas version 2.2.3 Numpy version 1.26.4 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw DDA - E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.raw DDA 25 commands to execute: CheckCentroid C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;C:\FragPipe\FragPipe-23.0\tools\batmass-io-1.35.1.jar org.nesvilab.fragpipe.util.CheckCentroid E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw 31 WorkspaceCleanInit [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\u0126651\AppData\Local\Temp\36d309d3-5b43-467c-bace-a70f9a55a135 MSFragger [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\python\python.exe C:\FragPipe\FragPipe-23.0\tools\msfragger_pep_split.py 10 "C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx107G" C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\MSFragger-4.3.jar E:\Ankita_MS\232_2025\02_03_Missed_cleavages\fragger.params E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.raw MSFragger move pepxml C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.pepXML E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pepXML MSFragger move pin C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pin MSFragger move pepxml C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.pepXML E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pepXML MSFragger move pin C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pin MSBooster [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -cp C:\FragPipe\FragPipe-23.0\tools\MSBooster-1.3.9.jar;C:\FragPipe\FragPipe-23.0\tools\batmass-io-1.35.1.jar mainsteps.MainClass --paramsList E:\Ankita_MS\232_2025\02_03_Missed_cleavages\msbooster_params.txt Percolator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-2_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-2_edited.pin Percolator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-3_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-3_edited.pin Percolator: Convert to pepxml [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 232_2025_KULeuven_FW-2.pin 232_2025_KULeuven_FW-2 232_2025_KULeuven_FW-2_percolator_target_psms.tsv 232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv interact-232_2025_KULeuven_FW-2 DDA 0.5 E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2_uncalibrated.mzML Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2_percolator_target_psms.tsv Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 232_2025_KULeuven_FW-3.pin 232_2025_KULeuven_FW-3 232_2025_KULeuven_FW-3_percolator_target_psms.tsv 232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv interact-232_2025_KULeuven_FW-3 DDA 0.5 E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3_uncalibrated.mzML Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3_percolator_target_psms.tsv Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv ProteinProphet [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\FASTAs\2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --picked --ion 0.05 --psm 005 --pep 0.05 --prot 0.05 --tag rev_ --pepxml E:\Ankita_MS\232_2025\02_03_Missed_cleavages --protxml E:\Ankita_MS\232_2025\02_03_Missed_cleavages\combined.prot.xml --razor PhilosopherReport [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe report WorkspaceClean [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck IonQuant [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\thermo -cp C:\FragPipe\FragPipe-23.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-23.0\tools\IonQuant-1.11.11.jar ionquant.IonQuant --threads 31 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --msstats 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt --modlist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt IonQuant [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\thermo -cp C:\FragPipe\FragPipe-23.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-23.0\tools\IonQuant-1.11.11.jar ionquant.IonQuant --threads 31 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --msstats 0 --annotation E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv=E:\Ankita_MS\232_2025\232_2025_02_03_TMT_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt --modlist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt TmtIntegrator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -jar C:\FragPipe\FragPipe-23.0\tools\TMT-Integrator-6.1.1.jar E:\Ankita_MS\232_2025\02_03_Missed_cleavages\tmt-integrator-conf.yml E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [CheckCentroid], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [WorkspaceCleanInit], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [MSFragger], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [MSBooster], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [Percolator], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [ProteinProphet], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [PhilosopherDbAnnotate], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [PhilosopherFilter], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [PhilosopherReport], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [WorkspaceClean], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [IonQuant], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [IonQuant], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] Cmd: [TmtIntegrator], Work dir: [E:\Ankita_MS\232_2025\02_03_Missed_cleavages] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\FASTAs\2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas~~~~~~~ >rev_sp|O00762|UBE2C_HUMAN Ubiquitin-conjugating enzyme E2 C OS=Homo sapiens OX=9606 GN=UBE2C PE=1 SV=1 >rev_tr|A0A9D4VZ63|A0A9D4VZ63_PEA F-box domain-containing protein OS=Pisum sativum OX=3888 GN=KIW84_076862 PE=4 SV=1 >rev_tr|A0A9D4WI28|A0A9D4WI28_PEA RPA-interacting protein OS=Pisum sativum OX=3888 GN=KIW84_050032 PE=4 SV=1 >rev_tr|A0A9D4X216|A0A9D4X216_PEA Uncharacterized protein OS=Pisum sativum OX=3888 GN=KIW84_057371 PE=4 SV=1 >rev_tr|A0A9D4XL24|A0A9D4XL24_PEA Nuclear transcription factor Y subunit OS=Pisum sativum OX=3888 GN=KIW84_045779 PE=3 SV=1 >rev_tr|A0A9D4Y592|A0A9D4Y592_PEA Expansin-like EG45 domain-containing protein OS=Pisum sativum OX=3888 GN=KIW84_034953 PE=4 SV=1 >rev_tr|A0A9D4YPX4|A0A9D4YPX4_PEA Uncharacterized protein OS=Pisum sativum OX=3888 GN=KIW84_011241 PE=4 SV=1 >rev_tr|A0A9D5ABJ3|A0A9D5ABJ3_PEA Conserved oligomeric Golgi complex subunit 1 OS=Pisum sativum OX=3888 GN=KIW84_064792 PE=3 SV=1 >rev_tr|A0A9D5AVI9|A0A9D5AVI9_PEA Methyltransferase type 11 domain-containing protein (Fragment) OS=Pisum sativum OX=3888 GN=KIW84_031670 PE=4 SV=1 >rev_tr|A0A9D5BEP2|A0A9D5BEP2_PEA Ubiquitin-like protease family profile domain-containing protein OS=Pisum sativum OX=3888 GN=KIW84_011287 PE=3 SV=1 >rev_tr|W0M1Z1|W0M1Z1_PEA Aquaporin PIP2-3 OS=Pisum sativum OX=3888 GN=PIP2-3 PE=2 SV=1 >tr|A0A9D4VZ59|A0A9D4VZ59_PEA Uncharacterized protein OS=Pisum sativum OX=3888 GN=KIW84_076246 PE=4 SV=1 >tr|A0A9D4WI24|A0A9D4WI24_PEA Uncharacterized protein OS=Pisum sativum OX=3888 GN=KIW84_066404 PE=4 SV=1 >tr|A0A9D4X212|A0A9D4X212_PEA Uncharacterized protein OS=Pisum sativum OX=3888 GN=KIW84_056983 PE=4 SV=1 >tr|A0A9D4XL20|A0A9D4XL20_PEA Natural resistance-associated macrophage protein 2, variant 2 OS=Pisum sativum OX=3888 GN=KIW84_045403 PE=3 SV=1 >tr|A0A9D4Y587|A0A9D4Y587_PEA DExH-box ATP-dependent RNA helicase DExH6 OS=Pisum sativum OX=3888 GN=KIW84_020504 PE=4 SV=1 >tr|A0A9D4YPW7|A0A9D4YPW7_PEA Zinc-finger domain-containing protein OS=Pisum sativum OX=3888 GN=KIW84_010783 PE=4 SV=1 >tr|A0A9D5ABI9|A0A9D5ABI9_PEA DUF674 family protein (Fragment) OS=Pisum sativum OX=3888 GN=KIW84_066376 PE=4 SV=1 >tr|A0A9D5AVI5|A0A9D5AVI5_PEA Cucumisin OS=Pisum sativum OX=3888 GN=KIW84_046411 PE=3 SV=1 >tr|A0A9D5BEN7|A0A9D5BEN7_PEA Glutathione hydrolase OS=Pisum sativum OX=3888 GN=KIW84_011233 PE=4 SV=1 >tr|Q9SYU1|Q9SYU1_PEA Dirigent protein OS=Pisum sativum OX=3888 GN=DRR206-c PE=3 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~annotation files~~~~~~~ E:\Ankita_MS\232_2025\232_2025_02_03_TMT_annotation.txt: 126 _126 127N _127N 127C _127C 128N _128N 128C _128C 129N _129N 129C _129C 130N _130N 130C _130C 131N _131N 131C _131C 132N _132N 132C _132C 133N _133N 133C _133C 134N _134N ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v23.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=C\:\\FASTAs\\2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas Table.editor=304.20715 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.channel-normalization-strategy=0 diann.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.min-site-prob=0.75 diann.mod-tag= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=2 diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.coadaptr.fpop.fpop_masses= fpop.coadaptr.fpop.run-fpop-coadaptr=false fpop.fragpipe.fpop.fpop-tmt=false fpop.fragpipe.fpop.label_control= fpop.fragpipe.fpop.label_fpop= fpop.fragpipe.fpop.region_size=1 fpop.fragpipe.fpop.run-fpop=false fpop.fragpipe.fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\FragPipe\\FragPipe-23.0\\tools\\diann\\1.8.2_beta_8\\windows\\DiaNN.exe fragpipe-config.bin-python=C\:\\FragPipe\\FragPipe-23.0\\python\\python.exe fragpipe-config.tools-folder=C\:\\FragPipe\\FragPipe-23.0\\tools freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.formula= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=1 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=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-im-model=false msbooster.find-best-rt-model=true msbooster.find-best-spectra-model=true msbooster.fragmentation-type=0 msbooster.im-model=DIA-NN msbooster.koina-url=https\://koina.wilhelmlab.org\:443/v2/models/ msbooster.predict-im=true msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=true msbooster.spectra-model=DIA-NN msbooster.spectral-library-path= msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=10 msfragger.allowed_missed_cleavage_2=2 msfragger.analyzer_types=all msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=-1/0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=5 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=134.5 msfragger.misc.fragger.clear-mz-lo=125.5 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=200 msfragger.misc.fragger.enzyme-dropdown-1=custom msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=10 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=-18.01056 79.96633 msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=FLMKRWY 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; 304.20715,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 304.20715,n^,true,1; 229.16293,S,false,1; 304.20715,K,false,1; 257.12756,K,false,1; 285.1437,K,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mzml=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.allowed_sites= opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --picked --ion 0.05 --psm 005 --pep 0.05 --prot 0.05 phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.override-defaults=false ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotate_assigned_mods=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.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_condPeaks=150 ptmshepherd.spectra_condRatio=0.0001 ptmshepherd.spectra_maxPrecursorCharge=4 ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.use_msfragger_localization=false ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true 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-fragment-tolerance=10 skyline.skyline-mods-mode=Default skyline.skyline-precursor-tolerance=10 skyline.use-ssl=false 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.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_temp_files=false tab-run.export_matched_fragments=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=false tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-16 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=-1 tmtintegrator.log2transformed=false tmtintegrator.max_pep_prob_thres=0.9 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_resolution=0 tmtintegrator.min_site_prob=-1 tmtintegrator.min_snr=0 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_d_tag=Pool tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=true tmtintegrator.tolerance=20 tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=E\:\\Ankita_MS\\232_2025\\02_03_Missed_cleavages workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.misc.sdrf-type=Default workflow.ram=0 workflow.threads=31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;C:\FragPipe\FragPipe-23.0\tools\batmass-io-1.35.1.jar org.nesvilab.fragpipe.util.CheckCentroid E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw 31 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="13:57:11" level=info msg="Executing Workspace v5.1.1" time="13:57:11" level=info msg="Removing workspace" time="13:57:11" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\u0126651\AppData\Local\Temp\36d309d3-5b43-467c-bace-a70f9a55a135 time="13:57:12" level=info msg="Executing Workspace v5.1.1" time="13:57:12" level=info msg="Creating workspace" time="13:57:12" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\python\python.exe C:\FragPipe\FragPipe-23.0\tools\msfragger_pep_split.py 10 "C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx107G" C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\MSFragger-4.3.jar E:\Ankita_MS\232_2025\02_03_Missed_cleavages\fragger.params E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.raw ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/fragger.params'), '--split1', WindowsPath('E:/Ankita_MS/232_2025/232_2025_KULeuven_FW-2.raw'), WindowsPath('E:/Ankita_MS/232_2025/232_2025_KULeuven_FW-3.raw')] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... Checking spectral files... 232_2025_KULeuven_FW-2.raw: Scans = 37546; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = true; MS1 ITMS = false; Isolation sizes = [0.4]; Instrument = Orbitrap Astral 232_2025_KULeuven_FW-3.raw: Scans = 37465; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = true; MS1 ITMS = false; Isolation sizes = [0.4]; Instrument = Orbitrap Astral ***********************************FIRST SEARCH************************************ Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all 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 = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 1612380 of length 8: 1404924 of length 9: 1187264 of length 10: 985751 of length 11: 804556 of length 12: 649929 of length 13: 519868 of length 14: 414339 of length 15: 326333 of length 16: 258588 of length 17: 200310 of length 18: 159961 of length 19: 125635 of length 20: 99424 of length 21: 79326 of length 22: 62406 of length 23: 49750 of length 24: 40492 of length 25: 31871 of length 26: 25445 of length 27: 20857 of length 28: 16520 of length 29: 13476 of length 30: 11214 of length 31: 9410 of length 32: 7323 of length 33: 6335 of length 34: 5513 of length 35: 4819 of length 36: 3873 of length 37: 3471 of length 38: 3013 of length 39: 2268 of length 40: 1935 of length 41: 1642 of length 42: 1550 of length 43: 1183 of length 44: 996 of length 45: 878 of length 46: 634 of length 47: 508 of length 48: 372 of length 49: 223 of length 50: 166 In total 9156731 peptides. Generated 21922228 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 448310224 fragments to be searched in 1 slices (4.18 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.99 s 001. 232_2025_KULeuven_FW-2.raw 11.3 s | deisotoping 0.4 s [progress: 37546/37546 (100%) - 16584 spectra/s] 2.3s 002. 232_2025_KULeuven_FW-3.raw 9.5 s | deisotoping 0.2 s [progress: 37465/37465 (100%) - 35681 spectra/s] 1.1s postprocessing 232_2025_KULeuven_FW-2.raw 0.2 s postprocessing 232_2025_KULeuven_FW-3.raw 0.1 s ***************************FIRST SEARCH DONE IN 0.603 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 0.56 0.79 | 0.03 0.48 | -0.05 1.78 | -0.20 1.77 002 | 0.90 0.75 | 0.04 0.49 | -0.62 1.78 | -0.16 1.75 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | 2278| 2495| 2565| 2571| 2304| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 2751| 2696| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 2683 -------|------- -------|------- Rm P. | 0 -------|------- Count | 2162 -------|------- New fragment_mass_tolerance = 15.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 0 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.863 MIN********* *******************************TOTAL TIME 1.466 MIN******************************** STARTED: DB split 1 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '0'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 298079 of length 8: 299660 of length 9: 302212 of length 10: 306273 of length 11: 307785 of length 12: 308565 of length 13: 310583 of length 14: 313599 of length 15: 312959 of length 16: 314006 of length 17: 312651 of length 18: 312623 of length 19: 310533 of length 20: 308875 of length 21: 305441 of length 22: 297932 of length 23: 290866 of length 24: 283898 of length 25: 273552 of length 26: 260764 of length 27: 247566 of length 28: 233853 of length 29: 218740 of length 30: 204792 of length 31: 188721 of length 32: 175139 of length 33: 158923 of length 34: 145119 of length 35: 132428 of length 36: 119036 of length 37: 107270 of length 38: 96329 of length 39: 86544 of length 40: 76336 of length 41: 68271 of length 42: 59428 of length 43: 50957 of length 44: 42148 of length 45: 31750 of length 46: 20487 of length 47: 12025 of length 48: 5959 of length 49: 2677 of length 50: 1217 In total 8516571 peptides. Generated 28092569 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1218777460 fragments to be searched in 1 slices (11.35 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.18 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.1 s [progress: 37546/37546 (100%) - 10666 spectra/s] 3.5s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 17857 spectra/s] 2.1s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.1 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.0 s ***************************MAIN SEARCH DONE IN 0.374 MIN*************************** *******************************TOTAL TIME 0.377 MIN******************************** DONE: DB split 1 of 10 STARTED: DB split 2 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '1'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 301275 of length 8: 303944 of length 9: 306085 of length 10: 309335 of length 11: 311803 of length 12: 313265 of length 13: 316022 of length 14: 319320 of length 15: 317482 of length 16: 318429 of length 17: 317974 of length 18: 318650 of length 19: 316690 of length 20: 315004 of length 21: 310540 of length 22: 302940 of length 23: 298528 of length 24: 289780 of length 25: 278342 of length 26: 265862 of length 27: 252624 of length 28: 238253 of length 29: 222262 of length 30: 208240 of length 31: 192675 of length 32: 177201 of length 33: 162802 of length 34: 147629 of length 35: 135510 of length 36: 121064 of length 37: 108625 of length 38: 97298 of length 39: 86301 of length 40: 77392 of length 41: 69224 of length 42: 60272 of length 43: 51345 of length 44: 42498 of length 45: 31987 of length 46: 21199 of length 47: 11981 of length 48: 5899 of length 49: 2820 of length 50: 1214 In total 8657585 peptides. Generated 28415719 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1233036246 fragments to be searched in 1 slices (11.48 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.22 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.4 s [progress: 37546/37546 (100%) - 11082 spectra/s] 3.4s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 17697 spectra/s] 2.1s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 2.8 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.1 s ***************************MAIN SEARCH DONE IN 0.376 MIN*************************** *******************************TOTAL TIME 0.379 MIN******************************** DONE: DB split 2 of 10 STARTED: DB split 3 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '2'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 298878 of length 8: 301193 of length 9: 304856 of length 10: 307651 of length 11: 310990 of length 12: 312212 of length 13: 313107 of length 14: 316863 of length 15: 316394 of length 16: 317079 of length 17: 316772 of length 18: 315987 of length 19: 314492 of length 20: 311831 of length 21: 309428 of length 22: 301933 of length 23: 295874 of length 24: 286569 of length 25: 276194 of length 26: 263740 of length 27: 250430 of length 28: 237292 of length 29: 221808 of length 30: 207084 of length 31: 191239 of length 32: 175621 of length 33: 161576 of length 34: 147116 of length 35: 135017 of length 36: 120396 of length 37: 108365 of length 38: 97703 of length 39: 86617 of length 40: 77343 of length 41: 68828 of length 42: 59267 of length 43: 50849 of length 44: 41594 of length 45: 31089 of length 46: 20214 of length 47: 11687 of length 48: 5710 of length 49: 2611 of length 50: 1174 In total 8602673 peptides. Generated 28378615 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1230192682 fragments to be searched in 1 slices (11.46 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.05 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.2 s [progress: 37546/37546 (100%) - 11319 spectra/s] 3.3s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 18374 spectra/s] 2.0s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.0 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.1 s ***************************MAIN SEARCH DONE IN 0.371 MIN*************************** *******************************TOTAL TIME 0.374 MIN******************************** DONE: DB split 3 of 10 STARTED: DB split 4 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '3'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 314993 of length 8: 317239 of length 9: 319884 of length 10: 322818 of length 11: 324365 of length 12: 325797 of length 13: 327790 of length 14: 331196 of length 15: 329607 of length 16: 331603 of length 17: 329819 of length 18: 328340 of length 19: 327273 of length 20: 324436 of length 21: 319974 of length 22: 312665 of length 23: 306250 of length 24: 297749 of length 25: 286039 of length 26: 272488 of length 27: 259502 of length 28: 244864 of length 29: 228217 of length 30: 213951 of length 31: 198507 of length 32: 182535 of length 33: 167305 of length 34: 151416 of length 35: 138570 of length 36: 124457 of length 37: 111992 of length 38: 100096 of length 39: 89755 of length 40: 79867 of length 41: 71077 of length 42: 62227 of length 43: 53163 of length 44: 44039 of length 45: 32988 of length 46: 21686 of length 47: 12572 of length 48: 6151 of length 49: 2869 of length 50: 1351 In total 8949482 peptides. Generated 29416273 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1273956886 fragments to be searched in 1 slices (11.86 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.31 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.2 s [progress: 37546/37546 (100%) - 10326 spectra/s] 3.6s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.4 s [progress: 37465/37465 (100%) - 17995 spectra/s] 2.1s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.0 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.4 s ***************************MAIN SEARCH DONE IN 0.389 MIN*************************** *******************************TOTAL TIME 0.392 MIN******************************** DONE: DB split 4 of 10 STARTED: DB split 5 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '4'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 302903 of length 8: 305369 of length 9: 307849 of length 10: 310796 of length 11: 313852 of length 12: 314676 of length 13: 316669 of length 14: 320235 of length 15: 319017 of length 16: 320831 of length 17: 319595 of length 18: 318370 of length 19: 317249 of length 20: 315206 of length 21: 312355 of length 22: 304410 of length 23: 297955 of length 24: 289740 of length 25: 277857 of length 26: 266084 of length 27: 252262 of length 28: 238512 of length 29: 222702 of length 30: 208146 of length 31: 192546 of length 32: 176607 of length 33: 162160 of length 34: 147414 of length 35: 135114 of length 36: 121048 of length 37: 109174 of length 38: 98059 of length 39: 87438 of length 40: 77899 of length 41: 69424 of length 42: 60557 of length 43: 52386 of length 44: 42683 of length 45: 32140 of length 46: 20979 of length 47: 11835 of length 48: 5933 of length 49: 2691 of length 50: 1131 In total 8679858 peptides. Generated 28454664 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1232266392 fragments to be searched in 1 slices (11.48 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.04 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.1 s [progress: 37546/37546 (100%) - 9093 spectra/s] 4.1s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 17943 spectra/s] 2.1s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.0 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.2 s ***************************MAIN SEARCH DONE IN 0.387 MIN*************************** *******************************TOTAL TIME 0.390 MIN******************************** DONE: DB split 5 of 10 STARTED: DB split 6 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '5'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 295054 of length 8: 295918 of length 9: 298727 of length 10: 302422 of length 11: 303641 of length 12: 304054 of length 13: 306050 of length 14: 309078 of length 15: 307998 of length 16: 308340 of length 17: 307193 of length 18: 307203 of length 19: 304600 of length 20: 302485 of length 21: 299626 of length 22: 291690 of length 23: 284982 of length 24: 277683 of length 25: 267597 of length 26: 255094 of length 27: 242115 of length 28: 228459 of length 29: 213602 of length 30: 199948 of length 31: 184359 of length 32: 170820 of length 33: 154784 of length 34: 141538 of length 35: 128823 of length 36: 115897 of length 37: 104437 of length 38: 93622 of length 39: 84181 of length 40: 74317 of length 41: 66349 of length 42: 57605 of length 43: 49429 of length 44: 40842 of length 45: 30665 of length 46: 19963 of length 47: 11569 of length 48: 5791 of length 49: 2609 of length 50: 1182 In total 8352341 peptides. Generated 27525570 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1191120164 fragments to be searched in 1 slices (11.09 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.86 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.6 s [progress: 37546/37546 (100%) - 8995 spectra/s] 4.2s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 18950 spectra/s] 2.0s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 2.9 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.2 s ***************************MAIN SEARCH DONE IN 0.392 MIN*************************** *******************************TOTAL TIME 0.395 MIN******************************** DONE: DB split 6 of 10 STARTED: DB split 7 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '6'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 298052 of length 8: 300269 of length 9: 302560 of length 10: 305377 of length 11: 307845 of length 12: 309152 of length 13: 311527 of length 14: 314523 of length 15: 312438 of length 16: 313145 of length 17: 312462 of length 18: 313288 of length 19: 311048 of length 20: 308729 of length 21: 304491 of length 22: 296953 of length 23: 292530 of length 24: 283843 of length 25: 271881 of length 26: 259848 of length 27: 246846 of length 28: 232721 of length 29: 217263 of length 30: 203365 of length 31: 188107 of length 32: 172762 of length 33: 158818 of length 34: 143720 of length 35: 131828 of length 36: 118062 of length 37: 105728 of length 38: 95002 of length 39: 84085 of length 40: 75324 of length 41: 67241 of length 42: 58690 of length 43: 50164 of length 44: 41432 of length 45: 31133 of length 46: 20614 of length 47: 11593 of length 48: 5780 of length 49: 2729 of length 50: 1168 In total 8494136 peptides. Generated 27843731 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1205528760 fragments to be searched in 1 slices (11.23 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.95 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.4 s [progress: 37546/37546 (100%) - 9946 spectra/s] 3.8s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.4 s [progress: 37465/37465 (100%) - 18556 spectra/s] 2.0s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 2.9 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.0 s ***************************MAIN SEARCH DONE IN 0.385 MIN*************************** *******************************TOTAL TIME 0.389 MIN******************************** DONE: DB split 7 of 10 STARTED: DB split 8 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '7'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 295827 of length 8: 297373 of length 9: 300770 of length 10: 304133 of length 11: 307278 of length 12: 308024 of length 13: 308709 of length 14: 312158 of length 15: 311363 of length 16: 311822 of length 17: 311388 of length 18: 310576 of length 19: 309286 of length 20: 306176 of length 21: 303367 of length 22: 295851 of length 23: 290041 of length 24: 280886 of length 25: 270202 of length 26: 257775 of length 27: 245227 of length 28: 232182 of length 29: 216740 of length 30: 201924 of length 31: 186622 of length 32: 171361 of length 33: 157656 of length 34: 143369 of length 35: 131359 of length 36: 117191 of length 37: 105263 of length 38: 95018 of length 39: 84465 of length 40: 75313 of length 41: 67025 of length 42: 57649 of length 43: 49435 of length 44: 40599 of length 45: 30349 of length 46: 19652 of length 47: 11285 of length 48: 5594 of length 49: 2539 of length 50: 1166 In total 8441988 peptides. Generated 27829117 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1203580736 fragments to be searched in 1 slices (11.21 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.19 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 0.6 s [progress: 37546/37546 (100%) - 11992 spectra/s] 3.1s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 17053 spectra/s] 2.2s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 2.9 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.2 s ***************************MAIN SEARCH DONE IN 0.359 MIN*************************** *******************************TOTAL TIME 0.363 MIN******************************** DONE: DB split 8 of 10 STARTED: DB split 9 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '8'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 311832 of length 8: 313649 of length 9: 316385 of length 10: 319331 of length 11: 320877 of length 12: 321685 of length 13: 323474 of length 14: 326853 of length 15: 324965 of length 16: 326561 of length 17: 324680 of length 18: 323408 of length 19: 322221 of length 20: 318850 of length 21: 314329 of length 22: 307145 of length 23: 300926 of length 24: 292221 of length 25: 280907 of length 26: 267010 of length 27: 254589 of length 28: 239922 of length 29: 223786 of length 30: 209715 of length 31: 194234 of length 32: 178577 of length 33: 163543 of length 34: 148076 of length 35: 135393 of length 36: 121670 of length 37: 109512 of length 38: 97959 of length 39: 87674 of length 40: 78104 of length 41: 69521 of length 42: 60605 of length 43: 52006 of length 44: 43011 of length 45: 32194 of length 46: 21161 of length 47: 12258 of length 48: 6048 of length 49: 2749 of length 50: 1325 In total 8800941 peptides. Generated 28907016 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1249785642 fragments to be searched in 1 slices (11.64 GB total) Operating on slice 1 of 1: Fragment index slice generated in 5.38 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.2 s [progress: 37546/37546 (100%) - 9834 spectra/s] 3.8s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.4 s [progress: 37465/37465 (100%) - 18410 spectra/s] 2.0s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.0 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.3 s ***************************MAIN SEARCH DONE IN 0.385 MIN*************************** *******************************TOTAL TIME 0.388 MIN******************************** DONE: DB split 9 of 10 STARTED: DB split 10 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), 'fragger.params', WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-2.mzBIN_calibrated'), WindowsPath('E:/Ankita_MS/232_2025/02_03_Missed_cleavages/split_peptide_index_tempdir/232_2025_KULeuven_FW-3.mzBIN_calibrated'), '--partial', '9'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 107 GB memory Checking database... ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 31 database_name = 2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = -1/0/1/2/3 mass_offsets = 0.0 use_detailed_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 = FLMKRWY search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 10 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 5 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 134.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 0 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 304.20715 n^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 304.20715 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 299567 of length 8: 301669 of length 9: 304173 of length 10: 306987 of length 11: 310041 of length 12: 310619 of length 13: 312264 of length 14: 315487 of length 15: 314098 of length 16: 315811 of length 17: 313939 of length 18: 313143 of length 19: 312044 of length 20: 309624 of length 21: 306489 of length 22: 298574 of length 23: 292123 of length 24: 283819 of length 25: 272185 of length 26: 260275 of length 27: 247142 of length 28: 233560 of length 29: 217846 of length 30: 203304 of length 31: 188093 of length 32: 172456 of length 33: 158129 of length 34: 143698 of length 35: 131469 of length 36: 117939 of length 37: 106377 of length 38: 95421 of length 39: 85083 of length 40: 75747 of length 41: 67417 of length 42: 58754 of length 43: 50988 of length 44: 41722 of length 45: 31128 of length 46: 20385 of length 47: 11470 of length 48: 5670 of length 49: 2598 of length 50: 1077 In total 8520404 peptides. Generated 27913868 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.08 Da. 1206506184 fragments to be searched in 1 slices (11.24 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.97 s 001. 232_2025_KULeuven_FW-2.mzBIN_calibrated 1.4 s [progress: 37546/37546 (100%) - 10418 spectra/s] 3.6s 002. 232_2025_KULeuven_FW-3.mzBIN_calibrated 0.2 s [progress: 37465/37465 (100%) - 15656 spectra/s] 2.4s postprocessing 232_2025_KULeuven_FW-2.mzBIN_calibrated 3.0 s postprocessing 232_2025_KULeuven_FW-3.mzBIN_calibrated 2.0 s ***************************MAIN SEARCH DONE IN 0.389 MIN*************************** *******************************TOTAL TIME 0.392 MIN******************************** DONE: DB split 10 of 10 ['C:\\FragPipe\\FragPipe-23.0\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx107G', WindowsPath('C:/FragPipe/FragPipe-23.0/tools/MSFragger-4.3/MSFragger-4.3.jar'), '--generate_expect_functions', '232_2025_KULeuven_FW-2_scores_histogram.tsv', '232_2025_KULeuven_FW-3_scores_histogram.tsv'] MSFragger version MSFragger-4.3 Batmass-IO version 1.35.4 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 Writing: 232_2025_KULeuven_FW-3 spectrum: 0 Writing: 232_2025_KULeuven_FW-2 spectrum: 0 Writing: 232_2025_KULeuven_FW-3 spectrum: 16384 Writing: 232_2025_KULeuven_FW-2 spectrum: 16384 Writing: 232_2025_KULeuven_FW-3 spectrum: 32768 Writing: 232_2025_KULeuven_FW-2 spectrum: 32768 Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.pepXML E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.pepXML E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar;/C:/FragPipe/FragPipe-23.0/lib/batmass-io-1.35.1.jar org.nesvilab.utils.FileMove --no-err E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -cp C:\FragPipe\FragPipe-23.0\tools\MSBooster-1.3.9.jar;C:\FragPipe\FragPipe-23.0\tools\batmass-io-1.35.1.jar mainsteps.MainClass --paramsList E:\Ankita_MS\232_2025\02_03_Missed_cleavages\msbooster_params.txt 2025-10-30 14:03:21 [INFO] - MSBooster v1.3.9 2025-10-30 14:03:21 [INFO] - TMT/iTRAQ mass detected in fragger.params as variable modification: 304.20715 2025-10-30 14:03:21 [INFO] - TMT/iTRAQ mass detected in fragger.params as fixed modification: 304.20715 2025-10-30 14:03:21 [INFO] - Creating output folder at E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster 2025-10-30 14:03:21 [INFO] - Using 31 threads 2025-10-30 14:03:23 [INFO] - Instrument detected: THERMOTOF 2025-10-30 14:03:23 [INFO] - NCE and fragmentation type detected: {HCD=32.00} 2025-10-30 14:03:23 [INFO] - Searching for best RT model for your data 2025-10-30 14:03:23 [INFO] - Searching the following models: [Prosit_2020_irt_TMT, DIA-NN] 2025-10-30 14:03:26 [INFO] - Choosing RT model based on top 10 consensus method 2025-10-30 14:03:26 [INFO] - Votes for DIA-NN: 10 2025-10-30 14:03:26 [INFO] - Votes for Prosit_2020_irt_TMT: 0 2025-10-30 14:03:26 [INFO] - ~~~~~~~~~~~~~~~~~~~~RT model chosen is DIA-NN~~~~~~~~~~~~~~~~~~~~ 2025-10-30 14:03:26 [INFO] - Searching for best spectra model for your data 2025-10-30 14:03:26 [INFO] - Searching the following models: [Prosit_2020_intensity_TMT, DIA-NN] 2025-10-30 14:03:26 [INFO] - Calibrating NCE for Prosit_2020_intensity_TMT ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:30 [INFO] - Best NCE for Prosit_2020_intensity_TMT after calibration is 35 2025-10-30 14:03:30 [INFO] - Choosing spectra model based on median method 2025-10-30 14:03:30 [INFO] - Median similarity for Prosit_2020_intensity_TMT is 0.9531 2025-10-30 14:03:30 [INFO] - Median similarity for DIA-NN is 0.9496 2025-10-30 14:03:30 [INFO] - ~~~~~~~~~~~~~~~~~~~~Spectra model chosen is Prosit_2020_intensity_TMT~~~~~~~~~~~~~~~~~~~~ 2025-10-30 14:03:30 [INFO] - Creating input file for createFull 2025-10-30 14:03:30 [INFO] - 62787 PSMs for prediction 2025-10-30 14:03:30 [INFO] - createFull input file generation took 116 milliseconds 2025-10-30 14:03:30 [INFO] - Input file at E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT_full.tsv 2025-10-30 14:03:30 [INFO] - Creating input file for Prosit_2020_intensity_TMT 2025-10-30 14:03:30 [INFO] - 62106 PSMs for prediction 2025-10-30 14:03:30 [INFO] - Prosit_2020_intensity_TMT input file generation took 225 milliseconds 2025-10-30 14:03:30 [INFO] - Input files in E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\jsonFiles 2025-10-30 14:03:30 [INFO] - Generating input file for DIA-NN 2025-10-30 14:03:30 [INFO] - Creating input file for Diann 2025-10-30 14:03:31 [INFO] - 62787 PSMs for prediction 2025-10-30 14:03:31 [INFO] - Writing DIA-NN input file 2025-10-30 14:03:31 [INFO] - Diann input file generation took 162 milliseconds 2025-10-30 14:03:31 [INFO] - Input file at E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT.tsv 2025-10-30 14:03:31 [INFO] - Calling Prosit_2020_intensity_TMT model ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:38 [INFO] - HTTP request and parse time in milliseconds: 6992 2025-10-30 14:03:39 [INFO] - Generating DIA-NN predictions 2025-10-30 14:03:39 [INFO] - C:\FragPipe\FragPipe-23.0\tools\diann\1.8.2_beta_8\windows\DiaNN.exe --lib E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT.tsv --predict --threads 31 --strip-unknown-mods --predict-n-frag 100 --mod TMT,304.20715 --original-mods 2025-10-30 14:03:39 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) 2025-10-30 14:03:39 [INFO] - Compiled on Sep 15 2022 18:28:57 2025-10-30 14:03:39 [INFO] - Current date and time: Thu Oct 30 14:03:39 2025 2025-10-30 14:03:39 [INFO] - CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i9-13900K 2025-10-30 14:03:39 [INFO] - SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 2025-10-30 14:03:39 [INFO] - Logical CPU cores: 32 2025-10-30 14:03:39 [INFO] - Predicted spectra will be saved in a binary format 2025-10-30 14:03:39 [INFO] - Thread number set to 31 2025-10-30 14:03:39 [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 2025-10-30 14:03:39 [INFO] - Deep learning predictor will predict 100 fragments 2025-10-30 14:03:39 [INFO] - Modification TMT with mass delta 304.207 added to the list of recognised modifications for spectral library-based search 2025-10-30 14:03:39 [INFO] - DIA-NN will not attempt to convert library modifications to the UniMod format 2025-10-30 14:03:39 [INFO] - 2025-10-30 14:03:39 [INFO] - 0 files will be processed 2025-10-30 14:03:39 [INFO] - [0:00] Loading spectral library E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT.tsv 2025-10-30 14:03:40 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2025-10-30 14:03:40 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 62787 precursors in 61821 elution groups. 2025-10-30 14:03:40 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction 2025-10-30 14:03:40 [INFO] - [0:00] Predicting spectra and IMs 2025-10-30 14:03:45 [INFO] - [0:05] Predicting RTs 2025-10-30 14:03:47 [INFO] - [0:07] Decoding predicted spectra and IMs 2025-10-30 14:03:47 [INFO] - [0:07] Decoding RTs 2025-10-30 14:03:47 [INFO] - [0:07] Saving the list of predictions to E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT.predicted.bin 2025-10-30 14:03:47 [INFO] - Finished 2025-10-30 14:03:48 [INFO] - Done generating DIA-NN predictions 2025-10-30 14:03:48 [INFO] - Model running took 8173 milliseconds 2025-10-30 14:03:48 [INFO] - Writing E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectra-Prosit_2020_intensity_TMT.koina.mgf 2025-10-30 14:03:48 [INFO] - Generating edited pin with following features: [unweightedSpectralEntropy, weightedSpectralEntropy, hypergeometricProbability, intersection, predRTrealUnits, deltaRTLOESS] 2025-10-30 14:03:48 [INFO] - Loading predicted spectra: E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectra-Prosit_2020_intensity_TMT.koina.mgf 2025-10-30 14:03:49 [INFO] - Loading predicted retention times: E:\Ankita_MS\232_2025\02_03_Missed_cleavages\MSBooster\spectraRT.predicted.bin 2025-10-30 14:03:49 [INFO] - Merging libraries 2025-10-30 14:03:49 [INFO] - E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pin has 35285 PSMs 2025-10-30 14:03:49 [INFO] - Processing pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2.pin 2025-10-30 14:03:49 [INFO] - Processing E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:50 [INFO] - Setting pin entries ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:51 [INFO] - RT regression using 1806 PSMs Iteration 1...2...3...4...5... 2025-10-30 14:03:51 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.1 2025-10-30 14:03:51 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:52 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:52 [INFO] - Edited pin file at E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2_edited.pin 2025-10-30 14:03:53 [INFO] - E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pin has 34470 PSMs 2025-10-30 14:03:53 [INFO] - Processing pin E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3.pin 2025-10-30 14:03:53 [INFO] - Processing E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:53 [INFO] - Setting pin entries ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:54 [INFO] - RT regression using 2380 PSMs Iteration 1...2...3...4...5... 2025-10-30 14:03:55 [INFO] - Best average bandwidth for mass from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.1 2025-10-30 14:03:55 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:56 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2025-10-30 14:03:56 [INFO] - Edited pin file at E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3_edited.pin 2025-10-30 14:03:56 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 7763 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-2_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-2_edited.pin Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-2_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-2_edited.pin Started Thu Oct 30 14:03:56 2025 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 232_2025_KULeuven_FW-2_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 304.20715n^ unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection pred_RT_real_units delta_RT_loess Found 35285 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 20534 positives and 14751 negatives, size ratio=1.39204 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 35 as initial direction. Could separate 2340 training set positives with q<0.01 in that direction. Split 2: Selected feature 8 as initial direction. Could separate 2143 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 2158 training set positives with q<0.01 in that direction. Found 3072 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3470 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4184 PSMs with q<0.01 Iteration 2: Estimated 4457 PSMs with q<0.01 Iteration 3: Estimated 4526 PSMs with q<0.01 Iteration 4: Estimated 4598 PSMs with q<0.01 Iteration 5: Estimated 4615 PSMs with q<0.01 Iteration 6: Estimated 4624 PSMs with q<0.01 Iteration 7: Estimated 4626 PSMs with q<0.01 Iteration 8: Estimated 4627 PSMs with q<0.01 Iteration 9: Estimated 4636 PSMs with q<0.01 Iteration 10: Estimated 4633 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2647 -0.1916 -0.3072 abs_ppm 0.0818 -0.1271 0.0305 isotope_error_negative 0.0878 0.0655 0.0646 isotope_error_0 0.1097 0.2315 0.2036 isotope_error_1 -0.0608 -0.1778 -0.2580 isotope_error_2 -0.2797 -0.0270 -0.0894 isotope_error_3_more -0.8391 -1.5580 -1.6695 log10_evalue -0.0945 0.4858 1.0846 hyperscore -0.2172 -0.6451 -0.6174 delta_hyperscore 1.5975 0.4938 0.6423 matched_ion_num -1.1046 -0.7838 -0.9981 complementary_ions -0.2456 0.0890 0.0252 ion_series -0.0282 -0.3550 -0.4341 weighted_average_abs_fragment_ppm -0.0138 -0.2327 -0.0772 length_7 -0.0778 -0.0129 -0.0800 length_8 -0.0040 0.1444 0.0671 length_9_30 0.4184 0.3361 0.3272 length_31 0.0000 0.0000 0.0000 ntt -0.2143 -0.2896 -0.7027 nmc 0.0000 0.0000 0.0000 charge_1 -0.2308 -0.2209 -0.3321 charge_2 0.0936 0.0691 0.0896 charge_3 0.1385 0.2144 0.3476 charge_4 0.2860 0.1120 0.2660 charge_5 0.0199 0.2134 0.1001 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 -0.0443 0.0517 -0.0020 15.9949M -0.3041 -0.4538 -0.6407 304.20715n^ 1.9352 1.9809 1.3023 unweighted_spectral_entropy 0.0555 -0.5186 0.1568 weighted_spectral_entropy 0.4424 0.9283 0.7365 hypergeometric_probability 0.0826 -0.2626 -0.1531 intersection 0.0025 -0.2397 0.0902 pred_RT_real_units -2.2473 -1.9681 -1.4288 delta_RT_loess -5.3034 -4.7453 -4.4944 m0 Found 4332 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20534 target PSMs and 14751 decoy PSMs. Calculating q values. Final list yields 4337 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.1980 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-3_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-3_edited.pin Percolator version 3.07.1, Build Date Jun 20 2024 13:21:08 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\FragPipe\FragPipe-23.0\tools\percolator_3_7_1\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 31 --results-psms 232_2025_KULeuven_FW-3_percolator_target_psms.tsv --decoy-results-psms 232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 232_2025_KULeuven_FW-3_edited.pin Started Thu Oct 30 14:03:59 2025 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 232_2025_KULeuven_FW-3_edited.pin Features: rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 304.20715n^ unweighted_spectral_entropy weighted_spectral_entropy hypergeometric_probability intersection pred_RT_real_units delta_RT_loess Found 34470 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 20726 positives and 13744 negatives, size ratio=1.508 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 35 as initial direction. Could separate 3173 training set positives with q<0.01 in that direction. Split 2: Selected feature 35 as initial direction. Could separate 2905 training set positives with q<0.01 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 2896 training set positives with q<0.01 in that direction. Found 4316 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3300 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5525 PSMs with q<0.01 Iteration 2: Estimated 5766 PSMs with q<0.01 Iteration 3: Estimated 5829 PSMs with q<0.01 Iteration 4: Estimated 5853 PSMs with q<0.01 Iteration 5: Estimated 5861 PSMs with q<0.01 Iteration 6: Estimated 5887 PSMs with q<0.01 Iteration 7: Estimated 5877 PSMs with q<0.01 Iteration 8: Estimated 5881 PSMs with q<0.01 Iteration 9: Estimated 5878 PSMs with q<0.01 Iteration 10: Estimated 5888 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1959 -0.2024 -0.4026 abs_ppm -0.0611 -0.0007 0.0176 isotope_error_negative -0.0212 0.2676 -0.0163 isotope_error_0 0.2083 0.2782 0.1915 isotope_error_1 -0.1047 -0.0998 -0.0713 isotope_error_2 -0.0189 -0.5659 -0.1210 isotope_error_3_more -1.0083 -1.8171 -1.5530 log10_evalue 0.2819 0.1448 0.1476 hyperscore -0.1542 -0.5612 -0.3706 delta_hyperscore 0.8355 0.4202 0.2371 matched_ion_num -0.8552 -0.8061 -0.5687 complementary_ions -0.1654 0.2271 0.2151 ion_series 0.0616 0.2218 0.1332 weighted_average_abs_fragment_ppm -0.0540 -0.1639 -0.1380 length_7 -0.0418 -0.1178 0.0020 length_8 0.0303 0.1749 0.0630 length_9_30 0.3484 0.3706 0.3733 length_31 0.0000 0.0000 0.0000 ntt 0.0365 -0.0702 -0.1101 nmc 0.0000 0.0000 0.0000 charge_1 -0.1122 -0.1992 -0.2730 charge_2 -0.0120 0.0735 0.1520 charge_3 0.1127 0.1240 0.1422 charge_4 0.2187 0.2483 0.1940 charge_5 0.1295 0.0385 0.0585 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 -0.2254 -0.1127 -0.2120 15.9949M -0.1020 -0.1718 -0.1460 304.20715n^ 1.4722 2.2443 1.6069 unweighted_spectral_entropy 0.5404 0.3131 0.3346 weighted_spectral_entropy 0.4778 0.7913 0.8670 hypergeometric_probability 0.0492 -0.2341 -0.3797 intersection -0.0509 -0.0216 -0.0784 pred_RT_real_units -2.7403 -3.2417 -2.1225 delta_RT_loess -5.3727 -5.9772 -4.2707 m0 Found 5717 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 20726 target PSMs and 13744 decoy PSMs. Calculating q values. Final list yields 5721 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.1650 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 232_2025_KULeuven_FW-2.pin 232_2025_KULeuven_FW-2 232_2025_KULeuven_FW-2_percolator_target_psms.tsv 232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv interact-232_2025_KULeuven_FW-2 DDA 0.5 E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2_percolator_target_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-2_percolator_decoy_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib/* org.nesvilab.fragpipe.tools.percolator.PercolatorOutputToPepXML 232_2025_KULeuven_FW-3.pin 232_2025_KULeuven_FW-3 232_2025_KULeuven_FW-3_percolator_target_psms.tsv 232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv interact-232_2025_KULeuven_FW-3 DDA 0.5 E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3_percolator_target_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 Percolator delete temp C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-23.0\lib\fragpipe-23.0.jar org.nesvilab.utils.FileDelete E:\Ankita_MS\232_2025\02_03_Missed_cleavages\232_2025_KULeuven_FW-3_percolator_decoy_psms.tsv Process 'Percolator delete temp' finished, exit code: 0 ProteinProphet [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_proteinprophet.txt time="14:04:08" 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 E:\Ankita_MS\232_2025\02_03_Missed_cleavages\interact-232_2025_KULeuven_FW-2.pep.xml... ...read in 0 1+, 3059 2+, 2172 3+, 344 4+, 95 5+, 22 6+, 0 7+ spectra with min prob 0.5 Reading in E:\Ankita_MS\232_2025\02_03_Missed_cleavages\interact-232_2025_KULeuven_FW-3.pep.xml... ...read in 0 1+, 3485 2+, 2720 3+, 410 4+, 112 5+, 10 6+, 0 7+ spectra with min prob 0.5 Initializing 8389 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database C:\FASTAs\2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........121000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........122000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........125000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........126000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........127000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........128000 .........:.........:.........:.........:.........:........ Total: 128588 Computing degenerate peptides for 5042 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6013 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6013 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6013 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6013 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=8.08293e-06, db_size=97192802 Computing MU for 6013 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="14:04:13" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\FASTAs\2024-09-23-decoys-contam-Pisum_staivum_UP001058974_2023_10_02.fasta.fas --prefix rev_ time="14:04:13" level=info msg="Executing Database v5.1.1" time="14:04:13" level=info msg="Annotating the database" time="14:04:13" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --picked --ion 0.05 --psm 005 --pep 0.05 --prot 0.05 --tag rev_ --pepxml E:\Ankita_MS\232_2025\02_03_Missed_cleavages --protxml E:\Ankita_MS\232_2025\02_03_Missed_cleavages\combined.prot.xml --razor time="14:04:13" level=info msg="Executing Filter v5.1.1" time="14:04:13" level=info msg="Processing peptide identification files" time="14:04:13" level=info msg="Parsing E:\\Ankita_MS\\232_2025\\02_03_Missed_cleavages\\interact-232_2025_KULeuven_FW-3.pep.xml" time="14:04:13" level=info msg="Parsing E:\\Ankita_MS\\232_2025\\02_03_Missed_cleavages\\interact-232_2025_KULeuven_FW-2.pep.xml" time="14:04:14" level=info msg="1+ Charge profile" decoy=0 target=0 time="14:04:14" level=info msg="2+ Charge profile" decoy=462 target=6082 time="14:04:14" level=info msg="3+ Charge profile" decoy=211 target=4681 time="14:04:14" level=info msg="4+ Charge profile" decoy=30 target=724 time="14:04:14" level=info msg="5+ Charge profile" decoy=17 target=190 time="14:04:14" level=info msg="6+ Charge profile" decoy=8 target=24 time="14:04:14" level=info msg="Database search results" ions=8384 peptides=7306 psms=12429 time="14:04:14" level=info msg="Converged to 6.22 % FDR with 11700 PSMs" decoy=728 threshold=0.500524 total=12428 time="14:04:14" level=info msg="Converged to 5.00 % FDR with 6243 Peptides" decoy=312 threshold=0.677026 total=6555 time="14:04:14" level=info msg="Converged to 5.00 % FDR with 7367 Ions" decoy=368 threshold=0.638706 total=7735 time="14:04:14" level=info msg="Protein inference results" decoy=674 target=2025 time="14:04:14" level=info msg="Converged to 4.91 % FDR with 693 Proteins" decoy=34 threshold=0.9181 total=727 time="14:04:14" level=info msg="Applying sequential FDR estimation" ions=7081 peptides=6012 psms=11028 time="14:04:14" level=info msg="Converged to 0.53 % FDR with 10969 PSMs" decoy=58 threshold=0.504618 total=11027 time="14:04:14" level=info msg="Converged to 0.57 % FDR with 5977 Peptides" decoy=34 threshold=0.50557 total=6011 time="14:04:14" level=info msg="Converged to 0.54 % FDR with 7042 Ions" decoy=38 threshold=0.505097 total=7080 time="14:04:14" level=info msg="Post processing identifications" time="14:04:14" level=info msg="Assigning protein identifications to layers" time="14:04:14" level=info msg="Processing protein inference" time="14:04:14" level=info msg="Synchronizing PSMs and proteins" time="14:04:14" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=7041 peptides=5976 proteins=693 psms=10967 time="14:04:14" level=info msg=Saving time="14:04:15" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe report time="14:04:15" level=info msg="Executing Report v5.1.1" time="14:04:15" level=info msg="Creating reports" time="14:04:15" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="14:04:15" level=info msg="Executing Workspace v5.1.1" time="14:04:15" level=info msg="Removing workspace" time="14:04:15" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\thermo -cp C:\FragPipe\FragPipe-23.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-23.0\tools\IonQuant-1.11.11.jar ionquant.IonQuant --threads 31 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --msstats 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt --modlist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt IonQuant version IonQuant-1.11.11 Batmass-IO version 1.35.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 107 GB memory 2025-10-30 14:04:15 [INFO] - Collecting variable modifications from all psm.tsv files... 2025-10-30 14:04:15 [INFO] - Loading and indexing all psm.tsv files... 2025-10-30 14:04:15 [INFO] - Indexing experiments... 2025-10-30 14:04:15 [INFO] - Indexing runs... 2025-10-30 14:04:15 [INFO] - Collecting all compensation voltages if applicable... 2025-10-30 14:04:17 [INFO] - 232_2025_KULeuven_FW-2 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash. 2025-10-30 14:04:17 [INFO] - There is no FAIMS in the dataset. 2025-10-30 14:04:17 [INFO] - Indexing proteins... 2025-10-30 14:04:17 [INFO] - Indexing sequences... 2025-10-30 14:04:17 [INFO] - Indexing peptides... 2025-10-30 14:04:17 [INFO] - Indexing ions... 2025-10-30 14:04:17 [INFO] - Indexing PSMs... 2025-10-30 14:04:18 [INFO] - Parameters: 2025-10-30 14:04:18 [INFO] - perform-ms1quant = 1 2025-10-30 14:04:18 [INFO] - perform-isoquant = 0 2025-10-30 14:04:18 [INFO] - isotol = 20.0 2025-10-30 14:04:18 [INFO] - isolevel = 2 2025-10-30 14:04:18 [INFO] - isotype = tmt10 2025-10-30 14:04:18 [INFO] - site-reports = 0 2025-10-30 14:04:18 [INFO] - msstats = 0 2025-10-30 14:04:18 [INFO] - threads = 31 2025-10-30 14:04:18 [INFO] - mztol = 10.0 2025-10-30 14:04:18 [INFO] - rttol = 1.0 2025-10-30 14:04:18 [INFO] - imtol = 0.05 2025-10-30 14:04:18 [INFO] - minisotopes = 1 2025-10-30 14:04:18 [INFO] - minscans = 1 2025-10-30 14:04:18 [INFO] - psm = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv 2025-10-30 14:04:18 [INFO] - multidir = null 2025-10-30 14:04:18 [INFO] - excludemods = 2025-10-30 14:04:18 [INFO] - minions = 1 2025-10-30 14:04:18 [INFO] - maxlfq = 0 2025-10-30 14:04:18 [INFO] - ibaq = 0 2025-10-30 14:04:18 [INFO] - normalization = 0 2025-10-30 14:04:18 [INFO] - minexps = 1 2025-10-30 14:04:18 [INFO] - minfreq = 0.0 2025-10-30 14:04:18 [INFO] - tp = 0 2025-10-30 14:04:18 [INFO] - mbr = 0 2025-10-30 14:04:18 [INFO] - mbrrttol = 1.0 2025-10-30 14:04:18 [INFO] - mbrimtol = 0.05 2025-10-30 14:04:18 [INFO] - mbrtoprun = 10 2025-10-30 14:04:18 [INFO] - mbrmincorr = 0.0 2025-10-30 14:04:18 [INFO] - ionmobility = 0 2025-10-30 14:04:18 [INFO] - ionfdr = 0.01 2025-10-30 14:04:18 [INFO] - peptidefdr = 1.0 2025-10-30 14:04:18 [INFO] - proteinfdr = 1.0 2025-10-30 14:04:18 [INFO] - light = 2025-10-30 14:04:18 [INFO] - medium = 2025-10-30 14:04:18 [INFO] - heavy = 2025-10-30 14:04:18 [INFO] - requantify = 0 2025-10-30 14:04:18 [INFO] - writeindex = 0 2025-10-30 14:04:18 [INFO] - locprob = 0.0 2025-10-30 14:04:18 [INFO] - uniqueness = 0 2025-10-30 14:04:18 [INFO] - intensitymode = 0 2025-10-30 14:04:18 [INFO] - formula = 2025-10-30 14:04:18 [INFO] - filelist = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt 2025-10-30 14:04:18 [INFO] - specdir = E:\Ankita_MS\232_2025 2025-10-30 14:04:18 [INFO] - modlist = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt 2025-10-30 14:04:18 [INFO] - mod masses: 2025-10-30 14:04:18 [INFO] - 15.9949 2025-10-30 14:04:18 [INFO] - 42.0106 2025-10-30 14:04:18 [INFO] - 57.02146 2025-10-30 14:04:18 [INFO] - 304.20715 2025-10-30 14:04:18 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2025-10-30 14:04:18 [INFO] - Loading E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw... 2025-10-30 14:04:22 [INFO] - Building index... 2025-10-30 14:04:22 [INFO] - Quantifying... 2025-10-30 14:04:23 [INFO] - Loading E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.raw... 2025-10-30 14:04:27 [INFO] - Building index... 2025-10-30 14:04:27 [INFO] - Quantifying... 2025-10-30 14:04:27 [INFO] - Updating Philosopher's tables... 2025-10-30 14:04:27 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 IonQuant [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -Dlibs.bruker.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\FragPipe-23.0\tools\MSFragger-4.3\ext\thermo -cp C:\FragPipe\FragPipe-23.0\tools\jfreechart-1.5.3.jar;C:\FragPipe\FragPipe-23.0\tools\IonQuant-1.11.11.jar ionquant.IonQuant --threads 31 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --msstats 0 --annotation E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv=E:\Ankita_MS\232_2025\232_2025_02_03_TMT_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt --modlist E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt IonQuant version IonQuant-1.11.11 Batmass-IO version 1.35.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 107 GB memory 2025-10-30 14:04:28 [INFO] - Collecting variable modifications from all psm.tsv files... 2025-10-30 14:04:28 [INFO] - Loading and indexing all psm.tsv files... 2025-10-30 14:04:28 [INFO] - Indexing experiments... 2025-10-30 14:04:28 [INFO] - Indexing runs... 2025-10-30 14:04:28 [INFO] - Collecting all compensation voltages if applicable... 2025-10-30 14:04:30 [INFO] - 232_2025_KULeuven_FW-2 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash. 2025-10-30 14:04:30 [INFO] - There is no FAIMS in the dataset. 2025-10-30 14:04:30 [INFO] - Indexing proteins... 2025-10-30 14:04:30 [INFO] - Indexing sequences... 2025-10-30 14:04:30 [INFO] - Indexing peptides... 2025-10-30 14:04:30 [INFO] - Indexing ions... 2025-10-30 14:04:30 [INFO] - Indexing PSMs... 2025-10-30 14:04:30 [INFO] - Parameters: 2025-10-30 14:04:30 [INFO] - perform-ms1quant = 0 2025-10-30 14:04:30 [INFO] - perform-isoquant = 1 2025-10-30 14:04:30 [INFO] - isotol = 20.0 2025-10-30 14:04:30 [INFO] - isolevel = 2 2025-10-30 14:04:30 [INFO] - isotype = tmt-16 2025-10-30 14:04:30 [INFO] - annotation = 02_03_Missed_cleavages/psm.tsv=E:\Ankita_MS\232_2025\232_2025_02_03_TMT_annotation.txt 2025-10-30 14:04:30 [INFO] - site-reports = 0 2025-10-30 14:04:30 [INFO] - msstats = 0 2025-10-30 14:04:30 [INFO] - threads = 31 2025-10-30 14:04:30 [INFO] - mztol = 10.0 2025-10-30 14:04:30 [INFO] - rttol = 1.0 2025-10-30 14:04:30 [INFO] - imtol = 0.05 2025-10-30 14:04:30 [INFO] - minisotopes = 1 2025-10-30 14:04:30 [INFO] - minscans = 1 2025-10-30 14:04:30 [INFO] - psm = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv 2025-10-30 14:04:30 [INFO] - multidir = null 2025-10-30 14:04:30 [INFO] - excludemods = 2025-10-30 14:04:30 [INFO] - minions = 1 2025-10-30 14:04:30 [INFO] - maxlfq = 0 2025-10-30 14:04:30 [INFO] - ibaq = 0 2025-10-30 14:04:30 [INFO] - normalization = 0 2025-10-30 14:04:30 [INFO] - minexps = 1 2025-10-30 14:04:30 [INFO] - minfreq = 0.0 2025-10-30 14:04:30 [INFO] - tp = 0 2025-10-30 14:04:30 [INFO] - mbr = 0 2025-10-30 14:04:30 [INFO] - mbrrttol = 1.0 2025-10-30 14:04:30 [INFO] - mbrimtol = 0.05 2025-10-30 14:04:30 [INFO] - mbrtoprun = 10 2025-10-30 14:04:30 [INFO] - mbrmincorr = 0.0 2025-10-30 14:04:30 [INFO] - ionmobility = 0 2025-10-30 14:04:30 [INFO] - ionfdr = 0.01 2025-10-30 14:04:30 [INFO] - peptidefdr = 1.0 2025-10-30 14:04:30 [INFO] - proteinfdr = 1.0 2025-10-30 14:04:30 [INFO] - light = 2025-10-30 14:04:30 [INFO] - medium = 2025-10-30 14:04:30 [INFO] - heavy = 2025-10-30 14:04:30 [INFO] - requantify = 0 2025-10-30 14:04:30 [INFO] - writeindex = 0 2025-10-30 14:04:30 [INFO] - locprob = 0.0 2025-10-30 14:04:30 [INFO] - uniqueness = 0 2025-10-30 14:04:30 [INFO] - intensitymode = 0 2025-10-30 14:04:30 [INFO] - formula = 2025-10-30 14:04:30 [INFO] - filelist = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\filelist_ionquant.txt 2025-10-30 14:04:30 [INFO] - specdir = E:\Ankita_MS\232_2025 2025-10-30 14:04:30 [INFO] - modlist = E:\Ankita_MS\232_2025\02_03_Missed_cleavages\modmasses_ionquant.txt 2025-10-30 14:04:30 [INFO] - mod masses: 2025-10-30 14:04:30 [INFO] - 15.9949 2025-10-30 14:04:30 [INFO] - 42.0106 2025-10-30 14:04:30 [INFO] - 57.02146 2025-10-30 14:04:30 [INFO] - 304.20715 2025-10-30 14:04:30 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2025-10-30 14:04:30 [INFO] - Loading and quantifying E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-2.raw... 2025-10-30 14:04:34 [INFO] - Loading and quantifying E:\Ankita_MS\232_2025\232_2025_KULeuven_FW-3.raw... 2025-10-30 14:04:38 [INFO] - Updating Philosopher's tables... 2025-10-30 14:04:38 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 TmtIntegrator [Work dir: E:\Ankita_MS\232_2025\02_03_Missed_cleavages] C:\FragPipe\FragPipe-23.0\jre\bin\java.exe -Xmx107G -jar C:\FragPipe\FragPipe-23.0\tools\TMT-Integrator-6.1.1.jar E:\Ankita_MS\232_2025\02_03_Missed_cleavages\tmt-integrator-conf.yml E:\Ankita_MS\232_2025\02_03_Missed_cleavages\psm.tsv TMT Integrator 6.1.1 Parameter Loading: 15 ms Check PSM tables, get genes, and build index: 110 ms Parsing and Filtering: 156 ms Preprocessing finished. Start to process GroupBy: 0 Take log and normalize data: 15 ms Group PSM: 16 ms Remove outliers: 38 ms Collapse: 124 ms Analyzing by group GENE: 2 ms Generate reports: 21 ms ----------------------------------------------------------------------- Start to process GroupBy: 1 Take log and normalize data: 10 ms Group PSM: 10 ms Remove outliers: 10 ms Collapse: 40 ms Analyzing by group PROTEIN_ID: 0 ms Generate reports: 20 ms ----------------------------------------------------------------------- Start to process GroupBy: 2 Take log and normalize data: 10 ms Group PSM: 0 ms Remove outliers: 8 ms Collapse: 60 ms Analyzing by group PEPTIDE: 2 ms Generate reports: 130 ms ----------------------------------------------------------------------- Execution time: 797 ms Process 'TmtIntegrator' finished, exit code: 0 Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021) (timsTOF ddaPASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020) (Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics 22:100538 (2023) (MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007) (Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003) (FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (Isobaric-labeling quantification) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020) (Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019) Task Runtimes: CheckCentroid: 0.00 minutes WorkspaceCleanInit: 0.01 minutes MSFragger: 6.13 minutes MSFragger move pepxml: 0.01 minutes MSFragger move pin: 0.01 minutes MSBooster: 0.59 minutes Percolator: 0.10 minutes Percolator: Convert to pepxml: 0.09 minutes Percolator delete temp: 0.01 minutes ProteinProphet: 0.08 minutes PhilosopherDbAnnotate: 0.00 minutes PhilosopherFilter: 0.02 minutes PhilosopherReport: 0.00 minutes WorkspaceClean: 0.00 minutes IonQuant: 0.38 minutes TmtIntegrator: 0.02 minutes Finalizer Task: 0.00 minutes =============================================================ALL JOBS DONE IN 7.5 MINUTES=============================================================