System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: N/A Version info: FragPipe version 22.0 MSFragger version 4.1 IonQuant version 1.10.27 diaTracer version 1.1.5 Philosopher version 5.1.1 LCMS files: Experiment/Group: 1 (if "spectral library generation" is enabled, all files will be analyzed together) - C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw DDA 20 commands to execute: CheckCentroid C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw 21 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\05df454c-7a3c-4505-877d-147fa69aa1b8 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\7415e4ec-1d60-4d76-ad55-bf8a6431027c MSFragger [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx14G C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\fragger.params C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pepXML C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pepXML MSFragger move pin C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin MSBooster [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -cp C:\Research_Software\fragpipe_v22\tools\MSBooster-1.2.31.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\msbooster_params.txt Percolator [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 21 --results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv --decoy-results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_edited.pin Percolator: Convert to pepxml [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1 AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv interact-AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1 DDA 0.5 C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_uncalibrated.mzML Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv ProteinProphet [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1 --protxml C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\combined.prot.xml --razor PhilosopherReport [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe report WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck IonQuant [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -Dlibs.bruker.dir=C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Research_Software\fragpipe_v22\tools\jfreechart-1.5.3.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar;C:\Research_Software\fragpipe_v22\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 21 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\filelist_ionquant.txt --modlist C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [CheckCentroid], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [WorkspaceCleanInit], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [WorkspaceCleanInit], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] Cmd: [MSFragger], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [MSBooster], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [Percolator], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [ProteinProphet], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [PhilosopherDbAnnotate], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [PhilosopherFilter], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [PhilosopherReport], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [WorkspaceClean], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] Cmd: [WorkspaceClean], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] Cmd: [IonQuant], Work dir: [C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.fasta.fas~~~~~~~ >PIERCE_88320 >rev_sp|P00004|CYC_HORSE Cytochrome c OS=Equus caballus OX=9796 GN=CYCS PE=1 SV=2 >rev_sp|P00761|TRYP_PIG Trypsin OS=Sus scrofa OX=9823 PE=1 SV=1 >rev_sp|P01031|CO5_HUMAN Complement C5 OS=Homo sapiens OX=9606 GN=C5 PE=1 SV=4 >rev_sp|P02443|KRA3A_SHEEP Keratin, high-sulfur matrix protein, IIIA3A OS=Ovis aries OX=9940 PE=1 SV=1 >rev_sp|P02768|ALBU_HUMAN Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2 >rev_sp|P08263|GSTA1_HUMAN Glutathione S-transferase A1 OS=Homo sapiens OX=9606 GN=GSTA1 PE=1 SV=3 >rev_sp|P12081|HARS1_HUMAN Histidine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=HARS1 PE=1 SV=2 >rev_sp|P35527|K1C9_HUMAN Keratin, type I cytoskeletal 9 OS=Homo sapiens OX=9606 GN=KRT9 PE=1 SV=3 >rev_sp|P63279|UBC9_HUMAN SUMO-conjugating enzyme UBC9 OS=Homo sapiens OX=9606 GN=UBE2I PE=1 SV=1 >rev_sp|Q14525|KT33B_HUMAN Keratin, type I cuticular Ha3-II OS=Homo sapiens OX=9606 GN=KRT33B PE=1 SV=3 >sp|O43790|KRT86_HUMAN Keratin, type II cuticular Hb6 OS=Homo sapiens OX=9606 GN=KRT86 PE=1 SV=1 >sp|P00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial OS=Bos taurus OX=9913 GN=GLUD1 PE=1 SV=2 >sp|P00791|PEPA_PIG Pepsin A OS=Sus scrofa OX=9823 GN=PGA PE=1 SV=3 >sp|P01133|EGF_HUMAN Pro-epidermal growth factor OS=Homo sapiens OX=9606 GN=EGF PE=1 SV=2 >sp|P02534|K1M1_SHEEP Keratin, type I microfibrillar 48 kDa, component 8C-1 OS=Ovis aries OX=9940 PE=1 SV=2 >sp|P02788|TRFL_HUMAN Lactotransferrin OS=Homo sapiens OX=9606 GN=LTF PE=1 SV=6 >sp|P09211|GSTP1_HUMAN Glutathione S-transferase P OS=Homo sapiens OX=9606 GN=GSTP1 PE=1 SV=2 >sp|P15252|REF_HEVBR Rubber elongation factor protein OS=Hevea brasiliensis OX=3981 PE=1 SV=2 >sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria OX=6100 GN=GFP PE=1 SV=1 >sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2 >sp|Q15323|K1H1_HUMAN Keratin, type I cuticular Ha1 OS=Homo sapiens OX=9606 GN=KRT31 PE=1 SV=3 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v22.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=C\:\\MSData_WorkDirectory\\fasta\\2024-07-14-decoys-contam-PRTC.fasta.fas Table.editor=10.008269 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\Research_Software\\fragpipe_v22\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-python=C\:\\Program Files\\Python39\\python.exe fragpipe-config.tools-folder=C\:\\Research_Software\\fragpipe_v22\\lib\\..\\tools freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=1 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-rt-model=false msbooster.find-best-spectra-model=false msbooster.koina-url= msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=true msbooster.spectra-model=DIA-NN msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 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=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 8.014199,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; 10.008269,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; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 0.01 --picked 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 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=NOSTACK KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=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.iterloc_maxEpoch=100 ptmshepherd.iterloc_mode=false ptmshepherd.localization_allowed_res= ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.print_full_glyco_params=false ptmshepherd.prob_mass=0.5 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=true run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 skyline.run-skyline=false skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-mode=0 skyline.skyline-mods-mode=Default speclibgen.convert-pepxml=true speclibgen.convert-psm=false speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.ignore_unannotated=true speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.philosopher-msstats=false tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=C\:\\MSData_WorkDirectory\\20240714-MWM_AT-0008_PRTCInjections\\fragpipe\\LFQMBR_500fmol_Heavy workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw 21 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="20:27:04" level=info msg="Executing Workspace v5.1.1" time="20:27:04" level=info msg="Removing workspace" time="20:27:04" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\05df454c-7a3c-4505-877d-147fa69aa1b8 time="20:27:04" level=info msg="Executing Workspace v5.1.1" time="20:27:04" level=info msg="Creating workspace" time="20:27:04" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="20:27:04" level=info msg="Executing Workspace v5.1.1" time="20:27:04" level=info msg="Removing workspace" time="20:27:04" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\morga\AppData\Local\Temp\7415e4ec-1d60-4d76-ad55-bf8a6431027c time="20:27:05" level=info msg="Executing Workspace v5.1.1" time="20:27:05" level=info msg="Creating workspace" time="20:27:05" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx14G C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\fragger.params C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 14 GB memory Checking database... Checking spectral files... C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw: Scans = 264; ITMS: false; FTMS: true; Isolation sizes = [1.6] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 21 database_name = C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 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 = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 8.014199 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 = 10.008269 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 995256 fragments to be searched in 1 slices (0.01 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.14 s 001. AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw 2.0 s | deisotoping 0.0 s [progress: 262/262 (100%) - 1272 spectra/s] 0.2s | postprocessing 0.0 s ***************************FIRST SEARCH DONE IN 0.064 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | Not enough data to perform mass calibration. Using the uncalibrated data. -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | 9| 9| 9| 9| 9| 10| 9| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 10| 10| 10| 10| 10| 10 -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 10 -------|------- -------|------- Rm P. | 0 -------|------- Count | 10 -------|------- New fragment_mass_tolerance = 25.000000 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 0 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.370 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 21 database_name = C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.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 = 25.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 8.014199 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 = 10.008269 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.13 Da. 995256 fragments to be searched in 1 slices (0.01 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.02 s 001. AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw 1.0 s | deisotoping 0.0 s [progress: 262/262 (100%) - 2278 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.2 s ***************************MAIN SEARCH DONE IN 0.027 MIN*************************** *******************************TOTAL TIME 0.461 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pepXML C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar;/C:/Research_Software/fragpipe_v22/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -cp C:\Research_Software\fragpipe_v22\tools\MSBooster-1.2.31.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\msbooster_params.txt 2024-07-14 20:27:33 [INFO] - MSBooster v1.2.31 2024-07-14 20:27:33 [INFO] - Using 21 threads 2024-07-14 20:27:33 [INFO] - Initializing C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_uncalibrated.mzML 2024-07-14 20:27:34 [INFO] - Could not detect instrument type. Setting to Lumos. If a different instrument was used, specify using '--instrument' via the command line or 'instrument=' in the param file. 2024-07-14 20:27:34 [INFO] - Fragmentation type detected: HCD 2024-07-14 20:27:34 [INFO] - NCE detected: 25.0 2024-07-14 20:27:34 [INFO] - Creating input file for createFull 2024-07-14 20:27:34 [INFO] - 4 PSMs for prediction 2024-07-14 20:27:34 [INFO] - createFull input file generation took 74 milliseconds 2024-07-14 20:27:34 [INFO] - Input file at C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\spectraRT_full.tsv 2024-07-14 20:27:34 [INFO] - Generating input file for DIA-NN 2024-07-14 20:27:34 [INFO] - Creating input file for Diann 2024-07-14 20:27:34 [INFO] - 4 PSMs for prediction 2024-07-14 20:27:34 [INFO] - Writing DIA-NN input file 2024-07-14 20:27:34 [INFO] - Diann input file generation took 2 milliseconds 2024-07-14 20:27:34 [INFO] - Input file at C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\spectraRT.tsv 2024-07-14 20:27:34 [INFO] - Generating DIA-NN predictions 2024-07-14 20:27:34 [INFO] - C:\Research_Software\fragpipe_v22\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\spectraRT.tsv --predict --threads 21 --strip-unknown-mods --predict-n-frag 100 2024-07-14 20:27:34 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) 2024-07-14 20:27:34 [INFO] - Compiled on Sep 15 2022 18:28:57 2024-07-14 20:27:34 [INFO] - Current date and time: Sun Jul 14 20:27:34 2024 2024-07-14 20:27:34 [INFO] - CPU: GenuineIntel Intel(R) Core(TM) Ultra 9 185H 2024-07-14 20:27:34 [INFO] - SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 2024-07-14 20:27:34 [INFO] - Logical CPU cores: 22 2024-07-14 20:27:34 [INFO] - Predicted spectra will be saved in a binary format 2024-07-14 20:27:34 [INFO] - Thread number set to 21 2024-07-14 20:27:34 [INFO] - DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option 2024-07-14 20:27:34 [INFO] - Deep learning predictor will predict 100 fragments 2024-07-14 20:27:34 [INFO] - 2024-07-14 20:27:34 [INFO] - 0 files will be processed 2024-07-14 20:27:34 [INFO] - [0:00] Loading spectral library C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\spectraRT.tsv 2024-07-14 20:27:34 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) 2024-07-14 20:27:34 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 4 precursors in 3 elution groups. 2024-07-14 20:27:34 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction 2024-07-14 20:27:34 [INFO] - [0:00] Predicting spectra and IMs 2024-07-14 20:27:34 [INFO] - [0:00] Predicting RTs 2024-07-14 20:27:34 [INFO] - [0:00] Decoding predicted spectra and IMs 2024-07-14 20:27:34 [INFO] - [0:00] Decoding RTs 2024-07-14 20:27:34 [INFO] - [0:00] Saving the list of predictions to C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\spectraRT.predicted.bin 2024-07-14 20:27:34 [INFO] - Finished 2024-07-14 20:27:34 [INFO] - Done generating DIA-NN predictions 2024-07-14 20:27:34 [INFO] - Model running took 349 milliseconds 2024-07-14 20:27:34 [INFO] - Generating edited pin with following features: [predRTrealUnits, unweightedSpectralEntropy, deltaRTLOESS] 2024-07-14 20:27:34 [INFO] - Loading predicted library 2024-07-14 20:27:34 [INFO] - Processing pin C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin 2024-07-14 20:27:34 [INFO] - C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin has 10 PSMs 2024-07-14 20:27:34 [INFO] - Processing C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_uncalibrated.mzML ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-14 20:27:34 [INFO] - Not enough high quality PSMs for RT regression with escore cutoff of 3.1622776E-4. Relaxing escore cutoff to 0.01 2024-07-14 20:27:34 [INFO] - RT regression using 3 PSMs java.lang.IllegalArgumentException: Histogram data cannot be empty!!! at org.knowm.xchart.Histogram.sanityCheck(Histogram.java:79) at org.knowm.xchart.Histogram.(Histogram.java:60) at Features.ScoreHistogram.(ScoreHistogram.java:147) at Features.PercolatorFormatter.editPin(PercolatorFormatter.java:679) at Features.MainClass.main(MainClass.java:1318) 2024-07-14 20:27:35 [INFO] - Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-14 20:27:35 [INFO] - Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% 2024-07-14 20:27:35 [INFO] - Edited pin file at C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_edited.pin java.lang.IllegalArgumentException: Histogram data cannot be empty!!! at org.knowm.xchart.Histogram.sanityCheck(Histogram.java:79) at org.knowm.xchart.Histogram.(Histogram.java:60) at Features.ScoreHistogram.(ScoreHistogram.java:147) at Features.PercolatorFormatter.editPin(PercolatorFormatter.java:679) at Features.MainClass.main(MainClass.java:1318) java.lang.IllegalArgumentException: Histogram data cannot be empty!!! at org.knowm.xchart.Histogram.sanityCheck(Histogram.java:79) at org.knowm.xchart.Histogram.(Histogram.java:60) at Features.ScoreHistogram.(ScoreHistogram.java:147) at Features.PercolatorFormatter.editPin(PercolatorFormatter.java:679) at Features.MainClass.main(MainClass.java:1318) 2024-07-14 20:27:35 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 741 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 21 --results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv --decoy-results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_edited.pin Percolator version 3.06.5, Build Date Feb 8 2024 10:07:48 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Research_Software\fragpipe_v22\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 21 --results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv --decoy-results-psms AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_edited.pin Started Sun Jul 14 20:27:35 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_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 pred_RT_real_units unweighted_spectral_entropy delta_RT_loess Found 10 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 10 positives and 0 negatives, size ratio=inf and pi0=1 Error: no decoy PSMs were provided. No-terminate flag set: ignoring error. Warning : the number of positive samples read is too small to perform a correct classification. Warning : the number of negative samples read is too small to perform a correct classification. Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 6 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 7 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 7 training set positives with q<0.01 in that direction. Found 0 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.0360 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 0 PSMs with q<0.01 Iteration 2: Estimated 0 PSMs with q<0.01 Iteration 3: Estimated 0 PSMs with q<0.01 Iteration 4: Estimated 0 PSMs with q<0.01 Iteration 5: Estimated 0 PSMs with q<0.01 Iteration 6: Estimated 0 PSMs with q<0.01 Iteration 7: Estimated 0 PSMs with q<0.01 Iteration 8: Estimated 0 PSMs with q<0.01 Iteration 9: Estimated 0 PSMs with q<0.01 Iteration 10: Estimated 0 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 0.0609 -0.1209 0.0086 abs_ppm 0.0000 0.0000 0.0000 isotope_error_negative 0.0000 0.0000 0.0000 isotope_error_0 0.0000 0.0000 0.0000 isotope_error_1 0.0000 0.0000 0.0000 isotope_error_2 0.0000 0.0000 0.0000 isotope_error_3_more -0.0130 -0.0138 0.0009 log10_evalue 0.0130 0.0138 -0.0009 hyperscore 0.0077 0.0070 -0.0139 delta_hyperscore 0.0000 0.0223 0.0038 matched_ion_num 0.0508 -0.0209 -0.0154 complementary_ions -0.0323 0.0566 0.0052 ion_series 0.0498 -0.1047 -0.0018 weighted_average_abs_fragment_ppm 0.0000 0.0000 0.0000 length_7 -0.0021 0.0011 0.0185 length_8 0.0021 -0.0011 -0.0185 length_9_30 0.0000 0.0000 0.0000 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 0.0487 0.0238 -0.0285 charge_2 -0.0487 -0.0238 0.0285 charge_3 0.0000 0.0000 0.0000 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.0000 0.0000 0.0000 15.9949M 0.0000 0.0000 0.0000 pred_RT_real_units -0.0098 0.0864 -0.0196 unweighted_spectral_entropy 0.0000 0.0000 0.0000 delta_RT_loess 0.3547 0.3633 0.4022 m0 Found 0 test set PSMs with q<0.01. No targets found with q<0.01 Resetting score vector, using default vector. Use --override flag to prevent this. Split 1: Selected feature 1 as initial direction. Could separate 6 training set positives with q<0.01 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 7 training set positives with q<0.01 in that direction. Split 3: Selected feature 1 as initial direction. Could separate 7 training set positives with q<0.01 in that direction. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 10 target PSMs and 0 decoy PSMs. Calculating q values. Final list yields 0 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). ERROR: Only 1 bin available for PEP estimation, no distinguishing feature present. No-terminate flag set: ignoring error and adding random noise to scores to break ties for PEP calculation. Logit transforming all scores prior to PEP calculation Processing took 0.5120 cpu seconds or 1 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pin AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1 AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv interact-AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1 DDA 0.5 C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp C:\Research_Software\fragpipe_v22\jre\bin\java.exe -cp C:\Research_Software\fragpipe_v22\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\filelist_proteinprophet.txt time="20:27:37" level=info msg="Executing ProteinProphet v5.1.1" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\interact-AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pep.xml... ...read in 0 1+, 8 2+, 2 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 4 peptide weights: 0%...50%...100% Calculating protein lengths and molecular weights from database C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.fasta.fas .........:.........:... Total: 238 Computing degenerate peptides for 3 proteins: 0%...100% Computing probabilities for 3 proteins. Loop 1: 0%...100% Loop 2: 0%...100% Computing probabilities for 3 proteins. Loop 1: 0%...100% Loop 2: 0%...100% Calculating sensitivity...and error tables... INFO: mu=2.52457e-08, db_size=158443 Computing MU for 3 proteins: 0%...100% time="20:27:38" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\MSData_WorkDirectory\fasta\2024-07-14-decoys-contam-PRTC.fasta.fas --prefix rev_ time="20:27:38" level=info msg="Executing Database v5.1.1" time="20:27:38" level=info msg="Annotating the database" time="20:27:38" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1 --protxml C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\combined.prot.xml --razor time="20:27:38" level=info msg="Executing Filter v5.1.1" time="20:27:38" level=info msg="Processing peptide identification files" time="20:27:38" level=info msg="Parsing C:\\MSData_WorkDirectory\\20240714-MWM_AT-0008_PRTCInjections\\fragpipe\\LFQMBR_500fmol_Heavy\\1\\interact-AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.pep.xml" time="20:27:38" level=info msg="1+ Charge profile" decoy=0 target=0 time="20:27:38" level=info msg="2+ Charge profile" decoy=0 target=8 time="20:27:38" level=info msg="3+ Charge profile" decoy=0 target=2 time="20:27:38" level=info msg="4+ Charge profile" decoy=0 target=0 time="20:27:38" level=info msg="5+ Charge profile" decoy=0 target=0 time="20:27:38" level=info msg="6+ Charge profile" decoy=0 target=0 time="20:27:38" level=info msg="Database search results" ions=4 peptides=3 psms=10 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 10 PSMs" decoy=0 threshold=1 total=10 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 3 Peptides" decoy=0 threshold=1 total=3 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 4 Ions" decoy=0 threshold=1 total=4 time="20:27:38" level=info msg="Protein inference results" decoy=0 target=3 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 3 Proteins" decoy=0 threshold=0.999 total=3 time="20:27:38" level=info msg="Applying sequential FDR estimation" ions=4 peptides=3 psms=10 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 10 PSMs" decoy=0 threshold=1 total=10 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 3 Peptides" decoy=0 threshold=1 total=3 time="20:27:38" level=info msg="Converged to 0.00 % FDR with 4 Ions" decoy=0 threshold=1 total=4 time="20:27:38" level=info msg="Post processing identifications" time="20:27:38" level=info msg="Assigning protein identifications to layers" time="20:27:38" level=info msg="Processing protein inference" time="20:27:38" level=info msg="Synchronizing PSMs and proteins" time="20:27:38" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=4 peptides=3 proteins=3 psms=10 time="20:27:38" level=info msg=Saving time="20:27:38" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe report time="20:27:38" level=info msg="Executing Report v5.1.1" time="20:27:38" level=info msg="Creating reports" time="20:27:38" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="20:27:39" level=info msg="Executing Workspace v5.1.1" time="20:27:39" level=info msg="Removing workspace" time="20:27:39" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1] C:\Research_Software\fragpipe_v22\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="20:27:39" level=info msg="Executing Workspace v5.1.1" time="20:27:39" level=info msg="Removing workspace" time="20:27:39" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy] C:\Research_Software\fragpipe_v22\jre\bin\java.exe -Xmx14G -Dlibs.bruker.dir=C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\Research_Software\fragpipe_v22\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Research_Software\fragpipe_v22\tools\jfreechart-1.5.3.jar;C:\Research_Software\fragpipe_v22\tools\batmass-io-1.33.4.jar;C:\Research_Software\fragpipe_v22\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 21 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --msstats 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0.75 --uniqueness 0 --multidir . --filelist C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\filelist_ionquant.txt --modlist C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\modmasses_ionquant.txt IonQuant version IonQuant-1.10.27 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 14 GB memory 2024-07-14 20:27:39 [WARNING] - There are only 1 experiments. Will not calculate MaxLFQ intensity. 2024-07-14 20:27:39 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-07-14 20:27:39 [INFO] - Loading and indexing all psm.tsv files... 2024-07-14 20:27:39 [INFO] - Collecting all compensation voltages if applicable... 2024-07-14 20:27:40 [INFO] - AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash. 2024-07-14 20:27:40 [INFO] - There is no FAIMS in the dataset. 2024-07-14 20:27:40 [WARNING] - There is only one run but mbr = 1. Changing mbr to 0. 2024-07-14 20:27:40 [INFO] - Parameters: 2024-07-14 20:27:40 [INFO] - perform-ms1quant = 1 2024-07-14 20:27:40 [INFO] - perform-isoquant = 0 2024-07-14 20:27:40 [INFO] - isotol = 20.0 2024-07-14 20:27:40 [INFO] - isolevel = 2 2024-07-14 20:27:40 [INFO] - isotype = tmt10 2024-07-14 20:27:40 [INFO] - site-reports = 1 2024-07-14 20:27:40 [INFO] - msstats = 1 2024-07-14 20:27:40 [INFO] - threads = 21 2024-07-14 20:27:40 [INFO] - mztol = 10.0 2024-07-14 20:27:40 [INFO] - rttol = 0.4 2024-07-14 20:27:40 [INFO] - imtol = 0.05 2024-07-14 20:27:40 [INFO] - minisotopes = 2 2024-07-14 20:27:40 [INFO] - minscans = 3 2024-07-14 20:27:40 [INFO] - psm = C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\1\psm.tsv 2024-07-14 20:27:40 [INFO] - multidir = C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\.\ 2024-07-14 20:27:40 [INFO] - excludemods = 2024-07-14 20:27:40 [INFO] - minions = 1 2024-07-14 20:27:40 [INFO] - maxlfq = 0 2024-07-14 20:27:40 [INFO] - ibaq = 0 2024-07-14 20:27:40 [INFO] - normalization = 1 2024-07-14 20:27:40 [INFO] - minexps = 1 2024-07-14 20:27:40 [INFO] - minfreq = 0.0 2024-07-14 20:27:40 [INFO] - tp = 0 2024-07-14 20:27:40 [INFO] - mbr = 0 2024-07-14 20:27:40 [INFO] - mbrrttol = 1.0 2024-07-14 20:27:40 [INFO] - mbrimtol = 0.05 2024-07-14 20:27:40 [INFO] - mbrtoprun = 10 2024-07-14 20:27:40 [INFO] - mbrmincorr = 0.0 2024-07-14 20:27:40 [INFO] - ionmobility = 0 2024-07-14 20:27:40 [INFO] - ionfdr = 0.01 2024-07-14 20:27:40 [INFO] - peptidefdr = 1.0 2024-07-14 20:27:40 [INFO] - proteinfdr = 1.0 2024-07-14 20:27:40 [INFO] - light = 2024-07-14 20:27:40 [INFO] - medium = 2024-07-14 20:27:40 [INFO] - heavy = 2024-07-14 20:27:40 [INFO] - requantify = 0 2024-07-14 20:27:40 [INFO] - writeindex = 0 2024-07-14 20:27:40 [INFO] - locprob = 0.75 2024-07-14 20:27:40 [INFO] - uniqueness = 0 2024-07-14 20:27:40 [INFO] - filelist = C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\filelist_ionquant.txt 2024-07-14 20:27:40 [INFO] - specdir = C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw 2024-07-14 20:27:40 [INFO] - modlist = C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\fragpipe\LFQMBR_500fmol_Heavy\modmasses_ionquant.txt 2024-07-14 20:27:40 [INFO] - mod masses: 2024-07-14 20:27:40 [INFO] - 8.014199 2024-07-14 20:27:40 [INFO] - 10.008269 2024-07-14 20:27:40 [INFO] - 15.9949 2024-07-14 20:27:40 [INFO] - 42.0106 2024-07-14 20:27:40 [INFO] - 57.02146 2024-07-14 20:27:40 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-07-14 20:27:40 [INFO] - Loading C:\MSData_WorkDirectory\20240714-MWM_AT-0008_PRTCInjections\raw\AT-0008_PRTC200fmol_HSS-C18-1mm_DDA35kTop6-1.raw... 2024-07-14 20:27:42 [INFO] - Building index... 2024-07-14 20:27:42 [INFO] - Quantifying... 2024-07-14 20:27:42 [INFO] - Updating Philosopher's tables... 2024-07-14 20:27:42 [INFO] - Combining experiments and estimating protein intensity... 2024-07-14 20:27:42 [INFO] - Generating modification reports... 2024-07-14 20:27:42 [INFO] - Done! Process 'IonQuant' 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) (Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021) (Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019) (Visualization with Skyline) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 26(7):966 (2010) =============================================================ALL JOBS DONE IN 0.7 MINUTES=============================================================