did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet?

EdwardSC625 commented 1 year ago

Describe the issue or question: As attached the log file, it stopped at somewhere ask if the peptideprophet is run. However, this function is enabled and i have tried different raw data, but same error pops up. log_2023-06-29_17-32-19.txt
Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

EdwardSC625 commented 1 year ago

System OS: Windows 10, Architecture: AMD64 Java Info: 20.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)

LCMS files: Experiment/Group: 230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368

C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d

17 commands to execute: WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck MSFragger [Work dir: C:\Users\DataProc5\Documents\Search_Results] java -jar -Dfile.encoding=UTF-8 -Xmx116G T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\MSFragger-3.2\MSFragger-3.2.jar C:\Users\DataProc5\Documents\Search_Results\fragger.params C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d MSFragger move pepxml java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib\fragpipe-15.0.jar;/T:/Software_version_timsTOF/FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML PeptideProphet: Workspace init [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp] T:\Software_versiontimsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_in_use.fasta.fas ..\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML PeptideProphet: Delete temp java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp Rewrite pepxml [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d ProteinProphet [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml PhilosopherDbAnnotate [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe database --annotate T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_inuse.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe database --annotate T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_inuse.fasta.fas --prefix rev PhilosopherFilter [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_versiontimsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368 --protxml C:\Users\DataProc5\Documents\Search_Results\combined.prot.xml PhilosopherReport [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe report WorkspaceClean [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368]
    Cmd: [MSFragger], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [PeptideProphet], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [ProteinProphet], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [PhilosopherFilter], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [PhilosopherReport], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\DataProc5\Documents\Search_Results]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=T\:\\Database_timsTOF\\MSfragger\\Human\\2023-03-30-decoys-contam-Human_uniprot_Apr2020_in_use.fasta.fas
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
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=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\Users\\DataProc5\\Software\\FragPipe-20.0(latestversionJune2023)\\IonQuant-1.9.8\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=T\:\\Software_version_timsTOF\\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\\MSFragger-3.2\\MSFragger-3.2.jar
fragpipe-config.bin-philosopher=T\:\\Software_version_timsTOF\\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\\Philosopher3.4.13\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\DataProc5\\anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
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.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
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=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=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=stricttrypsin
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
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
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=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.write_calibrated_mzml=true
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=1
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=true
opair.run-opair=true
opair.single_scan_type=true
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=true
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=true
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=25
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=true
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=3
saintexpress.run-saint-express=true
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
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.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
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=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=0.01
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
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.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=true
workdir=C\:\\Users\\DataProc5\\Documents\\Search_Results
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=24

WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:24:56] Executing Workspace v3.4.13
INFO[17:24:56] Removing workspace
WARN[17:24:56] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:24:56] Done
WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck INFO[17:24:59] Executing Workspace v3.4.13
INFO[17:24:59] Creating workspace
INFO[17:24:59] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --clean --nocheck INFO[17:25:01] Executing Workspace v3.4.13
INFO[17:25:01] Removing workspace
WARN[17:25:01] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:25:01] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:25:04] Executing Workspace v3.4.13
INFO[17:25:04] Creating workspace
INFO[17:25:04] Done
MSFragger [Work dir: C:\Users\DataProc5\Documents\Search_Results] java -jar -Dfile.encoding=UTF-8 -Xmx116G T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\MSFragger-3.2\MSFragger-3.2.jar C:\Users\DataProc5\Documents\Search_Results\fragger.params C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 20.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 116 GB memory Checking database... Checking spectral files... C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d: Scans = 16515 There is a mzBIN file from C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d converted with timsdata-2-7-0. Will use this mzBIN file. ***FIRST SEARCH**** Parameters: num_threads = 24 database_name = T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_in_use.fasta.fas decoyprefix = 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 write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 378063224 fragments to be searched in 1 slices (5.63 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.64 s

230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.mzBIN 23.6 s | deisotoping 1.8 s [progress: 82680/82680 (100%) - 20753 spectra/s] 4.0s | postprocessing 0.5 s ***FIRST SEARCH DONE IN 0.691 MIN**

***MASS CALIBRATION AND PARAMETER OPTIMIZATION* -----	---------------	---------------	---------------	---------------
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
Count	1	2	2	1	skip rest
-------	-------	-------	-------	-------	-------	-------	-------	-------
-------	-------	-------	-------	-------	-------	-------	-------
Peaks	500_0	300_0	200_0	175_0	150_1	125_1	100_1
-------	-------	-------	-------	-------	-------	-------	-------
Count	0	0	1	2	2	2	2
-------	-------	-------	-------	-------	-------	-------	-------
-------	-------
Int.	1
-------	-------
Count	0
-------	-------
-------	-------
Rm P.	1
-------	-------
Count	2
-------	-------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 100 New minimum_ratio = 0.010000 New intensity_transform = 0 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.973 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 24 database_name = T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_in_use.fasta.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 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 = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.03 Da. 378063224 fragments to be searched in 1 slices (5.63 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.19 s

230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.mzBIN 2.8 s | deisotoping 0.7 s [progress: 82680/82680 (100%) - 39185 spectra/s] 2.1s | postprocessing 0.5 s MAIN SEARCH DONE IN 0.186 MIN

***TOTAL TIME 2.850 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib\fragpipe-15.0.jar;/T:/Software_version_timsTOF/FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe workspace --init --nocheck INFO[17:28:01] Executing Workspace v3.4.13
INFO[17:28:01] Creating workspace
INFO[17:28:01] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp] T:\Software_versiontimsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Database_timsTOF\MSfragger\Human\2023-03-30-decoys-contam-Human_uniprot_Apr2020_in_use.fasta.fas ..\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML INFO[17:28:04] Executing PeptideProphet v3.4.13
Unknown file type. No file loaded.C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368/230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d Unknown file type. No file loaded.C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368/230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d file 1: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML processed altogether 3862 results INFO: Results written to file: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml

C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml
Building Commentz-Walter keyword tree...
Searching the tree...
Linking duplicate entries...
Printing results...

PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x8664)) AKeller@ISB read in 14 1+, 3218 2+, 573 3+, 55 4+, 2 5+, 0 6+, and 0 7+ spectra. Found 1939 Decoys, and 1923 Non-Decoys using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20......WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+).

model complete after 27 iterations INFO[17:28:27] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\fragpipe-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368] java -cp T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml C:\Users\DataProc5\Documents\HeLa_QC_Results\230629\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d Fixing pepxml: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml Writing output to: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml2002530809881171047.temp-rewrite Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: C:\Users\DataProc5\Documents\Search_Results] T:\Software_version_timsTOF\FragPipe-15.0&MSFragger-3.2(Inuse,May,2021)\Philosopher3.4.13\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml Deleting file: C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml Moving rewritten file to original location: [C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml2002530809881171047.temp-rewrite] -> [C:\Users\DataProc5\Documents\Search_Results\230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368\interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml] INFO[17:28:31] Executing ProteinProphet v3.4.13
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in C:/Users/DataProc5/Documents/Search_Results/230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368/interact-230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.pep.xml... Process 'ProteinProphet' finished, exit code: 1 Process returned non-zero exit code, stoppingdid not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

WARNING: no data - output file will be empty FATA[17:28:32] Cannot execute program. There was an error with ProteinProphet, please check your parameters and input files


Cancelling 7 remaining tasks

danielgeiszler commented 1 year ago

Either your data is bad or your search parameters don't match the data. You found zero peptides.

EdwardSC625 commented 1 year ago

weird thing is that when i try searching those previous MS data which run in same instrument and same method, and it works. So i guess the parameters is correct?

fcyu commented 1 year ago

If the same MS data worked previously but not now, the issue must be due to different parameters. If you are sure that the same .d worked before, you can share the log files from two searches with us to take a look if you like.

Best,

Fengchao

EdwardSC625 commented 1 year ago

log_2023-06-29_09-10-58.txt This search is run using same method in the instrument with same sample, and same parameters in the software, but it works perfectly.

Much thanks for your kind help.

fcyu commented 1 year ago

It was from a different data: 230628_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13363.d vs 230629_DDA_Hela_160ng_T_IO_40min_Slot1-6_1_13368.d!

EdwardSC625 commented 1 year ago

yes, 13363 is old MS data but using same parameter in both the instrument and the software. And 13363 works wells but 13368 are having the problem. 1336 3& 13368 are same samples but different injections.

I also checked the size of the raw data file as well as the chromatogram are similar so i assume there shouldn't be zero peptides

anesvi commented 1 year ago

If you see this problem with other files let us know. But we are not able to help you at this point as we do not have the ability to troubleshoot issues with specific files, and if no similar issues are reported by other users.

EdwardSC625 commented 1 year ago

log_2023-06-30_10-20-16.txt I also encountered similar problem when i am searching it using another PC.

May I kindly learn if there are any parameters in the MSFragger software that i can try to adjust for trouble-shooting? Thank you.

fcyu commented 1 year ago

I believe the issue is in your data, not the software. Please troubleshoot your sample preparation and data acquisition.

Best,

Fengchao

Nesvilab / FragPipe

did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? #1164