fcyu
commented
3 years ago It looks like an error from PTM-Shepherd. Danny @danielgeiszler , can you take a look when you have time?
Thanks,
Fengchao
Closed animesh closed 3 years ago
fcyu
commented
3 years ago It looks like an error from PTM-Shepherd. Danny @danielgeiszler , can you take a look when you have time?
Thanks,
Fengchao
danielgeiszler
commented
3 years ago Hi animesh,
Unfortunately, PTM-Shepherd can't process files that have spaces in their pathnames. It's something we're working on currently, but the only way around this currently is to rename your files and the folder name.
PTM-Shepherd will just provide summarizations of the mass shifts in your dataset. Depending on your intentions, it may not be necessary. Can you elaborate on what it is your goal with the open search is?
animesh
commented
3 years ago Removing the space in the file name seems to have worked @danielgeiszler 👍🏽 although i did not get much out of the open-search workflow (full run appended below), wondering if it is not optimized for timsTOFpro DDA data? Does it work for DIA BTW? We are looking for a modification in the sample which we don't know from beforehand but we have some idea that it is some sort of glycosylation. Do you thing glyco-workflow will have a better change is finding it?
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info:
FragPipe version 16.0
MSFragger version 3.3
Philosopher version 4.0.0 (build 1626989421)
LCMS files:
Experiment/Group: 210910_Finn_A_Coli_2_Slot1-38_1_206
- C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d
Experiment/Group: 210910_Finn_A_Sliv_1__Slot1-37_1_205
- C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d
31 commands to execute:
CheckCentroid
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx30G -cp "C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d 6
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
MSFragger [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx30G C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar C:\Users\animeshs\Desktop\FinnA\FP\fragger.params C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d
MSFragger move pepxml
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML
MSFragger move tsv
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.tsv C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.tsv
MSFragger move pin
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.pin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.pin
MSFragger move pepxml
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML
MSFragger move tsv
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.tsv C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.tsv
MSFragger move pin
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.pin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.pin
PeptideProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --combine 210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML
PeptideProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --combine 210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML
Rewrite pepxml [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d
Rewrite pepxml [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d
ProteinProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\animeshs\Desktop\FinnA\FP\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206 --protxml C:\Users\animeshs\Desktop\FinnA\FP\combined.prot.xml --razorbin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\.meta\razor.bin
PhilosopherFilter [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205 --protxml C:\Users\animeshs\Desktop\FinnA\FP\combined.prot.xml --razorbin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\.meta\razor.bin
PhilosopherReport [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe report
PhilosopherAbacus [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe abacus --razor --reprint --tag rev_ --protein 210910_Finn_A_Coli_2_Slot1-38_1_206 210910_Finn_A_Sliv_1__Slot1-37_1_205
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
PTMShepherd [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx30G -Dbatmass.io.libs.thermo.dir="C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\ext\thermo" -cp "C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\ptmshepherd-1.1.0.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\animeshs\Desktop\FinnA\FP\shepherd.config"
~~~~~~~~~~~~~~~~~~~~~~
Execution order:
Cmd: [START], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [CheckCentroid], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
Cmd: [MSFragger], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [PeptideProphet], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [ProteinProphet], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [PhilosopherReport], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [PhilosopherAbacus], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [WorkspaceClean], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
Cmd: [WorkspaceClean], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
Cmd: [WorkspaceClean], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
Cmd: [PTMShepherd], Work dir: [C:\Users\animeshs\Desktop\FinnA\FP]
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v16.0ui state cache
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=true
database.db-path=C\:\\Users\\animeshs\\Desktop\\FinnA\\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas
database.decoy-tag=rev_
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-msfragger=C\:\\Users\\animeshs\\Desktop\\Documents\\FragPipe-jre-16.0\\fragpipe\\tools\\MSFragger-3.3\\MSFragger-3.3.jar
fragpipe-config.bin-philosopher=C\:\\Users\\animeshs\\Desktop\\Documents\\philosopher_v4.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\intelpython\\python3.7\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
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=false
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
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.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
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.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.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.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
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.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01 --mapmods
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=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.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.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
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.remainder_masses=
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
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.im-cal=Automatic selection of a run as reference IM
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
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
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=-1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\Users\\animeshs\\Desktop\\FinnA\\FP
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=30
workflow.threads=6
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx30G -cp "C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d 6
Done in 0 ms.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:15:46] Executing Workspace v4.0.0
INFO[10:15:46] Removing workspace
WARN[10:15:46] Cannot read file. open .meta\meta.bin: The system cannot find the path specified.
INFO[10:15:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
INFO[10:15:47] Executing Workspace v4.0.0
INFO[10:15:47] Creating workspace
INFO[10:15:47] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:15:47] Executing Workspace v4.0.0
INFO[10:15:47] Removing workspace
WARN[10:15:47] Cannot read file. open .meta\meta.bin: The system cannot find the path specified.
INFO[10:15:47] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
INFO[10:15:48] Executing Workspace v4.0.0
INFO[10:15:48] Creating workspace
INFO[10:15:48] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:15:49] Executing Workspace v4.0.0
INFO[10:15:49] Removing workspace
WARN[10:15:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified.
INFO[10:15:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck
INFO[10:15:49] Executing Workspace v4.0.0
INFO[10:15:49] Creating workspace
INFO[10:15:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx30G C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar C:\Users\animeshs\Desktop\FinnA\FP\fragger.params C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d
MSFragger version MSFragger-3.3
Batmass-IO version 1.23.4
timsdata library version timsdata-2-8-7-1
(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: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 30 GB memory
Checking database...
Checking spectral files...
C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d: Scans = 13892
C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d: Scans = 16048
precursor_mass_mode = CORRECTED does not support specified spectral files. Using SELECTED instead.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 6
database_name = C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.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 = false
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_pin
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 (237.14773 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
Number of unique peptides
of length 7: 46449
of length 8: 45117
of length 9: 42390
of length 10: 41316
of length 11: 40933
of length 12: 39461
of length 13: 37802
of length 14: 36977
of length 15: 35387
of length 16: 34395
of length 17: 33056
of length 18: 31634
of length 19: 30256
of length 20: 29255
of length 21: 28011
of length 22: 27119
of length 23: 26076
of length 24: 24582
of length 25: 23055
of length 26: 21950
of length 27: 21111
of length 28: 20018
of length 29: 18466
of length 30: 17880
of length 31: 17003
of length 32: 15597
of length 33: 14789
of length 34: 13765
of length 35: 13203
of length 36: 12144
of length 37: 11209
of length 38: 10818
of length 39: 10099
of length 40: 9409
of length 41: 8775
of length 42: 8143
of length 43: 7147
of length 44: 6134
of length 45: 4699
of length 46: 3221
of length 47: 1850
of length 48: 1134
of length 49: 440
of length 50: 206
In total 922481 peptides.
Generated 1585744 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
70012408 fragments to be searched in 1 slices (1.04 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 2.39 s
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002. 210910_Finn_A_Sliv_1__Slot1-37_1_205.d
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002. 210910_Finn_A_Sliv_1__Slot1-37_1_205.d loading 99%679.1 s | deisotoping 0.0 s
[progress: 3603/3603 (100%) - 17490 spectra/s] 0.2s | postprocessing 0.0 s
***************************FIRST SEARCH DONE IN 23.626 MIN**************************
*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | 4.57 2.21 | -0.10 2.21 | 2.84 4.57 | -0.04 4.48
002 | 4.80 1.89 | -0.02 1.89 | 2.93 4.56 | 0.19 4.58
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50
-------|-------|-------|-------|-------|-------|-------|-------|-------
Count | skip | skip | 631| 629| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1
-------|-------|-------|-------|-------|-------|-------
Count | 638| 642| 641| 631| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
Int. | 1
-------|-------
Count | 540
-------|-------
-------|-------
Rm P. | 1
-------|-------
Count | 637
-------|-------
New fragment_mass_tolerance = 10 PPM
New use_topN_peaks = 175
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 0
New precursor_true_tolerance = 12.000000 PPM (tie breaker)
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.383 MIN*********
************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 6
database_name = C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -150.0
precursor_mass_upper = 500.0
precursor_mass_units = 0
data_type = 0
precursor_true_tolerance = 12.0
precursor_true_units = 1
fragment_mass_tolerance = 10.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mgf = 0
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = true
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_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = true
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 = 175
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
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 (237.14773 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
Number of unique peptides
of length 7: 46449
of length 8: 45117
of length 9: 42390
of length 10: 41316
of length 11: 40933
of length 12: 39461
of length 13: 37802
of length 14: 36977
of length 15: 35387
of length 16: 34395
of length 17: 33056
of length 18: 31634
of length 19: 30256
of length 20: 29255
of length 21: 28011
of length 22: 27119
of length 23: 26076
of length 24: 24582
of length 25: 23055
of length 26: 21950
of length 27: 21111
of length 28: 20018
of length 29: 18466
of length 30: 17880
of length 31: 17003
of length 32: 15597
of length 33: 14789
of length 34: 13765
of length 35: 13203
of length 36: 12144
of length 37: 11209
of length 38: 10818
of length 39: 10099
of length 40: 9409
of length 41: 8775
of length 42: 8143
of length 43: 7147
of length 44: 6134
of length 45: 4699
of length 46: 3221
of length 47: 1850
of length 48: 1134
of length 49: 440
of length 50: 206
In total 922481 peptides.
Generated 1585744 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.01 Da.
140024816 fragments to be searched in 1 slices (2.09 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 8.36 s
001. 210910_Finn_A_Coli_2_Slot1-38_1_206.mzBIN_calibrated 0.1 s
[progress: 1785/2710 (66%) - 177 spectra/s]
[progress: 2710/2710 (100%) - 228 spectra/s] 11.9s | postprocessing 0.5 s
002. 210910_Finn_A_Sliv_1__Slot1-37_1_205.mzBIN_calibrated 0.1 s
[progress: 2912/2912 (100%) - 390 spectra/s] 7.5s | postprocessing 0.4 s
***************************MAIN SEARCH DONE IN 0.525 MIN***************************
*******************************TOTAL TIME 24.533 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move tsv
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.tsv C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.tsv
Process 'MSFragger move tsv' finished, exit code: 0
MSFragger move pin
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.pin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move tsv
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.tsv C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.tsv
Process 'MSFragger move tsv' finished, exit code: 0
MSFragger move pin
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/animeshs/Desktop/Documents/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.pin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.pin
Process 'MSFragger move pin' finished, exit code: 0
PeptideProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --combine 210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML
PeptideProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --combine 210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML
INFO[10:40:29] Executing PeptideProphet v4.0.0
INFO[10:40:29] Executing PeptideProphet v4.0.0
Unknown file type. No file loaded.C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205/210910_Finn_A_Sliv_1__Slot1-37_1_205.d
Unknown file type. No file loaded.C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205/210910_Finn_A_Sliv_1__Slot1-37_1_205.d
file 1: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\210910_Finn_A_Sliv_1__Slot1-37_1_205.pepXML
Unknown file type. No file loaded.C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206/210910_Finn_A_Coli_2_Slot1-38_1_206.d
Unknown file type. No file loaded.C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206/210910_Finn_A_Coli_2_Slot1-38_1_206.d
file 1: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\210910_Finn_A_Coli_2_Slot1-38_1_206.pepXML
processed altogether 1823 results
processed altogether 1391 results
INFO: Results written to file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml
- C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml
INFO: Results written to file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml
- C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
- 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-x86_64)) AKeller@ISB
read in 26 1+, 1128 2+, 585 3+, 76 4+, 8 5+, 0 6+, and 0 7+ spectra.
Found 690 Decoys, and 1133 Non-Decoys
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
using search_offsets in mass 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 ...
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 34 1+, 1109 2+, 243 3+, 5 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 351 Decoys, and 1040 Non-Decoys
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
using search_offsets in mass 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: ...Iterations: ...............10..10............20........20..WARNING: Mixture model quality test failed for charge (1+).
....
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 (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 29 iterations
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[10:40:35] Done
Process 'PeptideProphet' finished, exit code: 0
INFO[10:40:36] Done
Process 'PeptideProphet' finished, exit code: 0
Rewrite pepxml [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Coli_2_Slot1-38_1_206.d
Fixing pepxml: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml
Writing output to: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml8033039908755870525.temp-rewrite
Deleting file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml
Moving rewritten file to original location: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml8033039908755870525.temp-rewrite] -> [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml C:\Users\animeshs\Desktop\FinnA\TTP\210910_Finn_A_Sliv_1__Slot1-37_1_205.d
Fixing pepxml: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml
Writing output to: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml2621978337474036611.temp-rewrite
Deleting file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml
Moving rewritten file to original location: [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml2621978337474036611.temp-rewrite] -> [C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
ProteinProphet [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\animeshs\Desktop\FinnA\FP\filelist_proteinprophet.txt
INFO[10:40:39] Executing ProteinProphet v4.0.0
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) (using degen pep info)
Reading in C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\interact.pep.xml...
...read in 0 1+, 0 2+, 150 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05
Reading in C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205\interact.pep.xml...
...read in 0 1+, 689 2+, 244 3+, 31 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05
Initializing 678 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/Users/animeshs/Desktop/FinnA/2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:....... Total: 14878
Computing degenerate peptides for 558 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 574 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 574 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 574 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 574 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing 525 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
INFO: mu=2.37771e-05, db_size=9155359
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
Computing MU for 574 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[10:40:40] Done
INFO[10:40:40] Executing Database v4.0.0
INFO[10:40:40] Annotating the database
INFO[10:40:41] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
INFO[10:40:42] Executing Database v4.0.0
INFO[10:40:42] Annotating the database
Process 'PhilosopherDbAnnotate' finished, exit code: 0
INFO[10:40:43] Done
PhilosopherDbAnnotate [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate C:\Users\animeshs\Desktop\FinnA\2021-09-21-decoys-contam-CelS2HisTageCOLIsLIVIDUS.fasta.fas --prefix rev_
INFO[10:40:44] Executing Database v4.0.0
INFO[10:40:44] Annotating the database
INFO[10:40:45] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206 --protxml C:\Users\animeshs\Desktop\FinnA\FP\combined.prot.xml --razorbin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\.meta\razor.bin
INFO[10:40:45] Executing Filter v4.0.0
INFO[10:40:45] Processing peptide identification files
INFO[10:40:45] 1+ Charge profile decoy=0 target=0
INFO[10:40:45] 2+ Charge profile decoy=0 target=0
INFO[10:40:45] 3+ Charge profile decoy=5 target=145
INFO[10:40:45] 4+ Charge profile decoy=0 target=0
INFO[10:40:45] 5+ Charge profile decoy=0 target=0
INFO[10:40:45] 6+ Charge profile decoy=0 target=0
INFO[10:40:45] Database search results ions=59 peptides=57 psms=150
INFO[10:40:45] Converged to 0.71 % FDR with 140 PSMs decoy=1 threshold=0.3489 total=141
INFO[10:40:45] Converged to 0.00 % FDR with 50 Peptides decoy=0 threshold=0.6191 total=50
INFO[10:40:45] Converged to 0.00 % FDR with 52 Ions decoy=0 threshold=0.6191 total=52
INFO[10:40:46] Protein inference results decoy=145 target=380
INFO[10:40:46] Converged to 1.18 % FDR with 169 Proteins decoy=2 threshold=0.9575 total=171
INFO[10:40:46] Applying sequential FDR estimation ions=48 peptides=46 psms=136
INFO[10:40:46] Converged to 0.00 % FDR with 136 PSMs decoy=0 threshold=0.3489 total=136
INFO[10:40:46] Converged to 0.00 % FDR with 46 Peptides decoy=0 threshold=0.8284 total=46
INFO[10:40:46] Converged to 0.00 % FDR with 48 Ions decoy=0 threshold=0.6546 total=48
INFO[10:40:46] Post processing identifications
INFO[10:40:46] Mapping modifications
INFO[10:40:46] Assigning protein identifications to layers
INFO[10:40:46] Processing protein inference
INFO[10:40:46] Synchronizing PSMs and proteins
INFO[10:40:46] Saving
INFO[10:40:46] Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205 --protxml C:\Users\animeshs\Desktop\FinnA\FP\combined.prot.xml --razorbin C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206\.meta\razor.bin
INFO[10:40:47] Executing Filter v4.0.0
INFO[10:40:47] Processing peptide identification files
INFO[10:40:47] 1+ Charge profile decoy=0 target=0
INFO[10:40:47] 2+ Charge profile decoy=110 target=579
INFO[10:40:47] 3+ Charge profile decoy=33 target=211
INFO[10:40:47] 4+ Charge profile decoy=5 target=26
INFO[10:40:47] 5+ Charge profile decoy=0 target=0
INFO[10:40:47] 6+ Charge profile decoy=0 target=0
INFO[10:40:47] Database search results ions=633 peptides=606 psms=964
INFO[10:40:47] Converged to 0.96 % FDR with 474 PSMs decoy=4 threshold=0.8898 total=478
INFO[10:40:47] Converged to 0.87 % FDR with 228 Peptides decoy=2 threshold=0.958 total=230
INFO[10:40:47] Converged to 0.80 % FDR with 248 Ions decoy=2 threshold=0.958 total=250
INFO[10:40:47] Protein inference results decoy=145 target=380
INFO[10:40:47] Converged to 1.18 % FDR with 169 Proteins decoy=2 threshold=0.9575 total=171
INFO[10:40:47] Applying sequential FDR estimation ions=251 peptides=230 psms=465
INFO[10:40:47] Converged to 0.43 % FDR with 463 PSMs decoy=2 threshold=0.897 total=465
INFO[10:40:47] Converged to 0.87 % FDR with 228 Peptides decoy=2 threshold=0.9087 total=230
INFO[10:40:47] Converged to 0.80 % FDR with 249 Ions decoy=2 threshold=0.9087 total=251
INFO[10:40:47] Post processing identifications
INFO[10:40:47] Mapping modifications
INFO[10:40:47] Assigning protein identifications to layers
INFO[10:40:48] Processing protein inference
INFO[10:40:48] Synchronizing PSMs and proteins
INFO[10:40:48] Saving
INFO[10:40:48] Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe report
INFO[10:40:48] Executing Report v4.0.0
INFO[10:40:48] Creating reports
INFO[10:40:48] Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe report
INFO[10:40:49] Executing Report v4.0.0
INFO[10:40:49] Creating reports
INFO[10:40:49] Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherAbacus [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe abacus --razor --reprint --tag rev_ --protein 210910_Finn_A_Coli_2_Slot1-38_1_206 210910_Finn_A_Sliv_1__Slot1-37_1_205
INFO[10:40:50] Executing Abacus v4.0.0
INFO[10:40:50] Processing combined file
INFO[10:40:50] Converged to 1.18 % FDR with 169 Proteins decoy=2 threshold=0.9575 total=171
INFO[10:40:50] Restoring protein results
INFO[10:40:50] Processing spectral counts
INFO[10:40:50] Processing peptide counts
INFO[10:40:50] Processing intensities
INFO[10:40:50] Creating Reprint reports
INFO[10:40:50] Done
Process 'PhilosopherAbacus' finished, exit code: 0
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:40:51] Executing Workspace v4.0.0
INFO[10:40:51] Removing workspace
INFO[10:40:51] Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:40:51] Executing Workspace v4.0.0
INFO[10:40:51] Removing workspace
INFO[10:40:51] Done
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Sliv_1__Slot1-37_1_205]
C:\Users\animeshs\Desktop\Documents\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:40:52] Executing Workspace v4.0.0
INFO[10:40:52] Removing workspace
INFO[10:40:52] Done
Process 'WorkspaceClean' finished, exit code: 0
PTMShepherd [Work dir: C:\Users\animeshs\Desktop\FinnA\FP]
C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx30G -Dbatmass.io.libs.thermo.dir="C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\ext\thermo" -cp "C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\ptmshepherd-1.1.0.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar;C:\Users\animeshs\Desktop\Documents\FragPipe-jre-16.0\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\animeshs\Desktop\FinnA\FP\shepherd.config"
PTM-Shepherd version 1.1.0(c) University of Michigan
Using Java 11.0.9.1 on 30720MB memory
Counting MS2 scans for dataset 210910_Finn_A_Coli_2_Slot1-38_1_206
136 MS2 scans present in dataset 210910_Finn_A_Coli_2_Slot1-38_1_206
Counting MS2 scans for dataset 210910_Finn_A_Sliv_1__Slot1-37_1_205
463 MS2 scans present in dataset 210910_Finn_A_Sliv_1__Slot1-37_1_205
Creating combined histogram
Generated histogram file for dataset 210910_Finn_A_Coli_2_Slot1-38_1_206 [-144 - 440]
Generated histogram file for dataset 210910_Finn_A_Sliv_1__Slot1-37_1_205 [-153 - 498]
Created combined histogram!
Running peak picking
Picked top 500 peaks
Removed 257 peaks with insufficient PSMs
Created summary table
Annotated summary table
Mapping modifications back into PSM lists
Created modification summary
Begin localization annotation
210910_Finn_A_Coli_2_Slot1-38_1_206 - 136 (541 ms, 139 ms)
210910_Finn_A_Sliv_1__Slot1-37_1_205 - 463 (592 ms, 313 ms)
Done
Created localization reports
Begin similarity and retention time annotation
Spectral data read into memory (134 ms)
210910_Finn_A_Coli_2_Slot1-38_1_206 - 136 (6 ms)
Spectral data read into memory (197 ms)
210910_Finn_A_Sliv_1__Slot1-37_1_205 - 463 (27 ms)
Done
Created similarity/RT reports
Combining and cleaning reports
Writing combined table for dataset 210910_Finn_A_Coli_2_Slot1-38_1_206
Writing combined table for dataset 210910_Finn_A_Sliv_1__Slot1-37_1_205
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\peaks.tsv
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\peaksummary.annotated.tsv
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\peaksummary.tsv
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\combined.tsv
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\combined.histo
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\global.locprofile.txt
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\global.simrtprofile.txt
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206.locprofile.txt
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206.simrtprofile.txt
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206.profile.tsv
Deleted file: C:\Users\animeshs\Desktop\FinnA\FP\210910_Finn_A_Coli_2_Slot1-38_1_206.histo
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Process 'PTMShepherd' 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)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020)
(Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Mol Cell Proteomics 20:100018 (2020)
(Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Label-free quantification/SILAC) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021)
(PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020)
(DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015)
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The search does not find many PSMs from your data. The reasons could be incorrect settings (enzyme, chemical labelling, database....) or your data. Please double check. There is no issue for your tools open search ddaPASEF data.
Open search does not support DIA.
Best,
Fengchao
animesh
commented
3 years ago I have loaded the analysis folder at https://drive.google.com/drive/folders/1g7Ofd_GWBO5l-zzwYivJP1dPmwtr8yZ_?usp=sharing , can you see if there is some issue with setup @fcyu 👍🏽
fcyu
commented
3 years ago Sure. I am quite busy recently, will take a look when I have time.
Best,
Fengchao
danielgeiszler
commented
3 years ago @animesh
Is this some sort of enriched data? Why do you have so few scans in general?
animesh
commented
3 years ago in a way, yes @danielgeiszler as it is a protein extracted from a gel-band so we are not expecting a lot (cf. MaxQuant reports about 100 ProteinIDs)
danielgeiszler
commented
3 years ago @animesh
So you're looking for a single modification on a single protein and you're not sure about the modification's mass? Do you know where on the protein it is?
I think this is a difficult problem, and doing open searches and searching entire databases on your enriched data is pulling in a bunch of noise. Even when doing the PeptideProphet modeling, the models were only able to converge for peptides at a 3+ charge state.
fcyu
commented
3 years ago Hi Danny,
I think this is what open search for. As long as the modification is abundant enough and not exists multiple times in one peptide, open search can find it.
Best,
Fengchao
danielgeiszler
commented
3 years ago @animesh
Can you describe more what you expect your data and modification to look like?
Should this dataset be extremely enriched for your modification, or just the protein it's on?
Are you sure that your modification weighs <500 Da, which is the mass range you used?
animesh
commented
3 years ago To be honest, we are really shooting here in the dark @danielgeiszler . What we know for sure is that one file has a protein roughly 500Da+ than other but this could be anywhere from ~100Da-1000Da and we expect it to be some sort of glycosylation? It should be in one file almost 100% and missing in the other file, so almost 0%... so far we have tried to proteases, GluC and Try/P, and as far as MaxQuant can see, it see both proteins in both files... so i guess the discriminatory peptide is not being caught by it. I was expecting the dependent-peptide to work but alas it fails https://groups.google.com/g/maxquant-list/c/g7ipwuMnUgI/m/Ve3KXm-vAAAJ ...
danielgeiszler
commented
3 years ago Hi @animesh
Sorry for the late reply, I missed the notification. Try increasing your mass range to 1500 Da or so in the MSFragger tab for the open search. You're only looking up to 500 Da, so you might be missing it if it's heavy.
animesh
commented
3 years ago looks like nothing much happened with 1500 @danielgeiszler , could crystal-C being not supported for this type of data be an issue? also is there a plan for making DIA work for open search too?
danielgeiszler
commented
3 years ago @animesh
Crystal-C shouldn't affect this, it only cleans up your search results. We don't have any plans to make DIA work for open search, but that wouldn't help in your case. If your modification is supposed to be there at high levels but it isn't showing up at all, there isn't much we can do to help you at this point. It could be a sample prep issue, which we have no control over. I'd suggest taking a look at your protein sequence and making sure that it produces peptides that can be found with your current settings, but there's nothing else we can do.
Good luck.
I am trying to run open-workflow on a timsTOFpro data but it is failing with "could not find mzData" message? I have loaded the output folder at https://drive.google.com/drive/folders/1U_n-hxpWwUq7EDjEC40sD-SC_ykMXeqt , let me know if more information is needed? I must mention that fragpipe did complain about crystal-c ...