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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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PTM-Shepherd becomes greyed out immediately after loading 1 mzML file #731

Closed Arthfael closed 2 years ago

Arthfael commented 2 years ago

Hi,

I just noticed an issue with the latest version of FragPipe (18.0): when I launch the GUI, I see that the PTMs tab is active and I can edit fields. PTM-Shepherd is set to active. As soon as I load one file, the tab becomes greyed out (PTM-Shepherd till shows as active, but I cannot edit anything). When I tried an Open Search, I did not see any global.modsummary.tsv file among the output files, and the Observed modification column in psm.tsv was empty. Best,

Armel

fcyu commented 2 years ago

Hi Armel,

Can you send us the log file of your open search?

Thanks,

Fengchao

Arthfael commented 2 years ago

Dear Fengchao,

Thank you very much, I have attached the log. Kind regards,

Armel

On Thu, Jun 23, 2022 at 3:35 PM Fengchao @.***> wrote:

Hi Armel,

Can you send us the log file of your open search?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/731#issuecomment-1164417510, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSHV4LIIDGA4ISUIW455VTVQRR3ZANCNFSM5ZT62ODA . You are receiving this because you authored the thread.Message ID: @.***>

System OS: Windows Server 2019, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.2.2

LCMS files: Experiment/Group: AF73_13

22 commands to execute: CheckCentroid C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx86G -cp "C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML 55 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\anicolas\AppData\Local\Temp\2\6a2a6ff1-b125-45e7-a983-ecdbc1568367 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\anicolas\AppData\Local\Temp\2\b48dc5cd-15d0-4181-a6e9-5e7e7153c255 MSFragger [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx86G C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar D:\groups_temp\Solgate\DIA\FragPipe\fragger.params D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML MSFragger move pepxml C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.pepXML D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pepXML MSFragger move pin C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.pin D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pin Crystal-C [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\thermo" -Xmx86G -cp "C:\FragPipe-jre-18.0\fragpipe\tools\original-crystalc-1.4.4.jar;C:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar;C:\FragPipe-jre-18.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\crystalc-0-AB24_AF73_13_20220520094053.pepXML.params D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pepXML Crystal-C: Delete temp C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\crystalc-0-AB24_AF73_13_20220520094053.pepXML.params PeptideProphet [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-_20220311.fasta.fas --combine AB24_AF73_13_20220520094053_c.pepXML Rewrite pepxml [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML PtmProphet [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe ptmprophet M:15.9949 --maxthreads 55 interact.pep.xml ProteinProphet [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\groups_temp\Solgate\DIA\FragPipe\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-20220311.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-20220311.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windowsamd64\philosopher.exe filter --sequential --mapmods --prot 0.01 --tag rev --pepxml D:\groups_temp\Solgate\DIA\FragPipe\AF73_13 --protxml D:\groups_temp\Solgate\DIA\FragPipe\combined.prot.xml --razor PhilosopherReport [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report SpecLibGen [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\Anaconda\python.exe -u C:\FragPipe-jre-18.0\fragpipe\tools\speclib\gen_con_spec_lib.py D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-_20220311.fasta.fas D:\groups_temp\Solgate\DIA\FragPipe\AF73_13 unused D:\groups_temp\Solgate\DIA\FragPipe\AF73_13 True unused use_easypqp noiRT;noIM 55 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\filelist_speclibgen.txt WorkspaceClean [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx86G -Dlibs.bruker.dir="C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\bruker" -Dlibs.thermo.dir="C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\thermo" -cp "C:\FragPipe-jre-18.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar;C:\FragPipe-jre-18.0\fragpipe\tools\IonQuant-1.8.0.jar" ionquant.IonQuant --threads 55 --ionmobility 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100000 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --light K0;R0 --medium K4.025107;R6.020129 --heavy K8.014199;R10.008269 --tp 0 --minfreq 0 --minions 2 --excludemods STY79.96633 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\groups_temp\Solgate\DIA\FragPipe\filelist_ionquant.txt


Execution order:

    Cmd: [START], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [CheckCentroid], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe\AF73_13]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [MSFragger], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [Crystal-C], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [PeptideProphet], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [PtmProphet], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [ProteinProphet], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [PhilosopherFilter], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [PhilosopherReport], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [SpecLibGen], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [WorkspaceClean], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe\AF73_13]
    Cmd: [WorkspaceClean], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]
    Cmd: [IonQuant], Work dir: [D:\groups_temp\Solgate\DIA\FragPipe]

>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries GN=KRT15 PE=2 SV=1
>rev_sp|P32241-4|VIPR1_HUMAN Isoform 4 of Vasoactive intestinal polypeptide receptor 1 OS=Homo sapiens OX=9606 GN=VIPR1
>rev_sp|Q5VZI3-2|TM268_HUMAN Isoform 2 of Transmembrane protein 268 OS=Homo sapiens OX=9606 GN=TMEM268
>rev_sp|Q969R2-6|OSBP2_HUMAN Isoform 6 of Oxysterol-binding protein 2 OS=Homo sapiens OX=9606 GN=OSBP2
>rev_sp|Q9ULJ8|NEB1_HUMAN Neurabin-1 OS=Homo sapiens OX=9606 GN=PPP1R9A PE=1 SV=2
>rev_tr|A0A286YF78|A0A286YF78_HUMAN D-3-phosphoglycerate dehydrogenase (Fragment) OS=Homo sapiens OX=9606 GN=PHGDH PE=1 SV=1
>rev_tr|B1AHC6|B1AHC6_HUMAN PHD finger protein 21B (Fragment) OS=Homo sapiens OX=9606 GN=PHF21B PE=1 SV=1
>rev_tr|E7EW82|E7EW82_HUMAN TRAF family member-associated NF-kappa-B activator OS=Homo sapiens OX=9606 GN=TANK PE=1 SV=1
>rev_tr|H0Y5U2|H0Y5U2_HUMAN Semaphorin-5B (Fragment) OS=Homo sapiens OX=9606 GN=SEMA5B PE=1 SV=1
>rev_tr|I3L4H9|I3L4H9_HUMAN Dynein axonemal heavy chain 2 (Fragment) OS=Homo sapiens OX=9606 GN=DNAH2 PE=1 SV=1
>rev_tr|X6RID7|X6RID7_HUMAN Cilia- and flagella-associated protein 70 (Fragment) OS=Homo sapiens OX=9606 GN=CFAP70 PE=1 SV=1
>sp|P32780|TF2H1_HUMAN General transcription factor IIH subunit 1 OS=Homo sapiens OX=9606 GN=GTF2H1 PE=1 SV=1
>sp|Q5W0Z9-3|ZDH20_HUMAN Isoform 3 of Palmitoyltransferase ZDHHC20 OS=Homo sapiens OX=9606 GN=ZDHHC20
>sp|Q969V5|MUL1_HUMAN Mitochondrial ubiquitin ligase activator of NFKB 1 OS=Homo sapiens OX=9606 GN=MUL1 PE=1 SV=1
>sp|Q9ULP9|TBC24_HUMAN TBC1 domain family member 24 OS=Homo sapiens OX=9606 GN=TBC1D24 PE=1 SV=2
>tr|A0A286YFE2|A0A286YFE2_HUMAN Stress-activated protein kinase JNK (Fragment) OS=Homo sapiens OX=9606 GN=MAPK10 PE=1 SV=1
>tr|B1AJR6|B1AJR6_HUMAN Protein-tyrosine-phosphatase OS=Homo sapiens OX=9606 GN=PTPRT PE=1 SV=1
>tr|E7EWM2|E7EWM2_HUMAN Centrosomal protein of 170 kDa OS=Homo sapiens OX=9606 GN=CEP170 PE=1 SV=1
>tr|H0Y662|H0Y662_HUMAN Proto-oncogene DBL (Fragment) OS=Homo sapiens OX=9606 GN=MCF2 PE=1 SV=1
>tr|I3L4Q0|I3L4Q0_HUMAN HCG1818442, isoform CRA_a OS=Homo sapiens OX=9606 GN=MCRIP1 PE=1 SV=1
>tr|X6RLJ0|X6RLJ0_HUMAN Complement C1q subcomponent subunit A (Fragment) OS=Homo sapiens OX=9606 GN=C1QA PE=1 SV=7
# FragPipe v18.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Fasta databases\\2022-06-23-decoys-contam-Homo_sapiens_-_uniprot-proteome_UP000005640_-_20220311.fasta.fas

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
Table.editor=0.984016
crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=0.01
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\FragPipe-jre-18.0\\fragpipe\\tools\\IonQuant-1.8.0.jar
fragpipe-config.bin-msfragger=C\:\\FragPipe-jre-18.0\\fragpipe\\tools\\MSFragger-3.5\\MSFragger-3.5.jar
fragpipe-config.bin-philosopher=C\:\\FragPipe-jre-18.0\\fragpipe\\tools\\philosopher_v4.2.2_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Anaconda\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=STY79.96633
ionquant.heavy=K8.014199;R10.008269
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=K0;R0
ionquant.locprob=0.75
ionquant.maxlfq=0
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=K4.025107;R6.020129
ionquant.minexps=1
ionquant.minfreq=0
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=0
ionquant.uniqueness=0
ionquant.use-labeling=true
ionquant.use-lfq=false
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.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.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=false
msfragger.mass_diff_to_variable_mod=1
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-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.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.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
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; 57.021464,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,KR,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=100
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.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --mapmods --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=M\:15.9949
ptmprophet.run-ptmprophet=true
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=25
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-diaumpire=false
run-psm-validation=true
run-validation-tab=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
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.glyco_qval=-1
tmtintegrator.groupby=-1
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.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\groups_temp\\Solgate\\DIA\\FragPipe
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=55

CheckCentroid C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx86G -cp "C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML 55 Done in 4103 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[11:40:50] Executing Workspace v4.2.2
INFO[11:40:50] Removing workspace
WARN[11:40:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:40:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\anicolas\AppData\Local\Temp\2\6a2a6ff1-b125-45e7-a983-ecdbc1568367 INFO[11:40:50] Executing Workspace v4.2.2
INFO[11:40:50] Creating workspace
INFO[11:40:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[11:40:51] Executing Workspace v4.2.2
INFO[11:40:51] Removing workspace
WARN[11:40:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:40:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\anicolas\AppData\Local\Temp\2\b48dc5cd-15d0-4181-a6e9-5e7e7153c255 INFO[11:40:52] Executing Workspace v4.2.2
INFO[11:40:52] Creating workspace
INFO[11:40:52] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\groups_temp\Solgate\DIA\FragPipe] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx86G C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar D:\groups_temp\Solgate\DIA\FragPipe\fragger.params D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML MSFragger version MSFragger-3.5 Batmass-IO version 1.25.5 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 Server 2019, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 86 GB memory Checking database... Checking spectral files... D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML: Scans = 60931 ***FIRST SEARCH**** Parameters: num_threads = 55 database_name = D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-_20220311.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 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 = CORRECTED 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_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 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 = 1 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 activation_types = all 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 = 57.021464 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: 337550 of length 8: 328678 of length 9: 326467 of length 10: 309905 of length 11: 294612 of length 12: 282513 of length 13: 275002 of length 14: 259551 of length 15: 246062 of length 16: 230766 of length 17: 216883 of length 18: 208235 of length 19: 203785 of length 20: 183791 of length 21: 176198 of length 22: 165254 of length 23: 154806 of length 24: 146959 of length 25: 138184 of length 26: 128833 of length 27: 123045 of length 28: 117551 of length 29: 107192 of length 30: 101543 of length 31: 95610 of length 32: 90314 of length 33: 84717 of length 34: 79353 of length 35: 72533 of length 36: 70249 of length 37: 64506 of length 38: 60383 of length 39: 54743 of length 40: 51919 of length 41: 48592 of length 42: 44817 of length 43: 37973 of length 44: 30905 of length 45: 23845 of length 46: 15942 of length 47: 10082 of length 48: 5856 of length 49: 3164 of length 50: 1856 In total 6010724 peptides. Generated 9711920 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 400206454 fragments to be searched in 1 slices (5.96 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.06 s

  1. AB24_AF73_13_20220520094053.mzML 5.0 s | deisotoping 3.5 s [progress: 60296/60296 (100%) - 14470 spectra/s] 4.2s | postprocessing 0.5 s ***FIRST SEARCH DONE IN 0.726 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 1.26 1.13 0.00 0.95 -0.54 2.25 0.01 2.26
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 6004 6173 6321 6230 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 6524 6530 6492 6538 6430 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 6601
------- -------
------- -------
Rm P. 0
------- -------
Count 6632
------- -------

New fragment_mass_tolerance = 10 PPM New use_topN_peaks = 150 New minimum_ratio = 0.010000 New intensity_transform = 1 New remove_precursor_peak = 0 New precursor_true_tolerance = 5.000000 PPM (tie breaker) ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.162 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 55 database_name = D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-_20220311.fasta.fas decoyprefix = rev precursor_mass_lower = -150.0 precursor_mass_upper = 500.0 precursor_mass_units = 0 data_type = 0 precursor_true_tolerance = 5.0 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 = CORRECTED 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_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 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 = 1 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 = 1 activation_types = all 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 = 1 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 = 57.021464 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: 337550 of length 8: 328678 of length 9: 326467 of length 10: 309905 of length 11: 294612 of length 12: 282513 of length 13: 275002 of length 14: 259551 of length 15: 246062 of length 16: 230766 of length 17: 216883 of length 18: 208235 of length 19: 203785 of length 20: 183791 of length 21: 176198 of length 22: 165254 of length 23: 154806 of length 24: 146959 of length 25: 138184 of length 26: 128833 of length 27: 123045 of length 28: 117551 of length 29: 107192 of length 30: 101543 of length 31: 95610 of length 32: 90314 of length 33: 84717 of length 34: 79353 of length 35: 72533 of length 36: 70249 of length 37: 64506 of length 38: 60383 of length 39: 54743 of length 40: 51919 of length 41: 48592 of length 42: 44817 of length 43: 37973 of length 44: 30905 of length 45: 23845 of length 46: 15942 of length 47: 10082 of length 48: 5856 of length 49: 3164 of length 50: 1856 In total 6010724 peptides. Generated 9711920 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.01 Da. 400206454 fragments to be searched in 1 slices (5.96 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.24 s

  1. AB24_AF73_13_20220520094053.mzBIN_calibrated 1.2 s [progress: 59961/59961 (100%) - 256 spectra/s] 234.5s | ramaping alternative proteins and postprocessing 16.4 s MAIN SEARCH DONE IN 4.464 MIN

***TOTAL TIME 7.352 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.pepXML D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.pin D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pin Process 'MSFragger move pin' finished, exit code: 0 Crystal-C [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\thermo" -Xmx86G -cp "C:\FragPipe-jre-18.0\fragpipe\tools\original-crystalc-1.4.4.jar;C:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar;C:\FragPipe-jre-18.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\crystalc-0-AB24_AF73_13_20220520094053.pepXML.params D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053.pepXML AB24_AF73_13_20220520094053.pepXML Done! The execution time is 0.29915 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C: Delete temp C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\crystalc-0-AB24_AF73_13_20220520094053.pepXML.params Process 'Crystal-C: Delete temp' finished, exit code: 0 PeptideProphet [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Fasta databases\2022-06-23-decoys-contam-Homosapiens-_uniprot-proteomeUP000005640-_20220311.fasta.fas --combine AB24_AF73_13_20220520094053_c.pepXML INFO[11:48:38] Executing PeptideProphet v4.2.2
file 1: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\AB24_AF73_13_20220520094053_c.pepXML processed altogether 55866 results INFO: Results written to file: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml

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 PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) @.*** read in 0 1+, 29549 2+, 19989 3+, 5330 4+, 787 5+, 178 6+, and 33 7+ spectra. Found 20684 Decoys, and 35182 Non-Decoys 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 (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations INFO[11:50:19] Done
Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml D:\groups_temp\Solgate\DIA\AB24_AF73_13_20220520094053.mzML Fixing pepxml: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml Writing output to: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml5660693342289564113.temp-rewrite Deleting file: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml Moving rewritten file to original location: [D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml5660693342289564113.temp-rewrite] -> [D:\groups_temp\Solgate\DIA\FragPipe\AF73_13\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 PtmProphet [Work dir: D:\groups_temp\Solgate\DIA\FragPipe\AF73_13] C:\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe ptmprophet M:15.9949 --maxthreads 55 interact.pep.xml INFO[11:50:21] Executing PTMProphet v4.2.2
INFO: Writing file interact.pep.xml.tmp.a14268 ...

Creating 1 threads Wait for threads to finish ... INFO: Reading file interact.pep.xml ... INFO: Applying PSM specific mass offset and tolerance ... ERROR: Cannot initialize for sequence: K[256]EVAGAKPHITAAEGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.04298.04298.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[225]VKPHSSFKPDNHVR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.04341.04341.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[522]HGELHEQFKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.04732.04732.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[147]AQVHAGGPAPHPCPR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.04943.04943.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[112]PKPDGPGGGPGGSHM[147]GGNYGDDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.04989.04989.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[141]LTHAQSTLDAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05064.05064.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: R[197]PAEDM[147]EEEQAFKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05250.05250.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: R[197]PAEDM[147]EEEQAFKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05253.05253.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: N[155]KPNM[147]SDPEESRGNDELVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05258.05258.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[154]HEEEPPQNM[147]KPQSGNDKPLSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05267.05267.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: R[108]PAEDMEEEQAFKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05270.05270.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[192]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05382.05382.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[192]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05397.05397.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[169]GVAINFVTEEDKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05418.05418.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[510]RHNSEKPPEPVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05568.05568.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[418]DVDTESPTKQK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05608.05608.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[308]VHHGVNQLKFAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05650.05650.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[191]ATYGKPVHHGVNQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05716.05716.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[114]ATYGKPVHHGVNQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05777.05777.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[114]ATYGKPVHHGVNQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05821.05821.4 Please specify modification and rerun PTMProphet ... ​ INFO: processed 1000/37727 spectrum_queries ERROR: Cannot initialize for sequence: K[256]EENSTEEQALEDQNAKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05902.05902.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[142]TM[147]RPQSFYDGSHSCAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05991.05991.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: S[128]STTSM[147]TSVPKPLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.05992.05992.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[225]VSRPATAAAAAAGSR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06013.06013.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[143]LQTGENHTSVDPR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06044.06044.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[135]LQTGENHTSVDPR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06050.06050.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[467]AKYDDIKK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06205.06205.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: E[385]QEPEKVDTEEDGKAEVASEK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06269.06269.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[98]PVKPTGGPGGGGTQTQQQM[147]NQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06325.06325.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[519]TGGPGGGGTQTQQQM[147]NQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06330.06330.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[569]GRPYDYNGPR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06340.06340.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[394]GAAM[147]VEM[147]ADGYAVDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06365.06365.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[142]NEQM[147]HQLVAAYK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06411.06411.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[161]AATSHVEGSGGVSAKGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06448.06448.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[338]AATSHVEGSGGVSAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06456.06456.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[162]VHQNSASDDAEASM[147]ISK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06688.06688.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[153]VHQNSASDDAEASM[147]ISK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06695.06695.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[112]EVDM[147]DTDAPQVSHKPGGEPK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06713.06713.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[383]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06750.06750.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[326]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06787.06787.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[326]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06805.06805.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[326]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06812.06812.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[383]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06813.06813.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[112]PGTNVAM[147]ASNQAVR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06841.06841.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[84]QEQGEGDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06851.06851.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: E[359]VKPPPGRPQPDSGR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06895.06895.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: E[254]VKPPPGRPQPDSGR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.06914.06914.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[151]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07024.07024.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: N[355]QVTQLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07066.07066.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: I[241]EQVDKEDEITEKK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07108.07108.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: D[156]PAQPM[147]SPGEATQSGARPADR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07157.07157.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: n[43]S[150]SPLYDEQGDARR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07292.07292.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: I[117]HEGCEEPATHNALAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07296.07296.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: I[117]HEGCEEPATHNALAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07321.07321.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: Y[204]LM[147]EEDEDAYKK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07336.07336.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: S[128]WVNQM[147]ESQTGEASK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07397.07397.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[77]VTEQGHELSNEER, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07414.07414.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: S[128]GSGTM[147]NLGGSLTR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07424.07424.2 Please specify modification and rerun PTMProphet ... ​ INFO: processed 2000/37727 spectrum_queries ERROR: Cannot initialize for sequence: E[401]EAEALYHSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07481.07481.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[395]AATSHVEGSGGVSAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07490.07490.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[143]ADHSSLTLGSGSSTTR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07493.07493.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[299]YEDEINKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07531.07531.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: n[43]S[479]KSESPKEPEQLR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07553.07553.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[169]AEIGIAM[147]GSGTAVAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07557.07557.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[128]MDLAQAGSTVESK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07636.07636.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[504]AKFENLCK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07650.07650.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: S[144]KAEAESLYQSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07682.07682.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[116]VGIWHCGSCM[147]K, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07687.07687.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: V[328]EATKNETSAPFK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07718.07718.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[631]QNVQLPR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07755.07755.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[383]HVNVGTIGHVDHGK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07846.07846.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[114]AFGKPQGTVAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07882.07882.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[114]AFGKPQGTVAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07884.07884.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[105]SHGEVISVPHK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07889.07889.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[593]GTEVQVDDIKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07890.07890.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[192]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07911.07911.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[105]SHGEVISVPHK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07934.07934.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[170]LEQYKEESKK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07936.07936.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[192]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07956.07956.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[135]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07984.07984.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[135]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.07987.07987.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[135]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08008.08008.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: F[188]M[147]SVQRPGPYDRPGTAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08095.08095.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[126]AHLM[147]EIQVNGGTVAEK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08145.08145.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: R[197]FDDAVVQSDM[147]K, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08147.08147.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[282]LPEYHVR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08198.08198.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[142]LSGM[147]ESYCVR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08200.08200.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[142]SPEM[147]DIQNPDDGAR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08205.08205.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: E[170]VDEQM[147]LNVQNK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08289.08289.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: Q[444]DAQVVLYR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08547.08547.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: V[140]LGEAM[147]TGISQNAK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08559.08559.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[308]ASGAPGQMGTASLLK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08616.08616.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: D[157]AINQGM[147]DEELERDEK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08758.08758.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: F[143]QDDNVEGDKVSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08867.08867.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: Q[255]APGNQDWHSAPLPGGEPSCVQK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08882.08882.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: P[338]PVHYNGPSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08913.08913.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[622]GAVITQIR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.08917.08917.3 Please specify modification and rerun PTMProphet ... ​ INFO: processed 3000/37727 spectrum_queries ERROR: Cannot initialize for sequence: R[197]PISADSAIM[147]NPASK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09020.09020.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: R[197]PISADSAIM[147]NPASK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09068.09068.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[144]GFEAASIK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09203.09203.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[69]APGAEFAPNKR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09271.09271.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[210]LTATPTPLGGM[147]TGFHM[147]QTEDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09382.09382.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: Y[204]M[147]PAVTSTPTVNQHETSTSK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09389.09389.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[141]HNQSTAINLNNPESQSM[147]HLETR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09400.09400.5 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: T[142]GTAEM[147]SSILEER, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09445.09445.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: S[143]GGGGGGGLGSGGSIR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09560.09560.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[126]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09573.09573.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[126]YAHTDCPGHADYVK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09590.09590.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[112]AQLCGAGM[147]AAVVDK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09613.09613.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[169]LGEM[147]WNNTAADDKQPYEK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09650.09650.4 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: K[169]LGEM[147]WNNTAADDKQPYEK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09657.09657.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[581]AHEVGWK, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09709.09709.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[77]QELGHSQSALASAQR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09824.09824.2 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: L[170]QQVLQMESHIQSTSDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09927.09927.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: G[98]TM[147]DDISQEEGSSQGEDSVSGSQR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.09954.09954.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: H[155]ELQANCYEEVKDR, unknown mods may exist in spectrum AB24_AF73_13_20220520094053.10007.10007.3 Please specify modification and rerun PTMProphet ... ERROR: Cannot initialize for sequence: A[128]GAGSATLSMAYAGAR, unk

fcyu commented 2 years ago

Hi Armel,

I can't reproduce your issue with the settings in your log file. But, I see that you changed some parameters, which causes the errors at the end of the log. Can you load the built-in open search workflow, and do not change the parameters unless they are necessary?

Best,

Fengchao