Error code 1

[sudarshancftri21a-maker]

PTMShepherd finished with exit code 1; process returned a non-zero exit code, stopping. Cancelling remaining items.
What is the solution I can obtain for this persistent error, even after making numerous parameter changes?

[fcyu]

Please share the whole log file.

Thanks,

Fengchao

[sudarshancftri21a-maker]

Hi, The requested log file is attached. Thanks, Sudarshan M

On Thu, Jan 1, 2026 at 8:26 PM Fengchao ***@***.***> wrote: *fcyu* left a comment (Nesvilab/FragPipe#2606) <#2606 (comment)> Please share the whole log file. Thanks, Fengchao — Reply to this email directly, view it on GitHub <#2606 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B4F27ITDDVO2QTWOFDNJGB34EUYR5AVCNFSM6AAAAACQOVG4PGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTOMBTG44TKOBXGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: N/A Version info: FragPipe version 24.0 DIA-Umpire version 2.3.3 diaTracer version 2.2.1 MSFragger version 4.4 Crystal-C version 1.5.10 MSBooster version 1.4.14 Percolator version 3.7.1 PTMProphet version 6.3.2 Metaproteomics version 1.0.1 Philosopher version 5.1.3-RC9 PTM-Shepherd version 3.0.11 IonQuant version 1.11.18 TMT-Integrator version 6.1.3 FragPipe-SpecLib version 0.1.58 DIA-NN version 1.8.2 beta 8 Skyline version 24.1.0.199 Pandas version 2.3.3 Numpy version 1.26.4 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - I:\MZML\IGMT.mzML DDA 16 commands to execute: CheckCentroid C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx16G -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar org.nesvilab.fragpipe.util.CheckCentroid I:\MZML\IGMT.mzML 7 WorkspaceCleanInit [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\User\AppData\Local\Temp\f8946ac3-76de-4e5e-aa9d-9769f9abd986 MSFragger [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx16G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar C:\Users\User\Documents\igmtnightserum\fragger.params I:\MZML\IGMT.mzML MSFragger move pepxml C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err I:\MZML\IGMT.pepXML C:\Users\User\Documents\igmtnightserum\IGMT.pepXML MSFragger move tsv C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err I:\MZML\IGMT.tsv C:\Users\User\Documents\igmtnightserum\IGMT.tsv Crystal-C [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Dlibs.thermo.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\thermo -Xmx16G -cp C:\FragPipe\FragPipe-24.0\tools\original-crystalc-1.5.10.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar;C:\FragPipe\FragPipe-24.0\tools\grppr-0.3.23.jar crystalc.Run C:\Users\User\Documents\igmtnightserum\crystalc-0-IGMT.pepXML.params C:\Users\User\Documents\igmtnightserum\IGMT.pepXML Crystal-C delete temp C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete C:\Users\User\Documents\igmtnightserum\crystalc-0-IGMT.pepXML.params PeptideProphet [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --decoy rev_ --database I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas --combine IGMT_c.pepXML Rewrite pepxml [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.util.RewritePepxml C:\Users\User\Documents\igmtnightserum\interact.pep.xml I:\MZML\IGMT.mzML ProteinProphet [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\User\Documents\igmtnightserum\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe database --annotate I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe filter --sequential --prot 0.01 --tag rev_ --pepxml C:\Users\User\Documents\igmtnightserum --protxml C:\Users\User\Documents\igmtnightserum\combined.prot.xml --razor PhilosopherReport [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe report PTMShepherd [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx16G -Dlibs.thermo.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\thermo -cp C:\FragPipe\FragPipe-24.0\tools\ptmshepherd-3.0.11.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar;C:\FragPipe\FragPipe-24.0\tools\commons-math3-3.6.1.jar;C:\FragPipe\FragPipe-24.0\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\FragPipe\FragPipe-24.0\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\User\Documents\igmtnightserum\shepherd.config" WorkspaceClean [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [CheckCentroid], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [MSFragger], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [Crystal-C], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [PeptideProphet], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [ProteinProphet], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [PhilosopherFilter], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [PhilosopherReport], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [PTMShepherd], Work dir: [C:\Users\User\Documents\igmtnightserum] Cmd: [WorkspaceClean], Work dir: [C:\Users\User\Documents\igmtnightserum] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas~~~~~~~

contam_sp|O00762|UBE2C_HUMAN Ubiquitin-conjugating enzyme E2 C OS=Homo sapiens OX=9606 GN=UBE2C PE=1 SV=1 contam_sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 contam_sp|P00915|CAH1_HUMAN Carbonic anhydrase 1 OS=Homo sapiens OX=9606 GN=CA1 PE=1 SV=2 contam_sp|P02439|KRB2B_SHEEP Keratin, high-sulfur matrix protein, B2B OS=Ovis aries OX=9940 PE=1 SV=1 contam_sp|P02753|RET4_HUMAN Retinol-binding protein 4 OS=Homo sapiens OX=9606 GN=RBP4 PE=1 SV=3 contam_sp|P08311|CATG_HUMAN Cathepsin G OS=Homo sapiens OX=9606 GN=CTSG PE=1 SV=2 contam_sp|P15252|REF_HEVBR Rubber elongation factor protein OS=Hevea brasiliensis OX=3981 PE=1 SV=2 contam_sp|P55957|BID_HUMAN BH3-interacting domain death agonist OS=Homo sapiens OX=9606 GN=BID PE=1 SV=1 contam_sp|P99999|CYC_HUMAN Cytochrome c OS=Homo sapiens OX=9606 GN=CYCS PE=1 SV=2 contam_sp|Q9NSB4|KRT82_HUMAN Keratin, type II cuticular Hb2 OS=Homo sapiens OX=9606 GN=KRT82 PE=1 SV=3 rev_contam_sp|P00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial OS=Bos taurus OX=9913 GN=GLUD1 PE=1 SV=2 rev_contam_sp|P00883|ALDOA_RABIT Fructose-bisphosphate aldolase A OS=Oryctolagus cuniculus OX=9986 GN=ALDOA PE=1 SV=2 rev_contam_sp|P02438|KRB2A_SHEEP Keratin, high-sulfur matrix protein, B2A OS=Ovis aries OX=9940 PE=1 SV=2 rev_contam_sp|P02741|CRP_HUMAN C-reactive protein OS=Homo sapiens OX=9606 GN=CRP PE=1 SV=1 rev_contam_sp|P08263|GSTA1_HUMAN Glutathione S-transferase A1 OS=Homo sapiens OX=9606 GN=GSTA1 PE=1 SV=3 rev_contam_sp|P15241|K2M2_SHEEP Keratin, type II microfibrillar, component 7C OS=Ovis aries OX=9940 PE=1 SV=1 rev_contam_sp|P51965|UB2E1_HUMAN Ubiquitin-conjugating enzyme E2 E1 OS=Homo sapiens OX=9606 GN=UBE2E1 PE=1 SV=1 rev_contam_sp|P81054|PLMP_GRIFR Peptidyl-Lys metalloendopeptidase OS=Grifola frondosa OX=5627 GN=MEP PE=1 SV=2 rev_contam_sp|Q9NSB2|KRT84_HUMAN Keratin, type II cuticular Hb4 OS=Homo sapiens OX=9606 GN=KRT84 PE=2 SV=2 rev_tr|A0A3Q1LZ90|A0A3Q1LZ90_BOVIN sp|Q2UVX4|CO3_BOVIN tr|A0AAA9RYV6|A0AAA9RYV6_BOVIN

~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v24.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=I\:\\database\\database\\2026-01-01-decoys-contam-repeatedremoved.fasta.fas crystalc.run-crystalc=true database.decoy-tag=rev_ diann.channel-normalization-strategy=0 diann.cmd-opts= diann.gene-level-report=false diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.mbr=false diann.medium= diann.min-site-prob=0.75 diann.mod-tag= diann.modified-peptide-level-report=true diann.peptide-level-report=true diann.protein-level-report=false diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=2 diann.redo-protein-inference=false diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.site-level-report=false diann.unrelated-runs=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.coadaptr.fpop.fpop_masses= fpop.coadaptr.fpop.run-fpop-coadaptr=false fpop.fragpipe.fpop.fpop-tmt=false fpop.fragpipe.fpop.label_control= fpop.fragpipe.fpop.label_fpop= fpop.fragpipe.fpop.region_size=1 fpop.fragpipe.fpop.run-fpop=false fpop.fragpipe.fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\FragPipe\\FragPipe-24.0\\tools\\diann\\1.8.2_beta_8\\windows\\DiaNN.exe fragpipe-config.bin-python=C\:\\FragPipe\\FragPipe-24.0\\python\\python.exe fragpipe-config.tools-folder=C\:\\FragPipe\\FragPipe-24.0\\tools freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.formula= ionquant.heavy= ionquant.imtol=0.05 ionquant.intensitymode=2 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=1 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 mbg.allow_chimeric=false mbg.expand_db=1 mbg.fdr=0.010 mbg.max_glycan_q=0.01 mbg.max_skips=0 mbg.min_glycans=2 mbg.min_psms=5 mbg.residues_to_add=HexNAc(1),Hex(1),Fuc(1),NeuAc(1),NH4(1),Na(1),Fe(1) mbg.run-mbg=false metaproteomics.cmd-line-opts= metaproteomics.delta-hyperscore=0.0 metaproteomics.host-name=Homo sapiens metaproteomics.iterations=3 metaproteomics.min-pept-cnt-per-prot=1 metaproteomics.min-uniq-pept-cnt=3 metaproteomics.min-uniq-pept-cnt-per-prot=1 metaproteomics.qvalue=0.01 metaproteomics.run-metaproteomics=false msbooster.find-best-im-model=false msbooster.find-best-rt-model=false msbooster.find-best-spectra-model=false msbooster.fragmentation-type=0 msbooster.im-model=DIA-NN msbooster.koina-url= msbooster.predict-im=true msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.rt-model=DIA-NN msbooster.run-msbooster=false msbooster.spectra-model=DIA-NN msbooster.spectral-library-path= msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.analyzer_types=all msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761 msfragger.diagnostic_intensity_filter=0.1 msfragger.digest-only=false msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y,Y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0 msfragger.labile_fragment_ion_series=b,y msfragger.labile_search_mode=nglycan msfragger.localize_delta_mass=true msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 203.07937 406.15874 568.21156 730.26438 349.13728 552.21665 714.26947 876.32229 892.3172 1038.37511 1054.37002 1095.39657 1184.43302 1200.42793 1216.42284 1241.45448 1257.44939 1298.47594 1362.48075 1378.47566 1387.51239 1403.5073 1419.50221 1444.53385 1460.52876 1501.55531 1540.52848 1548.54481 1549.56521 1564.53972 1565.56012 1581.55503 1589.57136 1590.59176 1605.56627 1606.58667 1622.58158 1647.61322 1663.60813 1694.60272 1702.5813 1704.63468 1710.59763 1726.59254 1727.61294 1736.64967 1751.62418 1752.64458 1767.61909 1768.63949 1784.6344 1809.66604 1825.66095 1850.69259 1864.63412 1866.6875 1872.65045 1888.64536 1897.68209 1907.71405 1913.677 1914.6974 1929.67191 1930.69231 1938.70864 1946.68722 1954.70355 1955.72395 1970.69846 1971.71886 1987.71377 1996.7505 2012.74541 2018.70836 2026.68694 2028.74032 2034.70327 2043.74 2053.77196 2059.73491 2060.75531 2069.76687 2075.72982 2076.75022 2091.72473 2092.74513 2100.76146 2110.79342 2116.75637 2117.77677 2132.75128 2133.77168 2141.78801 2142.80841 2149.76659 2157.78292 2158.80332 2174.79823 2188.73976 2190.79314 2204.77242 2205.79282 2206.81322 2215.82478 2220.76733 2221.78773 2222.80813 2236.76224 2237.78264 2238.80304 2245.79897 2246.81937 2256.85133 2261.79388 2262.81428 2263.83468 2272.84624 2277.78879 2278.80919 2279.82959 2287.84592 2294.8041 2295.8245 2303.84083 2311.81941 2313.87279 2320.85614 2336.85105 2350.79258 2350.83033 2352.84596 2361.88269 2366.82524 2382.82015 2391.85688 2393.87251 2407.85179 2423.8467 2424.8671 2425.8875 2432.88343 2434.89906 2439.84161 2440.86201 2448.87834 2457.87732 2459.9307 2464.87325 2475.92561 2482.90896 2498.90387 2539.93042 2553.9097 2555.92533 2569.90461 2570.92501 2580.95697 2585.89952 2586.91992 2596.95188 2601.89443 2619.93014 2621.98352 2628.96687 2642.94615 2351.85073 2643.94138 2658.94106 2659.93629 2674.93597 2676.9516 2701.98324 2715.96252 2716.98292 2717.97815 2731.95743 2732.97783 2747.95234 2759.0047 2481.88856 2772.98398 2788.97889 2789.99929 2800.03125 2804.9738 2805.9942 2861.00003 2864.03606 2876.99494 2878.01534 2892.98985 2894.01025 2896.05105 2908.98476 2910.00516 2919.04189 2627.94647 2921.05752 2935.0368 2937.0776 2946.08916 2951.03171 2952.05211 2967.02662 3007.05794 3009.07357 3023.05285 3025.06848 3039.04776 2756.98907 2465.89365 3048.08449 3055.04267 3064.0794 3067.11543 3080.07431 3081.09471 3083.11034 3083.13551 3096.06922 3147.11515 3165.16344 3210.13731 3226.13222 3228.17302 3229.16825 3242.12713 3244.16793 3258.12204 3276.15775 3284.17408 3292.15266 3372.19013 3405.20035 3421.19526 3432.24762 3155.13148 3446.2269 3448.24253 3462.22181 3478.21672 3517.22764 3533.22255 3549.21746 3575.2695 3591.26441 3594.30044 3607.25932 3663.28555 3679.28046 3704.3121 3720.30701 3737.32232 3753.31723 3769.31214 3785.30705 3797.37981 3866.36492 4028.41774 4102.45451 4118.44942 4134.44433 4307.54951 4323.54442 4393.54993 4758.68212 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 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=400 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=tsv_pepXML msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-200 msfragger.precursor_mass_mode=corrected msfragger.precursor_mass_units=0 msfragger.precursor_mass_upper=4000 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses=203.07937 msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,3; 6.020129,R,false,3 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=300 msfragger.write_calibrated_mzml=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.allowed_sites= opair.filterOxonium=true opair.glyco_db=HexNAc(1),HexNAc(2),HexNAc(2)Hex(1),HexNAc(2)Hex(2),HexNAc(1)Fuc(1),HexNAc(2)Fuc(1),HexNAc(2)Hex(1)Fuc(1),HexNAc(2)Hex(2)Fuc(1),HexNAc(2)Hex(3),HexNAc(2)Hex(3)Fuc(1),HexNAc(2)Hex(4),HexNAc(3)Hex(3),HexNAc(2)Hex(3)Fuc(2),HexNAc(2)Hex(4)Fuc(1),HexNAc(2)Hex(5),HexNAc(3)Hex(3)Fuc(1),HexNAc(3)Hex(4),HexNAc(4)Hex(3),HexNAc(2)Hex(5)Fuc(1),HexNAc(2)Hex(6),HexNAc(3)Hex(3)Fuc(2),HexNAc(3)Hex(4)Fuc(1),HexNAc(3)Hex(5),HexNAc(4)Hex(3)Fuc(1),HexNAc(4)Hex(4),HexNAc(5)Hex(3),HexNAc(2)Hex(7),HexNAc(3)Hex(4)NeuAc(1),HexNAc(3)Hex(4)Fuc(2),HexNAc(3)Hex(4)NeuGc(1),HexNAc(3)Hex(5)Fuc(1),HexNAc(3)Hex(6),HexNAc(4)Hex(3)NeuAc(1),HexNAc(4)Hex(3)Fuc(2),HexNAc(4)Hex(3)NeuGc(1),HexNAc(4)Hex(4)Fuc(1),HexNAc(4)Hex(5),HexNAc(5)Hex(3)Fuc(1),HexNAc(5)Hex(4),HexNAc(3)Hex(4)Fuc(1)NeuAc(1),HexNAc(2)Hex(8),HexNAc(6)Hex(3),HexNAc(3)Hex(4)Fuc(1)NeuGc(1),HexNAc(3)Hex(5)NeuAc(1),HexNAc(3)Hex(5)NeuGc(1),HexNAc(3)Hex(6)Fuc(1),HexNAc(4)Hex(3)Fuc(3),HexNAc(4)Hex(4)NeuAc(1),HexNAc(4)Hex(4)Fuc(2),HexNAc(4)Hex(4)NeuGc(1),HexNAc(4)Hex(5)Fuc(1),HexNAc(4)Hex(6),HexNAc(5)Hex(4)Fuc(1),HexNAc(5)Hex(5),HexNAc(6)Hex(3)Fuc(1),HexNAc(2)Hex(9),HexNAc(6)Hex(4),HexNAc(3)Hex(6)NeuAc(1),HexNAc(3)Hex(6)NeuGc(1),HexNAc(4)Hex(4)Fuc(1)NeuAc(1),HexNAc(7)Hex(3),HexNAc(4)Hex(4)Fuc(1)NeuGc(1),HexNAc(4)Hex(5)NeuAc(1),HexNAc(4)Hex(5)Fuc(2),HexNAc(4)Hex(5)NeuGc(1),HexNAc(4)Hex(6)Fuc(1),HexNAc(5)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(7),HexNAc(5)Hex(4)NeuAc(1),HexNAc(5)Hex(3)Fuc(1)NeuGc(1),HexNAc(5)Hex(4)Fuc(2),HexNAc(5)Hex(4)NeuGc(1),HexNAc(5)Hex(5)Fuc(1),HexNAc(5)Hex(6),HexNAc(6)Hex(3)Fuc(2),HexNAc(6)Hex(4)Fuc(1),HexNAc(3)Hex(6)Fuc(1)NeuAc(1),HexNAc(2)Hex(10),HexNAc(6)Hex(5),HexNAc(3)Hex(6)Fuc(1)NeuGc(1),HexNAc(4)Hex(4)Fuc(2)NeuAc(1),HexNAc(7)Hex(3)Fuc(1),HexNAc(4)Hex(5)Fuc(1)NeuAc(1),HexNAc(4)Hex(4)Fuc(2)NeuGc(1),HexNAc(4)Hex(5)Fuc(3),HexNAc(7)Hex(4),HexNAc(4)Hex(6)NeuAc(1),HexNAc(4)Hex(5)Fuc(1)NeuGc(1),HexNAc(4)Hex(6)Fuc(2),HexNAc(4)Hex(6)NeuGc(1),HexNAc(4)Hex(7)Fuc(1),HexNAc(5)Hex(4)Fuc(1)NeuAc(1),HexNAc(8)Hex(3),HexNAc(5)Hex(4)Fuc(1)NeuGc(1),HexNAc(5)Hex(5)NeuAc(1),HexNAc(5)Hex(5)Fuc(2),HexNAc(5)Hex(5)NeuGc(1),HexNAc(5)Hex(6)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1),HexNAc(6)Hex(3)Fuc(3),HexNAc(5)Hex(7),HexNAc(6)Hex(4)NeuAc(1),HexNAc(6)Hex(3)Fuc(1)NeuGc(1),HexNAc(6)Hex(4)Fuc(2),HexNAc(6)Hex(5)Fuc(1),HexNAc(2)Hex(11),HexNAc(6)Hex(6),HexNAc(4)Hex(5)NeuAc(2),HexNAc(4)Hex(5)Fuc(2)NeuAc(1),HexNAc(4)Hex(5)Fuc(4),HexNAc(7)Hex(4)Fuc(1),HexNAc(4)Hex(5)NeuAc(1)NeuGc(1),HexNAc(4)Hex(5)Fuc(2)NeuGc(1),HexNAc(4)Hex(6)Fuc(1)NeuAc(1),HexNAc(4)Hex(6)Fuc(3),HexNAc(4)Hex(5)NeuGc(2),HexNAc(4)Hex(6)Fuc(1)NeuGc(1),HexNAc(4)Hex(7)NeuAc(1),HexNAc(4)Hex(7)Fuc(2),HexNAc(5)Hex(4)NeuAc(2),HexNAc(5)Hex(4)Fuc(2)NeuAc(1),HexNAc(8)Hex(3)Fuc(1),HexNAc(5)Hex(4)NeuAc(1)NeuGc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(1),HexNAc(5)Hex(4)Fuc(2)NeuGc(1),HexNAc(5)Hex(5)Fuc(3),HexNAc(8)Hex(4),HexNAc(5)Hex(4)NeuGc(2),HexNAc(5)Hex(5)Fuc(1)NeuGc(1),HexNAc(5)Hex(6)NeuAc(1),HexNAc(5)Hex(6)Fuc(2),HexNAc(6)Hex(3)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)NeuGc(1),HexNAc(5)Hex(7)Fuc(1),HexNAc(6)Hex(3)Fuc(2)NeuGc(1),HexNAc(5)Hex(8),HexNAc(9)Hex(3),HexNAc(6)Hex(5)Fuc(2),HexNAc(6)Hex(6)Fuc(1),HexNAc(2)Hex(12),HexNAc(4)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(7),HexNAc(7)Hex(4)Fuc(2),HexNAc(4)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(4)Hex(5)Fuc(1)NeuGc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(6),HexNAc(5)Hex(5)NeuAc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(4)Fuc(1)NeuGc(2),HexNAc(5)Hex(5)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(3),HexNAc(6)Hex(3)Fuc(1)NeuAc(2),HexNAc(8)Hex(5),HexNAc(5)Hex(5)NeuGc(2),HexNAc(5)Hex(6)Fuc(1)NeuGc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(8)Fuc(1),HexNAc(9)Hex(3)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuGc(2),HexNAc(9)Hex(4),HexNAc(6)Hex(6)Fuc(2),HexNAc(6)Hex(7)Fuc(1),HexNAc(7)Hex(6)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(2),HexNAc(7)Hex(7),HexNAc(5)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)NeuAc(2),HexNAc(5)Hex(6)Fuc(2)NeuAc(1),HexNAc(8)Hex(5)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuGc(2),HexNAc(5)Hex(6)NeuAc(1)NeuGc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(2)NeuGc(1),HexNAc(8)Hex(6),HexNAc(5)Hex(6)NeuGc(2),HexNAc(5)Hex(9)Fuc(1),HexNAc(9)Hex(4)Fuc(1),HexNAc(6)Hex(6)Fuc(3),HexNAc(4)Hex(5)Fuc(3)NeuAc(2),HexNAc(4)Hex(5)Fuc(3)NeuAc(1),HexNAc(6)Hex(7)NeuAc(1),HexNAc(4)Hex(5)Fuc(3)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)NeuGc(1),HexNAc(4)Hex(5)Fuc(3)NeuGc(2),HexNAc(6)Hex(9),HexNAc(7)Hex(7)Fuc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)Fuc(3)NeuAc(1),HexNAc(7)Hex(8),HexNAc(5)Hex(6)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)Fuc(3)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuGc(2),HexNAc(8)Hex(7),HexNAc(6)Hex(6)NeuAc(1),HexNAc(6)Hex(6)NeuAc(2),HexNAc(6)Hex(6)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(1),HexNAc(9)Hex(6),HexNAc(6)Hex(6)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuGc(1),HexNAc(6)Hex(8)NeuAc(1),HexNAc(5)Hex(6)NeuAc(3),HexNAc(7)Hex(8)Fuc(1),HexNAc(5)Hex(6)NeuAc(2)NeuGc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)NeuAc(1)NeuGc(2),HexNAc(5)Hex(7)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(8)Fuc(4),HexNAc(5)Hex(6)NeuGc(3),HexNAc(5)Hex(7)Fuc(1)NeuGc(2),HexNAc(6)Hex(6)Fuc(1)NeuAc(2),HexNAc(6)Hex(6)Fuc(1)NeuAc(1),HexNAc(8)Hex(8),HexNAc(6)Hex(6)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)NeuAc(2),HexNAc(6)Hex(7)Fuc(4),HexNAc(9)Hex(6)Fuc(1),HexNAc(6)Hex(7)NeuAc(1)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuGc(2),HexNAc(6)Hex(8)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)NeuGc(2),HexNAc(5)Hex(6)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(7)Hex(8)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(5)Fuc(1)NeuAc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(3),HexNAc(5)Hex(6)Fuc(1)NeuGc(3),HexNAc(6)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(8)Hex(8)Fuc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuAc(2),HexNAc(8)Hex(9),HexNAc(6)Hex(7)Fuc(5),HexNAc(6)Hex(5)Fuc(1)NeuGc(3),HexNAc(6)Hex(11)Fuc(1),HexNAc(10)Hex(7),HexNAc(6)Hex(6)Fuc(1)NeuAc(3),HexNAc(6)Hex(6)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(6)Hex(7)NeuAc(3),HexNAc(6)Hex(7)Fuc(4)NeuAc(1),HexNAc(8)Hex(9)Fuc(1),HexNAc(6)Hex(7)NeuAc(2)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(4)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuGc(3),HexNAc(6)Hex(10)Fuc(1)NeuAc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(2),HexNAc(6)Hex(10)Fuc(1)NeuGc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(3),HexNAc(6)Hex(9)Fuc(1)NeuAc(2),HexNAc(6)Hex(9)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(9)Hex(9)Fuc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(2),HexNAc(9)Hex(10),HexNAc(7)Hex(8)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuGc(2),HexNAc(6)Hex(7)NeuAc(4),HexNAc(6)Hex(7)NeuAc(3)NeuGc(1),HexNAc(6)Hex(7)NeuAc(2)NeuGc(2),HexNAc(7)Hex(7)Fuc(1)NeuAc(3),HexNAc(7)Hex(7)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(9)Hex(10)Fuc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuAc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(3)NeuGc(1),HexNAc(7)Hex(6)Fuc(1)NeuAc(4),HexNAc(7)Hex(6)Fuc(1)NeuAc(3)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(7)Hex(8)Fuc(1)NeuGc(3),HexNAc(10)Hex(10)Fuc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(4),HexNAc(7)Hex(8)Fuc(1)NeuAc(4),HexNAc(8)Hex(9)Fuc(1)NeuAc(3),HexNAc(8)Hex(9)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(11)Hex(11)NeuAc(1),HexNAc(11)Hex(11)NeuGc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(4),HexNAc(9)Hex(10)Fuc(1)NeuAc(4) opair.max_glycans=1 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 4000.0 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 --prot 0.01 phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=true phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.override-defaults=false ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotate_assigned_mods=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=true ptmshepherd.annotation-unimod=false ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions=0,203.07937,406.15874,568.21156,730.26438,892.3172,349.137279 ptmshepherd.decoy_type=1 ptmshepherd.diag_ions=204.086646,186.076086,168.065526,366.139466,144.0656,138.055,512.197375,292.1026925,274.0921325,657.2349,243.026426,405.079246,485.045576,308.09761 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_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_lda=false ptmshepherd.glyco_lda_features=yscore,oxo,mass ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase=HexNAc(1),HexNAc(2),HexNAc(2)Hex(1),HexNAc(2)Hex(2),HexNAc(1)Fuc(1),HexNAc(2)Fuc(1),HexNAc(2)Hex(1)Fuc(1),HexNAc(2)Hex(2)Fuc(1),HexNAc(2)Hex(3),HexNAc(2)Hex(3)Fuc(1),HexNAc(2)Hex(4),HexNAc(3)Hex(3),HexNAc(2)Hex(3)Fuc(2),HexNAc(2)Hex(4)Fuc(1),HexNAc(2)Hex(5),HexNAc(3)Hex(3)Fuc(1),HexNAc(3)Hex(4),HexNAc(4)Hex(3),HexNAc(2)Hex(5)Fuc(1),HexNAc(2)Hex(6),HexNAc(3)Hex(3)Fuc(2),HexNAc(3)Hex(4)Fuc(1),HexNAc(3)Hex(5),HexNAc(4)Hex(3)Fuc(1),HexNAc(4)Hex(4),HexNAc(5)Hex(3),HexNAc(2)Hex(7),HexNAc(3)Hex(4)NeuAc(1),HexNAc(3)Hex(4)Fuc(2),HexNAc(3)Hex(4)NeuGc(1),HexNAc(3)Hex(5)Fuc(1),HexNAc(3)Hex(6),HexNAc(4)Hex(3)NeuAc(1),HexNAc(4)Hex(3)Fuc(2),HexNAc(4)Hex(3)NeuGc(1),HexNAc(4)Hex(4)Fuc(1),HexNAc(4)Hex(5),HexNAc(5)Hex(3)Fuc(1),HexNAc(5)Hex(4),HexNAc(3)Hex(4)Fuc(1)NeuAc(1),HexNAc(2)Hex(8),HexNAc(6)Hex(3),HexNAc(3)Hex(4)Fuc(1)NeuGc(1),HexNAc(3)Hex(5)NeuAc(1),HexNAc(3)Hex(5)NeuGc(1),HexNAc(3)Hex(6)Fuc(1),HexNAc(4)Hex(3)Fuc(3),HexNAc(4)Hex(4)NeuAc(1),HexNAc(4)Hex(4)Fuc(2),HexNAc(4)Hex(4)NeuGc(1),HexNAc(4)Hex(5)Fuc(1),HexNAc(4)Hex(6),HexNAc(5)Hex(4)Fuc(1),HexNAc(5)Hex(5),HexNAc(6)Hex(3)Fuc(1),HexNAc(2)Hex(9),HexNAc(6)Hex(4),HexNAc(3)Hex(6)NeuAc(1),HexNAc(3)Hex(6)NeuGc(1),HexNAc(4)Hex(4)Fuc(1)NeuAc(1),HexNAc(7)Hex(3),HexNAc(4)Hex(4)Fuc(1)NeuGc(1),HexNAc(4)Hex(5)NeuAc(1),HexNAc(4)Hex(5)Fuc(2),HexNAc(4)Hex(5)NeuGc(1),HexNAc(4)Hex(6)Fuc(1),HexNAc(5)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(7),HexNAc(5)Hex(4)NeuAc(1),HexNAc(5)Hex(3)Fuc(1)NeuGc(1),HexNAc(5)Hex(4)Fuc(2),HexNAc(5)Hex(4)NeuGc(1),HexNAc(5)Hex(5)Fuc(1),HexNAc(5)Hex(6),HexNAc(6)Hex(3)Fuc(2),HexNAc(6)Hex(4)Fuc(1),HexNAc(3)Hex(6)Fuc(1)NeuAc(1),HexNAc(2)Hex(10),HexNAc(6)Hex(5),HexNAc(3)Hex(6)Fuc(1)NeuGc(1),HexNAc(4)Hex(4)Fuc(2)NeuAc(1),HexNAc(7)Hex(3)Fuc(1),HexNAc(4)Hex(5)Fuc(1)NeuAc(1),HexNAc(4)Hex(4)Fuc(2)NeuGc(1),HexNAc(4)Hex(5)Fuc(3),HexNAc(7)Hex(4),HexNAc(4)Hex(6)NeuAc(1),HexNAc(4)Hex(5)Fuc(1)NeuGc(1),HexNAc(4)Hex(6)Fuc(2),HexNAc(4)Hex(6)NeuGc(1),HexNAc(4)Hex(7)Fuc(1),HexNAc(5)Hex(4)Fuc(1)NeuAc(1),HexNAc(8)Hex(3),HexNAc(5)Hex(4)Fuc(1)NeuGc(1),HexNAc(5)Hex(5)NeuAc(1),HexNAc(5)Hex(5)Fuc(2),HexNAc(5)Hex(5)NeuGc(1),HexNAc(5)Hex(6)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1),HexNAc(6)Hex(3)Fuc(3),HexNAc(5)Hex(7),HexNAc(6)Hex(4)NeuAc(1),HexNAc(6)Hex(3)Fuc(1)NeuGc(1),HexNAc(6)Hex(4)Fuc(2),HexNAc(6)Hex(5)Fuc(1),HexNAc(2)Hex(11),HexNAc(6)Hex(6),HexNAc(4)Hex(5)NeuAc(2),HexNAc(4)Hex(5)Fuc(2)NeuAc(1),HexNAc(4)Hex(5)Fuc(4),HexNAc(7)Hex(4)Fuc(1),HexNAc(4)Hex(5)NeuAc(1)NeuGc(1),HexNAc(4)Hex(5)Fuc(2)NeuGc(1),HexNAc(4)Hex(6)Fuc(1)NeuAc(1),HexNAc(4)Hex(6)Fuc(3),HexNAc(4)Hex(5)NeuGc(2),HexNAc(4)Hex(6)Fuc(1)NeuGc(1),HexNAc(4)Hex(7)NeuAc(1),HexNAc(4)Hex(7)Fuc(2),HexNAc(5)Hex(4)NeuAc(2),HexNAc(5)Hex(4)Fuc(2)NeuAc(1),HexNAc(8)Hex(3)Fuc(1),HexNAc(5)Hex(4)NeuAc(1)NeuGc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(1),HexNAc(5)Hex(4)Fuc(2)NeuGc(1),HexNAc(5)Hex(5)Fuc(3),HexNAc(8)Hex(4),HexNAc(5)Hex(4)NeuGc(2),HexNAc(5)Hex(5)Fuc(1)NeuGc(1),HexNAc(5)Hex(6)NeuAc(1),HexNAc(5)Hex(6)Fuc(2),HexNAc(6)Hex(3)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)NeuGc(1),HexNAc(5)Hex(7)Fuc(1),HexNAc(6)Hex(3)Fuc(2)NeuGc(1),HexNAc(5)Hex(8),HexNAc(9)Hex(3),HexNAc(6)Hex(5)Fuc(2),HexNAc(6)Hex(6)Fuc(1),HexNAc(2)Hex(12),HexNAc(4)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(7),HexNAc(7)Hex(4)Fuc(2),HexNAc(4)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(4)Hex(5)Fuc(1)NeuGc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(6),HexNAc(5)Hex(5)NeuAc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(4)Fuc(1)NeuGc(2),HexNAc(5)Hex(5)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(3),HexNAc(6)Hex(3)Fuc(1)NeuAc(2),HexNAc(8)Hex(5),HexNAc(5)Hex(5)NeuGc(2),HexNAc(5)Hex(6)Fuc(1)NeuGc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(8)Fuc(1),HexNAc(9)Hex(3)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuGc(2),HexNAc(9)Hex(4),HexNAc(6)Hex(6)Fuc(2),HexNAc(6)Hex(7)Fuc(1),HexNAc(7)Hex(6)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(2),HexNAc(7)Hex(7),HexNAc(5)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)NeuAc(2),HexNAc(5)Hex(6)Fuc(2)NeuAc(1),HexNAc(8)Hex(5)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuGc(2),HexNAc(5)Hex(6)NeuAc(1)NeuGc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(2)NeuGc(1),HexNAc(8)Hex(6),HexNAc(5)Hex(6)NeuGc(2),HexNAc(5)Hex(9)Fuc(1),HexNAc(9)Hex(4)Fuc(1),HexNAc(6)Hex(6)Fuc(3),HexNAc(4)Hex(5)Fuc(3)NeuAc(2),HexNAc(4)Hex(5)Fuc(3)NeuAc(1),HexNAc(6)Hex(7)NeuAc(1),HexNAc(4)Hex(5)Fuc(3)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)NeuGc(1),HexNAc(4)Hex(5)Fuc(3)NeuGc(2),HexNAc(6)Hex(9),HexNAc(7)Hex(7)Fuc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)Fuc(3)NeuAc(1),HexNAc(7)Hex(8),HexNAc(5)Hex(6)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(6)Fuc(3)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuGc(2),HexNAc(8)Hex(7),HexNAc(6)Hex(6)NeuAc(1),HexNAc(6)Hex(6)NeuAc(2),HexNAc(6)Hex(6)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(1),HexNAc(9)Hex(6),HexNAc(6)Hex(6)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuGc(1),HexNAc(6)Hex(8)NeuAc(1),HexNAc(5)Hex(6)NeuAc(3),HexNAc(7)Hex(8)Fuc(1),HexNAc(5)Hex(6)NeuAc(2)NeuGc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)NeuAc(1)NeuGc(2),HexNAc(5)Hex(7)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(5)Hex(8)Fuc(4),HexNAc(5)Hex(6)NeuGc(3),HexNAc(5)Hex(7)Fuc(1)NeuGc(2),HexNAc(6)Hex(6)Fuc(1)NeuAc(2),HexNAc(6)Hex(6)Fuc(1)NeuAc(1),HexNAc(8)Hex(8),HexNAc(6)Hex(6)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(6)Hex(7)NeuAc(2),HexNAc(6)Hex(7)Fuc(4),HexNAc(9)Hex(6)Fuc(1),HexNAc(6)Hex(7)NeuAc(1)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuGc(2),HexNAc(6)Hex(8)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)NeuGc(2),HexNAc(5)Hex(6)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(7)Hex(8)NeuGc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(5)Fuc(1)NeuAc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(3),HexNAc(5)Hex(6)Fuc(1)NeuGc(3),HexNAc(6)Hex(5)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(8)Hex(8)Fuc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuAc(2),HexNAc(8)Hex(9),HexNAc(6)Hex(7)Fuc(5),HexNAc(6)Hex(5)Fuc(1)NeuGc(3),HexNAc(6)Hex(11)Fuc(1),HexNAc(10)Hex(7),HexNAc(6)Hex(6)Fuc(1)NeuAc(3),HexNAc(6)Hex(6)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(6)Hex(7)NeuAc(3),HexNAc(6)Hex(7)Fuc(4)NeuAc(1),HexNAc(8)Hex(9)Fuc(1),HexNAc(6)Hex(7)NeuAc(2)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(4)NeuGc(1),HexNAc(6)Hex(6)Fuc(1)NeuGc(3),HexNAc(6)Hex(10)Fuc(1)NeuAc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(2),HexNAc(6)Hex(10)Fuc(1)NeuGc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(3),HexNAc(6)Hex(9)Fuc(1)NeuAc(2),HexNAc(6)Hex(9)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(9)Hex(9)Fuc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(2),HexNAc(9)Hex(10),HexNAc(7)Hex(8)Fuc(1)NeuAc(1)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuGc(2),HexNAc(6)Hex(7)NeuAc(4),HexNAc(6)Hex(7)NeuAc(3)NeuGc(1),HexNAc(6)Hex(7)NeuAc(2)NeuGc(2),HexNAc(7)Hex(7)Fuc(1)NeuAc(3),HexNAc(7)Hex(7)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(9)Hex(10)Fuc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(6)Hex(7)Fuc(1)NeuAc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(3)NeuGc(1),HexNAc(7)Hex(6)Fuc(1)NeuAc(4),HexNAc(7)Hex(6)Fuc(1)NeuAc(3)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(7)Hex(8)Fuc(1)NeuGc(3),HexNAc(10)Hex(10)Fuc(1),HexNAc(7)Hex(7)Fuc(1)NeuAc(4),HexNAc(7)Hex(8)Fuc(1)NeuAc(4),HexNAc(8)Hex(9)Fuc(1)NeuAc(3),HexNAc(8)Hex(9)Fuc(1)NeuAc(2)NeuGc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(1)NeuGc(2),HexNAc(11)Hex(11)NeuAc(1),HexNAc(11)Hex(11)NeuGc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(4),HexNAc(9)Hex(10)Fuc(1)NeuAc(4) 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.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.print_full_glyco_params=false ptmshepherd.prob_mass=0.5 ptmshepherd.remainder_masses=203.07937 ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=true ptmshepherd.run_diagextract_mode=true ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=true ptmshepherd.shuffle_decoy_intensities=false ptmshepherd.spectra_condPeaks=150 ptmshepherd.spectra_condRatio=0.0001 ptmshepherd.spectra_maxPrecursorCharge=4 ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.use_glycan_fragment_probs=false ptmshepherd.use_msfragger_localization=false ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true saintexpress.virtual-controls=100 skyline.fdr=1 skyline.generate-skyline-quant-report=false skyline.min-site-prob=0.75 skyline.mod-tag= skyline.run-skyline=false skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-fragment-tolerance=10 skyline.skyline-library-product-ions=12 skyline.skyline-mods-mode=Default skyline.skyline-precursor-tolerance=10 skyline.skyline-rt-tolerance=2 skyline.use-existing-skyline-document=false speclibgen.convert-pepxml=true speclibgen.convert-psm=false speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=Regular (not glyco) speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_temp_files=false tab-run.export_matched_fragments=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=0.01 tmtintegrator.groupby=-1 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_resolution=0 tmtintegrator.min_site_prob=-1 tmtintegrator.min_snr=0 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.philosopher-msstats=false tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_d_tag=Pool tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=true transfer-learning.credential= transfer-learning.instrument=Astral transfer-learning.keep-decoys=false transfer-learning.max-charge=3 transfer-learning.min-charge=2 transfer-learning.model-path= transfer-learning.nce=30 transfer-learning.output-format=tsv transfer-learning.peptides-to-predict=Whole FASTA file transfer-learning.perform-transfer-learning=true transfer-learning.predict-im=true transfer-learning.predict-ms2=true transfer-learning.predict-rt=true transfer-learning.predict-spectral-library=true transfer-learning.run-transfer-learning=false transfer-learning.spectral-library-path= workdir=C\:\\Users\\User\\Documents\\igmtnightserum workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.misc.sdrf-type=Default workflow.ram=16 workflow.threads=7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Xmx16G -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar org.nesvilab.fragpipe.util.CheckCentroid I:\MZML\IGMT.mzML 7 Done in 45.3 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --clean --nocheck time="21:12:27" level=info msg="Executing Workspace v5.1.3" time="21:12:27" level=info msg="Removing workspace" time="21:12:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe workspace --init --nocheck --temp C:\Users\User\AppData\Local\Temp\f8946ac3-76de-4e5e-aa9d-9769f9abd986 time="21:12:27" level=info msg="Executing Workspace v5.1.3" time="21:12:27" level=info msg="Creating workspace" time="21:12:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx16G C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\MSFragger-4.4.jar C:\Users\User\Documents\igmtnightserum\fragger.params I:\MZML\IGMT.mzML MSFragger version MSFragger-4.4 Batmass-IO version 1.36.5 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 16 GB memory Checking database... Checking spectral files... IGMT.mzML: Scans = 814; MS2 ITMS = false; MS2 FTMS = false; MS2 ASTMS = false; MS1 ITMS = false; Isolation sizes = [1.0]; Instrument = TripleTOF 5600 ***********************************FIRST SEARCH************************************ Parameters: num_threads = 7 database_name = I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas decoy_prefix = rev_ keep_decoys = 1 precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 use_detailed_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y, ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 973 of length 8: 996 of length 9: 1135 of length 10: 905 of length 11: 984 of length 12: 972 of length 13: 883 of length 14: 871 of length 15: 796 of length 16: 869 of length 17: 729 of length 18: 732 of length 19: 774 of length 20: 775 of length 21: 801 of length 22: 581 of length 23: 540 of length 24: 486 of length 25: 439 of length 26: 468 of length 27: 502 of length 28: 417 of length 29: 356 of length 30: 379 of length 31: 354 of length 32: 296 of length 33: 277 of length 34: 252 of length 35: 250 of length 36: 281 of length 37: 213 of length 38: 212 of length 39: 164 of length 40: 200 of length 41: 176 of length 42: 161 of length 43: 153 of length 44: 121 of length 45: 87 of length 46: 62 of length 47: 56 of length 48: 25 of length 49: 17 of length 50: 10 In total 20730 peptides. Generated 30020 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.10 Da. 1220022 fragments to be searched in 1 slices (0.01 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.11 s 001. IGMT.mzML 97.0 s | deisotoping 0.5 s [progress: 814/814 (100%) - 2332 spectra/s] 0.3s postprocessing IGMT.mzML 0.0 s ***************************FIRST SEARCH DONE IN 1.808 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | Not enough data to perform mass calibration. Using the uncalibrated data. -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | 5| 5| 1| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 5| 0| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 5 -------|------- -------|------- Rm P. | 0 -------|------- Count | 4 -------|------- New fragment_mass_tolerance = 5.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 0.539 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 7 database_name = I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas decoy_prefix = rev_ keep_decoys = 1 precursor_mass_lower = -200.0 precursor_mass_upper = 4000.0 precursor_mass_units = 0 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 5.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mzml = 1 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0.0/1038.3751/1054.37/1095.3966/1184.433/1200.428/1216.4229/1241.4545/1257.4493/1298.476/1362.4807/1378.4757/1387.5123/1403.5073/1419.5022/1444.5338/1460.5288/1501.5553/1540.5284/1548.5448/1549.5652/1564.5397/1565.5602/1581.555/1589.5714/1590.5918/1605.5663/1606.5867/1622.5815/1647.6132/1663.6082/1694.6027/1702.5813/1704.6346/1710.5977/1726.5925/1727.6129/1736.6497/1751.6241/1752.6445/1767.6191/1768.6395/1784.6344/1809.666/1825.661/1850.6926/1864.6342/1866.6875/1872.6504/1888.6454/1897.6821/1907.714/1913.677/1914.6974/1929.6719/1930.6923/1938.7086/1946.6873/1954.7035/1955.724/1970.6985/1971.7189/1987.7137/1996.7505/2012.7454/2018.7084/2026.6869/2028.7404/203.07938/2034.7032/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.7297/2076.7502/2091.7246/2092.745/2100.7615/2110.7935/2116.7563/2117.7769/2132.7512/2133.7717/2141.788/2142.8083/2149.7666/2157.783/2158.8032/2174.7983/2188.7397/2190.7932/2204.7725/2205.7927/2206.8132/2215.8247/2220.7673/2221.7878/2222.808/2236.7622/2237.7827/2238.803/2245.799/2246.8193/2256.8513/2261.794/2262.8142/2263.8347/2272.8462/2277.7888/2278.809/2279.8296/2287.846/2294.8042/2295.8245/2303.8408/2311.8193/2313.8728/2320.8562/2336.851/2350.7925/2350.8303/2351.8508/2352.846/2361.8826/2366.8252/2382.82/2391.857/2393.8726/2407.8518/2423.8467/2424.8672/2425.8875/2432.8835/2434.8992/2439.8416/2440.862/2448.8784/2457.8774/2459.9307/2464.8733/2465.8936/2475.9255/2481.8887/2482.909/2498.9038/2539.9304/2553.9097/2555.9253/2569.9045/2570.925/2580.957/2585.8994/2586.92/2596.952/2601.8945/2619.9302/2621.9834/2627.9465/2628.9668/2642.946/2643.9414/2658.9412/2659.9363/2674.936/2676.9517/2701.9832/2715.9624/2716.983/2717.9783/2731.9575/2732.9778/2747.9524/2756.989/2759.0046/2772.984/2788.979/2789.9993/2800.0312/2804.9739/2805.9941/2861.0/2864.0361/2876.9949/2878.0154/2892.9897/2894.0103/2896.051/2908.9849/2910.0051/2919.042/2921.0576/2935.0369/2937.0776/2946.089/2951.0317/2952.052/2967.0266/3007.0579/3009.0735/3023.0527/3025.0684/3039.0479/3048.0845/3055.0427/3064.0793/3067.1155/3080.0742/3081.0947/3083.1104/3083.1355/3096.0693/3147.1152/3155.1316/3165.1633/3210.1372/3226.1323/3228.173/3229.1682/3242.1272/3244.168/3258.122/3276.1577/3284.174/3292.1526/3372.1902/3405.2004/3421.1953/3432.2476/3446.2268/3448.2424/3462.222/3478.2168/349.13727/3517.2275/3533.2227/3549.2175/3575.2695/3591.2644/3594.3005/3607.2593/3663.2856/3679.2805/3704.312/3720.3071/3737.3223/3753.3171/3769.3123/3785.3071/3797.38/3866.365/4028.4177/406.15875/4102.4546/4118.449/4134.4443/4307.5493/4323.5444/4393.55/4758.682/552.2167/568.21155/714.2695/730.2644/876.32227/892.3172 use_detailed_offsets = 0 labile_search_mode = NGLYCAN restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y, labile_fragment_ion_series = b,y ion_series_definitions = diagnostic_intensity_filter = 0.1 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 remainder_fragment_masses = 203.07937 search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 973 of length 8: 996 of length 9: 1135 of length 10: 905 of length 11: 984 of length 12: 972 of length 13: 883 of length 14: 871 of length 15: 796 of length 16: 869 of length 17: 729 of length 18: 732 of length 19: 774 of length 20: 775 of length 21: 801 of length 22: 581 of length 23: 540 of length 24: 486 of length 25: 439 of length 26: 468 of length 27: 502 of length 28: 417 of length 29: 356 of length 30: 379 of length 31: 354 of length 32: 296 of length 33: 277 of length 34: 252 of length 35: 250 of length 36: 281 of length 37: 213 of length 38: 212 of length 39: 164 of length 40: 200 of length 41: 176 of length 42: 161 of length 43: 153 of length 44: 121 of length 45: 87 of length 46: 62 of length 47: 56 of length 48: 25 of length 49: 17 of length 50: 10 In total 20730 peptides. Generated 30020 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.00 Da. 2440044 fragments to be searched in 1 slices (0.02 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.20 s 001. IGMT.mzML 1.3 s | deisotoping 0.0 s [progress: 814/814 (100%) - 383 spectra/s] 2.1s postprocessing IGMT.mzML 4.4 s ***************************MAIN SEARCH DONE IN 0.251 MIN*************************** *******************************TOTAL TIME 2.597 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err I:\MZML\IGMT.pepXML C:\Users\User\Documents\igmtnightserum\IGMT.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar;/C:/FragPipe/FragPipe-24.0/lib/batmass-io-1.36.5.jar org.nesvilab.utils.FileMove --no-err I:\MZML\IGMT.tsv C:\Users\User\Documents\igmtnightserum\IGMT.tsv Process 'MSFragger move tsv' finished, exit code: 0 Crystal-C [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -Dlibs.thermo.dir=C:\FragPipe\FragPipe-24.0\tools\MSFragger-4.4\ext\thermo -Xmx16G -cp C:\FragPipe\FragPipe-24.0\tools\original-crystalc-1.5.10.jar;C:\FragPipe\FragPipe-24.0\tools\batmass-io-1.36.5.jar;C:\FragPipe\FragPipe-24.0\tools\grppr-0.3.23.jar crystalc.Run C:\Users\User\Documents\igmtnightserum\crystalc-0-IGMT.pepXML.params C:\Users\User\Documents\igmtnightserum\IGMT.pepXML IGMT.pepXML Done! The execution time is 0.08008 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C delete temp C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib\fragpipe-24.0.jar org.nesvilab.utils.FileDelete C:\Users\User\Documents\igmtnightserum\crystalc-0-IGMT.pepXML.params Process 'Crystal-C delete temp' finished, exit code: 0 PeptideProphet [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --decoy rev_ --database I:\database\database\2026-01-01-decoys-contam-repeatedremoved.fasta.fas --combine IGMT_c.pepXML Please wait. PeptideProphet is running. It can take a long time. time="21:15:11" level=info msg="Executing PeptideProphet v5.1.3" file 1: C:\Users\User\Documents\igmtnightserum\IGMT_c.pepXML processed altogether 19 results INFO: Results written to file: C:\Users\User\Documents\igmtnightserum\interact.pep.xml - Building Commentz-Walter keyword tree... - C:\Users\User\Documents\igmtnightserum\interact.pep.xml - Searching the tree... - Linking duplicate entries... - Printing results... 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: 0.0/1038.3751/1054.37/1095.3966/1184.433/1200.428/1216.4229/1241.4545/1257.4493/1298.476/1362.4807/1378.4757/1387.5123/1403.5073/1419.5022/1444.5338/1460.5288/1501.5553/1540.5284/1548.5448/1549.5652/1564.5397/1565.5602/1581.555/1589.5714/1590.5918/1605.5663/1606.5867/1622.5815/1647.6132/1663.6082/1694.6027/1702.5813/1704.6346/1710.5977/1726.5925/1727.6129/1736.6497/1751.6241/1752.6445/1767.6191/1768.6395/1784.6344/1809.666/1825.661/1850.6926/1864.6342/1866.6875/1872.6504/1888.6454/1897.6821/1907.714/1913.677/1914.6974/1929.6719/1930.6923/1938.7086/1946.6873/1954.7035/1955.724/1970.6985/1971.7189/1987.7137/1996.7505/2012.7454/2018.7084/2026.6869/2028.7404/203.07938/2034.7032/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.7297/2076.7502/2091.7246/2092.745/2100.7615/2110.7935/2116.7563/2117.7769/2132.7512/2133.7717/2141.788/2142.8083/2149.7666/2157.783/2158.8032/2174.7983/2188.7397/2190.7932/2204.7725/2205.7927/2206.8132/2215.8247/2220.7673/2221.7878/2222.808/2236.7622/2237.7827/2238.803/2245.799/2246.8193/2256.8513/2261.794/2262.8142/2263.8347/2272.8462/2277.7888/2278.809/2279.8296/2287.846/2294.8042/2295.8245/2303.8408/2311.8193/2313.8728/2320.8562/2336.851/2350.7925/2350.8303/2351.8508/2352.846/2361.8826/2366.8252/2382.82/2391.857/2393.8726/2407.8518/2423.8467/2424.8672/2425.8875/2432.8835/2434.8992/2439.8416/2440.862/2448.8784/2457.8774/2459.9307/2464.8733/2465.8936/2475.9255/2481.8887/2482.909/2498.9038/2539.9304/2553.9097/2555.9253/2569.9045/2570.925/2580.957/2585.8994/2586.92/2596.952/2601.8945/2619.9302/2621.9834/2627.9465/2628.9668/2642.946/2643.9414/2658.9412/2659.9363/2674.936/2676.9517/2701.9832/2715.9624/2716.983/2717.9783/2731.9575/2732.9778/2747.9524/2756.989/2759.0046/2772.984/2788.979/2789.9993/2800.0312/2804.9739/2805.9941/2861.0/2864.0361/2876.9949/2878.0154/2892.9897/2894.0103/2896.051/2908.9849/2910.0051/2919.042/2921.0576/2935.0369/2937.0776/2946.089/2951.0317/2952.052/2967.0266/3007.0579/3009.0735/3023.0527/3025.0684/3039.0479/3048.0845/3055.0427/3064.0793/3067.1155/3080.0742/3081.0947/3083.1104/3083.1355/3096.0693/3147.1152/3155.1316/3165.1633/3210.1372/3226.1323/3228.173/3229.1682/3242.1272/3244.168/3258.122/3276.1577/3284.174/3292.1526/3372.1902/3405.2004/3421.1953/3432.2476/3446.2268/3448.2424/3462.222/3478.2168/349.13727/3517.2275/3533.2227/3549.2175/3575.2695/3591.2644/3594.3005/3607.2593/3663.2856/3679.2805/3704.312/3720.3071/3737.3223/3753.3171/3769.3123/3785.3071/3797.38/3866.365/4028.4177/406.15875/4102.4546/4118.449/4134.4443/4307.5493/4323.5444/4393.55/4758.682/552.2167/568.21155/714.2695/730.2644/876.32227/892.3172 PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) ***@***.*** read in 0 1+, 10 2+, 7 3+, 2 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 9 Decoys, and 10 Non-Decoys WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). init with X! Tandem stricttrypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20 model complete after 21 iterations time="21:15:13" level=info msg=Done Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-24.0\lib/* org.nesvilab.fragpipe.util.RewritePepxml C:\Users\User\Documents\igmtnightserum\interact.pep.xml I:\MZML\IGMT.mzML Fixing pepxml: C:\Users\User\Documents\igmtnightserum\interact.pep.xml Writing output to: C:\Users\User\Documents\igmtnightserum\interact.pep.xml533240400343310195.temp-rewrite Deleting file: C:\Users\User\Documents\igmtnightserum\interact.pep.xml Moving rewritten file to original location: [C:\Users\User\Documents\igmtnightserum\interact.pep.xml533240400343310195.temp-rewrite] -> [C:\Users\User\Documents\igmtnightserum\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: C:\Users\User\Documents\igmtnightserum] C:\FragPipe\FragPipe-24.0\tools\Philosopher\philosopher-v5.1.3-RC9.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\User\Documents\igmtnightserum\filelist_proteinprophet.txt time="21:15:17" level=info msg="Executing ProteinProphet v5.1.3" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in C:\Users\User\Documents\igmtnightserum\interact.pep.xml... did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 WARNING: no data - output file will be empty time="21:15:18" level=error msg="Cannot execute program. there was an error with ProteinProp

[fcyu]

There are no IDs in your data. Please check the sample prep and parameter settings.

Thanks,

Fengchao