System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.25 Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: LC2_HILIC (if "spectral library generation" is enabled, all files will be analyzed together) - G:\WSY\S_2401600_LC2_20240202_01.mzML DDA 18 commands to execute: CheckCentroid D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx49G -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;D:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid G:\WSY\S_2401600_LC2_20240202_01.mzML 3 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\1abadf76-3a68-4c1b-b3de-991109447e19 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\8a4ab457-0e77-47be-adb9-ef3185e11739 MSFragger [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx49G D:\FragPipe-jre-19.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar G:\WSY\Output_LC2_20240222\fragger.params G:\WSY\S_2401600_LC2_20240202_01.mzML MSFragger move pepxml D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/D:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err G:\WSY\S_2401600_LC2_20240202_01.pepXML G:\WSY\Output_LC2_20240222\LC2_HILIC\S_2401600_LC2_20240202_01.pepXML MSFragger move tsv D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/D:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err G:\WSY\S_2401600_LC2_20240202_01.tsv G:\WSY\Output_LC2_20240222\LC2_HILIC\S_2401600_LC2_20240202_01.tsv PeptideProphet [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas --combine S_2401600_LC2_20240202_01.pepXML Rewrite pepxml [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml G:\WSY\S_2401600_LC2_20240202_01_calibrated.mzML PTMProphet [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n-terminus:42.0106,STY:79.9663,QC:-17.0265,E:-18.0106,N:568.2115,N:892.3172,N:1038.3751,N:1054.3700,N:1095.3966,N:1200.4280,N:1216.4229,N:1241.4545,N:1257.4493,N:1298.4760,N:1362.4807,N:1378.4757,N:1387.5123,N:1403.5073,N:1419.5022,N:1444.5338,N:1460.5288,N:1501.5553,N:1524.5336,N:1533.5703,N:1540.5284,N:1548.5448,N:1549.5652,N:1565.5601,N:1581.5551,N:1589.5714,N:1606.5867,N:1622.5815,N:1647.6132,N:1663.6082,N:1686.5864,N:1694.6027,N:1695.6232,N:1702.5813,N:1704.6346,N:1710.5977,N:1711.6180,N:1727.6129,N:1735.6293,N:1736.6497,N:1751.6241,N:1752.6445,N:1768.6395,N:1784.6344,N:1793.6711,N:1809.6660,N:1825.6610,N:1848.6392,N:1850.6926,N:1856.6555,N:1857.6759,N:1864.6342,N:1866.6875,N:1872.6504,N:1873.6709,N:1880.6667,N:1889.6658,N:1897.6821,N:1898.7025,N:1907.7140,N:1913.6770,N:1914.6974,N:1930.6923,N:1938.7086,N:1946.6873,N:1954.7035,N:1955.7240,N:1971.7189,N:1987.7137,N:1996.7505,N:2010.6920,N:2012.7454,N:2018.7084,N:2019.7288,N:2026.6869,N:2028.7404,N:2042.7196,N:2043.7400,N:2053.7720,N:2059.7349,N:2060.7554,N:2069.7668,N:2075.7297,N:2076.7502,N:2092.7451,N:2100.7615,N:2101.7817,N:2108.7400,N:2110.7935,N:2116.7563,N:2117.7769,N:2133.7717,N:2141.7881,N:2142.8083,N:2157.7830,N:2158.8032,N:2172.7449,N:2174.7983,N:2188.7397,N:2190.7932,N:2204.7725,N:2205.7927,N:2206.8132,N:2215.8247,N:2221.7878,N:2222.8081,N:2231.8196,N:2237.7827,N:2245.7991,N:2246.8193,N:2254.7979,N:2256.8513,N:2262.8142,N:2263.8347,N:2270.7930,N:2278.8091,N:2279.8296,N:2287.8459,N:2313.8728,N:2320.8562,N:2334.7976,N:2336.8511,N:2350.7925,N:2350.8303,N:2352.8459,N:2352.8711,N:2366.8252,N:2391.8569,N:2393.8726,N:2407.8518,N:2408.8721,N:2424.8672,N:2425.8875,N:2432.8833,N:2434.8992,N:2448.8784,N:2457.8772,N:2459.9307,N:2463.8403,N:2465.8936,N:2475.9255,N:2481.8887,N:2498.9038,N:2528.8782,N:2539.9304,N:2545.8933,N:2553.9097,N:2555.9253,N:2569.9045,N:2570.9250,N:2571.9453,N:2580.9570,N:2586.9199,N:2621.9834,N:2627.9465,N:2643.9414,N:2644.9617,N:2674.9360,N:2701.9832,N:2715.9624,N:2716.9829,N:2717.9783,N:2772.9839,N:2775.0247,N:2786.9631,N:2789.9993,N:2791.0198,N:2798.0156,N:2814.0105,N:2823.0095,N:2861.0000,N:2864.0361,N:2871.0571,N:2878.0154,N:2880.0310,N:2896.0510,N:2919.0420,N:2935.0369,N:2937.0776,N:2966.0315,N:2968.0471,N:3007.0579,N:3009.0735,N:3010.1191,N:3048.0845,N:3064.0793,N:3081.0947,N:3083.1104,N:3083.1355,N:3138.1162,N:3140.1570,N:3147.1152,N:3153.1157,N:3155.1316,N:3156.1519,N:3210.1372,N:3226.1323,N:3228.1731,N:3229.1682,N:3234.1484,N:3284.1741,N:3300.1689,N:3302.2097,N:3372.1902,N:3374.2058,N:3405.2004,N:3407.2412,N:3447.2473,N:3448.2424,N:3448.2676,N:3503.2483,N:3517.2275,N:3519.2683,N:3520.2637,N:3521.2842,N:3589.2488,N:3591.2644,N:3594.3005,N:3663.2856,N:3665.3013,N:3665.3264,N:3704.3120,N:3720.3069,N:3738.3428,N:3809.3435,N:3812.3794,N:3827.3540,N:3866.3650,N:3882.3599,N:3886.4163,N:3959.4326 MINPROB=0.5 MAXTHREADS=1 interact.pep.xml interact.mod.pep.xml ProteinProphet [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined G:\WSY\Output_LC2_20240222\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --psm 0.01 --tag rev_ --pepxml G:\WSY\Output_LC2_20240222\LC2_HILIC --protxml G:\WSY\Output_LC2_20240222\combined.prot.xml --razor PhilosopherReport [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx49G -Dlibs.thermo.dir=D:\FragPipe-jre-19.1\fragpipe\tools\MSFragger-4.0\ext\thermo -cp D:\FragPipe-jre-21.1\fragpipe\tools\ptmshepherd-2.0.6.jar;D:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar;D:\FragPipe-jre-21.1\fragpipe\tools\commons-math3-3.6.1.jar;D:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;D:\FragPipe-jre-21.1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "G:\WSY\Output_LC2_20240222\shepherd.config" WorkspaceClean [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [CheckCentroid], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [WorkspaceCleanInit], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [WorkspaceCleanInit], Work dir: [G:\WSY\Output_LC2_20240222\LC2_HILIC] Cmd: [MSFragger], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PeptideProphet], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PTMProphet], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [ProteinProphet], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PhilosopherDbAnnotate], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PhilosopherFilter], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PhilosopherReport], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [PTMShepherd], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [WorkspaceClean], Work dir: [G:\WSY\Output_LC2_20240222] Cmd: [WorkspaceClean], Work dir: [G:\WSY\Output_LC2_20240222\LC2_HILIC] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas~~~~~~~ >rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1 >rev_sp|Q9Y6W5|WASF2_HUMAN Actin-binding protein WASF2 OS=Homo sapiens OX=9606 GN=WASF2 PE=1 SV=3 >rev_tr|A0A1C9ZUT9|A0A1C9ZUT9_HUMAN MHC class I antigen (Fragment) OS=Homo sapiens OX=9606 GN=HLA-B PE=3 SV=1 >rev_tr|A0A5C2FZ54|A0A5C2FZ54_HUMAN IGL c1520_light_IGLV2-14_IGLJ1 (Fragment) OS=Homo sapiens OX=9606 PE=2 SV=1 >rev_tr|A0A7I2V5U6|A0A7I2V5U6_HUMAN Centrosome and spindle pole associated protein 1 (Fragment) OS=Homo sapiens OX=9606 GN=CSPP1 PE=1 SV=1 >rev_tr|B1AH77|B1AH77_HUMAN Rac family small GTPase 2 OS=Homo sapiens OX=9606 GN=RAC2 PE=1 SV=1 >rev_tr|C9JWG0|C9JWG0_HUMAN UTP--glucose-1-phosphate uridylyltransferase (Fragment) OS=Homo sapiens OX=9606 GN=UGP2 PE=1 SV=1 >rev_tr|F8VVN1|F8VVN1_HUMAN Cysteine and serine rich nuclear protein 2 (Fragment) OS=Homo sapiens OX=9606 GN=CSRNP2 PE=1 SV=1 >rev_tr|J3KS05|J3KS05_HUMAN Chromobox 1 (Fragment) OS=Homo sapiens OX=9606 GN=CBX1 PE=1 SV=8 >rev_tr|Q5TH07|Q5TH07_HUMAN Zinc finger MYND-type containing 8 (Fragment) OS=Homo sapiens OX=9606 GN=ZMYND8 PE=1 SV=1 >rev_tr|X6RM24|X6RM24_HUMAN Enolase superfamily member 1 (Fragment) OS=Homo sapiens OX=9606 GN=ENOSF1 PE=1 SV=1 >sp|Q9Y6V7|DDX49_HUMAN Probable ATP-dependent RNA helicase DDX49 OS=Homo sapiens OX=9606 GN=DDX49 PE=1 SV=1 >tr|A0A1C9ZUL2|A0A1C9ZUL2_HUMAN MHC class II antigen (Fragment) OS=Homo sapiens OX=9606 GN=HLA-DPB1 PE=4 SV=1 >tr|A0A5C2FZ51|A0A5C2FZ51_HUMAN IGL c2192_light_IGLV1-51_IGLJ2 (Fragment) OS=Homo sapiens OX=9606 PE=2 SV=1 >tr|A0A7I2V5U4|A0A7I2V5U4_HUMAN Aconitase 2 OS=Homo sapiens OX=9606 GN=ACO2 PE=1 SV=1 >tr|B1AH63|B1AH63_HUMAN Metallophosphoesterase domain containing 1 (Fragment) OS=Homo sapiens OX=9606 GN=MPPED1 PE=4 SV=1 >tr|C9JWF5|C9JWF5_HUMAN Basic leucine zipper and W2 domains 1 (Fragment) OS=Homo sapiens OX=9606 GN=BZW1 PE=1 SV=8 >tr|F8VVL7|F8VVL7_HUMAN Transmembrane protein 150A OS=Homo sapiens OX=9606 GN=TMEM150A PE=4 SV=1 >tr|J3KS03|J3KS03_HUMAN Nuclear prelamin A recognition factor (Fragment) OS=Homo sapiens OX=9606 GN=NARF PE=1 SV=1 >tr|Q5TGM7|Q5TGM7_HUMAN TUB like protein 1 (Fragment) OS=Homo sapiens OX=9606 GN=TULP1 PE=1 SV=1 >tr|X6RLY7|X6RLY7_HUMAN Calcium voltage-gated channel auxiliary subunit alpha2delta 4 OS=Homo sapiens OX=9606 GN=CACNA2D4 PE=4 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.1ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=G\:\\WSY\\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas Table.editor=CA_S13_786 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=true diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=D\:\\FragPipe-jre-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-ionquant=D\:\\FragPipe-jre-19.1\\fragpipe\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=D\:\\FragPipe-jre-19.1\\fragpipe\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=D\:\\FragPipe-jre-21.1\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\Administrator\\AppData\\Local\\Programs\\Python\\Python310\\python.exe freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.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=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=false msbooster.use-correlated-features=false msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 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.deisotope=1 msfragger.delta_mass_exclude_ranges=(-3.5,3.5) 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_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y,Y msfragger.fragment_mass_tolerance=50 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=nglycan msfragger.localize_delta_mass=true msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 568.21156 892.3172 1038.375109 1054.37002 1095.39657 1200.427929 1216.42284 1241.454479 1257.44939 1298.47594 1362.480749 1378.47566 1387.512388 1403.507299 1419.50221 1444.533849 1460.52876 1501.55531 1524.533569 1533.570297 1540.52848 1548.5448065 1549.565208 1565.560119 1581.55503 1589.5713565 1606.586669 1622.58158 1647.613219 1663.60813 1686.586389 1694.6027155 1695.623117 1702.5813 1704.63468 1710.5976265 1711.618028 1727.612939 1735.6292655 1736.649667 1751.6241765 1752.644578 1768.639489 1784.6344 1793.671128 1809.666039 1825.66095 1848.639209 1850.692589 1856.6555355 1857.675937 1864.63412 1866.6875 1872.6504465 1873.670848 1880.666773 1889.665759 1897.6820855 1898.702487 1907.71405 1913.6769965 1914.697398 1930.692309 1938.7086355 1946.68722 1954.7035465 1955.723948 1971.718859 1987.71377 1996.750498 2010.692029 2012.745409 2018.7083555 2019.728757 2026.68694 2028.74032 2042.719593 2043.7399945 2053.771959 2059.7349055 2060.755307 2069.76687 2075.7298165 2076.750218 2092.745129 2100.7614555 2101.781857 2108.74004 2110.79342 2116.7563665 2117.776768 2133.771679 2141.7880055 2142.808407 2157.7829165 2158.803318 2172.744849 2174.798229 2188.73976 2190.79314 2204.772413 2205.7928145 2206.813216 2215.824779 2221.7877255 2222.808127 2231.81969 2237.7826365 2245.798963 2246.8193645 2254.797949 2256.851329 2262.8142755 2263.834677 2270.79286 2278.8091865 2279.829588 2287.8459145 2313.87279 2320.856138 2334.797669 2336.851049 2350.79258 2350.830322 2352.84596 2352.871125 2366.825233 2391.856872 2393.87251 2407.851783 2408.8721845 2424.8670955 2425.887497 2432.883422 2434.89906 2448.878333 2457.877319 2459.930699 2463.8402655 2465.8936455 2475.92561 2481.8885565 2498.903869 2528.878053 2539.930419 2545.8933655 2553.909692 2555.92533 2569.904603 2570.9250045 2571.945406 2580.956969 2586.9199155 2621.983519 2627.9464655 2643.9413765 2644.961778 2674.935962 2701.983239 2715.962512 2716.9829135 2717.97815 2772.983973 2775.024776 2786.963246 2789.9992855 2791.019687 2798.015612000001 2814.010523 2823.009509 2861.0000195 2864.036059 2871.057149 2878.015332 2880.03097 2896.051046 2919.041882 2935.036793 2937.077596 2966.0313785 2968.0470165 3007.0579285 3009.0735665 3010.119133 3048.0844785 3064.0793895 3081.094702 3083.11034 3083.135505 3138.116163 3140.156966 3147.115149 3153.1158375 3155.1314755 3156.151877 3210.1372985 3226.1322095 3228.1730125 3229.168249 3234.148536000001 3284.174072 3300.168983 3302.209786 3372.1901185 3374.2057565 3405.200342 3407.241145 3447.2472935 3448.24253 3448.267695 3503.248353 3517.227626 3519.268429 3520.2636655 3521.284067 3589.2487615 3591.2643995 3594.300439 3663.285535 3665.301173 3665.326338 3704.312085 3720.306996 3738.34271 3809.343444 3812.3794835 3827.353993 3866.364905 3882.359816 3886.416257 3959.432629 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.output_report_topN_dia2=3 msfragger.override_charge=false msfragger.precursor_mass_lower=-50 msfragger.precursor_mass_mode=corrected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=50 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=N 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,true,3; -17.0265,nQnC,true,1; -18.0106,nE,true,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=true msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc 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 --mapmods --psm 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=true phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n-terminus\:42.0106,STY\:79.9663,QC\:-17.0265,E\:-18.0106,N\:568.2115,N\:892.3172,N\:1038.3751,N\:1054.3700,N\:1095.3966,N\:1200.4280,N\:1216.4229,N\:1241.4545,N\:1257.4493,N\:1298.4760,N\:1362.4807,N\:1378.4757,N\:1387.5123,N\:1403.5073,N\:1419.5022,N\:1444.5338,N\:1460.5288,N\:1501.5553,N\:1524.5336,N\:1533.5703,N\:1540.5284,N\:1548.5448,N\:1549.5652,N\:1565.5601,N\:1581.5551,N\:1589.5714,N\:1606.5867,N\:1622.5815,N\:1647.6132,N\:1663.6082,N\:1686.5864,N\:1694.6027,N\:1695.6232,N\:1702.5813,N\:1704.6346,N\:1710.5977,N\:1711.6180,N\:1727.6129,N\:1735.6293,N\:1736.6497,N\:1751.6241,N\:1752.6445,N\:1768.6395,N\:1784.6344,N\:1793.6711,N\:1809.6660,N\:1825.6610,N\:1848.6392,N\:1850.6926,N\:1856.6555,N\:1857.6759,N\:1864.6342,N\:1866.6875,N\:1872.6504,N\:1873.6709,N\:1880.6667,N\:1889.6658,N\:1897.6821,N\:1898.7025,N\:1907.7140,N\:1913.6770,N\:1914.6974,N\:1930.6923,N\:1938.7086,N\:1946.6873,N\:1954.7035,N\:1955.7240,N\:1971.7189,N\:1987.7137,N\:1996.7505,N\:2010.6920,N\:2012.7454,N\:2018.7084,N\:2019.7288,N\:2026.6869,N\:2028.7404,N\:2042.7196,N\:2043.7400,N\:2053.7720,N\:2059.7349,N\:2060.7554,N\:2069.7668,N\:2075.7297,N\:2076.7502,N\:2092.7451,N\:2100.7615,N\:2101.7817,N\:2108.7400,N\:2110.7935,N\:2116.7563,N\:2117.7769,N\:2133.7717,N\:2141.7881,N\:2142.8083,N\:2157.7830,N\:2158.8032,N\:2172.7449,N\:2174.7983,N\:2188.7397,N\:2190.7932,N\:2204.7725,N\:2205.7927,N\:2206.8132,N\:2215.8247,N\:2221.7878,N\:2222.8081,N\:2231.8196,N\:2237.7827,N\:2245.7991,N\:2246.8193,N\:2254.7979,N\:2256.8513,N\:2262.8142,N\:2263.8347,N\:2270.7930,N\:2278.8091,N\:2279.8296,N\:2287.8459,N\:2313.8728,N\:2320.8562,N\:2334.7976,N\:2336.8511,N\:2350.7925,N\:2350.8303,N\:2352.8459,N\:2352.8711,N\:2366.8252,N\:2391.8569,N\:2393.8726,N\:2407.8518,N\:2408.8721,N\:2424.8672,N\:2425.8875,N\:2432.8833,N\:2434.8992,N\:2448.8784,N\:2457.8772,N\:2459.9307,N\:2463.8403,N\:2465.8936,N\:2475.9255,N\:2481.8887,N\:2498.9038,N\:2528.8782,N\:2539.9304,N\:2545.8933,N\:2553.9097,N\:2555.9253,N\:2569.9045,N\:2570.9250,N\:2571.9453,N\:2580.9570,N\:2586.9199,N\:2621.9834,N\:2627.9465,N\:2643.9414,N\:2644.9617,N\:2674.9360,N\:2701.9832,N\:2715.9624,N\:2716.9829,N\:2717.9783,N\:2772.9839,N\:2775.0247,N\:2786.9631,N\:2789.9993,N\:2791.0198,N\:2798.0156,N\:2814.0105,N\:2823.0095,N\:2861.0000,N\:2864.0361,N\:2871.0571,N\:2878.0154,N\:2880.0310,N\:2896.0510,N\:2919.0420,N\:2935.0369,N\:2937.0776,N\:2966.0315,N\:2968.0471,N\:3007.0579,N\:3009.0735,N\:3010.1191,N\:3048.0845,N\:3064.0793,N\:3081.0947,N\:3083.1104,N\:3083.1355,N\:3138.1162,N\:3140.1570,N\:3147.1152,N\:3153.1157,N\:3155.1316,N\:3156.1519,N\:3210.1372,N\:3226.1323,N\:3228.1731,N\:3229.1682,N\:3234.1484,N\:3284.1741,N\:3300.1689,N\:3302.2097,N\:3372.1902,N\:3374.2058,N\:3405.2004,N\:3407.2412,N\:3447.2473,N\:3448.2424,N\:3448.2676,N\:3503.2483,N\:3517.2275,N\:3519.2683,N\:3520.2637,N\:3521.2842,N\:3589.2488,N\:3591.2644,N\:3594.3005,N\:3663.2856,N\:3665.3013,N\:3665.3264,N\:3704.3120,N\:3720.3069,N\:3738.3428,N\:3809.3435,N\:3812.3794,N\:3827.3540,N\:3866.3650,N\:3882.3599,N\:3886.4163,N\:3959.4326 MINPROB\=0.5 ptmprophet.run-ptmprophet=true ptmshepherd.adv_params=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.diagextract_mode=true ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=25 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=12.5 ptmshepherd.diagmine_fragMinSpecDiff=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=false ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=0.01 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_mode=true 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=1 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=3 ptmshepherd.precursor_mass_units=1 ptmshepherd.precursor_tol=8 ptmshepherd.print_decoys=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses=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.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true saintexpress.virtual-controls=100 speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=true tab-run.delete_temp_files=true 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.dont-run-fq-lq=false tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=0.01 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=true workdir=G\:\\WSY\\Output_LC2_20240222 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -Xmx49G -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;D:\FragPipe-jre-21.1\fragpipe\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid G:\WSY\S_2401600_LC2_20240202_01.mzML 3 Done in 7.7 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[14:23:50] Executing Workspace v5.1.0 INFO[14:23:50] Removing workspace INFO[14:23:50] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\1abadf76-3a68-4c1b-b3de-991109447e19 INFO[14:23:50] Executing Workspace v5.1.0 INFO[14:23:51] Creating workspace INFO[14:23:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[14:23:51] Executing Workspace v5.1.0 INFO[14:23:51] Removing workspace INFO[14:23:51] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\8a4ab457-0e77-47be-adb9-ef3185e11739 INFO[14:23:52] Executing Workspace v5.1.0 INFO[14:23:52] Creating workspace INFO[14:23:52] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx49G D:\FragPipe-jre-19.1\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar G:\WSY\Output_LC2_20240222\fragger.params G:\WSY\S_2401600_LC2_20240202_01.mzML MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 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: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 49 GB memory Checking database... Checking spectral files... G:\WSY\S_2401600_LC2_20240202_01.mzML: Scans = 85069; Isolation sizes = [1.6] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 3 database_name = G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 50.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 1 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-3.5,3.5) 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 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 variable_mod_03 = 79.96633 STY 2 variable_mod_04 = -17.0265 nQnC 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: 385226 of length 8: 377683 of length 9: 378870 of length 10: 358662 of length 11: 349172 of length 12: 333307 of length 13: 327633 of length 14: 309457 of length 15: 307150 of length 16: 283963 of length 17: 265192 of length 18: 254752 of length 19: 256310 of length 20: 229962 of length 21: 225979 of length 22: 219851 of length 23: 199950 of length 24: 198130 of length 25: 179261 of length 26: 172416 of length 27: 163535 of length 28: 151229 of length 29: 145121 of length 30: 133901 of length 31: 129954 of length 32: 119165 of length 33: 110339 of length 34: 103658 of length 35: 94666 of length 36: 92368 of length 37: 88688 of length 38: 85920 of length 39: 78458 of length 40: 72074 of length 41: 63897 of length 42: 67110 of length 43: 55440 of length 44: 47981 of length 45: 33580 of length 46: 24931 of length 47: 14848 of length 48: 8437 of length 49: 4201 of length 50: 2289 In total 7504716 peptides. Generated 167646147 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.25 Da. 9755884640 fragments to be searched in 4 slices (145.37 GB total) Operating on slice 1 of 4: Fragment index slice generated in 38.30 s 001. S_2401600_LC2_20240202_01.mzML 25.3 s | deisotoping 0.7 s [progress: 84056/84056 (100%) - 8336 spectra/s] 10.1s Operating on slice 2 of 4: Fragment index slice generated in 33.83 s 001. S_2401600_LC2_20240202_01.mzML 6.0 s | deisotoping 0.4 s [progress: 84056/84056 (100%) - 15971 spectra/s] 5.3s Operating on slice 3 of 4: Fragment index slice generated in 29.58 s 001. S_2401600_LC2_20240202_01.mzML 7.3 s | deisotoping 0.5 s [progress: 84056/84056 (100%) - 19104 spectra/s] 4.4s Operating on slice 4 of 4: Fragment index slice generated in 30.59 s 001. S_2401600_LC2_20240202_01.mzML 2.7 s | deisotoping 0.5 s [progress: 84056/84056 (100%) - 21754 spectra/s] 3.9s | postprocessing 0.6 s ***************************FIRST SEARCH DONE IN 6.100 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 0.39 1.79 | 0.14 1.15 | -1.57 2.56 | 0.06 2.41 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2 | 7 | 10 | 15 | 20 | 25 | 30 -------|-------|-------|-------|-------|-------|------- Count | 3245| 3114| skip rest -------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 150_1 | 100_1 -------|-------|-------|-------|------- Count | 3245| 3242| 3241| 3202 -------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 3060 -------|------- -------|------- Rm P. | 0 -------|------- Count | 3197 -------|------- New fragment_mass_tolerance = 7.000000 PPM New use_topN_peaks = 150 New minimum_ratio = 0.010000 New intensity_transform = 0 New remove_precursor_peak = 1 New precursor_true_tolerance = 5.000000 PPM ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 26.299 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 3 database_name = G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 5.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 1 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0/1038.3751/1054.37/1095.3966/1200.428/1216.4229/1241.4545/1257.4493/1298.476/1362.4807/1378.4757/1387.5123/1403.5073/1419.5022/1444.5338/1460.5288/1501.5553/1524.5336/1533.5703/1540.5284/1548.5448/1549.5652/1565.56/1581.555/1589.5714/1606.5867/1622.5815/1647.6132/1663.6082/1686.5864/1694.6027/1695.6232/1702.5813/1704.6346/1710.5977/1711.618/1727.6129/1735.6293/1736.6497/1751.6241/1752.6445/1768.6395/1784.6344/1793.6711/1809.666/1825.661/1848.6392/1850.6926/1856.6555/1857.6759/1864.6342/1866.6875/1872.6504/1873.6709/1880.6667/1889.6658/1897.6821/1898.7025/1907.714/1913.677/1914.6974/1930.6923/1938.7086/1946.6873/1954.7035/1955.724/1971.7189/1987.7137/1996.7505/2010.692/2012.7454/2018.7084/2019.7288/2026.6869/2028.7404/2042.7196/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.7297/2076.7502/2092.745/2100.7615/2101.7817/2108.74/2110.7935/2116.7563/2117.7769/2133.7717/2141.788/2142.8083/2157.783/2158.8032/2172.7449/2174.7983/2188.7397/2190.7932/2204.7725/2205.7927/2206.8132/2215.8247/2221.7878/2222.808/2231.8196/2237.7827/2245.799/2246.8193/2254.7979/2256.8513/2262.8142/2263.8347/2270.793/2278.809/2279.8296/2287.846/2313.8728/2320.8562/2334.7976/2336.851/2350.7925/2350.8303/2352.846/2352.871/2366.8252/2391.857/2393.8726/2407.8518/2408.872/2424.8672/2425.8875/2432.8833/2434.8992/2448.8784/2457.8772/2459.9307/2463.8403/2465.8936/2475.9255/2481.8887/2498.9038/2528.8782/2539.9304/2545.8933/2553.9097/2555.9253/2569.9045/2570.925/2571.9453/2580.957/2586.92/2621.9834/2627.9465/2643.9414/2644.9617/2674.936/2701.9832/2715.9624/2716.983/2717.9783/2772.984/2775.0247/2786.9631/2789.9993/2791.0198/2798.0156/2814.0105/2823.0095/2861.0/2864.0361/2871.0571/2878.0154/2880.031/2896.051/2919.042/2935.0369/2937.0776/2966.0315/2968.047/3007.0579/3009.0735/3010.1191/3048.0845/3064.0793/3081.0947/3083.1104/3083.1355/3138.1162/3140.157/3147.1152/3153.1157/3155.1316/3156.1519/3210.1372/3226.1323/3228.173/3229.1682/3234.1484/3284.174/3300.169/3302.2097/3372.1902/3374.2058/3405.2004/3407.2412/3447.2473/3448.2424/3448.2676/3503.2483/3517.2275/3519.2683/3520.2637/3521.2842/3589.2488/3591.2644/3594.3005/3663.2856/3665.3013/3665.3264/3704.312/3720.307/3738.3428/3809.3435/3812.3794/3827.354/3866.365/3882.3599/3886.4163/3959.4326/568.21155/892.3172 labile_search_mode = NGLYCAN restrict_deltamass_to = N precursor_mass_mode = CORRECTED localize_delta_mass = 1 delta_mass_exclude_ranges = (-3.5,3.5) 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 = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_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 variable_mod_03 = 79.96633 STY 3 variable_mod_04 = -17.0265 nQnC 1 variable_mod_05 = -18.0106 nE 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: 385226 of length 8: 377683 of length 9: 378870 of length 10: 358662 of length 11: 349172 of length 12: 333307 of length 13: 327633 of length 14: 309457 of length 15: 307150 of length 16: 283963 of length 17: 265192 of length 18: 254752 of length 19: 256310 of length 20: 229962 of length 21: 225979 of length 22: 219851 of length 23: 199950 of length 24: 198130 of length 25: 179261 of length 26: 172416 of length 27: 163535 of length 28: 151229 of length 29: 145121 of length 30: 133901 of length 31: 129954 of length 32: 119165 of length 33: 110339 of length 34: 103658 of length 35: 94666 of length 36: 92368 of length 37: 88688 of length 38: 85920 of length 39: 78458 of length 40: 72074 of length 41: 63897 of length 42: 67110 of length 43: 55440 of length 44: 47981 of length 45: 33580 of length 46: 24931 of length 47: 14848 of length 48: 8437 of length 49: 4201 of length 50: 2289 In total 7504716 peptides. Generated 305714459 modified peptides. Number of peptides with more than 5000 modification patterns: 40 Selected fragment index width 0.03 Da. 76321854032 fragments to be searched in 32 slices (1137.28 GB total) Operating on slice 1 of 32: Fragment index slice generated in 15.24 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.5 s [progress: 82913/82913 (100%) - 139 spectra/s] 595.1s Operating on slice 2 of 32: Fragment index slice generated in 14.63 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.5 s [progress: 82913/82913 (100%) - 150 spectra/s] 554.4s Operating on slice 3 of 32: Fragment index slice generated in 15.52 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.7 s [progress: 82913/82913 (100%) - 130 spectra/s] 637.5s Operating on slice 4 of 32: Fragment index slice generated in 16.57 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 108 spectra/s] 770.4s Operating on slice 5 of 32: Fragment index slice generated in 14.47 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.7 s [progress: 82913/82913 (100%) - 110 spectra/s] 754.3s Operating on slice 6 of 32: Fragment index slice generated in 15.18 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 113 spectra/s] 735.8s Operating on slice 7 of 32: Fragment index slice generated in 14.08 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 117 spectra/s] 709.9s Operating on slice 8 of 32: Fragment index slice generated in 15.20 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 118 spectra/s] 703.7s Operating on slice 9 of 32: Fragment index slice generated in 14.35 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 119 spectra/s] 697.6s Operating on slice 10 of 32: Fragment index slice generated in 13.09 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 117 spectra/s] 707.0s Operating on slice 11 of 32: Fragment index slice generated in 13.44 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 120 spectra/s] 691.1s Operating on slice 12 of 32: Fragment index slice generated in 13.42 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 119 spectra/s] 696.0s Operating on slice 13 of 32: Fragment index slice generated in 13.79 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 125 spectra/s] 663.6s Operating on slice 14 of 32: Fragment index slice generated in 12.36 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 128 spectra/s] 646.9s Operating on slice 15 of 32: Fragment index slice generated in 11.83 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 133 spectra/s] 622.8s Operating on slice 16 of 32: Fragment index slice generated in 11.89 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 128 spectra/s] 645.8s Operating on slice 17 of 32: Fragment index slice generated in 12.21 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 133 spectra/s] 621.1s Operating on slice 18 of 32: Fragment index slice generated in 12.07 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 132 spectra/s] 630.0s Operating on slice 19 of 32: Fragment index slice generated in 12.25 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 131 spectra/s] 631.4s Operating on slice 20 of 32: Fragment index slice generated in 11.60 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 125 spectra/s] 665.9s Operating on slice 21 of 32: Fragment index slice generated in 13.44 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 116 spectra/s] 715.5s Operating on slice 22 of 32: Fragment index slice generated in 12.46 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.7 s [progress: 82913/82913 (100%) - 126 spectra/s] 658.7s Operating on slice 23 of 32: Fragment index slice generated in 12.39 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.7 s [progress: 82913/82913 (100%) - 125 spectra/s] 663.7s Operating on slice 24 of 32: Fragment index slice generated in 12.49 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 127 spectra/s] 652.7s Operating on slice 25 of 32: Fragment index slice generated in 12.70 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 123 spectra/s] 675.6s Operating on slice 26 of 32: Fragment index slice generated in 12.61 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 124 spectra/s] 668.7s Operating on slice 27 of 32: Fragment index slice generated in 13.34 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.9 s [progress: 82913/82913 (100%) - 129 spectra/s] 642.9s Operating on slice 28 of 32: Fragment index slice generated in 11.87 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.7 s [progress: 82913/82913 (100%) - 125 spectra/s] 663.1s Operating on slice 29 of 32: Fragment index slice generated in 12.19 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.5 s [progress: 82913/82913 (100%) - 129 spectra/s] 641.2s Operating on slice 30 of 32: Fragment index slice generated in 10.40 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 140 spectra/s] 592.3s Operating on slice 31 of 32: Fragment index slice generated in 9.97 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.5 s [progress: 82913/82913 (100%) - 143 spectra/s] 579.5s Operating on slice 32 of 32: Fragment index slice generated in 10.44 s 001. S_2401600_LC2_20240202_01.mzBIN_calibrated 0.6 s [progress: 82913/82913 (100%) - 126 spectra/s] 656.2s | remapping alternative proteins and postprocessing 18.3 s ***************************MAIN SEARCH DONE IN 364.302 MIN*************************** *******************************TOTAL TIME 396.701 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/D:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err G:\WSY\S_2401600_LC2_20240202_01.pepXML G:\WSY\Output_LC2_20240222\LC2_HILIC\S_2401600_LC2_20240202_01.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib\fragpipe-21.1.jar;/D:/FragPipe-jre-21.1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err G:\WSY\S_2401600_LC2_20240202_01.tsv G:\WSY\Output_LC2_20240222\LC2_HILIC\S_2401600_LC2_20240202_01.tsv Process 'MSFragger move tsv' finished, exit code: 0 PeptideProphet [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas --combine S_2401600_LC2_20240202_01.pepXML Please wait. PeptideProphet is running. It can take a long time. INFO[21:00:37] Executing PeptideProphet v5.1.0 file 1: G:\WSY\Output_LC2_20240222\LC2_HILIC\S_2401600_LC2_20240202_01.pepXML processed altogether 28098 results INFO: Results written to file: G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml - G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... using N-glyc info 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: 0.0/1038.3751/1054.37/1095.3966/1200.428/1216.4229/1241.4545/1257.4493/1298.476/1362.4807/1378.4757/1387.5123/1403.5073/1419.5022/1444.5338/1460.5288/1501.5553/1524.5336/1533.5703/1540.5284/1548.5448/1549.5652/1565.56/1581.555/1589.5714/1606.5867/1622.5815/1647.6132/1663.6082/1686.5864/1694.6027/1695.6232/1702.5813/1704.6346/1710.5977/1711.618/1727.6129/1735.6293/1736.6497/1751.6241/1752.6445/1768.6395/1784.6344/1793.6711/1809.666/1825.661/1848.6392/1850.6926/1856.6555/1857.6759/1864.6342/1866.6875/1872.6504/1873.6709/1880.6667/1889.6658/1897.6821/1898.7025/1907.714/1913.677/1914.6974/1930.6923/1938.7086/1946.6873/1954.7035/1955.724/1971.7189/1987.7137/1996.7505/2010.692/2012.7454/2018.7084/2019.7288/2026.6869/2028.7404/2042.7196/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.7297/2076.7502/2092.745/2100.7615/2101.7817/2108.74/2110.7935/2116.7563/2117.7769/2133.7717/2141.788/2142.8083/2157.783/2158.8032/2172.7449/2174.7983/2188.7397/2190.7932/2204.7725/2205.7927/2206.8132/2215.8247/2221.7878/2222.808/2231.8196/2237.7827/2245.799/2246.8193/2254.7979/2256.8513/2262.8142/2263.8347/2270.793/2278.809/2279.8296/2287.846/2313.8728/2320.8562/2334.7976/2336.851/2350.7925/2350.8303/2352.846/2352.871/2366.8252/2391.857/2393.8726/2407.8518/2408.872/2424.8672/2425.8875/2432.8833/2434.8992/2448.8784/2457.8772/2459.9307/2463.8403/2465.8936/2475.9255/2481.8887/2498.9038/2528.8782/2539.9304/2545.8933/2553.9097/2555.9253/2569.9045/2570.925/2571.9453/2580.957/2586.92/2621.9834/2627.9465/2643.9414/2644.9617/2674.936/2701.9832/2715.9624/2716.983/2717.9783/2772.984/2775.0247/2786.9631/2789.9993/2791.0198/2798.0156/2814.0105/2823.0095/2861.0/2864.0361/2871.0571/2878.0154/2880.031/2896.051/2919.042/2935.0369/2937.0776/2966.0315/2968.047/3007.0579/3009.0735/3010.1191/3048.0845/3064.0793/3081.0947/3083.1104/3083.1355/3138.1162/3140.157/3147.1152/3153.1157/3155.1316/3156.1519/3210.1372/3226.1323/3228.173/3229.1682/3234.1484/3284.174/3300.169/3302.2097/3372.1902/3374.2058/3405.2004/3407.2412/3447.2473/3448.2424/3448.2676/3503.2483/3517.2275/3519.2683/3520.2637/3521.2842/3589.2488/3591.2644/3594.3005/3663.2856/3665.3013/3665.3264/3704.312/3720.307/3738.3428/3809.3435/3812.3794/3827.354/3866.365/3882.3599/3886.4163/3959.4326/568.21155/892.3172 init with X! Tandem stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 8113 2+, 10393 3+, 6931 4+, 2297 5+, 318 6+, and 46 7+ spectra. Found 10667 Decoys, and 17431 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+). . model complete after 27 iterations INFO[21:01:31] Done Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-21.1\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml G:\WSY\S_2401600_LC2_20240202_01_calibrated.mzML Fixing pepxml: G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml Writing output to: G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml14201012357757922830.temp-rewrite Deleting file: G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml Moving rewritten file to original location: [G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml14201012357757922830.temp-rewrite] -> [G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 PTMProphet [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\PTMProphet\PTMProphetParser.exe KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n-terminus:42.0106,STY:79.9663,QC:-17.0265,E:-18.0106,N:568.2115,N:892.3172,N:1038.3751,N:1054.3700,N:1095.3966,N:1200.4280,N:1216.4229,N:1241.4545,N:1257.4493,N:1298.4760,N:1362.4807,N:1378.4757,N:1387.5123,N:1403.5073,N:1419.5022,N:1444.5338,N:1460.5288,N:1501.5553,N:1524.5336,N:1533.5703,N:1540.5284,N:1548.5448,N:1549.5652,N:1565.5601,N:1581.5551,N:1589.5714,N:1606.5867,N:1622.5815,N:1647.6132,N:1663.6082,N:1686.5864,N:1694.6027,N:1695.6232,N:1702.5813,N:1704.6346,N:1710.5977,N:1711.6180,N:1727.6129,N:1735.6293,N:1736.6497,N:1751.6241,N:1752.6445,N:1768.6395,N:1784.6344,N:1793.6711,N:1809.6660,N:1825.6610,N:1848.6392,N:1850.6926,N:1856.6555,N:1857.6759,N:1864.6342,N:1866.6875,N:1872.6504,N:1873.6709,N:1880.6667,N:1889.6658,N:1897.6821,N:1898.7025,N:1907.7140,N:1913.6770,N:1914.6974,N:1930.6923,N:1938.7086,N:1946.6873,N:1954.7035,N:1955.7240,N:1971.7189,N:1987.7137,N:1996.7505,N:2010.6920,N:2012.7454,N:2018.7084,N:2019.7288,N:2026.6869,N:2028.7404,N:2042.7196,N:2043.7400,N:2053.7720,N:2059.7349,N:2060.7554,N:2069.7668,N:2075.7297,N:2076.7502,N:2092.7451,N:2100.7615,N:2101.7817,N:2108.7400,N:2110.7935,N:2116.7563,N:2117.7769,N:2133.7717,N:2141.7881,N:2142.8083,N:2157.7830,N:2158.8032,N:2172.7449,N:2174.7983,N:2188.7397,N:2190.7932,N:2204.7725,N:2205.7927,N:2206.8132,N:2215.8247,N:2221.7878,N:2222.8081,N:2231.8196,N:2237.7827,N:2245.7991,N:2246.8193,N:2254.7979,N:2256.8513,N:2262.8142,N:2263.8347,N:2270.7930,N:2278.8091,N:2279.8296,N:2287.8459,N:2313.8728,N:2320.8562,N:2334.7976,N:2336.8511,N:2350.7925,N:2350.8303,N:2352.8459,N:2352.8711,N:2366.8252,N:2391.8569,N:2393.8726,N:2407.8518,N:2408.8721,N:2424.8672,N:2425.8875,N:2432.8833,N:2434.8992,N:2448.8784,N:2457.8772,N:2459.9307,N:2463.8403,N:2465.8936,N:2475.9255,N:2481.8887,N:2498.9038,N:2528.8782,N:2539.9304,N:2545.8933,N:2553.9097,N:2555.9253,N:2569.9045,N:2570.9250,N:2571.9453,N:2580.9570,N:2586.9199,N:2621.9834,N:2627.9465,N:2643.9414,N:2644.9617,N:2674.9360,N:2701.9832,N:2715.9624,N:2716.9829,N:2717.9783,N:2772.9839,N:2775.0247,N:2786.9631,N:2789.9993,N:2791.0198,N:2798.0156,N:2814.0105,N:2823.0095,N:2861.0000,N:2864.0361,N:2871.0571,N:2878.0154,N:2880.0310,N:2896.0510,N:2919.0420,N:2935.0369,N:2937.0776,N:2966.0315,N:2968.0471,N:3007.0579,N:3009.0735,N:3010.1191,N:3048.0845,N:3064.0793,N:3081.0947,N:3083.1104,N:3083.1355,N:3138.1162,N:3140.1570,N:3147.1152,N:3153.1157,N:3155.1316,N:3156.1519,N:3210.1372,N:3226.1323,N:3228.1731,N:3229.1682,N:3234.1484,N:3284.1741,N:3300.1689,N:3302.2097,N:3372.1902,N:3374.2058,N:3405.2004,N:3407.2412,N:3447.2473,N:3448.2424,N:3448.2676,N:3503.2483,N:3517.2275,N:3519.2683,N:3520.2637,N:3521.2842,N:3589.2488,N:3591.2644,N:3594.3005,N:3663.2856,N:3665.3013,N:3665.3264,N:3704.3120,N:3720.3069,N:3738.3428,N:3809.3435,N:3812.3794,N:3827.3540,N:3866.3650,N:3882.3599,N:3886.4163,N:3959.4326 MINPROB=0.5 MAXTHREADS=1 interact.pep.xml interact.mod.pep.xml Please wait. PTMProphet is running. It can take a long time. [INFO:] Using statically set 15 PPM tolerance ... [INFO:] Writing file interact.pep.xml.tmp.a04112 ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact.pep.xml ... ​ [INFO:] processed 7000/8333 spectrum_queries WARNING: running job exception ... std::bad_alloc ... exiting ... [INFO:] done ... [INFO:] Computing EM Models ... [INFO:] Iterating PTM Model: ....5..done [INFO:] done ... [INFO:] done ... [INFO:] Creating 1 threads [INFO:] Wait for threads to finish ... [INFO:] Reading file interact.pep.xml ... ​ [INFO:] written 1000/8333 spectrum_queries WARNING: running job exception ... std::bad_alloc ... exiting ... [INFO:] done ... [INFO:] Writing file interact.mod.pep.xml ... 'chmod' �����ڲ����ⲿ���Ҳ���ǿ����еij��� ���������ļ��� [INFO:] done ... command "chmod 664 interact.mod.pep.xml" failed: Operation not permitted Process 'PTMProphet' finished, exit code: 0 ProteinProphet [Work dir: G:\WSY\Output_LC2_20240222] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined G:\WSY\Output_LC2_20240222\filelist_proteinprophet.txt INFO[21:32:08] Executing ProteinProphet v5.1.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.pep.xml... ...read in 0 1+, 1801 2+, 3416 3+, 2166 4+, 805 5+, 107 6+, 14 7+ spectra with min prob 0.05 Initializing 4575 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database g:/WSY/2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 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.........:.........:.........:.........:.........:.........:.........:.........:.........:.........297000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........298000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........299000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........300000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........301000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........302000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........303000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........304000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........305000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........306000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........307000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........308000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........309000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........310000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........311000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........312000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........313000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........314000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........315000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........316000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........317000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........318000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........319000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........320000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........321000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........322000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........323000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........324000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........325000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........326000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........327000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........328000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........329000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........330000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........331000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........332000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........333000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........334000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........335000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........336000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........337000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........338000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........339000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........340000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........341000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........342000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........343000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........344000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........345000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........346000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........347000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........348000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........349000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........350000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........351000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........352000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........353000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........354000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........355000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........356000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........357000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........358000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........359000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........360000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........361000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........362000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........363000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........364000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........365000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........366000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........367000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........368000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........369000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........370000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........371000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........372000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........373000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........374000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........375000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........376000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........377000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........378000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........379000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........380000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........381000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........382000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........383000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........384000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........385000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........386000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........387000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........388000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........389000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........390000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........391000 .........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry tr|Q6XGY1|Q6XGY1_HUMAN : U MSAGNGTPWDATWNITVQWLAVDIACRTLMFLKLMATYSAAFLPVVIGLDRQAAVLNPLGSRSGVRKLLGAAWGLSFLLAFPQLFLFHTVHUAGPDPFTQCVTKGSFKAQWQETTYNLFTFCCLFLLPLTAMAICYSRIVLSVSRPQTRKGSHAPAGEFALPRSFDNCPRVRLRALRLALLILLTFILCWTPYYLLGMWYWFSPTMLTEVPPSLSHILFLLGLLNAPLDPLLYGAFTLGCRRGHQELSIDSSKEGSGRMLQEEIHAFRQLEVQKTVTSRRAGETKGISITSI ......:.........:.........:.........:.........:.........392000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........393000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........394000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........395000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........396000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........397000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........398000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........399000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........400000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........401000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........402000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........403000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........404000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........405000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........406000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........407000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........408000 .........: Total: 408104 Computing degenerate peptides for 17968 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 19519 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=9.17229e-06, db_size=246455313 Computing MU for 19519 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[21:32:18] Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate G:\WSY\2024-02-22-decoys-uniprotkb_human_AND_model_organism_9606_2024_02_22.fasta.fas --prefix rev_ INFO[21:32:19] Executing Database v5.1.0 INFO[21:32:19] Annotating the database INFO[21:32:22] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: G:\WSY\Output_LC2_20240222\LC2_HILIC] D:\FragPipe-jre-21.1\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --psm 0.01 --tag rev_ --pepxml G:\WSY\Output_LC2_20240222\LC2_HILIC --protxml G:\WSY\Output_LC2_20240222\combined.prot.xml --razor INFO[21:32:23] Executing Filter v5.1.0 INFO[21:32:23] Processing peptide identification files INFO[21:32:23] Parsing G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.mod.pep.xml ERRO[21:32:23] Cannot read file. Error parsing the file Process 'PhilosopherFilter' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 5 remaining tasks