System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.28 Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: (if "spectral library generation" is enabled, all files will be analyzed together) - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F10.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F11.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F12.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F13.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F14.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F15.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F1_R.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F2.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F3.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F4.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F5.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F6.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F7.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F8.mzML DDA - C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F9.mzML DDA 2 commands to execute: CheckCentroid C:\Users\MSI13900K\Desktop\Fragpipe211\jre\bin\java.exe -Xmx38G -cp C:\Users\MSI13900K\Desktop\Fragpipe211\lib\fragpipe-21.1.jar;C:\Users\MSI13900K\Desktop\Fragpipe211\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F10.mzML 24 TmtIntegrator [Work dir: C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3] C:\Users\MSI13900K\Desktop\Fragpipe211\jre\bin\java.exe -Xmx38G -cp C:\Users\MSI13900K\Desktop\Fragpipe211\tools\tmt-integrator-5.0.7.jar TMTIntegrator C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3\tmt-integrator-conf.yml C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3\psm.tsv ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3] Cmd: [CheckCentroid], Work dir: [C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3] Cmd: [TmtIntegrator], Work dir: [C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of C:\Users\MSI13900K\Desktop\FastaFiles\2024-04-08-decoys-reviewed-contam-UP000005640.fas~~~~~~~ >contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1 >rev_sp|O43505|B4GA1_HUMAN Beta-1,4-glucuronyltransferase 1 OS=Homo sapiens OX=9606 GN=B4GAT1 PE=1 SV=1 >rev_sp|P0DME0|SETLP_HUMAN Protein SETSIP OS=Homo sapiens OX=9606 GN=SETSIP PE=1 SV=1 >rev_sp|P49662|CASP4_HUMAN Caspase-4 OS=Homo sapiens OX=9606 GN=CASP4 PE=1 SV=1 >rev_sp|Q14146|URB2_HUMAN Unhealthy ribosome biogenesis protein 2 homolog OS=Homo sapiens OX=9606 GN=URB2 PE=1 SV=2 >rev_sp|Q68DK2|ZFY26_HUMAN Zinc finger FYVE domain-containing protein 26 OS=Homo sapiens OX=9606 GN=ZFYVE26 PE=1 SV=4 >rev_sp|Q8IWB9|TEX2_HUMAN Testis-expressed protein 2 OS=Homo sapiens OX=9606 GN=TEX2 PE=1 SV=2 >rev_sp|Q8WVI7|PPR1C_HUMAN Protein phosphatase 1 regulatory subunit 1C OS=Homo sapiens OX=9606 GN=PPP1R1C PE=1 SV=1 >rev_sp|Q9BRC7|PLCD4_HUMAN 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-4 OS=Homo sapiens OX=9606 GN=PLCD4 PE=1 SV=1 >rev_sp|Q9NUP7|TRM13_HUMAN tRNA:m(4)X modification enzyme TRM13 homolog OS=Homo sapiens OX=9606 GN=TRMT13 PE=1 SV=2 >rev_sp|Q9Y6N1|COX11_HUMAN Cytochrome c oxidase assembly protein COX11, mitochondrial OS=Homo sapiens OX=9606 GN=COX11 PE=1 SV=3 >sp|O43623|SNAI2_HUMAN Zinc finger protein SNAI2 OS=Homo sapiens OX=9606 GN=SNAI2 PE=1 SV=1 >sp|P0DO97|CC192_HUMAN Coiled-coil domain-containing protein 192 OS=Homo sapiens OX=9606 GN=CCDC192 PE=4 SV=1 >sp|P49810|PSN2_HUMAN Presenilin-2 OS=Homo sapiens OX=9606 GN=PSEN2 PE=1 SV=1 >sp|Q14240|IF4A2_HUMAN Eukaryotic initiation factor 4A-II OS=Homo sapiens OX=9606 GN=EIF4A2 PE=1 SV=2 >sp|Q6AW86|Z324B_HUMAN Zinc finger protein 324B OS=Homo sapiens OX=9606 GN=ZNF324B PE=1 SV=1 >sp|Q8IWX5|SGPP2_HUMAN Sphingosine-1-phosphate phosphatase 2 OS=Homo sapiens OX=9606 GN=SGPP2 PE=1 SV=1 >sp|Q8WW59|SPRY4_HUMAN SPRY domain-containing protein 4 OS=Homo sapiens OX=9606 GN=SPRYD4 PE=1 SV=3 >sp|Q9BRT9|SLD5_HUMAN DNA replication complex GINS protein SLD5 OS=Homo sapiens OX=9606 GN=GINS4 PE=1 SV=1 >sp|Q9NVD3|SETD4_HUMAN SET domain-containing protein 4 OS=Homo sapiens OX=9606 GN=SETD4 PE=1 SV=1 >sp|Q9Y6Y8|S23IP_HUMAN SEC23-interacting protein OS=Homo sapiens OX=9606 GN=SEC23IP PE=1 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~annotation files~~~~~~~ C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\IodoTMT_annotation.txt: 126 sample-01 127N sample-02 128C sample-03 129N sample-04 130C sample-05 131N sample-06 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ 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=C\:\\Users\\MSI13900K\\Desktop\\FastaFiles\\2024-04-08-decoys-reviewed-contam-UP000005640.fas 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=C\:\\Users\\MSI13900K\\Desktop\\Fragpipe211\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-ionquant=C\:\\Users\\MSI13900K\\Desktop\\Fragpipe211\\tools\\IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=C\:\\Users\\MSI13900K\\Desktop\\Fragpipe211\\tools\\MSFragger-4.0\\MSFragger-4.0.jar fragpipe-config.bin-philosopher=C\:\\Users\\MSI13900K\\Desktop\\Fragpipe211\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\MSI13900K\\AppData\\Local\\Programs\\Python\\Python39\\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=1 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=true msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=3 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=0 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= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2/3 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=10000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=35 msfragger.num_enzyme_termini=3 msfragger.output_format=pepXML_pin 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=-10 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=10 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=false 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),false,-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,2; 42.0106,[^,false,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 87.99828,K,false,2; 417.22485,K,true,2; 42.0106,n^,false,1; 87.99828,n^,false,1; 417.22485,n^,true,1; 329.2266,C,false,2; 57.02146,C,false,2; 481.22314,C,false,2; 0.984016,N,false,2 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 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=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --picked --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=true phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,K\:417.2249,n\:417.2249 MINPROB\=0.5 ptmprophet.run-ptmprophet=true ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=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= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses=AcNterm\:42.0106, Probe\:87.99828, ProbeIodoTMT6plex\:417.22485, IodoTMT6plex\:329.2266, IAA\:57.02146, DTTIodoTMT6plex\:481.22314 quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=false saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false 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=ciRT 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=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=Skip extraction. Run TMT-Integrator only tmtintegrator.glyco_qval=-1 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=0.75 tmtintegrator.min_site_prob=0.75 tmtintegrator.mod_tag=n(417.2249),K(417.2249)\:probe tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=-1 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=true tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=C\:\\Users\\MSI13900K\\Desktop\\NormalSearching\\IodoTMT_Searching3 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\Users\MSI13900K\Desktop\Fragpipe211\jre\bin\java.exe -Xmx38G -cp C:\Users\MSI13900K\Desktop\Fragpipe211\lib\fragpipe-21.1.jar;C:\Users\MSI13900K\Desktop\Fragpipe211\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\MSI13900K\Desktop\NormalSearching\RawFiles\IodoTMT_Ectodomain_20230724\E_ZW_IodoTMT__20230724_F10.mzML 24 Done in 1.0 s. Process 'CheckCentroid' finished, exit code: 0 TmtIntegrator [Work dir: C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3] C:\Users\MSI13900K\Desktop\Fragpipe211\jre\bin\java.exe -Xmx38G -cp C:\Users\MSI13900K\Desktop\Fragpipe211\tools\tmt-integrator-5.0.7.jar TMTIntegrator C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3\tmt-integrator-conf.yml C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3\psm.tsv TMT-Integrator v5.0.7 Load parameters and check PSMs--- 0.00113 min. java.lang.StringIndexOutOfBoundsException: String index out of range: 10 at java.base/java.lang.StringLatin1.charAt(Unknown Source) at java.base/java.lang.String.charAt(Unknown Source) at integrate.LoadPsms(integrate.java:215) at integrate.run(integrate.java:48) at TMTIntegrator.main(TMTIntegrator.java:114) UpdateColumns--- 0.00380 min. Error at: C:\Users\MSI13900K\Desktop\NormalSearching\IodoTMT_Searching3\psm.tsv java.lang.StringIndexOutOfBoundsException: String index out of range: 10 Process 'TmtIntegrator' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 1 remaining tasks