# HG changeset patch # User galaxyp # Date 1720592100 0 # Node ID 14785481da2b6c763908611629a21f1184544274 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f diff -r 000000000000 -r 14785481da2b fragpipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fragpipe Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,65 @@ +#!/bin/bash + +# Modified version of the Bioconda wrapper of the script for command-line FragPipe, calling a local link to fragpipe instead of the version in $CONDA_PREFIX. +# Ensures the user agrees to MSFragger and IonQuant academic licenses. + +license_agreement_text=' +Please accept the academic license. + +FragPipe uses tools that are available freely for academic research and educational purposes only. + +Please provide license keys for MSFragger and IonQuant with the --msfragger_key and --ionquant_key flags. By passing these, you verify that you have read the ACADEMIC licenses for the MSFragger and IonQuant tools. You may obtain these keys by agreeing to the terms at http://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/.' + +declare -a fragpipe_args + +while [[ $# -gt 0 ]]; do + case "$1" in + --msfragger_key) + shift + msfragger_key=$1 + ;; + --ionquant_key) + shift + ionquant_key=$1 + ;; + --workflow) + fragpipe_args+=("$1") + shift + workflow_file="$1" + fragpipe_args+=("$1") + ;; + *) + fragpipe_args+=("$1") + ;; + esac + shift +done + +if [[ ! -z "$workflow_file" ]]; then + # Because the DIA-NN license is incompatible with bioconda, we remove the feature. + grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null + if [[ $? -eq 0 ]]; then + echo "Error: DIA-NN is disabled in the FragPipe bioconda package." + exit 1 + fi +fi + +if [[ -z $msfragger_key || -z $ionquant_key ]]; then + echo "$license_agreement_text" + exit 1 +else + msfragger --key $msfragger_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid MSFragger license key" + echo "$license_agreement_text" + exit 1 + fi + ionquant --key $ionquant_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid IonQuant license key" + echo "$license_agreement_text" + exit 1 + fi +fi + +sh fragpipe_local/bin/fragpipe "${fragpipe_args[@]}" diff -r 000000000000 -r 14785481da2b fragpipe.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fragpipe.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,276 @@ + + Data analysis for mass spectrometry-based proteomics + + macros.xml + + + + + + + + + fragpipe --help | grep 'FragPipe v' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + workflow_only or (output_options and 'workflow' in output_options) + + + + not workflow_only and output_options and 'log' in output_options + + + + + not workflow_only + + + + not workflow_only + + + + not workflow_only + + + + not workflow_only + + + + + + not workflow_only and output_options and 'combined_outputs' in output_options + + + + + + not workflow_only and 'concatenated_outputs' in output_options + + + not workflow_only and 'concatenated_outputs' in output_options + + + not workflow_only and 'concatenated_outputs' in output_options + + + not workflow_only and 'concatenated_outputs' in output_options + + + + + (not workflow_only) and ('Open' in wf['workflow_name']) + + + (not workflow_only) and ('Open' in wf['workflow_name']) + + + (not workflow_only) and ('Open' in wf['workflow_name']) + + + + + + (not workflow_only) and ('TMT' in wf['workflow_name']) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 14785481da2b genericize_db.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genericize_db.py Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +# +# Prefixes sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats with '>generic|' to avoid being misinterpreted by Philosopher. +# + +import re +import sys + +input_db_file = sys.argv[1] +output_db_file = sys.argv[2] + + +def sub_header(line): + return re.sub(r'^>(?!sp\||tr\||db\||AP_|NP_|YP_|XP_|WP_|ENSP|UniRef|nxp|generic)', '>generic|', line) + + +with open(input_db_file) as in_file, open(output_db_file, 'w') as out_file: + for line in in_file: + out_file.write(sub_header(line)) diff -r 000000000000 -r 14785481da2b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,1198 @@ + + msfragger_macros.xml + 20.0 + 0 + + + fragpipe + + + + + ['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N'] + ['114', '115', '116', '117'] + ['113', '114', '115', '116', '117', '118', '119', '121'] + + + + + + [a-zA-Z][a-zA-Z0-9_-]* + + + + + + + + + fp.manifest && + + #for $sf in $inputs + #set $i_name = $ln_name($sf) + ln -s '$sf' 'scans/${i_name}' && + #end for + ]]> + + + + + + + + + concat_\${f}; + fi; + awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.'); + mv \${i} \${t}; n=\$((n+1)); + done; + done + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + +
+ +
+ + + + + + + + + +
+ +
+ + + + + + + +
+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + + 0 + #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods]) + #end if + #for $k in $msfragger_dict.keys() + #set $kv = $k + '=' + str($msfragger_dict[$k]) + #set $wfk = 'msfragger.' + $k + #set $wfdict[$wfk] = str($msfragger_dict[$k]) + #end for + + @VALIDATION@ + @PTM_SHEPHERD@ + @LABEL_FREE_QUANTIFICATION@ + @ISOBARIC_QUANTIFICATION@ + + ## Populate the workflow with configuration and comment dictionary entries populated by tool params. + #for $comment in $comments +$comment + #end for + + #for $k in sorted($wfdict.keys()) + #set $kv = $k + '=' + str($wfdict[$k]) +$kv + #end for +#slurp]]> + + + + +
+ + +
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+ + + + +
+ + + + + + @RE_AA@,@RE_FLOAT@ + @RE_EXCLUDEMOD@(;\s*@RE_EXCLUDEMOD@)* + + + +
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+ + +
+ + ^\s*@RE_EXCLUDEMODS@\s*$ + + + + + + + + +
+
+ + +
+ + +
+ + +
+ + + + + + + +
+ + + + + + + + + +
+ + + ^TMT-\d? + + + Virtual or specify a Reference sample tag: pool or Bridge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability + + + + + + + + + + + + + + + + + + + + + + + + ^(none|[a-zA-Z]+\|)$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + + + +MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. + + +IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf + + +I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf + + +I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt + + +@MSFRAGGER_LICENSE_AGREEMENT@ +@IONQUANT_LICENSE_AGREEMENT@ +@THERMO_RAW_READER_LICENSE_AGREEMENT@ +@BRUKER_LICENSE_AGREEMENT@ + + + + + + value == True +
+@IONQUANT_LICENSE_AGREEMENT@ +

+@THERMO_RAW_READER_LICENSE_AGREEMENT@ +

+@BRUKER_LICENSE_AGREEMENT@ + ]]> + + + + + + 10.1038/s41592-020-0912-y + 10.1038/nmeth.4256 + 10.1038/s41467-020-17921-y + 10.1038/s41592-020-0967-9 + 10.1021/acs.jproteome.0c00119 + 10.1074/mcp.TIR120.002216 + 10.1074/mcp.TIR120.002048 + 10.1016/j.mcpro.2021.100077 + 10.1021/acs.jproteome.0c00544 + 10.1038/nmeth.3255 + + + + diff -r 000000000000 -r 14785481da2b msfragger_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msfragger_macros.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,1000 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12. + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + [+-]?\d+(\.\d*)? + ([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\]) + @RE_FLOAT@,@RE_AA@,\d + @RE_MOD@(;\s*@RE_MOD@)* + +
+ + + + + + + ^\s*@RE_MODS@\s*$ + + + + + + + + + + + + + + + + + +
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+ + + + + + + + Track top N unmodified peptide results separately from main results internally for boosting features. + Should be set to a number greater than output_report_topN if zero bin boosting is desired. + Default: 0 + + + + + + + Useful for recovery of modified peptides near C-terminal in open search. + Should be set to 0 (disabled) otherwise. + Default: 0 + + + + + +
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2591.9002 2213.8092 2594.9363 2595.9567 2649.9421 2666.9574 2610.9312 2611.9516 2665.937 2538.9352 2612.972 2683.9727 2393.8726 2539.9305 2684.968 2685.9884 2739.9738 2756.9891 2758.0095 2811.9949 2831.0259 2832.0463 2886.0317 2903.047 2902.0266 2957.0324 2974.0477 2830.0306 2904.0674 2958.0528 2975.0681 2976.0634 2977.0838 2978.1042 1419.5022 1565.5601 1710.5976 1856.6555 1987.7138 2001.693 2133.7717 2278.8092 2279.8296 1711.618 2002.7134 2147.7509 2424.8671 2425.8875 2292.7884 2569.9046 2570.925 2641.9257 2293.8088 2438.8463 2642.9461 2715.9625 2716.9829 2787.9836 2555.9254 2701.9833 2847.0208 2848.0412 2919.0419 2583.8838 2712.9264 2786.9632 2861 2862.0204 2916.0058 2933.0211 2920.0623 2991.063 2841.969 2990.0426 2993.0787 2994.0991 2992.0834 1218.4764 1306.4924 1380.5292 1526.5871 1542.582 1671.6246 1672.645 1688.6399 1759.6406 1817.6825 1833.6774 1834.6978 1907.7142 1979.7353 2053.7721 2124.7728 2125.7932 2198.8096 2199.83 2253.8154 2270.8307 1394.5084 1760.661 1905.6985 2141.7881 2286.8256 2287.846 2341.8314 2069.767 2215.8249 2360.8624 2361.8828 2415.8682 2432.8835 1980.7557 2142.8085 2433.9039 2506.9203 2507.9407 2561.9261 2578.9414 2231.8198 2377.8777 2522.9152 2523.9356 2577.921 2651.9578 2652.9782 2706.9636 2723.9789 2126.8136 2271.8511 2288.8664 2579.9618 2653.9986 2707.984 2724.9993 2668.9731 2669.9935 2740.9942 2794.9796 2416.8886 2798.0157 2799.0361 2853.0215 2870.0368 2814.0106 2815.031 2869.0164 2742.0146 2816.0514 2887.0521 2596.952 2743.0099 2888.0474 2889.0678 2943.0532 2960.0685 2961.0889 1482.5244 1790.6351 1848.677 1993.7145 2226.768 2429.8474 2156.7877 2534.8787 2609.9359 2737.9581 2214.8296 2359.8671 2592.9206 2667.9778 2796 2813.0153 2941.0375 2971.0116 1857.6759 2148.7713 2206.8132 2497.9086 2571.9454 2231.8449 2393.8977 2684.9931 2759.0299 2439.8667 2584.9042 2713.9468 2789.004 2863.0408 2934.0415 2555.9505 2847.0459 2921.0827 2729.9417 2858.9843 2988.0269 1581.555 1727.6129 1784.6344 1872.6504 1930.6923 2018.7083 2075.7298 2076.7502 2149.7666 2163.7458 2221.7877 2295.8245 2366.8252 2367.8456 2440.862 2441.8824 2512.8831 1873.6708 2164.7662 2222.8081 2309.8037 2513.9035 2586.9199 2587.9403 2658.941 2352.846 2498.9039 2643.9414 2644.9618 2454.8412 2657.9206 2731.9574 2732.9778 2803.9785 2789.9993 2791.0197 2455.8616 2600.8991 2804.9989 2878.0153 2879.0357 2950.0364 2935.0368 2936.0572 2937.0776 2717.9782 2864.0361 2745.9366 2874.9792 2949.016 2759.0048 2905.0627 2019.7287 2310.8241 2368.866 2659.9614 2733.9982 2601.9195 2746.957 2875.9996 2951.0568 2718.0033 2891.9945 2434.9243 2596.9771 2888.0725 2962.1093 2921.0576 2406.8565 2464.8984 2568.9093 2842.9894 2918.0466 2522.9403 2901.0313 2976.0885 2730.9621 2580.9822 2726.0197 2743.035 2959.0732 2871.0572 2905.0878 2893.0149 + + + 0/114.03169/193.99802/291.97492/406.00661 + 0 203.07937 406.15874 568.21156 730.26438 892.3172 + 0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 + 0 203.07937 365.1322 + 0 203.07937 365.1322 406.15874 568.21156 730.26438 892.3172 349.137279 + 0 203.07937 406.15874 568.21156 730.26438 349.137279 + + + +
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+ + + + + + + + diff -r 000000000000 -r 14785481da2b test-data/default/outputs/workflow.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/outputs/workflow.txt Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,308 @@ +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +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=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.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.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0.0 +msfragger.misc.fragger.clear-mz-lo=0.0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50.0 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +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=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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 --minprob 0.05 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +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.diagextract_mode=false +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_mode=false +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_mode=false +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.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=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.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +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=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b test-data/default/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test.fasta Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,72 @@ +>generic|U00096.3_prot_AAC76339.1_3292|30SribosomalsubunitproteinS3-Ecoli_MG1655 +MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP +AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI +TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA +DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK +>generic|OFI31430.1|phosphateacetyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN +STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS +LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE +QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA +TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG +ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV +QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA +AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM +TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF +FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD +VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN +TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQQ +>generic|OFI30005.1|serinehydroxymethyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP +GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMN +LAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGV +VDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL +AKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVE +VFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS +GIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA +>generic|OFI28972.1|translationelongationfactorTu,partial[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG +ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI +LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE +GDAEWEAKIIELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG +EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK +PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV +VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL +>generic|OFI28767.1|chitinase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MATSKLIQGDTITETTHAANGFDPATSDDKISYTSARVAKPVYNKYKNSTTKPKVFGYYT +DWSQYDSRLQGNMSQPGRGYDLTKVSPTAYDKLIFGFVGITGFRKIDTEDRDVVAEAAAL +CGKVKYEPTFLDPWGDFQSYINLGFDVSGWDVDPKTVTQSNAKGLLGALRDMQAKAKAAG +HTLALSMSIGGWSMSNGFHETAASDSSRKIFAKGVVKLFKQFPMFSEVDIDWEYPNNEGA +GNPFGPEDGANYALLIAELRKQLDSAGLSNVKISIAASAVTTIFDYAKVKDLMAAGLYGI +NLMTYDFFGTPWAETLGHHTNRKALEEGGWAVETIVDHLLAEGFSADRINIGYAGYTRNA +RQVEIESLSPLKGSYNPGSGPTTGSFESGTSEWYDVIYSYLDLENQKGRNGFNVYTDQVA +DADYLYSPESKLFLSLDTPRTVKAKGEYAAKLGLGGVFTWTIDQDNGVLVNAVREGLGYE +IESEVIDMEPFYFEGINVEKDEEQSDSDDAQKVNHAPKAAIELMVVGGSTVQLSGAGSSD +EDNDELSFSWGVPSQIDVADKTAEIIEVVVPEVSEKTAFQFTLFVRDCYNEPSSQQRFVL +TAVPALSQVQPEPEEEEEIIVPVPDEEEDTTPAEDDTPADDKTSPYAQWDASTVYGANWG +SFEIVSWKGHNYQVKWWSMGNQPDLNCGVGGAWTDLGAY +>generic|OFI28186.1|50SribosomalproteinL3[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAVQVTTGAKKANRV +TKPEAGHFAKAGVEAGRGLWEFRLAEGEEYTVGQSISVELFADVKKVDVTGTSKGKGFAG +TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV +DAERNLLLVKGGVPGATGCDLIVKPAVKA +>generic|AL009126.3_prot_CAB11777.1_1|chromosomalreplicationinitiatorinformationalATPase-BSU +MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPPDLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDINADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMYLSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK +>generic|AL009126.3_prot_CAB11778.1_2|DNApolymeraseIII(betasubunit)-BSU +MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY +>generic|AL009126.3_prot_CAB11779.1_3|RNAbindingproteininvolvedinribosomematuration-BSU +MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN +>generic|AL009126.3_prot_CAB11780.1_4|RecAfilament-DNAcomplexstabilisation,ssDNAanddsDNAbinding,ATPbinding-BSU +MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK +>generic|AL009126.3_prot_CAB11781.2_5|regulatorofextracellularmatrixformation-BSU +MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS +>generic|AL009126.3_prot_CAB11782.1_6|DNAgyrase(subunitB)-BSU +MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI +>generic|AL009126.3_prot_CAB11783.1_7|DNAgyrase(subunitA)-BSU +MSEQNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVIRRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDERRTEIVTSGLETIEDEDLIERENIVVTLTHNGYVKRLPASTYRSQKRGGKGVQGMGTNEDDFVEHLISTSTHDTILFFSNKGKVYRAKGYEIPEYGRTAKGIPIINLLEVEKGEWINAIIPVTEFNAELYLFFTTKHGVSKRTSLSQFANIRNNGLIALSLREDDELMGVRLTDGTKQIIIGTKNGLLIRFPETDVREMGRTAAGVKGITLTDDDVVVGMEILEEESHVLIVTEKGYGKRTPAEEYRTQSRGGKGLKTAKITENNGQLVAVKATKGEEDLMIITASGVLIRMDINDISITGRVTQGVRLIRMAEEEHVATVALVEKNEEDENEEEQEEV +>generic|AL009126.3_prot_CAB11784.1_8|conservedproteinofunknownfunction-BSU +MTYHEWKDLALFYSVESTQKFLEKVYILNGINDAKKNSFKNSERFIYFLKHAESFYKQAAYSPLEIKPILLFYGMAQLIKACLITRDPHYPSHTSVLAHGVTTRKRKKQNYCFSDDEVKIQRNGLCVHFMKHLFGQSDIVDERYTMKKLLMAIPELSDIFYFQQKERFMTKVEKDKNEIFVPEEVVINYKMSDSRFAEYMSHHYQWSFTKKNEHGLLFEISPQDKEPWTSTSLLFDMEKNQYYIPSQREQFLRLPEMTIHYLILYNVGMIARYETEWWYELLTQHISDDYVLIQQFLLVSEKKFPKYASQFLLHF +>generic|AL009126.3_prot_CAB11785.1_9|inosine-monophosphatedehydrogenase-BSU +MWESKFSKEGLTFDDVLLVPAKSEVLPRDVDLSVELTKTLKLNIPVISAGMDTVTESAMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSERGVITNPFFLTPDHQVFDAEHLMGKYRISGVPIVNNEEDQKLVGIITNRDLRFISDYSMKISDVMTKEELVTASVGTTLDEAEKILQKHKIEKLPLVDDQNKLKGLITIKDIEKVIEFPNSSKDIHGRLIVGAAVGVTGDTMTRVKKLVEANVDVIVIDTAHGHSQGVLNTVTKIRETYPELNIIAGNVATAEATRALIEAGADVVKVGIGPGSICTTRVVAGVGVPQITAIYDCATEARKHGKTIIADGGIKFSGDITKALAAGGHAVMLGSLLAGTSESPGETEIYQGRRFKVYRGMGSVAAMEKGSKDRYFQEENKKFVPEGIEGRTPYKGPVEETVYQLVGGLRSGMGYCGSKDLRALREEAQFIRMTGAGLRESHPHDVQITKESPNYTIS +>generic|AL009126.3_prot_CAB11786.1_10|D-alanyl-D-alaninecarboxypeptidase(penicillin-bindingprotein5)-BSU +MNIKKCKQLLMSLVVLTLAVTCLAPMSKAKAASDPIDINASAAIMIEASSGKILYSKNADKRLPIASMTKMMTEYLLLEAIDQGKVKWDQTYTPDDYVYEISQDNSLSNVPLRKDGKYTVKELYQATAIYSANAAAIAIAEIVAGSETKFVEKMNAKAKELGLTDYKFVNATGLENKDLHGHQPEGTSVNEESEVSAKDMAVLADHLITDYPEILETSSIAKTKFREGTDDEMDMPNWNFMLKGLVSEYKKATVDGLKTGSTDSAGSCFTGTAERNGMRVITVVLNAKGNLHTGRFDETKKMFDYAFDNFSMKEIYAEGDQVKGHKTISVDKGKEKEVGIVTNKAFSLPVKNGEEKNYKAKVTLNKDNLTAPVKKGTKVGKLTAEYTGDEKDYGFLNSDLAGVDLVTKENVEKANWFVLTMRSIGGFFAGIWGSIVDTVTGWF diff -r 000000000000 -r 14785481da2b test-data/default/test.manifest --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test.manifest Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,2 @@ +test1.mzML sample1 DDA +test2.mzML sample2 DDA diff -r 000000000000 -r 14785481da2b test-data/default/test1.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test1.mzML Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,721 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+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 +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= +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=(-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=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50.0 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +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_mode=false +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_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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.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=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=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=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 +workflow.description=

Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b test-data/tmt11/test.annotation --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.annotation Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,11 @@ +126 sample-01 +127N sample-02 +127C sample-03 +128N sample-04 +128C sample-05 +129N sample-06 +129C sample-07 +130N sample-08 +130C sample-09 +131N sample-10 +131C Bridge diff -r 000000000000 -r 14785481da2b test-data/tmt11/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.fasta Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,193 @@ +>sp|P22314|UBA1_HUMAN Ubiquitin-like modifier-activating enzyme 1 OS=Homo sapiens OX=9606 GN=UBA1 PE=1 SV=3 +MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLY +VLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLRE +EDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCH +NRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARH +GFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKK +ISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVA +LAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPI +MQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKYFLVGAGAIG +CELLKNFAMIGLGCGEGGEIIVTDMDTIEKSNLNRQFLFRPWDVTKLKSDTAAAAVRQMN +PHIRVTSHQNRVGPDTERIYDDDFFQNLDGVANALDNVDARMYMDRRCVYYRKPLLESGT +LGTKGNVQVVIPFLTESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDEFEGLFKQPA +ENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWADCVTWACHHWHTQYSN +NIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTG +SQDRAAVATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLP +GFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKSKLIAGKIIPAIATTTAA +VVGLVCLELYKVVQGHRQLDSYKNGFLNLALPFFGFSEPLAAPRHQYYNQEWTLWDRFEV +QGLQPNGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMPAAKLKERLDQPMTEIVS +RVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTIR +>sp|P31151|S10A7_HUMAN Protein S100-A7 OS=Homo sapiens OX=9606 GN=S100A7 PE=1 SV=4 +MSNTQAERSIIGMIDMFHKYTRRDDKIEKPSLLTMMKENFPNFLSACDKKGTNYLADVFE +KKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ +>sp|Q8TCU5|NMD3A_HUMAN Glutamate receptor ionotropic, NMDA 3A OS=Homo sapiens OX=9606 GN=GRIN3A PE=1 SV=2 +MRRLSLWWLLSRVCLLLPPPCALVLAGVPSSSSHPQPCQILKRIGHAVRVGAVHLQPWTT +APRAASRAPDDSRAGAQRDEPEPGTRRSPAPSPGARWLGSTLHGRGPPGSRKPGEGARAE +ALWPRDALLFAVDNLNRVEGLLPYNLSLEVVMAIEAGLGDLPLLPFSSPSSPWSSDPFSF +LQSVCHTVVVQGVSALLAFPQSQGEMMELDLVSLVLHIPVISIVRHEFPRESQNPLHLQL +SLENSLSSDADVTVSILTMNNWYNFSLLLCQEDWNITDFLLLTQNNSKFHLGSIINITAN +LPSTQDLLSFLQIQLESIKNSTPTVVMFGCDMESIRRIFEITTQFGVMPPELRWVLGDSQ +NVEELRTEGLPLGLIAHGKTTQSVFEHYVQDAMELVARAVATATMIQPELALIPSTMNCM +EVETTNLTSGQYLSRFLANTTFRGLSGSIRVKGSTIVSSENNFFIWNLQHDPMGKPMWTR +LGSWQGGKIVMDYGIWPEQAQRHKTHFQHPSKLHLRVVTLIEHPFVFTREVDDEGLCPAG +QLCLDPMTNDSSTLDSLFSSLHSSNDTVPIKFKKCCYGYCIDLLEKIAEDMNFDFDLYIV +GDGKYGAWKNGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTR +DTAAPIGAFMWPLHWTMWLGIFVALHITAVFLTLYEWKSPFGLTPKGRNRSKVFSFSSAL +NICYALLFGRTVAIKPPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGI +HDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVEYLKNDPEKLD +AFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTANISELISQYKSHGFM +DMLHDKWYRVVPCGKRSFAVTETLQMGIKHFSGLFVLLCIGFGLSILTTIGEHIVYRLLL +PRIKNKSKLQYWLHTSQRLHRAINTSFIEEKQQHFKTKRVEKRSNVGPRQLTVWNTSNLS +HDNRRKYIFSDEEGQNQLGIRIHQDIPLPPRRRELPALRTTNGKADSLNVSRNSVMQELS +ELEKQIQVIRQELQLAVSRKTELEEYQRTSRTCES +>sp|Q9HC84|MUC5B_HUMAN Mucin-5B OS=Homo sapiens OX=9606 GN=MUC5B PE=1 SV=3 +MGAPSACRTLVLALAAMLVVPQAETQGPVEPSWENAGHTMDGGAPTSSPTRRVSFVPPVT +VFPSLSPLNPAHNGRVCSTWGDFHYKTFDGDVFRFPGLCNYVFSEHCRAAYEDFNVQLRR +GLVGSRPVVTRVVIKAQGLVLEASNGSVLINGQREELPYSRTGLLVEQSGDYIKVSIRLV +LTFLWNGEDSALLELDPKYANQTCGLCGDFNGLPAFNEFYAHNARLTPLQFGNLQKLDGP +TEQCPDPLPLPAGNCTDEEGICHRTLLGPAFAECHALVDSTAYLAACAQDLCRCPTCPCA +TFVEYSRQCAHAGGQPRNWRCPELCPRTCPLNMQHQECGSPCTDTCSNPQRAQLCEDHCV +DGCFCPPGTVLDDITHSGCLPLGQCPCTHGGRTYSPGTSFNTTCSSCTCSGGLWQCQDLP +CPGTCSVQGGAHISTYDEKLYDLHGDCSYVLSKKCADSSFTVLAELRKCGLTDNENCLKA +VTLSLDGGDTAIRVQADGGVFLNSIYTQLPLSAANITLFTPSSFFIVVQTGLGLQLLVQL +VPLMQVFVRLDPAHQGQMCGLCGNFNQNQADDFTALSGVVEATGAAFANTWKAQAACANA +RNSFEDPCSLSVENENYARHWCSRLTDPNSAFSRCHSIINPKPFHSNCMFDTCNCERSED +CLCAALSSYVHACAAKGVQLSDWRDGVCTKYMQNCPKSQRYAYVVDACQPTCRGLSEADV +TCSVSFVPVDGCTCPAGTFLNDAGACVPAQECPCYAHGTVLAPGEVVHDEGAVCSCTGGK +LSCLGASLQKSTGCAAPMVYLDCSNSSAGTPGAECLRSCHTLDVGCFSTHCVSGCVCPPG +LVSDGSGGCIAEEDCPCVHNEATYKPGETIRVDCNTCTCRNRRWECSHRLCLGTCVAYGD +GHFITFDGDRYSFEGSCEYILAQDYCGDNTTHGTFRIVTENIPCGTTGTTCSKAIKLFVE +SYELILQEGTFKAVARGPGGDPPYKIRYMGIFLVIETHGMAVSWDRKTSVFIRLHQDYKG +RVCGLCGNFDDNAINDFATRSRSVVGDALEFGNSWKLSPSCPDALAPKDPCTANPFRKSW +AQKQCSILHGPTFAACRSQVDSTKYYEACVNDACACDSGGDCECFCTAVAAYAQACHDAG +LCVSWRTPDTCPLFCDFYNPHGGCEWHYQPCGAPCLKTCRNPSGHCLVDLPGLEGCYPKC +PPSQPFFNEDQMKCVAQCGCYDKDGNYYDVGARVPTAENCQSCNCTPSGIQCAHSLEACT +CTYEDRTYSYQDVIYNTTDGLGACLIAICGSNGTIIRKAVACPGTPATTPFTFTTAWVPH +STTSPALPVSTVCVREVCRWSSWYNGHRPEPGLGGGDFETFENLRQRGYQVCPVLADIEC +RAAQLPDMPLEELGQQVDCDRMRGLMCANSQQSPPLCHDYELRVLCCEYVPCGPSPAPGT +SPQPSLSASTEPAVPTPTQTTATEKTTLWVTPSIRSTAALTSQTGSSSGPVTVTPSAPGT +TTCQPRCQWTEWFDEDYPKSEQLGGDVESYDKIRAAGGHLCQQPKDIECQAESFPNWTLA +QVGQKVHCDVHFGLVCRNWEQEGVFKMCYNYRIRVLCCSDDHCRGRATTPPPTTELETAT +TTTTQALFSTPQPTSSPGLTRAPPASTTAVPTLSEGLTSPRYTSTLGTATTGGPTTPAGS +TEPTVPGVATSTLPTRSALPGTTGSLGTWRPSQPPTLAPTTMATSRARPTGTASTASKEP +LTTSLAPTLTSELSTSQAETSTPRTETTMSPLTNTTTSQGTTRCQPKCEWTEWFDVDFPT +SGVAGGDMETFENIRAAGGKMCWAPKSIECRAENYPEVSIDQVGQVLTCSLETGLTCKNE +DQTGRFNMCFNYNVRVLCCDDYSHCPSTPATSSTATPSSTPGTTWILTKPTTTATTTAST +GSTATPTSTLRTAPPPKVLTTTATTPTVTSSKATPSSSPGTATALPALRSTATTPTATSV +TPIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTATATTTGATGSVATPS +STPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTH +TATVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPP +VLTTTATTPAATSNTVTPSSALGTTHTPPVPNTMATTHGRSLPPSSPHTVRTAWTSATSG +ILGTTHITEPSTVTSHTLAATTGTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTTATS +RTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEWLDYSYPMPGPSGGDFDT +YSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCF +NYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTTESTGSTATPSSTPG +TTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTAT +ALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVHTSTVL +TTTATTTGATGSVATPSSTPGTAHTTKVLTTTTTGFTATPSSSPGTARTLPVWISTTTTP +TTRGSTVTPSSIPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITAT +GSTTNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLS +PSSPHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTE +SPPSPGTTTPGHTRATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEW +LDYSYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDF +GLVCRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTEQTTAA +TTTATTGSTAIPSSTPGTAPPPKVLTSTATTPTATSSKATSSSSPRTATTLPVLTSTATK +STATSFTPIPSFTLGTTGTLPEQTTTPMATMSTIHPSSTPETTHTSTVLTTKATTTRATS +SMSTPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTEPSTTATVTVPTGST +ATASSTRATAGTLKVLTSTATTPTVISSRATPSSSPGTATALPALRSTATTPTATSVTAI +PSSSLGTAWTRLSQTTTPTATMSTATPSSTPETVHTSTVLTTTTTTTRATGSVATPSSTP +GTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTHTAT +VLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPPVLT +TTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLPPSSPHTVRTAWTSATSGILG +TTHITEPSTVTSHTPAATTSTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTRGTSRTT +ATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDYSYPMPGPSGGDFDTYSN +IRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCFNYE +IRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTKLTTTATTTESTGSTATPSSTPGTTW +ILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTATALP +ALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTTT +ATTTRATGSVATPSSTPGTAHTTKVPTTTTTGFTVTPSSSPGTARTPPVWISTTTTPTTS +GSTVTPSSVPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLITTATTITATGST +TNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLSPSS +PHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTESPP +SPGTTTPGHTTATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDY +SYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLGELGQVVECSLDFGLV +CRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTT +ASTGSTATPSSTPGTAPPPKVLTSPATTPTATSSKATSSSSPRTATTLPVLTSTATKSTA +TSVTPIPSSTLGTTGTLPEQTTTPVATMSTIHPSSTPETTHTSTVLTTKATTTRATSSTS +TPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTELTTTATTTASTGSTATP +SSTPGTTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPSSS +PGTATALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVH +TSTVLTATATTTGATGSVATPSSTPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWIS +TTTTPTTTTPTTSGSTVTPSSIPGTTHTARVLTTTTTTVATGSMATPSSSTQTSGTPPSL +TTTATTITATGSTTNPSSTPGTTPITPVLTSTATTPAATSSKATSSSSPRTATTLPVLTS +TATKSTATSFTPIPSSTLWTTWTVPAQTTTPMSTMSTIHTSSTPETTHTSTVLTTTATMT +RATNSTATPSSTLGTTRILTELTTTATTTAATGSTATLSSTPGTTWILTEPSTIATVMVP +TGSTATASSTLGTAHTPKVVTTMATMPTATASTVPSSSTVGTTRTPAVLPSSLPTFSVST +VSSSVLTTLRPTGFPSSHFSTPCFCRAFGQFFSPGEVIYNKTDRAGCHFYAVCNQHCDID +RFQGACPTSPPPVSSAPLSSPSPAPGCDNAIPLRQVNETWTLENCTVARCVGDNRVVLLD +PKPVANVTCVNKHLPIKVSDPSQPCDFHYECECICSMWGGSHYSTFDGTSYTFRGNCTYV +LMREIHARFGNLSLYLDNHYCTASATAAAARCPRALSIHYKSMDIVLTVTMVHGKEEGLI +LFDQIPVSSGFSKNGVLVSVLGTTTMRVDIPALGVSVTFNGQVFQARLPYSLFHNNTEGQ +CGTCTNNQRDDCLQRDGTTAASCKDMAKTWLVPDSRKDGCWAPTGTPPTASPAAPVSSTP +TPTPCPPQPLCDLMLSQVFAECHNLVPPGPFFNACISDHCRGRLEVPCQSLEAYAELCRA +RGVCSDWRGATGGLCDLTCPPTKVYKPCGPIQPATCNSRNQSPQLEGMAEGCFCPEDQIL +FNAHMGICVQACPCVGPDGFPKFPGERWVSNCQSCVCDEGSVSVQCKPLPCDAQGQPPPC +NRPGFVTVTRPRAENPCCPETVCVCNTTTCPQSLPVCPPGQESICTQEEGDCCPTFRCRP +QLCSYNGTFYGVGATFPGALPCHMCTCLSGDTQDPTVQCQEDACNNTTCPQGFEYKRVAG +QCCGECVQTACLTPDGQPVQLNETWVNSHVDNCTVYLCEAEGGVHLLTPQPASCPDVSSC +RGSLRKTGCCYSCEEDSCQVRINTTILWHQGCETEVNITFCEGSCPGASKYSAEAQAMQH +QCTCCQERRVHEETVPLHCPNGSAILHTYTHVDECGCTPFCVPAPMAPPHTRGFPAQEAT +AV +>sp|Q9UBG3|CRNN_HUMAN Cornulin OS=Homo sapiens OX=9606 GN=CRNN PE=1 SV=1 +MPQLLQNINGIIEAFRRYARTEGNCTALTRGELKRLLEQEFADVIVKPHDPATVDEVLRL +LDEDHTGTVEFKEFLVLVFKVAQACFKTLSESAEGACGSQESGSLHSGASQELGEGQRSG +TEVGRAGKGQHYEGSSHRQSQQGSRGQNRPGVQTQGQATGSAWVSSYDRQAESQSQERIS +PQIQLSGQTEQTQKAGEGKRNQTTEMRPERQPQTREQDRAHQTGETVTGSGTQTQAGATQ +TVEQDSSHQTGRTSKQTQEATNDQNRGTETHGQGRSQTSQAVTGGHAQIQAGTHTQTPTQ +TVEQDSSHQTGSTSTQTQESTNGQNRGTEIHGQGRSQTSQAVTGGHTQIQAGSHTETVEQ +DRSQTVSHGGAREQGQTQTQPGSGQRWMQVSNPEAGETVPGGQAQTGASTESGRQEWSST +HPRRCVTEGQGDRQPTVVGEEWVDDHSRETVILRLDQGNLHTSVSSAQGQDAAQSEEKRG +ITARELYSYLRSTKP +>generic|con_K1C10_HUMAN|K1C10_HUMAN +MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRG +SSGGGCFGGSSGGYGGLGGFGGGSFHGSYGSSSFGGSYGGSFGGGNFGGGSFGGGSFGGG +GFGGGGFGGGFGGGFGGDGGLLSGNEKVTMQNLNDRLASYLDKVRALEESNYELEGKIKE +WYEKHGNSHQGEPRDYSKYYKTIDDLKNQILNLTTDNANILLQIDNARLAADDFRLKYEN +EVALRQSVEADINGLRRVLDELTLTKADLEMQIESLTEELAYLKKNHEEEMKDLRNVSTG +DVNVEMNAAPGVDLTQLLNNMRSQYEQLAEQNRKDAEAWFNEKSKELTTEIDNNIEQISS +YKSEITELRRNVQALEIELQSQLALKQSLEASLAETEGRYCVQLSQIQAQISALEEQLQQ +IRAETECQNTEYQQLLDIKIRLENEIQTYRSLLEGEGSSGGGGRGGGSFGGGYGGGSSGG +GSSGGGYGGGHGGSSGGGYGGGSSGGGSSGGGYGGGSSSGGHGGGSSSGGHGGSSSGGYG +GGSSGGGGGGYGGGSSGGGSSSGGGYGGGSSSGGHKSSSSGSVGESSSKGPRY +>generic|con_K2C1_HUMAN|K2C1_HUMAN +SRQFSSRSGYRSGGGFSSGSAGIINYQRRTTSSSTRRSGGGGGRFSSCGGGGGSFGAGGG +FGSRSLVNLGGSKSISISVARGGGRGSGFGGGYGGGGFGGGGFGGGGFGGGGIGGGGFGG +FGSGGGGFGGGGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSRER +EQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEPYFESFINNLRRR +VDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTNAENEFVTIKKDVDGAYMTKVDL +QAKLDNLQQEIDFLTALYQAELSQMQTQISETNVILSMDNNRSLDLDSIIAEVKAQNEDI +AQKSKAEAESLYQSKYEELQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISN +LQQSISDAEQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEIAT +YRTLLEGEESRMSGECAPNVSVSVSTSHTTISGGGSRGGGGGGYGSGGSSYGSGGGSYGS +GGGGGGGRGSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYRGGSGGGGGGSSGG +RGSGGGSSGGSIGGRGSSSGGVKSSGGSSSVRFVSTTYSGVTR +>sp|A0A087X1C5|CP2D7_HUMAN Putative cytochrome P450 2D7 OS=Homo sapiens OX=9606 GN=CYP2D7 PE=5 SV=1 +MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREAMVTRGEDTADRPPAPIYQVLGFGPRSQGVILSRYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFADQAGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLPHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAKKEKAKGSPESSFNDENLRIVVGNLFLAGMVTTSTTLAWGLLLMILHLDVQRGRRVSPGCPIVGTHVCPVRVQQEIDDVIGQVRRPEMGDQAHMPCTTAVIHEVQHFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWKKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVAAGQPRPSHSRVVSFLVTPSPYELCAVPR +>sp|A0A0B4J2F0|PIOS1_HUMAN Protein PIGBOS1 OS=Homo sapiens OX=9606 GN=PIGBOS1 PE=1 SV=1 +MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS +>sp|A0A0B4J2F2|SIK1B_HUMAN Putative serine/threonine-protein kinase SIK1B OS=Homo sapiens OX=9606 GN=SIK1B PE=5 SV=1 +MVIMSEFSADPAGQGQGQQKPLRVGFYDIERTLGKGNFAVVKLARHRVTKTQVAIKIIDKTRLDSSNLEKIYREVQLMKLLNHPHIIKLYQVMETKDMLYIVTEFAKNGEMFDYLTSNGHLSENEARKKFWQILSAVEYCHDHHIVHRDLKTENLLLDGNMDIKLADFGFGNFYKSGEPLSTWCGSPPYAAPEVFEGKEYEGPQLDIWSLGVVLYVLVCGSLPFDGPNLPTLRQRVLEGRFRIPFFMSQDCESLIRRMLVVDPARRITIAQIRQHRWMRAEPCLPGPACPAFSAHSYTSNLGDYDEQALGIMQTLGVDRQRTVESLQNSSYNHFAAIYYLLLERLKEYRNAQCARPGPARQPRPRSSDLSGLEVPQEGLSTDPFRPALLCPQPQTLVQSVLQAEMDCELQSSLQWPLFFPVDASCSGVFRPRPVSPSSLLDTAISEEARQGPGLEEEQDTQESLPSSTGRRHTLAEVSTRLSPLTAPCIVVSPSTTASPAEGTSSDSCLTFSASKSPAGLSGTPATQGLLGACSPVRLASPFLGSQSATPVLQAQGGLGGAVLLPVSFQEGRRASDTSLTQGLKAFRQQLRKTTRTKGFLGLNKIKGLARQVCQVPASRASRGGLSPFHAPAQSPGLHGGAAGSREGWSLLEEVLEQQRLLQLQHHPAAAPGCSQAPQPAPAPFVIAPCDGPGAAPLPSTLLTSGLPLLPPPLLQTGASPVASAAQLLDTHLHIGTGPTALPAVPPPRLARLAPGCEPLGLLQGDCEMEDLMPCSLGTFVLVQ +>sp|A0A0C5B5G6|MOTSC_HUMAN Mitochondrial-derived peptide MOTS-c OS=Homo sapiens OX=9606 GN=MT-RNR1 PE=1 SV=1 +MRWQEMGYIFYPRKLR +>sp|A0A0K2S4Q6|CD3CH_HUMAN Protein CD300H OS=Homo sapiens OX=9606 GN=CD300H PE=1 SV=1 +MTQRAGAAMLPSALLLLCVPGCLTVSGPSTVMGAVGESLSVQCRYEEKYKTFNKYWCRQPCLPIWHEMVETGGSEGVVRSDQVIITDHPGDLTFTVTLENLTADDAGKYRCGIATILQEDGLSGFLPDPFFQVQVLVSSASSTENSVKTPASPTRPSQCQGSLPSSTCFLLLPLLKVPLLLSILGAILWVNRPWRTPWTES +>sp|A0A0U1RRE5|NBDY_HUMAN Negative regulator of P-body association OS=Homo sapiens OX=9606 GN=NBDY PE=1 SV=1 +MGDQPCASGRSTLPPGNAREAKPPKKRCLLAPRWDYPEGTPNGGSTTLPSAPPPASAGLKSHPPPPEK +>sp|A0A1B0GTW7|CIROP_HUMAN Ciliated left-right organizer metallopeptidase OS=Homo sapiens OX=9606 GN=CIROP PE=1 SV=1 +MLLLLLLLLLLPPLVLRVAASRCLHDETQKSVSLLRPPFSQLPSKSRSSSLTLPSSRDPQPLRIQSCYLGDHISDGAWDPEGEGMRGGSRALAAVREATQRIQAVLAVQGPLLLSRDPAQYCHAVWGDPDSPNYHRCSLLNPGYKGESCLGAKIPDTHLRGYALWPEQGPPQLVQPDGPGVQNTDFLLYVRVAHTSKCHQETVSLCCPGWSTAAQSQLTAALTSWAQRRGFVMLPRLCLKLLGSSNLPTLASQSIRITGPSVIAYAACCQLDSEDRPLAGTIVYCAQHLTSPSLSHSDIVMATLHELLHALGFSGQLFKKWRDCPSGFSVRENCSTRQLVTRQDEWGQLLLTTPAVSLSLAKHLGVSGASLGVPLEEEEGLLSSHWEARLLQGSLMTATFDGAQRTRLDPITLAAFKDSGWYQVNHSAAEELLWGQGSGPEFGLVTTCGTGSSDFFCTGSGLGCHYLHLDKGSCSSDPMLEGCRMYKPLANGSECWKKENGFPAGVDNPHGEIYHPQSRCFFANLTSQLLPGDKPRHPSLTPHLKEAELMGRCYLHQCTGRGAYKVQVEGSPWVPCLPGKVIQIPGYYGLLFCPRGRLCQTNEDINAVTSPPVSLSTPDPLFQLSLELAGPPGHSLGKEQQEGLAEAVLEALASKGGTGRCYFHGPSITTSLVFTVHMWKSPGCQGPSVATLHKALTLTLQKKPLEVYHGGANFTTQPSKLLVTSDHNPSMTHLRLSMGLCLMLLILVGVMGTTAYQKRATLPVRPSASYHSPELHSTRVPVRGIREV +>sp|A0AV02|S12A8_HUMAN Solute carrier family 12 member 8 OS=Homo sapiens OX=9606 GN=SLC12A8 PE=1 SV=4 +MTQMSQVQELFHEAAQQDALAQPQPWWKTQLFMWEPVLFGTWDGVFTSCMINIFGVVLFLRTGWLVGNTGVLLGMFLVSFVILVALVTVLSGIGVGERSSIGSGGVYSMISSVLGGQTGGTIGLLYVFGQCVAGAMYITGFAESISDLLGLGNIWAVRGISVAVLLALLGINLAGVKWIIRLQLLLLFLLAVSTLDFVVGSFTHLDPEHGFIGYSPELLQNNTLPDYSPGESFFTVFGVFFPAATGVMAGFNMGGDLREPAASIPLGSLAAVGISWFLYIIFVFLLGAICTREALRYDFLIAEKVSLMGFLFLLGLYISSLASCMGGLYGAPRILQCIAQEKVIPALACLGQGKGPNKTPVAAICLTSLVTMAFVFVGQVNVLAPIVTINFMLTYVAVDYSYFSLSMCSCSLTPVPEPVLREGAEGLHCSEHLLLEKAPSYGSEGPAQRVLEGTLLEFTKDMDQLLQLTRKLESSQPRQGEGNRTPESQKRKSKKATKQTLQDSFLLDLKSPPSFPVEISDRLPAASWEGQESCWNKQTSKSEGTQPEGTYGEQLVPELCNQSESSGEDFFLKSRLQEQDVWRRSTSFYTHMCNPWVSLLGAVGSLLIMFVIQWVYTLVNMGVAAIVYFYIGRASPGLHLGSASNFSFFRWMRSLLLPSCRSLRSPQEQIILAPSLAKVDMEMTQLTQENADFATRDRYHHSSLVNREQLMPHY +>sp|A0AV96|RBM47_HUMAN RNA-binding protein 47 OS=Homo sapiens OX=9606 GN=RBM47 PE=1 SV=2 +MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY +>sp|A0AVF1|IFT56_HUMAN Intraflagellar transport protein 56 OS=Homo sapiens OX=9606 GN=TTC26 PE=1 SV=1 +MMLSRAKPAVGRGVQHTDKRKKKGRKIPKLEELLSKRDFTGAITLLEFKRHVGEEEEDTNLWIGYCAFHLGDYKRALEEYENATKEENCNSEVWVNLACTYFFLGMYKQAEAAGFKASKSRLQNRLLFHLAHKFNDEKKLMSFHQNLQDVTEDQLSLASIHYMRSHYQEAIDIYKRILLDNREYLALNVYVALCYYKLDYYDVSQEVLAVYLQQIPDSTIALNLKACNHFRLYNGRAAEAELKSLMDNASSSFEFAKELIRHNLVVFRGGEGALQVLPPLVDVIPEARLNLVIYYLRQDDVQEAYNLIKDLEPTTPQEYILKGVVNAALGQEMGSRDHMKIAQQFFQLVGGSASECDTIPGRQCMASCFFLLKQFDDVLIYLNSFKSYFYNDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSGESFSLLQLIANDCYKMGQFYYSAKAFDVLERLDPNPEYWEGKRGACVGIFQMIIAGREPKETLREVLHLLRSTGNTQVEYMIRIMKKWAKENRVSI diff -r 000000000000 -r 14785481da2b test-data/tmt11/test.manifest --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.manifest Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,2 @@ +test1.mzML sample1 DDA +test2.mzML sample2 DDA diff -r 000000000000 -r 14785481da2b test-data/tmt11/test1.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test1.mzML Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,716 @@ + + + + + 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Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,311 @@ +# Workflow: Default + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +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.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=(-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.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +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=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +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.diagextract_mode=false +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_mode=false +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_mode=false +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.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=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.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +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=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b workflows/LFQ-MBR.workflow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/LFQ-MBR.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: LFQ-MBR + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +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.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=(-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 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +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=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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 --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +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\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +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.diagextract_mode=false +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_mode=false +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_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=true +run-psm-validation=true +run-validation-tab=true +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=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=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.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +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=false +workflow.description=Perform closed search, followed by label free quantification with match-between-runs using IonQuant. If using mzML files, need to choose the right MS data type (Regular MS vs IM-MS). Need to assign runs to experiments. +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b workflows/Nonspecific-HLA.workflow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/Nonspecific-HLA.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: Nonspecific-HLA + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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=false +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +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.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=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=25 +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=1 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=5 +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=200 +msfragger.misc.fragger.enzyme-dropdown-1=nonspecific +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=0 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=15 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=- +msfragger.search_enzyme_cut_2=- +msfragger.search_enzyme_name_1=nonspecific +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,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=300 +msfragger.write_calibrated_mzml=false +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 --prot 1 +phi-report.pep-level-summary=true +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= +ptmprophet.run-ptmprophet=false +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.diagextract_mode=false +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_mode=false +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_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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.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=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=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=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.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +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=false +workflow.description=

Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b workflows/Open.workflow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/Open.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: Open + +crystalc.run-crystalc=true +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=true +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.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=false +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= +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=(-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 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=true +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-150 +msfragger.precursor_mass_mode=corrected +msfragger.precursor_mass_units=0 +msfragger.precursor_mass_upper=500 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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 1000.0 --clevel -2 +peptide-prophet.combine-pepxml=true +peptide-prophet.run-peptide-prophet=true +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=false +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 0.01 --mapmods +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= +ptmprophet.run-ptmprophet=false +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.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=25 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=12.5 +ptmshepherd.diagmine_fragMinSpecDiff=25 +ptmshepherd.diagmine_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=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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=true +ptmshepherd.spectra_maxfragcharge=1 +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=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=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +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=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=-1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=pool +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Open search workflow for PTM analysis. MSFragger localization-aware open search (LOS) algorithm, with deisotoping, mass calibration, parameter optimization, and monoisotope correction enabled. Mass range -150 to 500 Da. PeptideProphet with extended mass model. Crystal-C for artifact removal. Precursor ion quantification using Freequant. PTM-Shepherd for mass shift summarization. For faster run time, in MSFragger change the number of allowed missed cleavages to 1.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b workflows/TMT10.workflow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/TMT10.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: TMT10 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +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=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.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=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +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_mode=false +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_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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.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=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=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=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 +workflow.description=

Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff -r 000000000000 -r 14785481da2b workflows/TMT11.workflow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/TMT11.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: TMT11 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +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 +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=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.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=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +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=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +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_mode=false +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_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +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.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=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=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=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 +workflow.description=

Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5