| Previous changeset 14:e42225f8a659 (2021-07-08) Next changeset 16:74f5d355d156 (2022-07-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be" |
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modified:
macros.xml maxquant.xml |
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added:
maxquant_mqpar.xml modify_mqpar.py test-data/09/combined/txt/msmsScans.txt test-data/10/config.yml test-data/10/mqpar.xml test-data/mqpar/mqpar.xml test-data/mqpar/txt/allPeptides.txt test-data/mqpar/txt/evidence.txt test-data/mqpar/txt/modificationSpecificPeptides.txt test-data/mqpar/txt/mqpar.xml test-data/mqpar/txt/msms.txt test-data/mqpar/txt/msmsScans.txt test-data/mqpar/txt/mzRange.txt test-data/mqpar/txt/parameters.txt test-data/mqpar/txt/peptides.txt test-data/mqpar/txt/proteinGroups.txt test-data/mqpar/txt/summary.txt test-data/thermo.raw test-data/tmt_data_18.fasta test-data/tmt_data_18.mzXML |
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| diff -r e42225f8a659 -r 97a7f34fcb6a macros.xml --- a/macros.xml Thu Jul 08 22:45:35 2021 +0000 +++ b/macros.xml Wed Aug 11 09:24:23 2021 +0000 |
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| @@ -1,7 +1,8 @@ <?xml version="1.0" ?> <macros> <token name="@VERSION@">1.6.17.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX_MQPAR@">0</token> <token name="@VERSION_PTXQC@">1.0.10</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> <token name="@TMT2PLEX@"> @@ -60,6 +61,11 @@ - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True] - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True] </token> + <token name="@TMTPRO18PLEX@"> + @TMTPRO16PLEX@ + - [TMTpro18plex-Lys134C,TMTpro18plex-Nter134C,0,0,0,0,True] + - [TMTpro18plex-Lys135N,TMTpro18plex-Nter135N,0,0,0,0,True] + </token> <token name="@ITRAQ4PLEX@"> - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] @@ -131,11 +137,18 @@ cont_MYCO: - MYCOPLASMA - '1' + #if $varExists("mqpar_input"): + #import re + #set $mqpar_xml = open(str($mqpar_input), "r").read() + #set $matchingTimeWindow = re.search("matchingTimeWindow>(.*)./matchingTimeWindow", $mqpar_xml).group(1) + MQpar_MatchingTimeWindow_num: ${matchingTimeWindow} + #else: #if $search_opts.mbr.match_between_runs == 'True': MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window} #else: MQpar_MatchingTimeWindow_num: 0.0 #end if + #end if MatchBetweenRuns_wA: auto MQpar_firstSearchTol_num: 20.0 firstSearch_outOfCalWarnSD_num: 2.0 @@ -829,6 +842,10 @@ <expand macro="mod_option" value="TMTpro16plex-Lys133N"/> <expand macro="mod_option" value="TMTpro16plex-Lys133C"/> <expand macro="mod_option" value="TMTpro16plex-Lys134N"/> + <expand macro="mod_option" value="TMTpro18plex-Nter134C"/> + <expand macro="mod_option" value="TMTpro18plex-Nter135N"/> + <expand macro="mod_option" value="TMTpro18plex-Lys134C"/> + <expand macro="mod_option" value="TMTpro18plex-Lys135N"/> </xml> <xml name="citations"> <citations> |
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| diff -r e42225f8a659 -r 97a7f34fcb6a maxquant.xml --- a/maxquant.xml Thu Jul 08 22:45:35 2021 +0000 +++ b/maxquant.xml Wed Aug 11 09:24:23 2021 +0000 |
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| @@ -206,6 +206,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': @TMTPRO16PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex': + @TMTPRO18PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -251,6 +254,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': @TMTPRO16PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex': + @TMTPRO18PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -510,6 +516,7 @@ <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> <option value="tmtpro16plex">TMTpro16plex</option> + <option value="tmtpro18plex">TMTpro18plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -520,6 +527,7 @@ <when value="tmt10plex"/> <when value="tmt11plex"/> <when value="tmtpro16plex"/> + <when value="tmtpro18plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -565,6 +573,7 @@ <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> <option value="tmtpro16plex">TMTpro16plex</option> + <option value="tmtpro18plex">TMTpro18plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -575,6 +584,7 @@ <when value="tmt10plex"/> <when value="tmt11plex"/> <when value="tmtpro16plex"/> + <when value="tmtpro18plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -921,7 +931,7 @@ <output name="mqpar" file="07/mqpar.xml" lines_diff="4" /> <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" /> </test> - <!-- TMTpro16plex test --> + <!-- TMTpro16plex test --> <test expect_num_outputs="3"> <param name="ftype" value=".mzxml" /> <param name="fasta_files" value="tmt_data_16.fasta" /> @@ -945,6 +955,50 @@ <output name="mqpar" file="08/mqpar.xml" lines_diff="24" /> <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" /> </test> + <!-- TMTpro18plex test --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="tmt_data_18.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <repeat name="paramGroups"> + <param name="files" value="tmt_data_18.mzXML"/> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="fixedModifications" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms2" /> + <conditional name="iso_labels"> + <param name="labeling" value="tmtpro18plex" /> + </conditional> + </conditional> + </repeat> + <param name="do_it" value="False" /> + <param name="output" value="msmsScans" /> + <output name="msmsScans" file="09/combined/txt/msmsScans.txt"> + <assert_contents> + <has_text text="GANDSMMM" /> + </assert_contents> + </output> + </test> + <!-- Thermo RAW file test --> + <test expect_num_outputs="2"> + <param name="ftype" value=".thermo.raw" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value="^>.*\|(.*)\|.*$" /> + <param name="description_parse_rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" /> + <param name="min_unique_pep" value="1" /> + <repeat name="paramGroups"> + <param name="files" value="thermo.raw"/> + <param name="maxMissedCleavages" value="1"/> + <param name="variableModifications" value="Oxidation (M)" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="lfq" /> + </conditional> + </repeat> + <param name="output" value="config,mqpar" /> + <output name="config" file="10/config.yml" lines_diff="2" /> + <output name="mqpar" file="10/mqpar.xml" lines_diff="10" /> + </test> </tests> <help><![CDATA[ @@ -980,7 +1034,7 @@ - Tabular file with experimental design template: - - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template: + - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. Thermo RAW files are handled differently (see table below). This is a (syntactically) correct experimental design template: :: @@ -1003,6 +1057,18 @@ File4 1 (missing experiment) (File5 missing) + - However, “.raw” (Thermo) is considered a part of the filename: + + :: + + Name Fraction Experiment PTM + File1.raw 1 E1 False + File2.raw 2 E1 False + File3.raw 3 E1 False + File4.raw 1 E2 False + File5.raw 2 E2 False + File6.raw 3 E2 False + **Parameter Options** - Quantitation methods (in section parameter groups) |
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| diff -r e42225f8a659 -r 97a7f34fcb6a maxquant_mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mqpar.xml Wed Aug 11 09:24:23 2021 +0000 |
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| b'@@ -0,0 +1,204 @@\n+<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@">\n+ <macros>\n+ <xml name="output" token_format="tabular" token_label="default description" token_name="default">\n+ <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n+ <filter>\'@NAME@\' in output</filter>\n+ </data>\n+ </xml>\n+ <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">\n+ <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n+ <filter>\'@NAME@\' in output</filter>\n+ </data>\n+ </xml>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## link galaxy datasets to filenames accepted by maxquant\n+ #import re\n+ #set names = [re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($n.element_identifier)) for $n in $input_opts.infiles]\n+ #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]\n+ #for $target, $link in zip($infiles, $names_with_ext)\n+ #if str($input_opts.ftype) == \'.thermo.raw\':\n+ cp \'$target\' \'$link\' &&\n+ #else:\n+ ln -s \'$target\' \'$link\' &&\n+ #end if\n+ #end for\n+\n+ python3 \'$__tool_directory__/modify_mqpar.py\'\n+ #set inf = \',\'.join($names_with_ext)\n+ --infiles=\'$inf\'\n+ --version=@VERSION@\n+ --num_threads=\\${GALAXY_SLOTS:-1}\n+ --substitution_rx=\'@SUBSTITUTION_RX@\'\n+ --fasta_files=\'$fasta_files\'\n+ --description_parse_rule=\'$description_parse_rule\'\n+ --identifier_parse_rule=\'$identifier_parse_rule\'\n+ \'$mqpar_input\'\n+\n+ &&\n+ maxquant mqpar.xml\n+ #if \'log\' in $output:\n+ >> \'$log\'\n+ #end if\n+ && mv mqpar.xml combined/txt/mqpar.xml\n+ #if \'output_all\' in $output:\n+ &&\n+ tar -zcf \'$output_all\' ./combined/txt\n+ #end if\n+ \n+ #if $qc.do_it:\n+ &&\n+ Rscript \'$qr\' \'$qr_yaml\'\n+ #if \'log\' in $output:\n+ >> \'$log\' 2>&1\n+ #end if\n+ &&\n+ cp ./combined/txt/report_v@VERSION_PTXQC@_combined.pdf \'$ptxqc_report\'\n+ #end if\n+ ]]></command>\n+\n+ <configfiles>\n+ <expand macro="ptxqc"/>\n+ </configfiles>\n+\n+ <inputs>\n+ <conditional name="input_opts">\n+ <param name="ftype" type="select" label="choose the type of your input files">\n+ <option value=".thermo.raw">thermo.raw</option>\n+ <option value=".mzxml">mzXML</option>\n+ <option value=".mzml">mzML</option>\n+ </param>\n+ <when value=".thermo.raw"> \n+ <param multiple="true" name="infiles" type="data"\n+ format="thermo.raw" label="RAW Files"\n+ help="Specify one or more Thermo RAW files" />\n+ </when>\n+ <when value=".mzxml">\n+ <param multiple="true" name="infiles" type="data"\n+ format="mzXML" label="mzXML Files"\n+ help="Specify one or more mzXML files" />\n+ </when>\n+ <when value=".mzml">\n+ <param multiple="true" name="infiles" type="data"\n+ format="mzML" label="mzML Files"\n+ help="Specify one or more mzML files" />\n+ </when>\n+ </conditional>\n+ <param format="fasta" multiple="true" name="fasta_files"\n+ type="data" label="FASTA files"\n+ help="Specify one or more FASTA databases." />\n+ <param name="identifier_parse_rule" type="text"\n+ label="identifier parse rule" value="^>.*\\|(.*)\\|.*$">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="&apo'..b' <option value="modificationSpecificPeptides">modification specific peptides</option>\n+ <option value="ms3Scans">ms3 scans</option>\n+ <option value="msmsScans">msms scans</option>\n+ <option value="mzRange">mz range</option>\n+ <option value="peptideSection">peptide section</option>\n+ <option value="summary">summary</option>\n+ <option value="output_all">complete \'combined/txt/\' directory (compressed)</option>\n+ <option value="log">MaxQuant and PTXQC log</option>\n+ </param>\n+ </inputs>\n+\n+ <expand macro="outputs"/>\n+\n+ <tests>\n+ <test>\n+ <param name="ftype" value=".mzxml" />\n+ <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />\n+ <param name="fasta_files" value="bsa.fasta" />\n+ <param name="identifier_parse_rule" value=">([^\\s]*)" />\n+ <param name="description_parse_rule" value=">(.*)" />\n+ <param name="mqpar_input" value="mqpar/mqpar.xml" />\n+ <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />\n+ <output name="evidence">\n+ <assert_contents>\n+ <has_text text="AEFVEVTK" />\n+ </assert_contents>\n+ </output>\n+ <output name="msms">\n+ <assert_contents>\n+ <has_text text="ECCHGDLLECADDR" />\n+ </assert_contents>\n+ </output>\n+ <output name="allPeptides" file="mqpar/txt/allPeptides.txt" lines_diff="32" />\n+ <output name="msmsScans">\n+ <assert_contents>\n+ <has_text text="LLEEQVFMANGVSLQLQR" />\n+ </assert_contents>\n+ </output>\n+ <output name="mzRange" file="mqpar/txt/mzRange.txt" />\n+ <output name="parameters" file="mqpar/txt/parameters.txt" lines_diff="8"/>\n+ <output name="peptides">\n+ <assert_contents>\n+ <has_text text="VEVTKLVTDLTKVHKECCHGDLLECADDRA" />\n+ </assert_contents>\n+ </output>\n+ <output name="proteinGroups">\n+ <assert_contents>\n+ <has_text text="ENSBTAP00000007350" />\n+ </assert_contents>\n+ </output>\n+ <output name="summary" file="mqpar/txt/summary.txt" />\n+ <output name="modificationSpecificPeptides">\n+ <assert_contents>\n+ <has_text text="ECCHGDLLECADDR" />\n+ </assert_contents>\n+ </output>\n+ <output name="mqpar" file="mqpar/txt/mqpar.xml" lines_diff="8" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. \n+\n+This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible.\n+\n+**Input files**\n+\n+- Thermo raw file or mzXML file\n+ - The datatype has to be \'thermo.raw\' or \'mzXML\'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)\n+- mqpar.xml: \n+ - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager.\n+\n+**Output files**\n+\n+Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented. \n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r e42225f8a659 -r 97a7f34fcb6a modify_mqpar.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/modify_mqpar.py Wed Aug 11 09:24:23 2021 +0000 |
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| @@ -0,0 +1,34 @@ +"Modify a given mqpar.xml to run Galaxy MaxQuant with it." + +import argparse +import os + +from mqparam import MQParam + +parser = argparse.ArgumentParser() + +arguments = ('--infiles', + '--version', + '--num_threads', + '--substitution_rx', + '--fasta_files', + '--description_parse_rule', + '--identifier_parse_rule', + 'mqpar') + +for arg in arguments: + parser.add_argument(arg) + +args = parser.parse_args() + +mqpar_out = os.path.join(os.getcwd(), 'mqpar.xml') +infiles = [os.path.join(os.getcwd(), f) for f in args.infiles.split(',')] +mqparam = MQParam(args.mqpar, None, substitution_rx=args.substitution_rx) +if mqparam.version != args.version: + raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version)) +mqparam.translate(infiles) +mqparam.add_fasta_files(args.fasta_files.split(','), + {'identifierParseRule': args.identifier_parse_rule, + 'descriptionParseRule': args.description_parse_rule}) +mqparam.set_simple_param('numThreads', args.num_threads) +mqparam.write('mqpar.xml') |
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| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/09/combined/txt/msmsScans.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/09/combined/txt/msmsScans.txt Wed Aug 11 09:24:23 2021 +0000 |
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| @@ -0,0 +1,9 @@ +Raw file Scan number Retention time Ion injection time Total ion current Collision energy Summations Base peak intensity Elapsed time Identified Matched Reverse MS/MS IDs Sequence Length Filtered peaks m/z Mass Charge Type Fragmentation Mass analyzer Parent intensity fraction Fraction of total spectrum Base peak fraction Precursor full scan number Precursor intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Scan event number Modifications Modified sequence Proteins Score PEP Experiment Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Reporter intensity corrected 10 Reporter intensity corrected 11 Reporter intensity corrected 12 Reporter intensity corrected 13 Reporter intensity corrected 14 Reporter intensity corrected 15 Reporter intensity corrected 16 Reporter intensity corrected 17 Reporter intensity corrected 18 Reporter intensity 1 Reporter intensity 2 Reporter intensity 3 Reporter intensity 4 Reporter intensity 5 Reporter intensity 6 Reporter intensity 7 Reporter intensity 8 Reporter intensity 9 Reporter intensity 10 Reporter intensity 11 Reporter intensity 12 Reporter intensity 13 Reporter intensity 14 Reporter intensity 15 Reporter intensity 16 Reporter intensity 17 Reporter intensity 18 Reporter PIF Reporter fraction Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number +tmt_data_18 4 0.022647 -1 1555.1 35 0 429.62 -1 - -1 0 19 496.5587 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 0 2 3 +tmt_data_18 6 0.028164 -1 306.22 35 0 210 -1 - -1 0 3 562.254 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 1 3 5 +tmt_data_18 7 0.030756 -1 76712 0 0 6269.6 -1 - -1 0 84 1 NaN 0 PEAK CID FTMS NaN NaN NaN -1 NaN NaN 0 NaN 2 NaN NaN tmt_data_18.mzXML 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 437.7 465.76 538.68 473.42 0 662.1 803.52 0 1148.3 592.81 894.98 1139.6 977.11 1107.6 934.33 696.59 576.46 1213.5 NaN NaN NaN 0 2 3 5 +tmt_data_18 10 0.043625 -1 374.34 35 0 119.96 -1 - + -1 GANDSMMM 8 7 604.7506 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 3 Oxidation (M) _GANDSM(Oxidation (M))M(Oxidation (M))M(Oxidation (M))_ REV__sp|Q8N7M0|DYLT5_HUMAN 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 3 5 9 +tmt_data_18 14 0.05893 -1 417.62 35 0 66.299 -1 - -1 0 10 553.2144 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 NaN NaN tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 4 8 13 +tmt_data_18 39 0.17826 -1 136.05 35 0 61.009 -1 - + -1 QEMEPTR 7 3 404.2059 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Oxidation (M) _QEM(Oxidation (M))EPTR_ REV__sp|O15457|MSH4_HUMAN 4.59465663460819 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 5 32 38 +tmt_data_18 155 0.75055 -1 211.81 35 0 69.087 -1 - -1 PGTSGWDSCR 10 6 457.2214 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _PGTSGWDSCR_ CON__Q6KB66-1 0 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 6 147 154 +tmt_data_18 162 0.781 -1 239.53 35 0 62.874 -1 - + -1 MRLQIEQR 8 6 459.9375 NaN 0 PEAK CID ITMS NaN NaN NaN -1 NaN NaN 0 NaN 1 Unmodified _MRLQIEQR_ REV__sp|Q8ND30|LIPB2_HUMAN 4.96526132859811 0.01 tmt_data_18.mzXML 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NaN NaN NaN 0 7 153 161 |
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| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/10/config.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10/config.yml Wed Aug 11 09:24:23 2021 +0000 |
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| @@ -0,0 +1,38 @@ + + fastaFiles: [/tmp/tmps9fy8_y6/files/0/d/3/dataset_0d32c02a-47ca-47c8-83b6-1e955f377a96.dat] + parseRules: + identifierParseRule: '^>.*\|(.*)\|.*$' + descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$' + minUniquePeptides: 1 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] + useCounterparts: True + paramGroups: + - files: ['thermo.raw.thermo.raw'] + maxMissedCleavages: 1 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lfqMode: 1 + lfqNormType: 1 + lfqMinEdgesPerNode: 3 + lfqAvEdgesPerNode: 6 + lfqMinRatioCount: 2 + \ No newline at end of file |
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| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/10/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10/mqpar.xml Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,481 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmps9fy8_y6/files/0/d/3/dataset_0d32c02a-47ca-47c8-83b6-1e955f377a96.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>^>.*\\|(.*)\\|.*$</identifierParseRule>\n+\t\t\t<descriptionParseRule>^>.*\\|.*\\|[^ ]+ (.*) OS.*$</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>1</minUniquePeptides>\n+\t<useCounterparts>True</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>\n+\t<matchingIonMobilityWindow>0</matchingIonMobilityWindow>\n+\t<alignmentTimeWindow>0</alignmentTimeWindow>\n+\t<alignmentIonMobilityWindow>0</alignmentIonMobi'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/mqpar.xml Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,487 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>bsa.fasta</fastaFilePath>\n+\t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n+\t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>0</minUniquePeptides>\n+\t<useCounterparts>False</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>\n+\t<matchingIonMobilityWindow>0</matchingIonMobilityWindow>\n+\t<alignmentTimeWindow>0</alignmentTimeWindow>\n+\t<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>\n+\t<numberOfCandidatesMsms>15</numberOfCandidatesMsms>\n+\t<compositionPrediction>0</'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/allPeptides.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/allPeptides.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,405 @@\n+Raw file\tType\tCharge\tm/z\tMass\tUncalibrated m/z\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tMass fractional part\tMass deficit\tMass precision [ppm]\tMax intensity m/z 0\tRetention time\tRetention length\tRetention length (FWHM)\tMin scan number\tMax scan number\tIdentified\tReverse\tMS/MS IDs\tSequence\tLength\tModifications\tModified sequence\tProteins\tScore\tPEP\tIntensity\tIntensities\tIsotope pattern\tMS/MS Count\tMSMS Scan Numbers\tMSMS Isotope Indices\n+BSA_min_21\tMULTI\t2\t752.78847\t1503.5624\t752.78847\t8\t4\t2\t\t0.562384\t-0.16925473367246\t0.775183\t752.788732084711\t0.0728\t10.5\t0\t1\t31\t\t\t-1\t\t0\t\t\t\t0\tNaN\t29581\t0;10127.0834960938;21733.4140625;15751.8271484375;11119.455078125;0\t12711.455078125;9021.958984375\t0\t\t\n+BSA_min_21\tMULTI\t2\t485.29192\t968.5693\t485.29192\t22\t13\t3\t\t0.569296\t0.0837541655223504\t0.713993\t485.291493836352\t0.158\t29.2\t0\t1\t84\t\t\t-1\t\t0\t\t\t\t0\tNaN\t35127\t0;6617.423828125;22640.4897460938;31257.1982421875;34228.8039550781;35066.3161621094;22591.3203125;25334.1130371094;10954.4208984375;10387.701171875;5409.716796875;5679.3515625;3629.8916015625;3413.14501953125;0\t22239.669921875;10595.8701171875;3631.79956054688\t0\t\t\n+BSA_min_21\tMULTI\t1\t609.34313\t608.33585\t609.34313\t15\t10\t2\t\t0.335855\t0.0160203484621206\t0.653578\t609.343255068747\t0.14\t22.8\t0\t1\t66\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16988\t0;9840.98266601562;11124.4873046875;15963.8212890625;11129.7348632812;11067.9287109375;5360.87646484375;5169.17236328125;5964.7109375;5728.80078125;4231.7958984375;0\t9241.0615234375;7473.39013671875\t0\t\t\n+BSA_min_21\tMULTI\t2\t752.31297\t1502.6114\t752.31297\t9\t6\t2\t\t0.611386\t-0.119815223783917\t0.685468\t752.312709646655\t0.121\t14.7\t0\t1\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t40064\t0;4285.77001953125;11859.416015625;29434.9091796875;28467.7021484375;21782.734375;7783.14453125;0\t22226.8125;12791.9208984375\t1\t36\t0\n+BSA_min_21\tMULTI\t4\t835.11285\t3336.4223\t835.11285\t18\t7\t3\t\t0.422302\t-0.152452077995349\t0.513615\t835.363566648992\t0.151\t16.7\t0\t1\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t63787\t0;17149.9038085938;25055.0866699219;28565.6630859375;44055.3051757812;40159.6279296875;23483.638671875;9918.11328125;0\t0;20459.83203125;17639.462890625;9406.8017578125\t1\t41\t2\n+BSA_min_21\tMULTI\t1\t1129.4643\t1128.457\t1129.4643\t7\t4\t2\t\t0.456986\t-0.102104602059853\t1.36127\t1129.46329424631\t0.127\t10.5\t0\t7\t37\t\t\t-1\t\t0\t\t\t\t0\tNaN\t16468\t0;7075.529296875;14889.8579101562;13879.3891601562;10506.4604492188;0\t8219.6025390625;7768.6494140625\t0\t\t\n+BSA_min_21\tMULTI\t2\t529.23526\t1056.456\t529.23526\t11\t6\t2\t\t0.455969\t-0.0700012324659838\t0.57417\t529.23524702789\t0.144\t14.6\t0\t7\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t40276\t0;20066.6826171875;28887.369140625;34706.0693359375;23093.0561523438;20422.7763671875;4860.98779296875;0\t20563.033203125;14143.0361328125\t1\t30\t0\n+BSA_min_21\tMULTI\t2\t558.2828\t1114.551\t558.2828\t4\t2\t2\t\t0.55104\t-0.00165384098022514\t1.21174\t558.28243824793\t0.199\t6.41\t0\t25\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t10557\t0;6792.45678710938;8991.09375;0\t4918.08203125;4216.0205078125\t0\t\t\n+BSA_min_21\tMULTI\t2\t637.83382\t1273.6531\t637.83382\t8\t4\t2\t\t0.653089\t0.0272087376192758\t1.19726\t637.833851166233\t0.144\t10.6\t0\t13\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t23966\t0;12504.6166992188;19667.046875;14443.9584960938;9725.94287109375;0\t12625.1611328125;7041.8857421875\t0\t\t\n+BSA_min_21\tMULTI\t5\t840.76716\t4198.7994\t840.76716\t4\t2\t2\t\t0.799427\t-0.17202043738871\t0.862365\t841.167796873992\t0.215\t6.41\t0\t25\t43\t\t\t-1\t\t0\t\t\t\t0\tNaN\t27642\t0;8633.95654296875;12155.693359375;0\t0;0;6595.16845703125;5560.52490234375\t0\t\t\n+BSA_min_21\tMULTI\t3\t967.55492\t2899.6429\t967.55492\t7\t5\t2\t\t0.642938\t0.269101895641143\t1.61907\t967.889249718701\t0.225\t12.6\t0\t13\t48\t\t\t-1\t\t0\t\t\t\t0\tNaN\t25454\t0;5079.47021484375;4402.771484375;8270.53735351562;8089.029296875;7360.232421875;0\t0;7360.232421875;4058.29125976562\t0\t\t\n+BSA_min_21\tMULTI\t1\t371.20292\t370.19564\t371.20292\t5\t3\t2\t\t0.195642\t-0.0146479089494846\t3.73268\t371.20415036452\t0.304\t8.13\t0\t37\t60\t\t\t-1\t\t0\t\t\t\t0\tNaN\t11036\t0;9764.7158203125;13278.7290039062;8888.0634765625;0\t8888.0634765625;4521.07373046875\t0\t\t\n+BSA_min_21\tMULTI\t1\t375.19439\t374.18711\t375.19439\t19\t16\t2\t\t0.187112\t-0.0250141102352472\t0.737723\t375.19426'..b'9076.1640625;1087181.0390625;1083330.80859375;1064600.79492188;967271.58203125;760838.3828125;712827.775390625;711122.657226562;657815.7890625;639986.428710938;568138.3671875;498523.453125;0\t816282.4375;246289.265625;56386.8359375\t0\t\t\n+BSA_min_22\tMULTI\t2\t687.86486\t1373.7152\t687.86486\t34\t19\t2\t\t0.715162\t0.0432531900291906\t0.399097\t687.864771258339\t0.45\t30.4\t0\t19\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t154530\t0;17070.9765625;15239.01953125;37858.7900390625;49730.232421875;83999.640625;108620.02734375;78961.19921875;68455.525390625;103047.68359375;76193.4423828125;60915.087890625;103987.82421875;80639.453125;96846.3671875;59798.15625;50967.80859375;118319.59375;92429.69140625;0;0\t80212.90625;56705.4921875\t1\t81\t0\n+BSA_min_22\tMULTI\t2\t691.87178\t1381.729\t691.87178\t27\t17\t2\t\t0.72901\t0.0534145086980971\t0.579162\t691.872041785377\t0.504\t26.2\t0\t31\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t89847\t0;31056.8515625;24916.55859375;42320.4921875;33702.22265625;30072.40234375;54384.478515625;39607.3984375;67881.76171875;70223.21484375;56608.279296875;67995.814453125;48903.1484375;61068.0712890625;78135.9296875;60122.98046875;34629.55859375;20974.099609375;0\t45579.89453125;44678.484375\t0\t\t\n+BSA_min_22\tMULTI\t2\t760.30996\t1518.6054\t760.30996\t38\t21\t2\t\t0.605366\t-0.133192149836077\t0.532145\t760.310131649569\t0.405\t34.5\t0\t7\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t208680\t0;36578.73828125;35192.98046875;64308.9140625;105542.3984375;139310.45703125;114743.15234375;104284.55078125;173741.90625;124384.26171875;122811.6171875;118852.75390625;119179.0390625;95637.0078125;153314.75390625;109609.643554688;90966.337890625;97841.005859375;109332.62109375;95516.654296875;67384.787109375;43305.8515625;0\t130571.7890625;63446.5625\t0\t\t\n+BSA_min_22\tMULTI\t2\t771.36091\t1540.7073\t771.36091\t4\t2\t2\t\t0.707267\t-0.0414584089676282\t0.98934\t771.862096841899\t0.582\t3.25\t0\t94\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t91241\t0;51686.912109375;66223.453125;0\t30713.21875;35510.234375\t0\t\t\n+BSA_min_22\tMULTI\t1\t784.34691\t783.33964\t784.34691\t30\t15\t2\t\t0.339636\t-0.0607003816246561\t2.11829\t784.349756464299\t0.383\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t260350\t0;70757.70703125;189261.94140625;222351.78515625;199627.3203125;236004.41796875;230515.21875;190031.2265625;175600.515625;145150.48046875;144838.58203125;131776.0390625;109370.369140625;100637.03515625;105928.84375;90421.66015625;0\t176021.15625;68246.65625\t0\t\t\n+BSA_min_22\tMULTI\t1\t794.64688\t793.63961\t794.64688\t30\t15\t2\t\t0.639608\t0.234533860482884\t2.19164\t794.643543730692\t0.384\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t239190\t0;75799.166015625;182819.57421875;205794.7265625;190388.55078125;216829.5625;232016.9453125;192153.88671875;159977.91015625;138327.91796875;133145.87890625;134100.47265625;98902.771484375;91682.572265625;94544.208984375;90000.30859375;0\t154234.703125;77830.1171875\t0\t\t\n+BSA_min_22\tMULTI\t2\t882.35364\t1762.6927\t882.35364\t37\t10\t4\t\t0.692729\t-0.158109462239054\t0.252511\t882.3537934524\t0.506\t13.3\t0\t66\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t590530\t0;124034.1953125;163759.890625;282199.0859375;462152.302734375;567479.9140625;517910.6875;574728.921875;462919.96484375;487479.03125;390846.802734375;0\t260553.25;218559.125;96019.7890625;50340.6796875\t2\t79;76\t0;1\n+BSA_min_22\tMULTI\t1\t885.46037\t884.4531\t885.46037\t30\t15\t2\t\t0.453097\t0.00624859595677663\t0.233793\t885.460184927629\t0.523\t22\t0\t43\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t462900\t0;113598.3125;268971.296875;273512.21875;327821.2734375;293932.546875;284912.0546875;317776.6875;276913.546875;282582.9375;309678.84375;315305.8359375;341380.8984375;412443.2890625;350983.1953125;333208.1015625;0\t311737.5;106428.734375\t0\t\t\n+BSA_min_22\tMULTI\t2\t891.32977\t1780.645\t891.32977\t7\t4\t3\t\t0.644994\t-0.214102799046941\t1.52654\t891.330602133011\t0.564\t5.37\t0\t88\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t108770\t0;18189.900390625;36413.9580078125;95086.095703125;33709.892578125;0\t54638.015625;26095.5859375;17093.90234375\t0\t\t\n+BSA_min_22\tMULTI\t1\t998.47572\t997.46845\t998.47572\t8\t5\t2\t\t0.468446\t-0.0303893371509503\t1.07757\t998.476134677568\t0.575\t6.3\t0\t86\t97\t\t\t-1\t\t0\t\t\t\t0\tNaN\t69512\t0;24384.458984375;29209.26171875;59130.58984375;43881.052734375;60372.1484375;0\t43851.453125;18626.490234375\t0\t\t\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/evidence.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/evidence.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| @@ -0,0 +1,15 @@ +Sequence Length Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Acetyl (Protein N-term) Oxidation (M) Missed cleavages Proteins Leading proteins Leading razor protein Type Raw file MS/MS m/z Charge m/z Mass Uncalibrated - Calibrated m/z [ppm] Uncalibrated - Calibrated m/z [Da] Mass error [ppm] Mass error [Da] Uncalibrated mass error [ppm] Uncalibrated mass error [Da] Max intensity m/z 0 Retention time Retention length Calibrated retention time Calibrated retention time start Calibrated retention time finish Retention time calibration Match time difference Match m/z difference Match q-value Match score Number of data points Number of scans Number of isotopic peaks PIF Fraction of total spectrum Base peak fraction PEP MS/MS count MS/MS scan number Score Delta score Combinatorics Intensity Reverse Potential contaminant id Protein group IDs Peptide ID Mod. peptide ID MS/MS IDs Best MS/MS Oxidation (M) site IDs Taxonomy IDs +AEFVEVTK 8 Unmodified _AEFVEVTK_ 0 0 0 bsa;CON__P02769 bsa bsa MULTI-SECPEP BSA_min_21 461.747985839844 2 461.74765 921.480748 0 0 0.053791 2.4838E-05 0.053791 2.4838E-05 461.747684636513 0.52947 0.23399 0.52947 0.3685 0.60249 0 14 6 3 0 0 0 0.0055393 1 85 3.3922 3.3922 1 43060 + 0 2 0 0 0 0 +DDPHACYSTVFDK 13 Unmodified _DDPHACYSTVFDK_ 0 0 0 bsa;CON__P02769 bsa bsa MULTI-MSMS BSA_min_21 777.835021972656 2 777.830105 1553.64566 0 0 0.83593 0.00065021 0.83593 0.00065021 777.830735936543 0.47149 0.26748 0.47149 0.29786 0.56534 0 10 7 2 0 0 0 0.0081868 1 82 0 0 1 32583 + 1 2 1 1 1 1 +ECCHGDLLECADDR 14 Unmodified _ECCHGDLLECADDR_ 0 0 0 bsa;CON__P02769 bsa bsa MULTI-MSMS BSA_min_22 584.229736328125 3 583.892361 1748.65525 0 0 -1.1992 -0.00070022 -1.1992 -0.00070022 583.891878608632 0.42243 0.40142 0.42243 0.19137 0.59279 0 52 16 4 0 0 0 0.011617 2 60 4.06 4.06 1 341370 + 2 2 2 2 2;3 2 +ECCHGDLLECADDR 14 Unmodified _ECCHGDLLECADDR_ 0 0 0 bsa;CON__P02769 bsa bsa MULTI-MSMS BSA_min_22 875.332336425781 2 875.334903 1748.65525 0 0 0.27022 0.00023654 0.27022 0.00023654 875.335151892134 0.508 0.18103 0.508 0.41176 0.59279 0 16 8 3 0 0 0 0.011617 1 90 3.6449 3.6449 1 146170 + 3 2 2 2 4 4 +FNETTEK 7 Unmodified _FNETTEK_ 0 0 0 CON__REFSEQ:XP_585019 CON__REFSEQ:XP_585019 CON__REFSEQ:XP_585019 MULTI-SECPEP BSA_min_21 868.867431640625 1 868.404689 867.397412 0 0 1.5512 0.0013471 1.5512 0.0013471 868.405948529351 0.54676 0.26937 0.54676 0.33312 0.60249 0 14 7 2 0 0 0 0.0030372 1 57 0 0 1 40791 + 4 7 3 3 5 5 +GCTTTNSPSTPCQNCSR 17 Unmodified _GCTTTNSPSTPCQNCSR_ 0 0 0 CON__Q6IFU6 CON__Q6IFU6 CON__Q6IFU6 MSMS BSA_min_21 964.384521484375 2 964.388198 1926.76184 NaN NaN NaN NaN NaN NaN NaN 0.26375 1 0.26375 -0.23625 0.76375 0 0 0 0 0.016056 1 45 0 0 1 + 5 6 4 4 6 6 +GETGPAGPSGAPGPAGSR 18 Unmodified _GETGPAGPSGAPGPAGSR_ 0 0 0 CON__P04258 CON__P04258 CON__P04258 MSMS BSA_min_21 508.24755859375 3 508.246338 1521.71718 NaN NaN NaN NaN NaN NaN NaN 0.091825 1 0.091825 -0.40818 0.59183 0 0 0 0 0.014811 1 16 0 0 1 + 6 3 5 5 7 7 +LGQYTSPVAK 10 Unmodified _LGQYTSPVAK_ 0 0 0 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030 CON__P01030 MSMS BSA_min_21 532.293029785156 2 532.292756 1062.57096 NaN NaN NaN NaN NaN NaN NaN 0.057288 1 0.057288 -0.44271 0.55729 6.9389E-18 0 0 0 0.0086806 1 10 9.2141 9.2141 1 + 7 0 6 6 8 8 +TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ 0 0 0 CON__Q29443;CON__Q0IIK2 CON__Q29443 CON__Q29443 MULTI-MSMS BSA_min_21 463.896636962891 3 463.896757 1388.66844 0 0 0.22645 0.00010505 0.22645 0.00010505 463.896829521798 0.42161 0.33709 0.42161 0.2654 0.60249 0 18 9 3 0 0 0 0.0052683 2 67 2.8669 2.8669 1 99515 + 8 5 7 7 9;10 9 +TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ 0 0 0 CON__Q29443;CON__Q0IIK2 CON__Q29443 CON__Q29443 MULTI-MSMS BSA_min_21 695.341064453125 2 695.341498 1388.66844 0 0 1.6098 0.0011193 1.6098 0.0011193 695.342847214244 0.40624 0.23684 0.40624 0.29786 0.5347 -5.5511E-17 11 6 2 0 0 0 0.0052683 1 70 0 0 1 38431 + 9 5 7 7 11 11 +VLYDAEISQIHQSVTDTNVILSMDNSR 27 Unmodified _VLYDAEISQIHQSVTDTNVILSMDNSR_ 0 0 0 CON__P35908v2;CON__P35908 CON__P35908v2 CON__P35908v2 MULTI-SECPEP BSA_min_21 508.586730957031 6 508.921773 3047.48698 0 0 -0.029217 -1.4869E-05 -0.029217 -1.4869E-05 509.256120722166 0.35628 0.17335 0.35628 0.2654 0.43874 0 6 4 2 0 0 0 0.00066484 1 73 0 0 1 27010 + 10 4 8 8 12 12 +YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ 0 0 0 CON__P02676 CON__P02676 CON__P02676 MULTI-MSMS BSA_min_21 562.586242675781 3 562.584073 1684.73039 0 0 -0.094318 -5.3062E-05 -0.094318 -5.3062E-05 562.584772670959 0.49991 0.26937 0.49991 0.33312 0.60249 0 23 7 4 0 0 0 0.011617 1 80 0 0 1 78086 + 11 1 9 9 13 13 +YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ 0 0 0 CON__P02676 CON__P02676 CON__P02676 MULTI-MSMS BSA_min_21 843.877807617188 2 843.372472 1684.73039 0 0 1.6858 0.0014217 1.6858 0.0014217 843.374714279736 0.52265 0.19871 0.52265 0.40378 0.60249 0 16 5 4 0 0 0 0.011617 1 92 3.6449 3.6449 1 36340 + 12 1 9 9 14 14 +YICDNQDTISSK 12 Unmodified _YICDNQDTISSK_ 0 0 0 bsa;CON__P02769 bsa bsa MSMS BSA_min_21 722.326232910156 2 722.324656 1442.63476 NaN NaN NaN NaN NaN NaN NaN 0.25827 1 0.25827 -0.24173 0.75827 0 0 0 0 4.413E-09 1 44 24.343 7.7115 1 + 13 2 10 10 15 15 |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/modificationSpecificPeptides.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/modificationSpecificPeptides.txt Wed Aug 11 09:24:23 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Acetyl (Protein N-term) Oxidation (M) Missed cleavages Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Reverse Potential contaminant Intensity id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count Taxonomy IDs +AEFVEVTK Unmodified 921.48075 0.48074791 2 bsa;CON__P02769 yes no 0 0 0 0.52947 0.52947 2 0.0055393 85 BSA_min_21 3.3922 3.3922 + 43060 0 2 0 0 0 0 0 +DDPHACYSTVFDK Unmodified 1553.6457 0.64565776 2 bsa;CON__P02769 yes no 0 0 0 0.47149 0.47149 2 0.0081868 82 BSA_min_21 0 0 + 32583 1 2 1 1 1 1 1 +ECCHGDLLECADDR Unmodified 1748.6553 0.65525294 2 bsa;CON__P02769 yes no 0 0 0 0.46522 0.46522 2;3 0.011617 60 BSA_min_22 4.06 4.06 + 487540 2 2 2 2;3 2;3;4 2 3 +FNETTEK Unmodified 867.39741 0.39741221 7 CON__REFSEQ:XP_585019 yes yes 0 0 0 0.54676 0.54676 1 0.0030372 57 BSA_min_21 0 0 + 40791 3 7 3 4 5 5 0 +GCTTTNSPSTPCQNCSR Unmodified 1926.7618 0.76184328 6 CON__Q6IFU6 yes yes 0 0 0 0.26375 0.26375 2 0.016056 45 BSA_min_21 0 0 + 0 4 6 4 5 6 6 1 +GETGPAGPSGAPGPAGSR Unmodified 1521.7172 0.71718322 3 CON__P04258 yes yes 0 0 0 0.091825 0.091825 3 0.014811 16 BSA_min_21 0 0 + 0 5 3 5 6 7 7 1 +LGQYTSPVAK Unmodified 1062.571 0.5709599 0 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 yes no 0 0 0 0.057288 0.057288 2 0.0086806 10 BSA_min_21 9.2141 9.2141 + 0 6 0 6 7 8 8 1 +TSDANINWNNLK Unmodified 1388.6684 0.66844211 5 CON__Q29443;CON__Q0IIK2 yes no 0 0 0 0.41393 0.41393 2;3 0.0052683 98 BSA_min_21 2.8669 2.8669 + 137950 7 5 7 8;9 9;10;11 10 3 +VLYDAEISQIHQSVTDTNVILSMDNSR Unmodified 3047.487 0.48697886 4 CON__P35908v2;CON__P35908 yes no 0 0 0 0.35628 0.35628 6 0.00066484 73 BSA_min_21 0 0 + 27010 8 4 8 10 12 12 0 +YCGVPGEYWLGNDR Unmodified 1684.7304 0.73039044 1 CON__P02676 yes yes 0 0 0 0.51128 0.51128 2;3 0.011617 80 BSA_min_21 0 0 + 114430 9 1 9 11;12 13;14 13 2 +YICDNQDTISSK Unmodified 1442.6348 0.63475872 2 bsa;CON__P02769 yes no 0 0 0 0.25827 0.25827 2 4.413E-09 44 BSA_min_21 24.343 7.7115 + 0 10 2 10 13 15 15 1 \ No newline at end of file |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/mqpar.xml Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,487 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmpfjtbnut8/files/c/c/5/dataset_cc5df07a-ee7c-4aa9-a851-1d22973dc663.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n+\t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>0</minUniquePeptides>\n+\t<useCounterparts>False</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>\n+\t<matchingIonMobilityWindow>0</matchingIonMobilityWindow>\n+\t<alignmentTimeWindow>0</alignmentTimeWindow>\n+\t<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>\n+\t<numberOfCan'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/msms.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/msms.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| @@ -0,0 +1,17 @@ +Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score diffs Acetyl (Protein N-term) Oxidation (M) Proteins Charge Fragmentation Mass analyzer Type Scan event number Isotope index m/z Mass Mass error [ppm] Mass error [Da] Simple mass error [ppm] Retention time PEP Score Delta score Score diff Localization prob Combinatorics PIF Fraction of total spectrum Base peak fraction Precursor full scan number Precursor Intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Matches Intensities Mass deviations [Da] Mass deviations [ppm] Masses Number of matches Intensity coverage Peak coverage Neutral loss level ETD identification type Reverse All scores All sequences All modified sequences Reporter PIF Reporter fraction id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs +BSA_min_21 85 69 AEFVEVTK 8 0 Unmodified _AEFVEVTK_ 0 0 bsa;CON__P02769 2 CID FTMS MULTI-SECPEP 1 0 461.74765 921.48075 0.053791 2.4838E-05 NaN 0.50044 0.0055393 3.3922 3.3922 NaN NaN 1 0 0 0 84 8401.8173828125 1 0 0 b3 90 0.00372490351873012 10.6990826539628 348.151672363281 1 0.0187155550306724 0.00826446280991736 None Unknown 3.3921643866591;0 AEFVEVTK;LSVEAFEK _AEFVEVTK_;_LSVEAFEK_ 0 2 0 0 0 +BSA_min_21 82 67 DDPHACYSTVFDK 13 0 Unmodified _DDPHACYSTVFDK_ 0 0 bsa;CON__P02769 2 CID FTMS MULTI-MSMS 4 0 777.83011 1553.6457 0.83593 0.00065021 NaN 0.48088 0.0081868 0 0 NaN NaN 1 0 0 0 78 14602.341796875 1 0 0 0 0 0 None Unknown 0 DDPHACYSTVFDK _DDPHACYSTVFDK_ 1 2 1 1 1 +BSA_min_22 60 48 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 0 bsa;CON__P02769 3 CID FTMS MULTI-MSMS 2 1 583.89236 1748.6553 -1.1992 -0.00070022 NaN 0.34278 0.011617 4.06 4.06 NaN NaN 1 0 0 0 58 153296.796875 1 0 0 y2;b7 100;60 0.000875681750017065;0.0151950483749488 3.01808299667453;17.4197737863645 290.14501953125;872.287353515625 2 0.0345694906194995 0.016260162601626 None Unknown 4.06002529511453 ECCHGDLLECADDR _ECCHGDLLECADDR_ 2 2 2 2 2 +BSA_min_22 67 53 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 0 bsa;CON__P02769 3 CID FTMS MULTI-MSMS 1 0 583.89236 1748.6553 -1.1992 -0.00070022 NaN 0.3858 0.011617 0 0 NaN NaN 1 0 0 0 66 93077.6484375 0.590638368628048 -6 0.16876 0 0 0 None Unknown 0 ECCHGDLLECADDR _ECCHGDLLECADDR_ 3 2 2 2 2 +BSA_min_22 90 70 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 0 bsa;CON__P02769 2 CID FTMS MULTI-MSMS 2 0 875.3349 1748.6553 0.27022 0.00023654 NaN 0.52328 0.011617 3.6449 3.6449 NaN NaN 1 0 0 0 88 65524.953125 1 0 0 y10 80 -0.0168735156998991 -14.5021701256686 1163.5166015625 1 0.0263469586381965 0.00862068965517241 None Unknown 3.64492303257886 ECCHGDLLECADDR _ECCHGDLLECADDR_ 4 2 2 2 3 +BSA_min_21 57 46 FNETTEK 7 0 Unmodified _FNETTEK_ 0 0 CON__REFSEQ:XP_585019 1 CID FTMS MULTI-SECPEP 3 0 868.40469 867.39741 1.5512 0.0013471 NaN 0.33417 0.0030372 0 0 NaN NaN 1 0 0 0 54 12854.5830078125 0.610546493461869 -2 0.0649316666666667 0 0 0 None Unknown 0 FNETTEK _FNETTEK_ 5 7 3 3 4 +BSA_min_21 45 36 GCTTTNSPSTPCQNCSR 17 0 Unmodified _GCTTTNSPSTPCQNCSR_ 0 0 CON__Q6IFU6 2 CID FTMS MSMS 2 964.3882 1926.7618 NaN NaN NaN 0.26375 0.016056 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 GCTTTNSPSTPCQNCSR _GCTTTNSPSTPCQNCSR_ 6 6 4 4 5 +BSA_min_21 16 12 GETGPAGPSGAPGPAGSR 18 0 Unmodified _GETGPAGPSGAPGPAGSR_ 0 0 CON__P04258 3 CID FTMS MSMS 3 508.24634 1521.7172 NaN NaN NaN 0.091825 0.014811 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN a2 4 0.0013149045343539 8.2659354184025 159.075103759766 1 0.000881609535771964 0.00869565217391304 None Unknown 0;0 GETGPAGPSGAPGPAGSR;GSGAPGPAGSPGAPGTER _GETGPAGPSGAPGPAGSR_;_GSGAPGPAGSPGAPGTER_ 7 3 5 5 6 +BSA_min_21 10 7 LGQYTSPVAK 10 0 Unmodified _LGQYTSPVAK_ 0 0 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 2 CID FTMS MSMS 3 532.29276 1062.571 NaN NaN NaN 0.057288 0.0086806 9.2141 9.2141 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN y3;b2;b4 10;20;200 -0.00279849649376729;-0.00340676689998531;-0.00711106876252643 -8.82191072988591;-19.9090833143192;-15.3838714608204 317.221130371094;171.1162109375;462.241821289062 3 0.0308188417439214 0.0245901639344262 None Unknown 9.21405366890568;0;0 LGQYTSPVAK;AQYELIAQK;AQYEIIAQK _LGQYTSPVAK_;_AQYELIAQK_;_AQYEIIAQK_ 8 0 6 6 7 +BSA_min_21 67 54 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 0 CON__Q29443;CON__Q0IIK2 3 CID FTMS MULTI-MSMS 1 0 463.89676 1388.6684 0.22645 0.00010505 NaN 0.39389 0.0052683 0 0 NaN NaN 1 0 0 0 66 23524.845703125 0.459529453830584 -1 0.0348916666666667 0 0 0 None Unknown 0 TSDANINWNNLK _TSDANINWNNLK_ 9 5 7 7 8 +BSA_min_21 98 80 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 0 CON__Q29443;CON__Q0IIK2 3 CID FTMS MULTI-MSMS 5 1 463.89676 1388.6684 0.22645 0.00010505 NaN 0.57847 0.0052683 2.8669 2.8669 NaN NaN 1 0 0 0 93 7351.9912109375 0.14361227054852 4 NaN b9 6 -0.00485963613130025 -4.78099799382671 1016.44805908203 1 0.00268406539551173 0.00961538461538462 None Unknown 2.86688527480472 TSDANINWNNLK _TSDANINWNNLK_ 10 5 7 7 8 +BSA_min_21 70 57 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 0 CON__Q29443;CON__Q0IIK2 2 CID FTMS MULTI-MSMS 4 0 695.3415 1388.6684 1.6098 0.0011193 NaN 0.41019 0.0052683 0 0 NaN NaN 1 0 0 0 66 16808.548828125 0.978200928418143 -1 0.0348916666666667 0 0 0 None Unknown 0;0 TSDANINWNNLK;HVFAVDGAGEMLK _TSDANINWNNLK_;_HVFAVDGAGEM(Oxidation (M))LK_ 11 5 7 7 9 +BSA_min_21 73 59 VLYDAEISQIHQSVTDTNVILSMDNSR 27 0 Unmodified _VLYDAEISQIHQSVTDTNVILSMDNSR_ 0 0 CON__P35908v2;CON__P35908 6 CID FTMS MULTI-SECPEP 1 -2 508.92177 3047.487 -0.029217 -1.4869E-05 NaN 0.42964 0.00066484 0 0 NaN NaN 1 0 0 0 72 23982.154296875 1 0 0 0 0 0 None Unknown 0;0 VLYDAEISQIHQSVTDTNVILSMDNSR;NTMVVHEPSAHIQVQPNEFTVEIWSR _VLYDAEISQIHQSVTDTNVILSMDNSR_;_NTMVVHEPSAHIQVQPNEFTVEIWSR_ 12 4 8 8 10 +BSA_min_21 80 65 YCGVPGEYWLGNDR 14 0 Unmodified _YCGVPGEYWLGNDR_ 0 0 CON__P02676 3 CID FTMS MULTI-MSMS 2 0 562.58407 1684.7304 -0.094318 -5.3062E-05 NaN 0.46942 0.011617 0 0 NaN NaN 1 0 0 0 78 21744.55859375 0.743883342518387 -1 0.0342566666666667 0 0 0 None Unknown 0 YCGVPGEYWLGNDR _YCGVPGEYWLGNDR_ 13 1 9 9 11 +BSA_min_21 92 75 YCGVPGEYWLGNDR 14 0 Unmodified _YCGVPGEYWLGNDR_ 0 0 CON__P02676 2 CID FTMS MULTI-MSMS 3 1 843.37247 1684.7304 1.6858 0.0014217 NaN 0.54095 0.011617 3.6449 3.6449 NaN NaN 1 0 0 0 89 10235.505859375 1 0 0 y13 5 0.01796629868727 11.7993127121924 1522.65637207031 1 0.00360499788750048 0.00961538461538462 None Unknown 3.64492303257886 YCGVPGEYWLGNDR _YCGVPGEYWLGNDR_ 14 1 9 9 12 +BSA_min_21 44 35 YICDNQDTISSK 12 0 Unmodified _YICDNQDTISSK_ 0 0 bsa;CON__P02769 2 CID FTMS MSMS 1 722.32466 1442.6348 NaN NaN NaN 0.25827 4.413E-09 24.343 7.7115 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN y3;y8;y9;y10;b9 300;200;500;700;30 -0.00453549397497;-0.0138762988750614;-0.0167184231250985;-0.0175643623499582;-0.0019145705750816 -14.1212848085697;-15.5485287132689;-16.594286035641;-15.0442644146915;-1.70415154482157 321.181396484375;892.450927734375;1007.48071289062;1167.51220703125;1123.47436523438 5 0.182617971800349 0.0357142857142857 None Unknown 24.3433433825462;16.6318347984703 YICDNQDTISSK;YICENQDSISSK _YICDNQDTISSK_;_YICENQDSISSK_ 15 2 10 10 13 \ No newline at end of file |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/msmsScans.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/msmsScans.txt Wed Aug 11 09:24:23 2021 +0000 |
| b |
| b'@@ -0,0 +1,160 @@\n+Raw file\tScan number\tRetention time\tIon injection time\tTotal ion current\tCollision energy\tSummations\tBase peak intensity\tElapsed time\tIdentified\tMatched\tReverse\tMS/MS IDs\tSequence\tLength\tFiltered peaks\tm/z\tMass\tCharge\tType\tFragmentation\tMass analyzer\tParent intensity fraction\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tScan event number\tModifications\tModified sequence\tProteins\tScore\tPEP\tReporter PIF\tReporter fraction\tIntens Comp Factor\tCTCD Comp\tRawOvFtT\tAGC Fill\tScan index\tMS scan index\tMS scan number\n+BSA_min_21\t2\t0.01221\t-1\t47150\t35\t0\t12358\t-1\t-\t\t+\t-1\tEFWEPSDDEYK\t11\t150\t722.798704576355\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\tUnmodified\t_EFWEPSDDEYK_\tREV__CON__Q28107\t4.45112097361039\t0.022591673757553\t\t\tNaN\tNaN\tNaN\t0\t0\t0\t1\n+BSA_min_21\t3\t0.017623\t-1\t17297\t35\t0\t2580.2\t-1\t-\t\t\t-1\t \t0\t121\t594.555969238281\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t1\t0\t1\n+BSA_min_21\t4\t0.023405\t-1\t18183\t35\t0\t2001.2\t-1\t-\t\t\t-1\tGSGGSSAMCGGAGFGSR\t17\t142\t759.809204101563\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\tOxidation (M)\t_GSGGSSAM(Oxidation (M))CGGAGFGSR_\tCON__P50446\t0\t0.0160561546389173\t\t\tNaN\tNaN\tNaN\t0\t2\t0\t1\n+BSA_min_21\t5\t0.029038\t-1\t16124\t35\t0\t2760.5\t-1\t-\t\t\t-1\tDLGEEHFK\t8\t116\t487.732727050781\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\tUnmodified\t_DLGEEHFK_\tCON__P02769;bsa\t4.13698178514225\t0.0266825806985734\t\t\tNaN\tNaN\tNaN\t0\t3\t0\t1\n+BSA_min_21\t6\t0.034095\t-1\t16526\t35\t0\t4280.7\t-1\t-\t\t\t-1\t \t0\t113\t372.19735409279\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t4\t0\t1\n+BSA_min_21\t8\t0.04682\t-1\t65409\t35\t0\t8882.5\t-1\t-\t\t\t-1\t \t0\t122\t472.250845646481\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t5\t1\t7\n+BSA_min_21\t9\t0.051375\t-1\t13709\t35\t0\t4500\t-1\t-\t\t\t-1\t \t0\t114\t891.331298828125\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t6\t1\t7\n+BSA_min_21\t10\t0.057288\t-1\t8824.9\t35\t0\t1033.7\t-1\t+\t\t\t8\tLGQYTSPVAK\t10\t122\t532.293029785156\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\tUnmodified\t_LGQYTSPVAK_\tCON__ENSEMBL:ENSBTAP00000007350;CON__P01030\t9.21405366890568\t0.00868058904451287\t\t\tNaN\tNaN\tNaN\t0\t7\t1\t7\n+BSA_min_21\t11\t0.062452\t-1\t11430\t35\t0\t1724\t-1\t-\t\t\t-1\t \t0\t119\t538.768188476563\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t8\t1\t7\n+BSA_min_21\t12\t0.06764\t-1\t7136.7\t35\t0\t471.71\t-1\t-\t\t\t-1\tNECFLSHK\t8\t115\t517.73974609375\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\tUnmodified\t_NECFLSHK_\tCON__P02769;bsa\t1.32764519023524\t0.0381331571746415\t\t\tNaN\tNaN\tNaN\t0\t9\t1\t7\n+BSA_min_21\t14\t0.080647\t-1\t33.829\t35\t0\t18.526\t-1\t-\t\t\t-1\t \t0\t4\t1568.24185979966\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t13\t63387.5625\t1\t0\t0\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t10\t2\t13\n+BSA_min_21\t15\t0.086635\t-1\t7892.6\t35\t0\t2586\t-1\t-\t\t\t-1\t \t0\t111\t526.229125976563\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t11\t2\t13\n+BSA_min_21\t16\t0.091825\t-1\t6445.6\t35\t0\t396.47\t-1\t+\t\t\t7\tGETGPAGPSGAPGPAGSR\t18\t115\t508.24755859375\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\tUnmodified\t_GETGPAGPSGAPGPAGSR_\tCON__P04258\t0\t0.0148105555414328\t\t\tNaN\tNaN\tNaN\t0\t12\t2\t13\n+BSA_min_21\t17\t0.096923\t-1\t3111.3\t35\t0\t341.89\t-1\t-\t\t+\t-1\tHHSPSSGGAGLTMSK\t15\t112\t735.343090637035\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\tOxidation (M)\t_HHSPSSGGAGLTM(Oxidation (M))SK_\tREV__CON__Q9NSB4\t0\t0.0187837162948159\t\t\tNaN\tNaN\tNaN\t0\t13\t2\t13\n+BSA_min_21\t18\t0.10248\t-1\t5136.5\t35\t0\t339.91\t-1\t-\t\t+\t-1\tLVNMLEQHR\t9\t110\t570.301832275435\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\tUnmodified\t_LVNMLEQHR_\tREV__CON__Q6IME9\t0\t0.0333508993595612\t\t\tNaN\tNaN\tNaN\t0\t14\t2\t13\n+BSA_min_21\t20\t0.11574\t-1\t3120.2\t35\t0\t276.31\t-1\t-\t\t\t-1\t \t0\t114\t693.814799342839\t1385.61504575248\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t19\t25857.935546875\t0.752232476411029\t-2\t0.06875\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t15\t3\t19\n+BSA_min_21\t21\t0.12116\t-1\t2652.8\t35\t0\t180.5\t-1\t-\t\t\t-1\tEYEATLEECCAK\t12\t124\t751.810485839844\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tN'..b'.3\t35\t0\t158.2\t-1\t-\t\t\t-1\t \t0\t107\t1002.07797820268\t3003.21210520824\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t69\t44722.15234375\t0.0212647431022184\t8\t-0.16323\t3\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t57\t13\t69\n+BSA_min_22\t73\t0.42101\t-1\t700.97\t35\t0\t45.614\t-1\t-\t\t\t-1\t \t0\t62\t747.54713506966\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t69\t47683.56640625\t0.163391162978462\t9\t-0.185018333333333\t4\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t58\t13\t69\n+BSA_min_22\t75\t0.4333\t-1\t213.41\t35\t0\t43.272\t-1\t-\t\t\t-1\t \t0\t24\t1146.04347552057\t2290.07239810794\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t74\t102962.9140625\t0.243369234361311\t5\t-0.102611666666667\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t59\t14\t74\n+BSA_min_22\t76\t0.43931\t-1\t10561\t35\t0\t3357.8\t-1\t-\t\t\t-1\t \t0\t161\t882.353641063195\t1762.69272919319\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t74\t65622.515625\t0.300250632980892\t-5\t0.114316666666667\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t60\t14\t74\n+BSA_min_22\t77\t0.44516\t-1\t1115\t35\t0\t260.17\t-1\t-\t\t\t-1\t \t0\t45\t421.6946603681\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t74\t77002.7578125\t1\t0\t0\t3\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t61\t14\t74\n+BSA_min_22\t79\t0.45692\t-1\t12429\t35\t0\t2561.2\t-1\t-\t\t\t-1\t \t0\t159\t882.353641063195\t1762.69272919319\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t78\t125207.5546875\t0.480544973772156\t-2\t0.0532533333333333\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t62\t15\t78\n+BSA_min_22\t80\t0.46277\t-1\t3207.6\t35\t0\t297.68\t-1\t-\t\t\t-1\t \t0\t104\t519.302063818749\t1036.5895747043\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t78\t107721.2890625\t0.756074997274729\t-3\t0.0730283333333333\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t63\t15\t78\n+BSA_min_22\t81\t0.46789\t-1\t1712.2\t35\t0\t155.47\t-1\t-\t\t\t-1\t \t0\t80\t687.864857548912\t1373.71516216462\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t78\t62486.453125\t0.779007469574137\t-5\t0.120298333333333\t3\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t64\t15\t78\n+BSA_min_22\t82\t0.47339\t-1\t2066.8\t35\t0\t277.38\t-1\t-\t\t\t-1\t \t0\t102\t706.305530173543\t1410.59650741389\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t78\t46566.94140625\t0.933613855450418\t-2\t0.0532533333333333\t4\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t65\t15\t78\n+BSA_min_22\t84\t0.48564\t-1\t10930\t35\t0\t956.2\t-1\t-\t\t\t-1\t \t0\t149\t759.303833007813\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t66\t16\t83\n+BSA_min_22\t85\t0.4913\t-1\t5536.7\t35\t0\t592.18\t-1\t-\t\t\t-1\t \t0\t120\t586.330981400379\t1170.64740986756\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t83\t65373.234375\t1\t0\t0\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t67\t16\t83\n+BSA_min_22\t87\t0.50368\t-1\t592.85\t35\t0\t182.65\t-1\t-\t\t\t-1\t \t0\t45\t1502.25634765625\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t68\t17\t86\n+BSA_min_22\t89\t0.51803\t-1\t3787.5\t35\t0\t204.12\t-1\t-\t\t\t-1\t \t0\t118\t586.330981400379\t1170.64740986756\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t88\t87861.3359375\t0.892882174576085\t4\t-0.0718366666666667\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t69\t18\t88\n+BSA_min_22\t90\t0.52328\t-1\t3324.1\t35\t0\t503.57\t-1\t+\t\t\t4\tECCHGDLLECADDR\t14\t116\t875.335139472672\t1748.65572601214\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t88\t65524.953125\t1\t0\t0\t2\tUnmodified\t_ECCHGDLLECADDR_\tCON__P02769;bsa\t3.64492303257886\t0.0116170786220603\t\t\tNaN\tNaN\tNaN\t0\t70\t18\t88\n+BSA_min_22\t92\t0.53604\t-1\t1584.9\t35\t0\t55.739\t-1\t-\t\t\t-1\t \t0\t95\t594.555106701017\t1780.64349070325\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t73712.65625\t0.32216225208255\t-3\t0.0503366666666666\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t71\t19\t91\n+BSA_min_22\t93\t0.54179\t-1\t2714.4\t35\t0\t210.49\t-1\t-\t\t\t-1\t \t0\t109\t664.969909667969\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t72\t19\t91\n+BSA_min_22\t95\t0.55474\t-1\t3493.2\t35\t0\t289.39\t-1\t-\t\t\t-1\t \t0\t105\t613.754755665229\t1225.49495839726\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t94\t38025.9921875\t0.998631205980059\t5\tNaN\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t73\t20\t94\n+BSA_min_22\t98\t0.58882\t-1\t5962.2\t35\t0\t423.24\t-1\t-\t\t\t-1\t \t0\t117\t577.318870952338\t576.311594485738\t1\tMULTI\tCID\tFTMS\t0\t0\t0\t97\t938697.4375\t0.505617380261114\t10\tNaN\t1\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t74\t22\t97\n+BSA_min_22\t99\t0.59405\t-1\t2406.8\t35\t0\t329.59\t-1\t-\t\t\t-1\tLGSSCSGSGDSGR\t13\t104\t613.757507324219\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\tUnmodified\t_LGSSCSGSGDSGR_\tCON__Q5D862\t0\t0.022036437021241\t\t\tNaN\tNaN\tNaN\t0\t75\t22\t97\n+BSA_min_22\t100\t0.59926\t-1\t7827.3\t35\t0\t2715\t-1\t-\t\t\t-1\t \t0\t106\t891.338134765625\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\t \t \t \tNaN\tNaN\t\t\tNaN\tNaN\tNaN\t0\t76\t22\t97\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/mzRange.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/mzRange.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,3709 @@\n+Raw file\tm/z\tPeaks / Da\tSingle peaks / Da\tIsotope patterns / Da\tSingle isotope patterns / Da\tSILAC pairs / Da\tIdentified SILAC pairs / Da\tSILAC identification rate [%]\tMS/MS / Da\tIdentified MS/MS / Da\tIdentification rate 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|
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/parameters.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| @@ -0,0 +1,105 @@ +Parameter Value +Version 1.6.17.0 +User name niko +Machine name DESKTOP-I3UDKML +Date of writing 08/05/2021 17:10:11 +Include contaminants True +PSM FDR 0.01 +PSM FDR Crosslink 0.01 +Protein FDR 0.01 +Site FDR 0.01 +Use Normalized Ratios For Occupancy True +Min. peptide Length 7 +Min. score for unmodified peptides 0 +Min. score for modified peptides 40 +Min. delta score for unmodified peptides 0 +Min. delta score for modified peptides 6 +Min. unique peptides 0 +Min. razor peptides 1 +Min. peptides 1 +Use only unmodified peptides and True +Modifications included in protein quantification Oxidation (M);Acetyl (Protein N-term) +Peptides used for protein quantification Razor +Discard unmodified counterpart peptides True +Label min. ratio count 2 +Use delta score False +iBAQ False +iBAQ log fit False +Match between runs False +Find dependent peptides False +Fasta file /tmp/tmpfjtbnut8/files/c/c/5/dataset_cc5df07a-ee7c-4aa9-a851-1d22973dc663.dat +Decoy mode revert +Include contaminants True +Advanced ratios True +Fixed andromeda index folder +Combined folder location +Second peptides True +Stabilize large LFQ ratios True +Separate LFQ in parameter groups False +Require MS/MS for LFQ comparisons True +Calculate peak properties False +Main search max. combinations 200 +Advanced site intensities True +Write msScans table False +Write msmsScans table True +Write ms3Scans table True +Write allPeptides table True +Write mzRange table True +Write DIA fragments table False +Write pasefMsmsScans table True +Write accumulatedPasefMsmsScans table True +Max. peptide mass [Da] 4600 +Min. peptide length for unspecific search 8 +Max. peptide length for unspecific search 25 +Razor protein FDR True +Disable MD5 False +Max mods in site table 3 +Match unidentified features False +Epsilon score for mutations +Evaluate variant peptides separately True +Variation mode None +MS/MS tol. (FTMS) 20 ppm +Top MS/MS peaks per Da interval. (FTMS) 12 +Da interval. (FTMS) 100 +MS/MS deisotoping (FTMS) True +MS/MS deisotoping tolerance (FTMS) 7 +MS/MS deisotoping tolerance unit (FTMS) ppm +MS/MS higher charges (FTMS) True +MS/MS water loss (FTMS) True +MS/MS ammonia loss (FTMS) True +MS/MS dependent losses (FTMS) True +MS/MS recalibration (FTMS) False +MS/MS tol. (ITMS) 0.5 Da +Top MS/MS peaks per Da interval. (ITMS) 8 +Da interval. (ITMS) 100 +MS/MS deisotoping (ITMS) False +MS/MS deisotoping tolerance (ITMS) 0.15 +MS/MS deisotoping tolerance unit (ITMS) Da +MS/MS higher charges (ITMS) True +MS/MS water loss (ITMS) True +MS/MS ammonia loss (ITMS) True +MS/MS dependent losses (ITMS) True +MS/MS recalibration (ITMS) False +MS/MS tol. (TOF) 40 ppm +Top MS/MS peaks per Da interval. (TOF) 10 +Da interval. (TOF) 100 +MS/MS deisotoping (TOF) True +MS/MS deisotoping tolerance (TOF) 0.01 +MS/MS deisotoping tolerance unit (TOF) Da +MS/MS higher charges (TOF) True +MS/MS water loss (TOF) True +MS/MS ammonia loss (TOF) True +MS/MS dependent losses (TOF) True +MS/MS recalibration (TOF) False +MS/MS tol. (Unknown) 20 ppm +Top MS/MS peaks per Da interval. (Unknown) 12 +Da interval. (Unknown) 100 +MS/MS deisotoping (Unknown) True +MS/MS deisotoping tolerance (Unknown) 7 +MS/MS deisotoping tolerance unit (Unknown) ppm +MS/MS higher charges (Unknown) True +MS/MS water loss (Unknown) True +MS/MS ammonia loss (Unknown) True +MS/MS dependent losses (Unknown) True +MS/MS recalibration (Unknown) False +Site tables Oxidation (M)Sites.txt |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/peptides.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/peptides.txt Wed Aug 11 09:24:23 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +Sequence N-term cleavage window C-term cleavage window Amino acid before First amino acid Second amino acid Second last amino acid Last amino acid Amino acid after A Count R Count N Count D Count C Count Q Count E Count G Count H Count I Count L Count K Count M Count F Count P Count S Count T Count W Count Y Count V Count U Count O Count Length Missed cleavages Mass Proteins Leading razor protein Start position End position Unique (Groups) Unique (Proteins) Charges PEP Score Intensity Reverse Potential contaminant id Protein group IDs Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Taxonomy IDs MS/MS Count +AEFVEVTK LKAWSVARLSQKFPKAEFVEVTKLVTDLTK LSQKFPKAEFVEVTKLVTDLTKVHKECCHG K A E T K L 1 0 0 0 0 0 2 0 0 0 0 1 0 1 0 0 1 0 0 2 0 0 8 0 921.48075 bsa;CON__P02769 bsa 249 256 yes no 2 0.0055393 3.3922 43060 + 0 2 0 0 0 0 0 +DDPHACYSTVFDK LAKEYEATLEECCAKDDPHACYSTVFDKLK AKDDPHACYSTVFDKLKHLVDEPQNLIKQN K D D D K L 1 0 0 3 1 0 0 0 1 0 0 1 0 1 1 1 1 0 1 1 0 0 13 0 1553.6457 bsa;CON__P02769 bsa 387 399 yes no 2 0.0081868 0 32583 + 1 2 1 1 1 1 1 +ECCHGDLLECADDR VEVTKLVTDLTKVHKECCHGDLLECADDRA KECCHGDLLECADDRADLAKYICDNQDTIS K E C D R A 1 1 0 3 3 0 2 1 1 0 2 0 0 0 0 0 0 0 0 0 0 0 14 0 1748.6553 bsa;CON__P02769 bsa 267 280 yes no 2;3 0.011617 4.06 487540 + 2 2 2 2;3 2;3;4 2 3 +FNETTEK NMENPPECYRHAENRFNETTEKSLKIVQRE CYRHAENRFNETTEKSLKIVQRECEHFQNL R F N E K S 0 0 1 0 0 0 2 0 0 0 0 1 0 1 0 0 2 0 0 0 0 0 7 0 867.39741 CON__REFSEQ:XP_585019 CON__REFSEQ:XP_585019 401 407 yes yes 1 0.0030372 0 40791 + 3 7 3 4 5 5 0 +GCTTTNSPSTPCQNCSR ______________________________ TTTNSPSTPCQNCSRITNVSTISSNNGCHP K G C S R I 0 1 2 0 3 1 0 1 0 0 0 0 0 0 2 3 4 0 0 0 0 0 17 0 1926.7618 CON__Q6IFU6 CON__Q6IFU6 5 21 yes yes 2 0.016056 0 0 + 4 6 4 5 6 6 1 +GETGPAGPSGAPGPAGSR GPPGPVGPAGKSGDRGETGPAGPSGAPGPA GPAGPSGAPGPAGSRGPPGPQGPRGDKGET R G E S R G 3 1 0 0 0 0 1 6 0 0 0 0 0 0 4 2 1 0 0 0 0 0 18 0 1521.7172 CON__P04258 CON__P04258 1065 1082 yes yes 3 0.014811 0 0 + 5 3 5 6 7 7 1 +LGQYTSPVAK RKKRNVNFQKAIHEKLGQYTSPVAKRCCQD AIHEKLGQYTSPVAKRCCQDGLTRLPMART K L G A K R 1 0 0 0 0 1 0 1 0 0 1 1 0 0 1 1 1 0 1 1 0 0 10 0 1062.571 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030 689 698 yes no 2 0.0086806 9.2141 0 + 6 0 6 7 8 8 1 +TSDANINWNNLK KNTPEKGYLAVAVVKTSDANINWNNLKDKK VVKTSDANINWNNLKDKKSCHTAVDRTAGW K T S L K D 1 0 4 1 0 0 0 0 0 1 1 1 0 0 0 1 1 1 0 0 0 0 12 0 1388.6684 CON__Q29443;CON__Q0IIK2 CON__Q29443 438 449 yes no 2;3 0.0052683 2.8669 137950 + 7 5 7 8;9 9;10;11 9 3 +VLYDAEISQIHQSVTDTNVILSMDNSR QSKVDLLNQEIEFLKVLYDAEISQIHQSVT SVTDTNVILSMDNSRNLDLDSIIAEVKAQY K V L S R N 1 1 2 3 0 2 1 0 1 3 2 0 1 0 0 4 2 0 1 3 0 0 27 0 3047.487 CON__P35908v2;CON__P35908 CON__P35908v2 315 341 yes no 6 0.00066484 0 27010 + 8 4 8 10 12 12 0 +YCGVPGEYWLGNDR KQGFGNIATNAEGKKYCGVPGEYWLGNDRI KYCGVPGEYWLGNDRISQLTNMGPTKLLIE K Y C D R I 0 1 1 1 1 0 1 3 0 0 1 0 0 0 1 0 0 1 2 1 0 0 14 0 1684.7304 CON__P02676 CON__P02676 319 332 yes yes 2;3 0.011617 3.6449 114430 + 9 1 9 11;12 13;14 13 2 +YICDNQDTISSK GDLLECADDRADLAKYICDNQDTISSKLKE LAKYICDNQDTISSKLKECCDKPLLEKSHC K Y I S K L 0 0 1 2 1 1 0 0 0 2 0 1 0 0 0 2 1 0 1 0 0 0 12 0 1442.6348 bsa;CON__P02769 bsa 286 297 yes no 2 4.413E-09 24.343 0 + 10 2 10 13 15 15 1 |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/proteinGroups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/proteinGroups.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| @@ -0,0 +1,7 @@ +Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Intensity MS/MS count Only identified by site Reverse Potential contaminant id Peptide IDs Peptide is razor Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Oxidation (M) site positions Taxonomy IDs +CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 1;1 1;1 1;1 ; 2 1 1 1 0.6 0.6 0.6 192.79 1741 1741;1742 0 6.0615 0 1 + 0 6 True 6 7 8 8 -1;-1 +CON__P02676 CON__P02676 1 1 1 1 1 1 1 2.8 2.8 2.8 56.44 495 495 0 5.9349 114430 2 + 1 9 True 9 11;12 13;14 13 -1 +bsa;CON__P02769 bsa;CON__P02769 4;4 4;4 4;4 bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4; 2 4 4 4 7.7 7.7 7.7 69.293 607 607;607 0 30.634 563190 5 + 2 0;1;2;10 True;True;True;True 0;1;2;10 0;1;2;3;13 0;1;2;3;4;15 0;1;2;15 -1;-1 +CON__P04258 CON__P04258 1 1 1 1 1 1 1 1.2 1.2 1.2 138.44 1466 1466 0 5.8294 0 1 + 3 5 True 5 6 7 7 -1 +CON__P35908v2;CON__P35908 CON__P35908v2;CON__P35908 1;1 1;1 1;1 ; 2 1 1 1 4.2 4.2 4.2 65.432 639 639;645 0 7.1773 27010 0 + 4 8 True 8 10 12 12 -1;-1 +CON__Q29443;CON__Q0IIK2 CON__Q29443;CON__Q0IIK2 1;1 1;1 1;1 ; 2 1 1 1 1.8 1.8 1.8 75.829 685 685;704 0 6.2783 137950 3 + 5 7 True 7 8;9 9;10;11 9 -1;-1 |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/mqpar/txt/summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqpar/txt/summary.txt Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| @@ -0,0 +1,4 @@ +Raw file Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa] +BSA_min_21 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 18 82 0 124 40 0 84 10 6 0 4 8.1 15 0 4.8 10 1031 56 5.4 1 1.8 110 34 33 31 36 6 18 + 0.89167 1.1143 0.66988 0.8615 +BSA_min_22 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) False False 1 0 Standard 23 77 0 101 53 0 48 3 3 0 0 3 5.7 0 0 1 1675 61 3.6 1 1.6 294 43 41 15 15 10 23 + 0.73592 0.87072 0.46838 0.52262 +Total 41 159 0 225 93 0 132 13 9 0 4 5.8 9.7 0 3 11 2706 404 77 74 19 21 16 21 0.84717 1.0505 0.61231 0.77985 |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/thermo.raw |
| b |
| Binary file test-data/thermo.raw has changed |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/tmt_data_18.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt_data_18.fasta Wed Aug 11 09:24:23 2021 +0000 |
| [ |
| b'@@ -0,0 +1,593 @@\n+>sp|Q7LFL8|CXXC5_HUMAN CXXC-type zinc finger protein 5 OS=Homo sapiens OX=9606 GN=CXXC5 PE=1 SV=1\n+MSSLGGGSQDAGGSSSSSTNGSGGSGSSGPKAGAADKSAVVAAAAPASVADDTPPPERRN\n+KSGIISEPLNKSLRRSRPLSHYSSFGSSGGSGGGSMMGGESADKATAAAAAASLLANGHD\n+LAAAMAVDKSNPTSKHKSGAVASLLSKAERATELAAEGQLTLQQFAQSTEMLKRVVQEHL\n+PLMSEAGAGLPDMEAVAGAEALNGQSDFPYLGAFPINPGLFIMTPAGVFLAESALHMAGL\n+AEYPMQGELASAISSGKKKRKRCGMCAPCRRRINCEQCSSCRNRKTGHQICKFRKCEELK\n+KKPSAALEKVMLPTGAAFRWFQ\n+>sp|Q99698|LYST_HUMAN Lysosomal-trafficking regulator OS=Homo sapiens OX=9606 GN=LYST PE=1 SV=3\n+MSTDSNSLAREFLTDVNRLCNAVVQRVEAREEEEEETHMATLGQYLVHGRGFLLLTKLNS\n+IIDQALTCREELLTLLLSLLPLVWKIPVQEEKATDFNLPLSADIILTKEKNSSSQRSTQE\n+KLHLEGSALSSQVSAKVNVFRKSRRQRKITHRYSVRDARKTQLSTSDSEANSDEKGIAMN\n+KHRRPHLLHHFLTSFPKQDHPKAKLDRLATKEQTPPDAMALENSREIIPRQGSNTDILSE\n+PAALSVISNMNNSPFDLCHVLLSLLEKVCKFDVTLNHNSPLAASVVPTLTEFLAGFGDCC\n+SLSDNLESRVVSAGWTEEPVALIQRMLFRTVLHLLSVDVSTAEMMPENLRKNLTELLRAA\n+LKIRICLEKQPDPFAPRQKKTLQEVQEDFVFSKYRHRALLLPELLEGVLQILICCLQSAA\n+SNPFYFSQAMDLVQEFIQHHGFNLFETAVLQMEWLVLRDGVPPEASEHLKALINSVMKIM\n+STVKKVKSEQLHHSMCTRKRHRRCEYSHFMHHHRDLSGLLVSAFKNQVSKNPFEETADGD\n+VYYPERCCCIAVCAHQCLRLLQQASLSSTCVQILSGVHNIGICCCMDPKSVIIPLLHAFK\n+LPALKNFQQHILNILNKLILDQLGGAEISPKIKKAACNICTVDSDQLAQLEETLQGNLCD\n+AELSSSLSSPSYRFQGILPSSGSEDLLWKWDALKAYQNFVFEEDRLHSIQIANHICNLIQ\n+KGNIVVQWKLYNYIFNPVLQRGVELAHHCQHLSVTSAQSHVCSHHNQCLPQDVLQIYVKT\n+LPILLKSRVIRDLFLSCNGVSQIIELNCLNGIRSHSLKAFETLIISLGEQQKDASVPDID\n+GIDIEQKELSSVHVGTSFHHQQAYSDSPQSLSKFYAGLKEAYPKRRKTVNQDVHINTINL\n+FLCVAFLCVSKEAESDRESANDSEDTSGYDSTASEPLSHMLPCISLESLVLPSPEHMHQA\n+ADIWSMCRWIYMLSSVFQKQFYRLGGFRVCHKLIFMIIQKLFRSHKEEQGKKEGDTSVNE\n+NQDLNRISQPKRTMKEDLLSLAIKSDPIPSELGSLKKSADSLGKLELQHISSINVEEVSA\n+TEAAPEEAKLFTSQESETSLQSIRLLEALLAICLHGARTSQQKMELELPNQNLSVESILF\n+EMRDHLSQSKVIETQLAKPLFDALLRVALGNYSADFEHNDAMTEKSHQSAEELSSQPGDF\n+SEEAEDSQCCSFKLLVEEEGYEADSESNPEDGETQDDGVDLKSETEGFSASSSPNDLLEN\n+LTQGEIIYPEICMLELNLLSASKAKLDVLAHVFESFLKIIRQKEKNVFLLMQQGTVKNLL\n+GGFLSILTQDDSDFQACQRVLVDLLVSLMSSRTCSEELTLLLRIFLEKSPCTKILLLGIL\n+KIIESDTTMSPSQYLTFPLLHAPNLSNGVSSQKYPGILNSKAMGLLRRARVSRSKKEADR\n+ESFPHRLLSSWHIAPVHLPLLGQNCWPHLSEGFSVSLWFNVECIHEAESTTEKGKKIKKR\n+NKSLILPDSSFDGTESDRPEGAEYINPGERLIEEGCIHIISLGSKALMIQVWADPHNATL\n+IFRVCMDSNDDMKAVLLAQVESQENIFLPSKWQHLVLTYLQQPQGKRRIHGKISIWVSGQ\n+RKPDVTLDFMLPRKTSLSSDSNKTFCMIGHCLSSQEEFLQLAGKWDLGNLLLFNGAKVGS\n+QEAFYLYACGPNHTSVMPCKYGKPVNDYSKYINKEILRCEQIRELFMTKKDVDIGLLIES\n+LSVVYTTYCPAQYTIYEPVIRLKGQMKTQLSQRPFSSKEVQSILLEPHHLKNLQPTEYKT\n+IQGILHEIGGTGIFVFLFARVVELSSCEETQALALRVILSLIKYNQQRVHELENCNGLSM\n+IHQVLIKQKCIVGFYILKTLLEGCCGEDIIYMNENGEFKLDVDSNAIIQDVKLLEELLLD\n+WKIWSKAEQGVWETLLAALEVLIRADHHQQMFNIKQLLKAQVVHHFLLTCQVLQEYKEGQ\n+LTPMPREVCRSFVKIIAEVLGSPPDLELLTIIFNFLLAVHPPTNTYVCHNPTNFYFSLHI\n+DGKIFQEKVRSIMYLRHSSSGGRSLMSPGFMVISPSGFTASPYEGENSSNIIPQQMAAHM\n+LRSRSLPAFPTSSLLTQSQKLTGSLGCSIDRLQNIADTYVATQSKKQNSLGSSDTLKKGK\n+EDAFISSCESAKTVCEMEAVLSAQVSVSDVPKGVLGFPVVKADHKQLGAEPRSEDDSPGD\n+ESCPRRPDYLKGLASFQRSHSTIASLGLAFPSQNGSAAVGRWPSLVDRNTDDWENFAYSL\n+GYEPNYNRTASAHSVTEDCLVPICCGLYELLSGVLLILPDVLLEDVMDKLIQADTLLVLV\n+NHPSPAIQQGVIKLLDAYFARASKEQKDKFLKNRGFSLLANQLYLHRGTQELLECFIEMF\n+FGRHIGLDEEFDLEDVRNMGLFQKWSVIPILGLIETSLYDNILLHNALLLLLQILNSCSK\n+VADMLLDNGLLYVLCNTVAALNGLEKNIPMSEYKLLACDIQQLFIAVTIHACSSSGSQYF\n+RVIEDLIVMLGYLQNSKNKRTQNMAVALQLRVLQAAMEFIRTTANHDSENLTDSLQSPSA\n+PHHAVVQKRKSIAGPRKFPLAQTESLLMKMRSVANDELHVMMQRRMSQENPSQATETELA\n+QRLQRLTVLAVNRIIYQEFNSDIIDILRTPENVTQSKTSVFQTEISEENIHHEQSSVFNP\n+FQKEIFTYLVEGFKVSIGSSKASGSKQQWTKILWSCKETFRMQLGRLLVHILSPAHAAQE\n+RKQIFEIVHEPNHQEILRDCLSPSLQHGAKLVLYLSELIHNHQGELTEEELGTAELLMNA\n+LKLCGHKCIPPSASTKADLIKMIKEEQKKYETEEGVNKAAWQKTVNNNQQSLFQRLDSKS\n+KDISKIAADITQAVSLSQGNERKKVIQHIRGMYKVDLSASRHWQELIQQLTHDRAVWYDP\n+IYYPTSWQLDPTEGPNRERRRLQRCYLTIPNKYLLRDRQKSEDVVKPPLSYLFEDKTHSS\n+FSSTVKDKAASESIRVNRRCISVAPSRETAGELLLGKCGMYFVEDNASDTVESSSLQGEL\n+EPASFSWTYEEIKEVHKRWWQLRDNAVEIFLTNGRTLLLAFDNTKVRDDVYHNILTNNLP\n+NLLEYGNITALTNLWYTGQITNFEYLTHLNKHAGRSFNDLMQYPVFPFILADYVSETLDL\n+NDLLIYRNLSKPIAVQYKEKEDRYVDTYKYLEEEYRKGAREDDPMPPVQPYHYGSHYSNS\n+GTVLHFLVRMPPFTKMFLAYQDQSFDIPDRTFHSTNTTWRLSSFESMTDVKELIPEFFYL\n+PEFLVNREGFDFGVRQNGERVNHVNLPPWARNDPRLFILI'..b'LLNELGGFTITGKYLFGQPV\n+FRKVHAREHPILSTVITIADEYDDKQPLTSKEEEERRIAEMGRPILGEHTKLEVIIEESY\n+EFKSTVDKLIKKTNLALVVGTNSWREQFIEAITVSAGEDDDDDECGEEKLPSCFDYVMHF\n+LTVFWKVLFAFVPPTEYWNGWACFIVSILMIGLLTAFIGDLASHFGCTIGLKDSVTAVVF\n+VALGTSVPDTFASKVAATQDQYADASIGNVTGSNAVNVFLGIGVAWSIAAIYHAANGEQF\n+KVSPGTLAFSVTLFTIFAFINVGVLLYRRRPEIGGELGGPRTAKLLTSCLFVLLWLLYIF\n+FSSLEAYCHIKGF\n+>sp|O95544|NADK_HUMAN NAD kinase OS=Homo sapiens OX=9606 GN=NADK PE=1 SV=1\n+MEMEQEKMTMNKELSPDAAAYCCSACHGDETWSYNHPIRGRAKSRSLSASPALGSTKEFR\n+RTRSLHGPCPVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQ\n+PFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIIC\n+LGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRL\n+KVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVD\n+VYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVV\n+PAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFES\n+LAQCLHWNVRKKQAHFEEEEEEEEEG\n+>sp|P19878|NCF2_HUMAN Neutrophil cytosol factor 2 OS=Homo sapiens OX=9606 GN=NCF2 PE=1 SV=2\n+MSLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAF\n+TRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFA\n+CEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVG\n+KLFRPNERQVAQLAKKDYLGKATVVASVVDQDSFSGFAPLQPQAAEPPPRPKTPEIFRAL\n+EGEAHRVLFGFVPETKEELQVMPGNIVFVLKKGNDNWATVMFNGQKGLVPCNYLEPVELR\n+IHPQQQPQEESSPQSDIPAPPSSKAPGRPQLSPGQKQKEEPKEVKLSVPMPYTLKVHYKY\n+TVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPRDSNELVPLSEDSMKDAWGQVKNY\n+CLTLWCENTVGDQGFPDEPKESEKADANNQTTEPQLKKGSQVEALFSYEATQPEDLEFQE\n+GDIILVLSKVNEEWLEGECKGKVGIFPKVFVEDCATTDLESTRREV\n+>sp|Q5TAG4|NBPFC_HUMAN Neuroblastoma breakpoint family member 12 OS=Homo sapiens OX=9606 GN=NBPF12 PE=2 SV=3\n+MVVSAGPWSSEKAEMNILEINEKLRPQLAENKQQFRNLKERCFLTQLAGFLANRQKKYKY\n+EECKDLIKFMLRNERQFKEEKLAEQLKQAEELRQYKVLVHSQERELTQLREKLREGRDAS\n+RSLNEHLQALLTPDEPDKSQGQDLQEQLAEGCRLAQQLVQKLSPENDEDEDEDVQVEEDE\n+KVLESSAPREVQKAEESKVPEDSLEECAITCSNSHGPCDSIQPHKNIKITFEEDKVNSTV\n+VVDRKSSHDECQDALNILPVPGPTSSATNVSMVVSAGPLSSEKAEMNILEINEKLRPQLA\n+EKKQQFRSLKEKCFVTQLAGFLAKQQNKYKYEECKDLIKSMLRNELQFKEEKLAEQLKQA\n+EELRQYKVLVHSQERELTQLREKLREGRDASRSLNEHLQALLTPDEPDKSQGQDLQEQLA\n+EGCRLAQHLVQKLSPENDEDEDEDVQVEEDEKVLESSSPREMQKAEESKVPEDSLEECAI\n+TCSNSHGPCDSNQPHKNIKITFEEDKVNSSLVVDRESSHDECQDALNILPVPGPTSSATN\n+VSMVVSAGPLSSEKAEMNILEINEKLRPQLAEKKQQFRSLKEKCFVTQVACFLAKQQNKY\n+KYEECKDLLKSMLRNELQFKEEKLAEQLKQAEELRQYKVLVHSQERELTQLREKLREGRD\n+ASRSLNEHLQALLTPDEPDKSQGQDLQEQLAEGCRLAQHLVQKLSPENDNDDDEDVQVEV\n+AEKVQKSSSPREMQKAEEKEVPEDSLEECAITCSNSHGPYDSNQPHRKTKITFEEDKVDS\n+TLIGSSSHVEWEDAVHIIPENESDDEEEEEKGPVSPRNLQESEEEEVPQESWDEGYSTLS\n+IPPERLASYQSYSSTFHSLEEQQVCMAVDIGRHRWDQVKKEDQEATGPRLSRELLAEKEP\n+EVLQDSLDRCYSTPSVYLGLTDSCQPYRSAFYVLEQQRVGLAVDMDEIEKYQEVEEDQDP\n+SCPRLSRELLAEKEPEVLQDSLDRCYSTPSGYLELPDLGQPYRSAVYSLEEQYLGLALDV\n+DRIKKDQEEEEDQGPPCPRLSRELLEVVEPEVLQDSLDRCYSTPSSCLEQPDSCQPYRSS\n+FYALEEKHVGFSLDVGEIEKKGKGKKRRGRRSKKKRRRGRKEGEEDQNPPCPRLSRELLA\n+EKEPEVLQDSLDRWYSTPSVYLGLTDPCQPYRSAFYVLEQQRVGLAVDMDEIEKYQEVEE\n+DQDPSCPRLSRELLAEKEPEVLQDSLDRCYSTPSGYLELPDLGQPYRSAVYSLEEQYLGL\n+ALDVDRIKKDQEEEEDQGPPCPRLSRELLEVVEPEVLQDSLDRCYSTPSSCLEQPDSCQP\n+YRSSFYALEEKHVGFSLDVGEIEKKGKGKKRRGRRSKKKRRRGRKEGEEDQNPPCPRLNS\n+VLMEVEEPEVLQDSLDRCYSTPSMYFELPDSFQHYRSVFYSFEEQHITFALDMDNSFFTL\n+TVTSLHLVFQMGVIFPQ\n+>sp|Q15080|NCF4_HUMAN Neutrophil cytosol factor 4 OS=Homo sapiens OX=9606 GN=NCF4 PE=1 SV=2\n+MAVAQQLRAESDFEQLPDDVAISANIADIEEKRGFTSHFVFVIEVKTKGGSKYLIYRRYR\n+QFHALQSKLEERFGPDSKSSALACTLPTLPAKVYVGVKQEIAEMRIPALNAYMKSLLSLP\n+VWVLMDEDVRIFFYQSPYDSEQVPQALRRLRPRTRKVKSVSPQGNSVDRMAAPRAEALFD\n+FTGNSKLELNFKAGDVIFLLSRINKDWLEGTVRGATGIFPLSFVKILKDFPEEDDPTNWL\n+RCYYYEDTISTIKDIAVEEDLSSTPLLKDLLELTRREFQREDIALNYRDAEGDLVRLLSD\n+EDVALMVRQARGLPSQKRLFPWKLHITQKDNYRVYNTMP\n+>sp|P19404|NDUV2_HUMAN NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFV2 PE=1 SV=2\n+MFFSAALRARAAGLTAHWGRHVRNLHKTVMQNGAGGALFVHRDTPENNPDTPFDFTPENY\n+KRIEAIVKNYPEGHKAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYT\n+MYNRKPVGKYHIQVCTTTPCMLRNSDSILEAIQKKLGIKVGETTPDKLFTLIEVECLGAC\n+VNAPMVQINDNYYEDLTAKDIEEIIDELKAGKIPKPGPRSGRFSCEPAGGLTSLTEPPKG\n+PGFGVQAGL\n\\ No newline at end of file\n' |
| b |
| diff -r e42225f8a659 -r 97a7f34fcb6a test-data/tmt_data_18.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt_data_18.mzXML Wed Aug 11 09:24:23 2021 +0000 |
| [ |
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