Mercurial > repos > galaxyp > maxquant
changeset 4:dcd39bcc7481 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_mqpar.py Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,53 @@ +"""Create paramter xml file for a specific MaxQuant version from yaml or command line input +and a template parameter file. +""" + +import argparse +import os +import yaml + +from mqparam import MQParam + +parser = argparse.ArgumentParser() + +parser.add_argument('--yaml', '-y', help="""Yaml config file. Only those parameters differing +from the template need to be specified.""") + +parser.add_argument('--exp_design', '-e', help="Experimental design template as it is created by the MaxQuant GUI.") + +parser.add_argument('template', help="Template Parameter File.") + +parser.add_argument('--mqpar_out', '-o', help="Output file, will be ./mqpar.xml if omitted.") + +parser.add_argument('--substitution_rx', '-s', help="""Regular expression for filename substitution. +Necessary for usage in the Galaxy tool. Can usually be ignored.""") + +parser.add_argument('--version', '-v', help="""A version number. Raises exception if it doesn't +match the MaxQuant version of the template. For usage in the Galaxy tool.""") + +# in case numThreads is a environment variable, otherwise it can be specified in the yaml file as well +parser.add_argument('--num_threads', '-t', help="Number of threads to specify in mqpar.") +args = parser.parse_args() + +# edit file names, working dir is unknown at the time of galaxy tool configfile creation +if args.yaml: + with open(args.yaml) as f: + conf_dict = yaml.safe_load(f.read()) + + for n, pg in enumerate(conf_dict['paramGroups']): + for num, fl in enumerate(pg['files']): + if not fl.startswith('/'): + conf_dict['paramGroups'][n]['files'][num] = os.path.join(os.getcwd(), fl) + with open('yaml', 'w') as f: + yaml.safe_dump(conf_dict, stream=f) + args.yaml = 'yaml' + +kwargs = dict(yaml=args.yaml) +if args.substitution_rx: + kwargs['substitution_rx'] = args.substitution_rx +mqparam = MQParam(args.template, args.exp_design, **kwargs) +if args.version and mqparam.version != args.version: + raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version)) +mqparam.set_simple_param('numThreads', args.num_threads) + +mqparam.write(args.mqpar_out if args.mqpar_out else 'mqpar.xml')
--- a/init.py Thu Aug 15 08:09:00 2019 -0400 +++ b/init.py Sat Apr 11 11:49:19 2020 -0400 @@ -5,9 +5,7 @@ TODO: Append function: only add modifications that are not already present, add modification entries to conda maxquant -Authors: Damian Glaetzer <d.glaetzer@mailbox.org> - -Usage: init.py [-a] [-m MODS_FILE] [-e ENZYMES_FILE] +Usage: init.py [-m MODS_FILE] [-e ENZYMES_FILE] FILES are the modifications/enzymes.xml of MaxQuant, located at <ANACONDA_DIR>/pkgs/maxquant-<VERSION>/bin/conf/. (for conda installations) @@ -40,19 +38,20 @@ if args.modifications: mods_root = ET.parse(args.modifications).getroot() - mods = mods_root.findall('modification') standard_mods = [] label_mods = [] + iso_labels = [] for m in mods: if (m.findtext('type') == 'Standard' or m.findtext('type') == 'AaSubstitution'): standard_mods.append(m.get('title')) elif m.findtext('type') == 'Label': label_mods.append(m.get('title')) + elif m.findtext('type') == 'IsobaricLabel': + iso_labels.append(m.get('title')) if args.enzymes: enzymes_root = ET.parse(args.enzymes).getroot() - enzymes = enzymes_root.findall('enzyme') enzymes_list = [e.get('title') for e in enzymes] @@ -62,6 +61,8 @@ build_list(child, 'modification', standard_mods) elif child.get('name') == 'label' and args.modifications: build_list(child, 'label', label_mods) + elif child.get('name') == 'iso_labels' and args.modifications: + build_list(child, 'iso_labels', iso_labels) elif child.get('name') == 'proteases' and args.enzymes: build_list(child, 'proteases', enzymes_list)
--- a/macros.xml Thu Aug 15 08:09:00 2019 -0400 +++ b/macros.xml Sat Apr 11 11:49:19 2020 -0400 @@ -1,18 +1,185 @@ <?xml version="1.0" ?> <macros> - <token name="@VERSION@">1.6.3.4</token> + <token name="@VERSION@">1.6.10.43</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> - <xml name="output" token_format="tabular" token_label="default description" token_name="default"> - <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> - <filter>'@NAME@' in output_opts['output']</filter> - </data> + <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True] + - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True] + - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True] + - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True] + - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True] + - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True] + - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True] + - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True] + - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True] + - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True] + ]]></token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">maxquant</requirement> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="5.1.2">pyyaml</requirement> + <requirement type="package" version="0.92.6">r-ptxqc</requirement> + <requirement type="package" version="1.32">tar</requirement> + </requirements> </xml> - <xml name="output_option" token_label="default label" token_name="default"> - <option value="@NAME@">@LABEL@</option> + + <xml name="ptxqc"> + <configfile name="qr_yaml"> + PTXQC: + ReportFilename: + extended: yes + UseLocalMQPar: yes + NameLengthMax_num: 10.0 + OutputFormats: + - plainPDF + PlainPDF: + AddPageNumbers: 'on' + File: + Parameters: + #if $qc.do_it: + enabled: ${qc.parameters} + #end if + Summary: + #if $qc.do_it: + enabled: ${qc.summary} + #end if + IDRate: + Thresh_bad_num: 20.0 + Thresh_great_num: 35.0 + ProteinGroups: + #if $qc.do_it: + enabled: ${qc.proteingroups} + #end if + RatioPlot: + LabelIncThresh_num: 4.0 + IntensityThreshLog2_num: 25.0 + Evidence: + #if $qc.do_it: + enabled: ${qc.evidence} + #end if + ProteinCountThresh_num: 3500.0 + IntensityThreshLog2_num: 23.0 + PeptideCountThresh_num: 15000.0 + SpecialContaminants: + cont_MYCO: + - MYCOPLASMA + - '1' + MQpar_MatchingTimeWindow_num: 0.0 + MatchBetweenRuns_wA: auto + MQpar_firstSearchTol_num: 20.0 + firstSearch_outOfCalWarnSD_num: 2.0 + MQpar_mainSearchTol_num: 4.5 + MsMs: + #if $qc.do_it: + enabled: ${qc.msms} + #end if + MsMsScans: + #if $qc.do_it: + enabled: ${qc.msmsscans} + #end if + IonInjectionThresh_num: 10.0 + order: + qcMetric_PAR: 1.0 + qcMetric_PG_PCA: 3.0 + qcMetric_EVD_Top5Cont: 10.0 + qcMetric_PG_Ratio: 19.0 + qcMetric_EVD_UserContaminant: 20.0 + qcMetric_EVD_PeptideInt: 30.0 + qcMetric_EVD_ReporterInt: 31.0 + qcMetric_PG_RawInt: 32.0 + qcMetric_PG_LFQInt: 33.0 + qcMetric_PG_ReporterInt: 34.0 + qcMetric_MSMS_MissedCleavages: 40.0 + qcMetric_EVD_Charge: 100.0 + qcMetric_PG_Cont: 110.0 + qcMetric_MSMSScans_TopNoverRT: 120.0 + qcMetric_EVD_IDoverRT: 150.0 + qcMetric_EVD_RTPeakWidth: 170.0 + qcMetric_EVD_MBRAlign: 210.0 + qcMetric_EVD_MBRIdTransfer: 220.0 + qcMetric_EVD_MBRaux: 221.0 + qcMetric_MSMSScans_IonInjTime: 240.0 + qcMetric_MSMSScans_MSMSIntensity: 245.0 + qcMetric_EVD_MS2OverSampling: 250.0 + qcMetric_EVD_PreCal: 260.0 + qcMetric_EVD_PostCal: 270.0 + qcMetric_MSMS_MSMSDecal: 280.0 + qcMetric_SM_MSMSIdRate: 300.0 + qcMetric_MSMSScans_TopNID: 380.0 + qcMetric_MSMSScans_DepPep: 383.0 + qcMetric_EVD_MissingValues: 390.0 + qcMetric_EVD_PeptideCount: 400.0 + qcMetric_EVD_ProteinCount: 450.0 + qcMetric_AverageQualOverall: 9999.0 + </configfile> + <configfile name="qr"> + library(PTXQC) + library(yaml) + library(methods) + args = commandArgs(trailingOnly=TRUE) + yaml_config = yaml.load_file(input = args[1]) + r = createReport('./combined/txt', yaml_config) + cat(paste0("\nReport generated as '", r\$report_file, "'\n\n")) + </configfile> </xml> + <xml name="mod_option" token_value="default"> <option value="@VALUE@">@VALUE@</option> </xml> + <xml name="default_mod_option" token_value="default"> + <option selected="true" value="@VALUE@">@VALUE@</option> + </xml> + + <xml name="ptxqc-opts"> + <conditional name="qc"> + <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (at own risk)" + type="boolean" checked="false"/> + <when value="true"> + <param name="parameters" type="boolean" checked="true" + label="use parameters.txt?" truevalue="yes" falsevalue="no" /> + <param name="summary" type="boolean" checked="true" + label="use summary.txt?" truevalue="yes" falsevalue="no" /> + <param name="proteingroups" type="boolean" checked="true" + label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" /> + <param name="evidence" type="boolean" checked="true" + label="use evidence.txt?" truevalue="yes" falsevalue="no" /> + <param name="msms" type="boolean" checked="true" + label="use msms.txt?" truevalue="yes" falsevalue="no" /> + <param name="msmsscans" type="boolean" checked="true" + label="use msmsScans.txt?" truevalue="yes" falsevalue="no" /> + </when> + <when value="false"/> + </conditional> + </xml> + + <xml name="outputs"> + <outputs> + <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/> + <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/> + <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/> + <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/> + <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/> + <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/> + <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/> + <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/> + <expand macro="output_from_wdir" name="libraryMatch" label="library match"/> + <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/> + <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/> + <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/> + <expand macro="output_from_wdir" name="msmsScans" label="msms Scans"/> + <expand macro="output_from_wdir" name="mzRange" label="mz range"/> + <expand macro="output_from_wdir" name="peptideSection" label="peptide section"/> + <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/> + <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/> + <expand macro="output" name="log" format="txt" label="log"/> + <expand macro="output" name="config" format="txt" label="yaml config file"/> + <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report"> + <filter>qc['do_it'] == True</filter> + </data> + </outputs> + </xml> + <xml name="modification"> <expand macro="mod_option" value="Acetyl (K)"/> <expand macro="mod_option" value="Acetyl (Protein N-term)"/> @@ -430,6 +597,7 @@ <expand macro="mod_option" value="Cysteinyl"/> <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> </xml> + <xml name="label"> <expand macro="mod_option" value="Arg6"/> <expand macro="mod_option" value="Arg10"/> @@ -466,6 +634,7 @@ <expand macro="mod_option" value="Leu7"/> <expand macro="mod_option" value="Ile7"/> </xml> + <xml name="proteases"> <expand macro="mod_option" value="Trypsin"/> <expand macro="mod_option" value="Trypsin/P"/> @@ -481,5 +650,123 @@ <expand macro="mod_option" value="Chymotrypsin+"/> <expand macro="mod_option" value="Chymotrypsin"/> </xml> + + <xml name="iso_labels"> + <expand macro="mod_option" value="iTRAQ4plex-Nter114"/> + <expand macro="mod_option" value="iTRAQ4plex-Nter115"/> + <expand macro="mod_option" value="iTRAQ4plex-Nter116"/> + <expand macro="mod_option" value="iTRAQ4plex-Nter117"/> + <expand macro="mod_option" value="iTRAQ4plex-Lys114"/> + <expand macro="mod_option" value="iTRAQ4plex-Lys115"/> + <expand macro="mod_option" value="iTRAQ4plex-Lys116"/> + <expand macro="mod_option" value="iTRAQ4plex-Lys117"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter113"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter114"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter115"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter116"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter117"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter118"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter119"/> + <expand macro="mod_option" value="iTRAQ8plex-Nter121"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys113"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys114"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys115"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys116"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys117"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys118"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys119"/> + <expand macro="mod_option" value="iTRAQ8plex-Lys121"/> + <expand macro="mod_option" value="TMT2plex-Nter126"/> + <expand macro="mod_option" value="TMT2plex-Nter127"/> + <expand macro="mod_option" value="TMT2plex-Lys126"/> + <expand macro="mod_option" value="TMT2plex-Lys127"/> + <expand macro="mod_option" value="TMT6plex-Nter126"/> + <expand macro="mod_option" value="TMT6plex-Nter127"/> + <expand macro="mod_option" value="TMT6plex-Nter128"/> + <expand macro="mod_option" value="TMT6plex-Nter129"/> + <expand macro="mod_option" value="TMT6plex-Nter130"/> + <expand macro="mod_option" value="TMT6plex-Nter131"/> + <expand macro="mod_option" value="TMT8plex-Nter126C"/> + <expand macro="mod_option" value="TMT8plex-Nter127N"/> + <expand macro="mod_option" value="TMT8plex-Nter127C"/> + <expand macro="mod_option" value="TMT8plex-Nter128C"/> + <expand macro="mod_option" value="TMT8plex-Nter129N"/> + <expand macro="mod_option" value="TMT8plex-Nter129C"/> + <expand macro="mod_option" value="TMT8plex-Nter130C"/> + <expand macro="mod_option" value="TMT8plex-Nter131N"/> + <expand macro="mod_option" value="TMT10plex-Nter126C"/> + <expand macro="mod_option" value="TMT10plex-Nter127N"/> + <expand macro="mod_option" value="TMT10plex-Nter127C"/> + <expand macro="mod_option" value="TMT10plex-Nter128N"/> + <expand macro="mod_option" value="TMT10plex-Nter128C"/> + <expand macro="mod_option" value="TMT10plex-Nter129N"/> + <expand macro="mod_option" value="TMT10plex-Nter129C"/> + <expand macro="mod_option" value="TMT10plex-Nter130N"/> + <expand macro="mod_option" value="TMT10plex-Nter130C"/> + <expand macro="mod_option" value="TMT10plex-Nter131N"/> + <expand macro="mod_option" value="TMT11plex-Nter131C"/> + <expand macro="mod_option" value="TMT6plex-Lys126"/> + <expand macro="mod_option" value="TMT6plex-Lys127"/> + <expand macro="mod_option" value="TMT6plex-Lys128"/> + <expand macro="mod_option" value="TMT6plex-Lys129"/> + <expand macro="mod_option" value="TMT6plex-Lys130"/> + <expand macro="mod_option" value="TMT6plex-Lys131"/> + <expand macro="mod_option" value="TMT8plex-Lys126C"/> + <expand macro="mod_option" value="TMT8plex-Lys127N"/> + <expand macro="mod_option" value="TMT8plex-Lys127C"/> + <expand macro="mod_option" value="TMT8plex-Lys128C"/> + <expand macro="mod_option" value="TMT8plex-Lys129N"/> + <expand macro="mod_option" value="TMT8plex-Lys129C"/> + <expand macro="mod_option" value="TMT8plex-Lys130C"/> + <expand macro="mod_option" value="TMT8plex-Lys131N"/> + <expand macro="mod_option" value="TMT10plex-Lys126C"/> + <expand macro="mod_option" value="TMT10plex-Lys127N"/> + <expand macro="mod_option" value="TMT10plex-Lys127C"/> + <expand macro="mod_option" value="TMT10plex-Lys128N"/> + <expand macro="mod_option" value="TMT10plex-Lys128C"/> + <expand macro="mod_option" value="TMT10plex-Lys129N"/> + <expand macro="mod_option" value="TMT10plex-Lys129C"/> + <expand macro="mod_option" value="TMT10plex-Lys130N"/> + <expand macro="mod_option" value="TMT10plex-Lys130C"/> + <expand macro="mod_option" value="TMT10plex-Lys131N"/> + <expand macro="mod_option" value="TMT11plex-Lys131C"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys126"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys127"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys128"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys129"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys130"/> + <expand macro="mod_option" value="iodoTMT6plex-Cys131"/> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{cox2008maxquant, + title={MaxQuant enables high peptide identification rates, individualized + ppb-range mass accuracies and proteome-wide protein quantification}, + author={Cox, J{\"u}rgen and Mann, Matthias}, + journal={Nature biotechnology}, + volume={26}, + number={12}, + pages={1367}, + year={2008}, + publisher={Nature Publishing Group} + } + </citation> + <citation type="bibtex"> + @article{tyanova2016maxquant, + title={The MaxQuant computational platform for mass + spectrometry-based shotgun proteomics}, + author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen}, + journal={Nature protocols}, + volume={11}, + number={12}, + pages={2301}, + year={2016}, + publisher={Nature Publishing Group} + } + </citation> + <citation type="doi">10.1021/acs.jproteome.5b00780</citation> + </citations> + </xml> </macros> -
--- a/maxquant.xml Thu Aug 15 08:09:00 2019 -0400 +++ b/maxquant.xml Sat Apr 11 11:49:19 2020 -0400 @@ -1,114 +1,219 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@"> <macros> + <xml name="output" token_format="tabular" token_label="default description" token_name="default"> + <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> + <filter>'@NAME@' in output_opts['output']</filter> + </data> + </xml> + <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default"> + <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@"> + <filter>'@NAME@' in output_opts['output']</filter> + </data> + </xml> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@VERSION@">maxquant</requirement> - <requirement type="package" version="3.7">python</requirement> - </requirements> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import re - - python3 '$__tool_directory__/mqwrapper.py' + maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr + #if 'config' in $output_opts.output: + && + cp '$mq_conf' '$config' + #end if + #set infiles = [$name for $pg in $paramGroups for $name in $pg.files] + #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles] + #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names] + #for $target, $link in zip($infiles, $names_with_ext) + && + ln -s '$target' '$link' + #end for + && + python3 '$__tool_directory__/create_mqpar.py' + #if $search_opts.template + --exp_design='$search_opts.template' + #end if + --version=@VERSION@ --num_threads=\${GALAXY_SLOTS:-1} --substitution_rx='@SUBSTITUTION_RX@' - #if $input_opts.infile.select == "mzxml_files" - --mzxml_files='$input_opts.infile.mzxml_files' - #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files]) - #else - --raw_files='$input_opts.infile.raw_files' - #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.raw_files]) - #end if - --infile_names='$names' - --version='@VERSION@' - --fasta_files='$input_opts.fasta_files' - --identifier_parse_rule='$input_opts.identifier_parse_rule' - --description_parse_rule='$input_opts.description_parse_rule' + --yaml='$mq_conf' + mqpar.xml - --exp_design='$search_opts.template' - --missed_cleavages=$search_opts.missed_cleavages - --min_peptide_len=$search_opts.min_peptide_len - --max_peptide_mass=$search_opts.max_peptide_mass - --min_unique_pep=$search_opts.min_unique_pep - $search_opts.calc_peak_properties - $search_opts.match_between_runs - #if $search_opts.fixed_mods - --fixed_mods='$search_opts.fixed_mods' - #end if - #if $search_opts.var_mods - --var_mods='$search_opts.var_mods' - #end if - #if $search_opts.proteases - --proteases='$search_opts.proteases' - #end if - #if $search_opts.silac.light_mods - --light_mods='$search_opts.silac.light_mods' - #end if - #if $search_opts.silac.medium_mods - --medium_mods='$search_opts.silac.medium_mods' - #end if - #if $search_opts.silac.heavy_mods - --heavy_mods='$search_opts.silac.heavy_mods' - #end if - #if $search_opts.lfq.do_lfq == "--lfq_mode=1" - $search_opts.lfq.do_lfq.lfq_mode - --lfq_min_ratio_count=$search_opts.lfq.do_lfq.lfq_min_ratio_count - --lfq_min_edges_per_node=$search_opts.lfq.do_lfq.lfq_min_edges_per_node - --lfq_avg_edges_per_node=$search_opts.lfq.do_lfq.lfq_avg_edges_per_node - $search_opts.lfq.do_lfq.lfq_skip_norm - $search_opts.lfq.do_lfq.separate_lfq - $search_opts.lfq.do_lfq.lfq_stabilize_large_ratios - $search_opts.lfq.do_lfq.lfq_require_msms - #if $search_opts.lfq.do_lfq.do_ibaq == "--ibaq" - $search_opts.lfq.do_lfq.do_ibaq.ibaq - $search_opts.lfq.do_lfq.do_ibaq.ibaq_log_fit - #end if - $search_opts.lfq.do_lfq.advanced_site_intensities - #end if - - $output_opts.write_mztab - --evidence='$evidence' - --msms='$msms' - --parameters='$parameters' - --peptides='$peptides' - --proteinGroups='$proteinGroups' - --allPeptides='$allPeptides' - --libraryMatch='$libraryMatch' - --matchedFeatures='$matchedFeatures' - --modificationSpecificPeptides='$modificationSpecificPeptides' - --ms3Scans='$ms3Scans' - --msmsScans='$msmsScans' - --mzRange='$mzRange' - --peptideSection='$peptideSection' - --summary='$summary' - --mzTab='$mzTab' - --mqpar_out='$mqpar_out' - - #if 'log' in $output_opts.output - > '$log' - #end if - #if 'output_all' in $output_opts.output - && tar -zcf '$output_all' ./combined/txt + #if $output_opts.dry_run: + && + mkdir -p combined/txt + && + mv mqpar.xml combined/txt/mqpar.xml + #else: + && + maxquant mqpar.xml + #if 'log' in $output_opts.output: + > '$log' + #end if + && + mv mqpar.xml combined/txt/mqpar.xml + #if 'output_all' in $output_opts.output: + && + tar -zcf '$output_all' ./combined/txt + #end if + + #if $qc.do_it: + && + Rscript '$qr' '$qr_yaml' + #if 'log' in $output_opts.output: + >> '$log' 2>&1 + #end if + && + cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report' + #end if #end if ]]></command> + + <configfiles> + <configfile name="mq_conf"> + #import re + fastaFiles: [${input_opts.fasta_files}] + parseRules: + identifierParseRule: '${input_opts.identifier_parse_rule}' + descriptionParseRule: '${input_opts.description_parse_rule}' + minUniquePeptides: ${search_opts.min_unique_pep} + minPepLen: ${search_opts.min_peptide_len} + maxPeptideMass: ${search_opts.max_peptide_mass} + calcPeakProperties: ${search_opts.calc_peak_properties} + #set writeMzTab = "mzTab" in $output_opts.output + writeMzTab: $writeMzTab + #if $lfq_opts.do_ibaq.ibaq == 'True': + ibaq: ${lfq_opts.do_ibaq.ibaq} + ibaqLogFit: ${lfq_opts.do_ibaq.ibaqLogFit} + #end if + separateLfq: ${lfq_opts.separateLfq} + lfqStabilizeLargeRatios: ${lfq_opts.lfqStabilizeLargeRatios} + lfqRequireMsms: ${lfq_opts.lfqRequireMsms} + advancedSiteIntensities: ${lfq_opts.advancedSiteIntensities} + matchBetweenRuns: ${search_opts.match_between_runs} + paramGroups: + #for $pg in $paramGroups: + #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files] + #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names] + - files: $names_with_ext + maxMissedCleavages: ${pg.maxMissedCleavages} + #if $pg.fixedModifications: + fixedModifications: [${pg.fixedModifications}] + #else: + fixedModifications: [] + #end if + #if $pg.variableModifications: + variableModifications: [${pg.variableModifications}] + #else: + variableModifications: [] + #end if + #if $pg.enzymes: + enzymes: [${pg.enzymes}] + #else: + enzymes: [] + #end if + #if $pg.quant_method.select_quant_method == 'silac': + labelMods: + #if $pg.quant_method.light_labels: + - [${pg.quant_method.light_labels}] + #else: + - [] + #end if + #if $pg.quant_method.medium_labels: + - [${pg.quant_method.medium_labels}] + #else: + - [] + #end if + #if $pg.quant_method.heavy_labels: + - [${pg.quant_method.heavy_labels}] + #else: + - [] + #end if + #end if + #if $pg.quant_method.select_quant_method == 'lfq': + lfqMode: 1 + lfqSkipNorm: ${pg.quant_method.lfqSkipNorm} + lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode} + lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode} + lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount} + #end if + #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2': + lcmsRunType: 'Reporter ion MS2' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + isobaricLabels: + #if $pg.quant_method.iso_labels.labeling == 'custom': + #for $l in $pg.quant_method.iso_labels.iso_label: + - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] + #end for + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': + - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] + - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': + - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] + - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] + - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] + - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] + - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] + - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': + - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] + - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] + - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] + - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] + - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] + - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] + - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] + - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': + @TMT10PLEX@ + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': + @TMT10PLEX@ + - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': + - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] + - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False] + - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] + - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] + - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] + #end if + #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': + - [iodoTMT6plex-Cys126,'',0,0,0,0,True] + - [iodoTMT6plex-Cys127,'',0,0,0,0,True] + - [iodoTMT6plex-Cys128,'',0,0,0,0,True] + - [iodoTMT6plex-Cys129,'',0,0,0,0,True] + - [iodoTMT6plex-Cys130,'',0,0,0,0,True] + - [iodoTMT6plex-Cys131,'',0,0,0,0,True] + #end if + #end if + #end for + </configfile> + <expand macro="ptxqc"/> + </configfiles> + <inputs> <section name="input_opts" title="Input Options" expanded="True"> - <conditional name="infile"> - <param name="select" type="select" label="choose the type of your input files"> - <option value="raw_files">Thermo.raw</option> - <option value="mzxml_files">mzXML</option> - </param> - <when value="raw_files"> - <param multiple="true" name="raw_files" type="data" - format="thermo.raw" label="RAW Files" - help="Specify one or more Thermo RAW files" /> - </when> - <when value="mzxml_files"> - <param multiple="true" name="mzxml_files" type="data" - format="mzxml" label="mzXML Files" - help="Specify one or more mzXML files" /> - </when> - </conditional> + <param name="ftype" type="select" label="choose the type of your input files"> + <option value=".thermo.raw">thermo.raw</option> + <option value=".mzxml">mzxml</option> + <option value=".mzml">mzml</option> + </param> <param format="fasta" multiple="true" name="fasta_files" type="data" label="FASTA files" help="Specify one or more FASTA databases." /> @@ -135,168 +240,299 @@ <param format="tabular" name="template" type="data" optional="true" label="Specify an experimental design template (if needed). For detailed instructions see the help text." /> - <param type="integer" name="missed_cleavages" - label="missed cleavages" value="1"/> <param type="integer" name="min_peptide_len" label="minimum peptide length" value="7"/> <param type="integer" name="max_peptide_mass" label="maximum peptide mass" value="4600"/> <param type="integer" name="min_unique_pep" - label="minimum unique peptides" value="1" /> + label="minimum unique peptides" value="0" /> <param name="calc_peak_properties" type="boolean" checked="false" label="Calculate peak properties?" - truevalue="--calc_peak_properties" falsevalue="" /> + truevalue="True" falsevalue="False" /> <param name="match_between_runs" type="boolean" checked="false" label="Match between runs?" - truevalue="--match_between_runs" falsevalue="" /> - <param name="fixed_mods" type="select" label="fixed modifications" + truevalue="True" falsevalue="False" /> + </section> + + <repeat name="paramGroups" title="Parameter Group" min="1" default="1"> + <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true" + help="Only select infiles matching the filetype specified in the input options."/> + <param type="integer" name="maxMissedCleavages" + label="missed cleavages" value="2"/> + <param name="fixedModifications" type="select" label="fixed modifications" multiple="true" help="select zero or more fixed modifications"> <expand macro="modification"/> + <expand macro="default_mod_option" value="Carbamidomethyl (C)"/> + </param> + <param name="variableModifications" type="select" label="variable modifications" + multiple="true" help="select zero or more variable modifications"> + <expand macro="default_mod_option" value="Oxidation (M)"/> + <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> + <expand macro="modification"/> </param> - <param name="var_mods" type="select" label="variable modifications" - multiple="true" help="select zero or more variable modifications"> - <expand macro="modification"/> - </param> - <param name="proteases" type="select" label="proteases" + <param name="enzymes" type="select" label="proteases" multiple="true" help="select zero or more proteases"> + <expand macro="default_mod_option" value="Trypsin/P"/> <expand macro="proteases"/> </param> - <section title="label based quantitation" name="silac" expanded="false"> - <param name="light_mods" type="select" label="light labels" - multiple="true" help="select zero or more light modifications"> - <expand macro="label"/> - </param> - <param name="medium_mods" type="select" label="medium labels" - multiple="true" help="select zero or more medium modifications"> - <expand macro="label"/> - </param> - <param name="heavy_mods" type="select" label="heavy labels" - multiple="true" help="select zero or more heavy modifications"> - <expand macro="label"/> - </param> - </section> - <section title="label free quantification" name="lfq" expanded="false"> - <conditional name="do_lfq"> - <param name="lfq_mode" type="select" label="Perform LFQ?"> - <option value="">No</option> - <option value="--lfq_mode=1">Yes</option> - </param> - <when value="--lfq_mode=1"> - <param type="integer" name="lfq_min_ratio_count" - label="LFQ minimum ratio count" value="2"/> - <param type="integer" name="lfq_min_edges_per_node" - label="LFQ minimum number of neighbours" value="3"/> - <param type="integer" name="lfq_avg_edges_per_node" - label="LFQ average number of neighbours" value="6"/> - <param name="lfq_skip_norm" type="boolean" checked="false" - label="Skip normalization?" - truevalue="--lfq_skip_norm" falsevalue="" /> - <param name="separate_lfq" type="boolean" checked="false" - label="Separate LFQ in parameter Groups?" - truevalue="--separate_lfq" falsevalue="" /> - <param name="lfq_stabilize_large_ratios" type="boolean" checked="true" - label="Stabilize large LFQ ratios?" - truevalue="--lfq_stabilize_large_ratios" falsevalue="" /> - <param name="lfq_require_msms" type="boolean" checked="true" - label="Require MS/MS for LFQ comparisons?" - truevalue="--lfq_require_msms" falsevalue="" /> - <conditional name="do_ibaq"> - <param name="ibaq" type="select" label="iBAQ?"> - <option value="">No</option> - <option value="--ibaq">Yes</option> - </param> - <when value="--ibaq"> - <param name="ibaq_log_fit" type="boolean" checked="true" - label="Logarithmic fit?" - truevalue="--ibaq_log_fit" falsevalue="" /> - </when> - <when value=""> - </when> - </conditional> - <param name="advanced_site_intensities" type="boolean" checked="true" - label="Advanced site intensities?" - truevalue="--advanced_site_intensities" falsevalue="" /> - </when> - <when value=""> - </when> - </conditional> - </section> + <conditional name="quant_method"> + <param name="select_quant_method" type="select" label="Quantitation Methods" + help="Select a method if needed."> + <option value="">None</option> + <option value="lfq">label free quantification</option> + <option value="silac">label based quantification (SILAC)</option> + <option value="reporter_ion_ms2">reporter ion MS2</option> + </param> + <when value=""/> + <when value="silac"> + <param name="light_labels" type="select" label="light labels" + multiple="true" help="select zero or more light modifications"> + <expand macro="label"/> + </param> + <param name="medium_labels" type="select" label="medium labels" + multiple="true" help="select zero or more medium modifications"> + <expand macro="label"/> + </param> + <param name="heavy_labels" type="select" label="heavy labels" + multiple="true" help="select zero or more heavy modifications"> + <expand macro="label"/> + </param> + </when> + <when value="lfq"> + <param type="integer" name="lfqMinRatioCount" + label="LFQ minimum ratio count" value="2"/> + <param type="integer" name="lfqMinEdgesPerNode" + label="LFQ minimum number of neighbours" value="3"/> + <param type="integer" name="lfqAvEdgesPerNode" + label="LFQ average number of neighbours" value="6"/> + <param type="boolean" name="lfqSkipNorm" checked="true" + label="Skip normalization?" + truevalue="True" falsevalue="False" /> + </when> + <when value="reporter_ion_ms2"> + <conditional name="iso_labels"> + <param name="labeling" type="select" label="isobaric labeling" + help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> + <option value="custom">custom</option> + <option value="tmt2plex">TMT2plex</option> + <option value="tmt6plex">TMT6plex</option> + <option value="tmt8plex">TMT8plex</option> + <option value="tmt10plex">TMT10plex</option> + <option value="tmt11plex">TMT11plex</option> + <option value="itraq4plex">iTRAQ4plex</option> + <option value="itraq8plex">iTRAQ8plex</option> + <option value="iodotmt6plex">iodoTMT6plex</option> + </param> + <when value="tmt2plex"></when> + <when value="tmt6plex"></when> + <when value="tmt8plex"></when> + <when value="tmt10plex"></when> + <when value="tmt11plex"></when> + <when value="itraq4plex"></when> + <when value="itraq8plex"></when> + <when value="iodotmt6plex"></when> + <when value="custom"> + <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> + <param name="internallabel" type="select" label="internal label"> + <expand macro="iso_labels"/> + </param> + <param name="terminallabel" type="select" label="terminal label"> + <option value="">None</option> + <expand macro="iso_labels"/> + </param> + <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> + <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> + <param name="cp1" type="float" label="correction factor +1%" value="0.0"/> + <param name="cp2" type="float" label="correction factor +2%" value="0.0"/> + <param type="boolean" name="tmtlike" checked="false" + label="TMT-like" + truevalue="True" falsevalue="False" /> + </repeat> + </when> + </conditional> + </when> + </conditional> + </repeat> + + <section title="LFQ Options" name="lfq_opts" expanded="false"> + <param name="separateLfq" type="boolean" checked="false" + label="Separate LFQ in parameter Groups?" + truevalue="True" falsevalue="False" /> + <param name="lfqStabilizeLargeRatios" type="boolean" checked="true" + label="Stabilize large LFQ ratios?" + truevalue="True" falsevalue="False" /> + <param name="lfqRequireMsms" type="boolean" checked="true" + label="Require MS/MS for LFQ comparisons?" + truevalue="True" falsevalue="False" /> + <conditional name="do_ibaq"> + <param name="ibaq" type="select" label="iBAQ?"> + <option value="False">No</option> + <option value="True">Yes</option> + </param> + <when value="True"> + <param name="ibaqLogFit" type="boolean" checked="true" + label="Logarithmic fit?" + truevalue="True" falsevalue="False" /> + </when> + <when value="False"> + </when> + </conditional> + <param name="advancedSiteIntensities" type="boolean" checked="true" + label="Advanced site intensities?" + truevalue="True" falsevalue="False" /> </section> + <expand macro="ptxqc-opts"/> <section title="Output Options" name="output_opts" expanded="true"> - <param name="write_mztab" type="boolean" checked="false" - label="Write mztab file?" - truevalue="--write_mztab" falsevalue="" /> + <param name="dry_run" type="boolean" checked="false" + label="Only create config files? (i.e. for testing)" + truevalue="True" falsevalue="" /> <param type="select" name="output" label="Select the desired outputs." multiple="true" optional="false"> - <expand macro="output_option" name="proteinGroups" label="Protein Groups"/> - <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/> - <expand macro="output_option" name="peptides" label="Peptides"/> - <expand macro="output_option" name="evidence" label="Evidence"/> - <expand macro="output_option" name="parameters" label="Tabular Paramters"/> - <expand macro="output_option" name="msms" label="MSMS"/> - <expand macro="output_option" name="mzTab" label="mzTab"/> - <expand macro="output_option" name="allPeptides" label="all peptides"/> - <expand macro="output_option" name="libraryMatch" label="library match"/> - <expand macro="output_option" name="matchedFeatures" label="matched features"/> - <expand macro="output_option" name="modificationSpecificPeptides" label="modification specific peptides"/> - <expand macro="output_option" name="ms3Scans" label="ms3 scans"/> - <expand macro="output_option" name="msmsScans" label="msms scans"/> - <expand macro="output_option" name="mzRange" label="mz range"/> - <expand macro="output_option" name="peptideSection" label="peptide section"/> - <expand macro="output_option" name="summary" label="summary"/> - <expand macro="output_option" name="output_all" label="complete 'combined/txt/' directory (compressed)"/> - <expand macro="output_option" name="log" label="MaxQuant log"/> + <option value="proteinGroups">Protein Groups</option> + <option value="mqpar">mqpar.xml</option> + <option value="peptides">Peptides</option> + <option value="evidence">Evidence</option> + <option value="parameters">Tabular Paramters</option> + <option value="msms">MSMS</option> + <option value="mzTab">mzTab</option> + <option value="allPeptides">all peptides</option> + <option value="libraryMatch">library match</option> + <option value="matchedFeatures">matched features</option> + <option value="modificationSpecificPeptides">modification specific peptides</option> + <option value="ms3Scans">ms3 scans</option> + <option value="msmsScans">msms scans</option> + <option value="mzRange">mz range</option> + <option value="peptideSection">peptide section</option> + <option value="summary">summary</option> + <option value="output_all">complete 'combined/txt/' directory (compressed)</option> + <option value="log">MaxQuant and PTXQC log</option> + <option value="config">yaml config file</option> </param> </section> </inputs> - - <outputs> - <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/> - <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/> - <expand macro="output" name="peptides" label="MaxQuant Peptides"/> - <expand macro="output" name="evidence" label="MaxQuant Evidence"/> - <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/> - <expand macro="output" name="msms" label="MaxQuant MSMS"/> - <expand macro="output" name="mzTab" label="mzTab"/> - <expand macro="output" name="allPeptides" label="all peptides"/> - <expand macro="output" name="libraryMatch" label="library match"/> - <expand macro="output" name="matchedFeatures" label="matched features"/> - <expand macro="output" name="modificationSpecificPeptides" label="modification specific peptides"/> - <expand macro="output" name="ms3Scans" label="ms3 scans"/> - <expand macro="output" name="msmsScans" label="msms Scans"/> - <expand macro="output" name="mzRange" label="mz range"/> - <expand macro="output" name="peptideSection" label="peptide section"/> - <expand macro="output" name="summary" label="MaxQuant summary"/> - <expand macro="output" format="tar" name="output_all" label="'combined/txt/' directory"/> - <expand macro="output" name="log" format="txt" label="log"/> - </outputs> + + <expand macro="outputs"/> <tests> - <test> - <param name="select" value="mzxml_files" /> - <param name="mzxml_files" value="BSA_min_23.mzXML" /> + <!-- functional test with small mzXML file, no quantitation methods --> + <test expect_num_outputs="15"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_23.mzXML"/> + <param name="maxMissedCleavages" value="1"/> + <param name="fixedModifications" value="Carbamidomethyl (C)" /> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="enzymes" value="Trypsin/P" /> + </repeat> + <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" /> + <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/> + <output name="evidence" file="01/combined/txt/evidence.txt" /> + <output name="msms" file="01/combined/txt/msms.txt" /> + <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="4"/> + <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="4"/> + <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/> + <output name="mzRange" file="01/combined/txt/mzRange.txt" /> + <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/> + <output name="peptides" file="01/combined/txt/peptides.txt" /> + <output name="peptideSection" file="01/combined/txt/peptideSection.txt" /> + <output name="proteinGroups" file="01/combined/txt/proteinGroups.txt" /> + <output name="summary" file="01/combined/txt/summary.txt" /> + <output name="modificationSpecificPeptides" file="01/combined/txt/modificationSpecificPeptides.txt" /> + <output name="config" file="01/config.yml" lines_diff="2"/> + </test> + <!-- reporter ion ms2 + multiple param groups, testing yaml conf file and mqpar.xml only --> + <test expect_num_outputs="3"> + <param name="ftype" value=".mzxml" /> <param name="fasta_files" value="bsa.fasta" /> <param name="identifier_parse_rule" value=">([^\s]*)" /> <param name="description_parse_rule" value=">(.*)" /> - <param name="min_unique_pep" value="0" /> - <param name="fixed_mods" value="Carbamidomethyl (C)" /> - <param name="var_mods" value="Oxidation (M)" /> - <param name="proteases" value="Trypsin/P" /> - <param name="write_mztab" value="true" /> - <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" /> - <output name="evidence" file="single/combined/txt/evidence.txt" /> - <output name="msms" file="single/combined/txt/msms.txt" /> - <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/> - <output name="allPeptides" file="single/combined/txt/allPeptides.txt" /> - <output name="msmsScans" file="single/combined/txt/msmsScans.txt" /> - <output name="mzRange" file="single/combined/txt/mzRange.txt" /> - <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/> - <output name="peptides" file="single/combined/txt/peptides.txt" /> - <output name="peptideSection" file="single/combined/txt/peptideSection.txt" /> - <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" /> - <output name="summary" file="single/combined/txt/summary.txt" /> - <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_23.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="custom" /> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys126" /> + <param name="terminallabel" value="TMT2plex-Nter126" /> + <param name="tmtlike" value="True" /> + <param name="cp1" value="6.7" /> + <param name="cp2" value="3" /> + </repeat> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys127" /> + <param name="terminallabel" value="TMT2plex-Nter127" /> + <param name="tmtlike" value="True" /> + </repeat> + </conditional> + </conditional> + </repeat> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_22"/> + <param name="variableModifications" value="" /> + <param name="fixedModifications" value="" /> + <param name="enzymes" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms2" /> + <conditional name="iso_labels"> + <param name="labeling" value="itraq4plex" /> + </conditional> + </conditional> + </repeat> + <param name="dry_run" value="True" /> + <param name="output" value="config,mqpar,mzTab" /> + <output name="config" file="02/config.yml" lines_diff="2" /> + <!-- high difference due to unconsistant xml formatting in MQ --> + <output name="mqpar" file="02/mqpar.xml" lines_diff="24" /> + </test> + <!-- lfq, testing yaml conf file and mqpar.xml only --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="min_unique_pep" value="1" /> + <param name="ibaq" value="True" /> + <param name="ibaqLogFit" value="False" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_22"/> + <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="dry_run" value="True" /> + <param name="output" value="config,mqpar" /> + <output name="config" file="03/config.yml" lines_diff="2" /> + <output name="mqpar" file="03/mqpar.xml" lines_diff="10" /> + </test> + <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <param name="template" value="04/exp_design" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_23.mzXML,BSA_min_22"/> + <param name="fixedModifications" value="Carbamidomethyl (C)" /> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="enzymes" value="Trypsin/P" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="silac" /> + <param name="light_labels" value="Arg6,Lys4" /> + <param name="heavy_labels" value="Arg10,DimethLys8" /> + </conditional> + </repeat> + <param name="dry_run" value="True" /> + <param name="output" value="config,mqpar" /> + <output name="config" file="04/config.yml" lines_diff="2" /> + <output name="mqpar" file="04/mqpar.xml" lines_diff="12" /> </test> </tests> @@ -307,8 +543,9 @@ **Input files** -- Thermo raw file or mzXML file - - 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) +- Thermo raw files or mzXML files (in parameter group section): + - The datatype of all files has to be either 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) +- Fasta files: specify parse rules accordingly, default rules are compatible with uniprot - Optional files: - 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: @@ -340,37 +577,11 @@ - label based: - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections - label-free + - reporter ion ms2: either use the pre-defined labelings with correction factors set to 0 or specify a custom labeling **Output files** -Different output file options are available, most of them are part of the MaxQuant txt directory. +Different output file options are available, most of them are part of the MaxQuant txt directory. If ptxqc report ist selected, a quality control report will be created. ]]></help> - <citations> - <citation type="bibtex"> - @article{cox2008maxquant, - title={MaxQuant enables high peptide identification rates, individualized - ppb-range mass accuracies and proteome-wide protein quantification}, - author={Cox, J{\"u}rgen and Mann, Matthias}, - journal={Nature biotechnology}, - volume={26}, - number={12}, - pages={1367}, - year={2008}, - publisher={Nature Publishing Group} - } - </citation> - <citation type="bibtex"> - @article{tyanova2016maxquant, - title={The MaxQuant computational platform for mass - spectrometry-based shotgun proteomics}, - author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen}, - journal={Nature protocols}, - volume={11}, - number={12}, - pages={2301}, - year={2016}, - publisher={Nature Publishing Group} - } - </citation> - </citations> + <expand macro="citations"/> </tool>
--- a/mqparam.py Thu Aug 15 08:09:00 2019 -0400 +++ b/mqparam.py Sat Apr 11 11:49:19 2020 -0400 @@ -1,113 +1,174 @@ """ Create a project-specific MaxQuant parameter file. - -TODO: check validity of parsed experimental design template - add support for parameter groups - add reporter ion MS2 - add label free quantification - don't hardcode parse rules for fasta files - -Author: Damian Glaetzer <d.glaetzer@mailbox.org> """ +import copy import ntpath import os import re +import yaml import xml.etree.ElementTree as ET from itertools import zip_longest from xml.dom import minidom +def et_add_child(el, name, text, attrib=None): + "Add a child element to an xml.etree.ElementTree.Element" + child = ET.SubElement(el, name, attrib=attrib if attrib else {}) + child.text = str(text) + return child + + +class ParamGroup: + """Represents one parameter Group + """ + + def __init__(self, root): + """Initialize with its xml.etree.ElementTree root Element. + """ + self._root = copy.deepcopy(root) + + def set_list_param(self, key, vals): + """Set a list parameter. + """ + node = self._root.find(key) + if node is None: + raise ValueError('Element {} not found in parameter file' + .format(key)) + node.clear() + node.tag = key + for e in vals: + et_add_child(node, name='string', text=e) + + def set_simple_param(self, key, value): + """Set a simple parameter. + """ + node = self._root.find(key) + if node is None: + raise ValueError('Element {} not found in parameter file' + .format(key)) + node.text = str(value) + + def set_silac(self, light_labels, medium_labels, heavy_labels): + """Set label modifications. + """ + if medium_labels and not (heavy_labels or light_labels): # medium omly with heavy and light + raise Exception("Incorrect SILAC specification. Use medium only together with light and heavy labels.") + multiplicity = 3 if medium_labels else 2 if heavy_labels else 1 + max_label = str(max(len(light_labels) if light_labels else 0, + len(medium_labels) if medium_labels else 0, + len(heavy_labels) if heavy_labels else 0)) + self._root.find('multiplicity').text = str(multiplicity) + self._root.find('maxLabeledAa').text = max_label + node = self._root.find('labelMods') + node[0].text = ';'.join(light_labels) if light_labels else '' + if multiplicity == 3: + et_add_child(node, name='string', text=';'.join(medium_labels)) + if multiplicity > 1: + et_add_child(node, name='string', + text=';'.join(heavy_labels) if heavy_labels else '') + + def set_isobaric_label(self, internalLabel, terminalLabel, + cm2, cm1, cp1, cp2, tmtLike): + """Add isobaric label info. + Args: + internalLabel: string + terminalLabel: string + cm2: (float) correction factor + cm1: (float) correction factor + cp1: (float) correction factor + cp2: (float) correction factor + tmtLike: bool or string + Returns: + None + """ + iso_labels_node = self._root.find('isobaricLabels') + label = et_add_child(iso_labels_node, 'IsobaricLabelInfo', '') + et_add_child(label, 'internalLabel', internalLabel) + et_add_child(label, 'terminalLabel', terminalLabel) + for num, factor in (('M2', cm2), ('M1', cm1), ('P1', cp1), ('P2', cp2)): + et_add_child(label, 'correctionFactor' + num, + str(float(factor) if factor % 1 else int(factor))) + et_add_child(label, 'tmtLike', str(tmtLike)) + + class MQParam: """Represents a mqpar.xml and provides methods to modify some of its parameters. """ - fasta_template = """<FastaFileInfo> - <fastaFilePath></fastaFilePath> - <identifierParseRule></identifierParseRule> - <descriptionParseRule></descriptionParseRule> - <taxonomyParseRule></taxonomyParseRule> - <variationParseRule></variationParseRule> - <modificationParseRule></modificationParseRule> - <taxonomyId></taxonomyId> - </FastaFileInfo>""" - - def __init__(self, mqpar_out, mqpar_in, exp_design, - substitution_rx=r'[^\s\S]'): # no sub by default + def __init__(self, mqpar_in, exp_design=None, yaml=None, substitution_rx=r'[^\s\S]'): # no sub by default """Initialize MQParam class. mqpar_in can either be a template or a already suitable mqpar file. - >>> t = MQParam("test", './test-data/template.xml', None) - >>> t.root.tag - 'MaxQuantParams' - >>> (t.root.find('maxQuantVersion')).text - '1.6.3.4' + Args: + mqpar_in: a template parameter file + exp_design: a experimental design template (see MaxQuant documentation), + can be None + substitution_rx: a regular expression for replacements in the file names. + It is applied before comparing input file names (e.g. from the exp. design) """ - self.orig_mqpar = mqpar_in self.exp_design = exp_design - self.mqpar_out = mqpar_out - self.root = ET.parse(mqpar_in).getroot() - self.version = self.root.find('maxQuantVersion').text + self._root = ET.parse(mqpar_in).getroot() + self.version = self._root.find('maxQuantVersion').text # regex for substitution of certain file name characters self.substitution_rx = substitution_rx - - @staticmethod - def _add_child(el, name, text, attrib=None): - """Add a child element to an element. + self.pg_node = copy.deepcopy(self._root.find('parameterGroups')[0]) + self._paramGroups = [] + self.fasta_file_node = copy.deepcopy(self._root.find('fastaFiles')[0]) + if yaml: + self._from_yaml(yaml) - >>> t = MQParam("test", './test-data/template.xml', None) - >>> MQParam._add_child(t.root, "test", "test") - >>> t.root.find('test').text == "test" - True + def __getitem__(self, index): + """Return paramGroup if indexed with integer, else try to find + matching Element in XML root and return its text or None. """ - - child = ET.SubElement(el, name, attrib=attrib if attrib else {}) - child.text = str(text) + try: + return self._paramGroups[index] + except TypeError: + ret = self._root.find(index) + return ret.text if ret is not None else None @staticmethod def _check_validity(design, len_infiles): - "Perform some checks on the exp. design template" + """Perform some checks on the exp. design template""" design_len = len(design['Name']) + # 'Name' can be None, we need at least len_infiles valid entries match = len(list(filter(lambda x: bool(x), design['Name']))) if match < len_infiles: - raise Exception("Error parsing experimental design template: " + - "Found only {} matching entries ".format(design_len) + - "for {} input files".format(len_infiles)) + raise Exception(' '.join(["Error parsing experimental design template:", + "Found only {} matching entries".format(match), + "for {} input files".format(len_infiles)])) for i in range(0, design_len): - msg = "Error in line " + str(i + 2) + " of experimental design: " - if not (design['Name'][i] and design['Experiment'][i]): - raise Exception(msg + " Name or Experiment is empty.") + msg = "(in line " + str(i + 2) + " of experimental design) " + if not design['Experiment'][i]: + raise ValueError(msg + " Experiment is empty.") if design['PTM'][i].lower() not in ('true', 'false'): - raise Exception(msg + "Defines invalid PTM value, " + - "should be 'True' or 'False'.") + raise ValueError(msg + "Defines invalid PTM value, should be 'True' or 'False'.") try: int(design['Fraction'][i]) except ValueError as e: - raise Exception(msg + str(e)) + raise ValueError(msg + str(e)) - def _make_exp_design(self, infiles): - """Create a dict representing an experimental design from - an experimental design template and a list of input files. + def _make_exp_design(self, groups, files): + """Create a dict representing an experimental design from an + experimental design template and a list input files. If the experimental design template is None, create a default - design with one experiment for each input file, no fractions and - parameter group 0 for all files. - >>> t2 = MQParam("test", './test-data/template.xml', \ - './test-data/two/exp_design_template.txt') - >>> design = t2._make_exp_design(['./test-data/BSA_min_21.mzXML', \ - './test-data/BSA_min_22.mzXML']) - >>> design['Name'] - ['./test-data/BSA_min_21.mzXML', './test-data/BSA_min_22.mzXML'] - >>> design['Fraction'] - ['1', '2'] + design with one experiment for each input file and no fractions + for all files. + Args: + files: list of input file paths + groups: list of parameter group indices + Returns: + dict: The (complete) experimental design template """ - - design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")} + design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment", "paramGroup")} if not self.exp_design: - design["Name"] = infiles - design["Fraction"] = ('32767',) * len(infiles) - design["Experiment"] = [os.path.split(f)[1] for f in infiles] - design["PTM"] = ('False',) * len(infiles) + design["Name"] = files + design["Fraction"] = ('32767',) * len(files) + design["Experiment"] = [os.path.split(f)[1] for f in files] + design["PTM"] = ('False',) * len(files) + design["paramGroup"] = groups else: with open(self.exp_design) as design_file: index_line = design_file.readline().strip() @@ -116,25 +177,22 @@ if i in design: index.append(i) else: - raise Exception("Invalid column index in experimental" - + " design template: {}".format(i)) - + raise Exception("Invalid column index in experimental design template: {}".format(i)) for line in design_file: row = line.strip().split('\t') for e, i in zip_longest(row, index): - if i == "Fraction" and e == '': - e = 32767 + if i == "Fraction" and not e: + e = '32767' elif i == "PTM" and not e: e = 'False' design[i].append(e) - - # map infiles to names in exp. design template + # map files to names in exp. design template names = [] names_to_paths = {} # strip path and extension - for f in infiles: + for f in files: b = os.path.basename(f) - basename = b[:-6] if b.endswith('.mzXML') else b[:-11] + basename = b[:-11] if b.lower().endswith('.thermo.raw') else b.rsplit('.', maxsplit=1)[0] names_to_paths[basename] = f for name in design['Name']: # same substitution as in maxquant.xml, @@ -144,236 +202,157 @@ else None) # replace orig. file names with matching links to galaxy datasets design['Name'] = names - MQParam._check_validity(design, len(infiles)) - + design['paramGroup'] = groups + MQParam._check_validity(design, len(files)) return design - def add_infiles(self, infiles, interactive): + def add_infiles(self, infiles): """Add a list of raw/mzxml files to the mqpar.xml. If experimental design template was specified, modify other parameters accordingly. The files must be specified as absolute paths for maxquant to find them. - >>> t1 = MQParam("test", './test-data/template.xml', None) - >>> t1.add_infiles(('test1', ), True) - >>> t1.root.find("filePaths")[0].text - 'test1' - >>> t1.root.find("fractions")[0].text - '32767' - >>> len(t1.root.find("fractions")) - 1 - >>> t2 = MQParam("test", './test-data/template.xml', \ - './test-data/exp_design_test.txt') - >>> t2.add_infiles(('test-data/QEplus021874.thermo.raw', \ - 'test-data/QEplus021876.thermo.raw'), True) - >>> len(t2.root.find("filePaths")) - 2 - >>> t2.root.find("filePaths")[1].text - 'test-data/QEplus021876.thermo.raw' - >>> t2.root.find("experiments")[1].text - '2' - >>> t2.root.find("fractions")[0].text - '3' + Also add parameter Groups. + Args: + infiles: a list of infile lists. first dimension denotes the + parameter group. + Returns: + None """ - - # Create experimental design for interactive mode. - # In non-interactive mode only filepaths are modified, but - # their order from the original mqpar must be kept. - if interactive: - index = range(len(infiles)) - nodenames = ('filePaths', 'experiments', 'fractions', - 'ptms', 'paramGroupIndices', 'referenceChannel') - design = self._make_exp_design(infiles) - else: - index = [-1] * len(infiles) - # kind of a BUG: fails if filename starts with '.' - infilenames = [os.path.basename(f).split('.')[0] for f in infiles] - i = 0 - for child in self.root.find('filePaths'): - # either windows or posix path - win = ntpath.basename(child.text) - posix = os.path.basename(child.text) - basename = win if len(win) < len(posix) else posix - basename_with_sub = re.sub(self.substitution_rx, '_', - basename.split('.')[0]) - # match infiles to their names in mqpar.xml, - # ignore files missing in mqpar.xml - if basename_with_sub in infilenames: - index[i] = infilenames.index(basename_with_sub) - i += 1 - else: - raise ValueError("no matching infile found for " - + child.text) - - nodenames = ('filePaths', ) - design = {'Name': infiles} - + groups, files = zip(*[(num, f) for num, l in enumerate(infiles) for f in l]) + self._paramGroups = [ParamGroup(self.pg_node) for i in range(len(infiles))] + nodenames = ('filePaths', 'experiments', 'fractions', + 'ptms', 'paramGroupIndices', 'referenceChannel') + design = self._make_exp_design(groups, files) # Get parent nodes from document nodes = dict() for nodename in nodenames: - node = self.root.find(nodename) + node = self._root.find(nodename) if node is None: raise ValueError('Element {} not found in parameter file' .format(nodename)) nodes[nodename] = node node.clear() node.tag = nodename + # Append sub-elements to nodes (one per file) + for i, name in enumerate(design['Name']): + if name: + et_add_child(nodes['filePaths'], 'string', name) + et_add_child(nodes['experiments'], 'string', + design['Experiment'][i]) + et_add_child(nodes['fractions'], 'short', + design['Fraction'][i]) + et_add_child(nodes['ptms'], 'boolean', + design['PTM'][i]) + et_add_child(nodes['paramGroupIndices'], 'int', + design['paramGroup'][i]) + et_add_child(nodes['referenceChannel'], 'string', '') - # Append sub-elements to nodes (one per file) - for i in index: - if i > -1 and design['Name'][i]: - MQParam._add_child(nodes['filePaths'], 'string', - design['Name'][i]) - if interactive: - MQParam._add_child(nodes['experiments'], 'string', - design['Experiment'][i]) - MQParam._add_child(nodes['fractions'], 'short', - design['Fraction'][i]) - MQParam._add_child(nodes['ptms'], 'boolean', - design['PTM'][i]) - MQParam._add_child(nodes['paramGroupIndices'], 'int', 0) - MQParam._add_child(nodes['referenceChannel'], 'string', '') + def translate(self, infiles): + """Map a list of given infiles to the files specified in the parameter file. + Needed for the mqpar upload in galaxy. Removes the path and then tries + to match the files. + Args: + infiles: list or tuple of the input + Returns: + None + """ + # kind of a BUG: fails if filename starts with '.' + infilenames = [os.path.basename(f).split('.')[0] for f in infiles] + filesNode = self._root.find('filePaths') + files_from_mqpar = [e.text for e in filesNode] + filesNode.clear() + filesNode.tag = 'filePaths' + for f in files_from_mqpar: + # either windows or posix path + win = ntpath.basename(f) + posix = os.path.basename(f) + basename = win if len(win) < len(posix) else posix + basename_with_sub = re.sub(self.substitution_rx, '_', + basename.split('.')[0]) + # match infiles to their names in mqpar.xml, + # ignore files missing in mqpar.xml + if basename_with_sub in infilenames: + i = infilenames.index(basename_with_sub) + et_add_child(filesNode, 'string', infiles[i]) + else: + raise ValueError("no matching infile found for " + f) - def add_fasta_files(self, files, - identifier=r'>([^\s]*)', - description=r'>(.*)'): + def add_fasta_files(self, files, parse_rules={}): """Add fasta file groups. - >>> t = MQParam('test', './test-data/template.xml', None) - >>> t.add_fasta_files(('test1', 'test2')) - >>> len(t.root.find('fastaFiles')) - 2 - >>> t.root.find('fastaFiles')[0].find("fastaFilePath").text - 'test1' + Args: + files: (list) of fasta file paths + parseRules: (dict) the parse rules as (tag, text)-pairs + Returns: + None """ - fasta_node = self.root.find("fastaFiles") + fasta_node = self._root.find('fastaFiles') fasta_node.clear() - fasta_node.tag = "fastaFiles" - - for index in range(len(files)): - filepath = '<fastaFilePath>' + files[index] - identifier = identifier.replace('<', '<') - description = description.replace('<', '<') - fasta = self.fasta_template.replace('<fastaFilePath>', filepath) - fasta = fasta.replace('<identifierParseRule>', - '<identifierParseRule>' + identifier) - fasta = fasta.replace('<descriptionParseRule>', - '<descriptionParseRule>' + description) - ff_node = self.root.find('.fastaFiles') - fastaentry = ET.fromstring(fasta) - ff_node.append(fastaentry) + for f in files: + fasta_node.append(copy.deepcopy(self.fasta_file_node)) + fasta_node[-1].find('fastaFilePath').text = f + for rule in parse_rules: + fasta_node[-1].find(rule).text = parse_rules[rule] def set_simple_param(self, key, value): """Set a simple parameter. - >>> t = MQParam(None, './test-data/template.xml', None) - >>> t.set_simple_param('min_unique_pep', 4) - >>> t.root.find('.minUniquePeptides').text - '4' + Args: + key: (string) XML tag of the parameter + value: the text of the parameter XML node + Returns: + None """ - # map simple params to their node in the xml tree - simple_params = {'missed_cleavages': - '.parameterGroups/parameterGroup/maxMissedCleavages', - 'min_unique_pep': '.minUniquePeptides', - 'num_threads': 'numThreads', - 'calc_peak_properties': '.calcPeakProperties', - 'write_mztab': 'writeMzTab', - 'min_peptide_len': 'minPepLen', - 'max_peptide_mass': 'maxPeptideMass', - 'match_between_runs': 'matchBetweenRuns', - 'ibaq': 'ibaq', # lfq global options - 'ibaq_log_fit': 'ibaqLogFit', - 'separate_lfq': 'separateLfq', - 'lfq_stabilize_large_ratios': - 'lfqStabilizeLargeRatios', - 'lfq_require_msms': 'lfqRequireMsms', - 'advanced_site_intensities': - 'advancedSiteIntensities', - 'lfq_mode': # lfq param group options - '.parameterGroups/parameterGroup/lfqMode', - 'lfq_skip_norm': - '.parameterGroups/parameterGroup/lfqSkipNorm', - 'lfq_min_edges_per_node': - '.parameterGroups/parameterGroup/lfqMinEdgesPerNode', - 'lfq_avg_edges_per_node': - '.parameterGroups/parameterGroup/lfqAvEdgesPerNode', - 'lfq_min_ratio_count': - '.parameterGroups/parameterGroup/lfqMinRatioCount'} - - if key in simple_params: - node = self.root.find(simple_params[key]) - if node is None: - raise ValueError('Element {} not found in parameter file' - .format(simple_params[key])) - node.text = str(value) - else: - raise ValueError("Parameter not found.") + node = self._root.find(key) + if node is None: + raise ValueError('Element {} not found in parameter file' + .format(key)) + node.text = str(value) - def set_silac(self, light_mods, medium_mods, heavy_mods): - """Set label modifications. - >>> t1 = MQParam('test', './test-data/template.xml', None) - >>> t1.set_silac(None, ('test1', 'test2'), None) - >>> t1.root.find('.parameterGroups/parameterGroup/maxLabeledAa').text - '2' - >>> t1.root.find('.parameterGroups/parameterGroup/multiplicity').text - '3' - >>> t1.root.find('.parameterGroups/parameterGroup/labelMods')[1].text - 'test1;test2' - >>> t1.root.find('.parameterGroups/parameterGroup/labelMods')[2].text - '' + def _from_yaml(self, conf): + """Read a yaml config file. + Args: + conf: (string) path to the yaml conf file + Returns: + None """ - multiplicity = 3 if medium_mods else 2 if heavy_mods else 1 - max_label = str(max(len(light_mods) if light_mods else 0, - len(medium_mods) if medium_mods else 0, - len(heavy_mods) if heavy_mods else 0)) - multiplicity_node = self.root.find('.parameterGroups/parameterGroup/' - + 'multiplicity') - multiplicity_node.text = str(multiplicity) - max_label_node = self.root.find('.parameterGroups/parameterGroup/' - + 'maxLabeledAa') - max_label_node.text = max_label - - node = self.root.find('.parameterGroups/parameterGroup/labelMods') - node[0].text = ';'.join(light_mods) if light_mods else '' - if multiplicity == 3: - MQParam._add_child(node, name='string', text=';'.join(medium_mods)) - if multiplicity > 1: - MQParam._add_child(node, name='string', - text=';'.join(heavy_mods) if heavy_mods else '') + with open(conf) as f: + conf_dict = yaml.safe_load(f.read()) + paramGroups = conf_dict.pop('paramGroups') + self.add_infiles([pg.pop('files') for pg in paramGroups]) + for i, pg in enumerate(paramGroups): + silac = pg.pop('labelMods', False) + if silac: + self[i].set_silac(*silac) + isobaricLabels = pg.pop('isobaricLabels', False) + if isobaricLabels: + for l in isobaricLabels: + self[i].set_isobaric_label(*l) + for el in ['fixedModifications', 'variableModifications', 'enzymes']: + lst = pg.pop(el, None) + if lst is not None: + self[i].set_list_param(el, lst) + for key in pg: + self[i].set_simple_param(key, pg[key]) + fastafiles = conf_dict.pop('fastaFiles', False) + if fastafiles: + self.add_fasta_files(fastafiles, parse_rules=conf_dict.pop('parseRules', {})) + else: + raise Exception('No fasta files provided.') + for key in conf_dict: + self.set_simple_param(key, conf_dict[key]) - def set_list_params(self, key, vals): - """Set a list parameter. - >>> t = MQParam(None, './test-data/template.xml', None) - >>> t.set_list_params('proteases', ('test 1', 'test 2')) - >>> len(t.root.find('.parameterGroups/parameterGroup/enzymes')) - 2 - >>> t.set_list_params('var_mods', ('Oxidation (M)', )) - >>> var_mods = '.parameterGroups/parameterGroup/variableModifications' - >>> t.root.find(var_mods)[0].text - 'Oxidation (M)' + def write(self, mqpar_out): + """Write pretty formatted xml parameter file. + Compose it from global parameters and parameter Groups. """ - - params = {'var_mods': - '.parameterGroups/parameterGroup/variableModifications', - 'fixed_mods': - '.parameterGroups/parameterGroup/fixedModifications', - 'proteases': - '.parameterGroups/parameterGroup/enzymes'} - - if key in params: - node = self.root.find(params[key]) - if node is None: - raise ValueError('Element {} not found in parameter file' - .format(params[key])) - node.clear() - node.tag = params[key].split('/')[-1] - for e in vals: - MQParam._add_child(node, name='string', text=e) - else: - raise ValueError("Parameter {} not found.".format(key)) - - def write(self): - rough_string = ET.tostring(self.root, 'utf-8', short_empty_elements=False) + if self._paramGroups: + pg_node = self._root.find('parameterGroups') + pg_node.remove(pg_node[0]) + for group in self._paramGroups: + pg_node.append(group._root) + rough_string = ET.tostring(self._root, 'utf-8', short_empty_elements=False) reparsed = minidom.parseString(rough_string) pretty = reparsed.toprettyxml(indent="\t") even_prettier = re.sub(r"\n\s+\n", r"\n", pretty) - with open(self.mqpar_out, 'w') as f: + with open(mqpar_out, 'w') as f: print(even_prettier, file=f)
--- a/mqwrapper.py Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -""" -Run MaxQuant on a modified mqpar.xml. -Use maxquant conda package. -TODO: add support for parameter groups - -Authors: Damian Glaetzer <d.glaetzer@mailbox.org> - -based on the maxquant galaxy tool by John Chilton: -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant -""" - -import argparse -import os -import shutil -import subprocess - -import mqparam - -# build parser -parser = argparse.ArgumentParser() - -# input, special outputs and others -other_args = ('raw_files', 'mzxml_files', 'fasta_files', - 'description_parse_rule', 'identifier_parse_rule', - 'exp_design', 'output_all', - 'mqpar_out', 'infile_names', 'mzTab', - 'version', 'substitution_rx') - -# txt result files -txt_output = ('evidence', 'msms', 'parameters', - 'peptides', 'proteinGroups', 'allPeptides', - 'libraryMatch', 'matchedFeatures', - 'modificationSpecificPeptides', 'ms3Scans', - 'msmsScans', 'mzRange', 'peptideSection', - 'summary') - -# arguments for mqparam -# global -global_flags = ('calc_peak_properties', - 'write_mztab', - 'ibaq', - 'ibaq_log_fit', - 'separate_lfq', - 'lfq_stabilize_large_ratios', - 'lfq_require_msms', - 'advanced_site_intensities', - 'match_between_runs') - -global_simple_args = ('min_unique_pep', - 'num_threads', - 'min_peptide_len', - 'max_peptide_mass') - -# parameter group specific -param_group_flags = ('lfq_skip_norm',) - -param_group_simple_args = ('missed_cleavages', - 'lfq_mode', - 'lfq_min_edges_per_node', - 'lfq_avg_edges_per_node', - 'lfq_min_ratio_count') - -param_group_silac_args = ('light_mods', 'medium_mods', 'heavy_mods') - -list_args = ('fixed_mods', 'var_mods', 'proteases') - -arguments = ['--' + el for el in (txt_output - + global_simple_args - + param_group_simple_args - + list_args - + param_group_silac_args - + other_args)] - -flags = ['--' + el for el in global_flags + param_group_flags] - -for arg in arguments: - parser.add_argument(arg) -for flag in flags: - parser.add_argument(flag, action="store_true") - -args = vars(parser.parse_args()) - -# link infile datasets to names with correct extension -# for maxquant to accept them -files = (args['raw_files'] if args['raw_files'] - else args['mzxml_files']).split(',') -ftype = ".thermo.raw" if args['raw_files'] else ".mzXML" -filenames = args['infile_names'].split(',') -fnames_with_ext = [(a if a.endswith(ftype) - else os.path.splitext(a)[0] + ftype) - for a in filenames] - -for f, l in zip(files, fnames_with_ext): - os.symlink(f, l) - -# build mqpar.xml -mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml') -subprocess.run(('maxquant', '-c', mqpar_in)) -mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in - - -exp_design = args['exp_design'] if args['exp_design'] != 'None' else None -m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design, - substitution_rx=args['substitution_rx']) -if m.version != args['version']: - raise Exception('mqpar version is ' + m.version + - '. Tool uses version {}.'.format(args['version'])) - -# modify parameters, interactive mode if no mqpar_in was specified -m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], True) -m.add_fasta_files(args['fasta_files'].split(','), - identifier=args['identifier_parse_rule'], - description=args['description_parse_rule']) - -for e in (global_simple_args - + param_group_simple_args - + global_flags - + param_group_flags): - if args[e]: - m.set_simple_param(e, args[e]) - -for e in list_args: - if args[e]: - m.set_list_params(e, args[e].split(',')) - -if args['light_mods'] or args['medium_mods'] or args['heavy_mods']: - m.set_silac(args['light_mods'].split(',') if args['light_mods'] else None, - args['medium_mods'].split(',') if args['medium_mods'] else None, - args['heavy_mods'].split(',') if args['heavy_mods'] else None) - -m.write() - -# build and run MaxQuant command -cmd = ['maxquant', mqpar_out] - -subprocess.run(cmd, check=True, cwd='./') - -# copy results to galaxy database -for el in txt_output: - destination = args[el] - source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el)) - if destination != 'None' and os.path.isfile(source): - shutil.copy(source, destination) - -if args['mzTab'] != 'None': - source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab") - if os.path.isfile(source): - shutil.copy(source, args['mzTab'])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/allPeptides.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,167 @@ +Raw file Type Charge m/z Mass Uncalibrated m/z Resolution Number of data points Number of scans Number of isotopic peaks PIF Mass fractional part Mass deficit Mass precision [ppm] Max intensity m/z 0 Retention time Retention length Retention length (FWHM) Min scan number Max scan number Identified Reverse MS/MS IDs Sequence Length Modifications Modified sequence Proteins Score PEP Intensity Intensities Isotope pattern MS/MS Count MSMS Scan Numbers MSMS Isotope Indices +BSA_min_23 MULTI 3 710.69967 2129.0772 710.69967 NaN 5 3 2 0.0771919 0.0578164096173168 1.08086 711.033930698172 0.0366 8.26 0 1 25 -1 0 0 NaN 27555 0;16823.720703125;10726.12109375;6644.5966796875;0 7737.3974609375;9086.3232421875 0 +BSA_min_23 MULTI 3 1567.4354 4699.2845 1567.4354 NaN 5 3 2 0.284514 0.0828426326752378 7.31572 1568.10387245715 0.0671 8.26 0 1 25 -1 0 0 NaN 137580 0;23479.5932617188;59085.9194335938;20990.259765625;0 0;0;53540.3203125;7305.36279296875 0 +BSA_min_23 MULTI 2 466.26817 930.5218 466.26817 NaN 6 4 2 0.521797 0.0537564853223103 1.35299 466.26850803291 0.107 10.3 0 1 31 -1 0 0 NaN 33499 0;16896.8359375;13251.4482421875;29638.681640625;21903.5859375;0 22962.34375;6676.337890625 0 +BSA_min_23 MULTI 2 835.80692 1669.5993 835.80692 NaN 7 4 2 0.599289 -0.208726257088529 1.09635 835.807035746435 0.107 10.3 0 1 31 -1 0 0 NaN 35250 0;14611.8764648438;18125.6357421875;25099.0166015625;15365.583984375;0 16483.943359375;8615.0732421875 0 +BSA_min_23 MULTI 2 889.42648 1776.8384 889.42648 NaN 6 3 2 0.838398 -0.0189472723534436 2.69649 889.927320499287 0.107 8.26 0 1 25 -1 0 0 NaN 24592 0;9125.99072265625;13286.1201171875;16742.716796875;0 7208.8173828125;9533.8994140625 0 +BSA_min_23 MULTI 2 378.70717 755.39978 378.70717 NaN 4 2 2 0.399783 0.0122990350871532 2.65249 378.7066995797 0.119 6.22 0 13 31 -1 0 0 NaN 17113 0;15764.96875;12169.2568359375;0 9865.826171875;5910.52587890625 0 +BSA_min_23 MULTI 6 456.58136 2733.4445 456.58136 NaN 6 5 2 0.444504 0.14711979940148 1.25056 456.748107866223 0.139 12.6 0 7 43 -1 0 0 NaN 36582 0;9077.5439453125;13902.0874023438;19992.689453125;13010.4306640625;0;0 0;13844.125;6148.564453125 1 8 1 +BSA_min_23 MULTI 2 701.87367 1401.7328 701.87367 NaN 4 2 2 0.732779 0.0479819779827722 1.9101 701.87287295525 0.139 6.22 0 13 31 -1 0 0 NaN 19640 0;11736.2470703125;14934.2939453125;0 8433.541015625;6500.7529296875 0 +BSA_min_23 MULTI 2 903.84665 1805.6788 903.84665 NaN 14 5 3 0.67875 -0.191861895242255 0.538046 903.846381489202 0.128 12.5 0 1 37 -1 0 0 NaN 89876 0;22660.5712890625;48080.4096679688;66770.5043945313;78759.361328125;39740.7744140625;0 39216.41796875;30181.7421875;16944.533203125 1 27 0 +BSA_min_23 MULTI 3 487.53462 1459.582 487.53462 NaN 16 8 3 0.582041 -0.129367074224319 0.600339 487.53461224021 0.133 19 0 1 55 -1 0 0 NaN 84731 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0;5811.33935546875;6557.4794921875;7303.61962890625;9868.7724609375;15106.3935546875;5047.06591796875;0 9868.7724609375;6315.080078125 0 +BSA_min_23 MULTI 2 609.30165 1216.5887 609.30165 NaN 5 3 2 0.588746 -0.010884807340517 3.26112 609.801905531048 0.578 6.09 0 87 99 -1 0 0 NaN 18519 0;6848.39208984375;14504.1098632813;15519.5483398438;0 5654.28662109375;10022.16015625 0 +BSA_min_23 MULTI 2 626.82568 1251.6368 626.82568 NaN 8 5 2 0.636813 0.0210605159502393 0.950782 627.327160354538 0.556 10.1 0 75 99 -1 0 0 NaN 20467 0;7513.7216796875;15837.8994140625;13457.0910644531;10665.5668945313;6652.02783203125;0 7548.9072265625;10244.0595703125 0 +BSA_min_23 MULTI 3 635.60201 1903.7842 635.60201 NaN 11 4 3 0.784211 -0.131529739430107 0.651967 635.601854227925 0.587 8.25 0 81 99 -1 0 0 NaN 109400 0;11539.9194335938;49907.1435546875;64455.1904296875;94715.8671875;0 41372.8828125;37360.796875;15982.1875 1 93 0 +BSA_min_23 MULTI 2 722.29286 1442.5712 722.29286 NaN 11 4 3 0.571176 -0.132406498940327 0.598795 722.794557009268 0.587 8.25 0 81 99 -1 0 0 NaN 88555 0;19382.1572265625;29263.3842773438;56304.751953125;72047.59765625;0 31798.40625;40249.19140625;9051.69140625 2 94;97 0;0 +BSA_min_23 MULTI 2 731.29826 1460.582 731.29826 NaN 9 5 2 0.581963 -0.129905034647663 0.949227 731.799523381077 0.526 10.1 0 75 99 -1 0 0 NaN 29169 0;10700.2763671875;21935.4814453125;17981.1000976563;13056.220703125;17802.30078125;0 11073.208984375;11301.125 1 90 0 +BSA_min_23 MULTI 2 772.82766 1543.6408 772.82766 NaN 5 3 2 0.640772 -0.109302619518758 1.14656 772.827340413045 0.587 6.09 0 87 99 -1 0 0 NaN 33423 0;6804.890625;12703.8696289063;24380.708984375;0 15360.51953125;9020.189453125 0 +BSA_min_23 MULTI 3 776.67069 2326.9902 776.67069 NaN 7 3 3 0.990245 -0.120170237694765 1.89326 777.004331643663 0.571 6.09 0 87 99 -1 0 0 NaN 37194 0;6977.5546875;29906.751953125;25277;0 9063.5791015625;14645.7783203125;12678.326171875 0 +BSA_min_23 MULTI 1 837.43637 836.42909 837.43637 NaN 7 4 2 0.429093 0.0043357496634826 1.1693 837.436103089852 0.587 8.25 0 81 99 -1 0 0 NaN 73009 0;8795.1123046875;28166.4892578125;33590.7690429688;65961.154296875;0 53311.69140625;12649.462890625 0 +BSA_min_23 MULTI 2 882.84611 1763.6777 882.84611 NaN 12 7 3 0.677665 -0.17362702288824 0.463077 882.846072087715 0.563 13.8 0 65 99 -1 0 0 NaN 1179300 0;10685.890625;57645.44140625;185231.5625;292455.5625;750275.78125;1040647.75;871335.640625;0 494015.65625;379948.71875;166683.375 1 100 0 +BSA_min_23 MULTI 2 886.81224 1771.6099 886.81224 NaN 8 5 2 0.609919 -0.245021216350096 1.46251 887.31412154531 0.576 10.1 0 75 99 -1 0 0 NaN 29012 0;5249.1533203125;6298.3564453125;13226.2900390625;17856.4375;20045.5546875;0 8890.65234375;11784.896484375 0 +BSA_min_23 MULTI 1 899.44874 898.44146 899.44874 NaN 10 6 2 0.441463 -0.0118196933137824 0.501834 899.44868329937 0.563 11.9 0 71 99 -1 0 0 NaN 93356 0;10259.021484375;11104.9755859375;38988.1611328125;51494.2109375;83477.83203125;72926.943359375;0 61125.3359375;22352.49609375 0 +BSA_min_23 MULTI 2 973.90466 1945.7948 973.90466 NaN 7 4 2 0.794757 -0.14030840214582 1.22045 973.904958275679 0.587 8.25 0 81 99 -1 0 0 NaN 67032 0;22343.408203125;30602.4375;39709.193359375;30783.283203125;0 30783.283203125;12774.3359375 0 +BSA_min_23 MULTI 1 1012.4647 1011.4574 1012.4647 NaN 10 6 2 0.457396 -0.0478741148867812 0.638009 1012.46465963589 0.58 11.9 0 71 99 -1 0 0 NaN 45315 0;6566.83447265625;5892.9794921875;22179.6865234375;26302.4379882813;35693.482421875;39795.4755859375;0 31461.541015625;12683.193359375 0 +BSA_min_23 MULTI 2 1044.9323 2087.8501 1044.9323 NaN 6 4 2 0.850137 -0.150273671131799 1.9368 1045.43259299012 0.587 8.25 0 81 99 -1 0 0 NaN 22292 0;6181.01806640625;6017.2158203125;11961.13671875;13880.3842773438;0 6740.865234375;7139.51904296875 0 +BSA_min_23 MULTI 1 1164.5167 1163.5094 1164.5167 NaN 6 4 2 0.50944 -0.065774688654983 0.737118 1164.51651446826 0.569 8.25 0 81 99 -1 0 0 NaN 30247 0;5882.703125;19118.6171875;25656.2758789063;16791.0786132813;0 19902.078125;6989.12060546875 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/evidence.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,9 @@ +Sequence Length Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Oxidation (M) Missed cleavages Proteins Leading proteins Leading razor protein Type Raw file Experiment MS/MS m/z Charge m/z Mass Resolution 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 Reporter PIF Reporter fraction Reverse Potential contaminant id Protein group IDs Peptide ID Mod. peptide ID MS/MS IDs Best MS/MS Oxidation (M) site IDs +DSFDIIK 7 Unmodified _DSFDIIK_ 0 0 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 419.221313476563 2 419.221268 836.427984 NaN 0 0 0.54276 0.00022754 0.54276 0.00022754 419.22139467134 0.58669 0.13742 0.58669 0.46121 0.59862 0 11 4 3 0 0 0 8.9583E-05 1 96 0 0 1 768320 + 0 2 0 0 0 0 +LLESEECR 8 Unmodified _LLESEECR_ 0 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 CON__Q14CN4-1 MSMS BSA_min_23 BSA_min_23.mzXML 518.238220214844 2 518.242406 1034.47026 NaN NaN NaN NaN NaN NaN NaN NaN 0.50957 1 0.50957 0.0095717 1.0096 0 0 0 0 0.010121 1 86 1.6313 1.6313 1 + 1 6 1 1 1 1 +LVTDLTK 7 Unmodified _LVTDLTK_ 0 0 CON__P02769;bsa;CON__P02768-1 CON__P02769 CON__P02769 MSMS BSA_min_23 BSA_min_23.mzXML 395.239288330078 2 395.239461 788.46437 NaN NaN NaN NaN NaN NaN NaN NaN 0.010013 1 0.010013 -0.48999 0.51001 0 0 0 0 0.005963 1 2 0 0 1 + 2 0 2 2 2 2 +QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 629.358581542969 2 629.356085 1256.69762 NaN 0 0 0.76901 0.00048398 0.76901 0.00048398 629.356557471474 0.3521 0.47559 0.3521 0.12303 0.59862 0 33 14 3 0 0 0 0.0003393 2 52 0 0 1 84871 + 3 1 3 3 3;4 3 +QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 419.221313476563 3 419.906482 1256.69762 NaN 0 0 0.052788 2.2166E-05 0.052788 2.2166E-05 419.9067499241 0.32847 0.47559 0.32847 0.12303 0.59862 0 25 14 2 0 0 0 0.015457 1 96 0 0 1 57554 + 4 1 3 3 5 5 +SLSAIRER 8 Unmodified _SLSAIRER_ 0 1 CON__Q03247 CON__Q03247 CON__Q03247 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 465.766693115234 2 466.269616 930.524678 NaN 0 0 -3.0904 -0.0014409 -3.0904 -0.0014409 466.26850803291 0.10674 0.17216 0.10674 -0.014552 0.15761 0 6 4 2 0 0 0 0.015457 1 17 0 0 1 33499 + 5 5 4 4 6 6 +SQTSHRGYSASSAR 14 Unmodified _SQTSHRGYSASSAR_ 0 1 CON__P50446 CON__P50446 CON__P50446 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 747.855651855469 2 747.855835 1493.69712 NaN 0 0 0.34543 0.00025833 0.34543 0.00025833 747.856213318885 0.29902 0.26735 0.29902 0.19386 0.46121 0 11 7 2 0 0 0 0.0091697 1 53 0 0 1 59701 + 6 4 5 5 7 7 +TLGPWGQR 8 Unmodified _TLGPWGQR_ 0 0 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 457.746032714844 2 457.745776 913.477 NaN 0 0 -0.28456 -0.00013026 -0.28456 -0.00013026 457.745456355006 0.4547 0.40477 0.4547 0.19386 0.59862 -5.5511E-17 18 12 2 0 0 0 0.00018307 1 72 0 0 1 61894 + 7 3 6 6 8 8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/modificationSpecificPeptides.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,8 @@ +Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Oxidation (M) Missed cleavages Experiment BSA_min_23.mzXML Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Reverse Potential contaminant Intensity Intensity BSA_min_23.mzXML id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count +DSFDIIK Unmodified 836.42798 0.42798405 2 CON__ENSEMBL:ENSBTAP00000016046 yes yes 0 0 1 0.58669 0.58669 2 8.9583E-05 96 BSA_min_23 0 0 + 768320 768320 0 2 0 0 0 0 1 +LLESEECR Unmodified 1034.4703 0.47025958 6 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 yes no 0 0 1 0.50957 0.50957 2 0.010121 86 BSA_min_23 1.6313 1.6313 + 0 0 1 6 1 1 1 1 1 +LVTDLTK Unmodified 788.46437 0.46436956 0 CON__P02769;bsa;CON__P02768-1 yes no 0 0 1 0.010013 0.010013 2 0.005963 2 BSA_min_23 0 0 + 0 0 2 0 2 2 2 2 1 +QLELEKQLEK Unmodified 1256.6976 0.69761697 1 CON__ENSEMBL:ENSBTAP00000001528 yes yes 0 1 2 0.34029 0.34029 2;3 0.0003393 52 BSA_min_23 0 0 + 142430 142430 3 1 3 3;4 3;4;5 3 2 +SLSAIRER Unmodified 930.52468 0.52467841 5 CON__Q03247 yes yes 0 1 1 0.10674 0.10674 2 0.015457 17 BSA_min_23 0 0 + 33499 33499 4 5 4 5 6 6 0 +SQTSHRGYSASSAR Unmodified 1493.6971 0.69711648 4 CON__P50446 yes yes 0 1 1 0.29902 0.29902 2 0.0091697 53 BSA_min_23 0 0 + 59701 59701 5 4 5 6 7 7 1 +TLGPWGQR Unmodified 913.477 0.47699993 3 CON__ENSEMBL:ENSBTAP00000018574 yes yes 0 0 1 0.4547 0.4547 2 0.00018307 72 BSA_min_23 0 0 + 61894 61894 6 3 6 7 8 8 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/msms.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,10 @@ +Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score diffs 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_23 96 77 DSFDIIK 7 0 Unmodified _DSFDIIK_ 0 CON__ENSEMBL:ENSBTAP00000016046 2 CID FTMS MULTI-MSMS 1 0 419.22127 836.42798 0.54276 0.00022754 NaN 0.57043 8.9583E-05 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 DSFDIIK _DSFDIIK_ 0 2 0 0 0 +BSA_min_23 86 70 LLESEECR 8 0 Unmodified _LLESEECR_ 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 2 CID FTMS MSMS 5 518.24241 1034.4703 NaN NaN NaN 0.50957 0.010121 1.6313 1.6313 NaN NaN 1 0 0 0 81 10271.2001953125 1 0 0 y6 10 0.0135096433999706 16.6930827476743 809.2958984375 1 0.00309955136349784 0.00847457627118644 None Unknown 1.63126590808724;0;0 LLESEECR;LGSDMEDLR;QLNQEMEK _LLESEECR_;_LGSDMEDLR_;_QLNQEM(Oxidation (M))EK_ 1 6 1 1 1 +BSA_min_23 2 0 LVTDLTK 7 0 Unmodified _LVTDLTK_ 0 CON__P02769;bsa;CON__P02768-1 2 CID FTMS MSMS 1 395.23946 788.46437 NaN NaN NaN 0.010013 0.005963 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0;0 LVTDLTK;DSLLTLK _LVTDLTK_;_DSLLTLK_ 2 0 2 2 2 +BSA_min_23 52 42 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 2 CID FTMS MULTI-MSMS 3 0 629.35608 1256.6976 0.76901 0.00048398 NaN 0.30417 0.0003393 0 0 NaN NaN 1 0 0 0 49 47581.3515625 1 0 0 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 1 3 3 3 +BSA_min_23 82 66 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 2 CID FTMS MULTI-MSMS 1 1 629.35608 1256.6976 0.76901 0.00048398 NaN 0.48722 0.0003393 0 0 NaN NaN 1 0 0 0 81 28788.931640625 1 0 0 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 4 1 3 3 3 +BSA_min_23 96 77 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 3 CID FTMS MULTI-SECPEP 1 -2 419.90648 1256.6976 0.052788 2.2166E-05 NaN 0.57043 0.015457 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 5 1 3 3 4 +BSA_min_23 17 13 SLSAIRER 8 1 Unmodified _SLSAIRER_ 0 CON__Q03247 2 CID FTMS MULTI-SECPEP 4 -1 466.26962 930.52468 -3.0904 -0.0014409 NaN 0.096553 0.015457 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 SLSAIRER _SLSAIRER_ 6 5 4 4 5 +BSA_min_23 53 43 SQTSHRGYSASSAR 14 1 Unmodified _SQTSHRGYSASSAR_ 0 CON__P50446 2 CID FTMS MULTI-MSMS 4 0 747.85583 1493.6971 0.34543 0.00025833 NaN 0.30942 0.0091697 0 0 NaN NaN 1 0 0 0 49 27482.5703125 1 0 0 0 0 0 None Unknown 0;0 SQTSHRGYSASSAR;GLIDEVDQDFTSR _SQTSHRGYSASSAR_;_GLIDEVDQDFTSR_ 7 4 5 5 6 +BSA_min_23 72 58 TLGPWGQR 8 0 Unmodified _TLGPWGQR_ 0 CON__ENSEMBL:ENSBTAP00000018574 2 CID FTMS MULTI-MSMS 1 0 457.74578 913.477 -0.28456 -0.00013026 NaN 0.42593 0.00018307 0 0 NaN NaN 1 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 0 0 0 None Unknown 0;0 TLGPWGQR;IHVFNER _TLGPWGQR_;_IHVFNER_ 8 3 6 6 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/msmsScans.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,82 @@ +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 PIF Reporter fraction Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number +BSA_min_23 2 0.010013 -1 35863 35 0 15154 -1 + 2 LVTDLTK 7 103 395.239288330078 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 Unmodified _LVTDLTK_ bsa;CON__P02768-1;CON__P02769 0 1 BSA_min_23.mzXML NaN NaN NaN 0 0 0 1 +BSA_min_23 3 0.01458 -1 30585 35 0 3755 -1 - + -1 EHGLGSSHGSGSEYPR 16 164 552.918823242188 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 Unmodified _EHGLGSSHGSGSEYPR_ REV__CON__Q86YZ3;REV__CON__Q86YZ3;REV__CON__Q86YZ3 0 1 BSA_min_23.mzXML NaN NaN NaN 0 1 0 1 +BSA_min_23 4 0.020265 -1 11886 35 0 5306.3 -1 - + -1 IKNLDEITLHR 11 126 676.387463660037 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 Unmodified _IKNLDEITLHR_ REV__CON__Q148H6;REV__CON__Q7Z3Y7 0 1 BSA_min_23.mzXML NaN NaN NaN 0 2 0 1 +BSA_min_23 5 0.025633 -1 12813 35 0 1425.6 -1 - -1 EYEATLEECCAK 12 146 751.810668945313 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 Unmodified _EYEATLEECCAK_ bsa;CON__P02769 0 1 BSA_min_23.mzXML NaN NaN NaN 0 3 0 1 +BSA_min_23 6 0.031253 -1 10791 35 0 2980.7 -1 - + -1 CLNCFERWR 9 124 670.800842285156 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 Unmodified _CLNCFERWR_ REV__CON__P06868 0 1 BSA_min_23.mzXML NaN NaN NaN 0 4 0 1 +BSA_min_23 8 0.044372 -1 7950.3 35 0 925.49 -1 - + -1 TPLQYLHEFLSGILRAHVAPAVNGM 25 111 456.581360511828 2733.44450427137 6 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 Unmodified _TPLQYLHEFLSGILRAHVAPAVNGM_ REV__CON__REFSEQ:XP_092267 0 1 BSA_min_23.mzXML NaN NaN NaN 0 5 1 7 +BSA_min_23 9 0.049315 -1 13730 35 0 3362.2 -1 - -1 TSCSNANLEK 10 120 562.257629394531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 Unmodified _TSCSNANLEK_ CON__Q1A7A4 0 1 BSA_min_23.mzXML NaN NaN NaN 0 6 1 7 +BSA_min_23 10 0.05446 -1 8774.7 35 0 723.28 -1 - -1 0 121 589.203410887949 588.196134421349 1 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 7 1 7 +BSA_min_23 11 0.06018 -1 4436.2 35 0 280.8 -1 - -1 0 115 828.876770019531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 8 1 7 +BSA_min_23 12 0.065908 -1 3625.8 35 0 189.9 -1 - -1 GSCGIGGGIGGGSSR 15 112 639.798400878906 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 Unmodified _GSCGIGGGIGGGSSR_ CON__P02533;CON__P08779 1.5870418381875 1 BSA_min_23.mzXML NaN NaN NaN 0 9 1 7 +BSA_min_23 14 0.078957 -1 13236 35 0 4982.4 -1 - -1 0 137 883.333059829652 1764.6515667261 2 MULTI CID FTMS 0 0 0 13 171569.53125 0.0583552615411773 -4 NaN 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 10 2 13 +BSA_min_23 15 0.084805 -1 6304.6 35 0 393.58 -1 - -1 0 120 602.8994140625 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 11 2 13 +BSA_min_23 16 0.090573 -1 12119 35 0 1996 -1 - -1 0 135 648.602725143793 1942.78634603158 3 MULTI CID FTMS 0 0 0 13 52074.7734375 0.102435594507697 -16 NaN 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 12 2 13 +BSA_min_23 17 0.096553 -1 5932.3 35 0 1047.4 -1 - + -1 SAAKLPSEK 9 110 465.766693115234 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 Unmodified _SAAKLPSEK_ REV__CON__REFSEQ:XP_585019 0 1 BSA_min_23.mzXML NaN NaN NaN 0 13 2 13 +BSA_min_23 18 0.10154 -1 4161.5 35 0 213.29 -1 - -1 0 108 605.758117675781 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 14 2 13 +BSA_min_23 20 0.11439 -1 65173 35 0 21752 -1 - -1 0 102 387.700285234344 NaN 0 PEAK CID FTMS 0 0 0 19 5176.81640625 0.231645826498235 -7 NaN 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 15 3 19 +BSA_min_23 21 0.11842 -1 33705 35 0 7550.4 -1 - -1 0 123 430.226482307928 NaN 0 PEAK CID FTMS 0 0 0 19 7040.359375 0.343536017509867 -2 0.0701033333333334 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 16 3 19 +BSA_min_23 22 0.1234 -1 9502.6 35 0 474.56 -1 - 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-1 0 40 931.328202121546 1860.64185130989 2 MULTI CID FTMS 0 0 0 25 32505.169921875 0.556008699617638 -3 0.102683333333333 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 22 4 25 +BSA_min_23 29 0.16448 -1 3712.5 35 0 221.62 -1 - -1 0 134 730.799031095722 1459.58350925824 2 MULTI CID FTMS 0 0 0 25 39553.00390625 1 0 0 4 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 23 4 25 +BSA_min_23 30 0.17003 -1 5047.2 35 0 171.8 -1 - -1 0 108 585.918893568188 1754.73485130476 3 MULTI CID FTMS 0 0 0 25 27986.6171875 0.487805831250134 -2 0.0681233333333334 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 24 4 25 +BSA_min_23 32 0.18323 -1 3672.2 35 0 578.08 -1 - -1 0 95 597.209739443197 NaN 0 PEAK CID FTMS 0 0 0 31 45858.6953125 0.706827549584025 -2 0.0691516666666667 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 25 5 31 +BSA_min_23 33 0.18901 -1 10554 35 0 1235.3 -1 - -1 0 112 487.53462335476 1459.58204066448 3 MULTI CID FTMS 0 0 0 31 17205.21875 0.534308072152896 2 -0.07205 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 26 5 31 +BSA_min_23 34 0.19399 -1 794.02 35 0 70.921 -1 - -1 0 53 931.328202121546 1860.64185130989 2 MULTI CID FTMS 0 0 0 31 40352.77734375 0.775544041279623 -1 0.0365716666666666 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 27 5 31 +BSA_min_23 35 0.19977 -1 6966.5 35 0 1545.8 -1 - -1 EHEGAIYPDNTTDFQK 16 119 622.281005859375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 Unmodified _EHEGAIYPDNTTDFQK_ CON__ENSEMBL:ENSBTAP00000031900 0.0128211074556954 1 BSA_min_23.mzXML NaN NaN NaN 0 28 5 31 +BSA_min_23 36 0.20575 -1 2000.1 35 0 103.99 -1 - -1 0 122 843.968139648438 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 29 5 31 +BSA_min_23 38 0.21916 -1 3920.8 35 0 140.38 -1 - -1 0 120 703.140521860943 4212.79947236606 6 MULTI CID FTMS 0 0 0 37 38276.57421875 1 0 0 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 30 6 37 +BSA_min_23 39 0.22523 -1 7753.4 35 0 448.99 -1 - + -1 VNMYAEDVK 9 121 542.752915907862 NaN 0 PEAK CID FTMS 0 0 0 37 7960.71728515625 0.810623529138009 -1 0.0359233333333333 2 Oxidation (M) _VNM(Oxidation (M))YAEDVK_ REV__CON__H-INV:HIT000292931;REV__CON__P05787 0 1 BSA_min_23.mzXML NaN NaN NaN 0 31 6 37 +BSA_min_23 40 0.23041 -1 2121.2 35 0 123.11 -1 - -1 0 108 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 37 47932.00390625 1 0 0 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 32 6 37 +BSA_min_23 41 0.23643 -1 2589.1 35 0 109.74 -1 - -1 0 110 592.559742773291 1774.65739892007 3 MULTI CID FTMS 0 0 0 37 51832.45703125 1 0 0 4 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 33 6 37 +BSA_min_23 42 0.24218 -1 6786.4 35 0 300.4 -1 - -1 0 114 558.888078141406 1673.64240502442 3 MULTI CID FTMS 0 0 0 37 50127.9140625 0.805054408903464 -3 0.105075 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 34 6 37 +BSA_min_23 44 0.25533 -1 3829.3 35 0 182.71 -1 - + -1 WEAFIEEPFVSPLSLQKEFK 20 126 808.753845214844 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 Unmodified _WEAFIEEPFVSPLSLQKEFK_ REV__CON__Q2YDI2 3.05294695694606 1 BSA_min_23.mzXML NaN NaN NaN 0 35 7 43 +BSA_min_23 45 0.26131 -1 2056.8 35 0 123.91 -1 - -1 0 95 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 43 42148.32421875 1 0 0 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 36 7 43 +BSA_min_23 46 0.26732 -1 4217.2 35 0 207.39 -1 - -1 0 115 703.140521860943 4212.79947236606 6 MULTI CID FTMS 0 0 0 43 34525.390625 0.901997927706068 1 -0.0366366666666667 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 37 7 43 +BSA_min_23 47 0.27336 -1 4417.5 35 0 424.39 -1 - + -1 YYDEVLDQMR 10 112 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 43 36233.25 0.312245808501738 -5 0.176745 4 Oxidation (M) _YYDEVLDQM(Oxidation (M))R_ REV__CON__Q14CN4-1 0 1 BSA_min_23.mzXML NaN NaN NaN 0 38 7 43 +BSA_min_23 48 0.27939 -1 4893.8 35 0 478.46 -1 - + -1 LEENTQEIQKTIK 13 114 525.286926269531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 Unmodified _LEENTQEIQKTIK_ REV__CON__P17697 0 1 BSA_min_23.mzXML NaN NaN NaN 0 39 7 43 +BSA_min_23 50 0.29214 -1 2694.3 35 0 193.07 -1 - -1 0 118 844.169032154843 4215.80877844122 5 MULTI CID FTMS 0 0 0 49 18802.0625 1 0 0 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 40 8 49 +BSA_min_23 51 0.29815 -1 4123.5 35 0 362.12 -1 - + -1 YYDEVLDQMR 10 123 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 49 37438.125 0.322629010906119 -4 0.145258333333333 2 Oxidation (M) _YYDEVLDQM(Oxidation (M))R_ REV__CON__Q14CN4-1 0 1 BSA_min_23.mzXML NaN NaN NaN 0 41 8 49 +BSA_min_23 52 0.30417 -1 2801.3 35 0 563.75 -1 + 3 QLELEKQLEK 10 103 629.356568937177 1256.69858494115 2 MULTI CID FTMS 0 0 0 49 47581.3515625 1 0 0 3 Unmodified _QLELEKQLEK_ CON__ENSEMBL:ENSBTAP00000001528 0 1 BSA_min_23.mzXML NaN NaN NaN 0 42 8 49 +BSA_min_23 53 0.30942 -1 3120.2 35 0 230.29 -1 + 7 SQTSHRGYSASSAR 14 121 747.856093035124 1493.69763313705 2 MULTI CID FTMS 0 0 0 49 27482.5703125 1 0 0 4 Unmodified _SQTSHRGYSASSAR_ CON__P50446 0 1 BSA_min_23.mzXML NaN NaN NaN 0 43 8 49 +BSA_min_23 54 0.31497 -1 1089.3 35 0 99.892 -1 - -1 0 87 1177.44225204557 3529.3049267369 3 MULTI CID FTMS 0 0 0 49 22208.09765625 0.573548719035153 2 -0.0722016666666667 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 44 8 49 +BSA_min_23 56 0.32853 -1 4609.2 35 0 207.83 -1 - -1 0 134 808.5537109375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 45 9 55 +BSA_min_23 57 0.33454 -1 4781 35 0 347.22 -1 - -1 0 114 491.773453701772 981.532354470344 2 MULTI CID FTMS 0 0 0 55 66131.3984375 1 0 0 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 46 9 55 +BSA_min_23 58 0.33958 -1 3940 35 0 364.61 -1 - + -1 YYDEVLDQMR 10 120 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 55 46957.76171875 0.404665998035039 -3 0.10925 3 Oxidation (M) _YYDEVLDQM(Oxidation (M))R_ REV__CON__Q14CN4-1 0 1 BSA_min_23.mzXML NaN NaN NaN 0 47 9 55 +BSA_min_23 59 0.34561 -1 5227 35 0 382.1 -1 - -1 0 94 517.743469238281 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 48 9 55 +BSA_min_23 60 0.35072 -1 3062.2 35 0 407.26 -1 - -1 TEDGSDPPSGDFLTEGGGVR 20 101 664.964606092136 1991.87198887661 3 MULTI CID FTMS 0 0 0 55 33396.828125 0.665850940487736 5 -0.158593333333333 5 Unmodified _TEDGSDPPSGDFLTEGGGVR_ CON__P02672 0 1 BSA_min_23.mzXML NaN NaN NaN 0 49 9 55 +BSA_min_23 62 0.36446 -1 6953.5 35 0 2045.9 -1 - -1 0 98 460.254338656322 459.247062189722 1 MULTI CID FTMS 0 0 0 61 110063.5625 0.350472556233784 3 -0.0859683333333334 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 50 10 61 +BSA_min_23 63 0.36944 -1 3605.8 35 0 226.57 -1 - + -1 EGLVENGHMNGVK 13 128 700.332580566406 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 Oxidation (M) _EGLVENGHM(Oxidation (M))NGVK_ REV__CON__Q2KJ83 2.61985254508769 1 BSA_min_23.mzXML NaN NaN NaN 0 51 10 61 +BSA_min_23 64 0.37486 -1 1611.8 35 0 175.4 -1 - -1 0 101 1177.47028638169 1176.46300991509 1 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 52 10 61 +BSA_min_23 66 0.3885 -1 5670 35 0 829.98 -1 - -1 0 100 622.5341796875 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 53 11 65 +BSA_min_23 67 0.39452 -1 3085.9 35 0 186.47 -1 - -1 0 115 594.556274414063 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 54 11 65 +BSA_min_23 68 0.40026 -1 1992.2 35 0 98.298 -1 - -1 0 96 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 65 21625.0703125 0.451161406787757 5 -0.157466666666667 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 55 11 65 +BSA_min_23 69 0.40626 -1 1117.7 35 0 103 -1 - + -1 TTHISVNQMGSERLSEEGELK 21 76 1173.07641144645 2344.1382699597 2 MULTI CID FTMS 0 0 0 65 24950.53125 1 0 0 4 Unmodified _TTHISVNQMGSERLSEEGELK_ REV__CON__Q9H552 0 1 BSA_min_23.mzXML NaN NaN NaN 0 56 11 65 +BSA_min_23 70 0.41227 -1 2287.8 35 0 143.87 -1 - -1 0 138 1177.58276971623 2353.15098649927 2 MULTI CID FTMS 0 0 0 65 8500.6943359375 0.643644763729794 1 -0.0373533333333333 5 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 57 11 65 +BSA_min_23 72 0.42593 -1 5725.3 35 0 848.26 -1 + 8 TLGPWGQR 8 96 457.745646177304 913.476739421408 2 MULTI CID FTMS 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 1 Unmodified _TLGPWGQR_ CON__ENSEMBL:ENSBTAP00000018574 0 1 BSA_min_23.mzXML NaN NaN NaN 0 58 12 71 +BSA_min_23 73 0.43088 -1 1163.3 35 0 134.38 -1 - -1 0 65 1010.44003116945 4037.73101881139 4 MULTI CID FTMS 0 0 0 71 15265.9873046875 0.567392976805677 -2 0.0615566666666666 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 59 12 71 +BSA_min_23 74 0.43685 -1 4314.7 35 0 231.99 -1 - -1 0 113 585.918893568188 1754.73485130476 3 MULTI CID FTMS 0 0 0 71 21487.865234375 0.45287833588482 6 -0.168346666666667 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 60 12 71 +BSA_min_23 76 0.45047 -1 8334.6 35 0 1914.8 -1 - -1 0 119 447.536449992962 1339.58752057909 3 MULTI CID FTMS 0 0 0 75 40469.671875 0.9140992180924 1 -0.0369099999999999 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 61 13 75 +BSA_min_23 77 0.45584 -1 4436.9 35 0 793 -1 - -1 0 95 597.066144900786 2980.29434217093 5 MULTI CID FTMS 0 0 0 75 33103.19921875 0.991897253233573 1 -0.0369099999999999 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 62 13 75 +BSA_min_23 78 0.46188 -1 2747.5 35 0 299.93 -1 - -1 TEDGSDPPSGDFLTEGGGVR 20 106 664.964606092136 1991.87198887661 3 MULTI CID FTMS 0 0 0 75 18094.236328125 0.676187560804335 3 -0.0957016666666666 3 Unmodified _TEDGSDPPSGDFLTEGGGVR_ CON__P02672 0 1 BSA_min_23.mzXML NaN NaN NaN 0 63 13 75 +BSA_min_23 79 0.46792 -1 3792.1 35 0 320.32 -1 - -1 MLREHQELMSMK 12 127 782.86823361998 1563.72191430676 2 MULTI CID FTMS 0 0 0 75 24751.693359375 0.989113548898297 -1 0.0244116666666667 4 2 Oxidation (M) _M(Oxidation (M))LREHQELM(Oxidation (M))SMK_ CON__Q6NXH9 0 1 BSA_min_23.mzXML NaN NaN NaN 0 64 13 75 +BSA_min_23 80 0.4736 -1 1227.2 35 0 58.422 -1 - + -1 TTHISVNQMGSERLSEEGELK 21 96 1173.07641144645 2344.1382699597 2 MULTI CID FTMS 0 0 0 75 23081.546875 1 0 0 5 Unmodified _TTHISVNQMGSERLSEEGELK_ REV__CON__Q9H552 0 1 BSA_min_23.mzXML NaN NaN NaN 0 65 13 75 +BSA_min_23 82 0.48722 -1 6556.1 35 0 1271.7 -1 + 4 QLELEKQLEK 10 116 629.356568937177 1256.69858494115 2 MULTI CID FTMS 0 0 0 81 28788.931640625 1 0 0 1 Unmodified _QLELEKQLEK_ CON__ENSEMBL:ENSBTAP00000001528 0 1 BSA_min_23.mzXML NaN NaN NaN 0 66 14 81 +BSA_min_23 83 0.4925 -1 6615.3 35 0 545.34 -1 - -1 0 116 559.76878406336 1117.52301519352 2 MULTI CID FTMS 0 0 0 81 35334.84765625 0.949368528711517 -1 0.0369099999999999 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 67 14 81 +BSA_min_23 84 0.49762 -1 6183.7 35 0 2375.9 -1 - -1 0 125 972.401410273474 1942.78826761375 2 MULTI CID FTMS 0 0 0 81 19756.91796875 0.347354270628424 7 NaN 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 68 14 81 +BSA_min_23 85 0.50353 -1 3559.8 35 0 122.14 -1 - -1 0 116 681.999313403946 2042.97611081204 3 MULTI CID FTMS 0 0 0 81 11550.4775390625 0.629091502669348 2 -0.0587916666666667 4 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 69 14 81 +BSA_min_23 86 0.50957 -1 5114.2 35 0 640.76 -1 + 1 LLESEECR 8 118 518.240989833781 NaN 0 PEAK CID FTMS 0 0 0 81 10271.2001953125 1 0 0 5 Unmodified _LLESEECR_ CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1.63126590808724 1 BSA_min_23.mzXML NaN NaN NaN 0 70 14 81 +BSA_min_23 88 0.52259 -1 44411 35 0 18940 -1 - -1 0 134 385.207382835291 384.200106368691 1 MULTI CID FTMS 0 0 0 87 5929296.5 0.739051055541228 -3 0.0963616666666667 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 71 15 87 +BSA_min_23 89 0.52681 -1 3749.8 35 0 351.63 -1 - -1 0 100 597.066144900786 2980.29434217093 5 MULTI CID FTMS 0 0 0 87 19359.11328125 0.820197080002651 2 -0.04811 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 72 15 87 +BSA_min_23 90 0.53279 -1 3364.5 35 0 196.99 -1 - -1 0 128 731.29825780069 1460.58196266818 2 MULTI CID FTMS 0 0 0 87 10634.3564453125 0.960368079417471 -1 0.0350400000000001 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 73 15 87 +BSA_min_23 92 0.54611 -1 4680.5 35 0 301.84 -1 - -1 0 116 582.760858227368 1163.50716352154 2 MULTI CID FTMS 0 0 0 91 46220.83984375 0.762103661377976 -2 0.0587916666666667 1 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 74 16 91 +BSA_min_23 93 0.55132 -1 3773.2 35 0 552.59 -1 - -1 0 106 635.60201346581 1903.78421099763 3 MULTI CID FTMS 0 0 0 91 24284.580078125 0.586968526901584 -2 0.0587916666666667 2 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 75 16 91 +BSA_min_23 94 0.55721 -1 4670.5 35 0 438.63 -1 - -1 0 143 722.292864587666 1442.57117624213 2 MULTI CID FTMS 0 0 0 91 14970.0166015625 0.470778833500893 -2 0.0587916666666667 3 NaN NaN BSA_min_23.mzXML NaN NaN NaN 0 76 16 91 +BSA_min_23 96 0.57043 -1 15235 35 0 3357.3 -1 + 0 DSFDIIK 7 110 419.22149602984 836.428439126479 2 MULTI CID FTMS 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 1 Unmodified _DSFDIIK_ CON__ENSEMBL:ENSBTAP00000016046 0 1 BSA_min_23.mzXML NaN NaN NaN 0 77 17 95 +BSA_min_23 97 0.57533 -1 4806.4 35 0 539.18 -1 - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/mzTab.mzTab Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,49 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Complete +MTD mzTab-type Identification +MTD title null +MTD description null +MTD software[1] [MS, MS:1001583, MaxQuant,1.6.10.43] +COM [, CHEMMOD:57.0214637236, Carbamidomethyl (C),] +MTD fixed_mod[1] [, , CHEMMOD:57.0214637236,] +MTD fixed_mod[1]-site C +MTD fixed_mod[1]-position Anywhere +COM [, CHEMMOD:15.9949146221, Oxidation (M),] +MTD variable_mod[1] [, , CHEMMOD:15.9949146221,] +MTD variable_mod[1]-site M +MTD variable_mod[1]-position Anywhere +MTD protein_search_engine_score[1] [MS, MS:1002375, protein group-level combined FDRscore, ] +MTD peptide_search_engine_score[1] [MS, MS:1001250, local FDR, ] +MTD psm_search_engine_score[1] [MS, MS:1002338, Andromeda:score, ] +MTD psm_search_engine_score[2] [MS, MS:1002995, Andromeda:PEP, ] +MTD ms_run[1]-format [MS, MS:1002996, Andromeda:apl file format, ] +MTD ms_run[1]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.secpep.sil0_0.apl +MTD ms_run[1]-id_format [MS, MS:1000776, scan number only nativeID format, ] +MTD ms_run[2]-format [MS, MS:1002996, Andromeda:apl file format, ] +MTD ms_run[2]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.iso_0.apl +MTD ms_run[2]-id_format [MS, MS:1000776, scan number only nativeID format, ] + +PRH accession description taxid species database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] search_engine_score[1]_ms_run[2] num_psms_ms_run[1] num_psms_ms_run[2] num_peptides_distinct_ms_run[1] num_peptides_distinct_ms_run[2] num_peptides_unique_ms_run[1] num_peptides_unique_ms_run[2] ambiguity_members modifications protein_coverage opt_global_cv_MS:1002217_decoy_peptide +PRT CON__P02769 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 6.22453365714539 null null null null null null null null CON__P02769, bsa, CON__P02768-1 null 0.012 0 +PRT CON__ENSEMBL:ENSBTAP00000001528 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 7.46941253488722 null null null null null null null null CON__ENSEMBL:ENSBTAP00000001528 null 0.008 0 +PRT CON__ENSEMBL:ENSBTAP00000016046 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 8.04777465053044 null null null null null null null null CON__ENSEMBL:ENSBTAP00000016046 null 0.01 0 +PRT CON__ENSEMBL:ENSBTAP00000018574 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 7.73737648138078 null null null null null null null null CON__ENSEMBL:ENSBTAP00000018574 null 0.016 0 +PRT CON__P50446 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 6.03764269117454 null null null null null null null null CON__P50446 null 0.025 0 +PRT CON__Q03247 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 5.81086493552667 null null null null null null null null CON__Q03247 null 0.025 0 +PRT CON__Q14CN4-1 null null null null null [MS, MS:1002337, Andromeda, 1.6.10.43] 5.99478997658237 null null null null null null null null CON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5 null 0.016 0 + +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] search_engine_score[2] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_global_cv_MS:1000776_scan_number_only_nativeID_format opt_global_cv_MS:1002217_decoy_peptide +PSM DSFDIIK 1 CON__ENSEMBL:ENSBTAP00000016046 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 8.95829478642414E-05 null 0.570428333333333 2 419.22 419.22127 ms_run[2]:index=5 R R 646 652 96 0 +PSM LLESEECR 2 CON__Q14CN4-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 1.63126590808724 0.0101206876914345 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 +PSM LLESEECR 2 CON__Q3SY84 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 1.63126590808724 0.0101206876914345 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 +PSM LLESEECR 2 CON__Q9R0H5 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 1.63126590808724 0.0101206876914345 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 +PSM LVTDLTK 3 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00596302105559693 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 +PSM LVTDLTK 3 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00596302105559693 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 +PSM LVTDLTK 3 CON__P02768-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00596302105559693 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 +PSM QLELEKQLEK 4 CON__ENSEMBL:ENSBTAP00000001528 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00033930281684504 null 0.304175 2 629.36 629.35608 ms_run[2]:index=31 R Q 408 417 52 0 +PSM QLELEKQLEK 5 CON__ENSEMBL:ENSBTAP00000001528 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00033930281684504 null 0.487221666666667 2 629.36 629.35608 ms_run[2]:index=30 R Q 408 417 82 0 +PSM QLELEKQLEK 6 CON__ENSEMBL:ENSBTAP00000001528 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.015457350844535 null 0.570428333333333 3 419.91 419.90648 ms_run[1]:index=5 R Q 408 417 96 0 +PSM SLSAIRER 7 CON__Q03247 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.015457350844535 null 0.0965533333333333 2 466.27 466.26962 ms_run[1]:index=2 R F 190 197 17 0 +PSM SQTSHRGYSASSAR 8 CON__P50446 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.00916974606023747 null 0.309418333333333 2 747.86 747.85583 ms_run[2]:index=48 K V 9 22 53 0 +PSM TLGPWGQR 9 CON__ENSEMBL:ENSBTAP00000018574 1 null null [MS, MS:1002338, Andromeda:score, 1.6.10.43] 0 0.000183072671316044 null 0.425933333333333 2 457.75 457.74578 ms_run[2]:index=9 R D 20 27 72 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/parameters.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,105 @@ +Parameter Value +Version 1.6.10.43 +User name dglaetzer +Machine name FPROT-BEAST +Date of writing 02/25/2020 15:36:33 +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 D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta +Decoy mode revert +Include contaminants True +Advanced ratios True +Fixed andromeda index folder +Temporary 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 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/peptideSection.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,8 @@ +PEH sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[0] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[0] peptide_abundance_stdev_study_variable[0] peptide_abundance_std_error_study_variable[0] +PEP DSFDIIK null +PEP LLESEECR null +PEP LVTDLTK null +PEP QLELEKQLEK null +PEP SLSAIRER null +PEP SQTSHRGYSASSAR null +PEP TLGPWGQR null
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/peptides.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,8 @@ +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 Experiment BSA_min_23.mzXML Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count +DSFDIIK NHADIIFDITDGNLRDSFDIIKRYMDGMTV DITDGNLRDSFDIIKRYMDGMTVGVVRQVR R D S I K R 0 0 0 2 0 0 0 0 0 2 0 1 0 1 0 1 0 0 0 0 0 0 7 0 836.42798 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 646 652 yes yes 2 8.9583E-05 0 1 768320 768320 + 0 2 0 0 0 0 1 +LLESEECR SLKLALDMEIATYRKLLESEECRMSGEYPN EIATYRKLLESEECRMSGEYPNSVSISVIS K L L C R M 0 1 0 0 1 0 3 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 8 0 1034.4703 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 430 437 yes no 2 0.010121 1.6313 1 0 0 + 1 6 1 1 1 1 1 +LVTDLTK LSQKFPKAEFVEVTKLVTDLTKVHKECCHG AEFVEVTKLVTDLTKVHKECCHGDLLECAD K L V T K V 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 0 2 0 0 1 0 0 7 0 788.46437 CON__P02769;bsa;CON__P02768-1 CON__P02769 257 263 yes no 2 0.005963 0 1 0 0 + 2 0 2 2 2 2 1 +QLELEKQLEK QERKERERQEQERKRQLELEKQLEKQRELE QERKRQLELEKQLEKQRELERQREEERRKE R Q L E K Q 0 0 0 0 0 2 3 0 0 0 3 2 0 0 0 0 0 0 0 0 0 0 10 1 1256.6976 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 408 417 yes yes 2;3 0.0003393 0 2 142430 142430 + 3 1 3 3;4 3;4;5 3 2 +SLSAIRER RLAVYQAGASEGAERSLSAIRERFGPLVEQ ASEGAERSLSAIRERFGPLVEQGQSRAATL R S L E R F 1 2 0 0 0 0 1 0 0 1 1 0 0 0 0 2 0 0 0 0 0 0 8 1 930.52468 CON__Q03247 CON__Q03247 190 197 yes yes 2 0.015457 0 1 33499 33499 + 4 5 4 5 6 6 0 +SQTSHRGYSASSAR ______________________________ KSQTSHRGYSASSARVPGLNRSGFSSVSVC K S Q A R V 2 2 0 0 0 1 0 1 1 0 0 0 0 0 0 5 1 0 1 0 0 0 14 1 1493.6971 CON__P50446 CON__P50446 9 22 yes yes 2 0.0091697 0 1 59701 59701 + 5 4 5 6 7 7 1 +TLGPWGQR LRPLLLALLLASACRTLGPWGQRDDGGGEP LLASACRTLGPWGQRDDGGGEPESMEPRWG R T L Q R D 0 1 0 0 0 1 0 2 0 0 1 0 0 0 1 0 1 1 0 0 0 0 8 0 913.477 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 20 27 yes yes 2 0.00018307 0 1 61894 61894 + 6 3 6 7 8 8 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/proteinGroups.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,8 @@ +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 Peptides BSA_min_23.mzXML Razor + unique peptides BSA_min_23.mzXML Unique peptides BSA_min_23.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage BSA_min_23.mzXML [%] Intensity Intensity BSA_min_23.mzXML 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 +CON__P02769;bsa;CON__P02768-1 CON__P02769;bsa;CON__P02768-1 1;1;1 1;1;1 1;1;1 ;bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4; 3 1 1 1 1 1 1 1.2 1.2 1.2 69.293 607 607;607;609 0 6.2245 1.2 0 0 1 + 0 2 True 2 2 2 2 +CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 1 1 1 1 1 1 1 1 1 1 0.8 0.8 0.8 137.98 1222 1222 0 7.4694 0.8 142430 142430 2 + 1 3 True 3 3;4 3;4;5 3 +CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 1 1 1 1 1 1 1 1 1 1 1 1 1 77.456 706 706 0 8.0478 1 768320 768320 1 + 2 0 True 0 0 0 0 +CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 1 1 1 1 1 1 1 1 1 1 1.6 1.6 1.6 55.207 496 496 0 7.7374 1.6 61894 61894 1 + 3 6 True 6 7 8 8 +CON__P50446 CON__P50446 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 59.334 553 553 0 6.0376 2.5 59701 59701 1 + 4 5 True 5 6 7 7 +CON__Q03247 CON__Q03247 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 35.979 316 316 0 5.8109 2.5 33499 33499 0 + 5 4 True 4 5 6 6 +CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1;1;1 1;1;1 1;1;1 ;; 3 1 1 1 1 1 1 1.6 1.6 1.6 55.877 511 511;523;524 0 5.9948 1.6 0 0 1 + 6 1 True 1 1 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/combined/txt/summary.txt Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,3 @@ +Raw file Experiment 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_23 BSA_min_23.mzXML Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 1 Standard 19 81 0 111 51 0 60 7 5 0 2 6.3 9.8 0 3.3 7 1200 57 4.8 4 7 166 39 35 23 27 10 26 + 0.48635 0.52208 0.27503 0.30402 +Total 19 81 0 111 51 0 60 7 5 0 2 6.3 9.8 0 3.3 7 1200 166 39 35 23 27 10 26 0.48635 0.52208 0.27503 0.30402
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/config.yml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,22 @@ + + fastaFiles: [/tmp/tmpQsmPD9/files/7/b/e/dataset_7be42b54-5eac-4f1d-a6bb-0b85e8f1bd67.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: True + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + paramGroups: + - files: ['BSA_min_23.mzXML'] + maxMissedCleavages: 1 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/01/mqpar.xml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,451 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> + <identifierParseRule>>([^\s]*)</identifierParseRule> + <descriptionParseRule>>(.*)</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>False</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>0</minUniquePeptides> + <useCounterparts>False</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>True</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>session1</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> + </filePaths> + <experiments> + <string>BSA_min_23.mzXML</string> + </experiments> + <fractions> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + </paramGroupIndices> + <referenceChannel> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Standard</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>0</lfqMode> + <lfqSkipNorm>False</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>1</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + <string>Carbamidomethyl (C)</string> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>NaN</reporterMassTolerance> + <reporterPif>NaN</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>NaN</reporterFraction> + <reporterBasePeakRatio>NaN</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/02/config.yml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,45 @@ + + fastaFiles: [/tmp/tmpQsmPD9/files/7/b/e/dataset_7be42b54-5eac-4f1d-a6bb-0b85e8f1bd67.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: True + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + paramGroups: + - files: ['BSA_min_23.mzXML'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + lcmsRunType: 'Reporter ion MS2' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + isobaricLabels: + - ['TMT2plex-Lys126','TMT2plex-Nter126',0.0,0.0,6.7,3.0,True] + - ['TMT2plex-Lys127','TMT2plex-Nter127',0.0,0.0,0.0,0.0,True] + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [] + enzymes: [] + lcmsRunType: 'Reporter ion MS2' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + isobaricLabels: + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/02/mqpar.xml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,649 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> + <identifierParseRule>>([^\s]*)</identifierParseRule> + <descriptionParseRule>>(.*)</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>False</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>0</minUniquePeptides> + <useCounterparts>False</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>True</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>session1</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79589544172745E+308</fullMinMz> + <fullMaxMz>1.79589544172745E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> + <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_22.mzXML</string> + </filePaths> + <experiments> + <string>BSA_min_23.mzXML</string> + <string>BSA_min_22.mzxml</string> + </experiments> + <fractions> + <short>32767</short> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + <int>1</int> + </paramGroupIndices> + <referenceChannel> + <string/> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Reporter ion MS2</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>0</lfqMode> + <lfqSkipNorm>False</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>2</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + <IsobaricLabelInfo> + <internalLabel>TMT2plex-Lys126</internalLabel> + <terminalLabel>TMT2plex-Nter126</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>6.7</correctionFactorP1> + <correctionFactorP2>3</correctionFactorP2> + <tmtLike>True</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>TMT2plex-Lys127</internalLabel> + <terminalLabel>TMT2plex-Nter127</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>True</tmtLike> + </IsobaricLabelInfo> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>0.003</reporterMassTolerance> + <reporterPif>0</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>0</reporterFraction> + <reporterBasePeakRatio>0</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Reporter ion MS2</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>0</lfqMode> + <lfqSkipNorm>False</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>2</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + </fixedModifications> + <enzymes> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys114</internalLabel> + <terminalLabel>iTRAQ4plex-Nter114</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys115</internalLabel> + <terminalLabel>iTRAQ4plex-Nter115</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys116</internalLabel> + <terminalLabel>iTRAQ4plex-Nter116</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys117</internalLabel> + <terminalLabel>iTRAQ4plex-Nter117</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>0.003</reporterMassTolerance> + <reporterPif>0</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>0</reporterFraction> + <reporterBasePeakRatio>0</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/03/config.yml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,29 @@ + + fastaFiles: [/tmp/tmpQsmPD9/files/7/b/e/dataset_7be42b54-5eac-4f1d-a6bb-0b85e8f1bd67.dat] + parseRules: + identifierParseRule: '^>.*\|(.*)\|.*$' + descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$' + minUniquePeptides: 1 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + ibaq: True + ibaqLogFit: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + paramGroups: + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 1 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + lfqMode: 1 + lfqSkipNorm: True + lfqMinEdgesPerNode: 3 + lfqAvEdgesPerNode: 6 + lfqMinRatioCount: 2 + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/03/mqpar.xml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,451 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> + <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> + <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>True</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>1</minUniquePeptides> + <useCounterparts>False</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>False</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>session1</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79589544172745E+308</fullMinMz> + <fullMaxMz>1.79589544172745E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>D:\shared\dglaetzer\maxquant_tool\test3\BSA_min_22.mzXML</string> + </filePaths> + <experiments> + <string>BSA_min_22.mzxml</string> + </experiments> + <fractions> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + </paramGroupIndices> + <referenceChannel> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Standard</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>1</lfqMode> + <lfqSkipNorm>True</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>1</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + <string>Carbamidomethyl (C)</string> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>NaN</reporterMassTolerance> + <reporterPif>NaN</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>NaN</reporterFraction> + <reporterBasePeakRatio>NaN</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/04/config.yml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,26 @@ + + fastaFiles: [/home/galaxy/galaxy/database/files/000/dataset_4.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + paramGroups: + - files: ['BSA_min_23.mzXML', 'BSA_min_22.mzxml'] + maxMissedCleavages: 2 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + labelMods: + - [Arg6,Lys4] + - [] + - [Arg10,DimethLys8] + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/04/exp_design Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,3 @@ +Name Fraction Experiment PTM +BSA_min_22 1 e1 +BSA_min_23 2 e2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/04/mqpar.xml Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,458 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test2\bsa.fasta</fastaFilePath> + <identifierParseRule>>([^\s]*)</identifierParseRule> + <descriptionParseRule>>(.*)</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>False</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>0</minUniquePeptides> + <useCounterparts>False</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>False</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>session1</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79589544172745E+308</fullMinMz> + <fullMaxMz>1.79589544172745E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_22.mzXML</string> + <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_23.mzXML</string> + </filePaths> + <experiments> + <string>e1</string> + <string>e2</string> + </experiments> + <fractions> + <short>1</short> + <short>2</short> + </fractions> + <ptms> + <boolean>False</boolean> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + <int>0</int> + </paramGroupIndices> + <referenceChannel> + <string/> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string>Arg6;Lys4</string> + <string>Arg10;DimethLys8</string> + </labelMods> + <lcmsRunType>Standard</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>0</lfqMode> + <lfqSkipNorm>False</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>2</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>2</maxMissedCleavages> + <multiplicity>2</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + <string>Carbamidomethyl (C)</string> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>NaN</reporterMassTolerance> + <reporterPif>NaN</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>NaN</reporterFraction> + <reporterBasePeakRatio>NaN</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BSA_min_21.mzXML Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,2200 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd"> + <msRun scanCount="100" startTime="PT0.2912S" endTime="PT35.5222S"> + <parentFile fileName="file:///D:\shared\dglaetzer\maxquant_tool\test2\two/BSA_min_21.raw" + fileType="RAWData" + fileSha1="52125693477eda68b26bcebf7d345c550c6d3ef0"/> + <msInstrument msInstrumentID="1"> + <msManufacturer category="msManufacturer" value="Thermo Scientific"/> + <msModel category="msModel" value="LTQ Orbitrap XL"/> + <msIonisation category="msIonisation" value="nanoelectrospray"/> + <msMassAnalyzer category="msMassAnalyzer" value="orbitrap"/> + <msDetector category="msDetector" value="inductive detector"/> + <software type="acquisition" name="Xcalibur" version="2.5.5 SP2"/> + </msInstrument> + <msInstrument msInstrumentID="2"> + <msManufacturer category="msManufacturer" value="Thermo Scientific"/> + <msModel category="msModel" value="LTQ Orbitrap XL"/> + <msIonisation category="msIonisation" value="nanoelectrospray"/> + <msMassAnalyzer category="msMassAnalyzer" value="radial ejection linear ion trap"/> + <msDetector category="msDetector" value="electron multiplier"/> + <software type="acquisition" name="Xcalibur" version="2.5.5 SP2"/> + </msInstrument> + <dataProcessing centroided="1"> + <software type="conversion" name="ProteoWizard software" version="3.0.9706"/> + <processingOperation name="Conversion to mzML"/> + <software type="processing" name="ProteoWizard software" version="3.0.9706"/> + <comment>Thermo/Xcalibur peak picking</comment> + </dataProcessing> + <scan num="1" + scanType="Full" + centroided="1" + msLevel="1" + peaksCount="704" + polarity="+" + retentionTime="PT0.2912S" + lowMz="370.207275390625" + highMz="1609.848266601563" + basePeakMz="372.186614990234" + basePeakIntensity="1.998346e06" + totIonCurrent="2.1077186e07" + msInstrumentID="1"> + <peaks compressionType="zlib" + compressedLen="5188" + precision="32" + byteOrder="network" + 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+ </scan> + <scan num="97" + scanType="Full" + centroided="1" + msLevel="1" + peaksCount="679" + polarity="+" + retentionTime="PT34.9135S" + lowMz="371.011474609375" + highMz="1685.1826171875" + basePeakMz="395.239837646484" + basePeakIntensity="4.2699576e07" + totIonCurrent="1.21064016e08" + msInstrumentID="1"> + <peaks compressionType="zlib" + compressedLen="4905" + precision="32" + byteOrder="network" + 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--- a/test-data/single/combined/txt/allPeptides.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -Raw file Type Charge m/z Mass Uncalibrated m/z Resolution Number of data points Number of scans Number of isotopic peaks PIF Mass fractional part Mass deficit Mass precision [ppm] Max intensity m/z 0 Retention time Retention length Retention length (FWHM) Min scan number Max scan number Identified MS/MS IDs Sequence Length Modifications Modified sequence Proteins Score Intensity Intensities Isotope pattern MS/MS Count MSMS Scan Numbers MSMS Isotope Indices -BSA_min_23 MULTI 3 710.69967 2129.0772 710.69967 NaN 5 3 2 0.077192 0.0578164096173168 1.180035 711.033930698172 0.037 8.255 0 1 25 -1 0 NaN 27555 0;16823.720703125;10726.12109375;6644.5966796875;0 7737.3974609375;9086.3232421875 0 -BSA_min_23 MULTI 3 1567.4354 4699.2845 1567.4354 NaN 5 3 2 0.284514 0.0828426326752378 7.986968 1568.10387245715 0.067 8.255 0 1 25 -1 0 NaN 137580 0;23479.5932617188;59085.9194335938;20990.259765625;0 0;0;53540.3203125;7305.36279296875 0 -BSA_min_23 MULTI 2 466.26817 930.5218 466.26817 NaN 6 4 2 0.521797 0.0537564853223103 1.477127 466.26850803291 0.107 10.33 0 1 31 -1 0 NaN 33499 0;16896.8359375;13251.4482421875;29638.681640625;21903.5859375;0 22962.34375;6676.337890625 0 -BSA_min_23 MULTI 2 835.80692 1669.5993 835.80692 NaN 7 4 2 0.599289 -0.208726257088529 1.196939 835.807035746435 0.107 10.33 0 1 31 -1 0 NaN 35250 0;14611.8764648438;18125.6357421875;25099.0166015625;15365.583984375;0 16483.943359375;8615.0732421875 0 -BSA_min_23 MULTI 2 889.42648 1776.8384 889.42648 NaN 6 3 2 0.838398 -0.0189472723534436 2.943901 889.927320499287 0.107 8.255 0 1 25 -1 0 NaN 24592 0;9125.99072265625;13286.1201171875;16742.716796875;0 7208.8173828125;9533.8994140625 0 -BSA_min_23 MULTI 2 378.70717 755.39978 378.70717 NaN 4 2 2 0.399783 0.0122990350871532 2.895866 378.7066995797 0.119 6.221 0 13 31 -1 0 NaN 17113 0;15764.96875;12169.2568359375;0 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0;7211.73095703125;32638.8959960938;79787.74609375;74581.1875;40743.359375;31912.87890625;10748.6064453125;5496.4296875;0 40288.40234375;32200.93359375;13735.64453125 1 33 1 -BSA_min_23 MULTI 3 583.22015 1746.6386 583.22015 NaN 7 4 2 0.638625 -0.204828530265331 2.286815 583.220239813966 0.176 10.457 0 7 37 -1 0 NaN 42292 0;4036.83081054688;17411.11328125;19834.8046875;29221.802734375;0 17431.560546875;11790.2421875 0 -BSA_min_23 MULTI 3 635.60251 1903.7857 635.60251 NaN 11 5 3 0.785698 -0.130043202729439 1.119621 635.602244079812 0.167 12.618 0 7 43 -1 0 NaN 45493 0;8725.0478515625;17613.3891601563;33308.2824707031;39386.6171875;0;0 17209.375;13758.326171875;9491.1767578125 0 -BSA_min_23 MULTI 2 730.79903 1459.5835 730.79903 NaN 10 6 2 0.583509 -0.127899156014337 0.609982 730.799136547346 0.151 14.666 0 1 43 -1 0 NaN 77496 0;5839.765625;27434.9599609375;42471.279296875;58278.560546875;32345.4384765625;15650.7568359375;0 39553.00390625;19513.171875 1 29 0 -BSA_min_23 MULTI 2 996.94429 1991.874 996.94429 NaN 15 13 2 0.874033 -0.0822288372489766 0.911071 997.446155697545 0.123 28.656 0 7 87 -1 0 NaN 44879 0;20391.6489257813;28769.4560546875;39230.09765625;19622.400390625;13010.86328125;12843.5712890625;12676.279296875;15763.220703125;13381.2666015625;18258.947265625;16122.5546875;0;0;0 20617.05859375;21871.28515625 0 -BSA_min_23 MULTI 1 553.54774 552.54046 553.54774 NaN 5 4 2 0.540459 0.246290167421193 1.417869 553.548098212165 0.187 10.558 0 13 43 -1 0 NaN 28661 0;7194.10693359375;13920.0515136719;27294.748046875;9278.2734375;0 20645.99609375;9278.2734375 0 -BSA_min_23 MULTI 3 587.56748 1759.6806 587.56748 NaN 16 10 3 0.680607 -0.1688458310025 2.658571 587.569121985401 0.212 22.334 0 19 81 -1 0 NaN 57560 0;13109.6430664063;29217.251953125;50790.830078125;21790.4321289063;20568.8234863281;10979.0302734375;9119.8173828125;8416.8525390625;11413.40234375;0;0 24772.69140625;14722.291015625;11295.84765625 0 -BSA_min_23 MULTI 3 590.55881 1768.6546 590.55881 NaN 44 18 3 0.654589 -0.198991658837258 0.411116 590.558889154599 0.216 36.791 0 1 99 -1 0 NaN 1187800 0;6216.87548828125;36925.4790039063;184930.421875;385803.203125;733406.8125;1048139.10742188;905412.859375;792319.85546875;549991.755859375;589044.734375;506728.80859375;400140.365234375;396169.784179688;195725.788085938;105788.993164063;82565.4755859375;42732.5029296875;42157.044921875;0 871911.75;160150.890625;29449.3046875 0 -BSA_min_23 MULTI 3 590.58179 1768.7235 590.58179 NaN 9 5 3 0.723529 -0.130083827993076 4.805278 591.247820427107 0.227 12.954 0 25 61 -1 0 NaN 32803 0;9242.7578125;31178.3193359375;28945.6411132813;8860.56640625;9516.63671875;0 8819.9521484375;11911.1708984375;15289.587890625 0 -BSA_min_23 MULTI 3 591.22358 1770.6489 591.22358 NaN 11 6 3 0.648921 -0.205577517300526 3.134973 591.223392793869 0.181 14.934 0 13 55 -1 0 NaN 91403 0;19490.4609375;30658.0615234375;80654.2841796875;37342.1201171875;24294.84765625;19072.224609375;0 38292.2890625;32139.36328125;11321.0419921875 0 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4698.9374 1567.3197 NaN 9 7 2 0.937419 -0.264092711297053 3.412485 1568.32398965869 0.199 17.1 0 13 61 -1 0 NaN 89862 0;18336.91015625;24437.509765625;21274.6474609375;38593.7509765625;24568.837890625;22314.265625;0;0 0;0;14312.962890625;26823.41015625 0 -BSA_min_23 MULTI 2 441.71645 881.41834 441.71645 NaN 16 10 2 0.41834 -0.0271124766325102 0.367629 441.716375382017 0.139 23.006 0 1 65 -1 0 NaN 114490 0;5712.41015625;26837.841796875;55472.7392578125;102380.125;83058.240234375;69780.052734375;41715.6982421875;19781.36328125;16646.99609375;7474.2314453125;0 69811.8125;32568.3125 1 24 0 -BSA_min_23 MULTI 4 589.26254 2353.0211 589.26254 NaN 10 7 2 0.021052 -0.101337473261083 2.163457 589.513471781483 0.248 16.795 0 19 65 -1 0 NaN 86626 0;13832.5556640625;20902.3041992188;29452.2314453125;49581.69921875;13312.3544921875;13739.1064453125;12947.478515625;0 20231.46484375;29350.234375 0 -BSA_min_23 MULTI 3 589.2688 1764.7846 589.2688 NaN 10 7 2 0.784571 -0.0672303921774073 2.394204 589.269187431499 0.248 16.795 0 19 65 -1 0 NaN 96565 0;18051.07421875;23263.3901367188;38484.591796875;37740.23046875;17053.97265625;12810.2265625;17373.419921875;0 37740.23046875;28981.341796875 0 -BSA_min_23 MULTI 6 680.96393 4079.7399 680.96393 NaN 16 8 3 0.73991 -0.176770254570329 0.763825 681.298098346713 0.169 19.043 0 1 55 -1 0 NaN 69972 0;7875.16064453125;13812.1008300781;46568.4580078125;38948.9130859375;50431.388671875;44762.7075195313;26269.5;0;0 0;19749.041015625;25162.62109375;18991.82421875 0 -BSA_min_23 MULTI 3 694.975 2081.9032 694.975 NaN 4 2 2 0.903176 -0.0944992764948438 1.98739 695.308482832509 0.229 6.519 0 31 49 -1 0 NaN 43441 0;27048.9365234375;23994.908203125;0 12837.9169921875;14675.716796875 0 -BSA_min_23 MULTI 2 428.70867 855.40279 428.70867 NaN 11 7 2 0.40279 -0.030695093111035 1.073214 428.708371254103 0.285 16.376 0 31 75 -1 0 NaN 72480 0;10360.298828125;22505.4140625;65483.0126953125;49747.6396484375;35665.490234375;22419.4526367188;10354.0390625;0 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2 403.1609 804.30724 403.1609 NaN 7 6 2 0.307242 -0.10273887485755 4.842592 403.159823769958 0.557 11.938 0 71 99 -1 0 NaN 17595 0;3488.80078125;5058.57861328125;5149.92407226563;9366.63623046875;16003.2814941406;0;0 12698.837890625;4125.36669921875 0 -BSA_min_23 MULTI 1 401.4224 400.41513 401.4224 NaN 5 4 2 0.415128 0.190936921834407 13.525909 401.426492729968 0.48 8.652 0 75 99 -1 0 NaN 12501 0;12131.3984375;10847.1962890625;5505.88012695313;0;0 7007.498046875;5123.900390625 0 -BSA_min_23 MULTI 1 402.22123 401.21395 402.22123 NaN 12 8 2 0.213954 -0.0106045150496925 2.722259 402.221328891168 0.485 15.582 0 61 99 -1 0 NaN 85877 0;7818.44189453125;50336.5234375;18964.7890625;83337.447265625;46349.7744140625;70621.8837890625;75382.7255859375;69995.28125;0 74508.875;12651.0361328125 0 -BSA_min_23 MULTI 2 671.30281 1340.5911 671.30281 NaN 23 11 3 0.591063 -0.0656088245955289 0.312101 671.302827415245 0.477 22.125 0 43 99 -1 0 NaN 185360 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16679 0;9756.16552734375;12167.0639648438;5856.87719726563;0;0 7023.37158203125;6570.06201171875 0 -BSA_min_23 MULTI 2 542.31314 1082.6117 542.31314 NaN 7 5 2 0.611725 0.0737234033317691 0.695486 542.312962746134 0.556 10.085 0 75 99 -1 0 NaN 55111 0;13280.7685546875;28290.2578125;19233.314453125;29634.5625;9788.0546875;0 29634.5625;12601.22265625 0 -BSA_min_23 MULTI 3 585.91889 1754.7349 585.91889 NaN 27 14 2 0.734851 -0.112326726837182 1.772765 585.9203897338 0.212 29.803 0 13 95 -1 0 NaN 151700 0;25634;52852.154296875;83165.453125;104819.77734375;94229.328125;85360.95703125;67605.142578125;74073.81640625;70187.9453125;54396.115234375;44267.357421875;24930.5283203125;16429.5017089844;5700.82763671875;0 57372.453125;47447.32421875 2 30;74 0;1 -BSA_min_23 MULTI 5 597.06614 2980.2943 597.06614 NaN 37 11 4 0.294342 -0.116593226468922 0.472983 597.467119541279 0.428 22.125 0 43 99 -1 0 NaN 102270 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-0.0686896803804302 0.403533 447.870732206838 0.433 17.748 0 55 99 -1 0 NaN 114780 0;11778.837890625;23139.6025390625;68825.0380859375;106095.923828125;80380.0849609375;63801.41015625;49980.5732421875;27040.2021484375;23807.8686523438;0 44272.734375;47092.73046875;18533.521484375 1 76 0 -BSA_min_23 MULTI 2 457.74565 913.47674 457.74565 NaN 18 12 2 0.476739 0.0165401212738061 1.3063 457.745456355006 0.455 24.286 0 37 99 5 TLGPWGQR 8 Unmodified _TLGPWGQR_ CON__ENSEMBL:ENSBTAP00000018574 0 61894 0;16990.962890625;11575.6730957031;6160.38330078125;14041.025390625;32656.8212890625;44786.1005859375;54716.6572265625;55345.2353515625;39040.4921875;30755.6171875;35660.9853515625;0;0 43414.70703125;14701.8232421875 1 72 0 -BSA_min_23 MULTI 3 462.60021 1384.7788 462.60021 NaN 18 8 3 0.778798 0.101799265189584 0.724287 462.600287415821 0.502 15.582 0 61 99 -1 0 NaN 51167 0;6723.0703125;14707.15234375;44316.7954101563;47067.97265625;31669.6943359375;37648.8586425781;18663.072265625;11027.34765625;0 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NaN 37 10 4 0.852144 -0.17632784156649 0.491805 717.626027067929 0.408 19.942 0 49 99 -1 0 NaN 124890 0;22026.4995117188;58904.9892578125;117250.48828125;111492.02734375;105174.046875;101062.998046875;66927.7299804688;66607.2495117188;57809.5278320313;33717.2485351563;0 41750.08203125;50854.88671875;28232.26953125;14484.546875 0 -BSA_min_23 MULTI 6 386.12901 2310.7304 386.12901 NaN 4 2 2 0.730426 -0.372510238455106 4.169587 386.296780260594 0.587 4.323 0 91 99 -1 0 NaN 19777 0;10667.537109375;11550.3544921875;0 5064.693359375;6485.6611328125 0 -BSA_min_23 MULTI 1 386.96864 385.96136 386.96864 NaN 14 9 2 0.961364 -0.256178016890544 3.283629 386.967525717104 0.583 17.748 0 55 99 -1 0 NaN 51347 0;9129.955078125;11279.533203125;17809.572265625;24097.126953125;38355.6108398438;37379.2407226563;44880.3442382813;50983.2099609375;49828.7939453125;0 43493.59375;7938.8740234375 0 -BSA_min_23 MULTI 1 400.36713 399.35985 400.36713 NaN 16 10 2 0.359851 0.13614547589458 4.106837 400.36842042818 0.545 19.942 0 49 99 -1 0 NaN 78981 0;6156.287109375;12610.8056640625;16443.66796875;23166.564453125;37680.8334960938;69988.2421875;53991.6904296875;70495.287109375;76645.5185546875;74495.6787109375;0 65472.671875;17471.0625 0 -BSA_min_23 MULTI 7 401.15621 2801.0425 401.15621 NaN 11 7 2 0.042523 -0.285956722831543 2.568664 401.299140344645 0.578 13.784 0 65 99 -1 0 NaN 36821 0;7213.38037109375;6924.47998046875;17339.3579101563;16671.8857421875;19927.1689453125;23406.5014648438;4953.66796875;0 0;15112.5751953125;8411.234375 0 -BSA_min_23 MULTI 1 404.11303 403.10576 404.11303 NaN 16 9 2 0.105755 -0.119673584350551 3.455235 404.112031977039 0.583 17.748 0 55 99 -1 0 NaN 73469 0;13006.03125;21763.5092773438;30782.12109375;35696.5864257813;59794.9663085938;50389.5703125;69722.490234375;68714.9921875;61997.74609375;0 61997.74609375;9892.08203125 0 -BSA_min_23 MULTI 4 404.71106 1614.8151 404.71106 NaN 9 6 3 0.815121 0.0323063764612925 3.112679 404.961654054633 0.563 11.938 0 71 99 -1 0 NaN 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CON__ENSEMBL:ENSBTAP00000016046 0 768320 0;91299.93359375;241800.627929688;525219.90234375;753920.94140625;0 491425.375;219808.3125;42687.25390625 1 96 0 -BSA_min_23 MULTI 3 419.9065 1256.6977 419.9065 NaN 25 14 2 0.697683 0.0796025383165215 0.568655 419.9067499241 0.328 28.535 0 25 99 -1 0 NaN 57554 0;14390.53125;23922.302734375;24165.12890625;45028.5078125;31505.6552734375;47511.521484375;47811.853515625;28987.4296875;45375.6123046875;36277.5;25384.6372070313;30183.11328125;34972.8203125;22686.951171875;0 34948.3046875;22547.62890625 0 -BSA_min_23 MULTI 1 423.16235 422.15508 423.16235 NaN 28 11 3 0.155077 -0.0791138776144749 1.132056 423.162659610462 0.485 22.125 0 43 99 -1 0 NaN 525600 0;16769.75390625;35723.69140625;86788.763671875;151599.174804688;197071.871582031;238849.682617188;523878.314453125;329544.247070313;437148.26953125;456630.658203125;478603.056640625;0 439978.71875;62870.30859375;27823.416015625 0 -BSA_min_23 MULTI 1 423.15399 422.14671 423.15399 NaN 12 8 2 0.14671 -0.0874772228673919 0.244261 423.15400484274 0.578 15.582 0 61 99 -1 0 NaN 56980 0;10974.43359375;11466.44140625;17695.392578125;29738.080078125;42405.1352539063;49777.7587890625;52918.2924804688;55294.6079101563;0 49874.32421875;6935.59619140625 0 -BSA_min_23 MULTI 1 438.12074 437.11346 438.12074 NaN 14 7 2 0.113465 -0.127607350821677 4.801833 438.11835276147 0.563 13.784 0 65 99 -1 0 NaN 49183 0;12628.0346679688;18828.69140625;25120.1083984375;28692.1123046875;39040.9453125;47403.76953125;43417.169921875;0 25243.626953125;22160.142578125 0 -BSA_min_23 MULTI 2 472.23519 942.45582 472.23519 NaN 13 7 2 0.455821 -0.01770892971183 0.709379 472.235066999616 0.489 13.784 0 65 99 -1 0 NaN 56353 0;15947.7456054688;22278.6396484375;49859.734375;37677.9208984375;41839.669921875;29963.1635742188;33816.36328125;0 37885.62109375;14462.3369140625 0 -BSA_min_23 MULTI 3 512.90492 1535.6929 512.90492 NaN 12 6 2 0.692933 -0.0534854118236581 0.809488 512.90495520209 0.486 11.938 0 71 99 -1 0 NaN 39916 0;22260.3510742188;17784.23046875;29117.2568359375;23510.40234375;23676.2021484375;16407.2314453125;0 22463.94140625;14630.0244140625 0 -BSA_min_23 MULTI 2 536.75864 1071.5027 536.75864 NaN 7 4 2 0.502733 -0.0301585950960543 2.417234 537.260567742501 0.538 8.245 0 81 99 -1 0 NaN 20734 0;10059.73046875;17937.884765625;15345.3635253906;6743.6416015625;0 8550.685546875;9387.19921875 0 -BSA_min_23 MULTI 1 540.2454 539.23812 540.2454 NaN 13 7 2 0.238123 -0.0499263233698457 0.563837 540.24532444786 0.534 13.784 0 65 99 -1 0 NaN 54847 0;19292.154296875;33630.6376953125;45071.564453125;42212.9580078125;52232.3701171875;38198.8251953125;16618.658203125;0 42008.1484375;10444.9345703125 0 -BSA_min_23 MULTI 3 554.21555 1659.6248 554.21555 NaN 5 3 2 0.624827 -0.178600502911195 2.438908 554.215830630924 0.563 6.087 0 87 99 -1 0 NaN 29237 0;5868.830078125;20817.412109375;14182.5805664063;0 13458.6064453125;7358.8056640625 0 -BSA_min_23 MULTI 1 555.36421 554.35693 555.36421 NaN 11 6 2 0.356931 0.0619270308284285 0.459428 555.364097382042 0.545 11.938 0 71 99 -1 0 NaN 91371 0;11953.4111328125;56464.546875;61339.1220703125;87016.013671875;81907.529296875;69299.189453125;0 66361.0859375;22625.541015625 0 -BSA_min_23 MULTI 2 557.78935 1113.5641 557.78935 NaN 6 4 2 0.564147 0.0119075165016511 2.421348 557.790434802409 0.587 8.245 0 81 99 -1 0 NaN 16272 0;5989.40087890625;6732.34521484375;11646.4931640625;13934.3364257813;0 7986.845703125;5947.49072265625 0 -BSA_min_23 MULTI 2 559.76878 1117.523 559.76878 NaN 23 12 2 0.523015 -0.0310453934680481 0.427681 559.768803208661 0.515 24.286 0 37 99 -1 0 NaN 67211 0;30329.0063476563;50724.841796875;38037.4775390625;23608.0405273438;19378.5034179688;16818.5107421875;26791.890625;53347.1015625;57557.26953125;40855.7099609375;44248.58984375;6340.10107421875;0 37219.31640625;20337.953125 1 83 0 -BSA_min_23 MULTI 2 582.76086 1163.5072 582.76086 NaN 8 4 2 0.507164 -0.0680497736839243 0.460671 582.760715553871 0.587 8.245 0 81 99 -1 0 NaN 108980 0;29966.9487304688;59326.3994140625;83047.06640625;92434.69921875;0 60649.01953125;31785.6796875 1 92 0 -BSA_min_23 MULTI 2 602.33276 1202.651 602.33276 NaN 7 6 2 0.650966 0.0577468625917845 1.790633 602.333558802656 0.548 11.938 0 71 99 -1 0 NaN 19364 0;5811.33935546875;6557.4794921875;7303.61962890625;9868.7724609375;15106.3935546875;5047.06591796875;0 9868.7724609375;6315.080078125 0 -BSA_min_23 MULTI 2 609.30165 1216.5887 609.30165 NaN 5 3 2 0.588746 -0.010884807340517 3.455607 609.801905531048 0.578 6.087 0 87 99 -1 0 NaN 18519 0;6848.39208984375;14504.1098632813;15519.5483398438;0 5654.28662109375;10022.16015625 0 -BSA_min_23 MULTI 2 626.82568 1251.6368 626.82568 NaN 8 5 2 0.636813 0.0210605159502393 0.897662 627.327160354538 0.556 10.085 0 75 99 -1 0 NaN 20467 0;7513.7216796875;15837.8994140625;13457.0910644531;10665.5668945313;6652.02783203125;0 7548.9072265625;10244.0595703125 0 -BSA_min_23 MULTI 3 635.60201 1903.7842 635.60201 NaN 11 4 3 0.784211 -0.131529739430107 0.794887 635.601854227925 0.587 8.245 0 81 99 -1 0 NaN 109400 0;11539.9194335938;49907.1435546875;64455.1904296875;94715.8671875;0 41372.8828125;37360.796875;15982.1875 1 93 0 -BSA_min_23 MULTI 2 722.29286 1442.5712 722.29286 NaN 11 4 3 0.571176 -0.132406498940327 0.529807 722.794557009268 0.587 8.245 0 81 99 -1 0 NaN 88555 0;19382.1572265625;29263.3842773438;56304.751953125;72047.59765625;0 31798.40625;40249.19140625;9051.69140625 2 94;97 0;0 -BSA_min_23 MULTI 2 731.29826 1460.582 731.29826 NaN 9 5 2 0.581963 -0.129905034647663 1.015729 731.799523381077 0.526 10.085 0 75 99 -1 0 NaN 29169 0;10700.2763671875;21935.4814453125;17981.1000976563;13056.220703125;17802.30078125;0 11073.208984375;11301.125 1 90 0 -BSA_min_23 MULTI 2 772.32634 1542.6381 772.32634 NaN 16 12 3 0.638121 -0.111492432172099 0.832583 772.326445295162 0.587 24.286 0 37 99 -1 0 NaN 48065 0;8672.376953125;7721.82470703125;8208.14233398438;8694.4599609375;12981.9775390625;10428.1220703125;10370.2294921875;9308.8408203125;12825.458984375;17852.220703125;30189.3129882813;24380.708984375;0 19063.345703125;15360.51953125;9020.189453125 0 -BSA_min_23 MULTI 3 776.67069 2326.9902 776.67069 NaN 7 3 3 0.990245 -0.120170237694765 2.142655 777.004331643663 0.571 6.087 0 87 99 -1 0 NaN 37194 0;6977.5546875;29906.751953125;25277;0 9063.5791015625;14645.7783203125;12678.326171875 0 -BSA_min_23 MULTI 1 837.43637 836.42909 837.43637 NaN 7 4 2 0.429093 0.0043357496634826 1.321128 837.436103089852 0.587 8.245 0 81 99 -1 0 NaN 73009 0;8795.1123046875;28166.4892578125;33590.7690429688;65961.154296875;0 53311.69140625;12649.462890625 0 -BSA_min_23 MULTI 2 882.84611 1763.6777 882.84611 NaN 12 7 3 0.677665 -0.17362702288824 0.483171 882.846072087715 0.563 13.784 0 65 99 -1 0 NaN 1179300 0;10685.890625;57645.44140625;185231.5625;292455.5625;750275.78125;1040647.75;871335.640625;0 494015.65625;379948.71875;166683.375 1 100 0 -BSA_min_23 MULTI 2 886.81224 1771.6099 886.81224 NaN 8 5 2 0.609919 -0.245021216350096 1.522474 887.31412154531 0.576 10.085 0 75 99 -1 0 NaN 29012 0;5249.1533203125;6298.3564453125;13226.2900390625;17856.4375;20045.5546875;0 8890.65234375;11784.896484375 0 -BSA_min_23 MULTI 1 899.44874 898.44146 899.44874 NaN 10 6 2 0.441463 -0.0118196933137824 0.473138 899.44868329937 0.563 11.938 0 71 99 -1 0 NaN 93356 0;10259.021484375;11104.9755859375;38988.1611328125;51494.2109375;83477.83203125;72926.943359375;0 61125.3359375;22352.49609375 0 -BSA_min_23 MULTI 2 973.90466 1945.7948 973.90466 NaN 7 4 2 0.794757 -0.14030840214582 1.357784 973.904958275679 0.587 8.245 0 81 99 -1 0 NaN 67032 0;22343.408203125;30602.4375;39709.193359375;30783.283203125;0 30783.283203125;12774.3359375 0 -BSA_min_23 MULTI 1 1012.4647 1011.4574 1012.4647 NaN 10 6 2 0.457396 -0.0478741148867812 0.66179 1012.46465963589 0.58 11.938 0 71 99 -1 0 NaN 45315 0;6566.83447265625;5892.9794921875;22179.6865234375;26302.4379882813;35693.482421875;39795.4755859375;0 31461.541015625;12683.193359375 0 -BSA_min_23 MULTI 2 1044.9323 2087.8501 1044.9323 NaN 6 4 2 0.850137 -0.150273671131799 1.779455 1045.43259299012 0.587 8.245 0 81 99 -1 0 NaN 22292 0;6181.01806640625;6017.2158203125;11961.13671875;13880.3842773438;0 6740.865234375;7139.51904296875 0 -BSA_min_23 MULTI 2 1074.9485 2147.8825 1074.9485 NaN 7 5 2 0.882505 -0.145520540587768 1.74705 1074.94713499826 0.56 10.085 0 75 99 -1 0 NaN 47904 0;7807.28466796875;5717.341796875;13474.2958984375;16493.6396484375;19157.744140625;0 13474.2958984375;10645.7109375 0 -BSA_min_23 MULTI 1 1164.5167 1163.5094 1164.5167 NaN 6 4 2 0.50944 -0.065774688654983 0.883473 1164.51651446826 0.569 8.245 0 81 99 -1 0 NaN 30247 0;5882.703125;19118.6171875;25656.2758789063;16791.0786132813;0 19902.078125;6989.12060546875 0 -BSA_min_23 MULTI 1 1177.4707 1176.4634 1177.4707 NaN 18 7 3 0.463421 -0.117752640125445 0.401898 1177.47052434449 0.565 13.784 0 65 99 -1 0 NaN 191160 0;13462.1650390625;32176.0517578125;66198.634765625;127578.37890625;153005.427734375;176360.41015625;148912.65625;0 107823.8203125;52374.53515625;18917.345703125 1 64 0
--- a/test-data/single/combined/txt/evidence.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Sequence Length Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Oxidation (M) Missed cleavages Proteins Leading proteins Leading razor protein Type Raw file Experiment MS/MS m/z Charge m/z Mass Resolution 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 AIF MS/MS IDs Oxidation (M) site IDs -DSFDIIK 7 Unmodified _DSFDIIK_ 0 0 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 419.221313476563 2 419.221268 836.427984 NaN 0 0 0.54276 0.00022754 0.54276 0.00022754 419.22139467134 0.58669 0.13742 0.58669 0.46121 0.59862 0 11 4 3 0 0 0 0.010549 1 96 0 0 1 768320 + 0 2 0 0 0 0 -LLESEECR 8 Unmodified _LLESEECR_ 0 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 CON__Q14CN4-1 MSMS BSA_min_23 BSA_min_23.mzXML 518.238220214844 2 518.242406 1034.47026 NaN NaN NaN NaN NaN NaN NaN NaN 0.50957 1 0.50957 0.0095717 1.0096 0 0 0 0 0.0075205 1 86 1.6313 1.6313 1 + 1 5 1 1 1 1 -LVTDLTK 7 Unmodified _LVTDLTK_ 0 0 CON__P02769;bsa;CON__P02768-1 CON__P02769 CON__P02769 MSMS BSA_min_23 BSA_min_23.mzXML 395.239288330078 2 395.239461 788.46437 NaN NaN NaN NaN NaN NaN NaN NaN 0.010013 1 0.010013 -0.48999 0.51001 0 0 0 0 0.0046553 1 2 0 0 1 + 2 0 2 2 2 2 -QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 419.221313476563 3 419.906482 1256.69762 NaN 0 0 0.052788 2.2166E-05 0.052788 2.2166E-05 419.9067499241 0.32847 0.47559 0.32847 0.12303 0.59862 0 25 14 2 0 0 0 0.011549 1 96 0 0 1 57554 + 3 1 3 3 3 3 -SLSAIRER 8 Unmodified _SLSAIRER_ 0 1 CON__Q03247 CON__Q03247 CON__Q03247 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 465.766693115234 2 466.269616 930.524678 NaN 0 0 -3.0904 -0.0014409 -3.0904 -0.0014409 466.26850803291 0.10674 0.17216 0.10674 -0.014552 0.15761 0 6 4 2 0 0 0 0.011549 1 17 0 0 1 33499 + 4 4 4 4 4 4 -TLGPWGQR 8 Unmodified _TLGPWGQR_ 0 0 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 457.746032714844 2 457.745776 913.477 NaN 0 0 -0.28456 -0.00013026 -0.28456 -0.00013026 457.745456355006 0.4547 0.40477 0.4547 0.19386 0.59862 -5.5511E-17 18 12 2 0 0 0 0.01108 1 72 0 0 1 61894 + 5 3 5 5 5 5
--- a/test-data/single/combined/txt/modificationSpecificPeptides.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Oxidation (M) Missed cleavages Experiment BSA_min_23.mzXML Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count -DSFDIIK Unmodified 836.42798 0.42798405 2 CON__ENSEMBL:ENSBTAP00000016046 yes yes 0 0 1 0.58669 0.58669 2 0.010549 96 BSA_min_23 0 0 768320 768320 + 0 2 0 0 0 0 1 -LLESEECR Unmodified 1034.4703 0.47025958 5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 yes no 0 0 1 0.50957 0.50957 2 0.0075205 86 BSA_min_23 1.6313 1.6313 0 0 + 1 5 1 1 1 1 1 -LVTDLTK Unmodified 788.46437 0.46436956 0 CON__P02769;bsa;CON__P02768-1 yes no 0 0 1 0.010013 0.010013 2 0.0046553 2 BSA_min_23 0 0 0 0 + 2 0 2 2 2 2 1 -QLELEKQLEK Unmodified 1256.6976 0.69761697 1 CON__ENSEMBL:ENSBTAP00000001528 yes yes 0 1 1 0.32847 0.32847 3 0.011549 96 BSA_min_23 0 0 57554 57554 + 3 1 3 3 3 3 0 -SLSAIRER Unmodified 930.52468 0.52467841 4 CON__Q03247 yes yes 0 1 1 0.10674 0.10674 2 0.011549 17 BSA_min_23 0 0 33499 33499 + 4 4 4 4 4 4 0 -TLGPWGQR Unmodified 913.477 0.47699993 3 CON__ENSEMBL:ENSBTAP00000018574 yes yes 0 0 1 0.4547 0.4547 2 0.01108 72 BSA_min_23 0 0 61894 61894 + 5 3 5 5 5 5 1
--- a/test-data/single/combined/txt/msms.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs 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 ScanNumber 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 id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs -BSA_min_23 96 77 DSFDIIK 7 0 Unmodified _DSFDIIK_ 0 CON__ENSEMBL:ENSBTAP00000016046 2 CID FTMS MULTI-MSMS 1 0 419.22127 836.42798 0.54276 0.00022754 NaN 0.57043 0.010549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 DSFDIIK _DSFDIIK_ 0 2 0 0 0 -BSA_min_23 86 70 LLESEECR 8 0 Unmodified _LLESEECR_ 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 2 CID FTMS MSMS 5 518.24241 1034.4703 NaN NaN NaN 0.50957 0.0075205 1.6313 1.6313 NaN NaN 1 0 0 0 81 10271.2001953125 1 0 0 y6 11.7 0.0135096433999706 16.6930827476743 809.2958984375 1 0.00309955136349784 0.00847457627118644 None Unknown 1.63126590808724;0;0 LLESEECR;LGSDMEDLR;QLNQEMEK _LLESEECR_;_LGSDMEDLR_;_QLNQEM(ox)EK_ 1 5 1 1 1 -BSA_min_23 2 0 LVTDLTK 7 0 Unmodified _LVTDLTK_ 0 CON__P02769;bsa;CON__P02768-1 2 CID FTMS MSMS 1 395.23946 788.46437 NaN NaN NaN 0.010013 0.0046553 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0;0 LVTDLTK;DSLLTLK _LVTDLTK_;_DSLLTLK_ 2 0 2 2 2 -BSA_min_23 96 77 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 3 CID FTMS MULTI-SECPEP 1 -2 419.90648 1256.6976 0.052788 2.2166E-05 NaN 0.57043 0.011549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 1 3 3 3 -BSA_min_23 17 13 SLSAIRER 8 1 Unmodified _SLSAIRER_ 0 CON__Q03247 2 CID FTMS MULTI-SECPEP 4 -1 466.26962 930.52468 -3.0904 -0.0014409 NaN 0.096553 0.011549 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 SLSAIRER _SLSAIRER_ 4 4 4 4 4 -BSA_min_23 72 58 TLGPWGQR 8 0 Unmodified _TLGPWGQR_ 0 CON__ENSEMBL:ENSBTAP00000018574 2 CID FTMS MULTI-MSMS 1 0 457.74578 913.477 -0.28456 -0.00013026 NaN 0.42593 0.01108 0 0 NaN NaN 1 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 0 0 0 None Unknown 0;0 TLGPWGQR;IHVFNER _TLGPWGQR_;_IHVFNER_ 5 3 5 5 5
--- a/test-data/single/combined/txt/msmsScans.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -Raw file Scan number Retention time Ion injection time Total ion current Collision energy Summations Base peak intensity Elapsed time Identified 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 Experiment Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number -BSA_min_23 2 0.010013 -1 35863 35 0 0 -1 + 2 LVTDLTK 7 103 395.239288330078 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 Unmodified _LVTDLTK_ bsa;CON__P02768-1;CON__P02769 0 BSA_min_23.mzXML NaN NaN NaN 0 0 0 1 -BSA_min_23 3 0.01458 -1 30585 35 0 0 -1 - -1 0 164 552.918823242188 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 1 0 1 -BSA_min_23 4 0.020265 -1 11886 35 0 0 -1 - -1 0 126 676.387463660038 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 2 0 1 -BSA_min_23 5 0.025633 -1 12813 35 0 0 -1 - -1 0 146 751.810668945313 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 3 0 1 -BSA_min_23 6 0.031253 -1 10791 35 0 0 -1 - -1 0 124 670.800842285156 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 4 0 1 -BSA_min_23 8 0.044372 -1 7950.3 35 0 0 -1 - -1 0 111 456.581360511828 2733.44450427137 6 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 5 1 7 -BSA_min_23 9 0.049315 -1 13730 35 0 0 -1 - -1 0 120 562.257629394531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 6 1 7 -BSA_min_23 10 0.05446 -1 8774.7 35 0 0 -1 - -1 0 121 589.203410887949 588.196134421349 1 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 7 1 7 -BSA_min_23 11 0.06018 -1 4436.2 35 0 0 -1 - -1 0 115 828.876770019531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 8 1 7 -BSA_min_23 12 0.065908 -1 3625.8 35 0 0 -1 - -1 0 112 639.798400878906 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 9 1 7 -BSA_min_23 14 0.078957 -1 13236 35 0 0 -1 - -1 0 137 883.333059829652 1764.6515667261 2 MULTI CID FTMS 0 0 0 13 171569.53125 0.0583552615411773 -4 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 10 2 13 -BSA_min_23 15 0.084805 -1 6304.6 35 0 0 -1 - -1 0 120 602.8994140625 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 11 2 13 -BSA_min_23 16 0.090573 -1 12119 35 0 0 -1 - -1 0 135 648.602708784548 1942.78629695384 3 MULTI CID FTMS 0 0 0 13 52074.7734375 0.102435594507697 -16 NaN 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 12 2 13 -BSA_min_23 17 0.096553 -1 5932.3 35 0 0 -1 - -1 0 110 465.766693115234 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 13 2 13 -BSA_min_23 18 0.10154 -1 4161.5 35 0 0 -1 - -1 0 108 605.758117675781 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 14 2 13 -BSA_min_23 20 0.11439 -1 65173 35 0 0 -1 - -1 0 102 387.700285234344 NaN 0 PEAK CID FTMS 0 0 0 19 5176.81640625 0.231645826498235 -7 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 15 3 19 -BSA_min_23 21 0.11842 -1 33705 35 0 0 -1 - -1 0 123 430.226482307928 NaN 0 PEAK CID FTMS 0 0 0 19 7040.359375 0.343536017509867 -2 0.0701033333333334 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 16 3 19 -BSA_min_23 22 0.1234 -1 9502.6 35 0 0 -1 - -1 0 111 455.744353147131 NaN 0 PEAK CID FTMS 0 0 0 19 112493.5 0.827447086298523 -1 0.0355433333333333 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 17 3 19 -BSA_min_23 23 0.12833 -1 2553.5 35 0 0 -1 - -1 0 105 664.964606092136 1991.87198887661 3 MULTI CID FTMS 0 0 0 19 58531.14453125 1 0 0 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 18 3 19 -BSA_min_23 24 0.13435 -1 5665.1 35 0 0 -1 - -1 0 93 441.716446446474 881.418339959749 2 MULTI CID FTMS 0 0 0 19 40583.5390625 0.581327680935085 -1 0.0355433333333333 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 19 3 19 -BSA_min_23 26 0.14696 -1 4965.5 35 0 0 -1 - -1 0 111 972.401410273474 1942.78826761375 2 MULTI CID FTMS 0 0 0 25 65218.546875 0.578387033725099 -12 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 20 4 25 -BSA_min_23 27 0.15284 -1 3538.8 35 0 0 -1 - -1 0 124 903.846651631555 1805.67875032991 2 MULTI CID FTMS 0 0 0 25 39216.41796875 1 0 0 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 21 4 25 -BSA_min_23 28 0.15869 -1 612.01 35 0 0 -1 - -1 0 40 931.328202121547 1860.64185130989 2 MULTI CID FTMS 0 0 0 25 32505.169921875 0.556008699617638 -3 0.102683333333333 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 22 4 25 -BSA_min_23 29 0.16448 -1 3712.5 35 0 0 -1 - -1 0 134 730.799031095722 1459.58350925824 2 MULTI CID FTMS 0 0 0 25 39553.00390625 1 0 0 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 23 4 25 -BSA_min_23 30 0.17003 -1 5047.2 35 0 0 -1 - -1 0 108 585.918893568188 1754.73485130476 3 MULTI CID FTMS 0 0 0 25 27986.6171875 0.487805831250134 -2 0.0681233333333334 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 24 4 25 -BSA_min_23 32 0.18323 -1 3672.2 35 0 0 -1 - -1 0 95 597.209739443197 NaN 0 PEAK CID FTMS 0 0 0 31 45858.6953125 0.706827549584025 -2 0.0691516666666667 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 25 5 31 -BSA_min_23 33 0.18901 -1 10554 35 0 0 -1 - -1 0 112 487.53462335476 1459.58204066448 3 MULTI CID FTMS 0 0 0 31 17205.21875 0.534308072152896 2 -0.07205 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 26 5 31 -BSA_min_23 34 0.19399 -1 794.02 35 0 0 -1 - -1 0 53 931.328202121547 1860.64185130989 2 MULTI CID FTMS 0 0 0 31 40352.77734375 0.775544041279623 -1 0.0365716666666666 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 27 5 31 -BSA_min_23 35 0.19977 -1 6966.5 35 0 0 -1 - -1 0 119 622.281005859375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 28 5 31 -BSA_min_23 36 0.20575 -1 2000.1 35 0 0 -1 - -1 0 122 843.968139648438 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 29 5 31 -BSA_min_23 38 0.21916 -1 3920.8 35 0 0 -1 - -1 0 120 703.140521860943 4212.79947236606 6 MULTI CID FTMS 0 0 0 37 38276.57421875 1 0 0 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 30 6 37 -BSA_min_23 39 0.22523 -1 7753.4 35 0 0 -1 - -1 0 121 542.752915907862 NaN 0 PEAK CID FTMS 0 0 0 37 7960.71728515625 0.810623529138009 -1 0.0359233333333333 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 31 6 37 -BSA_min_23 40 0.23041 -1 2121.2 35 0 0 -1 - -1 0 108 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 37 47932.00390625 1 0 0 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 32 6 37 -BSA_min_23 41 0.23643 -1 2589.1 35 0 0 -1 - -1 0 110 592.559742773291 1774.65739892007 3 MULTI CID FTMS 0 0 0 37 51832.45703125 1 0 0 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 33 6 37 -BSA_min_23 42 0.24218 -1 6786.4 35 0 0 -1 - -1 0 114 558.888078141406 1673.64240502442 3 MULTI CID FTMS 0 0 0 37 50127.9140625 0.805054408903464 -3 0.105075 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 34 6 37 -BSA_min_23 44 0.25533 -1 3829.3 35 0 0 -1 - -1 0 126 808.753845214844 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 35 7 43 -BSA_min_23 45 0.26131 -1 2056.8 35 0 0 -1 - -1 0 95 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 43 42148.32421875 1 0 0 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 36 7 43 -BSA_min_23 46 0.26732 -1 4217.2 35 0 0 -1 - -1 0 115 703.140521860943 4212.79947236606 6 MULTI CID FTMS 0 0 0 43 34525.390625 0.901997927706068 1 -0.0366366666666667 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 37 7 43 -BSA_min_23 47 0.27336 -1 4417.5 35 0 0 -1 - -1 0 112 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 43 36233.25 0.312245808501738 -5 0.176745 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 38 7 43 -BSA_min_23 48 0.27939 -1 4893.8 35 0 0 -1 - -1 0 114 525.286926269531 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 39 7 43 -BSA_min_23 50 0.29214 -1 2694.3 35 0 0 -1 - -1 0 118 844.169032154843 4215.80877844122 5 MULTI CID FTMS 0 0 0 49 18802.0625 1 0 0 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 40 8 49 -BSA_min_23 51 0.29815 -1 4123.5 35 0 0 -1 - -1 0 123 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 49 37438.125 0.322629010906119 -4 0.145258333333333 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 41 8 49 -BSA_min_23 52 0.30417 -1 2801.3 35 0 0 -1 - -1 0 103 629.356568937177 1256.69858494115 2 MULTI CID FTMS 0 0 0 49 47581.3515625 1 0 0 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 42 8 49 -BSA_min_23 53 0.30942 -1 3120.2 35 0 0 -1 - -1 0 121 747.856093035124 1493.69763313705 2 MULTI CID FTMS 0 0 0 49 27482.5703125 1 0 0 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 43 8 49 -BSA_min_23 54 0.31497 -1 1089.3 35 0 0 -1 - -1 0 87 1177.44225204557 3529.3049267369 3 MULTI CID FTMS 0 0 0 49 22208.09765625 0.573548719035153 2 -0.0722016666666667 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 44 8 49 -BSA_min_23 56 0.32853 -1 4609.2 35 0 0 -1 - -1 0 134 808.5537109375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 45 9 55 -BSA_min_23 57 0.33454 -1 4781 35 0 0 -1 - -1 0 114 491.773453701772 981.532354470344 2 MULTI CID FTMS 0 0 0 55 66131.3984375 1 0 0 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 46 9 55 -BSA_min_23 58 0.33958 -1 3940 35 0 0 -1 - -1 0 120 674.296931013294 NaN 0 PEAK CID FTMS 0 0 0 55 46957.76171875 0.404665998035039 -3 0.10925 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 47 9 55 -BSA_min_23 59 0.34561 -1 5227 35 0 0 -1 - -1 0 94 517.743469238281 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 48 9 55 -BSA_min_23 60 0.35072 -1 3062.2 35 0 0 -1 - -1 0 101 664.964606092136 1991.87198887661 3 MULTI CID FTMS 0 0 0 55 33396.828125 0.665850940487736 5 -0.158593333333333 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 49 9 55 -BSA_min_23 62 0.36446 -1 6953.5 35 0 0 -1 - -1 0 98 460.254338656322 459.247062189722 1 MULTI CID FTMS 0 0 0 61 110063.5625 0.350472556233784 3 -0.0859683333333334 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 50 10 61 -BSA_min_23 63 0.36944 -1 3605.8 35 0 0 -1 - -1 0 128 700.332580566406 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 51 10 61 -BSA_min_23 64 0.37486 -1 1611.8 35 0 0 -1 - -1 0 101 1177.47069699992 1176.46342053332 1 MULTI CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 52 10 61 -BSA_min_23 66 0.3885 -1 5670 35 0 0 -1 - -1 0 100 622.5341796875 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 53 11 65 -BSA_min_23 67 0.39452 -1 3085.9 35 0 0 -1 - -1 0 115 594.556274414063 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 54 11 65 -BSA_min_23 68 0.40026 -1 1992.2 35 0 0 -1 - -1 0 96 686.596525404719 2056.76774681436 3 MULTI CID FTMS 0 0 0 65 21625.0703125 0.451161406787757 5 -0.157466666666667 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 55 11 65 -BSA_min_23 69 0.40626 -1 1117.7 35 0 0 -1 - -1 0 76 1173.07641144645 2344.1382699597 2 MULTI CID FTMS 0 0 0 65 24950.53125 1 0 0 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 56 11 65 -BSA_min_23 70 0.41227 -1 2287.8 35 0 0 -1 - -1 0 138 1177.58276971623 2353.15098649927 2 MULTI CID FTMS 0 0 0 65 8500.6943359375 0.643644763729794 1 -0.0373533333333333 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 57 11 65 -BSA_min_23 72 0.42593 -1 5725.3 35 0 0 -1 + 5 TLGPWGQR 8 96 457.745646177304 913.476739421408 2 MULTI CID FTMS 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 1 Unmodified _TLGPWGQR_ CON__ENSEMBL:ENSBTAP00000018574 0 BSA_min_23.mzXML NaN NaN NaN 0 58 12 71 -BSA_min_23 73 0.43088 -1 1163.3 35 0 0 -1 - -1 0 65 1010.44003116945 4037.73101881139 4 MULTI CID FTMS 0 0 0 71 15265.9873046875 0.567392976805677 -2 0.0615566666666666 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 59 12 71 -BSA_min_23 74 0.43685 -1 4314.7 35 0 0 -1 - -1 0 113 585.918893568188 1754.73485130476 3 MULTI CID FTMS 0 0 0 71 21487.865234375 0.45287833588482 6 -0.168346666666667 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 60 12 71 -BSA_min_23 76 0.45047 -1 8334.6 35 0 0 -1 - -1 0 119 447.536449992962 1339.58752057909 3 MULTI CID FTMS 0 0 0 75 40469.671875 0.9140992180924 1 -0.0369099999999999 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 61 13 75 -BSA_min_23 77 0.45584 -1 4436.9 35 0 0 -1 - -1 0 95 597.066144900786 2980.29434217093 5 MULTI CID FTMS 0 0 0 75 33103.19921875 0.991897253233573 1 -0.0369099999999999 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 62 13 75 -BSA_min_23 78 0.46188 -1 2747.5 35 0 0 -1 - -1 0 106 664.964606092136 1991.87198887661 3 MULTI CID FTMS 0 0 0 75 18094.236328125 0.676187560804335 3 -0.0957016666666666 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 63 13 75 -BSA_min_23 79 0.46792 -1 3792.1 35 0 0 -1 - -1 0 127 782.86823361998 1563.72191430676 2 MULTI CID FTMS 0 0 0 75 24751.693359375 0.989113548898297 -1 0.0244116666666667 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 64 13 75 -BSA_min_23 80 0.4736 -1 1227.2 35 0 0 -1 - -1 0 96 1173.07641144645 2344.1382699597 2 MULTI CID FTMS 0 0 0 75 23081.546875 1 0 0 5 NaN BSA_min_23.mzXML NaN NaN NaN 0 65 13 75 -BSA_min_23 82 0.48722 -1 6556.1 35 0 0 -1 - -1 0 116 629.356568937177 1256.69858494115 2 MULTI CID FTMS 0 0 0 81 28788.931640625 1 0 0 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 66 14 81 -BSA_min_23 83 0.4925 -1 6615.3 35 0 0 -1 - -1 0 116 559.768784063361 1117.52301519352 2 MULTI CID FTMS 0 0 0 81 35334.84765625 0.949368528711517 -1 0.0369099999999999 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 67 14 81 -BSA_min_23 84 0.49762 -1 6183.7 35 0 0 -1 - -1 0 125 972.401410273474 1942.78826761375 2 MULTI CID FTMS 0 0 0 81 19756.91796875 0.347354270628424 7 NaN 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 68 14 81 -BSA_min_23 85 0.50353 -1 3559.8 35 0 0 -1 - -1 0 116 681.999313403946 2042.97611081204 3 MULTI CID FTMS 0 0 0 81 11550.4775390625 0.629091502669348 2 -0.0587916666666667 4 NaN BSA_min_23.mzXML NaN NaN NaN 0 69 14 81 -BSA_min_23 86 0.50957 -1 5114.2 35 0 0 -1 + 1 LLESEECR 8 118 518.240989833781 NaN 0 PEAK CID FTMS 0 0 0 81 10271.2001953125 1 0 0 5 Unmodified _LLESEECR_ CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1.63126590808724 BSA_min_23.mzXML NaN NaN NaN 0 70 14 81 -BSA_min_23 88 0.52259 -1 44411 35 0 0 -1 - -1 0 134 385.207382835291 384.200106368691 1 MULTI CID FTMS 0 0 0 87 5929296.5 0.739051055541228 -3 0.0963616666666667 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 71 15 87 -BSA_min_23 89 0.52681 -1 3749.8 35 0 0 -1 - -1 0 100 597.066144900786 2980.29434217093 5 MULTI CID FTMS 0 0 0 87 19359.11328125 0.820197080002651 2 -0.04811 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 72 15 87 -BSA_min_23 90 0.53279 -1 3364.5 35 0 0 -1 - -1 0 128 731.29825780069 1460.58196266818 2 MULTI CID FTMS 0 0 0 87 10634.3564453125 0.960368079417471 -1 0.0350400000000001 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 73 15 87 -BSA_min_23 92 0.54611 -1 4680.5 35 0 0 -1 - -1 0 116 582.760858227368 1163.50716352154 2 MULTI CID FTMS 0 0 0 91 46220.83984375 0.762103661377976 -2 0.0587916666666667 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 74 16 91 -BSA_min_23 93 0.55132 -1 3773.2 35 0 0 -1 - -1 0 106 635.60201346581 1903.78421099763 3 MULTI CID FTMS 0 0 0 91 24284.580078125 0.586968526901584 -2 0.0587916666666667 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 75 16 91 -BSA_min_23 94 0.55721 -1 4670.5 35 0 0 -1 - -1 0 143 722.292864587666 1442.57117624213 2 MULTI CID FTMS 0 0 0 91 14970.0166015625 0.470778833500893 -2 0.0587916666666667 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 76 16 91 -BSA_min_23 96 0.57043 -1 15235 35 0 0 -1 + 0 DSFDIIK 7 110 419.22149602984 836.428439126479 2 MULTI CID FTMS 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 1 Unmodified _DSFDIIK_ CON__ENSEMBL:ENSBTAP00000016046 0 BSA_min_23.mzXML NaN NaN NaN 0 77 17 95 -BSA_min_23 97 0.57533 -1 4806.4 35 0 0 -1 - -1 0 129 722.292864587666 1442.57117624213 2 MULTI CID FTMS 0 0 0 95 26752.708984375 0.841322322069994 -1 0.0243583333333334 2 NaN BSA_min_23.mzXML NaN NaN NaN 0 78 17 95 -BSA_min_23 98 0.58084 -1 3667 35 0 0 -1 - -1 0 113 595.224647156549 NaN 0 PEAK CID FTMS 0 0 0 95 6964.16259765625 0.341923515563021 -1 0.0243583333333334 3 NaN BSA_min_23.mzXML NaN NaN NaN 0 79 17 95 -BSA_min_23 100 0.59414 -1 44171 35 0 0 -1 - -1 0 176 882.846108818038 1763.67766470288 2 MULTI CID FTMS 0 0 0 99 379571.375 0.768338756470332 1 NaN 1 NaN BSA_min_23.mzXML NaN NaN NaN 0 80 18 99
--- a/test-data/single/combined/txt/mzRange.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1881 +0,0 @@ -Raw file m/z Peaks / Da Single peaks / Da Isotope patterns / Da Single isotope patterns / Da SILAC pairs / Da Identified SILAC pairs / Da SILAC identification rate [%] MS/MS / Da Identified MS/MS / Da Identification rate [%] -BSA_min_23 111.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 112.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 113.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 114.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 115.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 116.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 117.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 118.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 119.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 120.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 121.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 122.199897766113 0 0 0 0 0 0 NaN 0 0 -BSA_min_23 123.199897766113 0 0 0 0 0 0 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48.85 -BSA_min_23 349.199897766113 38.06 1.291 5.703 0 0.2851 0.01371 4.81 0.02829 0.014 49.49 -BSA_min_23 350.199897766113 38.94 1.317 5.867 0 0.2934 0.01429 4.87 0.02864 0.01429 49.88 -BSA_min_23 351.199897766113 39.37 1.332 5.917 0 0.2959 0.01429 4.829 0.029 0.01429 49.26 -BSA_min_23 352.199897766113 39.8 1.346 5.967 0 0.2984 0.01429 4.788 0.02936 0.01429 48.66 -BSA_min_23 353.199897766113 40.23 1.361 6.017 0 0.3009 0.01429 4.748 0.02971 0.01429 48.08 -BSA_min_23 354.199897766113 40.66 1.376 6.067 0 0.3034 0.01429 4.709 0.03007 0.01429 47.51 -BSA_min_23 355.199897766113 41.09 1.39 6.117 0 0.3059 0.01429 4.671 0.03043 0.01429 46.95 -BSA_min_23 356.199897766113 41.51 1.405 6.167 0 0.3084 0.01429 4.633 0.03079 0.01429 46.4 -BSA_min_23 357.199897766113 41.94 1.42 6.217 0 0.3109 0.01429 4.596 0.03114 0.01429 45.87 -BSA_min_23 358.199897766113 42.37 1.434 6.267 0 0.3134 0.01429 4.559 0.0315 0.01429 45.35 -BSA_min_23 359.199897766113 42.8 1.449 6.317 0 0.3159 0.01429 4.523 0.03186 0.01429 44.84 -BSA_min_23 360.199897766113 43.23 1.464 6.367 0 0.3184 0.01429 4.487 0.03221 0.01429 44.35 -BSA_min_23 361.199897766113 43.66 1.478 6.417 0 0.3209 0.01429 4.452 0.03257 0.01429 43.86 -BSA_min_23 362.199897766113 44.09 1.493 6.467 0 0.3234 0.01429 4.418 0.03293 0.01429 43.38 -BSA_min_23 363.199897766113 44.51 1.508 6.517 0 0.3259 0.01429 4.384 0.03329 0.01429 42.92 -BSA_min_23 364.199897766113 44.94 1.522 6.567 0 0.3284 0.01429 4.351 0.03364 0.01429 42.46 -BSA_min_23 365.199897766113 45.37 1.537 6.617 0 0.3309 0.01429 4.318 0.034 0.01429 42.02 -BSA_min_23 366.199897766113 45.8 1.551 6.667 0 0.3334 0.01429 4.285 0.03436 0.01429 41.58 -BSA_min_23 367.199897766113 46.23 1.566 6.717 0 0.3359 0.01429 4.254 0.03471 0.01429 41.15 -BSA_min_23 368.199897766113 46.66 1.581 6.767 0 0.3384 0.01429 4.222 0.03507 0.01429 40.73 -BSA_min_23 369.199897766113 47.09 1.595 6.817 0 0.3409 0.01429 4.191 0.03543 0.01429 40.32 -BSA_min_23 370.199897766113 47.48 1.609 6.863 0 0.3431 0.01436 4.184 0.03607 0.01436 39.8 -BSA_min_23 371.199897766113 47.72 1.618 6.891 0 0.3446 0.01471 4.27 0.03786 0.01471 38.87 -BSA_min_23 372.199897766113 47.96 1.627 6.92 0 0.346 0.01507 4.356 0.03964 0.01507 38.02 -BSA_min_23 373.199897766113 48.21 1.636 6.949 0 0.3474 0.01543 4.441 0.04143 0.01543 37.24 -BSA_min_23 374.199897766113 48.45 1.645 6.977 0 0.3489 0.01579 4.525 0.04321 0.01579 36.53 -BSA_min_23 375.199897766113 48.69 1.654 7.006 0 0.3503 0.01614 4.608 0.045 0.01614 35.87 -BSA_min_23 376.199897766113 48.93 1.662 7.034 0 0.3517 0.0165 4.691 0.04679 0.0165 35.27 -BSA_min_23 377.199897766113 49.18 1.671 7.063 0 0.3531 0.01686 4.773 0.04857 0.01686 34.71 -BSA_min_23 378.199897766113 49.42 1.68 7.091 0 0.3546 0.01721 4.855 0.05036 0.01721 34.18 -BSA_min_23 379.199897766113 49.66 1.689 7.12 0 0.356 0.01757 4.936 0.05214 0.01757 33.7 -BSA_min_23 380.199897766113 49.91 1.698 7.149 0 0.3574 0.01793 5.016 0.05393 0.01793 33.25 -BSA_min_23 381.199897766113 50.15 1.707 7.177 0 0.3589 0.01829 5.096 0.05571 0.01829 32.82 -BSA_min_23 382.199897766113 50.39 1.716 7.206 0 0.3603 0.01864 5.174 0.0575 0.01864 32.42 -BSA_min_23 383.199897766113 50.63 1.725 7.234 0 0.3617 0.019 5.253 0.05929 0.019 32.05 -BSA_min_23 384.199897766113 50.88 1.734 7.263 0 0.3631 0.01936 5.33 0.06107 0.01936 31.7 -BSA_min_23 385.199897766113 51.12 1.743 7.291 0 0.3646 0.01971 5.408 0.06286 0.01971 31.36 -BSA_min_23 386.199897766113 51.36 1.752 7.32 0 0.366 0.02007 5.484 0.06464 0.02007 31.05 -BSA_min_23 387.199897766113 51.61 1.761 7.349 0 0.3674 0.02043 5.56 0.06643 0.02043 30.75 -BSA_min_23 388.199897766113 51.85 1.77 7.377 0 0.3689 0.02079 5.635 0.06821 0.02079 30.47 -BSA_min_23 389.199897766113 52.09 1.779 7.406 0 0.3703 0.02114 5.71 0.07 0.02114 30.2 -BSA_min_23 390.199897766113 52.33 1.787 7.434 0 0.3717 0.0215 5.784 0.07157 0.02143 29.94 -BSA_min_23 391.199897766113 52.58 1.796 7.463 0 0.3731 0.02186 5.858 0.07229 0.02143 29.64 -BSA_min_23 392.199897766113 52.82 1.805 7.491 0 0.3746 0.02221 5.931 0.073 0.02143 29.35 -BSA_min_23 393.199897766113 53.06 1.813 7.52 0 0.376 0.02257 6.003 0.07371 0.02143 29.07 -BSA_min_23 394.199897766113 53.31 1.822 7.549 0 0.3774 0.02293 6.075 0.07443 0.02143 28.79 -BSA_min_23 395.199897766113 53.55 1.83 7.577 0 0.3789 0.02329 6.146 0.07514 0.02143 28.52 -BSA_min_23 396.199897766113 53.79 1.839 7.606 0 0.3803 0.02364 6.217 0.07586 0.02143 28.25 -BSA_min_23 397.199897766113 54.03 1.847 7.634 0 0.3817 0.024 6.287 0.07657 0.02143 27.99 -BSA_min_23 398.199897766113 54.28 1.856 7.663 0 0.3831 0.02436 6.357 0.07729 0.02143 27.73 -BSA_min_23 399.199897766113 54.52 1.865 7.691 0 0.3846 0.02471 6.426 0.078 0.02143 27.47 -BSA_min_23 400.199897766113 54.76 1.873 7.72 0 0.386 0.02507 6.495 0.07871 0.02143 27.22 -BSA_min_23 401.199897766113 55.01 1.882 7.749 0 0.3874 0.02543 6.563 0.07943 0.02143 26.98 -BSA_min_23 402.199897766113 55.25 1.89 7.777 0 0.3889 0.02579 6.631 0.08014 0.02143 26.74 -BSA_min_23 403.199897766113 55.49 1.899 7.806 0 0.3903 0.02614 6.698 0.08086 0.02143 26.5 -BSA_min_23 404.199897766113 55.73 1.907 7.834 0 0.3917 0.0265 6.765 0.08157 0.02143 26.27 -BSA_min_23 405.199897766113 55.98 1.916 7.863 0 0.3931 0.02686 6.831 0.08229 0.02143 26.04 -BSA_min_23 406.199897766113 56.22 1.925 7.891 0 0.3946 0.02721 6.897 0.083 0.02143 25.82 -BSA_min_23 407.199897766113 56.46 1.933 7.92 0 0.396 0.02757 6.962 0.08371 0.02143 25.6 -BSA_min_23 408.199897766113 56.71 1.942 7.949 0 0.3974 0.02793 7.027 0.08443 0.02143 25.38 -BSA_min_23 409.199897766113 56.95 1.95 7.977 0 0.3989 0.02829 7.092 0.08514 0.02143 25.17 -BSA_min_23 410.199897766113 57.19 1.959 8.003 0 0.4001 0.02857 7.14 0.08586 0.02143 24.96 -BSA_min_23 411.199897766113 57.43 1.97 8.017 0 0.4009 0.02857 7.128 0.08657 0.02143 24.75 -BSA_min_23 412.199897766113 57.68 1.98 8.031 0 0.4016 0.02857 7.115 0.08729 0.02143 24.55 -BSA_min_23 413.199897766113 57.92 1.99 8.046 0 0.4023 0.02857 7.102 0.088 0.02143 24.35 -BSA_min_23 414.199897766113 58.16 2.001 8.06 0 0.403 0.02857 7.09 0.08871 0.02143 24.15 -BSA_min_23 415.199897766113 58.41 2.011 8.074 0 0.4037 0.02857 7.077 0.08943 0.02143 23.96 -BSA_min_23 416.199897766113 58.65 2.021 8.089 0 0.4044 0.02857 7.065 0.09014 0.02143 23.77 -BSA_min_23 417.199897766113 58.89 2.032 8.103 0 0.4051 0.02857 7.052 0.09086 0.02143 23.58 -BSA_min_23 418.199897766113 59.13 2.042 8.117 0 0.4059 0.02857 7.04 0.09157 0.02143 23.4 -BSA_min_23 419.199897766113 59.38 2.052 8.131 0 0.4066 0.02857 7.027 0.09229 0.02143 23.22 -BSA_min_23 420.199897766113 59.62 2.063 8.146 0 0.4073 0.02857 7.015 0.093 0.02143 23.04 -BSA_min_23 421.199897766113 59.86 2.073 8.16 0 0.408 0.02857 7.003 0.09371 0.02143 22.87 -BSA_min_23 422.199897766113 60.11 2.083 8.174 0 0.4087 0.02857 6.991 0.09443 0.02143 22.69 -BSA_min_23 423.199897766113 60.35 2.094 8.189 0 0.4094 0.02857 6.978 0.09514 0.02143 22.52 -BSA_min_23 424.199897766113 60.59 2.104 8.203 0 0.4101 0.02857 6.966 0.09586 0.02143 22.35 -BSA_min_23 425.199897766113 60.83 2.115 8.217 0 0.4109 0.02857 6.954 0.09657 0.02143 22.19 -BSA_min_23 426.199897766113 61.08 2.125 8.231 0 0.4116 0.02857 6.942 0.09729 0.02143 22.03 -BSA_min_23 427.199897766113 61.32 2.135 8.246 0 0.4123 0.02857 6.93 0.098 0.02143 21.87 -BSA_min_23 428.199897766113 61.56 2.146 8.26 0 0.413 0.02857 6.918 0.09871 0.02143 21.71 -BSA_min_23 429.199897766113 61.81 2.156 8.274 0 0.4137 0.02857 6.906 0.09943 0.02143 21.55 -BSA_min_23 430.199897766113 61.99 2.164 8.286 0 0.4143 0.02857 6.897 0.1001 0.0215 21.47 -BSA_min_23 431.199897766113 61.97 2.163 8.286 0 0.4143 0.02857 6.897 0.1009 0.02186 21.67 -BSA_min_23 432.199897766113 61.94 2.161 8.286 0 0.4143 0.02857 6.897 0.1016 0.02221 21.87 -BSA_min_23 433.199897766113 61.91 2.16 8.286 0 0.4143 0.02857 6.897 0.1023 0.02257 22.07 -BSA_min_23 434.199897766113 61.88 2.158 8.286 0 0.4143 0.02857 6.897 0.103 0.02293 22.26 -BSA_min_23 435.199897766113 61.85 2.157 8.286 0 0.4143 0.02857 6.897 0.1037 0.02329 22.45 -BSA_min_23 436.199897766113 61.82 2.155 8.286 0 0.4143 0.02857 6.897 0.1044 0.02364 22.64 -BSA_min_23 437.199897766113 61.79 2.154 8.286 0 0.4143 0.02857 6.897 0.1051 0.024 22.83 -BSA_min_23 438.199897766113 61.77 2.153 8.286 0 0.4143 0.02857 6.897 0.1059 0.02436 23.01 -BSA_min_23 439.199897766113 61.74 2.151 8.286 0 0.4143 0.02857 6.897 0.1066 0.02471 23.19 -BSA_min_23 440.199897766113 61.71 2.15 8.286 0 0.4143 0.02857 6.897 0.1073 0.02507 23.37 -BSA_min_23 441.199897766113 61.68 2.148 8.286 0 0.4143 0.02857 6.897 0.108 0.02543 23.54 -BSA_min_23 442.199897766113 61.65 2.147 8.286 0 0.4143 0.02857 6.897 0.1087 0.02579 23.72 -BSA_min_23 443.199897766113 61.62 2.145 8.286 0 0.4143 0.02857 6.897 0.1094 0.02614 23.89 -BSA_min_23 444.199897766113 61.59 2.144 8.286 0 0.4143 0.02857 6.897 0.1101 0.0265 24.06 -BSA_min_23 445.199897766113 61.57 2.143 8.286 0 0.4143 0.02857 6.897 0.1109 0.02686 24.23 -BSA_min_23 446.199897766113 61.54 2.141 8.286 0 0.4143 0.02857 6.897 0.1116 0.02721 24.39 -BSA_min_23 447.199897766113 61.51 2.14 8.286 0 0.4143 0.02857 6.897 0.1123 0.02757 24.55 -BSA_min_23 448.199897766113 61.48 2.138 8.286 0 0.4143 0.02857 6.897 0.113 0.02793 24.72 -BSA_min_23 449.199897766113 61.45 2.137 8.286 0 0.4143 0.02857 6.897 0.1137 0.02829 24.87 -BSA_min_23 450.199897766113 61.31 2.132 8.269 0 0.4134 0.02857 6.911 0.1141 0.0285 24.97 -BSA_min_23 451.199897766113 60.73 2.111 8.183 0 0.4091 0.02857 6.983 0.1134 0.02814 24.81 -BSA_min_23 452.199897766113 60.14 2.091 8.097 0 0.4049 0.02857 7.057 0.1127 0.02779 24.65 -BSA_min_23 453.199897766113 59.55 2.071 8.011 0 0.4006 0.02857 7.133 0.112 0.02743 24.49 -BSA_min_23 454.199897766113 58.97 2.05 7.926 0 0.3963 0.02857 7.21 0.1113 0.02707 24.33 -BSA_min_23 455.199897766113 58.38 2.03 7.84 0 0.392 0.02857 7.289 0.1106 0.02671 24.16 -BSA_min_23 456.199897766113 57.8 2.01 7.754 0 0.3877 0.02857 7.369 0.1099 0.02636 23.99 -BSA_min_23 457.199897766113 57.21 1.989 7.669 0 0.3834 0.02857 7.452 0.1091 0.026 23.82 -BSA_min_23 458.199897766113 56.63 1.969 7.583 0 0.3791 0.02857 7.536 0.1084 0.02564 23.65 -BSA_min_23 459.199897766113 56.04 1.948 7.497 0 0.3749 0.02857 7.622 0.1077 0.02529 23.47 -BSA_min_23 460.199897766113 55.45 1.928 7.411 0 0.3706 0.02857 7.71 0.107 0.02493 23.3 -BSA_min_23 461.199897766113 54.87 1.908 7.326 0 0.3663 0.02857 7.8 0.1063 0.02457 23.12 -BSA_min_23 462.199897766113 54.28 1.887 7.24 0 0.362 0.02857 7.893 0.1056 0.02421 22.94 -BSA_min_23 463.199897766113 53.7 1.867 7.154 0 0.3577 0.02857 7.987 0.1049 0.02386 22.75 -BSA_min_23 464.199897766113 53.11 1.847 7.069 0 0.3534 0.02857 8.084 0.1041 0.0235 22.57 -BSA_min_23 465.199897766113 52.53 1.826 6.983 0 0.3491 0.02857 8.183 0.1034 0.02314 22.38 -BSA_min_23 466.199897766113 51.94 1.806 6.897 0 0.3449 0.02857 8.285 0.1027 0.02279 22.18 -BSA_min_23 467.199897766113 51.35 1.786 6.811 0 0.3406 0.02857 8.389 0.102 0.02243 21.99 -BSA_min_23 468.199897766113 50.77 1.765 6.726 0 0.3363 0.02857 8.496 0.1013 0.02207 21.79 -BSA_min_23 469.199897766113 50.18 1.745 6.64 0 0.332 0.02857 8.606 0.1006 0.02171 21.59 -BSA_min_23 470.199897766113 49.57 1.724 6.546 0 0.3273 0.02843 8.686 0.1002 0.02136 21.31 -BSA_min_23 471.199897766113 48.87 1.704 6.417 0 0.3209 0.02771 8.638 0.1013 0.021 20.73 -BSA_min_23 472.199897766113 48.17 1.683 6.289 0 0.3144 0.027 8.587 0.1024 0.02064 20.17 -BSA_min_23 473.199897766113 47.47 1.662 6.16 0 0.308 0.02629 8.534 0.1034 0.02029 19.61 -BSA_min_23 474.199897766113 46.77 1.642 6.031 0 0.3016 0.02557 8.479 0.1045 0.01993 19.07 -BSA_min_23 475.199897766113 46.07 1.621 5.903 0 0.2951 0.02486 8.422 0.1056 0.01957 18.54 -BSA_min_23 476.199897766113 45.37 1.6 5.774 0 0.2887 0.02414 8.362 0.1066 0.01921 18.02 -BSA_min_23 477.199897766113 44.67 1.579 5.646 0 0.2823 0.02343 8.3 0.1077 0.01886 17.51 -BSA_min_23 478.199897766113 43.97 1.559 5.517 0 0.2759 0.02271 8.234 0.1088 0.0185 17.01 -BSA_min_23 479.199897766113 43.27 1.538 5.389 0 0.2694 0.022 8.165 0.1099 0.01814 16.52 -BSA_min_23 480.199897766113 42.57 1.517 5.26 0 0.263 0.02129 8.093 0.1109 0.01779 16.03 -BSA_min_23 481.199897766113 41.87 1.497 5.131 0 0.2566 0.02057 8.018 0.112 0.01743 15.56 -BSA_min_23 482.199897766113 41.17 1.476 5.003 0 0.2501 0.01986 7.938 0.1131 0.01707 15.1 -BSA_min_23 483.199897766113 40.47 1.455 4.874 0 0.2437 0.01914 7.855 0.1141 0.01671 14.64 -BSA_min_23 484.199897766113 39.77 1.434 4.746 0 0.2373 0.01843 7.766 0.1152 0.01636 14.2 -BSA_min_23 485.199897766113 39.07 1.414 4.617 0 0.2309 0.01771 7.673 0.1163 0.016 13.76 -BSA_min_23 486.199897766113 38.37 1.393 4.489 0 0.2244 0.017 7.575 0.1174 0.01564 13.33 -BSA_min_23 487.199897766113 37.67 1.372 4.36 0 0.218 0.01629 7.471 0.1184 0.01529 12.91 -BSA_min_23 488.199897766113 36.97 1.352 4.231 0 0.2116 0.01557 7.36 0.1195 0.01493 12.49 -BSA_min_23 489.199897766113 36.27 1.331 4.103 0 0.2051 0.01486 7.242 0.1206 0.01457 12.09 -BSA_min_23 490.199897766113 35.66 1.313 3.993 0 0.1996 0.01429 7.156 0.1214 0.01429 11.76 -BSA_min_23 491.199897766113 35.4 1.305 3.957 0 0.1979 0.01429 7.22 0.1214 0.01429 11.76 -BSA_min_23 492.199897766113 35.13 1.297 3.921 0 0.1961 0.01429 7.286 0.1214 0.01429 11.76 -BSA_min_23 493.199897766113 34.87 1.289 3.886 0 0.1943 0.01429 7.353 0.1214 0.01429 11.76 -BSA_min_23 494.199897766113 34.6 1.281 3.85 0 0.1925 0.01429 7.421 0.1214 0.01429 11.76 -BSA_min_23 495.199897766113 34.34 1.273 3.814 0 0.1907 0.01429 7.491 0.1214 0.01429 11.76 -BSA_min_23 496.199897766113 34.08 1.266 3.779 0 0.1889 0.01429 7.561 0.1214 0.01429 11.76 -BSA_min_23 497.199897766113 33.81 1.258 3.743 0 0.1871 0.01429 7.634 0.1214 0.01429 11.76 -BSA_min_23 498.199897766113 33.55 1.25 3.707 0 0.1854 0.01429 7.707 0.1214 0.01429 11.76 -BSA_min_23 499.199897766113 33.28 1.242 3.671 0 0.1836 0.01429 7.782 0.1214 0.01429 11.76 -BSA_min_23 500.199897766113 33.02 1.234 3.636 0 0.1818 0.01429 7.859 0.1214 0.01429 11.76 -BSA_min_23 501.199897766113 32.75 1.226 3.6 0 0.18 0.01429 7.936 0.1214 0.01429 11.76 -BSA_min_23 502.199897766113 32.49 1.218 3.564 0 0.1782 0.01429 8.016 0.1214 0.01429 11.76 -BSA_min_23 503.199897766113 32.23 1.211 3.529 0 0.1764 0.01429 8.097 0.1214 0.01429 11.76 -BSA_min_23 504.199897766113 31.96 1.203 3.493 0 0.1746 0.01429 8.18 0.1214 0.01429 11.76 -BSA_min_23 505.199897766113 31.7 1.195 3.457 0 0.1729 0.01429 8.264 0.1214 0.01429 11.76 -BSA_min_23 506.199897766113 31.43 1.187 3.421 0 0.1711 0.01429 8.351 0.1214 0.01429 11.76 -BSA_min_23 507.199897766113 31.17 1.179 3.386 0 0.1693 0.01429 8.439 0.1214 0.01429 11.76 -BSA_min_23 508.199897766113 30.9 1.171 3.35 0 0.1675 0.01429 8.529 0.1214 0.01429 11.76 -BSA_min_23 509.199897766113 30.64 1.163 3.314 0 0.1657 0.01429 8.621 0.1214 0.01429 11.76 -BSA_min_23 510.199897766113 30.58 1.162 3.31 0 0.1655 0.01421 8.589 0.1218 0.01421 11.67 -BSA_min_23 511.199897766113 31.36 1.185 3.431 0 0.1716 0.01386 8.077 0.1236 0.01386 11.21 -BSA_min_23 512.199897766113 32.14 1.207 3.553 0 0.1776 0.0135 7.6 0.1254 0.0135 10.77 -BSA_min_23 513.199897766113 32.92 1.23 3.674 0 0.1837 0.01314 7.154 0.1271 0.01314 10.34 -BSA_min_23 514.199897766113 33.7 1.253 3.796 0 0.1898 0.01279 6.737 0.1289 0.01279 9.917 -BSA_min_23 515.199897766113 34.48 1.276 3.917 0 0.1959 0.01243 6.346 0.1307 0.01243 9.508 -BSA_min_23 516.199897766113 35.26 1.299 4.039 0 0.2019 0.01207 5.978 0.1325 0.01207 9.111 -BSA_min_23 517.199897766113 36.03 1.322 4.16 0 0.208 0.01171 5.632 0.1343 0.01171 8.723 -BSA_min_23 518.199897766113 36.81 1.345 4.281 0 0.2141 0.01136 5.305 0.1361 0.01136 8.346 -BSA_min_23 519.199897766113 37.59 1.367 4.403 0 0.2201 0.011 4.997 0.1379 0.011 7.979 -BSA_min_23 520.199897766113 38.37 1.39 4.524 0 0.2262 0.01064 4.705 0.1396 0.01064 7.622 -BSA_min_23 521.199897766113 39.15 1.413 4.646 0 0.2323 0.01029 4.428 0.1414 0.01029 7.273 -BSA_min_23 522.199897766113 39.93 1.436 4.767 0 0.2384 0.009929 4.165 0.1432 0.009929 6.933 -BSA_min_23 523.199897766113 40.71 1.459 4.889 0 0.2444 0.009571 3.916 0.145 0.009571 6.601 -BSA_min_23 524.199897766113 41.48 1.482 5.01 0 0.2505 0.009214 3.678 0.1468 0.009214 6.277 -BSA_min_23 525.199897766113 42.26 1.505 5.131 0 0.2566 0.008857 3.452 0.1486 0.008857 5.962 -BSA_min_23 526.199897766113 43.04 1.527 5.253 0 0.2626 0.0085 3.236 0.1504 0.0085 5.653 -BSA_min_23 527.199897766113 43.82 1.55 5.374 0 0.2687 0.008143 3.03 0.1521 0.008143 5.352 -BSA_min_23 528.199897766113 44.6 1.573 5.496 0 0.2748 0.007786 2.833 0.1539 0.007786 5.058 -BSA_min_23 529.199897766113 45.38 1.596 5.617 0 0.2809 0.007429 2.645 0.1557 0.007429 4.771 -BSA_min_23 530.199897766113 45.99 1.614 5.714 0 0.2857 0.007071 2.475 0.1571 0.007143 4.545 -BSA_min_23 531.199897766113 45.92 1.61 5.714 0 0.2857 0.006714 2.35 0.1571 0.007143 4.545 -BSA_min_23 532.199897766113 45.86 1.607 5.714 0 0.2857 0.006357 2.225 0.1571 0.007143 4.545 -BSA_min_23 533.199897766113 45.79 1.604 5.714 0 0.2857 0.006 2.1 0.1571 0.007143 4.545 -BSA_min_23 534.199897766113 45.73 1.601 5.714 0 0.2857 0.005643 1.975 0.1571 0.007143 4.545 -BSA_min_23 535.199897766113 45.67 1.598 5.714 0 0.2857 0.005286 1.85 0.1571 0.007143 4.545 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0.007143 4.545 -BSA_min_23 547.199897766113 44.89 1.559 5.714 0 0.2857 0.001 0.35 0.1571 0.007143 4.545 -BSA_min_23 548.199897766113 44.83 1.556 5.714 0 0.2857 0.0006429 0.225 0.1571 0.007143 4.545 -BSA_min_23 549.199897766113 44.77 1.553 5.714 0 0.2857 0.0002858 0.1 0.1571 0.007143 4.545 -BSA_min_23 550.199897766113 44.72 1.549 5.721 0 0.2861 0 0 0.1574 0.007143 4.537 -BSA_min_23 551.199897766113 44.73 1.546 5.757 0 0.2879 0 0 0.1589 0.007143 4.496 -BSA_min_23 552.199897766113 44.75 1.543 5.793 0 0.2896 0 0 0.1603 0.007143 4.456 -BSA_min_23 553.199897766113 44.76 1.54 5.829 0 0.2914 0 0 0.1617 0.007143 4.417 -BSA_min_23 554.199897766113 44.77 1.537 5.864 0 0.2932 0 0 0.1631 0.007143 4.378 -BSA_min_23 555.199897766113 44.79 1.533 5.9 0 0.295 0 0 0.1646 0.007143 4.34 -BSA_min_23 556.199897766113 44.8 1.53 5.936 0 0.2968 0 0 0.166 0.007143 4.303 -BSA_min_23 557.199897766113 44.82 1.527 5.971 0 0.2986 0 0 0.1674 0.007143 4.266 -BSA_min_23 558.199897766113 44.83 1.524 6.007 0 0.3004 0 0 0.1689 0.007143 4.23 -BSA_min_23 559.199897766113 44.85 1.52 6.043 0 0.3021 0 0 0.1703 0.007143 4.195 -BSA_min_23 560.199897766113 44.86 1.517 6.079 0 0.3039 0 0 0.1717 0.007143 4.16 -BSA_min_23 561.199897766113 44.87 1.514 6.114 0 0.3057 0 0 0.1731 0.007143 4.125 -BSA_min_23 562.199897766113 44.89 1.511 6.15 0 0.3075 0 0 0.1746 0.007143 4.092 -BSA_min_23 563.199897766113 44.9 1.508 6.186 0 0.3093 0 0 0.176 0.007143 4.058 -BSA_min_23 564.199897766113 44.92 1.504 6.221 0 0.3111 0 0 0.1774 0.007143 4.026 -BSA_min_23 565.199897766113 44.93 1.501 6.257 0 0.3129 0 0 0.1789 0.007143 3.994 -BSA_min_23 566.199897766113 44.95 1.498 6.293 0 0.3146 0 0 0.1803 0.007143 3.962 -BSA_min_23 567.199897766113 44.96 1.495 6.329 0 0.3164 0 0 0.1817 0.007143 3.931 -BSA_min_23 568.199897766113 44.97 1.492 6.364 0 0.3182 0 0 0.1831 0.007143 3.9 -BSA_min_23 569.199897766113 44.99 1.488 6.4 0 0.32 0 0 0.1846 0.007143 3.87 -BSA_min_23 570.199897766113 45.01 1.485 6.433 0 0.3216 0 0 0.1856 0.007071 3.809 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45.75 1.467 6.711 0 0.3356 0 0 0.181 0.002429 1.342 -BSA_min_23 584.199897766113 45.81 1.465 6.733 0 0.3366 0 0 0.1806 0.002071 1.147 -BSA_min_23 585.199897766113 45.87 1.464 6.754 0 0.3377 0 0 0.1803 0.001714 0.9509 -BSA_min_23 586.199897766113 45.93 1.463 6.776 0 0.3388 0 0 0.1799 0.001357 0.7543 -BSA_min_23 587.199897766113 45.98 1.461 6.797 0 0.3399 0 0 0.1796 0.001 0.5569 -BSA_min_23 588.199897766113 46.04 1.46 6.819 0 0.3409 0 0 0.1792 0.0006429 0.3587 -BSA_min_23 589.199897766113 46.1 1.458 6.84 0 0.342 0 0 0.1789 0.0002858 0.1598 -BSA_min_23 590.199897766113 46.15 1.457 6.86 0 0.343 0 0 0.1791 0 0 -BSA_min_23 591.199897766113 46.17 1.456 6.874 0 0.3437 0 0 0.1816 0 0 -BSA_min_23 592.199897766113 46.19 1.455 6.889 0 0.3444 0 0 0.1841 0 0 -BSA_min_23 593.199897766113 46.21 1.454 6.903 0 0.3451 0 0 0.1866 0 0 -BSA_min_23 594.199897766113 46.23 1.453 6.917 0 0.3459 0 0 0.1891 0 0 -BSA_min_23 595.199897766113 46.25 1.452 6.931 0 0.3466 0 0 0.1916 0 0 -BSA_min_23 596.199897766113 46.28 1.451 6.946 0 0.3473 0 0 0.1941 0 0 -BSA_min_23 597.199897766113 46.3 1.449 6.96 0 0.348 0 0 0.1966 0 0 -BSA_min_23 598.199897766113 46.32 1.448 6.974 0 0.3487 0 0 0.1991 0 0 -BSA_min_23 599.199897766113 46.34 1.447 6.989 0 0.3494 0 0 0.2016 0 0 -BSA_min_23 600.199897766113 46.36 1.446 7.003 0 0.3501 0 0 0.2041 0 0 -BSA_min_23 601.199897766113 46.38 1.445 7.017 0 0.3509 0 0 0.2066 0 0 -BSA_min_23 602.199897766113 46.4 1.444 7.031 0 0.3516 0 0 0.2091 0 0 -BSA_min_23 603.199897766113 46.43 1.443 7.046 0 0.3523 0 0 0.2116 0 0 -BSA_min_23 604.199897766113 46.45 1.442 7.06 0 0.353 0 0 0.2141 0 0 -BSA_min_23 605.199897766113 46.47 1.441 7.074 0 0.3537 0 0 0.2166 0 0 -BSA_min_23 606.199897766113 46.49 1.44 7.089 0 0.3544 0 0 0.2191 0 0 -BSA_min_23 607.199897766113 46.51 1.439 7.103 0 0.3551 0 0 0.2216 0 0 -BSA_min_23 608.199897766113 46.53 1.438 7.117 0 0.3559 0 0 0.2241 0 0 -BSA_min_23 609.199897766113 46.55 1.437 7.131 0 0.3566 0 0 0.2266 0 0 -BSA_min_23 610.199897766113 46.55 1.435 7.139 0 0.3569 0 0 0.2286 0 0 -BSA_min_23 611.199897766113 46.43 1.43 7.117 0 0.3559 0 0 0.2286 0 0 -BSA_min_23 612.199897766113 46.32 1.426 7.096 0 0.3548 0 0 0.2286 0 0 -BSA_min_23 613.199897766113 46.21 1.421 7.074 0 0.3537 0 0 0.2286 0 0 -BSA_min_23 614.199897766113 46.09 1.416 7.053 0 0.3526 0 0 0.2286 0 0 -BSA_min_23 615.199897766113 45.98 1.412 7.031 0 0.3516 0 0 0.2286 0 0 -BSA_min_23 616.199897766113 45.86 1.407 7.01 0 0.3505 0 0 0.2286 0 0 -BSA_min_23 617.199897766113 45.75 1.402 6.989 0 0.3494 0 0 0.2286 0 0 -BSA_min_23 618.199897766113 45.63 1.398 6.967 0 0.3484 0 0 0.2286 0 0 -BSA_min_23 619.199897766113 45.52 1.393 6.946 0 0.3473 0 0 0.2286 0 0 -BSA_min_23 620.199897766113 45.41 1.388 6.924 0 0.3462 0 0 0.2286 0 0 -BSA_min_23 621.199897766113 45.29 1.384 6.903 0 0.3451 0 0 0.2286 0 0 -BSA_min_23 622.199897766113 45.18 1.379 6.881 0 0.3441 0 0 0.2286 0 0 -BSA_min_23 623.199897766113 45.06 1.374 6.86 0 0.343 0 0 0.2286 0 0 -BSA_min_23 624.199897766113 44.95 1.37 6.839 0 0.3419 0 0 0.2286 0 0 -BSA_min_23 625.199897766113 44.83 1.365 6.817 0 0.3409 0 0 0.2286 0 0 -BSA_min_23 626.199897766113 44.72 1.361 6.796 0 0.3398 0 0 0.2286 0 0 -BSA_min_23 627.199897766113 44.61 1.356 6.774 0 0.3387 0 0 0.2286 0 0 -BSA_min_23 628.199897766113 44.49 1.351 6.753 0 0.3376 0 0 0.2286 0 0 -BSA_min_23 629.199897766113 44.38 1.347 6.731 0 0.3366 0 0 0.2286 0 0 -BSA_min_23 630.199897766113 44.3 1.343 6.72 0 0.336 0 0 0.2287 0 0 -BSA_min_23 631.199897766113 44.35 1.342 6.749 0 0.3374 0 0 0.2294 0 0 -BSA_min_23 632.199897766113 44.41 1.341 6.777 0 0.3389 0 0 0.2301 0 0 -BSA_min_23 633.199897766113 44.47 1.341 6.806 0 0.3403 0 0 0.2309 0 0 -BSA_min_23 634.199897766113 44.53 1.34 6.834 0 0.3417 0 0 0.2316 0 0 -BSA_min_23 635.199897766113 44.58 1.339 6.863 0 0.3431 0 0 0.2323 0 0 -BSA_min_23 636.199897766113 44.64 1.338 6.891 0 0.3446 0 0 0.233 0 0 -BSA_min_23 637.199897766113 44.7 1.338 6.92 0 0.346 0 0 0.2337 0 0 -BSA_min_23 638.199897766113 44.75 1.337 6.949 0 0.3474 0 0 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--- a/test-data/single/combined/txt/mzTab.mzTab Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Complete -MTD mzTab-type Identification -MTD title null -MTD description null -MTD software[1] [MS, MS:1001583, MaxQuant,1.6.3.4] -COM [, CHEMMOD:57.0214637236, Carbamidomethyl (C),] -MTD fixed_mod[1] [, , CHEMMOD:57.0214637236,] -MTD fixed_mod[1]-site C -MTD fixed_mod[1]-position Anywhere -COM [, CHEMMOD:15.9949146221, Oxidation (M),] -MTD variable_mod[1] [, , CHEMMOD:15.9949146221,] -MTD variable_mod[1]-site M -MTD variable_mod[1]-position Anywhere -MTD protein_search_engine_score[1] [MS, MS:1002375, protein group-level combined FDRscore, ] -MTD peptide_search_engine_score[1] [MS, MS:1001250, local FDR, ] -MTD psm_search_engine_score[1] [MS, MS:1002338, Andromeda:score, ] -MTD psm_search_engine_score[2] [MS, MS:1002995, Andromeda:PEP, ] -MTD ms_run[1]-format [MS, MS:1002996, Andromeda:apl file format, ] -MTD ms_run[1]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.secpep.sil0_0.apl -MTD ms_run[1]-id_format [MS, MS:1000776, scan number only nativeID format, ] -MTD ms_run[2]-format [MS, MS:1002996, Andromeda:apl file format, ] -MTD ms_run[2]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.iso_0.apl -MTD ms_run[2]-id_format [MS, MS:1000776, scan number only nativeID format, ] - -PRH accession description taxid species database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] search_engine_score[1]_ms_run[2] num_psms_ms_run[1] num_psms_ms_run[2] num_peptides_distinct_ms_run[1] num_peptides_distinct_ms_run[2] num_peptides_unique_ms_run[1] num_peptides_unique_ms_run[2] ambiguity_members modifications protein_coverage opt_global_cv_MS:1002217_decoy_peptide -PRT CON__P02769 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.33205607832812 null null null null null null null null CON__P02769, bsa, CON__P02768-1 null 0.012 0 -PRT CON__ENSEMBL:ENSBTAP00000001528 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.93746772688895 null null null null null null null null CON__ENSEMBL:ENSBTAP00000001528 null 0.008 0 -PRT CON__ENSEMBL:ENSBTAP00000016046 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.97677849538172 null null null null null null null null CON__ENSEMBL:ENSBTAP00000016046 null 0.01 0 -PRT CON__ENSEMBL:ENSBTAP00000018574 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.95544937626172 null null null null null null null null CON__ENSEMBL:ENSBTAP00000018574 null 0.016 0 -PRT CON__Q03247 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.93746772688895 null null null null null null null null CON__Q03247 null 0.025 0 -PRT CON__Q14CN4-1 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.1237531147968 null null null null null null null null CON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5 null 0.016 0 - -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] search_engine_score[2] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_global_cv_MS:1000776_scan_number_only_nativeID_format opt_global_cv_MS:1002217_decoy_peptide -PSM DSFDIIK 1 CON__ENSEMBL:ENSBTAP00000016046 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.010549248059121 null 0.570428333333333 2 419.22 419.22127 ms_run[2]:index=5 R R 646 652 96 0 -PSM LLESEECR 2 CON__Q14CN4-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 -PSM LLESEECR 2 CON__Q3SY84 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 -PSM LLESEECR 2 CON__Q9R0H5 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0 -PSM LVTDLTK 3 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 -PSM LVTDLTK 3 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 -PSM LVTDLTK 3 CON__P02768-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0 -PSM QLELEKQLEK 4 CON__ENSEMBL:ENSBTAP00000001528 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0115486780155693 null 0.570428333333333 3 419.91 419.90648 ms_run[1]:index=5 R Q 408 417 96 0 -PSM SLSAIRER 5 CON__Q03247 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0115486780155693 null 0.0965533333333333 2 466.27 466.26962 ms_run[1]:index=2 R F 190 197 17 0 -PSM TLGPWGQR 6 CON__ENSEMBL:ENSBTAP00000018574 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0110802771561295 null 0.425933333333333 2 457.75 457.74578 ms_run[2]:index=9 R D 20 27 72 0 -
--- a/test-data/single/combined/txt/parameters.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -Parameter Value -Version 1.6.3.4 -User name dglaetzer -Machine name FPROT-BEAST -Date of writing 04/04/2019 17:32:37 -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) -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 D:\fasta\bsa.fasta -Decoy mode revert -Include contaminants True -Advanced ratios True -Fixed andromeda index folder -Temporary 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 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) 0.5 Da -Top MS/MS peaks per Da interval. (Unknown) 8 -Da interval. (Unknown) 100 -MS/MS deisotoping (Unknown) False -MS/MS deisotoping tolerance (Unknown) 0.15 -MS/MS deisotoping tolerance unit (Unknown) Da -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
--- a/test-data/single/combined/txt/peptideSection.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -PEH sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[0] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[0] peptide_abundance_stdev_study_variable[0] peptide_abundance_std_error_study_variable[0] -PEP DSFDIIK null -PEP LLESEECR null -PEP LVTDLTK null -PEP QLELEKQLEK null -PEP SLSAIRER null -PEP TLGPWGQR null
--- a/test-data/single/combined/txt/peptides.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -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 Experiment BSA_min_23.mzXML Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count -DSFDIIK NHADIIFDITDGNLRDSFDIIKRYMDGMTV DITDGNLRDSFDIIKRYMDGMTVGVVRQVR R D S I K R 0 0 0 2 0 0 0 0 0 2 0 1 0 1 0 1 0 0 0 0 0 0 7 0 836.42798 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 646 652 yes yes 2 0.010549 0 1 768320 768320 + 0 2 0 0 0 0 1 -LLESEECR SLKLALDMEIATYRKLLESEECRMSGEYPN EIATYRKLLESEECRMSGEYPNSVSISVIS K L L C R M 0 1 0 0 1 0 3 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 8 0 1034.4703 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 430 437 yes no 2 0.0075205 1.6313 1 0 0 + 1 5 1 1 1 1 1 -LVTDLTK LSQKFPKAEFVEVTKLVTDLTKVHKECCHG AEFVEVTKLVTDLTKVHKECCHGDLLECAD K L V T K V 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 0 2 0 0 1 0 0 7 0 788.46437 CON__P02769;bsa;CON__P02768-1 CON__P02769 257 263 yes no 2 0.0046553 0 1 0 0 + 2 0 2 2 2 2 1 -QLELEKQLEK QERKERERQEQERKRQLELEKQLEKQRELE QERKRQLELEKQLEKQRELERQREEERRKE R Q L E K Q 0 0 0 0 0 2 3 0 0 0 3 2 0 0 0 0 0 0 0 0 0 0 10 1 1256.6976 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 408 417 yes yes 3 0.011549 0 1 57554 57554 + 3 1 3 3 3 3 0 -SLSAIRER RLAVYQAGASEGAERSLSAIRERFGPLVEQ ASEGAERSLSAIRERFGPLVEQGQSRAATL R S L E R F 1 2 0 0 0 0 1 0 0 1 1 0 0 0 0 2 0 0 0 0 0 0 8 1 930.52468 CON__Q03247 CON__Q03247 190 197 yes yes 2 0.011549 0 1 33499 33499 + 4 4 4 4 4 4 0 -TLGPWGQR LRPLLLALLLASACRTLGPWGQRDDGGGEP LLASACRTLGPWGQRDDGGGEPESMEPRWG R T L Q R D 0 1 0 0 0 1 0 2 0 0 1 0 0 0 1 0 1 1 0 0 0 0 8 0 913.477 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 20 27 yes yes 2 0.01108 0 1 61894 61894 + 5 3 5 5 5 5 1
--- a/test-data/single/combined/txt/proteinGroups.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -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 Peptides BSA_min_23.mzXML Razor + unique peptides BSA_min_23.mzXML Unique peptides BSA_min_23.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage BSA_min_23.mzXML [%] Intensity Intensity BSA_min_23.mzXML 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 -CON__P02769;bsa;CON__P02768-1 CON__P02769;bsa;CON__P02768-1 1;1;1 1;1;1 1;1;1 ;bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4; 3 1 1 1 1 1 1 1.2 1.2 1.2 69.293 607 607;607;609 0 6.3321 1.2 0 0 1 + 0 2 True 2 2 2 2 -CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 1 1 1 1 1 1 1 1 1 1 0.8 0.8 0.8 137.98 1222 1222 0 5.9375 0.8 57554 57554 0 + 1 3 True 3 3 3 3 -CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 1 1 1 1 1 1 1 1 1 1 1 1 1 77.456 706 706 0 5.9768 1 768320 768320 1 + 2 0 True 0 0 0 0 -CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 1 1 1 1 1 1 1 1 1 1 1.6 1.6 1.6 55.207 496 496 0 5.9554 1.6 61894 61894 1 + 3 5 True 5 5 5 5 -CON__Q03247 CON__Q03247 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 35.979 316 316 0 5.9375 2.5 33499 33499 0 + 4 4 True 4 4 4 4 -CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1;1;1 1;1;1 1;1;1 ;; 3 1 1 1 1 1 1 1.6 1.6 1.6 55.877 511 511;523;524 0 6.1238 1.6 0 0 1 + 5 1 True 1 1 1 1
--- a/test-data/single/combined/txt/summary.txt Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Raw file Experiment 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_23 BSA_min_23.mzXML Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 1 Standard 19 81 0 111 51 0 60 4 2 0 2 3.6 3.92 NaN 3.33 6 1201 57 4.75 4 7.02 165 39 35 23.64 26.52 10 25.64 + 0.41463 0.43436 0.1789 0.18539 -Total 19 81 0 111 51 0 60 4 2 0 2 3.6 3.92 NaN 3.33 6 1201 165 39 35 23.64 26.52 10 25.64 0.41463 0.43436 0.1789 0.18539
--- a/test-data/single/mqpar.xml Thu Aug 15 08:09:00 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,426 +0,0 @@ -<?xml version="1.0" encoding="utf-8"?> -<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - <fastaFiles> - <FastaFileInfo> - <fastaFilePath>D:\fasta\bsa.fasta</fastaFilePath> - <identifierParseRule>>([^\s]*)</identifierParseRule> - <descriptionParseRule>>(.*)</descriptionParseRule> - <taxonomyParseRule></taxonomyParseRule> - <variationParseRule></variationParseRule> - <modificationParseRule></modificationParseRule> - <taxonomyId></taxonomyId> - </FastaFileInfo> - </fastaFiles> - <fastaFilesProteogenomics> - </fastaFilesProteogenomics> - <fastaFilesFirstSearch> - </fastaFilesFirstSearch> - <fixedSearchFolder></fixedSearchFolder> - <andromedaCacheSize>350000</andromedaCacheSize> - <advancedRatios>True</advancedRatios> - <pvalThres>0.005</pvalThres> - <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> - <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> - <rtShift>False</rtShift> - <separateLfq>False</separateLfq> - <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> - <lfqRequireMsms>True</lfqRequireMsms> - <decoyMode>revert</decoyMode> - <boxCarMode>all</boxCarMode> - <includeContaminants>True</includeContaminants> - <maxPeptideMass>4600</maxPeptideMass> - <epsilonMutationScore>True</epsilonMutationScore> - <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> - <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> - <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> - <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> - <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> - <minScoreModifiedPeptides>40</minScoreModifiedPeptides> - <secondPeptide>True</secondPeptide> - <matchBetweenRuns>False</matchBetweenRuns> - <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> - <matchBetweenRunsFdr>False</matchBetweenRunsFdr> - <dependentPeptides>False</dependentPeptides> - <dependentPeptideFdr>0</dependentPeptideFdr> - <dependentPeptideMassBin>0</dependentPeptideMassBin> - <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> - <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> - <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> - <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> - <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> - <msmsConnection>False</msmsConnection> - <ibaq>False</ibaq> - <top3>False</top3> - <independentEnzymes>False</independentEnzymes> - <useDeltaScore>False</useDeltaScore> - <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> - <taxonomyLevel>Species</taxonomyLevel> - <avalon>False</avalon> - <nModColumns>3</nModColumns> - <ibaqLogFit>False</ibaqLogFit> - <razorProteinFdr>True</razorProteinFdr> - <deNovoSequencing>False</deNovoSequencing> - <deNovoVarMods>True</deNovoVarMods> - <massDifferenceSearch>False</massDifferenceSearch> - <isotopeCalc>False</isotopeCalc> - <writePeptidesForSpectrumFile></writePeptidesForSpectrumFile> - <intensityPredictionsFile> - </intensityPredictionsFile> - <minPepLen>7</minPepLen> - <psmFdrCrosslink>0.01</psmFdrCrosslink> - <peptideFdr>0.01</peptideFdr> - <proteinFdr>0.01</proteinFdr> - <siteFdr>0.01</siteFdr> - <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> - <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> - <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> - <minPeptides>1</minPeptides> - <minRazorPeptides>1</minRazorPeptides> - <minUniquePeptides>0</minUniquePeptides> - <useCounterparts>False</useCounterparts> - <advancedSiteIntensities>True</advancedSiteIntensities> - <customProteinQuantification>False</customProteinQuantification> - <customProteinQuantificationFile></customProteinQuantificationFile> - <minRatioCount>2</minRatioCount> - <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods> - <string>Oxidation (M)</string> - </restrictMods> - <matchingTimeWindow>0</matchingTimeWindow> - <alignmentTimeWindow>0</alignmentTimeWindow> - <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms> - <numberOfCandidatesMsms>15</numberOfCandidatesMsms> - <compositionPrediction>0</compositionPrediction> - <quantMode>1</quantMode> - <massDifferenceMods> - </massDifferenceMods> - <mainSearchMaxCombinations>200</mainSearchMaxCombinations> - <writeMsScansTable>False</writeMsScansTable> - <writeMsmsScansTable>True</writeMsmsScansTable> - <writePasefMsmsScansTable>True</writePasefMsmsScansTable> - <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> - <writeMs3ScansTable>True</writeMs3ScansTable> - <writeAllPeptidesTable>True</writeAllPeptidesTable> - <writeMzRangeTable>True</writeMzRangeTable> - <writeMzTab>True</writeMzTab> - <disableMd5>False</disableMd5> - <cacheBinInds>True</cacheBinInds> - <etdIncludeB>False</etdIncludeB> - <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets> - <stackPeaks>False</stackPeaks> - <ms2PrecursorShift>0</ms2PrecursorShift> - <complementaryIonPpm>20</complementaryIonPpm> - <variationParseRule></variationParseRule> - <variationMode>none</variationMode> - <useSeriesReporters>False</useSeriesReporters> - <name>session1</name> - <maxQuantVersion>1.6.3.4</maxQuantVersion> - <tempFolder></tempFolder> - <pluginFolder></pluginFolder> - <numThreads>1</numThreads> - <emailAddress></emailAddress> - <smtpHost></smtpHost> - <emailFromAddress></emailFromAddress> - <fixedCombinedFolder></fixedCombinedFolder> - <fullMinMz>-1.79589544172745E+308</fullMinMz> - <fullMaxMz>1.79589544172745E+308</fullMaxMz> - <sendEmail>False</sendEmail> - <ionCountIntensities>False</ionCountIntensities> - <verboseColumnHeaders>False</verboseColumnHeaders> - <calcPeakProperties>False</calcPeakProperties> - <showCentroidMassDifferences>False</showCentroidMassDifferences> - <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <useDotNetCore>False</useDotNetCore> - <filePaths> - <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> - </filePaths> - <experiments> - <string>BSA_min_23.mzXML</string> - </experiments> - <fractions> - <short>32767</short> - </fractions> - <ptms> - <boolean>False</boolean> - </ptms> - <paramGroupIndices> - <int>0</int> - </paramGroupIndices> - <referenceChannel> - <string></string> - </referenceChannel> - <parameterGroups> - <parameterGroup> - <msInstrument>0</msInstrument> - <maxCharge>7</maxCharge> - <minPeakLen>2</minPeakLen> - <useMs1Centroids>False</useMs1Centroids> - <useMs2Centroids>False</useMs2Centroids> - <cutPeaks>True</cutPeaks> - <gapScans>1</gapScans> - <minTime>NaN</minTime> - <maxTime>NaN</maxTime> - <matchType>MatchFromAndTo</matchType> - <intensityDetermination>0</intensityDetermination> - <centroidMatchTol>8</centroidMatchTol> - <centroidMatchTolInPpm>True</centroidMatchTolInPpm> - <centroidHalfWidth>35</centroidHalfWidth> - <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> - <valleyFactor>1.4</valleyFactor> - <isotopeValleyFactor>1.2</isotopeValleyFactor> - <advancedPeakSplitting>False</advancedPeakSplitting> - <intensityThreshold>0</intensityThreshold> - <labelMods> - <string></string> - </labelMods> - <lcmsRunType>Standard</lcmsRunType> - <reQuantify>False</reQuantify> - <lfqMode>0</lfqMode> - <lfqSkipNorm>False</lfqSkipNorm> - <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> - <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> - <lfqMaxFeatures>100000</lfqMaxFeatures> - <neucodeMaxPpm>0</neucodeMaxPpm> - <neucodeResolution>0</neucodeResolution> - <neucodeResolutionInMda>False</neucodeResolutionInMda> - <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> - <fastLfq>True</fastLfq> - <lfqRestrictFeatures>False</lfqRestrictFeatures> - <lfqMinRatioCount>2</lfqMinRatioCount> - <maxLabeledAa>0</maxLabeledAa> - <maxNmods>5</maxNmods> - <maxMissedCleavages>1</maxMissedCleavages> - <multiplicity>1</multiplicity> - <enzymeMode>0</enzymeMode> - <complementaryReporterType>0</complementaryReporterType> - <reporterNormalization>0</reporterNormalization> - <neucodeIntensityMode>0</neucodeIntensityMode> - <fixedModifications> - <string>Carbamidomethyl (C)</string> - </fixedModifications> - <enzymes> - <string>Trypsin/P</string> - </enzymes> - <enzymesFirstSearch> - </enzymesFirstSearch> - <enzymeModeFirstSearch>0</enzymeModeFirstSearch> - <useEnzymeFirstSearch>False</useEnzymeFirstSearch> - <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> - <variableModifications> - <string>Oxidation (M)</string> - </variableModifications> - <useMultiModification>False</useMultiModification> - <multiModifications> - </multiModifications> - <isobaricLabels> - </isobaricLabels> - <neucodeLabels> - </neucodeLabels> - <variableModificationsFirstSearch> - </variableModificationsFirstSearch> - <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> - <additionalVariableModifications> - </additionalVariableModifications> - <additionalVariableModificationProteins> - </additionalVariableModificationProteins> - <doMassFiltering>True</doMassFiltering> - <firstSearchTol>20</firstSearchTol> - <mainSearchTol>4.5</mainSearchTol> - <searchTolInPpm>True</searchTolInPpm> - <isotopeMatchTol>2</isotopeMatchTol> - <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> - <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> - <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> - <checkMassDeficit>True</checkMassDeficit> - <recalibrationInPpm>True</recalibrationInPpm> - <intensityDependentCalibration>False</intensityDependentCalibration> - <minScoreForCalibration>70</minScoreForCalibration> - <matchLibraryFile>False</matchLibraryFile> - <libraryFile></libraryFile> - <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> - <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> - <matchLabelTimeTolMin>0</matchLabelTimeTolMin> - <reporterMassTolerance>NaN</reporterMassTolerance> - <reporterPif>NaN</reporterPif> - <filterPif>False</filterPif> - <reporterFraction>NaN</reporterFraction> - <reporterBasePeakRatio>NaN</reporterBasePeakRatio> - <timsHalfWidth>0</timsHalfWidth> - <timsStep>0</timsStep> - <timsResolution>0</timsResolution> - <timsMinMsmsIntensity>0</timsMinMsmsIntensity> - <timsRemovePrecursor>True</timsRemovePrecursor> - <timsIsobaricLabels>False</timsIsobaricLabels> - <timsCollapseMsms>True</timsCollapseMsms> - <crosslinkSearch>False</crosslinkSearch> - <crossLinker></crossLinker> - <minMatchXl>0</minMatchXl> - <minPairedPepLenXl>6</minPairedPepLenXl> - <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> - <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> - <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> - <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> - <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> - <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta> - <crosslinkCleaveModifications> - </crosslinkCleaveModifications> - <crosslinkFastaFiles> - </crosslinkFastaFiles> - <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode> - <peakRefinement>False</peakRefinement> - <isobaricSumOverWindow>True</isobaricSumOverWindow> - </parameterGroup> - </parameterGroups> - <msmsParamsArray> - <msmsParams> - <Name>FTMS</Name> - <MatchTolerance>20</MatchTolerance> - <MatchToleranceInPpm>True</MatchToleranceInPpm> - <DeisotopeTolerance>7</DeisotopeTolerance> - <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> - <DeNovoTolerance>10</DeNovoTolerance> - <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> - <Deisotope>True</Deisotope> - <Topx>12</Topx> - <TopxInterval>100</TopxInterval> - <HigherCharges>True</HigherCharges> - <IncludeWater>True</IncludeWater> - <IncludeAmmonia>True</IncludeAmmonia> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - <msmsParams> - <Name>ITMS</Name> - <MatchTolerance>0.5</MatchTolerance> - <MatchToleranceInPpm>False</MatchToleranceInPpm> - <DeisotopeTolerance>0.15</DeisotopeTolerance> - <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> - <Deisotope>False</Deisotope> - <Topx>8</Topx> - <TopxInterval>100</TopxInterval> - <HigherCharges>True</HigherCharges> - <IncludeWater>True</IncludeWater> - <IncludeAmmonia>True</IncludeAmmonia> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - <msmsParams> - <Name>TOF</Name> - <MatchTolerance>40</MatchTolerance> - <MatchToleranceInPpm>True</MatchToleranceInPpm> - <DeisotopeTolerance>0.01</DeisotopeTolerance> - <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.02</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> - <Deisotope>True</Deisotope> - <Topx>10</Topx> - <TopxInterval>100</TopxInterval> - <HigherCharges>True</HigherCharges> - <IncludeWater>True</IncludeWater> - <IncludeAmmonia>True</IncludeAmmonia> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - <msmsParams> - <Name>Unknown</Name> - <MatchTolerance>0.5</MatchTolerance> - <MatchToleranceInPpm>False</MatchToleranceInPpm> - <DeisotopeTolerance>0.15</DeisotopeTolerance> - <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> - <Deisotope>False</Deisotope> - <Topx>8</Topx> - <TopxInterval>100</TopxInterval> - <HigherCharges>True</HigherCharges> - <IncludeWater>True</IncludeWater> - <IncludeAmmonia>True</IncludeAmmonia> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - </msmsParamsArray> - <fragmentationParamsArray> - <fragmentationParams> - <Name>CID</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>HCD</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETD</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>PQD</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETHCD</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETCID</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>UVPD</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>Unknown</Name> - <Connected>False</Connected> - <ConnectedScore0>1</ConnectedScore0> - <ConnectedScore1>1</ConnectedScore1> - <ConnectedScore2>1</ConnectedScore2> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - </fragmentationParamsArray> -</MaxQuantParams>
--- a/test-data/template.xml Thu Aug 15 08:09:00 2019 -0400 +++ b/test-data/template.xml Sat Apr 11 11:49:19 2020 -0400 @@ -2,7 +2,7 @@ <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <fastaFiles> <FastaFileInfo> - <fastaFilePath></fastaFilePath> + <fastaFilePath>example.fasta</fastaFilePath> <identifierParseRule>>(.*)</identifierParseRule> <descriptionParseRule></descriptionParseRule> <taxonomyParseRule></taxonomyParseRule> @@ -88,8 +88,9 @@ <string>Acetyl (Protein N-term)</string> </restrictMods> <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> - <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> <numberOfCandidatesMsms>15</numberOfCandidatesMsms> <compositionPrediction>0</compositionPrediction> <quantMode>1</quantMode> @@ -107,15 +108,13 @@ <disableMd5>False</disableMd5> <cacheBinInds>True</cacheBinInds> <etdIncludeB>False</etdIncludeB> - <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets> - <stackPeaks>False</stackPeaks> <ms2PrecursorShift>0</ms2PrecursorShift> <complementaryIonPpm>20</complementaryIonPpm> <variationParseRule></variationParseRule> <variationMode>none</variationMode> <useSeriesReporters>False</useSeriesReporters> <name>templateSession</name> - <maxQuantVersion>1.6.3.4</maxQuantVersion> + <maxQuantVersion>1.6.10.43</maxQuantVersion> <tempFolder></tempFolder> <pluginFolder></pluginFolder> <numThreads>1</numThreads> @@ -150,11 +149,14 @@ <referenceChannel> <string></string> </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> <parameterGroups> <parameterGroup> <msInstrument>0</msInstrument> <maxCharge>7</maxCharge> <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> <useMs1Centroids>False</useMs1Centroids> <useMs2Centroids>False</useMs2Centroids> <cutPeaks>True</cutPeaks> @@ -263,14 +265,35 @@ <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> - <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta> - <crosslinkCleaveModifications> - </crosslinkCleaveModifications> + <crosslinkModifications> + </crosslinkModifications> <crosslinkFastaFiles> </crosslinkFastaFiles> - <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode></crosslinkMode> <peakRefinement>False</peakRefinement> <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath></diaLibraryPath> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> </parameterGroup> </parameterGroups> <msmsParamsArray> @@ -327,14 +350,14 @@ </msmsParams> <msmsParams> <Name>Unknown</Name> - <MatchTolerance>0.5</MatchTolerance> - <MatchToleranceInPpm>False</MatchToleranceInPpm> - <DeisotopeTolerance>0.15</DeisotopeTolerance> - <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>0.25</DeNovoTolerance> - <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> - <Deisotope>False</Deisotope> - <Topx>8</Topx> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> <TopxInterval>100</TopxInterval> <HigherCharges>True</HigherCharges> <IncludeWater>True</IncludeWater>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_mqparam.py Sat Apr 11 11:49:19 2020 -0400 @@ -0,0 +1,212 @@ +"""Tests for mqparam class. If testing a new MaxQuant version, +create a new parameter file using '<MAXQUANT_CMD> -c ./mqpar.xml' +""" + +import pytest +import xml.etree.ElementTree as ET +from mqparam import MQParam, ParamGroup + +TEMPLATE_PATH = './test-data/template.xml' + + +def mk_pg_root(): + mqpar = ET.parse(TEMPLATE_PATH).getroot() + return mqpar.find('.parameterGroups/parameterGroup') + + +class TestParamGroup: + def test_list_param(self): + t = ParamGroup(mk_pg_root()) + t.set_list_param('enzymes', ('test 1', 'test 2')) + assert len(t._root.find('enzymes')) == 2 + + t.set_list_param('variableModifications', ('Oxidation (M)', )) + assert t._root.find('variableModifications')[0].text == 'Oxidation (M)' + + with pytest.raises(ValueError): + t.set_list_param('foo', []) + + def test_simple_params(self): + t = ParamGroup(mk_pg_root()) + t.set_simple_param('fastLfq', False) + assert t._root.find('.fastLfq').text == 'False' + + with pytest.raises(ValueError): + t.set_simple_param('foo', 2) + + def test_silac(self): + t = ParamGroup(mk_pg_root()) + t.set_silac(None, None, ('Arg10', 'Lys4')) + assert t._root.find('.maxLabeledAa').text == '2' + assert t._root.find('.multiplicity').text == '2' + assert t._root.find('.labelMods')[1].text == 'Arg10;Lys4' + assert t._root.find('.labelMods')[0].text == '' + + def test_isobaric_label(self): + t = ParamGroup(mk_pg_root()) + t.set_isobaric_label('iTRAQ4plex-Lys114', 'iTRAQ4plex-Nter114', 0.3, 1, 1.2, 0, True) + + assert len(t._root.find('isobaricLabels')) == 1 + assert len(t._root.find('isobaricLabels')[0]) == 7 + + t.set_isobaric_label('iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115', 0.3, 1.0, 1.2, 0, True) + + assert len(t._root.find('isobaricLabels')) == 2 + + tag_list = [el.tag for el in t._root.find('isobaricLabels')[1]] + assert tag_list == ['internalLabel', 'terminalLabel', 'correctionFactorM2', + 'correctionFactorM1', 'correctionFactorP1', 'correctionFactorP2', + 'tmtLike'] + + text_list = [el.text for el in t._root.find('isobaricLabels')[1]] + assert text_list == ['iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115', + '0.3', '1', '1.2', '0', 'True'] + + +class TestMQParam: + + def test_version(self): + t = MQParam(TEMPLATE_PATH) + assert t._root.find('maxQuantVersion').text == '1.6.10.43' + + def test_validity_check(self): + design = {'Name': ['Test1', 'Test2'], + 'Fraction': ['2', 32767], + 'PTM': ['False', 'False'], + 'Experiment': ['e1', 'e1'], + 'paramGroup': [0, 0]} + + assert MQParam._check_validity(design, 2) is None + + design['Name'][0] = None + with pytest.raises(Exception): + MQParam._check_validity(design, 2) + design['Name'][0] = 'Test1' + + design['Experiment'][0] = '' + with pytest.raises(ValueError): + MQParam._check_validity(design, 2) + design['Experiment'][0] = 'e1' + + design['Fraction'][0] = 'foo' + with pytest.raises(ValueError): + MQParam._check_validity(design, 2) + + def test_exp_design(self, tmpdir): + # default experimental design when None is specified + t = MQParam(TEMPLATE_PATH) + design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML')) + assert design['Name'] == ('./Test1.mzXML', './Test2.mzXML') + assert design['Fraction'] == ('32767', '32767') + + # valid experimental design + e1 = tmpdir / "e1.txt" + e1.write('Name\tExperiment\tFraction\tPTM\nTest1\te1\nTest2\te1\t\tfalse') + t.exp_design = str(e1) + design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML')) + + assert design == {'Name': ['./Test1.mzXML', './Test2.mzXML'], + 'Experiment': ['e1', 'e1'], + 'Fraction': ['32767', '32767'], + 'PTM': ['False', 'false'], + 'paramGroup': (0, 0)} + + # invalid header + e2 = tmpdir / "e2.txt" + e2.write('Name\tExperiment\tFraction\tPTM\tparamGroup\n') + t.exp_design = str(e2) + + with pytest.raises(Exception): + design = t._make_exp_design(('./Test2.mzXML',), (0,)) + + def test_add_infiles(self): + t = MQParam(TEMPLATE_PATH) + t.add_infiles([('/path/Test1.mzXML', '/path/Test2.mzXML'), + ('/path/Test3.mzXML', '/path/Test4.mzXML')]) + + assert [e.text for e in t._root.find('filePaths')] == ['/path/Test1.mzXML', + '/path/Test2.mzXML', + '/path/Test3.mzXML', + '/path/Test4.mzXML'] + + assert [e.text for e in t._root.find('paramGroupIndices')] == ['0', '0', '1', '1'] + assert t[1] + + def test_translate(self): + t = MQParam(TEMPLATE_PATH) + t.add_infiles([('/posix/path/to/Test1.mzXML', + '/posix/path/to/Test2.mzXML'), + ('/path/dummy.mzXML',)]) # mqparam is not designed for windows + + t._root.find('filePaths')[2].text = r'D:\Windows\Path\Test3.mzXML' + + t.translate(('/galaxy/working/Test3.mzXML', + '/galaxy/working/Test1.mzXML', + '/galaxy/working/Test2.mzXML', + '/galaxy/working/Test4.mzXML')) + + assert [e.text for e in t._root.find('filePaths')] == ['/galaxy/working/Test1.mzXML', + '/galaxy/working/Test2.mzXML', + '/galaxy/working/Test3.mzXML'] + + def test_fasta_files(self): + t = MQParam(TEMPLATE_PATH) + t.add_fasta_files(('test1', 'test2'), + parse_rules={'identifierParseRule': r'>([^\s]*)'}) + assert len(t._root.find('fastaFiles')) == 2 + assert t._root.find('fastaFiles')[0].find("fastaFilePath").text == 'test1' + assert t._root.find('fastaFiles')[0].find("identifierParseRule").text == '>([^\\s]*)' + + def test_simple_param(self): + t = MQParam(TEMPLATE_PATH) + t.set_simple_param('minUniquePeptides', 4) + assert t._root.find('.minUniquePeptides').text == '4' + + with pytest.raises(ValueError): + t.set_simple_param('foo', 3) + + def test_from_yaml(self, tmpdir): + conf1 = tmpdir / "conf1.yml" + conf1.write(r""" + numThreads: 4 + fastaFiles: [test1.fasta,test2.fasta] + parseRules: + identifierParseRule: ^>.*\|(.*)\|.*$ + paramGroups: + - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0 + fixedModifications: [mod1,mod2] + lfqMode: 1 + - files: [Test3.mzXML,Test4.mzXML] # paramGroup 1 + labelMods: + - [] + - [] + - [label1,label2] + """) + + t = MQParam(TEMPLATE_PATH) + t._from_yaml(str(conf1)) + assert t['numThreads'] == '4' + assert [child.text for child in t[1]._root.find('labelMods')] == ['', 'label1;label2'] + + def test_write(self, tmpdir): + yaml_conf = tmpdir / "conf.yml" + yaml_conf.write(r""" + numThreads: 4 + fastaFiles: [test1.fasta,test2.fasta] + parseRules: + identifierParseRule: ^>.*\|(.*)\|.*$ + paramGroups: + - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0 + fixedModifications: [mod1] + variableModifications: [mod2,mod3] + maxMissedCleavages: 1 + """) + mqpar_out = tmpdir / "mqpar.xml" + + t = MQParam(TEMPLATE_PATH, yaml=str(yaml_conf)) + t.write(str(mqpar_out)) + + test = ET.parse(str(mqpar_out)).getroot() + assert test.find('numThreads').text == '4' + assert test.find('fastaFiles')[1].find('identifierParseRule').text == '^>.*\\|(.*)\\|.*$' + assert [el.text for el in test.find('parameterGroups')[0].find('variableModifications')] == ['mod2', 'mod3']