Mercurial > repos > galaxyp > maxquant_mqpar
changeset 0:256cc0e17454 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,27 @@ +GalaxyP - MaxQuant +================== + +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +* Tool ID: `maxquant_mqpar` +* Tool Type: `default` + + +Description +----------- + +Wrapper for the MaxQuant version available in conda. + + +Updating +-------- + +MaxQuant often changes the layout of its parameters file. +So changes to the code are likely to be necessary when +updating to a new version of MaxQuant. The init.py script +can be used to initialize the tool with a new list of +modifications or enzymes. From the tool dir run: + +./init.py -m MODIFICATIONS.XML -e ENZYMES.XML + +The location of these xml files usually is: +ANACONDA_DIR/bin/conf/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/init.py Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 +"""Initialize MaxQuant tool for use with a new version of +modifications/enzymes.xml. + +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] +FILES are the modifications/enzymes.xml of MaxQuant, located at +<ANACONDA_DIR>/pkgs/maxquant-<VERSION>/bin/conf/. +(for conda installations) + +Updates modification parameters in macros.xml. +""" + +import argparse +import re +import xml.etree.ElementTree as ET +from xml.dom import minidom + + +def build_list(node, name, mod_list, append=False): + """Build the modifications list in macros.xml""" + node.clear() + node.tag = 'xml' + node.set('name', name) + for m in mod_list: + ET.SubElement(node, 'expand', attrib={'macro': 'mod_option', + 'value': m}) + + +parser = argparse.ArgumentParser() +parser.add_argument("-m", "--modifications", + help="modifications.xml of maxquant") +parser.add_argument("-e", "--enzymes", + help="enzymes.xml of maxquant") +args = parser.parse_args() + +if args.modifications: + mods_root = ET.parse(args.modifications).getroot() + + mods = mods_root.findall('modification') + standard_mods = [] + label_mods = [] + 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')) + +if args.enzymes: + enzymes_root = ET.parse(args.enzymes).getroot() + + enzymes = enzymes_root.findall('enzyme') + enzymes_list = [e.get('title') for e in enzymes] + +macros_root = ET.parse('./macros.xml').getroot() +for child in macros_root: + if child.get('name') == 'modification' and args.modifications: + build_list(child, 'modification', standard_mods) + elif child.get('name') == 'label' and args.modifications: + build_list(child, 'label', label_mods) + elif child.get('name') == 'proteases' and args.enzymes: + build_list(child, 'proteases', enzymes_list) + +rough_string = ET.tostring(macros_root, 'utf-8') +reparsed = minidom.parseString(rough_string) +pretty = reparsed.toprettyxml(indent=" ") +even_prettier = re.sub(r"\n\s+\n", r"\n", pretty) +with open('./macros.xml', 'w') as f: + print(even_prettier, file=f)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0" ?> +<macros> + <token name="@VERSION@">1.6.3.4</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 ${on_string}" name="@NAME@"> + <filter>'@NAME@' in output</filter> + </data> + </xml> + <xml name="output_option" token_label="default label" token_name="default"> + <option value="@NAME@">@LABEL@</option> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mqpar.xml Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,214 @@ +<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@"> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">maxquant</requirement> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import re + + python3 '$__tool_directory__/mqwrapper.py' + --num_threads=\${GALAXY_SLOTS:-1} + --substitution_rx='@SUBSTITUTION_RX@' + #if $infile.select == "mzxml_files" + --mzxml_files='$infile.mzxml_files' + #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files]) + #else + --raw_files='$infile.raw_files' + #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files]) + #end if + --infile_names='$names' + --version='@VERSION@' + --fasta_files='$fasta_files' + --identifier_parse_rule='$identifier_parse_rule' + --description_parse_rule='$description_parse_rule' + --mqpar_in='$mqpar_in' + + --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='$mzTab' + --output_all='$output_all' + --mqpar_out='$mqpar_out' + + > '$log' + ]]></command> + <inputs> + <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 format="fasta" multiple="true" name="fasta_files" + type="data" label="FASTA files" + help="Specify one or more FASTA databases." /> + <param name="identifier_parse_rule" type="text" + label="identifier parse rule" value="^>.*\|(.*)\|.*$"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param name="description_parse_rule" type="text" + label="description parse rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" + help="Modify parse rules if needed"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param type="data" name="mqpar_in" format="xml" + label="mqpar.xml file with your search parameters. RAW file names + must match the names displayed in galaxy. Their paths + from the local machine are ignored. E.g. a file named + 'test01.raw' in galaxy can either be named 'test01.raw' or + 'D:\path\to\test01.raw' in the mqpar.xml."/> + + <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)"/> + </param> + </inputs> + + <outputs> + <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/> + <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/> + <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"/> + <data name="log" format="txt" + label="log"/> + </outputs> + + <tests> + <test> + <param name="select" value="mzxml_files" /> + <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <param name="mqpar_in" value="two/mqpar.xml" /> + <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" /> + <output name="evidence" file="two/combined/txt/evidence.txt" /> + <output name="msms" file="two/combined/txt/msms.txt" /> + <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/> + <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/> + <output name="msmsScans" file="two/combined/txt/msmsScans.txt" /> + <output name="mzRange" file="two/combined/txt/mzRange.txt" /> + <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/> + <output name="peptides" file="two/combined/txt/peptides.txt" /> + <output name="peptideSection" file="two/combined/txt/peptideSection.txt" /> + <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" /> + <output name="summary" file="two/combined/txt/summary.txt" /> + <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" /> + </test> + </tests> + <help><![CDATA[ +MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. + +This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred. + +**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) +- Optional files: + - mqpar.xml: + - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager. + +**Output files** + +Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented. + ]]></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> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mqparam.py Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,346 @@ +""" +Create a project-specific MaxQuant parameter file. + +TODO: check validity of parsed experimental design template + add support for parameter groups + add reporter ion MS2 + +Author: Damian Glaetzer <d.glaetzer@mailbox.org> +""" + +import ntpath +import os +import re +import xml.etree.ElementTree as ET +from itertools import zip_longest +from xml.dom import minidom + + +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 + """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' + """ + + 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 + # 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. + + >>> t = MQParam("test", './test-data/template.xml', None) + >>> MQParam._add_child(t.root, "test", "test") + >>> t.root.find('test').text == "test" + True + """ + + child = ET.SubElement(el, name, attrib=attrib if attrib else {}) + child.text = str(text) + + def _make_exp_design(self, infiles): + """Create a dict representing an experimental design from + an experimental design template and a list of 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 = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")} + 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) + else: + with open(self.exp_design) as design_file: + index_line = design_file.readline().strip() + index = [] + for i in index_line.split('\t'): + if i in design: + index.append(i) + else: + raise Exception("Invalid comlumn 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): + design[i].append(e) + + # map infiles to names in exp. design template + names = [] + names_to_paths = {} + # strip path and extension + for f in infiles: + b = os.path.basename(f) + basename = b[:-6] if b.endswith('.mzXML') else b[:-11] + names_to_paths[basename] = f + for name in design['Name']: + # same substitution as in maxquant.xml, + # when passing the element identifiers + fname = re.sub(self.substitution_rx, '_', name) + names.append(names_to_paths[fname] if fname in names_to_paths + else None) + # replace orig. file names with matching links to galaxy datasets + design['Name'] = names + + return design + + def add_infiles(self, infiles, interactive): + """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' + """ + + # 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} + + # Get parent nodes from document + nodes = dict() + for nodename in nodenames: + 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 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 add_fasta_files(self, files, + identifier=r'>([^\s]*)', + description=r'>(.*)'): + """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' + """ + fasta_node = self.root.find("fastaFiles") + fasta_node.clear() + fasta_node.tag = "fastaFiles" + + for index in range(len(files)): + filepath = '<fastaFilePath>' + files[index] + 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) + + 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' + """ + # 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', + '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.") + + 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 + '' + """ + 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 '') + + 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)' + """ + + 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) + 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: + print(even_prettier, file=f)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mqwrapper.py Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,99 @@ +""" +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', + 'mqpar_in', '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') + +global_simple_args = ('num_threads',) + +arguments = ['--' + el for el in (txt_output + + other_args + + global_simple_args)] + +for arg in arguments: + parser.add_argument(arg) + +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.link(f, l) + +# build mqpar.xml +mqpar_temp = os.path.join(os.getcwd(), 'mqpar.xml') +mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_temp +mqpar_in = args['mqpar_in'] + +exp_design = 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], False) +m.add_fasta_files(args['fasta_files'].split(','), + identifier=args['identifier_parse_rule'], + description=args['description_parse_rule']) + +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']) + +if args['output_all'] != 'None': + subprocess.run(('tar', '-zcf', args['output_all'], './combined/txt/'))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BSA_min_21.mzXML Sat Jul 20 04:53:23 2019 -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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bsa.fasta Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,12 @@ +>bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4 +MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPF +DEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEP +ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYY +ANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVA +RLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE +CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRR +HPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK +LGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL +NRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLP +DTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV +STQTALA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exp_design_test.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,3 @@ +Name Fraction Experiment PTM +QEplus021874 3 1 +QEplus021876 4 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/template.xml Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,428 @@ +<?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></fastaFilePath> + <identifierParseRule>>(.*)</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> + <string>Acetyl (Protein N-term)</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>False</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>templateSession</name> + <maxQuantVersion>1.6.3.4</maxQuantVersion> + <tempFolder></tempFolder> + <pluginFolder></pluginFolder> + <numThreads>1</numThreads> + <emailAddress></emailAddress> + <smtpHost></smtpHost> + <emailFromAddress></emailFromAddress> + <fixedCombinedFolder></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>file.example.RAW</string> + </filePaths> + <experiments> + <string>experiment.example</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>2</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> + <string>Acetyl (Protein N-term)</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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/allPeptides.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,408 @@ +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_21 MULTI 1 847.38839 846.38111 847.38839 NaN 7 6 2 0.381109 -0.0482261469993546 1.201046 847.387791819248 0.081 14.703 0 1 43 -1 0 NaN 19113 0;6793.9501953125;17268.0778808594;11640.9873046875;6699.59985351563;5769.13671875;0;0 13493.8720703125;4010.92431640625 0 +BSA_min_21 MULTI 2 723.80749 1445.6004 723.80749 NaN 7 6 2 0.600433 -0.104543113917543 2.322806 723.806797032529 0.117 14.703 0 1 43 -1 0 NaN 39557 0;8110.6953125;19435.744140625;29747.7436523438;30690.26953125;13858.6052246094;0;0 22715.69921875;8219.908203125 0 +BSA_min_21 MULTI 2 752.78847 1503.5624 752.78847 NaN 8 4 2 0.562393 -0.169245917260469 0.718395 752.788732084711 0.073 10.458 0 1 31 -1 0 NaN 29387 0;10127.0834960938;21733.4140625;15751.8271484375;11119.455078125;0 12711.455078125;9021.958984375 0 +BSA_min_21 MULTI 2 457.25346 912.49237 457.25346 NaN 16 10 2 0.492374 0.032627612403644 0.393188 457.253359375054 0.155 22.841 0 1 66 -1 0 NaN 59467 0;3735.79150390625;8995.0302734375;35687.0673828125;53174.9091796875;53788.833984375;43220.4130859375;26300.759765625;15439.015625;9543.25659179688;0;0 39425.62109375;16446.333984375 1 27 0 +BSA_min_21 MULTI 2 485.29192 968.56929 485.29192 NaN 22 13 3 0.569295 0.0837527808154164 0.60771 485.291493836352 0.158 29.17 0 1 84 -1 0 NaN 35092 0;6617.423828125;22640.4897460938;31257.1982421875;34228.8039550781;35066.3161621094;22591.3203125;25334.1130371094;10954.4208984375;10387.701171875;5409.716796875;5679.3515625;3629.8916015625;3413.14501953125;0 22239.669921875;10595.8701171875;3631.79956054688 0 +BSA_min_21 MULTI 1 609.34313 608.33585 609.34313 NaN 15 10 2 0.33585 0.0160151214452071 0.700196 609.343255068747 0.14 22.841 0 1 66 -1 0 NaN 16927 0;9840.98266601563;11124.4873046875;15963.8212890625;11129.7348632813;11067.9287109375;5360.87646484375;5169.17236328125;5964.7109375;5728.80078125;4231.7958984375;0 9241.0615234375;7473.39013671875 0 +BSA_min_21 MULTI 2 693.81484 1385.6151 693.81484 NaN 26 13 4 0.615131 -0.062251707645828 0.485084 693.814719759074 0.18 29.17 0 1 84 -1 0 NaN 80275 0;7327.79443359375;24553.93359375;45629.8364257813;58990.1015625;78488.80859375;45947.73046875;28370.5776367188;21553.2905273438;7933.5;5035.5166015625;6192.29931640625;0;0;0 34374.92578125;27593.28515625;12015.12109375;4505.4765625 2 20;38 0;1 +BSA_min_21 MULTI 2 752.31297 1502.6114 752.31297 NaN 9 6 2 0.611394 -0.119807465702706 0.803042 752.312709646655 0.121 14.703 0 1 43 -1 0 NaN 39800 0;4285.77001953125;11859.416015625;29434.9091796875;28467.7021484375;21782.734375;7783.14453125;0 22226.8125;12791.9208984375 1 36 0 +BSA_min_21 MULTI 4 835.11285 3336.4223 835.11285 NaN 18 7 3 0.4223 -0.152454285480871 0.475471 835.363566648992 0.151 16.655 0 1 48 -1 0 NaN 63753 0;17149.9038085938;25055.0866699219;28565.6630859375;44055.3051757813;40159.6279296875;23483.638671875;9918.11328125;0 0;20459.83203125;17639.462890625;9406.8017578125 1 41 2 +BSA_min_21 MULTI 1 1129.4643 1128.457 1129.4643 NaN 7 4 2 0.456983 -0.102107204594404 1.365982 1129.46329424631 0.127 10.543 0 7 37 -1 0 NaN 16363 0;7075.529296875;14889.8579101563;13879.3891601563;10506.4604492188;0 8219.6025390625;7768.6494140625 0 +BSA_min_21 MULTI 2 529.23526 1056.456 529.23526 NaN 11 6 2 0.45597 -0.069999862038685 0.525352 529.23524702789 0.144 14.61 0 7 48 -1 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0;6311.22607421875;8754.49487304688;8480.1240234375;0 0;6311.22607421875;4435.33447265625 0 +BSA_min_21 MULTI 1 890.51147 889.50419 890.51147 NaN 12 8 2 0.504193 0.0550214816486232 0.764025 890.511309054055 0.422 17.997 0 48 99 -1 0 NaN 32505 0;4910.841796875;17542.1821289063;16590.4404296875;29066.1064453125;23066.7353515625;9504.298828125;4884.37158203125;4831.18212890625;0 18355.962890625;10710.1435546875 0 +BSA_min_21 MULTI 3 987.56398 2959.6701 987.56398 NaN 9 7 2 0.67011 0.268662155433049 2.542496 988.232455202599 0.458 16.47 0 43 89 -1 0 NaN 28145 0;4842.390625;4339.55151367188;8024.91748046875;10535.5922851563;11118.5971679688;5135.18603515625;0;0 0;6473.9736328125;7065.58837890625 0 +BSA_min_21 MULTI 2 695.34262 1388.6707 695.34262 NaN 11 6 2 0.670679 -0.00810984752592958 0.76266 695.342847214244 0.406 14.211 0 54 93 8 TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ CON__Q0IIK2;CON__Q29443 0 38250 0;14984.2358398438;29819.1083984375;29084.7392578125;25871.509765625;17139.4765625;6280.5986328125;0 17183.125;13010.5595703125 1 70 0 +BSA_min_21 MULTI 2 890.35243 1778.6903 890.35243 NaN 16 7 3 0.690312 -0.167885838607617 0.841325 890.352365247965 0.422 16.162 0 60 99 -1 0 NaN 28853 0;10696.7241210938;25284.486328125;13905.8645019531;22343.8203125;11726.0463867188;10063.2033691406;4123.5986328125;0 10463.986328125;10160.248046875;4660.251953125 0 +BSA_min_21 MULTI 2 537.81687 1073.6192 537.81687 NaN 6 5 2 0.619187 0.0853225642406414 0.860704 537.816942841498 0.513 11.923 0 72 99 -1 0 NaN 15484 0;4765.35791015625;13641.2705078125;13395.4333496094;6628.81237792969;0;0 9669.9306640625;4510.712890625 0 +BSA_min_21 MULTI 2 751.81139 1501.6082 751.81139 NaN 9 6 2 0.608221 -0.122518328230854 0.939743 751.811796193494 0.492 14.039 0 66 99 -1 0 NaN 18992 0;5184.91064453125;10462.5234375;14045.6796875;9880.0263671875;5745.662109375;6069.99755859375;0 9001.66015625;5044.01953125 0 +BSA_min_21 MULTI 2 777.83075 1553.647 777.83075 NaN 10 7 2 0.646956 -0.107721302862501 0.523944 777.830735936543 0.471 16.049 0 54 99 0 DDPHACYSTVFDK 13 Unmodified _DDPHACYSTVFDK_ bsa;CON__P02769 0 32419 0;4814.0185546875;6059.36767578125;13234.7290039063;23648.78515625;21568.6884765625;13700.8950195313;0;0 14602.341796875;11081.0283203125 1 82 0 +BSA_min_21 MULTI 5 812.15609 4055.7441 812.15609 NaN 18 9 3 0.744064 -0.161577885562565 0.654153 812.356669084966 0.443 20.226 0 48 99 -1 0 NaN 49033 0;3445.51831054688;10195.0257568359;31522.841796875;29937.0932617188;25202.1640625;32384.310546875;23656.8525390625;6848.81201171875;0;0 0;16944.533203125;16791.10546875;9578.814453125 0 +BSA_min_21 MULTI 7 823.33076 5756.2644 823.33076 NaN 4 2 2 0.264359 -0.423522311275519 1.392371 823.760716101772 0.508 5.758 0 78 93 -1 0 NaN 25739 0;9439.15673828125;9841.84521484375;0 0;0;5113.29345703125;5769.67529296875 0 +BSA_min_21 MULTI 4 839.87032 3355.4522 839.87032 NaN 18 8 3 0.452161 -0.131346675770146 0.91301 840.120432111727 0.379 18.278 0 54 99 -1 0 NaN 53610 0;27595.84375;25173.5361328125;27216.892578125;21856.4345703125;20404.1889648438;18941.0786132813;6435.38842773438;0;0 0;17069.474609375;10947.2333984375;9059.63671875 0 +BSA_min_21 MULTI 2 843.37389 1684.7332 843.37389 NaN 16 5 4 0.733233 -0.0817443801904574 1.208973 843.374714279736 0.523 11.923 0 72 99 10 YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ CON__P02676 2.29958343542733 36308 0;19521.2788085938;18787.2817382813;35016.6455078125;20731.771484375;13503.7587890625;0 11023.345703125;10235.505859375;8751.0673828125;5006.7265625 1 92 1 +BSA_min_21 MULTI 2 430.2374 858.46024 430.2374 NaN 8 5 2 0.460239 0.0253472341734096 2.123673 430.236681252315 0.499 11.923 0 72 99 -1 0 NaN 11412 0;7067.99633789063;7718.81420898438;10310.3842773438;4820.31787109375;3255.27319335938;0 7577.419921875;4135.41796875 0 +BSA_min_21 MULTI 2 461.26081 920.50706 461.26081 NaN 8 5 2 0.507064 0.0436304272081998 0.41799 461.260747837569 0.53 11.923 0 72 99 -1 0 NaN 29551 0;9416.3076171875;20351.1962890625;15002.3862304688;26424.2915039063;15317.1875;0 19055.490234375;8401.8173828125 2 91;85 0;1 +BSA_min_21 MULTI 3 463.89686 1388.6688 463.89686 NaN 18 9 3 0.668755 -0.0100322521232101 0.58923 463.896829521798 0.422 20.226 0 48 99 7 TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ CON__Q0IIK2;CON__Q29443 2.86688527480472 99326 0;3691.8779296875;8363.6103515625;35855.0556640625;91369.7094726563;63194.5659179688;44804.7329101563;33870.9016113281;7351.9912109375;4699.16845703125;0 51193.3359375;32238.69921875;7937.67431640625 2 67;98 0;0 +BSA_min_21 MULTI 3 481.28091 1440.8209 481.28091 NaN 12 8 2 0.820902 0.118124598950317 0.682889 481.280974343372 0.422 18.278 0 54 99 -1 0 NaN 31820 0;4821.37646484375;6202.63916015625;23929.1845703125;17502.1655273438;13972.8552246094;11608.65625;3061.45141601563;4134.48291015625;0 15056.5234375;8872.6611328125 1 83 0 +BSA_min_21 MULTI 3 508.58654 1522.7378 508.58654 NaN 16 9 2 0.737798 -0.00266111302016725 0.37044 508.586455964423 0.436 20.226 0 48 99 -1 0 NaN 43197 0;3188.56469726563;12270.4814453125;30610.5615234375;31947.265625;36172.091796875;24363.2895507813;6752.63793945313;11374.64453125;5210.6572265625;0 23982.154296875;17929.1484375 1 73 0 +BSA_min_21 MULTI 3 518.89005 1553.6483 518.89005 NaN 10 6 2 0.648329 -0.106349495088807 2.163813 519.225386768445 0.489 13.933 0 60 99 -1 0 NaN 34132 0;4703.87841796875;9386.591796875;24898.04296875;23283.0537109375;22381.3276367188;11687.8979492188;0 14482.16796875;14514.39453125 0 +BSA_min_21 MULTI 2 559.7693 1117.524 559.7693 NaN 9 5 2 0.524044 -0.0300174134833924 1.58561 559.768801103529 0.538 11.923 0 72 99 -1 0 NaN 17843 0;10637.431640625;8693.818359375;14568.1103515625;15280.1772460938;5140.7861328125;0 11079.158203125;5793.765625 0 +BSA_min_21 MULTI 2 585.7691 1169.5236 585.7691 NaN 5 3 2 0.523646 -0.0543346692820705 1.749054 585.768767666226 0.547 7.711 0 84 99 -1 0 NaN 17919 0;10778.6171875;15199.0869140625;5375.859375;0 9397.6259765625;5801.4609375 0 +BSA_min_21 MULTI 2 736.29468 1470.5748 736.29468 NaN 7 4 2 0.574814 -0.141649943180482 0.716866 736.295043343221 0.547 9.825 0 78 99 -1 0 NaN 24544 0;9353.02294921875;15133.7646484375;18457.6469726563;9558.5673828125;0 11030.4052734375;7427.24169921875 0 +BSA_min_21 MULTI 1 400.22054 399.21327 400.22054 NaN 27 15 2 0.213268 -0.0103697768395818 3.726372 400.218150126271 0.525 32.798 0 13 99 -1 0 NaN 24628 0;9845.28271484375;10545.1369628906;10123.3044433594;10455.1870117188;9211.16625976563;8229.83984375;9206.7509765625;14777.1674804688;16875.1064453125;19460.97265625;13601.1586914063;13079.1025390625;16388.0617675781;10384.5908203125;0;0 16675.02734375;9548.97265625 0 +BSA_min_21 MULTI 2 428.77207 855.5296 428.77207 NaN 13 11 2 0.529595 0.0960516883171749 0.544283 428.772035034046 0.575 24.293 0 37 99 -1 0 NaN 30164 0;3511.56225585938;3825.44128417969;4139.3203125;5772.07836914063;7404.83642578125;13386.0244140625;8534.283203125;12096.677734375;19927.8129882813;6643.73095703125;6323.3876953125;0 20928.9609375;6643.73095703125 0 +BSA_min_21 MULTI 1 429.25182 428.24454 429.25182 NaN 20 17 2 0.244541 0.00754863192207722 1.029627 429.252563403712 0.56 36.88 0 1 99 -1 0 NaN 21907 0;4018.09741210938;4068.11657714844;4118.1357421875;9739.4833984375;6492.57470703125;11252.6904296875;10463.8779296875;12103.1279296875;10009.9326171875;13620.02734375;16490.888671875;12954.4306640625;15860.1767578125;11368.5771484375;18160.1590576172;19023.6843261719;0;0 17758.0390625;4103.048828125 0 +BSA_min_21 MULTI 2 461.74767 921.4808 461.74767 NaN 14 6 3 0.480796 0.0169143842105086 0.655256 461.747684636513 0.529 14.039 0 66 99 -1 0 NaN 43020 0;3919.46044921875;29991.630859375;44367.826171875;38897.6511230469;42091.376953125;25730.25;0 30971.01171875;13682.25390625;3505.40209960938 0 +BSA_min_21 MULTI 3 472.89075 1415.6504 472.89075 NaN 7 3 3 0.65043 -0.0407693455435947 0.632354 472.89081479184 0.584 7.711 0 84 99 -1 0 NaN 43845 0;5292.92138671875;19056.7224121094;40332.6684570313;0 19971.669921875;12813.8125;7547.18603515625 0 +BSA_min_21 MULTI 2 532.80294 1063.5913 532.80294 NaN 19 14 2 0.59133 0.0620782322844207 0.89098 532.802620518844 0.547 30.736 0 19 99 -1 0 NaN 25482 0;11658.3759765625;6371.7177734375;12925.6611328125;4947.52490234375;7325.11962890625;8809.7978515625;6300.15234375;5883.5234375;5946.2607421875;10242.828125;8520.94458007813;10986.2182617188;22045.3203125;21107.0229492188;0 16419.4296875;5625.890625 0 +BSA_min_21 MULTI 3 542.26956 1623.7869 542.26956 NaN 5 4 2 0.786864 -7.83552438861079E-05 0.784806 542.604027738255 0.584 9.825 0 78 99 -1 0 NaN 28086 0;2926.89282226563;4581.49865722656;11609.3940429688;8360.6865234375;0 8360.6865234375;11886.85546875 0 +BSA_min_21 MULTI 1 547.29498 546.28771 547.29498 NaN 6 4 2 0.287707 -0.00358565330816418 7.988923 547.298585048409 0.561 9.825 0 78 99 -1 0 NaN 11769 0;4716.59130859375;8972.32543945313;13359.6187744141;5820.453125;0 8671.9052734375;5404.3056640625 0 +BSA_min_21 MULTI 3 559.24853 1674.7238 559.24853 NaN 18 7 3 0.723758 -0.0866147410481517 0.554233 559.248698321496 0.508 16.162 0 60 99 -1 0 NaN 72140 0;11609.7485351563;18951.6411132813;42331.943359375;64517.6064453125;62426.8544921875;60428.4833984375;43004.3818359375;0 32104.572265625;26293.126953125;10454.2763671875 1 81 0 +BSA_min_21 MULTI 3 562.58402 1684.7302 562.58402 NaN 23 7 4 0.73023 -0.0847458212112997 0.962383 562.584772670959 0.5 16.162 0 60 99 9 YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ CON__P02676 0 78017 0;5475.34423828125;23366.1633300781;62110.6728515625;75243.3842773438;58874.4975585938;53664.9799804688;34079.66015625;0 29231.140625;23320.72265625;17257.232421875;6504.615234375 1 80 0 +BSA_min_21 MULTI 2 561.23974 1120.4649 561.23974 NaN 26 11 3 0.46493 -0.0904842882562207 0.46976 561.239571853106 0.559 24.293 0 37 99 -1 0 NaN 158810 0;9230.478515625;24284.412109375;37028.34375;38434.8486328125;28997.6025390625;28687.5771484375;53332.8349609375;102954.216796875;119394.01171875;153369.65625;140399.233398438;0 105331.609375;43806.62109375;9102.0419921875 1 51 0 +BSA_min_21 MULTI 2 568.79013 1135.5657 568.79013 NaN 5 3 2 0.565704 0.00334394678270655 0.615493 568.790191379726 0.547 7.711 0 84 99 -1 0 NaN 15135 0;5142.3740234375;12837.9770507813;9945.671875;0 7011.41748046875;5826.5595703125 0 +BSA_min_21 MULTI 7 570.45938 3986.1647 570.45938 NaN 5 4 2 0.164747 0.291111249103778 1.2616 570.745515761694 0.528 9.825 0 78 99 -1 0 NaN 26052 0;4088.34912109375;4003.96008300781;11493.7145996094;6710.23583984375;0 0;0;7574.1435546875;4088.34912109375 0 +BSA_min_21 MULTI 3 574.89513 1721.6636 574.89513 NaN 13 9 2 0.663562 -0.168403421289895 0.463748 574.895034712069 0.584 20.226 0 48 99 -1 0 NaN 40097 0;4399.6064453125;4485.24633789063;4570.88623046875;11549.9523925781;17705.712890625;15798.2470703125;19582.7353515625;24590.3408203125;0;0 16626.986328125;11371.765625 1 97 0 +BSA_min_21 MULTI 3 589.22449 1764.6516 589.22449 NaN 11 3 4 0.651639 -0.200100359993939 0.897766 589.224697893425 0.584 7.711 0 84 99 -1 0 NaN 757960 0;15533.0581054688;99619.0478515625;729715.87890625;0 310935.65625;245177.34375;124551.1015625;49051.77734375 1 94 0 +BSA_min_21 MULTI 3 614.63631 1840.8871 614.63631 NaN 5 4 2 0.887089 0.00028117336592004 0.694664 614.970769865097 0.566 9.825 0 78 99 -1 0 NaN 33552 0;4443.35693359375;4337.31420898438;15501.232421875;9923.19921875;0 11269.9609375;12581.9287109375 0 +BSA_min_21 MULTI 2 639.30668 1276.5988 639.30668 NaN 6 5 2 0.598809 -0.028426707325707 1.554277 639.307077797849 0.584 11.923 0 72 99 -1 0 NaN 15123 0;3943.39819335938;4584.02746582031;5224.65673828125;8266.45239257813;4789.61279296875;0 7565.39697265625;4789.61279296875 0 +BSA_min_21 MULTI 5 641.89233 3204.4253 641.89233 NaN 8 5 2 0.42529 -0.0887460879694117 2.09029 642.292985700728 0.512 11.923 0 72 99 -1 0 NaN 23941 0;3881.06884765625;11076.2985839844;12568.5817871094;10383.7104492188;3527.02392578125;0 0;4798.47021484375;8674.587890625 0 +BSA_min_21 MULTI 3 641.281 1920.8212 641.281 NaN 5 3 2 0.821166 -0.102411955036587 1.38797 641.280443916999 0.584 7.711 0 84 99 -1 0 NaN 34062 0;4565.6513671875;12665.3291015625;22596.490234375;0 13518.904296875;9077.5859375 0 +BSA_min_21 MULTI 3 649.6565 1945.9477 649.6565 NaN 14 5 3 0.947673 0.0125369676420632 0.936763 649.656254943024 0.554 11.923 0 72 99 -1 0 NaN 39608 0;8731.90551757813;25638.3276367188;28519.3139648438;33951.9521484375;25567.8647460938;0 18408.056640625;13551.5478515625;8707.236328125 2 96;87 0;1 +BSA_min_21 MULTI 2 659.31306 1316.6116 659.31306 NaN 24 6 5 0.611572 -0.0340688797505209 0.378473 659.313179263994 0.544 14.039 0 66 99 -1 0 NaN 675600 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0;113598.3125;268971.296875;273512.21875;327821.2734375;293932.546875;284912.0546875;317776.6875;276913.546875;282582.9375;309678.84375;315305.8359375;341380.8984375;412443.2890625;350983.1953125;333208.1015625;0 311737.5;106428.734375 0 +BSA_min_22 MULTI 2 891.32977 1780.645 891.32977 NaN 7 4 3 0.644993 -0.214103988484794 1.708541 891.330602133011 0.564 5.366 0 88 97 -1 0 NaN 108510 0;18189.900390625;36413.9580078125;95086.095703125;33709.892578125;0 54638.015625;26095.5859375;17093.90234375 0 +BSA_min_22 MULTI 1 998.47572 997.46844 998.47572 NaN 8 5 2 0.468444 -0.0303914675558872 0.989651 998.476134677568 0.575 6.3 0 86 97 -1 0 NaN 68746 0;24384.458984375;29209.26171875;59130.58984375;43881.052734375;60372.1484375;0 43851.453125;18626.490234375 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/evidence.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,11 @@ +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 Fraction 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 +DDPHACYSTVFDK 13 Unmodified _DDPHACYSTVFDK_ 0 0 CON__P02769;bsa CON__P02769 CON__P02769 MULTI-MSMS BSA_min_21 1 BSA_min_21.mzXML 777.835021972656 2 777.830105 1553.64566 NaN 0 0 0.83472 0.00064927 0.83472 0.00064927 777.830735936543 0.47149 0.26748 0.47149 0.29786 0.56534 0 10 7 2 0 0 0 0.0087938 1 82 0 0 1 32419 + 0 0 0 0 0 0 +ECCHGDLLECADDR 14 Unmodified _ECCHGDLLECADDR_ 0 0 CON__P02769;bsa CON__P02769 CON__P02769 MULTI-MSMS BSA_min_22 2 BSA_min_22.mzXML 584.229736328125 3 583.892361 1748.65525 NaN 0 0 -1.2 -0.00070066 -1.2 -0.00070066 583.891878608632 0.42243 0.40142 0.42243 0.19137 0.59279 0 52 16 4 0 0 0 0.012255 2 60 4.06 4.06 1 339840 + 1 0 1 1 1;2 1 +ECCHGDLLECADDR 14 Unmodified _ECCHGDLLECADDR_ 0 0 CON__P02769;bsa CON__P02769 CON__P02769 MULTI-MSMS BSA_min_22 2 BSA_min_22.mzXML 875.332336425781 2 875.334903 1748.65525 NaN 0 0 0.26945 0.00023586 0.26945 0.00023586 875.335151892134 0.508 0.18103 0.508 0.41176 0.59279 0 16 8 3 0 0 0 0.012255 1 90 3.6449 3.6449 1 145520 + 2 0 1 1 3 3 +GCTTTNSPSTPCQNCSR 17 Unmodified _GCTTTNSPSTPCQNCSR_ 0 0 CON__Q6IFU6 CON__Q6IFU6 CON__Q6IFU6 MSMS BSA_min_21 1 BSA_min_21.mzXML 964.384521484375 2 964.388198 1926.76184 NaN NaN NaN NaN NaN NaN NaN NaN 0.26375 1 0.26375 -0.23625 0.76375 0 0 0 0 0.016011 1 45 0 0 1 + 3 4 2 2 4 4 +LGQYTSPVAK 10 Unmodified _LGQYTSPVAK_ 0 0 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030 CON__P01030 MSMS BSA_min_21 1 BSA_min_21.mzXML 532.293029785156 2 532.292756 1062.57096 NaN NaN NaN NaN NaN NaN NaN NaN 0.057288 1 0.057288 -0.44271 0.55729 6.9389E-18 0 0 0 0.0074222 1 10 9.2141 9.2141 1 + 4 1 3 3 5 5 +TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ 0 0 CON__Q29443;CON__Q0IIK2 CON__Q29443 CON__Q29443 MULTI-MSMS BSA_min_21 1 BSA_min_21.mzXML 463.896636962891 3 463.896757 1388.66844 NaN 0 0 0.2251 0.00010442 0.2251 0.00010442 463.896829521798 0.42161 0.33709 0.42161 0.2654 0.60249 0 18 9 3 0 0 0 0.0053592 2 67 2.8669 2.8669 1 99326 + 5 3 4 4 6;7 6 +TSDANINWNNLK 12 Unmodified _TSDANINWNNLK_ 0 0 CON__Q29443;CON__Q0IIK2 CON__Q29443 CON__Q29443 MULTI-MSMS BSA_min_21 1 BSA_min_21.mzXML 695.341064453125 2 695.341498 1388.66844 NaN 0 0 1.6082 0.0011183 1.6082 0.0011183 695.342847214244 0.40624 0.23684 0.40624 0.29786 0.5347 -5.5511E-17 11 6 2 0 0 0 0.0053592 1 70 0 0 1 38250 + 6 3 4 4 8 8 +YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ 0 0 CON__P02676 CON__P02676 CON__P02676 MULTI-MSMS BSA_min_21 1 BSA_min_21.mzXML 562.586242675781 3 562.584073 1684.73039 NaN 0 0 -0.095012 -5.3452E-05 -0.095012 -5.3452E-05 562.584772670959 0.49991 0.26937 0.49991 0.33312 0.60249 0 23 7 4 0 0 0 0.012255 1 80 0 0 1 78017 + 7 2 5 5 9 9 +YCGVPGEYWLGNDR 14 Unmodified _YCGVPGEYWLGNDR_ 0 0 CON__P02676 CON__P02676 CON__P02676 MULTI-MSMS BSA_min_21 1 BSA_min_21.mzXML 843.877807617188 2 843.372472 1684.73039 NaN 0 0 1.6852 0.0014212 1.6852 0.0014212 843.374714279736 0.52265 0.19871 0.52265 0.40378 0.60249 0 16 5 4 0 0 0 0.012255 1 92 3.6449 3.6449 1 36308 + 8 2 5 5 10 10 +YICDNQDTISSK 12 Unmodified _YICDNQDTISSK_ 0 0 CON__P02769;bsa CON__P02769 CON__P02769 MSMS BSA_min_21 1 BSA_min_21.mzXML 722.326232910156 2 722.324656 1442.63476 NaN NaN NaN NaN NaN NaN NaN NaN 0.25827 1 0.25827 -0.24173 0.75827 0 0 0 0 3.6003E-09 1 44 24.343 7.7115 1 + 9 0 6 6 11 11
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/modificationSpecificPeptides.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,8 @@ +Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Oxidation (M) Missed cleavages Fraction Average Fraction Std. Dev. Fraction 1 Fraction 2 Experiment BSA_min_21.mzXML Experiment BSA_min_22.mzXML Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Intensity Intensity BSA_min_21.mzXML Intensity BSA_min_22.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 +DDPHACYSTVFDK Unmodified 1553.6457 0.64565776 0 CON__P02769;bsa yes no 0 0 1 0 1 1 0.47149 0.47149 2 0.0087938 82 BSA_min_21 0 0 32419 32419 0 + 0 0 0 0 0 0 1 +ECCHGDLLECADDR Unmodified 1748.6553 0.65525294 0 CON__P02769;bsa yes no 0 0 2 0 2 2 0.46522 0.46522 2;3 0.012255 60 BSA_min_22 4.06 4.06 485350 0 485350 + 1 0 1 1;2 1;2;3 1 3 +GCTTTNSPSTPCQNCSR Unmodified 1926.7618 0.76184328 4 CON__Q6IFU6 yes yes 0 0 1 0 1 1 0.26375 0.26375 2 0.016011 45 BSA_min_21 0 0 0 0 0 + 2 4 2 3 4 4 1 +LGQYTSPVAK Unmodified 1062.571 0.5709599 1 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 yes no 0 0 1 0 1 1 0.057288 0.057288 2 0.0074222 10 BSA_min_21 9.2141 9.2141 0 0 0 + 3 1 3 4 5 5 1 +TSDANINWNNLK Unmodified 1388.6684 0.66844211 3 CON__Q29443;CON__Q0IIK2 yes no 0 0 1 0 2 2 0.41393 0.41393 2;3 0.0053592 98 BSA_min_21 2.8669 2.8669 137580 137580 0 + 4 3 4 5;6 6;7;8 7 3 +YCGVPGEYWLGNDR Unmodified 1684.7304 0.73039044 2 CON__P02676 yes yes 0 0 1 0 2 2 0.51128 0.51128 2;3 0.012255 80 BSA_min_21 0 0 114330 114330 0 + 5 2 5 7;8 9;10 9 2 +YICDNQDTISSK Unmodified 1442.6348 0.63475872 0 CON__P02769;bsa yes no 0 0 1 0 1 1 0.25827 0.25827 2 3.6003E-09 44 BSA_min_21 24.343 7.7115 0 0 0 + 6 0 6 9 11 11 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/msms.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,13 @@ +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_21 82 67 DDPHACYSTVFDK 13 0 Unmodified _DDPHACYSTVFDK_ 0 CON__P02769;bsa 2 CID FTMS MULTI-MSMS 4 0 777.83011 1553.6457 0.83472 0.00064927 NaN 0.48088 0.0087938 0 0 NaN NaN 1 0 0 0 78 14602.341796875 1 0 0 0 0 0 None Unknown 0 DDPHACYSTVFDK _DDPHACYSTVFDK_ 0 0 0 0 0 +BSA_min_22 60 48 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 CON__P02769;bsa 3 CID FTMS MULTI-MSMS 2 1 583.89236 1748.6553 -1.2 -0.00070066 NaN 0.34278 0.012255 4.06 4.06 NaN NaN 1 0 0 0 58 153296.796875 1 0 0 y2;b7 138.2;64.3 0.000875681750017066;0.0151950483749488 3.01808299667453;17.4197737863645 290.14501953125;872.287353515625 2 0.0345694906307557 0.016260162601626 None Unknown 4.06002529511453 ECCHGDLLECADDR _ECCHGDLLECADDR_ 1 0 1 1 1 +BSA_min_22 67 53 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 CON__P02769;bsa 3 CID FTMS MULTI-MSMS 1 0 583.89236 1748.6553 -1.2 -0.00070066 NaN 0.3858 0.012255 0 0 NaN NaN 1 0 0 0 66 93077.6484375 0.590638368628048 -6 0.16876 0 0 0 None Unknown 0 ECCHGDLLECADDR _ECCHGDLLECADDR_ 2 0 1 1 1 +BSA_min_22 90 70 ECCHGDLLECADDR 14 0 Unmodified _ECCHGDLLECADDR_ 0 CON__P02769;bsa 2 CID FTMS MULTI-MSMS 2 0 875.3349 1748.6553 0.26945 0.00023586 NaN 0.52328 0.012255 3.6449 3.6449 NaN NaN 1 0 0 0 88 65524.953125 1 0 0 y10 82.6 -0.0168735156998991 -14.5021701256686 1163.5166015625 1 0.0263469586281723 0.00862068965517241 None Unknown 3.64492303257886 ECCHGDLLECADDR _ECCHGDLLECADDR_ 3 0 1 1 2 +BSA_min_21 45 36 GCTTTNSPSTPCQNCSR 17 0 Unmodified _GCTTTNSPSTPCQNCSR_ 0 CON__Q6IFU6 2 CID FTMS MSMS 2 964.3882 1926.7618 NaN NaN NaN 0.26375 0.016011 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 GCTTTNSPSTPCQNCSR _GCTTTNSPSTPCQNCSR_ 4 4 2 2 3 +BSA_min_21 10 7 LGQYTSPVAK 10 0 Unmodified _LGQYTSPVAK_ 0 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 2 CID FTMS MSMS 3 532.29276 1062.571 NaN NaN NaN 0.057288 0.0074222 9.2141 9.2141 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN y3;b2;b4 12.9;21.6;166.6 -0.00279849649376729;-0.00340676689998531;-0.00711106876252643 -8.82191072988591;-19.9090833143192;-15.3838714608204 317.221130371094;171.1162109375;462.241821289063 3 0.0308188417439214 0.0245901639344262 None Unknown 9.21405366890568;0;0 LGQYTSPVAK;AQYELIAQK;AQYEIIAQK _LGQYTSPVAK_;_AQYELIAQK_;_AQYEIIAQK_ 5 1 3 3 4 +BSA_min_21 67 54 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 CON__Q29443;CON__Q0IIK2 3 CID FTMS MULTI-MSMS 1 0 463.89676 1388.6684 0.2251 0.00010442 NaN 0.39389 0.0053592 0 0 NaN NaN 1 0 0 0 66 23524.845703125 0.459529453830584 -1 0.0348916666666667 0 0 0 None Unknown 0 TSDANINWNNLK _TSDANINWNNLK_ 6 3 4 4 5 +BSA_min_21 98 80 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 CON__Q29443;CON__Q0IIK2 3 CID FTMS MULTI-MSMS 5 1 463.89676 1388.6684 0.2251 0.00010442 NaN 0.57847 0.0053592 2.8669 2.8669 NaN NaN 1 0 0 0 93 7351.9912109375 0.14361227054852 4 NaN b9 5.8 -0.00485963613130025 -4.78099799382671 1016.44805908203 1 0.00268406539551173 0.00961538461538462 None Unknown 2.86688527480472 TSDANINWNNLK _TSDANINWNNLK_ 7 3 4 4 5 +BSA_min_21 70 57 TSDANINWNNLK 12 0 Unmodified _TSDANINWNNLK_ 0 CON__Q29443;CON__Q0IIK2 2 CID FTMS MULTI-MSMS 4 0 695.3415 1388.6684 1.6082 0.0011183 NaN 0.41019 0.0053592 0 0 NaN NaN 1 0 0 0 66 16808.548828125 0.978200928418143 -1 0.0348916666666667 0 0 0 None Unknown 0;0 TSDANINWNNLK;HVFAVDGAGEMLK _TSDANINWNNLK_;_HVFAVDGAGEM(ox)LK_ 8 3 4 4 6 +BSA_min_21 80 65 YCGVPGEYWLGNDR 14 0 Unmodified _YCGVPGEYWLGNDR_ 0 CON__P02676 3 CID FTMS MULTI-MSMS 2 0 562.58407 1684.7304 -0.095012 -5.3452E-05 NaN 0.46942 0.012255 0 0 NaN NaN 1 0 0 0 78 21744.55859375 0.743883342518387 -1 0.0342566666666667 0 0 0 None Unknown 0 YCGVPGEYWLGNDR _YCGVPGEYWLGNDR_ 9 2 5 5 7 +BSA_min_21 92 75 YCGVPGEYWLGNDR 14 0 Unmodified _YCGVPGEYWLGNDR_ 0 CON__P02676 2 CID FTMS MULTI-MSMS 3 1 843.37247 1684.7304 1.6852 0.0014212 NaN 0.54095 0.012255 3.6449 3.6449 NaN NaN 1 0 0 0 89 10235.505859375 1 0 0 y13 5.5 0.01796629868727 11.7993127121924 1522.65637207031 1 0.00360499788750048 0.00961538461538462 None Unknown 3.64492303257886 YCGVPGEYWLGNDR _YCGVPGEYWLGNDR_ 10 2 5 5 8 +BSA_min_21 44 35 YICDNQDTISSK 12 0 Unmodified _YICDNQDTISSK_ 0 CON__P02769;bsa 2 CID FTMS MSMS 1 722.32466 1442.6348 NaN NaN NaN 0.25827 3.6003E-09 24.343 7.7115 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN y3;y8;y9;y10;b9 300.5;246.4;476.9;729.7;28 -0.00453549397497;-0.0138762988750614;-0.0167184231250985;-0.0175643623499582;-0.0019145705750816 -14.1212848085697;-15.5485287132689;-16.594286035641;-15.0442644146915;-1.70415154482157 321.181396484375;892.450927734375;1007.48071289063;1167.51220703125;1123.47436523438 5 0.182617971514711 0.0357142857142857 None Unknown 24.3433433825462;16.6318347984703 YICDNQDTISSK;YICENQDSISSK _YICDNQDTISSK_;_YICENQDSISSK_ 11 0 6 6 9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/msmsScans.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,160 @@ +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 Fraction Experiment Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number +BSA_min_21 2 0.01221 -1 47150 35 0 0 -1 - -1 0 150 722.798704576355 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 0 0 1 +BSA_min_21 3 0.017623 -1 17297 35 0 0 -1 - -1 0 121 594.555969238281 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 1 0 1 +BSA_min_21 4 0.023405 -1 18183 35 0 0 -1 - -1 0 142 759.809204101563 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 2 0 1 +BSA_min_21 5 0.029038 -1 16124 35 0 0 -1 - -1 0 116 487.732727050781 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 3 0 1 +BSA_min_21 6 0.034095 -1 16526 35 0 0 -1 - -1 0 113 372.19735409279 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 4 0 1 +BSA_min_21 8 0.04682 -1 65409 35 0 0 -1 - -1 0 122 472.250845646481 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 5 1 7 +BSA_min_21 9 0.051375 -1 13709 35 0 0 -1 - -1 0 114 891.331298828125 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 6 1 7 +BSA_min_21 10 0.057288 -1 8824.9 35 0 0 -1 + 5 LGQYTSPVAK 10 122 532.293029785156 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 Unmodified _LGQYTSPVAK_ CON__ENSEMBL:ENSBTAP00000007350;CON__P01030 9.21405366890568 1 BSA_min_21.mzXML NaN NaN NaN 0 7 1 7 +BSA_min_21 11 0.062452 -1 11430 35 0 0 -1 - -1 0 119 538.768188476563 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 8 1 7 +BSA_min_21 12 0.06764 -1 7136.7 35 0 0 -1 - -1 0 115 517.73974609375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 9 1 7 +BSA_min_21 14 0.080647 -1 33.829 35 0 0 -1 - -1 0 4 1568.24185979966 NaN 0 PEAK CID FTMS 0 0 0 13 63387.5625 1 0 0 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 10 2 13 +BSA_min_21 15 0.086635 -1 7892.6 35 0 0 -1 - -1 0 111 526.229125976563 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 11 2 13 +BSA_min_21 16 0.091825 -1 6445.6 35 0 0 -1 - -1 0 115 508.24755859375 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 12 2 13 +BSA_min_21 17 0.096923 -1 3111.3 35 0 0 -1 - -1 0 112 735.343090637035 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 13 2 13 +BSA_min_21 18 0.10248 -1 5136.5 35 0 0 -1 - -1 0 110 570.301832275435 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 14 2 13 +BSA_min_21 20 0.11574 -1 3120.2 35 0 0 -1 - -1 0 114 693.814842092965 1385.61513125273 2 MULTI CID FTMS 0 0 0 19 25857.935546875 0.752232476411029 -2 0.06875 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 15 3 19 +BSA_min_21 21 0.12116 -1 2652.8 35 0 0 -1 - -1 0 124 751.810485839844 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 16 3 19 +BSA_min_21 22 0.12678 -1 3085 35 0 0 -1 - -1 0 102 672.697509765625 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 17 3 19 +BSA_min_21 23 0.13276 -1 2127.5 35 0 0 -1 - -1 0 120 960.878540039063 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 18 3 19 +BSA_min_21 24 0.13858 -1 2039.5 35 0 0 -1 - -1 0 120 964.882507324219 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 5 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 19 3 19 +BSA_min_21 26 0.15251 -1 11500 35 0 0 -1 - -1 0 127 518.23200061628 1034.44944829936 2 MULTI CID FTMS 0 0 0 25 49389.73046875 0.0109825061594874 -5 NaN 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 20 4 25 +BSA_min_21 27 0.15775 -1 4589.6 35 0 0 -1 - -1 0 101 457.253463518846 912.492374104492 2 MULTI CID FTMS 0 0 0 25 39425.62109375 1 0 0 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 21 4 25 +BSA_min_21 28 0.16272 -1 2946.3 35 0 0 -1 - -1 0 112 672.297790527344 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 3 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 22 4 25 +BSA_min_21 29 0.1687 -1 1729.9 35 0 0 -1 - -1 0 108 960.376098632813 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 4 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 23 4 25 +BSA_min_21 30 0.17459 -1 6259.6 35 0 0 -1 - -1 0 111 529.235261408654 1056.45596988411 2 MULTI CID FTMS 0 0 0 25 20563.033203125 1 0 0 5 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 24 4 25 +BSA_min_21 32 0.1879 -1 23439 35 0 0 -1 - -1 0 126 450.225605290271 NaN 0 PEAK CID FTMS 0 0 0 31 3407.88354492188 0.498620912407523 -1 0.0352683333333333 1 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 25 5 31 +BSA_min_21 33 0.19282 -1 3779.7 35 0 0 -1 - -1 0 112 707.71257651655 NaN 0 PEAK CID FTMS 0 0 0 31 36063.26953125 0.571979713244288 -5 0.174893333333333 2 NaN 1 BSA_min_21.mzXML NaN NaN NaN 0 26 5 31 +BSA_min_21 34 0.1989 -1 4361 35 0 0 -1 - 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-1 0 105 511.722861180277 1021.43116942735 2 MULTI CID FTMS 0 0 0 69 88299.2578125 0.90380053783557 -1 0.019775 2 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 56 13 69 +BSA_min_22 72 0.41503 -1 1824.3 35 0 0 -1 - -1 0 107 1002.07797774428 3003.21210383305 3 MULTI CID FTMS 0 0 0 69 44722.15234375 0.0212647431022184 8 -0.16323 3 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 57 13 69 +BSA_min_22 73 0.42101 -1 700.97 35 0 0 -1 - -1 0 62 747.54713506966 NaN 0 PEAK CID FTMS 0 0 0 69 47683.56640625 0.163391162978462 9 -0.185018333333333 4 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 58 13 69 +BSA_min_22 75 0.4333 -1 213.41 35 0 0 -1 - -1 0 24 1146.0434746856 2290.072396438 2 MULTI CID FTMS 0 0 0 74 102962.9140625 0.243369234361311 5 -0.102611666666667 1 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 59 14 74 +BSA_min_22 76 0.43931 -1 10561 35 0 0 -1 - -1 0 161 882.35364043549 1762.69272793778 2 MULTI CID FTMS 0 0 0 74 65622.515625 0.300250632980893 -5 0.114316666666667 2 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 60 14 74 +BSA_min_22 77 0.44516 -1 1115 35 0 0 -1 - 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-1 0 149 759.303833007813 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 66 16 83 +BSA_min_22 85 0.4913 -1 5536.7 35 0 0 -1 - -1 0 120 586.330980330897 1170.64740772859 2 MULTI CID FTMS 0 0 0 83 65373.234375 1 0 0 2 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 67 16 83 +BSA_min_22 87 0.50368 -1 592.85 35 0 0 -1 - -1 0 45 1502.25634765625 NaN 0 PEAK CID FTMS 0 0 0 -1 NaN NaN 0 NaN 1 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 68 17 86 +BSA_min_22 89 0.51803 -1 3787.5 35 0 0 -1 - -1 0 118 586.330980330897 1170.64740772859 2 MULTI CID FTMS 0 0 0 88 87861.3359375 0.892882174576085 4 -0.0718366666666667 1 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 69 18 88 +BSA_min_22 90 0.52328 -1 3324.1 35 0 0 -1 + 3 ECCHGDLLECADDR 14 116 875.335138792643 1748.65572465208 2 MULTI CID FTMS 0 0 0 88 65524.953125 1 0 0 2 Unmodified _ECCHGDLLECADDR_ bsa;CON__P02769 2.29958343542733 2 BSA_min_22.mzXML NaN NaN NaN 0 70 18 88 +BSA_min_22 92 0.53604 -1 1584.9 35 0 0 -1 - -1 0 95 594.55510633116 1780.64348959368 3 MULTI CID FTMS 0 0 0 91 73712.65625 0.32216225208255 -3 0.0503366666666666 1 NaN 2 BSA_min_22.mzXML NaN NaN NaN 0 71 19 91 +BSA_min_22 93 0.54179 -1 2714.4 35 0 0 -1 - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/mzRange.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,3709 @@ +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_21 118.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 119.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 120.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 121.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 122.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 123.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 124.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 125.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 126.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 127.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 128.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 129.061454772949 0 0 0 0 0 0 NaN 0 0 +BSA_min_21 130.061454772949 0 0 0 0 0 0 NaN 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/mzTab.mzTab Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,55 @@ +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/test2/two_mzxml_short/combined/andromeda/allspectra.cid.ftms.iso_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/test2/two_mzxml_short/combined/andromeda/allspectra.cid.ftms.iso_1.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] 24.4111732500507 null null null null null null null null CON__P02769, bsa null 0.064 0 +PRT CON__P01030 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.12946896793655 null null null null null null null null CON__P01030, CON__ENSEMBL:ENSBTAP00000007350 null 0.006 0 +PRT CON__P02676 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.91168885522525 null null null null null null null null CON__P02676 null 0.028 0 +PRT CON__Q29443 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.27089675212204 null null null null null null null null CON__Q29443, CON__Q0IIK2 null 0.018 0 +PRT CON__Q6IFU6 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.79558497906794 null null null null null null null null CON__Q6IFU6 null 0.035 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 DDPHACYSTVFDK 1 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00879376465973971 null 0.480878333333333 2 777.83 777.83011 ms_run[1]:index=121 K L 387 399 82 0 +PSM DDPHACYSTVFDK 1 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00879376465973971 null 0.480878333333333 2 777.83 777.83011 ms_run[1]:index=121 K L 387 399 82 0 +PSM ECCHGDLLECADDR 2 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 4.06002529511453 0.0122549387437507 null 0.342775 3 583.89 583.89236 ms_run[1]:index=147 K A 267 280 60 0 +PSM ECCHGDLLECADDR 2 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 4.06002529511453 0.0122549387437507 null 0.342775 3 583.89 583.89236 ms_run[1]:index=147 K A 267 280 60 0 +PSM ECCHGDLLECADDR 3 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0122549387437507 null 0.385801666666667 3 583.89 583.89236 ms_run[1]:index=146 K A 267 280 67 0 +PSM ECCHGDLLECADDR 3 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0122549387437507 null 0.385801666666667 3 583.89 583.89236 ms_run[1]:index=146 K A 267 280 67 0 +PSM ECCHGDLLECADDR 4 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 3.64492303257886 0.0122549387437507 null 0.523276666666667 2 875.34 875.3349 ms_run[1]:index=148 K A 267 280 90 0 +PSM ECCHGDLLECADDR 4 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 3.64492303257886 0.0122549387437507 null 0.523276666666667 2 875.34 875.3349 ms_run[1]:index=148 K A 267 280 90 0 +PSM GCTTTNSPSTPCQNCSR 5 CON__Q6IFU6 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0160108733047593 null 0.263751666666667 2 964.38 964.3882 ms_run[1]:index=170 K I 5 21 45 0 +PSM LGQYTSPVAK 6 CON__P01030 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 9.21405366890568 0.00742217230209436 null 0.0572883333333333 2 532.29 532.29276 ms_run[1]:index=35 K R 689 698 10 0 +PSM LGQYTSPVAK 6 CON__ENSEMBL:ENSBTAP00000007350 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 9.21405366890568 0.00742217230209436 null 0.0572883333333333 2 532.29 532.29276 ms_run[1]:index=35 K R 689 698 10 0 +PSM TSDANINWNNLK 7 CON__Q29443 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00535924051359045 null 0.393891666666667 3 463.9 463.89676 ms_run[1]:index=84 K D 438 449 67 0 +PSM TSDANINWNNLK 7 CON__Q0IIK2 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00535924051359045 null 0.393891666666667 3 463.9 463.89676 ms_run[1]:index=84 K D 438 449 67 0 +PSM TSDANINWNNLK 8 CON__Q29443 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 2.86688527480472 0.00535924051359045 null 0.578475 3 463.9 463.89676 ms_run[1]:index=85 K D 438 449 98 0 +PSM TSDANINWNNLK 8 CON__Q0IIK2 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 2.86688527480472 0.00535924051359045 null 0.578475 3 463.9 463.89676 ms_run[1]:index=85 K D 438 449 98 0 +PSM TSDANINWNNLK 9 CON__Q29443 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00535924051359045 null 0.41019 2 695.34 695.3415 ms_run[1]:index=86 K D 438 449 70 0 +PSM TSDANINWNNLK 9 CON__Q0IIK2 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00535924051359045 null 0.41019 2 695.34 695.3415 ms_run[1]:index=86 K D 438 449 70 0 +PSM YCGVPGEYWLGNDR 10 CON__P02676 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0122549387437507 null 0.469416666666667 3 562.58 562.58407 ms_run[1]:index=140 K I 319 332 80 0 +PSM YCGVPGEYWLGNDR 11 CON__P02676 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 3.64492303257886 0.0122549387437507 null 0.540946666666667 2 843.37 843.37247 ms_run[1]:index=141 K I 319 332 92 0 +PSM YICDNQDTISSK 12 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 24.3433433825462 3.60031720952497E-09 null 0.258266666666667 2 722.33 722.32466 ms_run[1]:index=94 K L 286 297 44 0 +PSM YICDNQDTISSK 12 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 24.3433433825462 3.60031720952497E-09 null 0.258266666666667 2 722.33 722.32466 ms_run[1]:index=94 K L 286 297 44 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/parameters.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,105 @@ +Parameter Value +Version 1.6.3.4 +User name dglaetzer +Machine name FPROT-BEAST +Date of writing 04/01/2019 13:43:35 +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 False +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/peptideSection.txt Sat Jul 20 04:53:23 2019 -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] search_engine_score[1]_ms_run[1] 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 DDPHACYSTVFDK null +PEP ECCHGDLLECADDR null +PEP GCTTTNSPSTPCQNCSR null +PEP LGQYTSPVAK null +PEP TSDANINWNNLK null +PEP YCGVPGEYWLGNDR null +PEP YICDNQDTISSK null
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/peptides.txt Sat Jul 20 04:53:23 2019 -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 Fraction Average Fraction Std. Dev. Fraction 1 Fraction 2 Experiment BSA_min_21.mzXML Experiment BSA_min_22.mzXML Intensity Intensity BSA_min_21.mzXML Intensity BSA_min_22.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 +DDPHACYSTVFDK LAKEYEATLEECCAKDDPHACYSTVFDKLK AKDDPHACYSTVFDKLKHLVDEPQNLIKQN K D D D K L 1 0 0 3 1 0 0 0 1 0 0 1 0 1 1 1 1 0 1 1 0 0 13 0 1553.6457 CON__P02769;bsa CON__P02769 387 399 yes no 2 0.0087938 0 1 0 1 1 32419 32419 0 + 0 0 0 0 0 0 1 +ECCHGDLLECADDR VEVTKLVTDLTKVHKECCHGDLLECADDRA KECCHGDLLECADDRADLAKYICDNQDTIS K E C D R A 1 1 0 3 3 0 2 1 1 0 2 0 0 0 0 0 0 0 0 0 0 0 14 0 1748.6553 CON__P02769;bsa CON__P02769 267 280 yes no 2;3 0.012255 4.06 2 0 2 2 485350 0 485350 + 1 0 1 1;2 1;2;3 1 3 +GCTTTNSPSTPCQNCSR ______________________________ TTTNSPSTPCQNCSRITNVSTISSNNGCHP K G C S R I 0 1 2 0 3 1 0 1 0 0 0 0 0 0 2 3 4 0 0 0 0 0 17 0 1926.7618 CON__Q6IFU6 CON__Q6IFU6 5 21 yes yes 2 0.016011 0 1 0 1 1 0 0 0 + 2 4 2 3 4 4 1 +LGQYTSPVAK RKKRNVNFQKAIHEKLGQYTSPVAKRCCQD AIHEKLGQYTSPVAKRCCQDGLTRLPMART K L G A K R 1 0 0 0 0 1 0 1 0 0 1 1 0 0 1 1 1 0 1 1 0 0 10 0 1062.571 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030 689 698 yes no 2 0.0074222 9.2141 1 0 1 1 0 0 0 + 3 1 3 4 5 5 1 +TSDANINWNNLK KNTPEKGYLAVAVVKTSDANINWNNLKDKK VVKTSDANINWNNLKDKKSCHTAVDRTAGW K T S L K D 1 0 4 1 0 0 0 0 0 1 1 1 0 0 0 1 1 1 0 0 0 0 12 0 1388.6684 CON__Q29443;CON__Q0IIK2 CON__Q29443 438 449 yes no 2;3 0.0053592 2.8669 1 0 2 2 137580 137580 0 + 4 3 4 5;6 6;7;8 6 3 +YCGVPGEYWLGNDR KQGFGNIATNAEGKKYCGVPGEYWLGNDRI KYCGVPGEYWLGNDRISQLTNMGPTKLLIE K Y C D R I 0 1 1 1 1 0 1 3 0 0 1 0 0 0 1 0 0 1 2 1 0 0 14 0 1684.7304 CON__P02676 CON__P02676 319 332 yes yes 2;3 0.012255 3.6449 1 0 2 2 114330 114330 0 + 5 2 5 7;8 9;10 9 2 +YICDNQDTISSK GDLLECADDRADLAKYICDNQDTISSKLKE LAKYICDNQDTISSKLKECCDKPLLEKSHC K Y I S K L 0 0 1 2 1 1 0 0 0 2 0 1 0 0 0 2 1 0 1 0 0 0 12 0 1442.6348 CON__P02769;bsa CON__P02769 286 297 yes no 2 3.6003E-09 24.343 1 0 1 1 0 0 0 + 6 0 6 9 11 11 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/proteinGroups.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,6 @@ +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_21.mzXML Peptides BSA_min_22.mzXML Razor + unique peptides BSA_min_21.mzXML Razor + unique peptides BSA_min_22.mzXML Unique peptides BSA_min_21.mzXML Unique peptides BSA_min_22.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Fraction average Fraction 1 Fraction 2 Q-value Score Sequence coverage BSA_min_21.mzXML [%] Sequence coverage BSA_min_22.mzXML [%] Intensity Intensity BSA_min_21.mzXML Intensity BSA_min_22.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__P02769;bsa 3;3 3;3 3;3 ;bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4 2 3 3 3 2 1 2 1 2 1 6.4 6.4 6.4 69.293 607 607;607 1.5 2 2 0 24.411 4.1 2.3 517770 32419 485350 5 + 0 0;1;6 True;True;True 0;1;6 0;1;2;9 0;1;2;3;11 0;1;11 +CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 CON__P01030;CON__ENSEMBL:ENSBTAP00000007350 1;1 1;1 1;1 ; 2 1 1 1 1 0 1 0 1 0 0.6 0.6 0.6 192.79 1741 1741;1742 1 1 0 6.1295 0.6 0 0 0 0 1 + 1 3 True 3 4 5 5 +CON__P02676 CON__P02676 1 1 1 1 1 1 1 1 0 1 0 1 0 2.8 2.8 2.8 56.44 495 495 1 2 0 5.9117 2.8 0 114330 114330 0 2 + 2 5 True 5 7;8 9;10 9 +CON__Q29443;CON__Q0IIK2 CON__Q29443;CON__Q0IIK2 1;1 1;1 1;1 ; 2 1 1 1 1 0 1 0 1 0 1.8 1.8 1.8 75.829 685 685;704 1 2 0 6.2709 1.8 0 137580 137580 0 3 + 3 4 True 4 5;6 6;7;8 6 +CON__Q6IFU6 CON__Q6IFU6 1 1 1 1 1 1 1 1 0 1 0 1 0 3.5 3.5 3.5 55.651 491 491 1 1 0 5.7956 3.5 0 0 0 0 1 + 4 2 True 2 3 4 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/combined/txt/summary.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,4 @@ +Raw file Experiment Fraction Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa] +BSA_min_21 BSA_min_21.mzXML 1 Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 0 Standard 18 82 0 125 39 0 86 9 6 0 3 7.2 15.38 NaN 3.49 6 1031 56 5.43 1 1.79 112 33 32 29.46 34.41 6 18.18 + 0.89087 1.1135 0.66933 0.8609 +BSA_min_22 BSA_min_22.mzXML 2 Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 0 Standard 23 77 0 101 53 0 48 3 3 0 0 2.97 5.66 NaN 0 1 1675 61 3.64 1 1.64 295 43 41 14.58 15.24 10 23.26 + 0.73591 0.87113 0.46826 0.52276 +Total 41 159 0 226 92 0 134 12 9 0 3 5.31 9.78 NaN 2.24 7 2706 407 76 73 18.67 20.17 16 21.05 0.84659 1.05 0.61188 0.77941
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/exp_design_template.txt Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,3 @@ +Name Fraction Experiment PTM +BSA_min_21 1 BSA_min_21.mzXML False +BSA_min_22 2 BSA_min_22.mzXML False
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two/mqpar.xml Sat Jul 20 04:53:23 2019 -0400 @@ -0,0 +1,432 @@ +<?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>False</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>2</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\test2\two_mzxml_short\BSA_min_21.mzXML</string> + <string>D:\shared\dglaetzer\maxquant_tool\test2\two_mzxml_short\BSA_min_22.mzXML</string> + </filePaths> + <experiments> + <string>BSA_min_21.mzXML</string> + <string>BSA_min_22.mzXML</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> + <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>NoMatching</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>2</maxNmods> + <maxMissedCleavages>0</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>