Mercurial > repos > galaxyp > maxquant
changeset 10:f522c08e900c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
| author | galaxyp |
|---|---|
| date | Fri, 12 Mar 2021 08:41:06 +0000 |
| parents | 37d669de2828 |
| children | d72c96ad9a16 |
| files | macros.xml maxquant.xml test-data/05/config.yml test-data/05/mqpar.xml test-data/06/config.yml test-data/06/mqpar.xml |
| diffstat | 6 files changed, 1471 insertions(+), 8 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Fri Feb 19 21:24:41 2021 +0000 +++ b/macros.xml Fri Mar 12 08:41:06 2021 +0000 @@ -65,7 +65,11 @@ cont_MYCO: - MYCOPLASMA - '1' + #if $search_opts.mbr.match_between_runs == 'True': + MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window} + #else: MQpar_MatchingTimeWindow_num: 0.0 + #end if MatchBetweenRuns_wA: auto MQpar_firstSearchTol_num: 20.0 firstSearch_outOfCalWarnSD_num: 2.0
--- a/maxquant.xml Fri Feb 19 21:24:41 2021 +0000 +++ b/maxquant.xml Fri Mar 12 08:41:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -89,7 +89,14 @@ lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios} lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms} advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities} - matchBetweenRuns: ${search_opts.match_between_runs} + matchBetweenRuns: ${search_opts.mbr.match_between_runs} + #if $search_opts.mbr.match_between_runs == 'True': + matchingTimeWindow: ${search_opts.mbr.matching_time_window} + matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window} + alignmentTimeWindow: ${search_opts.mbr.alignment_time_window} + alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window} + matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features} + #end if includeContaminants: ${search_opts.incl_contaminants} minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length} maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length} @@ -223,7 +230,78 @@ - [iodoTMT6plex-Cys130,'',0,0,0,0,True] - [iodoTMT6plex-Cys131,'',0,0,0,0,True] #end if - #end if + #end if + #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3': + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + #if $pg.quant_method.filter_by_pif.filter_pif == 'True': + reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif} + #else: + reporterPif: 0 + #end if + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: ${pg.quant_method.filter_by_pif.filter_pif} + isobaricLabels: + #if $pg.quant_method.iso_labels.labeling == 'custom': + #for $l in $pg.quant_method.iso_labels.iso_label: + - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] + #end for + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': + - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] + - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': + - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] + - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] + - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] + - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] + - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] + - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': + - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] + - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] + - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] + - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] + - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] + - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] + - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] + - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': + @TMT10PLEX@ + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': + @TMT10PLEX@ + - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': + - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] + - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False] + - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] + - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] + - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] + #end if + #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': + - [iodoTMT6plex-Cys126,'',0,0,0,0,True] + - [iodoTMT6plex-Cys127,'',0,0,0,0,True] + - [iodoTMT6plex-Cys128,'',0,0,0,0,True] + - [iodoTMT6plex-Cys129,'',0,0,0,0,True] + - [iodoTMT6plex-Cys130,'',0,0,0,0,True] + - [iodoTMT6plex-Cys131,'',0,0,0,0,True] + #end if + #end if #end for </configfile> <expand macro="ptxqc"/> @@ -276,10 +354,29 @@ label="Calculate peak properties" truevalue="True" falsevalue="False" help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/> - <param name="match_between_runs" type="boolean" checked="false" - label="Match between runs" - truevalue="True" falsevalue="False" - help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/> + <conditional name="mbr"> + <param name="match_between_runs" type="select" + label="Match between runs" + help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."> + <option value="False" selected="true">No</option> + <option value="True">Yes</option> + </param> + <when value="False"/> + <when value="True"> + <param name="matching_time_window" type="float" label="Match Time Window [min]" min="0" value="0.7" + help="The time window that is used in 'Match between runs' for the transfer of identifications."/> + <param name="matching_ion_mobility_window" type="float" label="Match Ion Mobility Window" min="0" value="0.05" + help="The ion mobility window that is used in 'Match between runs' for the transfer of identifications."/> + <param name="alignment_time_window" type="integer" label="Alignment Time Window [min]" min="0" value="20" + help="The time window that is used in retention time alignment to search for the best alignment function."/> + <param name="alignment_ion_mobility_window" type="integer" label="Alignment Ion Mobility" min="0" value="1" + help="The ion mobility window that is used in ion mobility alignment to search for the best alignment function."/> + <param name="match_unidentified_features" type="boolean" checked="false" + label="Match unidentified Features" + truevalue="True" falsevalue="False" + help="Also unidentified peptide features will be matched between runs. Their expression profiles over multiple samples are written into the table called 'matchedFeatures.txt'."/> + </when> + </conditional> <param name="incl_contaminants" type="boolean" checked="true" label="Include contaminants" truevalue="True" falsevalue="False" @@ -410,6 +507,7 @@ <option value="lfq">label free quantification</option> <option value="silac">label based quantification</option> <option value="reporter_ion_ms2">reporter ion MS2</option> + <option value="reporter_ion_ms3">reporter ion MS3</option> </param> <when value=""/> <when value="silac"> @@ -496,6 +594,60 @@ <when value="False"></when> </conditional> </when> + <when value="reporter_ion_ms3"> + <conditional name="iso_labels"> + <param name="labeling" type="select" label="isobaric labeling" + help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> + <option value="custom">custom</option> + <option value="tmt2plex">TMT2plex</option> + <option value="tmt6plex">TMT6plex</option> + <option value="tmt8plex">TMT8plex</option> + <option value="tmt10plex">TMT10plex</option> + <option value="tmt11plex">TMT11plex</option> + <option value="itraq4plex">iTRAQ4plex</option> + <option value="itraq8plex">iTRAQ8plex</option> + <option value="iodotmt6plex">iodoTMT6plex</option> + </param> + + <when value="tmt2plex"></when> + <when value="tmt6plex"></when> + <when value="tmt8plex"></when> + <when value="tmt10plex"></when> + <when value="tmt11plex"></when> + <when value="itraq4plex"></when> + <when value="itraq8plex"></when> + <when value="iodotmt6plex"></when> + <when value="custom"> + <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> + <param name="internallabel" type="select" label="internal label" help="contains Lys"> + <expand macro="iso_labels"/> + </param> + <param name="terminallabel" type="select" label="terminal label" help="contains Nter"> + <option value="">None</option> + <expand macro="iso_labels"/> + </param> + <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> + <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> + <param name="cp1" type="float" label="correction factor +1%" value="0.0"/> + <param name="cp2" type="float" label="correction factor +2%" value="0.0"/> + <param type="boolean" name="tmtlike" checked="false" + label="TMT-like" + truevalue="True" falsevalue="False"/> + </repeat> + </when> + </conditional> + <conditional name="filter_by_pif"> + <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF" + truevalue="True" falsevalue="False" + help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/> + <when value="True"> + <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" + max="1" + help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> + </when> + <when value="False"></when> + </conditional> + </when> </conditional> </repeat> @@ -632,6 +784,82 @@ <!-- high difference due to unconsistant xml formatting in MQ --> <output name="mqpar" file="02/mqpar.xml" lines_diff="24" /> </test> + <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only --> + <test expect_num_outputs="3"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <param name="incl_contaminants" value="False" /> <!-- non-default value --> + <param name="min_pep_length" value="7" /> <!-- non-default value --> + <param name="max_pep_length" value="24" /> <!-- non-default value --> + <param name="decoy_mode" value="randomize" /> <!-- non-default value --> + <param name="psm_fdr" value="0.5" /> <!-- non-default value --> + <param name="protein_fdr" value="0.4" /> <!-- non-default value --> + <section name="protein_quant"> + <param name="peptides_for_quantification" value="0"/><!-- non-default value --> + <conditional name="only_unmod_prot"> + <param name="unmod_prot" value="True"/> + <param name="mods_used_prot_quant" value="Pro5,Pro6"/> + </conditional> + </section> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_23.mzXML"/> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="fixedModifications" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms3" /> + <conditional name="iso_labels"> + <param name="labeling" value="custom" /> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys126" /> + <param name="terminallabel" value="TMT2plex-Nter126" /> + <param name="tmtlike" value="True" /> + <param name="cp1" value="6.7" /> + <param name="cp2" value="3" /> + </repeat> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys127" /> + <param name="terminallabel" value="TMT2plex-Nter127" /> + <param name="tmtlike" value="True" /> + </repeat> + </conditional> + <conditional name="filter_by_pif"> + <param name="filter_pif" value="False"/> + <param name="reporter_pif" + value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead --> + </conditional> + </conditional> + </repeat> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_22"/> + <param name="variableModifications" value="" /> + <param name="fixedModifications" value="" /> + <param name="enzymes" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms3"/> + <conditional name="iso_labels"> + <param name="labeling" value="itraq4plex"/> + </conditional> + <conditional name="filter_by_pif"> + <param name="filter_pif" value="True"/> + <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used --> + </conditional> + </conditional> + </repeat> + <param name="dry_run" value="True" /> + <param name="output" value="config,mqpar,mzTab" /> + <output name="config" file="06/config.yml" lines_diff="2"> + <assert_contents> + <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" /> + </assert_contents> + </output> + <output name="mqpar" file="06/mqpar.xml" lines_diff="6"> + <assert_contents> + <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." /> + </assert_contents> + </output> + </test> <!-- lfq, testing yaml conf file and mqpar.xml only --> <test expect_num_outputs="2"> <param name="ftype" value=".mzxml" /> @@ -654,6 +882,37 @@ <output name="config" file="03/config.yml" lines_diff="2" /> <output name="mqpar" file="03/mqpar.xml" lines_diff="10" /> </test> + <!-- Test for MBR --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value="^>.*\|(.*)\|.*$" /> + <param name="description_parse_rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" /> + <param name="min_unique_pep" value="1" /> + <param name="ibaq" value="True" /> + <param name="match_between_runs" value="True" /> + <param name="ibaqLogFit" value="False" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_22"/> + <param name="maxMissedCleavages" value="1"/> + <param name="variableModifications" value="Oxidation (M)" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="lfq" /> + </conditional> + </repeat> + <param name="dry_run" value="True" /> + <param name="output" value="config,mqpar" /> + <output name="config" file="05/config.yml" lines_diff="2"> + <assert_contents> + <has_text_matching expression="matchBetweenRuns\: True" /> + </assert_contents> + </output> + <output name="mqpar" file="05/mqpar.xml" lines_diff="4"> + <assert_contents> + <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." /> + </assert_contents> + </output> + </test> <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only --> <test expect_num_outputs="2"> <param name="ftype" value=".mzxml" /> @@ -744,7 +1003,7 @@ - for two channels: choose options from light and heavy sections - for three channels: choose options from light, medium and heavy sections - - reporter ion ms2: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling + - reporter ion ms2/ms3: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling - PTXQC quality control: quality control software creates an automatic quality control pdf report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/05/config.yml Fri Mar 12 08:41:06 2021 +0000 @@ -0,0 +1,45 @@ + + fastaFiles: [/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat] + parseRules: + identifierParseRule: '^>.*\|(.*)\|.*$' + descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$' + minUniquePeptides: 1 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + ibaq: True + ibaqLogFit: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: True + matchingTimeWindow: 0.7 + matchingIonMobilityWindow: 0.05 + alignmentTimeWindow: 20 + alignmentIonMobilityWindow: 1 + matchUnidentifiedFeatures: False + includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] + useCounterparts: True + paramGroups: + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 1 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lfqMode: 1 + lfqSkipNorm: True + lfqMinEdgesPerNode: 3 + lfqAvEdgesPerNode: 6 + lfqMinRatioCount: 2 + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/05/mqpar.xml Fri Mar 12 08:41:06 2021 +0000 @@ -0,0 +1,451 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat</fastaFilePath> + <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> + <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>revert</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>True</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>True</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>True</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.01</peptideFdr> + <proteinFdr>0.01</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>1</minUniquePeptides> + <useCounterparts>True</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> + <matchingTimeWindow>0.7</matchingTimeWindow> + <matchingIonMobilityWindow>0.05</matchingIonMobilityWindow> + <alignmentTimeWindow>20</alignmentTimeWindow> + <alignmentIonMobilityWindow>1</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>1</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>False</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>templateSession</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>/tmp/tmp0wswhy4o/job_working_directory/000/7/working/BSA_min_22.mzxml</string> + </filePaths> + <experiments> + <string>BSA_min_22.mzxml</string> + </experiments> + <fractions> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + </paramGroupIndices> + <referenceChannel> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Standard</lcmsRunType> + <reQuantify>False</reQuantify> + <lfqMode>1</lfqMode> + <lfqSkipNorm>True</lfqSkipNorm> + <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> + <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> + <lfqMaxFeatures>100000</lfqMaxFeatures> + <neucodeMaxPpm>0</neucodeMaxPpm> + <neucodeResolution>0</neucodeResolution> + <neucodeResolutionInMda>False</neucodeResolutionInMda> + <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes> + <fastLfq>True</fastLfq> + <lfqRestrictFeatures>False</lfqRestrictFeatures> + <lfqMinRatioCount>2</lfqMinRatioCount> + <maxLabeledAa>0</maxLabeledAa> + <maxNmods>5</maxNmods> + <maxMissedCleavages>1</maxMissedCleavages> + <multiplicity>1</multiplicity> + <enzymeMode>0</enzymeMode> + <complementaryReporterType>0</complementaryReporterType> + <reporterNormalization>0</reporterNormalization> + <neucodeIntensityMode>0</neucodeIntensityMode> + <fixedModifications> + <string>Carbamidomethyl (C)</string> + </fixedModifications> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>NaN</reporterMassTolerance> + <reporterPif>NaN</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>NaN</reporterFraction> + <reporterBasePeakRatio>NaN</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/06/config.yml Fri Mar 12 08:41:06 2021 +0000 @@ -0,0 +1,59 @@ + + fastaFiles: [/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: True + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + includeContaminants: False + minPeptideLengthForUnspecificSearch: 7 + maxPeptideLengthForUnspecificSearch: 24 + decoyMode: randomize + peptideFdr: 0.5 + proteinFdr: 0.4 + quantMode: 0 + restrictProteinQuantification: True + restrictMods: [Pro5,Pro6] + useCounterparts: True + paramGroups: + - files: ['BSA_min_23.mzXML'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: False + isobaricLabels: + - ['TMT2plex-Lys126','TMT2plex-Nter126',0.0,0.0,6.7,3.0,True] + - ['TMT2plex-Lys127','TMT2plex-Nter127',0.0,0.0,0.0,0.0,True] + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [] + enzymes: [] + enzymeMode: 0 + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + reporterPif: 0.8 + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: True + isobaricLabels: + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/06/mqpar.xml Fri Mar 12 08:41:06 2021 +0000 @@ -0,0 +1,645 @@ +<?xml version="1.0" ?> +<MaxQuantParams> + <fastaFiles> + <FastaFileInfo> + <fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath> + <identifierParseRule>>([^\s]*)</identifierParseRule> + <descriptionParseRule>>(.*)</descriptionParseRule> + <taxonomyParseRule/> + <variationParseRule/> + <modificationParseRule/> + <taxonomyId/> + </FastaFileInfo> + </fastaFiles> + <fastaFilesProteogenomics> + </fastaFilesProteogenomics> + <fastaFilesFirstSearch> + </fastaFilesFirstSearch> + <fixedSearchFolder/> + <andromedaCacheSize>350000</andromedaCacheSize> + <advancedRatios>True</advancedRatios> + <pvalThres>0.005</pvalThres> + <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> + <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> + <rtShift>False</rtShift> + <separateLfq>False</separateLfq> + <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> + <lfqRequireMsms>True</lfqRequireMsms> + <decoyMode>randomize</decoyMode> + <boxCarMode>all</boxCarMode> + <includeContaminants>False</includeContaminants> + <maxPeptideMass>4600</maxPeptideMass> + <epsilonMutationScore>True</epsilonMutationScore> + <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> + <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately> + <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides> + <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides> + <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides> + <minScoreModifiedPeptides>40</minScoreModifiedPeptides> + <secondPeptide>True</secondPeptide> + <matchBetweenRuns>False</matchBetweenRuns> + <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures> + <matchBetweenRunsFdr>False</matchBetweenRunsFdr> + <dependentPeptides>False</dependentPeptides> + <dependentPeptideFdr>0</dependentPeptideFdr> + <dependentPeptideMassBin>0</dependentPeptideMassBin> + <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> + <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> + <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> + <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> + <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> + <msmsConnection>False</msmsConnection> + <ibaq>False</ibaq> + <top3>False</top3> + <independentEnzymes>False</independentEnzymes> + <useDeltaScore>False</useDeltaScore> + <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> + <taxonomyLevel>Species</taxonomyLevel> + <avalon>False</avalon> + <nModColumns>3</nModColumns> + <ibaqLogFit>False</ibaqLogFit> + <razorProteinFdr>True</razorProteinFdr> + <deNovoSequencing>False</deNovoSequencing> + <deNovoVarMods>True</deNovoVarMods> + <massDifferenceSearch>False</massDifferenceSearch> + <isotopeCalc>False</isotopeCalc> + <writePeptidesForSpectrumFile/> + <intensityPredictionsFile> + </intensityPredictionsFile> + <minPepLen>7</minPepLen> + <psmFdrCrosslink>0.01</psmFdrCrosslink> + <peptideFdr>0.5</peptideFdr> + <proteinFdr>0.4</proteinFdr> + <siteFdr>0.01</siteFdr> + <minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch> + <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> + <minPeptides>1</minPeptides> + <minRazorPeptides>1</minRazorPeptides> + <minUniquePeptides>0</minUniquePeptides> + <useCounterparts>True</useCounterparts> + <advancedSiteIntensities>True</advancedSiteIntensities> + <customProteinQuantification>False</customProteinQuantification> + <customProteinQuantificationFile/> + <minRatioCount>2</minRatioCount> + <restrictProteinQuantification>True</restrictProteinQuantification> + <restrictMods> + <string>Pro5</string> + <string>Pro6</string> + </restrictMods> + <matchingTimeWindow>0</matchingTimeWindow> + <matchingIonMobilityWindow>0</matchingIonMobilityWindow> + <alignmentTimeWindow>0</alignmentTimeWindow> + <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> + <numberOfCandidatesMsms>15</numberOfCandidatesMsms> + <compositionPrediction>0</compositionPrediction> + <quantMode>0</quantMode> + <massDifferenceMods> + </massDifferenceMods> + <mainSearchMaxCombinations>200</mainSearchMaxCombinations> + <writeMsScansTable>False</writeMsScansTable> + <writeMsmsScansTable>True</writeMsmsScansTable> + <writePasefMsmsScansTable>True</writePasefMsmsScansTable> + <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> + <writeMs3ScansTable>True</writeMs3ScansTable> + <writeAllPeptidesTable>True</writeAllPeptidesTable> + <writeMzRangeTable>True</writeMzRangeTable> + <writeMzTab>True</writeMzTab> + <disableMd5>False</disableMd5> + <cacheBinInds>True</cacheBinInds> + <etdIncludeB>False</etdIncludeB> + <ms2PrecursorShift>0</ms2PrecursorShift> + <complementaryIonPpm>20</complementaryIonPpm> + <variationParseRule/> + <variationMode>none</variationMode> + <useSeriesReporters>False</useSeriesReporters> + <name>templateSession</name> + <maxQuantVersion>1.6.10.43</maxQuantVersion> + <tempFolder/> + <pluginFolder/> + <numThreads>1</numThreads> + <emailAddress/> + <smtpHost/> + <emailFromAddress/> + <fixedCombinedFolder/> + <fullMinMz>-1.79769313486232E+308</fullMinMz> + <fullMaxMz>1.79769313486232E+308</fullMaxMz> + <sendEmail>False</sendEmail> + <ionCountIntensities>False</ionCountIntensities> + <verboseColumnHeaders>False</verboseColumnHeaders> + <calcPeakProperties>False</calcPeakProperties> + <showCentroidMassDifferences>False</showCentroidMassDifferences> + <showIsotopeMassDifferences>False</showIsotopeMassDifferences> + <useDotNetCore>False</useDotNetCore> + <filePaths> + <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string> + <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string> + </filePaths> + <experiments> + <string>BSA_min_23.mzXML</string> + <string>BSA_min_22.mzxml</string> + </experiments> + <fractions> + <short>32767</short> + <short>32767</short> + </fractions> + <ptms> + <boolean>False</boolean> + <boolean>False</boolean> + </ptms> + <paramGroupIndices> + <int>0</int> + <int>1</int> + </paramGroupIndices> + <referenceChannel> + <string/> + <string/> + </referenceChannel> + <intensPred>False</intensPred> + <intensPredModelReTrain>False</intensPredModelReTrain> + <parameterGroups> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Reporter ion MS3</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/> + <enzymes> + <string>Trypsin/P</string> + </enzymes> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications> + <string>Oxidation (M)</string> + </variableModifications> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + <IsobaricLabelInfo> + <internalLabel>TMT2plex-Lys126</internalLabel> + <terminalLabel>TMT2plex-Nter126</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>6.7</correctionFactorP1> + <correctionFactorP2>3</correctionFactorP2> + <tmtLike>True</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>TMT2plex-Lys127</internalLabel> + <terminalLabel>TMT2plex-Nter127</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>True</tmtLike> + </IsobaricLabelInfo> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>0.003</reporterMassTolerance> + <reporterPif>0</reporterPif> + <filterPif>False</filterPif> + <reporterFraction>0</reporterFraction> + <reporterBasePeakRatio>0</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + <parameterGroup> + <msInstrument>0</msInstrument> + <maxCharge>7</maxCharge> + <minPeakLen>2</minPeakLen> + <diaMinPeakLen>2</diaMinPeakLen> + <useMs1Centroids>False</useMs1Centroids> + <useMs2Centroids>False</useMs2Centroids> + <cutPeaks>True</cutPeaks> + <gapScans>1</gapScans> + <minTime>NaN</minTime> + <maxTime>NaN</maxTime> + <matchType>MatchFromAndTo</matchType> + <intensityDetermination>0</intensityDetermination> + <centroidMatchTol>8</centroidMatchTol> + <centroidMatchTolInPpm>True</centroidMatchTolInPpm> + <centroidHalfWidth>35</centroidHalfWidth> + <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> + <valleyFactor>1.4</valleyFactor> + <isotopeValleyFactor>1.2</isotopeValleyFactor> + <advancedPeakSplitting>False</advancedPeakSplitting> + <intensityThreshold>0</intensityThreshold> + <labelMods> + <string/> + </labelMods> + <lcmsRunType>Reporter ion MS3</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/> + <enzymes/> + <enzymesFirstSearch> + </enzymesFirstSearch> + <enzymeModeFirstSearch>0</enzymeModeFirstSearch> + <useEnzymeFirstSearch>False</useEnzymeFirstSearch> + <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> + <variableModifications/> + <useMultiModification>False</useMultiModification> + <multiModifications> + </multiModifications> + <isobaricLabels> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys114</internalLabel> + <terminalLabel>iTRAQ4plex-Nter114</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys115</internalLabel> + <terminalLabel>iTRAQ4plex-Nter115</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys116</internalLabel> + <terminalLabel>iTRAQ4plex-Nter116</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + <IsobaricLabelInfo> + <internalLabel>iTRAQ4plex-Lys117</internalLabel> + <terminalLabel>iTRAQ4plex-Nter117</terminalLabel> + <correctionFactorM2>0</correctionFactorM2> + <correctionFactorM1>0</correctionFactorM1> + <correctionFactorP1>0</correctionFactorP1> + <correctionFactorP2>0</correctionFactorP2> + <tmtLike>False</tmtLike> + </IsobaricLabelInfo> + </isobaricLabels> + <neucodeLabels> + </neucodeLabels> + <variableModificationsFirstSearch> + </variableModificationsFirstSearch> + <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications> + <additionalVariableModifications> + </additionalVariableModifications> + <additionalVariableModificationProteins> + </additionalVariableModificationProteins> + <doMassFiltering>True</doMassFiltering> + <firstSearchTol>20</firstSearchTol> + <mainSearchTol>4.5</mainSearchTol> + <searchTolInPpm>True</searchTolInPpm> + <isotopeMatchTol>2</isotopeMatchTol> + <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm> + <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation> + <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation> + <checkMassDeficit>True</checkMassDeficit> + <recalibrationInPpm>True</recalibrationInPpm> + <intensityDependentCalibration>False</intensityDependentCalibration> + <minScoreForCalibration>70</minScoreForCalibration> + <matchLibraryFile>False</matchLibraryFile> + <libraryFile/> + <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm> + <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> + <matchLabelTimeTolMin>0</matchLabelTimeTolMin> + <reporterMassTolerance>0.003</reporterMassTolerance> + <reporterPif>0.8</reporterPif> + <filterPif>True</filterPif> + <reporterFraction>0</reporterFraction> + <reporterBasePeakRatio>0</reporterBasePeakRatio> + <timsHalfWidth>0</timsHalfWidth> + <timsStep>0</timsStep> + <timsResolution>0</timsResolution> + <timsMinMsmsIntensity>0</timsMinMsmsIntensity> + <timsRemovePrecursor>True</timsRemovePrecursor> + <timsIsobaricLabels>False</timsIsobaricLabels> + <timsCollapseMsms>True</timsCollapseMsms> + <crosslinkSearch>False</crosslinkSearch> + <crossLinker/> + <minMatchXl>0</minMatchXl> + <minPairedPepLenXl>6</minPairedPepLenXl> + <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> + <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> + <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> + <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> + <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> + <crosslinkModifications> + </crosslinkModifications> + <crosslinkFastaFiles> + </crosslinkFastaFiles> + <crosslinkSites> + </crosslinkSites> + <crosslinkNetworkFiles> + </crosslinkNetworkFiles> + <crosslinkMode/> + <peakRefinement>False</peakRefinement> + <isobaricSumOverWindow>True</isobaricSumOverWindow> + <isobaricWeightExponent>0.75</isobaricWeightExponent> + <diaLibraryType>0</diaLibraryType> + <diaLibraryPath/> + <diaPeptidePaths> + </diaPeptidePaths> + <diaEvidencePaths> + </diaEvidencePaths> + <diaMsmsPaths> + </diaMsmsPaths> + <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> + <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> + <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> + <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> + <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> + <diaScoreN>7</diaScoreN> + <diaMinScore>2.99</diaMinScore> + <diaPrecursorQuant>False</diaPrecursorQuant> + <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> + </parameterGroup> + </parameterGroups> + <msmsParamsArray> + <msmsParams> + <Name>FTMS</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>ITMS</Name> + <MatchTolerance>0.5</MatchTolerance> + <MatchToleranceInPpm>False</MatchToleranceInPpm> + <DeisotopeTolerance>0.15</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.25</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>False</Deisotope> + <Topx>8</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>TOF</Name> + <MatchTolerance>40</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>0.01</DeisotopeTolerance> + <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> + <DeNovoTolerance>0.02</DeNovoTolerance> + <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>10</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + <msmsParams> + <Name>Unknown</Name> + <MatchTolerance>20</MatchTolerance> + <MatchToleranceInPpm>True</MatchToleranceInPpm> + <DeisotopeTolerance>7</DeisotopeTolerance> + <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm> + <DeNovoTolerance>10</DeNovoTolerance> + <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> + <Deisotope>True</Deisotope> + <Topx>12</Topx> + <TopxInterval>100</TopxInterval> + <HigherCharges>True</HigherCharges> + <IncludeWater>True</IncludeWater> + <IncludeAmmonia>True</IncludeAmmonia> + <DependentLosses>True</DependentLosses> + <Recalibration>False</Recalibration> + </msmsParams> + </msmsParamsArray> + <fragmentationParamsArray> + <fragmentationParams> + <Name>CID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>HCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>PQD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETHCD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>ETCID</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>UVPD</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + <fragmentationParams> + <Name>Unknown</Name> + <Connected>False</Connected> + <ConnectedScore0>1</ConnectedScore0> + <ConnectedScore1>1</ConnectedScore1> + <ConnectedScore2>1</ConnectedScore2> + <InternalFragments>False</InternalFragments> + <InternalFragmentWeight>1</InternalFragmentWeight> + <InternalFragmentAas>KRH</InternalFragmentAas> + </fragmentationParams> + </fragmentationParamsArray> +</MaxQuantParams> +