Mercurial > repos > galaxyp > maxquant_mqpar

changeset 4:9cb7dcc07dae draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:25:06 +0000
parents 2d67fb758956
children
files macros.xml maxquant_mqpar.xml mqparam.py test-data/txt/mqpar.xml
diffstat 4 files changed, 491 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sat Apr 11 11:50:09 2020 -0400
+++ b/macros.xml	Fri Feb 19 21:25:06 2021 +0000
@@ -133,7 +133,7 @@
 
     <xml name="ptxqc-opts">
         <conditional name="qc">
-            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (at own risk)"
+            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)"
                    type="boolean" checked="false"/>
             <when value="true">
                 <param name="parameters" type="boolean" checked="true"
--- a/maxquant_mqpar.xml	Sat Apr 11 11:50:09 2020 -0400
+++ b/maxquant_mqpar.xml	Fri Feb 19 21:25:06 2021 +0000
@@ -31,14 +31,14 @@
     --fasta_files='$fasta_files'
     --description_parse_rule='$description_parse_rule'
     --identifier_parse_rule='$identifier_parse_rule'
-    '$mqpar'
+    '$mqpar_input'
 
     &&
     maxquant mqpar.xml
     #if 'log' in $output:
         >> '$log'
     #end if
-    && mv '$mqpar' combined/txt/mqpar.xml
+    && mv mqpar.xml combined/txt/mqpar.xml
     #if 'output_all' in $output:
         &&
         tar -zcf '$output_all' ./combined/txt
@@ -102,7 +102,7 @@
                 </valid>
             </sanitizer>
         </param>
-        <param type="data" name="mqpar" format="xml"
+        <param type="data" name="mqpar_input" 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
@@ -141,8 +141,8 @@
             <param name="fasta_files" value="bsa.fasta" />
             <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
             <param name="description_parse_rule" value="&gt;(.*)" />
-            <param name="mqpar" value="mqpar.xml" />
-            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" />
+            <param name="mqpar_input" value="mqpar.xml" />
+            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
             <output name="evidence" file="txt/evidence.txt" />
             <output name="msms" file="txt/msms.txt" lines_diff="2" />
             <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
@@ -153,6 +153,7 @@
             <output name="proteinGroups" file="txt/proteinGroups.txt" />
             <output name="summary" file="txt/summary.txt" />
             <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
+            <output name="mqpar" file="txt/mqpar.xml" lines_diff="8" />
         </test>
     </tests>
     <help><![CDATA[
--- a/mqparam.py	Sat Apr 11 11:50:09 2020 -0400
+++ b/mqparam.py	Fri Feb 19 21:25:06 2021 +0000
@@ -6,11 +6,12 @@
 import ntpath
 import os
 import re
-import yaml
 import xml.etree.ElementTree as ET
 from itertools import zip_longest
 from xml.dom import minidom
 
+import yaml
+
 
 def et_add_child(el, name, text, attrib=None):
     "Add a child element to an xml.etree.ElementTree.Element"
@@ -308,6 +309,23 @@
                              .format(key))
         node.text = str(value)
 
+    def set_list_param(self, key, values):
+        """Set a list parameter.
+        Args:
+            key: (string) XML tag of the parameter
+            values: the lit of values of the parameter XML node
+        Returns:
+            None
+        """
+        node = self._root.find(key)
+        if node is None:
+            raise ValueError('Element {} not found in parameter file'
+                             .format(key))
+        node.clear()
+        node.tag = key
+        for e in values:
+            et_add_child(node, name='string', text=e)
+
     def _from_yaml(self, conf):
         """Read a yaml config file.
         Args:
@@ -317,6 +335,7 @@
         """
         with open(conf) as f:
             conf_dict = yaml.safe_load(f.read())
+
         paramGroups = conf_dict.pop('paramGroups')
         self.add_infiles([pg.pop('files') for pg in paramGroups])
         for i, pg in enumerate(paramGroups):
@@ -325,8 +344,8 @@
                 self[i].set_silac(*silac)
             isobaricLabels = pg.pop('isobaricLabels', False)
             if isobaricLabels:
-                for l in isobaricLabels:
-                    self[i].set_isobaric_label(*l)
+                for ibl in isobaricLabels:
+                    self[i].set_isobaric_label(*ibl)
             for el in ['fixedModifications', 'variableModifications', 'enzymes']:
                 lst = pg.pop(el, None)
                 if lst is not None:
@@ -339,7 +358,10 @@
         else:
             raise Exception('No fasta files provided.')
         for key in conf_dict:
-            self.set_simple_param(key, conf_dict[key])
+            if key in ['restrictMods']:
+                self.set_list_param(key, conf_dict[key])
+            else:
+                self.set_simple_param(key, conf_dict[key])
 
     def write(self, mqpar_out):
         """Write pretty formatted xml parameter file.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/txt/mqpar.xml	Fri Feb 19 21:25:06 2021 +0000
@@ -0,0 +1,458 @@
+<?xml version="1.0" ?>
+<MaxQuantParams>
+	<fastaFiles>
+		<FastaFileInfo>
+			<fastaFilePath>/mnt/galaxy/data/003/dataset_3981.dat</fastaFilePath>
+			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
+			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
+			<taxonomyParseRule/>
+			<variationParseRule/>
+			<modificationParseRule/>
+			<taxonomyId/>
+		</FastaFileInfo>
+	</fastaFiles>
+	<fastaFilesProteogenomics>
+   </fastaFilesProteogenomics>
+	<fastaFilesFirstSearch>
+   </fastaFilesFirstSearch>
+	<fixedSearchFolder/>
+	<andromedaCacheSize>350000</andromedaCacheSize>
+	<advancedRatios>True</advancedRatios>
+	<pvalThres>0.005</pvalThres>
+	<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
+	<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
+	<rtShift>False</rtShift>
+	<separateLfq>False</separateLfq>
+	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
+	<lfqRequireMsms>True</lfqRequireMsms>
+	<decoyMode>revert</decoyMode>
+	<boxCarMode>all</boxCarMode>
+	<includeContaminants>True</includeContaminants>
+	<maxPeptideMass>4600</maxPeptideMass>
+	<epsilonMutationScore>True</epsilonMutationScore>
+	<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
+	<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
+	<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
+	<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
+	<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
+	<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
+	<secondPeptide>True</secondPeptide>
+	<matchBetweenRuns>False</matchBetweenRuns>
+	<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
+	<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
+	<dependentPeptides>False</dependentPeptides>
+	<dependentPeptideFdr>0</dependentPeptideFdr>
+	<dependentPeptideMassBin>0</dependentPeptideMassBin>
+	<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
+	<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
+	<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
+	<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
+	<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
+	<msmsConnection>False</msmsConnection>
+	<ibaq>False</ibaq>
+	<top3>False</top3>
+	<independentEnzymes>False</independentEnzymes>
+	<useDeltaScore>False</useDeltaScore>
+	<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
+	<taxonomyLevel>Species</taxonomyLevel>
+	<avalon>False</avalon>
+	<nModColumns>3</nModColumns>
+	<ibaqLogFit>False</ibaqLogFit>
+	<razorProteinFdr>True</razorProteinFdr>
+	<deNovoSequencing>False</deNovoSequencing>
+	<deNovoVarMods>True</deNovoVarMods>
+	<massDifferenceSearch>False</massDifferenceSearch>
+	<isotopeCalc>False</isotopeCalc>
+	<writePeptidesForSpectrumFile/>
+	<intensityPredictionsFile>
+   </intensityPredictionsFile>
+	<minPepLen>7</minPepLen>
+	<psmFdrCrosslink>0.01</psmFdrCrosslink>
+	<peptideFdr>0.01</peptideFdr>
+	<proteinFdr>0.01</proteinFdr>
+	<siteFdr>0.01</siteFdr>
+	<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
+	<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
+	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
+	<minPeptides>1</minPeptides>
+	<minRazorPeptides>1</minRazorPeptides>
+	<minUniquePeptides>0</minUniquePeptides>
+	<useCounterparts>False</useCounterparts>
+	<advancedSiteIntensities>True</advancedSiteIntensities>
+	<customProteinQuantification>False</customProteinQuantification>
+	<customProteinQuantificationFile/>
+	<minRatioCount>2</minRatioCount>
+	<restrictProteinQuantification>True</restrictProteinQuantification>
+	<restrictMods>
+		<string>Oxidation (M)</string>
+		<string>Acetyl (Protein N-term)</string>
+	</restrictMods>
+	<matchingTimeWindow>0</matchingTimeWindow>
+	<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
+	<alignmentTimeWindow>0</alignmentTimeWindow>
+	<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
+	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
+	<compositionPrediction>0</compositionPrediction>
+	<quantMode>1</quantMode>
+	<massDifferenceMods>
+   </massDifferenceMods>
+	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
+	<writeMsScansTable>False</writeMsScansTable>
+	<writeMsmsScansTable>True</writeMsmsScansTable>
+	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
+	<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
+	<writeMs3ScansTable>True</writeMs3ScansTable>
+	<writeAllPeptidesTable>True</writeAllPeptidesTable>
+	<writeMzRangeTable>True</writeMzRangeTable>
+	<writeMzTab>False</writeMzTab>
+	<disableMd5>False</disableMd5>
+	<cacheBinInds>True</cacheBinInds>
+	<etdIncludeB>False</etdIncludeB>
+	<ms2PrecursorShift>0</ms2PrecursorShift>
+	<complementaryIonPpm>20</complementaryIonPpm>
+	<variationParseRule/>
+	<variationMode>none</variationMode>
+	<useSeriesReporters>False</useSeriesReporters>
+	<name>session1</name>
+	<maxQuantVersion>1.6.10.43</maxQuantVersion>
+	<tempFolder/>
+	<pluginFolder/>
+	<numThreads>2</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>/mnt/galaxy/tmp/job_working_directory/003/3118/working/BSA_min_21.mzXML</string>
+		<string>/mnt/galaxy/tmp/job_working_directory/003/3118/working/BSA_min_22.mzxml</string>
+	</filePaths>
+	<experiments>
+		<string/>
+		<string/>
+	</experiments>
+	<fractions>
+		<short>32767</short>
+		<short>32767</short>
+	</fractions>
+	<ptms>
+		<boolean>False</boolean>
+		<boolean>False</boolean>
+	</ptms>
+	<paramGroupIndices>
+		<int>0</int>
+		<int>0</int>
+	</paramGroupIndices>
+	<referenceChannel>
+		<string/>
+		<string/>
+	</referenceChannel>
+	<intensPred>False</intensPred>
+	<intensPredModelReTrain>False</intensPredModelReTrain>
+	<parameterGroups>
+		<parameterGroup>
+			<msInstrument>0</msInstrument>
+			<maxCharge>7</maxCharge>
+			<minPeakLen>2</minPeakLen>
+			<diaMinPeakLen>2</diaMinPeakLen>
+			<useMs1Centroids>False</useMs1Centroids>
+			<useMs2Centroids>False</useMs2Centroids>
+			<cutPeaks>True</cutPeaks>
+			<gapScans>1</gapScans>
+			<minTime>NaN</minTime>
+			<maxTime>NaN</maxTime>
+			<matchType>MatchFromAndTo</matchType>
+			<intensityDetermination>0</intensityDetermination>
+			<centroidMatchTol>8</centroidMatchTol>
+			<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
+			<centroidHalfWidth>35</centroidHalfWidth>
+			<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
+			<valleyFactor>1.4</valleyFactor>
+			<isotopeValleyFactor>1.2</isotopeValleyFactor>
+			<advancedPeakSplitting>False</advancedPeakSplitting>
+			<intensityThreshold>0</intensityThreshold>
+			<labelMods>
+				<string/>
+			</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>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>
+				<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/>
+			<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>
+