mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
439 lines
18 KiB
XML
439 lines
18 KiB
XML
<?xml version="1.0" encoding="utf-8"?>
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<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<fastaFiles>
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<FastaFileInfo>
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<fastaFilePath>PLACEHOLDERyeast_UPS.fasta</fastaFilePath>
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<identifierParseRule>>([^\s]*)</identifierParseRule>
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<descriptionParseRule>>(.*)</descriptionParseRule>
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<taxonomyParseRule></taxonomyParseRule>
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<variationParseRule></variationParseRule>
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<modificationParseRule></modificationParseRule>
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<taxonomyId></taxonomyId>
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</FastaFileInfo>
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</fastaFiles>
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<fastaFilesProteogenomics></fastaFilesProteogenomics>
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<fastaFilesFirstSearch></fastaFilesFirstSearch>
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<fixedSearchFolder></fixedSearchFolder>
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<andromedaCacheSize>350000</andromedaCacheSize>
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<advancedRatios>True</advancedRatios>
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<pvalThres>0.005</pvalThres>
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<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
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<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
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<rtShift>False</rtShift>
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<separateLfq>False</separateLfq>
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<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
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<lfqRequireMsms>True</lfqRequireMsms>
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<decoyMode>revert</decoyMode>
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<boxCarMode>all</boxCarMode>
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<includeContaminants>True</includeContaminants>
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<maxPeptideMass>4600</maxPeptideMass>
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<epsilonMutationScore>True</epsilonMutationScore>
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<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
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<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
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<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
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<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
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<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
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<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
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<secondPeptide>True</secondPeptide>
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<matchBetweenRuns>True</matchBetweenRuns>
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<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
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<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
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<dependentPeptides>False</dependentPeptides>
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<dependentPeptideFdr>0</dependentPeptideFdr>
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<dependentPeptideMassBin>0</dependentPeptideMassBin>
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<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
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<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
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<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
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<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
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<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
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<msmsConnection>False</msmsConnection>
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<ibaq>False</ibaq>
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<top3>False</top3>
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<independentEnzymes>False</independentEnzymes>
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<useDeltaScore>False</useDeltaScore>
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<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
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<taxonomyLevel>Species</taxonomyLevel>
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<avalon>False</avalon>
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<nModColumns>3</nModColumns>
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<ibaqLogFit>False</ibaqLogFit>
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<razorProteinFdr>True</razorProteinFdr>
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<deNovoSequencing>False</deNovoSequencing>
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<deNovoVarMods>True</deNovoVarMods>
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<massDifferenceSearch>False</massDifferenceSearch>
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<isotopeCalc>False</isotopeCalc>
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<writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>
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<intensityPredictionsFile></intensityPredictionsFile>
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<minPepLen>7</minPepLen>
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<psmFdrCrosslink>0.01</psmFdrCrosslink>
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<peptideFdr>0.01</peptideFdr>
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<proteinFdr>0.01</proteinFdr>
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<siteFdr>0.01</siteFdr>
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<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
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<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
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<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
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<minPeptides>1</minPeptides>
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<minRazorPeptides>1</minRazorPeptides>
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<minUniquePeptides>0</minUniquePeptides>
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<useCounterparts>False</useCounterparts>
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<advancedSiteIntensities>True</advancedSiteIntensities>
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<customProteinQuantification>False</customProteinQuantification>
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<customProteinQuantificationFile></customProteinQuantificationFile>
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<minRatioCount>2</minRatioCount>
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<restrictProteinQuantification>True</restrictProteinQuantification>
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<restrictMods>
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<string>Oxidation (M)</string>
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<string>Acetyl (Protein N-term)</string>
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</restrictMods>
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<matchingTimeWindow>0.7</matchingTimeWindow>
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<matchingIonMobilityWindow>0.05</matchingIonMobilityWindow>
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<alignmentTimeWindow>20</alignmentTimeWindow>
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<alignmentIonMobilityWindow>1</alignmentIonMobilityWindow>
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<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
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<compositionPrediction>0</compositionPrediction>
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<quantMode>1</quantMode>
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<massDifferenceMods></massDifferenceMods>
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<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
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<writeMsScansTable>True</writeMsScansTable>
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<writeMsmsScansTable>True</writeMsmsScansTable>
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<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
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<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
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<writeMs3ScansTable>True</writeMs3ScansTable>
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<writeAllPeptidesTable>True</writeAllPeptidesTable>
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<writeMzRangeTable>True</writeMzRangeTable>
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<writeMzTab>True</writeMzTab>
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<disableMd5>False</disableMd5>
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<cacheBinInds>True</cacheBinInds>
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<etdIncludeB>False</etdIncludeB>
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<ms2PrecursorShift>0</ms2PrecursorShift>
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<complementaryIonPpm>20</complementaryIonPpm>
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<variationParseRule></variationParseRule>
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<variationMode>none</variationMode>
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<useSeriesReporters>False</useSeriesReporters>
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<name>Session1</name>
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<maxQuantVersion>1.6.10.43</maxQuantVersion>
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<tempFolder>PLACEHOLDERtemp</tempFolder>
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<pluginFolder></pluginFolder>
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<numThreads>2</numThreads>
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<emailAddress></emailAddress>
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<smtpHost></smtpHost>
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<emailFromAddress></emailFromAddress>
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<fixedCombinedFolder></fixedCombinedFolder>
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<fullMinMz>-1.79769313486232E+308</fullMinMz>
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<fullMaxMz>1.79769313486232E+308</fullMaxMz>
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<sendEmail>False</sendEmail>
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<ionCountIntensities>False</ionCountIntensities>
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<verboseColumnHeaders>False</verboseColumnHeaders>
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<calcPeakProperties>False</calcPeakProperties>
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<showCentroidMassDifferences>False</showCentroidMassDifferences>
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<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
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<useDotNetCore>False</useDotNetCore>
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<filePaths>
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<string>PLACEHOLDEROVEMB150205_12.raw</string>
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<string>PLACEHOLDEROVEMB150205_14.raw</string>
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</filePaths>
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<experiments>
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<string>Sample 1_Tr_1</string>
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<string>Sample 1_Tr_2</string>
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</experiments>
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<fractions>
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<short>1</short>
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<short>1</short>
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</fractions>
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<ptms>
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<boolean>False</boolean>
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<boolean>False</boolean>
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</ptms>
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<paramGroupIndices>
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<int>0</int>
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<int>0</int>
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</paramGroupIndices>
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<referenceChannel>
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<string></string>
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<string></string>
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</referenceChannel>
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<intensPred>False</intensPred>
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<intensPredModelReTrain>False</intensPredModelReTrain>
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<parameterGroups>
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<parameterGroup>
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<msInstrument>0</msInstrument>
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<maxCharge>7</maxCharge>
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<minPeakLen>2</minPeakLen>
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<diaMinPeakLen>2</diaMinPeakLen>
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<useMs1Centroids>False</useMs1Centroids>
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<useMs2Centroids>False</useMs2Centroids>
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<cutPeaks>True</cutPeaks>
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<gapScans>1</gapScans>
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<minTime>NaN</minTime>
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<maxTime>NaN</maxTime>
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<matchType>MatchFromAndTo</matchType>
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<intensityDetermination>0</intensityDetermination>
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<centroidMatchTol>8</centroidMatchTol>
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<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
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<centroidHalfWidth>35</centroidHalfWidth>
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<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
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<valleyFactor>1.4</valleyFactor>
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<isotopeValleyFactor>1.2</isotopeValleyFactor>
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<advancedPeakSplitting>False</advancedPeakSplitting>
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<intensityThreshold>0</intensityThreshold>
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<labelMods>
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<string></string>
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</labelMods>
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<lcmsRunType>Standard</lcmsRunType>
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<reQuantify>False</reQuantify>
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<lfqMode>1</lfqMode>
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<lfqSkipNorm>False</lfqSkipNorm>
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<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
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<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
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<lfqMaxFeatures>100000</lfqMaxFeatures>
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<neucodeMaxPpm>0</neucodeMaxPpm>
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<neucodeResolution>0</neucodeResolution>
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<neucodeResolutionInMda>False</neucodeResolutionInMda>
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<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
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<fastLfq>True</fastLfq>
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<lfqRestrictFeatures>False</lfqRestrictFeatures>
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<lfqMinRatioCount>2</lfqMinRatioCount>
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<maxLabeledAa>0</maxLabeledAa>
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<maxNmods>5</maxNmods>
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<maxMissedCleavages>2</maxMissedCleavages>
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<multiplicity>1</multiplicity>
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<enzymeMode>0</enzymeMode>
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<complementaryReporterType>0</complementaryReporterType>
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<reporterNormalization>0</reporterNormalization>
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<neucodeIntensityMode>0</neucodeIntensityMode>
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<fixedModifications>
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<string>Carbamidomethyl (C)</string>
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</fixedModifications>
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<enzymes>
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<string>Trypsin/P</string>
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</enzymes>
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<enzymesFirstSearch></enzymesFirstSearch>
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<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
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<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
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<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
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<variableModifications>
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<string>Oxidation (M)</string>
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<string>Acetyl (Protein N-term)</string>
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</variableModifications>
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<useMultiModification>False</useMultiModification>
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<multiModifications></multiModifications>
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<isobaricLabels></isobaricLabels>
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<neucodeLabels></neucodeLabels>
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<variableModificationsFirstSearch></variableModificationsFirstSearch>
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<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
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<additionalVariableModifications></additionalVariableModifications>
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<additionalVariableModificationProteins></additionalVariableModificationProteins>
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<doMassFiltering>True</doMassFiltering>
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<firstSearchTol>0.01</firstSearchTol>
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<mainSearchTol>0.8</mainSearchTol>
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<searchTolInPpm>True</searchTolInPpm>
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<isotopeMatchTol>2</isotopeMatchTol>
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<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
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<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
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<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
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<checkMassDeficit>True</checkMassDeficit>
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<recalibrationInPpm>True</recalibrationInPpm>
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<intensityDependentCalibration>False</intensityDependentCalibration>
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<minScoreForCalibration>70</minScoreForCalibration>
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<matchLibraryFile>False</matchLibraryFile>
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<libraryFile></libraryFile>
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<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
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<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
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<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
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<reporterMassTolerance>NaN</reporterMassTolerance>
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<reporterPif>NaN</reporterPif>
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<filterPif>False</filterPif>
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<reporterFraction>NaN</reporterFraction>
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<reporterBasePeakRatio>NaN</reporterBasePeakRatio>
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<timsHalfWidth>0</timsHalfWidth>
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<timsStep>0</timsStep>
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<timsResolution>0</timsResolution>
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<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
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<timsRemovePrecursor>True</timsRemovePrecursor>
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<timsIsobaricLabels>False</timsIsobaricLabels>
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<timsCollapseMsms>True</timsCollapseMsms>
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<crosslinkSearch>False</crosslinkSearch>
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<crossLinker></crossLinker>
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<minMatchXl>0</minMatchXl>
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<minPairedPepLenXl>6</minPairedPepLenXl>
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<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
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<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
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<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
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<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
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<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
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<crosslinkModifications></crosslinkModifications>
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<crosslinkFastaFiles></crosslinkFastaFiles>
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<crosslinkSites></crosslinkSites>
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<crosslinkNetworkFiles></crosslinkNetworkFiles>
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<crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
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<peakRefinement>False</peakRefinement>
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<isobaricSumOverWindow>True</isobaricSumOverWindow>
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<tisobaricWeightExponent>0.75</tisobaricWeightExponent>
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<diaLibraryType>0</diaLibraryType>
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<diaLibraryPath></diaLibraryPath>
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<diaPeptidePaths></diaPeptidePaths>
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<diaEvidencePaths></diaEvidencePaths>
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<diaMsmsPaths></diaMsmsPaths>
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<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
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<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
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<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
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<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
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<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
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<diaScoreN>7</diaScoreN>
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<diaMinScore>2.99</diaMinScore>
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<diaPrecursorQuant>False</diaPrecursorQuant>
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<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
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</parameterGroup>
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</parameterGroups>
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<msmsParamsArray>
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<msmsParams>
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<Name>FTMS</Name>
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<MatchTolerance>20</MatchTolerance>
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<MatchToleranceInPpm>True</MatchToleranceInPpm>
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<DeisotopeTolerance>7</DeisotopeTolerance>
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<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
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<DeNovoTolerance>10</DeNovoTolerance>
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<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
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<Deisotope>True</Deisotope>
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<Topx>12</Topx>
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<TopxInterval>100</TopxInterval>
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<HigherCharges>True</HigherCharges>
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<IncludeWater>True</IncludeWater>
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<IncludeAmmonia>True</IncludeAmmonia>
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<DependentLosses>True</DependentLosses>
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<Recalibration>False</Recalibration>
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</msmsParams>
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<msmsParams>
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<Name>ITMS</Name>
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<MatchTolerance>0.5</MatchTolerance>
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<MatchToleranceInPpm>False</MatchToleranceInPpm>
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<DeisotopeTolerance>0.15</DeisotopeTolerance>
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<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
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<DeNovoTolerance>0.25</DeNovoTolerance>
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<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
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<Deisotope>False</Deisotope>
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<Topx>8</Topx>
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<TopxInterval>100</TopxInterval>
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<HigherCharges>True</HigherCharges>
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<IncludeWater>True</IncludeWater>
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<IncludeAmmonia>True</IncludeAmmonia>
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<DependentLosses>True</DependentLosses>
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<Recalibration>False</Recalibration>
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</msmsParams>
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<msmsParams>
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<Name>TOF</Name>
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<MatchTolerance>40</MatchTolerance>
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<MatchToleranceInPpm>True</MatchToleranceInPpm>
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<DeisotopeTolerance>0.01</DeisotopeTolerance>
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<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
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<DeNovoTolerance>0.02</DeNovoTolerance>
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<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
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<Deisotope>True</Deisotope>
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<Topx>10</Topx>
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<TopxInterval>100</TopxInterval>
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<HigherCharges>True</HigherCharges>
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<IncludeWater>True</IncludeWater>
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<IncludeAmmonia>True</IncludeAmmonia>
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<DependentLosses>True</DependentLosses>
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<Recalibration>False</Recalibration>
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</msmsParams>
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<msmsParams>
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<Name>Unknown</Name>
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<MatchTolerance>20</MatchTolerance>
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<MatchToleranceInPpm>True</MatchToleranceInPpm>
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<DeisotopeTolerance>7</DeisotopeTolerance>
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<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
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<DeNovoTolerance>10</DeNovoTolerance>
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<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
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<Deisotope>True</Deisotope>
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<Topx>12</Topx>
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<TopxInterval>100</TopxInterval>
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<HigherCharges>True</HigherCharges>
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<IncludeWater>True</IncludeWater>
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<IncludeAmmonia>True</IncludeAmmonia>
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<DependentLosses>True</DependentLosses>
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<Recalibration>False</Recalibration>
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</msmsParams>
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</msmsParamsArray>
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<fragmentationParamsArray>
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<fragmentationParams>
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<Name>CID</Name>
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<Connected>False</Connected>
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<ConnectedScore0>1</ConnectedScore0>
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<ConnectedScore1>1</ConnectedScore1>
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<ConnectedScore2>1</ConnectedScore2>
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<InternalFragments>False</InternalFragments>
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<InternalFragmentWeight>1</InternalFragmentWeight>
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<InternalFragmentAas>KRH</InternalFragmentAas>
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</fragmentationParams>
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<fragmentationParams>
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<Name>HCD</Name>
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<Connected>False</Connected>
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<ConnectedScore0>1</ConnectedScore0>
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<ConnectedScore1>1</ConnectedScore1>
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<ConnectedScore2>1</ConnectedScore2>
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<InternalFragments>False</InternalFragments>
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<InternalFragmentWeight>1</InternalFragmentWeight>
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<InternalFragmentAas>KRH</InternalFragmentAas>
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</fragmentationParams>
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<fragmentationParams>
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<Name>ETD</Name>
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<Connected>False</Connected>
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<ConnectedScore0>1</ConnectedScore0>
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<ConnectedScore1>1</ConnectedScore1>
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<ConnectedScore2>1</ConnectedScore2>
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<InternalFragments>False</InternalFragments>
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<InternalFragmentWeight>1</InternalFragmentWeight>
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<InternalFragmentAas>KRH</InternalFragmentAas>
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</fragmentationParams>
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<fragmentationParams>
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<Name>PQD</Name>
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<Connected>False</Connected>
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<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>
|