--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two/mqpar.xml	Sat Jul 20 04:53:23 2019 -0400
@@ -0,0 +1,432 @@
+<?xml version="1.0" encoding="utf-8"?>
+<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+   <fastaFiles>
+      <FastaFileInfo>
+         <fastaFilePath>D:\fasta\bsa.fasta</fastaFilePath>
+         <identifierParseRule>>([^\s]*)</identifierParseRule>
+         <descriptionParseRule>>(.*)</descriptionParseRule>
+         <taxonomyParseRule></taxonomyParseRule>
+         <variationParseRule></variationParseRule>
+         <modificationParseRule></modificationParseRule>
+         <taxonomyId></taxonomyId>
+      </FastaFileInfo>
+   </fastaFiles>
+   <fastaFilesProteogenomics>
+   </fastaFilesProteogenomics>
+   <fastaFilesFirstSearch>
+   </fastaFilesFirstSearch>
+   <fixedSearchFolder></fixedSearchFolder>
+   <andromedaCacheSize>350000</andromedaCacheSize>
+   <advancedRatios>True</advancedRatios>
+   <pvalThres>0.005</pvalThres>
+   <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
+   <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
+   <rtShift>False</rtShift>
+   <separateLfq>False</separateLfq>
+   <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
+   <lfqRequireMsms>True</lfqRequireMsms>
+   <decoyMode>revert</decoyMode>
+   <boxCarMode>all</boxCarMode>
+   <includeContaminants>True</includeContaminants>
+   <maxPeptideMass>4600</maxPeptideMass>
+   <epsilonMutationScore>True</epsilonMutationScore>
+   <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
+   <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
+   <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
+   <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
+   <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
+   <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
+   <secondPeptide>False</secondPeptide>
+   <matchBetweenRuns>False</matchBetweenRuns>
+   <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
+   <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
+   <dependentPeptides>False</dependentPeptides>
+   <dependentPeptideFdr>0</dependentPeptideFdr>
+   <dependentPeptideMassBin>0</dependentPeptideMassBin>
+   <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
+   <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
+   <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
+   <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
+   <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
+   <msmsConnection>False</msmsConnection>
+   <ibaq>False</ibaq>
+   <top3>False</top3>
+   <independentEnzymes>False</independentEnzymes>
+   <useDeltaScore>False</useDeltaScore>
+   <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
+   <taxonomyLevel>Species</taxonomyLevel>
+   <avalon>False</avalon>
+   <nModColumns>3</nModColumns>
+   <ibaqLogFit>False</ibaqLogFit>
+   <razorProteinFdr>True</razorProteinFdr>
+   <deNovoSequencing>False</deNovoSequencing>
+   <deNovoVarMods>True</deNovoVarMods>
+   <massDifferenceSearch>False</massDifferenceSearch>
+   <isotopeCalc>False</isotopeCalc>
+   <writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>
+   <intensityPredictionsFile>
+   </intensityPredictionsFile>
+   <minPepLen>7</minPepLen>
+   <psmFdrCrosslink>0.01</psmFdrCrosslink>
+   <peptideFdr>0.01</peptideFdr>
+   <proteinFdr>0.01</proteinFdr>
+   <siteFdr>0.01</siteFdr>
+   <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
+   <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
+   <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
+   <minPeptides>1</minPeptides>
+   <minRazorPeptides>1</minRazorPeptides>
+   <minUniquePeptides>0</minUniquePeptides>
+   <useCounterparts>False</useCounterparts>
+   <advancedSiteIntensities>True</advancedSiteIntensities>
+   <customProteinQuantification>False</customProteinQuantification>
+   <customProteinQuantificationFile></customProteinQuantificationFile>
+   <minRatioCount>2</minRatioCount>
+   <restrictProteinQuantification>True</restrictProteinQuantification>
+   <restrictMods>
+      <string>Oxidation (M)</string>
+   </restrictMods>
+   <matchingTimeWindow>0</matchingTimeWindow>
+   <alignmentTimeWindow>0</alignmentTimeWindow>
+   <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms>
+   <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
+   <compositionPrediction>0</compositionPrediction>
+   <quantMode>1</quantMode>
+   <massDifferenceMods>
+   </massDifferenceMods>
+   <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
+   <writeMsScansTable>False</writeMsScansTable>
+   <writeMsmsScansTable>True</writeMsmsScansTable>
+   <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
+   <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
+   <writeMs3ScansTable>True</writeMs3ScansTable>
+   <writeAllPeptidesTable>True</writeAllPeptidesTable>
+   <writeMzRangeTable>True</writeMzRangeTable>
+   <writeMzTab>True</writeMzTab>
+   <disableMd5>False</disableMd5>
+   <cacheBinInds>True</cacheBinInds>
+   <etdIncludeB>False</etdIncludeB>
+   <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets>
+   <stackPeaks>False</stackPeaks>
+   <ms2PrecursorShift>0</ms2PrecursorShift>
+   <complementaryIonPpm>20</complementaryIonPpm>
+   <variationParseRule></variationParseRule>
+   <variationMode>none</variationMode>
+   <useSeriesReporters>False</useSeriesReporters>
+   <name>session1</name>
+   <maxQuantVersion>1.6.3.4</maxQuantVersion>
+   <tempFolder></tempFolder>
+   <pluginFolder></pluginFolder>
+   <numThreads>2</numThreads>
+   <emailAddress></emailAddress>
+   <smtpHost></smtpHost>
+   <emailFromAddress></emailFromAddress>
+   <fixedCombinedFolder></fixedCombinedFolder>
+   <fullMinMz>-1.79589544172745E+308</fullMinMz>
+   <fullMaxMz>1.79589544172745E+308</fullMaxMz>
+   <sendEmail>False</sendEmail>
+   <ionCountIntensities>False</ionCountIntensities>
+   <verboseColumnHeaders>False</verboseColumnHeaders>
+   <calcPeakProperties>False</calcPeakProperties>
+   <showCentroidMassDifferences>False</showCentroidMassDifferences>
+   <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
+   <useDotNetCore>False</useDotNetCore>
+   <filePaths>
+      <string>D:\shared\dglaetzer\maxquant_tool\test2\two_mzxml_short\BSA_min_21.mzXML</string>
+      <string>D:\shared\dglaetzer\maxquant_tool\test2\two_mzxml_short\BSA_min_22.mzXML</string>
+   </filePaths>
+   <experiments>
+      <string>BSA_min_21.mzXML</string>
+      <string>BSA_min_22.mzXML</string>
+   </experiments>
+   <fractions>
+      <short>1</short>
+      <short>2</short>
+   </fractions>
+   <ptms>
+      <boolean>False</boolean>
+      <boolean>False</boolean>
+   </ptms>
+   <paramGroupIndices>
+      <int>0</int>
+      <int>0</int>
+   </paramGroupIndices>
+   <referenceChannel>
+      <string></string>
+      <string></string>
+   </referenceChannel>
+   <parameterGroups>
+      <parameterGroup>
+         <msInstrument>0</msInstrument>
+         <maxCharge>7</maxCharge>
+         <minPeakLen>2</minPeakLen>
+         <useMs1Centroids>False</useMs1Centroids>
+         <useMs2Centroids>False</useMs2Centroids>
+         <cutPeaks>True</cutPeaks>
+         <gapScans>1</gapScans>
+         <minTime>NaN</minTime>
+         <maxTime>NaN</maxTime>
+         <matchType>NoMatching</matchType>
+         <intensityDetermination>0</intensityDetermination>
+         <centroidMatchTol>8</centroidMatchTol>
+         <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
+         <centroidHalfWidth>35</centroidHalfWidth>
+         <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
+         <valleyFactor>1.4</valleyFactor>
+         <isotopeValleyFactor>1.2</isotopeValleyFactor>
+         <advancedPeakSplitting>False</advancedPeakSplitting>
+         <intensityThreshold>0</intensityThreshold>
+         <labelMods>
+            <string></string>
+         </labelMods>
+         <lcmsRunType>Standard</lcmsRunType>
+         <reQuantify>False</reQuantify>
+         <lfqMode>0</lfqMode>
+         <lfqSkipNorm>False</lfqSkipNorm>
+         <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
+         <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
+         <lfqMaxFeatures>100000</lfqMaxFeatures>
+         <neucodeMaxPpm>0</neucodeMaxPpm>
+         <neucodeResolution>0</neucodeResolution>
+         <neucodeResolutionInMda>False</neucodeResolutionInMda>
+         <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
+         <fastLfq>True</fastLfq>
+         <lfqRestrictFeatures>False</lfqRestrictFeatures>
+         <lfqMinRatioCount>2</lfqMinRatioCount>
+         <maxLabeledAa>0</maxLabeledAa>
+         <maxNmods>2</maxNmods>
+         <maxMissedCleavages>0</maxMissedCleavages>
+         <multiplicity>1</multiplicity>
+         <enzymeMode>0</enzymeMode>
+         <complementaryReporterType>0</complementaryReporterType>
+         <reporterNormalization>0</reporterNormalization>
+         <neucodeIntensityMode>0</neucodeIntensityMode>
+         <fixedModifications>
+            <string>Carbamidomethyl (C)</string>
+         </fixedModifications>
+         <enzymes>
+            <string>Trypsin/P</string>
+         </enzymes>
+         <enzymesFirstSearch>
+         </enzymesFirstSearch>
+         <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
+         <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
+         <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
+         <variableModifications>
+            <string>Oxidation (M)</string>
+         </variableModifications>
+         <useMultiModification>False</useMultiModification>
+         <multiModifications>
+         </multiModifications>
+         <isobaricLabels>
+         </isobaricLabels>
+         <neucodeLabels>
+         </neucodeLabels>
+         <variableModificationsFirstSearch>
+         </variableModificationsFirstSearch>
+         <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
+         <additionalVariableModifications>
+         </additionalVariableModifications>
+         <additionalVariableModificationProteins>
+         </additionalVariableModificationProteins>
+         <doMassFiltering>True</doMassFiltering>
+         <firstSearchTol>20</firstSearchTol>
+         <mainSearchTol>4.5</mainSearchTol>
+         <searchTolInPpm>True</searchTolInPpm>
+         <isotopeMatchTol>2</isotopeMatchTol>
+         <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
+         <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
+         <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
+         <checkMassDeficit>True</checkMassDeficit>
+         <recalibrationInPpm>True</recalibrationInPpm>
+         <intensityDependentCalibration>False</intensityDependentCalibration>
+         <minScoreForCalibration>70</minScoreForCalibration>
+         <matchLibraryFile>False</matchLibraryFile>
+         <libraryFile></libraryFile>
+         <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
+         <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
+         <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
+         <reporterMassTolerance>NaN</reporterMassTolerance>
+         <reporterPif>NaN</reporterPif>
+         <filterPif>False</filterPif>
+         <reporterFraction>NaN</reporterFraction>
+         <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
+         <timsHalfWidth>0</timsHalfWidth>
+         <timsStep>0</timsStep>
+         <timsResolution>0</timsResolution>
+         <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
+         <timsRemovePrecursor>True</timsRemovePrecursor>
+         <timsIsobaricLabels>False</timsIsobaricLabels>
+         <timsCollapseMsms>True</timsCollapseMsms>
+         <crosslinkSearch>False</crosslinkSearch>
+         <crossLinker></crossLinker>
+         <minMatchXl>0</minMatchXl>
+         <minPairedPepLenXl>6</minPairedPepLenXl>
+         <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+         <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
+         <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
+         <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
+         <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
+         <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
+         <crosslinkCleaveModifications>
+         </crosslinkCleaveModifications>
+         <crosslinkFastaFiles>
+         </crosslinkFastaFiles>
+         <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
+         <peakRefinement>False</peakRefinement>
+         <isobaricSumOverWindow>True</isobaricSumOverWindow>
+      </parameterGroup>
+   </parameterGroups>
+   <msmsParamsArray>
+      <msmsParams>
+         <Name>FTMS</Name>
+         <MatchTolerance>20</MatchTolerance>
+         <MatchToleranceInPpm>True</MatchToleranceInPpm>
+         <DeisotopeTolerance>7</DeisotopeTolerance>
+         <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+         <DeNovoTolerance>10</DeNovoTolerance>
+         <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+         <Deisotope>True</Deisotope>
+         <Topx>12</Topx>
+         <TopxInterval>100</TopxInterval>
+         <HigherCharges>True</HigherCharges>
+         <IncludeWater>True</IncludeWater>
+         <IncludeAmmonia>True</IncludeAmmonia>
+         <DependentLosses>True</DependentLosses>
+         <Recalibration>False</Recalibration>
+      </msmsParams>
+      <msmsParams>
+         <Name>ITMS</Name>
+         <MatchTolerance>0.5</MatchTolerance>
+         <MatchToleranceInPpm>False</MatchToleranceInPpm>
+         <DeisotopeTolerance>0.15</DeisotopeTolerance>
+         <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+         <DeNovoTolerance>0.25</DeNovoTolerance>
+         <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+         <Deisotope>False</Deisotope>
+         <Topx>8</Topx>
+         <TopxInterval>100</TopxInterval>
+         <HigherCharges>True</HigherCharges>
+         <IncludeWater>True</IncludeWater>
+         <IncludeAmmonia>True</IncludeAmmonia>
+         <DependentLosses>True</DependentLosses>
+         <Recalibration>False</Recalibration>
+      </msmsParams>
+      <msmsParams>
+         <Name>TOF</Name>
+         <MatchTolerance>40</MatchTolerance>
+         <MatchToleranceInPpm>True</MatchToleranceInPpm>
+         <DeisotopeTolerance>0.01</DeisotopeTolerance>
+         <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+         <DeNovoTolerance>0.02</DeNovoTolerance>
+         <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+         <Deisotope>True</Deisotope>
+         <Topx>10</Topx>
+         <TopxInterval>100</TopxInterval>
+         <HigherCharges>True</HigherCharges>
+         <IncludeWater>True</IncludeWater>
+         <IncludeAmmonia>True</IncludeAmmonia>
+         <DependentLosses>True</DependentLosses>
+         <Recalibration>False</Recalibration>
+      </msmsParams>
+      <msmsParams>
+         <Name>Unknown</Name>
+         <MatchTolerance>0.5</MatchTolerance>
+         <MatchToleranceInPpm>False</MatchToleranceInPpm>
+         <DeisotopeTolerance>0.15</DeisotopeTolerance>
+         <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+         <DeNovoTolerance>0.25</DeNovoTolerance>
+         <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+         <Deisotope>False</Deisotope>
+         <Topx>8</Topx>
+         <TopxInterval>100</TopxInterval>
+         <HigherCharges>True</HigherCharges>
+         <IncludeWater>True</IncludeWater>
+         <IncludeAmmonia>True</IncludeAmmonia>
+         <DependentLosses>True</DependentLosses>
+         <Recalibration>False</Recalibration>
+      </msmsParams>
+   </msmsParamsArray>
+   <fragmentationParamsArray>
+      <fragmentationParams>
+         <Name>CID</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>HCD</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>ETD</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>PQD</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>ETHCD</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>ETCID</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>UVPD</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+      <fragmentationParams>
+         <Name>Unknown</Name>
+         <Connected>False</Connected>
+         <ConnectedScore0>1</ConnectedScore0>
+         <ConnectedScore1>1</ConnectedScore1>
+         <ConnectedScore2>1</ConnectedScore2>
+         <InternalFragments>False</InternalFragments>
+         <InternalFragmentWeight>1</InternalFragmentWeight>
+         <InternalFragmentAas>KRH</InternalFragmentAas>
+      </fragmentationParams>
+   </fragmentationParamsArray>
+</MaxQuantParams>