Mercurial > repos > galaxyp > maxquant
comparison test-data/06/mqpar.xml @ 12:0839f84def5e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
| author | galaxyp |
|---|---|
| date | Sun, 20 Jun 2021 16:37:41 +0000 |
| parents | f522c08e900c |
| children | 837224ad1694 |
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| 11:d72c96ad9a16 | 12:0839f84def5e |
|---|---|
| 1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
| 2 <MaxQuantParams> | 2 <MaxQuantParams> |
| 3 <fastaFiles> | 3 <fastaFiles> |
| 4 <FastaFileInfo> | 4 <FastaFileInfo> |
| 5 <fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath> | 5 <fastaFilePath>/tmp/tmpyzym30dx/files/b/9/7/dataset_b97123e2-9db4-407c-bd7f-b69d65fc32cc.dat</fastaFilePath> |
| 6 <identifierParseRule>>([^\s]*)</identifierParseRule> | 6 <identifierParseRule>>([^\s]*)</identifierParseRule> |
| 7 <descriptionParseRule>>(.*)</descriptionParseRule> | 7 <descriptionParseRule>>(.*)</descriptionParseRule> |
| 8 <taxonomyParseRule/> | 8 <taxonomyParseRule/> |
| 9 <variationParseRule/> | 9 <variationParseRule/> |
| 10 <modificationParseRule/> | 10 <modificationParseRule/> |
| 17 </fastaFilesFirstSearch> | 17 </fastaFilesFirstSearch> |
| 18 <fixedSearchFolder/> | 18 <fixedSearchFolder/> |
| 19 <andromedaCacheSize>350000</andromedaCacheSize> | 19 <andromedaCacheSize>350000</andromedaCacheSize> |
| 20 <advancedRatios>True</advancedRatios> | 20 <advancedRatios>True</advancedRatios> |
| 21 <pvalThres>0.005</pvalThres> | 21 <pvalThres>0.005</pvalThres> |
| 22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> | |
| 23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> | |
| 24 <rtShift>False</rtShift> | 22 <rtShift>False</rtShift> |
| 25 <separateLfq>False</separateLfq> | 23 <separateLfq>False</separateLfq> |
| 26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> | 24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> |
| 27 <lfqRequireMsms>True</lfqRequireMsms> | 25 <lfqRequireMsms>True</lfqRequireMsms> |
| 28 <decoyMode>randomize</decoyMode> | 26 <decoyMode>randomize</decoyMode> |
| 46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> | 44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> |
| 47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> | 45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> |
| 48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> | 46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> |
| 49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> | 47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> |
| 50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> | 48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> |
| 51 <msmsConnection>False</msmsConnection> | |
| 52 <ibaq>False</ibaq> | 49 <ibaq>False</ibaq> |
| 53 <top3>False</top3> | 50 <top3>False</top3> |
| 54 <independentEnzymes>False</independentEnzymes> | 51 <independentEnzymes>False</independentEnzymes> |
| 55 <useDeltaScore>False</useDeltaScore> | 52 <useDeltaScore>False</useDeltaScore> |
| 56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> | 53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> |
| 98 </massDifferenceMods> | 95 </massDifferenceMods> |
| 99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> | 96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> |
| 100 <writeMsScansTable>False</writeMsScansTable> | 97 <writeMsScansTable>False</writeMsScansTable> |
| 101 <writeMsmsScansTable>True</writeMsmsScansTable> | 98 <writeMsmsScansTable>True</writeMsmsScansTable> |
| 102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> | 99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> |
| 103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> | 100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> |
| 104 <writeMs3ScansTable>True</writeMs3ScansTable> | 101 <writeMs3ScansTable>True</writeMs3ScansTable> |
| 105 <writeAllPeptidesTable>True</writeAllPeptidesTable> | 102 <writeAllPeptidesTable>True</writeAllPeptidesTable> |
| 106 <writeMzRangeTable>True</writeMzRangeTable> | 103 <writeMzRangeTable>True</writeMzRangeTable> |
| 104 <writeDiaFragmentTable>False</writeDiaFragmentTable> | |
| 107 <writeMzTab>True</writeMzTab> | 105 <writeMzTab>True</writeMzTab> |
| 108 <disableMd5>False</disableMd5> | 106 <disableMd5>False</disableMd5> |
| 109 <cacheBinInds>True</cacheBinInds> | 107 <cacheBinInds>True</cacheBinInds> |
| 110 <etdIncludeB>False</etdIncludeB> | 108 <etdIncludeB>False</etdIncludeB> |
| 111 <ms2PrecursorShift>0</ms2PrecursorShift> | 109 <ms2PrecursorShift>0</ms2PrecursorShift> |
| 112 <complementaryIonPpm>20</complementaryIonPpm> | 110 <complementaryIonPpm>20</complementaryIonPpm> |
| 113 <variationParseRule/> | 111 <variationParseRule/> |
| 114 <variationMode>none</variationMode> | 112 <variationMode>none</variationMode> |
| 115 <useSeriesReporters>False</useSeriesReporters> | 113 <useSeriesReporters>False</useSeriesReporters> |
| 116 <name>templateSession</name> | 114 <name>templateSession</name> |
| 117 <maxQuantVersion>1.6.10.43</maxQuantVersion> | 115 <maxQuantVersion>1.6.17.0</maxQuantVersion> |
| 118 <tempFolder/> | |
| 119 <pluginFolder/> | 116 <pluginFolder/> |
| 120 <numThreads>1</numThreads> | 117 <numThreads>1</numThreads> |
| 118 <batchSize>1</batchSize> | |
| 121 <emailAddress/> | 119 <emailAddress/> |
| 122 <smtpHost/> | 120 <smtpHost/> |
| 123 <emailFromAddress/> | 121 <emailFromAddress/> |
| 124 <fixedCombinedFolder/> | 122 <fixedCombinedFolder/> |
| 125 <fullMinMz>-1.79769313486232E+308</fullMinMz> | 123 <fullMinMz>-1.79769313486232E+308</fullMinMz> |
| 128 <ionCountIntensities>False</ionCountIntensities> | 126 <ionCountIntensities>False</ionCountIntensities> |
| 129 <verboseColumnHeaders>False</verboseColumnHeaders> | 127 <verboseColumnHeaders>False</verboseColumnHeaders> |
| 130 <calcPeakProperties>False</calcPeakProperties> | 128 <calcPeakProperties>False</calcPeakProperties> |
| 131 <showCentroidMassDifferences>False</showCentroidMassDifferences> | 129 <showCentroidMassDifferences>False</showCentroidMassDifferences> |
| 132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences> | 130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences> |
| 133 <useDotNetCore>False</useDotNetCore> | 131 <useDotNetCore>True</useDotNetCore> |
| 132 <profilePerformance>False</profilePerformance> | |
| 134 <filePaths> | 133 <filePaths> |
| 135 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string> | 134 <string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_23.mzXML</string> |
| 136 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string> | 135 <string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_22.mzxml</string> |
| 137 </filePaths> | 136 </filePaths> |
| 138 <experiments> | 137 <experiments> |
| 139 <string>BSA_min_23.mzXML</string> | 138 <string>BSA_min_23.mzXML</string> |
| 140 <string>BSA_min_22.mzxml</string> | 139 <string>BSA_min_22.mzxml</string> |
| 141 </experiments> | 140 </experiments> |
| 155 <string/> | 154 <string/> |
| 156 <string/> | 155 <string/> |
| 157 </referenceChannel> | 156 </referenceChannel> |
| 158 <intensPred>False</intensPred> | 157 <intensPred>False</intensPred> |
| 159 <intensPredModelReTrain>False</intensPredModelReTrain> | 158 <intensPredModelReTrain>False</intensPredModelReTrain> |
| 159 <lfqTopNPeptides>0</lfqTopNPeptides> | |
| 160 <parameterGroups> | 160 <parameterGroups> |
| 161 <parameterGroup> | 161 <parameterGroup> |
| 162 <msInstrument>0</msInstrument> | 162 <msInstrument>0</msInstrument> |
| 163 <maxCharge>7</maxCharge> | 163 <maxCharge>7</maxCharge> |
| 164 <minPeakLen>2</minPeakLen> | 164 <minPeakLen>2</minPeakLen> |
| 165 <diaMinPeakLen>2</diaMinPeakLen> | 165 <diaMinPeakLen>1</diaMinPeakLen> |
| 166 <useMs1Centroids>False</useMs1Centroids> | 166 <useMs1Centroids>False</useMs1Centroids> |
| 167 <useMs2Centroids>False</useMs2Centroids> | 167 <useMs2Centroids>False</useMs2Centroids> |
| 168 <cutPeaks>True</cutPeaks> | 168 <cutPeaks>True</cutPeaks> |
| 169 <gapScans>1</gapScans> | 169 <gapScans>1</gapScans> |
| 170 <minTime>NaN</minTime> | 170 <minTime>NaN</minTime> |
| 176 <centroidHalfWidth>35</centroidHalfWidth> | 176 <centroidHalfWidth>35</centroidHalfWidth> |
| 177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> | 177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> |
| 178 <valleyFactor>1.4</valleyFactor> | 178 <valleyFactor>1.4</valleyFactor> |
| 179 <isotopeValleyFactor>1.2</isotopeValleyFactor> | 179 <isotopeValleyFactor>1.2</isotopeValleyFactor> |
| 180 <advancedPeakSplitting>False</advancedPeakSplitting> | 180 <advancedPeakSplitting>False</advancedPeakSplitting> |
| 181 <intensityThreshold>0</intensityThreshold> | 181 <intensityThresholdMs1>0</intensityThresholdMs1> |
| 182 <intensityThresholdMs2>0</intensityThresholdMs2> | |
| 182 <labelMods> | 183 <labelMods> |
| 183 <string/> | 184 <string/> |
| 184 </labelMods> | 185 </labelMods> |
| 185 <lcmsRunType>Reporter ion MS3</lcmsRunType> | 186 <lcmsRunType>Reporter ion MS3</lcmsRunType> |
| 186 <reQuantify>False</reQuantify> | 187 <reQuantify>False</reQuantify> |
| 187 <lfqMode>0</lfqMode> | 188 <lfqMode>0</lfqMode> |
| 188 <lfqSkipNorm>False</lfqSkipNorm> | 189 <lfqNormClusterSize>80</lfqNormClusterSize> |
| 189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> | 190 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> |
| 190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> | 191 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> |
| 191 <lfqMaxFeatures>100000</lfqMaxFeatures> | 192 <lfqMaxFeatures>100000</lfqMaxFeatures> |
| 192 <neucodeMaxPpm>0</neucodeMaxPpm> | 193 <neucodeMaxPpm>0</neucodeMaxPpm> |
| 193 <neucodeResolution>0</neucodeResolution> | 194 <neucodeResolution>0</neucodeResolution> |
| 275 <timsResolution>0</timsResolution> | 276 <timsResolution>0</timsResolution> |
| 276 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> | 277 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> |
| 277 <timsRemovePrecursor>True</timsRemovePrecursor> | 278 <timsRemovePrecursor>True</timsRemovePrecursor> |
| 278 <timsIsobaricLabels>False</timsIsobaricLabels> | 279 <timsIsobaricLabels>False</timsIsobaricLabels> |
| 279 <timsCollapseMsms>True</timsCollapseMsms> | 280 <timsCollapseMsms>True</timsCollapseMsms> |
| 280 <crosslinkSearch>False</crosslinkSearch> | 281 <crossLinkingType>0</crossLinkingType> |
| 281 <crossLinker/> | 282 <crossLinker/> |
| 282 <minMatchXl>0</minMatchXl> | 283 <minMatchXl>0</minMatchXl> |
| 283 <minPairedPepLenXl>6</minPairedPepLenXl> | 284 <minPairedPepLenXl>6</minPairedPepLenXl> |
| 284 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> | 285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> |
| 285 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> | 286 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> |
| 297 <crosslinkMode/> | 298 <crosslinkMode/> |
| 298 <peakRefinement>False</peakRefinement> | 299 <peakRefinement>False</peakRefinement> |
| 299 <isobaricSumOverWindow>True</isobaricSumOverWindow> | 300 <isobaricSumOverWindow>True</isobaricSumOverWindow> |
| 300 <isobaricWeightExponent>0.75</isobaricWeightExponent> | 301 <isobaricWeightExponent>0.75</isobaricWeightExponent> |
| 301 <diaLibraryType>0</diaLibraryType> | 302 <diaLibraryType>0</diaLibraryType> |
| 302 <diaLibraryPath/> | 303 <diaLibraryPaths> |
| 304 </diaLibraryPaths> | |
| 303 <diaPeptidePaths> | 305 <diaPeptidePaths> |
| 304 </diaPeptidePaths> | 306 </diaPeptidePaths> |
| 305 <diaEvidencePaths> | 307 <diaEvidencePaths> |
| 306 </diaEvidencePaths> | 308 </diaEvidencePaths> |
| 307 <diaMsmsPaths> | 309 <diaMsmsPaths> |
| 310 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> | 312 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> |
| 311 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> | 313 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> |
| 312 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> | 314 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> |
| 313 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> | 315 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> |
| 314 <diaScoreN>7</diaScoreN> | 316 <diaScoreN>7</diaScoreN> |
| 315 <diaMinScore>2.99</diaMinScore> | 317 <diaMinScore>1.99</diaMinScore> |
| 316 <diaPrecursorQuant>False</diaPrecursorQuant> | 318 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> |
| 317 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> | 319 <diaXgBoostSubSample>0.9</diaXgBoostSubSample> |
| 320 <centroidPosition>0</centroidPosition> | |
| 321 <diaQuantMethod>7</diaQuantMethod> | |
| 322 <diaFeatureQuantMethod>2</diaFeatureQuantMethod> | |
| 323 <lfqNormType>1</lfqNormType> | |
| 324 <diaTopNForQuant>10</diaTopNForQuant> | |
| 325 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> | |
| 326 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> | |
| 327 <diaPrecursorFilterType>0</diaPrecursorFilterType> | |
| 328 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> | |
| 329 <diaMinPrecursorScore>0.5</diaMinPrecursorScore> | |
| 330 <diaMinProfileCorrelation>0</diaMinProfileCorrelation> | |
| 331 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> | |
| 332 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> | |
| 333 <diaXgBoostEstimators>580</diaXgBoostEstimators> | |
| 334 <diaXgBoostGamma>0.9</diaXgBoostGamma> | |
| 335 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> | |
| 336 <diaGlobalMl>True</diaGlobalMl> | |
| 337 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> | |
| 338 <diaMassWindowFactor>3.3</diaMassWindowFactor> | |
| 339 <diaRtPrediction>False</diaRtPrediction> | |
| 340 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> | |
| 341 <diaNoMl>False</diaNoMl> | |
| 342 <diaPermuteRt>False</diaPermuteRt> | |
| 343 <diaPermuteCcs>False</diaPermuteCcs> | |
| 344 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> | |
| 345 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> | |
| 346 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> | |
| 347 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> | |
| 318 </parameterGroup> | 348 </parameterGroup> |
| 319 <parameterGroup> | 349 <parameterGroup> |
| 320 <msInstrument>0</msInstrument> | 350 <msInstrument>0</msInstrument> |
| 321 <maxCharge>7</maxCharge> | 351 <maxCharge>7</maxCharge> |
| 322 <minPeakLen>2</minPeakLen> | 352 <minPeakLen>2</minPeakLen> |
| 323 <diaMinPeakLen>2</diaMinPeakLen> | 353 <diaMinPeakLen>1</diaMinPeakLen> |
| 324 <useMs1Centroids>False</useMs1Centroids> | 354 <useMs1Centroids>False</useMs1Centroids> |
| 325 <useMs2Centroids>False</useMs2Centroids> | 355 <useMs2Centroids>False</useMs2Centroids> |
| 326 <cutPeaks>True</cutPeaks> | 356 <cutPeaks>True</cutPeaks> |
| 327 <gapScans>1</gapScans> | 357 <gapScans>1</gapScans> |
| 328 <minTime>NaN</minTime> | 358 <minTime>NaN</minTime> |
| 334 <centroidHalfWidth>35</centroidHalfWidth> | 364 <centroidHalfWidth>35</centroidHalfWidth> |
| 335 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> | 365 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> |
| 336 <valleyFactor>1.4</valleyFactor> | 366 <valleyFactor>1.4</valleyFactor> |
| 337 <isotopeValleyFactor>1.2</isotopeValleyFactor> | 367 <isotopeValleyFactor>1.2</isotopeValleyFactor> |
| 338 <advancedPeakSplitting>False</advancedPeakSplitting> | 368 <advancedPeakSplitting>False</advancedPeakSplitting> |
| 339 <intensityThreshold>0</intensityThreshold> | 369 <intensityThresholdMs1>0</intensityThresholdMs1> |
| 370 <intensityThresholdMs2>0</intensityThresholdMs2> | |
| 340 <labelMods> | 371 <labelMods> |
| 341 <string/> | 372 <string/> |
| 342 </labelMods> | 373 </labelMods> |
| 343 <lcmsRunType>Reporter ion MS3</lcmsRunType> | 374 <lcmsRunType>Reporter ion MS3</lcmsRunType> |
| 344 <reQuantify>False</reQuantify> | 375 <reQuantify>False</reQuantify> |
| 345 <lfqMode>0</lfqMode> | 376 <lfqMode>0</lfqMode> |
| 346 <lfqSkipNorm>False</lfqSkipNorm> | 377 <lfqNormClusterSize>80</lfqNormClusterSize> |
| 347 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> | 378 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> |
| 348 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> | 379 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> |
| 349 <lfqMaxFeatures>100000</lfqMaxFeatures> | 380 <lfqMaxFeatures>100000</lfqMaxFeatures> |
| 350 <neucodeMaxPpm>0</neucodeMaxPpm> | 381 <neucodeMaxPpm>0</neucodeMaxPpm> |
| 351 <neucodeResolution>0</neucodeResolution> | 382 <neucodeResolution>0</neucodeResolution> |
| 447 <timsResolution>0</timsResolution> | 478 <timsResolution>0</timsResolution> |
| 448 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> | 479 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> |
| 449 <timsRemovePrecursor>True</timsRemovePrecursor> | 480 <timsRemovePrecursor>True</timsRemovePrecursor> |
| 450 <timsIsobaricLabels>False</timsIsobaricLabels> | 481 <timsIsobaricLabels>False</timsIsobaricLabels> |
| 451 <timsCollapseMsms>True</timsCollapseMsms> | 482 <timsCollapseMsms>True</timsCollapseMsms> |
| 452 <crosslinkSearch>False</crosslinkSearch> | 483 <crossLinkingType>0</crossLinkingType> |
| 453 <crossLinker/> | 484 <crossLinker/> |
| 454 <minMatchXl>0</minMatchXl> | 485 <minMatchXl>0</minMatchXl> |
| 455 <minPairedPepLenXl>6</minPairedPepLenXl> | 486 <minPairedPepLenXl>6</minPairedPepLenXl> |
| 456 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> | 487 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> |
| 457 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> | 488 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> |
| 469 <crosslinkMode/> | 500 <crosslinkMode/> |
| 470 <peakRefinement>False</peakRefinement> | 501 <peakRefinement>False</peakRefinement> |
| 471 <isobaricSumOverWindow>True</isobaricSumOverWindow> | 502 <isobaricSumOverWindow>True</isobaricSumOverWindow> |
| 472 <isobaricWeightExponent>0.75</isobaricWeightExponent> | 503 <isobaricWeightExponent>0.75</isobaricWeightExponent> |
| 473 <diaLibraryType>0</diaLibraryType> | 504 <diaLibraryType>0</diaLibraryType> |
| 474 <diaLibraryPath/> | 505 <diaLibraryPaths> |
| 506 </diaLibraryPaths> | |
| 475 <diaPeptidePaths> | 507 <diaPeptidePaths> |
| 476 </diaPeptidePaths> | 508 </diaPeptidePaths> |
| 477 <diaEvidencePaths> | 509 <diaEvidencePaths> |
| 478 </diaEvidencePaths> | 510 </diaEvidencePaths> |
| 479 <diaMsmsPaths> | 511 <diaMsmsPaths> |
| 482 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> | 514 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> |
| 483 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> | 515 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> |
| 484 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> | 516 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> |
| 485 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> | 517 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> |
| 486 <diaScoreN>7</diaScoreN> | 518 <diaScoreN>7</diaScoreN> |
| 487 <diaMinScore>2.99</diaMinScore> | 519 <diaMinScore>1.99</diaMinScore> |
| 488 <diaPrecursorQuant>False</diaPrecursorQuant> | 520 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> |
| 489 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> | 521 <diaXgBoostSubSample>0.9</diaXgBoostSubSample> |
| 522 <centroidPosition>0</centroidPosition> | |
| 523 <diaQuantMethod>7</diaQuantMethod> | |
| 524 <diaFeatureQuantMethod>2</diaFeatureQuantMethod> | |
| 525 <lfqNormType>1</lfqNormType> | |
| 526 <diaTopNForQuant>10</diaTopNForQuant> | |
| 527 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> | |
| 528 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> | |
| 529 <diaPrecursorFilterType>0</diaPrecursorFilterType> | |
| 530 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> | |
| 531 <diaMinPrecursorScore>0.5</diaMinPrecursorScore> | |
| 532 <diaMinProfileCorrelation>0</diaMinProfileCorrelation> | |
| 533 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> | |
| 534 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> | |
| 535 <diaXgBoostEstimators>580</diaXgBoostEstimators> | |
| 536 <diaXgBoostGamma>0.9</diaXgBoostGamma> | |
| 537 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> | |
| 538 <diaGlobalMl>True</diaGlobalMl> | |
| 539 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> | |
| 540 <diaMassWindowFactor>3.3</diaMassWindowFactor> | |
| 541 <diaRtPrediction>False</diaRtPrediction> | |
| 542 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> | |
| 543 <diaNoMl>False</diaNoMl> | |
| 544 <diaPermuteRt>False</diaPermuteRt> | |
| 545 <diaPermuteCcs>False</diaPermuteCcs> | |
| 546 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> | |
| 547 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> | |
| 548 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> | |
| 549 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> | |
| 490 </parameterGroup> | 550 </parameterGroup> |
| 491 </parameterGroups> | 551 </parameterGroups> |
| 492 <msmsParamsArray> | 552 <msmsParamsArray> |
| 493 <msmsParams> | 553 <msmsParams> |
| 494 <Name>FTMS</Name> | 554 <Name>FTMS</Name> |