Mercurial > repos > galaxyp > maxquant

comparison test-data/10/mqpar.xml @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
parents
children 8934bc76bb52
comparison
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14:e42225f8a659 15:97a7f34fcb6a
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>/tmp/tmps9fy8_y6/files/0/d/3/dataset_0d32c02a-47ca-47c8-83b6-1e955f377a96.dat</fastaFilePath>
6 <identifierParseRule>^&gt;.*\|(.*)\|.*$</identifierParseRule>
7 <descriptionParseRule>^&gt;.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule>
8 <taxonomyParseRule/>
9 <variationParseRule/>
10 <modificationParseRule/>
11 <taxonomyId/>
12 </FastaFileInfo>
13 </fastaFiles>
14 <fastaFilesProteogenomics>
15 </fastaFilesProteogenomics>
16 <fastaFilesFirstSearch>
17 </fastaFilesFirstSearch>
18 <fixedSearchFolder/>
19 <andromedaCacheSize>350000</andromedaCacheSize>
20 <advancedRatios>True</advancedRatios>
21 <pvalThres>0.005</pvalThres>
22 <rtShift>False</rtShift>
23 <separateLfq>False</separateLfq>
24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
25 <lfqRequireMsms>True</lfqRequireMsms>
26 <decoyMode>revert</decoyMode>
27 <boxCarMode>all</boxCarMode>
28 <includeContaminants>True</includeContaminants>
29 <maxPeptideMass>4600</maxPeptideMass>
30 <epsilonMutationScore>True</epsilonMutationScore>
31 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
32 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
33 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
34 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
35 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
36 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
37 <secondPeptide>True</secondPeptide>
38 <matchBetweenRuns>False</matchBetweenRuns>
39 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
40 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
41 <dependentPeptides>False</dependentPeptides>
42 <dependentPeptideFdr>0</dependentPeptideFdr>
43 <dependentPeptideMassBin>0</dependentPeptideMassBin>
44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
49 <ibaq>False</ibaq>
50 <top3>False</top3>
51 <independentEnzymes>False</independentEnzymes>
52 <useDeltaScore>False</useDeltaScore>
53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
54 <taxonomyLevel>Species</taxonomyLevel>
55 <avalon>False</avalon>
56 <nModColumns>3</nModColumns>
57 <ibaqLogFit>False</ibaqLogFit>
58 <razorProteinFdr>True</razorProteinFdr>
59 <deNovoSequencing>False</deNovoSequencing>
60 <deNovoVarMods>True</deNovoVarMods>
61 <massDifferenceSearch>False</massDifferenceSearch>
62 <isotopeCalc>False</isotopeCalc>
63 <writePeptidesForSpectrumFile/>
64 <intensityPredictionsFile>
65 </intensityPredictionsFile>
66 <minPepLen>7</minPepLen>
67 <psmFdrCrosslink>0.01</psmFdrCrosslink>
68 <peptideFdr>0.01</peptideFdr>
69 <proteinFdr>0.01</proteinFdr>
70 <siteFdr>0.01</siteFdr>
71 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
72 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
73 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
74 <minPeptides>1</minPeptides>
75 <minRazorPeptides>1</minRazorPeptides>
76 <minUniquePeptides>1</minUniquePeptides>
77 <useCounterparts>True</useCounterparts>
78 <advancedSiteIntensities>True</advancedSiteIntensities>
79 <customProteinQuantification>False</customProteinQuantification>
80 <customProteinQuantificationFile/>
81 <minRatioCount>2</minRatioCount>
82 <restrictProteinQuantification>True</restrictProteinQuantification>
83 <restrictMods>
84 <string>Oxidation (M)</string>
85 <string>Acetyl (Protein N-term)</string>
86 </restrictMods>
87 <matchingTimeWindow>0</matchingTimeWindow>
88 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
89 <alignmentTimeWindow>0</alignmentTimeWindow>
90 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
91 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
92 <compositionPrediction>0</compositionPrediction>
93 <quantMode>1</quantMode>
94 <massDifferenceMods>
95 </massDifferenceMods>
96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
97 <writeMsScansTable>False</writeMsScansTable>
98 <writeMsmsScansTable>True</writeMsmsScansTable>
99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
101 <writeMs3ScansTable>True</writeMs3ScansTable>
102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
103 <writeMzRangeTable>True</writeMzRangeTable>
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
105 <writeMzTab>False</writeMzTab>
106 <disableMd5>False</disableMd5>
107 <cacheBinInds>True</cacheBinInds>
108 <etdIncludeB>False</etdIncludeB>
109 <ms2PrecursorShift>0</ms2PrecursorShift>
110 <complementaryIonPpm>20</complementaryIonPpm>
111 <variationParseRule/>
112 <variationMode>none</variationMode>
113 <useSeriesReporters>False</useSeriesReporters>
114 <name>templateSession</name>
115 <maxQuantVersion>1.6.17.0</maxQuantVersion>
116 <pluginFolder/>
117 <numThreads>1</numThreads>
118 <batchSize>1</batchSize>
119 <emailAddress/>
120 <smtpHost/>
121 <emailFromAddress/>
122 <fixedCombinedFolder/>
123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
124 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
125 <sendEmail>False</sendEmail>
126 <ionCountIntensities>False</ionCountIntensities>
127 <verboseColumnHeaders>False</verboseColumnHeaders>
128 <calcPeakProperties>False</calcPeakProperties>
129 <showCentroidMassDifferences>False</showCentroidMassDifferences>
130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
131 <useDotNetCore>True</useDotNetCore>
132 <profilePerformance>False</profilePerformance>
133 <filePaths>
134 <string>/tmp/tmps9fy8_y6/job_working_directory/000/3/working/thermo.raw.thermo.raw</string>
135 </filePaths>
136 <experiments>
137 <string>thermo.raw.thermo.raw</string>
138 </experiments>
139 <fractions>
140 <short>32767</short>
141 </fractions>
142 <ptms>
143 <boolean>False</boolean>
144 </ptms>
145 <paramGroupIndices>
146 <int>0</int>
147 </paramGroupIndices>
148 <referenceChannel>
149 <string/>
150 </referenceChannel>
151 <intensPred>False</intensPred>
152 <intensPredModelReTrain>False</intensPredModelReTrain>
153 <lfqTopNPeptides>0</lfqTopNPeptides>
154 <parameterGroups>
155 <parameterGroup>
156 <msInstrument>0</msInstrument>
157 <maxCharge>7</maxCharge>
158 <minPeakLen>2</minPeakLen>
159 <diaMinPeakLen>1</diaMinPeakLen>
160 <useMs1Centroids>False</useMs1Centroids>
161 <useMs2Centroids>False</useMs2Centroids>
162 <cutPeaks>True</cutPeaks>
163 <gapScans>1</gapScans>
164 <minTime>NaN</minTime>
165 <maxTime>NaN</maxTime>
166 <matchType>MatchFromAndTo</matchType>
167 <intensityDetermination>0</intensityDetermination>
168 <centroidMatchTol>8</centroidMatchTol>
169 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
170 <centroidHalfWidth>35</centroidHalfWidth>
171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
172 <valleyFactor>1.4</valleyFactor>
173 <isotopeValleyFactor>1.2</isotopeValleyFactor>
174 <advancedPeakSplitting>False</advancedPeakSplitting>
175 <intensityThresholdMs1>0</intensityThresholdMs1>
176 <intensityThresholdMs2>0</intensityThresholdMs2>
177 <labelMods>
178 <string/>
179 </labelMods>
180 <lcmsRunType>Standard</lcmsRunType>
181 <reQuantify>False</reQuantify>
182 <lfqMode>1</lfqMode>
183 <lfqNormClusterSize>80</lfqNormClusterSize>
184 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
185 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
186 <lfqMaxFeatures>100000</lfqMaxFeatures>
187 <neucodeMaxPpm>0</neucodeMaxPpm>
188 <neucodeResolution>0</neucodeResolution>
189 <neucodeResolutionInMda>False</neucodeResolutionInMda>
190 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
191 <fastLfq>True</fastLfq>
192 <lfqRestrictFeatures>False</lfqRestrictFeatures>
193 <lfqMinRatioCount>2</lfqMinRatioCount>
194 <maxLabeledAa>0</maxLabeledAa>
195 <maxNmods>5</maxNmods>
196 <maxMissedCleavages>1</maxMissedCleavages>
197 <multiplicity>1</multiplicity>
198 <enzymeMode>0</enzymeMode>
199 <complementaryReporterType>0</complementaryReporterType>
200 <reporterNormalization>0</reporterNormalization>
201 <neucodeIntensityMode>0</neucodeIntensityMode>
202 <fixedModifications>
203 <string>Carbamidomethyl (C)</string>
204 </fixedModifications>
205 <enzymes>
206 <string>Trypsin/P</string>
207 </enzymes>
208 <enzymesFirstSearch>
209 </enzymesFirstSearch>
210 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
211 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
212 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
213 <variableModifications>
214 <string>Oxidation (M)</string>
215 </variableModifications>
216 <useMultiModification>False</useMultiModification>
217 <multiModifications>
218 </multiModifications>
219 <isobaricLabels>
220 </isobaricLabels>
221 <neucodeLabels>
222 </neucodeLabels>
223 <variableModificationsFirstSearch>
224 </variableModificationsFirstSearch>
225 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
226 <additionalVariableModifications>
227 </additionalVariableModifications>
228 <additionalVariableModificationProteins>
229 </additionalVariableModificationProteins>
230 <doMassFiltering>True</doMassFiltering>
231 <firstSearchTol>20</firstSearchTol>
232 <mainSearchTol>4.5</mainSearchTol>
233 <searchTolInPpm>True</searchTolInPpm>
234 <isotopeMatchTol>2</isotopeMatchTol>
235 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
236 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
237 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
238 <checkMassDeficit>True</checkMassDeficit>
239 <recalibrationInPpm>True</recalibrationInPpm>
240 <intensityDependentCalibration>False</intensityDependentCalibration>
241 <minScoreForCalibration>70</minScoreForCalibration>
242 <matchLibraryFile>False</matchLibraryFile>
243 <libraryFile/>
244 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
245 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
246 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
247 <reporterMassTolerance>NaN</reporterMassTolerance>
248 <reporterPif>NaN</reporterPif>
249 <filterPif>False</filterPif>
250 <reporterFraction>NaN</reporterFraction>
251 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
252 <timsHalfWidth>0</timsHalfWidth>
253 <timsStep>0</timsStep>
254 <timsResolution>0</timsResolution>
255 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
256 <timsRemovePrecursor>True</timsRemovePrecursor>
257 <timsIsobaricLabels>False</timsIsobaricLabels>
258 <timsCollapseMsms>True</timsCollapseMsms>
259 <crossLinkingType>0</crossLinkingType>
260 <crossLinker/>
261 <minMatchXl>0</minMatchXl>
262 <minPairedPepLenXl>6</minPairedPepLenXl>
263 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
264 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
265 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
266 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
267 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
268 <crosslinkModifications>
269 </crosslinkModifications>
270 <crosslinkFastaFiles>
271 </crosslinkFastaFiles>
272 <crosslinkSites>
273 </crosslinkSites>
274 <crosslinkNetworkFiles>
275 </crosslinkNetworkFiles>
276 <crosslinkMode/>
277 <peakRefinement>False</peakRefinement>
278 <isobaricSumOverWindow>True</isobaricSumOverWindow>
279 <isobaricWeightExponent>0.75</isobaricWeightExponent>
280 <diaLibraryType>0</diaLibraryType>
281 <diaLibraryPaths>
282 </diaLibraryPaths>
283 <diaPeptidePaths>
284 </diaPeptidePaths>
285 <diaEvidencePaths>
286 </diaEvidencePaths>
287 <diaMsmsPaths>
288 </diaMsmsPaths>
289 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
290 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
291 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
292 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
293 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
294 <diaScoreN>7</diaScoreN>
295 <diaMinScore>1.99</diaMinScore>
296 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
297 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
298 <centroidPosition>0</centroidPosition>
299 <diaQuantMethod>7</diaQuantMethod>
300 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
301 <lfqNormType>1</lfqNormType>
302 <diaTopNForQuant>10</diaTopNForQuant>
303 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
304 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
305 <diaPrecursorFilterType>0</diaPrecursorFilterType>
306 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
307 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
308 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
309 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
310 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
311 <diaXgBoostEstimators>580</diaXgBoostEstimators>
312 <diaXgBoostGamma>0.9</diaXgBoostGamma>
313 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
314 <diaGlobalMl>True</diaGlobalMl>
315 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
316 <diaMassWindowFactor>3.3</diaMassWindowFactor>
317 <diaRtPrediction>False</diaRtPrediction>
318 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
319 <diaNoMl>False</diaNoMl>
320 <diaPermuteRt>False</diaPermuteRt>
321 <diaPermuteCcs>False</diaPermuteCcs>
322 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
323 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
324 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
325 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
326 </parameterGroup>
327 </parameterGroups>
328 <msmsParamsArray>
329 <msmsParams>
330 <Name>FTMS</Name>
331 <MatchTolerance>20</MatchTolerance>
332 <MatchToleranceInPpm>True</MatchToleranceInPpm>
333 <DeisotopeTolerance>7</DeisotopeTolerance>
334 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
335 <DeNovoTolerance>10</DeNovoTolerance>
336 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
337 <Deisotope>True</Deisotope>
338 <Topx>12</Topx>
339 <TopxInterval>100</TopxInterval>
340 <HigherCharges>True</HigherCharges>
341 <IncludeWater>True</IncludeWater>
342 <IncludeAmmonia>True</IncludeAmmonia>
343 <DependentLosses>True</DependentLosses>
344 <Recalibration>False</Recalibration>
345 </msmsParams>
346 <msmsParams>
347 <Name>ITMS</Name>
348 <MatchTolerance>0.5</MatchTolerance>
349 <MatchToleranceInPpm>False</MatchToleranceInPpm>
350 <DeisotopeTolerance>0.15</DeisotopeTolerance>
351 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
352 <DeNovoTolerance>0.25</DeNovoTolerance>
353 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
354 <Deisotope>False</Deisotope>
355 <Topx>8</Topx>
356 <TopxInterval>100</TopxInterval>
357 <HigherCharges>True</HigherCharges>
358 <IncludeWater>True</IncludeWater>
359 <IncludeAmmonia>True</IncludeAmmonia>
360 <DependentLosses>True</DependentLosses>
361 <Recalibration>False</Recalibration>
362 </msmsParams>
363 <msmsParams>
364 <Name>TOF</Name>
365 <MatchTolerance>40</MatchTolerance>
366 <MatchToleranceInPpm>True</MatchToleranceInPpm>
367 <DeisotopeTolerance>0.01</DeisotopeTolerance>
368 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
369 <DeNovoTolerance>0.02</DeNovoTolerance>
370 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
371 <Deisotope>True</Deisotope>
372 <Topx>10</Topx>
373 <TopxInterval>100</TopxInterval>
374 <HigherCharges>True</HigherCharges>
375 <IncludeWater>True</IncludeWater>
376 <IncludeAmmonia>True</IncludeAmmonia>
377 <DependentLosses>True</DependentLosses>
378 <Recalibration>False</Recalibration>
379 </msmsParams>
380 <msmsParams>
381 <Name>Unknown</Name>
382 <MatchTolerance>20</MatchTolerance>
383 <MatchToleranceInPpm>True</MatchToleranceInPpm>
384 <DeisotopeTolerance>7</DeisotopeTolerance>
385 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
386 <DeNovoTolerance>10</DeNovoTolerance>
387 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
388 <Deisotope>True</Deisotope>
389 <Topx>12</Topx>
390 <TopxInterval>100</TopxInterval>
391 <HigherCharges>True</HigherCharges>
392 <IncludeWater>True</IncludeWater>
393 <IncludeAmmonia>True</IncludeAmmonia>
394 <DependentLosses>True</DependentLosses>
395 <Recalibration>False</Recalibration>
396 </msmsParams>
397 </msmsParamsArray>
398 <fragmentationParamsArray>
399 <fragmentationParams>
400 <Name>CID</Name>
401 <Connected>False</Connected>
402 <ConnectedScore0>1</ConnectedScore0>
403 <ConnectedScore1>1</ConnectedScore1>
404 <ConnectedScore2>1</ConnectedScore2>
405 <InternalFragments>False</InternalFragments>
406 <InternalFragmentWeight>1</InternalFragmentWeight>
407 <InternalFragmentAas>KRH</InternalFragmentAas>
408 </fragmentationParams>
409 <fragmentationParams>
410 <Name>HCD</Name>
411 <Connected>False</Connected>
412 <ConnectedScore0>1</ConnectedScore0>
413 <ConnectedScore1>1</ConnectedScore1>
414 <ConnectedScore2>1</ConnectedScore2>
415 <InternalFragments>False</InternalFragments>
416 <InternalFragmentWeight>1</InternalFragmentWeight>
417 <InternalFragmentAas>KRH</InternalFragmentAas>
418 </fragmentationParams>
419 <fragmentationParams>
420 <Name>ETD</Name>
421 <Connected>False</Connected>
422 <ConnectedScore0>1</ConnectedScore0>
423 <ConnectedScore1>1</ConnectedScore1>
424 <ConnectedScore2>1</ConnectedScore2>
425 <InternalFragments>False</InternalFragments>
426 <InternalFragmentWeight>1</InternalFragmentWeight>
427 <InternalFragmentAas>KRH</InternalFragmentAas>
428 </fragmentationParams>
429 <fragmentationParams>
430 <Name>PQD</Name>
431 <Connected>False</Connected>
432 <ConnectedScore0>1</ConnectedScore0>
433 <ConnectedScore1>1</ConnectedScore1>
434 <ConnectedScore2>1</ConnectedScore2>
435 <InternalFragments>False</InternalFragments>
436 <InternalFragmentWeight>1</InternalFragmentWeight>
437 <InternalFragmentAas>KRH</InternalFragmentAas>
438 </fragmentationParams>
439 <fragmentationParams>
440 <Name>ETHCD</Name>
441 <Connected>False</Connected>
442 <ConnectedScore0>1</ConnectedScore0>
443 <ConnectedScore1>1</ConnectedScore1>
444 <ConnectedScore2>1</ConnectedScore2>
445 <InternalFragments>False</InternalFragments>
446 <InternalFragmentWeight>1</InternalFragmentWeight>
447 <InternalFragmentAas>KRH</InternalFragmentAas>
448 </fragmentationParams>
449 <fragmentationParams>
450 <Name>ETCID</Name>
451 <Connected>False</Connected>
452 <ConnectedScore0>1</ConnectedScore0>
453 <ConnectedScore1>1</ConnectedScore1>
454 <ConnectedScore2>1</ConnectedScore2>
455 <InternalFragments>False</InternalFragments>
456 <InternalFragmentWeight>1</InternalFragmentWeight>
457 <InternalFragmentAas>KRH</InternalFragmentAas>
458 </fragmentationParams>
459 <fragmentationParams>
460 <Name>UVPD</Name>
461 <Connected>False</Connected>
462 <ConnectedScore0>1</ConnectedScore0>
463 <ConnectedScore1>1</ConnectedScore1>
464 <ConnectedScore2>1</ConnectedScore2>
465 <InternalFragments>False</InternalFragments>
466 <InternalFragmentWeight>1</InternalFragmentWeight>
467 <InternalFragmentAas>KRH</InternalFragmentAas>
468 </fragmentationParams>
469 <fragmentationParams>
470 <Name>Unknown</Name>
471 <Connected>False</Connected>
472 <ConnectedScore0>1</ConnectedScore0>
473 <ConnectedScore1>1</ConnectedScore1>
474 <ConnectedScore2>1</ConnectedScore2>
475 <InternalFragments>False</InternalFragments>
476 <InternalFragmentWeight>1</InternalFragmentWeight>
477 <InternalFragmentAas>KRH</InternalFragmentAas>
478 </fragmentationParams>
479 </fragmentationParamsArray>
480 </MaxQuantParams>
481