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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>mzQuantML</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| </buildSpec> | ||
| <natures> | ||
| </natures> | ||
| </projectDescription> |
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| <!------------------> | ||
| <!-- PROTEIN LIST --> | ||
| <!------------------> | ||
| <ProteinList> | ||
| <protein AccesionRef=""><!--link to mzIdentML--> | ||
| <groupReference ref="groupA"> | ||
| <mean_abundance> | ||
| </groupReference> | ||
| <groupReference ref="groupB"> | ||
| </groupReference> | ||
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| </protein> | ||
| </ProteinList> | ||
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| <!------------------> | ||
| <!-- PEPTIDE LIST --> | ||
| <!------------------> | ||
| <PeptideList> | ||
| <peptide matchedFeatureRef="X1"/> | ||
| <sequence/> | ||
| <modifications/> | ||
| <identificationRef=""/><!--link to mzIdentML--> | ||
| </peptide> | ||
| </PeptideList> | ||
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| <!------------------> | ||
| <!-- FEATURE LIST --> | ||
| <!------------------> | ||
| <FeatureList> | ||
| <MatchedFeature id="X1"> | ||
| <masterRT=""> | ||
| <window=""> | ||
| <group ref="A"><!-- may have mean intensity--> | ||
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| <!-- group has | ||
| mean intensity | ||
| standard deviation | ||
| --> | ||
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| <group_member ref="1"> | ||
| <!-- CV VALUES: --> | ||
| abundance | ||
| intensity | ||
| scores | ||
| std | ||
| mean | ||
| . | ||
| . | ||
| rt and m/z (in label free) | ||
| boundary points (in gel-based) | ||
| </group_member> | ||
| <group_member id="2"> | ||
| </group_member> | ||
| <group_member id="3"> | ||
| </group_member> | ||
| <group_member id="4"> | ||
| </group_member> | ||
| </group> | ||
| <group ref="B"> | ||
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| </group> | ||
| </MatchedFeatures> | ||
| <FeatureList> | ||
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| <!-- Note: | ||
| 1. Run => One raw file | ||
| --> | ||
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| <!-----------------> | ||
| <!-- GROUPS --> | ||
| <!-----------------> | ||
| <!-- OPTION 1 for groups representation --> | ||
| <groups> <!-- List of technical replicates // RUNS in label free --> | ||
| <!-- List of technical replicates // RUNS in label-based. Its is needed links between groups (isn't it?) --> | ||
| <group id="A" name =""> | ||
| <groupMember id="A.1" name=""> | ||
| <spectrumFileREF=""/> | ||
| </groupMember> | ||
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| <chemistrydetails> <!-- for SILAC --> | ||
| <massShift="x Daltons"/> | ||
| </chemistrydetails> | ||
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| </group> | ||
| <group id="B" name=""> | ||
| <groupMember id="B.1" name=""> | ||
| <spectrumFileREF=""/> | ||
| </groupMember> | ||
| </group> | ||
| </groups> | ||
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| <!-- OPTION 2 for groups representation --> | ||
| <!-- in SILAC should be: --> | ||
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| <!-- Run could be 1 raw file, (or could be multiple files that are notionally merged) - likely to be difficult --> | ||
| <run> | ||
| </groupA> | ||
| </groupB> | ||
| </run> | ||
| <!-- in label free should be: --> | ||
| <run> | ||
| </groupA> | ||
| </run> | ||
| <run> | ||
| </groupB> | ||
| </run> | ||
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| <!--------------------> | ||
| <!-- PROTOCOLS --> | ||
| <!--------------------> | ||
| <protocols> | ||
| <!--thresholds like minimum number of peptide for quantify a proteins --> | ||
| <!--alignment (from spectra files to FeatureList) --> | ||
| <!--quantExpression (in label free, from featureList to ProteinAbundanceList) --> | ||
| </protocols> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,149 @@ | ||
| <!------------------> | ||
| <!-- PROTEIN LIST --> | ||
| <!------------------> | ||
| <ProteinList> | ||
| <protein AccesionRef=""><!--link to mzIdentML--> | ||
| <groupReference ref="groupA"> | ||
| <mean_abundance> | ||
| </groupReference> | ||
| <groupReference ref="groupB"> | ||
| </groupReference> | ||
| <proteinRatios> | ||
| </proteinRatios> | ||
| <peptideReferenceList> | ||
| <peptideRef="P1"> | ||
| </peptideReferenceList> | ||
| </protein> | ||
| </ProteinList> | ||
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| <!------------------> | ||
| <!-- PEPTIDE LIST --> | ||
| <!------------------> | ||
| <PeptideList> | ||
| <!-- Note: for SILAC, it will be 4 peptides (in this example) | ||
| e.g. A1 X B1 - one peptide - one matched feature | ||
| A2 X B2 - one peptide - one matched feature | ||
| A3 X B3 - one peptide - one matched feature | ||
| A4 X B4 - one peptide - one matched feature | ||
| unless retention time alignment, in that case may only have one peptide ID and one matched feature | ||
| --> | ||
| <peptide id="P1" matchedFeatureRef="X1"/> | ||
| <sequence/> | ||
| <modifications/> | ||
| <identificationRef=""/><!--link to mzIdentML--> | ||
| <cvparams..> | ||
| ratio | ||
| p-values | ||
| group_correlation | ||
| ... | ||
| </cvparams..> | ||
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| </peptide> | ||
| <peptide matchedFeatureRef="X2"/> | ||
| <sequence/> | ||
| <modifications/> | ||
| <identificationRef=""/><!--link to mzIdentML--> | ||
| </peptide> | ||
| </PeptideList> | ||
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| <!------------------> | ||
| <!-- FEATURE LIST --> | ||
| <!------------------> | ||
| <FeatureList> | ||
| <!-- Note: for SILAC, it will be 4 matched features (in this example) --> | ||
| <MatchedFeature id="X1"> | ||
| <masterRT=""> | ||
| <window=""> | ||
| <group ref="A"><!-- may have mean intensity--> | ||
| <!-- CV VALUES: --> | ||
| <!-- group has | ||
| mean intensity | ||
| standard deviation | ||
| --> | ||
| <!-- Note: group member is equivalent to a chromatogram peak --> | ||
| <group_member ref="1"> | ||
| <!-- CV VALUES: --> | ||
| abundance | ||
| intensity | ||
| scores | ||
| charge state | ||
| . | ||
| . | ||
| rt and m/z (in label free) | ||
| boundary points (in gel-based) | ||
| </group_member> | ||
| <group_member id="2"> | ||
| </group_member> | ||
| <group_member id="3"> | ||
| </group_member> | ||
| <group_member id="4"> | ||
| </group_member> | ||
| </group> | ||
| <group ref="B"> | ||
| </group> | ||
| </MatchedFeatures> | ||
| <FeatureList> | ||
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| <!-- Note: | ||
| 1. Run => One raw file | ||
| --> | ||
|
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||
| <!-----------------> | ||
| <!-- GROUPS --> | ||
| <!-----------------> | ||
| <!-- OPTION 1 for groups representation --> | ||
| <groups> <!-- List of technical replicates // RUNS in label free --> | ||
| <!-- List of technical replicates // RUNS in label-based. Its is needed links between groups (isn't it?) --> | ||
| <group id="A" name =""> | ||
| <groupMember id="A.1" name=""> | ||
| <spectrumFileREF=""/> | ||
| </groupMember> | ||
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| <chemistrydetails> <!-- for SILAC --> | ||
| <massShift="x Daltons"/> | ||
| </chemistrydetails> | ||
|
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| </group> | ||
| <group id="B" name=""> | ||
| <groupMember id="B.1" name=""> | ||
| <spectrumFileREF=""/> | ||
| </groupMember> | ||
| </group> | ||
| </groups> | ||
|
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||
| <!-- OPTION 2 for groups representation --> | ||
| <!-- in SILAC should be: --> | ||
|
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||
| <!-- Run could be 1 raw file, (or could be multiple files that are notionally merged) - likely to be difficult --> | ||
| <run> | ||
| </groupA> | ||
| </groupB> | ||
| </run> | ||
| <!-- in label free should be: --> | ||
| <run> | ||
| </groupA> | ||
| </run> | ||
| <run> | ||
| </groupB> | ||
| </run> | ||
|
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| <!--------------------> | ||
| <!-- PROTOCOLS --> | ||
| <!--------------------> | ||
| <protocols> | ||
| <!--thresholds like minimum number of peptide for quantify a proteins --> | ||
| <!--alignment (from spectra files to FeatureList) --> | ||
| <!--quantExpression (in label free, from featureList to ProteinAbundanceList) --> | ||
| </protocols> |
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