[Psidev-ms-dev] mzML chromatograms

[Andreas B. <be...@in...>]

Hi all,

currently I am working on implementing the chromatogram support. I  
have noticed that there are no mapping rules for the precursor  
activation of chromatograms. I think it is necessary to port the  
following rules from spectrum to chromatograms.

         <CvMappingRule id="precursor_activation_must" cvElementPath="/ 
mzML/run/spectrumList/spectrum/precursorList/precursor/activation/ 
cvParam/@accession" requirementLevel="MUST" scopePath="/mzML/run/ 
spectrumList/spectrum/precursorList/precursor/activation"  
cvTermsCombinationLogic="AND">
           <CvTerm termAccession="MS:1000044" useTerm="true"  
termName="dissociation method" isRepeatable="true"  
allowChildren="true" cvIdentifierRef="MS"></CvTerm>
         </CvMappingRule>

         <CvMappingRule id="precursor_activation_may" cvElementPath="/ 
mzML/run/spectrumList/spectrum/precursorList/precursor/activation/ 
cvParam/@accession" requirementLevel="MAY" scopePath="/mzML/run/ 
spectrumList/spectrum/precursorList/precursor/activation"  
cvTermsCombinationLogic="OR">
           <CvTerm termAccession="MS:1000510" useTerm="false"  
termName="precursor activation attribute" isRepeatable="true"  
allowChildren="true" cvIdentifierRef="MS"></CvTerm>
         </CvMappingRule>

Additionally, a precursor type can also have selectedIons specified.  
Which does not make much sense in my opinion (at least in the use  
cases I am aware of). Should there be something like an empty mapping  
rule, such that no cv is allowed for chromatogram/precursor/ 
selectedIon (which simply results in no useful information if this tag  
is present in a chromatogram)?

Another question would be how to handle chromatograms that are defined  
via spectra. For SRM or SIM it is quite clear that these spectra can  
be converted into chromatograms. But what about other types? Are there  
any "guidelines" for converters what to convert to chromatograms and  
what to keep as spectra, e.g. for mzXML -> mzML converters?

One minor thing, the psi-ms ontology defines three terms, MS:1000804 !  
electromagnetic radiation spectrum, MS:1000805 ! emission spectrum, MS: 
1000806 ! absorption spectrum all children of spectrum type. The  
corresponding chromatogram terms, however, have a hierarchy, the  
emission and absorption chromatogram terms are children of  
electromagnetic radiation chromatogram, was that intended?

Cheers,
A.


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