Hi Eric,
This solution seems good. Maybe a required 'order' attribute at the
IntermediateProduct element would be easier to validate instead of the
ms level terms. On the other hand, the Product list in mzML is ordered
just by order of appearance. Any of these solutions would do, since more
than one IntermediateProduct will be extremely rare. So I'm fine with
'ms level' if this is what the majority prefers.
More important is how to define different collision energies for the
different steps as Steffen brought up some time ago. Is the proposal to
have configuration elements in IntermediateProduct and Product?
Regards
Fredrik
On 2011-05-04 01:49, Eric Deutsch wrote:
>
> Hi everyone, at the last call it seems like the preferred plan to
> support MS3 in TraML as suggested by the reviewers was via an
> <intermediateProduct> element, so this would look something like this:
>
> <Transition>
>
> <Precursor>
>
> <cvParam cvRef="MS" accession="MS:1000827" name="isolation window
> target m/z" value="862.94" …../>
>
> <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
>
> </Precursor>
>
> <intermediateProduct>
>
> <cvParam cvRef="MS" accession="MS:1000827" name="isolation window
> target m/z" value="427.34" …../>
>
> <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
>
> </intermediateProduct>
>
> <Product>
>
> <cvParam cvRef="MS" accession="MS:1000827" name="selection window
> target m/z" value="540.57" ……/>
>
> <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
>
> </Product>
>
> <InterpretationList>...</InterpretationList>
>
> <RetentionTime>...</RetentionTime>
>
> <ConfigurationList>...</ConfigurationList>
>
> </Transition>
>
> This seems to neatly solve the problem that the intermediate product
> is a product but is also a precursor and trying to shove them in
> either <Precursor> or <Product> led to problems.
>
> Note also that Precursor and IntermediateProduct have the term
> "isolation window target m/z".
>
> While Product has a "selection window target m/z".
>
> I believe this was the consensus on the call and seems to make sense.
>
> Comments from anyone out there on this? Does this seem like a tidy
> solution?
>
> Since order matters, how do we differentiate between the possibility
> of multiple intermediate products? Shall we require the ms level term?
>
> <intermediateProduct>
>
> <cvParam cvRef="MS" accession="MS:1000827" name="isolation window
> target m/z" value="427.34" …../>
>
> <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
>
> <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
>
> </intermediateProduct>
>
> In theory a validator could enforce sequential ms levels beginning
> with 2, but it might not be easy with the current framework.
>
> What do you think?
>
> Thanks,
>
> Eric
>
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