[Psidev-ms-dev] IntermediateProduct?

[Eric D. <Eri...@sy...>]

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