Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

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

Ah, I see, so you'd like to see:



<Precursor>

  <CvParam cvRef="MS" accession="MS:1000xxx" name="precursor m/z"
value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

  <CvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>

</Precursor>

<Product>

  <CvParam cvRef="MS" accession="MS:1000xxx" name="product m/z"
value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

  <CvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>

</Product>



Thanks,

Eric







> -----Original Message-----

> From: Matthew Chambers [mailto:mat...@va...]

> Sent: Thursday, December 17, 2009 2:28 PM

> To: Mass spectrometry standard development

> Subject: Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

>

> In our CV, the m/z term is a unit, not the name of the measurement. If

> you recall, we had the same problem in mzML. We solved it by making

> specific terms with m/z in the name, but not the whole name. So it

> should be:

>

> <CvParam cvRef="MS" accession="xxx" name="<some kind of> m/z"

> value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"

> unitName="m/z" />

>

>

> -Matt

>

> Eric Deutsch wrote:

> >> Also, the precursor and product elements use cvParams for m/z, but

> just

> >> like mzML's selectedIon elements, we can't use the m/z unit as the

> main

> >> term for this. We could either re-use selected ion m/z (awkward?) or

> we

> >> could add a new term.

> >>

> >

> > Sorry, I'm not understanding this issue. Can you expand on this?

> Currently

> > we have:

> >

> > <Precursor>

> >   <CvParam cvRef="MS" accession="MS:1000040" name="m/z"

> value="862.9467"/>

> >   <CvParam cvRef="MS" accession="MS:1000041" name="charge state"

> > value="2"/>

> > </Precursor>

> >

> > What's wrong with this and what are you proposing?

> >

> > Thanks,

> > Eric

> >

> >

>

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