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

[Fredrik L. <Fre...@im...>]

I think it would be fine to reuse 'isolation window target m/z', 
MS:1000827, here. It is reflecting the target value for isolation, both 
for precursor and product.

Thanks

Fredrik

Eric Deutsch wrote:
>
> 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... 
> <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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