Re: [Psidev-ms-dev] precursor m/z encoding

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

Hi Darren, there is already an <isolationWindow> element for this. So I
think it should look like this:

  <precursor spectrumRef="S2">
         <isolationWindow>
               <cvParam cvRef="MS" accession="MS:1000040" name="m/z"  
value="796.8"/>
        </isolationWindow>
        <selectedIonList count="1">
             <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000040" name="m/z"  
value="797.3"/>
                 <cvParam cvRef="MS" accession="MS:1000042"
name="intensity" value="120053"/>
             </selectedIon>
        </selectedIonList>
        ...
  </precursor>

But the monoisotopic issue is interesting. Maybe under m/z, we should
have:

m/z
 \_ monoisotopic m/z
 \_ average m/z

Thoughts?

Eric


> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Darren Kessner
> Sent: Tuesday, May 27, 2008 1:38 PM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] precursor m/z encoding
> 
> Hi all,
> 
> Just came across an issue in my lab involving precursor encoding.  For
> ms2 scans, we want to know both the isolation m/z and the precursor
> monoisotopic m/z, which may be different.  The isolation m/z is what
> is recorded in the filter string.  The monoisotopic m/z may be
> recorded by the instrument, or it may be calculated by analyzing the
> parent survey scan.
> 
> Here's a suggestion for how to encode this:
> 
>   <precursor spectrumRef="S2">
>         <selectedIonList count="1">
>              <selectedIon>
>                  <cvParam cvRef="MS" accession="MS:1000040" name="m/z"
> value="796.8"/>
>                  <cvParam cvRef="MS" accession="MS:1000xxx"
> name="monoisotopic m/z" value="797.3"/>
>              </selectedIon>
>         </selectedIonList>
>         ...
>   </precursor>
> 
> 
> Does this seem reasonable?  If so, we'll need a term for "monoisotopic
> m/z" -- we have "monoisotopic mass" only.
> 
> 
> Darren
> 
> 
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