Re: [Psidev-ms-dev] mzML comments

[Wilfred H T. <Ta...@ap...>]

psi...@li... wrote on 08/12/2008 03:38:52 
PM:

> 
> In that case 
>  - the definition for "full scan" ("Feature of the ion trap mass 
> spectrometer where MS data is acquired over a mass range.") is very 
misleading

Actually the definition for "full scan" might be considered accurate if 
read the right way without the ion trap qualification, but the definition 
for "zoom scan" is clearly misleading - "Feature of the ion trap mass 
spectrometer where MSMS data is acquired over a certain mass range."

>  - why is there a "product ion scan"? 
> 
> Also, wouldn't it make sense for there to be a one-to-one 
> correspondence between the entries under "scanning method" and the 
> entries under "spectrum type"? After all, a spectrum is the result 
> of a scan. Any reason why there should not be a one-to-one 
correspondence? 
> 
> Thanks, 
> Wilfred 
> 
> 

> 
> Matt Chambers <mat...@va...> 
> Sent by: psi...@li... 
> 08/08/2008 06:07 AM 
> 
> Please respond to
> Mass spectrometry standard development 
<psi...@li...>
> 
> To
> 
> Mass spectrometry standard development 
<psi...@li...> 
> 
> cc
> 
> Subject
> 
> Re: [Psidev-ms-dev] mzML comments
> 
> 
> 
> 
> Hi Wilfred,
> 
> I didn't realize we hadn't responded to your suggestions for these 
> terms. We did discuss them on a WG call. The consensus, IIRC, was that 
> MS1 scan and MSn scan are already fully encapsulated by the "full scan" 
> term (in concert with the "MS level" term), and that precursor ion 
> spectrum and constant neutral loss spectrum will be added to the CV. The 

> process is that someone checks out the CV from CVS, makes some valid 
> changes (readable by OBO-Edit), and then someone with commit access to 
> CVS would check it in. Yes, we need a more detailed and explicit process 

> than that; we're working on it! :)
> 
> -Matt
> 
> 
> Wilfred H Tang wrote:
> >
> > Does the lack of dissent mean that the proposal is accepted? :)
> >
> > What is the process for incorporating this into the psi-ms.obo file?
> >
> > Thanks,
> > Wilfred
> >
> >
> > Any thoughts regarding the comments below?
> >
> > For the last point, I would like to propose to add the following terms 

> > to the controlled vocabulary:
> >
> > [Term]
> > id: MS:9999999
> > name: MS1 scan
> > def: "The specific scan function or process that records a MS1 
> > spectrum." [PSI:MS]
> > is_a: MS:1000020 ! scanning method
> >
> > [Term]
> > id: MS:9999999
> > name: MSn scan
> > def: "The specific scan function or process that records a MSn 
> > spectrum." [PSI:MS]
> > is_a: MS:1000020 ! scanning method
> >
> > [Term]
> > id: MS:9999999
> > name: precursor ion spectrum
> > def: "Spectrum generated by scanning precursor m/z while monitoring a 
> > fixed product m/z" [PSI:MS]
> > is_a: MS:1000524 ! data file content
> > is_a: MS:1000559 ! spectrum type
> >
> > [Term]
> > id: MS:9999999
> > name: constant neutral loss spectrum
> > def: "Spectrum generated by scanning precursor m/z and product m/z 
> > simultaneously, maintaining a constant difference between the two" 
> > [PSI:MS]
> > is_a: MS:1000524 ! data file content
> > is_a: MS:1000559 ! spectrum type
> >
> > Thanks,
> > Wilfred
> 
> 
> 
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