Re: [Psidev-ms-dev] mzML comments

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

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
 - 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
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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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