Re: [Psidev-ms-dev] mzML comments

[Matt C. <mat...@va...>]

The full scan definition is wrong in that full scans can be done on many 
different types of MS instruments.

I have been working under the impression that the "spectrum type" refers 
to a brief meaning of a spectrum (the current term definition for 
"spectrum type" is woefully inadequate), whereas "scanning method" 
refers to the technique used to acquire the scan(s). This interpretation 
may be too vague to capture in the CV, though. We will discuss this 
further and clarify it. :)

The scanning method definition ("Describes the acquisition data type 
produced by a tandem mass spectrometry experiment.") is also wrong 
because not all scans are tandem MS.

It makes little sense to me to have spectrum type and scanning method 
have a one-to-one correspondence because it implies redundant terms.

The terms "precursor ion scan" and "product ion scan" seems to mean a 
scanning role/purpose instead of a scanning method/technique. The 
role/purpose terms are, I think, redundant with their "spectrum type" 
counterparts. The method/technique terms are not. I may be missing 
something about "precursor/product ion scan" though - are they not 
simply an MSn spectrum acquired with a full scan (m/z range)?

-Matt


Wilfred H Tang wrote:
>
> 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
> Please respond to
> Mass spectrometry standard development 
> <psi...@li...>
>
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> To
> 	Mass spectrometry standard development 
> <psi...@li...>
> cc
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> Subject
> 	Re: [Psidev-ms-dev] mzML comments
>
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> 	
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>
>
>
> 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
>