Re: [Psidev-ms-dev] mzML comments

[Marc S. <st...@in...>]

Hi all,

I didn't get the difference between "scan method" and "spectrum type" 
either, so I parse "spectrum type" only.
I'm not convinced we need "scan method" at all.

Another related question:
Is it ok to have "MSn spectrum" spectrum type and "ms level" = 1?
If so, when should the type "MS1 spectrum" be used?

-Marc

Matt Chambers wrote:
> 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...>
>>
>>
>> 	
>> 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
>>>       
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>