Re: [Psidev-ms-dev] mzML comments

[Fredrik L. <Fre...@im...>]

Hi Marc,

Yes, the comment is no longer valid and should be removed. I'll forward 
to the ms-vocab list so that it's not forgotten again.

Fredrik

Marc Sturm wrote:
> I for got something:
>
> In the CV I found the following note for the "ms level" term:
> "The attribute 'ms level' should be encoded in the homonymous XML 
> attribute of the element 'dx:Spectrum', and not using the CvParam element."
>
> Is it still valid, or has someone simply forgotten to remove it?
>
> -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
>>>>       
>>>>         
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