Re: [Psidev-ms-dev] Unique scan numbers

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

That's an interesting edge case for the nativeID. I am inclined to 
suggest that the nativeID be put in the acquisition, or that spectral 
combination be rethought entirely. Since a combined spectrum is 
essentially a "meta-spectrum" and not a real spectrum (at least I would 
think about it that way), we could use a separate element entirely to 
encode combinations. The combinations themselves would not have any of 
the normal attributes or cvParams of a <spectrum>, just a list of 
references to the actual <spectrum> elements elsewhere in the file. This 
would be a better way in terms of avoiding (meta)data loss.  It would be 
reasonable to allow the <metaspectrum> or <combined_spectrum> to have 
binaryDataArrays containing the combined data, though, since that would 
take the most time to regenerate. But if the spectra are combined before 
putting them in the file, you lose the data from the individual 
acquisitions.

-Matt


Rune Schjellerup Philosof wrote:
> Eric Deutsch wrote:
>   
>> So it seems like the final suggestion is something like:
>>   <spectrum index="18" id="S2,4,6" >
>>     <scan nativeScanReference="2,4,6">
>>     </scan>
>>   </spectrum>
>>   
>>     
>
> that would be
> <spectrum><spectrumDescription><scan nativeScanReference="2,4,6">
>
> This would work for cases when each spectrum refers to a single native scan.
> But aren't there support for having a spectrum that is for instance a 
> combination of several native scans?
>
> [Term]
> id: MS:1000570
> name: spectra combination
> def: "Method used to combine the mass spectra." [PSI:MS]
> relationship: part_of MS:1000442 ! spectrum
>
>
> What to do in this case?
>
>
> --
> Rune