Re: [Psidev-ms-dev] binaryArrayData lengths

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

>> i like that idea of being able to annotate a small subset of the peaks 
>> in a spectrum.
>> This is e.g. needed when assigning ion types for MS/MS: b1, b2, ..., y1, 
>> y2, ..., y7-H2O, ...
>> Most of the peaks are simply noise and so only a minority of peaks will 
>> have an annotation.
>> Using a full-sized array would be possible, but a waste of space.
>> In my opinion, there should be a recommended way to do such a thing. 
>> What do you suggest?
>>
>> Before i forget: Is it possible to annotate peaks with strings? 
>> Otherwise we would have to use some kind of dictionary to assign ion 
>> type an integer index.
>>     
>
> The annotation of a mass spectrum with fragment ion types and indices 
> presents a significant amount of processing of the original mass spec 
> data, as well as a certain type of 'inference' (uncertainty, and often 
> ambiguity!) that has nothing to do with the mass spectrometer, but 
> relates to an identification algorithm of some description.
>
> As such, I don't think we want to annotate this information in mzML at 
> all, or encourage people to do so. The scope of mzML should remain 
> limited to the instrument output (with possibly some signal processing 
> done by the instrument software).
>
> Fragment ion annotation should therefore be held elsewhere, and the PSI 
> is actually creating analysisXML for the purpose of recording 
> identification algorithm output (such as fragment ion assignment). 
> analysisXML will link back to the mzML files used as input, and through 
> this link, peak annotation can be extracted.
>   
The fragment ion annotation was only an example. It's true that mzML is not the right place for it. But i still think that there should be a way to annotate a subset of the peaks with arbitrary data. I could imagine several usecases for such a feature.

- Marc