Re: [Psidev-ms-dev] binaryArrayData lengths

[Lennart M. <len...@eb...>]

Hi Marc,


> 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.


Cheers,

lnnrt.
> 
> -Marc
> 
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