Re: [Psidev-ms-dev] analysisXML/mzIdent & quantitation

[Chris T. <chr...@eb...>]

Hi Jen. Just a quick response before all the Americans wake up :)

Basically analysisXML has this structure that allows a number of 
(sub)schema 'modules' to be plugged into a 'core' bit. This 
means that in one incarnation it is a model of peptide/protein 
identification, with a description of data source, engine and 
parameters in one bit, the reults in the next one and finally 
the 'knowledge' in the third.

For quantitation, there will be a similar set of modules (to cut 
to the chase, they aren't there yet except as stubs afaik). 
Basically these too may split three ways (although it isn't 
immediately clear to me what will be in the third bit, possibly 
nothing). Number one would be a 'how did I measure intensities 
and with what data' bit; number two being the 'here's the actual 
measured amounts after scaling, normalising, taking ratios etc.

As I say though, it isn't there yet afaik. And I stand to be 
corrected once this post has been seen by those more fully in 
the know than I.

Cheers, Chris.


Jennifer Siepen wrote:
> Hi,
> 
> I am new to the list and have a query about analysisXML/mzIdent. Here at 
> Manchester we have a number of groups carrying out studies with 
> quantitation in proteomics. My query is how does analysisXML/mzIdent 
> cope with quantitation, and are relative and absolute quantitation both 
> catered for?
> 
> Many thanks for any help/information,
> 
> Jennifer
> 

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