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

[Randy J. <rkj...@in...>]

Jennifer,

As Chris indicated, analysisXML has been designed for storing 
quantitation results.  Both chromatographic (label-free) and 
spectrometric (labeled) quantitation where considered along with the 
'protein/peptide identification' use case.  There are two sub-schema in 
the current draft which address quantitation: quant_method.xsd and 
quant_result.xsd.  These are currently implemented as controlled 
vocabulary schema.  We need to create a proper vocabulary for 
quantitation to use these schema.  Alternatively they can be used as 
examples for creating more specific sub-schema for representing 
quantitation results using explicitly named parameters as elements 
rather than simply using a CV.  The goal is to have a standard HUPO 
quantitation schema developed with the participation and review of the 
entire PSI.

If you have ideas about alternatives to a simple flat CV for they type 
of quantitation results you have, let me know and we can develop some 
prototype sub-schema to test.

Thanks,
Randy


Chris Taylor wrote:

> 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
>>
>