Re: [Psidev-ms-dev] dataXML and spectral library support

[Pierre-Alain B. <pie...@is...>]

Thanks Karl for these proposals.
Timewise, I believe we can define and decide how to support library 
searches in the way you propose in Lyon.
Will you be available there (do you have the possibility to come) or in 
another way remotely in case?

Pierre-Alain


Karl Clauser wrote:
>
> Hi folks,
>
> >- Do we support properly the spectrum "library" use case?
>
>             dataXML is supposed to be for MS instrument raw data, not 
> interpreted data, i.e. with assignments. That is what analysisXML is 
> intended for.
>
> I do not espouse the view that dataXML should contain peptide 
> interpretation for individual MS/MS scans (db, de-novo, or otherwise). 
> dataXML is sensibly intended for spectral information, raw or 
> processed. Association of the interpretation information and the 
> individual spectrum in the dataXML file could come from analysisXML or 
> elsewhere.
>
>  
>
> The extent to which dataXML could usefully and easily support spectral 
> libraries is to facilitate that a dataXML file could contain a 
> collection of MS/MS spectra that may have been derived from one or 
> more LC/MS/MS runs. I personally envision that all spectra are at 
> least derived from the same type of instrument
>
> To effectively meet that objective the schema simply needs to support:
>
> 1.       A spectrum name as a string (I expect this would not contain 
> a full path but instead be more like a .dta or .pkl name: 
> runame.firstScanNum.LastScanNum.charge.pkl)
>
> 2.       Spectral parameters on a per spectrum basis: i.e. resolution, 
> dissociation mode, collision energy
>
> 3.       Index attribute expansion where there can be additional 
> attributes other than scan number in the index element: i.e. spectrum 
> Name, precursor m/z, precursor charge. These would be used for sorting 
> and rapid access to selectively retrieve individual scans. Personally 
> I favor the index as a separate file rather than appended to the end 
> as in mzXML.
>
>  
>
> --Karl
>
> ---------------------------------------------------
>
> Karl R. Clauser
>
> Research Scientist III
>
> Broad Institute of MIT and Harvard
>
> 7 Cambridge Center
>
> Cambridge, MA 02142
>
> Ph. 617-324-9719
>
> E-mail: cl...@br... <mailto:cl...@br...>
>
>  
>
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-- 
--
 Dr. Pierre-Alain Binz
 Swiss Institute of Bioinformatics
 Proteome Informatics Group
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 Tel: +41-22-379 50 50
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 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html