Re: [Psidev-pi-dev] Fragment ion information

[Angel P. <an...@ma...>]

I'm fine with inclusion of calls.
-a

On Thu, Jul 3, 2008 at 8:57 AM, Lennart Martens <len...@eb...>
wrote:

> Dear PSI-PI'ers,
>
>
> I recently came across a discussion related to the inclusion of fragment
> ions (as called by the search engine during identification) in the
> analysisXML format (see issue 28 on the Google tracker, direct link:
> http://code.google.com/p/psi-pi/issues/detail?id=28).
>
> It somehow seems that popular opinion is against inclusion of this vital
> piece of information, and that makes me very worried. One of the
> comments on the issue page in fact is that fragment ion calling is
> algorithm specific (which is true), and therefore should not be a part
> of analysisXML.
> I'd actually like to use this same datum to strongly argue the other
> way: since the calling is algorithm specific, it is next to impossible
> to reconstruct the original calling after analysisXML export. So
> essentially, a vital piece of information (the ability of the spectrum
> to support the peptide identification as judged by the algorithm) is
> thrown away during analysisXML conversion or output.
>
> I also believe that the difficulty in annotating which fragments are
> called from the spectrum is definitely not insurmountable. The link with
> mzML should be there anyway (otherwise you would not even be able to
> retrieve the spectrum the identification was made from, an unthinkable
> scenario), so inclusion of this is trivial (as in: already there).
> Additionally, the unambiguous reference to the exact peak called in the
> spectrum is also trivial: simply copy in the actual mass - or more
> likely: m/z - in the analysisXML tag. Ion type should be easy enough to
> annotate (there are only so many ion types, and these can be modelled in
> CV), while charge state is a call made by the algorithm anyway, and can
> therefore also be included easily. So this essentially fully backs up
> Andy Jones' suggested tag format on the issue 28 page. And Andy has
> included some other information, such as 'subsequence' and 'theoretical
> mass' which people are free to dicuss the usefulness of (as it probably
> constitutes redundant information).
>
> So my conclusion is: it's relatively easy to do, will capture vital
> information about the identification and how it was established, and
> conserves irreplacable data.
> So consider any weight I might have to be formally thrown behind
> including this in version 1.0!
>
> Let the argument (re-)commence!
>
>
> Cheers,
>
> lnnrt.
>
> -------------------------------------------------------------------------
> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
> Studies have shown that voting for your favorite open source project,
> along with a healthy diet, reduces your potential for chronic lameness
> and boredom. Vote Now at http://www.sourceforge.net/community/cca08
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>



-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility
806 Biological Research Building
421 Curie Blvd.
Philadelphia, PA 19104-6160
215-573-3736