[Psidev-ms-dev] [Fwd: Re: [Psidev-gps-dev] PepXML]

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

-------- Original Message --------
Subject: Re: [Psidev-gps-dev] PepXML
Date: Tue, 03 May 2005 10:12:17 +0100
From: Chris Taylor <ch...@eb...>
To: psi...@li...

Hiya.

PepXML is (when considered together with protXML) a functional
equivalent to what will be mzIdent, but currently it is not clear how
close they will be to each other. mzIdent may itself (as a result of
discussions in Siena, that included an ISB representative) be split into
two parts; 'first-level' inferences -- your direct conclusions about
'what flew down you mass spec', allowing us to consider
non-proteomics-specific applications also such as metabolomics or
lipidomics; and 'second-level' inferences -- what (in the world of
peptides and other protein-related thingies) you assert about the
content of your source material (which may have been trypsin-digested or
whatever). No current name for the second format afaik and as I say it
is not yet settled, just likely.

Iirc (and forgice me ISBers if this is waaay off) there is some
redundancy (in the normal form database sense) between pepXML and
protXML, so that they can best do the jobs they are intended for, which
is to sit comfortably in the 'Trans-Proteomic Pipeline' from ISB (an
inter-compatible suite of tools and formats).

Cheers, Chris.


Arn...@sa... wrote:
> Hello,
> 
> Any idea how PepXML fits into the PSI standards - is the predecessor of mzIdent?
> 
> Any clarification is welcome.
> 
> 	+kind regards,
> 
> 	Arne
> 
> 
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~