Re: [Psidev-pi-dev] AnalysisXML PMF Example

[Jones, A. <And...@li...>]

Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.

The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.

I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.

Cheers
Andy

 



> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 16 October 2008 13:54
> To: psi...@li...
> Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
> 
> Hi Andy,
> 
> For PMF, with Mascot, (and all other search engines as far as I know),
> there is no score assigned to matching a single peak to an individual
> peptide. A score for one peak in isolation would have little meaning -
> you can only really score the match of the complete spectrum.
> 
> David
> 
> Jones, Andy wrote:
> > Hi David,
> >
> > You may be right that the parameter should be optionally anyway, but in this
> > particular example is there not some score assigned to the peptide-spectrum
> > identification?
> >
> > In the equivalent MS/MS example, we have:
> >
> >             <pf:cvParam accession="PI:00171" name="mascot:score"
> > cvRef="PSI-PI" value="62.72" />
> >             <pf:cvParam accession="PI:00172" name="mascot:expectation value"
> > cvRef="PSI-PI" value="0.000863428353297988" />
> >             <pf:cvParam accession="PI:99999" name="mascot_rank"
> > cvRef="PSI-PI" value="1" />
> >
> > Are the same sort of scores not valid for PMF as well...?
> >
> > Cheers
> > Andy
> >
> >
> >> -----Original Message-----
> >> From: David Creasy [mailto:dc...@ma...]
> >> Sent: 16 October 2008 12:29
> >> To: psi...@li...
> >> Subject: [Psidev-pi-dev] AnalysisXML PMF Example
> >>
> >> Hi All,
> >>
> >> There's an example PMF file here:
> >>
> >> http://code.google.com/p/psi-
> pi/source/browse/trunk/examples/PMF_example.axml
> >>
> >> The only small problem that I can see is that for
> >>  <SpectrumIdentificationItem>
> >>
> >> the schema has:
> >>   <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
> >> maxOccurs="unbounded"/>
> >>   <xsd:element ref="pf:Param" maxOccurs="unbounded"/>
> >>
> >> and I can't think of any required CV here
> >>
> >> To find it, search for
> >> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
> >> to say here here"
> >>
> >> I suggest that we have minOccurs=0 for pfParam here unless anyone
> disagrees?
> >>
> >> David
> >>
> >> --
> >> David Creasy
> >> Matrix Science
> >> 64 Baker Street
> >> London W1U 7GB, UK
> >> Tel: +44 (0)20 7486 1050
> >> Fax: +44 (0)20 7224 1344
> >>
> >> dc...@ma...
> >> http://www.matrixscience.com
> >>
> >> Matrix Science Ltd. is registered in England and Wales
> >> Company number 3533898
> >>
> >>
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> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> dc...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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