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

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> Is the PMF example any clearer now?
> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml

Looks good to me now. I think there's a chance that people may find the way
results are separated into SpectrumIdentificationItems and ProteinHypotheses
slightly confusing since the separation makes less sense for PMF than MS/MS but
we probably have to live with this if we want to re-use the same general model
structures.

> For the MS-MS, I wonder if we should have 'rank' as an attribute for
> <SpectrumIdentificationItem> rather than using CV since I think it will
> be common across all search engines?
> (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment).

I'm in favour of this change, although it would have to be an optional attribute
(and well documented) since it makes no sense for PMF data.

Cheers
Andy

> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 17 October 2008 12:53
> To: Jones, Andy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
> 
> I've updated the four Mascot MSMS examples and the PMF example as
> discussed in the call.
> 
> Is the PMF example any clearer now?
> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml
> 
> Corresponding Mascot report can be seen here:
> http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat
> 
> For the MS-MS, I wonder if we should have 'rank' as an attribute for
> <SpectrumIdentificationItem> rather than using CV since I think it will
> be common across all search engines?
> (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment).
> 
> David
> 
> Jones, Andy wrote:
> > New schema uploaded by SVN with changes agreed on the call:
> >
> >
> >
> >
> >
> > - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle
> > PMF data)
> >
> > - Altered documentation for SpectrumIdentificationItem to clarify that
> > this is a single peptide-spectrum identification
> >
> > - Altered documentation for SpectrumIdentificationResult – one
> > SpectrumIdentificationResult for one spectrum
> >
> > - Moved spectrumID and SpectraData_ref as attributes of
> > SpectrumIdentificationResult, and made these composite unique, removed
> > SpectrumElement
> >
> >
> >
> >
> >
> > Andy
> >
> >
> >
> >
> >
> > *From:* Pierre-Alain Binz [mailto:pie...@is...]
> > *Sent:* 16 October 2008 14:26
> > *To:* Jones, Andy
> > *Cc:* psi...@li...
> > *Subject:* Re: [Psidev-pi-dev] AnalysisXML PMF Example
> >
> >
> >
> > Actually, there might be a score associated with each peptide - peak
> > couple, similar to "weights" that coulld be attributed to a specific
> > fragment ion match in a MS/MS spectrum. But at the end, even if a
> > software goes through this, and maybe scores the peptides in an
> > intermediary process, it will at the end always link a spectrum with one
> > or more molecule(s) (in the case of PMF the molecule(s) is(are)
> > proteins). It can annotate the spectrum, either with potential peptides
> > of fragments, respectively. Anyway, we have not encoded any scores to
> > the interpretation of fragment ions in MS/MS spectra. Similarly, we
> > wouldn't do it for PMF. Annotation is the sole point of discussion,
> > which I think we want to postone for v2, right?
> >
> >
> > Pierre-Alain
> >
> > Jones, Andy wrote:
> >
> > 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... <mailto:psidev-pi-
> de...@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... <mailto:psidev-pi-
> de...@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... <mailto: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... <mailto: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