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

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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: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... <mailto: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
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>              
> 
>             dc...@ma... <mailto:dc...@ma...>
> 
>             http://www.matrixscience.com
> 
>              
> 
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>     --
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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
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>      
> 
>     dc...@ma... <mailto:dc...@ma...>
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>     http://www.matrixscience.com
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>     Matrix Science Ltd. is registered in England and Wales
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>     Company number 3533898
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