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Re: [Psidev-pi-dev] AnalysisXML PMF Example
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From: David C. <dc...@ma...> - 2008-10-16 12:53:46
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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 >> >> >> ------------------------------------------------------------------------- >> 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 >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------- > 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 > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- 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 |
