Menu
▾
▴
Re: [Psidev-pi-dev] Reporting identifications passing threshold
|
From: David C. <dc...@ma...> - 2008-12-15 16:03:00
|
Hi, Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem really looks wrong to me - it's a global value, so we shouldn't have to report it for each spectrum... (Not to be confused with "PI:00250" name="local FDR" which is also under SpectrumIdentificationItem) However, there are arguments for putting it in two separate places: a) <AdditionalSearchParams> You choose a FDR and the search/analysis software only creates a list of peptides within that FDR - therefore it is a 'search' parameter. b) <SpectrumIdentificationList> You do the search against a forward and decoy database. From the results you calculate the global FDR. In this case, I suppose it's part of the results. As far as I'm aware, the net effect for the consumer of the AnalysisXML document is the same. We don't want to allow the same cv term in two places, so I'd vote for having it under <AdditionalSearchParams> Any other thoughts? David Jones, Andy wrote: > Hi all, > > I want to insert the following text into the spec document but the first example > probably will not validate, since this would not be counted as a valid mapping > for AdditionalSearchParams: > > <pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI" value = > "0.01"/> > > Can we update this mapping or someone suggest a suitable example CV term for > setting a threshold for peptide-spectrum matches. > > Also, feel free to suggest any amendments to this text. > > Cheers > Andy > > > > 7.1.4 Reporting peptide and protein identifications passing a significance > threshold > > The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis> have > a mandatory Boolean attribute passThreshold that allows a file producer to > indicate that an identification has passed a given threshold or that it has been > manually validated. Depending on the intended purpose of the file, the file > producer MAY wish to report a number of identifications that fall below the > given significance threshold, for example to allow global statistics to be > performed which is not possible if only identifications passing the threshold > are reported. If the file producer does not want to indicate that a threshold > has been set, all identifications MUST have passThreshold = “true”. Thresholds > for peptide-spectrum matches or for protein identification can be encoded as > instances of <cvParam> within <SpectrumDetectionProtocol> or > <ProteinDetectionProtocol> for example as follows: > > <SpectrumIdentificationProtocol id="SEQUEST_proto" > AnalysisSoftware_ref="SEQUEST_SW"> > <SearchType> > <pf:cvParam accession="PI:00083" name="ms-ms search" > cvRef="PSI-PI"/> > </SearchType> > <AdditionalSearchParams> > <pf:cvParam accession="PI:00364" name="pep:global FDR" > cvRef="PSI-PI" value = "0.01"/> > ... > > > <ProteinDetectionProtocol id="PDP_MascotParser_1" > AnalysisSoftware_ref="AS_mascot_parser"> > <AnalysisParams> > <pf:cvParam accession="PI:00316" name="mascot:SigThreshold" cvRef="PSI-PI" > value="0.05"/> > … > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > 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 |
