Re: [Psidev-pi-dev] Reporting identifications passing threshold

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Hi David,

> 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)

Agreed but I wasn't suggesting this ;-) I put it under
SpectrumIdentificationProtocol. 

Currently, PI:00364 is set as a child term of:

[Term]
id: PI:00213
name: search result details
def: "Scores and global result characteristics

So I guess it would be fine to map to this from either AdditionalSearchParams or
from SpectrumIdentificationList. Just to be clear, I was suggesting the term be
used for a very specific purpose though - documenting which identifications are
flagged with passThreshold = "true". It shouldn't impact how many results are
actually output by the search engine. I would also vote for putting this as
AdditionalSearchParams.

Cheers,
Andy

> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 15 December 2008 16:03
> To: psi...@li...
> Subject: Re: [Psidev-pi-dev] Reporting identifications passing threshold
> 
> 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"/>
> > 	…
> >
> >
> >
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> --
> David Creasy
> Matrix Science
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