[Psidev-pi-dev] Reporting identifications passing threshold

[Jones, A. <And...@li...>]

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"/>
	…