[Psidev-pi-dev] Issue 45 in psi-pi: Number of peptides / proteins to be reported

[<cod...@go...>]

Comment #1 on issue 45 by andrewrobertjones: Number of peptides / proteins  
to be reported
http://code.google.com/p/psi-pi/issues/detail?id=45

I think we can support this for SpectrumIdentifications with no schema  
change. We
can encourage data producers to produce large number of spectrum  
identifications.
The identifications deemed "correct" are the ones referenced from
ProteinDetectionHypotheses. This then also supports the use case of peptide
identification scores being boosted once a protein detection has been made.  
PRIDE
can make a call on how many of the SpectrumIdentifications to load.

This does not solve the FDR problem for proteins though. However, I think  
the
solution of creating two different instance documents would be okay. If  
sending to
PRIDE, just send the list of proteins found. If using analysisXML as an  
intermediate
format, send a long list of proteins (and peptides) with no set criteria  
for what
is "correct".

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