[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

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

Comment #18 on issue 49 by dcreasy: Issues / schema updates prior to  
version 1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

Sorry, this is not good timing...
We currently have:

<SpectrumIdentificationResult ... >
   <SpectrumIdentificationItem  ... >
     <PeptideEvidence isDecoy="true" DBSequence_Ref="XYZ">

In the existing examples of using decoy, where each  
<SpectrumIdentificationItem>
always has a <PeptideEvidence> this works just fine.

The Mascot examples (which don't currently have a decoy search example)  
show the
possibility of saving all matches to spectra, enabling further statistical  
analysis
of the results. This is done by saving a <SpectrumIdentificationItem>  
without
<PeptideEvidence> for 'junk' matches. However, without the  
<PeptideEvidence> element,
there is no way to know if the match was to a decoy sequence. I think that  
the
isDecoy should be an attribute of <SpectrumIdentificationItem> or possibly  
<Peptide>.
Without this change, I think this means we can't fulfil use case #4 without  
huge file
bloat. Too late to change???

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings