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Support for peptide-level properties in future versions #80

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
In discussion with Lukas Kall, he pointed out to me that it appears mzid 
appears to have limited support for capturing properties of peptide 
identification (as opposed to PSMs). q-values, local FDR, p-values etc can all 
be calculated for peptides (after redundant PSM info has been removed). It is 
possible to envisage workarounds for encoding such values on all PSMs for a 
given peptide or the best PSM for a given peptide, but neither situation is 
ideal.

If and when there is an mzid version 2, this is something we might consider for 
inclusion

Original issue reported on code.google.com by andrewro...@googlemail.com on 21 Aug 2013 at 3:23

GoogleCodeExporter commented 8 years ago 
We have an encoding for how to do this in the mzidLibrary, using cvParams - 
placing scores on _every_ PSM (independent of rank or score) supporting the 
same peptide, then we need to add a CvParam for "best PSM per peptide", plus a 
note in specification doc about doing this an example file

Original comment by andrewro...@googlemail.com on 31 Jan 2014 at 4:31