[Psidev-pi-dev] OMSSA example doc - a few questions

[Jennifer S. <jen...@ma...>]

Hi,

I am in the process of trying to put together an example instance 
document for OMSSA and have a few questions.  To make things more 
complicated I have gone for an example where I run the search on a 
concatenated forward/reverse database.  At the moment I have all the 
results in the analysisXML file i.e. in the ConceptualMoleculeCollection 
I am listing all proteins and peptides identified including the reverse 
sequences.  I am unsure if (a) I am supposed to be listing all results 
and (b) if all results are supposed to be listed how I mark the reverse 
ones as decoy or does it not matter?

I am also listing all results (forward and reverse) in DataCollection.  
The next step for me would be to calculate false discovery rates based 
upon the OMSSA results and select 'good' peptides, I am not sure where 
these results would be reported? 

A quick question relates to the 'PeptideEvidence'. One of the attributes 
is "pre" as in the previous flanking sequence.  If my peptide is the 
N-terminal peptide what would pre be? pre="" or  pre="-"? or does it not 
matter?

Finally the database searched was a custom database, is there anywhere 
to report how a database was generated?  Sometimes we also search 
peptide databases i.e. the database would have the same number of 
'protein' entries as the original but there would only be one peptide 
per protein would I be able to report how many peptides are in the 
underlying database searched - would it be a cvParam?

Thanks,

Jenny