Hi all, I am running PeptideProphet, iProphet and ProteinProphet (TPP 4.6.3) on Q Exactive data searched with Comet, Myrimatch and OMSSA. I wondered if the NSP model should be disabled in ProteinProphet when it is enabled in iProphet? I got confused because it seems Petunia enables the NSP model both in iprophet and proteinprophet by default (ie. when xinteract runs with the -ip option).
Another question is that when I compare decoy estimated protein FDRs to ProteinProphet modelled FDRs, ProteinProphet seems a bit optimistic (decoy based FDR of 0.1% corresponds to ~0.02% model FDR). This is with NSP enabled in iProphet and disabled in ProteinProphet. How should I deal with discrepancy, ie. should I take the decoy or probability based FDR to select a probability cutoff? I have attached some examples for a search with myrimatch only. These are the commands I used to generate the graphs: xinteract -Nmyrimatch.pep.xml -OAP -p0 -a%ExperimentFolder% -dDECOY0 -E%ExperimentTag% *.pep.xml InterProphetParser myrimatch.pep.xml myrimatch.ipro.pep.xml ProphetModels.pl -i myrimatch.ipro.pep.xml -k -r 0.25 -d "DECOY1" ProteinProphet myrimatch.ipro.pep.xml myrimatch.prot.xml IPROPHET NONSP ProtProphModels.pl -k -r 0.25 -d DECOY1 -i myrimatch.prot.xml The graphs are: myrimatch_all.ipro.pep_FDR_10pc: PeptideProphet/iProphet decoy vs model FDR, all models enabled myrimatch_nonsp.ipro.pep_FDR_10pc: PeptideProphet/iProphet decoy vs model FDR, NSP model disabled in iProphet myrimatch_nonsp.prot_FDR_5pc: ProteinProphet decoy vs model FDR, NSP model disabled in ProteinProphet myrimatch_all.prot_FDR_5pc: ProteinProphet decoy vs model FDR, NSP model enabled in iProphet and ProteinProphet Thanks in advance! Kind regards, Rene -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
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