Hi all,
I have a question about FDR estimation for protein identification (using reversed decoy database together with target database in a single file). I can estimate the probability threshold for peptides to get for example 1% FDR. My question is how to use this peptide probability threshold for protein identification? Do I have to filter out peptides below the probability threshold before ProteinProphet analysis(how?)? Or do I have to run ProteinProphet, then filter out peptides below the threshold and then estimate FDR for proteins? Or just etimate FDR on the protein level? What is the right way ? This is probably a silly question but I am confused about information I found in different papers, sometimes there are FDR estimations on the protein level only, sometimes there are FDR for peptides only and sometimes one can found info like „FDRs for both peptides and proteins were x%“. Thank you Pavel -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
