Dear all, I have a dataset that I was trying to apply both peptide-level and protein-level FDR. I have found some publications which set for example a FDR below 1% for protein and peptide assignments, and I was wondering how it was done. Can someone help me with this?
1. Is it possible to filter out peptides below the probability threshold (1% FDR in PeptideProphet) before ProteinProphet analysis? In this case, only the list of peptides matching this cutoff would be used to assemble the list of proteins with ProteinProphet. 2. The other option would be filtering peptides after ProteinProphet, based on the probabilities calculated in PeptideProphet. Is it possible? I have noticed that ProteinProphet does not allow to filter out peptides based on PeptideProphet calculated FDR. So, is it possible to apply both peptide-level FDR based on PeptideProphet and protein-level FDR based on ProteinProphet, for the same dataset? Thank you!! Luciana -- 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/d/optout.
