Hello all, I am using the new TPP 4.7.1 and running database searches using both Tandem and Comet, which I then plan to analyze using PeptideProphet, InterProphet, ProteinProphet, and PTMProphet. My question is about the best practice for determining peptide probability filters before submitting the peptides to ProteinProphet.
Is using the default filter of 0.05 on the the PeptideProphet interface appropriate? Or should it be based on the roc error rates from the output pep.xml file? Also, is it appropriate to filter the peptides based on the InterProphet probabilities? And if so, is there a command line option to do so through the TPP interface? Thank you, Kirill Borziak -- 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. For more options, visit https://groups.google.com/d/optout.
