Hello, In the MSFragger publication the authors adopt an extended mass model when processing the data with peptide prophet which allows mass-shift-dependent FDR estimation.
I don't really see how you could implement this with the standard versions of peptide prophet - is the version of peptide prophet they used available? In addition, is this a valid option for a small dataset resulting in a couple of thousand PSMs only? The number of PSMs per dM bin might be quite small... Any help would be much appreciated, Alastair -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
