Hi Bo, Not sure if this is what you need, but the FDR formula at the PSM level is eq. 14 on page 5391 of this paper: Keller, A., Nesvizhskii, A. I., Kolker, E. Aebersold, R., 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74 (20), 5383–5392. It's based on posterior probabilities of the PSMs.
For proteins, the formula is the same, but here the probabilities are those of the proteins (which are based on the modified probabilities of the PSMs). Cheers, Bjorn On Thursday, 24 April 2014 15:53:15 UTC+2, Bo wrote: > > Hi, > Does anyone know TPP how to calculate the PSM-level FDR and peptide-level > FDR? > Many thanks and best regards! > Bo > -- 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.
