Please see the section called "Estimation of FDR" in the iProphet paper found here:
http://www.mcponline.org/content/10/12/M111.007690.long also http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237071/ The tool in TPP Petunia that can be used to do both PSM and Peptide FDR estimation using decoys is found in: Decoy -> Decoy Peptide Validation The tool in TPP Petunia for protein level FDR estimation using decoys Decoy -> Decoy Protein Validation -David On Thu, May 1, 2014 at 10:06 AM, Bjorn <[email protected]> wrote: > 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. > -- 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.
