Hi David, I got it. Thank you so much. Best regards! Bo 在 2014年5月2日星期五UTC+8上午2时24分17秒，David Shteynberg写道： > > 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] > <javascript:>>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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > >
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