Hi Peter, For more information on what Mike explains, I recommend this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773710/ Also, be careful about distinguishing whether your FDR<=1% is at the unique peptide level or the peptide spectrum match (PSM) level. The same phenomenon occurs between PSM FDR and unique peptide FDR as between unique peptide FDR and protein FDR. Namely, true discoveries are more likely to be repeated, and therefore 1% FDR at the PSM level will grow above 1% for unique peptides and again further for proteins, as Mike noted. Your choice to include only proteins with >1 hit does improve this growth in FDR, by applying a secondary filter, but it is by no means foolproof with modern mass spectrometers and multi-run data sets, depending on the number of spectra you collected versus the number of proteins considered in your search. I have seen million spectrum data sets where FDR was seriously underestimated against a human FASTA with proteins for ~23,000 genes. A good way to gain some insight on your true FDR is to have decoy proteins in your FASTA that are never exposed to any of your search criteria. This allows you to double-check FDR estimates from the statistical tools you use. Once you gain familiarity with your tools, this may be come less necessary, but I have seen statistical tools get these numbers wrong, for exactly these reasons. Good luck with your FDR statistics. --Brendan On Tuesday, November 26, 2013 8:52:25 PM UTC-8, zion wrote: > > Dear All: > > If there are some confident peptide ids at FDR<=1% at the peptide level, > when inferring proteins by confident peptides and at least one unique > peptide, CAN i say that at the protein level, its FDR<=1%? > Many thanks, > > -Peter > -- 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/groups/opt_out.
