Hi, >From what I understand, the simplest ways to calculate FDR using a Target-Decoy search are:-
1. Run a Concatenate target and decoy database search. The formula would be : 2 *number(decoys)/ number(target+decoys) - See Elias and Gygi , Nat Methods. 2007 Mar;4(3):207-14. 2. Run Separate target and decoy searches. The formula would be: number(decoys)/number(targets). See Kall et al J Proteome Res. 2008 Jan;7(1):29-34 I think your formula should be the first one. Members, please correct me if I am wrong. Regards, Amit Kumar Yadav Senior Research Fellow (SRF-CSIR) IGIB, New Delhi (India) MassWiz Web server MassWiz sourceforge project MassWiki On Wed, Nov 24, 2010 at 6:39 PM, Bjorn <[email protected]> wrote: > > Hello all, > > I am trying to find my way through the different interpretations and > calculations of the FDR, but I'm a bit lost where it comes to the > PeptideProphet. > > So far, I know that the simplest calculation is (decoy_hits/ > target_hits). So, I ran X!tandem on my dataset (target DB + > concatenated decoy DB) and then ran PeptideProphet on the resulting > pep.xml file (not setting the decoy option!). > I then set a certain probability threshold (say 0.85) and looked at > the number of spectra (e.g. 1200 of 1500). Setting the protein text to > decoy gives me, e.g. 50 hits. The FDR for a prob. of 0.85 would then > be 50/1150. If I look at the table displayed in the PeptideProphet, > the FDR I found is almost spot-on with the number in the table. The > thing is that if I lower my probabilty threshold, the FDRs in the > table stay relatively low, while the FDRs I calculate with the above > formula go up. Is there any extra correction being done in the > PeptideProphet (like correct for the percentage of incorrect target > hits (PIT) as described by Kall et al in 2008)? > Or am I missing something vital here? > > Furthermore, how is the estimated number of correct assignments > calculated? I can't seem to find the correct formula to come to that > number? I assume it is related to the surface under the curve plotted > with the correct identifications? > > Many questions, but I hope someone can help me with this. > > Best regards, > > bjorn > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
