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.
