Hi, I have a question about acceptable protein group probability and FDR settings. Is it acceptable to use protein hits with lower protein group probability (eg 50%) if it gives an estimated FDR (as calculated by looking at the decoys) of ~1%? If it is acceptable, why do all the papers simply report protein group probability >= 90%?
Is it not acceptable to report things from an FDR perspective and then state that the score cutoff (ie the probabilty cutoff) to achieve this was 50%? Or does "50%" mean that half of the protein are probably not true (which does not seem accurate based on the decoy FDR estimations....)? Can we rely on such proteins (with 1%FDR cutoff but low protein group/low peptide probability (eg. 50%)) to be a true hit from the spectrum standpoint? Any input on acceptability/reliability of low probability hits (with 1% FDR cutoff) are welcome. Thanks Vidya -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/olsoZQfY3TgJ. 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.
