Table 12.
Comparison between the single-pass search (the search Y-1) and various two-pass search methods (the searches Y-10 to Y-13)
| Search# | Spectra | Database | PMTol | MSR2 | EmpiricalFDR fixed | FactFDR fixed | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| IsTwoPass | 2th decoy1 | Ntarget | FactFDR(%) | p-value(%) | Ntarget | EmpiricalFDR(%) | |||||
| Y-1 | Y-Small+AB-TC | Yeast+AT | 30 ppm | No | Rev | N/A | 2574/1988 | 1.0/1.3 | 50.1/22.7 | 2588/1759 | 1.0/0.5 |
| Y-10 | Y-Small+AB-TC | Yeast+AT | 30 ppm | Yes | Trad3 | No | 5361/5744 | 15.9/20.1 | 0.0/0.0 | 3260/2655 | 0.6/0.3 |
| Y-11 | Y-Small+AB-TC | Yeast+AT | 30 ppm | Yes | Trad | Yes | 4114/3925 | 7.3/10.1 | 0.0/0.0 | 3102/2320 | 0.9/0.5 |
| Y-12 | Y-Small+AB-TC | Yeast+AT | 30 ppm | Yes | BK4 | No | 3529/3089 | 1.2/1.0 | 24.9/45.0 | 3262/3074 | 0.7/0.9 |
| Y-13 | Y-Small+AB-TC | Yeast+AT | 30 ppm | Yes | BK | Yes | 3137/2514 | 1.1/1.1 | 40.1/39.3 | 3103/2521 | 1.0/0.8 |
For the searches Y-10 and Y-11, the traditional second pass decoy database was used to estimate FDR (see text). For the searches Y-12 and Y-13, the decoy database proposed by Bern et al. [25] was used. Also, for the searches Y-11 and Y-13, the matched spectrum removal (MSR) step was used.
Low Fisher p-values in Y-10 and Y-11 illustrate that using the traditional second pass decoy database results in significant underestimation of the true FDR.
1The decoy database for the second pass search; 2Whether the matched spectrum removal step was used; 3The traditional decoy database; 4The BK decoy database.