Table 6.
Comparison between searches against databases of different sizes
| Search# | Spectra | Database | PMTol | DB size | EmpiricalFDR fixed | FactFDR fixed | |||
|---|---|---|---|---|---|---|---|---|---|
| Ntarget | FactFDR(%) | p-value(%) | Ntarget | EmpiricalFDR(%) | |||||
| I-1 | ISB-02 | ISB | 2.5 Da | 7,440 | 2329/1009 | 5.8/4.4 | 10.9/30.9 | 2279/1024 | 3.9/5.7 |
| I-3 | ISB-02 | ISB+Yeast | 2.5 Da | 3,019,432 | 1578/602 | 4.7/5.1 | 40.8/50.3 | 1583/596 | 5.1/3.9 |
| I-14 | ISB-02+AB-TC | ISB | 2.5 Da | 7,440 | 2262/984 | 5.8/4.5 | 5.7/34.5 | 2221/995 | 4.0/6.0 |
| I-5 | ISB-02+AB-TC | ISB+Yeast | 2.5 Da | 3,019,432 | 1490/569 | 5.0/5.8 | 50.2/31.2 | 1480/553 | 4.5/4.3 |
| I-7 | ISB-02+AB-TC | ISB+AT | 2.5 Da | 13,475,763 | 1320/441 | 4.6/4.1 | 36.6/38.0 | 1342/464 | 5.8/7.3 |
| Y-5 | Y-Small+AB-TC | Yeast | 30 ppm | 3,011,992 | 3340/2734 | 1.2/1.0 | 30.0/50.1 | 3209/2717 | 0.8/1.0 |
| Y-1 | Y-Small+AB-TC | Yeast+AT | 30 ppm | 16,480,315 | 2574/1988 | 1.0/1.3 | 50.1/22.7 | 2588/1759 | 1.0/0.5 |
As expected, for smaller databases, TDA yielded more resulting PSMs. Fisher p-values were higher than 5% for all cases, which indicates that the FDR estimation via empirical FDR is reliable regardless of the database size.