Table 3 Comparison of different methods on the control datasets
From: A nonparametric model for quality control of database search results in shotgun proteomics
Instrument type | Methods | Expected FPR = 0.05 | Expected FPR = 0.01 | ||||
|---|---|---|---|---|---|---|---|
| Â | Â | Validated matches/false positives | Actual FPR | Sensitivity (%) | Validated matches/false positives | Actual FPR | Sensitivity (%) |
LCQ | M1 | 652/30 | 0.046 | 74.3 | 581/15 | 0.026 | 69.1 |
| Â | M2 | 735/34 | 0.046 | 84.1 | 587/9 | 0.015 | 69.3 |
| Â | M3 | 765/28 | 0.037 | 87.9 | 699/10 | 0.014 | 82.2 |
LTQ | M1 | 5507/156 | 0.028 | 71.0 | 4761/48 | 0.010 | 62.6 |
| Â | M2 | 5818/197 | 0.034 | 74.6 | 4640/20 | 0.004 | 61.6 |
| Â | M3 | 6681/271 | 0.041 | 85.1 | 5652/61 | 0.011 | 74.2 |
LTQ/FT | M1 | 2554/69 | 0.027 | 83.7 | 2135/30 | 0.014 | 70.9 |
| Â | M2 | 2111/46 | 0.022 | 69.6 | 1411/15 | 0.011 | 46.8 |
| Â | M3 | 2594/67 | 0.026 | 87.5 | 2210/33 | 0.015 | 74.5 |