From: A nonparametric model for quality control of database search results in shotgun proteomics
Instrument type | Charge state | Expected FPR = 0.05 | Expected FPR = 0.01 | ||||
---|---|---|---|---|---|---|---|
 |  | Total matches/false positive matches | Actual FPR | Estimated FPR | Total matches/false positive matches | Actual FPR | Estimated FPR |
LCQ | +1 | 62/3 | 0.048 | 0.030 | 57/2 | 0.035 | 0.000 |
 | +2 | 521/23 | 0.044 | 0.049 | 464/6 | 0.012 | 0.009 |
 | +3 | 181/2 | 0.011 | 0.043 | 178/2 | 0.011 | 0.000 |
LTQ | +1 | 447/43 | 0.096 | 0.048 | 242/9 | 0.037 | 0.008 |
 | +2 | 4,623/169 | 0.037 | 0.050 | 3,961/26 | 0.007 | 0.010 |
 | +3 | 1,611/59 | 0.037 | 0.050 | 1,449/26 | 0.018 | 0.010 |
LTQ/FT | +1 | 168/18 | 0.107 | 0.047 | 124/12 | 0.097 | 0.000 |
 | +2 | 1,861/43 | 0.023 | 0.049 | 1,543/14 | 0.009 | 0.009 |
 | +3 | 565/6 | 0.011 | 0.048 | 543/7 | 0.007 | 0.007 |