Table 2 Number of PSMs output by PeptideProphet, Percolator, and OLCS-Ranker
From: A cost-sensitive online learning method for peptide identification
Dataset | Method | FDR = 0.02 | FDR = 0.04 | ||||
|---|---|---|---|---|---|---|---|
Targets | Decoys | Ratio | Targets | Decoys | Ratio | ||
Yeast | PepProphet | 1379 | 13 | 0.206 | 1436 | 29 | 0.214 |
Percolator | 1225 | 12 | 0.183 | 1366 | 27 | 0.204 | |
OLCS-Ranker | 1374 | 13 | 0.205 | 1467 | 29 | 0.219 | |
Ups1 | PepProphet | 506 | 5 | 0.056 | 545 | 11 | 0.061 |
Percolator | 471 | 4 | 0.052 | 554 | 11 | 0.062 | |
OLCS-Ranker | 473 | 4 | 0.053 | 528 | 10 | 0.059 | |
Tal08 | PepProphet | 911 | 9 | 0.092 | 948 | 20 | 0.096 |
Percolator | 1036 | 10 | 0.105 | 1059 | 21 | 0.107 | |
OLCS-Ranker | 1140 | 10 | 0.115 | 1156 | 22 | 0.117 | |
Tal08-large | PepProphet | 14966 | 152 | 0.354 | 15516 | 317 | 0.367 |
Percolator | 15793 | 159 | 0.374 | 16164 | 329 | 0.383 | |
OLCS-Ranker | 15706 | 157 | 0.372 | 16078 | 327 | 0.381 | |
Velos-mips | PepProphet | 116533 | 1177 | 0.558 | 120080 | 2450 | 0.575 |
Percolator | 116046 | 1172 | 0.556 | 120952 | 2468 | 0.579 | |
OLCS-Ranker | 117084 | 1182 | 0.561 | 120033 | 2448 | 0.575 | |
Velos-nomips | PepProphet | 166790 | 1684 | 0.542 | 173935 | 3549 | 0.566 |
Percolator | 165174 | 1668 | 0.537 | 174361 | 3558 | 0.567 | |
OLCS-Ranker | 170722 | 1723 | 0.555 | 177007 | 3611 | 0.576 | |