Table 2. Comparison of Percolator and Q-ranker on 17 and 37 feature data sets.
Each entry in the table indicates the number of accepted PSMs for the given algorithm (column) on the given data set at the given specified q value (row). Entries in boldface indicate that this algorithm performed better than the other algorithm for this data set and q value threshold.
| 17 features | 37 features | ||||
|---|---|---|---|---|---|
| Data set | q value | Percolator | Q-ranker | Percolator | Q-ranker |
| Yeast trypsin | 0.01 | 5917 | 5885 | 5983 | 6072 |
| 0.05 | 6793 | 6940 | 6813 | 7501 | |
| 0.1 | 7168 | 7610 | 7200 | 8430 | |
|
| |||||
| Yeast elastase | 0.01 | 1389 | 1380 | 1491 | 1615 |
| 0.05 | 1806 | 1851 | 1958 | 2140 | |
| 0.1 | 2103 | 2196 | 2301 | 2561 | |
|
| |||||
| Yeast chymotrypsin | 0.01 | 2077 | 2086 | 2158 | 2312 |
| 0.05 | 2576 | 2620 | 2680 | 2844 | |
| 0.1 | 2914 | 2961 | 3057 | 3214 | |
|
| |||||
| Worm trypsin | 0.01 | 5116 | 5031 | 5192 | 5238 |
| 0.05 | 5864 | 6119 | 5830 | 6419 | |
| 0.1 | 6169 | 6730 | 6146 | 7128 | |