Table 4. Average Percentage Recall at 99% Precision for Eight Model-Peptide Spectrum Datasets with Respect to Various Synthetic Reference Labels.
| Reference | Threshold | Positive/Negative | X!Tandem | Mascot | MS search | HMM |
|---|---|---|---|---|---|---|
| X!Tandem (E-value) | 0.1 | 93/12 | — | 59% | 54% | 53% |
| 0.05 | 90/15 | — | 56% | 54% | 54% | |
| 0.01 | 79/26 | — | 48% | 37% | 43% | |
| 0.001 | 61/44 | — | 38% | 14% | 32% | |
| Mascot (E-value) | 0.1 | 38/67 | 38% | — | 33% | 40% |
| 0.05 | 34/71 | 42% | — | 35% | 34% | |
| 0.01 | 26/79 | 45% | — | 26% | 33% | |
| MS search (match factor) | 0.8 | 52/63 | 46% | 61% | — | 60% |
| 0.9 | 62/53 | 36% | 55% | — | 49% | |
| 0.95 | 72/43 | 32% | 42% | — | 46% |
Training spectra and spectra with no reference score excluded.