Table 4.
Automated versus manual peptide and phosphosite assignments
| Automated Curation with ProPhosSI |
||||
|---|---|---|---|---|
| Phosphopeptides |
Phosphosites |
|||
| Pass | Fail | Pass | Fail | |
| Orbitrap (all PSM) | ||||
| Manual Curation | ||||
| Pass | 60 | 17 | 41 | 5 |
| Fail | 12 | 79 | 6 | 13 |
| Q-Star (all PSM) | ||||
| Manual Curation | ||||
| Pass | 101 | 52 | 69 | 17 |
| Fail | 19 | 161 | 17 | 33 |
| Orbitrap (Rank 1 PSM) | ||||
| Manual Curation | ||||
| Pass | 32 | 5 | 31 | 3 |
| Fail | 6 | 37 | 2 | 2 |
| Q-star (Rank 1 PSM) | ||||
| Manual curation | ||||
| Pass | 53 | 30 | 53 | 15 |
| Fail | 9 | 58 | 2 | 2 |
The results from independent manual curation were compared with results from the automated validation. Each individual PSM and site observation is considered for each experiment and additionally for the subset of data that only includes top ranked MASCOT PSMs.