Table 4.
Expected errors
| Case | Expected errors Plimit = 0.9 | Expected errors Plimit = 0.95 | Expected errors Plimit = 0.99 |
| MS/MS Pi ≥ Plimit | 0.00915 (9%) | 0.00517 (5%) | 0.00137 (1%) |
| MS/MS Pi ≥ Plimit, Npeptide observed > 1 | 0.00884 (9%) | 0.00506 (5%) | 0.00136 (1%) |
| Consensus peptide best Pi, Pi ≥ Plimit | 0.01027 (10%) | 0.00510 (5%) | 0.00120 (1%) |
| Consensus peptide best Pi, Pi ≥ Plimit, Npeptide observed >1 | 0.00272 (3%) | 0.00215 (2%) | 0.00078 (1%) |
Expected errors in the Saccharomyces PeptideAtlas are calculated for four cases and lower probability limits (Plimit = 0.9, 0.95, 0.99): the assigned probability P of each MS/MS is used for all Pi ≥ Plimit; the assigned probability P of each MS/MS is used for all Pi ≥ Plimit where the associated peptide has been seen in the S. cerevisiae PeptideAtlas more than once'; the best probability for each unique peptide sequence is used for all Pi ≥ Plimit; the best probability for each unique peptide sequence is used for all Pi ≥ Plimit when the peptide has been seen in the S. cerevisiae PeptideAtlas more than once.