Table II. Spectra identified by incorporation of the detected modifications into sequence database search and by peptide propagation among spectral pairs with PEP ≤ 0.02 for the ISB standard protein mix data set. (*For each detected modification, the number of identified spectra is the number of spectra identified as peptides with this modification; for semispecific digestion, it is the number of spectra identified as semitryptic peptides.).
| Digestion mode | Considered modification | Number of spectra identified as modified/semitryptic peptides* |
|
|---|---|---|---|
| Database search | Propagation (PEP ≤ 0.02) | ||
| Full-specific | Calcium (D, E and peptide C-terminus) | 142 | 488 |
| Sodium (D, E and peptide C-terminus) | 205 | 372 | |
| Deamidation (N and Q) | 165 | 98 | |
| Carbamidomethyl DTT (C) | 82 | 0 | |
| Dehydration (T, S, D, and E at peptide N-termimus) | 14 | 0 | |
| Acetaldehyde (H, K and peptide N-termimus) | 38 | 0 | |
| Semispecific | None | 218 | 14 |
| Total | 864 | 972 | |