Table 2. Parameters Used in the Mascot Search Engine for the Analysis of Each Downloaded Project from the PRIDE Database.
| Project Accession | Precursor mass tolerance (ppm) | Fragment mass tolerance (Da) | Missed cleavages | Fixed modifications | Variable modifications |
|---|---|---|---|---|---|
| PXD001468 | 20 | 0.05 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| PXD002367 | 10 | 0.5 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| Acetyl (Protein N-term) | |||||
| PXD001242 | 20 | 0.05 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| PXD000754 | 20 | 1 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| PXD000605 | 20 | 0.05 | 2 | iTRAQ4plex114 (K) | iTRAQ4plex114 (Y) |
| Methylthio (C) | Oxidation (M) | ||||
| PXD000004 | 20 | 0.05 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| Label: 13C(6) (K) | |||||
| PRD000269 | 20 | 0.05 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| PXD002145 | 10 | 0.5 | 2 | Carbamidomethyl (C) | Oxidation (M) |
| Acetyl (Protein N-term) |