Table 2. Number of peptides, proteins and protein groups that were positively identified with at least 1 peptide and 99% confidence with Mascot, Sequest and the combination of the two search engines.
| Fractionation approach | MASCOT | SEQUEST | MASCOT+SEQUEST | ||||||
| Peptides | Proteins | Protein Groups | Peptides | Proteins | Protein Groups | Peptides | Proteins | Protein Groups | |
| ProteoMiner | 363 | 147 | 72 | 1551 | 305 | 136 | 1914 | 318 | 139 |
| ProteoPrep20 | 897 | 232 | 131 | 1798 | 323 | 183 | 2695 | 334 | 186 |
| ProteoExtract+ProteoPrep20 | 861 | 258 | 112 | 1668 | 418 | 161 | 2529 | 429 | 163 |