Table 3.
Comparison of Separation Methods According to the Number of Total Proteins, Unique Peptides, Total Peptides, Average Percent Sequence Coverage, Average Protein Scores (log E), and False Discovery Rate (FDR)
| Total Proteins |
||||||||
|---|---|---|---|---|---|---|---|---|
| Mascot | X!Tandem | Unique Peptides | Total Peptides | % Unique/Total | Avg % Sequence Coverage | Avg Protein Scores (log E) | %FDR | |
| pH-RP | 266 | 299 | 749 | 870 | 86.1 | 13.1 | −16.3 | 1.16 |
| cProt | 241 | 252 | 731 | 1036 | 70.6 | 19.4 | −19.3 | 1.03 |
| hrProt+Urea | 255 | 287 | 977 | 1509 | 64.7 | 19.3 | −24.9 | 1.05 |
| hrProt | 281 | 271 | 1110 | 1848 | 60.1 | 19.8 | −27.3 | 1.07 |
| Offline SCX | 81 | 105 | 172 | 232 | 74.1 | 8.3 | −8.1 | 1.35 |
| Online SCX | 178 | 199 | 369 | 857 | 43.1 | 9.4 | −9.7 | 1.17 |
| Gel | 139 | 157 | 354 | 476 | 74.4 | 9.5 | −12.2 | 1.35 |