Table IV.
Search results of a large scale data set filtered by mass accuracy of the parent ion, the peptide length, missed cleavage rules, and charge
| Search methoda | Peptide IDsb | MH+ | MH22+ | MH33+ | Unique peptides | Protein IDs (1-pep cases)c |
|---|---|---|---|---|---|---|
| Mascot | ||||||
| Normal | 46,603 | 4,179 | 23,745 | 18,679 | 7,717 | 1,760 (732) |
| Decoy | 1,881 | 346 | 987 | 548 | 1,069 | 1,017 (971) |
| FDR (%) | 4.0 | 8.3 | 4.2 | 2.9 | 13.9 | 58 |
| Sequest | ||||||
| Normal | 47,344 | 4,115 | 24,368 | 18,861 | 7,861 | 1,730 (689) |
| Decoy | 1,754 | 242 | 975 | 537 | 931 | 873 (824) |
| FDR (%) | 3.7 | 5.9 | 4.0 | 2.9 | 12 | 50 |
| SM consensus | ||||||
| Normal | 44,303 | 3,877 | 23,111 | 17,315 | 7,227 | 1,441 (449) |
| Decoy | 427 | 60 | 254 | 113 | 216 | 186 (183) |
| FDR (%) | 1.0 | 1.6 | 1.1 | 0.7 | 3.0 | 13 |
| XM consensus | ||||||
| Normal | 37,589 | 3,008 | 19,836 | 14,745 | 6,640 | 1,359 (438) |
| Decoy | 185 | 37 | 134 | 14 | 81 | 80 (79) |
| FDR (%) | 0.5 | 1.2 | 0.7 | 0.1 | 1.2 | 5.9 |
Results are shown for Mascot search and consensus between Sequest and Mascot using the IPI human database or decoy database and consensus between X!Hunter and Mascot where X!Hunter searches xSS and decoy xSS. There were 90,411 total MS/MS in this data set. For all search results, the assignments were filtered to allow charge up to 3, at least 9 amino acids, following missed cleavage rules, and parent ion mass accuracy within −2 to +7 ppm.
Total MS/MS identified are shown along with the breakdown of MH+, MH22+, and MH33+ cases and total unique peptide sequences.
The total number of protein assignments accepted by these filters is shown, and in parentheses the number of cases that are supported by only one peptide (1-pep cases) is shown. For example, there were 1,760 proteins found in the normal Mascot search of which 732 were protein identifications (IDs) supported by only one peptide.