Table 2. Comparing Cross-Link Identifications Validated Using the Target–Decoy Approach against the Structural Modela.
| FDR | target–target hits | ||||
|---|---|---|---|---|---|
|
| |||||
| total | distance computable | distance ≥24.0 Å | percentage | ||
| 1% | intraprotein | 132 (36) | 105 (28) | 1 (1) | 0.95% (3.57%) |
| interprotein | 84 (25) | 59 (15) | 3 (3) | 5.08% (20.0%) | |
| 5% | intraprotein | 134 (38) | 107 (30) | 1 (1) | 0.93% (3.33%) |
| interprotein | 87 (27) | 62 (17) | 5 (5) | 8.06% (29.4%) | |
a
The total numbers of PSMs, the numbers of PSMs for which the Cα –Cα distance were computable, and the numbers of PSMs for which the Cα – Cα distance exceeded 24.0 Å are illustrated. The numbers in the parentheses correspond to the unique peptide pairs. The FDR was estimated at the unique peptide-pair level.