Table 4. Numbers of PSMs and Unique Cross-Linked Peptides (in the Parentheses) Identified by XLSearch, xQuest, and Kojak, Separated into Intraprotein and Interprotein Cross-Linksa.
| FDR | methods | E. coli | Expanded E. coli | Human | Expanded Humanb | Expanded Humanc | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||||
| intra | inter | intra | inter | intra | inter | intra | inter | intra | inter | ||
| FDR estimated at PSM level | |||||||||||
| 1% | XLSearch | 134 (38) | 84 (25) | 192 (51) | 115 (33) | 66 (33) | 115 (60) | 74 (36) | 116 (61) | 74 (36) | 119 (63) |
| xQuest | 32 (10) | 38 (10) | 14 (4) | 2 (1) | 40 (21) | 52 (30) | 19 (7) | 18 (10) | 19 (7) | 19 (11) | |
| Kojak | 47 (15) | 23 (8) | 50 (15) | 22 (9) | 63 (23) | 42 (23) | 8 (4) | 7 (5) | 8 (4) | 8 (6) | |
| 5% | XLSearch | 225 (59) | 128 (34) | 260 (67) | 130 (35) | 185 (79) | 231 (113) | 158 (71) | 208 (106) | 158 (71) | 218 (110) |
| xQuest | 108 (35) | 103 (25) | 14 (4) | 2 (1) | 244 (89) | 251 (120) | 44 (21) | 59 (33) | 44 (21) | 60 (34) | |
| Kojak | 54 (15) | 25 (9) | 64 (16) | 25 (9) | 78 (29) | 46 (27) | 61 (22) | 39 (22) | 61 (22) | 45 (28) | |
| FDR estimated at unique peptide pair level | |||||||||||
| 1% | XLSearch | 132 (36) | 84 (25) | 192 (51) | 113 (32) | 66 (33) | 88 (50) | 74 (36) | 109 (58) | 74 (36) | 112 (60) |
| xQuest | 32 (10) | 38 (10) | 14 (4) | 2 (1) | 40 (21) | 52 (30) | 19 (7) | 18 (10) | 19 (7) | 19 (11) | |
| Kojak | 47 (15) | 23 (8) | 50 (15) | 22 (9) | 63 (23) | 42 (23) | 8 (4) | 7 (5) | 8 (4) | 8 (6) | |
| 5% | XLSearch | 134 (38) | 87 (27) | 197 (53) | 115 (33) | 161 (70) | 210 (109) | 103 (49) | 164 (85) | 103 (49) | 170 (87) |
| xQuest | 32 (10) | 38 (10) | 14 (4) | 2 (1) | 44 (21) | 53 (30) | 40 (21) | 52 (30) | 40 (21) | 53 (31) | |
| Kojak | 47 (15) | 23 (8) | 50 (15) | 22 (9) | 71 (25) | 46 (27) | 8 (4) | 7 (5) | 8 (4) | 8 (6) | |
a
FDR was estimated at both the PSM level and the unique peptide pair level and separately for intraprotein and interprotein cross-links. The corresponding Venn diagrams are shown in Figure 4. The searches were performed against 56 ribosomal proteins (E. coli), 56 ribosomal and 34 associated proteins (Expanded E. coli), eight TAF proteins (Human), eight TAF proteins, and 50 arbitrary proteins (Expanded Human).
b
Note that for the search against the Expanded Human database, we separately listed the target–target PSMs that do not contain peptides from the 50 arbitrary proteins, and.
c
Note that for the search against the Expanded Human database, we separately listed the target–target PSMs that include peptides from the 50 arbitrary proteins.