Table 2.
Characteristics of measured and analyzed EndoPro and trypsin datasets.
| Protease | pH | Digestion time | Fragmentation | Byonic semispecific search | ||||
|---|---|---|---|---|---|---|---|---|
| # MS2 scans | #PSMs 0.1 FDR | # unique peptides | # unique proteins | % identification | ||||
| Trypsin | 8.5 | ON | ETD/EThcD/HCD | 163 823 | 109 682 | 35 330 | 5036 | 67% |
| EndoPro | 2 | 1 h | ETD/EThcD/HCD | 152 064 | 54 251 | 13 631 | 2633 | 36% |
| EndoPro | 2 | ON | ETD/EThcD/HCD | 151 115 | 57 722 | 15 264 | 2439 | 38% |
| EndoPro | 5.5 | 1 h | ETD/EThcD/HCD | 155 229 | 68 902 | 18 268 | 2810 | 44% |
| EndoPro | 5.5 | ON | ETD/EThcD/HCD | 155 565 | 60 318 | 17 378 | 2621 | 39% |
| EndoPro cumulative | 613 973 | 241 193 | 38 004 | 4715 | 39% | |||