Table 1. LFQbench metrics summary of the dataset TripleTOF 6600 - 64w.
Iteration 1 | Iteration 2 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Median CV of Human |
Number of IDs |
Valid quantification ratios |
Overlap Yeast–Human (arctanh) |
Overlap Ecoli–Human (arctanh) |
Median CV of Human |
Number of IDs |
Valid quantification ratios |
Overlap Yeast–Human (arctanh) |
Overlap Ecoli–Human (arctanh) |
||
peptides | OpenSWATH | 6.5% | 40,726 | 36,098 | 2.12 | 2.24 | 8.2% | 40,728 | 35,944 | 2.10 | 2.26 |
SWATH2.0 | 6.6% | 35,517 | 35,517 | 2.14 | 2.11 | 6.1% | 35,489 | 26,303 | 2.49 | 2.52 | |
Skyline | 7.4% | 40,804 | 34,103 | 1.91 | 1.85 | 6.9% | 42,517 | 37,977 | 2.13 | 2.14 | |
Spectronaut | 5.9% | 42,439 | 37,120 | 1.97 | 1.90 | 6.2% | 42,325 | 36,292 | 2.11 | 2.26 | |
DIA-Umpire | 13.2% | 36,332 | 28,785 | 1.74 | 1.98 | 12.9% | 36,249 | 25,677 | 1.82 | 2.18 | |
proteins | OpenSWATH | 5.4% | 4,632 | 4,343 | 2.30 | 2.56 | 6.4% | 4,636 | 4,352 | 2.51 | 2.60 |
SWATH2.0 | 5.6% | 4,323 | 4,323 | 2.37 | 2.36 | 6.1% | 3,946 | 3,371 | 2.42 | 2.56 | |
SWATH2.0 (built-in) | 6.0% | 6,178 | 6,178 | 2.23 | 2.03 | ||||||
Skyline | 5.9% | 4,518 | 4,140 | 2.03 | 2.15 | 5.5% | 4,692 | 4,456 | 2.37 | 2.43 | |
Spectronaut | 3.3% | 4,692 | 4,346 | 2.13 | 2.18 | 3.3% | 4,675 | 4,300 | 2.31 | 2.50 | |
DIA-Umpire | 12.0% | 3,795 | 3,379 | 2.12 | 2.30 | 12.3% | 3,673 | 3,111 | 2.13 | 2.85 | |
DIA-Umpire (built-in) | 13.1% | 4,849 | 4,489 | 1.78 | 1.94 |