Table 1. LFQbench metrics summary of the dataset TripleTOF 6600 - 64w.
Number of protein and peptide identifications, number of valid quantification ratios and calculated hyperbolic arctangents (atanh) transformed AUQC values for separation between (yeast vs. human) and (E.coli vs human) for the dataset TripleTOF 6600 - 64 windows. A valid quantification ratio is defined in LFQbench as the ratio of a peptide or protein present in at least one technical replicate in both samples A and B that falls into a validity range (defined as the range of expectation (a maximum difference of 5 standard deviations from the average) defined by the sample set composition and the spread of the log2-ratios observed for each species. Very few cases (if any) fall out of this range, as it can be checked at the LFQbench logs (metrics file) under the “invalid, out of validity range” section. For better readability of the separation values, a color scale is applied to all separation values, from full red (worst separation value of all shown) to full green (best separation value of all shown). Raw AUQC values for separation are provided in Supplementary Table 2.
| 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 | ||||||