Table 1 SWATH acquisition parameters studied during the screening and optimization DoE experiments with upper and lower ranges explored
Experiment | SWATH acquisition parameters | Role | Lower range | Upper range |
|---|---|---|---|---|
Screening design | Protein to deplete (µg) | Continuous | 400 | 600 |
Gradient length (min) | Continuous | 30 | 90 | |
MS/MS accumulation time (ms) | Continuous | 50 | 250 | |
Number of SWATH windows | Continuous | 20 | 83 | |
MS mass range (m/z) | Categorical | 400–800 | 350–1200 | |
MS/MS mass range (m/z) | Categorical | 400–1200 | 100–1800 | |
SWATH window width | Categorical | Fixed | Variable | |
Optimization design | MS/MS accumulation time (ms) | Continuous | 20 | 60 |
Number of SWATH windows | Continuous | 60 | 100 |