Table 1. Parameters of the Best DIA-MS Method Per Chromatographic Gradient Tested.
| method ID | gradient (min) | window size (m/z) | placement | mass range (m/z) | cycle time (s) | points per peak | peptide count | peptide CV | protein count | protein CV |
|---|---|---|---|---|---|---|---|---|---|---|
| 120 min–1 | 120 | 16 | staggered | 450–950 | 2.91 | 5.14 (±3.42) | 10,590 (±218.09) | 15.42 (±20.78) | 1678 (±10.44) | 14.94 (±25.24) |
| 120 min–11 | 120 | 1.4 | DDA | 350–1800 | 1.2 | 7486 (±187.09) | 16.05 (±22.27) | 1323 (±24.33) | 19.36 (±25.43) | |
| 60 min–1 | 60 | 16 | staggered | 450–950 | 2.91 | 3.86 (±2.16) | 9053 (±114.9) | 17.6 (±20.92) | 1452 (±12.12) | 17.52 (±23.68) |
| 45 min–1 | 45 | 16 | staggered | 400–1000 | 3.37 | 3.56 (±1.76) | 7951 (±54.01) | 22.52 (±23.55) | 1337 (±19.63) | 22.75 (±28.1) |
| 30 min–1 | 30 | 24 | staggered | 450–950 | 1.95 | 3.88 (±2.06) | 6091 (±18.33) | 17.87 (±22.53) | 1125 (±10.6) | 18.13 (±27.6) |