Table 1.
Transition settings used in Skyline when importing hybrid-DIA or SureQuant data
| Transition settings | HybridDIA | SureQuant | |
|---|---|---|---|
| Full-Scan | |||
| MS filtering | |||
| Isotope peaks included | None | Count | |
| Peaks | NA | 1 | |
| Precursor mass analyzer | NA | Orbitrap | |
| Resolving power, At | NA | 60,000, 400 mz | |
| MS/MS filtering | |||
| Acquisition method | PRM | SureQuant | |
| Product mass analyzer | Orbitrap | Centroided | |
| Resolving power, At | 30,000, 400 mz | ||
| Mass accuracy | 10 ppm | ||
| Include all matching scans | TRUE | TRUE | |
| Filter | |||
| Peptides | |||
| Precursor charges | 2,3,4 | 2,3,4 | |
| Ion charges | 1,2,3,4 | 1,2,3,4 | |
| Ion types | y | y,b | |
| Instrument | |||
| Min m/z | 160 | 160 | |
| Max m/z | 3000 | 3000 | |
| Method match tolerance m/z | 0.001 | 0.001 | |
| Triggered chromatogram acquisition | FALSE | TRUE | |