Dear Skyline users,
Can someone help me with understanding and choosing the right settings to process Waters DIA data acquired in MSe with SONAR option?
So far, I was always using Acquisition method: DIA with Isolation scheme: All Ions, when using Waters MSe data.
I have recently added SONAR acquisition mode: Quadrupole scan, 400-900 m/z with 50 Da windows, which means according to Waters terminology, 200 bins/500 Da * 50 = 20 bins.
I was wondering if I need to process this data as SWATH (with windows of 20Da) or still as All ions?
The "SWATH" approach does not seem to work in extracting MSMS data.
Any recommendation or confirmation about the isolation scheme to chose in SKYLINE?
Thanks in advance for your help
Christophe Folly