Hi,
We're evaluating some Astral data with Skyline doc previously optimized for PRM on Lumos Fusion (MS2 filtering matched Fusion Orbi res 60K, At 400 m/z and selected PRM and Orbitrap as instrument in the MS2 filtering). I would like to know if you've observed any issues or have experience with Astral run in targeted mode. We use the latest Skyline Daily build Skyline-daily (64-bit) 24.1.1.202 (c511d22bf). We noticed the Astral data seems very noisy with very choppy peak shape so curious if alternate instrument selection (under full scan filter settings), resolution, etc. would improve this (we already have Savitzky-Golay smoothing active). The Astral experiment acquires targeted MS2 scans for ~60 peptide precursors. The Astral method has Experiment 1 and 2 in parallel: Exp 1 set as Orbi for full scan MS and resolution of 240K, while Exp 2 Astral MS2 scans were set for 1.6Da isolation and 20ms injection. Should Skyline MS2 filter be PRM & Orbitrap or should it be TOF (PRM?)? What would be optimum resolution for Astral MS2...80K? Are there any other settings we should be concerned with, especially since this instrument is scanning so much faster than our older instrument?
Thanks!
Monica