As of release 3.5, Skyline's small molecule support includes the ability to explicitly set many vendor-specific instrument tuning parameters on a per-precursor basis.
The "Insert Transition List" dialog for small molecules now has columns for importing various vendor-specific values such as "S-Lens", "Cone Voltage", "Declustering Potential" and "Compensation Voltage", along with the previously implemented ability to explicitly set "Collision Energy", "Retention Time" "Retention Time Window", "Drift Time", and "Drift Time High Energy Offset". These values can also be modified in the Document Grid.
These values can also be modified in the document grid for peptides (formerly this was only possible for small molecules).
By default S-Lens values are not written: a new checkbox in the Export Method dialog enables this for appropriate Thermo outputs. On the commandline side, there is a new argument "exp-use-s-lens" for this.