To learn more about using Skyline with SureQuant take a look at this tutorial. Here is the supplemental data for the tutorial.
As of Skyline-Daily 18.104.22.168, Skyline-Daily has support for "Triggered Acquisition" methods.
A Triggered Acquisition method is one where the mass spectrometer has been told to begin collecting MS2 scans for one analyte when the mass spectrometer sees particular transitions for a different precursor.
This will enable Skyline to work better with assays such as Thermo's SureQuant Targeted Mass Spec Assay Kits
The Transition Settings > Instrument tab will have a "Triggered Acquisition" checkbox which tells Skyline that there may be large gaps between the points in an analyte's chromatograms.
When Triggered Acquisition is selected, Skyline will detect these gaps and make sure that integration boundaries do not cross these gaps. Also, Skyline will perform no background subtraction when Triggered Acquisition is enabled.
For more information, see the attached PowerPoint.