Hi Judy,

Skyline is capable of handling all of these methods of data acquisition. In the cases A and C, the scan header information provides all that Skyline needs to know and therefore the experiment should be set up as "Targeted" in Settings...Transition Settings...Full-Scan...Acquisition Method. You would also need to pay attention to Settings...Transition Settings...Method match tolerance m/z. In the case of wide-window isolation - essentially equivalent of DIA/SWATH - in principle you could make this work by setting setting ...Method match tolerance m/z to be extremely wide but instead might consider setting Settings...Transition Settings...Full-Scan...Acquisition Method to DIA and then defining custom DIA windows depending on your actual instrument method.

Sincerely,
Jake Jaffe

Hi Jake,

Thank you for the help. Have you run multiplexed PRM before like the Figure 2C? Do you know how Thermo Q exactive pair the precursors from the inclusion list?

Thank you,
Judy

It will just proceed down the list in the order that you have the targets.