We need more information. What type of QTOF? Q Exactive is usually achieved with File > Export > Isolation List - Thermo Q Exactive, and using the output as an inclusion list. If you need more than that, I can probably have someone in our lab jump on the thread and explain in more detail.

For Bruker and SCIEX TOF instruments, you can usually use File > Export > Method, and provide a template method (as long as you have instrument control software on the computer) and Skyline will inject the isolation list into the right place in those template methods.

For Waters and Agilent, you again have to rely on File > Export > Isolation list, and if you need more information on how to get the exported files into a template TOF method for PRM, I can try to find someone to give you more detailed information, but it would help to know your TOF instrument. So, I know who to pester.

Good luck with your comparison. Sounds interesting.

--Brendan