The first thing to try is to use File > Export > Transition List to get just the corresponding transition list which Skyline is trying to inject into the Altis template method. Have a close look at the transition list and see if you can figure out what Thermo software is complaining about. Maybe try the operation yourself manually by bringing up the Thermo method editor on the template and trying to import the transition list.

You could also open the transition list in Excel and sort the rows by precursor m/z and product m/z and see if you see any duplicate Q1/Q3 pairs.

These are the best ways to figure out what is going wrong. Let us know when you figure it out if there is something we could be doing better even if it is just a clearer error message.

Good luck. Thanks for posting the screenshot.

--Brendan

Thank you for your rapid response. I exported the transition list and imported it directly to the Altis method, and there were duplicated pairs of precursor and product ions, which caused errors when imported. We are wondering how to adjust the settings or change things from Skyline to prevent it from generating the redundant precursor-product pairs? For the details, please find the errors when we import the transition list created by Skyline.