If the MS/MS Filtering Acquisition Method is "PRM" and "Retention Time Filtering" is set to either "Use only scans within X minutes of MS/MS IDs" or "Use only scans within X minutes of predicted RT", then Skyline should change the text of the option to red and the tooltip should explain why it's a bad idea to use this with PRM.

Also if the acquisition method is changed to "PRM" then the Retention time filtering option should be changed to "Include all matching scans", although the original value of that option should be remembered so that if they subsequently change the acquisition method to something else the Retention time filtering setting can be set back to the value it had before.