As I might have whined about in the past, making pasefDIA windows can be some tricky business. We gave up and had an expert come in, load up his method, and we just run that one. Some other group wasn't satisfied with that method and made a program to make optimal methods!
The program is really straight-forward to install and run on what appears to be every operating system and you can get it here.
The dividends for optimizing windows for phosphoproteomics shown in the study are seriously impressive compared to just running a canned method.