Hi Dietmar,
You are not the first to have requested this. I have posted this as an issue to our issues list:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=453

With any luck we will implement a solution by the next public release. Sorry we don't already have this for you.

Thanks for your feedback!

--Brendan

I also wish for this, any chance to get my vote as well? :)

Skyfall,

We have not implemented any enhancements to the way that enzymes work in Skyline but we have tried to improve the experience of working with non-tryptic peptides (or, specifically, peptides which do not match the currently chosen enzyme).

Specifically, if you have a spectral library which contains all of the peptides that you are interested in, you can use the "Add All" button in the Spectral Library Explorer to add all of the peptides from the library to the document regardless of whether the peptide could have been generated by the current enzyme.
You can get to the Spectral Library Explorer with the "View > Spectral Libraries" menu item in Skyline 24.1 or "View > Libraries > Library Explorer" in Skyline-daily.

A different way of getting arbitrary peptides into the document is using the "Edit > Insert > Peptides" menu item.

After you have all of these peptides in your document you can assort them into the correct proteins using the "Refine > Associate Proteins" menu item.

In Skyline 24.1, non-tryptic peptides would end up in a separate list of peptides, but, in Skyline-daily we have improved the experience so these peptides will end up associated with the correct protein even though the enzyme could not have produced them.

If you are still having trouble working with your non-tryptic peptides in Skyline let us know more detail about what you are doing and we might be able to come up with a way to make it work better.
-- Nick

great, thanks. I didn't know about those options!