Nothing that simple. A lot of people are using spectral libraries from DDA data as a starting point, and Skyline makes it easy to limit your peptide selection to only what is available in a spectral library. There are some predictive tools that try to achieve this, and one (PREGO) can be found in the Skyline Tool Store, but we have not been super impressed with their performance compared with an empirical assessment.

I guess I would recommend starting with the Targeted Method Editing tutorial, if you have not already, and follow that with the Targeted Method Refinement tutorial to get a sense for how this problem can be approached in Skyline.

--Brendan

Hi Brendan
Thanks for this. I mean specifically which Camino acids, combination of amino acid and position of amino acids are ruled out?

That can be heuristically controlled through the check list in the Peptide Settings - Filter tab under "Exclude peptides containing", but it requires you to make your own decisions about what to exclude/include. Some of the default options there are aimed at things some people have felt make peptides less ideally "quantotypic", but we make no claims as to how correct they are. These filters themselves are completely customizable and should support any type of filtering by amino acid combination and modification existence you desire.

Perhaps this is helpful. Otherwise, back to the tutorials or post something a lot more specific with screenshots of what you are finding and hoping to find.