Hi Chengkang,
Skyline, as you know, has built in domain knowledge for proteomics - understands the way proteins and peptides fragment - but other classes of molecules have entirely different behaviors. So while Skyline can also deal with generalized molecules ("smALL molecules", as some say), there can be a lot of domain knowledge needed to make a truly useful tool for specific kinds of molecules.
Happily, Skyline's external tools interface enables others to bring their domain knowledge to Skyline. LipidCreator is an excellent example of this, a very nice front end for describing lipids and feeding that information into Skyline, written by Skyline users with only a very tiny bit of help from the Skyline team.
Perhaps you're interested in doing something like that for your field?
Best Regards,
Brian Pratt |