Skyline can be used with all types of molecules, but you have to tell Skyline the chemical formulas (or m/z) of the precursors and the fragment ions in order for Skyline to know what chromatograms to extract.

Skyline really only understands the fragmentation of peptide sequences along the backbone. For all other types of molecules you have to tell Skyline exactly what molecules and fragments to expect.

You might be able to find spectral libraries containing fragmentation information about your molecules. Skyline understands NIST libraries (.msp), Spectrast (.sptxt), XHunter (.xlf) as well as our own BiblioSpec (.blib) formats.

If you want to learn about how to provide Skyline with a list of molecules to extract chromatograms for, the Small Molecule Targets tutorial might be a good place to start:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule
-- Nick