If you open a document with a library and peptides that match its spectra, and then in transition settings turn off aut-select of transitions, and remove y and b ions from the ion types list. Okay that, and you will see that none of the previously selected transitions appear to match the spectral library, and the dot-product values will all be zero. We don't want Skyline to rank ions from types that are not in the ion types list, but it would be preferable if it still matched them when they are present in both the spectrum and the transition list. So that the match is indicated in the transition icon and the intensity can be correctly used in the dot-product.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.