Currently Skyline chooses a single spectrum for each peptide-charge combination from which to choose transitions and calculate dot products. This may be either a spectrum matching a light or heavy precursor for that charge state. If the library/libraries contain both the light and heavy spectrum, the light will be used. If multiple libraries are present the first library to contain the spectrum will be used.

It should be possible to view all potential matching spectra in the library graph UI, and override the default choice, since it may not be the best available spectrum. In the future we might also want to think more about how people choose the best available spectrum, and have Skyline use similar heuristics to make the best choice automatically more often.

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Eva added the combo box to view secondary spectrum matches a while ago. The button to change manually the choice of spectrum will have to wait until next release, because Eva has had to focus on other things, and we are closing down v0.7

Unlikely to make our priority list with so few requests after so many years.

This has been requested again. Perhaps we should reconsider.