View > Library Match is just the old View > MS/MS Spectrum renamed.
Where are your measured spectra? Are they in a different library than the one you generated from Prosit? If so, then I think you have 2 options:
- Uncheck the right-click > Prosit menu item, but leave "Mirror" checked. This should then give you a toolbar option allowing you to choose which libraries to mirror against each other, and you can mirror your Prosit library against your empirically measured library.
- Either remove the Prosit library (you can Undo this operation) or make it second in the Peptide Settings > Library order. This should get Skyline choosing your empirical spectra above the Prosit library spectra, and then mirroring with dynamically queried Prosit spectra in the Library Match view should give you what you are asking for.
The Targeted Method Editing tutorial covers working with multiple libraries (though, not with Prosit).
If your empirical MS/MS spectra are not in a separate library, then I will need to understand better what you are trying to achieve.
Thanks for posting to the Skyline support board.