I am not sure that I understand your question.
If you want to get the prosit dot product values, I think the thing to do is to create a .blib file from Prosit.
That is, go to:
Settings > Peptide Settings > Library
and push the "Build" button and choose "Prosit" as the "Data source".
This will create a spectral library (.blib) file containing the peptides in your Skyline document where the spectra have the intensities that were predicted by Prosit.
Then, when you are using the library in your Skyline document the Library Dot Product values will be the dot product against the predicted prosit spectra.
Does that answer your question?
I might have misunderstood your question. Could you post a screenshot of what you are looking at?
It might also help me understand if you send us your Skyline document. In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here: