The dotp in that mirror plot is the dotp between the two spectra in the plot and is currently correctly showing what we expect. While the dotp in the document grid is showing the dotp between your measured peak areas and the matching library spectrum peaks.
Originally, Tobi R. implemented this as it seems you are requesting and only calculated a dotp between peaks that had signal in both spectra in the mirror plot. I didn't feel that was such a great idea, because it can give great dotp values between measured and Prosit predicted spectra where Prosit predicts very intense peaks which are entirely missing in the measured spectrum.
We could, of course, put this back as an option, but I disagree that this is the desired default behavior. I guess you might want 3 options?
- Full spectrum dotp (what you get today)
- Peaks with signal in both spectra dotp (what Tobi R. originally implemented)
- Peaks for only targeted transitions dotp
This #3 may actually be what you are asking for and best matches how the Library Dot Product gets calculated in the document grid. The value in the mirror plot, however, was originally designed to give us insight into how well Prosit was doing at predicting compared to measured spectra, since that would inform how your targeted transitions are chosen, and not how well ions match once your targeted transitions are already chosen, which as I have explained might easily ignore all of the ions Prosit predicts as the most intense.
That is, does it really matter that Prosit matches relative intensities well between a measured spectrum and its 10-15 most intense peaks, if it gets 1-5 entirely wrong?
I understand that in your manufactured case, this is what you want to see, but I think it is less likely to be generally useful, and it is certainly not a case where you can prove that Skyline is just getting this calculation wrong. It is the right calculation for what it intends to show, even if it disagrees with what the document grid is showing, which has a totally different intent.
Do you want us to expose new options? Do you agree with the possible options I have listed above?
Thanks for your feedback.