Dear Skyline support,
I've noticed a couple of times that the values of idotp can change drastically if certain precursor transitions are turned off and on again. In the attached Skyline document, the idotp values are all around 0.3-0.45 (pretty low for how they visually look) yet if I disable and then re-enable the monoisotopic precursor transition, my idotp values increase at least two-fold (0.84 - 0.94).
The final idotp values look to be correct based on the workaround, but I could imagine this could cause some trouble for people that don't know about it and automatically filter their transitions based on idotp.
Cheers,
Chris