Hi there,
I have been using the new "synchronize integration" setting heavily. It reduces my processing time astronomically so THANK YOU!

However, I have observed some bugs I would like to report. The only working example I have of these bugs is in a batch that I am preparing for a manuscript, so if it would be of use I would prefer to share it privately.

-When synchronizing integration for a molecule that uses a surrogate IS, there seems to be some effect on the surrogate IS integration (which should not happen since the surrogate molecule is a completely different molecule).

-In the "synchronize integration" window, if you choose to synchronize according to analyte concentration Skyline encounters an unexpected error.

-(May or may not be a bug) - when you synchronize integration for a molecule that has a matched IS, the synchronization of the two is independent - i.e., you must synchronize the unlabeled version and then synchronize the labeled version separately. This is unlike how Skyline normally works where adjusting integration on the unlabeled set of a pair of matched analytes/internal standards is automatically applied to the matched IS. I actually kind of like that this is separate since at times the IS is deuterated (as opposed to having heavy carbon) and deuterons in place of hydrogens causes a shift in RT such that a matched analyte/internal standard pair may actually have slightly different RT's.

Please let me know if I need to elaborate more or share my skyline doc with you (I can share a more detailed explanation of the where the error is at that time). Thanks!