If you are unable to update these requests, this may not be the best place for this discussion, as I am not exactly sure how you will respond to me. Maybe it would be better to use the support board, and I can post to the issues list once I understand the issue and that a code change in Skyline is needed. I would expect you to have an easier time attaching a powerpoint file to a support request also. I have attached your file to this response.
Okay, this does look like a problem that requires a code fix. Is this new in Skyline-daily, or do you see the same issue in the Skyline 3.7 release?
Are you extracting any fragment ion chromatograms at all?
We recently changed Skyline to reduce MS1 chromatograms to the range of MS/MS chromatograms if they are present, which is an important improvement for PRM, but even so, I would agree that this should be done at the peptide level and not the precursor level. So, that all precursors for the same peptide have the same chromatogram range.
I am sure we can get this fixed to meet your needs. I just need to understand the context a bit better.
Thanks for posting the issue and providing the screenshots.