Sorry for the long wait on a reply. This message came during a month of travel in Europe. I am back, and catching up on things that slipped by during that time.
The short answer, unfortunately, is that I have seen this before, but haven't managed to code a solution for it yet. I will try very hard to get to this before the next release, but it doesn't seem to have become really blocking to anyone, and we do have a great deal of pressing work right now. So, I still can't get to it immediately. I have two other direct emails about it in the past 6 months, but it would be great if you could turn this email report into a post to the Skyline issues list (Help > Issues from inside Skyline).
Thanks for taking the time to make this report.
On Mon, Jul 2, 2012 at 8:08 AM, Jonathan Worboys <Jonathan.Worboys@icr.ac.uk> wrote:
I have been using Skyline for a while and have come across this issue. It seems that if you have two peptides with the same precursor mass it cannot display the chromatograms properly as can be seen in the attached png file. It seems when the two peptide acquisition times overlap you can see this spiky line. Have you come across this at all? I have looked at the file in pinpoint and it displays it normally so i am not sure why it is happening.