We do have an audit trail now, which we are working on getting published soon in the journal Bioinformatics. Hopefully, we can resubmit the favorably reviewed paper within the next few days.
There is a published tutorial on how it works already, though:
Make sure you use Skyline-daily in doing the tutorial. It contains fixes to issues we have discovered since version 20.1 was released.
It is not a fully 21 CFR part 11 compliant workflow. We decided to take this first large step toward that goal when we had the opportunity with a very talented undergraduate developer named Tobi Rohde, and he and Rita Chupalov on the team managed to get the work integrated with Panorama. But, we stopped short of a fully encrypted log with keys controlled by a secure Panorama Server, which would be required to achieve 21 CFR Part 11 compliance. Nor are we far enough along to fully understand the standards body that would test our work and declare it in compliance.
So far we have left it "research-grade" audit logging as complete as we felt we could make it within our current resources, since we didn't really have a funding source willing to drive requirements and ensure meeting them was fully funded.
I just noticed you are from Novartis, which is interesting, because this work was at least in part inspired by a discussion with someone from Novartis at the 2017 DIA/SWATH course at ETH. Unfortunately, I lost contact with him after that.
Anyway, we feel we have designed toward the end goal of 21 CFR Part 11 compliance, but only within out own means with no fully funded mandate to reach that end goal.
Thanks for your interest and for making contact through the Skyline support board.