Hello,

I'm using Skyline-daily (64-bit, 3.6.1.10775) analyzing PRM data. The file was created in January, and I have been updating Skyline-daily as new versions were released. I'm constantly adding new PRM (.raw) files from a Q-Exactive to this file. I have done lots of manual peak integration and Remove Peak on many of the samples (over 70 samples, 22 prec, 1600 transitions). Each sample is acquired with two methods, and therefore to import a new sample I do: Import/Results.../Add One New Replicate/type a sample name and choose the two new .raw files for import. I have now noticed that after the import of a new sample all my manual peak integrations and Remove Peak selections are reset in the older samples. How do I ensure Skyline retains my manual integration/Remove Peak modifications?

Thank you,

Dominik

Hi Dominik,
Thanks for your report. You are not the second to report this, but the first to get it on the issues list.

It appears that what was supposed to be a minimal fix (committed with r10761) for a less common issue had a small logic flaw that caused this issue.

I promise it will be fixed in the next Skyline-daily release and, hopefully, a new test added to catch something like this in the future.

If you want to return to a version of Skyline without this flaw, you should be able to go through the steps to uninstall Skyline-daily, which will present you with the option to remove it completely or return to the previous version. I believe that returning to the previous version should fix the problem for you. Also, I would be very interested to hear if it did not.

Thanks again for your report.

--Brendan

This turned to be much worse than I originally thought. Luckily, I had a file from an earlier report. It only impacted files with over 1000 transitions, but if you save one of those files the flag that tells Skyline a peak is a manual integration is not saved, which means the file is corrupted. The next time the saved file is opened, many changes, including importing new data will cause the peaks to get reset.

Thanks for raising the priority on this issue with your report.

--Brendan

This has been fixed and released in Skyline-daily 3.6.1.10828, and a special one-time release has been made as 3.6.1.10828 that can be used to fix any saved documents with this issue (using Edit > Refine > Repair User Set).

Thanks for reporting this! It turns out it has been broken since 3.6.1.10690 on March 31st.

--Brendan