Peak inversion over y-axis with new skyline version

Peak inversion over y-axis with new skyline version dhaupt  2024-02-02 08:11

Hi Skyline Team,

I recently downloaded the latest update ( and now all of my peaks appear split with the earlier half of the peak being above the y-axis and the later half falling below the y-axis. The peak areas themselves don't appear to be affected, however, I can't seem to figure out how to fix this. I sent multiple files to a colleague using an older version of skyline and they observed typical peak shapes. Wondering if there is a way to disable this or if there is a way to revert to an older version of skyline. Will attach a screenshot of an example chromatogram along with my skyline project so you can check my settings. Thanks for your help.

Dan Haupt

Nick Shulman responded:  2024-02-02 08:28
You should right-click on the chromatogram graph and choose "Transform > None".

It looks like you have chosen "Transform > Second Derivative". With that option selected, Skyline displays the second derivative of the chromatogram instead of the chromatogram intensities themselves. The second derivative of the chromatogram is probably only useful for getting insights into Skyline's peak detection algorithm. The first step of Skyline's peak detection algorithm involves finding the points where the second derivative crosses the X-axis.

Earlier versions of Skyline would not display the portion of the graph that is below the X-axis. Skyline 23.1 chooses a lower bound for the Y-axis which enables you to see the negative portions of the second derivative graph.

By the way, if you want to send your Skyline document, you should use the "File > Share" menu item.
That menu item will create a .zip file containing the .sky file that you attached as well as other supporting files including extracted chromatograms (the .skyd file).
-- Nick