color mismatch

color mismatch tkoller  2019-07-26

I am analyzing data in the ‘molecule interface’ and it seems that there is a color mismatch going on within the Peak Areas and elution plots. The most abundant ion in the elution is m/z 133, however, in the peak area it is shown as m/z238 (but it should be m/z 133). The other peak areas are also wrong: m/z 133 should always be the most abundant one. (Skyline (64-bit) on Windows 10 Enterprise).

Nick Shulman responded:  2019-07-26
Can you send us your Skyline document? I will figure out what is going on.

In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

-- Nick
Nick Shulman responded:  2019-07-26

In your screenshot, I just noticed the peak area bar graph is using a logarithmic scale.
Skyline is displaying the peak areas for each of the transitions on a stacked bar graph.
When there is a logarithmic scale, whichever transition Skyline chooses to put on top of the bar graph is going to be squished down the most because of the behavior of logarithms.

You can right-click on the bar graph and uncheck "Log Scale" to make it use a linear scale.
-- Nick