In a call with Agilent today, Sarah Stowe demonstrated a bug in Skyline where her document has one replicate that's ion mobility data, and another that isn't. If she shows the heatmap view of a scan in the IM replicate then clicks on a chromatogram in the non-IM replicate, the view is a strange mix of heatmap and stick view - proper axis labels but everything clumped down at zero and showing the color blobs instead of the sticks.

I don't have any repro data handy but I imagine it's not too hard to show - probably just take an IM-containing file, and an mzML representation of that which has had the IM dimension collapsed.

This would go to Rita once you have files to reproduce the problem.

OK, repro files attached. The png image shows the unwanted effect, the .sky.zip contains a loaded Skyline doc that shows the problem:

select the "data" tab
click on the precursor chromatogram
make sure the spectrum viewer is set to show the IM heatmap
leave that window op, select the "preQC" tab
click on the precursor chromatogram
spectrum viewer may show nothing at all, click the magnifying glass icon
may need to switch back and forth once or twice to see it

hmm, files didn't attach - data set too large. I'll email that to Rita as https://drive.google.com/file/d/1A_Lnpq47ByD3sJAQhChOsHwP_97Jk2g2/view?usp=drive_web

So, what's the desired behavior should be? Fall back to sticks if no-IM replicate is selected? What if used clicks on an IM replicate after that? Should the last user choice be remembered, or should it just stick with sticks?

I would think that yes, it would fall back to the stick view if the heatmap is inappropriate for the current replicate, and just stay that way if IM replicate is reselected.

This is kind of an unusual scenario so I'm not sure it's worth trying to do some kind of per-replicate mode save, and this simplified behavior would at least be easy to understand.