So, it appears that the cause of the confusion is that you have Explicit Collision Energy set on all your transitions.

Not that we think it is right for Skyline to just silently export the single explicit CE for each transition when you have clearly indicated you want a transition list for CE optimization in the method/transition list export form, but that is what is causing this. You can easily work around the issue by doing the following:

• View > Document Grid
• Views > Small Molecule Transition List
• Select all cells in the Explicit Collision Energy column (select the top cell and ctrl-shift-down-arrow)
• Press the Delete key

That said, I am not entirely clear this is what you want. I could imagine that what you were intending was to have Skyline export a transition list with 11 CE values per transition centered around your explicit CE values, and that seems like it could now have the benefit of allowing second-round CE optimization. That if we enabled that, you could:

• Perform first round CE optimization based on your linear equation
• Save optimal CE information for every transition where an apex intensity was observed in the middle of the measured CE values
• Set Explicit CE on any transition where apex intensity was observed on an extreme CE value
• Perform second round CE optimization centered around the explicit CE values for only the transitions with an extreme apex

Then, consider what you think should happen when you click the OK button in the Export Transition List form for a document with Explicit CE values. Should we warn:

This document contains Explicit Collision Energy settings. Skyline will ignore these for collision energy optimization.

OK Cancel

Offer an option:

This document contains Explicit Collision Energy settings. How would you like to handle these?

(o) Optimize around the Explicit Collision Energy values when present ( ) Ignore them and optimize around the values predicted by "Small Molecules" predictor

OK Cancel

Something else? Just silently do one or the other option?

At least it is clear that just silently giving you only 1 entry per transition is not the right thing to do. At least you can still achieve the linear equation option through a bit more work.

Thanks for reporting this issue.

--Brendan

P.S. - Your CV Histogram issue is totally the new intended behavior. If you look closely you should still be able to find a tab in your layout for the CV Histogram, probably it is right next to the tab labeled "Replication Comparison" in the partial screen grab you posted in the PowerPoint slide (about 2/3 down on the left edge). It is now possible to show multiple graphs for peak area and retention time at the same time.

However, I can see that this is confusing. So, we are just going to remove the check marks in the menus and let them always just active the forms (as they already do). Check marks in the menus are more appropriate anyway when the menu item can be used to turn on and off the option. These are on-only menu items.

Thanks again for the feedback.