Can we have a look at the Skyline document? You can use Skyline's File>Share menu item to create a .sky.zip file containing all the pertinent files. It would be useful to see one of your MSe files too.

Thanks for using the Skyline support board,

Brian Pratt

Can you send us your Skyline document?
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.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

That error message makes it sound like you do not have any transitions in the Targets tree.
You might be able to correct this by right-clicking on something in the Targets tree and choosing "Pick Children".

For everything in the Targets tree, Skyline keeps track of whether you are the one deciding which children it has, or whether Skyline is managing that.
When you bring up the child picker window there is a magic wand button which can toggle between the two states.
Also, you can put everything into the Skyline is managing state by going to:
Refine > Advanced
and checking the checkbox next to the "Auto-select all..." items.
If you check the checkbox next to "Auto-select all...Transitions" then the settings on the "Filter" tab at "Settings > Transition Settings" will have an effect.
-- Nick

Thank you both for your response. After a bit of tinkering, I think I figured it out? I wasn't adding a library to search against, since we are doing pretty pure untargeted (with the plan to build our in-house library as we go). I assumed I could generate a targets list de novo. Once I added a public .msp file to build the targets list against, then it worked.

I will look into generating my own library from my own data to improve the matches.

Thanks!