If your Skyline document contains the peptides that you are interested in, you can go to the "Library" tab at "Settings > Peptide Settings" and push the "Build" button and choose "Koina" as the "Data source".
After you have built the Koina library you should make it so that that library is the first (or only) library selected in the list of libraries at on the "Library" tab at "Settings > Peptide Settings".
Then you should go to the "Library" tab at "Settings > Transition Settings" and put the number "n" into the "Pick X product ions" textbox and make sure that "From filtered ion charges and types" is selected.
On the "Filter" tab, make sure that "Ion charges" and "Ion types" are the ion charges and types that you are interested in.

Then, go to "Refine > Advanced" and check the checkbox next to "Auto-select all...Transitions".

After you have done that, the Skyline document will contain the top N transitions from the library that was predicted by Koina.
You can then create a custom report including the transitions. The predicted retention time is available as the column "Retention time calculator score". It's not a real retention time-- it's an iRT value, which is a retention time normalized to approximately the range of 0 to 100.

You can learn more about custom reports in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick

Thanks Nick,

That is super helpful - one issue is that the "Retention time calculator score" gives us "#N/A" values when we export the report. Do we need to define Koina as an RT prediction calculator under peptide settings somehow?

Thanks again,
Vincent

Oops. I left out some important steps.

When you are building the library using Koina, make sure that you choose something in the "iRT standard peptides" dropdown in the "Build library" dialog.
Then, after the library has been built, Skyline will offer to create an iRT predictor for you and add the iRT standards to your document.
After you have done that you will see values in the "Retention time calculator score" column.
-- Nick