When you Import Results into a Skyline document, Skyline always uses the default peak picking model.
In order to pick peaks using your trained model you would need to use the "Refine > Reintegrate" menu item.

We do believe that a trained peak picking model will do better than the default model. The other thing that it does is give you "Detection Q-Value" and "Detection Z-Score" values that you can find in the Document Grid which will tell you how good the peaks are.

If you are using Skyline-daily, then there is a command line command "--exp-mprophet-features" that you can use to export mProphet features.
This command is not available in Skyline 23.1.

We will be releasing Skyline 24.1 in a week or two, and Skyline 24.1 will also support the "--exp-mprophet-features" command.
-- Nick

Hi Nick, Thank you so much for the reply. It was helpful. However I do have one question, I'm not sure how I see the "Detection Q-Value" and "Detection Z-Score" values. Do I add it into a report file?
-Anirudh

Yes, you would need to create a custom report with the "Detection Q-value" and "Detection Z-score" columns on them.

If you would like to learn more about custom reports you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

When you are editing a report definition, there is a binoculars button on the toolbar at the top of the Edit Report form which will let you search for a column by name.
-- Nick