This is a short guide to demonstrate enabling Koina in Skyline and building a Koina library for a set of target peptides. For this guide we will use a small FASTA of abundant proteins.

Download the attached FASTA file:
https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=29ff5efd-e725-103d-b4e5-22f535560118&name=some-proteins.fasta

Open Skyline and start with a blank document.

• Click the Tools menu, then click Options.

• Select the Koina tab and select the intensity and retention time models to use to build the library:

• Click the OK button.

Import the FASTA file you downloaded:

• Click the Settings menu, then click Peptide Settings and select the Library tab:

• Click the Build button.

The Build Library dialog will appear:

• Give the library a name and click the Browse button to choose where to save the library.
• Select Koina as the Data Source.
• Click the Finish button to begin building the library and close the dialog.
• Back on peptide settings' library tab, click the checkbox to enable the library:

• Click the OK button to close the peptide settings dialog.
• Dock the library spectrum graph in the main document area by dragging the title bar.

• Expand a protein in the target tree and click on a peptide.

• Right click on the library spectrum and click "Mirror".
• Right click there again and click "Koina".

You will see the generated-on-the-fly Koina spectrum on top compared to the locally stored Koina spectrum mirrored on the bottom:

• Go back to Koina settings in Tools -> Options and change to a different model.

• Select another peptide to refresh the graph with the new Koina model.

You will now see the generated-on-the-fly Koina spectrum on top is different than the locally stored Koina mirror spectrum:

You can keep changing the Koina model or NCE to see how the spectrum changes compared to the local one.