You need to add those peptides to your Skyline document. Skyline does not know how to add them for you.
In order for Skyline to add those peptides to your document, Skyline would need to know which charge states and transitions are supposed to be measured. For the built-in iRT standards that Skyline knows about, Skyline knows which charge states and transitions.
If you have measured these peptides before, you probably have a Skyline document that already has those peptides in it. You could start by copying those peptides out of that document (you can select the peptides in the Targets tree, and do "Edit > Copy", and then paste them into a different Skyline document).
You can always add peptides to your document using the menu item:
Edit > Insert > Peptides
and Skyline will give you precursors and transitions based on your settings at Settings > Transition Settings
It might be helpful if you look at the iRT tutorial: