If you want to create a BiblioSpec spectral library with all of the tryptic peptides from a FASTA file, you would first use the menu item "File > Import > FASTA" and point Skyline at your FASTA file with all of your proteins of interest.
Skyline will add all of the tryptic peptides to the document.

Then you should go to the "Libraries" tab at "Settings > Peptide Settings" and push the "Build" button.

On the "Build Library" dialog, be sure to select the option "Koina".

Then Skyline will create a .blib spectral library with the spectra for all of the peptides predicted by Koina.

To answer your other question, if you have imported QQQ chromatograms into Skyline, you can create a spectral library using the menu item:
File > Export > Spectral Library

Skyline will create a spectral library where the m/z's are the product m/z's of the Transitions in the Skyline document, and the intensities are the integrated chromatogram peak areas.

If you want to learn about importing QQQ chromatograms into Skyline I would recommend the Targeted Method Editing tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit
as well as the Targeted Method Refinement tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_refine

-- Nick

Thank you Nick,
The in-silico spectral library are not peptides and are not in a FASTA format. Is there a way that I can generate my own file, with precursor and fragment ions that I want to search against ?

I am not sure I understand what you are trying to do.
If you have a list of precursor and product m/z's, the way that you would import them into Skyline is with the "File > Import > Transition List" menu item.

If you are interested in using Skyline for small molecules and not peptides, then I would recommend the Small Molecule Targets tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule
-- Nick