Yes, Skyline is a great tool for what you want to do.
You will use the menu item:
File > Import > FASTA
to read in your FASTA file which will add all of the tryptic peptides to your document.
Then, you probably need to go to:
Settings > Transitions Settings > Full Scan
and change MS/MS filtering Acquisition Method to "PRM".
Also, change, the "Retention time filtering" option to "Include all matching scans".
You probably also want to change MS1 filtering isotope peaks included to something other than "None" if you would like Skyline to extract MS1 chromatograms in addition to the PRM chromatograms.
Then, you will export your isolation list using the menu item:
File > Export > Isolation List
After you have collected data on your mass spectrometer you will tell Skyline to extract chromatograms from your raw files using the menu item:
File > Import > Results
There are a lot of tutorials on this page:
Probably, the best tutorial for you to look at is the PRM tutorial: