Are you using your triple quad in the mode where the Q3 scans across a range of m/z's so that you end up collecting MS2 spectra?
I am not very familiar with that sort of data from a triple quad, but if they look like MS2 spectra then you should be able to use a peptide search engine on it.
Skyline has a peptide search engine built in called "MSAmanda". In order to tell Skyline to perform a peptide search on your data using MSAmanda, you would use the menu item:
File > Import > Peptide Search
On the first page of the Import Peptide Search wizard, tell Skyline that you are starting from "DDA raw".
Here is the tutorial for doing that sort of peptide search in Skyline: