You need a Peptide Search tool. There are a lot of them out there and we are unaware of any that Skyline does not currently support. The complete list can be found here:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries

Some of them require converting your instrument data files (.wiff) to other formats, like Mascot General Format (MGF) or mzXML or mzML, all of which you can do with the ProteoWizard tool msconvert or MSConvertGUI (installers here: http://proteowizard.sourceforge.net/download.html).

Hope this helps. Good luck with your DDA data processing.

--Brendan