Skyline is not very good at extracting chromatograms from DDA data.
The reason is that, because a particular precursor does not get sampled on a reliable schedule, the chromatograms tend to have long straight lines connecting the points where a matching precursor happened to have been selected for fragmentation.
Despite this, it is possible to extract chromatograms from DDA data.
On the "Full Scan" tab at "Settings > Transition Settings" you would choose "DDA" for the MS/MS filtering Acquisition Method.
You also need to choose something other than "None" under the MS1 filtering Isotope Peaks Included. Skyline will not extract DDA chromatograms unless you also tell Skyline to extract MS1 chromatograms at the same time.
Can you send us your Skyline document and one or more of your .raw files?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including whatever chromatograms you may have extracted.
The Share Document dialog also gives you the option to include raw files in the .zip file, or you could send them to us separately.
Files which are less than 50MB can be attached to these support request. You can always upload larger files here:
https://skyline.ms/files.url
I am not the expert on using FAIMS with Skyline. I think you end up doing something on the "Settings > Transition Settings > Ion Mobility" tab.
One thing you can always do is import the results without any compensation voltage filtering which will probably result in jagged-looking chromatograms. After you verify that chromatogram extraction works you could then figure out how to apply compensation voltage filtering using the Transition Settings Ion Mobility or maybe just setting the "Explicit Ion Mobility" values for your molecules in the Document Grid.
-- Nick