Did you use D3 leucine in your labeling experiment? One limitation of the TurnoveR tool is that it only works with deuterated leucine.

If you did do a D3 leucine experiment then it is conceivable that the tool will work with your data.

One thing you could do is send us your Skyline document and I could see if I can get this to work.
In Skyline you can use the menu item:
File > Share to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

If your experiment did not use D3 Leucine then TurnoveR will not work with your data but we still might be able to help you with the math to calculate half lives.
--Nick