I am not sure I understand your question.
One thing to keep in mind with Skyline is that Skyline only knows how to quantify things using chromatogram peak areas. Many people who use TMT want to quantify things using a single spectrum. (And, I believe, often that spectrum is an MS3 spectrum). Skyline does not make it easy to get those sort of numbers out of a mass spec data file.
I know some people do use TMT with Skyline, but I am not sure what sort of experiments they are doing.
If you would like to learn more about what Skyline is capable of, you should take a look at the tutorials.
The absolute quantification tutorial talks about looking at heavy to light ratios: