It is possible to use TMT with Skyline but Skyline might be missing a few features to make it easy.

One thing to know about using TMT with Skyline is that the way to tell Skyline about the TMT reporter ions is on the "Filter" tab at "Settings > Transition Settings".
Whenever you want Skyline to extract chromatograms for fragment ions which are not attached to any amino acids of the peptide, you need to add the fragment ion to the "Special ions" list on the "Filter" tab at "Settings > Transition Settings".
When your reporter ions have a checkmark next to them in that Special ions list box, you will be able to add the transitions to the Targets tree.

When Skyline has extracted chromatograms for your TMT reporter ions, you will be able to see their peak areas using the "Transition Results" report in the Document Grid.

We have had plans to add features to make TMT more useful in Skyline. One feature which is missing from Skyline is the ability to treat these different TMT reporter ions as different samples to use in a Group Comparison. Unfortunately, the Group Comparison feature in Skyline does not know anything about TMT reporter ions, so you will have to do your analysis in another tool such as by exporting a CSV file and analyzing it in Microsoft Excel.

Another feature which is missing from Skyline is correcting for the spillover of signal in different channels. When you purchase your TMT reagents, it includes some information about the isotopic composition of the reagents and what corrections need to be applied. To get the most accurate results some sort of matrix math needs to be performed to deconvolute the spillover, and Skyline does not do that either.

You can learn more about Custom Reports here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick