This is obviously interesting - and surprisingly easy to pull off. The data is processed in FragPipe and one of the output sheets is put into these python tools to identify the complementary fragment ions.
I like the figure above because they use 2 very similar peptides labeled with TMT and demonstrate that they can clearly find clean complementary fragment ion pairs. Oh yeah, here is the paper.
They really really don't want to do any spectral deconvolution so they only used 3 of the TMTProC tags that give them clusters of complementary ions 4 Da apart. The open suggestion is here the whole time that if you aren't afraid of deconvoluting your complementary ion clusters - you can obviously do more than a 3-plex DIA experiment.
This is a really nice read with the appropriate controls included as well as a way to dramatically increase the throughput of some DIA proteomics workflows on basically any mass analyzer. Worth a read for sure.
If you type "TMTc" into the blog search bar you'll find a lot of stuff over the years. This is one old post that goes more into what this is and why it can be valuable.
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