The use of the complementary region of a reporter ion tag is not new, but it has been somewhat limited in utility due to the relatively low plexing capabilities.
You know how those Tandem Mass Things all have the exact same mass? It's because they swap isotopes between the reporter thing (red above) down around 100 m/z that you normally quan off of and this balance region thing (blue above) that we typically just forget about.
However, it's really noisy down around 100 m/z, and for a lot of instruments it is 1) impossible to scan down that low 2) annoying to scan that low (because if you lower your lower limit you also have to lower your upper limit), so the complementary tags have always had a bit of a following, but -- ouch. You're stuck to plexing 5at most 5 samples at once?
Would it be a better option with some adjusted tag chemistry and 3 more channels? Sure looks like it!
Not only does the complementary approach beat SPS MS3 in some cases in this comparison (I think the comparison was a Fusion 1 and the authors are very clear about the hardware advancements in the subsequent generations) the very best looking files out of the ones I've downloaded? They're CID, yo.
Check out how clean the complementary ion region is here! There is a lot less noise in the higher m/z range in shotgun samples. If you thought that you'd pushed your trusty high mileage hardware to and/or well beyond it's limits and you're having trouble competing with the big spenders out there with the newer gizmos? I probably couldn't recommend this new study more! Tighten up that quan while still getting a solid high (or higher) plexing number!
Oh. Wait. Does processing it look like an absolute nightmare?
Less fun details: The resolution that you use will be important to what channels you can and can not use. As your instrument probably decreases in relative resolution as the relative m/z increases, those big ions will coalesce with the natural C13 isotopes, so you'll lose a channel or two. That's why you probably can't use the N/C swapping at all unless you really crank up the resolution numbers. Still cool. Still highly recommended.