I always err toward MS2-based reporter ion experiments. I know the accuracy is better with the MS3 based methods, but my problem is always trying to get to the protein(s) that everyone is so interested in and I can't take the speed hit.
This relatively simple looking new approach shows that by deconvolution and intelligent use of the TMT complementary ion fragments you can have it all!
The use of the high mass fragments that still carry TMT fragment tags is not new, these authors described TMTc a few years ago --and there is a free Proteome Discoverer node from IMP that will allow you to utilize them, but TMTc+ takes it a couple steps further. By adjusting conditions to bias toward the formation of the complement ions and by taking the shape of the ion isolation window into account they demonstrate massive improvements in this approach.
How massive? Ummm....more quantified proteins than a label free approach?!? If true, this is paradigm flipping stuff. Every study I've ever seen has shown throwing in the reporter ion tag to decrease the number of IDs compared to label free approaches and I think we all just accept it as the trade off for being able to multiplex a bunch of samples at once. But...if you actually get more IDs -- or even no loss -- the next question is why wouldn't you use TMT for every experiment (where your n < something crazy, of course)
This study was just accepted by ACS, so I changed the link above to the direct toward that version of the paper. The preprint is still available at bioRxiv here.
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