This revolutionary new application note is making the rounds on LinkedIn and I'm largely just floored by the fact that you can multiplex on the TIMSTOFs!
Apparently the trick is that you use every other TMTPro channel, since you can't get full baseline separation of every N/C TMT reporter ion pair with the TIMSTOFs and it would be patently irresponsible to try and do quantification without that separation.
They even go to "single cell equivalents" which means they diluted HeLa / K562 and some other cell line digests down to a 100% theoretical yield of a digested single cell, labeled those and - HeLa/K562 and the other cell line separate by PCA. The do it pretty fast, using the Whisper 120 method and TMT 9-plex. If they didn't have any blanks or QCs this workflow could do more than 1000 "cells"/day. And who needs blanks and QCs anyway?
If you are going to attempt this groundbreaking application, you probably want to not use just the "n" channels. If you can pick any channels you want you're better off alternating N/C because at this resolution, using the N channels alone will give you the maximum amount of cross talk between your isotopic impurities.
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