Have you ever tried to combine multiple TMT studies? I'm paraphrasing, but Akhilesh Pandey said "two will work, and three is okay, but the amount of loss by your fourth plex makes it not worth it" and I have found that to be 100% true in my hands. Our sampling is stochaistic, which is fun to say, but I'm not sure that I'm using the word correctly. The Venn diagram of the peptides that you're able to fragment and identify in each plex that you add gets progressively less overlapping. In today's instruments that are blindingly fast, we're getting loads more fragment ions but that doesn't necessarily translate to higher percentages of actual identified ones.
Isobaric match between runs (IMBR) allows you to link data from fragmented but not identified peptides back to the identified ones from other plexes.
I'm legit blown away. There are at least 10 different studies on hard drives sitting around here that this should help with.
Oh, and they built a new algorithm to normalize without using a pooled channel. 'Cause, you know, this wasn't incredible enough. And these appear to now be built into MaxQuant and Perseus now!
TIME TO UPDATE YOUR MAXQUANT VERSION!
Follow-up:
I was on a conference call the other day and someone said that we needed more tools for combining TMT plexes. If you're not about to start updating your MaxQuant after reading this post, you should 100% check out IRS from Phil Wilmarth. You'll need to use R to do this, but you can pretty much follow anything Phil does and copypasta what he writes directly into R and just run it.
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