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!
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.