Thursday, May 26, 2016

Special Epigenetics issue of MCP!

In January MCP did a big ol' issue focused on epigenetics. Personally, I'd rather ignore this whole interplay between protein back to influence the DNA level because, honestly, I don't think my brain is big enough to think about it. If we have 1e9 proteoforms isn't that enough mechanisms to completely control a human system?

Unfortunately it seems like mounting evidence is building that we need to think about this stuff...or, at least...someone has to....and this special issue gives us a perspective of where we are right now.

A good starting point is this introduction from Mike Washburn, Ying Ming Zhou and Ben Garcia.

Counting the introduction, there are 19 articles here. If this is your field -- congrats, here is a new book on the topic! Other technologies are working on epigenetics as well, but here you can see that we've got the tools to take this confusing field head on. A study from Don Hunt's group applies ETD to histones and the Kelleher lab contributes some quantification via Top-Down of specific histone methyltransferase.

There is some great work in here and, holy cow, it shows how far we've gotten with our understanding of PTM interplay and with just our understanding of epigenetics as a whole. It isn't all sunshine and rainbows, though. Even a quick read through of some of the discussions will tell you that -- yes, we've got the best tools we've ever had, AND we can do some great stuff... but this is still a very big and complicated and relatively new field of biology and we have quite a way to go yet to fully understand what epigenetics really is. I'm glad people are interested in working on it!

One of the last articles is this gem from Gene Hart-Smith et al., that discusses how general shotgun proteomics searches don't do a good job with protein methylation data. My spidey sense warns me of a theme this year -- FDR and PTMs? Of course, they propose some solutions, but I expect some interesting conversations in San Antonio regarding how we improve our PSM confidence.

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