Over at the entertaining culture-blog 2Blowhards, the comments to this post (on people who feel deficient in math ability) include a mention of proteomics, which prompted Michael Blowhard to say:
"Proteomics" -- even the word is scary. I wonder how people in the field are going to communicate the substance and importance of what they're up to to civilians ... A challenge, I guess."
A challenge that I'm willing to take up! It's not my exact field, of course, but close enough. I'm starting a new category for posts like this, when I (and the readership here, in the comments) try to explain some technical buzzword-laden area in language that intelligent non-scientists can profit from. So. . .proteomics.
The place to start, most likely, is where the word came from. It's a direct steal from "genomics", the study of genomes, which are the total DNA sequences of a species (or individuals of a species). Back a few years ago when the human genome was being sequenced for the first time (all the individual A T C G letters being read off), it became clear that the number of genes that humans carry around was very much on the low side of what most people expected. (The human genome, as we have it today, is a composite - the number of people in the world who have their complete genome read can be counted on one hand. That's going to change drastically in the years to come as the process gets cheaper, faster, and more useful).
The reason why people expected more genes relates to what a gene is: a stretch of DNA that's read off (transcribed) and turned into a specific protein. That's DNA's job; it's a set of coded instructions to make proteins. But, as it happens, we have a lot more different proteins than we have genes. Clearly, something more happens downstream of the DNA part of the process.
A lot of things happen, actually. Those first-made proteins get altered in all sorts of ways. The same protein can be folded into different shapes, for starters (we're just now recognizing how important a process this is in some diseases). Proteins can also be clipped into smaller ones by many different routes, and at any stage they'll be decorated with molecular tinsel like sugars and lipids and phosphates. All of those can totally change a protein's function. This gives you some idea of where all that diversity is coming from - and why sequencing the human genome, huge and necessary accomplishment though it was, was nowhere near the end of the story.
Proteins spend their time interacting with other proteins. If you think of a cell in your body as a large irregularly shaped bag, full of intricate (and somewhat squishy) 3-D jigsaw pieces which are constantly sluicing around assembling or sliding past each other, you'll have a pretty reasonable idea of what it's like in there. Any given cell will contain thousands upon thousands of different proteins, many of which are doing multiple jobs depending on the time and place. Proteomics is the attempt to understand which proteins are doing what, when, with whom, and why.
It hardly needs saying, but we're just at the very beginning of that study. We have some tools to track these interactions, and they're far better than anything people had twenty or thirty years ago, but they're still rather crude compared to what we need. Huge signaling networks get uncovered and extended, and are found to touch upon others for reasons that are unclear. All sorts of feedback loops and backup systems are sketched in, and many pathways have been missed (or, alternatively, assigned too much importance) because they only operate under certain special conditions that our assays may overemphasize or skip entirely.
This project is much harder than the deciphering of the genome, and will take much longer. But that's because it's much closer to the real-time workings of a living organism, which means that comprehension, when it comes, will be still more valuable. Really substantial sums are being spent on this stuff, along with serious brainpower and computing resources. Progress will be jerky, irregular, infuriating, and of very great interest indeed.