Sunday, February 21, 2016

Environmental proteomics tackles viral "dark matter"!!!

If it seems like I'm making fun, I'm doing it wrong. I'm totally not. Environmental proteomics (there's definitely better names for it!) is super cool. I think that we've wanted to do it for a long time, and we finally have the technology (and really innovative researchers) to use mass spectrometry to better understand how our environment works.

Want further proof? Check out this sweet new paper at PNAS:

This is more than just a catchy title, turns out "dark matter" is a hot topic in science right now (and something in this context I've never heard of before).  What does dark matter mean here? Its all the biomaterial out there that we have no idea what it is or does.

For some cool reading on viral dark matter, check out this New Yorker article from last year. A researcher states that there is probably 1e31 phages on Earth (vastly outnumbering every other organism on earth combined) and that we really know very very little about them.

Sounds like a job for some Orbitraps to me!!!  And some genomics. And some really really smart data analysis.

How do you get started in looking at viral dark matter? start with FASP digesting about 80 LITERS of sea water. And then you break out the MudPit. We're talking low abundance and super low copy number. An Orbitrap classic did MudPits of 72 hours in length. For the Q Exactive work they could get data to work with out of 8 hour run times, and an Orbitrap Velos Pro fell somewhere in the middle.  Once they got their HUGE data files, they used an assembled metagenome that is tremendously huge. I'm a little fuzzy on the FASTA details, but the assembled entries are between 2e5 and 1e6 protein entries.

Cause every data point needs to be evaluated, the data was thrown against Sequest (with DTA select and with Percolator separately) and through the TPP, using X!Tandem and some robust statistics were used to combine that data.

So how do you define success with an experiment like this?

What if you found a high level of peptides present from some new proteins that are very similar to known capsid protein structurally (capsid is the protein on the outside of a virus...or phage, more correctly, I think...), but no one has ever characterized it before?!?!  And what if you find that protein, now that you know to look for it in sea water all over the planet and this illuminates some of that "dark matter" a little?

I think that is EXACTLY how you define success with a project like this one. This is a solid study all the way around and just a great coffee read!

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