Friday, June 21, 2019

Is 2019 the year of Single Cell Proteomics?

Image borrowed/taken from this great paper above.

In a field growing as rapidly in every direction as ours, it's impossible to pick a direction that it is going in. It really is, but half way through the year I'm going to type loudly on this keyboard every other person earth who has ever touched it has hated (it's this one, and it's awesome)


Before I start or continue rambling I'd like to point out something that I didn't know until a few months ago.

Did you know that single cell genomics doesn't give you a complete picture of the genomics stuff in that single cell?

IT TOTALLY DOESN'T! The genomics people like to hang over our heads -- "there will never be an equivalent for PCR in proteins". Maybe there won't be. But...this paper is 1.23 pages long and yes it is a few years ago, but...

....and they are not getting anywhere near complete transcriptome coverage. (Grain of salt, here obviously, I know less of what I'm typing about here than normal), but I've got it on good authority from an expert in this stuff (what up, Joe!) that they aren't getting a whole genome or transcriptome out of a single cell. Is that an "the emperor didn't win the popular vote" level surprise to you as well? Okay. So...what about proteomics?

I dunno. What if there are 2 single cell proteomics meetings this year? Does that do anything for you?

One just happened, so let's skip it. If you don't register for a conference 3 months in advance you obviously lose, right?

What's important is this one! (Jokes aside, you should register soon. It's free, and looks awesome!)

Wait. FIRST? Do you mean that we got to something in proteomics in the 21st century before Europe did!! About time! Take that you rest of the world people with your fancy pants schools where you learn stuff. We're first in single cell proteomics right now thanks to a red blooded American who grew up right here in Dallas, gosh darned Texas, named Nikolai Slavov.

I've never met anyone from the Slavov lab, I'm pretty sure. I've kicked some emails around, but I think if you are on this blog you'd think we played on the same AMERICAN football team in middle school. I just really like this lab's work and general philosophy. Slavov lab seems to be juuuuust a little over the status quo in the way science is disseminated to the world. Like -- waiting 6 months for a journal to finally format your paper for publishing, or -- if you aren't part of the right society or you couldn't attend a meeting for whatever reason, then you miss out on all of it.)

Case in point?

Who hasn't tried ScoPE-MS at this point? Most people I know tried it a year before the paper was printed. Yo. Dick Smith's lab had a killer poster on ScoPE-MS at ASMS where they threw in their technology (NanoPots) and it improved everything.  The info got out fast. People tried it. It worked, but had challenges and one of the powerhouse labs in our field jumped in with some improvements.

More pertinent case in point? I couldn't go to Boston for the Single Cell meeting. I've got a job and dogs to feed. I missed out, right?

BOOM. They're all here. No membership required. No expiration date on the talks. Free access for everyone.

Okay -- so this is maybe the coolest part -- and the example of why we need science to move faster (I know we're trying!)

Peter Kharchenko demonstrating a re-analysis of a new bioRXiV paper that came out just 2 days before he spoke!

Yes. There are downsides to the preprint process, like, yes, you can be totally wrong and everyone will see it and you'll feel dumb and maybe they wasted time that a reviewer would have saved everyone from. Peer review should never go away, but open rapid access to awesome new scientific advances should be screamed from rooftops and written in blood on pancakes and this is one of the clearest success stories of this model that I know of

Pumped for the future. Lets knock down paywalls and give our talks online free access -- cause, just maybe, the next top mind in our field is in Bhutan or Malawi or Paraguay and keeping all our results in our special clubs is the only thing standing between us and that person coming in and revolutionizing all of it.

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