Friday, November 22, 2019

Wanna go fast?!? SPEED Acid digestion!

I'm going to start off by admitting I mostly moved this paper up the blogging queue so I would have excuses to put more Ricky Bobby quotes on this blog.  However, there are clearly some jewels in here. It might seem off topic, but -- THERE ARE MICROBIOME STANDARDS FROM ATCC!!! -- and they use one for the gut microbiome in this study. I've written a lot of commercial groups that do genetics microbiome standards to see if they had anything for proteomics and I've been ignored. Probably because everyone in the world but me knows that ATCC has already locked up that market? Great. I hear they make good standards and it looks to me like they'll be perfect for metaproteomics and metabolomics. 

With the dozens (hundreds?) of sample prep methodologies out there, why would you use this one? Cause...

...that was a joke...

SPEED isn't a crazy fast digestion method like FLASH or sTRAP (which can be killer fast, if you want to use it that way -- I've noticed it used slower in the literature, because our typical overnight digestion can be pretty darned convenient). The goal here appears to be to minimize sample handling, because that should always be our goal.

I stole the overview of the method as the top image in the post and it should expand if you click it. I really really like one part of it. The turbidity measurement for protein concentation. <1 minute to know what my protein concentration is? Now...that being said....I've not found nanodrop to be the most accurate way of measuring proteins and turbidity seems even a step back from that. (As always, please keep in mind I'm not good very good at sample prep and my decreasing vision and hand eye coordination aren't exactly helping (thanks sensescence! you're the best!). If that is linear and sensitive, that would save a lot of time.

Here, microwave digestion is used as a first step for the hardest of samples (10 seconds for gram positives with an 800W microwave [Much less time than you'd need for Shake 'n Bake. Yes. That just happened]) it isn't used as the ultimate digestion method. Trypsin is still employed as the final digestion reagent.

The authors are quick to point out that while this method has some great pluses -- like no detergents, there are some obvious concerns --

--- they look at phosphorylations in this study.

How's it do? On the microbiome standard it appears to outperform iST by a lot and even beats STrap. If you'd like to check out the data it has been uploaded to ProteomeXchange as PXD011189, but hasn't been made live yet.

Hey authors! This is two papers in one weekend. Don't forget to tell the repositories when you're papers get accepted so all us nosy people can actually start digging through them.

Do we have a new number 1 digestion method? I'd like to see more data from other people before thinking this beats the current number 1 (which I'd call STrap right now).

And you know you can't have 2 number 1s -- cause then you'd have 11.

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