Thursday, February 19, 2015

Know someone who doesn't think mass spec can be reproducible and accurate? Send them this paper!

Man, this is awesome.  What is it that we hear about proteomics from the naysayers?  Interlab variability?  Poor reproducibility?  Next time you hear that send them this paper from Sue Abbatiello, Birgit Schilling and D.R. Mani et al., (in press and open access at MCP!)

What is it?  A concerted freaking effort that shows, conclusively that if we eliminate the dumb variables we're all always messing with and use the same prep and instrument methods and use a good quality control that we can get precise and reproducible quantification of peptides from human plasma -- in any lab.  The proof?  11 labs, 14 different LC-MS systems.  The same data!!!

And they didn't go after albumin for a "proof of concept".  They quantified 27 different cancer linked proteins and controls.  Something around 125 peptides!

One really interesting observation is that they did abundant protein depletion -- and were still reproducible.  A lot of previous observations had suggested that doing abundant protein depletion wreaks havoc on your plasma samples.  There is some solid data here that pointedly refutes that.  Sure, you can introduce variability if you do a lazy job depleting your plasma, but it looks like you can also do a great job (probably following the same protocol helps...)

I cut this image (please don't sue me...this thing is open access and I should eventually learn the details of what that really means) out of the paper!  Digestion and processing at individual sites!

Yes, I'm over excited.  Yes, this is the first paper I've read after opening a terrific chardonnay.  But that doesn't dilute that this is an incredible, thorough, and impressive paper from some top notch researchers at some great labs.  If you're into validation, I can't recommend this paper enough.

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