Thursday, September 20, 2018

Need some inspiration? REAL CLINICAL PROTEOMICS. This is what we can do today!!

Okay -- cool developments with our toys aside for a second -- this might be one of my all-time favorite papers. If you can look at that picture without getting inspired by how far proteomics has come -- AND WHAT WE MIGHT DO NEXT?? you probably didn't click the right link to end up here.

I think I might have passed by this paper once because I didn't know what a lot of the words were in that title. 

To be honest -- I have one criticism of this paper. The title is terrible. 

What I would have made the title --

 In a clinically relevant time frame we can help diagnose a cancer patient and pick a personalized therapy to kill their tumor and massively increase the chance the patient survives!!  

How'd they do it? They did label free proteomics on slides (? pretty sure?)  from an excised tumor as well as the surrounding stromal tissue. 

They rapid tip digest it (they use the rapid reduction/alkylation together method as well) and they pop 1ug of peptides onto an inhouse 40cm column (probably cost them $5 to make?) on a Q Exactive HF. Yup, just an HF. Like the one that is running brain digests from mice with generalized anxiety disorders or something in your lab right now that you were considering trading in for something more expensive to run mouse brain digest with? Same one! 

They use the always free MaxQuant and Perseus for the data processing and downstream analysis/stats. 

Why am I fixating on prices? Because the first argument in clinical anything (at least in the US) is "how can we make an absurd profit for our shareholders again this year if the test we charge $8000 for costs more than $1.16 to actually run? Do you think we're running a charity in this hospital?!?!?" 

This group just showed us that we could do personalized proteomics to help patients TODAY with an aging benchtop Orbitrap (that will fit neatly into any clinical lab -- have you seen how much smaller colorimetric blood analyzers are now? They're tiny!  Boom -- put an HF there). If you consider free software, virtually no cost for reagents (10uL of acetonitrile and some trypsin) and I don't think we're too far off that $1.16 target for the assay cost. We can stop talking about personalized medicine and actually start doing it already! 

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