Monday, January 10, 2022

Getting more out of your (FLAG tag) experiments with FAIMS!


FLAG tags are for when you absolutely want to pull down a protein of interest to the point that you're willing to mutate your organism so you can pull down your flag tagged proteins with Anti-Flag. (Not these guys, these things).  

What are the challenges? Well, to do this the hard way, I'll cut from the abstract. 

Of this paper (almost forgot the paper link again!)

My interpretation is that when you use these proteins you've got a shitload of them around and it's hard to see past them to your targets. 

FAIMS time! 

Of course it helps. That's what it does. They experiment with settings to dig past their FLAG-tagged target protein that is 99% or 99.9% of their mixture. What is really cool here, I think, is how well the FAIMS unit works on their Orbitrap Fusion 2 (Luminati). 

They run the same samples on their FAIMS equipped Lumos compared to a non-FAIMS equipped Exploris 480 and Orbitrap Fusion 3 (Eclaire) -- and the Fusion 2 + FAIMS wins every comparison in the study. At one point they get 81% more peptides in the experiment than the Exploris 480! 

I don't know what they're charging for the FAIMS these days, but if you were looking for a boost in capabilities for some tough matrices I bet you'd spend less on this unit (minus your massive N2 usage) than you would on a whole new system! 

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