Sunday, January 28, 2024

Crosslinking proteomics plus AlphaFold2 = higher confidence data all around!

 



I can't really assess how good this new toolkit is, but it makes sense and the illustrations are gorgeous!  


My argument for why it is worth posting is that I've never once put crosslinking reagent into some proteins (or....well....had someone else do it) and have my spectra improve. Those chemicals generally do the opposite. Then, particularly if you're using a fancy tribrid with the real time crosslinking stuff, a lot of the data you get is ion trap (blech) and it's tough to really tell what is what. 

XLMS-tools (on git?lab?) is an ambitious way to leverage the fancy predictive capabilities of AlphaFold 2 to increase you confidence in those putative identifications - AND the opposite. 

Sounds smart, the software and data is publicly available and the use of proteins in open/closed configurations as spotchecks is a compelling argument.

Funny thing I learned at EuBiC is that AlphaFold has very strict high mass cutoffs, so this probably wouldn't help you much for a big protein. To fold big proteins they cut the sequences into little chunks and fold those. Which....is probably less dumb than it sounds. But that's AlphaFold's problem, not this nice new study. 


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