Thanks to all the journals allowing Open Peer Review and allowing me to sign about half of the 30 or so papers I've reviewed recently, it's pretty clear to people how unproductive I think things like this title are. Even if, as in here, I really do like the paper.
I think I'm just old, for real, but I do think that if you've got cool biology in your paper but you've got the instrument front and center you're doing yourself a disservice. 10 years from now that instrument is going to be $100k from second party vendors or $50k on Ebay without an ionization source or accompanying PC and no one is going to look at the biology in your paper.
However - this is some pretty amazing crosslinking data. And that's my point, I guess. It's a nice study. FAIMS helps a lot with crosslinking on both an Eclipse and Astral, but stepped collision energy - while helpful on the Tribrid, has minimum effects on the Astral. Higher CE helps a lot. There is also a neat toolkit I heard mentioned at iHUPO called "Raw Vegetable" which I assumed someone said but actually meant "Raw Beans" (which I love). You also get a cool step-by-step breakdown on how to optimize crosslink data analysis in Proteome Discoverer. They do some filtering inside the software and break it down at every level. Super helpful for anyone using that toolkit in their lab (I think they use 3.1).
Worth noting, they used the freely available MSAnnika node for the crosslinking, which is pretty cool to see it in use - and optimized through.
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