Friday, January 18, 2019
LOPIT-DC: Subcellular proteomics returns -- in a much more accessible form!
LOPIT, HyperLOPIT (excuse capitalization spelling and hyphens that all may be wrong) has appeared on this blog more than once. It's brilliant and provides a way for quantitative proteomics with subcellular fractionation. We're often not doing ourselves any favors by mixing all the organelles from loads of different cells together, but fractionating beyond that seems really really hard.
LOPIT -- as smart as it is -- never cracked my list of "I have to find someone who needs data like this so I can do it" protocols. Primarily because it looked REAAAAALLLLY hard for someone who isn't good at sample prep things. I'm not the only person who was thinking this, I guess....
Let's fix that right now!
The figure at the top that was stolen from this nice open paper shows the old protocol on the left and the new protocol on the right!
Set a timer on your gradient centrifugation and then pull your subcellular fraction? I can do that! End up with single TMTplex experiment for analysis? I can do that as well. I bet you I can even take these files from PRIDE (PXD0112554) and process them in something that doesn't start and end with the letter "R"!
And -- get this --BOOM! -- mass spectrometrist friendly Shiny Web Interface!!
Is LOPIT easy now? No, that's probably a stretch. But these tweaks have made it far easier than it was before -- and what other technique can possibly get you these results? Nothing I've ever seen!
Kudos to these authors. Could they have sat back and established a monopoly on subcellular localization proteomics? Probably. Instead, they took the time and made this amazing technique far more approachable for the rest of us.