Fuck. This new preprint is awesome. For real....this is really really good, and I saw some stuff about it on LinkedIn and assumed it was blown out of proportion. Its not. It's really really cool.
What if you found a really good in vivo model that you could control well to try and dissect what and how single cells actually regulate protein abundance. There are amazing resources for protein turnover and mechanisms in bulk digests, but nothing comprehensive in single cells. I mean...we couldn't actually do that...yet...right?
In this case they specifically narrowed in on mouse tracheal cells. Then they metabolically pulsed the mouse diet. Then they did single cell transcriptomics and single cell proteomics (with multiplexing, to get 4,200 cells) and worked backward to figure out
What proteins correlate with transcript regulation, which work backward to protein regulation and which are regulated by clearance (what I'd call turnover, but they make a point that in vivo there are more than one way to drop the abundace of the protein in a cell.
It's the kind of basic science stuff that you know needs to be done with single cell proteomics so we can take that step forward and do applications - but...funding mechanisms are all pretty heavily biased toward actually applying it.
For the mass spec side, multiplexed DIA was used...there might be some details missing in the method section for the labeling but it's based on a previous referenced work. It's essentially mTRAQ with DIA. 4,200 cells with an average depth of 800 or 900 proteins.
I gotta run, but I'll be revisiting this one later.
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