Wait. How many proteins are in the nucleus?

 

Ummm...okay... so I stand corrected.... Thank you ProteinAtlas! 

https://www.proteinatlas.org/humanproteome/subcellular/nucleoplasm

So...I'm surprised by a whole lot of this. I'd personally expected that when we got around to doing single nuclei proteomics that there wouldn't be a lot there. 

Something like 

HISTONES

and all the AHNAKs

and that would be about it. Sure, some transcription factors, but they're low copy number at the best of times.

And there is a whole lot more going on there which doesn't make much sense to me at all, and that's okay.

So far we've seen two studies with single nuclei proteomics, one published and one that I'm sure will show up any day now.

In this one, Derks et al., used multiplexed DIA reagents on a TIMSTOF SCP and optimized out some carrier channel levels for the nuclei. Across the study I count around 1,800 protein groups in their data, however the actual protein IDs are missing from a lot of the processed data. I assume that's so they can do unbiased clustering downstream. SCP-Viz requires an identifier to perform clustering which makes it harder for me to reanalyze the data, but it's still a big number. Mun et al., 

did a far smaller number of nuclei, but did it with label free diaPASEF. I've got to dig back into their numbers but they were also far larger than I'd expected (see eroneous assumptions above...)