Maybe it has something to do with my common spatial proximity to a certain neuroscience postdoc, but I've definitely heard that neural proteomics is some tough stuff to do. There are limitations due to lots of things, including low relative protein amount to lipids and other less interesting biomolecules as well as just historic limitations of mass spec sensitivity.
A lot of mouse brain proteomics has come out of Max Planck over the years, and they just decided to show us in this new article in Nature Neuroscience just where you can get with today's methods and technology.
Mouse brains taken out, mouse brains chopped into the correct sub-regions, proteins extracted, peptides subjected to simple StageTip fractionation and then full out label free proteomics with a Q Exactive HF.
The sensitivity problems of the past are history with simple fractionation and a Q Exactive. There is plenty of material in a region of a tiny mouse brain to get full proteome coverage. The output is incredible. Their base group ran about 12k proteins and anywhere from hundreds to thousands of proteins show differential expression across the various sub-types.
To sweeten the analysis, they went ahead and did RNA-Seq on these brain regions and compared both the IDs and the quantification -- cause, you know, why not!
I'll throw it out there that I'm pretty impressed by the data integration they demonstrate in Perseus in these 2 data sets. And the fact they draw some really interesting conclusions on the processes leading to neural cell differentiation is just icing on the cake here!
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