Graphical abstract

Brain transcriptome and connectome maps are being generated, but an equivalent effort on the proteome is currently lacking. Here we performed high-resolution mass spectrometry-based proteomics for in-depth analysis of the mouse brain and its major brain regions and cell types. Comparisons of the 12,934 identified proteins in oligodendrocytes, astrocytes, microglia and cortical neurons with deep sequencing data of the transcriptome indicated deep coverage of the proteome. Cell-type specific proteins defined as ten-fold more abundant than average expression, represent about a tenth of the total proteome.

The mass spectrometry proteomics data can be accessed through the ProteomeXchange Consortium