Integrating quantitative proteomic and transcriptomic datasets promises valuable insights in unraveling the molecular mechanisms of the brain. We concentrate on recent studies using mass spectrometry and microarray data to investigate transcript and protein abundance in normal and diseased neural tissues. Highlighted are dual spatial maps of these molecules obtained using voxelation of the mouse brain. We demonstrate that the relationship between transcript and protein levels displays a specific anatomical distribution, with greatest fidelity in midline structures and the hypothalamus. Genes are also identified that have strong correlations between mRNA and protein abundance. In addition, transcriptomic and proteomic analysis of mouse models of Parkinson's disease are discussed.