More than three hundreds of genes related to brain diseases have been identified in human genome analysis. However, there are few information on the gene products (proteins) that give us the most important idea on the biological mechanism of the disease formation. Brain proteomics have been concentrated on the disease related to the brain tumor and neuronal apoptosis that involve many regulator proteins for cellular processes, such as cell cycle, DNA repair, apoptosis, etc. Many factors contribute to control their activations, and their downstream responses also depend on the cellular environment or other modifying factors in the cells of the central nervous system (CNS). To compile the information of the brain protein structures and functions related to the pathogenesis, and to make use of the information to the clinical application, proteomic study for the brain tissue/cells must be crucial. We have been constructing proteome maps of mouse and human brain by two-dimensional electrophoresis (2-D) and listing the information of protein expression profiles in the data bank. In this review, our proteomic approaches on the specific brain tissue and cellular proteins that relate to the neuronal apoptosis and brain tumor were introduced with two functional proteomic strategies; 1) Differential proteomic display (comparative 2-D) of brain tissue proteins, 2) Affinity cellular proteomic mapping; detection of specific binding proteins that associate with the target gene products using micro affinity columns. Our final goal on this study is to contribute to the advancement of medical science as well as brain science by constructing the proteomic database covered the gamut of protein information of the CNS disease related concerns.
