Human Brain Proteome Atlas (HBPA) aims to provide a draft map of the spatial human brain proteome to support researches on normal brain function and disease. Currently, HBPA contains 4310 protein expression profiles across 29 broadmann areas in cerebral cortex obtained from iTRAQ-based 2DLC-MS/MS analyses. This dataset reveals that proteomic profile of a brain area is highly correlated with its anatomical and functional characteristics.