Defining the proteomes encoded by each chromosome and characterizing proteins related to human illnesses are among the goals of the Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease-driven HPP. Following these objectives, we investigated the proteomes of the human anterior temporal lobe (ATL) and corpus callosum (CC) collected postmortem from eight subjects. Using a label-free GeLC-MS/MS approach, we identified 2,454 proteins in the ATL and 1,887 in the CC through roughly 7,500 and 5,500 peptides respectively. Considering that the ATL is a gray matter region while the CC is a white matter, they presented proteomes specific to their functions. Besides, 38 proteins were found to be differentially expressed between the two regions. Furthermore, the proteome datasets were classified according to their chromosomal origin and five proteins were evidenced at MS level for the first time. We identified 70 proteins of the chromosome 15 - one of them for the first time by MS - which were submitted to an in silico pathway analysis. These revealed branch point proteins associated to Prader-Willi and Angelman syndromes and dyskeratosis congenital, which are chromosome 15 associated diseases. Data presented here can be a useful for brain disorders studies as well as for contributing to the C-HPP initiative. Our data are publicly available as resource data to C-HPP participant groups at http://yoda.iq.ufrj.br/Daniel/chpp2013. Additionally, the mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000547 for the corpus callosum and PXD000548 for the anterior temporal lobe.