Deep brain stimulation (DBS) is a neurosurgical procedure that provides therapeutic benefits for movement and affective disorders. The nucleus basalis of Meynert (NBM) and substantia nigra (SN) are considered target areas to apply DBS. Even though the degeneration of NBM and SN underlies the cognitive decline observed in neurological diseases, the protein knowledge derived from both areas is scarce. We have characterized the proteome present in both subcortical brain areas using the Triple TOF 5600 mass spectrometer, identifying 2775 and 3469 proteoforms in NBM and SN respectively. Data mining of MS-generated proteomic data have revealed that: i) 675 proteins tend to localize to synaptic ending, ii) 61% of the global dataset is also present in human CSF and/or plasma, and iii) 894 proteins have not been previously identified in healthy brain by MS. The correlation of NBM and SN proteomic expression profiles with human brain transcriptome data available at Allen Brain Atlas has revealed protein evidence for 250 genes considered with brain-wide expression and 112 genes with region-specific expression in human brain. In addition, protein datasets have been classified according to their chromosomal origin, increasing the current proteome coverage in healthy human brain. The nucleus basalis of Meynert and substantia nigra are brain areas of clinical interest to apply the deep brain stimulation (DBS) technology in neurosurgery. Our proteomic characterization has revealed 675 proteins involved in the regulation of synaptic transmission, electrical machinery, and neurotransmitter release in both DBS target areas. Moreover, 2599 identified proteins present capacity to be secreted to the CSF and plasma. Our data contribute to a further step towards the characterization of the anatomical atlas of the human brain proteome, detecting 652 proteins that are common between different basal ganglia structures. This article is part of a Special Issue entitled: HUPO 2014.