Shotgun mass spectrometry analysis of the human thalamus proteome

The thalamus plays pivotal roles in the central nervous system as relay center for organizing information, such as auditory and visual senses from diverse brain regions and their re-distribution to the cerebral cortex. Brain diseases including schizophrenia, Parkinson's disease, epilepsy, and bipolar disorder have been associated with the thalamus. We performed a shotgun proteome analysis of iTRAQ-labeled tryptic peptides of human mediodorsal thalamus protein extracts coming from two healthy male and two healthy female subjects. The shotgun workflow consisted of IEF fractionation, RP LC and MALDI-TOF/TOF mass spectrometric analysis. We were able to identify 542 proteins that are involved in different biological processes and from diverse cellular localizations. A considerable fraction of these proteins had not been identified by traditional proteomics methods such as 2-DE. The thalamus proteome contributes to the knowledge of the human brain proteome and future applications in basic and clinical research.