Shotgun proteomics involves the analysis of peptides obtained by enzymatic digestions of proteins and subsequent identification via tandem mass spectrometry. This approach is an effective method for studying global protein expression in neuronal systems. The method described here is a quantitative shotgun neuroproteomics method using amine-specific isobaric tags for a relative and absolute quantitation (iTRAQ)-based workflow. We will provide the technical details for sample preparation, two-dimensional liquid chromatography, tandem mass spectrometry, database search, and statistical analysis to identify differentially expressed proteins. We will use a recent study on a rat model of multiple sclerosis, experimental autoimmune encephalomyelitis to illustrate the successful application of this method.