This chapter covers the selected applications of mass spectrometry and highlights its power to support diverse studies focusing on the mammalian brain. Microdialysis employs a semipermeable hollow-fiber membrane implanted in the tissue. It allows for the sampling of chemicals from the extracellular space of the brain, when the implanted probe is perfused at low flow rates and usually with a solution mimicking the composition of the cerebrospinal fluid (CSF). The reversed-phase ion-pair liquid chromatography (LC) coupled with positive-ion electrospray ionization (ESI) tandem mass spectrometry (MS/MS) has been shown to detect ACh with low limit of detection (1.4 fmol) and, thus, to measure this neurotransmitter and related endogenous compounds in rat brain microdialysates. Neuropeptides collected by microdialysis can be preconcentrated and desalted by reversed-phase LC, and subsequently supplied directly onto a micro- or nanoflow-LC column for gradient elution, and ESI-MS as well as MS/MS analysis. The separation and visualization of complex protein mixtures are commonly performed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 2D-PAGE followed by in-gel protease (trypsin) digestion, matrix-assisted laser desorption/ionization (MALDI)/time-of-flight (TOF) mass spectrometry, and sequence database searching is the technique most frequently used in today's neuroproteomics studies.