Ethanol exposure causes neurotoxicity, where neuroinflammation has been proposed to contribute to ethanol neurotoxicity. In addition to astroglia, microglia, as resident immune cells in the central nervous system, have been implicated as a key contributor to the neuroimmune and inflammatory processes. However, little is known regarding the role of microglia in alcohol-induced neuronal dysfunction. In this chapter, we describe a method that provides an effective and unbiased global-scale analysis for relative quantitation of protein expression in microglial cells to elucidate the molecular mechanisms underlying microglial activation after ethanol exposure. The approach involves stable isotope labeling with amino acids in cell culture followed by mass spectrometric analysis of stable isotope-labeled proteins derived from cultured microglial cells and represents a powerful tool that can be used for general assessment of microglial response at the protein level.