Characterization of microorganisms is critical for the diagnosis and subsequent treatment of infectious diseases, as well as for the detection of biohazards in the environment. Matrixassisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry (MS) have both been used to analyze microorganisms. There are a number of advantages to using MALDI-MS for the direct identification of bacteria, including the high speed and sensitivity of the technique, the simplified mass spectra obtained (predominantly singly charged ions), and the approach tolerance to contaminants. ESI-MS allows on-line detection to be combined with sample purification, concentration, and separation techniques, such as microdialysis, solid phase extraction, liquid chromatography, and capillary electrophoresis (CE). Thus, ESI-MS has become a powerful tool for the analysis of complex systems.