In medical microbiology, the identification of microorganisms in clinical specimens is a key step for successful therapy. In the last few years, new technologies have emerged for routine identification, among which matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a technology that appears very promising as it is currently becoming established in microbiological laboratories worldwide. MALDI-TOF MS allows the identification of microorganisms - bacteria as well as fungi - by so called intact-cell mass spectrometry, and the comparison of a sample’s mass spectrum to reference mass spectra in a database. The key factors to the success of this technology are: i) the fact that a uniform sample preparation procedure is utilized for many different types of microorganisms, ii) the short time to a result, and 3) the comparatively low cost per analysis. Additionally, mass spectrometry based identification can be readily expanded to different microbiological fields, including food, industrial and veterinary microbiology.
In this chapter, the basic principles of MALDI-TOF MS are briefly described, followed by an introduction to intact-cell mass spectrometry of microorganisms and mass based identification. Further, limits of the technology are reviewed in the light of expected future developments. Finally, possible consequences of the broad introduction of MALDI-TOF MS based on microbial identification systems for practical and theoretical issues of medical microbiology are discussed.