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Microorganisms are involved in all aspects of human life and are closely related to human disease and health. Mass spectrometry (MS) is a promising technique for microorganism characterization, with high throughput, high sensitivity, and high accuracy. This chapter provides an overview of rapid microorganism detection based on MS. The MS techniques for microorganism determination including matrix-assisted laser desorption/ionization time-of-flight MS, electrospray ionization MS, and ambient ionization MS are summarized. In addition, the applications of MS-based microorganism detection in clinical laboratories, environmental science, and the food industry are described. Finally, this chapter discusses the challenges and prospects of MS-based microorganism detection.

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