Maximizing the taxonomic resolution of MALDI-TOF-MS-based approaches to bacterial characterization: From culture conditions through data analysis

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be a rapid, effective, and sensitive tool for characterizing diverse bacteria. Historically, the primary application of this technology has been to identify bacteria at the genus and species levels in a few minutes. The most commonly used identification method involves matching mass spectra of unknown bacteria to reference spectra in commercially available databases with the assistance of manufacturer-created algorithms. Recently, there has been keen interest in enhancing the taxonomic resolution of MALDI to characterize bacteria at the strain and subspecies levels. Often, categorization of strains sharing similar traits, differentiation of closely related strains, and/or identification of a single strain are desired. Strain-level characterization is important in the development of counter-bioterrorism strategies, prevention of food contamination, and rapid diagnosis of bacterial infections. This chapter focuses on factors, including culture medium, sample preparation, data acquisition, and data analysis that affect strain-level characterization. In addition, the chapter highlights techniques and treatments that offer promise to improve the taxonomic resolution of MALDI-TOF MS-enabled approaches to bacterial characterization.