Chapter 3: MALDI-TOF Mass Fingerprinting for Rapid Identification of Bacteria: Data Analysis and Algorithm Development

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of microorganisms. In a typical MALDI-TOF MS analysis of microorganisms, spectra of unknown samples are compared to reference libraries of spectra of known microorganisms by spectral pattern matching. This chapter provides an overview of the data analysis workflow for MALDI-TOF MS-based identification of microorganisms, including spectrum preprocessing, spectral matching, and result interpretation. The existing computational methods for the three steps of data analysis and available software solutions are summarized. In addition, bioinformatic methods that do not require a reference spectral library are introduced as alternatives to typical spectral matching approaches. Finally, the current challenges and outlook of MALDI-TOF MS data analysis for microorganism identification are discussed.