MALDI TOF MS profiling of bacteria at the strain level: A review

Since the advent of the use of matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight mass spectrometry (TOF MS) as a tool for microbial characterization, efforts to increase the taxonomic resolution of the approach have been made. The rapidity and efficacy of the approach have suggested applications in counter‐bioterrorism, prevention of food contamination, and monitoring the spread of antibiotic‐resistant bacteria. Strain‐level resolution has been reported with diverse bacteria, using library‐based and bioinformatics‐enabled approaches. Three types of characterization at the strain level have been reported: strain categorization, strain differentiation, and strain identification. Efforts to enhance the library‐based approach have involved sample pre‐treatment and data reduction strategies. Bioinformatics approaches have leveraged the ever‐increasing amount of publicly available genomic and proteomic data to attain strain‐level characterization. Bioinformatics‐enabled strategies have facilitated strain characterization via intact biomarker identification, bottom‐up, and top‐down approaches. Rigorous quantitative and advanced statistical analyses have fostered success at the strain level with both approaches. Library‐based approaches can be limited by effects of sample preparation and culture conditions on reproducibility, whereas bioinformatics‐enabled approaches are typically limited to bacteria, for which genetic and/or proteomic data are available. Biological molecules other than proteins produced in strain‐specific manners, including lipids and lipopeptides, might represent other avenues by which strain‐level resolution might be attained. Immunological and lectin‐based chemistries have shown promise to enhance sensitivity and specificity. Whereas the limits of the taxonomic resolution of MALDI TOF MS profiling of bacteria appears bacterium‐specific, recent data suggest that these limits might not yet have been reached. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:188–217, 2013