Mass spectrometry: A powerful tool for the identification of wine-related bacteria and yeasts

Abstract

Traditional methods for identifying microorganisms in microbiology laboratories are based on microscopic and biochemical methods (phenotyping) and gene sequencing identification techniques (genotyping). However in the past decade, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been established as a new reliable, rapid, and inexpensive automatable method for identifying a wide array of bacteria, archaea, fungi, dermatophytes and even viruses. Its "molecular-phenotypic”-based methodology is based on the reproducible detection of protein mass patterns (proteomic profile) obtained from whole cells, cell lysates, or crude bacterial extracts. Microbial MALDI-TOF MS mass spectra can be regarded as snapshots of the protein composition of the strains under study. Many of the mass spectral signals have been assigned as high-abundance proteins with housekeeping functions, such as basic ribosomal proteins or DNA-binding proteins. These proteins are highly conserved and consistently expressed under nearly all growth conditions. They can thus be regarded as robust biomarker candidates of the respective microorganism and their identification. As ribosomal protein genealogies mirror the rRNA genes reconstructed phylogenies, the mass spectra show congruency with the genealogy of microorganisms, and hence, can be implemented as a valuable analytical tool for polyphasic approaches in microbial systematics. For microbial characterization by MALDI-TOF MS, the protein mass spectra can be analyzed in two principally different ways, library-based approaches and bioinformatics-enabled approaches. Considering the more widespread application of library-based approaches to profile microorganisms at the species and even subspecies level, this review will focus on challenges and limits associated with this MS profiling technique and its successful real-world application of identifying microbes involved in the winemaking process.