Matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometry (TOF MS) is now accepted as a quick, easy-to-use, cost-effective, and accurate technique for the identification of microorganisms. However, the successful identification of microorganisms is dependent upon careful attention to factors such as growth conditions, extraction methods, mass spectral data collection, and data analysis procedures. Currently, most microorganism identification has been limited to the species level, and only a limited number of publications have been successful in achieving strain-level identification. In this work, a "cell-free" approach is introduced where peptide analytes secreted by several Saccharomyces cerevisiae strains during their growth period are analyzed. The analysis of the cell supernatant generates mass spectral patterns that are specific to each strain. The patterns generated in combination with a robust data analysis workflow using the open-source programs MALDIquant and Mass-Up allows for strain-level identification of S. cerevisiae. The cell-free approach using the yeast supernatant to accurately identify yeast strains is presented here as a proof of concept. Graphical Abstract.
Keywords: Cell-free approach; MALDI-TOF MS; MALDIquant; Mass-Up; Microorganism identification; S. cerevisiae strain identification.