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  • Review Article
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Mass spectrometry tools for the classification and identification of bacteria

Nature Reviews Microbiology volume 8, pages 74–82 (2010)Cite this article

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Key Points

  • Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry has become an important tool in the life sciences. Recently, mass spectrometry methods have been developed that are tailored to the rapid classification and identification of bacteria and other microorganisms.

  • MALDI-based protein mass pattern detection ('profiling') is an inexpensive and straightforward approach for bacterial classification and identification. The method can easily distinguish bacteria on the genus, species and, sometimes, subspecies level.

  • MALDI-based resequencing is an accurate, flexible and efficient alternative to conventional DNA sequencing applications in microbiology.

  • ESI-based detection of PCR products is a fast epidemiological tool for the analysis of microorganisms.

  • The three mass spectrometry approaches can be cleverly combined to provide comprehensive tools for bacterial detection.

  • Automated, standardized protocols and mature software packages for the mass spectrometry analysis of bacteria are available.

  • The methods can be easily adapted by microbiology laboratories using either academic or commercial protocols.

Abstract

Mass spectrometry has become an important analytical tool in biology in the past two decades. In principle, mass spectrometry offers high-throughput, sensitive and specific analysis for many applications in microbiology, including clinical diagnostics and environmental research. Recently, several mass spectrometry methods for the classification and identification of bacteria and other microorganisms, as well as new software analysis tools, have been developed. In this Review we discuss the application range of these mass spectrometry procedures and their potential for successful transfer into microbiology laboratories.

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Figure 1: Matrix-assisted laser desorption/ionization protein mass pattern approach.
Figure 2: Matrix-assisted laser desorption/ionization-based resequencing.
Figure 3: Electrospray ionization analysis of PCR products.

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Acknowledgements

We thank M. Kostrzewa, T. Maier, J. Sauer and C. Honisch for discussions and C.-T. Han for critical reading of the manuscript. We also thank S. Holzhauser, V. Nicolaysen and A. Freiwald for help with the figures. Our work is supported by the German Ministry for Education and Research (BMBF; grant number 0315082), the National Genome Research Net (NGFN; grant number 01 GS 0828), the European Union (FP7/2007-2013, under grant agreement number [HEALTH-F4-2008-201418], entitled READNA), and the Max Planck Society. We apologize to all whose work is not covered here owing to space limitations.

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  1. Max Planck Institute for Molecular Genetics, Otto-Warburg Laboratory, Ihnestrasse 63-73, Berlin, D-14195, Germany

    Sascha Sauer & Magdalena Kliem

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Correspondence to Sascha Sauer.

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DATABASES

Entrez Genome Project

Bacillus anthracis

Bacteroides fragilis

Escherichia coli str. K-12 substr. MG1655

Haemophilus influenzae

Neisseria meningitidis

Staphylococcus aureus

Streptococcus pyogenes

FURTHER INFORMATION

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Mass Spectrometry – a Textbook

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Glossary

Enzyme-linked immunosorbent assay

(ELISA). A common serological test for the presence of particular antigens, using specific antibody binding and an enzyme to generate reporter label molecules.

Pulsed-field gel electrophoresis

(PFGE). A variation on the standard gel electrophoresis such that an alternating voltage gradient is applied to improve the separation of biomolecules such as large nucleic acids.

GC–MS

Gas chromatography–mass spectrometry coupling, a technique that is applied to isolate the components of volatile samples in the gas phase and to seamlessly identify and potentially quantify the single components by a mass spectrometer.

Matrix-assisted laser desorption/ionization

(MALDI). A soft method for the generation of ions that uses laser bombardment of crystals containing analyte molecules and an excess of matrix molecules that absorb laser light of a specific wavelength.

Electrospray ionization

(ESI). A soft technique for the generation of ions in aerosols.

Unsupervised hierarchical clustering

A procedure for statistical data analysis that uses clustering algorithms to find successive data clusters using previously generated clusters, which can be represented in a tree structure termed a dendrogram.

Multilocus sequence typing

A molecular biology method for the typing of multiple genomic loci, which is applied to analyse isolates of bacterial species using the DNA sequences of internal fragments of multiple housekeeping genes. The first protocol has been established for Neisseria meningitidis, the causative pathogen of meningococcal meningitis and septicaemia.

Euclidean distance

A mathematical term that describes the distance between two points, which can be verified by application of the Pythagorean theorem.

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Sauer, S., Kliem, M. Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol 8, 74–82 (2010). https://doi.org/10.1038/nrmicro2243

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