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Phylogenetic classification and identification of bacteria by mass spectrometry

Nature Protocols volume 4, pages 732–742 (2009)Cite this article

Abstract

Bacteria are a convenient source of intrinsic marker proteins, which can be detected efficiently by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The patterns of protein masses observed can be used for accurate classification and identification of bacteria. Key to the reliability of the method is a robust and standardized procedure for sample preparations, including bacterial culturing, chemical treatment for bacterial cell wall disruption and for protein extraction, and mass spectrometry analysis. The protocol is an excellent alternative to classical microbiological classification and identification procedures, requiring minimal sample preparation efforts and costs. Without cell culturing, the protocol takes in general <1 h.

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Figure 1: A general overview of the procedure.
Figure 2: A mass spectrum of an E. coli sample.
Figure 3: Phylogenetic classification of a number of bacteria.

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Acknowledgements

We thank Drs Markus Kostrzewa and Thomas Maier (Bruker Daltonics), Dr Michael Kube (MPI for Molecular Genetics) and Prof. Klaus Geider (JKI Dossenheim) for valuable help in setting up the system described in this protocol, fruitful scientific discussions and the provided test samples. We also thank Dr Chung-Ting Han (MPI for Molecular Genetics) and Drs Kostrzewa and Maier for critical reading of the paper. This work was supported by the German Ministry for Education and Research (BMBF, Grant no. 0315082), the National Genome Research Net (NGFN, Grant no. 01 GS 0828), the European Union (FP7/2007-2013, under grant agreement no. HEALTH-F4-2008-201418 entitled READNA) and the Max Planck Society.

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  1. Max Planck Institute for Molecular Genetics, Otto-Warburg-Laboratory, Berlin, Germany

    Anja Freiwald & Sascha Sauer

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  1. Anja Freiwald
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Correspondence to Sascha Sauer.

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Freiwald, A., Sauer, S. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 4, 732–742 (2009). https://doi.org/10.1038/nprot.2009.37

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