Surfing the metabolome. Application of high resolution mass spectrometry to the analysis of single cell organisms

PhD ceremony: Mr. R.A. Scheltema, 13.15 uur, Academiegebouw, Broerstraat 5, Groningen

Thesis: Surfing the metabolome. Application of high resolution mass spectrometry to the analysis of single cell organisms

Promotor(s): prof. R.C. Jansen, prof. R. Breitling

Faculty: Mathematics and Natural Sciences

Untargeted metabolomics provides researchers with a window into the metabolic state of an organism at any point during its development. As the metabolome often provides the closest correlate to the phenotype under investigation, this approach promises to be an efficient strategy to uncover novel biological processes. The methodology is very suitable for the characterization of single cell organisms, as these can be cultured in sufficiently high volumes for generating metabolite levels detectable with modern mass spectrometry equipment. The relative homogeneity of the cultures ensures a representative reflection of the intracellular metabolite contents.

The recorded datasets are however complex, requiring extensive strategies for extracting the relevant information. A typical profile contains not only a large number of real metabolite signals, but also a large amount of noise of different types, including many signals caused by derivative analytes (e.g., isotopes, adducts and fragments). The challenge is to detect, identify and quantify, and compare the real metabolite signals in a reliable way.

The principal aim of the work leading up to this thesis, has been the development of bioinformatics strategies and tools for the analysis of rich metabolomics datasets recorded from single cell organisms. For this purpose we studied the protozoan parasite Leishmania donovani and the Gram-positive bacterium Streptomyces coelicolor in close collaboration with the Department of Parasitology at the Institute of Tropical Medicine Antwerp and the Microbial Physiology Research Group at the University of Groningen, respectively. Part 1 describes the experimental protocol for running mass spectrometry analysis and newly developed approaches for analyzing the recorded data. Part 2 describes the two biological studies, which led to the identification of metabolic actors in observed drug resistance in L. donovani and the response to salt shock in S. coelicolor. Part 3 discusses our perspective of metabolomics research and outlines some future research directions.