High throughput metabolomics

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In many areas of both basic and applied biological research there is a pressing demand for large scale metabolome studies with thousands of strains, compounds, or conditions. This applies for example to functional genomics, causal elucidation of regulatory networks, mapping of gene-environment interactions in quantitative traits, inhibitor screens, toxicology studies, metabotyping of clinical samples, etc. Unfortunately, current metabolomics platforms have only limited throughput, typically up to 50 samples per day and instrument. To enable novel holistic studies, we continuously develop means to achieve massively higher throughput.

A conceptually very simple strategy to increase throughput is to omit chromatography and directly inject samples on a mass spectrometer with high resolving power. Since all analytes coelute simultaneously, this approach can't resolve compounds (isomers) with the same molecular weight and potentially suffers form ion suppression, poor reproducibility, matrix effects, etc.

We successfully addressed these potential issues and eventually established robust flow injection - MS to analyze about 2'000 samples/day in microbes, yeasts, or (adherent) cells. A completely novel IT solution for data management, processing, mining, and visualization was deployed to enable large-scale studies and intelligently exploit the data-set size. The whole pipeline works at native MS resolution (about 0.001 Da), and allows monitoring several thousands of biological features in complex extracts. Despite only a fraction can be putatively annotated based on accurate mass, the typical coverage is of >300 metabolites as listed from genomic reconstructions. The system scales well as demonstrated by a recent genome-wide analysis of E. coli single knockout mutants comprehensive of more than 35'000 independent injections on a single instrument within 5 weeks. Details on the platform were initially published by Fuhrer et al in 2011. Since then, however, we kept on continuosly improving sensitivity and performance by implementing newest developments in instruments, technology, and software.

Over the last few years, we injected > 500'000 samples. This system has become the essential workhorse of our approach and has delivered key insights in an steadily increasing number of own and external publications.


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  • Fuhrer T, Heer D, Begemann B, Zamboni N, High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection - time-of-flight mass spectrometry, Anal Chem. 2011; 83(18): 7074-7080 Pubmed doi
  • Fuhrer T, Zamboni N, High-throughput discovery metabolomics, Curr Opin Biotechnol, 2015 (31), 73-78 Pubmed doi 
  • Link H, Fuhrer T, et al. Real-time metabolome profiling of the metabolic switch between starvation and growthNat Methods, 2015, doi
  • Citations at Google Scholar
  • Sévin DC, Sauer U. (2014) Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nat Chem Biol. 2014 Apr;10(4):266-72 Pubmed
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Fri Apr 28 20:03:52 CEST 2017
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