Fast sampling for quantitative microbial metabolomics: new aspects on cold methanol quenching: metabolite co-precipitation


The intra- and extracellular concentrations of 16 metabolites were measured in chemostat (D = 0.1 h−1) anaerobic cultures of the yeast Saccharomyces cerevisiae CEN.PK-113-7D growing on minimal medium. Two independent sampling workflows were employed: (i) conventional cold methanol quenching and (ii) a differential approach. Metabolites were quantified in different sample fractions (total, extracellular, quenching supernatant, methanol/water extract and pellet) in order to derive their mass balance. The differential method in combination with absolute metabolite quantification by gas-chromatography with isotope dilution mass spectrometry (GC–IDMS) was used as a benchmark to assess quality of the cold methanol quenching procedure. Quantitative comparison of metabolite concentrations in all fractions collected by different quenching techniques indicates asystematic loss of the total mass of various metabolites in course of the cold methanol quenching. Pellet resulting from the cold methanol quenching besides biomass contains considerable amounts of precipitated inorganic salts from the fermentation media. Quantitative analysis has revealed significant co-precipitation of polar extracellular metabolites together with these salts. This phenomenon is especially significant for metabolites with large extracellular mass-fraction. We report that the co-precipitation is a hitherto neglected phenomenon and concluded that its degree strongly linked to culturing conditions (i.e. media composition) and chemical properties of the particular metabolite. Thus, intracellular metabolite levels measured from samples collected by cold methanol quenching might be uncertain and variably biased due to corruption by described phenomena.


DOI: 10.1007/s11306-014-0700-8

Projects: MOSES

Publication type: Not specified

Journal: Metabolomics

Citation: Metabolomics 11(2) : 286

Date Published: 1st Apr 2015

Registered Mode: Not specified

Authors: Maksim Zakhartsev, Oliver Vielhauer, Thomas Horn, Xuelian Yang, Matthias Reuss

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Zakhartsev, M., Vielhauer, O., Horn, T., Yang, X., & Reuss, M. (2014). Fast sampling for quantitative microbial metabolomics: new aspects on cold methanol quenching: metabolite co-precipitation. In Metabolomics (Vol. 11, Issue 2, pp. 286–301). Springer Science and Business Media LLC.

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Created: 1st Nov 2015 at 17:50

Last updated: 8th Dec 2022 at 17:26

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