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Updated: May 22, 2026
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Sample Preparation for Single Cell Mass Spectrometry Metabolomics Studies: Combined Cell Washing, Quenching, Drying, and Storage
Published on: September 16, 2025
Fast sampling of the cellular metabolome
Walter M Van Gulik1, Andre B Canelas, Hilal Taymaz-Nikerel
1Department of Biotechnology, Delft University of Technology, Delft, The Netherlands. w.m.vangulik@tudelft.nl
Methods in Molecular Biology (Clifton, N.J.)
|May 29, 2012
Summary
Accurate microbial metabolomics requires rapid quenching and extraction to preserve metabolite levels. A differential method is presented to accurately measure intracellular metabolites in prokaryotes by subtracting extracellular levels.
Area of Science:
- Microbial metabolomics
- Biochemistry
- Analytical chemistry
Background:
- Accurate microbial metabolomics requires rapid sampling, quenching, and extraction to prevent metabolite degradation and ensure reliable measurements.
- A significant challenge is differentiating intracellular metabolites from extracellular ones, especially in prokaryotes, as standard quenching methods can cause metabolite leakage.
Purpose of the Study:
- To provide an overview of established sampling, quenching, and extraction methods for microbial metabolomics.
- To present detailed protocols for quantitative metabolomics in both eukaryotic and prokaryotic microorganisms.
- To address the challenge of extracellular metabolite interference in microbial metabolomics.
Main Methods:
- Review of literature on microbial metabolomics sampling, quenching, and extraction techniques.
- Development and description of protocols for rapid sampling, quenching, and extraction.
- Application of a differential method using total broth and supernatant samples for intracellular metabolite quantification.
Main Results:
- Established protocols for rapid sampling, quenching, and extraction suitable for microbial metabolomics.
- Demonstrated a differential method for accurate intracellular metabolite quantification in prokaryotes.
- Provided a comprehensive approach applicable to both eukaryotic and prokaryotic microorganisms.
Conclusions:
- The presented methods enable accurate snapshots of the microbial metabolome.
- The differential method effectively overcomes challenges posed by extracellular metabolites in prokaryotes.
- These protocols facilitate high-throughput, quantitative metabolomics for diverse microorganisms.
