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Gas Chromatography–Mass Spectrometry (GC–MS)

Gas Chromatography–Mass Spectrometry (GC–MS)

Gas chromatography–mass spectrometry (GC–MS) is the combination of analytical techniques of gas chromatography and mass spectrometry in a single instrument for analyzing a mixture of compounds. The gas chromatograph separates the compounds in the mixture, and the mass spectrometer analyzes each compound separately to determine the molecular masses and molecular structures.
A gas chromatograph consists of a long, narrow capillary column with a polysiloxane coating on the inner wall....

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Updated: Jan 8, 2026

Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry GC-MS-based Metabolomics

Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry GC-MS-based Metabolomics

Published on: June 6, 2018

Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.

Nikita Denisov¹, Fabian Springer¹, Amber Brauer-Nikonow¹

¹Molecular Systems Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Analytical and Bioanalytical Chemistry

|December 15, 2025

Summary

Researchers developed a new GC-MS/MS method to quantify 120 gut bacteria metabolites. This tool aids in understanding microbiota-host metabolic interactions and their role in diseases.

Keywords:

Bacterial metabolites DNA stabilization buffers GC-MS/MS Gut microbiota

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Last Updated: Jan 8, 2026

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Published on: June 6, 2018

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Published on: December 15, 2011

Area of Science:

Microbiome research
Metabolomics
Analytical chemistry

Background:

Gut microbiota metabolites significantly impact host physiology and disease development.
Accurate quantification of these metabolites is crucial for understanding host-microbe interactions.
Existing methods may have limitations in scope or sensitivity.

Purpose of the Study:

To develop and validate a sensitive gas chromatography-tandem mass spectrometry (GC-MS/MS) method.
To quantify a broad range of 120 volatile and semi-volatile gut microbial metabolites.
To enable absolute metabolite quantification in various biological matrices.

Main Methods:

Gas chromatography-coupled tandem mass spectrometry (GC-MS/MS) utilizing multiple-reaction-monitoring (MRM).
Quantification of 120 target compounds including short-chain fatty acids, indols, and organic acids.
Use of isotopically labeled internal standards for absolute quantification.

Main Results:

Developed a GC-MS/MS method capable of quantifying 120 microbial metabolites with high sensitivity (0.45 pmol to 1 nmol).
Successfully applied the method to diverse sample types: plasma, liver, feces, and intestinal contents from mice.
Demonstrated quantification in stool samples preserved in DNA stabilization buffers, compatible with microbiome sequencing.

Conclusions:

The novel GC-MS/MS method provides a robust tool for absolute quantification of gut microbiota metabolites.
This analytical advancement facilitates deeper investigation into microbiota-host metabolic crosstalk.
The method supports research into the role of microbial metabolites in health and diseases like metabolic disorders and cancer.