Understanding the Role of Mass Spectrometry in Metabolomics

Metabolomics – the study of metabolites (such as sugars, lipids, and amino acids) present in cells, tissues, or organisms – provides wide ranging insights into cellular processes and the physiological state of an organism at a given point in time.

This makes metabolomic data particularly useful for researchers that investigate disease mechanisms and drug discovery, but also for any research investigating the mechanics within a cell.

In this article, we are going to investigate the critical role that mass spectrometry plays in studying metabolomics, and some of the different methods and techniques that are used in this ever-evolving field.

Quantitative Metabolomics: A Deep Dive

Metabolomics is used to describe the study of small molecules, quantitative metabolomics takes this one step further by providing accurate measurement of concentrations or relative abundance of metabolites in biological samples.

Overview of metabolomics and metabolites
Image: Chemistry Department NMR Research Facility of the University of Oxford

The data allows for the study of metabolite levels between different samples or conditions, hence enabling the discovery of metabolic changes associated with diseases, responses to treatment, or other biological processes.

For quantitative metabolomics to work, samples are often compared to known standards or labeled with isotopes to facilitate accurate quantification. There are two main approaches in quantitative metabolomics: targeted and untargeted.

Targeted quantitative metabolomics focuses on a predefined set of metabolites and is typically used when there is a specific hypothesis to be tested. Untargeted quantitative metabolomics on the other hand, focuses on the comprehensive analysis of all detectable metabolites in a sample without bias towards specific metabolites.

The Role of Mass Spectrometry in Metabolomics

Mass spectrometry (MS) is used to study metabolomics because of its sensitivity, selectivity, and capability to analyze a variety of metabolites at high-throughput.

But for data generated by mass spectrometry to be most effective, it is often coupled with additional equipment – such as gas chromatography (GC) or liquid chromatography (LC) – to separate molecules or molecule fragments, based on polarity and size before they enter the detector.

Gas Chromatography – Mass Spectrometry (GC-MS)

GC-MS combines gas chromatography with mass spectrometry for detection. The GC component separates volatile compounds in the sample, which then enter the mass spectrometer for detection, making the method particularly suitable for analyzing small, volatile, and thermally stable metabolites.

Liquid Chromatography – Mass Spectrometry (LC-MS)

In LC-MS, liquid chromatography is used to separate a sample, before quantification by a mass spectrometer. This technique is particularly useful for studying complex biological samples with a high degree of variability, and can handle a wider range of metabolites, including larger, non-volatile, or thermally unstable species.

Tandem Mass Spectrometry (MS/MS)

Tandem Mass Spectrometry – also referred to as MS/MS or MS2 – involves multiple mass spectrometry selection, typically with some form of fragmentation occurring in between.

For metabolomic studies, MS/MS is often used for the identification of unknown metabolites providing structural information that can aid in identifying the original molecule, by causing the selected ions to fragment and analyzing the results.

Sample Preparation for Mass Spectrometry in Metabolomics

When it comes to using mass spectrometry for metabolomics, sample preparation directly impacts the quality and reproducibility of the data obtained, which is why proper care and attention must be taken. Whilst there are varying techniques available for consideration, it is important to consider the sample type, and the properties of the metabolite(s) of interest.


Metabolites are extracted from the sample using solvents, with the type of solvent used depending on the polarity of the metabolites. Polar metabolites are often extracted using polar solvents such as methanol or water, while nonpolar metabolites can be extracted using solvents like chloroform.


Precipitation is a technique used to remove proteins from biological samples, and the remaining supernatant, containing the metabolites, is collected for analysis.


Derivatization involves chemically modifying metabolites to ensure they are volatile enough for analysis.

Solid-Phase Extraction

Solid-phase extraction (SPE) and liquid-liquid extraction (LLE) are techniques used to purify and concentrate metabolites, removing unwanted components from the sample.

Applications of Mass Spectrometry in Metabolomics

The study of metabolomics provides a range of insights that help researchers to better understand cells, tissues, and whole organisms. Using mass spectrometry often provides insights into specific areas of research, outlined below.

Identification & Quantification of Metabolites

Due to high sensitivity and specificity, identification and quantification of metabolites is often achieved through labeling strategies or by comparing to known standards. The measurement and quantification of metabolite concentrations provides wide ranging insights into metabolic pathways and interactions.

Metabolic Profiling & Biomarker Discovery

Metabolic profiling allows for characterization of a complete set of metabolites in a biological sample, making it possible to identify specific metabolites or patterns of metabolites that serve as biomarkers for certain diseases or conditions.

Disease Diagnosis & Drug Development

Changes in metabolite levels can provide early signs of disease or insights into disease progression. In drug development, metabolomics can be used to understand how drugs are metabolized to identify potential side effects, and monitor treatment efficacy.


Mass spectrometry is a powerful and versatile analytical tool, and has become an integral part of metabolomics research. Due to its versatility in identifying and quantifying a wide range of metabolites from complex biological samples has opened up exciting avenues for the study of metabolism.

At Silantes, we offer an extensive range of metabolite and amino acid standards designed to ensure precision and reliability in your research. If you are looking for help with your metabolomic research, our team of experts is available to discuss your research and experimentation challenges, just reach out to our customer service team.


What is metabolomics used for?

Metabolomics is the study of the metabolome, the complete set of small-molecule chemicals found within a biological sample that are used to understand biochemical processes, identify biomarkers for disease and monitor therapeutic intervention.

How is mass spectrometry used in metabolomics?

Mass spectrometry (MS) is used to identify and quantify metabolites in a sample, which can detect hundreds of metabolites in a single experiment. This information can help scientists understand metabolic pathways, and identify biomarkers and disease states.

What are the methods used in metabolomics?

The study of metabolomics typically relies on mass spectrometry (MS) or nuclear magnetic resonance (NMR) spectroscopy to detect, identify and quantify metabolites in biological samples.

How do you analyze metabolomics data?

Information generated from MS and NMR relies on advanced computational and statistical tools to analyze and interpret the data generated. However, these instruments and tools are only as good as the sample preparation and the quality of data generated through experimentation.

What is the best method to be used to analyze a metabolome?

The best method to analyze the metabolome depends on the research and sample type that is being investigated. Different instrumentation provides different levels of information, and raw data must be properly analyzed using data analysis tools to generate information that is of use to researchers.

What type of sample is studied in metabolomics?

The study of metabolomics allows for a wide range of different sample types to be investigated – including but not limited to – blood, urine, tissue and cell samples, soil and water. The sample type that is being investigated should be most applicable to the metabolic disease or pathway of interest.

What is the difference between metabolites and metabolomes?

Metabolites are the individual small molecule chemicals involved in metabolism that allow for the chemical reactions that maintain life. The metabolome refers to a complete set of metabolites found within a biological system.