Definition of Metabolomics. How Metabolomics works? Major applications of Metabolomics

What is Metabolomics?

Definition of Metabolomics: It is the large-scale scientific study of small molecules, commonly known as metabolites produced as a result of metabolism in a biological system

Metabolism is the sum total of chemical reactions occurring within the cell that is essential for survival of an organism.

How to study metabolomics?

How metabolomics works? Metabolomics workflow

Step 1: Collection of biological samples from blood, urine, tissue etc.

Step 2: Data acquisition using Nuclear magnetic Resonance (NMR) or Mass Spectroscopy (MS) (both GC-MS and LC-MS).

The chemicals are identified and quantified using NMR and MS

Step 3: Spectral processing

Spectral processing is a methodological approach aimed at accurately identifying and quantifying the features in the sample spectra of a metabolomics study. Spectral processing is also necessary to guarantee that each final measurement will refer to the same metabolomic feature in all samples.

Spectral processing is done to avoid any errors or to improve signal quality

Step 4:  Data analysis using biostatistics tools

a)     For identification of biomarkers

Biomarkers are “objective indications of medical state observed from outside the patient – which can be measured accurately and reproducibly”. If samples are collected from a group of patients with a particular pathological condition, if a unique chemical is present in all the samples; that can serve as a biomarker.


      Decreased choline and linoleic acid in serum of lung cancer patients.

      Elevated 3-hydroxypropionic acid reduced pyruvic acid (specific) in serum of gastric cancer patients.

b)     Metabolite identification of spectral data using metabolite databases like METLIN and Human Metabolome Database (HMDB)

 Step 5: Biological Interpretation

The analysis of metabolomic data can often be used to build models that attempt to describe the observed data.

Using metabolic pathway databases like KEGG Kyoto Encyclopedia of Genes and Genomes (KEGG), small molecule pathway database (SMPDB) etc to understand the role and impact of these chemicals in different metabolic pathways and finally proposing a biological model based on correlation-based network analysis.

Metabolomics researchers uses wide variety of software tools to analyze metabolomic data at the pathway level that includes Paintomics, and Cytoscape. Both are efficient pathway visualization tools.

Major Applications of Metabolomics:

a) Biomarker discovery

b) Toxicity studies: In drug safety studies and food safety studies

c) Environmental metabolomics: To assess effect of different chemical pollutants on our metabolic profile.

To study the changes in metabolic profile of organisms in different environments

d) Plant metabolomics:  to study the metabolic mechanisms underlying plant responses to adverse environmental conditions (abiotic stress) and/or plant–attacker interactions (biotic stress) that adversely affect plant growth and development.

-Identification and enhanced production of useful plant metabolites

-to understand the chemical footprints during different phases of growth and development of plants and marker-assisted selection for high-yielding varieties or plants with more beneficial nutrients.

e) Microbial metabolomics: functional gene research, microbial identification, metabolic pathways, antibiotic resistance, industrial biotechnology, synthesis biology, and enzyme discovery.

Alonso, A., Marsal, S., & Julià, A. (2015). Analytical methods in untargeted metabolomics: state of the art in 2015. Frontiers in bioengineering and biotechnology3, 23

Misra, B. B. (2021). New software tools, databases, and resources in metabolomics: Updates from 2020. Metabolomics17(5), 1-24.

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