Metabolism is the assembly of biochemical reactions in living organisms, the material basis for life maintenance of living organisms, and an important basis for the study of life activities. Metabolomics studies the endogenous metabolic activities of life under the influence of the internal and external environments, including the detection and analysis of metabolite types and quantities and their change patterns, thus studying the nature of the occurrence and development of collective life activities. Compared to other omics technologies, metabolomics offers several advantages:

• Changes in the type and quantity of metabolites are easy to detect.
• The technical means are simpler compared to genomics and proteomics.
• Compared with genomics and of proteomics, the number of metabolites is small and easy to detect, verify and analyze.
• Changes in metabolite levels can reveal the physiopathological state of the organism in real time.

What Can Metabolomics Tell Us?

Metabolomics offers a wealth of information that can be leveraged across multiple disciplines. By analyzing the metabolome, researchers can:

Identify Biomarkers: Metabolites can serve as valuable biomarkers for various diseases. For instance, altered metabolite profiles have been associated with cancer, diabetes, cardiovascular diseases, and neurodegenerative disorders.

Uncover Drug Targets: Metabolomics aids in the identification of potential therapeutic targets by highlighting specific metabolites or metabolic pathways that are dysregulated in diseases. This information enables the development of targeted therapies aimed at restoring normal metabolic balance.

Understand Biological Pathways: Metabolomics allows researchers to map and comprehend intricate metabolic pathways, unveiling the interplay between genes, proteins, and metabolites. This understanding can be crucial in elucidating the mechanisms of diseases and identifying novel therapeutic interventions.

Assess Environmental Impact: Environmental metabolomics focuses on studying the effects of environmental factors, such as pollutants or toxins, on the metabolome. By identifying metabolic alterations induced by environmental stressors, researchers can assess the impact on ecosystems and human health.

Why is Metabolomics Difficult?

Metabolomics presents several challenges that must be addressed to ensure reliable and reproducible results:

Sample Complexity:

Biological samples used in metabolomics, such as blood, urine, tissues, or cells, are inherently complex. They contain a vast array of metabolites with a wide dynamic range of concentrations. The presence of high-abundance compounds, such as amino acids and lipids, can mask the detection of lower-abundance metabolites, leading to challenges in identifying and quantifying specific metabolites of interest. Strategies such as sample fractionation, enrichment techniques, or targeted extraction methods are employed to mitigate the complexity of samples and enhance the detection of low-abundance metabolites.

Metabolite Identification:

Metabolite identification is a critical challenge in metabolomics. While advanced analytical techniques like mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy provide valuable information about the mass and structure of metabolites, confidently identifying metabolites from complex spectra remains a complex task. Several factors contribute to this challenge, including the presence of isomers or structurally similar compounds, database limitations, and spectral overlap. To overcome these challenges, researchers rely on techniques such as tandem MS, high-resolution MS, and the use of reference standards and databases for metabolite identification.

Data Analysis:

Metabolomics generates vast amounts of data, often referred to as "big data." Effective data analysis is crucial for extracting meaningful insights from this data deluge. However, metabolomics data analysis is complex and requires sophisticated computational tools, statistical methods, and bioinformatics expertise. Data processing, feature extraction, statistical analysis, metabolite quantification, and multivariate analysis are essential steps in metabolomic data analysis. Additionally, data normalization and quality control procedures are critical for ensuring the reliability and comparability of metabolomics data across different samples or studies.

Data Integration and Interpretation:

Metabolomics often involves integrating data from multiple analytical platforms, such as different types of mass spectrometers or NMR instruments. Integrating data from different platforms poses challenges due to variations in instrument performance, sensitivity, and data formats. Data integration approaches and normalization techniques are employed to address these challenges and enable meaningful comparisons and analysis across datasets. Furthermore, the interpretation of metabolomic data requires expertise in metabolite pathway analysis, statistical modeling, and systems biology approaches to unravel the biological significance of the observed metabolic changes.

Standardization and Reproducibility:

Standardization and reproducibility are essential aspects of metabolomics research. Variability in sample collection, storage, extraction methods, analytical techniques, and data processing can introduce bias and affect the reproducibility of results. Establishing standardized protocols and quality control measures is crucial to ensure consistency and comparability of metabolomics data across different laboratories and studies. The development of metabolomics-specific reporting standards, such as the Metabolomics Standards Initiative (MSI), promotes data reproducibility and facilitates data sharing and collaboration in the metabolomics community.

Which Methods Are Used in Metabolomics?

Metabolomics can be divided into untargeted and targeted metabolomics depending on the purpose of the study.

Untargeted metabolomics is a comprehensive and systematic analysis of endogenous metabolites in organisms, and is an unbiased metabolomic analysis that can identify new biomarkers. Targeted metabolomics focuses on the study of a specific class of metabolites.

As both metabolomics approaches have their own advantages and disadvantages. Untargeted metabolomics is unbiased and provides a comprehensive and systematic response to the metabolomic profile of living organisms, but is less reproducible and has a limited linear range. Targeted metabolomics, on the other hand, has improved reproducibility and sensitivity, simple metabolite confirmation, and a wide linear range, but requires a prior knowledge background and is a biased metabolomic analysis method. Therefore, in practice, both are often used in combination and work together.