Precision medicine, Space exploration, drug discovery to characterization of dark chemical space of habitats and organisms, metabolomics takes a centre stage in providing answers to diverse biological, biochemical, and environmental questions.​


Metabolite Screening & Identification

What is metabolomics?

Metabolomics is the study of endo/exogenous metabolites, called metabolome, which is a collection of low molecular weight (50-1500 Da) compounds with a wide range of physicochemical properties. Measuring the metabolome provides important information about the functional status of a biological system. Metabolomics recently caught up with complementary efforts to understand the genomes, transcriptomes, and proteomes to establish holistic pictures of the biological system 

  • Endogenous Molecules - (Produced by the organism itself) fatty acids, organic acids, sugars, Vitamins.

  • Exogenous Metabolites – (External from the organism) Drugs, Environmental toxicants


The approach can be divided into targeted and untargeted approaches. Targeted approaches require prior knowledge of the molecule(s) of interest to design tailored analytical methods. Untargeted approaches aim to detect many metabolites as possible in a sample with subsequent annotation and identification, usually involving databases searches (e.g., METLIN or MS-DIAL) as well as comparison with authentic synthetic materials.​

Applications of Metabolomics

In Human Diseases:
One of the most important applications of metabolomics in the study of human diseases is in the field of oncobiology. Because tumor cells are highly proliferative and have a high transcription and translation rates, as well as a higher energy demand, they have special metabolic requirements when compared to normal cells and frequently lose many regulatory functions. Thus, one of the greatest challenges in medicine is the use of metabolomics in predicting the appearance of tumor cells. Initially, putative metabolic biomarkers for cancer detection and/or assessment of efficacy of anticancer treatment are discovered in preclinical analyses, followed by the validation of these biomarkers in biofluids (blood, urine, prostatic secretions, etc.) 

However, there are several gaps in the knowledge of the cancer metabolome. The metabolite profile could vary among the different tumor types making it difficult to generalize findings across tumor groups. There are also technical difficulties encountered while performing metabolomic assays that may hinder the characterization of a tumor metabolome, including sample-to-sample variation, the sensitivity and the physiological status of the tumor. 

Another application of metabolomics in the field of human health includes nutrigenomics. The term nutrigenomics is associated with the interaction of the diet and the genes and reflects the change in gene expression that takes place after the exposure to different nutrients. The identification of certain compounds that would have the ability to act on the expression of target genes is extremely important in preventing diseases such as cancer. Moreover, this interaction could influence the absorption, digestion, and the elimination of metabolites. Thus, the metabolomic approach may allow the discovery of bioprotective foods.

In Plant Biotechnology: 
Plant metabolites are involved in many resistance and stress responses and also contribute to the color, taste, aroma, and scent of fruits and flowers. The biochemical phenotype of an organism is the final result of interactions between the genotype and the environmental stimuli; but it is also modulated by intracellular physiological fluctuations that are part of homeostasis. Thus, the simultaneous identification and quantification of metabolites is necessary to understand the dynamics of the metabolome, analyze fluxes in metabolic pathways and decipher the role of each metabolite following various stimuli. The challenge of metabolomics is to find changes in biochemical pathways, and metabolic networks that might correlate with the physiological and developmental phenotype of a cell, tissue, or organism.

Plant metabolomics is being increasingly used for understanding other processes such as the cellular responses to stress conditions. The metabolic readjustment to sulfur deficiency is an example of this. A close relationship was found between sulfur assimilation, nitrogen, lipid, and purine metabolism and enhanced photorespiration. Metabolomics has also been applied to the study of the cold stress response. Other applications include metabolic engineering of biochemical pathways, gene function discovery, and engineering pathways for pharmaceuticals production are as follows:

Environmental metabolomics
Metabolomics can also be applied to characterize the ways in which an organism interacts with its environment. Studying these environmental interactions and assessing the function and health of an organism at a molecule level can reveal useful information about the effect of environment on an organism’s health. This can also be applied to a wider population to provide data for other fields of research, such as ecology.

Future perspectives
Metabolomics technology will be combined with more emerging technologies to provide a guarantee for the development of metabolomics. Metabolomics based on MS will be more perfect, and all kinds of combined techniques, such as LC/MS and GC/MS, will provide a scientific basis for solving the problem of metabolite research and elucidating metabolic pathways. Mass spectrometry continues to play a leading role as an important analytical tool in the field of metabolomics. Advances in this field have enabled the discovery of many putative disease biomarkers and provided insight into the pathogenesis of various diseases. Numerous studies have also been tested, including early disease detection, treatment prediction and prognosis, monitoring treatment and recurrence testing. Given the extreme complexity of biological mixtures, most MS analytical methods involve the use of LC, GC or CE. However, rapidly growing applications using evolving separation methods and protocols offer opportunities and challenges. Clearly, developments in chromatographic methods have been effective in separating metabolites and increasing the number of metabolites detected. However, one major challenge is the inability to compare and correlate the results of these studies, which are performed on the same or similar samples obtained by independent research groups. This is the main bottleneck in the development of this field. Other factors such as sample preparation, sample matrix and residual effects can also lead to data variability. To overcome these challenges, it is necessary to shift from the conventionally used relative metabolite concentration measurements to a more reliable absolute concentration determination, which will be independent of the analytic platform, method and protocol used. This method is not straightforward for MS, but it is very important.

Metabolomic analysis must accurately determine even the slightest changes of molecular profile related to disease, disease progression, therapeutic intervention, genetic modification or environmental variation.
Patterns in cells and biofluids that are characteristic (a “fingerprint”) of the nature of the site of the action. These patterns can be evaluated using spectroscopic/ spectrometric techniques combined with multivariate statistical methods to gain insight into the molecular response of a biological system.


What is flux analysis?
Flux analysis is used for the metabolic network to determine the rate at which the metabolites in the metabolomic network are synthesized. Reactions with greater flux is significant in the network because the rate at which the product is synthesized will decide the outcome of the network. 

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