Metabolomics is the study of small molecules within a biological system. Its popularity has soared in the past decade thanks to its potential to provide information on the overall physiological state of an organism.
Metabolomics techniques would not be possible without high-sensitivity, high-resolution techniques such as mass spectrometry. High-resolution mass spectrometry (HRMS) provides the highest degree of structural information.
Ghaste et al. recently reviewed the two most common HRMS techniques used in metabolomics: Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap-based mass spectrometry.1
Introduction of the Orbitrap mass analyzer has been key in metabolomics studies. Thanks to its ability to be coupled with liquid and gas chromatography, a growing number of studies now employ HRMS in metabolomics research.
The authors point out that HRMS techniques have several advantages over other commonly used methods, such as gas chromatography and capillary electrophoresis, in studying the metabolome:
- The capacity to resolve analytes at the 1–3 ppm level, which dramatically improves characterization of complex mixtures.
- Increased mass accuracy and acquisition rates, which are particularly important in fingerprinting studies.
- The availability of various ion source or fragmentation techniques, which allows flexibility in the approach to a metabolomics experiment.
- The ability to perform stepwise fragmentation in multiple-stage mass spectrometry experiments, which is useful for confident metabolite identification.
Ghaste et al. discuss some of the latest developments in HRMS metabolomics. These include shotgun-based approaches based on direct infusion mass spectrometry (DIMS), hyphenated techniques, and mass spectrometry imaging.
Shotgun-based approaches based on DIMS negate the complex preprocessing steps associated with other techniques. They have several advantages in large-scale metabolomics studies where speed of analysis is most important. These techniques are especially useful in fingerprinting.
Hyphenated techniques, such as gas chromatography–mass spectrometry (GC-MS), are used to overcome issues related to sample complexity. The GC-enabled quadrupole linear Hybrid Ion Trap-Orbitrap mass spectrometer technology (Thermo Scientific), which is capable of sub-parts-per-million accuracy, has brought about significant technical advances in HRMS-based metabolomics. Its performance is highlighted in studies determining the dioxins and furans in environmental samples and in the profiling of primary metabolites in Arabidopsis thaliana extracts.
In their review, Ghaste et al. highlight the fact that the GC quadrupole-Orbitrap mass spectrometer is a promising instrument for both untargeted and targeted metabolomics studies.
Mass spectrometry imaging approaches can provide spatial information to help locate metabolites and other small molecules in tissues or organs. MALDI combined with HRMS is the most common imaging technique used. A study in the review, which used a MALDI LTQ Orbitrap XL mass spectrometer (Thermo Scientific), showed the distribution of lipids at cellular resolution in cotton embryos.
Ghaste et al. also reviewed recent developments of novel approaches for processing HRMS data. They highlight that recent improvements in instrumentation have been complemented by the development of new data-processing algorithms, software and databases. Many of these are available in the public domain.
Popular, recently developed programs and databases mentioned in the review include the National Institute of Standards and Technology (NIST) search program; the METLIN metabolite database from the Scripps Center for Metabolomics and Mass Spectrometry; and the Web server MassTRIX, which helps with assignment of bulk chemical formulae. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the Madison Metabolomics Consortium Database (MMCD), the Human Metabolome Database (HMDB), DrugBank, and the LIPID Metabolites and Pathway Strategy (LIPIDMAPS) database are also mentioned.
The authors predict even more improvement in instrumentation and processing software in the near future and hope to soon see increased community efforts in standardizing metabolomics data standards, expanding bioinformatics tools and making available metabolomics data repositories.
1. Ghaste, M., Mistrik R., and Shulaev, V. (2016) “Applications of Fourier transform ion cyclotron resonance (FT-ICR) and orbitrap based high resolution mass spectrometry in metabolomics and lipidomics,” International Journal of Molecular Sciences, 17(6) (p. 816), doi: 10.3390/ijms17060816.
Post Author: Kathryn Loydall. Kathryn is a science and medical writer with a background in protein chemistry, biochemistry and applied biology. She enjoys making science accessible to a lay audience through writing, illustrations and media. Originally from the UK, she moved to Vancouver Island in 2008 to complete her PhD focussed on sepsis research and x-ray crystallography of monoclonal antibodies. In 2012, Kathryn left the lab behind to start freelancing as a science and medical writer and editor, and hasn’t looked back since.