Metabolite annotations based on the integration of mass spectral information
Open accessAbstract
A large number of metabolites are found in each plant, most of which have not yet been identified. Development of a methodology is required to deal systematically with unknown metabolites, and to elucidate their biological roles in an integrated 'omics' framework. Here we report the development of a 'metabolite annotation' procedure. The metabolite annotation is a process by which structures and functions are inferred for metabolites. Tomato (Solanum lycopersicum cv. Micro-Tom) was used as a model for this study using LC-FTICR-MS. Collected mass spectral features, together with predicted molecular formulae and putative structures, were provided as metabolite annotations for 869 metabolites. Comparison with public databases suggests that 494 metabolites are novel. A grading system was introduced to describe the evidence supporting the annotations. Based on the comprehensive characterization of tomato fruit metabolites, we identified chemical building blocks that are frequently found in tomato fruit tissues, and predicted novel metabolic pathways for flavonoids and glycoalkaloids. These results demonstrate that metabolite annotation facilitates the systematic analysis of unknown metabolites and biological interpretation of their relationships, which provide a basis for integrating metabolite information into the system-level study of plant biology.
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Up to 200,000 different metabolites are estimated to occur in the plant kingdom, and combinations of several hundreds of secondary metabolites generally characterize each edible plant.
“Up to 200,000 different metabolites are estimated to occur in the plant kingdom, and combinations of several hundreds of secondary metabolites generally characterize each edible plant (6,64,65).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [65]
Metabolomics applied to foods has enabled identification of many novel food constituents that are naturally present in food species or formed during food processing.
“The application of metabolomics to foods has allowed the identification of a large variety of novel food constituents that are either naturally present in the food species or formed during food processing (65,173,174).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [65]
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- Authors
- Iijima, Y., Nakamura, Y., Ogata, Y., Tanaka, K., Sakurai, N., Suda, K., Suzuki, T., Suzuki, H., Okazaki, K., Kitayama, M., Kanaya, S., Aoki, K., & Shibata, D.
- Affiliations
- Kazusa DNA Research Institute (JP)
- International Pacific University Women's College (JP)
- Nara Institute of Science and Technology (JP)
- Corresponding author
- Aoki, Koh
- ORCID
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2008-02-07
- Volume
- 54
- Issue
- 5
- Pages
- 949-962
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- PMC
- PMC2440531
- OpenAlex
- W2136555527
- Cited by
- 283
- References
- 46
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 1 · 2023: 10 · 2022: 11 · 2021: 10 · 2020: 16 · 2019: 15 · 2018: 12 · 2017: 18 · 2016: 17 · 2015: 10 · 2014: 25 · 2013: 28 · 2012: 16
- FWCI
- 12.47
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The Plant Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Chiba University
- University of California, Davis
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant biochemistry and biosynthesis
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- metabolite annotation, unknown metabolites, novel metabolites, flavonoids, glycoalkaloids, metabolic pathway prediction, plant metabolomics
- MeSH terms
- Chromatography, Liquid, Plants, Spectrophotometry, Ultraviolet, Mass Spectrometry, Databases, Factual, Spectroscopy, Fourier Transform Infrared
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