ArticleThe Plant cell2014
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Compositional Analysis of Grape Berries: Mapping the Global Metabolism of Grapes.Foods (Basel, Switzerland) · 2024Article
- Insights into Tissue-Specific Specialized Metabolism in Wampee (Foods (Basel, Switzerland) · 2024Article
- Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- Depicting the genetic and metabolic panorama of chemical diversity in the tea plant.Plant biotechnology journal · 2024Article
- Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat.The Plant cell · 2024Article
- QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits.Molecular plant · 2023Article
- Multilayered regulation of secondary metabolism in medicinal plants.Molecular horticulture · 2023Review
- Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2023Article
- [A novel method for efficient screening and annotation of important pathway-associated metabolites based on the modified metabolome and probe molecules].Se pu = Chinese journal of chromatography · 2022Article
- Flexible and digestible wood caused by viral-induced alteration of cell wall composition.Current biology : CB · 2022Article
- Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches.Genomics, proteomics & bioinformatics · 2022Article
- Past accomplishments and future challenges of the multi-omics characterization of leaf growth.Plant physiology · 2022Review
- Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration.Nature communications · 2022Article
- Polyphenol-Enriched Extracts ofMolecules (Basel, Switzerland) · 2022Article
- Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation.Frontiers in molecular biosciences · 2022Review
- Metabolic diversity in a collection of wild and cultivatedFrontiers in molecular biosciences · 2022Article
- Strategies for structure elucidation of small molecules based on LC-MS/MS data from complex biological samples.Computational and structural biotechnology journal · 2022Review
- Graph Properties of Mass-Difference Networks for Profiling and Discrimination in Untargeted Metabolomics.Frontiers in molecular biosciences · 2022Article
- Sample Preparation, Data Acquisition, and Data Analysis forMethods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
9 authors.
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Abstract
Plant metabolomics is increasingly used for pathway discovery and to elucidate gene function. However, the main bottleneck is the identification of the detected compounds. This is more pronounced for secondary metabolites as many of their pathways are still underexplored. Here, an algorithm is presented in which liquid chromatography-mass spectrometry profiles are searched for pairs of peaks that have mass and retention time differences corresponding with those of substrates and products from well-known enzymatic reactions. Concatenating the latter peak pairs, called candidate substrate-product pairs (CSPP), into a network displays tentative (bio)synthetic routes. Starting from known peaks, propagating the network along these routes allows the characterization of adjacent peaks leading to their structure prediction. As a proof-of-principle, this high-throughput cheminformatics procedure was applied to the Arabidopsis thaliana leaf metabolome where it allowed the characterization of the structures of 60% of the profiled compounds. Moreover, based on searches in the Chemical Abstract Service database, the algorithm led to the characterization of 61 compounds that had never been described in plants before. The CSPP-based annotation was confirmed by independent MS(n) experiments. In addition to being high throughput, this method allows the annotation of low-abundance compounds that are otherwise not amenable to isolation and purification. This method will greatly advance the value of metabolomics in systems biology.
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