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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks
Plant Cell, Volume 26, No. 3, Year 2014
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Description
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 MSn 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. © 2014 American Society of Plant Biologists. All rights reserved.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC4001402/bin/supp_26_3_929__index.html
https://efashare.b-cdn.net/share/pmc/articles/PMC4001402/bin/supp_tpc.113.122242_tpc122242_SupplementalData.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC4001402/bin/supp_tpc.113.122242_tpc122242_Supplemental_DS1.xls
Authors & Co-Authors
Morreel, Kris
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Saeys, Yvan
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Dima, Oana
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Lu, Fachuang
United States, Madison
University of Wisconsin-madison
Van de Peer, Y.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
South Africa, Pretoria
University of Pretoria
Vanholme, Ruben
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Ralph, John
United States, Madison
University of Wisconsin-madison
Vanholme, Bartel T.M.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Boeŕjan, Wout A.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Statistics
Citations: 110
Authors: 9
Affiliations: 4
Identifiers
Doi:
10.1105/tpc.113.122242
ISSN:
10404651
e-ISSN:
1532298X
Research Areas
Genetics And Genomics