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Metabolomics Data Analysis, Visualization, and Integration

  • Protocol
Plant Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 406))

Summary

Metabolomics is the large-scale analysis of metabolites and as such requires bioinformatics tools for data analysis, visualization, and integration. This chapter describes the basic composition of chromatographically coupled mass spectrometry (MS) data sets used in metabolomics and describes in detail the steps necessary for extracting large-scale qualitative and quantitative information. This process involves noise filtering, peak picking and deconvolution, peak identification, peak alignment, and the creation of a final data matrix for statistical processing. Multivariate tools for comparative analysis are presented and illustrated using data for Medicago truncatula. Additional tools for visualizing and integrating metabolomics data within a biological context are discussed. Two tables are provided listing current metabolomics data processing and visualization software. Because metabolomics is rapidly maturing, a final section is presented concerning the need for data standardization and current efforts.

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Acknowledgments

The Sumner lab is supported by The National Science Foundation Plant Genome Research Program Award no. DBI-0109732, NSF 2010 MCB-0520283, NSF 2010 MCB-0520140, State of Oklahoma, and The Samuel Roberts Noble Foundation.

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Authors and Affiliations

  1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK

    Lloyd W Sumner

  2. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK

    Ewa Urbanczyk-Wochniak

  3. Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO

    Corey D Broeckling

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  1. Lloyd W Sumner
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  2. Ewa Urbanczyk-Wochniak
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  3. Corey D Broeckling
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Editors and Affiliations

  1. Primary Industries Research Victoria, Plant Genetics and Genomics,Victorian AgriBiosciences Centre, La Trobe University, Bundoora, Victoria, Australia

    David Edwards

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Sumner, L.W., Urbanczyk-Wochniak, E., Broeckling, C.D. (2005). Metabolomics Data Analysis, Visualization, and Integration. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology™, vol 406. Humana Press. https://doi.org/10.1007/978-1-59745-535-0_20

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  • DOI: https://doi.org/10.1007/978-1-59745-535-0_20

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-653-5

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