Protocol

Plant Bioinformatics

Volume 406 of the series Methods in Molecular Biology™ pp 409-436

Metabolomics Data Analysis, Visualization, and Integration

  • Lloyd W SumnerAffiliated withPlant Biology Division, The Samuel Roberts Noble Foundation
  • , Ewa Urbanczyk-WochniakAffiliated withPlant Biology Division, The Samuel Roberts Noble Foundation
  • , Corey D BroecklingAffiliated withDepartment of Horticulture and Landscape Architecture, Colorado State University

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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.

Key Words

Metabolite analysis metabolic profiling metabolomics data processing statistical analysis data visualization data integration functional genomics