Metabolomics data analysis, visualization, and integration.
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.
Sumner
Lloyd W
LW
The Samuel Roberts Nobel Foundation, Plant Biology Division, Ardmore, OK, USA.
Urbanczyk-Wochniak
Ewa
E
Broeckling
Corey D
CD
D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D016247:Information Storage and Retrieval / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D046913:Medicago truncatula / Q000378:metabolism; D055432:Metabolomics / Q000379:methods* / Q000706:statistics & numerical data; D015999:Multivariate Analysis; D012984:Software; D014584:User-Computer Interface