PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments

Preeti Bais,Tom Walk,Kate Dreher,Eve Syrkin Wurtele,B Markus Lange,Stephanie M Moon,Oliver Fiehn,Julie A Dickerson,Ruth Welti,Vladimir Shulaev,Seung Y Rhee,Gert Wohlgemuth,Basil J Nikolau,Yves Sucaet,Lloyd W Sumner,Mary R Roth,Lenore Barkan,Philip M Dixon ,Ricardo Leitão ,Kongwang He

doi:10.1104/pp.109.151027

Abstract

PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. Widespread public access to well-annotated metabolomics datasets is essential for establishing metabolomics as a functional genomics tool. PM integrates metabolomics data generated from different analytical platforms from multiple laboratories along with the key visualization tools such as ratio and error plots. Visualization tools can quickly show how one condition compares to another and which analytical platforms show the largest changes. The database tries to capture a complete annotation of the experiment metadata along with the metabolite abundance databased on the evolving Metabolomics Standards Initiative. PM can be used as a platform for deriving hypotheses by enabling metabolomic comparisons between genetically unique Arabidopsis (Arabidopsis thaliana) populations subjected to different environmental conditions. Each metabolite is linked to relevant experimental data and information from various annotation databases. The portal also provides detailed protocols and tutorials on conducting plant metabolomics experiments to promote metabolomics in the community. PM currently houses Arabidopsis metabolomics data generated by a consortium of laboratories utilizing metabolomics to help elucidate the functions of uncharacterized genes. PM is publicly available at http://www.plantmetabolomics.org.

Highlights

PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data
Standards for the annotation of metabolomics experiments are still under active development and the metadata types collected in PM are based on the recommendations of the Metabolomics Standards Initiative (MSI; Fiehn et al, 2007a) and the Minimal Information for a Metabolomic Experiment (Bino et al, 2004) standards
MSI attempts to capture the complete annotation of metabolomics experiments and includes metadata of the experiments along with the metabolite abundance data

Summary

DESIGN REQUIREMENTS AND FUNCTIONALITY

PM allows users to explore and interpret data sets and put them in a biological context This requires the integration of relative metabolite abundance along with the metadata of the experimental conditions including growth, harvest, and storage conditions of sample tissue, sample extraction, and instrument parameters. The MSI specifies the minimum amount of metadata from the metabolomics experiments that must be reported so that experiments can be replicated and results can be verified These minimum data include descriptions of biological study design, sample preparation, data acquisition, data processing, and data analysis procedures. Experimental metadata provides information about the growth and harvesting regimen, including the temperature, illumination, duration of growth, humidity, and storage parameters, which were used to produce the Arabidopsis tissue samples for analysis. The public can access the data online or download it for use in other applications

DESIGN OF EXPERIMENTS

CONCLUSION