PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments

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.In the post genomics era, metabolomics is fast emerging as a vital source of information to aid in solving systems biology puzzles with an emphasis on metabolic solutions. Metabolomics is the science of measuring the pool sizes of metabolites (small molecules of M r #

Recommendations for Reporting Metabolite Data

“…Our recommendations include methods for sampling, extraction and storage, metabolite identification, processing of large sample numbers, and recommendations for reporting the methods of metabolite identification and the levels of certainty in metabolite quantification. Good suggestions for standards in reporting chemical ontology and supporting metadata have already been made by Sumner et al (2007) and Bais et al (2010).…”

Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis

“…Based on a comparison of our data set and the PlantMetabolomics.org data set (Bais et al, 2010, we report at least partial mutual data complementarity (comparing only GC-MS metabolomics; Fig. 3A).…”

“…When we compared the mutants on our list (Supplemental Table S1) with those generated by the Arabidopsis 2010 Plant Metabolomics Consortium (Bais et al, 2010Quanbeck et al, 2012;Hur et al, 2013; http://www.metnetdb.org/pmr/), we found that on both, pad4-1 (Arabidopsis Biological Resource Center identifier CS3806; AT3G52430, encoding the ARABIDOPSIS PHYTOALEXIN DEFICIENT4 [PAD4] a/b-hydrolase superfamily protein; Fig. 3A) was analyzed by GC-MS.…”

“…pap1-D; indicated by the arrow). Bais et al, 2010Bais et al, , 2012. A, Venn diagram of the mutants analyzed by the two projects.…”

“…Fernie et al (2011) have also presented additional practical recommendations for reporting metabolome data. In this context, Bais et al (2010Bais et al ( , 2012 developed the first metabolite profiling database with statistical data analysis tools for Arabidopsis mutants using multiple analytical instruments. The data include MSI-compliant experimental metadata and freely available metabolite profiles.…”