Metabolomic Tool Kit

Tools and resources for the analysis, visualization and characterization of metabolomic data, including publically available metabolomic databases of interest to plant science researchers.


AraCyc is a metabolic pathway database for Arabidopsis thaliana that contains information about both predicted and experimentally determined pathways, reactions, compounds, genes and enzymes. The Omics viewer is a software for displaying large scale data such as microarray gene expression results or proteomic data in the context of biochemical pathways.

Arabidopsis Metabolomics Consortium

An NSF-funded multi-institutional project that is developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes. The Consortium has established metabolomic platforms that detect approximately 1,800 metabolites, of which 900 are chemically defined. There is a useful page on protocols and tutorials too. 

From the abstract: (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. Visualization tools can quickly show how one condition compares to another and which analytical platforms show the largest changes. PM can be used as a platform for deriving hypotheses by enabling metabolomic comparisons between genetically unique Arabidopsis populations subjected to different environmental conditions. Each metabolite is linked to relevant experimental data and information from various annotation databases. 

Golm Metabolome Database

Golm Metabolome Database facilitates the search for and dissemination of reference mass spectra from biologically active metabolites quantified using gas chromatography (GC) coupled to mass spectrometry (MS).

Information on Metabolomics at TAIR

A collection of links to tools and resources for metabolomics


Web-based analysis tool that can be used to superimpose transcriptome and metabolome data onto plant metabolic pathway maps. Available for a number of plants, including Arabidopsis and tomato.

From the abstract: We report here a new metabolic pathway database, KaPPA-View4, which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This representation would help to discover, for example, novel functions of a transcription factor that regulates genes on a metabolic pathway.


KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for primary and secondary metabolism, cellular processes, signalling, and organismal systems. 

Madison Metabolomics Consortium

A searchable database of information on small molecules of biological interest gathered from electronic databases and the scientific literature. Information on each molecule includes the names and synonyms, structure, and NMR and MS data where available. 

From the published article: We have developed the Madison Metabolomics Consortium (MMC) Database, a web-based tool that contains data pertaining to biologically relevant small molecules from a variety of species.The MMCD6 contains information on >20,000 metabolites and other small molecules of biological interest. These molecules, which were chosen from entries in such databases as KEGG, BioCyc, and PDB, represent a collection of primary and secondary metabolites, xenobiotics and common small-molecule contaminants.


From the abstract: MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. It can group genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes; group hundreds of metabolites into pathways or groups of structurally related compounds; and use these groupings to organise and display experimental data sets onto diagrams of the users' choice.

Mass Bank

Mass Bank is a database containing electron-ionization mass spectrometry(EI-MS), fast atom bombardment MS, and electrospray ionization (ESI)-MSn data of authentic compounds of metabolites, volatile natural and synthetic compounds. 

From the abstract: MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da).  MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS2 data on an identical compound under different collision-induced dissociation conditions. MassBank is useful for the identification of chemical compounds and the publication of experimental data.


The MassBase database is fundamental for metabolomics, which provides raw mass chromatograms from various biological samples and text-file data processed from the raw chromatograms. You can view the raw or processed chromatograms of your interest and also download the files of interest or even in bulk all datasets.


MetaboLights, a database for metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments and is a collaborative multi-laboratory effort including groups specialising in plant metabolism.

Metabolomics Society

The Metabolomics Society is an international society of metabolomics researchers. Their website has many useful pages, including jobs, a list of databases, and tutorials


PASMet is a web-based platform for predicting, modelling and analysing metabolic systems. It is a non-commercial and user-friendly tool for assisting non-experts in mathematical modelling, computing or programming to work on computational biology

Pathway Tools Information Site

Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology, including development, visualisation of model-organism databases. 

From the abstract: The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms.

Plant Metabolic Network

The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants.

From the abstract: We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. These resources can be searched by text or BLAST, browsed, and downloaded from our project website (

Plant MetGenMAP

Plant MetGenMAP is a visualization and analysis package that allows to identify changed pathways and enriched GO terms from gene expression and/or metabolite profile data and to visualize the profile data in a biochemical pathway context. The syste supports a number of plant species, including Arabidopsis, rice, and tomato. 

From the abstract: Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways.


PRIMe is a Web- based service that provides data sets of metabolites measured by multidimensional NMR spectroscopy, GC-MS, LC-MS and CE-MS together with analytical tools to promote integrated approaches using comprehensive data sets within the metabolome and transcriptome.

From the abstract: The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses. In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting for the analysis of mRNA expression. Use of the tools and database can contribute to the analysis of biological events at the levels of metabolites and gene expression.


Promex is a mass spectral reference database. The database consists of tryptic peptide fragmentation mass spectra derived from plants, including Arabidopsis, rice, tomato and maize.

ReSpect for Phytochemicals

From the website: RIKEN MSn spectral database for phytochemicals (ReSpect) is a collection of literature and in-house MSn spectra data for research on plant metabolomics. More than 8649 spectra records are available.