Tools and Resources
Food Composition Tables
A number of organizations worldwide maintain food composition tables to help to provide consumers with nutritional information about the food they eat. These include the Canadian Nutrient Files, CIQUAL French Food Composition Table and the New Zealand Food Composition Database.
Given the diversity and the rapidly growing number of known food metabolites, well-curated databases are of utmost importance for keeping track of this information. Some databases have been developed as part of FOODBALL and are more specific for the food metabolome: FooDB, Phenol-Explorer, FoodComEx and PhytoHub.
- FooDB is a comprehensive resource on food constituents and their chemical and biological data.
- Exposome Explorer is the first database dedicated to biomarkers of exposure to environmental risk factors for diseases.
- FoodComEx is a new chemical library created to facilitate the exchange of standards for food compounds.
- PhytoHub contains detailed information about dietary phytochemicals and their human metabolites.
- Knapsack is an extensive species-metabolite database for plants, including edible and non-edible plants.
- HMDB is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.
- ChEBI is a freely available dictionary of molecular entities focused on ‘small’ chemical entities.
- The Dictionary of Food Compounds contains entries describing natural components of food raw materials and products as well as compounds added to foods or formed in the course of storage or processing.
- Dr. Duke's contains detailed information about dietary phytochemicals and their human metabolites.
Metabolite identification in metabolomic studies relies on the comparison of generated spectra with those in curated databases. To facilitate this, there are a number of online publically accessible spectral libraries, including:
- BMRB: The Biological Magnetic Resonance Data Bank, a repository of NMR spectra for biological macromolecules and metabolites.
- GMD: The Golm Metabolome Database, a reference GC-MS database for biologically active metabolites.
- HMDB: The Human Metabolome Database, containing searchable spectra for human metabolites.
- MassBank: A repository of MS spectra from endogenous and exogenous substances.
- METLIN: A repository of MS/MS spectra and metabolite information.
Data analysis is a key step in foodomics. Fortunately, some excellent tools exist for metabolomics data analysis, including:
- MetaboAnalyst: A comprehensive online software suite for statistical analysis of metabolomics data.
- Bayesil: A web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum, or cerebrospinal fluid.
- MATLAB: A widely used numerical computing environment.
- mixOmics: An R package for the integration of multiple ‘omics’ datasets (e.g. metabolomics, transcriptomics, proteomics) using unsupervised or supervised multivariate data analysis.
- SIMCA: A tool for multivariate statistical analysis.
- Workflow4Metabolomics: A collaborative portal dedicated to metabolomics data processing, analysis, and annotation for Metabolomics community.
Identification and Prediction Tools
Several tools for compound identification in mass spectrometry and NMR are available, as well as tools for the in silico prediction of food-derived metabolic compounds:
- MetFusion: A tool that integrates compound identification strategies.
- MetFrag: A tool for computer assisted identification of metabolite mass spectra using in silico fragmentation.
- MyCompoundID: A web-based resource for identification of compounds of interest based on chemical properties of a molecule, such as accurate mass and fragment ion spectral pattern generated by mass spectrometry.
- Bayesil: A web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid.
- CFM-ID: A server that uses Competitive Fragmentation Modeling to identify metabolites in spectra generated by ESI-MS/MS.
- LipidBlast: A computer-generated MS/MS database that can be used to annotate and identify lipids.
- Meteor Nexus: A software program that predicts metabolites from input structures using lipophilicity, structural features, and transformation likelihoods.
Finding the right standard for confirming the identity of a marker can be quite challenging.
- FoodComEX: FoodComEx is a new chemical library initiated in the FoodBAll project to facilitate the sharing of not easily accessible standards for food compounds and their human metabolites.
- eMolecules: eMolecules is a free chemical structure search engine with millions of public domain structures from vendors worldwide.
- Extrasynthese: For 30 years Extrasynthese had provided highly purified reference phytochemicals.
- ZINC: ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats.
Ongoing international initiatives include:
- Metabolomics Society: The Metabolomics Society is dedicated to promoting the growth, use and understanding of metabolomics in the life sciences.
- Metabolomics Workbench: A national and international repository for metabolomics data and metadata that provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more.
- MetaboLights: A database for metabolomics experiments and derived information.
- COSMOS: A consortium of leading European groups in metabolomics.
- MetabolomeXchange: An international data aggregation and notification service for metabolomics.