Madison-Qingdao Metabolomics Consortium Database (MMCD)

Category Metabolomics/Metabonomics>Knowledge Bases/Databases/Tools

Abstract The Madison-Qingdao Metabolomics Consortium Database (MMCD) is a resource for metabolomics research based on nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS).

The goal of MMCD has been to support high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples.

MMCD currently serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature.

Each metabolite entry in the MMCD is supported by information in an average of 50 separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available;

NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and extensive links to images, references, and other public databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and PubChem.

The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

MMCD Data content --

The flexible design of the MMCD allows the database to modify both its content and informatics tools in response to needs of the metabolomics community. The database gives emphasis to Arabidopsis thaliana.

However it can also apply to other organisms. MMCD collects links to mainstream cheminformatics and bioinformatics databases/websites, such as KEGG, PubChem, ChEBI, PDB, and HMDB.

The entry for each compound in the MMCD contains two-dimensional and three-dimensional representations of the covalent structure, calculated masses for different mono-isotopic compositions, and empirically predicted chemical shifts and, where available, experimental NMR chemical shifts and liquid chromatography-mass spectrometry (LC-MS) data collected under defined conditions.

Summary of the content of the Madison-Qingdao Metabolomics Consortium Database (MMCD):

1) Data related to NMR spectroscopy in the MMCD -

2) Data related to mass spectrometry -

3) Data related to structure -

4) Basic properties -

Such as: Name, IUPAC name, synonym, CAS, formula, average mass, water solubility, LogP, etc.

5) Links to chemical and biological informatics databases/websites -

Such as: PubChem, ChemIDplus, KEGG, CHEBI, HMDB, BioCyc, UM-BBD, NIST Chemistry WebBook, NMRShiftDB and wwwPDB.

6) Miscellaneous data -

MMCD Search, browse, and analysis functionalities --

The MMCD is equipped with a very flexible and efficient query system.

Data in the MMCD database can be accessed through any of the five (5) search engines.

The five (5) search categories are:

With the “what you see is what you search” (WYSIWYS) interface, the user can combine all five search types.

Searches are activated by clicking on the corresponding gold bar. Once activated, the search section can be deactivated (folded back) by clicking on its title.

After finishing a query, pushing the “reset” button will clear all previous input so that the system is ready for a new search.

The five search modules work together in an additive manner. Any search component that is activated is included in the current search.

For example, one can search on a particular molecular formula (“Structure-based Search”) with specified chemical shift values (“NMR-based Search”) and limit the search to metabolites believed to be associated with Arabidopsis (“Miscellanea”).

The batch mode search feature enables high-throughput searching. Batch mode searching is available for the Text-based, NMR-based, and MASS-based search sections.

Clicking on the “Batch Mode” bar switches the search engine to batch mode and enables data input from a file.

In batch mode, the MMCD provides a true high-throughput search engine that enables automated qualitative and quantitative analysis of metabolite mixtures upon uploading files with NMR and/or MS data.

System Requirements

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Manufacturer Web Site Madison-Qingdao Metabolomics Consortium Database (MMCD)

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G6G Abstract Number 20670

G6G Manufacturer Number 104311