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Madison-Qingdao Metabolomics Consortium Database


Reference: Q. Cui, I. A. Lewis, A. D. Hegeman, M. E. Anderson, J. Li, C. F. Schulte, W. M. Westler, H. R. Eghbalnia, M. R. Sussman, and J. L. Markley; "Metabolite identification via the Madison Metabolomics Consortium Database", Nature Biotechnology, 26,162 (2008)


Introduction

This database, which is maintained by the National Magnetic Resonance Facility at Madison, is a resource for metabolomics research based on nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). The goal of the Madison-Qingdao Metabolomics Consortium Database (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.

overview

The figure above shows summary of the information content of the Madison-Qingdao Metabolomics Consortium Database (MMCD) and queries that it supports. The MMCD is a hub for NMR and MS spectral data from databases and the literature (or collected in-house), information about metabolites, links to external websites containing information about metabolites, and relevant calculated parameters. The versatile web-based query interface supports single queries typed into the interface or batch queries specified by uploaded files.

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 (12C14N, 13C14N, 12C15N, 13C15N), empirically predicted chemical shifts and, where available, experimental NMR chemical shifts and 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

Experimental data collected under standard conditions (spectra, peak list, assignments)

Literature data

Chemical shifts from theoretical calculations (by Gaussian 03)

Empirically predicted chemical shifts

2. Data related to mass spectrometery

Isotopomer masses for: 12C14N / 13C14N / 12C15N / 13C15N

LC-MS data collected under defined conditions

3. Data related to structure

String presentation: SMILES, InChI

2D mol file

3D mol file

Canonicalized atom-ID

4. Basic properties

e.g., Name, IUPAC name, synonym, CAS, formula, average mass, water solubility, LogP, etc.

5. Links to chemical and biological informatics databases/websites:

e.g., PubChem, ChemIDplus, KEGG, CHEBI, HMDB, BioCyc, UM-BBD, NIST Chemistry WebBook, NMRShiftDB and wwwPDB

6. Miscellaneous data.

Reference, data source, organism, etc.

For local MMC use: order status, vendor, and location

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 search engines located in the panel to the left. The five search categories are: text search, molecular structure search, NMR parameter search, MS parameter search, and miscellaneous criteria search. 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.

Users of the MMCD are encouraged to use the following acknowledgement: "This work utilized the MMC Database supported by NIH grants R21 DK070297 and P41 RR02301."

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