HMDB

HMDB provides a comprehensive, curated database of human small-molecule metabolites with associated concentration, reference NMR and MS spectra, pathway, enzyme, gene, SNP, and disease annotations to support metabolomics and clinical research.

Key Features:

• Comprehensive Data Collection: Version 2.0 contains records for over 6,800 fully annotated metabolites, more than 4,400 metabolites with biofluid or tissue concentration data, and reference spectra for over 790 compounds.
• Extensive Data Fields: Each metabolite entry contains an average of 90 data fields including names, synonyms, structural information, physico-chemical properties, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme and gene sequence data, and SNP and mutation details.
• Experimental Data Integration: The database integrates experimental metabolite concentration data derived from hundreds of mass spectrometry (MS) and nuclear magnetic resonance (NMR) analyses of human samples such as urine, blood, and cerebrospinal fluid.
• Enhanced Search and Spectral Tools: HMDB supports text, sequence, chemical structure, and relational queries and implements improved algorithms for spectral matching and chemical substructure searches, as well as pathway searching tools and interactive metabolic maps.

Scientific Applications:

• Metabolite identification and annotation: Use of reference NMR and MS spectra and spectral matching algorithms to identify and annotate small-molecule metabolites.
• Clinical biochemistry and biomarker discovery: Analysis of biofluid concentration data to identify disease-associated metabolites and monitor physiological changes.
• Organ transplant monitoring: Metabolite profiling to assess organ function, viability, and detect rejection episodes post-transplantation.
• Systems biology and pathway analysis: Integration of pathway information with enzyme and gene sequence data, including SNP and mutation details, to support mechanistic and integrative studies.

Methodology:

Provides text, sequence, chemical structure, and relational query capabilities; implements spectral matching algorithms and chemical substructure searches; integrates reference NMR and MS spectra, pathway searching tools, and experimental MS/NMR concentration data.