HMDB: a knowledgebase for the human metabolome

Abstract

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

“…The results of our accurate mass measurements annotated in Figure 1B agree with previously published data from isotope labeling studies carried out on U [16]. We have reinterpreted this labeling data, which was originally only discussed in terms of 15 N, 13 C, and 18 O labeling [16], to include the results from dissociation of [5,6-D 2 ]uracil that had not previously been explained but are critical in explaining several dissociation pathways. Based on this interpretation, the composition and atom position of each product-ion and all neutral losses are presented in Table 1, which is the starting point for our spectral interpretation.…”

“…Such de novo identification aims to correlate observed spectral features in MS/MS to the structures of investigated species based on established reactivity for a class of compounds [4,[6][7][8][9]. The idea of using MS/MS as stand-alone identification tool is of increasing interest and is also being addressed using other more general approaches intended to generalize dissociation pathways [10], to automate data analysis [11], or to compile spectra in databases [12,13].…”

The role of metabolomics in determination of new dietary biomarkers

“…all metabolites will be detected once they are present in concentrations above the limit of detection. Two-dimensional (2D) NMR experiments such as TOCSY, 1 H J-RES and 1 H- 13 C HSQC are important to use in conjunction with one-dimensional spectra for metabolite identification (21) and to compare with reference databases such as the Human Metabolome Database (22) and Biological Magnetic Resonance Databank (23) . In addition, one-dimensional and 2D NMR experiments offer the potential to identify previously unknown metabolites (24) .…”

Qualitative Metabolome Analysis of Human Cerebrospinal Fluid by13C-/12C-Isotope Dansylation Labeling Combined with Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

“…The detected ion pairs can be searched against a database for putative metabolite identification or a library of standards for definitive identification. In this work, putative identification is based on the accurate mass matches of the dansylated metabolites with the human endogenous metabolites found in the Human Metabolome Database (HMDB) (about 8000 metabolite entries) [30]. Definitive identification is based on matches of accurate masses and retention times to a 13 C-/ 12 C-labeled authentic standards library (220 standards; see below).…”