Abstract
Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.
Highlights
Metabolomics is a branch of ‘‘omics’’ research primarily concerned with the high-throughput identification and quantification of small molecule (,1500 Da) metabolites in the metabolome [1,2]
With the release of the Human Metabolome Database (HMDB) [4,5] and other related compound or spectral resources such as KEGG [6], LipidMaps [7], PubChem [8], ChEBI [9], MMCD [10], Metlin [11] and MassBank [12], we believe the field has taken an important step towards making metabolomics studies much more quantitative and far more expansive in terms of metabolite coverage
A complete listing of the identity and quantity of endogenous metabolites that can be detected in human serum is available in the Serum Metabolome Database (SMDB: http:// www.serummetabolome.ca)
Summary
Metabolomics is a branch of ‘‘omics’’ research primarily concerned with the high-throughput identification and quantification of small molecule (,1500 Da) metabolites in the metabolome [1,2]. Metabolomics currently lacks the quantitative horsepower that characterizes the other ‘‘omics’’ sciences This limitation has mostly arisen because metabolomics has, until recently, lacked the electronic database equivalent of GenBank or UniProt [2] for compound identification. With the release of the Human Metabolome Database (HMDB) [4,5] and other related compound or spectral resources such as KEGG [6], LipidMaps [7], PubChem [8], ChEBI [9], MMCD [10], Metlin [11] and MassBank [12], we believe the field has taken an important step towards making metabolomics studies much more quantitative and far more expansive in terms of metabolite coverage. Following our comprehensive characterization of the cerebrospinal fluid metabolome [15] we continue with a comprehensive characterization of the human serum metabolome
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