Journal ArticleDOI
Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics
Marie Brown,Warwick B. Dunn,Paul D. Dobson,Yogendra Patel,Catherine L. Winder,Sue Francis-McIntyre,Paul Begley,Kathleen M. Carroll,David Broadhurst,Andy Tseng,Neil Swainston,Irena Spasic,Royston Goodacre,Douglas B. Kell +13 more
TLDR
The combination of accurate mass data for a large collection of metabolites, theoretical isotope abundance data and knowledge of the different ion types detected provided a greater number of electrospray mass spectrometric signals which were putatively identified and with greater confidence in the samples studied.Abstract:
The chemical identification of mass spectrometric signals in metabolomic applications is important to provide conversion of analytical data to biological knowledge about metabolic pathways. The complexity of electrospray mass spectrometric data acquired from a range of samples (serum, urine, yeast intracellular extracts, yeast metabolic footprints, placental tissue metabolic footprints) has been investigated and has defined the frequency of different ion types routinely detected. Although some ion types were expected (protonated and deprotonated peaks, isotope peaks, multiply charged peaks) others were not expected (sodium formate adduct ions). In parallel, the Manchester Metabolomics Database (MMD) has been constructed with data from genome scale metabolic reconstructions, HMDB, KEGG, Lipid Maps, BioCyc and DrugBank to provide knowledge on 42,687 endogenous and exogenous metabolite species. The combination of accurate mass data for a large collection of metabolites, theoretical isotope abundance data and knowledge of the different ion types detected provided a greater number of electrospray mass spectrometric signals which were putatively identified and with greater confidence in the samples studied. To provide definitive identification metabolite-specific mass spectral libraries for UPLC-MS and GC-MS have been constructed for 1,065 commercially available authentic standards. The MMD data are available at http://dbkgroup.org/MMD/.read more
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
Warwick B. Dunn,David Broadhurst,David Broadhurst,Paul Begley,Eva Zelena,Sue Francis-McIntyre,Nadine Anderson,Marie Brown,Joshau D Knowles,Antony Halsall,John N. Haselden,Andrew W. Nicholls,Ian D. Wilson,Douglas B. Kell,Royston Goodacre +14 more
TL;DR: The experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years is described.
Journal ArticleDOI
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles
Masahiro Sugimoto,David T.W. Wong,David T.W. Wong,Akiyoshi Hirayama,Tomoyoshi Soga,Masaru Tomita +5 more
TL;DR: A comprehensive metabolite analysis of saliva samples obtained from 215 individuals using capillary electrophoresis time-of-flight mass spectrometry identified 57 principal metabolites that can be used to accurately predict the probability of being affected by each individual disease.
Journal ArticleDOI
Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy
Warwick B. Dunn,David Broadhurst,Helen J. Atherton,Helen J. Atherton,Royston Goodacre,Julian L. Griffin +5 more
TL;DR: An introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided and the applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed.
Journal ArticleDOI
Modern analytical techniques in metabolomics analysis
TL;DR: The combined use of modern instrumental analytical approaches has unravelled the ideal outcomes in metabolomics, and is beneficial to increase the coverage of detected metabolites that can not be achieved by single-analysis techniques.
References
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Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules
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