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2019 | OriginalPaper | Buchkapitel

6. Metabonomics

verfasst von : Toby Athersuch

Erschienen in: Unraveling the Exposome

Verlag: Springer International Publishing

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Abstract

The exposome concept places substantial weight on the internal chemical milieu of individuals, as this is the primary integrator of the human genome and the wider external environment. Small molecule metabolites of both endogenous and exogenous origin are involved in a plethora of cellular and systemic functions, and collectively contribute to the mechanistic linkage of exposures, responses, and associated adverse outcomes. Temporal and spatial responses of metabolic phenotypes to various environmental stimuli provide a direct report on multiple interacting and conditional processes that are modulated by numerous factors including diet, lifestyle, pharmaceutical use, microbial activity, age, sex, and many others. Measuring and integrating information about the human metabolome represents a critical part of the path toward understanding the environmental determinants of chronic disease.
The size and diversity of the chemical space that metabolites occupy means that measuring the human metabolome via serum, urine, or other biofluids or tissues represents a huge analytical challenge, addressed by the application of high-resolution platforms, typically incorporating liquid- and/or gas-chromatography for separation, and nuclear magnetic resonance spectroscopy and/or mass spectrometry for detection. Advances in the performance of these platforms now permit the measurement of many hundreds or thousands of metabolites, in either targeted or untargeted assays. The focus of this chapter is on the utility of the different analytical platforms, their complementarity, and application to large-scale sample set analysis. Considerations for data analysis and integration with other omics, exposure, and outcome data are discussed, alongside approaches for interpreting findings in the context of the human exposome.

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Literatur
Zurück zum Zitat Abbiss H, Rawlinson C, Maker GL, Trengove R (2015) Assessment of automated trimethylsilyl derivatization protocols for GC–MS-based untargeted metabolomic analysis of urine. Metabolomics 11:1908–1921CrossRef Abbiss H, Rawlinson C, Maker GL, Trengove R (2015) Assessment of automated trimethylsilyl derivatization protocols for GC–MS-based untargeted metabolomic analysis of urine. Metabolomics 11:1908–1921CrossRef
Zurück zum Zitat Anton G, Wilson R, Yu Z-H, Prehn C, Zukunft S, Adamski J et al (2015) Pre-analytical sample quality: metabolite ratios as an intrinsic marker for prolonged room temperature exposure of serum samples. Kim KH, editor. PLoS One e0121495:10 Anton G, Wilson R, Yu Z-H, Prehn C, Zukunft S, Adamski J et al (2015) Pre-analytical sample quality: metabolite ratios as an intrinsic marker for prolonged room temperature exposure of serum samples. Kim KH, editor. PLoS One e0121495:10
Zurück zum Zitat Athersuch T (2016) Metabolome analyses in exposome studies: profiling methods for a vast chemical space. Arch Biochem Biophys 589:177–186CrossRef Athersuch T (2016) Metabolome analyses in exposome studies: profiling methods for a vast chemical space. Arch Biochem Biophys 589:177–186CrossRef
Zurück zum Zitat Balog J, Szaniszlo T, Schaefer K-C, Dénes J, Lopata A, Godorhazy L et al (2010) Identification of biological tissues by rapid evaporative ionization mass spectrometry. Anal Chem 82:7343–7350CrossRef Balog J, Szaniszlo T, Schaefer K-C, Dénes J, Lopata A, Godorhazy L et al (2010) Identification of biological tissues by rapid evaporative ionization mass spectrometry. Anal Chem 82:7343–7350CrossRef
Zurück zum Zitat Bamba T, Shimonishi N, Matsubara A, Hirata K, Nakazawa Y, Kobayashi A et al (2008) High throughput and exhaustive analysis of diverse lipids by using supercritical fluid chromatography-mass spectrometry for metabolomics. J Biosci Bioeng 105:460–469CrossRef Bamba T, Shimonishi N, Matsubara A, Hirata K, Nakazawa Y, Kobayashi A et al (2008) High throughput and exhaustive analysis of diverse lipids by using supercritical fluid chromatography-mass spectrometry for metabolomics. J Biosci Bioeng 105:460–469CrossRef
Zurück zum Zitat Bamba T, Lee JW, Matsubara A, Fukusaki E (2012) Metabolic profiling of lipids by supercritical fluid chromatography/mass spectrometry. J Chromatogr A 1250:212–219CrossRef Bamba T, Lee JW, Matsubara A, Fukusaki E (2012) Metabolic profiling of lipids by supercritical fluid chromatography/mass spectrometry. J Chromatogr A 1250:212–219CrossRef
Zurück zum Zitat Bartel J, Krumsiek J, Schramm K, Adamski J, Gieger C, Herder C et al (2015) The human blood metabolome-transcriptome interface. Inouye M, editor. PLoS Genet e1005274:11 Bartel J, Krumsiek J, Schramm K, Adamski J, Gieger C, Herder C et al (2015) The human blood metabolome-transcriptome interface. Inouye M, editor. PLoS Genet e1005274:11
Zurück zum Zitat Beckett AH (2008) Metabolic oxidation of aliphatic basic nitrogen atoms and their α-carbon atoms. Xenobiotica 1:365–384CrossRef Beckett AH (2008) Metabolic oxidation of aliphatic basic nitrogen atoms and their α-carbon atoms. Xenobiotica 1:365–384CrossRef
Zurück zum Zitat Beckonert O, Keun HC, Ebbels TMD, Bundy J, Holmes E, Lindon JC et al (2007) Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2:2692–2703CrossRef Beckonert O, Keun HC, Ebbels TMD, Bundy J, Holmes E, Lindon JC et al (2007) Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2:2692–2703CrossRef
Zurück zum Zitat Beckonert O, Coen M, Keun HC, Wang Y (2010) High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc 5(6):1019–1032CrossRef Beckonert O, Coen M, Keun HC, Wang Y (2010) High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc 5(6):1019–1032CrossRef
Zurück zum Zitat Benton HP, Want E, Keun HC, Amberg A, Plumb RS, Goldfain-Blanc F et al (2012) Intra- and interlaboratory reproducibility of ultra performance liquid chromatography-time-of-flight mass spectrometry for urinary metabolic profiling. Anal Chem 84:2424–2432CrossRef Benton HP, Want E, Keun HC, Amberg A, Plumb RS, Goldfain-Blanc F et al (2012) Intra- and interlaboratory reproducibility of ultra performance liquid chromatography-time-of-flight mass spectrometry for urinary metabolic profiling. Anal Chem 84:2424–2432CrossRef
Zurück zum Zitat Blaise BJ, Correia G, Tin A, Young JH, Vergnaud A-C, Lewis M et al (2016) Power analysis and sample size determination in metabolic phenotyping. Anal Chem 88:5179–5188CrossRef Blaise BJ, Correia G, Tin A, Young JH, Vergnaud A-C, Lewis M et al (2016) Power analysis and sample size determination in metabolic phenotyping. Anal Chem 88:5179–5188CrossRef
Zurück zum Zitat Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C et al (2013) The human urine metabolome. Dzeja P, editor. PLoS One e73076:8 Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C et al (2013) The human urine metabolome. Dzeja P, editor. PLoS One e73076:8
Zurück zum Zitat Budde K, Gök Ö-N, Pietzner M, Meisinger C, Leitzmann M, Nauck M et al (2016) Quality assurance in the pre-analytical phase of human urine samples by 1H NMR spectroscopy. Arch Biochem Biophys 589:10–17CrossRef Budde K, Gök Ö-N, Pietzner M, Meisinger C, Leitzmann M, Nauck M et al (2016) Quality assurance in the pre-analytical phase of human urine samples by 1H NMR spectroscopy. Arch Biochem Biophys 589:10–17CrossRef
Zurück zum Zitat Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA et al (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42:D459–D471CrossRef Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA et al (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42:D459–D471CrossRef
Zurück zum Zitat Chan ECY, Pasikanti KK, Nicholson JK (2011) Global urinary metabolic profiling procedures using gas chromatography-mass spectrometry. Nat Protoc 6:1483–1499CrossRef Chan ECY, Pasikanti KK, Nicholson JK (2011) Global urinary metabolic profiling procedures using gas chromatography-mass spectrometry. Nat Protoc 6:1483–1499CrossRef
Zurück zum Zitat Cherney DP, Ekman DR, Dix DJ, Collette TW (2007) Raman spectroscopy-based metabolomics for differentiating exposures to triazole fungicides using rat urine. Anal Chem 79:7324–7332CrossRef Cherney DP, Ekman DR, Dix DJ, Collette TW (2007) Raman spectroscopy-based metabolomics for differentiating exposures to triazole fungicides using rat urine. Anal Chem 79:7324–7332CrossRef
Zurück zum Zitat Contrepois K, Jiang L, Snyder M (2015) Optimized analytical procedures for the untargeted metabolomic profiling of human urine and plasma by combining hydrophilic interaction (HILIC) and reverse-phase liquid chromatography (RPLC)-mass spectrometry. Mol Cell Proteomics 14:1684–1695CrossRef Contrepois K, Jiang L, Snyder M (2015) Optimized analytical procedures for the untargeted metabolomic profiling of human urine and plasma by combining hydrophilic interaction (HILIC) and reverse-phase liquid chromatography (RPLC)-mass spectrometry. Mol Cell Proteomics 14:1684–1695CrossRef
Zurück zum Zitat Creek DJ, Chokkathukalam A, Jankevics A, Burgess KEV, Breitling R, Barrett MP (2012) Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Anal Chem 84:8442–8447CrossRef Creek DJ, Chokkathukalam A, Jankevics A, Burgess KEV, Breitling R, Barrett MP (2012) Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Anal Chem 84:8442–8447CrossRef
Zurück zum Zitat Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF et al (2008) Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol 26:162–164CrossRef Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF et al (2008) Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol 26:162–164CrossRef
Zurück zum Zitat Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I (2015a) Review on Ion Mobility Spectrometry. Part 1: current instrumentation. Analyst 140:1376–1390CrossRef Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I (2015a) Review on Ion Mobility Spectrometry. Part 1: current instrumentation. Analyst 140:1376–1390CrossRef
Zurück zum Zitat Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I (2015b) Review on Ion Mobility Spectrometry. Part 2: hyphenated methods and effects of experimental parameters. Analyst 140:1391–1410CrossRef Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I (2015b) Review on Ion Mobility Spectrometry. Part 2: hyphenated methods and effects of experimental parameters. Analyst 140:1391–1410CrossRef
Zurück zum Zitat Damjanovich L, Darzi A, Nicholson JK (2013) Intraoperative tissue identification using rapid evaporative ionization mass spectrometry. Sci Transl Med 5(194):194ra93 Damjanovich L, Darzi A, Nicholson JK (2013) Intraoperative tissue identification using rapid evaporative ionization mass spectrometry. Sci Transl Med 5(194):194ra93
Zurück zum Zitat Damsten MC, Commandeur JNM, Fidder A, Hulst AG, Touw D, Noort D et al (2007) Liquid chromatography/tandem mass spectrometry detection of covalent binding of acetaminophen to human serum albumin. Drug Metab Dispos 35:1408–1417CrossRef Damsten MC, Commandeur JNM, Fidder A, Hulst AG, Touw D, Noort D et al (2007) Liquid chromatography/tandem mass spectrometry detection of covalent binding of acetaminophen to human serum albumin. Drug Metab Dispos 35:1408–1417CrossRef
Zurück zum Zitat Davidson RL, Weber RJM, Liu H, Sharma-Oates A, Viant MR (2016) Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Gigascience 5:10CrossRef Davidson RL, Weber RJM, Liu H, Sharma-Oates A, Viant MR (2016) Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Gigascience 5:10CrossRef
Zurück zum Zitat Davies SK, Ang JE, Revell VL, Holmes B, Mann A, Robertson FP et al (2014) Effect of sleep deprivation on the human metabolome. PNAS 111:10761–10766CrossRef Davies SK, Ang JE, Revell VL, Holmes B, Mann A, Robertson FP et al (2014) Effect of sleep deprivation on the human metabolome. PNAS 111:10761–10766CrossRef
Zurück zum Zitat Dénes J, Katona M, Hosszú Á, Czuczy N, Takáts Z (2009) Analysis of biological fluids by direct combination of solid phase extraction and desorption electrospray ionization mass spectrometry. Anal Chem 81:1669–1675CrossRef Dénes J, Katona M, Hosszú Á, Czuczy N, Takáts Z (2009) Analysis of biological fluids by direct combination of solid phase extraction and desorption electrospray ionization mass spectrometry. Anal Chem 81:1669–1675CrossRef
Zurück zum Zitat Dénes J, Szabó E, Robinette SL, Szatmári I, Szőnyi L, Kreuder JG et al (2012) Metabonomics of newborn screening dried blood spot samples: a novel approach in the screening and diagnostics of inborn errors of metabolism. Anal Chem 84:10113–10120CrossRef Dénes J, Szabó E, Robinette SL, Szatmári I, Szőnyi L, Kreuder JG et al (2012) Metabonomics of newborn screening dried blood spot samples: a novel approach in the screening and diagnostics of inborn errors of metabolism. Anal Chem 84:10113–10120CrossRef
Zurück zum Zitat Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR et al (2014) Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping. Anal Chem 86:9887–9894CrossRef Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR et al (2014) Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping. Anal Chem 86:9887–9894CrossRef
Zurück zum Zitat Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD et al (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS 104:1777–1782CrossRef Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD et al (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS 104:1777–1782CrossRef
Zurück zum Zitat Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N et al (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6:1060–1083CrossRef Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N et al (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6:1060–1083CrossRef
Zurück zum Zitat Dunn WB, Lin W, Broadhurst D, Begley P, Brown M, Zelena E et al (2014) Molecular phenotyping of a UK population: defining the human serum metabolome. Metabolomics 11:9–26CrossRef Dunn WB, Lin W, Broadhurst D, Begley P, Brown M, Zelena E et al (2014) Molecular phenotyping of a UK population: defining the human serum metabolome. Metabolomics 11:9–26CrossRef
Zurück zum Zitat Ellis DI, Goodacre R (2006) Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy. Analyst 131:875–885CrossRef Ellis DI, Goodacre R (2006) Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy. Analyst 131:875–885CrossRef
Zurück zum Zitat Ellis JK, Athersuch TJ, Thomas LD, Teichert F, Pérez-Trujillo M, Svendsen C et al (2012) Metabolic profiling detects early effects of environmental and lifestyle exposure to cadmium in a human population. BMC Med 10:61CrossRef Ellis JK, Athersuch TJ, Thomas LD, Teichert F, Pérez-Trujillo M, Svendsen C et al (2012) Metabolic profiling detects early effects of environmental and lifestyle exposure to cadmium in a human population. BMC Med 10:61CrossRef
Zurück zum Zitat Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2:155–168CrossRef Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2:155–168CrossRef
Zurück zum Zitat Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N et al (2007) The metabolomics standards initiative (MSI). Metabolomics 3:175–178CrossRef Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N et al (2007) The metabolomics standards initiative (MSI). Metabolomics 3:175–178CrossRef
Zurück zum Zitat Fink T, Reymond J-L (2007) Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery. J Chem Inf Model 47:342–353CrossRef Fink T, Reymond J-L (2007) Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery. J Chem Inf Model 47:342–353CrossRef
Zurück zum Zitat García A, Barbas C (2010) Gas chromatography-mass spectrometry (GC-MS)-based metabolomics. In: Fan J-B (ed) Metabolic profiling. Humana Press, Totowa, NJ, pp 191–204 García A, Barbas C (2010) Gas chromatography-mass spectrometry (GC-MS)-based metabolomics. In: Fan J-B (ed) Metabolic profiling. Humana Press, Totowa, NJ, pp 191–204
Zurück zum Zitat Ghaste M, Mistrik R, Shulaev V (2016) Applications of fourier transform ion cyclotron resonance (FT-ICR) and orbitrap based high resolution mass spectrometry in metabolomics and lipidomics. Int J Mol Sci 17(6):pii: E816CrossRef Ghaste M, Mistrik R, Shulaev V (2016) Applications of fourier transform ion cyclotron resonance (FT-ICR) and orbitrap based high resolution mass spectrometry in metabolomics and lipidomics. Int J Mol Sci 17(6):pii: E816CrossRef
Zurück zum Zitat Gieger C, Geistlinger L, Altmaier E, Hrabé de Angelis M, Kronenberg F, Meitinger T et al (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4:e1000282CrossRef Gieger C, Geistlinger L, Altmaier E, Hrabé de Angelis M, Kronenberg F, Meitinger T et al (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4:e1000282CrossRef
Zurück zum Zitat Gika HG, Theodoridis GA, Wilson ID (2008) Liquid chromatography and ultra-performance liquid chromatography–mass spectrometry fingerprinting of human urine. J Chromatogr A 1189:314–322CrossRef Gika HG, Theodoridis GA, Wilson ID (2008) Liquid chromatography and ultra-performance liquid chromatography–mass spectrometry fingerprinting of human urine. J Chromatogr A 1189:314–322CrossRef
Zurück zum Zitat Giskeødegård GF, Davies SK, Revell VL, Keun H, Skene DJ (2015) Diurnal rhythms in the human urine metabolome during sleep and total sleep deprivation. Sci Rep 5:14843CrossRef Giskeødegård GF, Davies SK, Revell VL, Keun H, Skene DJ (2015) Diurnal rhythms in the human urine metabolome during sleep and total sleep deprivation. Sci Rep 5:14843CrossRef
Zurück zum Zitat Gray N, Zia R, King A, Patel VC, Wendon J, McPhail MJW et al (2017) High-speed quantitative UPLC-MS analysis of multiple amines in human plasma and serum via precolumn derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate: application to acetaminophen-induced liver failure. Anal Chem 89:2478–2487CrossRef Gray N, Zia R, King A, Patel VC, Wendon J, McPhail MJW et al (2017) High-speed quantitative UPLC-MS analysis of multiple amines in human plasma and serum via precolumn derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate: application to acetaminophen-induced liver failure. Anal Chem 89:2478–2487CrossRef
Zurück zum Zitat Guthrie R, Susi A (1963) A simple phenylalanine method for detecting phenylketonuria in large populations of newborn infants. Pediatrics 32:338–343 Guthrie R, Susi A (1963) A simple phenylalanine method for detecting phenylketonuria in large populations of newborn infants. Pediatrics 32:338–343
Zurück zum Zitat Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N et al (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463CrossRef Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N et al (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463CrossRef
Zurück zum Zitat Haug K, Salek RM, Conesa P, Hastings J (2013) MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 41:D781–D786CrossRef Haug K, Salek RM, Conesa P, Hastings J (2013) MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 41:D781–D786CrossRef
Zurück zum Zitat Haug K, Salek RM, Steinbeck C (2017) Global open data management in metabolomics. Curr Opin Chem Biol 36:58–63CrossRef Haug K, Salek RM, Steinbeck C (2017) Global open data management in metabolomics. Curr Opin Chem Biol 36:58–63CrossRef
Zurück zum Zitat Hebels DGAJ, Georgiadis P, Keun HC, Athersuch TJ, Vineis P, Vermeulen R et al (2013) Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ Health Perspect 121(4):480–487CrossRef Hebels DGAJ, Georgiadis P, Keun HC, Athersuch TJ, Vineis P, Vermeulen R et al (2013) Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ Health Perspect 121(4):480–487CrossRef
Zurück zum Zitat Hernandes VV, Barbas C, Dudzik D (2017) A review of blood sample handling and pre-processing for metabolomics studies. Electrophoresis 38(18):2232–2241CrossRef Hernandes VV, Barbas C, Dudzik D (2017) A review of blood sample handling and pre-processing for metabolomics studies. Electrophoresis 38(18):2232–2241CrossRef
Zurück zum Zitat Hicks AA, Pramstaller PP, Johansson Å, Vitart V, Rudan I, Ugocsai P et al (2009) Genetic determinants of circulating sphingolipid concentrations in European populations. Gibson G, editor. PLoS Genet e1000672:5 Hicks AA, Pramstaller PP, Johansson Å, Vitart V, Rudan I, Ugocsai P et al (2009) Genetic determinants of circulating sphingolipid concentrations in European populations. Gibson G, editor. PLoS Genet e1000672:5
Zurück zum Zitat Holmes E, Nicholson JK (2008) Human metabolic phenotyping and metabolome wide association studies. Oncogenes meet metabolism. Springer, Berlin, Heidelberg, pp 227–249 Holmes E, Nicholson JK (2008) Human metabolic phenotyping and metabolome wide association studies. Oncogenes meet metabolism. Springer, Berlin, Heidelberg, pp 227–249
Zurück zum Zitat Holmes E, Loo RL, Cloarec O, Coen M, Tang H, Maibaum E et al (2007) Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem 79:2629–2640CrossRef Holmes E, Loo RL, Cloarec O, Coen M, Tang H, Maibaum E et al (2007) Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem 79:2629–2640CrossRef
Zurück zum Zitat Holmes E, Wilson ID, Nicholson JK (2008) Metabolic phenotyping in health and disease. Cell 134:714–717CrossRef Holmes E, Wilson ID, Nicholson JK (2008) Metabolic phenotyping in health and disease. Cell 134:714–717CrossRef
Zurück zum Zitat Holmes E, Stamler J, Nicholson JK (2010) Opening up the “Black Box”: metabolic phenotyping and metabolome-wide association studies in epidemiology. J Clin Epidemiol 63(9):970–979CrossRef Holmes E, Stamler J, Nicholson JK (2010) Opening up the “Black Box”: metabolic phenotyping and metabolome-wide association studies in epidemiology. J Clin Epidemiol 63(9):970–979CrossRef
Zurück zum Zitat Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K et al (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45:703–714CrossRef Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K et al (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45:703–714CrossRef
Zurück zum Zitat Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham CR (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443CrossRef Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham CR (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443CrossRef
Zurück zum Zitat Huan T, Forsberg EM, Rinehart D, Johnson CH (2017) Systems biology guided by XCMS Online metabolomics. Nat Methods 14(5):461–462CrossRef Huan T, Forsberg EM, Rinehart D, Johnson CH (2017) Systems biology guided by XCMS Online metabolomics. Nat Methods 14(5):461–462CrossRef
Zurück zum Zitat IARC (2012) Chemical agents and related occupations. Benzo[α]pyrene. IARC Monogr Eval Carcinog Risk Chem Man 100F:111–144 IARC (2012) Chemical agents and related occupations. Benzo[α]pyrene. IARC Monogr Eval Carcinog Risk Chem Man 100F:111–144
Zurück zum Zitat Illig T, Gieger C, Zhai G, Römisch-Margl W, Wang Sattler R, Prehn C et al (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42:137–141CrossRef Illig T, Gieger C, Zhai G, Römisch-Margl W, Wang Sattler R, Prehn C et al (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42:137–141CrossRef
Zurück zum Zitat Jansen RJ, Argos M, Tong L, Li J, Rakibuz-Zaman M, Islam MT et al (2016) Determinants and consequences of arsenic metabolism efficiency among 4,794 individuals: demographics, lifestyle, genetics, and toxicity. Cancer Epidemiol Biomark Prev 25(2):381–390CrossRef Jansen RJ, Argos M, Tong L, Li J, Rakibuz-Zaman M, Islam MT et al (2016) Determinants and consequences of arsenic metabolism efficiency among 4,794 individuals: demographics, lifestyle, genetics, and toxicity. Cancer Epidemiol Biomark Prev 25(2):381–390CrossRef
Zurück zum Zitat Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J et al (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 22:1601–1606CrossRef Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J et al (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 22:1601–1606CrossRef
Zurück zum Zitat Jones DP (2016) Sequencing the exposome: a call to action. Toxicol Rep 3:29–45CrossRef Jones DP (2016) Sequencing the exposome: a call to action. Toxicol Rep 3:29–45CrossRef
Zurück zum Zitat Jones DR, Wu Z, Chauhan D, Anderson KC, Peng J (2014) A nano ultra-performance liquid chromatography–high resolution mass spectrometry approach for global metabolomic profiling and case study on drug-resistant multiple myeloma. Anal Chem 86:3667–3675CrossRef Jones DR, Wu Z, Chauhan D, Anderson KC, Peng J (2014) A nano ultra-performance liquid chromatography–high resolution mass spectrometry approach for global metabolomic profiling and case study on drug-resistant multiple myeloma. Anal Chem 86:3667–3675CrossRef
Zurück zum Zitat Kamlage B, Maldonado SG, Bethan B, Peter E, Schmitz O, Liebenberg V et al (2014) Quality markers addressing preanalytical variations of blood and plasma processing identified by broad and targeted metabolite profiling. Clin Chem 60:399–412CrossRef Kamlage B, Maldonado SG, Bethan B, Peter E, Schmitz O, Liebenberg V et al (2014) Quality markers addressing preanalytical variations of blood and plasma processing identified by broad and targeted metabolite profiling. Clin Chem 60:399–412CrossRef
Zurück zum Zitat Karagas MR, Gossai A, Pierce B, Ahsan H (2015) Drinking water arsenic contamination, skin lesions, and malignancies: a systematic review of the global evidence. Curr Envir Health Rep 2:52–68CrossRef Karagas MR, Gossai A, Pierce B, Ahsan H (2015) Drinking water arsenic contamination, skin lesions, and malignancies: a systematic review of the global evidence. Curr Envir Health Rep 2:52–68CrossRef
Zurück zum Zitat Kassner MK, Charney R, Fernandez FM (2008) Novel approach to employing SFC for metabolomics research. In: Aiche annual meeting, conference proceeding Kassner MK, Charney R, Fernandez FM (2008) Novel approach to employing SFC for metabolomics research. In: Aiche annual meeting, conference proceeding
Zurück zum Zitat Kastenmüller G, Raffler J, Gieger C, Suhre K (2015) Genetics of human metabolism: an update. Hum Mol Genet 24(R1):R93–R101CrossRef Kastenmüller G, Raffler J, Gieger C, Suhre K (2015) Genetics of human metabolism: an update. Hum Mol Genet 24(R1):R93–R101CrossRef
Zurück zum Zitat Keun HC, Athersuch TJ (2010) Nuclear magnetic resonance (NMR)-based metabolomics. In: Fan J-B (ed) Metabolic profiling. Humana Press, Totowa, NJ, pp 321–334 Keun HC, Athersuch TJ (2010) Nuclear magnetic resonance (NMR)-based metabolomics. In: Fan J-B (ed) Metabolic profiling. Humana Press, Totowa, NJ, pp 321–334
Zurück zum Zitat Keun HC, Beckonert O, Griffin JL, Richter C, Moskau D, Lindon JC, Nicholson JK et al (2002) Cryogenic probe 13C NMR spectroscopy of urine for metabonomic studies. Anal Chem 74:4588–4593CrossRef Keun HC, Beckonert O, Griffin JL, Richter C, Moskau D, Lindon JC, Nicholson JK et al (2002) Cryogenic probe 13C NMR spectroscopy of urine for metabonomic studies. Anal Chem 74:4588–4593CrossRef
Zurück zum Zitat Kim K, Mall C, Taylor SL, Hitchcock S, Zhang C, Wettersten HI et al (2014) Mealtime, temporal, and daily variability of the human urinary and plasma metabolomes in a tightly controlled environment. Brennan L, editor. PLoS One e86223:9 Kim K, Mall C, Taylor SL, Hitchcock S, Zhang C, Wettersten HI et al (2014) Mealtime, temporal, and daily variability of the human urinary and plasma metabolomes in a tightly controlled environment. Brennan L, editor. PLoS One e86223:9
Zurück zum Zitat Kim S, Thiessen PA, Bolton EE, Chen J (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213CrossRef Kim S, Thiessen PA, Bolton EE, Chen J (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213CrossRef
Zurück zum Zitat Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S et al (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 81:10038–10048CrossRef Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S et al (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 81:10038–10048CrossRef
Zurück zum Zitat Lewis MR, Pearce JTM, Spagou K, Green M, Dona AC, Yuen AHY et al (2016) Development and application of ultra-performance liquid chromatography-TOF MS for precision large scale urinary metabolic phenotyping. Anal Chem 88:9004–9013CrossRef Lewis MR, Pearce JTM, Spagou K, Green M, Dona AC, Yuen AHY et al (2016) Development and application of ultra-performance liquid chromatography-TOF MS for precision large scale urinary metabolic phenotyping. Anal Chem 88:9004–9013CrossRef
Zurück zum Zitat Li N, Song YP, Tang H, Wang Y (2016) Recent developments in sample preparation and data pre-treatment in metabonomics research. Arch Biochem Biophys 589:4–9CrossRef Li N, Song YP, Tang H, Wang Y (2016) Recent developments in sample preparation and data pre-treatment in metabonomics research. Arch Biochem Biophys 589:4–9CrossRef
Zurück zum Zitat Lindon JC, Nicholson JK, Holmes E, Everett JR (2000) Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids. Concepts Magn Reson 12:289–320CrossRef Lindon JC, Nicholson JK, Holmes E, Everett JR (2000) Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids. Concepts Magn Reson 12:289–320CrossRef
Zurück zum Zitat Lindon JC, Nicholson JK, Holmes E, Keun HC (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23(7):833–838CrossRef Lindon JC, Nicholson JK, Holmes E, Keun HC (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23(7):833–838CrossRef
Zurück zum Zitat Loo RL, Coen M, Ebbels T, Cloarec O, Maibaum E, Bictash M et al (2009) Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies. Anal Chem 81:5119–5129CrossRef Loo RL, Coen M, Ebbels T, Cloarec O, Maibaum E, Bictash M et al (2009) Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies. Anal Chem 81:5119–5129CrossRef
Zurück zum Zitat Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O et al (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Molecular Systems Biology. EMBO Press 3:135 Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O et al (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Molecular Systems Biology. EMBO Press 3:135
Zurück zum Zitat Maier TV, Schmitt-Kopplin P (2016) Capillary electrophoresis in metabolomics. Methods Mol Biol 1483:437–470CrossRef Maier TV, Schmitt-Kopplin P (2016) Capillary electrophoresis in metabolomics. Methods Mol Biol 1483:437–470CrossRef
Zurück zum Zitat Maitre L, Lau C-HE, Vizcaino E, Robinson O, Casas M, Siskos AP et al (2017) Assessment of metabolic phenotypic variability in children’s urine using (1)H NMR spectroscopy. Sci Rep 7:46082CrossRef Maitre L, Lau C-HE, Vizcaino E, Robinson O, Casas M, Siskos AP et al (2017) Assessment of metabolic phenotypic variability in children’s urine using (1)H NMR spectroscopy. Sci Rep 7:46082CrossRef
Zurück zum Zitat Marchand J, Martineau E, Guitton Y, Dervilly-Pinel G, Giraudeau P (2017) Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics. Curr Opin Biotechnol 43:49–55CrossRef Marchand J, Martineau E, Guitton Y, Dervilly-Pinel G, Giraudeau P (2017) Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics. Curr Opin Biotechnol 43:49–55CrossRef
Zurück zum Zitat Martin J-C, Maillot M, Mazerolles G, Verdu A, Lyan B, Migné C et al (2015) Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study. Metabolomics 11:807–821CrossRef Martin J-C, Maillot M, Mazerolles G, Verdu A, Lyan B, Migné C et al (2015) Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study. Metabolomics 11:807–821CrossRef
Zurück zum Zitat McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM et al (2013) Criteria for the use of omics-based predictors in clinical trials. Nature 502:317–320CrossRef McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM et al (2013) Criteria for the use of omics-based predictors in clinical trials. Nature 502:317–320CrossRef
Zurück zum Zitat Melkonian S, Argos M, Hall MN, Chen Y, Parvez F, Pierce B et al (2013) Urinary and dietary analysis of 18,470 bangladeshis reveal a correlation of rice consumption with arsenic exposure and toxicity. States JC, editor. PLoS One e80691:8 Melkonian S, Argos M, Hall MN, Chen Y, Parvez F, Pierce B et al (2013) Urinary and dietary analysis of 18,470 bangladeshis reveal a correlation of rice consumption with arsenic exposure and toxicity. States JC, editor. PLoS One e80691:8
Zurück zum Zitat Miller GW, Jones DP (2014) The nature of nurture: refining the definition of the exposome. Toxicol Sci 137(1):1–2CrossRef Miller GW, Jones DP (2014) The nature of nurture: refining the definition of the exposome. Toxicol Sci 137(1):1–2CrossRef
Zurück zum Zitat Moros G, Chatziioannou AC, Gika HG, Raikos N, Theodoridis G (2017) Investigation of the derivatization conditions for GC-MS metabolomics of biological samples. Bioanalysis 9:53–65CrossRef Moros G, Chatziioannou AC, Gika HG, Raikos N, Theodoridis G (2017) Investigation of the derivatization conditions for GC-MS metabolomics of biological samples. Bioanalysis 9:53–65CrossRef
Zurück zum Zitat Nakamura Y, Afendi FM, Parvin AK, Ono N, Tanaka K, Hirai Morita A et al (2014) KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiol 55:e7CrossRef Nakamura Y, Afendi FM, Parvin AK, Ono N, Tanaka K, Hirai Morita A et al (2014) KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiol 55:e7CrossRef
Zurück zum Zitat Nicholson G, Rantalainen M, Maher AD, Li JV, Malmodin D, Ahmadi KR et al (2011) Human metabolic profiles are stably controlled by genetic and environmental variation. Mol Syst Biol 7:525–525CrossRef Nicholson G, Rantalainen M, Maher AD, Li JV, Malmodin D, Ahmadi KR et al (2011) Human metabolic profiles are stably controlled by genetic and environmental variation. Mol Syst Biol 7:525–525CrossRef
Zurück zum Zitat Nicholson JK, Wilson ID (2003) Understanding “global” systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2:668–676CrossRef Nicholson JK, Wilson ID (2003) Understanding “global” systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2:668–676CrossRef
Zurück zum Zitat Nicholson JK, Lindon JC, Holmes E (1999) “Metabonomics”: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29:1181–1189CrossRef Nicholson JK, Lindon JC, Holmes E (1999) “Metabonomics”: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29:1181–1189CrossRef
Zurück zum Zitat Oliver S (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378CrossRef Oliver S (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378CrossRef
Zurück zum Zitat Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW et al (2014a) Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem 87:1137–1144CrossRef Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW et al (2014a) Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem 87:1137–1144CrossRef
Zurück zum Zitat Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S et al (2014b) Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem 86:3985–3993CrossRef Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S et al (2014b) Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem 86:3985–3993CrossRef
Zurück zum Zitat Peter Guengerich F, Shimada T (1998) Activation of procarcinogens by human cytochrome P450 enzymes. Mutat Res 400:201–213CrossRef Peter Guengerich F, Shimada T (1998) Activation of procarcinogens by human cytochrome P450 enzymes. Mutat Res 400:201–213CrossRef
Zurück zum Zitat Petersen A-K, Zeilinger S, Kastenmüller G, Römisch-Margl W, Brugger M, Peters A et al (2014) Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits. Hum Mol Genet 23:534–545CrossRef Petersen A-K, Zeilinger S, Kastenmüller G, Römisch-Margl W, Brugger M, Peters A et al (2014) Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits. Hum Mol Genet 23:534–545CrossRef
Zurück zum Zitat Pierce BL, Tong L, Argos M, Gao J, Jasmine F (2013) Arsenic metabolism efficiency has a causal role in arsenic toxicity: Mendelian randomization and gene-environment interaction. Int J Epidemiol 42(6):1862–1871CrossRef Pierce BL, Tong L, Argos M, Gao J, Jasmine F (2013) Arsenic metabolism efficiency has a causal role in arsenic toxicity: Mendelian randomization and gene-environment interaction. Int J Epidemiol 42(6):1862–1871CrossRef
Zurück zum Zitat Pitt JJ (2010) Newborn screening. Clin Biochem Rev 31(2):57–68 Pitt JJ (2010) Newborn screening. Clin Biochem Rev 31(2):57–68
Zurück zum Zitat Plumb RS, Shockcor J, Holmes E, Nicholson JK (2010) Global metabolic profiling procedures for urine using UPLC–MS. Nat Protoc 5(6):1005–1018CrossRef Plumb RS, Shockcor J, Holmes E, Nicholson JK (2010) Global metabolic profiling procedures for urine using UPLC–MS. Nat Protoc 5(6):1005–1018CrossRef
Zurück zum Zitat Posma JM, Robinette SL, Holmes E, Nicholson JK (2014) MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. Bioinformatics 30:893–895CrossRef Posma JM, Robinette SL, Holmes E, Nicholson JK (2014) MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. Bioinformatics 30:893–895CrossRef
Zurück zum Zitat Posma JM, Garcia-Perez I, Heaton JC, Burdisso P, Mathers JC, Draper J et al (2017) Integrated analytical and statistical two-dimensional spectroscopy strategy for metabolite identification: application to dietary biomarkers. Anal Chem 89:3300–3309CrossRef Posma JM, Garcia-Perez I, Heaton JC, Burdisso P, Mathers JC, Draper J et al (2017) Integrated analytical and statistical two-dimensional spectroscopy strategy for metabolite identification: application to dietary biomarkers. Anal Chem 89:3300–3309CrossRef
Zurück zum Zitat Psychogios N, Hau DD, Peng J, Guo AC, Mandal R (2011) The human serum metabolome. PLoS One 6(2):e16957CrossRef Psychogios N, Hau DD, Peng J, Guo AC, Mandal R (2011) The human serum metabolome. PLoS One 6(2):e16957CrossRef
Zurück zum Zitat Qi Y, Song Y, Gu H, Fan G, Chai Y (2014) Global metabolic profiling using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry. Methods Mol Biol 1198:15–27CrossRef Qi Y, Song Y, Gu H, Fan G, Chai Y (2014) Global metabolic profiling using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry. Methods Mol Biol 1198:15–27CrossRef
Zurück zum Zitat Ramautar R, Somsen GW, de Jong GJ (2017) CE-MS for metabolomics: developments and applications in the period 2014-2016. Rassi El Z, editor. Electrophoresis 38:190–202CrossRef Ramautar R, Somsen GW, de Jong GJ (2017) CE-MS for metabolomics: developments and applications in the period 2014-2016. Rassi El Z, editor. Electrophoresis 38:190–202CrossRef
Zurück zum Zitat Rappaport SM, Barupal DK, Wishart D, Vineis P, Scalbert A (2014) The blood exposome and its role in discovering causes of disease. Environ Health Perspect 122:769CrossRef Rappaport SM, Barupal DK, Wishart D, Vineis P, Scalbert A (2014) The blood exposome and its role in discovering causes of disease. Environ Health Perspect 122:769CrossRef
Zurück zum Zitat Reymond J-L, van Deursen R, Blum LC, Ruddigkeit L (2010) Chemical space as a source for new drugs. Med Chem Commun 1:30–38CrossRef Reymond J-L, van Deursen R, Blum LC, Ruddigkeit L (2010) Chemical space as a source for new drugs. Med Chem Commun 1:30–38CrossRef
Zurück zum Zitat Reymond J-L, Ruddigkeit L, Blum L, van Deursen R (2012) The enumeration of chemical space. Wiley Interdiscip Rev Comput Mol Sci 2:717–733CrossRef Reymond J-L, Ruddigkeit L, Blum L, van Deursen R (2012) The enumeration of chemical space. Wiley Interdiscip Rev Comput Mol Sci 2:717–733CrossRef
Zurück zum Zitat Robinette SL, Lindon JC, Nicholson JK (2013) Statistical spectroscopic tools for biomarker discovery and systems medicine. Anal Chem 85:5297–5303CrossRef Robinette SL, Lindon JC, Nicholson JK (2013) Statistical spectroscopic tools for biomarker discovery and systems medicine. Anal Chem 85:5297–5303CrossRef
Zurück zum Zitat Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A et al (2016) Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics 12:14CrossRef Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A et al (2016) Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics 12:14CrossRef
Zurück zum Zitat Ruddigkeit L, van Deursen R, Blum LC, Reymond J-L (2012) Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. J Chem Inf Model 52:2864–2875CrossRef Ruddigkeit L, van Deursen R, Blum LC, Reymond J-L (2012) Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. J Chem Inf Model 52:2864–2875CrossRef
Zurück zum Zitat Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J et al (2015) COordination of standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics 11:1587–1597CrossRef Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J et al (2015) COordination of standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics 11:1587–1597CrossRef
Zurück zum Zitat Sampson JN, Boca SM, Shu XO, Stolzenberg-Solomon RZ, Matthews CE, Hsing AW et al (2013) Metabolomics in epidemiology: sources of variability in metabolite measurements and implications. Cancer Epidemiol Biomark Prev 22:631–640CrossRef Sampson JN, Boca SM, Shu XO, Stolzenberg-Solomon RZ, Matthews CE, Hsing AW et al (2013) Metabolomics in epidemiology: sources of variability in metabolite measurements and implications. Cancer Epidemiol Biomark Prev 22:631–640CrossRef
Zurück zum Zitat Sansone S-A, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R et al (2007) The metabolomics standards initiative. Nat Biotechnol 25:846–848 Sansone S-A, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R et al (2007) The metabolomics standards initiative. Nat Biotechnol 25:846–848
Zurück zum Zitat Scalbert A, Brennan L, Manach C, Andres-Lacueva C, Dragsted LO, Draper J et al (2014) The food metabolome: a window over dietary exposure. Am J Clin Nutr 99:1286–1308CrossRef Scalbert A, Brennan L, Manach C, Andres-Lacueva C, Dragsted LO, Draper J et al (2014) The food metabolome: a window over dietary exposure. Am J Clin Nutr 99:1286–1308CrossRef
Zurück zum Zitat Schmelzer K, Fahy E, Subramaniam S, Dennis EA (2007) The lipid maps initiative in lipidomics. Methods Enzymol 432:171–183CrossRef Schmelzer K, Fahy E, Subramaniam S, Dennis EA (2007) The lipid maps initiative in lipidomics. Methods Enzymol 432:171–183CrossRef
Zurück zum Zitat Shimada T, Oda Y, Gillam EMJ, Guengerich FP, Inoue K (2001) Metabolic activation of polycyclic aromatic hydrocarbons and other procarcinogens by cytochromes P450 1A1 and P450 1B1 allelic variants and other human cytochromes P450 in Salmonella typhimurium NM2009. Drug Metab Dispos 29:1176–1182 Shimada T, Oda Y, Gillam EMJ, Guengerich FP, Inoue K (2001) Metabolic activation of polycyclic aromatic hydrocarbons and other procarcinogens by cytochromes P450 1A1 and P450 1B1 allelic variants and other human cytochromes P450 in Salmonella typhimurium NM2009. Drug Metab Dispos 29:1176–1182
Zurück zum Zitat Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y et al (2017) Interlaboratory reproducibility of a targeted metabolomics platform for analysis of human serum and plasma. Anal Chem 89:656–665CrossRef Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y et al (2017) Interlaboratory reproducibility of a targeted metabolomics platform for analysis of human serum and plasma. Anal Chem 89:656–665CrossRef
Zurück zum Zitat Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR et al (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27:747–751CrossRef Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR et al (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27:747–751CrossRef
Zurück zum Zitat Spagou K, Wilson ID, Masson P, Theodoridis G, Raikos N, Coen M et al (2010) HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. Anal Chem 83:382–390CrossRef Spagou K, Wilson ID, Masson P, Theodoridis G, Raikos N, Coen M et al (2010) HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. Anal Chem 83:382–390CrossRef
Zurück zum Zitat Strittmatter N, Rebec M, Jones EA, Golf O, Abdolrasouli A, Balog J et al (2014) Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry. Anal Chem 86:6555–6562CrossRef Strittmatter N, Rebec M, Jones EA, Golf O, Abdolrasouli A, Balog J et al (2014) Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry. Anal Chem 86:6555–6562CrossRef
Zurück zum Zitat Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C et al (2016) Metabolomics Workbench: an international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res 44:D463–D470CrossRef Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C et al (2016) Metabolomics Workbench: an international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res 44:D463–D470CrossRef
Zurück zum Zitat Suhre K, Meisinger C, Döring A, Altmaier E, Belcredi P, Gieger C et al (2010) Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. Breant B, editor. PLoS One e13953:5 Suhre K, Meisinger C, Döring A, Altmaier E, Belcredi P, Gieger C et al (2010) Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. Breant B, editor. PLoS One e13953:5
Zurück zum Zitat Suhre K, Wallaschofski H, Raffler J, Friedrich N (2011) A genome-wide association study of metabolic traits in human urine. Nature 43(6):565–569 Suhre K, Wallaschofski H, Raffler J, Friedrich N (2011) A genome-wide association study of metabolic traits in human urine. Nature 43(6):565–569
Zurück zum Zitat Suhre K, Raffler J, Kastenmüller G (2016) Biochemical insights from population studies with genetics and metabolomics. Arch Biochem Biophys 589:168–176CrossRef Suhre K, Raffler J, Kastenmüller G (2016) Biochemical insights from population studies with genetics and metabolomics. Arch Biochem Biophys 589:168–176CrossRef
Zurück zum Zitat Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M et al (2016) Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12:109CrossRef Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M et al (2016) Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12:109CrossRef
Zurück zum Zitat Takáts Z, Wiseman JM, Gologan B, Cooks RG (2004) Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 306:471–473CrossRef Takáts Z, Wiseman JM, Gologan B, Cooks RG (2004) Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 306:471–473CrossRef
Zurück zum Zitat Takáts Z, Wiseman JM, Cooks RG (2005) Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology. J Mass Spectrom 40:1261–1275CrossRef Takáts Z, Wiseman JM, Cooks RG (2005) Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology. J Mass Spectrom 40:1261–1275CrossRef
Zurück zum Zitat Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45(D1):D353–D361CrossRef Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45(D1):D353–D361CrossRef
Zurück zum Zitat Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G (2012) XCMS online: a web-based platform to process untargeted metabolomic data. Anal Chem 84:5035–5039CrossRef Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G (2012) XCMS online: a web-based platform to process untargeted metabolomic data. Anal Chem 84:5035–5039CrossRef
Zurück zum Zitat Teahan O, Gamble S, Holmes E, Waxman J, Nicholson JK, Bevan C et al (2006) Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem 78:4307–4318CrossRef Teahan O, Gamble S, Holmes E, Waxman J, Nicholson JK, Bevan C et al (2006) Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem 78:4307–4318CrossRef
Zurück zum Zitat Thévenot EA, Roux A, Xu Y, Ezan E, Junot C (2015) Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. J Proteome Res 14(8):3322–3335CrossRef Thévenot EA, Roux A, Xu Y, Ezan E, Junot C (2015) Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. J Proteome Res 14(8):3322–3335CrossRef
Zurück zum Zitat Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK et al (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol 31:419–425CrossRef Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK et al (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol 31:419–425CrossRef
Zurück zum Zitat Thomas L, Hodgson S, Nieuwenhuijsen M, Jarup L (2007) Early renal damage in a population environmentally exposed to cadmium—the Avonmouth Pilot Study. Epidemiology 18:S123CrossRef Thomas L, Hodgson S, Nieuwenhuijsen M, Jarup L (2007) Early renal damage in a population environmentally exposed to cadmium—the Avonmouth Pilot Study. Epidemiology 18:S123CrossRef
Zurück zum Zitat Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408CrossRef Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408CrossRef
Zurück zum Zitat Uppal K, Walker DI, Liu K, Li S, Go Y-M, Jones DP (2016) Computational metabolomics: a framework for the million metabolome. Chem Res Toxicol 29:1956–1975CrossRef Uppal K, Walker DI, Liu K, Li S, Go Y-M, Jones DP (2016) Computational metabolomics: a framework for the million metabolome. Chem Res Toxicol 29:1956–1975CrossRef
Zurück zum Zitat Van Deemter JJ, Zuiderweg FJ, Klinkenberg A (1956) Longitudinal diffusion and resistance to mass transfer as causes of nonideality in chromatography. Chem Eng Sci 5:271–289CrossRef Van Deemter JJ, Zuiderweg FJ, Klinkenberg A (1956) Longitudinal diffusion and resistance to mass transfer as causes of nonideality in chromatography. Chem Eng Sci 5:271–289CrossRef
Zurück zum Zitat Vineis P, Veldhoven K, Chadeau-Hyam M, Athersuch TJ (2013) Advancing the application of omics-based biomarkers in environmental epidemiology. Environ Mol Mutagen 54(7):461CrossRef Vineis P, Veldhoven K, Chadeau-Hyam M, Athersuch TJ (2013) Advancing the application of omics-based biomarkers in environmental epidemiology. Environ Mol Mutagen 54(7):461CrossRef
Zurück zum Zitat Vineis P, Chadeau-Hyam M, Gmuender H, Gulliver J, Herceg Z, KLEINJANS J et al (2017) The exposome in practice: design of the EXPOsOMICS project. Int J Hyg Environ Health 220:142–151CrossRef Vineis P, Chadeau-Hyam M, Gmuender H, Gulliver J, Herceg Z, KLEINJANS J et al (2017) The exposome in practice: design of the EXPOsOMICS project. Int J Hyg Environ Health 220:142–151CrossRef
Zurück zum Zitat Vlaanderen JJ, Janssen NA, Hoek G, Keski-Rahkonen P, Barupal DK, Cassee FR et al (2017) The impact of ambient air pollution on the human blood metabolome. Environ Res 156:341–348CrossRef Vlaanderen JJ, Janssen NA, Hoek G, Keski-Rahkonen P, Barupal DK, Cassee FR et al (2017) The impact of ambient air pollution on the human blood metabolome. Environ Res 156:341–348CrossRef
Zurück zum Zitat Vrijheid M, Slama R, Robinson O, Chatzi L, Coen M, van den Hazel P et al (2014) The human early-life exposome (HELIX): project rationale and design. Environ Health Perspect 122(6):535–544CrossRef Vrijheid M, Slama R, Robinson O, Chatzi L, Coen M, van den Hazel P et al (2014) The human early-life exposome (HELIX): project rationale and design. Environ Health Perspect 122(6):535–544CrossRef
Zurück zum Zitat Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J et al (2010) Global metabolic profiling procedures for urine using UPLC|[ndash]|MS. Nat Protoc 5:1005–1018CrossRef Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J et al (2010) Global metabolic profiling procedures for urine using UPLC|[ndash]|MS. Nat Protoc 5:1005–1018CrossRef
Zurück zum Zitat Warth B, Levin N, Rinehart D, Teijaro J, Benton HP, Siuzdak G (2017) Metabolizing data in the cloud. Trends Biotechnol 35:481–483CrossRef Warth B, Levin N, Rinehart D, Teijaro J, Benton HP, Siuzdak G (2017) Metabolizing data in the cloud. Trends Biotechnol 35:481–483CrossRef
Zurück zum Zitat Wild CP (2005) Complementing the genome with an “exposome”: the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomark Prev 14:1847–1850CrossRef Wild CP (2005) Complementing the genome with an “exposome”: the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomark Prev 14:1847–1850CrossRef
Zurück zum Zitat Wild CP (2012) The exposome: from concept to utility. Int J Epidemiol 41:24–32CrossRef Wild CP (2012) The exposome: from concept to utility. Int J Epidemiol 41:24–32CrossRef
Zurück zum Zitat Wild CP, Scalbert A, Herceg Z (2013) Measuring the exposome: a powerful basis for evaluating environmental exposures and cancer risk. Environ Mol Mutagen 54:480–499CrossRef Wild CP, Scalbert A, Herceg Z (2013) Measuring the exposome: a powerful basis for evaluating environmental exposures and cancer risk. Environ Mol Mutagen 54:480–499CrossRef
Zurück zum Zitat WILSON I, Plumb R, Granger J, Major H, WILLIAMS R, LENZ E (2005a) HPLC-MS-based methods for the study of metabonomics. J Chromatogr B 817:67–76CrossRef WILSON I, Plumb R, Granger J, Major H, WILLIAMS R, LENZ E (2005a) HPLC-MS-based methods for the study of metabonomics. J Chromatogr B 817:67–76CrossRef
Zurück zum Zitat Wilson ID, Nicholson JK, Castro-Perez J, Granger JH, Johnson KA, Smith BW et al (2005b) High resolution “ultra performance” liquid chromatography coupled to oa-tof mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J Proteome Res 4:591–598CrossRef Wilson ID, Nicholson JK, Castro-Perez J, Granger JH, Johnson KA, Smith BW et al (2005b) High resolution “ultra performance” liquid chromatography coupled to oa-tof mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J Proteome Res 4:591–598CrossRef
Zurück zum Zitat Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong Y et al (2008) The human cerebrospinal fluid metabolome. J Chromatogr B 871:164–173CrossRef Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong Y et al (2008) The human cerebrospinal fluid metabolome. J Chromatogr B 871:164–173CrossRef
Zurück zum Zitat Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y et al (2012) HMDB 3.0—the human metabolome database in 2013. Nucleic Acids Res 41:D801–D807CrossRef Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y et al (2012) HMDB 3.0—the human metabolome database in 2013. Nucleic Acids Res 41:D801–D807CrossRef
Zurück zum Zitat Wist J (2017) Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges. A special issue of the associate ed, editor. Magn Reson Chem 55:22–28CrossRef Wist J (2017) Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges. A special issue of the associate ed, editor. Magn Reson Chem 55:22–28CrossRef
Zurück zum Zitat Xia J, Sinelnikov IV, Han B, Wishart DS (2015) MetaboAnalyst 3.0—making metabolomics more meaningful. Nucl Acids Res 43(W1):W251–W257CrossRef Xia J, Sinelnikov IV, Han B, Wishart DS (2015) MetaboAnalyst 3.0—making metabolomics more meaningful. Nucl Acids Res 43(W1):W251–W257CrossRef
Zurück zum Zitat Xiao R, Zhang X, Rong Z, Xiu B, Yang X, Wang C et al (2016) Non-invasive detection of hepatocellular carcinoma serum metabolic profile through surface-enhanced Raman spectroscopy. Nanomedicine 12:2475–2484CrossRef Xiao R, Zhang X, Rong Z, Xiu B, Yang X, Wang C et al (2016) Non-invasive detection of hepatocellular carcinoma serum metabolic profile through surface-enhanced Raman spectroscopy. Nanomedicine 12:2475–2484CrossRef
Zurück zum Zitat Xu X, Veenstra TD, Fox SD, Roman JM, Issaq HJ, Falk R et al (2005) Measuring fifteen endogenous estrogens simultaneously in human urine by high-performance liquid chromatography-mass spectrometry. Anal Chem 77:6646–6654CrossRef Xu X, Veenstra TD, Fox SD, Roman JM, Issaq HJ, Falk R et al (2005) Measuring fifteen endogenous estrogens simultaneously in human urine by high-performance liquid chromatography-mass spectrometry. Anal Chem 77:6646–6654CrossRef
Zurück zum Zitat Yin P, Lehmann R, Xu G (2015) Effects of pre-analytical processes on blood samples used in metabolomics studies. Anal Bioanal Chem 407:4879–4892CrossRef Yin P, Lehmann R, Xu G (2015) Effects of pre-analytical processes on blood samples used in metabolomics studies. Anal Bioanal Chem 407:4879–4892CrossRef
Zurück zum Zitat Zhao L, Pickering G (2011) Paracetamol metabolism and related genetic differences. Drug Metab Rev 43:41–52CrossRef Zhao L, Pickering G (2011) Paracetamol metabolism and related genetic differences. Drug Metab Rev 43:41–52CrossRef
Zurück zum Zitat Zheng X, Zhao A, Xie G, Chi Y, Zhao L (2013) Melamine-induced renal toxicity is mediated by the gut microbiota. Sci Transl Med 5(172):172ra22CrossRef Zheng X, Zhao A, Xie G, Chi Y, Zhao L (2013) Melamine-induced renal toxicity is mediated by the gut microbiota. Sci Transl Med 5(172):172ra22CrossRef
Zurück zum Zitat Zubarev RA, Makarov A (2013) Orbitrap mass spectrometry. Anal Chem 85:5288–5296CrossRef Zubarev RA, Makarov A (2013) Orbitrap mass spectrometry. Anal Chem 85:5288–5296CrossRef
Metadaten
Titel
Metabonomics
verfasst von
Toby Athersuch
Copyright-Jahr
2019
DOI
https://doi.org/10.1007/978-3-319-89321-1_6