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Methods in Pharmacology and Toxicology Teresa Whei-Mei Fan Andrew N. Lane Editors Richard M. Higashi The Handbook of Metabolomics M P T ETHODS IN H A R M A C O L O G Y A N D OXICOLO GY SeriesEditor Y. James Kang For further volumes: http://www.springer.com/series/7653 The Handbook of Metabolomics Edited by Teresa Whei-Mei Fan and Richard M. Higashi Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA Andrew N. Lane Departments of Medicine and Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA Editors TeresaWhei-MeiFan AndrewN.Lane DepartmentofChemistry DepartmentsofMedicineandChemistry CenterforRegulatoryandEnvironmental CenterforRegulatoryandEnvironmental AnalyticalMetabolomics(CREAM), AnalyticalMetabolomics(CREAM), andJamesGrahamBrownCancerCenter andJamesGrahamBrownCancerCenter UniversityofLouisville UniversityofLouisville Louisville,KY,USA Louisville,KY,USA RichardM.Higashi DepartmentofChemistry CenterforRegulatoryandEnvironmental AnalyticalMetabolomics(CREAM), andJamesGrahamBrownCancerCenter UniversityofLouisville Louisville,KY,USA ISSN1557-2153 ISSN1940-6053(electronic) ISBN978-1-61779-617-3 ISBN978-1-61779-618-0(eBook) DOI10.1007/978-1-61779-618-0 SpringerNewYorkHeidelbergDordrechtLondon LibraryofCongressControlNumber:2012935107 ªSpringerScience+BusinessMediaNewYork2012 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.Exemptedfromthis legalreservationarebriefexcerptsinconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyfor thepurposeofbeingenteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. 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Printedonacid-freepaper HumanaPressisabrandofSpringer SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Metabolomicsisarapidlyexpandingfieldthatprovidesalinkbetweenfunctional biology (phenotypes)and the inner workings ofcells in tissues or whole organisms. Thetechnol- ogies of metabolomics are being taken up by academic researchers, increasingly in the medicalfield,andespeciallybythebiotechandpharmaceuticalcompanies. Thegoalofthehandbookistoprovidereaderswiththecurrentstateofmetabolomic development and the integration of metabolomics with transcriptomics and proteomics. Theseaspectsareillustratedbyresearcheffortsrelatedtotoxicologyandpharmacology. The 14 contributions deal with a critical discussion of topics ranging from sample preparationandconsiderations(bothlaboratoryandclinical),analyticalmethodologiesfor metabolite and isotopomer profiling, to metabolic flux modeling, database construction, and integration of “omics” for systems biochemical understanding. The handbook includesextensivebibliographiesandresources. Louisville,KY,USA TeresaWhei-MeiFan AndrewN.Lane RichardM.Higashi v Contents Preface.................................................................... v Contributors............................................................... ix 1 IntroductiontoMetabolomics ........................................... 1 TeresaWhei-MeiFan,AndrewN.Lane,andRichardM.Higashi 2 ConsiderationsofSamplePreparationforMetabolomicsInvestigation.......... 7 TeresaWhei-MeiFan 3 ClinicalAspectsofMetabolomics ......................................... 29 MichaelBousamraII,JamieDay,TeresaWhei-MeiFan, GoetzKloecker,AndrewN.Lane,andDonaldM.Miller 4 StructuralMassSpectrometryforMetabolomics............................. 61 RichardM.Higashi 5 MetabolomicApplicationsofInductivelyCoupledPlasma-Mass Spectrometry(ICP-MS)................................................. 99 RobHenryandTeresaCassel 6 PrinciplesofNMRforApplicationsinMetabolomics ........................ 127 AndrewN.Lane 7 NovelNMRandMSApproachestoMetabolomics .......................... 199 IanA.Lewis,MichaelR.Shortreed,AdrianD.Hegeman, andJohnL.Markley 8 MetabolicFluxAnalysis ................................................. 231 TaeHoonYang 9 IntroductiontoMetabolicControlAnalysis(MCA) ......................... 279 MaliackalPouloJoy,TimothyC.Elston,AndrewN.Lane, JeffreyM.Macdonald,andMartaCascante 10 ApplicationofTracer-BasedMetabolomicsandFluxAnalysis inTargetedCancerDrugDesign ......................................... 299 MartaCascante,VitalySelivanov,andAntonioRamos-Montoya 11 NoninvasiveFluxomicsinMammalsbyNuclearMagnetic ResonanceSpectroscopy................................................. 321 JustynaWolak,KayvanRahimi-Keshari,RexE.Jeffries, MaliackalPouloJoy,AbigailTodd,PeterPediatitakis,BrianJ.Dewar, JasonH.Winnike,OlegFavorov,TimothyC.Elston,LeeM.Graves, JohnKurhanzewicz,DanielVigneron,EkhsonHolmuhamedov,and JeffreyM.Macdonald 12 CompositionalAnalysisofPhospholipidsbyMassSpectrometry andPhosphorus-31NuclearMagneticResonanceSpectroscopy ............... 393 M.CeciliaYappert vii viii Contents 13 TheHumanCycPathway-GenomeDatabaseandPathwayToolsSoftware asToolsforImagingandAnalyzingMetabolomicsData...................... 419 PedroRomero 14 Metabolomics-EditedTranscriptomicsAnalysis(META) ..................... 439 TeresaWhei-MeiFan Index..................................................................... 481 Contributors MICHAEL BOUSAMRA II (cid:1) Department of Surgery, University of Louisville, Louisville, KY, USA MARTA CASCANTE (cid:1) Department of Biochemistry and Molecular Biology, Associated Unit to CSIC, Institute of Biomedicine of University of Barcelona (IBUB) and IDIBAPS (Institut d’Investigacions Biome`diques August Pi i Sunyer), Barcelona, Spain TERESA CASSEL (cid:1) Center for Regulatory and Environmental Analytical Metabolomics (CREAM), University of Louisville, Louisville, KY, USA JAMIE DAY (cid:1) James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA BRIAN J. DEWAR (cid:1) Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA TIMOTHY C. ELSTON (cid:1) Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA TERESAWHEI-MEI FAN (cid:1) Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA OLEG FAVOROV (cid:1) Department of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA LEE M. GRAVES (cid:1) Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA ADRIAND.HEGEMAN (cid:1) DepartmentofHorticulturalScience,UniversityofMinnesota, St. Paul, MN, USA ROB HENRY (cid:1) Thermo Fisher Scientific, Bremen, Germany RICHARD M. HIGASHI (cid:1) Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA EKHSON HOLMUHAMEDOV (cid:1) Department of Cell and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA REX E. JEFFRIES (cid:1) Department of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA MALIACKAL POULO JOY (cid:1) Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA GOETZ KLOECKER (cid:1) Department of Medicine and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA JOHN KURHANEWICZ (cid:1) Departments of Radiology and Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA ANDREW N. LANE (cid:1) Departments of Medicine and Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA ix