Mass Spectrometry for Metabolomics PDF
Preview Mass Spectrometry for Metabolomics
Methods in Molecular Biology 2571 Raúl González-Domínguez Editor Mass Spectrometry for Metabolomics M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Mass Spectrometry for Metabolomics Edited by Raúl González-Domínguez Instituto de Investigación e Innovación Biomédica de Cádiz, Hospital Universitario Puerta del Mar, Cádiz, Spain Editor Rau´lGonza´lez-Dom´ınguez InstitutodeInvestigacio´n eInnovacio´nBiome´dicadeCa´diz HospitalUniversitarioPuertadelMar Ca´diz,Spain ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2698-6 ISBN978-1-0716-2699-3 (eBook) https://doi.org/10.1007/978-1-0716-2699-3 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2023 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductionon microfilmsorinanyotherphysicalway,andtransmissionorinformation storageand retrieval,electronicadaptation, computersoftware,orbysimilar ordissimilar methodologynow knownorhereafter developed. 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Preface Mass spectrometry (MS) has become the most widely employed analytical technique in metabolomics because of its sensitivity, selectivity, and broad coverage thanks to the avail- ability of multiple instrumental configurations. This book provides a comprehensive over- viewofstate-of-the-artmetabolomicsmethodsbasedonMS,andtheirapplicationinfood, nutrition, and biomedical research. In this volume of the Methods in Molecular Biology series, 22 chapters are assembled covering hot topics related to sample preparation, chro- matographic and electrophoretic separation, MS-based analysis, as well as data processing andanalysis. Thefirstpartofthisbookiscomprisedofinnovativemetabolomicsapproachesinfood scienceandnutritionresearch.Chapter1presentsanovelmethodbasedonreversed-phase liquid chromatography (RPLC) coupled with diode array detector and MS for high- throughput, comprehensive, and quantitative fingerprinting of a broad range of phenolic compounds and related metabolites in different food products. In Chaps. 2 and 3, the authors explain how to analyze volatile metabolites in vinegar samples by applying solid- phase microextraction (SPME) and stir bar sorptive extraction (SBSE) techniques in com- bination with gas chromatography–mass spectrometry (GC-MS). Chapter 4 describes the application of untargeted metabolomics based on liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) for the discovery of food intake biomarkers in blood and urine samples. Finally, Chap. 5 illustrates the potential of metabolomics to investigate the anti-proliferative capacity of bioactive compounds from fruit by-products againstcoloncancercells. Inthesecondpart,wegather14chaptersfocusedontheapplicationofmetabolomicsin biomedical research. Chapters 6, 7 and 8 describe complementary MS-based hyphenated platforms for untargeted metabolomics of common biological fluids (e.g., blood, urine), namely reversed-phase liquid chromatography (RPLC, Chap. 6), hydrophilic interaction liquid chromatography (HILIC, Chap. 7), and capillary electrophoresis (CE, Chap. 8). In relationtoCE-basedmetabolomics,Chaps.9and10presentnovelanalyticaldevelopments for direct analysis of highly saline samples using in-capillary preconcentration and for enhancing the analysis of acidic metabolites using chemical derivatization, respectively. Chapter 11 outlines a metabolomics multi-platform, based on the combination of RPLC andHILIC,tocapturetheplasmaanderythrocytemetabolomesbehindchildhoodobesity and insulin resistance. In this vein, Chap. 12 details how to characterize the plasmatic and erythroid multi-elemental biodistribution in childhood obesity using a method based on protein precipitation under non-denaturing conditions and further analysis by inductively coupled plasma mass spectrometry. The last chapters of this part ofthe book deal with the analysis of other tissues and biological samples. Chapter 13 presents an untargeted meta- bolomics workflow for brain tissue analysis based on two LC-MS methods combining reversed-phase and HILIC chromatography, whereas Chap. 14 focuses on the targeted determination of cholesterol in liver by GC-MS. The next three chapters revolve around the potential of MS to characterize ocular samples. In Chap. 15, the authors describe a simple method for the preparation and metabolomics analysis of aqueous humor samples usingRPLC-MSandHILIC-MS.Chapter16tacklestheanalysisofserotoninandL-DOPA in ocular tissues by imaging mass spectrometry. On the other hand, the method described v vi Preface under Chap. 17 explains how to conduct isobaric incorporation of C13-histidine for the assessment of remyelination in the optic nerve. Chapter 18 details an innovative workflow for the isolation and lipidomics analysis of extracellular vesicles from human breast milk. Finally, Chap. 19 introduces a robust LC-HRMS-based metabolomics and lipidomics platformfor theinvestigationofculturedhepaticcelllines. To conclude, this book also includes three chapters addressing the importance of data processing and statistical analysis in MS-based metabolomics. Chapter 20 reviews the available tools and resources for conducting each of the steps usually required in metabo- lomicsdataprocessing,namelydatapreprocessing,dataanalysis,annotation,andfunctional analysis. In Chap. 21, a typical data processing procedure is provided for the analysis and qualitycontroloftargetedmetabolomicsLC-MS-baseddata.Thefinalchapterpresentsan instrument-agnostizingmethodologyforLC-MSaimedtoprovidestandardizedandcom- parablechromatographicfingerprintsregardlessoftheinstrument. In summary, this volume in the Methods in Molecular Biology series represents a collection of the expertise of leading scientists in the field of metabolomics and mass spectrometry research. Considering its multidisciplinary scope, I hope a broad target audiencewillbenefitofthistimelybook,includingchemists,biochemists,biologists,nutri- tionists, clinicians, and other experts working in the growing and exciting field of metabolomics. Ca´diz,Spain Rau´lGonza´lez-Domı´nguez Contents Preface ..................................................................... v Contributors................................................................. xi 1 ComprehensiveandHigh-ThroughputMethodforQuantitative FingerprintingofPhenolicCompounds ..... ....... ........ ....... ........ 1 Rau´lGonza´lez-Domı´nguez,AnaSayago,Marı´aSantos-Martı´n, andA´ngelesFerna´ndez-Recamales 2 DeterminationofVolatileMetabolitesinVinegarbySolid-Phase Microextraction–GasChromatography–MassSpectrometry (SPME–GC–MS) .......... ........ ....... ....... ........ ....... ........ 13 RemediosCastroandEnriqueDura´n-Guerrero 3 DeterminationofVolatileMetabolitesinVinegarbyStirBarSorptive Extraction–GasChromatography–MassSpectrometry (SBSE–GC–MS).... ....... ........ ....... ....... ...... .. .... ... ........ 21 EnriqueDura´n-GuerreroandRemediosCastro 4 DiscoveryofFoodIntakeBiomarkersUsingMetabolomics ...... .... ........ 33 LeticiaLacalle-Bergeron,DavidIzquierdo-Sandoval, JuanV.Sancho,andTaniaPortole´s 5 MetabolomicCharacterizationoftheAntiproliferativeActivity ofBioactiveCompoundsfromFruitBy-ProductsAgainst ColonCancerCells ........ ........ ....... ....... ........ ....... ........ 45 GerardoAlvarez-Rivera,AlbertoValde´s,andAlejandro Cifuentes 6 UntargetedMetabolomicsbyLiquidChromatography–MassSpectrometry inBiomedicalResearch ..... ........ ... .... ...... ......... ....... ........ 57 CaridadDı´azandCarmenGonza´lez-Olmedo 7 UntargetedMetabolomicsforDisease-SpecificSignatures..... ....... ........ 71 ConstantinaChalikiopoulou,Jose´CarlosG(cid:1)omez-Tamayo, andTheodoraKatsila 8 MetabolomicsAnalysisofBlood,Urine,andSalivaSamplesBased onCapillaryElectrophoresis–MassSpectrometry..... ........ ....... ........ 83 MasahiroSugimotoandYumiAizawa 9 CapillaryElectrophoresis–MassSpectrometryfor theDirectAnalysis ofMetabolitesinHighlySalineSamplesUsingIn-Capillary Preconcentration.... ....... ........ ....... ....... ..... ... ....... ........ 95 MarlienvanMeverandRawiRamautar 10 ChemicalDerivatizationtoEnhanceCapillaryElectrophoresis MassSpectrometricAnalysisofAcidicMetabolites inMammalianCells........ ........ ....... ....... ........ ....... ........ 105 MarlienvanMeverandRawiRamautar vii viii Contents 11 UntargetedMetabolomicsBasedonLiquidChromatography–Mass Spectrometryfor theAnalysisofPlasmaandErythrocyteSamples inChildhoodObesity ...... ........ ....... ....... ........ ....... ........ 115 A´lvaro Gonza´lez-Domı´nguez,MarinaArmeni,OttoSavolainen, AlfonsoMarı´aLechuga-Sancho,RikardLandberg, andRau´lGonza´lez-Domı´nguez 12 CharacterizationofthePlasmaticandErythroidMultielemental BiodistributioninChildhoodObesityUsingaHigh-Throughput MethodforSizeFractionationofMetalSpecies...... ........ ....... ........ 123 A´lvaro Gonza´lez-Domı´nguez,Marı´aMilla´n-Martı´nez, DanielSa´nchez-Rodas,AlfonsoMarı´aLechuga-Sancho, andRau´lGonza´lez-Domı´nguez 13 AnalysisofBrainMetabolitesUsingTwoComplementary Ultrahigh-PerformanceLiquidChromatography–Mass SpectrometryMethods ..... ........ ....... ....... ........ ...... ....... .. 133 AlexaM.Jauregui,SofiaE.Parellada,EmilyNeag, andSanjoyK.Bhattacharya 14 AnalysisofCholesterolfromtheLiverUsingGasChromatography–Mass Spectrometry....... ....... ........ ....... ....... ........ ....... ........ 143 MeherA.Saleem,BetsyBenitez,CharlesYaros,GabrielleYamar, andSanjoyK.Bhattacharya 15 MetabolomicsAnalysisofAqueousHumorBasedonLiquid Chromatography–MassSpectrometry ....... ....... ........ ....... ........ 149 KarolinaPietrowska,DianaAnnaDmuchowska,AdamKretowski, andMichalCiborowski 16 AnalysesandLocalizationofSerotoninandL-DOPAinOcularTissues byImagingMassSpectrometry..... ....... .... .... ........ ....... ........ 157 VarunKrishnan,SeanMeehan,ColinHayter,andSanjoyK.Bhattacharya 17 IsobaricIncorporationofC13-Histidinefor theAssessment ofRemyelination .......... ........ ....... ....... ........ ....... ........ 169 FaithChristineHarvey,AnddreOsmarValdivia,ColinHayter, andSanjoyK.Bhattacharya 18 IsolationandLipidomicScreeningofHumanMilk ExtracellularVesicles ....... ........ ....... ....... ...... .. ....... ........ 177 VictoriaRamos-Garcia,IsabelTen-Dome´nech,AbelAlbiach-Delgado, MartaG(cid:1)omez-Ferrer,PilarSepu´lveda,AnnaParra-Llorca, LauraCampos-Berga,AlbaMoreno-Gime´nez,GuillermoQuinta´s, andJuliaKuligowski 19 MassSpectrometry-BasedUntargetedMetabolomicsandLipidomics PlatformstoAnalyzeCellCultureExtracts.......... ........ ....... ........ 189 EliasIturrospe,KatyenyManueladaSilva,MariavandeLavoir, RaniRobeyns,MatthiasCuykx,TamaraVanhaecke, AlexanderL.N.vanNuijs,andAdrianCovaci 20 DataProcessingandAnalysisinMassSpectrometry-Based Metabolomics...... ....... ........ ....... ....... ........ ....... ........ 207 A´ngelaPeralbo-Molina,PolSol`a-Santos,AlexandrePerera-Lluna, andEduardoChicano-Ga´lvez Contents ix 21 DataProcessingandAnalysisinLiquidChromatography–Mass Spectrometry-BasedTargetedMetabolomics........ ........ ....... ........ 241 MasahiroSugimoto,YumiAizawa,andAtsumiTomita 22 Instrument-AgnostizingMethodologyforLiquidChromatography–Mass SpectrometrySystems ...... ........ ....... ....... ........ ....... ........ 257 Rosalı´aL(cid:1)opez-Ruı´z,SandraMartı´n-Torres,AnaM.Jime´nez-Carvelo, RobertoRomero-Gonza´lez,andLuisCuadros-Rodrı´guez Index ...................................................................... 271
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