Plant metabolomics: methods and protocols

351 Pages·2018·9.17 MB·English

by  Carla António (editor)

Methods in
Molecular Biology 1778
Carla António Editor
Plant
Metabolomics
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Plant Metabolomics
Methods and Protocols
Edited by
Carla António
Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier,
Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
Editor
CarlaAnto´nio
PlantMetabolomicsLaboratory
InstitutodeTecnologiaQu´ımicaeBiolo´gicaAnto´nioXavier
UniversidadeNovadeLisboa(ITQBNOVA)
Oeiras,Portugal
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7818-2 ISBN978-1-4939-7819-9 (eBook)
https://doi.org/10.1007/978-1-4939-7819-9
LibraryofCongressControlNumber:2018940501
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Dedication
InMemoryoftheLateProfessorTsutomuMasujima.
CarlaAnto´nio
Preface
Studiesoftheplantmetabolomeincludetheanalysisofawiderangeofchemicalspecieswith
verydiversephysico-chemicalproperties,andtherefore,powerfulanalyticalmethodologies
are required for the separation, characterization, and quantification of this vast compound
diversitypresentinplantbiologicalsamples.
Due to its high sensitivity, mass spectrometry (MS) is one main analytical technology
driving plant metabolomics studies, typically coupled to liquid chromatography (LC-MS)
and gas chromatography (GC-MS). However, currently, there is a growing interest in
narrowing metabolomics analyses down to the tissue or single-cell level. These can be
achieved using mass spectrometry imaging (MSI) approaches and live single-cell mass
spectrometry (LSC-MS), respectively. MSI is a developing technique designed to achieve
spatial analysis of the metabolites present in a plant tissue (or specific section) that is
commonly performed in situ with ionization techniques, such as matrix-assisted laser
desorptionionization(MALDI)andlaserablationelectrosprayionization(LAESI).Indeed,
major achievements in LSC-MS, pioneered by the group of the late Professor Tsutomu
Masujima,havepavedthewayforsensitive,high-resolutionsingle-cellplantanalysisthatwill
increasingly challenge our current view of the cell mechanisms on a single-cell level.
Nonetheless, the need for standardizing key steps in plant metabolomics experiments is
stillconsideredacriticalissue.
ThisbookunitesdiverseMS-basedprotocols,fromsamplepreparationandextractionof
plantprimaryandsecondarymetabolites(e.g.,arangeofsugars,lipids,phytohormones,and
volatile organic compounds) to metabolite analysis, using exclusively highly sensitive
MS-basedmethodologies,followedbyfrontlinebioinformaticsand/ormathematicalmod-
elingapproachestoproducereliablebiologicaldatainterpretation.
I hope that both new and well-established researchers in the plant metabolomics field
findinthisbookhelpfulguidelinesandusefullaboratory-basedprotocolsforsettinguptheir
routineplantmetabolomicsexperiments.
Last but not least, I would like to express my heartfelt thanks to all contributors who
madethisbookpossibleandProfessorJohnWalker for theopportunitytotakeontherole
of editor for what I hope will be an ultimate source of updated MS-based protocols in the
subjectofPlantMetabolomics.
Oeiras,Portugal CarlaAnt(cid:1)onio
vii
Contents
Preface ..................................................................... vii
Contributors................................................................. xi
PART I REVIEW CHAPTERS
1 TheImportanceofExperimentalDesign,QualityAssurance,
andControlinPlantMetabolomicsExperiments ........................... 3
MarinaC.M.Martins,CamilaCaldana,LuciaDanielaWolf,
andLuisGuilhermeFurlandeAbreu
2 StandardKeyStepsinMassSpectrometry-BasedPlantMetabolomics
Experiments:InstrumentPerformanceandAnalyticalMethodValidation...... 19
AnaMargaridaRodriguesandCarlaAnt(cid:1)onio
3 GuidelinesforSampleNormalizationtoMinimizeBatchVariation
forLarge-ScaleMetabolicProfilingofPlantNaturalGeneticVariance......... 33
SalehAlseekh,SiWu,YarivBrotman,andAlisdairR.Fernie
4 GasChromatography–MassSpectrometry-Based13C-LabelingStudies
inPlantMetabolomics................................................... 47
Vale´riaF.Lima,LeonardoPerezdeSouza,ThomasC.R.Williams,
AlisdairR.Fernie,andDaniloM.Daloso
5 CarbonAtomicSurveyforIdentificationofSelectedMetabolicFluxes ........ 59
LeonardoPerezdeSouza,AlisdairR.Fernie,andTakayukiTohge
PART II MASS SPECTROMETRY-BASED METHODOLOGY CHAPTERS
6 QuantificationofLow-AbundantPhosphorylatedCarbohydrates
UsingHILIC-QqQ-MS/MS............................................. 71
TiagoF.JorgeandCarlaAnt(cid:1)onio
7 QuantificationofSolubleSugarsandSugarAlcoholsbyLC-MS/MS.......... 87
ReginaFeilandJohnEdwardLunn
8 UntargetedAnalysisofSemipolarCompoundsbyLC-MS
andTargetedAnalysisofFattyAcidsbyGC-MS/GC-FID:
FromPlantCultivationtoExtractPreparation.............................. 101
CamilleBe´nard,Se´bastienAcket,YannickRossez,OlivierFernandez,
ThierryBerton,YvesGibon,andCe´cileCabasson
9 ExtractionofPlantLipidsforLC-MS-BasedUntargetedPlantLipidomics..... 125
ThusithaW.T.RupasingheandUteRoessner
10 Semi-targetedLipidomicsofPlantAcylLipidsUsingUPLC-HR-MS
inCombinationwithaData-IndependentAcquisitionMode................. 137
MohamedA.SalemandPatrickGiavalisco
ix
x Contents
11 PlantLipidomicsUsingUPLC-QTOF-MS ................................ 157
YozoOkazakiandKazukiSaito
12 TargetedLC-MSAnalysisforPlantSecondaryMetabolites .................. 171
TakafumiShimizu,MutsumiWatanabe,AlisdairR.Fernie,
andTakayukiTohge
13 AnUHPLC-MS/MSMethodforTargetProfilingofStress-Related
Phytohormones ........................................................ 183
OndrˇejNova´kandKristy´naFlokova´
14 ACompletePipelineforGeneratingaHigh-Resolution
LC-MS-BasedReferenceMassSpectraLibrary ............................. 193
NirShahaf,AsaphAharoni,andIlanaRogachev
15 QuantificationofSugarsandOrganicAcidsinBiologicalMatrices
UsingGC-QqQ-MS .................................................... 207
NirupamaSamanmalieJayasinghe,HimashaMendis,UteRoessner,
andDanielAnthonyDias
16 AcquisitionofVolatileCompoundsbyGasChromatography–Mass
Spectrometry(GC-MS).................................................. 225
Jose´G.Vallarino,AlexanderErban,InesFehrle,AlisdairR.Fernie,
JoachimKopka,andSoniaOsorio
17 MassSpectrometryImaging(MSI)forPlantMetabolomics.................. 241
BerinA.BoughtonandDinaizThinagaran
18 LaserAblationElectrosprayIonization-MassSpectrometry
Imaging(LAESI-MS)forSpatiallyResolvedPlantMetabolomics............. 253
DesalegnW.Etalo,CarmenDı´ez-Sim(cid:1)on,RicC.H.deVos,
andRobertD.Hall
19 LiveSingle-CellMassSpectrometry(LSC-MS)forPlantMetabolomics ....... 269
KeikoMasuda,YasmineAbouleila,AhmedAli,ToshioYanagida,
andTsutomuMasujima
PART III DATA ANALYSIS & STATISTICS CHAPTERS
20 StatisticalandMultivariateAnalysisofMS-BasedPlant
MetabolomicsData ..................................................... 285
CarstenJaegerandJanLisec
21 IntegrationofPlantMetabolomicsDatawithMetabolicNetworks:
ProgressesandChallenges ............................................... 297
NadineT¨opfer,SamuelM.D.Seaver,andAsaphAharoni
22 UnderstandingtheFunctionalityofaBiologicalSystemasaWhole:
ComparativeDataAnalysis............................................... 311
IsabelOrf
23 Regression-BasedModelingofComplexPlantTraitsBased
onMetabolomicsData .................................................. 321
FranciscodeAbreueLima,LydiaLeifels,andZoranNikoloski
24 MathematicalModelingApproachesinPlantMetabolomics.................. 329
LisaFu¨rtauer,JakobWeiszmann,WolframWeckwerth,andThomasNa€gele
Index ...................................................................... 349
Contributors
YASMINEABOULEILA (cid:1) LaboratoryforSingle-CellMassSpectrometry,QuantitativeBiology
Center,RIKEN,Osaka,Japan
LUIS GUILHERMEFURLANDE ABREU (cid:1) BrazilianBioethanolScienceandTechnology
Laboratory(CTBE),BrazilianCenter forResearchinEnergyandMaterials(CNPEM),
Campinas,SP,Brazil
FRANCISCODEABREUELIMA (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-
Golm,Germany
SE´BASTIENACKET (cid:1) SorbonneUniversite´s,Universite´deTechnologiedeCompie`gne,UMR
CNRS7025,Ge´nieEnzymatiqueetCellulaire,Compie`gneCedex,France
ASAPHAHARONI (cid:1) DepartmentofPlantandEnvironmentalSciences,FacultyofBiochemistry,
WeizmannInstituteofScience,Rehovot,Israel
AHMEDALI (cid:1) LaboratoryforSingle-CellMassSpectrometry,QuantitativeBiologyCenter,
RIKEN,Osaka,Japan
SALEHALSEEKH (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany;CenterofPlantSystemBiologyandBiotechnology,Plovdiv,Bulgaria
CARLAANTO´NIO (cid:1) PlantMetabolomicsLaboratory,InstitutodeTecnologiaQuı´mica
eBiol(cid:1)ogicaAnt(cid:1)onioXavier,UniversidadeNovadeLisboa(ITQBNOVA),Oeiras,
Portugal
CAMILLEBE´NARD (cid:1) ServicedePharmacologieetImmunoanalyse(SPI),MetaboHUB-Paris,
CEA,INRA,Universite´ParisSaclay,Gif-sur-YvetteCedex,France;UMR1332Biologie
duFruitetPathologie,CentreINRAdeNouvelleAquitaine-Bordeaux,INRA,Univ.
Bordeaux,Villenaved’Ornon,France;PlateformeMe´tabolomeBordeaux,PHENOME,
MetaboHUB,CentreINRAdeNouvelleAquitaine-Bordeaux,INRA,CNRS,Univ.
Bordeaux,Villenaved’Ornon,France
THIERRYBERTON (cid:1) UMR1332BiologieduFruitetPathologie,CentreINRAdeNouvelle
Aquitaine-Bordeaux,INRA,Univ.Bordeaux,Villenaved’Ornon,France;Plateforme
Me´tabolomeBordeaux,PHENOME,MetaboHUB,CentreINRAdeNouvelleAquitaine-
Bordeaux,INRA,CNRS,Univ.Bordeaux,Villenaved’Ornon,France
BERIN A.BOUGHTON (cid:1) MetabolomicsAustralia,SchoolofBioSciences,TheUniversity
ofMelbourne,Parkville,VIC,Australia
YARIVBROTMAN (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany;DepartmentofLifeSciences,Ben-GurionUniversityoftheNegev,Beersheba,
Israel
CE´CILECABASSON (cid:1) Plateforme Me´tabolomeBordeaux,PHENOME,MetaboHUB,Centre
INRAdeNouvelleAquitaine-Bordeaux,INRA,CNRS,Univ.Bordeaux,Villenave
d’Ornon,France;UMR1332BiologieduFruitetPathologie,CentreINRAdeNouvelle-
AquitaineBordeaux,INRA,Univ.Bordeaux,Villenaved’Ornon,France
CAMILACALDANA (cid:1) BrazilianBioethanolScienceandTechnologyLaboratory(CTBE),
BrazilianCenterforResearchinEnergyandMaterials(CNPEM),Campinas,SP,Brazil;
Max-PlanckPartnerGroup,BrazilianBioethanolScienceandTechnologyLaboratory
(CTBE/CNPEM),Campinas,Brazil;MaxPlanckInstituteofMolecularPlantPhysiology,
Potsdam-Golm,Germany
xi
xii Contributors
CARMENDI´EZ-SIMO´N (cid:1) LaboratoryofPlantPhysiology,WageningenUniversityand
Research,Wageningen,TheNetherlands
DANILOM.DALOSO (cid:1) DepartamentodeBioquı´micaeBiologiaMolecular,Universidade
FederaldoCeara´,Fortaleza,CE,Brazil
DANIELANTHONYDIAS (cid:1) MetabolomicsAustralia,SchoolofBioSciences,TheUniversity
ofMelbourne,Parkville,VIC,Australia;SchoolofHealthandBiomedicalSciences,
DisciplineofLaboratoryMedicine,RMITUniversity,Bundoora,VIC,Australia
ALEXANDERERBAN (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
DESALEGNW.ETALO (cid:1) NetherlandsInstituteofEcology,Wageningen,TheNetherlands
LISAFU¨RTAUER (cid:1) DepartmentofEcogenomicsandSystemsBiology,FacultyofLifeSciences,
UniversityofVienna,Vienna,Austria
INESFEHRLE (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,Germany
REGINAFEIL (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,Germany
OLIVIERFERNANDEZ (cid:1) UMR1332BiologieduFruitetPathologie,CentreINRAdeNouvelle
Aquitaine-Bordeaux,INRA,Univ.Bordeaux,Villenaved’Ornon,France
ALISDAIR R.FERNIE (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
KRISTY´NAFLOKOVA´ (cid:1) LaboratoryofGrowthRegulators,CentreoftheRegionHana´ for
BiotechnologicalandAgriculturalResearch,InstituteofExperimentalBotanyoftheCzech
AcademyofSciences,Olomouc,CzechRepublic;FacultyofScience,Palacky´ University,
Olomouc,CzechRepublic;PlantHormoneBiology,SwammerdamInstituteforLife
Sciences,UniversityofAmsterdam,Amsterdam,TheNetherlands
PATRICKGIAVALISCO (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
YVESGIBON (cid:1) UMR1332BiologieduFruitetPathologie,CentreINRAdeNouvelle
Aquitaine-Bordeaux,INRA,Univ.Bordeaux,Villenaved’Ornon,France;Plateforme
Me´tabolomeBordeaux,PHENOME,MetaboHUB,CentreINRAdeNouvelleAquitaine-
Bordeaux,INRA,CNRS,Univ.Bordeaux,Villenaved’Ornon,France
ROBERTD.HALL (cid:1) LaboratoryofPlantPhysiology,WageningenUniversityandResearch,
Wageningen,TheNetherlands;BusinessUnitBioscience,WageningenUniversityand
Research,Wageningen,TheNetherlands;NetherlandsMetabolomicsCentre,Leiden,The
Netherlands
CARSTENJAEGER (cid:1) MolecularCancerResearchCenter(MKFZ),
Charite´-Universita€tsmedizinBerlin,Berlin,Germany;BerlinInstituteofHealth(BIH),
Berlin,Germany
NIRUPAMA SAMANMALIE JAYASINGHE (cid:1) MetabolomicsAustralia,SchoolofBioSciences,
TheUniversityofMelbourne,Parkville,VIC,Australia;RacingAnalyticalServicesLtd.,
Flemington,VIC,Australia
TIAGOF.JORGE (cid:1) PlantMetabolomicsLaboratory,InstitutodeTecnologiaQuı´mica
eBiol(cid:1)ogicaAnt(cid:1)onioXavier,UniversidadeNovadeLisboa(ITQBNOVA),Oeiras,
Portugal
JOACHIMKOPKA (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
LYDIALEIFELS (cid:1) MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
VALE´RIAF.LIMA (cid:1) DepartamentodeBioquı´micaeBiologiaMolecular,UniversidadeFederal
doCeara´,Fortaleza,CE,Brazil