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ofsmallmoleculechemicalsfoundwithina
biologicalsample.[1]Thebiologicalsample
Mainpage

canbeacell,acellularorganelle,anorgan,

Contents

atissue,atissueextract,abiofluidoran

Featuredcontent

entireorganism.Thesmall

Currentevents

moleculechemicalsfoundinagiven

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metabolomemayincludeboth

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endogenousmetabolitesthatarenaturally
producedbyanorganism(suchasamino
acids,organicacids,nucleicacids,fatty

Figure1.Anillustrationofthe
pyramidoflifewhichshowsthe
varyinginfluenceoftheenvironment
andphysiologyonthegenome,
proteomeandmetabolome.

acids,amines,sugars,vitamins,co

Communityportal

factors,pigments,antibiotics,etc.)aswellasexogenouschemicals(suchas

Recentchanges

drugs,environmentalcontaminants,foodadditives,toxinsandotherxenobiotics)

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thatarenotnaturallyproducedbyanorganism.[2][3]Inotherwords,thereisbothan
endogenousmetabolomeandanexogenousmetabolome.Theendogenous

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metabolomecanbefurthersubdividedtoincludea"primary"anda"secondary"

Relatedchanges

metabolome(particularlywhenreferringtoplantormicrobialmetabolomes).

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Aprimarymetaboliteisdirectlyinvolvedinthenormalgrowth,development,and

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reproduction.Asecondarymetaboliteisnotdirectlyinvolvedinthoseprocesses,but

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usuallyhasimportantecologicalfunction.Secondarymetabolitesmay
includepigments,antibioticsorwasteproductsderivedfrompartially
metabolizedxenobiotics.Toqualifyasametabolite,ortobeconsideredtobepartof
themetabolome,asmallmoleculemusttypicallyhaveamolecularweight<1500
Da.[2]Thismeansthatmoleculessuchasglycolipids,polysaccharides,

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shortpeptides(<14aminoacids)andsmalloligonucleotides(<5bases)canbe

Printableversion

regardedasmetabolitesorconstituentsofthemetabolome.Ontheotherhand,

Languages

verylargemacromoleculessuchasproteins,messengerRNA,ribosomal

Bosanski

RNA,microRNAandDNAaredefinitelynotmetabolitesandarenotconsideredto

Catal

bepartofthemetabolome.Thestudyofthemetabolomeiscalledmetabolomics.

Deutsch

SeeFigure1forapictureoftherelationshipbetweendifferentomes.

Espaol

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Galego

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https://en.wikipedia.org/wiki/Metabolome

1 Origins
2 Measuringthemetabolome
3 Metabolomedatabases
3.1 TheHumanMetabolomeDatabase
3.1.1 Humanbiofluidmetabolomes
3.2 YeastMetabolomeDatabase

Figure2.Anillustrationofthe
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Polski

relationshipbetweensensitivity(or
lowerdetectionlimitinconcentration
units)andthenumberofmetabolites
detected(usingaLog10scale)via
differentmetabolomicstechnologies.

3.3 TheEscherichiacoliMetabolome

Database

/srpski
Srpskohrvatski/

4 Seealso
5 References
6 Externallinks

Svenska
TingVit

Editlinks

Origins

[ edit ]

Thewordmetabolomeappearstobeablendingofthewordsmetaboliteand
chromosome.Itwasconstructedtoimplythatmetabolitesareindirectlyencoded
bygenesoractongenesandgeneproducts.Thetermmetabolomewasfirst
usedin1998[1][4]andwaslikelycoinedtomatchwithexistingbiologicalterms
referringtothecompletesetofgenes(thegenome),thecompletesetofproteins
(theproteome)andthecompletesetoftranscripts(thetranscriptome).Thefirst
bookonmetabolomicswaspublishedin2003.[5]Thefirstjournaldedicatedto
metabolomics(titledsimplyMetabolomics)waslaunchedin2005andiscurrently
editedbyDr.RoystonGoodacre.Someofthemoresignificantearlypaperson
metabolomeanalysisarelistedinthereferencesbelow[6][7][8][9]

Measuringthemetabolome

[ edit ]

Themetabolomereflectstheinteractionbetweenanorganismsgenomeandits
environment.Asaresult,anorganismsmetabolomecanserveasanexcellent
probeofitsphenotype(i.e.theproductofitsgenotypeandits
environment).Metabolitescanbemeasured(identified,quantifiedorclassified)
usinganumberofdifferenttechnologiesincludingNMRspectroscopyandmass
spectrometry.Mostmassspectrometry(MS)methodsmustbecoupledtovarious
formsofliquidchromatography(LC),gaschromatography(GC)orcapillary
electrophoresis(CE)tofacilitatecompoundseparation.Eachmethodistypically
abletoidentifyorcharacterize505000differentmetabolitesormetabolite
featuresatatime,dependingontheinstrumentorprotocolbeingused.See
Figure2foranillustrationoftherelationshipbetweendifferentanalyticalmethods
andtheirsensitivity.Currentlyitisnotpossibletoanalyzetheentirerangeof
metabolitesbyasingleanalyticalmethod.
Nuclearmagneticresonance(NMR)spectroscopyisananalyticalchemistry
techniquethatmeasurestheabsorptionofradiofrequencyradiationofspecificnuclei
whenmoleculescontainingthosenucleiareplacedinstrongmagneticfields.The
frequency(i.e.thechemicalshift)atwhichagivenatomornucleusabsorbsis
highlydependentonthechemicalenvironment(bonding,chemicalstructure
nearestneighbours,solvent)ofthatatominagivenmolecule.TheNMRabsorption
patternsproduceresonancepeaksatdifferentfrequenciesordifferentchemical
shiftsthiscollectionofpeaksiscalledaNMRspectrum.Becauseeachchemical
compoundhasadifferentchemicalstructure,eachcompoundwillhaveaunique
(oralmostunique)NMRspectrum.Asaresult,NMRisparticularlyusefulforthe
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characterization,identificationandquantificationofsmallmolecules,suchas
metabolites.ThewidespreaduseofNMRforclassicalmetabolicstudies,along
withitsexceptionalcapacitytohandlecomplexmetabolitemixturesislikelythe
reasonwhyNMRwasoneofthefirsttechnologiestobewidelyadoptedforroutine
metabolomemeasurements.Asananalyticaltechnique,NMRisnondestructive,
nonbiased,easilyquantifiable,requireslittleornoseparation,permitsthe
identificationofnovelcompoundsanditneedsnochemicalderivatization.NMRis
particularlyamenabletodetectingcompoundsthatarelesstractabletoLC
MSanalysis,suchassugars,aminesorvolatileliquidsorGCMSanalysis,suchas
largemolecules(>500Da)orrelativelynonreactivecompounds.NMRisnotavery
sensitivetechniquewithalowerlimitofdetectionofabout5M.Typically50150
compoundscanbeidentifiedbyNMRbasedmetabolomicstudies.
Massspectrometryisananalyticaltechniquethatmeasuresthemasstocharge
ratioofmolecules.Moleculesormolecularfragmentsaretypicallychargedor
ionizedbysprayingthemthroughachargedfield(electrosprayionization),
bombardingthemwithelectronsfromahotfilament(electronionization)orblasting
themwithalaserwhentheyareplacedonspeciallycoatedplates(matrixassisted
laserdesorptionionization).Thechargedmoleculesarethenpropelledthrough
spaceusingelectrodesormagnetsandtheirspeed,rateofcurvature,orother
physicalcharacteristicsaremeasuredtodeterminetheirmasstochargeratio.
Fromthesedatathemassoftheparentmoleculecanbedetermined.Further
fragmentationofthemoleculethroughcontrolledcollisionswithgasmoleculesor
withelectronscanhelpdeterminethestructureofmolecules.Veryaccuratemass
measurementscanalsobeusedtodeterminetheelementalformulasorelemental
compositionofcompounds.Mostformsofmassspectrometryrequiresomeformof
separationusingliquidchromatographyorgaschromatography.Thisseparation
stepisrequiredtosimplifytheresultingmassspectraandtopermitmoreaccurate
compoundidentification.Somemassspectrometrymethodsalsorequirethatthe
moleculesbederivatizedorchemicallymodifiedsothattheyaremoreamenable
forchromatographicseparation(thisisparticularlytrueforGCMS).Asananalytical
technique,MSisaverysensitivemethodthatrequiresverylittlesample(<1ngof
materialor<10Lofabiofluid)andcangeneratesignalsfor1000sofmetabolites
fromasinglesample.MSinstrumentscanalsobeconfiguredforveryhigh
throughputmetabolomeanalyses(100sto1000sofsamplesaday).Quantification
ofmetabolitesandthecharacterizationofnovelcompoundstructuresismore
difficultbyMSthanbyNMR.LCMSisparticularlyamenabletodetecting
hydrophobicmolecules(lipids,fattyacids)andpeptideswhileGCMSisbestfor
detectingsmallmolecules(<500Da)andhighlyvolatilecompounds
(esters,amines,ketones,alkanes,thiols).
Unlikethegenomeoreventheproteome,themetabolomeisahighlydynamic
entitythatcanchangedramatically,overaperiodofjustsecondsorminutes.Asa
result,thereisgrowinginterestinmeasuringmetabolitesovermultipletimeperiods
orovershorttimeintervalsusingmodifiedversionsofNMRorMSbased
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metabolomics

Metabolomedatabases

[ edit ]

Becauseanorganismsmetabolomeislargelydefinedbyitsgenome,different
specieswillhavedifferentmetabolomes.Indeed,thefactthatthemetabolomeofa
tomatoisdifferentthanthemetabolomeofanappleisthereasonwhythesetwo
fruitstastesodifferent.Furthermore,differenttissues,
differentorgansandbiofluidsassociatedwiththoseorgansandtissuescanalso
havedistinctlydifferentmetabolomes.Thefactthatdifferentorganismsand
differenttissues/biofluidshavesuchdifferentmetabolomeshasledtothe
developmentofanumberoforganismspecificofbiofluidspecificmetabolome
databases.SomeofthebetterknownmetabolomedatabasesincludetheHuman
MetabolomeDatabaseorHMDB,[10]theYeastMetabolome
DatabaseorYMDB,[11]theE.coliMetabolomeDatabaseorECMDB,[12]the
ArabidopsismetabolomedatabaseorAraCyc[13]aswellastheUrineMetabolome
Database,[14]theCerebrospinalFluid(CSF)MetabolomeDatabase[15]andthe
SerumMetabolomeDatabase.[16]Thelatterthreedatabasesarespecifictohuman
biofluids.Anumberofverypopulargeneralmetabolitedatabasesalsoexist
includingKEGG,[17]MetaboLights,[18]theGolmMetabolome
Database,[19]MetaCyc,[20]LipidMaps[21]andMetlin.[22]Metabolomedatabasescan
bedistinguishedfrommetabolitedatabasesinthatmetabolitedatabasescontain
lightlyannotatedorsynopticmetabolitedatafrommultipleorganismswhile
metabolomedatabasescontainrichlydetailedandheavilyreferencedchemical,
pathway,spectralandmetaboliteconcentrationdataforspecificorganisms.

TheHumanMetabolomeDatabase

[ edit ]

TheHumanMetabolomeDatabaseisafreelyavailable,openaccessdatabase
containingdetaileddataonmorethan40,000metabolitesthathavealreadybeen
identifiedorarelikelytobefoundinthehumanbody.TheHMDBcontainsthree
kindsofinformation:1)chemicalinformation,2)clinicalinformation,and3)
biochemicalinformation.Thechemicaldataincludes>40,000metabolitestructures
withdetaileddescriptions,extensivechemicalclassifications,synthesisinformation
andobserved/calculatedchemicalproperties.Italsocontainsnearly10,000
experimentallymeasuredNMR,GCMSandLC/MSspectrafrommorethan1100
differentmetabolites.Theclinicalinformationincludesdataon>10,000metabolite
biofluidconcentrations,metaboliteconcentrationinformationonmorethan600
differenthumandiseasesandpathwaydataformorethan200differentinborn
errorsofmetabolism.Thebiochemicalinformationincludesnearly6000protein
(andDNA)sequencesandmorethan5000biochemicalreactionsthatarelinkedto
thesemetaboliteentries.TheHMDBsupportsawidevarietyofonlinequeries
includingtextsearches,chemicalstructuresearches,sequencesimilaritysearches
andspectralsimilaritysearches.Thismakesitparticularlyusefulformetabolomic
researcherswhoareattemptingtoidentifyorunderstandmetabolitesinclinical
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metabolomicstudies.ThefirstversionoftheHMDBwasreleasedinJan.12007
andwascompiledbyscientistsattheUniversityofAlbertaandtheUniversityof
Calgary.Atthattimetheyreporteddataon2,500metabolites,1,200drugsand
3,500foodcomponents.Sincethenthesescientistshavegreatlyexpandedthe
collection.ThelatestversionoftheHMDB(version3.5)contains>16,000
endogenousmetabolites,>1500drugsand>22,000foodconstituentsorfood
metabolites.[23]
Humanbiofluidmetabolomes [ edit ]
ScientistsattheUniversityofAlbertahavebeensystematicallycharacterizing
specificbiofluidmetabolomesincludingtheserummetabolome,[16]theurine
metabolome,[14]thecerebrospinalfluid(CSF)metabolome[15]andthesaliva
metabolome.Theseeffortshaveinvolvedbothexperimentalmetabolomicanalysis
(involvingNMR,GCMS,ICPMS,LCMSandHPLCassays)aswellasextensive
literaturemining.Accordingtotheirdata,thehumanserummetabolomecontainsat
least4200differentcompounds(includingmanylipids),thehumanurine
metabolomecontainsatleast3000differentcompounds(including100sofvolatiles
andgutmicrobialmetabolites),thehumanCSFmetabolomecontainsnearly500
differentcompoundswhilethehumansalivametabolomecontainsapproximately
400differentmetabolites,includingmanybacterialproducts.

YeastMetabolomeDatabase

[ edit ]

TheYeastMetabolomeDatabaseisafreelyaccessible,onlinedatabaseof>2000
smallmoleculemetabolitesfoundinorproducedbySaccharomyces
cerevisiae(Bakersyeast).TheYMDBcontainstwokindsofinformation:1)
chemicalinformationand2)biochemicalinformation.Thechemicalinformationin
YMDBincludes2027metabolitestructureswithdetailedmetabolitedescriptions,
extensivechemicalclassifications,synthesisinformationandobserved/calculated
chemicalproperties.Italsocontainsnearly4000NMR,GCMSandLC/MSspectra
obtainedfrommorethan500differentmetabolites.Thebiochemicalinformation
inYMDBincludes>1100protein(andDNA)sequencesand>900biochemical
reactions.TheYMDBsupportsawidevarietyofqueriesincludingtextsearches,
chemicalstructuresearches,sequencesimilaritysearchesandspectralsimilarity
searches.Thismakesitparticularlyusefulformetabolomicresearcherswhoare
studyingyeastasamodelorganismorwhoarelookingintooptimizingthe
productionoffermentedbeverages(wine,beer).

TheEscherichiacoliMetabolomeDatabase

[ edit ]

TheE.ColiMetabolomeDatabaseisafreelyaccessible,onlinedatabaseof>2700
smallmoleculemetabolitesfoundinorproducedbyEscherichiacoli(E.colistrain
K12,MG1655).TheECMDBcontainstwokindsofinformation:1)chemical
informationand2)biochemicalinformation.Thechemicalinformationincludes
morethan2700metabolitestructureswithdetailedmetabolitedescriptions,
extensivechemicalclassifications,synthesisinformationandobserved/calculated
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chemicalproperties.Italsocontainsnearly5000NMR,GCMSandLCMSspectra
frommorethan600differentmetabolites.Thebiochemicalinformationincludes
>1600protein(andDNA)sequencesand>3100biochemicalreactionsthatare
linkedtothesemetaboliteentries.TheECMDBsupportsmanydifferenttypesof
onlinequeriesincludingtextsearches,chemicalstructuresearches,sequence
similaritysearchesandspectralsimilaritysearches.Thismakesitparticularlyuseful
formetabolomicresearcherswhoarestudyingE.coliasamodelorganism.

Seealso

[ edit ]

Tumormetabolome

Metabolismportal

Proteinelectrophoresis
Proteinsequencing.

References

[ edit ]

1.^ a bOliver,SGWinsonMKKellDBBaganzF(September1998)."Systematic
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4.^Tweeddale,HNotleyMcRobbLFerenciT.(Oct1998)."Effectofslowgrowthon
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10.^Wishart,DSTzurDKnoxCetal.(January2007)."HMDB:theHuman
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11.^Jewison,T.NeveuV,LeeJ,KnoxC,LiuP,MandalR,MurthyRK,SinelnikovI,Guo
AC,WilsonM,DjoumbouYandWishartDS.(Jan2012)."TheYeastMetabolome
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KrishnamurthyRWishartDS(Jan2013)."ECMDB:theE.coliMetabolome
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13.^Mueller,LAZhangPRheeSY.(June2003)."AraCyc:abiochemicalpathway
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14.^ a bBouatra,SAziatF,MandalR,GuoAC,WilsonMR,KnoxC,BjorndahlTC,
KrishnamurthyR,SaleemF,LiuP,DameZT,PoelzerJ,HuynhJ,YallouFS,
PsychogiosN,DongE,BogumilR,RoehringC,WishartDS.(Sep2013)."Thehuman
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DS.(Apr2012)."Multiplatformcharacterizationofthehumancerebrospinalfluid
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KrishnamurthyR,EisnerR,GautamB,YoungN,XiaJ,KnoxC,DongE,HuangP,
HollanderZ,PedersenTL,SmithSR,BamforthF,GreinerR,McManusB,Newman
JW,GoodfriendT,WishartDS.(Feb2011)."Thehumanserummetabolome." .PLoS
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WilliamsM,NeumannS,RoccaSerraP,MaguireE,GonzlezBeltrnA,SansoneSA,
GriffinJL,SteinbeckC.(2013)."MetaboLightsanopenaccessgeneralpurpose
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Externallinks

[ edit ]
Lookupmetabolomein
Wiktionary,thefree
dictionary.

Categories: Metabolism

Systemsbiology

Bioinformatics

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