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1、commentaryTheprosandconsofpeptide-centricproteomicsMarkWDuncan,RuediAebersold&RichardMCaprioliRecommendationsonhowbesttoexploitthestrengthsofpeptide-centricproteomicsandavoiditspitfalls.eptide-centricapproaches—sometimesalsoraisesomecautionarynotesandmakesomeisassigneda
2、score,andthepeptidesequencePreferredtoasshotgunstrategiesorbot-recommendationsspecificallyforendusers.inthedatabasewiththebestscore,abovetom-upproteomics—arenowwidelyadoptedsomepredeterminedthreshold,isgener-asameansofidentifyingproteinspresentinRationaleforpeptide-cent
3、ricapproachesallyassumedtobecorrect.Typically,ifthebiologicalmixtures.SuchapproachesinvolveAlthoughtheexactnumberofhumanproteinthresholdisnotmet,noassignmentismade.thesequence-specificcleavageofacomplex,productsremainsunknown,itextendsfarOnceatandemmassspectrumisassigne
4、daprotein-containingsampletocreateamix-beyondtheestimated20,000orsoprotein-cod-peptidesequence,thedatabase(s)ofknowntureofpeptidesofmuchgreatercomplexity.inggenesinthegenome.ConsiderationoftheproteinsissearchedtodefinetheantecedentTheunderlyingassumptionofthisstrategyli
5、kelynumberoftranscriptionalvariantspre-protein(s)incorporatingit.Theoverallpro-isthatproteinsintheoriginalsamplecanbedicts>100,000codedproteins1.However,thecessisrepresentedinFigure1.identifiedbymeansofmassspectrometrymainsourceofproteincomplexityistheubiq-Thisisapowerf
6、ulstrategy,andthereare(MS)-mediatedidentificationoftheircon-uitousincorporationof>200post-translationalfewpracticalalternatives.Forexample,Edmanstituentpeptides.Thetypeofinstrumenta-modifications,includingphosphorylationandanalysiswouldrequireisolationandpurifica-tionco
7、mmonlyusedinthisanalysisisliquidglycosylation2.Consequently,genesfrequentlytionofeachindividualproteinfollowedbychromatography(LC)andelectrosprayion-serveasthepredecessorsofmultiplestructur-exhaustiveresidue-by-residuesequencing.izationtandemmassspectrometry(MS/MS),ally
8、distinctproductsandevenminorstructuralTheprocesswouldbetimeconsuming,costlybutanotherapproachgainingpopularity
