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1、perspectiveOptionsandconsiderationswhenselectingaquantitativeproteomicsstrategyBrunoDomon1&RuediAebersold1,2Thevastmajorityofproteomicstudiestodatehavereliedonmassspectra,commonlygeneratedbycollisionalactivation,aremassspectrometrictechniquestoidentify,andinsomecasesrecordedandusedtodeter
2、minetheaminoacidsequenceoftheselectedquantify,peptidesthathavebeengeneratedbyproteolysis.peptides.Finally,theproteinspresentinthesampleareinferredfromCurrentapproachesdifferinthetypesofinstrumentused,theirtheensembleofidentifiedpeptides.Inthemostcommonimplementa-performanceprofiles,theman
3、nerinwhichtheyinterfacewithtionofthemethod,theprecursorionsareselectedautomaticallyfrombiologicalresearchstrategies,andtheirrelianceonandusetheionsdetectedinasurveyscanimmediatelyprecedingtheionselec-ofpriorinformation.Here,weconsiderthethreemainmasstion,aprocessreferredtoasdata-dependent
4、analysis(DDA).Whenspectrometry(MS)-basedproteomicapproachesusedtoday:combinedwithanappropriatestable-isotopelabelingstrategy,theseshotgun(ordiscovery),directedandtargetedstrategies.Weproteinidentificationmethodsalsopermitrelative(involvingcompari-discusstheprinciplesofeachtechnique,theirs
5、trengthsandsontoareferencesample)orabsolutequantificationoftheidentifiedweaknessesandthedependenceoftheirperformanceprofilesonproteins2,4.Thevariousmethodsdifferintherequirementsforsamplethecompositionofthebiologicalsample.Ourgoalistoprovidepreparation,theextentofsamplefractionationandthe
6、level(proteinarationalframeworkforselectingstrategiesoptimallysuitedtoorpeptide)atwhichfractionationisperformed,thetypeofmassspec-addressthespecificresearchissueunderconsideration.trometerusedandtheirneedsindataprocessingtools5.Mostcommonimplementationsrelyonelectrosprayionizationdirectly
7、coupledtoanTheproteomeismorethanthemeretranslationoftheprotein-codinginstrumentforliquidchromatography.However,alternativeorcomple-regionsofagenome.Processessuchasalternativesplicing,proteinmentarymethodsbasedonmatrix-assistedlaserdesorptionioniza-processingandpost-
