Chapter 22 Gel-Based Proteome Analysis

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1、CHAPTER22Gel-BasedProteomeAnalysisINTRODUCTIONProteomicsisanewdisciplinethatoriginatedinthemid-1990sandhasgrownrapidlyinaveryshorttime.Aswithmanynewfields,thereissomedisagreementconcerningwhatproteomicsreallyencompasses,andsomefeelthatproteomicsissimplyanewnamefortheproteinbiochem

2、istrystudiesthatmanyhavebeenpursuingforyears.However,thesebroaddefinitionsdonotaccuratelyreflecttheparadigmshiftdrivenbyseveralkeyenablingtechnologicaladvancesinthe1990sthatledtothebirthofproteomicsasauniqueapproachtobiology,namelyavailabilityofcompletegenomesequencesandhighsensi-

3、tivitymassspectrometrymethodstoidentifyproteins.Perhapsthebestcurrentdefinitionofproteomicsis“anylarge-scaleprotein-basedsystematicanalysisoftheproteomeordefinedsub-proteomefromacell,tissue,orentireorganism.”Proteomicsisthelogicalnextstepaftergenomesequencing,andshouldenhanceourun

4、derstandingofcellularanddiseaseprocesses,aswellasourabilitytodevelopnewtherapies.However,proteomicsismorecomplicatedandmorechallengingthansequenc-inggenomesbecausegenomesarefiniteandusuallystaticoverthelifetimeofacellwhileproteomesareconstantlychanging.Inaddition,theproteinreperto

5、ireofhighereu-karyotesisfargreaterthanthenumberofopenreadingframesinthegenomebecauseindividualgenesoftenproducemanydifferentproteinproductsthathaveimportantfunctionaldifferences.Theseincludealternativelysplicedproteinsandheterogeneouspost-translationalmodifications.Thischapterwill

6、describegel-basedmethodsandrelatedtechnologiesforanalyzingproteomes.Afuturechapterwilladdressnon-gelbasedmethodsofseparatingandanalyzingproteomesincludingmulti-dimensionalchromatographicseparationscoupleddirectlytomassspectrometers.Antibodyandotherproteinarrayswillbedescribedaswel

7、l.Subsequentchapterswilladdresstargetedproteomesandproteomebioinformatics.Thecurrentchapterbeginswithageneraloverviewofproteomics(UNIT22.1)focusingonthethreemostcommontypesofproteomestudies:1)quantitativeproteinprofilecom-parisons,2)analysisofprotein-proteininteractions,and3)compo

8、sitionalanalysisofsimpleproteomes