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1AnAlgorithmicApproachtoPeptideSequencingviaTandemMassSpectrometryMing-YangKaoDepartmentofComputerScienceNorthwesternUniversityEvanston,IllinoisU.S.A.2CollaboratorsofThisProjectUniversityofSouthernCalifornia•TingChenHarvardMedicalSchool•GeorgeM.Church•JohnRush•MatthewTepel3PerspectivesAkeygoalofbioinformatics:Tostudybiologicalsystemsbasedonglobalknowledgeofgenomes,transcriptomes,andproteomes.•Genome:entiresetsofmaterialsinthechromosomes.•Transcriptome:entiresetsofgenetranscripts.•Proteome:entiresetsofproteins.Genome(DNA)Transcriptome(RNA)Proteome(Protein)4PerspectivesAkeygoalofbioinformatics:Tostudybiologicalsystemsbasedonglobalknowledgeofgenomes,transcriptomes,andproteomes.•Genome:entiresetsofmaterialsinthechromosomes.•Transcriptome:entiresetsofgenetranscripts.•Proteome:entiresetsofproteins.Genome(DNA)Transcriptome(RNA)Proteome(Protein)thistalk’sfocus5Proteomics•Proteome:allproteinsencodedwithinagenome–halfmillionsdistinctproteins(temporal,spatial,modifications)–~30,000humangenes–mRNAandproteinexpressionsmaynotcorrelate•Proteomics:studyofproteinexpressionbybiologicalsystems–relativeabundanceandstability;post-translationalmodifications–fluctuationsasaresponsetoenvironmentandalteredcellularneeds–correlationsbetweenproteinexpressionanddiseasestate–protein-proteininteractions,proteincomplexes•Technologies:–2Dgelelectrophoresis–massspectrometry–yeasttwo-hybridsystem–proteinchipsthistalk’sfocus6AKeyStepofProteomics•Howtosequenceproteins?•Howtosequenceproteinpeptides?(thistalk’sfocus)7OutlineofThisTalk1.ProblemFormulation(Biology)2.ProblemFormulation(ComputerScience)3.BasicComputationalTechniques4.ImprovedComputationalComplexityandMoreRobustAlgorithms5.Conclusions8OutlineofThisTalk(1)1.ProblemFormulation(Biology)2.ProblemFormulation(ComputerScience)3.BasicComputationalTechniques4.ImprovedComputationalComplexityandMoreRobustAlgorithms5.Conclusions9ProteinIdentification:HPLC-MS-MSMassSpectrometerFragmentation&IonizationMassSpectrometerDeNovoPeptideSequencingProteinDatabaseSearchHPLCMass/ChargeTandemMassSpectrumMass/ChargeProteinsPeptidesOnePeptideB-ions/Y-ions10ProteinIdentification:HPLC-MS-MSMassSpectrometerFragmentation&IonizationMassSpectrometerDeNovoPeptideSequencingProteinDatabaseSearchHPLCMass/ChargeTandemMassSpectrumMass/ChargeProteinsPeptidesOnePeptideB-ions/Y-ions11PeptideFragmentationandIonizationB-ionY-ionComplementary:Mass(B-ion)+Mass(Y-ion)=Mass(peptide)+4H+O12B-ionsandY-ions)(Peptide321RRR)()()(321321211RRRbRRbRbionsbAll)()()(321332231RRRyRRyRyionsyAllFragmentation19,113TandemMassSpectrumMass/Charge2005088.033100400175.113274.112361.121430.213448.22514RawTandemMassSpectrum15PredictionfromRawTandemMassSpectrum16ProteinDatabaseSearchFindthepeptidesequencesinaproteindatabasethatoptimallyfitthespectrum.•Itdoesnotworkifthetargetpeptidesequenceisnotinthedatabase.•Itdoesnotworkifthereisanunknownmodificationatsomeaminoacid.•Itisveryslowbecauseitmustsearchtheentiredatabase.•E.g.,SEQUEST,Yates,Univ.ofWashington.17DeNovoPeptideSequencingProblem•Input:(1)themassWofanunknowntargetpeptide,and(2)asetSofthemassesofsomeorallb-ionsandy-ionsofthepeptide.•Output:apeptidePsuchthat(1)mass(P)=Wand(2)SisasubsetofalltheionmassesofP.Mass/Charge50100274.112361.121PeptideMass429.212DaltonsP=SWR,Mass(P)=429.212,Ions(P)={88.033,175.113,274.112,361.121,430.213,448.225}18TandemMassSpectrumMass/Charge2005088.033100400175.113274.112361.121430.213448.225PeptideMass429.212Daltons19AminoAcidMassTableA71.08M131.19C103.14N114.1D115.09P97.12E129.12Q128.13F147.18R156.19G57.05S87.08H137.14T101.11I113.16V99.13K128.17W186.21L113.16Y163.1820Feature1AllB-ionsformaforwardmassladder.Mass/Charge2005088.033100400175.113274.112361.121430.213448.225SWRPeptideMass429.212Daltonsb1b2b3121Feature2AllY-ionsformareversemassladder.Mass/Charge2005088.033100400175.113274.112361.121430.213448.225SWRRWSPeptideMass429.212Daltonsy1y2y31922BasicDifficulty#1ItisunknownwhetheranionisaB-ionoranY-ion.Mass/Charge2005088.033100400175.113274.112361.121430.213448.225PeptideMass429.212Daltons23BasicDifficulty#2Therearemissingions.Mass/Charge20050100400274.112361.121Ion1Ion2PeptideMass429.212Daltons24Feature3(toourRescue)ComplementaryIonPairs:b1/y2andb2/y1Mass/Charge2005088.033100400175.113274.112361.121430.213448.225SWRRWSPeptideMass429.212Daltonsy1y2y3b1b2b325OutlineofThisTalk(2)1.ProblemFormulation(Biology)2.ProblemFormulation(ComputerScience)3.BasicComputationalTechniques4.ImprovedComputationalComplexityandMoreRobustAlgorithms5.Conclusions26FormulatingtheComputationalProblem1.T=analphabetof20charactersa1,a2,…,a20.2.twospecialcharacters:alphaandbeta.3.themassofalpha=1,themassofbeta=19,themassofaiismi.4.Apeptidesequenceisx1,x2,x3,…,xn-1,xn,whereeachxiisfromT.5.Ab-ionisx0,x1,x2,…,xiforsome1=i=n,wherex0=alpha.6.Ay-ionisxi,…,xn-2,xn-1,xn,xn+1forsome1=i=n,wherexn+1=beta.27DeNovoPeptideSequencingProblem•Input:(1)themassWofanunknowntargetpeptide,and(2)asetSofthemassesofsomeorallb-ionsandy-ionsofthepeptide.•Output:apeptidePsuchthat(1)mas
本文标题:SequencingviaTandemMass
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