鸟枪法蛋白质学的介绍

ADVANCEMENTINPROTEININFERENCEFROMSHOTGUNPROTEOMICSUSINGPEPTIDEDETECTABILITYOverview•ShotgunProteomics•ProteinInferenceProblem•ProteinIdentificationUsingPeptideDetectability•Results•LimitationsandImprovementsDegeneratePeptidesRatSample/RatIPIDatabase60%Nesvizhskii,A.I.andAebersold,R.(2005)Interpretationofshotgunproteomicdata:theproteininferenceproblem.Mol.CellProteomics,4,1419–1440.ProteinInferenceProblemSolution1*(A,E)*Solution2*(B,C,D)****MinimumProteinSet11PossibleSolutionsNesvizhskii,A.I.andAebersold,R.(2005)Interpretationofshotgunproteomicdata:theproteininferenceproblem.Mol.CellProteomics,4,1419–1440.IdentifiedPeptides12345678910Proteins1234261235417810966910GMPSA5331323222001GreedyMinimumProteinSetAlgorithmNesvizhskii,A.I.andAebersold,R.(2005)Interpretationofshotgunproteomicdata:theproteininferenceproblem.Mol.CellProteomics,4,1419–1440.ResolvingAmbiguitydetectabilityofapeptide–theprobabilitythatthepeptidewillbeobservedinastandardsampleanalyzedbyastandardproteomicsroutineTang,H.,Arnold,R.J.,Alves,P.,Xun,Z.,Clemmer,D.E.,Novotny,M.V.,Reilly,J.P.&Radivojac,P.(2006).Acomputationalapproachtowardlabel-freeproteinquantificationusingpredictedpeptidedetectability.Bioinformatics,(2006)22(14):e481-e488FactorsaffectingPeptideDetectionFourclassesoffactors1)Chemicalpropertiesofthepeptide(andparentprotein)2)Limitationsofpeptideidentificationprotocol3)Abundanceofthepeptideinthesample4)PresenceofotherpeptidesthatcompetefordetectionMeanAccuracy:71%MeanAUC:78%Synthetic:~30%ofpeptidesidentifiedReal:~10%ofpeptidesidentifiedPeptideDetectabilityPredictionIdentifiedPeptides12345678910ProteinsMinimumMissedPeptides124542614578692710245323175569101411723121532401MissedpeptideMDAPIdentifiedPeptides12345678910ProteinsLDFA124542614578692710245323175569101457629810314117231215324210210RESULTSGMPSALDFASyntheticSamplewith12Proteins7correctproteins10correctproteins5tiedproteins1tiedprotein1incorrecttiedproteinGMPSAvsLDFAinaR.norvegicussampleGMPSALDFARatSample/RatIPIDatabase234694IndistinguishablepairsGMPSAvsLDFAGMPSALDFA247275Totalproteinsidentified62%81%Percentofproteinsassignedwithnoties153224Totalassignmentswithnoties149Proteinsassignedduetouniquepeptides475TotalunambiguousassignmentsexcludingtheproteinswithuniquepeptidesIdentifiedProteinsUnambiguouslyIdentifiedProteinsLimitationsandImprovements•Includemissed-cleavagepeptides•Includelowerscoringpeptidestoaidinthedifferentiationoftiedproteins•Includepeptidesidentifiedwithcharges+1and+3•Trainonotheranalyticalplatforms•StudytheeffectsofdetectabilitypredictiononalgorithmresultsPublications•PSB2007–Alves,P.,Arnold,R.,Novotny,M.,Radivojac,P.,Reilly,J.,Tang,H.(2007).AdvancementinProteinInferencefromShotgunProteomicsUsingPeptideDetectability.Pac.Symp.Biocomput.,(2007)12:409-420•ISMB2006–Tang,H.,Arnold,R.J.,Alves,P.,Xun,Z.,Clemmer,D.E.,Novotny,M.V.,Reilly,J.P.&Radivojac,P.(2006).Acomputationalapproachtowardlabel-freeproteinquantificationusingpredictedpeptidedetectability.Bioinformatics,(2006)22(14):e481-e488.Acknowledgements•PredragRadivojac•HaixuTang•RandyArnold•IUSchoolofInformatics•IUChemistryDept.