鸟枪法蛋白质学的介绍.pptxVIP

ADVANCEMENT IN PROTEIN INFERENCE FROM SHOTGUNPROTEOMICS USING PEPTIDE DETECTABILITYOverviewShotgun ProteomicsProtein Inference ProblemProtein Identification Using Peptide DetectabilityResultsLimitations and ImprovementsDegenerate Peptides60%Rat Sample/Rat IPI DatabaseNesvizhskii, A.I. and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell Proteomics, 4, 1419–1440.Protein Inference ProblemSolution 1 * (A, E)**Minimum Protein SetSolution 2 * (B, C, D)** 11 Possible Solutions*Nesvizhskii, A.I. and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell Proteomics, 4, 1419–1440.GMPSAProteinsGreedy Minimum Protein Set AlgorithmIdentified Peptides 12345678910 4 2 6 1 2 323312026 95 4 1 7 81 2 352310 9 610310Nesvizhskii, A.I. and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell Proteomics, 4, 1419–1440.Resolving Ambiguitydetectability of a peptide – the probability that the peptide will be observed in a standard sample analyzed by a standard proteomics routineTang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P. Radivojac, P. (2006). A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics, (2006) 22 (14): e481-e488 Factors affecting Peptide DetectionFour classes of factorsChemical properties of the peptide (and parent protein)Limitations of peptide identification protocolAbundance of the peptide in the samplePresence of other peptides that compete for detectionPeptide Detectability PredictionSynthetic : ~30% of peptides identifiedReal : ~10% of peptides identifiedMean Accuracy : 71%Mean AUC : 78%Minimum Missed PeptidesIdentified Peptides Proteins1245426141172312345678910Missed peptide14578692712153241017556910MDADFAProteinsIdentified Peptides 14576298103124542614117231234567891021457869271215324