메뉴 건너뛰기




Volumn 5, Issue 1, 2012, Pages 3-20

A review of statistical methods for protein identification using tandem mass spectrometry

Author keywords

Bayesian methods; Mass spectrometry; Proteomics

Indexed keywords


EID: 84859193599     PISSN: 19387989     EISSN: 19387997     Source Type: Journal    
DOI: 10.4310/sii.2012.v5.n1.a2     Document Type: Review
Times cited : (58)

References (38)
  • 1
    • 49749121622 scopus 로고    scopus 로고
    • HUGIN, a shell for building Bayesian belief universes for expert systems
    • Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, 1990. ISBN 1-55860-125-2
    • Andersen, S. K., Olesen, K. G. and Jensen, F. V. HUGIN, a shell for building Bayesian belief universes for expert systems, pages 332-337. Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, 1990. ISBN 1-55860-125-2.
    • Andersen, S.K.1    Olesen, K.G.2    Jensen, F.V.3
  • 3
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289-300, 1995.
    • (1995) Journal of the Royal Statistical Society B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 0003857778 scopus 로고    scopus 로고
    • A gentle tutorial of the EM algorithm and its application to parameter estimation for Gaussian mixture and hidden Markov models
    • Bilmes, J. A gentle tutorial of the EM algorithm and its application to parameter estimation for Gaussian mixture and hidden Markov models. http://ssli.ee.washington.edu/~bilmes/mypubs/bilmes1997-em.pdf, 1998.
    • (1998)
    • Bilmes, J.1
  • 5
    • 0141955057 scopus 로고    scopus 로고
    • A method for reducing the time required to match protein sequences with tandem mass spectra
    • Craig, R. and Beavis, R. C. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid communications in mass spectrometry, 17:2310-2316, 2003.
    • (2003) Rapid communications in mass spectrometry , vol.17 , pp. 2310-2316
    • Craig, R.1    Beavis, R.C.2
  • 6
    • 1542784653 scopus 로고    scopus 로고
    • Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association
    • Efron, B., Tibshirani, R., Storey, J.D., and Tusher, V. Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association, 96(456):1151-1161, 2001.
    • (2001) , vol.96 , Issue.456 , pp. 1151-1161
    • Efron, B.1    Tibshirani, R.2    Storey, J.D.3    Tusher, V.4
  • 7
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E. and Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods, 4(3):207-214, 2007.
    • (2007) Nature Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 8
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., and Yates, III, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry, 5:976-989, 1994.
    • (1994) Journal of the American Society for Mass Spectrometry , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 9
    • 34548802987 scopus 로고    scopus 로고
    • Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/peptide sequence false match frequencies
    • Feng, J., Naiman, D. Q., and Cooper, B. Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/peptide sequence false match frequencies. Bioinformatics, 23(17):2210-2217, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2210-2217
    • Feng, J.1    Naiman, D.Q.2    Cooper, B.3
  • 10
    • 59849093889 scopus 로고    scopus 로고
    • Prediction of high-responding peptides for targeted protein assays by mass spectrometry
    • Fusaro, V. A., Mani, D. R., Mesirov, J. P., and Carr, S. A. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nature Biotechnology, 27(2):190-198, 2009.
    • (2009) Nature Biotechnology , vol.27 , Issue.2 , pp. 190-198
    • Fusaro, V.A.1    Mani, D.R.2    Mesirov, J.P.3    Carr, S.A.4
  • 11
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mrna abundance in yeast
    • Gygi, S. P., Rochon, Y., Franza, B., and Aebersold, R. Correlation between protein and mrna abundance in yeast. Mol. Cell. Biol., 19(3):1720-1730, 1999.
    • (1999) Mol. Cell. Biol. , vol.19 , Issue.3 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.3    Aebersold, R.4
  • 12
    • 65249121948 scopus 로고    scopus 로고
    • Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures
    • Hoopmann, M. R., Merrihew, G. E., von Haller, P. D., and MacCoss, M. J. Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. Journal of Proteome Research, 8(4):1870-1875, 2009.
    • (2009) Journal of Proteome Research , vol.8 , Issue.4 , pp. 1870-1875
    • Hoopmann, M.R.1    Merrihew, G.E.2    von Haller, P.D.3    MacCoss, M.J.4
  • 13
    • 34047112748 scopus 로고    scopus 로고
    • Emergence of novel color vision in mice engineered to express a human cone photopigment
    • Jacobs, G. H., Williams, G. A., Cahill, H., and Nathans, J. Emergence of novel color vision in mice engineered to express a human cone photopigment. Science, 315(5819):1723-1725, 2007.
    • (2007) Science , vol.315 , Issue.5819 , pp. 1723-1725
    • Jacobs, G.H.1    Williams, G.A.2    Cahill, H.3    Nathans, J.4
  • 14
    • 35748972060 scopus 로고    scopus 로고
    • A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets
    • Käll, L., Canterbury, J., Weston, J., Noble, W. S., and MacCoss, M. J. A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets. Nature Methods, 4:923-25, 2007.
    • (2007) Nature Methods , vol.4 , pp. 923-925
    • Käll, L.1    Canterbury, J.2    Weston, J.3    Noble, W.S.4    MacCoss, M.J.5
  • 15
    • 0003037529 scopus 로고
    • Reducibility among combinatorial problems
    • R. E. Miller and J. W. Thatcher, editors. Plenum Press
    • Karp, R. M. Reducibility among combinatorial problems. In R. E. Miller and J. W. Thatcher, editors, Complexity of Computer Computations, pages 85-103. Plenum Press, 1972.
    • (1972) Complexity of Computer Computations , pp. 85-103
    • Karp, R.M.1
  • 16
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search
    • Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search. Analytical Chemistry, 74:5383-5392, 2002.
    • (2002) Analytical Chemistry , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
    • Kim, S., Gupta, N., and Pevzner, P. A. Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases. Journal of Proteome Research, 7:3354-3363, 2008.
    • (2008) Journal of Proteome Research , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 19
    • 77955459838 scopus 로고    scopus 로고
    • A nested mixture model for protein identification using mass spectrometry
    • Li, Q., MacCoss, M. J., and Stephens, M. A nested mixture model for protein identification using mass spectrometry. Annals of Applied Sciences, 4(2):962-987, 2010.
    • (2010) Annals of Applied Sciences , vol.4 , Issue.2 , pp. 962-987
    • Li, Q.1    MacCoss, M.J.2    Stephens, M.3
  • 22
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • Nesvizhskii, A. I. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Journal of Proteomics, 73(11):2092-2123, 2010.
    • (2010) Journal of Proteomics , vol.73 , Issue.11 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 23
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry, 75:4646-4658, 2003.
    • (2003) Analytical Chemistry , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 24
    • 74549222857 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Advanced online publication, November
    • Pan, Q., Shai, O., Lee, L. J., Frey, B. J., and Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Advanced online publication, November 2008.
    • (2008)
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 26
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J. C., Creasy, D. M., and Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20:3551-3567, 1999.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 29
    • 77949695293 scopus 로고    scopus 로고
    • Scaffold: A bioinformatic tool for validating ms/ms-based proteomic studies
    • Searle, B. C. Scaffold: A bioinformatic tool for validating ms/ms-based proteomic studies. PROTEOMICS, 10(6):1265-1269, 2010.
    • (2010) PROTEOMICS , vol.10 , Issue.6 , pp. 1265-1269
    • Searle, B.C.1
  • 30
    • 77957339566 scopus 로고    scopus 로고
    • Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
    • Serang, O., MacCoss, M. J., and Noble, W. S. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. Journal of Proteome Research, 9(10):5346-5357, 2010.
    • (2010) Journal of Proteome Research , vol.9 , Issue.10 , pp. 5346-5357
    • Serang, O.1    MacCoss, M.J.2    Noble, W.S.3
  • 31
    • 38349166945 scopus 로고    scopus 로고
    • A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry
    • Shen, C., Wang, Z., Shankar, G., Zhang, X., and Li, L. A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. Bioinformatics, 24:202-208, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 202-208
    • Shen, C.1    Wang, Z.2    Shankar, G.3    Zhang, X.4    Li, L.5
  • 33
    • 0036393898 scopus 로고    scopus 로고
    • DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
    • Tabb, D. L., McDonald, W. H., and Yates, III, J. R. DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. Journal of Proteome Research, 1(1):21-26, 2002.
    • (2002) Journal of Proteome Research , vol.1 , Issue.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2    Yates III, J.R.3
  • 35
    • 0030987210 scopus 로고    scopus 로고
    • Initial genetic characterization of the 1918 Spanish influenza virus
    • Taubenberger, J. K., Reid, A. H., Krafft, A. E., Bijwaard, K. E., and Fanning, T. G. Initial genetic characterization of the 1918 Spanish influenza virus. Science, 275(5307): 1793-1796, 1997.
    • (1997) Science , vol.275 , Issue.5307 , pp. 1793-1796
    • Taubenberger, J.K.1    Reid, A.H.2    Krafft, A.E.3    Bijwaard, K.E.4    Fanning, T.G.5
  • 36
    • 84988779772 scopus 로고    scopus 로고
    • Correctness of local probability propagation in graphical models with loops
    • Weiss, Y. Correctness of local probability propagation in graphical models with loops. Neural Computation, 12(1):1-41, 2000.
    • (2000) Neural Computation , vol.12 , Issue.1 , pp. 1-41
    • Weiss, Y.1
  • 38
    • 34948874252 scopus 로고    scopus 로고
    • Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
    • Zhang, B., Chambers, M. C., and Tabb, D. L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Journal of Proteome Research, 6(9):3549-3557, 2007.
    • (2007) Journal of Proteome Research , vol.6 , Issue.9 , pp. 3549-3557
    • Zhang, B.1    Chambers, M.C.2    Tabb, D.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.