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Volumn 8, Issue 3, 2009, Pages 547-557

Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN DERIVATIVE;

EID: 63049091003     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700558-MCP200     Document Type: Article
Times cited : (33)

References (52)
  • 1
    • 33644898528 scopus 로고    scopus 로고
    • Automated protein identification by tandem mass spectrometry: Issues and strategies
    • Hernandez, P., Muller, M., and Appel, R. D. (2006) Automated protein identification by tandem mass spectrometry: issues and strategies. Mass Spectrom. Rev. 25, 235-254
    • (2006) Mass Spectrom. Rev , vol.25 , pp. 235-254
    • Hernandez, P.1    Muller, M.2    Appel, R.D.3
  • 2
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 4
    • 18744398125 scopus 로고    scopus 로고
    • Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book
    • Sadygov, R. G., Cociorva, D., and Yates, J. R. (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat. Methods 1, 195-202
    • (2004) Nat. Methods , vol.1 , pp. 195-202
    • Sadygov, R.G.1    Cociorva, D.2    Yates, J.R.3
  • 5
    • 34250885089 scopus 로고    scopus 로고
    • Complexity and scoring function of MS/MS peptide de novo sequencing
    • Xu, C., and Ma, B. (2006) Complexity and scoring function of MS/MS peptide de novo sequencing. Comput. Syst. Bioinformatics Conf. 2006, 5, 361-369
    • (2006) Comput. Syst. Bioinformatics Conf , vol.2006 , Issue.5 , pp. 361-369
    • Xu, C.1    Ma, B.2
  • 6
    • 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, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 7
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence data-bases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence data-bases using mass spectrometry data. Electrophoresis 20, 3551-3567
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 8
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: Towards high-throughput tandem mass spectrometry data identification
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T., and Magnin, J. (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463
    • (2003) Proteomics , vol.3 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 9
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 10
    • 24044468693 scopus 로고    scopus 로고
    • Valid data from large-scale proteomics studies
    • Chamrad, D., and Meyer, H. E. (2005) Valid data from large-scale proteomics studies. Nat. Methods 2, 647-648
    • (2005) Nat. Methods , vol.2 , pp. 647-648
    • Chamrad, D.1    Meyer, H.E.2
  • 11
    • 33750622611 scopus 로고    scopus 로고
    • Challenges and opportunities in proteomic data analysis
    • Domon, B., and Aebersold, R. (2006) Challenges and opportunities in proteomic data analysis. Mol. Cell. Proteomics 5, 1921-1926
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1921-1926
    • Domon, B.1    Aebersold, R.2
  • 12
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 13
    • 3042735127 scopus 로고    scopus 로고
    • The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data
    • Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol. Cell. Proteomics 3, 531-533
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 531-533
    • Carr, S.1    Aebersold, R.2    Baldwin, M.3    Burlingame, A.4    Clauser, K.5    Nesvizhskii, A.6
  • 14
    • 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, J. R. (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26
    • (2002) J. Proteome Res , vol.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2    Yates, J.R.3
  • 15
    • 14844360847 scopus 로고    scopus 로고
    • Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: The human proteome
    • Qian, W. J., Liu, T., Monroe, M. E., Strittmatter, E. F., Jacobs, J. M., Kangas, L. J., Petritis, K., Camp, D. G., and Smith, R. D. (2005) Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res. 4, 53-62
    • (2005) J. Proteome Res , vol.4 , pp. 53-62
    • Qian, W.J.1    Liu, T.2    Monroe, M.E.3    Strittmatter, E.F.4    Jacobs, J.M.5    Kangas, L.J.6    Petritis, K.7    Camp, D.G.8    Smith, R.D.9
  • 16
    • 12744280774 scopus 로고    scopus 로고
    • AMASS: Software for automatically validating the quality of MS/MS spectrum from SEQUEST results
    • Sun, W., Li, F., Wang, J., Zheng, D., and Gao, Y. (2004) AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results. Mol. Cell. Proteomics 3, 1194-1199
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1194-1199
    • Sun, W.1    Li, F.2    Wang, J.3    Zheng, D.4    Gao, Y.5
  • 17
    • 3142729873 scopus 로고    scopus 로고
    • RScore: A peptide randomicity score for evaluating tandem mass spectra
    • Li, F., Sun, W., Gao, Y., and Wang, J. (2004) RScore: a peptide randomicity score for evaluating tandem mass spectra. Rapid Commun. Mass Spectrom. 18, 1655-1659
    • (2004) Rapid Commun. Mass Spectrom , vol.18 , pp. 1655-1659
    • Li, F.1    Sun, W.2    Gao, Y.3    Wang, J.4
  • 18
    • 32544455331 scopus 로고    scopus 로고
    • Randomized sequence databases for tandem mass spectrometry peptide and protein identification
    • Higdon, R., Hogan, J. M., Van Belle, G., and Kolker, E. (2005) Randomized sequence databases for tandem mass spectrometry peptide and protein identification. OMICS 9, 364-379
    • (2005) OMICS , vol.9 , pp. 364-379
    • Higdon, R.1    Hogan, J.M.2    Van Belle, G.3    Kolker, E.4
  • 19
    • 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. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
    • (2007) Nat. Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 20
    • 38649125220 scopus 로고    scopus 로고
    • Semisupervised model-based validation of Peptide identifications in mass spectrometry-based proteomics
    • Choi, H., and Nesvizhskii, A. I. (2008) Semisupervised model-based validation of Peptide identifications in mass spectrometry-based proteomics. J. Proteome Res. 7, 254-265
    • (2008) J. Proteome Res , vol.7 , pp. 254-265
    • Choi, H.1    Nesvizhskii, A.I.2
  • 21
    • 38649083116 scopus 로고    scopus 로고
    • (200$) Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
    • Choi, H., Ghosh, D., and Nesvizhskii, A. I. (200$) Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteome Res. 7, 286-292
    • J. Proteome Res , vol.7 , pp. 286-292
    • Choi, H.1    Ghosh, D.2    Nesvizhskii, A.I.3
  • 22
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii, A., Roos, F. F., Grossmann, J., Vogelzang, M., Eddes, J. S., Gruissem, W., Baginsky, S., and Aebersold, R. (2006) Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol. Cell. Proteomics 5, 652-670
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4    Eddes, J.S.5    Gruissem, W.6    Baginsky, S.7    Aebersold, R.8
  • 23
    • 40749116092 scopus 로고    scopus 로고
    • A nonparametric model for quality control of database search results in shotgun proteomics
    • Jiyang, Z., Jianqi, L., Xin, L., Hongwei, X., Yunping, Z., and Fuchu, H. (2008) A nonparametric model for quality control of database search results in shotgun proteomics. BMC Bioinformatics 9, 29
    • (2008) BMC Bioinformatics , vol.9 , pp. 29
    • Jiyang, Z.1    Jianqi, L.2    Xin, L.3    Hongwei, X.4    Yunping, Z.5    Fuchu, H.6
  • 24
    • 1842681979 scopus 로고    scopus 로고
    • Standard mixtures for proteome studies
    • Purvine, S., Picone, A. F., and Kolker, E. (2004) Standard mixtures for proteome studies. OMICS 8, 79-92
    • (2004) OMICS , vol.8 , pp. 79-92
    • Purvine, S.1    Picone, A.F.2    Kolker, E.3
  • 25
    • 38649094868 scopus 로고    scopus 로고
    • The Standard Protein Mix Database: A diverse data set to assist in the production of improved peptide and protein identification software tools
    • Klimek, J., Eddes, J. S., Hohmann, L., Jackson, J., Peterson, A., Letarte, S., Gafken, P. R., Katz, J. E., Mallick., P., and Lee, H. (2008) The Standard Protein Mix Database: a diverse data set to assist in the production of improved peptide and protein identification software tools. J. Proteome Res. 7, 96-103
    • (2008) J. Proteome Res , vol.7 , pp. 96-103
    • Klimek, J.1    Eddes, J.S.2    Hohmann, L.3    Jackson, J.4    Peterson, A.5    Letarte, S.6    Gafken, P.R.7    Katz, J.E.8    Mallick, P.9    Lee, H.10
  • 30
    • 36549047947 scopus 로고    scopus 로고
    • A new strategy to filter out false positive identifications of peptides in SEQUEST database search results
    • Zhang, J., Li, J., Xie, H., Zhu, Y., and He, F. (2007) A new strategy to filter out false positive identifications of peptides in SEQUEST database search results. Proteomics 7, 4036-4044
    • (2007) Proteomics , vol.7 , pp. 4036-4044
    • Zhang, J.1    Li, J.2    Xie, H.3    Zhu, Y.4    He, F.5
  • 31
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 3908-3922
    • (2004) Anal. Chem , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 32
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A., Nesvizhskii, A., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
    • (2002) Anal. Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.2    Kolker, E.3    Aebersold, R.4
  • 33
    • 25144455555 scopus 로고    scopus 로고
    • Fully nonparametric probability density function estimation with finite gaussian mixture models
    • Calcutta, India, December 11-13, The International Association for Pattern Recognition
    • Archambeau, C., and Vedeysen, M. (2003) Fully nonparametric probability density function estimation with finite gaussian mixture models, in 5th International Conference on Advances in Pattern Recognition, Calcutta, India, December 11-13, 2003, pp. 81-84, The International Association for Pattern Recognition
    • (2003) 5th International Conference on Advances in Pattern Recognition , pp. 81-84
    • Archambeau, C.1    Vedeysen, M.2
  • 35
    • 34147173417 scopus 로고    scopus 로고
    • On the proper use of mass accuracy in proteomics
    • Zubarev, R., and Mann, M. (2007) On the proper use of mass accuracy in proteomics. Mol. Cell. Proteomics 6, 377-381
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 377-381
    • Zubarev, R.1    Mann, M.2
  • 36
    • 43849101253 scopus 로고    scopus 로고
    • Comparison of Mascot and XITandem performance for low and high accuracy mass spectrometry and the development of an adjusted mascot threshold
    • Brosch, M., Swamy, S., Hubbard, T., and Choudhary, J. (2008) Comparison of Mascot and XITandem performance for low and high accuracy mass spectrometry and the development of an adjusted mascot threshold. Mol. Cell. Proteomics 7, 962-970
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 962-970
    • Brosch, M.1    Swamy, S.2    Hubbard, T.3    Choudhary, J.4
  • 37
    • 23944451618 scopus 로고    scopus 로고
    • An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis
    • Kapp, E. A., Schutz, F., Connolly, L. M., Chakel, J. A., Meza, J. E., Miller, C. A., Fenyo, D., Eng, J. K., Adkins, J. N., and Omenn, G. S. (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 5, 3475-3490
    • (2005) Proteomics , vol.5 , pp. 3475-3490
    • Kapp, E.A.1    Schutz, F.2    Connolly, L.M.3    Chakel, J.A.4    Meza, J.E.5    Miller, C.A.6    Fenyo, D.7    Eng, J.K.8    Adkins, J.N.9    Omenn, G.S.10
  • 38
    • 20844457100 scopus 로고    scopus 로고
    • Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra
    • Chen, Y., Kwon, S. W., Kim, S. C., and Zhao, Y. (2005) Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J. Proteome Res. 4, 998-1005
    • (2005) J. Proteome Res , vol.4 , pp. 998-1005
    • Chen, Y.1    Kwon, S.W.2    Kim, S.C.3    Zhao, Y.4
  • 41
    • 33745839886 scopus 로고    scopus 로고
    • Retention prediction of peptides based on uninformative variable elimination by partial least squares
    • Put, R., Daszykowski, M., Baczek, T., and Vander Heyden, Y. (2006) Retention prediction of peptides based on uninformative variable elimination by partial least squares. J. Proteome Res. 5, 1618-1625
    • (2006) J. Proteome Res , vol.5 , pp. 1618-1625
    • Put, R.1    Daszykowski, M.2    Baczek, T.3    Vander Heyden, Y.4
  • 42
    • 0042972838 scopus 로고    scopus 로고
    • A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores
    • Anderson, D. C., Li, W., Payan, D. G., and Noble, W. S. (2003) A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2, 137-146
    • (2003) J. Proteome Res , vol.2 , pp. 137-146
    • Anderson, D.C.1    Li, W.2    Payan, D.G.3    Noble, W.S.4
  • 43
    • 2942577596 scopus 로고    scopus 로고
    • Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics
    • Baczek, T., Bucinski, A., Ivanov, A. R., and Kaliszan, R. (2004) Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics. Anal. Chem. 76, 1726-1732
    • (2004) Anal. Chem , vol.76 , pp. 1726-1732
    • Baczek, T.1    Bucinski, A.2    Ivanov, A.R.3    Kaliszan, R.4
  • 44
    • 13844307725 scopus 로고    scopus 로고
    • Prediction of high-performance liquid chromatography retention of peptides with the use of quantitative structure-retention relationships
    • Kaliszan, R., Baczek, T., Cimochowska, A., Juszczyk, P., Wiśniewska, K., and Grzonka, Z. (2005) Prediction of high-performance liquid chromatography retention of peptides with the use of quantitative structure-retention relationships. Proteomics 5, 409-415
    • (2005) Proteomics , vol.5 , pp. 409-415
    • Kaliszan, R.1    Baczek, T.2    Cimochowska, A.3    Juszczyk, P.4    Wiśniewska, K.5    Grzonka, Z.6
  • 45
    • 33645467062 scopus 로고    scopus 로고
    • Improved classification of mass spectrometry database search results using newer machine learning approaches
    • Ulintz, P. J., Zhu, J., Qin, Z. S., and Andrews, P. C. (2006) Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol. Cell. Proteomics 5, 497-509
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 497-509
    • Ulintz, P.J.1    Zhu, J.2    Qin, Z.S.3    Andrews, P.C.4
  • 46
    • 26844559371 scopus 로고    scopus 로고
    • Charge state estimation for tandem mass spectrometry proteomics
    • Hogan, J. M., Higdon, R., Kolker, N., and Kolker, E. (2005) Charge state estimation for tandem mass spectrometry proteomics. OMICS 9, 233-250
    • (2005) OMICS , vol.9 , pp. 233-250
    • Hogan, J.M.1    Higdon, R.2    Kolker, N.3    Kolker, E.4
  • 47
    • 20444459841 scopus 로고    scopus 로고
    • Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
    • Huang, Y., Triscari, J. M., Tseng, G. C., Pasa-Tolic, L., Lipton, M. S., Smith, R. D., and Wysocki, V. H. (2005) Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 77, 5800-5813
    • (2005) Anal. Chem , vol.77 , pp. 5800-5813
    • Huang, Y.1    Triscari, J.M.2    Tseng, G.C.3    Pasa-Tolic, L.4    Lipton, M.S.5    Smith, R.D.6    Wysocki, V.H.7
  • 50
    • 17644368549 scopus 로고    scopus 로고
    • The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry
    • Fridman, T., Razumovskaya, J., Verberkmoes, N., Hurst, G., Protopopescu, V., and Xu, Y. (2005) The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry. J. Bioinform. Comput. Biol. 3, 455-476
    • (2005) J. Bioinform. Comput. Biol , vol.3 , pp. 455-476
    • Fridman, T.1    Razumovskaya, J.2    Verberkmoes, N.3    Hurst, G.4    Protopopescu, V.5    Xu, Y.6
  • 51
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyö, D., and Beavis, R. C. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768-774
    • (2003) Anal. Chem , vol.75 , pp. 768-774
    • Fenyö, D.1    Beavis, R.C.2
  • 52
    • 4444249998 scopus 로고    scopus 로고
    • Matthiesen, R., Bunkenborg, J., Stensballe, A., Jensen, O. N., Welinder, K. G., and Bauw, G. (2004) Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics 4, 2583-2589
    • Matthiesen, R., Bunkenborg, J., Stensballe, A., Jensen, O. N., Welinder, K. G., and Bauw, G. (2004) Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics 4, 2583-2589


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