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Volumn 7, Issue 6, 2008, Pages 1135-1145

Properties of average score distributions of SEQUEST: The probability ratio method

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL ERROR; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; MASS SPECTROMETRY; NONPARAMETRIC TEST; PEPTIDE ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROBABILITY; SCORING SYSTEM;

EID: 46749136858     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700239-MCP200     Document Type: Article
Times cited : (123)

References (35)
  • 1
    • 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., III (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 III, J.R.3
  • 2
    • 0029644596 scopus 로고
    • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
    • Yates, J. R., III, Eng, J. K., McCormack, A. L., and Schieltz, D. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436
    • (1995) Anal. Chem , vol.67 , pp. 1426-1436
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 3
    • 0029645432 scopus 로고
    • Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
    • Yates, J. R., III, Eng, J. K., and McCormack, A. L. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202-3210
    • (1995) Anal. Chem , vol.67 , pp. 3202-3210
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 5
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 19, 242-247
    • (2001) Nat Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 6
    • 0037277179 scopus 로고    scopus 로고
    • Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
    • Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50
    • (2003) J. Proteome Res , vol.2 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 8
    • 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., II, 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 II, D.G.8    Smith, R.D.9
  • 9
    • 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. I., 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.I.2    Kolker, E.3    Aebersold, R.4
  • 10
    • 0037953090 scopus 로고    scopus 로고
    • Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
    • Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., and Yates, J. R., III (2003) Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75, 2470-2477
    • (2003) Anal. Chem , vol.75 , pp. 2470-2477
    • Tabb, D.L.1    MacCoss, M.J.2    Wu, C.C.3    Anderson, S.D.4    Yates III, J.R.5
  • 11
    • 0043064042 scopus 로고    scopus 로고
    • A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
    • Sadygov, R. G., and Yates, J. R., III (2003) A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal. Chem. 75, 3792-3798
    • (2003) Anal. Chem , vol.75 , pp. 3792-3798
    • Sadygov, R.G.1    Yates III, J.R.2
  • 12
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: An algorithm for evaluating SEQUEST database search results
    • Moore, R. E., Young, M. K., and Lee, T. D. (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 13, 378-386
    • (2002) J. Am. Soc. Mass Spectrom , vol.13 , pp. 378-386
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 13
    • 0036828724 scopus 로고    scopus 로고
    • Probability-based validation of protein identifications using a modified SEQUEST algorithm
    • MacCoss, M. J., Wu, C. C., and Yates, J. R., III (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599
    • (2002) Anal. Chem , vol.74 , pp. 5593-5599
    • MacCoss, M.J.1    Wu, C.C.2    Yates III, J.R.3
  • 14
    • 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
  • 15
    • 1842423492 scopus 로고    scopus 로고
    • A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST
    • Razumovskaya, J., Olman, V., Xu, D., Uberbacher, E. C., VerBerkmoes, N. C., Hettich, R. L., and Xu, Y. (2004) A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics 4, 961-969
    • (2004) Proteomics , vol.4 , pp. 961-969
    • Razumovskaya, J.1    Olman, V.2    Xu, D.3    Uberbacher, E.C.4    VerBerkmoes, N.C.5    Hettich, R.L.6    Xu, Y.7
  • 17
    • 10044248655 scopus 로고    scopus 로고
    • Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST
    • Lopez-Ferrer, D., Martinez-Bartolome, S., Villar, M., Campillos, M., Martin-Maroto, F., and Vazquez, J. (2004) Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal. Chem. 76, 6853-6860
    • (2004) Anal. Chem , vol.76 , pp. 6853-6860
    • Lopez-Ferrer, D.1    Martinez-Bartolome, S.2    Villar, M.3    Campillos, M.4    Martin-Maroto, F.5    Vazquez, J.6
  • 18
    • 0035829361 scopus 로고    scopus 로고
    • Controlling the false discovery rate in behavior genetics research
    • Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav. Brain Res. 125, 279-284
    • (2001) Behav. Brain Res , vol.125 , pp. 279-284
    • Benjamini, Y.1    Drai, D.2    Elmer, G.3    Kafkafi, N.4    Golani, I.5
  • 19
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100, 9440-9445
    • (2003) Proc. Natl. Acad. Sci. U. S. A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 20
    • 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
  • 21
    • 0036211823 scopus 로고    scopus 로고
    • RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
    • Field, H. I., Fenyo, D., and Beavis, R. C. (2002) RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36-47
    • (2002) Proteomics , vol.2 , pp. 36-47
    • Field, H.I.1    Fenyo, D.2    Beavis, R.C.3
  • 22
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., and Gygi, S. P. (2004) Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219
    • (2004) Nat. Biotechnol , vol.22 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4    Gygi, S.P.5
  • 23
    • 0002451984 scopus 로고    scopus 로고
    • SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database
    • Bafna, V., and Edwards, N. (2001) SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 17, Suppl. 1, S13-S21
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Bafna, V.1    Edwards, N.2
  • 24
    • 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
  • 27
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyo, 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
    • Fenyo, D.1    Beavis, R.C.2
  • 29
    • 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
  • 30
    • 2542640024 scopus 로고    scopus 로고
    • Protein identification by mass spectrometry. Issues to be considered
    • Baldwin, M. A. (2004) Protein identification by mass spectrometry. Issues to be considered. Mol. Cell. Proteomics 3, 1-9
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1-9
    • Baldwin, M.A.1
  • 31
    • 0037171444 scopus 로고    scopus 로고
    • Prolactin is a component of the human synovial liquid and modulates the growth and chondrogenic differentiation of bone marrow-derived mesenchymal stem cells
    • Ogueta, S., Munoz, J., Obregon, E., Delgado-Baeza, E., and Garcia-Ruiz, J. P. (2002) Prolactin is a component of the human synovial liquid and modulates the growth and chondrogenic differentiation of bone marrow-derived mesenchymal stem cells. Mol. Cell. Endocrinol. 190, 51-63
    • (2002) Mol. Cell. Endocrinol , vol.190 , pp. 51-63
    • Ogueta, S.1    Munoz, J.2    Obregon, E.3    Delgado-Baeza, E.4    Garcia-Ruiz, J.P.5
  • 32
    • 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. I., 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.I.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4    Eddes, J.S.5    Gruissem, W.6    Baginsky, S.7    Aebersold, R.8
  • 33
    • 24744455665 scopus 로고    scopus 로고
    • Automatic quality assessment of peptide tandem mass spectra
    • Bern, M., Goldberg, D., McDonald, W. H., and Yates, J. R., III (2004) Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 20, Suppl. 1, i49-i54
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Bern, M.1    Goldberg, D.2    McDonald, W.H.3    Yates III, J.R.4
  • 35
    • 1542617945 scopus 로고    scopus 로고
    • Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases
    • Sadygov, R. G., Liu, H., and Yates, J. R. (2004) Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 76, 1664-1671
    • (2004) Anal. Chem , vol.76 , pp. 1664-1671
    • Sadygov, R.G.1    Liu, H.2    Yates, J.R.3


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