메뉴 건너뛰기




Volumn 80, Issue , 2013, Pages 123-131

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

Author keywords

Peptides; Shotgun proteomics; Statistics

Indexed keywords

PEPTIDE; PROTEOME;

EID: 84873695876     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.12.007     Document Type: Article
Times cited : (49)

References (37)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 84855269263 scopus 로고    scopus 로고
    • Computational mass spectrometry-based proteomics
    • Käll L., Vitek O. Computational mass spectrometry-based proteomics. PLoS Comput Biol 2011, 7:e1002277.
    • (2011) PLoS Comput Biol , vol.7
    • Käll, L.1    Vitek, O.2
  • 3
    • 84857476737 scopus 로고    scopus 로고
    • Computational and statistical analysis of protein mass spectrometry data
    • Noble W., MacCoss M. Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol 2012, 8:e1002296.
    • (2012) PLoS Comput Biol , vol.8
    • Noble, W.1    MacCoss, M.2
  • 4
    • 79952309062 scopus 로고    scopus 로고
    • Quality assessments of peptide-spectrum matches in shotgun proteomics
    • Granholm V., Käll L. Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 2011, 11:1086-1093.
    • (2011) Proteomics , vol.11 , pp. 1086-1093
    • Granholm, V.1    Käll, L.2
  • 5
    • 0000453490 scopus 로고
    • Statistical "discoveries" and effect-size estimation
    • Sorić B. Statistical "discoveries" and effect-size estimation. J Am Stat Assoc 1989, 84:608-610.
    • (1989) J Am Stat Assoc , vol.84 , pp. 608-610
    • Sorić, B.1
  • 6
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 1995, 57:289-300.
    • (1995) J R Stat Soc Ser B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey J., Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100:9440.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440
    • Storey, J.1    Tibshirani, R.2
  • 8
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: an algorithm for evaluating SEQUEST database search results
    • Moore R., Young M., Lee T. Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom 2002, 13:378-386.
    • (2002) J Am Soc Mass Spectrom , vol.13 , pp. 378-386
    • Moore, R.1    Young, M.2    Lee, T.3
  • 9
    • 77449146854 scopus 로고    scopus 로고
    • Target-decoy search strategy for mass spectrometry-based proteomics
    • Elias J., Gygi S. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol 2010, 604:55.
    • (2010) Methods Mol Biol , vol.604 , pp. 55
    • Elias, J.1    Gygi, S.2
  • 10
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyö D., Beavis R. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 2003, 75:768-774.
    • (2003) Anal Chem , vol.75 , pp. 768-774
    • Fenyö, D.1    Beavis, R.2
  • 11
    • 65249097774 scopus 로고    scopus 로고
    • Statistical calibration of the SEQUEST XCorr function
    • Klammer A., Park C., Noble W. Statistical calibration of the SEQUEST XCorr function. J Proteome Res 2009, 8:2106-2113.
    • (2009) J Proteome Res , vol.8 , pp. 2106-2113
    • Klammer, A.1    Park, C.2    Noble, W.3
  • 12
    • 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., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.2    Kolker, E.3    Aebersold, R.4
  • 13
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim S., Gupta N., Pevzner P. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 2008, 7:3354-3363.
    • (2008) J Proteome Res , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.3
  • 15
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii A., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003, 75:4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 16
    • 57449099865 scopus 로고    scopus 로고
    • Maxquant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
    • Cox J., Mann M. Maxquant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26:1367-1372.
    • (2008) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 17
    • 77957339566 scopus 로고    scopus 로고
    • Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
    • Serang O., MacCoss M., Noble W. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J Proteome Res 2010, 9:5346-5357.
    • (2010) J Proteome Res , vol.9 , pp. 5346-5357
    • Serang, O.1    MacCoss, M.2    Noble, W.3
  • 18
    • 72149093828 scopus 로고    scopus 로고
    • Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
    • Reiter L., Claassen M., Schrimpf S., Jovanovic M., Schmidt A., Buhmann J., et al. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics 2009, 8:2405.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2405
    • Reiter, L.1    Claassen, M.2    Schrimpf, S.3    Jovanovic, M.4    Schmidt, A.5    Buhmann, J.6
  • 19
    • 82755181926 scopus 로고    scopus 로고
    • Two-dimensional target decoy strategy for shotgun proteomics
    • Bern M., Kil Y. Two-dimensional target decoy strategy for shotgun proteomics. J Proteome Res 2011, 10:5296-5301.
    • (2011) J Proteome Res , vol.10 , pp. 5296-5301
    • Bern, M.1    Kil, Y.2
  • 20
    • 21044459357 scopus 로고    scopus 로고
    • A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results
    • Weatherly D., Atwood J., Minning T., Cavola C., Tarleton R., Orlando R. A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results. Mol Cell Proteomics 2005, 4:762.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 762
    • Weatherly, D.1    Atwood, J.2    Minning, T.3    Cavola, C.4    Tarleton, R.5    Orlando, R.6
  • 21
    • 35748972060 scopus 로고    scopus 로고
    • Semi-supervised learning for peptide identification from shotgun proteomics datasets
    • Käll L., Canterbury J., Weston J., Noble W., MacCoss M. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 4:923-925.
    • (2007) Nat Methods , vol.4 , pp. 923-925
    • Käll, L.1    Canterbury, J.2    Weston, J.3    Noble, W.4    MacCoss, M.5
  • 22
    • 51349096085 scopus 로고    scopus 로고
    • Improved ranking functions for protein and modification-site identifications
    • Bern M., Goldberg D. Improved ranking functions for protein and modification-site identifications. J Comput Biol 2008, 15:705-719.
    • (2008) J Comput Biol , vol.15 , pp. 705-719
    • Bern, M.1    Goldberg, D.2
  • 23
    • 80053387432 scopus 로고    scopus 로고
    • IProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    • Shteynberg D., Deutsch E., Lam H., Eng J., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011, 10.
    • (2011) Mol Cell Proteomics , vol.10
    • Shteynberg, D.1    Deutsch, E.2    Lam, H.3    Eng, J.4    Sun, Z.5    Tasman, N.6
  • 24
    • 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. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010, 73:2092-2123.
    • (2010) J Proteomics , vol.73 , pp. 2092-2123
    • Nesvizhskii, A.1
  • 25
    • 79955870431 scopus 로고    scopus 로고
    • On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics
    • Granholm V., Noble W., Käll L. On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics. J Proteome Res 2011, 10:2671-2678.
    • (2011) J Proteome Res , vol.10 , pp. 2671-2678
    • Granholm, V.1    Noble, W.2    Käll, L.3
  • 26
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • Käll L., Storey J., MacCoss M., Noble W. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7:29-34.
    • (2008) J Proteome Res , vol.7 , pp. 29-34
    • Käll, L.1    Storey, J.2    MacCoss, M.3    Noble, W.4
  • 28
  • 29
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey J. A direct approach to false discovery rates. J R Stat Soc Ser B (Stat Methodol) 2002, 64:479-498.
    • (2002) J R Stat Soc Ser B (Stat Methodol) , vol.64 , pp. 479-498
    • Storey, J.1
  • 30
    • 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., Hohmann L., Jackson J., Peterson A., Letarte S., et al. 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 2008, 7:96-103.
    • (2008) J Proteome Res , vol.7 , pp. 96-103
    • Klimek, J.1    Eddes, J.2    Hohmann, L.3    Jackson, J.4    Peterson, A.5    Letarte, S.6
  • 31
    • 34948874252 scopus 로고    scopus 로고
    • Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
    • Zhang B., Chambers M., Tabb D. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 2007, 6:3549-3557.
    • (2007) J Proteome Res , vol.6 , pp. 3549-3557
    • Zhang, B.1    Chambers, M.2    Tabb, D.3
  • 33
    • 46249114017 scopus 로고    scopus 로고
    • Rapid and accurate peptide identification from tandem mass spectra
    • Park C., Klammer A., Käll L., MacCoss M., Noble W. Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 2008, 7:3022-3027.
    • (2008) J Proteome Res , vol.7 , pp. 3022-3027
    • Park, C.1    Klammer, A.2    Käll, L.3    MacCoss, M.4    Noble, W.5
  • 34
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng J., McCormack A., Yates J. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.1    McCormack, A.2    Yates, J.3
  • 35
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu H., Sadygov R., Yates J. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
    • (2004) Anal Chem , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.2    Yates, J.3
  • 36
    • 12244270638 scopus 로고    scopus 로고
    • Differential proteomics via probabilistic peptide identification scores
    • Colinge J., Chiappe D., Lagache S., Moniatte M., Bougueleret L. Differential proteomics via probabilistic peptide identification scores. Anal Chem 2005, 77:596-606.
    • (2005) Anal Chem , vol.77 , pp. 596-606
    • Colinge, J.1    Chiappe, D.2    Lagache, S.3    Moniatte, M.4    Bougueleret, L.5
  • 37
    • 63549095080 scopus 로고    scopus 로고
    • Qvality: non-parametric estimation of q-values and posterior error probabilities
    • Käll L., Storey J., Noble W. Qvality: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics 2009, 25:964-966.
    • (2009) Bioinformatics , vol.25 , pp. 964-966
    • Käll, L.1    Storey, J.2    Noble, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.