메뉴 건너뛰기




Volumn 8, Issue 10, 2009, Pages 2227-2242

Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT;

EID: 71049189969     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800462-MCP200     Document Type: Article
Times cited : (106)

References (46)
  • 3
    • 38649090064 scopus 로고    scopus 로고
    • False discovery rates and related statistical concepts in mass spectrometry-based proteomics
    • DOI 10.1021/pr700747q
    • Choi, H., and Nesvizhskii, A. I. (2008) False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J. Proteome Res. 7, 47-50 (Pubitemid 351171114)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 47-50
    • Choi, H.1    Nesvizhskii, A.I.2
  • 4
    • 38649129079 scopus 로고    scopus 로고
    • Posterior error probabilities and false discovery rates: Two sides of the same coin
    • DOI 10.1021/pr700739d
    • Käll, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. J. Proteome Res. 7, 40-44 (Pubitemid 351171112)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 40-44
    • Kall, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 5
    • 34548409217 scopus 로고    scopus 로고
    • Experimental and statistical considerations to avoid false conclusions in proteomic studies using differential in-gel electrophoresis
    • Karp, N. A., McCormick, P. S., Russell, M. R., and Lilley, K. S. (2007) Experimental and statistical considerations to avoid false conclusions in proteomic studies using differential in-gel electrophoresis. Mol. Cell. Proteomics 6, 1354-1364
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1354-1364
    • Karp, N.A.1    McCormick, P.S.2    Russell, M.R.3    Lilley, K.S.4
  • 7
    • 4544270574 scopus 로고    scopus 로고
    • DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results
    • Kreil, D. P., Karp, N. A., and Lilley, K. S. (2004) DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics 20, 2026-2034
    • (2004) Bioinformatics , vol.20 , pp. 2026-2034
    • Kreil, D.P.1    Karp, N.A.2    Lilley, K.S.3
  • 9
    • 26844492976 scopus 로고    scopus 로고
    • A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
    • Li, X. J., Yi, E. C., Kemp, C. J., Zhang, H., and Aebersold, R. (2005) A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 4, 1328-1340
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1328-1340
    • Li, X.J.1    Yi, E.C.2    Kemp, C.J.3    Zhang, H.4    Aebersold, R.5
  • 10
    • 11144260096 scopus 로고    scopus 로고
    • Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: Missing data, normalization, and statistics
    • DOI 10.1021/pr049886m
    • Chang, J., Van Remmen, H., Ward, W. F., Regnier, F. E., Richardson, A., and Cornell, J. (2004) Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics. J. Proteome Res. 3, 1210-1218 (Pubitemid 40040375)
    • (2004) Journal of Proteome Research , vol.3 , Issue.6 , pp. 1210-1218
    • Chang, J.1    Van Remmen, H.2    Ward, W.F.3    Regnier, F.E.4    Richardson, A.5    Cornell, J.6
  • 13
    • 3042562270 scopus 로고    scopus 로고
    • Genomics, prior probability, and statistical tests of multiple hypotheses
    • DOI 10.1101/gr.2156804
    • Manly, K. F., Nettleton, D., and Hwang, J. T. (2004) Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res. 14, 997-1001 (Pubitemid 38811535)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 997-1001
    • Manly, K.F.1    Nettleton, D.2    Gene Hwang, J.T.3
  • 14
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15
    • (2002) Nucleic Acids Res. , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 16
    • 33750092954 scopus 로고    scopus 로고
    • Statistical analysis of the experimental variation in the proteomic characterization of human plasma by two-dimensional difference gel electrophoresis
    • DOI 10.1021/pr060100p
    • Corzett, T. H., Fodor, I. K., Choi, M. W., Walsworth, V. L., Chromy, B. A., Turteltaub, K. W., and McCutchen-Maloney, S. L. (2006) Statistical analysis of the experimental variation in the proteomic characterization of human plasma by two-dimensional difference gel electrophoresis. J. Proteome Res. 5, 2611-2619 (Pubitemid 44595163)
    • (2006) Journal of Proteome Research , vol.5 , Issue.10 , pp. 2611-2619
    • Corzett, T.H.1    Fodor, I.K.2    Choi, M.W.3    Walsworth, V.L.4    Chromy, B.A.5    Turteltaub, K.W.6    McCutchen-Maloney, S.L.7
  • 17
    • 17444386712 scopus 로고    scopus 로고
    • Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis
    • Meunier, B., Bouley, J., Piec, I., Bernard, C., Picard, B., and Hocquette, J. F. (2005) Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis. Anal. Biochem. 340, 226-230
    • (2005) Anal. Biochem. , vol.340 , pp. 226-230
    • Meunier, B.1    Bouley, J.2    Piec, I.3    Bernard, C.4    Picard, B.5    Hocquette, J.F.6
  • 18
    • 13244258397 scopus 로고    scopus 로고
    • Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics
    • Karp, N. A., Griffin, J. L., and Lilley, K. S. (2005) Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics. Proteomics 5, 81-90
    • (2005) Proteomics , vol.5 , pp. 81-90
    • Karp, N.A.1    Griffin, J.L.2    Lilley, K.S.3
  • 20
    • 17844394177 scopus 로고    scopus 로고
    • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
    • Listgarten, J., and Emili, A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419-434
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 21
    • 38149060091 scopus 로고    scopus 로고
    • Proteomic profiling using mass spectrometry - Does normalising by total ion current potentially mask some biological differences?
    • Cairns, D. A., Thompson, D., Perkins, D. N., Stanley, A. J., Selby, P. J., and Banks, R. E. (2008) Proteomic profiling using mass spectrometry - does normalising by total ion current potentially mask some biological differences? Proteomics 8, 21-27
    • (2008) Proteomics , vol.8 , pp. 21-27
    • Cairns, D.A.1    Thompson, D.2    Perkins, D.N.3    Stanley, A.J.4    Selby, P.J.5    Banks, R.E.6
  • 22
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex mixtures from tandem mass spectra
    • Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., and Yates, J. R. (2004) Automated approach for quantitative analysis of complex mixtures from tandem mass spectra. Nat. Methods 1, 39-45
    • (2004) Nat. Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 23
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide studies
    • Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genome-wide 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
  • 24
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
    • Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 25
    • 33750620682 scopus 로고    scopus 로고
    • Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: Non-label methods comparison, q-values and LOWESS curve fitting
    • Xia, Q., Wang, T., Park, Y., Lamont, R. J., and Hackett, M. (2007) Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: non-label methods comparison, q-values and LOWESS curve fitting. Int. J. Mass Spectrom. 259, 105-116
    • (2007) Int. J. Mass Spectrom. , vol.259 , pp. 105-116
    • Xia, Q.1    Wang, T.2    Park, Y.3    Lamont, R.J.4    Hackett, M.5
  • 27
    • 0031734090 scopus 로고    scopus 로고
    • Implication of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256
    • Fegatella, F., Lim, J., Kjelleberg, S., and Cavicchioli, R. (1998) Implication of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 64, 4433-4438
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4433-4438
    • Fegatella, F.1    Lim, J.2    Kjelleberg, S.3    Cavicchioli, R.4
  • 28
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254
    • (1976) Anal. Biochem. , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 29
    • 0000094597 scopus 로고
    • Microcomputer-assisted biomass determination of plankton bacteria on scanning electron micrographs
    • Krambeck, C., Krambeck, H. J., and Overbeck, J. (1981) Microcomputer-assisted biomass determination of plankton bacteria on scanning electron micrographs. Appl. Environ. Microbiol. 42, 142-149
    • (1981) Appl. Environ. Microbiol. , vol.42 , pp. 142-149
    • Krambeck, C.1    Krambeck, H.J.2    Overbeck, J.3
  • 30
    • 0032767720 scopus 로고    scopus 로고
    • An assessment of protein profiles from the marine oligotraphic ultramicrobacterium, Sphingomonas sp. strain RB2256
    • Fegatella, F., Ostrowski, M., and Cavicchioli, R. (1999) An assessment of protein profiles from the marine oligotraphic ultramicrobacterium, Sphingomonas sp. strain RB2256. Electrophoresis 20, 2094-2098
    • (1999) Electrophoresis , vol.20 , pp. 2094-2098
    • Fegatella, F.1    Ostrowski, M.2    Cavicchioli, R.3
  • 31
    • 0029927505 scopus 로고    scopus 로고
    • Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels
    • Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858
    • (1996) Anal. Chem. , vol.68 , pp. 850-858
    • Shevchenko, A.1    Wilm, M.2    Vorm, O.3    Mann, M.4
  • 33
    • 0032190378 scopus 로고    scopus 로고
    • Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography- microspray and nanospray mass spectrometry
    • Gatlin, C. L., Kleemann, G. R., Hays, L. G., Link, A. J., and Yates, J. R., 3rd (1998) Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem. 263, 93-101
    • (1998) Anal. Biochem. , vol.263 , pp. 93-101
    • Gatlin, C.L.1    Kleemann, G.R.2    Hays, L.G.3    Link, A.J.4    Yates III, J.R.5
  • 34
    • 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., 3rd (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 III, J.R.3
  • 35
    • 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
    • DOI 10.1021/pr025556v
    • 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 (Pubitemid 36207189)
    • (2003) Journal of Proteome Research , vol.2 , Issue.1 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 36
    • 0346122950 scopus 로고    scopus 로고
    • A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
    • MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., and Yates, J. R., 3rd (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75, 6912-6921
    • (2003) Anal. Chem. , vol.75 , pp. 6912-6921
    • MacCoss, M.J.1    Wu, C.C.2    Liu, H.3    Sadygov, R.4    Yates III, J.R.5
  • 37
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka, R., and Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299-314
    • (1996) J. Comput. Graph. Stat. , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 39
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Article3
    • Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Star. Appl. Genet. Mol. Biol. 3, Article3
    • (2004) Star. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 40
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. P. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sin. 12, 111-139
    • (2002) Stat. Sin. , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 41
    • 0023904423 scopus 로고
    • Light scattering and cell volumes in osmotically stressed and frozen-thawed cells
    • McGann, L. E., Walterson, M. L., and Hogg, L. M. (1988) Light scattering and cell volumes in osmotically stressed and frozen-thawed cells. Cytometry 9, 33-38
    • (1988) Cytometry , vol.9 , pp. 33-38
    • McGann, L.E.1    Walterson, M.L.2    Hogg, L.M.3
  • 43
    • 0036012343 scopus 로고    scopus 로고
    • Replicated microarray data
    • Lonnstedt, I., and Speed, T. P. (2002) Replicated microarray data. Stat. Sin. 12, 31-46
    • (2002) Stat. Sin. , vol.12 , pp. 31-46
    • Lonnstedt, I.1    Speed, T.P.2
  • 44
    • 33947172745 scopus 로고    scopus 로고
    • Identification of differentially expressed genes and false discovery rate in microarray studies
    • Gusnanto, A., Calza, S., and Pawitan, Y. (2007) Identification of differentially expressed genes and false discovery rate in microarray studies. Curr. Opin. Lipidol. 18, 187-193
    • (2007) Curr. Opin. Lipidol. , vol.18 , pp. 187-193
    • Gusnanto, A.1    Calza, S.2    Pawitan, Y.3
  • 45
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. A 57, 289-300
    • (1995) J. R. Stat. Soc. Ser. A , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.