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Volumn 6, Issue 10, 2007, Pages 4019-4024

YPED: A web-accessible database system for protein expression analysis

Author keywords

DIGE; ICAT; iTRAQ; Mass spectrometry; MudPIT; Protein expression database; Proteomics

Indexed keywords

PHOSPHOPROTEIN; TRYPSIN;

EID: 35649019880     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070325f     Document Type: Article
Times cited : (31)

References (35)
  • 1
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Brown, P. O.; Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 1999, 21(1 Suppl), 33-37.
    • (1999) Nat. Genet , vol.21 , Issue.1 SUPPL. , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 2
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422(6928), 198-207.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 3
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon, B.; Aebersold, R. Mass spectrometry and protein analysis. Science 2006, 312(5771), 212-217.
    • (2006) Science , vol.312 , Issue.5771 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 4
    • 35648989233 scopus 로고    scopus 로고
    • Wilkins, M. R.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F., Eds. Proteome research : new frontiers in functional genomics. Springer: Berlin ; New York, 1997; p xviii, 243 p.
    • Wilkins, M. R.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F., Eds. Proteome research : new frontiers in functional genomics. Springer: Berlin ; New York, 1997; p xviii, 243 p.
  • 6
    • 0035106351 scopus 로고    scopus 로고
    • Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19(3), 242-247.
    • Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19(3), 242-247.
  • 7
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17(10), 994-999.
    • (1999) Nat. Biotechnol , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 8
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1(5), 376-386.
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 9
    • 33847174067 scopus 로고    scopus 로고
    • Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research
    • Wiese, S.; Reidegeld, K. A.; Meyer, H. E.; Warscheid, B. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007, 7(3), 340-350.
    • (2007) Proteomics , vol.7 , Issue.3 , pp. 340-350
    • Wiese, S.1    Reidegeld, K.A.2    Meyer, H.E.3    Warscheid, B.4
  • 10
    • 0037434977 scopus 로고    scopus 로고
    • Biomedical informatics for proteomics
    • Boguski, M. S.; McIntosh, M. W. Biomedical informatics for proteomics. Nature 2003, 422(6928), 233-237.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 233-237
    • Boguski, M.S.1    McIntosh, M.W.2
  • 12
    • 9144233086 scopus 로고    scopus 로고
    • Garwood, K.; McLaughlin, T.; Garwood, C.; Joens, S.; Morrison, N.; Taylor, C. F.; Carroll, K.; Evans, C.; Whetton, A. D.; Hart, S.; Stead, D.; Yin, Z.; Brown, A. J.; Hesketh, A.; Chater, K.; Hansson, L.; Mewissen, M.; Ghazal, P.; Howard, J.; Lilley, K. S.; Gaskell, S. J.; Brass, A.; Hubbard, S. J.; Oliver, S. G.; Paton, N. W. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004, 5(1), 68.
    • Garwood, K.; McLaughlin, T.; Garwood, C.; Joens, S.; Morrison, N.; Taylor, C. F.; Carroll, K.; Evans, C.; Whetton, A. D.; Hart, S.; Stead, D.; Yin, Z.; Brown, A. J.; Hesketh, A.; Chater, K.; Hansson, L.; Mewissen, M.; Ghazal, P.; Howard, J.; Lilley, K. S.; Gaskell, S. J.; Brass, A.; Hubbard, S. J.; Oliver, S. G.; Paton, N. W. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004, 5(1), 68.
  • 13
    • 33947434519 scopus 로고    scopus 로고
    • Automated reporting from gel-based proteomics experiments using the open source Proteios database application
    • Levander, F.; Krogh, M.; Warell, K.; Garden, P.; James, P.; Hakkinen, J. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 2007, 7(5), 668-674.
    • (2007) Proteomics , vol.7 , Issue.5 , pp. 668-674
    • Levander, F.1    Krogh, M.2    Warell, K.3    Garden, P.4    James, P.5    Hakkinen, J.6
  • 14
    • 30744438115 scopus 로고    scopus 로고
    • Rauch, A.; Bellew, M.; Eng, J.; Fitzgibbon, M.; Holzman, T.; Hussey, P.; Igra, M.; Maclean, B.; Lin, C. W.; Detter, A.; Fang, R.; Faca, V.; Gafken, P.; Zhang, H.; Whiteaker, J.; States, D.; Hanash, S.; Paulovich, A.; McIntosh, M. W. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 2006, 5(1), 112-121.
    • Rauch, A.; Bellew, M.; Eng, J.; Fitzgibbon, M.; Holzman, T.; Hussey, P.; Igra, M.; Maclean, B.; Lin, C. W.; Detter, A.; Fang, R.; Faca, V.; Gafken, P.; Zhang, H.; Whiteaker, J.; States, D.; Hanash, S.; Paulovich, A.; McIntosh, M. W. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 2006, 5(1), 112-121.
  • 15
    • 33644875983 scopus 로고    scopus 로고
    • Jones, P.; Cote, R. G.; Martens, L.; Quinn, A. F.; Taylor, C. F.; Derache, W.; Hermjakob, H.; Apweiler, R. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 2006, 34(Database issue), D659-D663.
    • Jones, P.; Cote, R. G.; Martens, L.; Quinn, A. F.; Taylor, C. F.; Derache, W.; Hermjakob, H.; Apweiler, R. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 2006, 34(Database issue), D659-D663.
  • 17
    • 0029983427 scopus 로고    scopus 로고
    • Federated two-dimensional electrophoresis database: A simple means of publishing two-dimensional electrophoresis data
    • Appel, R. D.; Bairoch, A.; Sanchez, J. C.; Vargas, J. R.; Golaz, O.; Pasquali, C.; Hochstrasser, D. F. Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data. Electrophoresis 1996, 17(3), 540-546.
    • (1996) Electrophoresis , vol.17 , Issue.3 , pp. 540-546
    • Appel, R.D.1    Bairoch, A.2    Sanchez, J.C.3    Vargas, J.R.4    Golaz, O.5    Pasquali, C.6    Hochstrasser, D.F.7
  • 19
    • 33750345305 scopus 로고    scopus 로고
    • Minimum Reporting Requirements for Proteomics: A MIAPE Primer
    • Taylor, C. F. Minimum Reporting Requirements for Proteomics: A MIAPE Primer. Proteomics 2006, 6 Suppl 2, 39-44.
    • (2006) Proteomics , vol.6 , Issue.SUPPL. 2 , pp. 39-44
    • Taylor, C.F.1
  • 20
    • 35649007561 scopus 로고    scopus 로고
    • NCBI Taxonomy web page. http://www.ncbi.nlm.nih.gov/Taxonomy/ taxonomyhome.html.
    • NCBI Taxonomy web page
  • 22
    • 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.; Yates, J. R., III. 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(11), 976-989.
    • (1994) J. Am. Soc. Mass Spectrom , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 23
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18), 3551-3567.
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 24
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9), 1466-1467.
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 25
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean, B.; Eng, J. K.; Beavis, R. C.; McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 2006, 22(22), 2830-2832.
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2830-2832
    • MacLean, B.1    Eng, J.K.2    Beavis, R.C.3    McIntosh, M.4
  • 26
    • 33746930864 scopus 로고    scopus 로고
    • Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst Biol 2005, 1, 2005 0017.
    • Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst Biol 2005, 1, 2005 0017.
  • 27
    • 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.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74(20), 5383-5392.
    • (2002) Anal. Chem , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 28
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75(17), 4646-4658.
    • (2003) Anal. Chem , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 29
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotopecoded affinity tags and mass spectrometry
    • Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotopecoded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19(10), 946-951.
    • (2001) Nat. Biotechnol , vol.19 , Issue.10 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 30
    • 0344737959 scopus 로고    scopus 로고
    • Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
    • Li, X. J.; Zhang, H.; Ranish, J. A.; Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 2003, 75(23), 6648-6657.
    • (2003) Anal. Chem , vol.75 , Issue.23 , pp. 6648-6657
    • Li, X.J.1    Zhang, H.2    Ranish, J.A.3    Aebersold, R.4
  • 33
    • 33745686436 scopus 로고    scopus 로고
    • Probabilistic enrichment of phosphopeptides by their mass defect
    • Bruce, C.; Shifman, M. A.; Miller, P.; Gulcicek, E. E. Probabilistic enrichment of phosphopeptides by their mass defect. Anal. Chem. 2006, 78(13), 4374-4382.
    • (2006) Anal. Chem , vol.78 , Issue.13 , pp. 4374-4382
    • Bruce, C.1    Shifman, M.A.2    Miller, P.3    Gulcicek, E.E.4
  • 34
    • 35648944991 scopus 로고    scopus 로고
    • Libra web page. http://tools.proteomecenter.org/Libra.php.
    • Libra web page


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.