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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. 17:1999;994-999.
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Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
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Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA. 97:2000;9390-9395.
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This is a good example of multidimensional peptide chromatography based on physico-chemical properties to profile a human subproteome from blood serum.
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Adkins J.N., Varnum S.M., Auberry K.J., Moore R.J., Angell N.H., Smith R.D., Springer D.L., Pounds J.G. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics. 1:2002;947-955 This is a good example of multidimensional peptide chromatography based on physico-chemical properties to profile a human subproteome from blood serum.
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Mol Cell Proteomics
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Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags
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This paper describes classification of the proteome using multidimensional chromatography using ICAT-based quantification.
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Gygi S.P., Rist B., Griffin T.J., Eng J., Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res. 1:2002;47-54 This paper describes classification of the proteome using multidimensional chromatography using ICAT-based quantification.
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J Proteome Res
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Gygi, S.P.1
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Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
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Han D.K., Eng J., Zhou H., Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol. 19:2001;946-951.
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Nat Biotechnol
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Han, D.K.1
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Li J., Steen H., Gygi S.P. Protein profiling with cleavable isotope coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol Cell Proteomics. 2:2003;1198-1204.
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Mol Cell Proteomics
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Proteomics
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This paper describes identification of a functional protein complex using tandem affinity tags and MS to build up a protein interaction network.
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Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147 This paper describes identification of a functional protein complex using tandem affinity tags and MS to build up a protein interaction network.
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Gavin, A.C.1
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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
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This paper reports another example of profiling protein complexes.
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Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:2002;180-183 This paper reports another example of profiling protein complexes.
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Nature
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Ho, Y.1
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This is a good example of proteomic analysis on cellular machinery.
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Rappsilber J., Ryder U., Lamond A.I., Mann M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12:2002;1231-1245 This is a good example of proteomic analysis on cellular machinery.
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Genome Res
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Rappsilber, J.1
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Comprehensive proteomic analysis of the human spliceosome
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This paper provides an example of a subproteome study on the human spliceosome complex.
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Zhou Z., Licklider L.J., Gygi S.P., Reed R. Comprehensive proteomic analysis of the human spliceosome. Nature. 419:2002;182-185 This paper provides an example of a subproteome study on the human spliceosome complex.
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Nature
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Zhou, Z.1
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Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 148:2000;635-651.
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Directed proteomic analysis of the human nucleolus
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This paper gives an example of MS analysis on a subcellular fraction.
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Andersen J.S., Lyon C.E., Fox A.H., Leung A.K., Lam Y.W., Steen H., Mann M., Lamond A.I. Directed proteomic analysis of the human nucleolus. Curr Biol. 12:2002;1-11 This paper gives an example of MS analysis on a subcellular fraction.
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Curr Biol
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Andersen, J.S.1
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Approaching complete peroxisome characterization by gas-phase fractionation
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This paper describes improved coverage of peroxisome profiling using a gas phase fractionation technique.
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Yi E.C., Marelli M., Lee H., Purvine S.O., Aebersold R., Aitchison J.D., Goodlett D.R. Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis. 23:2002;3205-3216 This paper describes improved coverage of peroxisome profiling using a gas phase fractionation technique.
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Electrophoresis
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Yi, E.C.1
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A method for the comprehensive proteomic analysis of membrane proteins
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This paper discusses technological development on proteomic analysis, particularly on membrane proteins.
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Wu C.C., MacCoss M.J., Howell K.E., Yates J.R. A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol. 21:2003;532-538 This paper discusses technological development on proteomic analysis, particularly on membrane proteins.
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Nat Biotechnol
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Wu, C.C.1
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Bergquist J., Gobom J., Blomberg A., Roepstorff P., Ekman R. Identification of nuclei associated proteins by 2D-gel electrophoresis and mass spectrometry. J Neurosci Methods. 109:2001;3-11.
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J Neurosci Methods
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The study of macromolecular complexes by quantitative proteomics
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This is a good example of identification of functional protein complexes and discrimination of real components of a complex from contaminant proteins using quantitative proteomics.
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Ranish J.A., Yi E.C., Leslie D.M., Purvine S.O., Goodlett D.R., Eng J., Aebersold R. The study of macromolecular complexes by quantitative proteomics. Nat Genet. 33:2003;349-355 This is a good example of identification of functional protein complexes and discrimination of real components of a complex from contaminant proteins using quantitative proteomics.
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Nat Genet
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Ranish, J.A.1
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Aebersold, R.7
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Quantitative proteomic analysis of chromatin-associated factors
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Shiio Y., Eisenman R.N., Yi E.C., Donohoe S., Goodlett D.R., Aebersold R. Quantitative proteomic analysis of chromatin-associated factors. J Am Soc Mass Spectrom. 14:2003;696-703.
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J Am Soc Mass Spectrom
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Shiio, Y.1
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Yi, E.C.3
Donohoe, S.4
Goodlett, D.R.5
Aebersold, R.6
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27
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0037337310
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A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
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This paper reports another MS-based approach to identify protein complexes from background binding using quantitative proteomics by differentially label proteins in EGF-stimulated versus unstimulated cells using stable isotopic amino acids in cell culture (SILAC).
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Blagoev B., Kratchmarova I., Ong S.E., Nielsen M., Foster L.J., Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol. 21:2003;315-318 This paper reports another MS-based approach to identify protein complexes from background binding using quantitative proteomics by differentially label proteins in EGF-stimulated versus unstimulated cells using stable isotopic amino acids in cell culture (SILAC).
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Nat Biotechnol
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Blagoev, B.1
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Mass spectrometry-based proteomics
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Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature. 422:2003;198-207.
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Nature
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Tyers M., Mann M. From genomics to proteomics. Nature. 422:2003;193-197.
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Nature
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Sechi S., Oda Y. Quantitative proteomics using mass spectrometry. Curr Opin Chem Biol. 7:2003;70-77.
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Curr Opin Chem Biol
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Shotgun identification of protein modifications from protein complexes and lens tissue
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This paper reports on proteomics analysis of a complex protein mixture and post-translational modification.
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MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A. et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA. 99:2002;7900-7905 This paper reports on proteomics analysis of a complex protein mixture and post-translational modification.
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Proc Natl Acad Sci USA
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MacCoss, M.J.1
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Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
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This paper describes a method to enrich N-terminal peptides using the diagonal chromatography approach.
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Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol. 21:2003;566-569 This paper describes a method to enrich N-terminal peptides using the diagonal chromatography approach.
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Nat Biotechnol
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Simplification of complex peptide mixtures for proteomic analysis: Reversible biotinylation of cysteinyl peptides
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Spahr C.S., Susin S.A., Bures E.J., Robinson J.H., Davis M.T., McGinley M.D., Kroemer G., Patterson S.D. Simplification of complex peptide mixtures for proteomic analysis: reversible biotinylation of cysteinyl peptides. Electrophoresis. 21:2000;1635-1650.
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Electrophoresis
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A solid-phase-based stable isotope tagging method is discussed.
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Zhou H., Ranish J.A., Watts J.D., Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol. 20:2002;512-515 A solid-phase-based stable isotope tagging method is discussed.
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Nat Biotechnol
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Zhou, H.1
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Quantitative chemical proteomics for identifying candidate drug targets
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Oda Y., Owa T., Sato T., Boucher B., Daniels S., Yamanaka H., Shinohara Y., Yokoi A., Kuromitsu J., Nagasu T. Quantitative chemical proteomics for identifying candidate drug targets. Anal Chem. 75:2003;2159-2165.
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Anal Chem
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Quantitative proteomic analysis of Myc oncoprotein function
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Shiio Y., Donohoe S., Yi E.C., Goodlett D.R., Aebersold R., Eisenman R.N. Quantitative proteomic analysis of Myc oncoprotein function. EMBO J. 21:2002;5088-5096.
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EMBO J
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The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation
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Von Haller P.D., Yi E., Donohoe S., Vaughn K., Keller A., Nesvizhskii A.I., Eng J., Li X.J., Goodlett D.R., Aebersold R. et al. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Mol Cell Proteomics. 2:2003;428-442.
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Mol Cell Proteomics
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Eng, J.7
Li, X.J.8
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Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
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Baliga N.S., Pan M., Goo Y.A., Yi E.C., Goodlett D.R., Dimitrov K., Shannon P., Aebersold R., Ng W.V., Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci USA. 99:2002;14913-14918.
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Proc Natl Acad Sci USA
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Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways
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This is a good example of the application of quantitative proteomics using ICAT reagents to address biological questions.
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Guina T., Purvine S.O., Yi E.C., Eng J., Goodlett D.R., Aebersold R., Miller S.I. Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc Natl Acad Sci USA. 100:2003;2771-2776 This is a good example of the application of quantitative proteomics using ICAT reagents to address biological questions.
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Proc Natl Acad Sci USA
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Guina, T.1
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Aebersold, R.6
Miller, S.I.7
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Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
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Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:2001;929-934.
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