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Volumn 8, Issue 1, 2004, Pages 66-75

Chemical probes and tandem mass spectrometry: A strategy for the quantitative analysis of proteomes and subproteomes

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYSTEINE; GLYCOPEPTIDE; HISTIDINE; ISOTOPE; LECTIN; METHIONINE; NITROGEN; PEPTIDE; PROTEOME; TRYPTOPHAN;

EID: 1042275609     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2003.12.001     Document Type: Review
Times cited : (135)

References (76)
  • 1
    • 0033904796 scopus 로고    scopus 로고
    • Proteomics: The industrialization of protein chemistry
    • Patterson S.D. Proteomics: the industrialization of protein chemistry. Curr Opin Biotechnol. 11:2000;413-418.
    • (2000) Curr Opin Biotechnol , vol.11 , pp. 413-418
    • Patterson, S.D.1
  • 2
    • 0033535961 scopus 로고    scopus 로고
    • Accurate quantitation of protein expression and site-specific phosphorylation
    • Oda Y., Huang K., Cross F.R., Cowburn D., Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA. 96:1999;6591-6596.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 6591-6596
    • Oda, Y.1    Huang, K.2    Cross, F.R.3    Cowburn, D.4    Chait, B.T.5
  • 5
    • 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. 17:1999;994-999.
    • (1999) Nat Biotechnol , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 6
    • 0035582244 scopus 로고    scopus 로고
    • An automated multidimensional protein identification technology for shotgun proteomics
    • Wolters D.A., Washburn M.P., Yates J.R. III An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem. 73:2001;5683-5690.
    • (2001) Anal Chem , vol.73 , pp. 5683-5690
    • Wolters, D.A.1    Washburn, M.P.2    Yates III, J.R.3
  • 7
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn M.P., Wolters D., Yates J.R. III Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 19:2001;242-247.
    • (2001) Nat Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 8
    • 0034662907 scopus 로고    scopus 로고
    • Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
    • 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.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 9390-9395
    • Gygi, S.P.1    Corthals, G.L.2    Zhang, Y.3    Rochon, Y.4    Aebersold, R.5
  • 9
    • 0003206867 scopus 로고    scopus 로고
    • Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry
    • This is a good example of multidimensional peptide chromatography based on physico-chemical properties to profile a human subproteome from blood serum.
    • 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.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 947-955
    • Adkins, J.N.1    Varnum, S.M.2    Auberry, K.J.3    Moore, R.J.4    Angell, N.H.5    Smith, R.D.6    Springer, D.L.7    Pounds, J.G.8
  • 10
    • 0036391454 scopus 로고    scopus 로고
    • Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags
    • This paper describes classification of the proteome using multidimensional chromatography using ICAT-based quantification.
    • 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.
    • (2002) J Proteome Res , vol.1 , pp. 47-54
    • Gygi, S.P.1    Rist, B.2    Griffin, T.J.3    Eng, J.4    Aebersold, R.5
  • 11
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • 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.
    • (2001) Nat Biotechnol , vol.19 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 12
    • 1042284932 scopus 로고    scopus 로고
    • Protein profiling with cleavable isotope coded affinity tag (cICAT) reagents: The yeast salinity stress response
    • 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.
    • (2003) Mol Cell Proteomics , vol.2 , pp. 1198-1204
    • Li, J.1    Steen, H.2    Gygi, S.P.3
  • 14
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 17:1999;1030-1032.
    • (1999) Nat Biotechnol , vol.17 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 15
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • This paper describes identification of a functional protein complex using tandem affinity tags and MS to build up a protein interaction network.
    • 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.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6    Schultz, J.7    Rick, J.M.8    Michon, A.M.9    Cruciat, C.M.10
  • 16
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • This paper reports another example of profiling protein complexes.
    • 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.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5    Adams, S.L.6    Millar, A.7    Taylor, P.8    Bennett, K.9    Boutilier, K.10
  • 17
    • 0036674269 scopus 로고    scopus 로고
    • Large-scale proteomic analysis of the human spliceosome
    • This is a good example of proteomic analysis on cellular machinery.
    • 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.
    • (2002) Genome Res , vol.12 , pp. 1231-1245
    • Rappsilber, J.1    Ryder, U.2    Lamond, A.I.3    Mann, M.4
  • 18
    • 0037068447 scopus 로고    scopus 로고
    • Comprehensive proteomic analysis of the human spliceosome
    • This paper provides an example of a subproteome study on the human spliceosome complex.
    • 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.
    • (2002) Nature , vol.419 , pp. 182-185
    • Zhou, Z.1    Licklider, L.J.2    Gygi, S.P.3    Reed, R.4
  • 19
    • 0034695924 scopus 로고    scopus 로고
    • The yeast nuclear pore complex: Composition, architecture, and transport mechanism
    • 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.
    • (2000) J Cell Biol , vol.148 , pp. 635-651
    • Rout, M.P.1    Aitchison, J.D.2    Suprapto, A.3    Hjertaas, K.4    Zhao, Y.5    Chait, B.T.6
  • 20
    • 0037039159 scopus 로고    scopus 로고
    • Directed proteomic analysis of the human nucleolus
    • This paper gives an example of MS analysis on a subcellular fraction.
    • 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.
    • (2002) Curr Biol , vol.12 , pp. 1-11
    • Andersen, J.S.1    Lyon, C.E.2    Fox, A.H.3    Leung, A.K.4    Lam, Y.W.5    Steen, H.6    Mann, M.7    Lamond, A.I.8
  • 22
    • 0036747350 scopus 로고    scopus 로고
    • Approaching complete peroxisome characterization by gas-phase fractionation
    • This paper describes improved coverage of peroxisome profiling using a gas phase fractionation technique.
    • 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.
    • (2002) Electrophoresis , vol.23 , pp. 3205-3216
    • Yi, E.C.1    Marelli, M.2    Lee, H.3    Purvine, S.O.4    Aebersold, R.5    Aitchison, J.D.6    Goodlett, D.R.7
  • 23
    • 0038561131 scopus 로고    scopus 로고
    • A method for the comprehensive proteomic analysis of membrane proteins
    • This paper discusses technological development on proteomic analysis, particularly on membrane proteins.
    • 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.
    • (2003) Nat Biotechnol , vol.21 , pp. 532-538
    • Wu, C.C.1    MacCoss, M.J.2    Howell, K.E.3    Yates, J.R.4
  • 24
    • 0035882269 scopus 로고    scopus 로고
    • Identification of nuclei associated proteins by 2D-gel electrophoresis and mass spectrometry
    • 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.
    • (2001) J Neurosci Methods , vol.109 , pp. 3-11
    • Bergquist, J.1    Gobom, J.2    Blomberg, A.3    Roepstorff, P.4    Ekman, R.5
  • 25
    • 0037370399 scopus 로고    scopus 로고
    • The study of macromolecular complexes by quantitative proteomics
    • 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.
    • 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.
    • (2003) Nat Genet , vol.33 , pp. 349-355
    • Ranish, J.A.1    Yi, E.C.2    Leslie, D.M.3    Purvine, S.O.4    Goodlett, D.R.5    Eng, J.6    Aebersold, R.7
  • 27
    • 0037337310 scopus 로고    scopus 로고
    • A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    • 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).
    • 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).
    • (2003) Nat Biotechnol , vol.21 , pp. 315-318
    • Blagoev, B.1    Kratchmarova, I.2    Ong, S.E.3    Nielsen, M.4    Foster, L.J.5    Mann, M.6
  • 28
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature. 422:2003;198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 29
    • 0037434980 scopus 로고    scopus 로고
    • From genomics to proteomics
    • Tyers M., Mann M. From genomics to proteomics. Nature. 422:2003;193-197.
    • (2003) Nature , vol.422 , pp. 193-197
    • Tyers, M.1    Mann, M.2
  • 30
    • 0037304325 scopus 로고    scopus 로고
    • Quantitative proteomics using mass spectrometry
    • Sechi S., Oda Y. Quantitative proteomics using mass spectrometry. Curr Opin Chem Biol. 7:2003;70-77.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 70-77
    • Sechi, S.1    Oda, Y.2
  • 31
    • 18444391517 scopus 로고    scopus 로고
    • Shotgun identification of protein modifications from protein complexes and lens tissue
    • This paper reports on proteomics analysis of a complex protein mixture and post-translational modification.
    • 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.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7900-7905
    • MacCoss, M.J.1    McDonald, W.H.2    Saraf, A.3    Sadygov, R.4    Clark, J.M.5    Tasto, J.J.6    Gould, K.L.7    Wolters, D.8    Washburn, M.9    Weiss, A.10
  • 32
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • This paper describes a method to enrich N-terminal peptides using the diagonal chromatography approach.
    • 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.
    • (2003) Nat Biotechnol , vol.21 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4    Staes, A.5    Thomas, G.R.6    Vandekerckhove, J.7
  • 33
    • 0016321645 scopus 로고
    • Diagonal chromatography for the selective purification of tyrosyl peptides
    • Cruickshank W.H., Malchy B.L., Kaplan H. Diagonal chromatography for the selective purification of tyrosyl peptides. Can J Biochem. 52:1974;1013-1017.
    • (1974) Can J Biochem , vol.52 , pp. 1013-1017
    • Cruickshank, W.H.1    Malchy, B.L.2    Kaplan, H.3
  • 35
    • 0036246088 scopus 로고    scopus 로고
    • Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry
    • A solid-phase-based stable isotope tagging method is discussed.
    • 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.
    • (2002) Nat Biotechnol , vol.20 , pp. 512-515
    • Zhou, H.1    Ranish, J.A.2    Watts, J.D.3    Aebersold, R.4
  • 38
    • 33746408762 scopus 로고    scopus 로고
    • 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
    • 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.
    • (2003) Mol Cell Proteomics , vol.2 , pp. 428-442
    • Von Haller, P.D.1    Yi, E.2    Donohoe, S.3    Vaughn, K.4    Keller, A.5    Nesvizhskii, A.I.6    Eng, J.7    Li, X.J.8    Goodlett, D.R.9    Aebersold, R.10
  • 40
    • 0037418318 scopus 로고    scopus 로고
    • Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways
    • This is a good example of the application of quantitative proteomics using ICAT reagents to address biological questions.
    • 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.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 2771-2776
    • Guina, T.1    Purvine, S.O.2    Yi, E.C.3    Eng, J.4    Goodlett, D.R.5    Aebersold, R.6    Miller, S.I.7
  • 42
    • 0346668314 scopus 로고    scopus 로고
    • Use of proteomics methodology to evaluate inflammatory protein expression in tendinitis
    • Harris R.D., Nindl G., Balcavage W.X., Weiner W., Johnson M.T. Use of proteomics methodology to evaluate inflammatory protein expression in tendinitis. Biomed Sci Instrum. 39:2003;493-499.
    • (2003) Biomed Sci Instrum , vol.39 , pp. 493-499
    • Harris, R.D.1    Nindl, G.2    Balcavage, W.X.3    Weiner, W.4    Johnson, M.T.5
  • 43
    • 0036748438 scopus 로고    scopus 로고
    • Tagless extraction-retentate chromatography: A new global protein digestion strategy for monitoring differential protein expression
    • Weinberger S.R., Viner R.I., Ho P. Tagless extraction-retentate chromatography: a new global protein digestion strategy for monitoring differential protein expression. Electrophoresis. 23:2002;3182-3192.
    • (2002) Electrophoresis , vol.23 , pp. 3182-3192
    • Weinberger, S.R.1    Viner, R.I.2    Ho, P.3
  • 44
    • 0038271634 scopus 로고    scopus 로고
    • Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: Identification of more than 800 Escherichia coli proteins
    • This paper reports on a useful method to study methionine-containing peptides based on the diagonal chromatography concept.
    • Gevaert K., Van Damme J., Goethals M., Thomas G.R., Hoorelbeke B., Demol H., Martens L., Puype M., Staes A., Vandekerckhove J. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics. 1:2002;896-903 This paper reports on a useful method to study methionine-containing peptides based on the diagonal chromatography concept.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 896-903
    • Gevaert, K.1    Van Damme, J.2    Goethals, M.3    Thomas, G.R.4    Hoorelbeke, B.5    Demol, H.6    Martens, L.7    Puype, M.8    Staes, A.9    Vandekerckhove, J.10
  • 45
    • 0038608603 scopus 로고    scopus 로고
    • An approach to quantitative proteome analysis by labeling tryptophan residues
    • A method for targeting tryptophan-containing peptides has been proposed.
    • Kuyama H., Watanabe M., Toda C., Ando E., Tanaka K., Nishimura O. An approach to quantitative proteome analysis by labeling tryptophan residues. Rapid Commun Mass Spectrom. 17:2003;1642-1650 A method for targeting tryptophan-containing peptides has been proposed.
    • (2003) Rapid Commun Mass Spectrom , vol.17 , pp. 1642-1650
    • Kuyama, H.1    Watanabe, M.2    Toda, C.3    Ando, E.4    Tanaka, K.5    Nishimura, O.6
  • 47
    • 0037040565 scopus 로고    scopus 로고
    • Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates
    • Wang S., Zhang X., Regnier F.E. Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates. J Chromatogr A. 949:2002;153-162.
    • (2002) J Chromatogr a , vol.949 , pp. 153-162
    • Wang, S.1    Zhang, X.2    Regnier, F.E.3
  • 48
    • 0020713174 scopus 로고
    • Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes
    • Bause E. Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes. Biochem J. 209:1983;331-336.
    • (1983) Biochem J , vol.209 , pp. 331-336
    • Bause, E.1
  • 49
    • 0037685263 scopus 로고    scopus 로고
    • Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins
    • This paper describes MS analysis of protein glycosylations using the combined techniques of lectin affinity purification and isotope-coded tagging.
    • Kaji H., Saito H., Yamauchi Y., Shinkawa T., Taoka M., Hirabayashi J., Kasai K., Takahashi N., Isobe T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol. 21:2003;667-672 This paper describes MS analysis of protein glycosylations using the combined techniques of lectin affinity purification and isotope-coded tagging.
    • (2003) Nat Biotechnol , vol.21 , pp. 667-672
    • Kaji, H.1    Saito, H.2    Yamauchi, Y.3    Shinkawa, T.4    Taoka, M.5    Hirabayashi, J.6    Kasai, K.7    Takahashi, N.8    Isobe, T.9
  • 50
    • 0038699625 scopus 로고    scopus 로고
    • Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    • This paper describes a method to identify and quantify N-linked glycoproteins. It also applies the method to enrich cell surface proteins and efficiently profile serum proteins by removing albumin from serum samples.
    • Zhang H., Li X.J., Martin D.B., Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol. 21:2003;660-666 This paper describes a method to identify and quantify N-linked glycoproteins. It also applies the method to enrich cell surface proteins and efficiently profile serum proteins by removing albumin from serum samples.
    • (2003) Nat Biotechnol , vol.21 , pp. 660-666
    • Zhang, H.1    Li, X.J.2    Martin, D.B.3    Aebersold, R.4
  • 51
    • 0037524357 scopus 로고    scopus 로고
    • O-GlcNAc turns twenty: Functional implications for post-translational modification of nuclear and cytosolic proteins with a sugar
    • Wells L., Hart G.W. O-GlcNAc turns twenty: functional implications for post-translational modification of nuclear and cytosolic proteins with a sugar. FEBS Lett. 546:2003;154-158.
    • (2003) FEBS Lett , vol.546 , pp. 154-158
    • Wells, L.1    Hart, G.W.2
  • 52
    • 0001607910 scopus 로고    scopus 로고
    • Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications
    • Analysis of O-GlcNAc modification using β-elimination and Michael addition reaction is described. Also described is a strategy to distinguish O-GlcNAc modification at serine or threonine from phosphorylation modification using this approach.
    • Wells L., Vosseller K., Cole R.N., Cronshaw J.M., Matunis M.J., Hart G.W. Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol Cell Proteomics. 1:2002;791-804 Analysis of O-GlcNAc modification using β-elimination and Michael addition reaction is described. Also described is a strategy to distinguish O-GlcNAc modification at serine or threonine from phosphorylation modification using this approach.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 791-804
    • Wells, L.1    Vosseller, K.2    Cole, R.N.3    Cronshaw, J.M.4    Matunis, M.J.5    Hart, G.W.6
  • 53
    • 0035241690 scopus 로고    scopus 로고
    • Mass spectrometry in proteomics
    • Aebersold R., Goodlett D.R. Mass spectrometry in proteomics. Chem Rev. 101:2001;269-295.
    • (2001) Chem Rev , vol.101 , pp. 269-295
    • Aebersold, R.1    Goodlett, D.R.2
  • 54
    • 0034602654 scopus 로고    scopus 로고
    • Analysis of receptor signaling pathways by mass spectrometry: Identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors
    • Pandey A., Podtelejnikov A.V., Blagoev B., Bustelo X.R., Mann M., Lodish H.F. Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc Natl Acad Sci USA. 97:2000;179-184.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 179-184
    • Pandey, A.1    Podtelejnikov, A.V.2    Blagoev, B.3    Bustelo, X.R.4    Mann, M.5    Lodish, H.F.6
  • 55
    • 0032479322 scopus 로고    scopus 로고
    • Colony-stimulating factor-1 stimulates the formation of multimeric cytosolic complexes of signaling proteins and cytoskeletal components in macrophages
    • Yeung Y.G., Wang Y., Einstein D.B., Lee P.S., Stanley E.R. Colony-stimulating factor-1 stimulates the formation of multimeric cytosolic complexes of signaling proteins and cytoskeletal components in macrophages. J Biol Chem. 273:1998;17128-17137.
    • (1998) J Biol Chem , vol.273 , pp. 17128-17137
    • Yeung, Y.G.1    Wang, Y.2    Einstein, D.B.3    Lee, P.S.4    Stanley, E.R.5
  • 56
    • 0036652968 scopus 로고    scopus 로고
    • A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: Identification of a novel protein, Frigg, as a protein kinase a substrate
    • This is an example of identification of phospho-Ser/Thr proteins based on phospho-specific antibodies.
    • Gronborg M., Kristiansen T.Z., Stensballe A., Andersen J.S., Ohara O., Mann M., Jensen O.N., Pandey A. A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol Cell Proteomics. 1:2002;517-527 This is an example of identification of phospho-Ser/Thr proteins based on phospho-specific antibodies.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 517-527
    • Gronborg, M.1    Kristiansen, T.Z.2    Stensballe, A.3    Andersen, J.S.4    Ohara, O.5    Mann, M.6    Jensen, O.N.7    Pandey, A.8
  • 57
    • 0037151026 scopus 로고    scopus 로고
    • A method to identify serine kinase substrates. Akt phosphorylates a novel adipocyte protein with a Rab GTPase-activating protein (GAP) domain
    • This is another example of profiling serine phosphorylation using phospho-specific antibodies and MS.
    • Kane S., Sano H., Liu S.C., Asara J.M., Lane W.S., Garner C.C., Lienhard G.E. A method to identify serine kinase substrates. Akt phosphorylates a novel adipocyte protein with a Rab GTPase-activating protein (GAP) domain. J Biol Chem. 277:2002;22115-22118 This is another example of profiling serine phosphorylation using phospho-specific antibodies and MS.
    • (2002) J Biol Chem , vol.277 , pp. 22115-22118
    • Kane, S.1    Sano, H.2    Liu, S.C.3    Asara, J.M.4    Lane, W.S.5    Garner, C.C.6    Lienhard, G.E.7
  • 58
    • 0037131411 scopus 로고    scopus 로고
    • Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs
    • This paper describes the development of phospho-specific antibodies that are broadly reactive to the consensus phosphorylation motif of certain kinases.
    • Zhang H., Zha X., Tan Y., Hornbeck P.V., Mastrangelo A.J., Alessi D.R., Polakiewicz R.D., Comb M.J. Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J Biol Chem. 277:2002;39379-39387 This paper describes the development of phospho-specific antibodies that are broadly reactive to the consensus phosphorylation motif of certain kinases.
    • (2002) J Biol Chem , vol.277 , pp. 39379-39387
    • Zhang, H.1    Zha, X.2    Tan, Y.3    Hornbeck, P.V.4    Mastrangelo, A.J.5    Alessi, D.R.6    Polakiewicz, R.D.7    Comb, M.J.8
  • 60
    • 0033565503 scopus 로고    scopus 로고
    • Immobilized gallium(III) affinity chromatography of phosphopeptides
    • Posewitz M.C., Tempst P. Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal Chem. 71:1999;2883-2892.
    • (1999) Anal Chem , vol.71 , pp. 2883-2892
    • Posewitz, M.C.1    Tempst, P.2
  • 61
    • 0036198435 scopus 로고    scopus 로고
    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • This paper describes the improvement of specificity of IMAC-based phospho-peptides enrichment by methyl-esterification.
    • Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol. 20:2002;301-305 This paper describes the improvement of specificity of IMAC-based phospho-peptides enrichment by methyl-esterification.
    • (2002) Nat Biotechnol , vol.20 , pp. 301-305
    • Ficarro, S.B.1    McCleland, M.L.2    Stukenberg, P.T.3    Burke, D.J.4    Ross, M.M.5    Shabanowitz, J.6    Hunt, D.F.7    White, F.M.8
  • 62
    • 0842299091 scopus 로고    scopus 로고
    • Identification of novel phosphorylation sites on Xenopus laevis Aurora a and analysis of phosphopeptide enrichment by immobilized metal-affinity chromatography
    • Haydon C.E., Eyers P.A., Aveline-Wolf L.D., Resing K.A., Maller J.L., Ahn N.G. Identification of novel phosphorylation sites on Xenopus laevis Aurora A and analysis of phosphopeptide enrichment by immobilized metal-affinity chromatography. Mol Cell Proteomics. 2:2003;1055-1067.
    • (2003) Mol Cell Proteomics , vol.2 , pp. 1055-1067
    • Haydon, C.E.1    Eyers, P.A.2    Aveline-Wolf, L.D.3    Resing, K.A.4    Maller, J.L.5    Ahn, N.G.6
  • 63
    • 0037305895 scopus 로고    scopus 로고
    • Tackling the phosphoproteome: Tools and strategies
    • Kalume D.E., Molina H., Pandey A. Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol. 7:2003;64-69.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 64-69
    • Kalume, D.E.1    Molina, H.2    Pandey, A.3
  • 64
    • 0035072715 scopus 로고    scopus 로고
    • A systematic approach to the analysis of protein phosphorylation
    • Zhou H., Watts J.D., Aebersold R. A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol. 19:2001;375-378.
    • (2001) Nat Biotechnol , vol.19 , pp. 375-378
    • Zhou, H.1    Watts, J.D.2    Aebersold, R.3
  • 65
    • 0035067251 scopus 로고    scopus 로고
    • Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome
    • Oda Y., Nagasu T., Chait B.T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol. 19:2001;379-382.
    • (2001) Nat Biotechnol , vol.19 , pp. 379-382
    • Oda, Y.1    Nagasu, T.2    Chait, B.T.3
  • 66
    • 0035356565 scopus 로고    scopus 로고
    • Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses
    • Goshe M.B., Conrads T.P., Panisko E.A., Angell N.H., Veenstra T.D., Smith R.D. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal Chem. 73:2001;2578-2586.
    • (2001) Anal Chem , vol.73 , pp. 2578-2586
    • Goshe, M.B.1    Conrads, T.P.2    Panisko, E.A.3    Angell, N.H.4    Veenstra, T.D.5    Smith, R.D.6
  • 67
    • 0033827629 scopus 로고    scopus 로고
    • Comparative quantification and identification of phosphoproteins using stable isotope labeling and liquid chromatography/mass spectrometry
    • Weckwerth W., Willmitzer L., Fiehn O. Comparative quantification and identification of phosphoproteins using stable isotope labeling and liquid chromatography/mass spectrometry. Rapid Commun Mass Spectrom. 14:2000;1677-1681.
    • (2000) Rapid Commun Mass Spectrom , vol.14 , pp. 1677-1681
    • Weckwerth, W.1    Willmitzer, L.2    Fiehn, O.3
  • 68
    • 0042861519 scopus 로고    scopus 로고
    • Phosphospecific proteolysis for mapping sites of protein phosphorylation
    • This is an excellent example of method development on mapping serine/threonine phosphorylated sites by proteolysis specific to the phosphorylated sites.
    • Knight Z.A., Schilling B., Row R.H., Kenski D.M., Gibson B.W., Shokat K.M. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat Biotechnol. 21:2003;1047-1054 This is an excellent example of method development on mapping serine/threonine phosphorylated sites by proteolysis specific to the phosphorylated sites.
    • (2003) Nat Biotechnol , vol.21 , pp. 1047-1054
    • Knight, Z.A.1    Schilling, B.2    Row, R.H.3    Kenski, D.M.4    Gibson, B.W.5    Shokat, K.M.6
  • 69
    • 0037161303 scopus 로고    scopus 로고
    • Direct identification of a G protein ubiquitination site by mass spectrometry
    • Marotti L.A. Jr., Newitt R., Wang Y., Aebersold R., Dohlman H.G. Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry. 41:2002;5067-5074.
    • (2002) Biochemistry , vol.41 , pp. 5067-5074
    • Marotti, L.A.Jr.1    Newitt, R.2    Wang, Y.3    Aebersold, R.4    Dohlman, H.G.5
  • 70
    • 0041706156 scopus 로고    scopus 로고
    • A proteomics approach to understanding protein ubiquitination
    • This paper provides the first demonstration of large-scale proteomics analysis on protein ubiquitination.
    • Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 21:2003;921-926 This paper provides the first demonstration of large-scale proteomics analysis on protein ubiquitination.
    • (2003) Nat Biotechnol , vol.21 , pp. 921-926
    • Peng, J.1    Schwartz, D.2    Elias, J.E.3    Thoreen, C.C.4    Cheng, D.5    Marsischky, G.6    Roelofs, J.7    Finley, D.8    Gygi, S.P.9
  • 71
    • 0038434056 scopus 로고    scopus 로고
    • A superfamily of protein tags: Ubiquitin, SUMO and related modifiers
    • Schwartz D.C., Hochstrasser M. A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem Sci. 28:2003;321-328.
    • (2003) Trends Biochem Sci , vol.28 , pp. 321-328
    • Schwartz, D.C.1    Hochstrasser, M.2
  • 72
    • 0033593013 scopus 로고    scopus 로고
    • Activity-based protein profiling: The serine hydrolases
    • Liu Y., Patricelli M.P., Cravatt B.F. Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci USA. 96:1999;14694-14699.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 14694-14699
    • Liu, Y.1    Patricelli, M.P.2    Cravatt, B.F.3
  • 73
    • 0033835372 scopus 로고    scopus 로고
    • Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools
    • Greenbaum D., Medzihradszky K.F., Burlingame A., Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem Biol. 7:2000;569-581.
    • (2000) Chem Biol , vol.7 , pp. 569-581
    • Greenbaum, D.1    Medzihradszky, K.F.2    Burlingame, A.3    Bogyo, M.4
  • 74
    • 0036391485 scopus 로고    scopus 로고
    • Design and synthesis of class-selective activity probes for protein tyrosine phosphatases
    • An activity-based protein probe for phosphatase is discussed.
    • Lo L.C., Pang T.L., Kuo C.H., Chiang Y.L., Wang H.Y., Lin J.J. Design and synthesis of class-selective activity probes for protein tyrosine phosphatases. J Proteome Res. 1:2002;35-40 An activity-based protein probe for phosphatase is discussed.
    • (2002) J Proteome Res , vol.1 , pp. 35-40
    • Lo, L.C.1    Pang, T.L.2    Kuo, C.H.3    Chiang, Y.L.4    Wang, H.Y.5    Lin, J.J.6
  • 75
    • 0038361307 scopus 로고    scopus 로고
    • Discovering potent and selective reversible inhibitors of enzymes in complex proteomes
    • This paper discusses competitive profiling of serine hydrolyse inhibitors using chemical probes and provides a potential method for screening enzyme inhibitors.
    • Leung D., Hardouin C., Boger D.L., Cravatt B.F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat Biotechnol. 21:2003;687-691 This paper discusses competitive profiling of serine hydrolyse inhibitors using chemical probes and provides a potential method for screening enzyme inhibitors.
    • (2003) Nat Biotechnol , vol.21 , pp. 687-691
    • Leung, D.1    Hardouin, C.2    Boger, D.L.3    Cravatt, B.F.4
  • 76
    • 0036022519 scopus 로고    scopus 로고
    • Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype
    • This paper describes a study using a library with a sulfonate ester chemotype to screen complex proteomes for activity-dependent protein activities and provides a useful method for future drug screen.
    • Adam G.C., Sorensen E.J., Cravatt B.F. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat Biotechnol. 20:2002;805-809 This paper describes a study using a library with a sulfonate ester chemotype to screen complex proteomes for activity-dependent protein activities and provides a useful method for future drug screen.
    • (2002) Nat Biotechnol , vol.20 , pp. 805-809
    • Adam, G.C.1    Sorensen, E.J.2    Cravatt, B.F.3


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