메뉴 건너뛰기




Volumn 4, Issue 9, 2005, Pages 1328-1340

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; GLYCOPEPTIDE; PEPTIDE; PROTEIN; PROTEOME;

EID: 26844492976     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M500141-MCP200     Document Type: Article
Times cited : (164)

References (39)
  • 1
    • 0037434980 scopus 로고    scopus 로고
    • From genomics to proteomics
    • Tyers, M., and Mann, M. (2003) From genomics to proteomics. Nature 422, 193-197
    • (2003) Nature , vol.422 , pp. 193-197
    • Tyers, M.1    Mann, M.2
  • 2
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 3
    • 0037434981 scopus 로고    scopus 로고
    • Disease proteomics
    • Hanash, S. (2003) Disease proteomics. Nature 422, 226-232
    • (2003) Nature , vol.422 , pp. 226-232
    • Hanash, S.1
  • 4
    • 0037434977 scopus 로고    scopus 로고
    • Biomedical informatics for proteomics
    • Boguski, M. S., and McIntosh, M. W. (2003) Biomedical informatics for proteomics. Nature 422, 233-237
    • (2003) Nature , vol.422 , pp. 233-237
    • Boguski, M.S.1    McIntosh, M.W.2
  • 5
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
    • (2001) Nat. Biotechnol. , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 6
    • 0036535357 scopus 로고    scopus 로고
    • Analysis of quantitative proteomic data generated via multidimensional protein identification technology
    • Washburn, M. P., Ulaszek, R., Deciu, C., Schieltz, D. M., and Yates, J. R., III (2002) Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74, 1650-1657
    • (2002) Anal. Chem. , vol.74 , pp. 1650-1657
    • Washburn, M.P.1    Ulaszek, R.2    Deciu, C.3    Schieltz, D.M.4    Yates III, J.R.5
  • 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., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 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
  • 8
    • 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., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951
    • (2001) Nat. Biotechnol. , vol.19 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 9
    • 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., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
    • (2002) Mol. Cell Proteomics , vol.1 , 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
  • 10
    • 0037337310 scopus 로고    scopus 로고
    • A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    • Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., and Mann, M. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318
    • (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
  • 11
    • 0033535961 scopus 로고    scopus 로고
    • Accurate quantitation of protein expression and site-specific phosphorylation
    • Oda, Y., Huang, K., Cross, F. R., Cowburn, D., and Chait, B. T. (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U. S. A. 96, 6591-6596
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 6591-6596
    • Oda, Y.1    Huang, K.2    Cross, F.R.3    Cowburn, D.4    Chait, B.T.5
  • 12
  • 14
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 15
    • 0024289037 scopus 로고
    • Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons
    • Karas, M., and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299-2301
    • (1988) Anal. Chem. , vol.60 , pp. 2299-2301
    • Karas, M.1    Hillenkamp, F.2
  • 17
    • 0035241690 scopus 로고    scopus 로고
    • Mass spectrometry in proteomics
    • Aebersold, R., and Goodlett, D. R. (2001) Mass spectrometry in proteomics. Chem. Rev. 101, 269-295
    • (2001) Chem. Rev. , vol.101 , pp. 269-295
    • Aebersold, R.1    Goodlett, D.R.2
  • 18
    • 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., and Yates, J. R., III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 19
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence data-bases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence data-bases using mass spectrometry data. Electrophoresis 20, 3551-3567
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 20
    • 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., and Aebersold, R. (2003) Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75, 6648-6657
    • (2003) Anal. Chem. , vol.75 , pp. 6648-6657
    • Li, X.J.1    Zhang, H.2    Ranish, J.A.3    Aebersold, R.4
  • 21
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 24
    • 4444371652 scopus 로고    scopus 로고
    • Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
    • Blagoev, B., Ong, S. E., Kratchmarova, I., and Mann, M. (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22, 1139-1145
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1139-1145
    • Blagoev, B.1    Ong, S.E.2    Kratchmarova, I.3    Mann, M.4
  • 25
    • 3042739098 scopus 로고    scopus 로고
    • A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry
    • Li, X. J., Pedrioli, P. G., Eng, J., Martin, D., Yi, E. C., Lee, H., and Aebersold, R. (2004) A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal. Chem. 76, 3856-3860
    • (2004) Anal. Chem. , vol.76 , pp. 3856-3860
    • Li, X.J.1    Pedrioli, P.G.2    Eng, J.3    Martin, D.4    Yi, E.C.5    Lee, H.6    Aebersold, R.7
  • 26
    • 10744233766 scopus 로고    scopus 로고
    • Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
    • Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S., Kumar, P., Anderle, M., and Becker, C. H. (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75, 4818-4826
    • (2003) Anal. Chem. , vol.75 , pp. 4818-4826
    • Wang, W.1    Zhou, H.2    Lin, H.3    Roy, S.4    Shaler, T.A.5    Hill, L.R.6    Norton, S.7    Kumar, P.8    Anderle, M.9    Becker, C.H.10
  • 27
    • 14344250874 scopus 로고    scopus 로고
    • Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry
    • Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T. G., Foss, E., Mao, Y., and Emili, A. (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 3, 984-997
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 984-997
    • Radulovic, D.1    Jelveh, S.2    Ryu, S.3    Hamilton, T.G.4    Foss, E.5    Mao, Y.6    Emili, A.7
  • 28
    • 0037106398 scopus 로고    scopus 로고
    • Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry
    • Bondarenko, P. V., Chelius, D., and Shaler, T. A. (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 74, 4741-4749
    • (2002) Anal. Chem. , vol.74 , pp. 4741-4749
    • Bondarenko, P.V.1    Chelius, D.2    Shaler, T.A.3
  • 30
    • 0038699625 scopus 로고    scopus 로고
    • Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    • Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666
    • (2003) Nat. Biotechnol. , vol.21 , pp. 660-666
    • Zhang, H.1    Li, X.J.2    Martin, D.B.3    Aebersold, R.4
  • 32
    • 0024700097 scopus 로고
    • A theory for multidirectional signal decomposition: The wavelet representation
    • Mallat, S. G. (1989) A theory for multidirectional signal decomposition: the wavelet representation. IEEE Trans. Pattern Anal. Mach. Intell. 11, 674-693
    • (1989) IEEE Trans. Pattern Anal. Mach. Intell. , vol.11 , pp. 674-693
    • Mallat, S.G.1
  • 34
    • 58149209843 scopus 로고
    • Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
    • Senko, M. W., Beu, S. C., and McLafferty, F. W. (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229-233
    • (1995) J. Am. Soc. Mass Spectrom. , vol.6 , pp. 229-233
    • Senko, M.W.1    Beu, S.C.2    McLafferty, F.W.3
  • 35
    • 0035632456 scopus 로고    scopus 로고
    • Isotopic deconvolution of matrix-assisted laser desorption/ionization mass spectra for substance-class specific analysis of complex samples
    • Wehofsky, M., Hoffmann, R., Hubert, M., and Spengler, B. (2001) Isotopic deconvolution of matrix-assisted laser desorption/ionization mass spectra for substance-class specific analysis of complex samples. Eur. J. Mass Spectrom. 7, 39-46
    • (2001) Eur. J. Mass Spectrom. , vol.7 , pp. 39-46
    • Wehofsky, M.1    Hoffmann, R.2    Hubert, M.3    Spengler, B.4
  • 36
    • 0242354113 scopus 로고    scopus 로고
    • Shifts in peptide and protein charge state distributions with varying spray tip orifice diameter in nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry
    • Li, Y., and Cole, R. B. (2003) Shifts in peptide and protein charge state distributions with varying spray tip orifice diameter in nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 75, 5739-5746
    • (2003) Anal. Chem. , vol.75 , pp. 5739-5746
    • Li, Y.1    Cole, R.B.2
  • 37
    • 0025853823 scopus 로고
    • Deamidation of soluble CD4 at asparagine-52 results in reduced binding capacity for the HIV-1 envelope glycoprotein gp120
    • Teshima, G., Porter, J., Yim, K., Ling, V., and Guzzetta, A. (1991) Deamidation of soluble CD4 at asparagine-52 results in reduced binding capacity for the HIV-1 envelope glycoprotein gp120. Biochemistry 30, 3916-3922
    • (1991) Biochemistry , vol.30 , pp. 3916-3922
    • Teshima, G.1    Porter, J.2    Yim, K.3    Ling, V.4    Guzzetta, A.5
  • 38
    • 12244255362 scopus 로고    scopus 로고
    • Microfluidic chip for peptide analysis with an integrated HPLC column, sample enrichment column, and nanoelectrospray tip
    • Yin, H., Killeen, K., Brennen, R., Sobek, D., Werlich, M., and van de Goor, T. (2005) Microfluidic chip for peptide analysis with an integrated HPLC column, sample enrichment column, and nanoelectrospray tip. Anal. Chem. 77, 527-533
    • (2005) Anal. Chem. , vol.77 , pp. 527-533
    • Yin, H.1    Killeen, K.2    Brennen, R.3    Sobek, D.4    Werlich, M.5    van de Goor, T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.