Recent advances in gel-based proteome profiling techniques

Applied Biochemistry and Biotechnology - Part B Molecular Biotechnology

Volumn 28, Issue 1, 2004, Pages 63-76

  Hu, Yi ^a   Huang, Xuan ^a   Chen, Grace Y J ^a   Yao, Shao Q ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

DIGE; Fluorescence; ICAT; Isotope labeling; Proteomics; SDS PAGE; Two dimensional

Indexed keywords

ACRYLICS; ELECTROPHORESIS; GELS; MOLECULAR BIOLOGY; POLYAMIDES; PROBES; RADIOISOTOPES;

DIGE; GEL ELECTROPHORESIS; ICAT; ISOTAPE LABELING; PROTEOMICS; SDS-PAGE;

PROTEINS;

FLUORESCENT DYE; PROTEIN; RADIOISOTOPE; ISOTOPE; PROTEOME;

ANALYTIC METHOD; DNA MICROARRAY; GEL MOBILITY SHIFT ASSAY; INTERMETHOD COMPARISON; ISOTOPE LABELING; MOLECULAR DYNAMICS; MOLECULAR PROBE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS; HUMAN; METHODOLOGY;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FLUORESCENT DYES; HUMANS; ISOTOPES; PROTEOME; PROTEOMICS;

EID: 13844270303     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1385/MB:28:1:63     Document Type: Review

References (58)

1. Chen, G. Y. J., Uttamchandani, M., Lue, Y. P. R., Lesaicherre, M. L., and Yao, S. Q. (2003) Array-based technologies and their applications in proteomics. Curr. Top. Med. Chem. 3, 705-724.
2. Lockhart, D. J. and Winzeler, E. A. (2000) Genomics, gene expression and DNA arrays. Nature. 405, 827-836.
3. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720-1730.
4. Adam, G. C., Sorensen, E. J., and Cravatt, B. F. (2002) Chemical strategies for functional proteomics. Mol. Cell Proteomics 1, 781-790.
5. Hu, Y., Wang, G., Chen, G. Y. J., Fu, X., and Yao, S. Q. (2003) Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 24, 1458-1470.
6. Patton, W. F. (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21, 1123-1144.
7. Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
8. Huang, X., Tan, E. L. P., Chen, G. Y. J., and Yao, S. Q. (2003) Enzyme-targeting small molecule probes for proteomics application. Appl. Genomics and Proteomics, in press.
9. MacBeath, G. (2001) Proteomics comes to the surface. Nat. Biotechnol. 19, 828-829.
10. Zhu, H., Bilgin, M., Bangham, R., et al. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101-2105.
11. Lesaicherre, M. L., Lue, Y. P. R., Chen, G. Y. J., Zhu, Q., and Yao, S. Q. (2002) Intein-mediated biotinylation of proteins and its application in a protein microarray, J. Am. Chem. Soc. 124, 8768-8769.
12. Chen, G. Y. J., Uttamchandani, M., Zhu, Q., Wang, G., and Yao, S. Q. (2003) Developing a strategy for activity-based detection of enzymes in a protein microarray. Chembiochem. 4, 336-339.
13. Lesaicherre, M. L., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2002) Developing site-specific immobilization strategies of peptides in a microarray. Bioorg. Med. Chem. Lett. 12, 2079-2083.
14. Lesaicherre, M. L., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2002) Antibody-based fluorescence detection of kinase activity on a peptide array. Bioorg. Med. Chem. Lett. 12, 2085-2088.
15. Zhu, Q., Uttamchandani, M., Li, D.B., Lesaicherre, M. L., and Yao, S. Q. (2003) An enzymatic profiling system in a small-molecule microarray. Org. Lett. 5, 1257-1260.
16. Uttamchandani, M., Chan, E. W. S., Chen, G. Y. J., and Yao, S. Q. (2003) Combinatorial peptide microarrays for the rapid determination of kinase specificity. Bioorg. Med. Chem. Lett. 13, 2997-3000.
17. Unlu, M., Morgan, M. E., and Minden, J. S. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077.
18. Tonge, R., Shaw, J., Middleton, B., et al. (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377-396.
19. Gharbi, S., Gaffney, P., Yang, A., et al. (2002) Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol. Cell. Proteomics 1, 91-98.
20. Gade, D., Thiermann, J., Markowsky, D., and Rabus, R. (2003) Evaluation of two-dimensional difference gel electrophoresis for protein profiling: soluble proteins of the marine bacterium Pirellula sp. strain 1. J. Mol. Microbiol. Biotechnol. 5, 240-251.
21. Lee, J. R., Baxter, T. M., Yamaguchi, H., Wang, T. C., Goldenring, J. R., and Anderson, M. G. (2003) Differential protein analysis of spasmolytic polypeptide expressing metaplasia using laser capture microdissection and two-dimensional difference gel electrophoresis. Appl. Immunohistochem. Mol. Morphol. 11, 188-193.
22. Zhou, G., Li, H., DeCamp, D., et al. (2002) 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol. Cell. Proteomics 1, 117-124.
23. Van Den Bergh, G., Clerens, S., Vandesande, F., and Arckens, L. (2003) Reversed-phase high-performance liquid chromatography prefractionation prior to two-dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat. Electrophoresis 24, 1471-1481.
24. Yan, J. X., Devenish, A. T., Wait, R., Stone, T., Lewis, S., and Fowler, S. (2002) Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2, 1682-1698.
25. Shaw, J., Rowlinson, R., Nickson, J., et al. (2003) Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 3, 1181-1195.
26. Steinberg, T. H., Pretty On Top, K., Berggren, K. N., et al. (2001) Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots. Proteomics 1, 841-855.
27. Steinberg, T. H., Agnew, B. J., Gee, K. R., et al. (2003) Global quantitative phosphoprotein analysis using multiplexed proteomics technology. Proteomics 3, 1128-1144.
28. Patton, W. F. (2002) Detection technologies in proteome analysis. J Chromatogr. B Analyt. Technol. Biomed. Life Sci. 771, 3-31.
29. Schulenberg, B., Beechem, J. M., and Patton, W. F. (2003) Mapping glycosylation changes related to cancer using the multiplexed proteomics technology: a protein differential display approach. J Chromatogr. B Analyt. Technol. Biomed. Life Sci. 793, 127-139.
30. Monribot-Espagne, C. and Boucherie, H. (2002) Differential gel exposure: a new methodology for the two-dimensional comparison of protein samples. Proteomics 2, 229-240.
31. 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.
32. Turecek, F. (2002) Mass spectrometry in coupling with affinity capture-release and isotope-coded affinity tags for quantitative protein analysis. J. Mass Spectrom. 37, 1-14.
33. Smolka, M., Zhou, H., and Aebersold, R. (2002) Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell Proteomics 1, 19-29.
34. Vido, K., Spector, D., Lagniel, G., Lopez, S., Toledano, M. B., and Labarre, J. (2001) A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J. Biol. Chem. 276, 8469-8474.
35. Maillet, I., Lagniel, G., Perrot, M., Boucherie, H., and Labarre, J. (1996) Rapid identification of yeast proteins on two-dimensional gels. J. Biol. Chem. 271, 10263-10270.
36. Bro, C., Regenberg, B., Lagniel, G., Labarre, J., Montero-Lomeli, M., and Nielsen, J. (2003) Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J. Biol. Chem. 278, 32141-32149.
37. Jiang, H. and English, A. M. (2002) Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 1, 345-350.
38. Krijgsveld, J., Ketting, R. F., Mahmoudi, T., et al. (2003) Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 21, 927-931.
39. Yeargin, J. and Haas, M. (1995) Elevated levels of wild-type p53 induced by radiolabeling of cells leads to apoptosis or sustained growth arrest. Curr. Biol. 5, 423-431.
40. Jeffery, D. A. and Boygo, M. (2003) Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. 14, 87-95.
41. Liu, Y., Patricelli, M. P., and Cravatt, B. F. (1999) Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. USA 96, 14,694-14,699.
42. Wang, G., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2003) Solid-phase synthesis of peptide vinyl sulfones and their uses in large-scale proteomic experiments. Org. Lett. 5, 737-740.
43. Zhu, Q., Huang, X., Chen, G. Y. J., and Yao, S. Q. (2003) Activity-based fluorescent probes that targets phosphatases. Tetrahedron Lett. 44, 2669-2672.
44. Liau, M. L., Panicker, R. C., and Yao, S. Q. (2003) Design and synthesis of an affinity probe that targets caspases in proteomic experiments. Tetrahedron Lett. 44, 1043-1046.
45. Speers, A. E., Adam, G. C., and Cravatt, B. F. (2003) Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc. 125, 4686-4687.
46. Papp, B., Pal, C., and Hurst, L. D. (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424, 194-197.
47. Govorun, V. M. and Archakov, A. I. (2002) Proteomic technologies in modern biomedical science. Biochemistry (Mosc) 67, 1109-1123.
48. Auerbach, D., Thaminy, S., Hottiger, M. O., and Stagljar, I. (2002) The post-genomic era of interactive proteomics: facts and perspectives. Proteomics 2, 611-623.
49. Fromont-Racine, M., Rain, J. C., and Legrain, P. (1997) Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16, 277-282.
50. Stagljar, I., Korostensky, C., Johnsson, N., and te Heesen, S. (1998) A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA 95, 5187-5192.
51. Uetz, P., Giot, L., Cagney, G., et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
52. Puig, O., Caspary, F., Rigaut, G., et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229.
53. Gavin, A. C., Bosche, M., Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
54. Nelson, T. J., Backlund, P. S.. Jr., Yergey, A. L., and Alkon, D. L. (2002) Isolation of protein subpopulations undergoing protein-protein interactions. Mol. Cell. Proteomics 1, 253-259.
55. 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.
56. Wu, C. C. and Yates, J. R., III. (2003) The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 21, 262-267.
57. Wu, C. C., MacCoss, M. J., Howell, K. E., and Yates, J. R., III. (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 21, 532-538.
58. Mann, M., Jensen, O. N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255-261.