High resolution protein display by two-dimensional electrophoresis

Current Analytical Chemistry

Volumn 5, Issue 2, 2009, Pages 106-115

  Van den Bergh, Gert ^a   Arckens, Lutgarde ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

2 D DIGE; Glycosylation; Phosphorylation; Protein prefractionation; Proteomics; Two dimensional electrophoresis

Indexed keywords

CHROMATOGRAPHY; ELECTROPHORESIS; MOLECULAR BIOLOGY;

2-D DIGE; GLYCOSYLATIONS; HIGH RESOLUTION; LARGE-SCALE ANALYSIS; PREFRACTIONATION; PROTEIN EXPRESSIONS; PROTEIN PREFRACTIONATION; PROTEOMICS; TECHNICAL ADVANCES; TWO DIMENSIONAL ELECTROPHORESIS;

PROTEINS;

EID: 67649949033     PISSN: 15734110     EISSN: None     Source Type: Journal    
DOI: 10.2174/157341109787846199     Document Type: Review

References (77)

1. O'Farrell, P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem., 1975, 250, 4007-21.
2. Klose, J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik, 1975, 26, 231-43.
3. rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol., 2001, 19, 242-47.
4. Gevaert, K.; Goethals, M.; Martens, L.; Van Damme, J.; Staes, A.; Thomas, G.R.; Vandekerckhove, J. Exploring proteomes and analysing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol., 2003, 21, 566-69.
5. Gevaert, K.; Van Damme, P.; Martens, L.; Vandekerckhove, J. Diagonal reverse-phase chromatography applications in peptidecentric proteomics: ahead of catalogue-omics? Anal. Biochem., 2005, 345, 18-29.
6. 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, 994-99.
7. DeSouza, L.; Diehl, G.; Rodrigues, M.J.; Guo, J.; Romaschin, A.D.; Colgan, T.J.; Siu, K.W. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res., 2005, 4, 377-86.
8. Choe, L.H.; Aggarwal, K.; Franck, Z.; Lee, K.H. A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis, 2005, 26, 2437-49.
9. Wu, W.W.; Wang, G.; Baek, S.J.; Shen, R.F. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res., 2006, 5, 651-58.
10. Simpson, R. Proteins and Proteomics, Cold Spring Harbor Laboratory Press: Woodbury NY, 2003.
11. Westermeier, R.; Postel, W.; Weser, J.; Gorg, A. High-resolution two-dimensional electrophoresis with isoelectric focusing in immobilized pH gradients. J. Biochem. Biophys. Methods, 1983, 8, 321-30.
12. Görg, A.; Obermaier, C.; Boguth, G.; Harder, A.; Scheibe, B.; Wildgruber, R.; Weiss, W. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis, 2000, 21, 1037-53.
13. Görg, A.; Weiss, W.; Dunn, M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics, 2004, 4, 3665-85.
14. Miller, I.; Crawford, J.; Gianazza, E. Protein stains for proteomic applications: which, when, why? Proteomics, 2006, 6, 5385-408.
15. Bernhardt, J.; Buttner, K.; Scharf, C.; Hecker, M. Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis, 1999, 20, 2225-40.
16. Hecker, M.; Volker, U. Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics, 2004, 4, 3727-50.
17. Berggren, K.; Chernokalskaya, E.; Steinberg, T.H.; Kemper, C.; Lopez, M.F.; Diwu, Z.; Haugland, R.P.; Patton, W.F. Backgroundfree, high sensitivity staining of proteins in one- and twodimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis, 2000, 21, 2509-21.
18. Bell, P.J.; Karuso, P. Epicocconone, a novel fluorescent compound from the fungus epicoccumnigrum. J. Am. Chem. Soc., 2003, 125, 9304-5.
19. Mackintosh, J.A.; Choi, H.Y.; Bae, S.H.; Veal, D.A.; Bell, P.J.; Ferrari, B.C.; Van Dyk, D.D.; Verrills, N.M.; Paik, Y.K.; Karuso, P. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics, 2003, 3, 2273-88.
20. Raman, B.; Cheung, A.; Marten, M.R. Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie. Electrophoresis, 2002, 23, 2194-202.
21. Rosengren, A.T.; Salmi, J.M.; Aittokallio, T.; Westerholm, J.; Lahesmaa, R.; Nyman, T.A.; Nevalainen, O.S. Comparison of PDQuest and Progenesis software packages in the analysis of twodimensional electrophoresis gels. Proteomics, 2003, 3, 1936-46.
22. Stasyk, T.; Huber, L.A. Zooming in: fractionation strategies in proteomics. Proteomics, 2004, 4, 3704-16.
23. Craven, R.A.; Banks, R.E. Laser capture microdissection and proteomics: possibilities and limitation. Proteomics, 2001, 1, 1200-4.
24. Shaw, J.; Rowlinson, R.; Nickson, J.; Stone, T.; Sweet, A.; Williams, K.; Tonge, R. Evaluation of saturation labelling twodimensional difference gel electrophoresis fluorescent dyes. Proteomics, 2003, 3, 1181-95.
25. Huber, L.A.; Pfaller, K.; Vietor, I. Organelle proteomics: implications for subcellular fractionation in proteomics. Circ. Res., 2003, 92, 962-68.
26. Vercauteren, F.G.; Flores, G.; Ma, W.; Chabot, J.G.; Geenen, L.; Clerens, S.; Fazel, A.; Bergeron, J.J.; Srivastava, L.K.; Arckens, L.; Quirion, R. An organelle proteomic method to study neurotransmission-related proteins, applied to a neurodevelopmental model of schizophrenia. Proteomics, 2007, 7, 3569-79.
27. Zischka, H.; Weber, G.; Weber, P.J.; Posch, A.; Braun, R.J.; Bühringer, D.; Schneider, U.; Nissum, M.; Meitinger, T.; Ueffing, M.; Eckerskorn, C. Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis. Proteomics, 2003, 3, 906-16.
28. Rabilloud, T.; Kieffer, S.; Procaccio, V.; Louwagie, M.; Courchesne, P.L.; Patterson, S.D.; Martinez, P.; Garin, J.; Lunardi, J. Two-dimensional electrophoresis of human placental mitochondria and protein identification by mass spectrometry: toward a human mitochondrial proteome. Electrophoresis, 1998, 19, 1006-14.
29. Murayama, K.; Fujimura, T.; Morita, M.; Shindo, N. One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles. Electrophoresis, 2001, 22, 2872-80.
30. Kernec, F.; Ünlü, M.; Labeikovsky, W.; Minden, J.S.; Koretsky, A.P. Changes in the mitochondrial proteome from mouse hearts deficient in creatine kinase. Physiol. Genomics, 2001, 6, 117-28.
31. Molloy, M.P.; Herbert, B.R.; Walsh, B.J.; Tyler, M.I.; Traini, M.; Sanchez, J.C.; Hochstrasser, D.F.; Williams, K.L.; Gooley, A.A. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis, 1998, 19, 837-44.
32. Taylor, C.M.; Pfeiffer, S.E. Enhanced resolution of glycosylphosphatidylinositol-anchored and transmembrane proteins from the lipid-rich myelin membrane by two-dimensional gel electrophoresis. Proteomics, 2003, 3, 1303-12.
33. Helling, S.; Schmitt, E.; Joppich, C.; Schulenborg, T.; Müllner, S.; Felske-Müller, S.; Wiebringhaus, T.; Becker, G.; Linsenmann, G.; Sitek, B.; Lutter, P.; Meyer, H.E.; Marcus, K. 2-D differential membrane proteome analysis of scarce protein samples. Proteomics, 2006, 6, 4506-13.
34. Badock, V.; Steinhusen, U.; Bommert, K.; Otto, A. Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography. Electrophoresis, 2001, 22, 2856-64.
35. Van den Bergh, G.; Clerens, S.; Vandesande, F.; Arckens, L. 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, 2003, 24, 1471-81.
36. Shin, J.H.; Krapfenbauer, K.; Lubec, G. Large-scale identification of cytosolic mouse brain proteins by chromatographic prefractionation. Electrophoresis, 2006, 27, 2799-813.
37. Görg, A.; Boguth, G.; Kopf, A.; Reil, G.; Parlar, H.; Weiss, W. Sample prefractionation with Sephadex isoelectric focusing prior to narrow pH range two-dimensional gels. Proteomics, 2002, 2, 1652-57.
38. Rill, R.L.; Al-Sayah, M.A. Peptide separations by slab gel electrophoresis in pluronic F127 polymer liquid crystals. Electrophoresis, 2004, 25, 1249-54.
39. McDonough, J.; Marban, E. Optimization of IPG strip equilibration for the basic membrane protein mABC1. Proteomics, 2005, 5, 2892-95.
40. Herbert, B.; Galvani, M.; Hamdan, M.; Olivieri, E.; MacCarthy, J.; Pedersen, S.; Righetti, P.G. Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how? Electrophoresis, 2001, 22, 2046-57.
41. Thulasiraman, V.; Lin, S.; Gheorghiu, L.; Lathrop, J.; Lomas, L.; Hammond, D.; Boschetti, E. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis, 2005, 26, 3561-71.
42. Righetti, P.G.; Castagna, A.; Antonioli, P.; Boschetti, E. Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis, 2005, 26, 297-319.
43. Righetti, P.G.; Boschetti, E.; Lomas, L.; Citterio, A. Protein Equalizer Technology: the quest for a "democratic proteome". Proteomics, 2006, 6, 3980-92.
44. Lam, K.S.; Salmon, S.E.; Hersh, E.M.; Hruby, V.J.; Kazmierski, W.M.; Knapp, R.J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature, 1991, 354, 82-84.
45. Castagna, A.; Cecconi, D.; Sennels, L.; Rappsilber, J.; Guerrier, L.; Fortis, F.; Boschetti, E.; Lomas, L.; Righetti, P.G. Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res., 2005, 4, 1917-30.
46. Greenough, C.; Jenkins, R.E.; Kitteringham, N.R.; Pirmohamed, M.; Park, B.K.; Pennington, S.R. A method for the rapid depletion of albumin and immunoglobulin from human plasma. Proteomics, 2004, 4, 3107-11.
47. Granger, J.; Siddiqui, J.; Copeland, S.; Remick, D. Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics, 2005, 5, 4713-18.
48. Ünlü, M.; Morgan, M.E.; Minden, J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis, 1997, 18, 2071-77.
49. Tonge, R.; Shaw, J.; Middleton, B.; Rowlinson, R.; Rayner, S.; Young, J.; Pognan, F.; Hawkins, E.; Currie, I.; Davison, M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics, 2001, 1, 377-96.
50. Van den Bergh, G.; Arckens, L. Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics. Curr. Opin. Biotechnol., 2004, 15, 38-43.
51. Van den Bergh, G.; Clerens, S.; Cnops, L.; Vandesande, F.; Arckens, L. Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat. J. Neurochem., 2003, 85, 193-205.
52. Van den Bergh, G.; Clerens, S.; Firestein, B.L.; Burnat, K.; Arckens, L. Development and plasticity-related changes in protein expression patterns in cat visual cortex: a fluorescent twodimensional difference gel electrophoresis approach. Proteomics, 2006, 6, 3821-32.
53. Zhou, G.; Li, H.; DeCamp, D.; Chen, S.; Shu, H.; Gong, Y.; Flaig, M.; Gillespie, J.W.; Hu, N.; Taylor, P.R.; Emmert-Buck, M.R.; Liotta, L.A.; Petricoin, E.F.; 3rd, Zhao, Y. 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol. Cell. Proteomics, 2002, 1, 117-24.
54. Sakai, J.; Ishikawa, H.; Kojima, S.; Satoh, H.; Yamamoto, S.; Kanaoka, M. Proteomic analysis of rat heart in ischemia and ischemiareperfusion using fluorescence two-dimensional difference gel electrophoresis. Proteomics, 2003, 3, 1318-24.
55. Alban, A.; David, S.O.; Bjorkesten, L.; Andersson, C.; Sloge, E.; Lewis, S.; Currie, I. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics, 2003, 3, 36-44.
56. Gade, D.; Thiermann, J.; Markowsky, D.; Rabus, R. Evaluation of two-dimensional difference gel electrophoresis for protein profiling. Soluble proteins of the marine bacterium Pirellula sp. strain 1. J. Mol. Microbiol. Biotechnol., 2003, 5, 240-51.
57. Knowles, M.R.; Cervino, S.; Skynner, H.A.; Hunt, S.P.; de Felipe, C.; Salim, K.; Meneses-Lorente, G.; McAllister, G.; Guest, P.C. Multiplex proteomic analysis by two-dimensional differential ingel electrophoresis. Proteomics, 2003, 3, 1162-71.
58. Seike, M.; Kondo, T.; Mori, Y.; Gemma, A.; Kudoh, S.; Sakamoto, .; Yamada, T.; Hirohashi, S. Proteomic analysis of intestinal epithelial cells expressing stabilized beta-catenin. Cancer Res., 2003, 63, 4641-47.
59. Wheelock, A.M.; Zhang, L.; Tran, M.U.; Morin, D.; Penn, S.; Buckpitt, A.R.; Plopper, C.G. Isolation of rodent airway epithelial cell proteins facilitates in vivo proteomics studies of lung toxicity. Am. J. Physiol. Lung Cell. Mol. Physiol., 2004, 286, L399-410.
60. Kondo, T.; Seike, M.; Mori, Y.; Fujii, K.; Yamada, T.; Hirohashi, S. Application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool. Proteomics, 2003, 3, 1758-66.
61. Kondo, T.; Hirohashi, S. Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics. Nat. Protoc., 2006, 1, 2940-56.
62. Wilson, K.E.; Marouga, R.; Prime, J.E.; Pashby, D.P.; Orange, P.R.; Crosier, S.; Keith, A.B.; Lathe, R.; Mullins, J.; Estibeiro, P.; Bergling, H.; Hawkins, E.; Morris, C.M. Comparative proteomic analysis using samples obtained with laser microdissection and saturation dye labelling. Proteomics, 2005, 5, 3851-58.
63. Maeda, K.; Finnie, C.; Svensson, B. Cy5 maleimide labelling for sensitive detection of free thiols in native protein extracts: identification of seed proteins targeted by barley thioredoxin hisoforms. Biochem. J., 2004, 378, 497-507.
64. Biron, D.G.; Brun, C.; Lefevre, T.; Lebarbenchon, C.; Loxdale, H.D.; Chevenet, F.; Brizard, J.P.; Thomas, F. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics, 2006, 6, 5577-96.
65. Karp, N.A.; Kreil, D.P.; Lilley, K.S. Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics, 2004, 4, 1421-32.
66. Fodor, I.K.; Nelson, D.O.; Alegria-Hartman, M.; Robbins, K.; Langlois, R.G.; Turteltaub, K.W.; Corzett, T.H.; McCutchen-Maloney, S.L. Statistical challenges in the analysis of twodimensional difference gel electrophoresis experiments using De-Cyder. Bioinformatics, 2005, 21, 3733-40.
67. Reiner, A.; Yekutieli, D.; Benjamini, Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 2003, 19, 368-75.
68. Kreil, D.P.; Karp, N.A.; Lilley, K.S. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics, 2004, 20, 2026-34.
69. Yokoo, H.; Kondo, T.; Fujii, K.; Yamada, T.; Todo, S.; Hirohashi, S. Proteomic signature corresponding to alpha fetoprotein expression in liver cancer cells. Hepatology, 2004, 40, 609-17.
70. Hoorn, E.J.; Hoffert, J.D.; Knepper, M.A. Combined proteomics and pathways analysis of collecting duct reveals a protein regulatory network activated in vasopressin escape. J. Am. Soc. Nephrol., 2005, 16, 2852-63.
71. Chen, Z.; Southwick, K.; Thulin, C.D. Initial analysis of the phosphoproteome of Chinese hamster ovary cells using electrophoresis. J. Biomol. Tech., 2004, 15, 249-56.
72. Soskic, V.; Gorlach, M.; Poznanovic, S.; Boehmer, F.D.; Godovac-Zimmermann, J. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor. Biochemistry, 1999, 38, 1757-64.
73. Gravel, P.; Walzer, C.; Aubry, C.; Balant, L.P.; Yersin, B.; Hochstrasser, D.F.; Guimon, J. New alterations of serum glycoproteins in alcoholic and cirrhotic patients revealed by high resolution two-dimensional gel electrophoresis. Biochem. Biophys. Res. Commun., 1996, 220, 78-85.
74. Schulenberg, B.; Aggeler, R.; Beechem, J.M.; Capaldi, R.A.; Patton, W.F. Analysis of steady-state protein phosphorylation in mitochondria using a novel fluorescent phosphosensor dye. J. Biol. Chem., 2003, 278, 27251-55.
75. Steinberg, T.H.; Pretty On Top, K.; Berggren, K.N.; Kemper, C.; Jones, L.; Diwu, Z.; Haugland, R.P.; Patton, W.F. Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots. Proteomics, 2001, 1, 841-55.
76. Hart, C.; Schulenberg, B.; Steinberg, T.H.; Leung, W.Y.; Patton, W.F. Detection of glycoproteins in polyacrylamide gels and on electroblots using Pro-Q Emerald 488 dye, a fluorescent periodate Schiff-base stain. Electrophoresis, 2003, 24, 588-98.
77. Schulenberg, B.; Beechem, J.M.; Patton, W.F. Mapping glycosylation changes related to cancer using the Multiplexed Proteomics technology: a protein differential display approach. J. Chromatogr. B Anal. Technol. Biomed. Life Sci., 2003, 793, 127-39.