All about DIGE: Quantification technology for differential-display 2D-gel proteomics

Expert Review of Proteomics

Volumn 1, Issue 4, 2004, Pages 401-409

  Lilley, Kathryn S ^a   Friedman, David B ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

2D DIGE; 2D PAGE; Minimal CyDyes; Quantitative proteomics; Saturation CyDyes

Indexed keywords

BIOLOGICAL MARKER; PROTEOME;

BIOTECHNOLOGY; DIAGNOSTIC TEST; IMAGE DISPLAY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; SENSITIVITY ANALYSIS; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS; TWO DIMENSIONAL GEL ELECTROPHORESIS; ANIMAL; ARTICLE; BRAIN LEVEL; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MOUSE;

ANIMALS; BRAIN CHEMISTRY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION PROFILING; MICE; PROTEOME; PROTEOMICS;

EID: 27744583045     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.1.4.401     Document Type: Review

References (46)

1. Petricoin EF, Wulfkuhle J, Espina V, Liotta LA. Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. J. Proteome Res. 3, 209-217 (2004).
2. Malone J, Radabaugh M, Leimgruber R, Gerstenecker G. Practical aspects of fluorescent staining for proteomic applications. Electrophoresis 22, 919-932 (2001).
3. Ünlü M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077 (1997).
4. Lilley KS, Razzaq A, Dupree P. Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. Curr. Opin. Chem. Biol. 6, 46-50 (2002).
5. Tonge R, Shaw J, Middleton B et al. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377-396 (2001).
6. Shaw J, Rowlinson R, Nickson J et al. Evaluation of saturation labeling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 3, 1181-1195 (2003).
7. Wheeler JX, Wait R, Stone T et al. Mass spectrometric analysis of maleimide CyDye labeled model peptides. Rapid Commun. Mass Spectrom. 17, 2563-2566 (2003).
8. Alban A, David SO, Bjorkesten L et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 36-44 (2003).
9. Knowles MR, Cervino S, Skynner HA et al. Multiplex proteomic analysis by two-dimensional differential in-gel electrophoresis Proteomics 3, 1162-1171 (2003).
10. Friedman DB, Hill S, Keller JW et al. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 4, 793-811 (2004).
11. Wang D, Jensen R, Gendeh G, Williams K, Pallavicini MG. Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4. J. Proteome Res. 3, 627-635 (2004).
12. Prabakaran S, Swatton JE, Ryan MM et al. Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Mol. Psychiatry 9, 684-697 (2004).
13. Zhang YQ, Matthies HJ, Mancuso J et al. The Drosophila fragile X-related gene regulates axoneme differentiation during spermatogenesis. Dev. Biol. 270, 290-307 (2004).
14. Seike M, Kondo T, Fujii K et al. Proteomic signature of human cancer cells. Proteomics 4, 2776-2788 (2004).
15. Yokoo H, Kondo T, Fujii K, Yamada T, Todo S, Hirohashi S. Proteomic signature corresponding to alpha fetoprotein expression in liver cancer cells. Hepatology 40, 609-617 (2004).
16. 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. 5, 240-251 (2003).
17. Gharbi S, Gaffney P, Yang A et al. Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol. Cell. Proteomics 1, 91-98 (2002).
18. Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnol. 20, 512-515 (2002).
19. Hu Y, Wang G, Chen GY, Fu X, Yao SQ. Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 24, 1458-1470 (2003).
20. Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol. Cell. Biol. 24, 8276-8287 (2004).
21. Gong L, Puri M, Unlu M et al. Drosophila ventral furrow morphogenesis: a proteomic analysis. Development 131, 643-656 (2004).
22. Kernec F, Unlu M, Labeikovsky W, Minden JS, Koretsky AP. Changes in the mitochondrial proteome from mouse hearts deficient in creatine kinase. Physiol. Genomics 6, 117-128 (2001).
23. Skynner HA, Rosahl TW, Knowles MR et al. Alterations of stress related proteins in genetically altered mice revealed by two-dimensional differential in-gel electrophoresis analysis. Proteomics 2, 1018-1025 (2002).
24. Sakai J, Ishikawa H, Kojima S, Satoh H, Yamamoto S, Kanaoka M. Proteomic analysis of rat heart in ischemia and ischemia-reperfusion using fluorescence two-dimensional difference gel electrophoresis. Proteomics 3, 1318-1324 (2003).
25. 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 3, 1758-1766 (2003).
26. 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 h isoforms. Biochem. J. 378, 497-507 (2004).
27. Zuo X, Echan L, Hembach P et al. Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two-dimensional gels and using one-dimensional gels for insoluble and large proteins. Electrophoresis 22, 1603-1615 (2001).
28. Gorg 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 2, 1652-1657 (2002).
29. Klose J, Nock C, Herrmann M et al. Genetic analysis of the mouse brain proteome. Electrophoresis 24, 1471-1481 (2003).
30. 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 24, 1471-1481 (2003).
31. Santoni V, Molloy M, Rabilloud T. Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 1054-1070 (2000).
32. Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591-6596 (1999).
33. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994-999 (1999).
34. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456-2465 (2001).
35. Mason DE, Liebler DC. Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. J. Proteome Res. 2, 265-272 (2003).
36. 15N-metabolic labeling. Anal. Chem. 73, 2132-2139 (2001).
37. Ong S, Blagoev B, Kratchmarova I et al. 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).
38. Krijgsveld J, Ketting R, Mahmoudi T et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nature Biotechnol. 21, 927-931 (2003).
39. Li J, Steen H, Gygi SP. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol. Cell. Proteomics 2, 1198-1204 (2003).
40. Ross P, Huang Y, Marchese J et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics (2004) (In Press).
41. Chaurand P, Stoeckli M, Caprioli RM. Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal. Chem. 71, 5263-5270 (1999).
42. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nature Med. 7, 493-496 (2001).
43. Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM. Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clin. Cancer Res. 10, 981-987 (2004).
44. Reyzer ML, Hsieh Y, Ng K, Korfmacher WA, Caprioli RM. Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 38, 1081-1092 (2003).
45. Yanagisawa K, Shyr Y, Xu BJ et al. Proteomic patterns of tumor subsets in non-small-cell lung cancer. Lancet 362, 433-439 (2003).
46. Haab BB. Methods and applications of antibody microarrays in cancer research. Proteomics 3, 2116-2122 (2003).