2D protein electrophoresis: Can it be perfected?

Current Opinion in Biotechnology

Volumn 10, Issue 1, 1999, Pages 16-21

  Celis, Julio E ^a   Gromov, Pavel ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSTIC TEST; DRUG DEVELOPMENT; DRUG INDUSTRY; GENE EXPRESSION; HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 0032948126     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(99)80004-4     Document Type: Article

References (40)

1. Celis JE, Bravo R Two-Dimensional Gel Electrophoresis of Proteins: Methods and Applications. 1984;Academic Press, New York.
2. Celis JE, Østergaard M, Jensen NA, Gromova I, Rasmussen HH, Gromov P Human and mouse proteomic databases: novel resources in the protein universe. FEBS Lett. 430:1998;64-72.
3. Wilkins MR, Williams KL, Appel RD, Hochstrasser DF Proteomic Research: New Frontiers in Functional Genomics (Principles and Practice). 1997;Springer Verlag, Berlin. Perhaps the most comprehensive compendium of proteome data published so far. It describes the elements of proteome technology, points towards future developments, and highlights areas of research where proteomic technologies are making an impact.
4. Williams KL Strategies in Proteome Research. In Electrophoresis. 19:1998;1853-2050. This special issue of Electrophoresis gives an overall perspective of the potential and limitations of the proteome technology. It includes some applications of the technology in cell biology.
5. O'Farrell PH High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 250:1975;4007-4021.
6. O'Farrell PZ, Goodman HM, O'Farrell PH High resolution two-dimensional electrophoresis of basic as well as acidic proteins. Cell. 12:1977;1133-1141.
7. 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. 26:1975;231-243.
8. Celis JE, Gromov PS, Østergaard M, Gromova I, Madsen P, Varmark H, Jensen NA, Rasmussen HH: Human proteomic databases: a novel resource for functional genomics in health and disease. Progr Biophys Mol Biol 1999, in press.
9. Anderson NL, Anderson NG Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis. 19:1998;1853-1861. An overview of the beginning of the proteomic field, previously called 'Molecular Anatomy Programme'. In additon, it emphasizes the need for comprehensive quantitative studies of reasonably large datasets.
10. Walsh BJ, Molloy MP, Williams KL The Australian Proteome Analysis Facility (APAF): assembling large scale proteomics through integration and automation. Electrophoresis. 19:1998;1883-1890. This paper describes the setting-up of a national core facility for high-throughput proteomics studies. Examples of human tears and Dictiostelium discoideum are given.
11. Celis JE Proteomics: key technology in drug discovery. Drug Discov Today. 3:1998;193-195.
12. Mullner S, Neumann T, Lottspeich F Proteomics - a new way for drug target discovery. Arzneimittelforschung. 48:1998;93-95.
13. Celis JE, Carter N, Hunter T, Shotton D, Simons K, Small JV Cell Biology: A laboratory Handbook, vol 4, edn 2. 1997;Academic Press, New York.
14. Aebersold RH, Teplow DB, Hood LE, Kent SB Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis. J Biol Chem. 261:1986;4229-4238.
15. Matsudaira P Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 262:1987;10035-10038.
16. Bauw G, Van Damme J, Puype M, Vandekerckhove J, Gesser B, Ratz GP, Lauridsen JB, Celis JE Protein-electroblotting and microsequencing strategies in generating protein data bases from two-dimensional gels. Proc Natl Acad Sci USA. 86:1989;7701-7705.
17. Mann M, Wilm M Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem. 66:1994;4390-4399.
18. Yates JR, Eng JK, McCormack AL, Schieltz D Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 67:1995;1426-1436.
19. Schevchenko A, Wilm M, Mann M Peptide sequencing by mass spectrometry for homology searches and cloning genes. J Protein Chem. 16:1997;481-490. The authors describe how to sequence peptide fragments from proteins recovered from gels using mass spectrometry at the low picomole to fentomole levels.
20. Celis JE, Lauridsen JB, Basse B Determination of antibody specificity by Western blotting and immunoprecipitation. Celis JE, Carter N, Hunter T, Simons K, Small JV. Cell Biology: A Laboratory Handbook, edn 2. 1997;429-438 Academic Press, New York.
21. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al.: Life with 6000 genes. Science 1996, 274:546, 563-567.
22. Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tome P, Aggarwal A, Bajorek Eet al. A gene map of the human genome. Science. 274:1996;540-546.
23. Duncan R, McConkey EH How many proteins are there in a typical mammalian cell? Clin Chem. 28:1982;749-755.
24. Celis JE, Rasmussen HH, Leffers H, Madsen P, Honore B, Gesser B, Dejgaard K, Vandekerckhove J Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing. FASEB J. 5:1991;2200-2208.
25. Celis JE, Rasmussen HH, Gromov P, Olsen E, Madsen P, Leffers H, Honore B, Dejgaard K, Vorum H, Kristensen DB The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways. Electrophoresis. 16:1995;2177-2240.
26. Gooley AA, Packer NH The importance of protein co- and post-translational modifications in proteome projects. Wilkins MR, Williams KL, Appel RD, Hochstrasser DF Proteome Research: New Frontiers in Functional Genomics (Principles and Practice). 1997;Springer Verlag, Berlin. This overviews post-translational modifications and outlines important features that distinguish proteomic from genomic projects. It also describes procedures to determine the nature and localization of the modifications.
27. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, Westermeier R, Postel W Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods. 6:1982;317-339.
28. Görg A, Postel W, Gunther S The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis. 9:1988;531-546.
29. Righetti PG, Bossi A Isoelectric focusing in immobilised pH gradients: an update. J Chromatogr B Biomed Sci Appl. 699:1997;77-89. A review of the latest developments on isoelectric focusing in immobilised pH gradients; it highlights the advantages of combining this technique with SDS-PAGE to obtain a high resolution gel separation procedure.
30. Görg A, Boguth G, Obermaier C, Weiss W Two-dimensional electrophoresis of proteins in an immobilized pH 4-12 gradient. Electrophoresis. 19:1998;1516-1519.
31. Righetti PG, Bossi A Isoelectric focusing in immobilized pH gradients: recent analytical and preparative developments. Anal Biochem. 247:1997;1-10.
32. Bjellqvist B, Basse B, Olsen E, Celis JE Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis. 15:1994;529-539.
33. Nawrocki A, Larsen MR, Podtelejnikov AV, Jensen ON, Mann M, Roepstorff P, Görg A, Fey SJ, Larsen PM Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification. Electrophoresis. 19:1998;1024-1035. A thorough comparison between yeast protein patterns obtained by using carrier ampholyte- and IPG-based 2D gel technology. It clearly emphasizes the need of using protein identification techniques (MALDI-MS) to assess the identity of polypeptides having similar coordinates, that is molecular weight and pI.
34. Görg A, Obermaier C, Boguth G, Csodas A, Diaz JJ, Madjar JJ Very alkaline immobilised pH gradients for two-dimensional electrophoresis of ribosomal and nuclear proteins. Electrophoresis. 18:1997;328-337. HeLa, mouse liver ribosomes and chicken erythrocyte histones were separated using highly reproducible very alkaline pH gradients.
35. Klose J, Kobalz U Two-dimensional electrophoresis of proteins: an update protocol and implications for a functional analysis of the genome. Electrophoresis. 16:1995;1034-1059.
36. Tang W, Harrata AK, Lee CS Two-dimensional analysis of recombinant E. coli proteins using capillary isoelectric focusing electrospray ionization mass spectrometry. Anal Chem. 69:1997;3177-3182.
37. Rabilloud T, Adessi C, Giraudel A, Lunardi J Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis. 18:1997;307-316. Detergents and chaotropes are used to improve the solubility and 2D gel resolution of membrane proteins.
38. Chevallet M, Santoni V, Poinas A, Rouquie D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis. 19:1998;1901-1909.
39. Gromov P, Celis JE Blot overlay assay for identification of GTP-binding proteins. Celis JE, Carter N, Hunter T, Shotton D, Simons K, Small JV. Cell Biology: A Laboratory Handbook, edn 2. 1997;Academic Press, New York.
40. Steinberg TH, Haugland RP, Singer VL Application of SYPRO orange and SYPRO red protein gel stains. Anal Biochem. 239:1996;238-245.