Making blind robots see: The synergy between fluorescent dyes and imaging devices in automated proteomics

BioTechniques

Volumn 28, Issue 5, 2000, Pages 944-957

  Patton, Wayne F ^a  

^a MOLECULAR PROBES INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CELLULAR DISTRIBUTION; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN SYNTHESIS;

EID: 0034075850     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/00285rv01     Document Type: Article

References (65)

1. Alba, F., A. Bermudez, S. Bartolome and J. Daban. 1996. Detection of five nanograms of protein by two-minute Nile red staining of unfixed SDS gels. BioTechniques 21:625-626.
2. Alba, F. and J. Daban. 1998. Rapid fluorescent monitoring of total protein patterns on sodium dodecyl sulfate-polyacrylamide gels and western blots before immunodetection and sequencing. Electrophoresis 19:2407-2411.
3. Allen, R. and B. Budowle. 1999. Protein Staining and Identification Techniques. BioTechniques Molecular Laboratory Methods Series, Eaton Publishing, Natick, MA.
4. Anderson, L. and J. Seilhamer. 1997. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537.
5. Berggren, K., T. Steinberg, C. Kemper, M. Lopez, C. Chernokalskaya, Z. Diwu, R. Haugland and W. Patton. Background-free, high-sensitivity staining of proteins in one-and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis (In Press).
6. Berggren, K., T. Steinberg, W. Lauber, J. Carroll, M. Lopez, E. Chernokalskaya, L. Zieske, Z. Diwu, R. Haugland and W. Patton. 1999. A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports. Anal. Biochem. 272:129-143.
7. Bermudez, A., J. Daban, J. Garcia and E. Mendez. 1994. Direct blotting, sequencing and immunodetection of proteins after five-minute staining of SDS and SDS-treated IEF gels with Nile Red. BioTechniques 16:621-624.
8. Berndt, P., U. Hobohm and H. Langen. 1999. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20:3521-3526.
9. Blomberg, A., L. Blomberg, J. Norbeck, S. Fey, P. Mose-Larsen, M. Larsen, P. Roepstorff, H. Degand, M. Boutry et al. 1995. Interlaboratory reproducibility of yeast protein patterns analyzed by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 16:1935-1945.
10. Boulikas, T. 1995. Phosphorylation of transcription factors and control of the cell cycle. Crit. Rev. Eukaryot. Gene Expr. 5:1-77.
11. Brush, M. 1998. Dye hard: protein gel staining products. The Scientist 12:16-22.
12. Daban, J., S. Bartolome and A. Bermudez. 1996. Rapid staining of proteins in polyacrylamide gels, p. 179-185. In J. Walker (Ed.), The Protein Protocols Handbook. Humana Press, Totowa, NJ.
13. Daban, J., S. Bartolome and M. Samso. 1991. Use of the hydrophobic probe Nile Red for the fluorescent staining of protein bands in sodium dodecyl sulfate-polyacrylamide gels. Anal. Biochem. 199:169-174.
14. Fey, S., A. Nawrocki, M. Larsen, A. Gorg, P. Roepstorff, G. Skews, R. Williams and P. Larsen. 1997. Proteome analysis of Saccharomyces cerevisiae: a methodological outline. Electrophoresis 18:1361-1372.
15. Gharahdaghi, F., C. Weinberg, D. Meagher, B. Imai and S. Mische. 1999. Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20:601-605.
16. Gwynne, P. and G. Page. 1999. Protein + protein interactions. Science 286::1759-1773.
17. Gygi, S., B. Rist, S. Gerber, F. Turecek, M. Gelb and R. Aebersold. 1999 Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-999.
18. Gygi, S., Y. Rochon, B. Franza and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730.
19. Hamby, R. 1996. A sensitive fluorescent gel stain. Am. Biotechnol. Lab. 14:12.
20. Hamby, R. 1997. A fluorescent gel stain for detection of proteins following 1-D, 2-D and native polyacrylamide gel electrophoresis. Biotechnol. Int. 1:339-343.
21. Hardie, D. 1990. Roles of protein kinases and phosphatases in signal transduction. Symp. Soc. Exp. Biol. 44:241-255.
22. 2-induced filamin redistribution in endothelial cells is modulated by the cyclic AMP dependent protein kinase pathway. J. Cell. Physiol. 172:373-381.
23. Hastie, L., W. Patton, H. Hechtman and D. Shepro. 1997. Hydrogen peroxide-induced filamin translocation in an in vitro model of reoxygenation injury; inhibition by iron chelators and superoxide radical scavengers. Free Radic. Biol. Med. 22:955-966.
24. 2-induced filamin redistribution in endothelial cells. J. Cell. Biochem. 68:511-524.
25. Holton, W. 1994. CCD technology has brought profound changes to the world of bioimaging. BioPhotonics I:43-51.
26. Hucho, F. and K. Buchner. 1997. Signal transduction and protein kinases: the long way from the plasma membrane into the nucleus. Naturwissenschaften 84:281-290.
27. Humphrey-Smith, I. and W. Blackstock. 1997. Proteome analysis: genomics via the output rather than the input code. J. Protein Chem. 16:537-544.
28. Johnson, B. 1999. All's well that ends well; a profile of specially microwell plates. The Scientist 13:16.
29. Karin, M. 1994. Signal transduction from the cell surface to the nucleus through the phosphorylation of transcription factors. Curr. Opin. Cell. Biol. 6:415-424.
30. Krause, E., H. Wenschuh and P. Jungblut. 1999. The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71:4160-4165.
31. Lim, M., W. Patton, N. Shojaee, M. Lopez, K. Spofford and D. Shepro. 1997. A luminescent europium complex for the sensitive detection of proteins and nucleic acids immobilized on membrane supports. Anal. Biochem. 245: 184-195.
32. Lopez, M. 1998. Proteomic databases: road-maps for drug discovery. Am. Biotechnol. Lab. 16:8-9.
33. Lopez, M. 1999. Automating proteome analysis: from soup to nuts. Am. Biotechnol. Lab. 17:44-45.
34. Lopez, M. 1999 Proteome analysis I. Gene products are where the biological action is. J. Chromatogr. B 722:191-202.
35. Lopez, M. and W. Patton. 1997. Reproducibility of polypeptide spot positions in two-dimensional gels run using carrier ampholytes in the isoelectric focusing dimension. Electrophoresis 18:338-343.
36. Mullner, S., T. Neumann and F. Lottspeich. 1998. Proteomics - a new way for drug target discovery. Arzneimittelforschung 48:93-95.
37. Nowak, R. 1995. Entering the postgenome era. Science 270:368-369.
38. Oda, Y., K. Huang, F. Cross, D. Cowburn and B. Chait. 1999. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96:6591-6596.
39. O'Farrell, P. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250:4007-4021.
40. Patton, W. 1995. Biologist's perspective on analytical imaging systems as applied to protein gel electrophoresis. J. Chromatogr. A 698:55-87.
41. Patton, W. 1999. Proteome analysis II. Protein subcellular redistribution: linking physiology to genomics via the proteome and separation technologies involved. J. Chromatogr. B 722:203-223.
42. Patton, W., H. Erdjument-Bromage, A. Marks, M. Taubman and P. Tempst. 1995 Components of the protein synthesis and folding machinery are induced in both hyperplastic and hypertrophic vascular smooth muscle cells. Identification by comparative protein phenotyping and micro-sequencing. J. Biol. Chem. 270:21404-21410.
43. Patton, W., M. Lim and D. Shepro. 1999. Image acquisition in 2-D electrophoresis, p. 353-362. In A. Link (Ed.), Methods in Molecular Biology, Volume 112. 2-D Proteome Analysis Protocols. Humana Press, Totowa, NJ.
44. Patton, W., M. Lim and D. Shepro. 1999. Protein detection using reversible metal chelate stains, p. 331-339. In A. Link (Ed.), Methods in Molecular Biology, Volume 112. 2-D Proteome Analysis Protocols. Humana Press, Totowa, NJ.
45. Patton, W., M. Pluskal, W. Skea, J. Buecker, M. Lopez, R. Zimmerman, L. Belanger and P. Hatch. 1990. Development of a dedicated two-dimensional gel electrophoresis system that provides optimal reproducibility and polypeptide resolution. BioTechniques 8:518-527.
46. Quadroni, M. and P. James. 1999. Proteomics and automation. Electrophoresis 20:664-677.
47. Rabilloud, T. 1999. Silver staining of 2-D electrophoresis gels, p. 297-305. In A. Link (Ed.), Methods in Molecular Biology, Volume 112, 2-D Proteome Analysis Protocols. Humana Press, Totowa, NJ.
48. Rabilloud, T. 2000. Detecting proteins separated by 2-D gel electrophoresis. Anal. Chem. 72:48A-55A
49. Ramm, P. 1999. Imaging systems in assay screening. Drug Discovery Today 4:401-410.
50. Scangos, G. 1997. Drug discovery in the postgenomic era. Nat. Biotechnol. 15:1220-1221.
51. Shevchenko, A., M. Wilm, O. Vorm and M. Mann. 1996. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68:850-858.
52. Steinberg, T., E. Chernokalskaya, K. Berggren, M. Lopez, Z. Diwu, R. Haugland and W. Patton. 2000. Ultrasensitive fluorescence protein detection in isoelectric focusing gels using a ruthenium metal chelate stain. Electrophoresis 21:486-496.
53. Steinberg, T., R. Haugland and V. Singer. 1996 Applications of SYPRO Orange and SYPRO Red protein gel stains. Anal. Biochem. 239:238-245.
54. Steinberg, T., L. Jones, R. Haugland and V. Singer. 1996. SYPRO Orange and SYPRO Red protein gel stains: one-step fluorescent staining of denaturing gels for detection of nanogram levels of protein. Anal. Biochem. 239:223-237.
55. Steinberg, T., W. Lauber, K. Berggren, C. Kemper, S. Vue and W. Patton. 2000. Fluorescence detection of proteins in SDS-polyacrylamide gels using environmentally benign, non-fixative, saline solution. Electrophoresis 21:497-508.
56. Steinberg, T., H. White and V. Singer. 1997. Optimal filter combinations for photographing SYPRO Orange or SYPRO Red dye-stained gels. Anal. Biochem. 248:168-172.
57. Sutherland, J. 1993. Electronic imaging of electrophoretic gels and blots, p. 1-42. In A. Chrambach. M. Dunn and B. Radola (Eds.), Advances in Electrophoresis, Volume 6. VCH Publishers, New York.
58. Unlu, M., M. Morgan and J. Minden. 1997. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071-2077.
59. Urwin, V. and P. Jackson. 1993. Two-dimensional polyacrylamide gel electrophoresis of proteins labeled with the fluorophore monobromobimane prior to first-dimensional isoelectric focusing: imaging of the fluorescent protein spot patterns using a cooled charge-coupled device. Anal. Biochem. 209:57-62.
60. Wang, Q., W. Patton, E. Chiang, H. Hechtman and D. Shepro. 1996. Bradykinin-induced filamin translocation in endothelial cells; regulation by calcium, protein kinases and protein phosphatases. J. Cell. Biochem. 62:383-396.
61. Wang, Q., W. Patton, H. Hechtman and D. Shepro. 1997. A novel, anti-inflammatory peptide inhibits endothelial cell cytoskeletal rearrangement, nitric oxide synthase translocation and paracellular permeability increases. J. Cell. Physiol. 172:171-182.
62. Wang, Q., W. Patton, H. Hechtman and D. Shepro. 1997. Activation of endothelial cell kinin receptors leads to intracellular calcium increases and filamin translocation: regulation by protein kinase C. Cell. Signal. 9:595-602.
63. Wilkins, M., E. Gasteiger, J. Sanchez, A. Bairoch and D. Hochstrasser. 1998. Two dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number. Electrophoresis 19:1501-1505.
64. Wirth, P. and A. Romano. 1995. Staining methods in gel electrophoresis, including the use of multiple detection methods. J. Chromatogr. A. 698:123-143.
65. Woods, A., A. Huang, R. Cotter, G. Pasternack, D. Pardoll and E. Jaffee. 1995. Simplified high sensitivity sequencing of MHC class I-associated, immunoreactive peptides using matrix assisted laser desorption/ionization mass spectrometry. Anal. Biochem. 226:15-25.