Proteomics studies of traumatic brain injury

International Review of Neurobiology

Volumn 61, Issue , 2004, Pages 215-240

  Wang, Kevin K W ^a,b,c   Ottens, Andrew ^a,b,c   Haskins, William ^a,b,c   Liu, Ming Cheng ^a,b,c   Kobeissy, Firas ^a,b,c   Denslow, Nancy ^a,b   Chen, SuShing ^a,b   Hayes, Ronald L ^b,c  

^a UNIVERSITY OF FLORIDA HEALTH   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ANIMAL; BIOLOGY; BRAIN INJURY; DISEASE MODEL; HUMAN; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; BRAIN INJURIES; COMPUTATIONAL BIOLOGY; DISEASE MODELS, ANIMAL; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MASS SPECTROMETRY; PROTEOME; PROTEOMICS;

EID: 16544392510     PISSN: 00747742     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0074-7742(04)61009-9     Document Type: Article

References (74)

1. Adkins, J. N., Varnum, S. M., Auberry, K.J., Moore, R.J., Angell, N. H., Smith, R. D., Springer, D. L., and Pounds, J. G. (2002). Toward a human blood scrum proteome: Analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell Proteomics 1, 947-955.
2. Aebersold, R., and Watts, J. D. (2002). The need for national centers for proteomics. Nature Biotech. 20(7), 651.
3. Appel, R. D., Bairoch, A., and Hochstrasser, D. F. (1999). 2-D databases on the World Wide Web in methods in molecular biology. In "2-D Proteome Analysis Protocols" (A. J. Link, Ed.), vol. 112, pp. 383-391. Humana Press, Totowa, NJ.
4. Axelrod, R. (1976). "Structure of Decision." Princeton University Press, Princeton, NJ.
5. Bienvenut, W. V., Deon, C., Pasquarello, C., Campbell, J. M., Sanchez, J. C., Vestal, M. L., and Hochstrasser, D. F. (2002). Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins. Proteomics 2, 868-876.
6. Bjellqvist, B., Ek, K., Righetti, P. G., Gianazza, E., Gorg, A., and Westermeier, R. (1982). Isoelectric focusing in immobilized pH gradients: Principle, methodology and some applications. J. Biochem. Biophys. Methods 6, 317-339.
7. Boguslavsky, J. (2003). Resolving the proteome by relying on 2DE methods. Drug Discovery Develop. 6(7), 57-60.
8. Cattell, R. G. G. (Ed.) (1996). "The Object Database Standard: ODMG-93." Morgan Kaufmann, San Mateo, CA.
9. Chakravarti, D. N., Chakrarti, B., and Moutsatsos, I. (2003). Informatic tools for proteome profiling. High throughput proteomics; protein arrays. BioTechnoques 3(Suppl.), 4-15.
10. Chen, S. (1988). Knowledge acquisition on neural networks, uncertainty and intelligent systems. In "Lecture Notes in Computer Science" (B. Bouchon, L. Saitta, and R. R. Yager, Eds.), vol. 313, pp. 281-289. Springer-Verlag.
11. Chen, I. A., and Markowitz, V. M. (1995). An overview of the object protocol model (OPM) and the OPM data management tools. Information Systems 20, 393-418.
12. Chen, S., (1986). Some extensions of probabilistic logic, Proc. AAAI Workshop on Uncertainty in Artificial Intelligence, Philadelphia, August 8-10, 1986, pp. 43-48, an extended version appeared in "Uncertainty in Artificial Intelligence," vol. 2, (L. N. Kanal, and J. F. Lemmer Eds.), North-Holland, Amsterdam, Holland.
13. Chen, S. (1987). Automated reasoning on neural networks: A probabilistic approach. IEEE First International Conference on Neural Networks, San Diego, June 21-24, 1987.
14. Chen, S. (2000a). Knowledge discovery of gene functions and metabolic pathways. IEEE BioInformatic and Biomedical Engineering Conference, Washington, November 2000.
15. Chen, S. (1998). "Digital Libraries: The Life Cycle of Information." BE Publisher, Columbus, OH.
16. Davidsson, P., Westman-Brinkmalm, A., Nilsson, C. L., Lindbjer, M., Paulson, L., Andreasen, N., Sjogren, M., and Blennow, K. (2002). Proteome analysis of cerebrospinal fluid proteins in Alzheimer patients. Neuroreport 13(5), 611-615.
17. Denslow, N. D., Michel, M. E., Temple, M. D., Hsu, C., Saatman, K., and Hayes, R. L. (2003). Application of proteomics technology to the field of neurotrauma. J. Neurotrauma 20, 401-407.
18. Derra, S. (2003). Lab-on-a-chip technologies emerging from infancy. Drug Disc. Develop. 6(5), 40-45.
19. Dixon, C. E., Clifton, G. L., Lighthall J. W., Yaghmai, A. A., and Hayes, R. L. (1991). A controlled cortical impact model of traumatic brain injury in the rat. J. Neurosci. Methods 39(3), 253-262.
20. Fang, Z., Polacco, M., Chen, S., Schroeder, S., Hancock, D., Sanchez, H., and Coe, E. (2003). cMap: The comparative genetic map viewer. Bioinformatics 19, 416-417.
21. Finnie, J. (2001). Animal models of traumatic brain injury: A review. Aust. Vet. J. 79(9), 628-633.
22. Fountoulakis, M., Hardmaier, R., Schuller, E., and Lubec, G. (2000). Differences in protein level between neonatal and adult brain. Electrophoresis 21(3), 673-678.
23. Fountoulakis, M., Schuller, E., Hardmeier, R., Berndt, P., and Lubec, G. (1999). Rat brain proteins: Two-dimensional protein database and variations in the expression level. Electrophoresis 20(18), 3572-3579.
24. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940-6945.
25. Goldknopf, I., Park, H. R., and Kuerer, H. M. (2003). Merging diagnostics with therapeutic proteomics. IVD Technology 9(1), 1-6.
26. Gorg, A., Postel, W., and Gunther, S. (1988). The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9, 531-546.
27. Grant, S. G., and Blackstock, W. P. (2001). Proteomics in neuroscience: From protein to network. J. Neurosci. 21(21), 8315-8318.
28. Grant, S. G. N., and Husi, H. (2001). Proteomics of multiprotein complexes: Answering fundamental questions in neuroscience. Trends Biotechnol. (Suppl. 10), S49-S54.
29. Graslund, S., Falk, R., Brundell, E., Hoog, C., and Stahl, S. (2002). A high-stringency proteomics concept aimed for generation of antibodies specific for cDNA-encoded proteins. Biotechnol. Appl. Biochem. 35(Pt 2), 75-82.
30. 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.
31. Gygi, S. P., et al. (2000). Mass spectrometry and proteomics. Analytical Techniques 4, 489-494.
32. Hanash, S. (2004). HUPO initiatives relevant to clinical proteomics. Mol. Cell Proteomics. 298-301.
33. Hanash, S. M. (2003). Disease proteomics. Nature 422(6928), 226-232.
34. Hayes, R. L., Newcomb, J. K., Pike, B. R., and DeFord, S. M. (2001). Contributions of calpains and caspases to cell death following traumatic brain injury. In "Head Trauma: Basic, Preclinical and Clinical Aspects" (L. P. Miller and R. L. Hayes, Eds.), vol. 10, pp. 219-237. Wiley & Sons, New York, NY.
35. Hochstrasser, D. F., Sanchez, J. C., and Appel, R. D. (2002). Proteomics and its trends facing nature's complexity. Proteomics 2(7), 807-812.
36. James, P. (2002). Chips for proteomics; a new tool or just hype? High throughput proteomics; protein arrays BioTechniques 12(Suppl.), 14-23.
37. Janssen, D. (2003). Major approaches to identifying key PTMs. Genomics and Proteomics 3(1), 38-41.
38. Jungblut, P., Thiede, B., Zimny-Arndt, U., Muller, E. C., Scheler, C., and Wittmann-Liebold, B. (1996). Resolution power of two-dimensional electrophoresis and identification of proteins from gels. Electrophoresis 17, 839-847.
39. Kitano, II. (2000). Perspectives on systems biology, "New Generation Computing," Vol. 18, No. 3. Ohm-sha, Springer-Verlag, New York Inc.
40. Kitano, H. (2002a). Systems biology: A brief overview. Science 295(5560), 1662-1664.
41. Kitano, H. (2002b). Computational systems biology. Nature 420(6912), 206-210 (review).
42. Kohn, M. C., and Letzkus, W. J. (1983). A graph theoretical analysis of metabolic regulation. J. Theoretical Biology 100, 293-304.
43. Kosko, B. (1986). Fuzzy cognitive maps. Int. J. Man-Machine Studies 24, 65-75.
44. Kusnezow, W., and Hoheisel, J. D. (2002). Antibody microarrays: Promises and problems. High throughput proteomics; protein arrays. Bio Tech. 12(Suppl.), 14-23.
45. Lemkin, P. F. (1997). Comparing two-dimensional electrophoretic gel images across the Internet. Electrophoresis 18, 2759-2773.
46. Lu, B., and Chen, T. (2003). A suffix tree approach to the interpretation of tandem mass spectra: Applications to peptides of non-specific digestion and post-translational modifications. Bioinformatics 19(Suppl. 2), II113-II121.
47. Lubec, G., Krapfenbauer, K., and Fountoulakis, M. (2003). Proteomics in brain research: Potentials and limitations. Prog. Neurobiol. 69(3), 193-211.
48. Mendes, P. (1993). GEPASI: A software package for modelling the dynamics, steady, states and control of biochemical and other systems. Comput. Appli. Biosci. 9, 563-571.
49. Mendes, P. (1997). Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
50. Meyer, H. E., Klose, J., and Hamacher, M. (2003). HBPP and the pursuit of standardisation. Lancet Neurol. 2(11), 657-658.
51. Moody, M. D. (2001). Array-based ELISAs for high-throughput analysis of human cytokines. Bio Tech. 31, 186-194.
52. Patton, W. F. (2002). Detection technologies in proteome analysis. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 771(1-2), 3-31.
53. Peng, J., Elias, J. E., Thoreen, C. C., Licldider, L. J., and Gygi, S. P. (2003). Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large scale protein analysis: The yeast proteome. J. Proteome Res. 2, 43-50.
54. Peng, J., and Gygi, S. P. (2001). Proteomics: The move to mixtures. J. Mass. Spectrom. 36(10), 1083-1091.
55. Pike, B. R., Flint, J., Dave, J. R., Lu, X.-C. M., Wang, K. K. W., Tortella, F. C., and Hayes, R. L. (2004). Accumulation of calpain and caspase-3 proteolytic fragments of brain-derived all-spectrin in CSF after middle cerebral artery occlusion in rats. J. Cereb. Blood Flow Metab. 24(1), 98-106.
56. Pike, B. R., Flint, J., Dutta, S., Johnson, E., Wang, K. K. W., and Hayes, R. L. (2001). Accumulation of non-erythroid all-spectrin and calpain-cleaved all-spectrin breakdown products in cerebrospinal fluid after traumatic brain injury in rats. J. Neurochem. 78, 1297-1306.
57. Raabe, A., Grolms, C., and Seifert, V. (1999). Serum markers of brain damage and outcome prediction in patients after severe head injury. Br. J. Neurosurg. 13, 56-59.
58. Raghupathi, R., Graham, D. I., and McIntosh, T. K. (2000). Apoptosis after traumatic brain injury. J. Neurotrauma 17(10), 927-938.
59. Reddy, V. N., Mavrovouniotis, M. L., and Liebman, M. N. (1993). Petri net representations in metabolic pathways. Proc. ISMB 1, 328-336.
60. Reyes, D. R., Iossifidis, D., Auroux, P. A., and Manz, A. (2002). Micro total analysis systems. I. Introduction, theory, and technology. Anal. Chem. 74(12), 2623-2636.
61. Romner, B., Ingebrigtsen, T., Kongstad, P., and Borgesen, S. E. (2000). Traumatic brain damage: Serum S-100 protein measurements related to neuroradiological findings. J. Neurotrauma 17(8), 641-647.
62. Schäfer, H., Marcus, K., Sickmann, A., Herrmann, M., Klosc, J., and Meyer, H. E. (2003). Identification of phosphorylation and acetylation sites in alphaA-crystallin of the eye lens (mus musculus) after two-dimensional gel electrophoresis. Anal. Bioanal. Chem. 376(7), 966-972.
63. Schwartz, D. C., and Hochstrasser, M. (2003). A superfamily of protein tags: Ubiquitin, SUMO and related modifiers. Trends Biochem. Sci. 28(6), 321-328.
64. Service, R. F. (2001). Gold rush-High-speed biologists search for gold in proteins. Science 294(5549), 2074-2077.
65. Shi, H., Rodrigucz, O., Shang, Y., and Chen, S. (2002). Integrating adaptive and intelligent techniques into a web-based environment for active learning. In "Intelligent Systems: Technology and Applications" (C. T. Leondes, Ed.), vol. 4, pp. 229-260. CRG Press, Boca Raton, Fla.
66. Smith, R. D. (2000). Probing proteomes-seeing the whole picture? Nat. BioTech. 18, 1041-1042.
67. Somogyi, R., and Sniegoski, C. A. (1996). Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation. Complexity 1, 45-63.
68. Tabb, D. L., McDonald, W. H., and Yates, J. R. (2002). DTASelcct and contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26.
69. 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(11), 2071-2077.
70. Wiesner, A. (2004). Detection of tumor markers with ProteinChip technology. Curr. Pharm. Biotechnol. 5(1), 45-67.
71. Van, 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(12), 1682-1698.
72. Yates, J. R., III, Carmack, E., Hays, L., Link, A. J., and Eng, J. K. (1999). Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry. In "Methods in Molecular Biology" (A. J. Link, Ed.), vol. 112, pp. 553-569. Human Press, Totowa, N. J.
73. Yates, J. R., Morgan, S. F., Gatlin, C. L., Griffin, P. R., and Eng, J. K. (1998). Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis. Anal. Chem. 70, 3557-3565.
74. Zhang, W. R., Chen, S., and Bezdek, J. C. (1989). PooI2: A generic system for cognitive map development and decision analysis. IEEE Trans. SMC 19, 31-39.