Progress in tumor proteomics

World Chinese Journal of Digestology

Volumn 10, Issue 12, 2002, Pages 1436-1440

  Long, Y Z ^a   Fan, X G ^a   Li, N ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA MICROARRAY; GENOMICS; PROTEOMICS; REVIEW; TUMOR GROWTH;

EID: 0036913757     PISSN: 10093079     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (72)

1. Compagni A, Christofori G. Recent advances in research on multistage tumorigenesis. Br J Cancer 2000;83:1-5
2. Livingston DM, Shivdasani R. Toward mechanism-based cancer care. JAMA 2001;285:588-593
3. Duelli DM, Lazebnik YA. Primary cells suppress oncogene-dependent apoptosis. Nat Cell Biol 2000;11:859-862
4. Stambolic V, Mak TW, Woodgett JR. Modulation of cellular apoptotic potential: Contributions to oncogenesis. Oncogene 1999; 18:6094-6103
5. Alaiya AA, Franzen B, Auer G, Linder S. Cancer proteomics: From identification of novel markers to creation of artifical learning models for tumor classification. Electrophoresis 2000;21:1210-1217
6. Bidart JM, Thuillier F, Augereau C, Chalas J, Daver A, Jacob N, Labrousse F, Voitot H. Kinetics of serum tumor marker concentrations and usefulness in clinical monitoring. Clin Chem 1999; 45:1695-1707
7. Steams V, Yamauchi H, Hayes DF. Circulating tumor markers in breast cancer: Accepted utilities and novel prospects. Breast Cancer Res Treat 1998;52:239-259
8. Srinivas PR, Verma M, Zhao Y, Srivastava S. Proteomics for cancer biomarker discovery. Clin Chem 2002;48:1160-1169
9. Lindblom A, Liljigren A. Tumor markers in malignancies. Br Med J 2000;320:424-427
10. Sturgeon C. Practice guidelines for tumor marker use in the clinic. Clin Chem 2002;48:1151-1159
11. Rappsilber J, Mann M. What does it mean to identify a protein in proteomics? Trends Biochem Sci 2002;27:74-78
12. Chambers G, Lawrie L, Cash P, Murray GI. Proteomics: A new approach to the study of disease. J Pathol 2000;192:280-288
13. Banks RE, Dunn MJ, Hochstrasser DF, Sanchez JC, Blackstock W, Pappin DJ, Selby PJ. Proteomics: New perspectives, new biomedical opportunities. Lancet 2000;356:1749-1756
14. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M. The sequence of the human genome. Science 2001;291:1304-1351
15. Meri S, Baumann M. Proteomics: Posttranslational modifications, immune responses and current analytical tools. Biomol Eng 2001; 18:213-220
16. Nalivaeva NN, Turner AJ. Post-translational modifications of proteins: Acetylcholinesterase as a model system. Proteomics 2001;1:735-747
17. Williams KL. Genomes and proteomes: Towards a multidimensional view of biology. Electrophoresis 1999;20:678-688
18. Pandey A, Mann M. Proteomics to study genes and genomes. Nature 2000;405:837-846
19. Graves PR, Haystead TA. Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 2002;66:39-63
20. Naaby-Hansen S, Waterfield MD, Cramer R. Proteomics-postgenomic cartography to understand gene function. Trends Pharmacol Sci 2001;22:376-384
21. O'Donovan C, Apweiler R, Bairoch A. The human proteomics initiative (HPI). Trends Biotechnol 2001;19:178-181
22. Steiner S, Anderson NL. Expression profiling in toxicology potentials and limitations. Toxicol Lett 2000;112:467-471
23. Dongre AR, Opiteck G, Cosand WL, Hefta SA. Proteomics in the post-genome age. Biopolymers 2001;60:206-211
24. Herrmann PC, Liotta LA, Petricoin EF 3rd. Cancer proteomics: The state of the art. Dis Markers 2001;17:49-57
25. Opiteck GJ, Ramirez SM, Jorgenson JW, Moseley MA 3rd. Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal Biochem 1998;258:349-361
26. Davidsson P, Westman A, Puchades M, Nilsson CL, Blennow K. Characterization of proteins from human cerebrospinal fluid by a combination of preparative two-dimensional liquid-phase electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 1999;71:642-647
27. Tragas C, Pawliszyn J. On-line coupling of high performance gel filtration chromatography with imaged capillary isoelectric focusing using a membrane interface. Electrophoresis 2000;21:227-237
28. Tsugita A, Kawakami T, Uchida T, Sakai T, Kamo M, Matsui T, Watanabe Y, Morimasa T, Hosokawa K, Toda T. Proteome analysis of mouse brain: Two-dimensional electrophoresis profiles of tissue proteins during the course of aging. Electrophoresis 2000; 21:1853-1871
29. Fountoulakis M, Berndt P, Boelsterli UA, Crameri F, Winter M, Albertini S, Suter L. Two-dimensional database of mouse liver proteins: Changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Electrophoresis 2000;21:2148-2161
30. Colvis CM, Duglas-Tabor Y, Werth KB, Vieira NE, Kowalak JA, Janjani A, Yergey AL, Garland DL. Tracking pathology with proteomics: Identification of in vivo degradation products of alphaB-crystallin. Electrophoresis 2000;21:2219-2227
31. Jung E, Heller M, Sanchez JC, Hochstrasser DF. Proteomics meets cell biology: The establishment of subcellular proteomes. Electrophoresis 2000;21:3369-3377
32. Fenyo D. Identifying the proteome: Software tools. Curr Opin Biotechnol 2000;11:391-395
33. Molloy MP. Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients. Anal Biochem 2000;10; 280:1-10
34. Herbert B. Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 1999;20:660-663
35. Cordwell SJ, Nouwens AS, Verrills NM, Basseal DJ, Walsh BJ. Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis 2000;21:1094-1103
36. Hoving S, Voshol H, van Oostrum J. Towards high performance two-dimensional gel electrophoresis using ultrazoom gels. Electrophoresis 2000;21:2617-2621
37. Lopez MF, Kristal BS, Chernokalskaya E, Lazarev A, Shestopalov AI, Bogdanova A, Robinson M. High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation. Electrophoresis 2000;21:3427-3440
38. Issaq HJ. The role of separation science in proteomics research. Electrophoresis 2001;22:3629-3638
39. Bergman AC, Benjamin T, Alaiya A, Waltham M, Sakaguchi K, Franzen B, Linder S, Bergman T, Auer G, Appella E, Wirth PJ, Jornvall H. Identification of gel-separated tumor marker proteins by mass spectrometry. Electrophoresis 2000;21:679-686
40. Patton WF. Making blind robots see: The synergy between fluorescent dyes and imaging devices in automated proteomics. Biotechniques 2000;28:944-957
41. Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996;68:850-858
42. Craven RA, Banks RE. Laser capture microdissection and proteomics: Possibilities and limitation. Proteomics 2001;1:1200-1204
43. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2002;2:3-10
44. Klose J. Large-gel 2D electrophoresis. Methods Mol Biol 1999;112: 147-172
45. Packer NH, Pawlak A, Kett WC, Gooley AA, Redmond JW, Williams KL. Proteome analysis of glycoforms: A review of strategies for the microcharacterisation of glycoproteins separated by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 1997;18:452-460
46. Muller DR, Schindler P, Coulot M, Voshol H, van Oosstrum J. Mass spectrometric characterization of stathmin isoforms separated by 2-D PAGE. J Mass Spectrom 1999;34:336-345
47. Yates JR 3rd. Mass spectrometry and the age of the proteome. J Mass Spectrom 1998;33:1-19
48. Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 2001;70:437-473
49. Guilhaus M, Selby D, Mlynski V. Orthogonal acceleration time-of-flight mass spectrometry. Mass Spectrom Rev 2000;19:65-107
50. Marshall AG, Hendrickson CL, Jackson GS. Fourier transform ion cyclotron resonance mass spectrometry: A primer. Mass Spectrom Rev 1998;17:1-35
51. Shevchenko A, Loboda A, Shevchenko A, Ens W, Standing KG. MALDI quadrupole time-of-flight mass spectrometry: A powerful tool for proteomic research. Anal Chem 2000;72:2132-2141
52. Lahm HW, Langen H. Mass spectrometry: A tool for the identification of proteins separated by gels. Electrophoresis 2000;21: 2105-2114
53. Adamczyk M, Gebler JC, Wu J. Charge derivatization of peptides to simplify their sequencing with an ion trap mass spectrometer. Rapid Commun Mass Spectrom 1999;13:1413-1422
54. Peng J, Gygi SP. Proteomics: The move to mixtures. J Mass Spectrom 2001;36:1083-1091
55. Verma M, Wright GL Jr, Hanash SM, Gopal-Srivastava R, Srivastava S. Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. Ann N Y Acad Sci 2001;945:103-115
56. Yates JR 3rd. Database searching using mass spectrometry data. Electrophoresis 1998;19:893-900
57. Larsen MR, Roepstorff P. Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis. Fresenius J Anal Chem 2000;366: 677-690
58. Lee KH. Proteomics: A technology-driven and technology-limited discovery science. Trends Biotechnol 2001;19:217-222
59. Yarmush ML, Jayaraman A. Advances in proteomic technologies. Annu Rev Biomed Eng 2002;4:349-373
60. Ong SE, Pandey A. An evaluation of the use of two-dimensional gel electrophoresis in proteomics. Biomol Eng 2001;18:195-205
61. Vihinen M. Bioinformatics in proteomics. Biomol Eng 2001;18: 241-248
62. Wojcik J, Schachter V. Proteomic databases and software on the web. Brief Bioin 2000;1:250-259
63. Mann M, Pandey A. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem Sci 2001;26:54-61
64. Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem 2001;73:1917-1926
65. Maggio ET, Ramnarayan K. Recent developments in computational proteomics. Trends Biotechnol 2001;19:266-272
66. Sarto C, Frutiger S, Cappellano F, Sanchez JC, Doro G, Catanzaro F, Hughes GJ, Hochstrasser DF, Mocarelli P. Modified expression of plasma glutathione peroxidase and manganese superoxidise dismutase in human renal cell carcinoma. Electrophoresis 1999; 20:3458-3466
67. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, Liotta LA. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572-577
68. Tan C, Li J, Wang J, Xiang Q, Zhang X, Dong L, Shen S, Liang S, Li G. Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection. Proteomics 2002;2:306-312
69. Tan S, Seow TK, Liang RC, Koh S, Lee CP, Chung MC, Hooi SC. Proteome analysis of butyrate-treated human colon cancer cells (HT-29). Int J Cancer 2002;98:523-531
70. Marshall T, Williams KM. Proteomics and its impact upon biomedical science. Br J Biomed Sci 2002;59:47-64
71. Lawrie LC, Fothergill JE, Murray GI. Spot the differences: Proteomics in cancer research. Lancet Oncol 2001;2:270-277
72. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 2002;416:507-511