Proteomics In Clinical Laboratory Diagnosis

Advances in Clinical Chemistry

Volumn 39, Issue , 2005, Pages 159-184

  Shoshan, Stacy H ^a   Admon, Arie ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; TUMOR MARKER;

BIOLOGY; DIAGNOSIS, MEASUREMENT AND ANALYSIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; MASS SPECTROMETRY; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN MICROARRAY; PROTEOMICS; REVIEW;

BIOLOGICAL MARKERS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; LABORATORY TECHNIQUES AND PROCEDURES; MASS SPECTROMETRY; PROTEIN ARRAY ANALYSIS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 23244460589     PISSN: 00652423     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2423(04)39006-2     Document Type: Review

References (93)

1. Hanash S. Disease proteomics. Nature 422 6928 (2003) 226-232
2. Patterson S.D., and Aebersold R.H. Proteomics: The first decade and beyond. Nat Genet 33 Suppl. (2003) 311-323
3. Zolg J.W., and Langen H. How industry is approaching the search for new diagnostic markers and biomarkers. Mol Cell Proteomics 3 4 (2004) 345-354
4. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250 10 (1975) 4007-4021
5. 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 3 (1975) 231-243
6. Celis J.E., and Gromov P. Proteomics in translational cancer research: Toward an integrated approach. Cancer Cell 3 1 (2003) 9-15
7. Gorg A., Obermaier C., Boguth G., et al. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21 6 (2000) 1037-1053
8. Lauber W.M., Carroll J.A., Dufield D.R., Kiesel J.R., Radabaugh M.R., and Malone J.P. Mass spectrometry compatibility of two-dimensional gel protein stains. Electrophoresis 22 5 (2001) 906-918
9. White I.R., Pickford R., Wood J., Skehel J.M., Gangadharan B., and Cutler P. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 25 17 (2004) 3048-3054
10. Kang C., Kim H.J., Kang D., Jung D.Y., and Suh M. Highly sensitive and simple fluorescence staining of proteins in sodium dodecyl sulfate-polyacrylamide-based gels by using hydrophobic tail-mediated enhancement of fluorescein luminescence. Electrophoresis 24 19-20 (2003) 3297-3304
11. Wittke S., Kaiser T., and Mischak H. Differential polypeptide display: The search for the elusive target. J Chromatogr B 803 1 (2004) 17-26
12. Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 6928 (2003) 198-207
13. Le Gac S., Carlier J., Camart J.C., Cren-Olive C., and Rolando C. Monoliths for microfluidic devices in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 808 1 (2004) 3-14
14. Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60 20 (1988) 2299-2301
15. Hutchens T.W., and Yip T.-T. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun Mass Spectrom 7 7 (1993) 576-580
16. Fenn J.B., Mann M., Meng C.K., Wong S.F., and Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 246 4926 (1989) 64-71
17. Biemann K., and Scoble H.A. Characterization by tandem mass spectrometry of structural modifications in proteins. Science 237 4818 (1987) 992-998
18. Ornstein D.K., Gillespie J.W., Paweletz C.P., et al. Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines. Electrophoresis 21 11 (2000) 2235-2242
19. Homola J. Present and future of surface plasmon resonance biosensors. Anal Bioanal Chem 19 (2003) 19
20. McDonnell J.M. Surface plasmon resonance: Towards an understanding of the mechanisms of biological molecular recognition. Curr Opin Chem Biol 5 5 (2001) 572-577
21. de Wildt R.M., Mundy C.R., Gorick B.D., and Tomlinson I.M. Antibody arrays for high-throughput screening of antibody-antigen interactions. Nat Biotechnol 18 9 (2000) 989-994
22. MacBeath G. Protein microarrays and proteomics. Nat Genet 32 Suppl. (2002) 526-532
23. Michaud G.A., Salcius M., Zhou F., et al. Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 21 12 (2003) 1509-1512
24. Walter G., Bussow K., Lueking A., and Glokler J. High-throughput protein arrays: Prospects for molecular diagnostics. Trends Mol Med 8 6 (2002) 243-250
25. Robinson W.H., DiGennaro C., Hueber W., et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med 8 3 (2002) 295-301
26. Cutler P. Protein arrays: The current state-of-the-art. Proteomics 3 1 (2003) 3-18
27. Zhu H., Bilgin M., and Snyder M. Proteomics. Annu Rev Biochem 72 (2003) 783-812
28. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., and Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 90 11 (1993) 5011-5015
29. Mann M., Hojrup P., and Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mas Spectrom 22 6 (1993) 338-345
30. Pappin D.J.C., Hojrup P., and Bleasby A.J. Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3 6 (1993) 327-332
31. James P., Quadroni M., Carafoli E., and Gonnet G. Protein identification by mass profile fingerprinting. Biochem Biophys Res Comm 195 1 (1993) 58-64
32. Yates J.R., Speicher S., Griffin P.R., and Hunkapiller T. Peptide mass maps: A highly informative approach to protein identification. Anal Biochem 214 2 (1993) 397-408
33. Nesvizhskii A.I., and Aebersold R. Analysis, statistical validation and dissemination of large- scale proteomics datasets generated by tandem MS. Drug Discov Today 9 4 (2004) 173-181
34. Palmblad M., Ramstrom M., Markides K.E., Hakansson P., and Bergquist J. Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal Chem 74 22 (2002) 5826-5830
35. Beer I., Barnea E., Ziv T., and Admon A. Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 4 4 (2004) 950-960
36. Radulovic D., Jelveh S., Ryu S., et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid-chromatography-tandem mass spectrometry. Mol Cell Proteomics 21 (2004) 21
37. Gambari R., Borgatti M., Altomare L., et al. Applications to cancer research of "lab-on-a-chip" devices based on dielectrophoresis (DEP). Technol Cancer Res Treat 2 1 (2003) 31-40
38. Belov M.E., Anderson G.A., Wingerd M.A., et al. An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J Am Soc Mass Spectrom 15 2 (2004) 212-232
39. Zhang X., Leung S.M., Morris C.R., and Shigenaga M.K. Evaluation of a novel, integrated approach using functionalized magnetic beads, bench-top MALDI-TOF-MS with prestructured sample supports, and pattern recognition software for profiling potential biomarkers in human plasma. J Biomol Tech 15 3 (2004) 167-175
40. Wong Y.F., Cheung T.H., Lo K.W., et al. Protein profiling of cervical cancer by protein-biochips: Proteomic scoring to discriminate cervical cancer from normal cervix. Cance Lett 211 2 (2004) 227-234
41. Quadroni M., and James P. Proteomics and automation. Electrophoresis 20 4-5 (1999) 664-677
42. Triolo A., Altamura M., Cardinali F., Sisto A., and Maggi C.A. Mass spectrometry and combinatorial chemistry: A short outline. J Mas Spectrom 36 12 (2001) 1249-1259
43. Petricoin E.F., Ardekani A.M., Hitt B.A., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359 9306 (2002) 572-577
44. Conrads T.P., Fusaro V.A., Ross S., et al. High-resolution serum proteomic features for ovarian cancer detection. Endocr Relat Cancer 11 2 (2004) 163-178
45. Cohen L.S., Escobar P.F., Scharm C., Glimco B., and Fishman D.A. Three-dimensional power Doppler ultrasound improves the diagnostic accuracy for ovarian cancer prediction. Gynecol Oncol 82 1 (2001) 40-48
46. Diamandis E.P. Point: Proteomic patterns in biological fluids: Do they represent the future of cancer diagnostics?. Clin Chem 49 8 (2003) 1272-1275
47. Hanash S.M. Global profiling of gene expression in cancer using genomics and proteomics. Curr Opin Mol Ther 3 6 (2001) 538-545
48. Hirsch J., Hansen K.C., Burlingame A.L., and Matthay M.A. Proteomics: Current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 287 1 (2004) L1-L23
49. Rosenblatt K.P., Bryant-Greenwood P., Killian J.K., et al. Serum proteomics in cancer diagnosis and management. Annu Rev Med 55 (2004) 97-112
50. Srinivas P.R., Verma M., Zhao Y., and Srivastava S. Proteomics for cancer biomarker discovery. Clin Chem 48 8 (2002) 1160-1169
51. Wulfkuhle J.D., Liotta L.A., and Petricoin E.F. Proteomic applications for the early detection of cancer. Nat Rev Cancer 3 4 (2003) 267-275
52. Petricoin E., Wulfkuhle J., Espina V., and Liotta L.A. Clinical proteomics: Revolutionizing disease detection and patient tailoring therapy. J Proteome Res 3 2 (2004) 209-217
53. Turner B.J., Weiner M., Yang C., and TenHave T. Predicting adherence to colonoscopy or flexible sigmoidoscopy on the basis of physician appointment-keeping behavior. Ann Intern Med 140 7 (2004) 528-532
54. Liotta L.A., and Kohn E.C. The microenvironment of the tumour-host interface. Nature 411 6835 (2001) 375-379
55. Xu B.J., Caprioli R.M., Sanders M.E., and Jensen R.A. Direct analysis of laser capture microdissected cells by MALDI mass spectrometry. J Am Soc Mass Spectrom 13 11 (2002) 1292-1297
56. Emmert-Buck M.R., Bonner R.F., Smith P.D., et al. Laser capture microdissection. Science 274 5289 (1996) 998-1001
57. Choudhary J., and Grant S.G. Proteomics in postgenomic neuroscience: The end of the beginning. Nat Neurosci 7 5 (2004) 440-445
58. Dreger M. Proteome analysis at the level of subcellular structures. Eur J Biochem 270 4 (2003) 589-599
59. Tang N., Tornatore P., and Weinberger S.R. Current developments in SELDI affinity technology. Mas Spectrom Rev 23 1 (2004) 34-44
60. Joo W.A., Lee D.Y., and Kim C.W. Development of an effective sample preparation method for the proteome analysis of body fluids using 2-D gel electrophoresis. Biosci Biotechnol Biochem 67 7 (2003) 1574-1577
61. Yu L.R., Zhou M., Conrads T.P., and Veenstra T.D. Diagnostic proteomics: Serum proteomic patterns for the detection of early stage cancers. Dis Marker 19 4-5 (2003) 209-218
62. Anderson N.L., and Anderson N.G. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1 11 (2002) 845-867
63. Ahmed N., Barker G., Oliva K., et al. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum. Proteomics 3 10 (2003) 1980-1987
64. Pieper R., Su Q., Gatlin C.L., Huang S.T., Anderson N.L., and Steiner S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3 4 (2003) 422-432
65. Georgiou H.M., Rice G.E., and Baker M.S. Proteomic analysis of human plasma: Failure of centrifugal ultrafiltration to remove albumin and other high molecular weight proteins. Proteomics 1 12 (2001) 1503-1506
66. Zhou M., Lucas D.A., Chan K.C., et al. An investigation into the human serum "interactome.". Electrophoresis 25 9 (2004) 1289-1298
67. Mehta A.I., Ross S., Lowenthal M.S., et al. Biomarker amplification by serum carrier protein binding. Dis Marker 19 1 (2003) 1-10
68. Orchard S., Hermjakob H., and Apweiler R. The proteomics standards initiative. Proteomics 3 7 (2003) 1374-1376
69. Wilkins M.R., Sanchez J.C., Gooley A.A., et al. Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13 (1996) 19-50
70. Chaurand P., Schwartz S.A., and Caprioli R.M. Assessing protein patterns in disease using imaging mass spectrometry. J Proteome Res 3 2 (2004) 245-252
71. Chaurand P., Schwartz S.A., Billheimer D., Xu B.J., Crecelius A., and Caprioli R.M. Integrating histology and imaging mass spectrometry. Anal Chem 76 4 (2004) 1145-1155
72. Schwartz S.A., Weil R.J., Johnson M.D., Toms S.A., and Caprioli R.M. Protein profiling in brain tumors using mass spectrometry: Feasibility of a new technique for the analysis of protein expression. Clin Cance Res 10 3 (2004) 981-987
73. Mouledous L., Hunt S., Harcourt R., Harry J., Williams K.L., and Gutstein H.B. Navigated laser capture microdissection as an alternative to direct histological staining for proteomic analysis of brain samples. Proteomics 3 5 (2003) 610-615
74. Poon T.C., and Johnson P.J. Proteome analysis and its impact on the discovery of serological tumor markers. Clin Chim Acta 313 1-2 (2001) 231-239
75. Jain K.K. Role of proteomics in diagnosis of cancer. Technol Cancer Res Treat 1 4 (2002) 281-286
76. Rai A.J., and Chan D.W. Cancer proteomics: Serum diagnostics for tumor marker discovery. Ann NY Acad Sci 1022 (2004) 286-294
77. Kennedy S. Proteomic profiling from human samples: The body fluid alternative. Toxicol Lett 120 1-3 (2001) 379-384
78. Mian S., Ball G., Hornbuckle J., et al. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics 3 9 (2003) 1725-1737
79. Kim S.I., Voshol H., van Oostrum J., Hastings T.G., Cascio M., and Glucksman M.J. Neuroproteomics: Expression profiling of the brain's proteomes in health and disease. Neurochem Res 29 6 (2004) 1317-1331
80. Belov L., de la Vega O., dos Remedios C.G., Mulligan S.P., and Christopherson R.I. Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cance Res 61 11 (2001) 4483-4489
81. Iba T., Kigawa J., Kanamori Y., et al. Expression of the c-myc gene as a predictor of chemotherapy response and a prognostic factor in patients with ovarian cancer. Cancer Sci 95 5 (2004) 418-423
82. Wang J.Y., Hsieh J.S., Chen C.C., et al. Alterations of APC, c-met, and p53 genes in tumor tissue and serum of patients with gastric cancers. J Surg Res 120 2 (2004) 242-248
83. Perkins G.L., Slater E.D., Sanders G.K., and Prichard J.G. Serum tumor markers. Am Fam Physician 68 6 (2003) 1075-1082
84. Scanlan M.J., Gure A.O., Jungbluth A.A., Old L.J., and Chen Y.T. Cancer/testis antigens: An expanding family of targets for cancer immunotherapy. Immunol Rev 188 (2002) 22-32
85. Parmiani G., Castelli C., Dalerba P., et al. Cancer immunotherapy with peptide-based vaccines: What have we achieved? Where are we going?. J Natl Cancer Inst 94 11 (2002) 805-818
86. Mocellin S., Rossi C.R., Nitti D., Lise M., and Marincola F.M. Dissecting tumor responsiveness to immunotherapy: The experience of peptide-based melanoma vaccines. Biochim Biophys Acta 1653 2 (2003) 61-71
87. Disis M.L., Gooley T.A., Rinn K., et al. Generation of T-cell immunity to the HER-2/neu protein after active immunization with HER-2/neu peptide-based vaccines. J Clin Oncol 20 11 (2002) 2624-2632
88. Le Naour F., Brichory F., Misek D.E., Brechot C., Hanash S.M., and Beretta L. A distinct repertoire of autoantibodies in hepatocellular carcinoma identified by proteomic analysis. Mol Cel Proteomics 1 3 (2002) 197-203
89. Chen G., Gharib T.G., Wang H., et al. Protein profiles associated with survival in lung adenocarcinoma. PNAS 100 23 (2003) 13537-13542
90. Bouwman K., Qiu J., Zhou H., et al. Microarrays of tumor cell derived proteins uncover a distinct pattern of prostate cancer serum immunoreactivity. Proteomics 3 11 (2003) 2200-2207
91. Kaiser T., Kamal H., Rank A., et al. Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation. Blood 104 2 (2004) 340-349
92. Walker C.M., Moody D.J., Stites D.P., and Levy J.A. CD8+ lymphocytes can control HIV infection in vitro by suppressing virus replication. Science 234 4783 (1986) 1563-1566
93. Zhang L., Yu W., He T., et al. Contribution of Human alpha-Defensin 1, 2, and 3 to the Anti-HIV-1 Activity of CD8 Antiviral Factor. Science 298 5595 (2002) 995-1000