Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins

Drug Discovery Today

Volumn 13, Issue 23-24, 2008, Pages 1042-1051

  Zolla, Lello ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; BIOLOGICAL MARKER; ORGANIC COMPOUND; PEPTIDE; PLASMA PROTEIN;

DRUG DESIGN; DRUG MECHANISM; HUMAN; MOLECULAR THERAPY; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW;

BIOLOGICAL MARKERS; BLOOD PROTEINS; DRUG DESIGN; HUMANS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS;

EID: 55749085423     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2008.09.013     Document Type: Review

References (73)

1. Cottingham K. HUPO plasma proteome project: challenges and future directions. J. Proteome Res. 5 (2006) 1298
2. Omenn G.S. The human proteome organization plasma proteome project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses. Proteomics 4 (2004) 1235-1240
3. Shen Y., et al. Characterization of the human blood plasma proteome. Proteomics 5 (2005) 4034-4045
4. Jacobs J.M. Utilizing human blood plasma for proteomic biomarker discovery. J. Proteome Res. 4 (2005) 1073-1085
5. Barelli S., et al. Oxidation of proteins: basic principles and perspectives for blood proteomics. Proteomics Clin. Appl. 2 (2008) 142-157
6. D'Amici G.M., et al. Proteomic analysis of RBC membrane protein degradation during blood storage. J. Proteome Res. 6 (2007) 3242-3255
7. Richter R., et al. Composition of the peptide fraction in human blood plasma: database of circulating human peptides. J. Chromatogr. B Biomed. Sci. Appl. 726 (1999) 25-35
8. Torchilin V.P., and Lukyanov A.N. Peptide and protein drug delivery to and into tumors: challenges and solutions. Drug Discov. Today 8 (2003) 259-266
9. Colcher D., et al. Effects of genetic engineering on the pharmacokinetics of antibodies. Q. J. Nucl. Med. 43 (1999) 132-139
10. Adkins J.N., et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 1 (2002) 947-955
11. Pieper R., et al. Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3 (2003) 422-432
12. Zolotarjova N., et al. Differences among techniques for high-abundant protein depletion. Proteomics 5 (2005) 3304-3313
13. Huang L., et al. Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics 5 (2005) 3314-3328
14. Liu T., et al. Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol. Cell. Proteomics 5 (2006) 2167-2174
15. Tang H.-Y., et al. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 5 (2005) 3329-3342
16. Nissum M., et al. Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis. Proteomics 7 (2007) 4218-4227
17. Boschetti E., and Righetti P.G. The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species. J. Proteome 71 (2008) 255-264
18. Wasinger V., et al. Prefractionation, enrichment, desalting and depleting of low volume and low abundance proteins and peptides using the MF10. Methods Mol. Biol. 424 (2008) 257-275
19. Zhou M., et al. An investigation into the human serum interactome. Electrophoresis 25 (2004) 1289-1298
20. Rifai N., et al. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24 (2006) 971-983
21. Marko-Varga G., and Fehniger T. Proteomics and disease - the challenges for technology and discovery. J. Proteome Res. 3 (2004) 167-178
22. Petricoin E., et al. Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. J. Proteome Res. 3 (2004) 209-217
23. Hanash S.M., et al. Mining the plasma proteome for cancer biomarkers. Nature 452 (2008) 571-579
24. Omenn G.S. Strategies for plasma proteomic profiling of cancers. Proteomics 6 (2006) 5662-5673
25. Simpson R.J., et al. Proteomics-driven cancer biomarker discovery: looking to the future. Curr. Opin. Chem. Biol. 12 (2008) 72-77
26. Wan C., et al. Dysregulation of retinoid transporters expression in body fluids of schizophrenia patients. J. Proteome Res. 5 (2006) 3213-3216
27. Vadiraja B.B. Comparative plasma proteome analysis of lymphoma-bearing SJL mice. J. Proteome Res. 4 (2005) 1814-1825
28. Josic D., et al. Proteomic characterization of inter-alpha inhibitor proteins from human plasma. Proteomics 6 (2006) 2874-2885
29. Sjoholt G., et al. Proteomic strategies for Individualizing therapy of acute myeloid leukemia (AML). Curr. Pharm. Biotechnol. 7 (2006) 159-170
30. Rosenfeld R.G. Pharmacogenomics and pharmacoproteomics in the evaluation and management of short stature. Eur. J. Endocrinol. 157 (2007) S27-S31
31. Tyers M., and Mann M. From genomics to proteomics. Nature 422 (2003) 193-197
32. Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207
33. Pusch W., et al. Mass spectrometry-based clinical proteomics. Pharmacogenomics 4 (2003) 463-476
34. Garbett N.C. Calorimetry outside the box: a new window into the plasma proteome. Biophys. J. 94 (2008) 1377-1383
35. Hood L.M., and Perlmutter R.M. The impact of systems approaches on biological problems in drug discovery. Nat. Biotechnol. 22 (2004) 1215-1217
36. Patil S.T., et al. Identifying pharmacodynamic protein markers of centrally active drugs in humans: a pilot study in a novel clinical model. J. Proteome Res. 6 (2007) 955-966
37. Dunning B.E., et al. Alpha cell function in health and disease: influence of glucagon-like peptide-1. Diabetologia 48 (2005) 1700-1713
38. Jiang X., et al. Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Proteomics 8 (2008) 686-705
39. White Forest M. Quantitative phosphoproteomic analysis of signaling network dynamics. Curr. Opin. Biotechnol. 19 (2008) 404-409
40. Hunter T. Signaling - 2000 and beyond. Cell 100 (2000) 113-127
41. Wulfkuhle J.D., et al. Technology insight: pharmacoproteomics for cancer - promises of patient-tailored medicine using protein microarrays. Nat. Clin. Pract. Oncol. 3 (2006) 256-268
42. Krutzik P.O., et al. High-content single-cell drug screening with phosphospecific flow cytometry. Nat. Chem. Biol. 4 (2008) 132-142
43. Haab B.B. Antibody arrays in cancer research. Mol. Cell. Proteomics 4 (2005) 377-383
44. Zhu H., and Snyder M. Protein chip technology. Curr. Opin. Chem. Biol. 7 (2003) 55-56
45. Paweletz C.P., et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20 (2001) 1981-1989
46. Angenendt P. Progress in protein and antibody microarray technology. Drug Discov. Today 10 (2005) 503-511
47. LaBaer J., and Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9 (2005) 14-19
48. Eckel-Passow J.E., et al. Experimental design and analysis of antibody microarrays: applying methods from cDNA arrays. Cancer Res. 65 (2005) 2985-2989
49. Petricoin E.F., et al. Clinical proteomics: translating bench side promise into bedside reality. Nat. Rev. Drug Discov. 1 (2002) 683-695
50. Leuking A., et al. Protein biochips: a new and versatile platform technology for molecular medicine. Drug Discov. Today 10 (2005) 789-794
51. Tanner S., et al. Accurate annotation of peptide modifications through unrestrictive database search. J. Proteome Res. 7 (2008) 170-181
52. Salomon A.R., et al. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 443-448
53. Wissing J., et al. Chemical proteomic analysis reveals alternative modes of action for pyrido2 3-dpyrimidine kinase inhibitors. Mol. Cell. Proteomics 3 (2004) 1181-1193
54. Godl K., et al. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15434-15439
55. Cecconi D., et al. Proteomic analysis of pancreatic ductal carcinoma cells treated with 5-aza-2′-deoxycytidine. Electrophoresis 24 (2003) 1871-1878
56. Cecconi D., et al. Proteomic analysis of pancreatic endocrine tumor cell lines treated with the histone deacetylase inhibitor trichostatin A. Proteomics 7 (2007) 1644-1653
57. Milli A., et al. A proteomic approach for evaluating the cell response to a novel histone deacetylase inhibitor in colon cancer cells. BBA-Protein Proteom 1784 (2008) 1702-1710
58. Chapal N. Pharmacoproteomic approach to the study of drug mode of action, toxicity, and resistance: applications in diabetes and cancer. Fund. Clin. Pharmacol. 18 (2004) 413-422
59. Petricoin E.F., et al. Toxicoproteomics: serum proteomic pattern diagnostics for early detection of drug induced cardiac toxicities and cardioprotection. Toxicol. Pathol. 32 Suppl. 1 (2004) 122-130
60. Joo W.A., et al. Proteomic analysis of plasma proteins of workers exposed to benzene. Mutat. Res. 558 (2004) 35-44
61. Qian W.J., et al. Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics 5 (2005) 572-584
62. Kap-Soon N., et al. Protein biomarkers in the plasma of workers occupationally exposed to polycyclic aromatic hydrocarbons. Proteomics 4 (2004) 3505-3513
63. Ren Y., et al. The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome. Proteomics 4 (2004) 3477-3484
64. Chen J.H., et al. Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 17039-17044
65. Huanga J., et al. The application of inductively coupled plasma mass spectrometry in pharmaceutical and biomedical analysis. J. Pharmaceut. Biomed. Anal. 40 (2006) 227-234
66. Lopez-Farre A.J., et al. Relationship between vitamin d binding protein and aspirin resistance in coronary ischemic patients: a proteomic study. J. Proteome Res. 6 (2007) 2481-2487
67. Steen H., and Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5 (2004) 699-711
68. Yates III J.R., et al. Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6 (2005) 702-714
69. Goodman S.R., et al. The human red blood cell proteome and interactome. Exp. Biol. Med. 232 (2007) 1391-1408
70. Kurdia, A. et al. (2007) Centrality measures for the human red blood cell interactome. Engineering in Medicine and Biology Workshop, pp. 98-101, IEEE Dallas
71. Chaurasia G., et al. UniHI: an entry gate to the human protein interactome. Nucleic Acids Res. 35 Database issue (2007) D590-D594
72. Balasubramanian R., et al. A graph theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics 20 (2004) 3353-3362
73. Liumbruno G., et al. Transfusion medicine in the era of proteomics. J. Proteomics 71 (2008) 34-45