Proteomic technologies for the discovery of type 1 diabetes biomarkers

Journal of Diabetes Science and Technology

Volumn 4, Issue 4, 2010, Pages 993-1002

  Zhi, Wenbo ^a   Purohit, Sharad ^a   Carey, Colleen ^a   Wang, Meiyao ^a   She, Jin Xiong ^a  

^a MEDICAL COLLEGE OF GEORGIA   (United States)

Author keywords

Depletion; Enrichment; Mass spectrometry; Protein biomarker; Proteomics; Type 1 diabetes mellitus

Indexed keywords

BIOLOGICAL MARKER; PROTEIN;

ARTICLE; CHEMISTRY; GENETICS; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MULTIVARIATE ANALYSIS; PROTEOMICS;

BIOLOGICAL MARKERS; DIABETES MELLITUS, TYPE 1; HUMANS; MULTIVARIATE ANALYSIS; PROTEINS; PROTEOMICS;

EID: 77955630295     PISSN: None     EISSN: 19322968     Source Type: Journal    
DOI: 10.1177/193229681000400431     Document Type: Review

References (33)

1. Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG 2nd, Smith RD. Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res. 2005;4(4):1073-85.
2. Simpson RJ, Bernhard OK, Greening DW, Moritz RL. Proteomicsdriven cancer biomarker discovery: looking to the future. Curr Opin Chem Biol. 2008;12(1):72-7.
3. Li F, Fang Y, Xiao ZQ, Chen ZC. Clinical proteomics: the application of proteomics in the research of clinical medicine. Prog Biochem Biophys. 2006;33(1):5-9.
4. Purohit S, She JX. Biomarkers for type 1 diabetes. Int J Clin Exp Med. 2008;1(2):98-116.
5. Sosenko JM, Krischer JP, Palmer JP, Mahon J, Cowie C, Greenbaum CJ, Cuthbertson D, Lachin JM, Skyler JS, Diabetes Prevention Trial-Type 1 Study Group. A risk score for type 1 diabetes derived from autoantibody-positive participants in the diabetes prevention trial-type 1. Diabetes Care. 2008;31(3):528-33.
6. Maurya P, Meleady P, Dowling P, Clynes M. Proteomic approaches for serum biomarker discovery in cancer. Anticancer Res. 2007;27(3A):1247-55.
7. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics. 2005;4(10):1487-502.
8. Asara JM, Christofk HR, Freimark LM, Cantley LC. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics. 2008;8(5):994-9.
9. Anderson L. Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J Physiol. 2005;563(Pt 1):23-60.
10. Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG 2nd, Smith RD. Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res. 2005;4(4):1073-85.
11. Gong Y, Li X, Yang B, Ying W, Li D, Zhang Y, Dai S, Cai Y, Wang J, He F, Qian X. Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res. 2006;5(6):1379-87.
12. Righetti PG, Boschetti E, Lomas L, Citterio A. Protein Equalizer Technology: the quest for a "democratic proteome." Proteomics. 2006;6(14):3980-92.
13. Brand J, Haslberger T, Zolg W, Pestlin G, Palme S. Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics. 2006;6(11):3236-42.
14. Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics. 2005;5(13):3292-303.
15. Sennels L, Salek M, Lomas L, Boschetti E, Righetti PG, Rappsilber J. Proteomic analysis of human blood serum using peptide library beads. J Proteome Res. 2007;6(10):4055-62.
16. Boschetti E, Lomas L, Citterio A, Righetti PG. Romancing the "hidden proteome," Anno Domini two zero zero seven. J Chromatogr A. 2007;1153(1-2):277-90.
17. Elias JE, Haas W, Faherty BK, Gygi SP. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods. 2005;2(9):667-75.
18. Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Görg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ. Guidelines for the next 10 years of proteomics. Proteomics. 2006;6(1):4-8.
19. Liu T, Qian WJ, Mottaz HM, Gritsenko MA, Norbeck AD, Moore RJ, Purvine SO, Camp DG 2nd, Smith RD. Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics. 2006;5(11):2167-74.
20. Yocum AK, Yu K, Oe T, Blair IA. Effect of immunoaffinity depletion of human serum during proteomic investigations. J Proteome Res. 2005;4(5):1722-31.
21. Sihlbom C, Kanmert I, Bahr H, Davidsson P. Evaluation of the Combination of Bead Technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J Proteome Res. 2008;7(9):4191-8.
22. Dwivedi RC, Krokhin OV, Cortens JP, Wilkins JA. Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization. J Proteome Res. 2010;9(2):1144-9.
23. Hartwig S, Czibere A, Kotzka J, Passlack W, Haas R, Eckel J, Lehr S. Combinatorial hexapeptide ligand libraries (ProteoMiner): an innovative fractionation tool for differential quantitative clinical proteomics. Arch Physiol Biochem. 2009;115(3):155-60.
24. Wang H, Hanash S. Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom Rev. 2005;24(3):413-26.
25. Horn A, Kreusch S, Bublitz R, Hoppe H, Cumme GA, Schulze M, Moore T, Ditze G, Rhode H. Multidimensional proteomics of human serum using parallel chromatography of native constituents and microplate technology. Proteomics. 2006;6(2):559-70.
26. Assiddiq BF, Williamson JC, Snijders AP, Cook K, Dickman MJ. Multidimensional liquid phase protein separations in conjunction with stable isotope labelling for quantitative proteomics. Proteomics. 2007;7(21):3826-34.
27. Wang H, Chang-Wong T, Tang HY, Speicher DW. Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes. J Proteome Res. 2010;9(2):1032-40.
28. Fang Y, Robinson DP, Foster LJ. Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. J Proteome Res. 2010;9(4):1902-12.
29. Sundsten T, Eberhardson M, Göransson M, Bergsten P. The use of proteomics in identifying differentially expressed serum proteins in humans with type 2 diabetes. Proteome Sci. 2006;4:22.
30. Kim HJ, Cho EH, Yoo JH, Kim PK, Shin JS, Kim MR, Kim CW. Proteome analysis of serum from type 2 diabetics with nephropathy. J Proteome Res. 2007;6(2):735-43.
31. Cho WC, Yip TT, Chung WS, Leung AW, Cheng CH, Yue KK. Differential expression of proteins in kidney, eye, aorta, and serum of diabetic and non-diabetic rats. J Cell Biochem. 2006;99(1):256-68.
32. Riaz S, Alam SS, Akhtar MW. Proteomic identification of human serum biomarkers in diabetes mellitus type 2. J Pharm Biomed Anal. 2010;51(5):1103-7.
33. Purohit S, Podolsky R, Schatz D, Muir A, Hopkins D, Huang YH, She JX. Assessing the utility of SELDI-TOF and model averaging for serum proteomic biomarker discovery. Proteomics. 2006;6(24):6405-15.