Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies

Inflammatory Bowel Diseases

Volumn 15, Issue 4, 2009, Pages 616-629

  Alex, Philip ^a   Gucek, Marjan ^b   Li, Xuhang ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Biomarkers; Crohn's disease; Inflammatory bowel disease (IBD); Proteomics; Ulcerative colitis

Indexed keywords

BIOLOGICAL MARKER; DETERGENT; EDETIC ACID; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PARAFFIN;

ANALYTIC METHOD; BODY FLUID; CELL COMPARTMENTALIZATION; CELL FRACTIONATION; CELL ISOLATION; CELL MEMBRANE; CELL ORGANELLE; CELL SPECIFICITY; CELL TYPE; CELLULAR DISTRIBUTION; CHROMATOGRAPHY; CROHN DISEASE; DISEASE MARKER; ENTERITIS; EPITHELIUM CELL; HUMAN; IMMUNOCOMPETENT CELL; ISOTOPE LABELING; LASER CAPTURE MICRODISSECTION; MASS SPECTROMETRY; MULTI EPITOPE LIGAND CARTOGRAPHY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN GLYCOSYLATION; PROTEIN LOCALIZATION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; TISSUE CULTURE CELL; TWO DIMENSIONAL GEL ELECTROPHORESIS; UBIQUITINATION; ULCERATIVE COLITIS; IMMUNOLOGY; METHODOLOGY; PATHOPHYSIOLOGY;

BIOLOGICAL MARKERS; HUMANS; INFLAMMATORY BOWEL DISEASES; PROTEOMICS;

EID: 67650189497     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1002/ibd.20652     Document Type: Review

References (135)

1. Podolsky DK. Inflammatory bowel disease. N Engl J Med. 2002;347: 417-429.
2. Loftus EV Jr. Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology. 2004;126:1504-1517.
3. Kappelman MD, Rifas-Shiman SL, Kleinman K, et al. The prevalence and geographic distribution of Crohn's disease and ulcerative colitis in the United States. Clin Gastroenterol Hepatol. 2007;5:1424-1429.
4. Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007;448:427-434.
5. Cho JH. The genetics and immunopathogenesis of inflammatory bowel disease. Nat Rev Immunol. 2008;8:458-466.
6. Mamula P, Telega GW, Markowitz JE, et al. Inflammatory bowel disease in children 5 years of age and younger. Am J Gastroenterol. 2002;97:2005-2010.
7. Lutgens MW, Vleggaar FP, Schipper ME, et al. High frequency of early colorectal cancer in inflammatory bowel disease. Gut. 2008 (in press).
8. Hawk ET, Levin B. Colorectal cancer prevention. J Clin Oncol. 2005; 23:378-391.
9. Cravatt BF, Simon GM, Yates JR. The biological impact of massspectrometry-based proteomics. Nature. 2007;450:991-1000.
10. Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature. 2008;452:571-579.
11. Chaerkady R, Pandey A. Applications of proteomics to lab diagnosis. Annu Rev Pathol. 2008;3:485-498.
12. Gulcicek EE, Colangelo CM, McMurray W, et al. Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. Curr Protoc Bioinformatics. 2005;13:13.1.
13. Reinders J, Sickmann A. Modificomics: posttranslational modifications beyond protein phosphorylation and glycosylation. Biomol Eng. 2007; 24:169-177.
14. Walsh CT, Garneau-Tsodikova S, Gatto GJJ. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl. 2005;44:7342-7372.
15. Felley-Bosco E, Andre M. Proteomics and chronic inflammatory bowel diseases. Pathol Res Pract. 2004;200:129-133.
16. Feng JT, Shang S, Beretta L. Proteomics for the early detection and treatment of hepatocellular carcinoma. Oncogene. 2006; 25:3810-3817.
17. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006;312:212-217.
18. Scigelova M, Makarov A. Orbitrap mass analyzer - overview and applications in proteomics. Proteomics. 2006;6(suppl 2):16-21.
19. Schmidt A, Gehlenborg N, Bodenmiller B, et al. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics. 2008 (in press).
20. Weichart D, Gobom J, Klopfleisch S, et al. Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells. J Biol Chem. 2006;281:2380-2389.
21. Chen X, Sun L, Yu Y, et al. Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics. 2007;4:25-37.
22. Haqqani AS, Kelly JF, Stanimirovic DB. Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags. Methods Mol Biol. 2008;439:225-240.
23. Han DK, Eng J, Zhou H, et al. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol. 2001;19:946-951.
24. Gruhler S, Kratchmarova I. Stable isotope labeling by amino acids in cell culture (SILAC). Methods Mol Biol. 2008;424:101-111.
25. Ong SE, Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc. 2006;1:2650-2660.
26. Guo Y, Singleton PA, Rowshan A, et al. Quantitative proteomics analysis of human endothelial cell membrane rafts: evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Mol Cell Proteomics. 2007;6:689-696.
27. Pan S, Aebersold R. Quantitative proteomics by stable isotope labeling and mass spectrometry. Methods Mol Biol. 2007;367:209-218.
28. Donowitz M, Singh S, Salahuddin FF, et al. Proteome of the small intestinal brush border of the NHERF1 knock out mouse: up regulation of transporters and pro-proliferation molecules. Gastroenterology. 2008;134:A266-A266.
29. Bertone P, Snyder M. Advances in functional protein microarray technology. FEBS J. 2005;272:5400-5411.
30. Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mech Ageing Dev. 2007;128:161-167.
31. Speer R, Wulfkuhle JD, Liotta LA, et al. Reverse-phase protein microarrays for tissue-based analysis. Curr Opin Mol Ther. 2005;7:240-245.
32. Kader HA, Tchernev VT, Satyaraj E, et al. Protein microarray analysis of disease activity in pediatric inflammatory bowel disease demonstrates elevated serum PLGF, IL-7, TGF-beta1, and IL-12p40 levels in Crohn's disease and ulcerative colitis patients in remission versus active disease. Am J Gastroenterol. 2005;100:414-423.
33. Alex P, Frank MB, Sutton C, et al. Distinct Th1/Th2/Th17 profiles identified in gene and cytokine expression signatures from patients with inflammatory bowel disease. Gastroenterology. 2007;132:A698-A699.
34. Alex P, Zachos NC, Nguyen T, et al. Distinct cytokine patterns identified from multiplex profiles of murine DSS and TNBS-induced colitis. Inflamm Bowel Dis. 2008 (in press).
35. Sullivan S, Zh-H, Cuffari C, et al. Identification and validation of serological IBD biomarkers by a novel high throughput proteomic approach using high density protein chip technology. Gastroenterology. 2006;130:A24-A24.
36. Vermeulen N, Vermeire S, Michiels G, et al. Protein microarray experiments for profiling of the autoimmune response in inflammatory bowel disease; identification of PHLA1. Gastroenterology. 2008;134: A197-A197.
37. Schubert P, Hoffman MD, Sniatynski MJ, et al. Advances in the analysis of dynamic protein complexes by proteomics and data processing. Anal Bioanal Chem. 2006;386:482-493.
38. Berndt U, Bartsch S, Philipsen L, et al. Proteomic analysis of the inflamed intestinal mucosa reveals distinctive immune response profiles in Crohn's disease and ulcerative colitis. J Immunol. 2007;179:295-304.
39. Feitelson JS, Simonian MH, Dewald H, et al. Proteome Partitioning and Fractionation. Drug Discovery Channel: Tutorial. 2006;26:12.
40. Fountain D, Ralston M, Higgins N, et al. Liquid nitrogen freezers: a potential source of microbial contamination of hematopoietic stem cell components. Transfusion. 1997;37:585-591.
41. Morandell S, Stasyk T, Grosstessner-Hain K, et al. Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics. 2006;6:4047-4056.
42. Mustafa D, Kros JM, Luider T. Combining laser capture microdissection and proteomics techniques. Methods Mol Biol. 2008;428:159-178.
43. Kohn EC, Azad N, Annunziata C, et al. Proteomics as a tool for biomarker discovery. Dis Markers. 2007;23:411-417.
44. Paik YK, Kim H, Lee EY, et al. Overview and introduction to clinical proteomics. Methods Mol Biol. 2008;428:1-31.
45. Veenstra TD, Conrads TP, Hood BL, et al. Biomarkers: mining the biofluid proteome. Mol Cell Proteomics. 2005;4:409-418.
46. Meuwis MA, Fillet M, Geurts P, et al. Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling. Biochem Pharmacol. 2007;73:1422-1433.
47. Meuwis MA, Fillet M, Lutteri L, et al. Proteomics for prediction and characterization of response to infliximab in Crohn's disease: a pilot study. Clin Biochem. 2008;41:960-967.
48. Nanni P, Parisi D, Roda G, et al. Serum protein profiling in patients with inflammatory bowel diseases-sing selective solid-phase bulk extraction, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemometric data analysis. Rapid Commun Mass Spectrom. 2007;21:4142-4148.
49. Subramanian V, Subramanian D, Pollok RC. Serum protein signatures determined by mass spectrometry (SELDI-ToF) accurately distinguishes Crohn's disease (CD) from ulcerative colitis (UC). Gastroenterology. 2008;134:A196-A196.
50. Laroux FS, Pavlick KP, Wolf RE, et al. Dysregulation of intestinal mucosal immunity: implications in inflammatory bowel disease. News Physiol Sci. 2001;16:272-277.
51. Clark RA, Nauseef WM. Isolation and functional analysis of neutrophils. Curr Protoc Immunol. 2001;7:7.23.
52. Kanof ME, Smith PD, Zola H. Isolation of whole mononuclear cells from peripheral blood and cord blood. Curr Protoc Immunol. 2001;7:7.1.
53. Bini L, Pacini S, Liberatori S, et al. Extensive temporally regulated reorganization of the lipid raft proteome following T-cell antigen receptor triggering. Biochem J. 2003;369:301-309.
54. Loyet KM, Ouyang W, Eaton DL, et al. Proteomic profiling of surface proteins on Th1 and Th2 cells. J Proteome Res. 2005;4:400-409.
55. Peirce MJ, Wait R, Begum S, et al. Expression profiling of lymphocyte plasma membrane proteins. Mol Cell Proteomics. 2004;3:56-65.
56. Salonen JM, Valmu L, Ronnholm G, et al. Proteome analysis of B-cell maturation. Proteomics. 2006;6:5152-5168.
57. Liu BG, Cao YB, Cao YY, et al. Altered protein profile of lymphocytes in an antigen-specific model of colitis: a comparative proteomic study. Inflamm Res. 2007;56:377-384.
58. Barderas MG, Darde VM, Duran MC, et al. Characterization of circulating human monocytes by proteomic analysis. Methods Mol Biol. 2007;357:319-328.
59. Hryniewicz-Jankowska A, Choudhary PK, Goodman SR. Variation in the monocyte proteome. Exp Biol Med (Maywood). 2007;232:967-976.
60. Wang X, Zhao H, Andersson R. Proteomics and leukocytes: an approach to understanding potential molecular mechanisms of inflammatory responses. J Proteome Res. 2004;3:921-929.
61. Pabst MJ, Pabst KM, Handsman DB, et al. Proteome of monocyte priming by lipopolysaccharide, including changes in interleukin-1beta and leukocyte elastase inhibitor. Proteome Sci. 2008;6:13.
62. Pereira SR, Faca VM, Gomes GG, et al. Changes in the proteomic profile during differentiation and maturation of human monocyte-derived dendritic cells stimulated with granulocyte macrophage colony stimulating factor/interleukin-4 and lipopolysaccharide. Proteomics. 2005;5:1186-1198.
63. Caruso R, Fina D, Peluso I, et al. A functional role for interleukin-21 in promoting the synthesis of the T-cell chemoattractant, MIP-3alpha, by gut epithelial cells. Gastroenterology. 2007;132:166-175.
64. Cheon JH, Kim JS, Kim JM, et al. Plant sterol guggulsterone inhibits nuclear factor-kappaB signaling in intestinal epithelial cells by blocking IkappaB kinase and ameliorates acute murine colitis. Inflamm Bowel Dis. 2006;12:1152-1161.
65. Conklin LS, Cuffari C, Saatian B, et al. Inherent differences in 6MP transport in human lymphocytes: correlation with drug-induced cytotoxicity. Gastroenterology. 2008;134:A69-A69.
66. Hardwidge PR, Rodriguez-Escudero I, Goode D, et al. Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem. 2004;279:20127-20136.
67. Higgins LM, Frankel G, Douce G, et al. Citrobacter rodentium infection in mice elicits a mucosal Th1 cytokine response and lesions similar to those in murine inflammatory bowel disease. Infect Immun. 1999; 67:3031-3039.
68. Barcelo-Batllori S, Andre M, Servis C, et al. Proteomic analysis of cytokine induced proteins in human intestinal epithelial cells: implications for inflammatory bowel diseases. Proteomics. 2002;2:551-560.
69. Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics. 2006;6:4106-4114.
70. Guo T, Wang W, Rudnick PA, et al. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem. 2007;55:763-772.
71. Naylor S. Genomic and proteomic sample preparation: higher throughput solutions. 26-27th April, 2004, World Trade Center, Boston, MA, USA. Expert Rev Proteomics. 2004;1:11-16.
72. Nakazawa A, Watanabe M, Kanai T, et al. Functional expression of costimulatory molecule CD86 on epithelial cells in the inflamed colonic mucosa. Gastroenterology. 1999;117:536-545.
73. Brandsch C, Friedl P, Lange K, et al. Primary culture and transfection of epithelial cells of human small intestine. Scand J Gastroenterol. 1998;33:833-838.
74. Mohammadpour HA. Isolation and culture of human colon epithelial cells using a modified explant technique employing a noninjurious approach. Methods Mol Med. 2005;107:237-247.
75. Bjerknes M, Cheng H. Methods for the isolation of intact epithelium from the mouse intestine. Anat Rec. 1981;199:565-574.
76. Mizoguchi E, Xavier RJ, Reinecker HC, et al. Colonic epithelial functional phenotype varies with type and phase of experimental colitis. Gastroenterology. 2003;125:148-161.
77. Grossmann J, Maxson JM, Whitacre CM, et al. New isolation technique to study apoptosis in human intestinal epithelial cells. Am J Pathol. 1998;153:53-62.
78. Vaandrager AB, Bot AG, De Vente J, et al. Atriopeptins and Escherichia coli enterotoxin STa have different sites of action in mammalian intestine. Gastroenterology. 1992;102:1161-1169.
79. Donowitz M, Singh S, Salahuddin FF, et al. Proteome of murine jejunal brush border membrane vesicles. J Proteome Res. 2007;6:4068-4079.
80. Bhattacharya SH, Gal AA, Murray KK. Laser capture microdissection MALDI for direct analysis of archival tissue. J Proteome Res. 2003;2:95-98.
81. Gutstein HB, Morris JS. Laser capture sampling and analytical issues in proteomics. Expert Rev Proteomics. 2007;4:627-637.
82. Yuki T, Ishihara S, Rumi MA, et al. Increased expression of midkine in the rat colon during healing of experimental colitis. Am J Physiol Gastrointest Liver Physiol. 2006;291:G735-43.
83. Ryan P, Bennett MW, Aarons S, et al. PCR detection of Mycobacterium paratuberculosis in Crohn's disease granulomas isolated by laser capture microdissection. Gut. 2002;51:665-670.
84. Ryan P, Kelly RG, Lee G, et al. Bacterial DNA within granulomas of patients with Crohn's disease - detection by laser capture microdissection and PCR. Am J Gastroenterol. 2004;99:1539-1543.
85. Stasyk T, Huber LA. Zooming in: fractionation strategies in proteomics. Proteomics. 2004;4:3704-3716.
86. Andersen JS, Mann M. Organellar proteomics: turning inventories into insights. EMBO Rep. 2006;7:874-879.
87. Li X, Leu S, Cheong A, et al. Akt2, phosphatidylinositol 3-kinase, and PTEN are in lipid rafts of intestinal cells: role in absorption and differentiation. Gastroenterology. 2004;126:122-135.
88. Sato K, Yang XL, Yudate T, et al. Dectin-2 is a pattern recognition receptor for fungi that couples with the Fc receptor gamma chain to induce innate immune responses. J Biol Chem. 2006;281:38854-38866.
89. Li X, Sullivan S, Conklin L, et al. Identification of differentially expressed proteins in biopsies of IBD patients using zoom 2D gel coupled with DIGE and LC-MS/MS. Gastroenterology. 2007;132: A239-A239.
90. Li X, Donowitz M. Density gradient fractionation. Exocytosis and endocytosis. Methods Mol Biol. 2007;440:97-111.
91. O'Morain C, Smethurst P, Levi J, et al. Subcellular fractionation of rectal biopsy homogenates from patients with inflammatory bowel disease. Scand J Gastroenterol. 1985;20:209-214.
92. Seminario MC, Bunnell SC. Signal initiation in T-cell receptor microclusters. Immunol Rev. 2008;221:90-106.
93. Molloy MP, Herbert BR, Walsh BJ, et al. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis. 1998;19:837-844.
94. Baribault H, Penner J, Iozzo RV, et al. Colorectal hyperplasia and inflammation in keratin 8-deficient FVB/N mice. Genes Dev. 1994;8: 2964-2973.
95. Zhang L, Wang X, Peng X, et al. Immunoaffinity purification of plasma membrane with secondary antibody superparamagnetic beads for proteomic analysis. J Proteome Res. 2007;6:34-43.
96. Person MD, Shen J, Traner A, et al. Protein fragment domains identified using 2D gel electrophoresis/MALDI-TOF. J Biomol Tech. 2006; 17:145-156.
97. Marko-Varga G, Lindberg H, Lofdahl CG, et al. Discovery of biomarker candidates within disease by protein profiling: principles and concepts. J Proteome Res. 2005;4:1200-1212.
98. Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics. 2004;1:401-409.
99. Friedman DB, Lilley KS. Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol. 2008;428:93-124.
100. Shkoda A, Werner T, Daniel H, et al. Differential protein expression profile in the intestinal epithelium from patients with inflammatory bowel disease. J Proteome Res. 2007;6:1114-1125.
101. Hsieh SY, Shih TC, Yeh CY, et al. Comparative proteomic studies on the pathogenesis of human ulcerative colitis. Proteomics. 2006;6:5322-5331.
102. Drew JE, Padidar S, Horgan G, et al. Salicylate modulates oxidative stress in the rat colon: a proteomic approach. Biochem Pharmacol. 2006;72:204-216.
103. Swanson SK, Washburn MP. The continuing evolution of shotgun proteomics. Drug Discov Today. 2005;10:719-725.
104. Mumby M, Brekken D. Phosphoproteomics: new insights into cellular signaling. Genome Biol. 2005;6:230.
105. Olsen JV, Blagoev B, Gnad F, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006;127:635-648.
106. Mertins P, Eberl HC, Renkawitz J, et al. Investigation of protein tyrosine phosphatase 1B function by quantitative proteomics. Mol Cell Proteomics. 2008 (in press).
107. Molina H, Horn DM, Tang N, et al. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007;104:2199-2204.
108. Macek B, Mijakovic I, Olsen JV, et al. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics. 2007;6:697-707.
109. Wang Z, Gucek M, Hart GW. Crosstalk between O-GlcNAc and O-phosphate: global and site-specific phosphorylation dynamics in response to elevated GLCNacylation. Proc Natl Acad Sci U S A. 2008 (in press).
110. Wu J, Katrekar A, Honigberg LA, et al. Identification of substrates of human protein-tyrosine phosphatase PTPN22. J Biol Chem. 2006;281: 11002-11010.
111. Siu R, Fladd C, Rotin D. N-cadherin is an in vivo substrate for protein tyrosine phosphatase sigma (PTPsigma) and participates in PTPsigma-mediated inhibition of axon growth. Mol Cell Biol. 2007;27:208-219.
112. Zhong J, Molina H, Pandey A. Phosphoproteomics. Curr Protoc Protein Sci. 2007;24:24.4.
113. Sarker R, Gronborg M, Cha B, et al. CK2 binds to the C-terminus of NHE3 and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Mol Biol Cell. 2008 (in press).
114. Li Y, Lin H, Deng C, et al. Highly selective and rapid enrichment of phosphorylated peptides using gallium oxide-coated magnetic microspheres for MALDI-TOF-MS and nano-LC-ESI-MS/MS/MS analysis. Proteomics. 2008;8:238-249.
115. Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics. 2008;8:832-851.
116. Ohtsubo K, Marth JD. Glycosylation in cellular mechanisms of health and disease. Cell. 2006;126:855-867.
117. Freeze HH, Aebi M. Altered glycan structures: the molecular basis of congenital disorders of glycosylation. Curr Opin Struct Biol. 2005;15: 490-498.
118. Qiu R, Regnier FE. Comparative glycoproteomics of N-linked complex-type glycoforms containing sialic acid in human serum. Anal Chem. 2005;77:7225-7231.
119. Mills PB, Mills K, Johnson AW, et al. Analysis by matrix assisted laser desorption/ionisation-time of flight mass spectrometry of the post-translational modifications of alpha 1-antitrypsin isoforms separated by two-dimensional polyacrylamide gel electrophoresis. Proteomics. 2001;1:778-786.
120. Furusawa T, Rakwal R, Nam HW, et al. Comprehensive royal jelly (RJ) proteomics using one- and two-dimensional proteomics platforms reveals novel RJ proteins and potential phospho/glycoproteins. J Proteome Res. 2008;7:3194-3229.
121. Takahashi N, Masuda K, Hiraki K, et al. N-glycan structures of squid rhodopsin. Eur J Biochem. 2003;270:2627-2632.
122. Ishii A, Ikenaka K, Pfeiffer SE. The N-glycan profile of mouse myelin, a specialized central nervous system membrane. J Neurochem. 2007; 103(suppl 1):25-31.
123. Campbell BJ, Yu LG, Rhodes JM. Altered glycosylation in inflammatory bowel disease: a possible role in cancer development. Glycoconj J. 2001, 18:851-8.
124. Tysk C, Riedesel H, Lindberg E, et al. Colonic glycoproteins in monozygotic twins with inflammatory bowel disease. Gastroenterology. 1991;100(2):419-23.
125. Heazlewood CK, Cook MC, Eri R, et al. Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis, PLoS Med. 2008 4;5(3):e54.
126. Seyfried NT, Xu P, Duong DM, et al. Systematic approach for validating the ubiquitinated proteome. Anal Chem. 2008;80:4161-4169.
127. Taylor C, Jobin C. Ubiquitin protein modification and signal transduction: implications for inflammatory bowel diseases. Inflamm Bowel Dis. 2005;11:1097-1107.
128. Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol. 2005;7:750-757.
129. Peng J, Schwartz D, Elias JE, et al. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003;21:921-926.
130. Hitchcock AL, Auld K, Gygi SP, et al. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc Natl Acad Sci U S A. 2003;100:12735-12740.
131. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics: MCP. 2002; 1:845-867.
132. Issaq HJ, Xiao Z, Veenstra TD. Serum and plasma proteomics. Chem Rev. 2007;107:3601-3620.
133. Zhou M, Conrads TP, Veenstra TD. Proteomics approaches to biomarker detection. Brief Funct Genomic Proteomic. 2005;4:69-75.
134. Boyle MD, Hess JL, Nuara AA, et al. Application of immunoproteomics to rapid cytokine detection. Methods. 2006;38:342-350.
135. Hess JL, Blazer L, Romer T, et al. Immunoproteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2005;815:65-75.