Proteomic methodologies and their application in colorectal cancer research

Critical Reviews in Clinical Laboratory Sciences

Volumn 46, Issue 5-6, 2009, Pages 319-342

  Ikonomou, Georgia ^a   Samiotaki, Martina ^a   Panayotou, George ^a  

^a BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

Author keywords

Biological markers; Colorectal neoplasms; Diagnostics; Electrophoresis; High pressure liquid chromatography; Mass spectrometry; Post translational modifications; Proteomic

Indexed keywords

CA 19-9 ANTIGEN; DNA MARKER;

CANCER RESEARCH; CANCER STAGING; CAPILLARY ELECTROPHORESIS; CARCINOGENESIS; CELL FRACTIONATION; COLORECTAL CANCER; ELECTROPHORESIS; FECES ANALYSIS; FLUORESCENCE ACTIVATED CELL SORTING; GLYCOSYLATION; LASER CAPTURE MICRODISSECTION; MASS SPECTROMETRY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MICROARRAY; PROTEIN PROCESSING; PROTEOMICS; REVIEW; TUMOR CELL; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ADENOCARCINOMA; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COLORECTAL NEOPLASMS; ELECTROPHORESIS; HUMANS; MASS SPECTROMETRY; NEOPLASM PROTEINS; PROGNOSIS; PROTEIN ARRAY ANALYSIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 71849104219     PISSN: 10408363     EISSN: 1549781X     Source Type: Journal    
DOI: 10.3109/10408360903375277     Document Type: Review

References (213)

1. Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, Tun MJ. Cancer statistics, 2008. CA Cancer J Clin 2008; 58:71-96.
2. Ferlay J, Autier P, Boniol M, Heanue M, Colombet M, Boyle P. Estimates of the cancer incidence and mortality in Europe in 2006. Ann Oncol 2007; 18:581-592. (Pubitemid 46359643)
3. Boyle P, Ferlay J. Mortality and survival in breast and colorectal cancer. Nat Clin Pract Oncol 2005; 2:424-425.
4. Coleman MP, Quaresma M, Berrino F, Lutz JM, De Angelis R, Capocaccia R, Baili P, Rachet B, Gatta G, Hakulinen T, Micheli A, Sant M, Weir HK, Elwood JM, Tsukuma H, Koifman S, GA ES, Francisci S, Santaquilani M, Verdecchia A, Storm HH, Young JL. Cancer survival in fve continents: a worldwide population-based study (CONCORD). Lancet Oncol 2008; 9:730-756.
5. Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell 1990; 61:759-767.
6. Morson BC. Evolution of cancer of the colon and rectum. Cancer 1974; 34(Suppl3):845-849.
7. Rex DK Johnson DA Anderson JC, Schoenfeld PS, Burke CA, Inadomi JM. American College of Gastroenterology guidelines for colorectal cancer screening 2008. Am J Gastroenterol 2009; 104:739-750.
8. Gold P, Freedman SO. Specifc carcinoembryonic antigens of the human digestive system. J Exp Med 1965; 122: 467-481.
9. Wanebo HJ, Rao B, Pinsky CM, Hofman RG, Stearns M, Schwartz MK, Oettgen HF. Preoperative carcinoembryonic antigen level as a prognostic indicator in colorectal cancer. N Engl J Med 1978; 299:448-451.
10. Fletcher RH. Carcinoembryonic antigen. Ann Intern Med 1986; 104:66-73.
11. Goslin R, O'Brien MJ, Steele G, Mayer R, Wilson R, Corson JM, Zamcheck N. Correlation of plasma CEA and CEA tissue staining in poorly diferentiated colorectal cancer. Am J Med 1981; 71:246-253.
12. Rognum TO, Torud E, Elgjo K, Brandtzaeg P, Orjasaeter H, Nygaard K. Large-bowel carcinomas with diferent ploidy, related to secretory component, IgA, and CEA in epithelium and plasma. Br J Cancer 1982; 45:921-934.
13. Gerber MA, Tung SN. Carcinoembryonic antigen in normal and diseased liver tissue. Am J Pathol 1978; 92: 671-679.
14. Sugarbaker PH. Carcinoembryonic antigen (CEA) assays in obstructive colorectal cancer. Ann Surg 1976; 184: 752-757.
15. Alexander JC, Silverman NA, Chretien PB. Efect of age and cigarette smoking on carcinoembryonic antigen levels. JAMA 1976; 235:1975-1979.
16. Locker GY, Hamilton S, Harris J, Jessup JM, Kemeny N, Macdonald JS, Somerfeld MR, Hayes DF, Bast RC Jr. ASCO 2006 update of recommendations for the use of tumor markers in gastrointestinal cancer. J Clin Oncol 2006; 24:5313-5327.
17. Magnani JL, Nilsson B, Brockhaus M, Zopf D, Steplewski Z, Koprowski H, Ginsburg V. A monoclonal antibody-defned antigen associated with gastrointestinal cancer is a ganglioside containing sialylated lacto-N-fucopentaose II. J Biol Chem 1982; 257:14365-14369.
18. Koprowski H, Herlyn M, Steplewski Z, Sears HF. Specifc antigen in serum of patients with colon carcinoma. Science 1981; 212:53-55.
19. Hundt S, Haug U, Brenner H. Blood markers for early detection of colorectal cancer: a systematic review. Cancer Epidemiol Biomarkers Prev 2007; 16:1935-1953.
20. Ryan BM, Lefort F, McManus R, Daly J, Keeling PW, Weir DG, Kelleher D. A prospective study of circulating mutant KRAS2 in the serum of patients with colorectal neoplasia: strong prognostic indicator in postoperative follow up. Gut 2003; 52:101-108.
21. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Tornton K, Agrawal N, Sokoll L, Szabo SA, Kinzler KW, Vogelstein B, Diaz LA Jr. Circulating mutant DNA to assess tumor dynamics. Nat Med 2008; 14:985-990.
22. Calistri D, Rengucci C, Bocchini R, Saragoni L, Zoli W, Amadori D. Fecal multiple molecular tests to detect colo-rectal cancer in stool. Clin Gastroenterol Hepatol 2003; 1:377-383.
23. Boynton KA, Summerhayes IC, Ahlquist DA, Shuber AP. DNA integrity as a potential marker for stool-based detection of colorectal cancer. Clin Chem 2003; 49:1058-1065.
24. Ahlquist DA, Skoletsky JE, Boynton KA, Harrington JJ, Mahoney DW, Pierceall WE, Tibodeau SN, Shuber AP. Colorectal cancer screening by detection of altered human DNA in stool: feasibility of a multitarget assay panel. Gastroenterology 2000; 119:1219-1227.
25. Guidoboni M, Gafa R, Viel A, Doglioni C, Russo A, Santini A, Del Tin L, Macri E, Lanza G, Boiocchi M, Dolcetti R. Microsatellite instability and high content of activated cyto-toxic lymphocytes identify colon cancer patients with a favorable prognosis. Am J Pathol 2001; 159:297-304.
26. Herman JG. Hypermethylation pathways to colorec-tal cancer. Implications for prevention and detection. Gastroenterol Clin North Am 2002; 31:945-958.
27. Smith AJ, Stern HS, Penner M, Hay K, Mitri A, Bapat BV, Gallinger S. Somatic APC and K-ras codon 12 mutations in aberrant crypt foci from human colons. Cancer Res 1994; 54:5527-5530.
28. Fearnhead NS, Britton MP, Bodmer WF. Te ABC of APC. Hum Mol Genet 2001; 10:721-733.
29. Sidransky D, Tokino T, Hamilton SR, Kinzler KW, Levin B, Frost P, Vogelstein B. Identifcation of ras oncogene mutations in the stool of patients with curable colorectal tumors. Science 1992; 256:102-105.
30. Caldas C, Hahn SA, Hruban RH, Redston MS, Yeo CJ, Kern SE. Detection of K-ras mutations in the stool of patients with pancreatic adenocarcinoma and pancreatic ductal hyperplasia. Cancer Res 1994; 54:3568-3573.
31. Samuels Y, Wang Z, Bardelli A, Silliman N, Ptak J, Szabo S, Yan H, Gazdar A, Powell SM, Riggins GJ, Willson JK, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE. High frequency of mutations of the PIK3CA gene in human cancers. Science 2004; 304:554. (Pubitemid 38541907)
32. Iacopetta B. TP53 mutation in colorectal cancer. Hum Mutat 2003; 21:271-276.
33. Booth RA. Minimally invasive biomarkers for detection and staging of colorectal cancer. Cancer Lett 2007; 249:87-96.
34. Kambara T, Simms LA, Whitehall VL, Spring KJ, Wynter C V, Walsh MD, Barker MA, Arnold S, McGivern A, Matsubara N, Tanaka N, Higuchi T, Young J, Jass JR, Leggett BA. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut 2004; 53:1137-1144.
35. Kondo Y, Issa J P. Epigenetic changes in colorectal cancer. Cancer Metastasis Rev 2004; 23:29-39.
36. Chan AO, Broaddus RR, Houlihan PS, Issa JP, Hamilton SR, Rashid A. CpG island methylation in aberrant crypt foci of the colorectum. Am J Pathol 2002; 160:1823-1830.
37. Lenhard K, Bommer GT, Asutay S, Schauer R, Brabletz T, Goke B, Lamerz R, Kolligs FT. Analysis of promoter methylation in stool: a novel method for the detection of colorectal cancer. Clin Gastroenterol Hepatol 2005; 3:142-149.
38. Zou H, Harrington JJ, Shire AM, Rego RL, Wang L, Campbell ME, Oberg AL, Ahlquist DA. Highly methylated genes in colorectal neoplasia: implications for screening. Cancer Epidemiol Biomarkers Prev 2007; 16:2686-2696.
39. Ahlquist DA, Sargent DJ, Loprinzi CL, Levin TR, Rex DK, Ahnen DJ, Knigge K, Lance MP, Burgart LJ, Hamilton SR, Allison JE, Lawson MJ, Devens ME, Harrington JJ, Hillman SL. Stool DNA and occult blood testing for screen detection of colorectal neoplasia. Ann Intern Med 2008; 149:441-450.
40. Dong SM, Traverso G, Johnson C, Geng L, Favis R, Boynton K, Hibi K, Goodman SN, D'Allessio M, Paty P, Hamilton SR, Sidransky D, Barany F, Levin B, Shuber A, Kinzler KW, Vogelstein B, Jen J. Detecting colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst 2001; 93:858-865.
41. Fehm T, Sagalowsky A, Cliford E, Beitsch P, Saboorian H, Euhus D, Meng S, Morrison L, Tucker T, Lane N, Ghadimi BM, Heselmeyer-Haddad K, Ried T, Rao C, Uhr J. Cytogenetic evidence that circulating epithelial cells in patients with carcinoma are malignant. Clin Cancer Res 2002; 8:2073-2084.
42. Mostert B, Sleijfer S, Foekens JA, Gratama JW. Circulating tumor cells (CTCs): Detection methods and their clinical relevance in breast cancer. Cancer Treat Rev 2009; 35: 463-474.
43. Mocellin S, Keilholz U, Rossi CR, Nitti D. Circulating tumor cells: the 'leukemic phase' of solid cancers. Trends Mol Med 2006; 12:130-139.
44. Cohen SJ, Punt CJ, Iannotti N, Saidman BH, Sabbath KD, Gabrail NY, Picus J, Morse M, Mitchell E, Miller MC, Doyle GV, Tissing H, Terstappen LW, Meropol NJ. Relationship of circulating tumor cells to tumor response, progression-free survival, and overall survival in patients with metastatic colorectal cancer. J Clin Oncol 2008; 26:3213-3221.
45. Herbert B, Harry E. Difcult proteins. Methods Mol Biol 2009; 519:47-63.
46. Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Mullner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Tiel A, Tiery J, Uefng M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomic: current state and future felds of application in fuid proteomic. Clin Chem Lab Med 2009; 47:724-744.
47. Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purifcation of trace components in complex biological samples for proteomic analysis. J Chromatogr A 2007; 1168:190-210; discussion 189.
48. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, Gutkind JS. Proteomic analysis of laser-captured parafn-embedded tissues: a molecular portrait of head and neck cancer progression. Clin Cancer Res 2008; 14:1002-1014.
49. Hwang SI, Tumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, Eng J, Wright ME, Han DK. Direct cancer tissue pro-teomic: a method to identify candidate cancer biomarkers from formalin-fxed parafn-embedded archival tissues. Oncogene 2007; 26:65-76.
50. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. Science 1996; 274:998-1001.
51. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G, Geho DH, Petricoin EF 3rd, Liotta LA. Laser-capture microdissection. Nat Protoc 2006; 1:586-603.
52. Godfrey W, Rudd CJ, Iyer S, Recktenwald D. Purifcation of cellular and organelle populations by fuorescence-activated cell sorting for proteome analysis. In Walker J, Ed. Te Proteomic Protocols Handbook. Pp. 67-78. Totowa, NJ: Humana Press, 2005.
53. Weber G, Wildgruber R. Free-fow electrophoresis system for proteomic applications. Methods Mol Biol 2008; 384: 703-716.
54. Kohlheyer D, Eijkel JC, van den Berg A, Schasfoort RB. Miniaturizing free-fow electrophoresis-a critical review. Electrophoresis 2008; 29:977-993.
55. Cortez C, Tomaskovic-Crook E, Johnston AP, Scott AM, Nice EC, Heath JK, Caruso F. Infuence of size, surface, cell line, and kinetic properties on the specifc binding of A33 antigen-targeted multilayered particles and capsules to colorectal cancer cells. ACS Nano 2007; 1:93-102.
56. Reymond MA, Sanchez JC, Hughes GJ, Gunther K, Riese J, Tortola S, Peinado MA, Kirchner T, Hohenberger W, Hochstrasser D F, Kockerling F. Standardized characterization of gene expression in human colorectal epithelium by two-dimensional electrophoresis. Electrophoresis 1997; 18:2842-2848.
57. Koga Y, Yasunaga M, Katayose S, Moriya Y, Akasu T, Fujita S, Yamamoto S, Baba H, Matsumura Y. Improved recovery of exfoliated colonocytes from feces using newly developed immunomagnetic beads. Gastroenterol Res Pract 2008; 2008:605273.
58. Rothacker J, Ramsay RG, Ciznadija D, Gras E, Neylon CB, Elwood NJ, Bouchier-Hayes D, Gibbs P, Rosenthal MA, Nice EC. A novel magnetic bead-based assay with high sensitivity and selectivity for analysis of telomerase in exfoliated cells from patients with bladder and colon cancer. Electrophoresis 2007; 28:4435-4446.
59. Ackermann BL, Berna MJ. Coupling immunoafnity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomic 2007; 4:175-186.
60. Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, Veenstra TD, Adkins JN, Pounds JG, Fagan R, Lobley A. Te human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomic 2004; 3:311-326.
61. Anderson NL, Anderson NG. Te human plasma pro-teome: history, character, and diagnostic prospects. Mol Cell Proteomic 2002; 1:845-867.
62. Boschetti E, Giorgio Righetti P. Hexapeptide combinatorial ligand libraries: the march for the detection of the low-abundance proteome continues. Biotechniques 2008; 44:663-665.
63. Boschetti E, Righetti PG. Te art of observing rare protein species in proteomes with peptide ligand libraries. Proteomic 2009; 9:1492-1510.
64. 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; 7:4191-4198.
65. Fang X, Zhang WW. Afnity separation and enrichment methods in proteomic analysis. J Proteomic 2008; 71:284-303.
66. Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomic. Nat Protoc 2006; 1:1872-1878.
67. Mann M, Kelleher NL. Precision proteomic: the case for high resolution and high mass accuracy. Proc Natl Acad Sci USA 2008; 105:18132-18138.
68. Yates J, Ruse CI, Nakorchevsky A. Proteomic by mass spec-trometry: approaches, advances, and applications. Annu Rev Biomed Eng 2009; 11:49-79.
69. O'Farrell PH. High resolution two-dimensional electro-phoresis of proteins. J Biol Chem 1975; 250:4007-4021.
70. Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomic Clin Appl 2009; 3:155-172.
71. Gorg A, Drews O, Luck C, Weiland F, Weiss W. 2-DE with IPGs. Electrophoresis 2009; 30(Suppl 1):S122-S132.
72. Unlu M, Morgan ME, Minden JS. Diference gel electro-phoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997; 18:2071-2077.
73. Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Cofey RJ, Caprioli RM. Proteome analysis of human colon cancer by two-dimensional diference gel electrophoresis and mass spectrometry. Proteomic 2004; 4:793-811.
74. Timms JF, Cramer R. Diference gel electrophoresis. Proteomic 2008, 8:4886-4897.
75. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difer-ence gel electrophoresis incorporating a pooled internal standard. Proteomic 2003; 3:36-44.
76. Viswanathan S, Unlu M, Minden JS. Two-dimensional difference gel electrophoresis. Nat Protoc 2006; 1:1351-1358.
77. Rais I, Karas M, Schagger H. Two-dimensional electro-phoresis for the isolation of integral membrane proteins and mass spectrometric identifcation. Proteomic 2004; 4:2567-2571.
78. Williams AA, Fakayode SO, Huang X, Warner IM. Use of multivariate analysis for optimization of separation parameters and prediction of migration time, resolution, and resolution per unit time in micellar electrokinetic chroma-tography. Electrophoresis 2006; 27:4127-4140.
79. Chait BT. Chemistry. Mass spectrometry: bottom-up or top-down? Science 2006; 314:65-66.
80. Bantschef M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomic: a critical review. Anal Bioanal Chem 2007; 389:1017-1031.
81. Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identif-cation technology. Nat Biotechnol 2001; 19:242-247.
82. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomic. Mol Cell Proteomic 2002; 1:376-386.
83. Kruger M, Moser M, Ussar S, Tievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fassler R, Mann M. SILAC mouse for quantitative proteomic uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008, 134:353-364.
84. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded afnity tags. Nat Biotechnol 1999; 17: 994-999.
85. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomic 2004; 3:1154-1169.
86. Wolf-Yadlin A, Hautaniemi S, Laufenburger DA, White FM. Multiple reaction monitoring for robust quantitative pro-teomic analysis of cellular signaling networks. Proc Natl Acad Sci USA 2007; 104:5860-5865.
87. Wang M, You J, Bemis KG, Tegeler TJ, Brown DP. Label-free mass spectrometry-based protein quantifcation technologies in proteomic analysis. Brief Funct Genomic Proteomic 2008; 7:329-339.
88. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantifcation of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 2003; 100:6940-6945.
89. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomic 2006; 5:573-588.
90. Ye H, Hill J, Kaufman J, Gryniewicz C, Han X. Detection of protein modifcations and counterfeit protein pharmaceuticals using isotope tags for relative and absolute quantifcation and matrix-assisted laser desorption/ioni-zation tandem time-of-fight mass spectrometry: studies of insulins. Anal Biochem 2008; 379:182-191.
91. Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA. A human proteome detection and quantitation project. Mol Cell Proteomic 2009; 8:883-886.
92. Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomic 2007; 6:2212-2229.
93. Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomic 2007; 6:1809-1817.
94. Kitteringham NR, Jenkins RE, Lane CS, Elliott VL, Park BK. Multiple reaction monitoring for quantitative biomarker analysis in proteomic and metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1229-1239.
95. Jafe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verifcation. Mol Cell Proteomic 2008; 7: 1952-1962.
96. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohof D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Multi-site assessment of the precision and reproducibility of multiple reaction mon-itoring-based measurements of proteins in plasma. Nat Biotechnol 2009; 27:633-641.
97. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identifcation by searching sequence databases using mass spectrometry data. Electrophoresis 1999; 20:3551-3567.
98. Eng JK, McCormack AL, Yates JRI. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994; 5:976-989.
99. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004; 20:1466-1467.
100. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrom-etry. Anal Chem 2003; 75:4646-4658.
101. Reinders J, Sickmann A. Modifcomics: posttranslational modifcations beyond protein phosphorylation and glyco-sylation. Biomol Eng 2007; 24:169-177.
102. Sickmann A, Mreyen M, Meyer HE. Identifcation of modi-fed proteins by mass spectrometry. IUBMB Life 2002; 54:51-57.
103. Diella F, Gould CM, Chica C, Via A, Gibson TJ. Phospho. ELM: a database of phosphorylation sites-update 2008. Nucleic Acids Res 2008; 36:D240-D244.
104. Ranzinger R, Herget S, Wetter T, von der Lieth CW. GlycomeDB-integration of open-access carbohydrate structure databases. BMC Bioinformatics 2008; 9:384.
105. Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y. SysPTM-a systematic resource for proteomic research of post-trans-lational modifcations. Mol Cell Proteomic 2009;8:1839-1849.
106. Taylor AD, Hancock WS, Hincapie M, Taniguchi N, Hanash SM. Towards an integrated proteomic and gly-comic approach to fnding cancer biomarkers. Genome Med 2009; 1:57.
107. Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts JD. Mass-spectrometric identifcation and relative quantifcation of N-linked cell surface glycoproteins. Nat Biotechnol 2009; 27:378-386.
108. Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R. Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomic 2009; 8:624-638.
109. Andersson L, Porath J. Isolation of phosphoproteins by immobilized metal (Fe3+) afnity chromatography. Anal Biochem 1986; 154:250-254.
110. Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ. Highly selective enrichment of phosphor-ylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomic 2005; 4:873-886.
111. Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B, Heck AJ. Selective isolation at the femtomole level of phosphopep-tides from proteolytic digests using 2D-NanoLC-ESI-MS/ MS and titanium oxide precolumns. Anal Chem 2004; 76:3935-3943.
112. Stensballe A, Jensen ON, Olsen JV, Haselmann KF, Zubarev RA. Electron capture dissociation of singly and multiply phosphorylated peptides. Rapid Commun Mass Spectrom 2000; 14:1793-1800.
113. Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Gref Z, Keri G, Stemmann O, Mann M. Kinase-selective enrichment enables quantitative phosphopro-teomic of the kinome across the cell cycle. Mol Cell 2008; 31:438-448.
114. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specifc phosphorylation dynamics in signaling networks. Cell 2006; 127:635-648.
115. Schreiber TB, Mausbacher N, Breitkopf SB, Grundner-Culemann K, Daub H. Quantitative phosphoproteomic-an emerging key technology in signal-transduction research. Proteomic 2008; 8:4416-4432.
116. Huang PH, White FM. Phosphoproteomic: unraveling the signaling web. Mol Cell 2008; 31:777-781.
117. Yu LF, Wang J, Zou B, Lin MC, Wu YL, Xia HH, Sun YW, Gu Q, He H, Lam SK, Kung HF, Wong BC. XAF1 mediates apoptosis through an extracellular signal-regulated kinase pathway in colon cancer. Cancer 2007; 109:1996-2003.
118. Siuti N, Kelleher NL. Decoding protein modifcations using top-down mass spectrometry. Nat Methods 2007; 4:817-821.
119. Wu S, Yang F, Zhao R, Tolic N, Robinson EW, Camp DG, Smith RD, Pasa-Tolic L. Integrated workfow for characterizing intact phosphoproteins from complex mixtures. Anal Chem 2009;81:4210-4219.
120. MacBeath G. Protein microarrays and proteomic. Nat Genet 2002; 32 Suppl: 526-532.
121. Pollard HB, Srivastava M, Eidelman O, Jozwik C, Rothwell SW, Mueller GP, Jacobowitz DM, Darling T, Guggino WB, Wright J, Zeitlin PL, Paweletz CP. Protein microarray platforms for clinical proteomic. Proteomic Clin Appl 2007; 1:934-952.
122. Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. Biomol Eng 2006; 23:77-88.
123. Spurrier B, Honkanen P, Holway A, Kumamoto K, Terashima M, Takenoshita S, Wakabayashi G, Austin J, Nishizuka S. Protein and lysate array technologies in cancer research. Biotechnol Adv 2008; 26:361-369.
124. Spurrier B, Ramalingam S, Nishizuka S. Reverse-phase protein lysate microarrays for cell signaling analysis. Nat Protoc 2008; 3:1796-1808.
125. Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 2004; 96:353-356.
126. Poon TC. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomic 2007; 4:51-65.
127. Villanueva J, Philip J, DeNoyer L, Tempst P. Data analysis of assorted serum peptidome profles. Nat Protoc 2007; 2:588-602.
128. Metzger J, Schanstra JP, Mischak H. Capillary electrophore-sis-mass spectrometry in urinary proteome analysis: current applications and future developments. Anal Bioanal Chem 2009; 393:1431-1442.
129. Ramautar R, Somsen GW, de Jong GJ. CE-MS in metabo-lomics. Electrophoresis 2009; 30:276-291.
130. McDonnell LA, Heeren RM. Imaging mass spectrometry. Mass Spectrom Rev 2007; 26:606-643.
131. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med 2001; 7:493-496.
132. Franck J, Arafah K, Elayed M, Bonnel D, Vergara D, Jacquet A, Vinatier D, Wisztorski M, Day R, Fournier I, Salzet M. MALDI imaging: State of the art technology in clinical pro-teomic. Mol Cell Proteomic 2009; 8: 2023-2033.
133. Camp RL, Neumeister V, Rimm DL. A decade of tissue micro-arrays: progress in the discovery and validation of cancer biomarkers. J Clin Oncol 2008; 26:5630-5637.
134. Fredriksson S, Gullberg M, Jarvius J, Olsson C, Pietras K, Gustafsdottir SM, Ostman A, Landegren U. Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol 2002; 20:473-477.
135. Song Y. Bead arrays: An introduction to multiplexed bead-based assays for proteins. In Matson RS, Ed. Microarray Methods and Protocols. Pp. 111-126. Boca Raton, FL: CRC Press, 2009.
136. Blow N. Antibodies: Te generation game. Nature 2007; 447:741-744.
137. Ponten F, Jirstrom K, Uhlen M. Te Human Protein Atlas-a tool for pathology. J Pathol 2008; 216:387-393.
138. Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantschef M, Bennett KL, Bjorling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfeld E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagne P, Gelf C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjerno K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Korner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Lobke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Tongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A. Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 2008; 26:164-167.
139. Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A. Human Proteinpedia: a unifed discovery resource for proteomic research. Nucleic Acids Res 2009; 37:D773-D781.
140. Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R. PRIDE: a public repository of protein and peptide identifcations for the proteomic community. Nucleic Acids Res 2006, 34: D659-D663.
141. Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomic work-fows. EMBO Rep 2008; 9:429-434.
142. Rodriguez H, Snyder M, Uhlen M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Ponten F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R. Recommendations from the 2008 International Summit on Proteomic Data Release and Sharing Policy: The Amsterdam Principles. J Proteome Res 2009; 8:3689-3692.
143. Saito H, Oda Y, Sato T, Kuromitsu J, Ishihama Y. Multiplexed two-dimensional liquid chromatography for MALDI and nanoelectrospray ionization mass spectrometry in pro-teomic. J Proteome Res 2006; 5:1803-1807.
144. Hofmann P, Ji H, Moritz RL, Connolly LM, Frecklington DF, Layton MJ, Eddes JS, Simpson RJ. Continuous free-fow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: a non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomic 2001; 1:807-818.
145. Zhang N, Li N, Li L. Liquid chromatography MALDI MS/ MS for membrane proteome analysis. J Proteome Res 2004; 3:719-727.
146. Choi DS, Lee JM, Park GW, Lim HW, Bang JY, Kim YK, Kwon KH, Kwon HJ, Kim KP, Gho YS. Proteomic analysis of microvesicles derived from human colorectal cancer cells. J Proteome Res 2007; 6:4646-4655.
147. Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ. Diference gel electrophoresis analysis of Ras-transformed fbroblast cell-derived exosomes. Electrophoresis 2008; 29:2660-2671.
148. Mathias RA, Lim JW, Ji H, Simpson RJ. Isolation of extracellular membranous vesicles for proteomic analysis. Methods Mol Biol 2009; 528:227-242.
149. Gouyer V, Fontaine D, Dumont P, de Wever O, Fontayne-Devaud H, Leteurtre E, Truant S, Delacour D, Drobecq H, Kerckaert JP, de Launoit Y, Bracke M, Gespach C, Desseyn JL, Huet G. Autocrine induction of invasion and metastasis by tumor-associated trypsin inhibitor in human colon cancer cells. Oncogene 2008; 27:4024-4033.
150. Turck N, Richert S, Gendry P, Stutzmann J, Kedinger M, Leize E, Simon-Assmann P, Van Dorsselaer A, Launay JF. Proteomic analysis of nuclear proteins from proliferative and diferentiated human colonic intestinal epithelial cells. Proteomic 2004; 4:93-105.
151. Miyamoto S. Clinical applications of glycomic approaches for the detection of cancer and other diseases. Curr Opin Mol Ter 2006; 8:507-513.
152. Vercoutter-Edouart AS, Slomianny MC, Dekeyzer-Beseme O, Haeuw JF, Michalski JC. Glycoproteomic and glycomics investigation of membrane N-glycosylproteins from human colon carcinoma cells. Proteomic 2008; 8:3236-3256.
153. Saint-Guirons J, Zeqiraj E, Schumacher U, Greenwell P, Dwek M. Proteome analysis of metastatic colorectal cancer cells recognized by the lectin Helix pomatia agglutinin (HPA). Proteomic 2007; 7:4082-4089.
154. Leroy C, Fialin C, Sirvent A, Simon V, Urbach S, Poncet J, Robert B, Jouin P, Roche S. Quantitative phosphoproteomic reveals a cluster of tyrosine kinases that mediates SRC invasive activity in advanced colon carcinoma cells. Cancer Res 2009; 69:2279-2286.
155. Leech SH, Evans CA, Shaw L, Wong CH, Connolly J, Grifths JR, Whetton AD, Corfe BM. Proteomic analyses of intermediate flaments reveals cytokeratin8 is highly acetylated-implications for colorectal epithelial homeosta-sis. Proteomic 2008; 8:279-288.
156. Saldanha RG, Xu N, Molloy MP, Veal DA, Baker MS. Diferential proteome expression associated with uroki-nase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer. J Proteome Res 2008; 7:4792-4806.
157. Gu S, Liu Z, Pan S, Jiang Z, Lu H, Amit O, Bradbury EM, Hu CA, Chen X. Global investigation of p53-induced apoptosis through quantitative proteomic profling using comparative amino acid-coded tagging. Mol Cell Proteomic 2004; 3:998-1008.
158. Rahman-Roblick R, Roblick UJ, Hellman U, Conrotto P, Liu T, Becker S,
159. Wang P, Lo A, Young JB, Song JH, Lai R, Kneteman NM, Hao C, Li L. Targeted quantitative mass spectrometric identifcation of diferentially expressed proteins between Bax-expressing and defcient colorectal carcinoma cells. J Proteome Res 2009; 8:3403-3414.
160. Ikonomou G, Samiotaki M, Pintzas A, Panayotou G. Proteomic analysis of HRAS-mediated oncogenic transformation of a human colon adenocarcinoma cell line-an approach to identify novel therapeutic targets. FEBS Journal 2008; 275 (Suppl 1):334.
161. Ji H, Moritz RL, Kim YS, Zhu HJ, Simpson RJ. Analysis of Ras-induced oncogenic transformation of NIH-3T3 cells using diferential-display 2-DE proteomic. Electrophoresis 2007; 28:1997-2008.
162. Kim S, Lee YZ, Kim YS, Bahk YY. A Proteomic approach for protein-profling the oncogenic ras induced transformation (H-, K-, and N-Ras) in NIH/3T3 mouse embryonic fbroblasts. Proteomic 2008; 8:3082-3093.
163. Mathias RA, Wang B, Ji H, Kapp EA, Moritz RL, Zhu HJ, Simpson RJ. Secretome-based proteomic profling of Ras-transformed MDCK cells reveals extracellular modulators of epithelial-mesenchymal transition. J Proteome Res 2009; 8:2827-2837.
164. Xu BJ, Li J, Beauchamp RD, Shyr Y, Li M, Washington MK, Yeatman TJ, Whitehead RH, Cofey RJ, Caprioli RM. Identifcation of early intestinal neoplasia protein biomark-ers using laser capture microdissection and MALDI MS. Mol Cell Proteomic 2009; 8:936-945.
165. Zhao L, Liu L, Wang S, Zhang YF, Yu L, Ding YQ. Diferential proteomic analysis of human colorectal carcinoma cell lines metastasis-associated proteins. J Cancer Res Clin Oncol 2007; 133:771-782.
166. Catimel B, Rothacker J, Catimel J, Faux M, Ross J, Connolly L, Clippingdale A, Burgess AW, Nice E. Biosensor-based micro-afnity purifcation for the proteomic analysis of protein complexes. J Proteome Res 2005; 4:1646-1656.
167. Andre M, Le Caer JP, Greco C, Planchon S, El Nemer W, Boucheix C, Rubinstein E, Chamot-Rooke J, Le Naour F. Proteomic analysis of the tetraspanin web using LC-ESI-MS/MS and MALDI-FTICR-MS. Proteomic 2006; 6:1437-1449.
168. Le Naour F, Andre M, Greco C, Billard M, Sordat B, Emile J F, Lanza F, Boucheix C, Rubinstein E. Profling of the tetraspanin web of human colon cancer cells. Mol Cell Proteomic 2006; 5:845-857.
169. Shin YK, Yoo BC, Chang HJ, Jeon E, Hong SH, Jung MS, Lim SJ, Park JG. Down-regulation of mitochondrial F1F0-ATP synthase in human colon cancer cells with induced 5-fuorouracil resistance. Cancer Res 2005; 65:3162-3170.
170. Skvortsov S, Sarg B, Loefer-Ragg J, Skvortsova I, Lindner H, Werner Ott H, Lukas P, Illmensee K, Zwierzina H. Diferent proteome pattern of epidermal growth factor receptor-positive colorectal cancer cell lines that are responsive and nonresponsive to C225 antibody treatment. Mol Cancer Ter 2004; 3:1551-1558.
171. Zhang JT, Liu Y. Use of comparative proteomic to identify potential resistance mechanisms in cancer treatment. Cancer Treat Rev 2007; 33:741-756.
172. Ma Y, Ding Z, Qian Y, Shi X, Castranova V, Harner EJ, Guo L. Predicting cancer drug response by proteomic profling. Clin Cancer Res 2006; 12:4583-4589.
173. Drew JE, Rucklidge GJ, Duncan G, Lufty A, Farquharson AJ, Reid MD, Russell WR, Morrice PC, Arthur JR, Duthie GG. A proteomic approach to identify changes in protein profles in pre-cancerous colon. Biochem Biophys Res Commun 2005; 330:81-87.
174. Wenzel U, Herzog A, Kuntz S, Daniel H. Protein expression profling identifes molecular targets of quercetin as a major dietary favonoid in human colon cancer cells. Proteomic 2004; 4:2160-2174.
175. Herzog A, Kuntz S, Daniel H, Wenzel U. Identifcation of biomarkers for the initiation of apoptosis in human preneo-plastic colonocytes by proteome analysis. Int J Cancer 2004; 109:220-229.
176. Dihal AA, van der Woude H, Hendriksen PJ, Charif H, Dekker LJ, Ijsselstijn L, de Boer VC, Alink GM, Burgers PC, Rietjens IM, Woutersen RA, Stierum RH. Transcriptome and proteome profling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glyco-lysis. Proteomic 2008; 8:45-61.
177. Herzog A, Kindermann B, Doring F, Daniel H, Wenzel U. Pleiotropic molecular efects of the pro-apoptotic dietary constituent favone in human colon cancer cells identifed by protein and mRNA expression profling. Proteomic 2004; 4:2455-2464.
178. Winkelmann I, Diehl D, Oesterle D, Daniel H, Wenzel U. Te suppression of aberrant crypt multiplicity in colonic tissue of 1,2-dimethylhydrazine-treated C57BL/6J mice by dietary favone is associated with an increased expression of Krebs cycle enzymes. Carcinogenesis 2007; 28:1446-1454.
179. Winkelmann I, Nassl AM, Daniel H, Wenzel U. Proteome response in HT-29 human colorectal cancer cells to two apoptosis-inducing compounds with diferent mode of action. Int J Cancer 2008; 122:2223-2232.
180. 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.
181. Fillet M, Cren-Olive C, Renert AF, Piette J, Vandermoere F, Rolando C, Merville MP. Diferential expression of proteins in response to ceramide-mediated stress signal in colon cancer cells by 2-D gel electrophoresis and MALDI-TOF-MS. J Proteome Res 2005; 4:870-880.
182. Lee SY, Kim GT, Roh SH, Song JS, Kim HJ, Hong SS, Kwon SW, Park JH. Proteome changes related to the anti-cancer activity of HT29 cells by the treatment of ginsenoside Rd. Pharmazie 2009; 64:242-247.
183. Lee SY, Kim GT, Roh SH, Song JS, Kim HJ, Hong SS, Kwon SW, Park JH. Proteomic analysis of the anti-cancer efect of 20S-ginsenoside Rg3 in human colon cancer cell lines. Biosci Biotechnol Biochem 2009; 73:811-816.
184. Duthie SJ, Mavrommatis Y, Rucklidge G, Reid M, Duncan G, Moyer MP, Pirie LP, Bestwick CS. Te response of human colonocytes to folate defciency in vitro: functional and pro-teomic analyses. J Proteome Res 2008; 7:3254-3266.
185. Ward DG, Suggett N, Cheng Y, Wei W, Johnson H, Billingham LJ, Ismail T, Wakelam MJ, Johnson PJ, Martin A. Identifcation of serum biomarkers for colon cancer by proteomic analysis. Br J Cancer 2006; 94:1898-1905.
186. Liu XP, Shen J, Li ZF, Yan L, Gu J. A serum proteomic pattern for the detection of colorectal adenocarcinoma using surface enhanced laser desorption and ionization mass spec-trometry. Cancer Invest 2006; 24:747-753.
187. Ward DG, Nyangoma S, Joy H, Hamilton E, Wei W, Tselepis C, Steven N, Wakelam MJ, Johnson PJ, Ismail T, Martin A. Proteomic profling of urine for the detection of colon cancer. Proteome Sci 2008; 6:19.
188. Stulik J, Hernychova L, Porkertova S, Knizek J, Macela A, Bures J, Jandik P, Langridge JI, Jungblut PR. Proteome study of color-ectal carcinogenesis. Electrophoresis 2001; 22:3019-3025.
189. Rho JH, Qin S, Wang JY, Roehrl MH. Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. J Proteome Res 2008; 7:2959-2972.
190. Alfonso P, Nunez A, Madoz-Gurpide J, Lombardia L, Sanchez L, Casal JI. Proteomic expression analysis of colo-rectal cancer by two-dimensional diferential gel electro-phoresis. Proteomic 2005; 5:2602-2611.
191. Kim HJ, Kang HJ, Lee H, Lee ST, Yu MH, Kim H, Lee C. Identifcation of S100A8 and S100A9 as Serological Markers for serological markers for colorectal cancer. J Proteome Res 2009;8:1368-1379.
192. States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confdence protein identifcations from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006; 24:333-338.
193. Brunagel G, Vietmeier BN, Bauer AJ, Schoen RE, Getzenberg RH. Identifcation of nuclear matrix protein alterations associated with human colon cancer. Cancer Res 2002; 62:2437-2442. (Pubitemid 34411729)
194. Leman ES, Schoen RE, Magheli A, Sokoll LJ, Chan DW, Getzenberg RH. Evaluation of colon cancer-specifc antigen 2 as a potential serum marker for colorectal cancer. Clin Cancer Res 2008; 14:1349-1354.
195. Leman ES, Schoen RE, Weissfeld JL, Cannon GW, Sokoll LJ, Chan DW, Getzenberg RH. Initial analyses of colon cancer-specifc antigen (CCSA)-3 and CCSA-4 as color-ectal cancer-associated serum markers. Cancer Res 2007; 67:5600-5605.
196. Polley AC, Mulholland F, Pin C, Williams EA, Bradburn DM, Mills SJ, Mathers JC, Johnson IT. Proteomic analysis reveals feld-wide changes in protein expression in the morphologically normal mucosa of patients with colorectal neoplasia. Cancer Res 2006; 66:6553-6562.
197. Roblick UJ, Hirschberg D, Habermann JK, Palmberg C, Becker S, Kruger S, Gustafsson M, Bruch HP, Franzen B, Ried T, Bergmann T, Auer G, Jornvall H. Sequential pro-teome alterations during genesis and progression of colon cancer. Cell Mol Life Sci 2004; 61:1246-1255.
198. Mazzanti R, Giulivi C. Coordination of nuclear-and mito-chondrial-DNA encoded proteins in cancer and normal colon tissues. Biochim Biophys Acta 2006; 1757:618-623.
199. Alfonso P, Canamero M, Fernandez-Carbonie F, Nunez A, Casal JI. Proteome analysis of membrane fractions in colo-rectal carcinomas by using 2D-DIGE saturation labeling. J Proteome Res 2008; 7:4247-4255.
200. Madoz-Gurpide J, Canamero M, Sanchez L, Solano J, Alfonso P, Casal JI. A proteomic analysis of cell signaling alterations in colorectal cancer. Mol Cell Proteomic 2007; 6:2150-2164.
201. Zhao L, Wang H, Li J, Liu Y, Ding Y. Overexpression of Rho GDP-dissociation inhibitor alpha is associated with tumor progression and poor prognosis of colorectal cancer. J Proteome Res 2008; 7:3994-4003.
202. Pei H, Zhu H, Zeng S, Li Y, Yang H, Shen L, Chen J, Zeng L, Fan J, Li X, Gong Y, Shen H. Proteome analysis and tissue microarray for profling protein markers associated with lymph node metastasis in colorectal cancer. J Proteome Res 2007; 6:2495-2501.
203. Duncan R, Carpenter B, Main LC, Telfer C, Murray GI. Characterisation and protein expression profling of annex-ins in colorectal cancer. Br J Cancer 2008; 98:426-433.
204. Coghlin C, Carpenter B, Dundas SR, Lawrie LC, Telfer C, Murray GI. Characterization and over-expression of chaper-onin t-complex proteins in colorectal cancer. J Pathol 2006; 210:351-357.
205. Dundas SR, Lawrie LC, Rooney PH, Murray GI. Mortalin is over-expressed by colorectal adenocarcinomas and correlates with poor survival. J Pathol 2005; 205:74-81.
206. Kim H, Kang HJ, You KT, Kim SH, Lee KY, Kim TI, Kim C, Song SY, Kim HJ, Lee C, Kim H. Suppression of human selenium-binding protein 1 is a late event in colorec-tal carcinogenesis and is associated with poor survival. Proteomic 2006; 6:3466-3476.
207. Carpenter B, McKay M, Dundas SR, Lawrie LC, Telfer C, Murray GI. Heterogeneous nuclear ribonucleoprotein K is over expressed, aberrantly localised and is associated with poor prognosis in colorectal cancer. Br J Cancer 2006; 95:921-927.
208. Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional separations-based shotgun proteomic. Chem Rev 2007; 107:3654-3686.
209. Han X, Aslanian A, Yates JR, 3rd. Mass spectrometry for proteomic. Curr Opin Chem Biol 2008; 12:483-490.
210. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y,. Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant P V, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. Te genomic landscapes of human breast and colorectal cancers. Science 2007; 318:1108-1113.
211. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. Te consensus coding sequences of human breast and colorectal cancers. Science 2006; 314:268-274.
212. Stratton MR, Campbell PJ, Futreal PA. Te cancer genome. Nature 2009; 458:719-724.
213. Petricoin E F, 3rd, Bichsel VE, Calvert VS, Espina V, Winters M, Young L, Belluco C, Trock BJ, Lippman M, Fishman DA, Sgroi DC, Munson PJ, Esserman LJ, Liotta LA. Mapping molecular networks using proteomic: a vision for patient-tailored combination therapy. J Clin Oncol 2005; 23:3614-3621