Proteomic methodologies and their application in colorectal cancer research

References

• Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, Thun MJ. Cancer statistics, 2008. CA Cancer J Clin 2008; 58:71–96.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Boyle P, Ferlay J. Mortality and survival in breast and colorectal cancer. Nat Clin Pract Oncol 2005; 2:424–425.
   Google Scholar
• 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 five continents: a worldwide population-based study (CONCORD). Lancet Oncol 2008; 9:730–756.
   PubMed Web of Science ®Google Scholar
• Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell 1990; 61:759–767.
   PubMed Web of Science ®Google Scholar
• Morson BC. Evolution of cancer of the colon and rectum. Cancer 1974; 34(Suppl3):845–849.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Gold P, Freedman SO. Specific carcinoembryonic antigens of the human digestive system. J Exp Med 1965; 122: 467–481.
   PubMed Web of Science ®Google Scholar
• Wanebo HJ, Rao B, Pinsky CM, Hoffman 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.
   PubMed Web of Science ®Google Scholar
• Fletcher RH. Carcinoembryonic antigen. Ann Intern Med 1986; 104:66–73.
   PubMed Web of Science ®Google Scholar
• 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 differentiated colorectal cancer. Am J Med 1981; 71:246–253.
   PubMed Web of Science ®Google Scholar
• Rognum TO, Thorud E, Elgjo K, Brandtzaeg P, Orjasaeter H, Nygaard K. Large-bowel carcinomas with different ploidy, related to secretory component, IgA, and CEA in epithelium and plasma. Br J Cancer 1982; 45:921–934.
   PubMed Web of Science ®Google Scholar
• Gerber MA, Thung SN. Carcinoembryonic antigen in normal and diseased liver tissue. Am J Pathol 1978; 92:671–679.
   PubMed Web of Science ®Google Scholar
• Sugarbaker PH. Carcinoembryonic antigen (CEA) assays in obstructive colorectal cancer. Ann Surg 1976; 184:752–757.
   Google Scholar
• Alexander JC, Silverman NA, Chretien PB. Effect of age and cigarette smoking on carcinoembryonic antigen levels. JAMA 1976; 235:1975–1979.
   PubMed Web of Science ®Google Scholar
• Locker GY, Hamilton S, Harris J, Jessup JM, Kemeny N, Macdonald JS, Somerfield 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.
   PubMed Web of Science ®Google Scholar
• Magnani JL, Nilsson B, Brockhaus M, Zopf D, Steplewski Z, Koprowski H, Ginsburg V. A monoclonal antibody-defined antigen associated with gastrointestinal cancer is a ganglioside containing sialylated lacto-N-fucopentaose II. J Biol Chem 1982; 257:14365–14369.
   PubMed Web of Science ®Google Scholar
• Koprowski H, Herlyn M, Steplewski Z, Sears HF. Specific antigen in serum of patients with colon carcinoma. Science 1981; 212:53–55.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Ahlquist DA, Skoletsky JE, Boynton KA, Harrington JJ, Mahoney DW, Pierceall WE, Thibodeau 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.
   PubMed Web of Science ®Google Scholar
• 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 cytotoxic lymphocytes identify colon cancer patients with a favorable prognosis. Am J Pathol 2001; 159:297–304.
   PubMed Web of Science ®Google Scholar
• Herman JG. Hypermethylation pathways to colorectal cancer. Implications for prevention and detection. Gastroenterol Clin North Am 2002; 31:945–958.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fearnhead NS, Britton MP, Bodmer WF. The ABC of APC. Hum Mol Genet 2001; 10:721–733.
   PubMed Web of Science ®Google Scholar
• Sidransky D, Tokino T, Hamilton SR, Kinzler KW, Levin B, Frost P, Vogelstein B. Identification of ras oncogene mutations in the stool of patients with curable colorectal tumors. Science 1992; 256:102–105.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Iacopetta B. TP53 mutation in colorectal cancer. Hum Mutat 2003; 21:271–276.
   PubMed Web of Science ®Google Scholar
• Booth RA. Minimally invasive biomarkers for detection and staging of colorectal cancer. Cancer Lett 2007; 249:87–96.
   PubMed Web of Science ®Google Scholar
• Kambara T, Simms LA, Whitehall VL, Spring KJ, Wynter CV, 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.
   PubMed Web of Science ®Google Scholar
• Kondo Y, Issa JP. Epigenetic changes in colorectal cancer. Cancer Metastasis Rev 2004; 23:29–39.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Fehm T, Sagalowsky A, Clifford 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Mocellin S, Keilholz U, Rossi CR, Nitti D. Circulating tumor cells: the ‘leukemic phase’ of solid cancers. Trends Mol Med 2006; 12:130–139.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Herbert B, Harry E. Difficult proteins. Methods Mol Biol 2009; 519:47–63.
   Google Scholar
• 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, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomic: current state and future fields of application in fluid proteomic. Clin Chem Lab Med 2009; 47:724–744.
   PubMed Web of Science ®Google Scholar
• Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomic analysis. J Chromatogr A 2007; 1168:190–210; discussion 189.
   PubMed Web of Science ®Google Scholar
• Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, Gutkind JS. Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Clin Cancer Res 2008; 14:1002–1014.
   PubMed Web of Science ®Google Scholar
• Hwang SI, Thumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, Eng J, Wright ME, Han DK. Direct cancer tissue proteomic: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2007; 26:65–76.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Godfrey W, Rudd CJ, Iyer S, Recktenwald D. Purification of cellular and organelle populations by fluorescence-activated cell sorting for proteome analysis. In Walker J, Ed. The Proteomic Protocols Handbook. Pp. 67–78. Totowa, NJ: Humana Press, 2005.
   Google Scholar
• Weber G, Wildgruber R. Free-flow electrophoresis system for proteomic applications. Methods Mol Biol 2008; 384:703–716.
   Google Scholar
• Kohlheyer D, Eijkel JC, van den Berg A, Schasfoort RB. Miniaturizing free-flow electrophoresis - a critical review. Electrophoresis 2008; 29:977–993.
   PubMed Web of Science ®Google Scholar
• Cortez C, Tomaskovic-Crook E, Johnston AP, Scott AM, Nice EC, Heath JK, Caruso F. Influence of size, surface, cell line, and kinetic properties on the specific binding of A33 antigen-targeted multilayered particles and capsules to colorectal cancer cells. ACS Nano 2007; 1:93–102.
   PubMed Web of Science ®Google Scholar
• Reymond MA, Sanchez JC, Hughes GJ, Gunther K, Riese J, Tortola S, Peinado MA, Kirchner T, Hohenberger W, Hochstrasser DF, Kockerling F. Standardized characterization of gene expression in human colorectal epithelium by two-dimensional electrophoresis. Electrophoresis 1997; 18:2842–2848.
   Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   Google Scholar
• Ackermann BL, Berna MJ. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomic 2007; 4:175–186.
   PubMed Web of Science ®Google Scholar
• Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, Veenstra TD, Adkins JN, Pounds JG, Fagan R, Lobley A. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomic 2004; 3:311–326.
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomic 2002; 1:845–867.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomic 2009; 9:1492–1510.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J Proteomic 2008; 71:284–303.
   PubMed Web of Science ®Google Scholar
• Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomic. Nat Protoc 2006; 1:1872–1878.
   PubMed Web of Science ®Google Scholar
• Mann M, Kelleher NL. Precision proteomic: the case for high resolution and high mass accuracy. Proc Natl Acad Sci USA 2008; 105:18132–18138.
   PubMed Web of Science ®Google Scholar
• Yates J, Ruse CI, Nakorchevsky A. Proteomic by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 2009; 11:49–79.
   PubMed Web of Science ®Google Scholar
• O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975; 250:4007–4021.
   PubMed Web of Science ®Google Scholar
• Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomic Clin Appl 2009; 3:155–172.
   PubMed Web of Science ®Google Scholar
• Gorg A, Drews O, Luck C, Weiland F, Weiss W. 2-DE with IPGs. Electrophoresis 2009; 30(Suppl 1):S122–S132.
   Google Scholar
• Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997; 18:2071–2077.
   PubMed Web of Science ®Google Scholar
• Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomic 2004; 4:793–811.
   PubMed Web of Science ®Google Scholar
• Timms JF, Cramer R. Difference gel electrophoresis. Proteomic 2008, 8:4886–4897.
   PubMed Web of Science ®Google Scholar
• 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 difference gel electrophoresis incorporating a pooled internal standard. Proteomic 2003; 3:36–44.
   PubMed Web of Science ®Google Scholar
• Viswanathan S, Unlu M, Minden JS. Two-dimensional difference gel electrophoresis. Nat Protoc 2006; 1:1351–1358.
   PubMed Web of Science ®Google Scholar
• Rais I, Karas M, Schagger H. Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomic 2004; 4:2567–2571.
   PubMed Web of Science ®Google Scholar
• 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 chromatography. Electrophoresis 2006; 27:4127–4140.
   Google Scholar
• Chait BT. Chemistry. Mass spectrometry: bottom-up or top-down? Science 2006; 314:65–66.
   PubMed Web of Science ®Google Scholar
• Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomic: a critical review. Anal Bioanal Chem 2007; 389:1017–1031.
   PubMed Web of Science ®Google Scholar
• Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001; 19:242–247.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Kruger M, Moser M, Ussar S, Thievessen 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.
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999; 17: 994–999.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci USA 2007; 104:5860–5865.
   PubMed Web of Science ®Google Scholar
• Wang M, You J, Bemis KG, Tegeler TJ, Brown DP. Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 2008; 7:329–339.
   PubMedGoogle Scholar
• Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 2003; 100:6940–6945.
   PubMed Web of Science ®Google Scholar
• Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomic 2006; 5:573–588.
   PubMed Web of Science ®Google Scholar
• Ye H, Hill J, Kauffman J, Gryniewicz C, Han X. Detection of protein modifications and counterfeit protein pharmaceuticals using isotope tags for relative and absolute quantification and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry: studies of insulins. Anal Biochem 2008; 379:182–191.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Jaffe 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 verification. Mol Cell Proteomic 2008; 7:1952–1962.
   PubMed Web of Science ®Google Scholar
• 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, Ransohoff 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 monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009; 27:633–641.
   PubMed Web of Science ®Google Scholar
• Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999; 20:3551–3567.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004; 20:1466–1467.
   PubMed Web of Science ®Google Scholar
• Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003; 75:4646–4658.
   PubMed Web of Science ®Google Scholar
• Reinders J, Sickmann A. Modificomics: posttranslational modifications beyond protein phosphorylation and glycosylation. Biomol Eng 2007; 24:169–177.
   Google Scholar
• Sickmann A, Mreyen M, Meyer HE. Identification of modified proteins by mass spectrometry. IUBMB Life 2002; 54:51–57.
   Google Scholar
• 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.
   Google Scholar
• Ranzinger R, Herget S, Wetter T, von der Lieth CW. GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics 2008; 9:384.
   Google Scholar
• 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-translational modifications. Mol Cell Proteomic 2009;8:1839-1849.
   Google Scholar
• Taylor AD, Hancock WS, Hincapie M, Taniguchi N, Hanash SM. Towards an integrated proteomic and glycomic approach to finding cancer biomarkers. Genome Med 2009; 1:57.
   Google Scholar
• Wollscheid B, Bausch-Fluck D, Henderson C, O’Brien R, Bibel M, Schiess R, Aebersold R, Watts JD. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol 2009; 27:378–386.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Andersson L, Porath J. Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem 1986; 154:250–254.
   PubMed Web of Science ®Google Scholar
• Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomic 2005; 4:873–886.
   PubMed Web of Science ®Google Scholar
• Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B, Heck AJ. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 2004; 76:3935–3943.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M. Kinase-selective enrichment enables quantitative phosphoproteomic of the kinome across the cell cycle. Mol Cell 2008; 31:438–448.
   PubMed Web of Science ®Google Scholar
• Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006; 127:635–648.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Huang PH, White FM. Phosphoproteomic: unraveling the signaling web. Mol Cell 2008; 31:777–781.
   PubMedGoogle Scholar
• 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.
   Google Scholar
• Siuti N, Kelleher NL. Decoding protein modifications using top-down mass spectrometry. Nat Methods 2007; 4:817–821.
   PubMed Web of Science ®Google Scholar
• Wu S, Yang F, Zhao R, Tolic N, Robinson EW, Camp DG, Smith RD, Pasa-Tolic L. Integrated workflow for characterizing intact phosphoproteins from complex mixtures. Anal Chem 2009;81:4210–4219.
   PubMed Web of Science ®Google Scholar
• MacBeath G. Protein microarrays and proteomic. Nat Genet 2002; 32 Suppl: 526–532.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. Biomol Eng 2006; 23:77–88.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Spurrier B, Ramalingam S, Nishizuka S. Reverse-phase protein lysate microarrays for cell signaling analysis. Nat Protoc 2008; 3:1796–1808.
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 2004; 96:353–356.
   PubMed Web of Science ®Google Scholar
• Poon TC. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomic 2007; 4:51–65.
   PubMed Web of Science ®Google Scholar
• Villanueva J, Philip J, DeNoyer L, Tempst P. Data analysis of assorted serum peptidome profiles. Nat Protoc 2007; 2:588–602.
   Google Scholar
• Metzger J, Schanstra JP, Mischak H. Capillary electrophoresis-mass spectrometry in urinary proteome analysis: current applications and future developments. Anal Bioanal Chem 2009; 393:1431–1442.
   Google Scholar
• Ramautar R, Somsen GW, de Jong GJ. CE-MS in metabolomics. Electrophoresis 2009; 30:276–291.
   PubMed Web of Science ®Google Scholar
• McDonnell LA, Heeren RM. Imaging mass spectrometry. Mass Spectrom Rev 2007; 26:606–643.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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 proteomic. Mol Cell Proteomic 2009; 8: 2023–2033.
   Google Scholar
• Camp RL, Neumeister V, Rimm DL. A decade of tissue microarrays: progress in the discovery and validation of cancer biomarkers. J Clin Oncol 2008; 26:5630–5637.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Blow N. Antibodies: The generation game. Nature 2007; 447:741–744.
   PubMed Web of Science ®Google Scholar
• Ponten F, Jirstrom K, Uhlen M. The Human Protein Atlas–a tool for pathology. J Pathol 2008; 216:387–393.
   PubMed Web of Science ®Google Scholar
• Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff 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, Dransfield 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, Gelfi 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, Thongboonkerd 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.
   PubMed Web of Science ®Google Scholar
• 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 unified discovery resource for proteomic research. Nucleic Acids Res 2009; 37:D773–D781.
   PubMed Web of Science ®Google Scholar
• Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R. PRIDE: a public repository of protein and peptide identifications for the proteomic community. Nucleic Acids Res 2006, 34:D659–D663.
   PubMed Web of Science ®Google Scholar
• Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomic workflows. EMBO Rep 2008; 9:429–434.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Saito H, Oda Y, Sato T, Kuromitsu J, Ishihama Y. Multiplexed two-dimensional liquid chromatography for MALDI and nanoelectrospray ionization mass spectrometry in proteomic. J Proteome Res 2006; 5:1803–1807.
   Google Scholar
• Hoffmann P, Ji H, Moritz RL, Connolly LM, Frecklington DF, Layton MJ, Eddes JS, Simpson RJ. Continuous free-flow 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.
   Google Scholar
• Zhang N, Li N, Li L. Liquid chromatography MALDI MS/MS for membrane proteome analysis. J Proteome Res 2004; 3:719–727.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ. Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes. Electrophoresis 2008; 29:2660–2671.
   PubMed Web of Science ®Google Scholar
• Mathias RA, Lim JW, Ji H, Simpson RJ. Isolation of extracellular membranous vesicles for proteomic analysis. Methods Mol Biol 2009; 528:227–242.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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 differentiated human colonic intestinal epithelial cells. Proteomic 2004; 4:93–105.
   PubMed Web of Science ®Google Scholar
• Miyamoto S. Clinical applications of glycomic approaches for the detection of cancer and other diseases. Curr Opin Mol Ther 2006; 8:507–513.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMedGoogle Scholar
• Leech SH, Evans CA, Shaw L, Wong CH, Connolly J, Griffiths JR, Whetton AD, Corfe BM. Proteomic analyses of intermediate filaments reveals cytokeratin8 is highly acetylated–implications for colorectal epithelial homeostasis. Proteomic 2008; 8:279–288.
   Google Scholar
• Saldanha RG, Xu N, Molloy MP, Veal DA, Baker MS. Differential proteome expression associated with urokinase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer. J Proteome Res 2008; 7:4792–4806.
   PubMed Web of Science ®Google Scholar
• 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 profiling using comparative amino acid-coded tagging. Mol Cell Proteomic 2004; 3:998–1008.
   PubMed Web of Science ®Google Scholar
• Rahman-Roblick R, Roblick UJ, Hellman U, Conrotto P, Liu T, Becker S, Hirschberg D, Jornvall H, Auer G, Wiman KG. p53 targets identified by protein expression profiling. Proc Natl Acad Sci USA 2007; 104:5401–5406.
   PubMed Web of Science ®Google Scholar
• Wang P, Lo A, Young JB, Song JH, Lai R, Kneteman NM, Hao C, Li L. Targeted quantitative mass spectrometric identification of differentially expressed proteins between Bax-expressing and deficient colorectal carcinoma cells. J Proteome Res 2009; 8:3403–3414.
   Google Scholar
• 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.
   Google Scholar
• Ji H, Moritz RL, Kim YS, Zhu HJ, Simpson RJ. Analysis of Ras-induced oncogenic transformation of NIH-3T3 cells using differential-display 2-DE proteomic. Electrophoresis 2007; 28:1997–2008.
   Google Scholar
• Kim S, Lee YZ, Kim YS, Bahk YY. A Proteomic approach for protein-profiling the oncogenic ras induced transformation (H-, K-, and N-Ras) in NIH/3T3 mouse embryonic fibroblasts. Proteomic 2008; 8:3082–3093.
   PubMed Web of Science ®Google Scholar
• Mathias RA, Wang B, Ji H, Kapp EA, Moritz RL, Zhu HJ, Simpson RJ. Secretome-based proteomic profiling of Ras-transformed MDCK cells reveals extracellular modulators of epithelial-mesenchymal transition. J Proteome Res 2009; 8:2827–2837.
   PubMed Web of Science ®Google Scholar
• Xu BJ, Li J, Beauchamp RD, Shyr Y, Li M, Washington MK, Yeatman TJ, Whitehead RH, Coffey RJ, Caprioli RM. Identification of early intestinal neoplasia protein biomarkers using laser capture microdissection and MALDI MS. Mol Cell Proteomic 2009; 8:936–945.
   PubMed Web of Science ®Google Scholar
• Zhao L, Liu L, Wang S, Zhang YF, Yu L, Ding YQ. Differential proteomic analysis of human colorectal carcinoma cell lines metastasis-associated proteins. J Cancer Res Clin Oncol 2007; 133:771–782.
   PubMed Web of Science ®Google Scholar
• Catimel B, Rothacker J, Catimel J, Faux M, Ross J, Connolly L, Clippingdale A, Burgess AW, Nice E. Biosensor-based micro-affinity purification for the proteomic analysis of protein complexes. J Proteome Res 2005; 4:1646–1656.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Le Naour F, Andre M, Greco C, Billard M, Sordat B, Emile JF, Lanza F, Boucheix C, Rubinstein E. Profiling of the tetraspanin web of human colon cancer cells. Mol Cell Proteomic 2006; 5:845–857.
   PubMedGoogle Scholar
• 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-fluorouracil resistance. Cancer Res 2005; 65:3162–3170.
   PubMed Web of Science ®Google Scholar
• Skvortsov S, Sarg B, Loeffler-Ragg J, Skvortsova I, Lindner H, Werner Ott H, Lukas P, Illmensee K, Zwierzina H. Different proteome pattern of epidermal growth factor receptor-positive colorectal cancer cell lines that are responsive and nonresponsive to C225 antibody treatment. Mol Cancer Ther 2004; 3:1551–1558.
   Google Scholar
• Zhang JT, Liu Y. Use of comparative proteomic to identify potential resistance mechanisms in cancer treatment. Cancer Treat Rev 2007; 33:741–756.
   PubMed Web of Science ®Google Scholar
• Ma Y, Ding Z, Qian Y, Shi X, Castranova V, Harner EJ, Guo L. Predicting cancer drug response by proteomic profiling. Clin Cancer Res 2006; 12:4583–4589.
   PubMed Web of Science ®Google Scholar
• 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 profiles in pre-cancerous colon. Biochem Biophys Res Commun 2005; 330:81–87.
   PubMed Web of Science ®Google Scholar
• Wenzel U, Herzog A, Kuntz S, Daniel H. Protein expression profiling identifies molecular targets of quercetin as a major dietary flavonoid in human colon cancer cells. Proteomic 2004; 4:2160–2174.
   PubMed Web of Science ®Google Scholar
• Herzog A, Kuntz S, Daniel H, Wenzel U. Identification of biomarkers for the initiation of apoptosis in human preneoplastic colonocytes by proteome analysis. Int J Cancer 2004; 109:220–229.
   PubMed Web of Science ®Google Scholar
• 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 profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis. Proteomic 2008; 8:45–61.
   PubMed Web of Science ®Google Scholar
• Herzog A, Kindermann B, Doring F, Daniel H, Wenzel U. Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling. Proteomic 2004; 4:2455–2464.
   PubMed Web of Science ®Google Scholar
• Winkelmann I, Diehl D, Oesterle D, Daniel H, Wenzel U. The suppression of aberrant crypt multiplicity in colonic tissue of 1,2-dimethylhydrazine-treated C57BL/6J mice by dietary flavone is associated with an increased expression of Krebs cycle enzymes. Carcinogenesis 2007; 28:1446–1454.
   Google Scholar
• Winkelmann I, Nassl AM, Daniel H, Wenzel U. Proteome response in HT-29 human colorectal cancer cells to two apoptosis-inducing compounds with different mode of action. Int J Cancer 2008; 122:2223–2232.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fillet M, Cren-Olive C, Renert AF, Piette J, Vandermoere F, Rolando C, Merville MP. Differential 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Lee SY, Kim GT, Roh SH, Song JS, Kim HJ, Hong SS, Kwon SW, Park JH. Proteomic analysis of the anti-cancer effect of 20S-ginsenoside Rg3 in human colon cancer cell lines. Biosci Biotechnol Biochem 2009; 73:811–816.
   PubMed Web of Science ®Google Scholar
• Duthie SJ, Mavrommatis Y, Rucklidge G, Reid M, Duncan G, Moyer MP, Pirie LP, Bestwick CS. The response of human colonocytes to folate deficiency in vitro: functional and proteomic analyses. J Proteome Res 2008; 7:3254–3266.
   PubMed Web of Science ®Google Scholar
• Ward DG, Suggett N, Cheng Y, Wei W, Johnson H, Billingham LJ, Ismail T, Wakelam MJ, Johnson PJ, Martin A. Identification of serum biomarkers for colon cancer by proteomic analysis. Br J Cancer 2006; 94:1898–1905.
   PubMed Web of Science ®Google Scholar
• 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 spectrometry. Cancer Invest 2006; 24:747–753.
   PubMed Web of Science ®Google Scholar
• Ward DG, Nyangoma S, Joy H, Hamilton E, Wei W, Tselepis C, Steven N, Wakelam MJ, Johnson PJ, Ismail T, Martin A. Proteomic profiling of urine for the detection of colon cancer. Proteome Sci 2008; 6:19.
   PubMedGoogle Scholar
• Stulik J, Hernychova L, Porkertova S, Knizek J, Macela A, Bures J, Jandik P, Langridge JI, Jungblut PR. Proteome study of colorectal carcinogenesis. Electrophoresis 2001; 22:3019–3025.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Alfonso P, Nunez A, Madoz-Gurpide J, Lombardia L, Sanchez L, Casal JI. Proteomic expression analysis of colo-rectal cancer by two-dimensional differential gel electrophoresis. Proteomic 2005; 5:2602–2611.
   PubMed Web of Science ®Google Scholar
• Kim HJ, Kang HJ, Lee H, Lee ST, Yu MH, Kim H, Lee C. Identification of S100A8 and S100A9 as Serological Markers for serological markers for colorectal cancer. J Proteome Res 2009;8:1368–1379.
   PubMed Web of Science ®Google Scholar
• States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006; 24:333–338.
   PubMed Web of Science ®Google Scholar
• Brunagel G, Vietmeier BN, Bauer AJ, Schoen RE, Getzenberg RH. Identification of nuclear matrix protein alterations associated with human colon cancer. Cancer Res 2002; 62:2437–2442.
   PubMed Web of Science ®Google Scholar
• Leman ES, Schoen RE, Magheli A, Sokoll LJ, Chan DW, Getzenberg RH. Evaluation of colon cancer-specific antigen 2 as a potential serum marker for colorectal cancer. Clin Cancer Res 2008; 14:1349–1354.
   PubMed Web of Science ®Google Scholar
• Leman ES, Schoen RE, Weissfeld JL, Cannon GW, Sokoll LJ, Chan DW, Getzenberg RH. Initial analyses of colon cancer-specific antigen (CCSA)-3 and CCSA-4 as colorectal cancer-associated serum markers. Cancer Res 2007; 67:5600–5605.
   PubMed Web of Science ®Google Scholar
• Polley AC, Mulholland F, Pin C, Williams EA, Bradburn DM, Mills SJ, Mathers JC, Johnson IT. Proteomic analysis reveals field-wide changes in protein expression in the morphologically normal mucosa of patients with colorectal neoplasia. Cancer Res 2006; 66:6553–6562.
   PubMed Web of Science ®Google Scholar
• 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 proteome alterations during genesis and progression of colon cancer. Cell Mol Life Sci 2004; 61:1246–1255.
   PubMedGoogle Scholar
• Mazzanti R, Giulivi C. Coordination of nuclear- and mitochondrial-DNA encoded proteins in cancer and normal colon tissues. Biochim Biophys Acta 2006; 1757:618–623.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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 profiling protein markers associated with lymph node metastasis in colorectal cancer. J Proteome Res 2007; 6:2495–2501.
   PubMed Web of Science ®Google Scholar
• Duncan R, Carpenter B, Main LC, Telfer C, Murray GI. Characterisation and protein expression profiling of annexins in colorectal cancer. Br J Cancer 2008; 98:426–433.
   PubMed Web of Science ®Google Scholar
• Coghlin C, Carpenter B, Dundas SR, Lawrie LC, Telfer C, Murray GI. Characterization and over-expression of chaperonin t-complex proteins in colorectal cancer. J Pathol 2006; 210:351–357.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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 colorectal carcinogenesis and is associated with poor survival. Proteomic 2006; 6:3466–3476.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional separations-based shotgun proteomic. Chem Rev 2007; 107:3654–3686.
   PubMed Web of Science ®Google Scholar
• Han X, Aslanian A, Yates JR, 3rd. Mass spectrometry for proteomic. Curr Opin Chem Biol 2008; 12:483–490.
   PubMed Web of Science ®Google Scholar
• 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 PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007; 318:1108–1113.
   PubMed Web of Science ®Google Scholar
• 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. The consensus coding sequences of human breast and colorectal cancers. Science 2006; 314:268–274.
   PubMed Web of Science ®Google Scholar
• Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009; 458:719–724.
   PubMed Web of Science ®Google Scholar
• Petricoin EF, 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.
   PubMed Web of Science ®Google Scholar