A strategy for precise and large scale identification of core fucosylated glycoproteins

Molecular and Cellular Proteomics

Volumn 8, Issue 5, 2009, Pages 913-923

  Jia, Wei ^a,b   Lu, Zhuang ^a,c   Fu, Yan ^d   Wang, Hai Peng ^d   Wang, Le Heng ^d   Chi, Hao ^d   Yuan, Zuo Fei ^d   Zheng, Zhao Bin ^a   Song, Li Na ^a   Han, Huan Huan ^a   Liang, Yi Min ^a   Wang, Jing Lan ^a   Cai, Yun ^a   Zhang, Yu Kui ^c   Deng, Yu Lin ^c   Ying, Wan Tao ^a   He, Si Min ^d   Qian, Xiao Hong ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

^c BEIJING INSTITUTE OF TECHNOLOGY   (China)

^d INSTITUTE OF COMPUTING TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN; PLASMA PROTEIN;

ARTICLE; CONTROLLED STUDY; FUCOSYLATION; HUMAN; LIVER CELL CARCINOMA; MASS SPECTROMETRY; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ACETYLGLUCOSAMINE; AMINO ACID SEQUENCE; BIOMEDICAL RESEARCH; FUCOSE; GLYCOPEPTIDES; GLYCOPROTEINS; GLYCOSYLATION; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEOMICS; ULTRAFILTRATION;

EID: 67449100987     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800504-MCP200     Document Type: Article

References (29)

1. Parodi, A. J. (2000) Protein glucosylation and its role in protein folding. Annu. Rev. Biochem. 69, 69-93
2. Walsh, G., and Jefferis, R. (2006) Post-translational modifications in the context of therapeutic proteins. Nat. Biotechnol. 24, 1241-1252
3. Dwek, R. A., Butters, T. D., Piatt, F. M., and Zitzmann, N. (2002) Targeting glycosylation as a therapeutic approach. Nat. Rev. Drug Discov. 1, 65-75
4. Kondo, A., Li, W., Nakagawa, T., Nakano, M., Koyama, N., Wang, X., Gu, J., Miyoshi, E., and Taniguchi, N. (2006) From glycomics to functional glycomics of sugar chains: identification of target proteins with functional changes using gene targeting mice and knock down cells of FUT8 as examples. Biochim. Biophys. Acta 1764, 1881-1889
5. Ma, B., Simala-Grant, J. L., and Taylor, D. E. (2006) Fucosylation in prokaryotes and eukaryotes. Glycobiology 16, 158-184
6. Wang, X., Inoue, S., Gu, J., Miyoshi, E., Noda, K., Li, W., Mizuno-Horikawa, Y., Nakano, M., Asahi, M., Takahashi, M., Uozumi, N., Ihara, S., Lee, S. H., Ikeda, Y., Yamaguchi, Y., Aze, Y., Tomiyama, Y., Fujii, J., Suzuki, K., Kondo, A., Shapiro, S. D., Lopez-Otin, C., Kuwaki, T., Okabe, M., Honke, K., and Taniguchi, N. (2005) Dysregulation of TGF-β1 receptor activation leads to abnormal lung development and emphysema-like phenotype in core fucose deficient mice. Proc. Natl. Acad. Sci. U. S. A. 102, 15791-15796 (Pubitemid 41552821)
7. Wang, X., Gu, J., Ihara, H., Miyoshi, E., Honke, K., and Taniguchi, N. (2006) Core fucosylation regulates epidermal growth factor receptor-mediated intracellular signaling. J. Biol. Chem. 281, 2572-2577 (Pubitemid 43845717)
8. Block, T. M., Comunale, M. A., Lowman, M., Steel, L. F., Romano, P. R., Fimmel, C., Tennant, B. C., London, W. T., Evans, A. A., Blumberg, B. S., Dwek, R. A., Mattu, T. S., and Mehta, A. S. (2005) Use of targeted glycoproteomics to identify serum glycoproteins that correlate with liver cancer in woodchucks and humans. Proc. Natl. Acad. Sci. U. S. A. 102, 779-784 (Pubitemid 40282742)
9. Comunale, M. A., Lowman, M., Long, R. E., Krakover, J., Philip, R., Seehofer, S., Evans, A. A., Hann, H. W., Block, T. M., and Mehta, A. S. (2006) Proteomic analysis of serum associated fucosylated glycoproteins in the development of primary hepatocellular carcinoma. J. Proteome Res. 5, 308-315
10. Okuyama, N., Ide, Y., Nakano, M., Nakagawa, T., Yamanaka, K., Moriwaki, K., Murata, K., Ohigashi, H., Yokoyama, S., Eguchi, H., Ishikawa, O., Ito, T, Kato, M., Kasahara, A., Kawano, S., Gu, J., Taniguchi, N., and Miyoshi, E. (2006) Fucosylated haptoglobin is a novel marker for pancreatic cancer a detailed analysis of the oligosaccharide structure and a possible mechanism for fucosylation. Int. J. Cancer 118, 2803-2808 (Pubitemid 43673360)
11. Barrabés, S., Pagès-Pons, L., Radcliffe, C. M., Tabarés, G., Fort, E., Royle, L., Harvey, D. J., Moenner, M., Dwek, R. A., Rudd, P. M., De Llorens, R., and Peracaula, R. (2007) Glycosylation of serum ribonuclease 1 indicates a major endothelial origin and reveals an increase in core fucosylation in pancreatic cancer. Glycobioiogy 17, 388-400 (Pubitemid 46432010)
12. Geng, F., Shi, B. Z., Yuan, Y. F., and Wu, X. Z. (2004) The expression of core fucosylated E-cadherin in cancer cells and lung cancer patients: prognostic implications. Cell Res. 14, 423-433 (Pubitemid 43231805)
13. Saldova, R., Royle, L., Radcliffe, C. M., Abd Hamid, U. M., Evans, R., Arnold, J. N., Banks, R. E., Hutson, R., Harvey, D. J., Antrobus, R., Petrescu, S. M., Dwek, R. A., and Rudd, P. M. (2007) Ovarian cancer is associated with changes in glycosylation in both acute-phase proteins and IgG. Glycobioiogy 17, 1344-1356 (Pubitemid 350131311)
14. Tabarés, G., Radcliffe, C. M., Barrabés, S., Ramírez, M., Aleixandre, R. N., Hoesel, W., Dwek, R. A, Rudd, P. M., Peracaula, R., and de Llorens, R. (2006) Different glycan structures in prostate-specific antigen from prostate cancer sera in relation to seminal plasma PSA. Glycobioiogy 16, 132-145 (Pubitemid 43125969)
15. Drake, R. R., Schwegler, E. E., Malik, G., Diaz, J., Block, T, Mehta, A., and Semmes, O. J. (2006) Lectin capture strategies combined with mass spectrometry for the discovery of serum glycoprotein biomarkers. Mol. Cell. Proteomics 5, 1957-1967 (Pubitemid 44688203)
16. Wright, L. M., Kreikemeier, J. T., and Fimmel, C. J. (2007) A concise review of serum markers for hepatocellular cancer. Cancer Detect. Prev. 31, 35-44 (Pubitemid 46367447)
17. Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666 (Pubitemid 36638093)
18. Kaji, H., Saito, H., Yamauchi, Y., Shinkawa, T., Taoka, M., Hirabayashi, J., Kasai, K., Takahashi, N., and Isobe, T. (2003) Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat. Biotechnol. 21, 667-672 (Pubitemid 36638094)
19. Zhao, J., Simeone, D. M., Heidt, D., Anderson, M. A., and Lubman, D. M. (2006) Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: application to pancreatic cancer serum. J. Proteome Res. 5, 1792-1802 (Pubitemid 44036154)
20. Hägglund, P., Bunkenborg, J., Elortza, F., Jensen, O. N., and Roepstorff, P. (2004) A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. J. Proteome Res. 3, 556-566 (Pubitemid 39207360)
21. Hägglund, P., Matthiesen, R., Elortza, F., Højrup, P., Roepstorff, P., Jensen, O. N., and Bunkenborg, J. (2007) An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J. Proteome Res. 6, 3021-3031 (Pubitemid 47310187)
22. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50 (Pubitemid 36207189)
23. Alvarez-Manilla, G., Atwood, J., III, Guo, Y., Warren, N. L., Orlando, R., and Pierce, M. (2006) Tools for glycoproteomic analysis: size exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites. J. Proteome Res. 5, 701-708 (Pubitemid 43364110)
24. Tarentino, A. L., Quinones, G., Changchien, L. M., and Plummer, T. H. (1993) Multiple endoglycosidase F activities expressed by Flavobacterium meningosepticum endoglycosidases F2 and F3. J. Biol. Chem. 268, 9702-9708
25. Wuhrer, M., Catalina, M. I., Deelder, A. M., and Hokke, C. H. (2007) Glycoproteomics based on tandem mass spectrometry of glycopeptides. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 849, 115-128 (Pubitemid 46529311)
26. Fu, Y., Yang, Q., Sun, R., Li, D., Zeng, R., Ung, C. X., and Gao, W. (2004) Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 20, 1948-1954 (Pubitemid 39199057)
27. Li, D., Fu, Y., Sun, R., Ung, C. X., Wei, Y., Zhou, H., Zeng, R., Yang, Q., He, S., and Gao, W. (2005) pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics 21, 3049-3050 (Pubitemid 40916431)
28. Wang, L. H., Li, D. Q., Fu, Y., Wang, H. P., Zhang, J. F., Yuan, Z. F., Sun, R. X., Zeng, R., He, S. M., and Gao, W. (2007) pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun. Mass Spectrom. 21, 2985-2991 (Pubitemid 47401434)
29. Miyoshi, E., and Nakano, M. (2008) Fucosylated haptoglobin is a novel marker for pancreatic cancen detailed analyses of oligosaccharide structures. Proteomics 8, 3257-3262