Deciphering the glycocode: the complexity and analytical challenge of glycomics

Current Opinion in Chemical Biology

Volumn 11, Issue 3, 2007, Pages 300-305

  Pilobello, Kanoelani T ^a   Mahal, Lara K ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCAN; LECTIN;

ACETYLATION; AFFINITY CHROMATOGRAPHY; ANALYTIC METHOD; BIOSYNTHESIS; GLYCOBIOLOGY; GLYCOSYLATION; HIGH THROUGHPUT SCREENING; HUMAN; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHYLATION; MICROARRAY ANALYSIS; PROTEIN PURIFICATION; REVIEW; SULFATION;

CARBOHYDRATES; LECTINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 34250693209     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2007.05.002     Document Type: Review

References (40)

1. Haltiwanger R.S., and Lowe J.B. Role of glycosylation in development. Annu Rev Biochem 73 (2004) 491-537
2. Ohtsubo K., and Marth J.D. Glycosylation in cellular mechanisms of health and disease. Cell 126 (2006) 855-867. An excellent review covering the latest knowledge on disease-related glycobiology.
3. Stenutz R., Weintraub A., and Widmalm G. The structures of Escherichia coli O-polysaccharide antigens. FEMS Microbiol Rev 30 (2006) 382-403
4. 12 structures for a reducing hexasaccharide: the isomer barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology 4 (1994) 759-767
5. Aoki K.F., Yamaguchi A., Okuno Y., Akutsu T., Ueda N., Kanehisa M., and Mamitsuka H. Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform 14 (2003) 134-143
6. Naka R., Kamoda S., Ishizuka A., Kinoshita M., and Kakehi K. Analysis of total N-glycans in cell membrane fractions of cancer cells using a combination of serotonin affinity chromatography and normal phase chromatography. J Proteome Res 5 (2006) 88-97
7. Comelli E.M., Head S.R., Gilmartin T., Whisenant T., Haslam S.M., North S.J., Wong N.K., Kudo T., Narimatsu H., Esko J.D., et al. A focused microarray approach to functional glycomics: transcriptional regulation of the glycome. Glycobiology 16 (2006) 117-131. Using a combination of glycomic profiling by MS and gene expression profiling with a glycogene-specific microarray, the authors demonstrate the power of integrating systems-based data in understanding glycan biosynthesis.
8. An H.J., Ninonuevo M., Aguilan J., Liu H., Lebrilla C.B., Alvarenga L.S., and Mannis M.J. Glycomics analyses of tear fluid for the diagnostic detection of ocular rosacea. J Proteome Res 4 (2005) 1981-1987
9. Kirmiz C., Li B., An H.J., Clowers B.H., Chew H.K., Lam K.S., Ferrige A., Alecio R., Borowsky A.D., Sulaimon S., et al. A serum glycomics approach to breast cancer biomarkers. Mol Cell Proteomics 6 (2007) 43-55
10. An H.J., Miyamoto S., Lancaster K.S., Kirmiz C., Li B., Lam K.S., Leiserowitz G.S., and Lebrilla C.B. Profiling of glycans in serum for the discovery of potential biomarkers for ovarian cancer. J Proteome Res 5 (2006) 1626-1635
11. Hanneman A.J., Rosa J.C., Ashline D., and Reinhold V.N. Isomer and glycomer complexities of core GlcNAcs in Caenorhabditis elegans. Glycobiology 16 (2006) 874-890
12. Liu X., McNally D.J., Nothaft H., Szymanski C.M., Brisson J.R., and Li J. Mass spectrometry-based glycomics strategy for exploring N-linked glycosylation in eukaryotes and bacteria. Anal Chem 78 (2006) 6081-6087
13. Zaia J. Mass spectrometry of oligosaccharides. Mass Spectrom Rev 23 (2004) 161-227
14. Guerardel Y., Chang L.Y., Maes E., Huang C.J., and Khoo K.H. Glycomic survey mapping of zebrafish identifies unique sialylation pattern. Glycobiology 16 (2006) 244-257
15. Tseng K., Xie Y., Seeley J., Hedrick J.L., and Lebrilla C.B. Profiling with structural elucidation of the neutral and anionic O-linked oligosaccharides in the egg jelly coat of Xenopus laevis by Fourier transform mass spectrometry. Glycoconj J 18 (2001) 309-320
16. Zhang J., Xie Y., Hedrick J.L., and Lebrilla C.B. Profiling the morphological distribution of O-linked oligosaccharides. Anal Biochem 334 (2004) 20-35
17. Shimaoka H., Kuramoto H., Furukawa J.I., Miura Y., Kurogochi M., Kita Y., Hinou H., Shinohara Y., and Nishimura S.I. One-pot solid-phase glycoblotting and probing by transoximization for high-throughput glycomics and glycoproteomics. Chemistry 13 (2007) 1664-1673
18. Lohse A., Martins R., Jorgensen M.R., and Hindsgaul O. Solid-phase oligosaccharide tagging (SPOT): validation on glycolipid-derived structures. Angew Chem Int Ed Engl 45 (2006) 4167-4172
19. Uematsu R., Furukawa J.I., Nakagawa H., Shinohara Y., Deguchi K., Monde K., and Nishimura S.I. High throughput quantitative glycomics and glycoform-focused proteomics of murine dermis and epidermis. Mol Cell Proteomics 4 (2005) 1977-1989. A nice study in which new hydroxylamine-based isotope tags are developed for differential glycomics. This technique is then used to assess relative differences in different mouse dermal layers.
20. Mechref Y., and Novotny M.V. Miniaturized separation techniques in glycomic investigations. J Chromatogr B Analyt Technol Biomed Life Sci 841 (2006) 65-78
21. von der Lieth C.W., Lutteke T., and Frank M. The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra. Biochim Biophys Acta 1760 (2006) 568-577
22. Goldberg D., Bern M., Li B., and Lebrilla C.B. Automatic determination of O-glycan structure from fragmentation spectra. J Proteome Res 5 (2006) 1429-1434
23. n. Anal Chem 77 (2005) 6250-6262
24. n data. Anal Chem 77 (2005) 6271-6279
25. n spectral library. Anal Chem 77 (2005) 6263-6270
26. Lohmann K.K., and von der Lieth C.W. GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. Nucleic Acids Res 32 (2004) W261-W266
27. Joshi H.J., Harrison M.J., Schulz B.L., Cooper C.A., Packer N.H., and Karlsson N.G. Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data. Proteomics 4 (2004) 1650-1664
28. Goldberg D., Sutton-Smith M., Paulson J., and Dell A. Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. Proteomics 5 (2005) 865-875. This paper describes Cartoonist, a biosynthetically informed N-glycan annotation program for MALDI-TOF MS spectra. Such programs are the first step towards making glycomic MS possible for the non-expert.
29. Tsui Z.C., Chen Q.R., Thomas M.J., Samuel M., and Cui Z. A method for profiling gangliosides in animal tissues using electrospray ionization-tandem mass spectrometry. Anal Biochem 341 (2005) 251-258
30. Rudiger H., and Gabius H.J. Plant lectins: occurrence, biochemistry, functions and applications. Glycoconj J 18 (2001) 589-613
31. Pilobello K.T., Krishnamoorthy L., Slawek D., and Mahal L.K. Development of a lectin microarray for the rapid analysis of protein glycopatterns. ChemBioChem 6 (2005) 985-989
32. Hsu K.L., Pilobello K.T., and Mahal L.K. Analyzing the dynamic bacterial glycome with a lectin microarray approach. Nat Chem Biol 2 (2006) 153-157. Using a lectin microarray, the authors distinguish between closely related Escherichia coli strains. This is the first paper describing the use of lectin microarrays for microbial glycoprofiling.
33. Angeloni S., Ridet J.L., Kusy N., Gao H., Crevoisier F., Guinchard S., Kochhar S., Sigrist H., and Sprenger N. Glycoprofiling with micro-arrays of glycoconjugates and lectins. Glycobiology 15 (2005) 31-41
34. Zheng T., Peelen D., and Smith L.M. Lectin arrays for profiling cell surface carbohydrate expression. J Am Chem Soc 127 (2005) 9982-9983
35. Kuno A., Uchiyama N., Koseki-Kuno S., Ebe Y., Takashima S., Yamada M., and Hirabayashi J. Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling. Nat Methods 2 (2005) 851-856
36. Ebe Y., Kuno A., Uchiyama N., Koseki-Kuno S., Yamada M., Sato T., Narimatsu H., and Hirabayashi J. Application of lectin microarray to crude samples: differential glycan profiling of lec mutants. J Biochem (Tokyo) 139 (2006) 323-327
37. Hsu K.L., and Mahal L.K. A lectin microarray approach for the rapid analysis of bacterial glycans. Nat Protocols 1 (2006) 543-549. This protocol paper gives complete instructions on how to construct and to use a lectin microarray for glycoprofiling.
38. Manimala J.C., Roach T.A., Li Z., and Gildersleeve J.C. High-throughput carbohydrate microarray analysis of 24 lectins. Angew Chem Int Ed Engl 45 (2006) 3607-3610
39. Manimala J.C., Li Z., Jain A., VedBrat S., and Gildersleeve J.C. Carbohydrate array analysis of anti-Tn antibodies and lectins reveals unexpected specificities: implications for diagnostic and vaccine development. ChemBioChem 6 (2005) 2229-2241
40. Hirabayashi J. Lectin-based structural glycomics: glycoproteomics and glycan profiling. Glycoconj J 21 (2004) 35-40