1 Glycopeptide Analysis: Recent Developments and Applications By: Heather Desaire* Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66045 *To whom correspondence should be addressed. Phone: (785) 864-3015 Email: [email protected]MCP Papers in Press. Published on February 6, 2013 as Manuscript R112.026567 Copyright 2013 by The American Society for Biochemistry and Molecular Biology, Inc. by guest on November 16, 2018 http://www.mcponline.org/ Downloaded from
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Glycopeptide Analysis: Recent Developments and Applications
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Glycopeptide Analysis: Recent Developments and Applications
By: Heather Desaire*
Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66045 *To whom correspondence should be addressed. Phone: (785) 864-3015 Email: [email protected]
MCP Papers in Press. Published on February 6, 2013 as Manuscript R112.026567
Copyright 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
References 1. Quinton. L., Gilles, N., Smargiasso, N., Kiehne, A., De Pauw, E. (2011) An Unusual Family of Glycosylated Peptides Isolated from Dendroaspis angusticeps Venom and Characterized by Combination of Collision Induced and Electron Transfer Dissociation. J. Am. Soc. Mass Spectrom. 22, 1891-1897. 2. Wang, D. D., Hincapie, M., Rejtar, T., Karger, B. L. (2011) Ultrasensitive Characterization of Site-Specific Glycosylation of Affinity-Purified Haptoglobin from Lung Cancer Patient Plasma Using 10 mu m i.d. Porous Layer Open Tubular Liquid Chromatography-Linear Ion Trap Collision-Induced Dissociation/Electron Transfer Dissociation Mass Spectrometry. Anal Chem., 83, 2029-2037. 3. Li, Y., Tian, Y. A., Rezai, T., Prakash, A., Lopez, M. F., Dan, D. W., Zhang, H. (2011) Simultaneous Analysis of Glycosylated and Sialylated Prostate-Specific Antigen Revealing Differential Distribution of Glycosylated Prostate-Specific Antigen Isoforms in Prostate Cancer Tissues. Anal Chem., 83, 240-245. 4. Dalpathado, D. S., Irungu, J., Go, E. P., Nortan, K., Bousfield, G. R., Desaire, H. (2006) Comparative Glycomics of the Glycoprotein Follicle-Stimulating Hormone (FSH): Glycopeptide Analysis of Isolates from Two Mammalian Species. Biochemistry, 45, 8665-8673. 5. Gimenez, E., Ramos-Hernan, R., Benavente, F., Barbosa, J., Sanz-Nebot, V. (2012) Analysis of Recombinant Human Erythropoietin Glycopeptides by Capillary Electrophoresis Electrospray-Time of Flight Mass Apectrometry. Anal. Chimica Acta. 709, 81-90. 6. Grass, J., Pabst, M., Chang, M., Wozny, M., Altmann, F. (2011) Analysis of Recombinant Human Follicle-Stimulating Hormone (FSH) by Mass Spectrometric Approaches. Anal. Bioanal. Chem. 400, 2427-2438. 7. Zhu, X. G., Borchers, C., Bienstock, R. J., Tomer, K. B. (2000) Mass Spectrometric Characterization of the Glycosylation Pattern of HIV-gp120 Expressed in CHO Cells. Biochemistry, 39, 11194-11204. 8. Go, E. P., Irungu, J., Zhang, Y., Dalpathado, D. S., Liao, H.-X., Sutherland, L. L., Alam, S. M., Haynes, B. F., Desaire, H. (2008) Glycosylation Site-Specific Analysis of HIV Envelope Proteins (JR-FL and CON-S) Reveals Major Differences in Glycosylation Site Occupancy, Glycoform Profiles, and Antigenic Epitopes’ Accessibility. J. Proteome Resch. 7(4), 1660-1674. 9. Go, E. P., Chang, Q., Liao, H.-X., Sutherland, L. L., Alam, S. M., Haynes, B. F., Desaire, H. (2009) Glycosylation Site-Specific Analysis of Clade C HIV-1 Envelope Proteins. J. Proteome Resch. 8, 4231-4242. 10. Go, E. P., Hewawasam, G., Liao, H. X., Chen, H., Ping, L. H., Anderson, J. A., Hua D, C., Haynes, B.F., Desaire, H. (2011) Characterization of Glycosylation Profile of HIV-1 Transmitted/Founder Envelopes by Mass Spectrometry. J. Virology.85(16), 8270-8284.
11. Poon, T. C., Mok, T. S., Chan, A. T., Chan, C. M., Leong, V., Tsui, S. H., Leung, T. W., Wong, H. T., Ho, S. K., Johnson, P. J. (2002) Quantification and Utility of Monosialylated Alpha-Fetoprotein in the Diagnosis of Hepatocellular Carcinoma with Nondiagnostic Serum Total Alpha-Fetoprotein Clin. Chem. 48 (7), 1021–1027. 12. Peracaula, R., Tabares, G., Royle, L., Harvey, D. J., Dwek, R. A., Rudd, P. M., de Llorens, R. (2003) Altered Glycosylation Pattern Allows the Distinction Between Prostate-Specific Antigen (PSA) from Normal and Tumor Origins Glycobiology 13 (6), 457–470. 13. Kuzmanov, U., Jiang, N., Smith, C. R., Soosaipillai, A., Diamandis, E. P. (2009) Differential N-Glycosylation of Kallikrein 6 Derived from Ovarian Cancer Cells or the Central Nervous System Mol. Cell. Proteomics 8 (4), 791–798. 14. Sasaki, H., Ochi, N., Dell, A., Fukuda, M. (1988) Site Specific Glycosylation Analysis of Human Recombinant Erythropoietin. Analysis of Glycopeptides or Peptides at Each Glycosylation Site by Fast Atom Bombardment Mass Spectrometry. Biochemistry, 27, 8618-8626. 15. RahbekNielsen, H., Roepstorff, P., Reischl, H., Qozny, M., Koll, H., Haselbeck, A. (1997) Glycopeptide Profiling of Human Urinary Erythropoietin by Matrix-Assisted Laser Desorption /Ionization Mass Spectrometry. J. Mass Spectrom. 32, 948-958. 16. Takegawa, Y., Ito, H., Keira, T., Deguchi, K. et al. (2008) Profiling of N- and O-Glycopeptides of Erythropoietin by Capillary Zwitterionic Type of Hydrophilic Interaction Chromatography/Electrospray Ionization Mass Spectrometry. J. Sep. Sci. 31, 1585-1593. 17. Zaia, J. (2008) Mass Spectrometry and the Emerging Field of Glycomics. Chemistry & Biology, 15, 881-892. 18. Harvey, D. J. (2005) Proteomic Analysis of Glycosylation: Structural Determination of N- and O-linked Glycans by Mass Spectrometry. Expert Rev. Proteomics. 2, 87-101. 19. Rebecchi, K. R., Desaire, H. (2011) Recent Mass Spectrometric Based Methods in Quantitative N-linked Glycoproteomics. Current Proteomics 8(4), 269-277. 20. Wuhrer, M., Stam, J. C., van de Geijn, F. E., Koeleman, C. A. M., Verrips, C. T., Dolhain, R. J. E. M., Hokke, C., Deelder, A. M. (2007) Glycosylation Profiling of Immunoglobulin G (IgG) Subclasses from Human Serum. Proteomics, 7(22), 4070-4081. 21. Selman, M. H. J., McDonnell, L.A., Palmblad, M., Ruhaak, R., Deelder, A. M., Wuhrer, M. (2010) Immunoglobulin G Glycopeptide Profiling by Matrix-Assisted Laser Desorption Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem., 82(3), 1073-1081. 22. Qiu, R. Regnier, F. E. (2005) Comparative Glycoproteomics of N-Linked Complex-Type Glycoforms Containing Sialic Acid in Human Serum. Anal. Chem., 77(22), 7225-7231.
23. Lee, H.-J., Na, K., Choi, E.-Y., Kim, K. S., Kim, H., Paik, Y.-K. (2010) Simple Method for Quantitative Analysis of N-Linked Glycoproteins in Hepatocellular Carcinoma Specimens. J. Proteome Res., 9(1), 308-318. 24. Drake, P. M., Schilling, B., Niles, R. K., Braten, M., Johansen, E., Liu, H. C., Lerch, M., Sorensen, D. J., Li, B. S., Allen, S., Hall, S. C., Witkowska, H. E., Regnier, F. E., Gibson, B. W., Fisher, S. J. (2011) A Lectin Affinity Workflow Targeting Glycosite-Specific, Cancer-Related Carbohydrate Structures in Trypsin-Digested Human Plasma. Anal Biochem. 408, 71-85. 25. Wada, Y., Tajiri, M., Yoshida, S. (2004) Hydrophilic Affinity Isolation and MALDI Multiple-Stage Tandem Mass Spectrometry of Glycopeptides for Glycoproteomics. Anal. Chem., 76(22), 6560-6565. 26. Lin, C. Y., Ma, Y. C., Pai, P. J., Her, G. R. (2012) A Comparative Study of Glycoprotein Concentration, Glycoform Profile, and Glycosylation Site Occupancy Using Isotope Labeling and Electrospray Linear Ion Trap Mass Spectrometery. Anal. Chim. Acta 728, 49-66. 27. Rebecchi, K. R., Wenke, J. L., Go, E. P., Desaire, H. (2009) Label-free Quantitation: A New Glycoproteomics Approach. J. Am. Soc. Mass Spectrom., 20(6), 1048-1059. 28. Zhang, Y., Go, E. P., Desaire, H. (2008) Maximizing Coverage of Glycosylation Heterogeneity in MALDI-MS Analysis of Glycoproteins with up to 27 Glycosylation Sites. Anal. Chem., 80(9), 3144-3158. 29. Yeh, C. H., Chen, S.H., Li, D. T., Lin, H. P., Huang, H. J., Chang, C. I., Shih, W. L., Charn, C. L., Shi, F. K., Hus, J. L. (2012) Magnetic Bead-Based Hydrophilic Interaction Liquid Chromatography for Glycopeptide Enrichments. J. Chromatog. A. 1224, 70-78. 30. Qauner, G., Deelder, A. M., Wuhrer, M. (2011) Recent Advances in Hydrophilic Interaction Liquid Chromatography (HILIC) for Structural Glycomics. Electrophoresis, 32, 3456-3466. 31. Hua, S., Nwosu, C. C., Strum, J. S., Seipert, R. R., An, H. J., Zivkovik, A. M., German, J. B., Lebrilla, C. B. (2012) Site-Specific Protein Glycosylation Analysis With Glycan Isomer Differentiation. Anal. Bianal. Chem 403, 1291-1302. 32. Thaysen-Andersen, M., Wilkinson, B. L., Payne, R. J., Packer, N. H. (2011) Site-Specific Characterisation of Densely O-Glycosylated Mucin-Type Peptides Using Electron Transfer Dissociation ESI-MS/MS. Electrophoresis, 32, 3536-3545. 33. Creese, A. J., Cooper, H. J. (2012) Separation and Identification of Isomeric Glycopeptides by High Field Asymmetric Waveform Ion Mobility Spectrometry. Anal. Chem. 84, 2597-2601. 34. Desaire, H., Hua, D. (2009) When Can Glycopeptides be Assigned Based Solely on High Resolution Mass Data? Int. J. Mass Spec. 287, 21-26.
35. Hanisch, F. G. (2011) Top-Down Sequencing of O-Glycoproteins by In-Source Decay Matrix-Assisted Laser Desoprtion Ionization Mass Spectrometry for Glycosylation Site Analysis. Anal. Chem. 83, 4829-4837. 36. Segu, Z. M., Mechref, Y. (2010) Characterizing Protein Glycosylation Sites Through Higher-Energy C-Trap Dissociation. Rapid Comm. Mass Spectrom. 24, 1217-1225. 37. Scott, N. E., Parker, B. L., Connolly, A. M., Paulech, J., Edwards, A. V. G., Crossett, B., Falconer, L., Kolarich, D., Djordjevic, S. P., Hojrup, P., Packer, N. H., Larsen, M. R., Cordwell, S. J. (2011) Simultaneous Glcan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni. Mol. Cell. Proteomics, 10, 1-18. 38. Hart-Smith, G., Raftery, M. J. (2012) Detection and Characterization of Low Abundance Glycopeptides Via Higher-Energy C-Trap Dissociation and Orbitrap Mass Analysis. J. Am. Soc. Mass Spectrom. 23, 124-140. 39. Ko, B. J., Brodbelt, J. S. (2011) 193 nm Ultraviolet Photodissociation of Deprotonated Sialylated Oligosaccharides. Anal. Chem. 83, 8192-8200. 40. Cooper, C. A., Gasteiger, E., Packer, N. H. (2001) GlycoMod – A Software Tool for Determining Glycosylation Compositions From Mass Spectrometric Data. Proteomics. 1, 340-349. 41. Go, E. P., Rebecchi, K. R., Dalpathado, D. S., Bandu, M. L., Zhang, Y., Desaire, H. (2007) GlycoPep DB: A Tool for Glycopeptide Analysis Using a “Smart Search”. Anal. Chem. 79, 1708-1713. 42. Deshpande, N., Jensen, P. H., Packer, N. H., Kolarich, D. (2010) GlycoSpectrumScan: Fishing Glycopeptides from MS Spectra of Protease Digests of Human Colostrum sIgA. J. Proteome Res. 9, 1063-1075. 43. Ozohanics, O., Krenyacz, J., Ludányi, K., Pollreisz, F., Vékey, K., Drahos, L. (2008) GlycoMiner: A New Software Tool to Elucidate Glycopeptide Composition. Rapid Commun. Mass. Spectrom. 22, 3245-3254. 44. Woodin, C. L., Hua, D., Maxon, M., Rebecchi, K. R., Go, E. P., Desaire, H. (2012) GlycoPep Grader: A Web-Based Utility for Assigning the Composition of N-Linked Glycopeptides. Anal. Chem. 84, 4821-4829. 45. Wu, Y., Mechref, Y., Klouckova, I., Novotny, M. V., Tang, H. (2007) A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry. Systems Biology and Computational Proteomics. Ideker, T.; Bafna, V., Eds. Springer Berlin/Heidelberg: Vol. 4532, pp 96-107. 46. Mayampurath, M. A., Wu, Y., Segu, Z. M., Mechref, Y., Tang, H. X. (2011) Improving Confidence in Detection and Characterization of Protein N-Glycosylation Sites and Microheterogeneity. Rapid Comm Mass Spectrom. 25, 2007-2019.
47. Singh, C., Zampronio, C. G., Creese, A. J., Cooper, H. J. (2012) Higher Energy Collision Dissociation (HCD) Product Ion-Triggered Electron Transfer Dissociation (ETD) Mass Spectrometry for the Analysis of N-Linked Glycoproteins. J. Proteome Resch. 11, 4517-4525.
Figure 1. Comparison of the glycopeptides identified from human and equine follicle stimulating hormone (FSH). Proteins were isolated from pituitary extracts, digested with proteinase K, and characterize by ESI-MS. The glycans are described using the following key: Square = HexNAc; circle = hexose; triangle = fucoses; diamond = sialic acid. Structures were inferred based on fragmentation data and biological precedence. Glycoforms in boxes are uniquely identified in one of the two species. Data adapted from reference 4. Figure 2. Recent developments using porous-layer open tubular columns for separation and analysis of glycopeptides. A) Base peak chromatogram of 10 fmol tryptic digest of haptoglobin using PLOT-LTQ-CID/ETD-MS platform. B) MS data showing seven glycoforms identified in a site-specific manner on one of haptoglobin’s glycosylation sites. Glycan structures are depicted using the same conventions as described in Figure 1. Data provided by Professor Barry Karger, Northeastern University.
Figure 3: Comparison of two fragmentation methods for glycopeptides. A) Collision induced dissociation data of an N-linked glycopeptide from RNAse B. B) Electron transfer dissociation data for the same glycopeptide. Both data sets were acquired on a LTQ-Velos linear ion trap (Thermo). Glycan structures are depicted using the same conventions as described in Figure 1. Data provided by Zhikai Zhu, University of Kansas.
Figure 4. MS/MS data of doubly deprotonated [2Ant2SiA - 2H]2- (A) by CID and (B) by 193 nm UVPD with 10 pulses; and the product ions assigned from (C) CID and (D) UVPD. Data provided by Professor Jennifer Brodbelt, University of Texas, Austin. by guest on N
Figure 1. Comparison of the glycopeptides identified from human and equine follicle stimulating hormone (FSH). Proteins were isolated from pituitary extracts, digested with proteinase K, and characterize by ESI-MS. Glycoforms in boxes are uniquely identified in one of the two species. Data adapted from reference 4.
Figure 2. Recent developments using porous-layer open tubular columns for separation and analysis of glycopeptides. A) Base peak chromatogram of 10 fmol tryptic digest of haptoglobin using PLOT-LTQ-CID/ETD-MS platform. B) MS data showing seven glycoforms identified in a site-specific manner on one of haptoglobin’s glycosylation sites. Data provided by Professor Barry Karger, Northeastern University.
Figure 3: Comparison of two fragmentation methods for glycopeptides. A) Collision induced dissociation data of an N-linked glycopeptide from RNAse B. B) Electron transfer dissociation data for the same glycopeptide. Both data sets were acquired on a LTQ-Velos linear ion trap (Thermo). Data provided by Zhikai Zhu, University of Kansas.
Figure 4. MS/MS data of doubly deprotonated [2Ant2SiA - 2H]2- (A) by CID and (B) by 193 nm UVPD with 10 pulses; and the product ions assigned from (C) CID and (D) UVPD. Data provided by Professor Jennifer Brodbelt, University of Texas, Austin.