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Ion Mobility-Mass Spectrometry of Glycoconjugates

  • Weston B. StruweEmail author
  • David J. Harvey
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2084)

Abstract

Glycoconjugates are diverse biomolecules that are dynamically assembled to regulate and fine-tune numerous cellular processes. Their biosynthesis is nontemplate-driven, achieved stepwise in discrete locations within the cell, giving rise to a range of complex branched structures that pose a significant challenge in structural biology. Mass spectrometry is the leading method for analysis of glycoconjugates, and the addition of ion mobility has proven valuable for improving structural assignments of individual glycans in complex biological mixtures. In this chapter, we briefly discuss recent applications of IM for glycomics and describe how to acquire, interpret, and analyze IM-MS data for the analysis of glycans.

Key words

Glycosylation Mass spectrometry Ion mobility Glycomics Collision cross section 

References

  1. 1.
    Struwe WB, Pagel K, Benesch JL et al (2016) GlycoMob: an ion mobility-mass spectrometry collision cross section database for glycomics. Glycoconj J 33:399–404PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Gray CJ, Thomas B, Upton R et al (2016) Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta 1860:1688–1709PubMedCrossRefPubMedCentralGoogle Scholar
  3. 3.
    Hofmann J, Pagel K (2017) Glycan analysis by ion mobility-mass spectrometry. Angew Chem Int Ed Engl 56:8342–8349PubMedCrossRefPubMedCentralGoogle Scholar
  4. 4.
    Manz C, Pagel K (2018) Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy. Curr Opin Chem Biol 42:16–24PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Struwe WB, Baldauf C, Hofmann J et al (2016) Ion mobility separation of deprotonated oligosaccharide isomers – evidence for gas-phase charge migration. Chem Commun (Camb) 52:12353–12356CrossRefGoogle Scholar
  6. 6.
    Mucha E, Stuckmann A, Marianski M et al (2019) In-depth structural analysis of glycans in the gas phase. Chem Sci 10:1272–1284PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    May JC, Goodwin CR, Lareau NM et al (2014) Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer. Anal Chem 86:2107–2116PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Harvey DJ, Scarff CA, Edgeworth M et al (2013) Travelling wave ion mobility and negative ion fragmentation for the structural determination of N-linked glycans. Electrophoresis 34:2368–2378PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Harvey DJ, Sobott F, Crispin M et al (2011) Ion mobility mass spectrometry for extracting spectra of N-glycans directly from incubation mixtures following glycan release: application to glycans from engineered glycoforms of intact, folded HIV gp120. J Am Soc Mass Spectrom 22:568–581PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Guttman M, Lee KK (2016) Site-specific mapping of sialic acid linkage isomers by ion mobility spectrometry. Anal Chem 88:5212–5217PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Hinneburg H, Hofmann J, Struwe WB et al (2016) Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry. Chem Commun 52:4381–4384CrossRefGoogle Scholar
  12. 12.
    Hofmann J, Stuckmann A, Crispin M et al (2017) Identification of Lewis and blood group carbohydrate epitopes by ion mobility-tandem-mass spectrometry fingerprinting. Anal Chem 89:2318–2325PubMedCrossRefPubMedCentralGoogle Scholar
  13. 13.
    Harvey DJ, Struwe WB (2018) Structural studies of fucosylated N-glycans by ion mobility mass spectrometry and collision-induced fragmentation of negative ions. J Am Soc Mass Spectrom 29:1179–1193PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Harvey DJ, Royle L, Radcliffe CM et al (2008) Structural and quantitative analysis of N-linked glycans by matrix-assisted laser desorption ionization and negative ion nanospray mass spectrometry. Anal Biochem 376:44–60PubMedCrossRefPubMedCentralGoogle Scholar
  15. 15.
    Harvey DJ, Scarff CA, Edgeworth M et al (2016) Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans. J Mass Spectrom 51:219–235PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Huang YT, Dodds ED (2013) Ion mobility studies of carbohydrates as group I adducts: isomer specific collisional cross section dependence on metal ion radius. Anal Chem 85:9728–9735PubMedCrossRefPubMedCentralGoogle Scholar
  17. 17.
    Struwe WB, Benesch JL, Harvey DJ et al (2015) Collision cross sections of high-mannose N-glycans in commonly observed adduct states – identification of gas-phase conformers unique to [M−H](−) ions. Analyst 14:6799–6803CrossRefGoogle Scholar
  18. 18.
    Harvey DJ, Scarff CA, Edgeworth M et al (2016) Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans. J Mass Spectrom 51:1064–1079PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Harvey DJ, Seabright GE, Vasiljevic S et al (2018) Isomer information from ion mobility separation of high-mannose glycan fragments. J Am Soc Mass Spectrom 29:972–988PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Harvey DJ, Watanabe Y, Allen JD et al (2018) Collision cross sections and ion mobility separation of fragment ions from complex N-glycans. J Am Soc Mass Spectrom 29:1250–1261PubMedCrossRefPubMedCentralGoogle Scholar
  21. 21.
    Hinneburg H, Hofmann J, Struwe WB et al (2016) Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry. Chem Commun (Camb) 52:4381–4384CrossRefGoogle Scholar
  22. 22.
    Hofmann J, Struwe WB, Scarff CA et al (2014) Estimating collision cross sections of negatively charged N-glycans using traveling wave ion mobility-mass spectrometry. Anal Chem 86:10789–10795PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Bitto D, Harvey DJ, Halldorsson S et al (2015) Determination of N-linked glycosylation in viral glycoproteins by negative ion mass spectrometry and ion mobility. Methods Mol Biol 1331:93–121PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Royle L, Radcliffe CM, Dwek RA et al (2006) Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions. Methods Mol Biol 347:125–143PubMedPubMedCentralGoogle Scholar
  25. 25.
    Jensen PH, Karlsson NG, Kolarich D et al (2012) Structural analysis of N- and O-glycans released from glycoproteins. Nat Protoc 7:1299–1310PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Karlsson NG, Schulz BL, Packer NH (2004) Structural determination of neutral O-linked oligosaccharide alditols by negative ion LC-electrospray-MSn. J Am Soc Mass Spectrom 15:659–672PubMedCrossRefPubMedCentralGoogle Scholar
  27. 27.
    Seo Y, Andaya A, Leary JA (2012) Preparation, separation, and conformational analysis of differentially sulfated heparin octasaccharide isomers using ion mobility mass spectrometry. Anal Chem 84:2416–2423PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Turnbull JE, Miller RL, Ahmed Y et al (2010) Glycomics profiling of heparan sulfate structure and activity. Methods Enzymol 480:65–85PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Kolarich D, Jensen PH, Altmann F et al (2012) Determination of site-specific glycan heterogeneity on glycoproteins. Nat Protoc 7:1285–1298PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Stavenhagen K, Hinneburg H, Kolarich D et al (2017) Site-specific N- and O-glycopeptide analysis using an integrated C18-PGC-LC-ESI-QTOF-MS/MS approach. Methods Mol Biol 1503:109–119PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Bornsen KO, Mohr MD, Widmer HM (1995) Ion-exchange and purification of carbohydrates on a Nafion(R) membrane as a new sample pretreatment for matrix-assisted laser-desorption ionization mass-spectrometry. Rapid Commun Mass Spectrom 9:1031–1034CrossRefGoogle Scholar
  32. 32.
    Hernandez H, Robinson CV (2007) Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nat Protoc 2:715–726PubMedCrossRefPubMedCentralGoogle Scholar
  33. 33.
    Harvey DJ (2005) Fragmentation of negative ions from carbohydrates: Part 1. Use of nitrate and other anionic adducts for the production of negative ion electrospray spectra from N-linked carbohydrates. J Am Soc Mass Spectrom 16:622–630PubMedCrossRefPubMedCentralGoogle Scholar
  34. 34.
    Harvey DJ (2005) Fragmentation of negative ions from carbohydrates: Part 2. Fragmentation of high-mannose N-linked glycans. J Am Soc Mass Spectrom 16:631–646PubMedCrossRefPubMedCentralGoogle Scholar
  35. 35.
    Harvey DJ (2005) Fragmentation of negative ions from carbohydrates: Part 3. Fragmentation of hybrid and complex N-linked glycans. J Am Soc Mass Spectrom 16:647–659PubMedCrossRefPubMedCentralGoogle Scholar
  36. 36.
    Harvey DJ, Abrahams JL (2016) Fragmentation and ion mobility properties of negative ions from N-linked carbohydrates: Part 7. Reduced glycans. Rapid Commun Mass Spectrom 30:627–634PubMedCrossRefPubMedCentralGoogle Scholar
  37. 37.
    Harvey DJ, Edgeworth M, Krishna BA et al (2014) Fragmentation of negative ions from N-linked carbohydrates: Part 6. Glycans containing one N-acetylglucosamine in the core. Rapid Commun Mass Spectrom 28:2008–2018PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Harvey DJ, Jaeken J, Butler M et al (2010) Fragmentation of negative ions from N-linked carbohydrates: Part 4. Fragmentation of complex glycans lacking substitution on the 6-antenna. J Mass Spectrom 45:528–535PubMedCrossRefPubMedCentralGoogle Scholar
  39. 39.
    Harvey DJ, Rudd PM (2011) Fragmentation of negative ions from N-linked carbohydrates: Part 5. Anionic N-linked glycans. Int J Mass Spectrom 305:120–130CrossRefGoogle Scholar
  40. 40.
    Thalassinos, K., Grabenauer, M., Slade, S. E., Hilton, G. R., Bowers, M. T. and Scrivens, J. H. (2009) Characterisation of phosphorylated peptides using travelling wave-based and drift cell ion mobility mass spectrometry. Analytical Chemistry 81:248–254.PubMedCrossRefPubMedCentralGoogle Scholar
  41. 41.
    Domon B, Costello CE (1988) A systematic nomenclature for carbohydrate fragmentations in FAB-MS MS spectra of glycoconjugates. Glycoconj J 5:397–409CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
  2. 2.Department of Biochemistry, Oxford Glycobiology InstituteUniversity of OxfordOxfordUK
  3. 3.Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK

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