Abstract
This chapter describes the utility of ion mobility-mass spectrometry (IM-MS) for the detection and characterization of glycoproteins and associated glycoconjugates. IM-MS provides separations in two dimensions; one on the basis of molecular surface area or structure, and the other on molecular mass which creates the ability to differentiate biomolecular classes and isobaric species. When applied to the characterization of glycoproteins, IM-MS separates peptides from the associated glycans in the same digest without purification, and can also be used to separate different isomeric glycans which is a significant challenge in current glycomic studies. The chapter details the methodologies to use IM-MS for the study of glycans and glycoproteins for an audience ranging from new and potential practitioners to those already utilizing the technique.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bahl OP (1992) Glycoconjugates: composition, structure, and function. Marcel Dekker, New York, NY
Gorelik E, Galili U, Raz A (2001) On the role of cell surface carbohydrates and their binding proteins (lectins) in tumor metastasis. Cancer Metastasis Rev 20:245–277
Montreuil J, Vliegenthart JFG, Schachter H (1995) Glycoproteins I. Elsevier Science, New York, NY
Apweiler R, Hermjakob H, Sharon N (1999) On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta 1473:4–8
Rudd PM, Elliott T, Cresswell P, Wilson IA, Dwek RA (2001) Glycosylation and the immune system. Science 291:2370–2376
Taylor ME, Drickamer K (2006) Introduction to glycobiology. Oxford University Press, Oxford, UK
Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME (eds) (2009) Essentials of glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Woodbury, NY
McLean JA, Ruotolo BT, Gillig KJ, Russell DH (2005) Ion mobility-mass spectrometry: a new paradigm for proteomics. Int J Mass Spectrom 240:301–315
Clemmer DE, Jarrold MF (1997) Ion mobility measurements and their applications to clusters and biomolecules. J Mass Spectrom 32:577–592
Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH Jr (2008) Ion mobility-mass spectrometry. J Mass Spectrom 43:1–22
Mason EA, McDaniel EW (1988) Transport properties of ions in gases. Wiley, Indiana-polis, IN
Baumbach J (2006) Process analysis using ion mobility spectrometry. Anal Bioanal Chem 384:1059–1070
Eiceman GA, Karpas Z (2005) Ion mobility spectrometry, 2nd edn. CRC Press, Boca Raton, FL
McAfee KB Jr, Edelson D (1963) Identification and mobility of ions in a Townsend discharge by time-resolved mass spectrometry. Proc Phys Soc Lond 81:382–384
Barnes WS, Martin DW, McDaniel EW (1961) Mass spectrographic identification of the ion observed in hydrogen mobility experiments. Phys Rev Lett 6:110–111
Gieniec J, Mack LL, Nakamae K, Gupta C, Kumar V, Malcolm D (1984) Electrospray mass spectroscopy of macromolecules: application of an ion-drift spectrometer. Biomed Mass Spectrom 11:259–268
von Helden G, Wyttenbach T, Bowers MT (1995) Inclusion of a MALDI ion source in the ion chromatography technique: conformational information on polymer and biomolecular ions. Int J Mass Spectrom Ion Process 146–147:349–364
Shelimov KB, Clemmer DE, Hudgins RR, Jarrold MF (1997) Protein structure in vacuo: gas-phase confirmations of BPTI and cytochrome c. J Am Chem Soc 119:2240–2248
von Helden G, Wyttenbach T, Bowers MT (1995) Conformation of macromolecules in the gas-phase—use of matrix-assisted laser-desorption methods in ion chromatography. Science 267:1483–1485
Wyttenbach T, vonHelden G, Bowers MT (1996) Gas-phase conformation of biological molecules: bradykinin. J Am Chem Soc 118:8355–8364
Myung S, Lee YJ, Moon MH, Taraszka J, Sowell R, Koeniger S, Hilderbrand AE, Valentine SJ, Cherbas L, Cherbas P, Kaufmann TC, Miller DF, Mechref Y, Novotny MV, Ewing MA, Sporleder CR, Clemmer DE (2003) Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract. Anal Chem 75:5137–5145
Isailovic D, Kurulugama RT, Plasencia MD, Stokes ST, Kyselova Z, Goldman R, Mechref Y, Novotny MV, Clemmer DE (2008) Profiling of human serum glycans associated with liver cancer and cirrhosis by IMS-MS. J Proteome Res 7:1109–1117
Liu X, Plasencia M, Ragg S, Valentine SJ, Clemmer DE (2004) Development of high throughput dispersive LC-ion mobility-TOFMS techniques for analysing the human plasma proteome. Brief Funct Genomic Proteomic 3:177–186
Liu XY, Valentine SJ, Plasencia MD, Trimpin S, Naylor S, Clemmer DE (2007) Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom 18:1249–1264
Valentine SJ, Plasencia MD, Liu XY, Krishnan M, Naylor S, Udseth HR, Smith RD, Clemmer DE (2006) Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res 5:2977–2984
Liu XY, Miller BR, Rebec GV, Clemmer DE (2007) Protein expression in the striatum and cortex regions of the brain for a mouse model of Huntington’s disease. J Proteome Res 6:3134–3142
Taraszka JA, Kurulugama R, Sowell RA, Valentine SJ, Koeniger SL, Arnold RJ, Miller DF, Kaufman TC, Clemmer DE (2005) Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods. J Proteome Res 4:1223–1237
Benesch JLP, Ruotolo BT, Simmons DA, Robinson CV (2007) Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev 107:3544–3567
Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, Robinson CV (2005) Evidence for macromolecular protein rings in the absence of bulk water. Science 310:1658–1661
Ruotolo BT, Hyung SJ, Robinson PM, Giles K, Bateman RH, Robinson CV (2007) Ion mobility-mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. Angew Chem Int Ed Engl 46:8001–8004
Jackson SN, Ugarov M, Egan T, Post JD, Langlais D, Schultz JA, Woods AS (2007) MALDI-ion mobility-TOFMS imaging of lipids in rat brain tissue. J Mass Spectrom 42:1093–1098
McLean JA, Ridenour WB, Caprioli RM (2007) Profiling and imaging of tissues by imaging ion mobility-mass spectrometry. J Mass Spectrom 42:1099–1105
Mason EA, McDaniel EW (1988) Transport properties of ions in gases. Wiley, New York, NY, pp 31–102
Dugourd P, Hudgins RR, Clemmer DE, Jarrold MF (1997) High-resolution ion mobility measurements. Rev Sci Instrum 68:1122–1129
Merenbloom SI, Glaskin RS, Henson ZB, Clemmer DE (2009) High-resolution ion cyclotron mobility spectrometry. Anal Chem 81:1482–1487
Wyttenbach T, Kemper PR, Bowers MT (2001) Design of a new electrospray ion mobility mass spectrometer. Int J Mass Spectrom 212:13–23
Dwivedi P, Wu P, Klopsch SJ, Puzon GJ, Xun L, Hill HH Jr (2008) Metabolic profiling by ion mobility mass spectrometry (IMMS). Metabolomics 4:63–80
Furche F, Ahlrichs R, Weis P, Jacob C, Gilb S, Bierweiler T, Kappes MM (2002) The structures of small gold cluster anions as determined by a combination of ion mobility measurements and density functional calculations. J Chem Phys 117:6982–6990
Ruotolo BT, Verbeck GF, Thomson LM, Woods AS, Gillig KJ, Russell DH (2002) Distinguishing between phosphorylated and nonphosphorylated peptides with ion mobility-mass spectrometry. J Proteome Res 1:303–306
Tao L, McLean JR, McLean JA, Russell DH (2007) A collision cross-section database of singly-charged peptide ions. J Am Soc Mass Spectrom 18:1232–1238
Mason EA (1984) Ion mobility: its role in plasma chromatography. In: Carr TW (ed) Plasma chromatography. Plenum, New York, NY, pp 43–93
Revercomb HE, Mason EA (1975) Theory of plasma chromatography/gaseous electrophoresis. Review. Anal Chem 47:970–983
Fenn LS, McLean JA (2008) Biomolecular structural separations by ion mobility-mass spectrometry. Anal Bioanal Chem 391:905–909
Giles K, Pringle SD, Worthington KR, Little D, Wildgoose JL, Bateman RH (2004) Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Commun Mass Spectrom 18:2401–2414
Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH (2007) An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom 261:1–12
Ruotolo BT, Benesch JLP, Sandercock AM, Hyung S-J, Robinson CV (2008) Ion mobility-mass spectrometry analysis of large protein complexes. Nat Protoc 3:1139–1152
Williams JP, Scrivens JH (2008) Coupling desorption electrospray ionisation and neutral desorption/extractive electrospray ionisation with a travelling-wave based ion mobility mass spectrometer for the analysis of drugs. Rapid Commun Mass Spectrom 22:187–196
Vakhrushev SY, Langridge J, Campuzano I, Hughes C, Peter-Katalinic J (2008) Ion mobility mass spectrometry analysis of human glycourinome. Anal Chem 80:2506–2513
Riba-Garcia I, Giles K, Bateman RH, Gaskell SJ (2008) Evidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry. J Am Soc Mass Spectrom 19:609–613
Gidden J, Bowers MT (2003) Gas-phase conformations of deprotonated trinucleotides (dGTT(−), dTGT(−), and dTTG(−)): the question of zwitterion formation. J Am Soc Mass Spectrom 14:161–170
Gidden J, Bowers MT (2003) Gas-phase conformations of deprotonated and protonated mononucleotides determined by ion mobility and theoretical modeling. J Phys Chem B 107:12829–12837
Shvartsburg AA, Jarrold MF (1996) An exact hard-spheres scattering model for the mobilities of polyatomic ions. Chem Phys Lett 261:86–91
Wyttenbach T, Witt M, Bowers MT (2000) On the stability of amino acid zwitterions in the gas phase: the influence of derivatization, proton affinity, and alkali ion addition. J Am Chem Soc 122:3458–3464
Fenn LS, McLean JA (2011) Structural resolution of carbohydrate positional and structural isomers based on gas-phase ion mobility-mass spectrometry. Phys Chem Chem Phys 13:2196–2205
Williams JP, Grabenauer M, Holland RJ, Carpenter CJ, Wormald MR, Giles K, Harvey DJ, Bateman RH, Scrivens JH, Bowers MT (2010) Characterization of simple isomeric oligosaccharides and the rapid separation of glycan mixtures by ion mobility mass spectrometry. Int J Mass Spectrom 298(1–3):119–127
Fenn LS, Kliman M, Mahsut A, Zhao SR, McLean JA (2009) Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples. Anal Bioanal Chem 394:235–244
Lee S, Wyttenbach T, Bowers MT (1997) Gas phase structures of sodiated oligosaccharides by ion mobility/ion chromatography methods. Int J Mass Spectrom Ion Process 167–168:605–614
Hoaglund CS, Valentine SJ, Clemmer DE (1997) An ion trap interface for ESI Ion mobility experiments. Anal Chem 69:4156–4161
Liu Y, Clemmer DE (1997) Characterizing oligosaccharides using injected-ion mobility/mass spectrometry. Anal Chem 69:2504–2509
Leavell MD, Gaucher SP, Leary JA, Taraszka JA, Clemmer DE (2002) Conformational studies of Zn-ligand-hexose diastereomers using ion mobility measurements and density functional theory calculations. J Am Soc Mass Spectrom 13:284–293
Clowers BH, Dwivedi P, Steiner WE, Hill HH, Bendiak B (2005) Separation of sodiated isobaric disaccharides and trisaccharides using electrospray ionization-atmospheric pressure ion mobility-time of flight mass spectrometry. J Am Soc Mass Spectrom 16:660–669
Clowers BH, Hill HH Jr (2005) Mass analysis of mobility-selected ion populations using dual gate, ion mobility, quadrupole ion trap mass spectrometry. Anal Chem 77:5877–5885
Dwivedi P, Bendiak B, Clowers BH, Hill HH Jr (2007) Rapid resolution of carbohydrate isomers by electrospray ionization ambient pressure ion mobility spectrometry-time-of-flight mass spectrometry (ESI-APIMS-TOFMS). J Am Soc Mass Spectrom 18:1163–1175
Zhu M, Bendiak B, Clowers B, Hill H (2009) Ion mobility-mass spectrometry analysis of isomeric carbohydrate precursor ions. Anal Bioanal Chem 394:1853–1867
Yamagaki T, Sato A (2009) Peak width-mass correlation in CID MS/MS of isomeric oligosaccharides using traveling-wave ion mobility mass spectrometry. J Mass Spectrom 44:1509–1517
Yamagaki T, Sato A (2009) Isomeric oligosaccharides analyses using negative-ion electrospray ionization ion mobility spectrometry combined with collision-induced dissociation MS/MS. Anal Sci 25:985–988
Gabryelski W, Froese KL (2003) Rapid and sensitive differentiation of anomers, linkage, and position isomers of disaccharides using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). J Am Soc Mass Spectrom 14:265–277
Olivova P, Chen W, Chakraborty AB, Gebler JC (2008) Determination of N-glycosylation sites and site heterogeneity in a monoclonal antibody by electrospray quadrupole ion-mobility time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 22:29–40
Plasencia MD, Isailovic D, Merenbloom SI, Mechref Y, Clemmer DE (2008) Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS. J Am Soc Mass Spectrom 19:1706–1715
Schenauer MR, Meissen JK, Seo Y, Ames JB, Leary JA (2009) Heparan sulfate separation, sequencing, and isomeric differentiation: ion mobility spectrometry reveals specific iduronic and glucuronic acid-containing hexasaccharides. Anal Chem 81:10179–10185
Jin L, Barran PE, Deakin JA, Lyon M, Uhrin D (2005) Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling. Phys Chem Chem Phys 7:3464–3471
McCullough BJ, Kalapothakis JM, Taylor K, Clarke DJ, Eastwood H, Campopiano D, MacMillan D, Dorin J, Barran PE (2010) Binding a heparin derived disaccharide to defensin inspired peptides: insights to antimicrobial inhibition from gas-phase measurements. Phys Chem Chem Phys 12:3589–3596
Bagal D, Valliere-Douglass JF, Balland A, Schnier PD (2010) Resolving disulfide structural isoforms of IgG2 monoclonal antibodies by ion mobility mass spectrometry. Anal Chem 82:6751–6755
Harvey DJ (2003) Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates and glycoconjugates. Int J Mass Spectrom 226:1–35
Harvey DJ (1999) Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates. Mass Spectrom Rev 18:349–450
Harvey DJ (2001) Identification of protein-bound carbohydrates by mass spectrometry. Proteomics 1:311–328
An HJ, Lebrilla CB (2010) Structure elucidation of native N- and O-linked glycans by tandem mass spectrometry (tutorial). Mass Spectrom Rev 30(4):560–578
Henderson SC, Valentine SJ, Counterman AE, Clemmer DE (1998) ESI/Ion trap/ion mobility/time-of-flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures. Anal Chem 71:291–301
Hoaglund CS, Valentine SJ, Sporleder CR, Reilly JP, Clemmer DE (1998) Three-dimensional ion mobility/TOFMS analysis of electrosprayed biomolecules. Anal Chem 70:2236–2242
Clemmer Cross Section Database. http://www.indiana.edu/∼clemmer/Research/cross%20section%20database/cs%20database.htm. Accessed 30 Aug 2010
Ridenour WB, Kliman M, McLean JA, Caprioli RM (2010) Structural characterization of phospholipids and peptides directly from tissue sections by MALDI traveling-wave ion mobility-mass spectrometry. Anal Chem 82:1881–1889
Park Z-Y, Russell DH (2000) Thermal denaturation: a useful technique in peptide mass mapping. Anal Chem 72:2667–2670
Cleland WW (1964) Dithiothreitol, a new protective reagent for SH groups*. Biochemistry 3:480–482
Smythe CV (1936) The reaction of iodoacetate and of iodoacetamide with various sulfhydryl groups, with urease, and with yeast preparations. J Biol Chem 114:601–612
Kuster B, Harvey DJ (1997) Ammonium containing buffers should be avoided during enzymatic release of glycans from glycoproteins when followed by reducing terminal derivatization. Glycobiology 7:vii–ix
Pace CN (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131:266–280
Shirley BA (1995) Urea and guanidine hydrochloride denaturation curves. Methods Mol Biol 40:177–190
Fenn LS, McLean JA (2009) Simultaneous glycoproteomics on the basis of structure using ion mobility-mass spectrometry. Mol Biosyst 5:1298–1302
Lareau NM, Fenn LS, McLean JA (2012) Simultaneous glycomics, proteomics, and lipidomics using ion mobility-mass spectrometry. Anal Chem (in preparation).
Acknowledgements
Financial support for this work was provided by the National Institutes of Health (1R01GM092218-01 and RC2DA028981), the US Defense Threat Reduction Agency (HDTRA-09-1-0013), Vanderbilt University College of Arts and Sciences, Vanderbilt Institute of Chemical Biology, and Vanderbilt Institute for Integrative Biosystems Research and Engineering. We thank Nichole M. Lareau for critical comments and assistance with this manuscript. Richard M. Caprioli (Vanderbilt University, Department of Biochemistry) and the Vanderbilt University Mass Spectrometry Research Center for use of the Synapt HDMS. The carbohydrate compounds, LacNAc, Lec, Lac, B tetra type 1, 2′F-B type 2, LNT, LeALex, Di-Lec, Di-LeA, LNnT, Galα3-type1, B2-tri, Pk, P1 tri, Tri-LacNAc, H-type2-LN-LN, P1 penta, P1 antigen, GNLNLN, and 3′SLN-Lec, were provided by the Carbohydrate Synthesis/Protein Expression Core of The Consortium for Functional Glycomics funded by the National Institute of General Medical Sciences grant GM62116.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Fenn, L.S., McLean, J.A. (2013). Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics. In: Kohler, J., Patrie, S. (eds) Mass Spectrometry of Glycoproteins. Methods in Molecular Biology, vol 951. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-146-2_12
Download citation
DOI: https://doi.org/10.1007/978-1-62703-146-2_12
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-145-5
Online ISBN: 978-1-62703-146-2
eBook Packages: Springer Protocols