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Quantitative Analysis of Glycoprotein Glycans

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Mass Spectrometry of Glycoproteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 951))

Abstract

The ability to quantitatively determine changes in the N- and O-linked glycans is an essential component of comparative glycomics. Multiple strategies are available to by which this can be accomplished, including; both label free approaches and isotopic labeling strategies. The focus of this chapter is to describe each of these approaches while providing insight into their strengths and weaknesses, so that glycomic investigators can make an educated choice of the strategy that is best suited for their particular application.

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References

  1. Liu H, Sadygov RG, Yates JR III (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201

    Article  CAS  PubMed  Google Scholar 

  2. Radulovic D, Jelveh S, Ryu S, Hamilton TG, Foss E, Mao Y, Emili A (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 3:984–997

    Article  CAS  PubMed  Google Scholar 

  3. Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S (2005) Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77:2187–2200

    Article  CAS  PubMed  Google Scholar 

  4. Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75:4818–4826

    Article  CAS  PubMed  Google Scholar 

  5. Goshe MB, Smith RD (2003) Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 14:101–109

    Article  CAS  PubMed  Google Scholar 

  6. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5:2339–2347

    Article  CAS  PubMed  Google Scholar 

  7. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4:1487–1502

    Article  CAS  PubMed  Google Scholar 

  8. Hendrickson EL, Xia Q, Wang T, Leigh JA, Hackett M (2006) Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics. Analyst 131:1335–1341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Tao WA, Aebersold R (2003) Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr Opin Biotechnol 14:110–118

    Article  CAS  PubMed  Google Scholar 

  10. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  CAS  PubMed  Google Scholar 

  11. Liu P, Regnier FE (2002) An isotope coding strategy for proteomics involving both amine and carboxyl group labeling. J Proteome Res 1:443–450

    Article  CAS  PubMed  Google Scholar 

  12. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386

    Article  CAS  PubMed  Google Scholar 

  13. Rao KC, Carruth RT, Miyagi M (2005) Proteolytic 18O labeling by peptidyl-Lys metalloendopeptidase for comparative proteomics. J Proteome Res 4:507–514

    Article  CAS  PubMed  Google Scholar 

  14. Schnolzer M, Jedrzejewski P, Lehmann WD (1996) Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17:945–953

    Article  CAS  PubMed  Google Scholar 

  15. Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL (2005) Quantitative analysis of both protein expression and serine/threonine post-translational modifications through stable isotope labeling with dithiothreitol. Proteomics 5:388–398

    Article  CAS  PubMed  Google Scholar 

  16. Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, Hart GW (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol Cell Proteomics 1:791–804

    Article  CAS  PubMed  Google Scholar 

  17. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73:2836–2842

    Article  CAS  PubMed  Google Scholar 

  18. Ong SE, Foster LJ, Mann M (2003) Mass spectrometric-based approaches in quantitative proteomics. Methods 29:124–130

    Article  CAS  PubMed  Google Scholar 

  19. Wada Y, Azadi P, Costello CE, Dell A, Dwek RA et al (2007) Comparison of the methods for profiling glycoprotein glycans—HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. Glycobiology 17:411–422

    Article  CAS  PubMed  Google Scholar 

  20. Aoki K, Perlman M, Lim JM, Cantu R, Wells L, Tiemeyer M (2007) Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryo. J Biol Chem 282:9127–9142

    Article  CAS  PubMed  Google Scholar 

  21. Sutton CW, O’Neill JA, Cottrell JS (1994) Site-specific characterization of glycoprotein carbohydrates by exoglycosidase digestion and laser-desorption mass spectrometry. Anal Biochem 218:34–46

    Article  CAS  PubMed  Google Scholar 

  22. Kang P, Mechref Y, Klouckova I, Novotny MV (2005) Solid-phase permethylation of glycans for mass spectrometric analysis. Rapid Commun Mass Spectrom 19:3421–3428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kang P, Mechre Y, Novotny MV (2008) High-throughput solid-phase permethylation of glycans prior to mass spectrometry. Rapid Commun Mass Spectrom 22:721–734

    Article  CAS  PubMed  Google Scholar 

  24. Karlsson NG, Wilson NL, Wirth HJ, Dawes P, Joshi H, Packer NH (2004) Negative ion graphitised carbon nano-liquid chromatography/mass spectrometry increases sensitivity for glycoprotein oligosaccharide analysis. Rapid Commun Mass Spectrom 18:2282–2292

    Article  CAS  PubMed  Google Scholar 

  25. Orlando R, Leymarie N, Keck R (2010) Results of the 2010 Glycoprotein Research Group’s (gPRG) study on quantitative glycoprotein analysis. J Biomol Tech 21(3 suppl):S17

    PubMed Central  Google Scholar 

  26. Yuan J, Hashii N, Kawasaki N, Itoh S, Kawanishi T, Hayakawa T (2005) Isotope tag method for quantitative analysis of carbohydrates by liquid chromatography–mass spectrometry. J Chromatogr A 1067:145–152

    Article  CAS  PubMed  Google Scholar 

  27. Hitchcock AM, Costello CE, Zaia J (2006) Glycoform quantification of chondroitin/dermatan sulfate using an LC/MS/MS platform. Biochemistry 45:2350–2361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hsu J, Chang SJ, Franz AH (2006) MALDI-TOF and ESI-MS analysis of oligosaccharides labeled with a new multifunctional oligosaccharide tag. J Am Soc Mass Spectrom 17:194–204

    Article  CAS  PubMed  Google Scholar 

  29. Bowman MJ, Zaia J (2007) Tags for the stable isotopic labeling of carbohydrates and quantitative analysis by mass spectrometry. Anal Chem 79:5777–5784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Xie Y, Liu J, Zhang J, Hedrick JL, Lebrilla CB (2004) Method for the comparative glycomic analyses of O-linked, mucin-type oligosaccharides. Anal Chem 76:5186–5197

    Article  CAS  PubMed  Google Scholar 

  31. Alvarez-Manilla G, Warren NL, Abney T, Atwood J III, Azadi P, York WS, Pierce M, Orlando R (2007) Tools for glycomics: relative quantitation of glycans by isotopic permethylation using 13CH3I. Glycobiology 17:677–687

    Article  CAS  PubMed  Google Scholar 

  32. Kang P, Mechref Y, Kyselova Z, Goetz JA, Novotny MV (2007) Comparative glycomic mapping through quantitative permethylation and stable-isotope labeling. Anal Chem 79:6064–6073

    Article  CAS  PubMed  Google Scholar 

  33. Botelho JC, Atwood JA III, Cheng L, Alvarez-Manilla G, York WS, Orlando R (2008) Quantification by isobaric labeling (QUIBL) for the comparative glycomic study of O-linked glycans. Int J Mass Spectrom 278(2–3):137–142

    Article  CAS  Google Scholar 

  34. Atwood JA III, Cheng L, Alvarez-Manilla G, Warren NL, York WS, Orlando R (2008) Quantitation by isobaric labeling: applications to glycomics. J Proteome Res 7:367–374

    Article  CAS  PubMed  Google Scholar 

  35. Orlando R, Lim J, Atwood JA III, Angel PM, Fang M, Alvarez-Manilla G, Moremen KW, York WS, Tiemeyer M, Pierce M, Dalton S, Wells L (2009) IDAWG: metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells. J Proteome Res 8:3816–3823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Ron Orlando .

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Orlando, R. (2013). Quantitative Analysis of Glycoprotein Glycans. 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_13

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  • DOI: https://doi.org/10.1007/978-1-62703-146-2_13

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-145-5

  • Online ISBN: 978-1-62703-146-2

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