Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins

Journal of Proteome Research

Volumn 11, Issue 9, 2012, Pages 4517-4525

  Singh, Charandeep ^a   Zampronio, Cleidiane G ^a   Creese, Andrew J ^a   Cooper, Helen J ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

ETD; glycosylation; HCD; N linked glycosylation; post translational modification; tandem mass spectrometry; ZIC HILIC

Indexed keywords

GLYCAN; GLYCOPEPTIDE; GLYCOPROTEIN; HYDRONIUM ION; IMMUNOGLOBULIN G; MANNOSE; N ACETYLGLUCOSAMINE; RIBONUCLEASE; TRYPSIN;

AMINO ACID SEQUENCE; ARTICLE; COLLISION INDUCED DISSOCIATION MASS SPECTROMETRY; ELECTRON TRANSFER DISSOCIATION MASS SPECTROMETRY; HIGHER ENERGY COLLISION DISSOCIATION MASS SPECTROMETRY; HYDROPHILIC INTERACTION CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DATABASE;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; GLYCOPROTEINS; GLYCOSYLATION; HUMANS; IONS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 84866084330     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300257c     Document Type: Article

References (34)

1. Apweiler, R.; Hermjakob, H.; Sharon, N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database Biochim. Biophys. Acta, Gen. Subj. 1999, 1473 (1) 4-8
2. Khoury, G. A.; Baliban, R. C.; Floudas, C. A., Proteome-wide post-translational modification statistics: Frequency analysis and curation of the SWISS-PROT database. Sci. Rep. 2011, 1, article 90, doi: 10.1038/srep00090.
3. Marth, J. D.; Ohtsubo, K. Glycosylation in cellular mechanisms of health and disease Cell 2006, 126 (5) 855-867 (Pubitemid 44310784)
4. Varki, A. Biological roles of oligosaccharides-All of the theories are correct Glycobiology 1993, 3 (2) 97-130 (Pubitemid 23132602)
5. Go, E. P.; Chang, Q.; Liao, H.-X.; Sutherland, L. L.; Alam, S. M.; Haynes, B. F.; Desaire, H. Glycosylation site-specific analysis of Clade C HIV-1 envelope proteins J. Proteome Res. 2009, 8 (9) 4231-4242
6. Zhang, M.; Gaschen, B.; Blay, W.; Foley, B. L.; Haigwood, N.; Kuiken, C.; Korber, B. Tracking global patterns of N-linked glycosylation site variation in highly variable glycoproteins: HIV, SIV and HCV envelopes and influenza hemagglutinin Glycobiology 2004, 14 (12) 1229-1246 (Pubitemid 39585357)
7. Dijk, W.; Turner, G. A.; Mackiewicz, A. Changes in glycosylation of acute-phase proteins in health and disease: Occurence, regulation and function Glycoconjugate J. 1984, 1 (1) 5-14
8. Higai, K.; Aoki, Y.; Azuma, Y.; Matsumoto, K. Glycosylation of site-specific glycans of α1-acid glycoprotein and alterations in acute and chromic inflammation Biochim. Biophys. Acta 2005, 1725 (1) 128-135 (Pubitemid 41169183)
9. Hochepied, T.; Berger, F. G.; Baumann, H.; Libert, C. α1-acid glycoprotein: An acute phase protein with inflammatory and immunomodulation properties Cytokine Growth Factor Rev. 2003, 14 (1) 25-34 (Pubitemid 36098429)
10. Kandzia, S.; Grammel, N.; Grabenhorst, E.; Conradt, H. S. Quantitative N-glycan mapping of glycoprotein therapeutics by HPAEC-PAD: Glycosylation chracteristics of different recombinant EPO products. In Cells and Culture, Proceedings of the 20th ESACT Meeting; Springer: Dordrecht, 2010; pp 867-871.
11. Raju, T. S.; Briggs, J. B.; Borge, S. M.; Jones, A. J. S. Species-specific variation in glycosylation of IgG: evidence for the species-specific sialylation and branch-specific galactosylation and importance for engineering recombinant glycoprotein therapeutics Glycobiology 2000, 10 (5) 477-486 (Pubitemid 30216089)
12. Imperiali, B.; O'Connor, S. E. Effect of N-linked glycosylation on glycopeptide and glycoprotein structure Curr. Opin. Chem. Biol. 1999, 3 (6) 643-649
13. Hagglund, P.; Bunkenborg, J.; Elortza, F.; Jensen, O. N.; Roepstorff, P. A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sutes using HILIC enrichment and partial deglycosylation J. Proteome Res. 2004, 3 (3) 556-566 (Pubitemid 39207360)
14. Hagglund, P.; Matthiesen, R.; Elortza, F.; Hojrup, P.; Roepstorff, P.; Jensen, O. N.; Bunkenborg, J. An enzymatic deglycosylation scheme enabling idneitification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins J. Proteome Res. 2007, 6 (8) 3021-3031 (Pubitemid 47310187)
15. Tarentino, A. L.; Gomez, C. M.; Plummer, T. H. Deglycosylation of asparagine-linked glycans by peptide:N-glycosidase F Biochemistry 1985, 24 (17) 4665-4671 (Pubitemid 15233719)
16. Hakansson, K.; Cooper, H. J.; Emmett, M. R.; Costello, C. E.; Marshall, A. G.; Nilsson, C. L. ECD and IRMPD MS/MS of an N-glycosylated tryptic peptide to yield complementary sequence information Anal. Chem. 2001, 73 (18) 4530-4536
17. Mikesh, L. M.; Ueberheide, B.; Chi, A.; Coon, J. J.; Syka, J. E. P.; Shabanowitz, J.; Hunt, D. F. The utility of ETD mass spectrometry in proteomic analysis Biochim. Biophys. Acta, Proteins Proteomics 2006, 1764 (12) 1811-1822 (Pubitemid 44895029)
18. Mirgorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Localization of O-glycosylation sites in peptides by ECD in a Fourier transform mass spectrometer Anal. Chem. 1999, 71 (20) 4431-4436
19. Alley, W. R., Jr; Mechref, Y.; Novotny, M. V. Characterisation of glycopeptides by combining collision-induced dissociation and electron transfer dissociation mass spectrometry data Rapid Commun. Mass Spectrom. 2009, 23 (1) 161-170
20. Catalina, M. I.; Koeleman, C. A. M.; Deelder, A. M.; Wuhrer, M. Electron transfer dissociation of N-glycopeptides: loss of the entire N-glycosylated asparagine side chain Rapid Commun. Mass Spectrom. 2007, 21 (6) 1053-1061 (Pubitemid 46426828)
21. 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. Simultaneous glycan-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 2011, 10 (2 M000031
22. Olsen, J. V.; Macek, B.; Lange, O.; Makarov, A.; Horning, S.; Mann, M. Higher-energy C-trap dissociation for peptide modification analysis Nat. Methods 2007, 4 (9) 709-712 (Pubitemid 47338163)
23. Segu, Z. M.; Mechref, Y. Characterising protein glycosylation sites through higher-energy C-trap dissociation Rapid Commun. Mass Spectrom. 2010, 24 (9) 1217-1225
24. Hart-Smith, G.; Raftery, M. J. Detection and characterisation of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis J. Am. Soc. Mass Spectrom. 2012, 23, 124-140
25. Zhao, P.; Viner, R.; Teo, C. F.; Boons, G.-J.; Horn, D. M.; Wells, L. Combining high-energy C-trap dissociation and electron transfer dissociation for protein O -GlcNAc modification site assignment J. Proteome Res. 2011, 10 (9) 4088-4104
26. Sweet, S. M. M.; Bailey, C. M.; Cunningham, D. L.; Heath, J. K.; Cooper, H. J. Large-scale localization of protein phosphorylation by electron capture dissociation mass spectrometry Mol. Cell. Proteomics 2009, 8 (5) 904-912
27. Sweet, S. M. M.; Creese, A. J.; Cooper, H. J. Strategy for the identification of sites of phosphorylation in proteins: Neutral loss triggered electron capture dissociation Anal. Chem. 2006, 78 (21) 7563-7569 (Pubitemid 44707666)
28. Creese, A. J.; Grant, M. M.; Chapple, I. L. C.; Cooper, H. J. On-line liquid chromatography neutral-loss triggered ETD mass spectrometry for the targeted analysis of citrullinated peptides Anal. Methods 2011, 3 (2) 259-266
29. Steentoft, C.; Vakhrushev, S. Y.; Vester-Christinasen, M. B.; Schjoldager, K. T.-B. G.; Kong, Y.; Bennett, E. P.; Mandel, U.; Wandall, H.; Levery, S. B.; Clausen, H. Mining the O-glycoproteome using sinc-finger nuclease-glycoengineered SimpleCell lines Nat. Methods 2011, 8 (11) 977-982
30. Zhang, Y.; Ficarro, S. B.; Li, S.; Marto, J. A. Optimized orbitrap HCD for quantitative analysis of phosphopeptides J. Am. Soc. Mass Spectrom. 2009, 20, 1425-1434
31. Domon, B.; Costello, C. E. A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates Glycoconjugate J. 1988, 5 (4) 397-409 (Pubitemid 19031141)
32. Sweet, S. M. M.; Jones, A. W.; Cunningham, D. L.; Heath, J. K.; Cooper, H. J. Database search strategies for proteomic datasets generated by ECD mass spectrometry J. Proteome Res. 2009, 8 (12) 5475-5484
33. Perdivara, I.; Peddada, S. D.; Miller, F. W.; Tomer, K. B.; Deterding, L. J. Mass spectrometric determination of IgG subclass-specific glycosylation profiles in siblings discordant for myositis syndromes J. Proteome Res. 2011, 10 (7) 2969-2978
34. Zhang, L.; Lu, H.; Yang, P. Specific enrichment methods for glycoproteome research Anal. Bioanal. Chem. 2010, 396 (1) 199-203