Top-down tandem mass spectrometry on RNase A and B using a Qh/FT-ICR hybrid mass spectrometer

Proteomics

Volumn 14, Issue 10, 2014, Pages 1174-1184

  Bourgoin Voillard, Sandrine ^a   Leymarie, Nancy ^a   Costello, Catherine E ^a  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Collision induced dissociation (CID); Electron capture dissociation (ECD); Electron transfer dissociation (ETD); Glycoproteomics; Infrared multiphoton dissociation (IRMPD)

Indexed keywords

GLYCAN; PROTON; RIBONUCLEASE; RIBONUCLEASE A; GLYCOPROTEIN; PANCREATIC RIBONUCLEASE; PEPTIDE FRAGMENT;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL REACTION; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRON CAPTURE DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; ELECTRON TRANSPORT; GLYCOSYLATION; INFRARED MULTIPHOTON DISSOCIATION; MASS SPECTROMETER; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROTON TRANSPORT; TANDEM MASS SPECTROMETRY; DISSOCIATION; FRAGMENTATION REACTION; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; SEQUENCE ANALYSIS; VIBRATION; ANIMAL; BOVINAE; CHEMISTRY; DEVICES; METABOLISM; MOLECULAR GENETICS; PROCEDURES; PROTEOMICS;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; GLYCOPROTEINS; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEOMICS; RIBONUCLEASE, PANCREATIC; RIBONUCLEASES; TANDEM MASS SPECTROMETRY;

EID: 84899846994     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300433     Document Type: Article

References (47)

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 1999, 1473, 4-8.
2. Varki, A., Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 1993, 3, 97-130.
3. Dwek, R. A., Glycobiology: toward understanding the function of sugars. Chem. Rev. 1996, 96, 683-720.
4. Kornfeld, R., Kornfeld, S., Assembly of asparagine-linked oligosaccharides. Annu. Rev. Biochem. 1985, 54, 631-664.
5. Vance, B. A., Wu, W., Ribaudo, R. K., Segal, D. M., Kearse, K. P., Multiple dimeric forms of human CD69 result from differential addition of N-glycans to typical (Asn-X-Ser/Thr) and atypical (Asn-X-Cys) glycosylation motifs. J. Biol. Chem. 1997, 272, 23117-23122.
6. Halim, A., Rüetschi, U., Larson, G., Nilsson, J., LC-MS/MS Characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins. J. Proteome Res., 2013, 12, 573-584.
7. Geyer, H., Geyer, R., Strategies for analysis of glycoprotein glycosylation. Biochimica. Biophy Acta Proteins roteomics. 2006, 1764, 1853-1869.
8. Wuhrer, M., Catalina, M. I., Deelder, A. M., Hokke, C. H., Glycoproteomics based on tandem mass spectrometry of glycopeptides. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 849, 115-128.
9. Reid, G. E., Stephenson, J. L., Jr., McLuckey, S. A., Tandem mass spectrometry of Ribonuclease A and B: N-linked glycosylation site analysis of whole protein ions. Anal. Chem. 2002, 74, 577-583.
10. Siuti, N., Kelleher, N. L., Decoding protein modifications using top-down mass spectrometry. Nat. Methods 2007, 4, 817-821.
11. Cui, W., Rohrs, H.W., Gross, M.L., Top-down mass spectrometry: recent developments, applications and perspectives. Analyst 2011, 136, 3854-3864.
12. Gault, J., Malosse, C., Duménil, G., Chamot-Rooke, J., A combined mass spectrometry strategy for complete posttranslational modification mapping of Neisseria meningitidis major pilin. J. Mass Spectrom. 2013, 48, 1199-1206.
13. Vestal, M. L., Juhasz, P., Martin, S. A., Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1995, 9, 1044-1050
14. Taichriba, A., Pelzingb, M., Pellegrinoc, C., Rossic, M., Neusüß, C., High resolution TOF MS coupled to CE for the analysis of isotopically resolved intact proteins. J. Proteomics 2011, 74, 958-966.
15. Zhang, Y., Sinaiko, A. R., Nelsestuen, G. L., Glycoproteins and glycosylation_ Apolipoprotein C3 glycoforms by top-down MALDI-TOF mass spectrometry. Methods Mol. Biol. 2012, 909, 141-150.
16. Fornelli, L., Damoc, E., Thomas, P. M., Kelleher, N. L. et al., Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS. Mol. Cell. Proteomics 2012, 11, 1758-1767.
17. Senko, M. W., Speir, J. P., McLafferty, F. W., Collisional activation of large multiply charged ions using Fourier transform mass spectrometry. Anal. Chem. 1994, 66, 2801-2808.
18. Little, D. P., Spier, J. P., Senko, M. W., O'Connor, P. B., McLafferty, F. W., Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal. Chem. 1994, 66, 2809-2815.
19. Zubarev, R. A., Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol. 2004, 15, 12-16.
20. Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., Hunt, D. F., Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528-9533.
21. Adamson, J. T., Håkansson, K., Infrared multiphoton dissociation and electron capture dissociation of high-mannose type glycopeptides. J. Proteome Res. 2006, 5, 493-501.
22. Håkansson, K., Cooper, H. J., Emmet, M. R., Costello, C. E. et al., Electron capture dissociation and infrared multiphoton dissociation MS/MS of an N-glycosylated tryptic peptide to yield complementary sequence information. Anal. Chem. 2001, 73, 4530-4536.
23. Wiesner, J., Premsler, T., Sickmann, A., Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 2008, 8, 4466-4483.
24. Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J. et al., The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 2006, 1764, 1811-1822.
25. Catalina, M. I., Koeleman, C. A. M., Deelder, A. M., Wuher, M., Electron transfer dissociation of N-glycopeptides: loss of the entire N-glycosylated asparagine side chain. Rapid Commun. Mass Spectrom. 2007, 21, 1053-1061.
26. Tsybin, Y. O., Witt, M., Baykut, G., Kjeldsen, F., Hakansson, P., Combined infrared multiphoton dissociation and electron capture dissociation with a hollow electron beam in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 2003, 17, 1759-1768.
27. Gorshkov, M. V., Masselon, C. D., Nikolaev, E. N., Udseth, H. R. et al., Considerations for electron capture dissociation efficiency in FTICR mass spectrometry. Int. J. Mass Spectrom. 2004, 234, 131-136.
28. Han, H., Xia, Y., Yang, M., McLuckey, S. A., Rapidly alternating transmission mode Electron-transfer dissociation and collisional activation for the characterization of polypeptide Ions. Anal. Chem. 2008, 80, 3492-3497.
29. Campbell, J. L., Hager, J. W., Le Blanc, J. C. Y., On performing simultaneous electron transfer dissociation and collision-induced dissociation on multiply protonated peptides in a linear ion trap. J. Am. Soc. Mass Spectrom. 2009, 20, 1672-1683.
30. Nagy, K., Vékey, K., Imre, T., Ludányi, K. et al., Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry of human alpha-1-acid glycoprotein. Anal. Chem. 2004, 76, 4998-5005.
31. Balaguer, E., Neusüss, C., Glycoprotein characterization combining intact protein and glycan analysis by capillary electrophoresis-electrospray ionization-mass spectrometry. Anal. Chem. 2006, 78, 5384-5393.
32. Baek, W. O., Vijayalakshmi, M. A., Effect of chemical glycosylation of RNase A on the protein stability and surface histidines accessibility in immobilized metal ion affinity electrophoresis (IMAGE) system. Biochim. Biophys. Acta 1997, 1336, 394-402.
33. Tsybin, Y. O., Hendrickson, C. L., Beu, S. C., Marshall, A. G., Impact of ion magnetron motion on electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry. Int. J. Mass Spectrom. 2006, 256, 144-149.
34. Tong, R. T. W., Infusini, G., Cui, W., Perlman, D. H. et al., BUPID-Top-Down: database search and assignment of top-down MS/MS Data. Proceedings of the 57th American Society Conference on Mass Spectrometry and Allied Topics, Philadelphia, PA 2009.
35. Horn, D. M., Zubarev, R. A., McLafferty, F. W., Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332
36. Horn, D. M., Ge, Y., McLafferty, F. W., Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 2000, 72, 4778-4784.
37. Zabrouskov, V., Han, X., Welker, E., Zhai, H. et al., Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry 2006, 45, 987-992.
38. Hall, Z., Robinson, C.V., Do charge state signatures guarantee protein conformations? J. Am. Soc. Mass Spectrom. 2012, 23, 1161-1168.
39. Skinner, O. S., Breuker, K., McLafferty, F. W., Charge site mass spectra: conformation-sensitive components of the electron capture dissociation spectrum of a protein. J. Am. Soc. Mass Spectrom. 2013, 24, 807-810.
40. Alley, Jr., W. R., Mechref, Y., Novotny, M. V., Characterization of glycopeptides by combining collision-induced dissociation and electron-transfer dissociation mass spectrometry data. Rapid Commun. Mass Spectrom. 2009, 23, 161-170.
41. Konn, D. O., Murrell, J., Despeyroux, D., Comparison of the effects of ionization mechanism, analyte concentration, and ion "cool-times" on the internal energies of peptide ions produced by electrospray and atmospheric pressure matrix-assisted laser desorption ionization. J. Am. Soc. Mass Spectrom. 2005, 16, 743-751.
42. Sleno, L., Volmer, D. A., Ion activation methods for tandem mass spectrometry, J. Mass Spectrom. 2004, 39, 1091-1112.
43. Dongre, A. R., Jones, J. L., Somogyi, A., Wysocki, V. H., Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model. J. Am. Chem. Soc. 1996, 118, 8365-8374.
44. Paizs, B., Suhai, S., Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
45. Zubarev, R. A., Kelleher, N. L., McLafferty, F. W., Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process, J. Am. Chem. Soc. 1998, 120, 3265-3266.
46. Zubarev, R. A., Haselmann, K. F., Budnik, B., Kjeldsen, F., Jensen, F., Towards an understanding of the mechanism of electron capture dissociation: a historical perspective. Eur. J. Mass Spectrom. 2002, 8, 337-349.
47. Williams, R. L., Greene, S. M., McPherson, A., The crystal structure of ribonuclease B at 2.5-A resolution. J. Biol. Chem. 1987, 262, 16020-16031.