Electron transfer dissociation of modified peptides and proteins

Current Pharmaceutical Biotechnology

Volumn 12, Issue 10, 2011, Pages 1558-1567

  Zhou, Yuping ^a   Dong, Jia ^a   Vachet, Richard W ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Collision induced dissociation; Glycosylation; Mass spectrometry; Methylation; MS MS; Nitration; Oxidation; Phosphorylation; Post translational modification; Sulfation

Indexed keywords

ASPARAGINE; ASPARTIC ACID; DISULFIDE; PEPTIDE;

ARTICLE; CHEMICAL REACTION; COLLISIONALLY ACTIVATED DISSOCIATION; DEAMINATION; ELECTRON TRANSFER DISSOCIATION; GLYCOSYLATION; HUMAN; ISOMERIZATION; METHYLATION; NITRATION; NITROSYLATION; NONHUMAN; OXIDATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; SULFONATION;

EID: 80053533242     PISSN: 13892010     EISSN: 18734316     Source Type: Journal    
DOI: 10.2174/138920111798357230     Document Type: Article

References (75)

1. Ficarro, S. B.; McCleland, M. L.; Stukenberg, P. T.; Burke, D. J.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F.; White, F. M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol., 2002, 20 (3), 301-305.
2. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villen, J.; Li, J.; Cohn, M. A.; Cantley, L. C.; Gygi, S. P. Largescale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci., 2004, 101 (33), 12130-12135.
3. 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 (13), 3265-3266.
4. 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., 2004, 101 (26), 9528-9533.
5. Simons, J. Mechanisms for S-S and N-C-alpha bond cleavage in peptide ECD and ETD mass spectrometry. Chem. Phys. Lett., 2010, 484(4-6), 81-95.
6. Kjeldsen, F.; Giessing, A. M. B.; Ingrell, C. R.; Jensen, O. N. Peptide Sequencing and Characterization of Post-Translational Modifications by Enhanced Ion-Charging and Liquid Chromatography Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal. Chem., 2007, 79 (24), 9243-9252.
7. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome. Science, 2002, 298 (5600), 1912-1916, 1933-1934.
8. Coon, J. J.; Syka, J. E. P.; Shabanowitz, J.; Hunt, D. F. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques, 2005, 38 (4), 519,521,523.
9. Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Soc., 2007, 104 (7), 2199-2204.
10. Swaney, D. L.; Wenger, C. D.; Thomson, J. A.; Coon, J. J. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Soc., 2009, 106 (4), 995-1000.
11. Palumbo, A. M.; Reid, G. E. Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS3. Anal. Chem., 2008, 80 (24), 9735-9747.
12. Aguiar, M.; Haas, W.; Beausoleil, S. A.; Rush, J.; Gygi, S. P. Gasphase rearrangements do not affect site localization reliability in phosphoproteomics data sets. J. Proteome Res., 2010, 9 (6), 3103-3107.
13. Swaney, D. L.; McAlister, G. C.; Wirtala, M.; Schwartz, J. C.; Syka, J. E. P.; Coon, J. J. Supplemental activation method for highefficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal. Chem., 2007, 79 (2), 477-485.
14. Domon, B.; Bodenmiller, B.; Carapito, C.; Hao, Z.; Huehmer, A.; Aebersold, R. Electron transfer dissociation in conjunction with collision activation to investigate the drosophila melanogaster phosphoproteome. J. Proteome Res., 2009, 8 (6), 2633-2639.
15. Wu, S.-L.; Huehmer, A. F. R.; Hao, Z.; Karger, B. L. On-line lc-ms approach combining collision-induced dissociation (CID), electrontransfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with posttranslational modifications. J. Proteome Res., 2007, 6 (11), 4230-4244.
16. Coon, J. J.; Ueberheide, B.; Syka, J. E. P.; Dryhurst, D. D.; Ausio, J.; Shabanowitz, J.; Hunt, D. F. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci., 2005, 102 (27), 9463-9468.
17. Gunawardena, H. P.; Emory, J. F.; McLuckey, S. A. Phosphopeptide anion characterization via sequential charge inversion and electron-transfer dissociation. Anal. Chem., 2006, 78 (11), 3788-3793.
18. Coon, J. J.; Shabanowitz, J.; Hunt, D. F.; Syka, J. E. P. Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom., 2005, 16 (6), 880-882.
19. Huzarska, M.; Ugalde, I.; Kaplan, D. A.; Hartmer, R.; Easterling, M. L.; Polfer, N. C. Negative electron transfer dissociation of deprotonated phosphopeptide anions: choice of radical cation reagent and competition between electron and proton transfer. Anal. Chem., 2010, 82 (7), 2873-2878.
20. Chi, A.; Huttenhower, C.; Geer, L. Y.; Coon, J. J.; Syka, J. E. P.; Bai, D. L.; Shabanowitz, J.; Burke, D. J.; Troyanskaya, O. G.; Hunt, D. F. Analysis of phosphorylation sites on proteins from saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci., 2007, 104 (7), 2193-2198.
21. Zabrouskov, V.; Ge, Y.; Schwartz, J.; Walker, J. W. Unraveling molecular complexity of phosphorylated human cardiac troponin I by top down electron capture dissociation/electron transfer dissociation mass spectrometry. Mol. Cell Proteomics, 2008, 7 (10), 1838-1849.
22. Ahmad, I.; Hoessli, D. C.; Walker-Nasir, E.; Rafik, S. M.; Shakoori, A. R.; Nasir ud, D. Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation. Nucleic Acids Res., 2006, 34 (1), 175-184.
23. Alley, W. R., Jr.; 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 (1), 161-170.
24. Morelle, W.; Canis, K.; Chirat, F.; Faid, V.; Michalski, J.-C. The use of mass spectrometry for the proteomic analysis of glycosylation. Proteomics, 2006, 6 (14), 3993-4015.
25. Hogan, J. M.; Pitteri, S. J.; Chrisman, P. A.; McLuckey, S. A. Complementary structural information from a tryptic N-linked glycopeptide via electron transfer ion/ion reactions and collisioninduced dissociation. J. Proteome Res., 2005, 4 (2), 628-632.
26. 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.
27. Housley Michael, P.; Udeshi Namrata, D.; Rodgers Joseph, T.; Shabanowitz, J.; Puigserver, P.; Hunt Donald, F.; Hart Gerald, W. A PGC-1alpha-O-GlcNAc transferase complex regulates FoxO transcription factor activity in response to glucose. J. Biol. Chem., 2009, 284 (8), 5148-57.
28. Klein, A. L.; Berkaw, M. N.; Buse, M. G.; Ball, L. E. O-linked Nacetylglucosamine modification of insulin receptor substrate-1 occurs in close proximity to multiple SH2 domain binding motifs. Mol. Cell. Proteomics, 2009, 8 (12), 2733-2745.
29. Schroeder, M. J.; Webb, D. J.; Shabanowitz, J.; Horwitz, A. F.; Hunt, D. F. Methods for the detection of paxillin post-translational modifications and interacting proteins by mass spectrometry. J. Proteome Res., 2005, 4 (5), 1832-1841.
30. Housley, M. P.; Rodgers, J. T.; Udeshi, N. D.; Kelly, T. J.; Shabanowitz, J.; Hunt, D. F.; Puigserver, P.; Hart, G. W. OGlcNAc Regulates foxO activation in response to glucose. J. Biol. Chem., 2008, 283 (24), 16283-16292.
31. Perdivara, I.; Petrovich, R.; Alliquant, B.; Deterding, L. J.; Tomer, K. B.; Przybylski, M. Elucidation of o-glycosylation structures of the β-amyloid precursor protein by liquid chromatography-mass spectrometry using electron transfer dissociation and collision induced dissociation. J. Proteome Res., 2009, 8 (2), 631-642.
32. Chalkley, R. J.; Thalhammer, A.; Schoepfer, R.; Burlingame, A. L. Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc. Natl. Acad. Sci., 2009, 106 (22), 8894-8899.
33. Christiansen, M. N.; Kolarich, D.; Nevalainen, H.; Packer, N. H.; Jensen, P. H. Challenges of determining o-glycopeptide heterogeneity: a fungal glucanase model system. Anal. Chem., 2010, 82 (9), 3500-3509.
34. Berlett, B. S.; Stadtman, E. R. Protein oxidation in aging, disease, and oxidative stress. J. Biol. Chem., 1997, 272 (33), 20313-20316.
35. Sclavi, B.; Sullivan, M.; Chance, M. R.; Brenowitz, M.; Woodson, S. A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 1998, 279 (5358), 1940-1943.
36. Hambly, D. M.; Gross, M. L. Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. J. Am. Soc. Mass Spectrom., 2005, 16 (12), 2057-2063.
37. Takamoto, K.; Chance, M. R. Radiolytic protein footprinting with mass Spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct., 2006, 35, 251-276.
38. Konermann, L.; Stocks, B. B.; Pan, Y.; Tong, X. Mass spectrometry combined with oxidative labeling for exploring protein structure and folding. Mass Spectrom. Rev., 2010, 29 (4), 651-667.
39. Zhao, F.; GhezzoSchoneich, E.; Aced, G. I.; Hong, J. Y.; Milby, T.; Schoneich, C. Metal-catalyzed oxidation of histidine in human growth hormone - Mechanism, isotope effects, and inhibition by a mild denaturing alcohol. J. Biol. Chem., 1997, 272 (14), 9019-9029.
40. Schoneich, C. Mechanisms of metal-catalyzed oxidation of histidine to 2-oxo-histidine in peptides and proteins. J. Pharm. Biomed. Anal., 2000, 21 (6), 1093-1097.
41. Bridgewater, J. D.; Vachet, R. W. Metal-catalyzed oxidation reactions and mass spectrometry: The roles of ascorbate and different oxidizing agents in determining Cu-protein-binding sites. Anal. Biochem., 2005, 341 (1), 122-130.
42. Bridgewater, J. D.; Lim, J.; Vachet, R. W. Using metal-catalyzed oxidation reactions and mass spectrometry to identify amino acidresidues within 10 angstrom of the metal in Cu-binding proteins. J. Am. Soc. Mass Spectrom., 2006, 17 (11), 1552-1559.
43. Lim, J.; Vachet, R. W. Development of a methodology based on metal-catalyzed oxidation reactions and mass spectrometry to determine the metal binding sites in copper metalloproteins. Anal. Chem., 2003, 75 (5), 1164-1172.
44. Srikanth, R.; Wilson, J.; Bridgewater, J. D.; Numbers, J. R.; Lim, J.; Olbris, M. R.; Kettani, A.; Vachet, R. W. Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation. J. Am. Soc. Mass Spectrom., 2007, 18 (8), 1499-1506.
45. Burlet, O.; Yang, C. Y.; Gaskell, S. J. Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: evidence for intraionic interactions. J. Am. Soc. Mass Spectrom., 1992, 3 (4), 337-44.
46. Tsaprailis, G.; Nair, H.; Somogyi, A.; Wysocki, V. H.; Zhong, W.; Futrell, J. H.; Summerfield, S. G.; Gaskell, S. J. Influence of secondary structure on the fragmentation of protonated peptides. J. Am. Chem. Soc., 1999, 121 (22), 5142-5154.
47. Wang, Y.; Vivekananda, S.; Men, L.; Zhang, Q. Fragmentation of protonated ions of peptides containing cysteine, cysteine sulfinic acid, and cysteine sulfonic acid. J. Am. Soc. Mass Spectrom., 2004, 15 (5), 697-702.
48. Jiang, X.; Smith, J. B.; Abraham, E. C. Identification of MS-MS fragment diagnostic for methionine sulfoxide. J. Mass Spectrom., 1996, 31 (11), 1309-1310.
49. Bridgewater, J. D.; Srikanth, R.; Lim, J.; Vachet, R. W. The effect of histidine oxidation on the dissociation patterns of peptide ions. J. Am. Soc. Mass Spectrom, 2007, 18 (3), 553-562.
50. Srikanth, R.; Wilson, J.; Vachet, R. W. Correct identification of oxidized histidine residues using electron-transfer dissociation. J. Mass Spectrom, 2009, 44 (5), 755-762.
51. Snijders, A. P. L.; Hung, M.-L.; Wilson, S. A.; Dickman, M. J. Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry. J. Am. Soc. Mass Spectrom, 2010, 21 (1), 88-96.
52. Srahl, B. O.; Allis, C. D. The language of covalent histone modifications. Nature (London), 2000, 403 (6765), 41-45.
53. Chen, D.; Han, M.; Hong, H.; Koh, S. S.; Huang, S.-M.; Schurter, B. T.; Aswad, D. W.; Stallcup, M. R. Regulation of transcription by a protein methyltransferase. Science, 1999, 284 (5423), 2174-2177.
54. Wang, H.; Straubinger, R. M.; Aletta, J. M.; Cao, J.; Duan, X.; Yu, H.; Qu, J. Accurate Localization and Relative Quantification of Arginine Methylation Using Nanoflow Liquid Chromatography Coupled to Electron Transfer Dissociation and Orbitrap Mass Spectrometry. J. Am. Soc. Mass Spectrom, 2009, 20 (3), 507-519.
55. Xiong, L.; Ping, L.; Yuan, B.; Wang, Y. Methyl group migration during the fragmentation of singly charged ions of trimethyllysinecontaining peptides: precaution of using ms/ms of singly charged ions for interrogating peptide methylation. J. Am. Soc. Mass Spectrom, 2009, 20 (6), 1172-1181.
56. Fuchs, R.; Budzikiewicz, H. Rearrangement reactions in the electrospray ionization mass spectra of pyoverdins. Int. J. Mass Spectrom, 2001, 210/211 (1-3), 603-612.
57. Patriksson, A.; Adams, C.; Kjeldsen, F.; Raber, J.; van der Spoel, D.; Zubarev, R. A. Prediction of NCα bond cleavage frequencies in electron capture dissociation of Trp-cage dications by force-field molecular dynamics simulations. Int. J. Mass Spectrom., 2006, 248 (3), 124-135.
58. Crizer, D. M.; McLuckey, S. A. Electron transfer dissociation of amide nitrogen methylated polypeptide cations. J. Am. Soc. Mass Spectrom., 2009, 20 (7), 1349-1354.
59. Phanstiel, D.; Brumbaugh, J.; Berggren, W. T.; Conard, K.; Feng, X.; Levenstein, M. E.; McAlister, G. C.; Thomson, J. A.; Coon, J. J. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc. Natl. Acad. Sci. Early Edition, 2008, 105(11), 4093-4098.
60. Kozlik, P.; Baehler, M.; Puentener, C.; Zerbe, O.; Bigler, L.; Altorfer, H. R. N-Nitrosylation potential of mono-Ndesethylamiodarone at physiological pH. J. Pharm. Biomed. Anal., 2004, 34 (2), 399-407.
61. Goedecke, A.; Schrader, J.; Reinartz, M. Nitric oxide-mediated protein modification in cardiovascular physiology and pathology. Proteomics Clin. Appl., 2008, 2 (6), 811-822.
62. Stamler, J. S.; Lamas, S.; Fang, F. C. Nitrosylation: The prototypic redox-based signaling mechanism. Cell, 2001, 106 (6), 675-683.
63. 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 and Proteomics, 2006, 1764 (12), 1811-1822.
64. Jones, A. W.; Mikhailov, V. A.; Iniesta, J.; Cooper, H. J. Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides. J. Am. Soc. Mass Spectrom, 2010, 21 (2), 268-277.
65. Medzihradszky, K. F.; Darula, Z.; Perlson, E.; Fainzilber, M.; Chalkley, R. J.; Ball, H.; Greenbaum, D.; Bogyo, M.; Tyson, D. R.; Bradshaw, R. A.; Burlingame, A. L. O-sulfonation of serine and threonine: Mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes. Mol. Cell Proteomics, 2004, 3 (5), 429-440.
66. Strott, C. A. Sulfonation and molecular action. Endocr. Rev., 2002, 23(5), 703-732.
67. Medzihradszky, K. F.; Guan, S.; Maltby, D. A.; Burlingame, A. L. Sulfopeptide fragmentation in electron-capture and electrontransfer dissociation. J. Am. Soc. Mass Spectrom, 2007, 18 (9), 1617-1624.
68. Liu, H.; Hakansson, K. Electron capture dissociation of tyrosine Osulfated peptides complexed with divalent metal cations. Anal. Chem., 2006, 78 (21), 7570-7576.
69. Clarke, S. Propensity for spontaneous succinimide formation from aspartyl and asparagine residues in cellular proteins. Int. J. Pept. Proteins Res., 1987, 30(6), 808-821.
70. Cournoyer, J. J.; Pittman, J. L.; Ivleva, V. B.; Fallows, E.; Waskell, L.; Costello, C. E.; O'Connor, P. B. Deamidation: Differentiation of aspartyl from isoaspartyl products in peptides by ECD. Protein Sci., 2005, 14 (2), 452-463.
71. Yang, H.; Zubarev, R. A. Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides. Electrophoresis, 2010, 31(11), 1764-1772.
72. Chan, W. Y. K.; Chan, T. W. D.; O'Conner, P. B. Electron transfer dissocaition with supplemental activation to differentiate aspartic and isoaspartic residues in doubly charged peptide cations. J. Am. Soc. Mass Spectrom, 2010, 21(6), 1012-1015.
73. Ni, W.; Dai, S.; Karger, B. F.; Zhou, Z. S. Analysis of isoaspartic acid by selective proteolysis with asp-n and electron tansfer dissociation mass spectrometry. Anal. Chem., 2010, 82 (17), 7485-7491.
74. Chrisman, P. A.; Pitteri, S. J.; Hogan, J. M.; McLuckey, S. A. SO-•2 electron transfer ion/ion reactions with disulfide linked polypeptide ions. J. Am. Soc. Mass Spectrom, 2005, 16 (7), 1020-1030.
75. Sobott, F.; Watt, S. J.; Smith, J.; Edelmann, M. J.; Kramer, H. B.; Kessler, B. M. Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination. J. Am. Soc. Mass Spectrom, 2009, 20 (9), 1652-1659.