Biotechnology Letters

, Volume 28, Issue 14, pp 1047–1059

Electron Capture Dissociation Mass Spectrometry in Characterization of Peptides and Proteins

Review

Abstract

Electron capture dissociation (ECD) represents one of the most recent and significant advancements in tandem mass spectrometry (MS/MS) for the identification and characterization of polypeptides. In comparison with the conventional fragmentation techniques, such as collisionally activated dissociation (CAD), ECD provides more extensive sequence fragments, while allowing the labile modifications to remain intact during backbone fragmentation—an important attribute for characterizing post-translational modifications. Herein, we present a brief overview of the ECD technique as well as selected applications in characterization of peptides and proteins. Case studies including characterization and localization of amino acid glycosylation, methionine oxidation, acylation, and “top–down” protein mass spectrometry using ECD will be presented. A recent technique, coined as electron transfer dissociation (ETD), will be also discussed briefly.

Key words

Electron capture dissociation Electron transfer dissociation Electrospray ionization Fourier transform mass spectrometry Post-translational modifications 

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References

  1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207PubMedCrossRefGoogle Scholar
  2. Beu SC, Senko MW, Quinn JP, Wampler FM III, McLafferty FW (1993) Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules. J Am Soc Mass Spectrom 4:557–565CrossRefGoogle Scholar
  3. Borchers CH, Thapar R, Petrotchenko EV, Torres MP, Speir JP, Easterling M, Dominski Z, Marzluff WF (2006) Combined top–down and bottom–up proteomics identifies a phsophorylation site in stem-loop-binding proteins that contributes to high-affinity RNA binding. Proc Natl Acad Sci USA 103:3094–3099PubMedCrossRefGoogle Scholar
  4. Breuker K, Oh H-B, Lin C, Carpenter BK, McLafferty FW (2004) Nonergodic and conformational control of the electron capture dissociation of protein molecules. Proc Natl Acad Sci USA 101:14011–14016PubMedCrossRefGoogle Scholar
  5. Chalmers MJ, Mackay CL, Hendrickson CL, Wittke S, Walden M, Mischak H, Fliser D, Just I, Marshall AG (2005) Combined top–down and bottom–up mass spectrometric approach to characterization of biomarkers for renal disease. Anal Chem 77:7163–7171PubMedCrossRefGoogle Scholar
  6. Chu J-W, Yin J, Brooks BR, Wang DIC, Ricci MS, Brems DN, Trout BL (2004) A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. J Pharm Sci 93:3096–3102PubMedCrossRefGoogle Scholar
  7. Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J, Shabanowitz J, Hunt DF (2005) Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci USA 102:9463–9468PubMedCrossRefGoogle Scholar
  8. Cooper HJ, Heath JK, Jaffray E, Hay RT, Lam TT, Marshall AG (2004) Identification of sites of ubiquitination in proteins: a Fourier transform ion cyclotron resonance mass spectrometry approach. Anal Chem 76:6982–6988PubMedCrossRefGoogle Scholar
  9. Cooper HJ, Hakansson K, Marshall AG (2005) The role of electron capture dissociation in biomolecular analysis. Mass Spectrom Rev 24:201–222PubMedCrossRefGoogle Scholar
  10. Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM (2005) NovoHMM: a hidden Markon model for de novo peptide sequencing. Anal Chem 77:7265–7273PubMedCrossRefGoogle Scholar
  11. Foldvari M, Attah-Poku S, Hu J, Li Q, Hughes H, Babiuk LA, Kruger S (1998) Palmitoyl derivatives of interferon alpha: potential for cutaneous delivery. J Pharm Sci 87:1203–1208PubMedCrossRefGoogle Scholar
  12. Foldvari M, Baca-Estrada ME, He Z, Hu J, Attah-Poku S, King M (1999) Dermal and transdermal delivery of protein pharmaceuticals: lipid-based delivery systems for interferon alpha. Biotechnol Appl Biochem 30:129–137PubMedGoogle Scholar
  13. Frokjaer S, Otzen DE (2005) Protein drug stability: a formulation challenge. Nature Rev Drug Discov 4:298–306CrossRefGoogle Scholar
  14. Fuchs F (2002) Quality control of biotechnology-derived vaccines: technical and regulatory considerations. Biochimie 84:1173–1179PubMedCrossRefGoogle Scholar
  15. Ge Y, Lawhorn BG, El-Naggar M, Strauss E, Park JH, Begley TP, McLafferty FW (2002) Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc 124:672–678PubMedCrossRefGoogle Scholar
  16. Gervais A, Hammel Y-A, Pelloux S, Lepage P, Baer G, Carte N, Sorokine O, Strub J-M, Koerner R, Leize E, Van Dorsselaer A (2003) Glycosylation of human recombinant gonadotrophins: characterization and batch-to-batch consistency. Glycobiology 13:179–189PubMedCrossRefGoogle Scholar
  17. Gitlin G, Tsarbopoulos A, Patel ST, Sydor W, Pramanik BN, Jacobs S, Westreich L, Mittelman S, Bausch JN (1996) Isolation and characterization of a mono-methioninesulfoxide variant of interferon alpha-2b. Pharm Res 13:762–769PubMedCrossRefGoogle Scholar
  18. Guan Z (2002) Identification and localization of the fatty acid modification in ghrelin by electron capture dissociation. J Am Soc Mass Spectrom 13:1443–1447PubMedCrossRefGoogle Scholar
  19. Guan Z, Kelleher NL, Oȁ9Connor PB, Aaserud DJ, Little DP, McLafferty FW (1996) 193 nm photodissociation of larger multiply-charged biomolecules. Int J Mass Spectrom 157/158:357–364CrossRefGoogle Scholar
  20. Guan Z, Yates NA, Bakhtiar R (2003) Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation. J Am Soc Mass Spectrom 14:605–613PubMedCrossRefGoogle Scholar
  21. Haag R, Kratz F (2006) Polymer therapeutics: concepts and applications. Angew Chem Int Ed Engl 45:1198–1215PubMedCrossRefGoogle Scholar
  22. Haselmann KF, Budnik BA, Olsen JV, Nielsen ML, Reis CA, Clausen H, Johnsen AH, Zubarev RA (2001) Advantages of external accumulation for electron capture dissociation in Fourier transform mass spectrometry. Anal Chem 73:2998–3005PubMedCrossRefGoogle Scholar
  23. Hermeling S, Crommelin DJA, Schellekens H, Jiskoot W (2004) Structure-immunogenicity relationships of therapeutic proteins. Pharm Res 21:897–903PubMedCrossRefGoogle Scholar
  24. Janis LJ, Davis GC (1994) Analytical strategies for the determination of protein modifications. Dev Biol Stand 83:135–142PubMedGoogle Scholar
  25. Jaracz S, Chen J, Kuznetsova LV, Ojima I (2005) Recent advances in tumor-targeting anticancer drug conjugates. Bioorg Med Chem 13:5043–5054PubMedCrossRefGoogle Scholar
  26. Jefferis R (2005) Glycosylation of recombinant antibody therapeutics. Biotechnol Prog 21:11–16PubMedCrossRefGoogle Scholar
  27. Jones JJ, Wilkins CL, Cai Y, Beitle RR, Liyanage R, Lay JO (2005) Real-time monitoring of recombinant bacterial proteins by mass spectrometry. Biotechnol Prog 21:1754–1758PubMedCrossRefGoogle Scholar
  28. Kelleher NL (2004) Top–down proteomics. Anal Chem 76:197A–203APubMedCrossRefGoogle Scholar
  29. Kelleher NL, Lin HY, Valaskovic GA, Aaserud DJ, Fridriksson EK, McLafferty FW (1999) Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J Am Chem Soc 121:806–812CrossRefGoogle Scholar
  30. Kleinnijenhuis AJ, Duursma MC, Breukink E, Heeren RMA, Heck AJR (2003) Localization of intramolecular monosulfide bridges in lantibiotics determined with electron capture induced dissociation. Anal Chem 75:3219–3225PubMedCrossRefGoogle Scholar
  31. Loo JA, Edmonds CG, Udseth HR, Smith RD (1990) Effect of reducing disulfide-containing proteins on electrospray Ionization mass spectra. Anal Chem 62:693–698PubMedCrossRefGoogle Scholar
  32. Lundblad RL, Bradshaw RA (1997) Applications of site-specific chemical modification in the manufacture of biopharmaceuticals: I. An overview. Biotechnol Appl Biochem 26:143–151PubMedGoogle Scholar
  33. Marshall AG, Hendrickson CL, Jackson GS (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17:1–35PubMedCrossRefGoogle Scholar
  34. Marshall AG, Hendrickson CL, Shi SD (2002) Scaling MS plateaus with high-resolution FT-ICRMS. Anal Chem 74:252A–259APubMedCrossRefGoogle Scholar
  35. McLafferty FW, Horn DM, Breuker K, Ge Y, Lewis MA, Cerda B, Zubarev RA, Carpenter BK (2001) Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J Am Soc Mass Spectrom 12:245–249PubMedCrossRefGoogle Scholar
  36. McLuckey SA (1992) Principles of collisional activation in analytical mass spectrometry. J Am Soc Mass Spectrom 3:599–614CrossRefGoogle Scholar
  37. Medzihradszky KF, Zhang X, Chalkley RJ, Guan S, McFarland MA, Chalmers MJ, Marshall AG, Diaz RL, Allis CD, Burlingame AL (2004) Characterization of Tetrahymena Histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS). Mol Cell Proteomics 3:872–886PubMedCrossRefGoogle Scholar
  38. Meng F, Forbes AJ, Miller LM, Kelleher NL (2005) Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom Rev 24:126–134PubMedCrossRefGoogle Scholar
  39. Mirgorodskaya E, Roepstorff P, Zubarev RA (1999) Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal Chem 71:4431–4436PubMedCrossRefGoogle Scholar
  40. Molineux G (2003) Pegylation: engineering improved biopharmaceuticals for oncology. Pharmacotherapy 23:3S–8SPubMedCrossRefGoogle Scholar
  41. Molineux G (2004) The design and development of pegfilgrastim (PEG-rmetHuG-CSF, Neulasta®). Curr Pharm Design 10:1235–1244CrossRefGoogle Scholar
  42. Murano G (1997) FDA perspective on specifications for biotechnology products: from IND to PLA. Dev Biol Stand 91:3–13PubMedGoogle Scholar
  43. Nemeth-Cawley JF, Tangarone BS, Rouse JC (2003) “Top down” characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J Proteomics 2:495–505Google Scholar
  44. Oȁ9Connor PB, Cournoyer JJ, Pitteri SJ, Chrisman PA, McLuckey SA (2006) Differentiation of aspartic and isoaspartic acids using electron transfer dissociation. J Am Soc Mass Spectrom 17:15–19CrossRefGoogle Scholar
  45. Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846PubMedCrossRefGoogle Scholar
  46. Pesavento JJ, Kim Y-B, Taylor GK, Kelleher NL (2004) Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. J Am Chem Soc 126:3386–3387PubMedCrossRefGoogle Scholar
  47. Peter-Katalinic J (2005) Methods in enzymology: O-glycosylation of proteins. Meth Enzymol 405:139–171PubMedCrossRefGoogle Scholar
  48. Peterman SM, Dufresne CP, Horning S (2005) The use of a hybrid linear trap/FT-ICR mass spectrometer for on-line high resolution/high mass accuracy bottom–up sequencing. J Biomol Tech 16:112–124PubMedGoogle Scholar
  49. Reid GE, McLuckey SA (2002) “Top down” protein characterization via tandem mass spectrometry. J Mass Spectrom 37:663–675PubMedCrossRefGoogle Scholar
  50. Resh MD (2004) Membrane targeting of lipid modified signal transduction proteins. Subcell Biochem 37:217–232PubMedGoogle Scholar
  51. Roberts MJ, Bentley MD, Harris JM (2002) Chemistry and peptide and protein PEGylation. Adv Drug Deliv Rev 54:459–476PubMedCrossRefGoogle Scholar
  52. Rouse JC, McClellan JE, Patel HK, Jankowski MA, Porter TJ (2005) Top–down characterization of protein pharmaceuticals by liquid chromatography/mass spectrometry: application to recombinant factor IX comparability-a case study. Methods Mol Biol 308:435–460PubMedGoogle Scholar
  53. Roy I, Gupta MN (2004) Freeze-drying of proteins: some emerging concerns. Biotechnol Appl Biochem 39:165–177PubMedCrossRefGoogle Scholar
  54. Ryan TE, Patterson SD (2002) Proteomics: drug target discovery on an industrial scale. Trends Biotechnol 20:S45–S51PubMedCrossRefGoogle Scholar
  55. Savitski MM, Nielsen ML, Zubarev RA (2005) New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse score, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell Proteomics 4:1180–1188PubMedCrossRefGoogle Scholar
  56. Schellekens H (2005) Factors influencing the immunogenicity of therapeutic proteins. Nephrol. Dial. Transplant 20 Suppl. 6:vi3-vi9PubMedCrossRefGoogle Scholar
  57. Schey KL, Finley EL (2000) Identification of peptide oxidation by tandem mass spectrometry. Acc Chem Res 33:299–306PubMedCrossRefGoogle Scholar
  58. Schroeder MJ, Webb DJ, Shabanowitz J, Horwitz AF, Hunt DF (2005) Methods for the detection of paxillin post-translational modifications and interacting proteins by mass spectrometry. J Proteome Res 4:1831–1841CrossRefGoogle Scholar
  59. Senko MW, Speir JP, McLafferty FW (1994) Collisional activation of large multiply charged ions using Fourier transform mass spectrometry. Anal Chem 66:2801–2808PubMedCrossRefGoogle Scholar
  60. Sheffield WP (2001) Modification of clearance of therapeutic and potentially therapeutic proteins. Current Drug Targets: Cardiovas Hemat Dis 1:1–22CrossRefGoogle Scholar
  61. Shi SDH, Hemling ME, Carr SA, Horn DM, Lindh I, McLafferty FW (2001) Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal Chem 73:19–22PubMedCrossRefGoogle Scholar
  62. Sinclair AM, Elliott S (2005) Glycoengineering: the effect of glycosylation on the properties of therapeutic proteins. J Pharm Sci 94:1626–1635PubMedCrossRefGoogle Scholar
  63. Sleno L, Volmer DA (2004) Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39:1091–1112PubMedCrossRefGoogle Scholar
  64. Smith RA, Dewdney JM, Fears R, Poste G (1993) Chemical derivatization of therapeutic proteins. Trends Biotechnol 11:397–403PubMedCrossRefGoogle Scholar
  65. Smith RG, Jiang H, Sun Y (2005) Developments in ghrelin biology and potential clinical relevance. Trends Endocrinol Metab 16:436–442PubMedCrossRefGoogle Scholar
  66. Stadtman ER, Van Remmen H, Richardson A, Wehr NB, Levine RL (2005) Methionine oxidation and aging. Biochim Biophys Acta 1703:135–140PubMedGoogle Scholar
  67. Strupat K (2005) Molecular weight determination of peptides and proteins by ESI and MALDI. Meth Enzymol 405:1–36PubMedCrossRefGoogle Scholar
  68. Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101:9528–9533PubMedCrossRefGoogle Scholar
  69. Sze S-K, Ge Y, Oh H-B, McLafferty FW (2002) Top–down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc Natl Acad Sci USA 99:1774–1779PubMedCrossRefGoogle Scholar
  70. Tang L, Persky AM, Hochhaus G, Meibohm B (2004) Pharmacokinetic aspects of biotechnology products. J␣Pharm Sci 93:2184–2204PubMedCrossRefGoogle Scholar
  71. Tang WH, Halpern BR, Shilov IV, Seymour SL, Keating SP, Loboda A, Patel AA, Schaeffer DA, Nuwaysir LM (2005) Discovering known and unanticipated protein modifications using MS/MS database searching. Anal Chem 77:3931–3946PubMedCrossRefGoogle Scholar
  72. Walsh CT, Garneau-Tsodikova S, Gatto GJ (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed 44:7342–7372CrossRefGoogle Scholar
  73. Wang W (1999) Instability, stabilization, and formulation of liquid protein pharmaceuticals. Int J Pharm 185:129–188PubMedCrossRefGoogle Scholar
  74. Wu AM, Senter PD (2005) Arming antibodies: prospects and challenges for immunoconjugates. Nat Biotechnol 23:1137–1146PubMedCrossRefGoogle Scholar
  75. Wurn FM (2004) Production of recombinant protein therapeutics in cultivated mammalian cells. Nat Biotechnol 22:1393–1398CrossRefGoogle Scholar
  76. Wysocki VH, Resing KA, Zhang Q, Cheng G (2005) Mass spectrometry of peptides and proteins. Methods 35:211–222PubMedCrossRefGoogle Scholar
  77. Yates JR (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Struct 33:297–316CrossRefGoogle Scholar
  78. Zabrouskov V, Han X, Welker E, Zhai H, Lin C, van Wijk KJ, Scheraga HA, McLafferty FW (2006) Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry 45:987–992PubMedCrossRefGoogle Scholar
  79. Zubarev RA (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom Rev 22:57–77PubMedCrossRefGoogle Scholar
  80. Zubarev RA (2004) Electron capture dissociation mass spectrometry. Curr Opin Biotechnol 15:12–16PubMedCrossRefGoogle Scholar
  81. Zubarev RA, Kelleher NL, McLafferty FW (1998) Electron capture dissociation of multiply charged protein cations: a nonergodic process. J Am Chem Soc 120:3265–3266CrossRefGoogle Scholar
  82. Zubarev RA, Kruger NA, Fridriksson EK, Lewis MA, Horn DM, Carpenter BK, McLafferty FW (1999) Electron capture dissociation of gaseous multiply-charged proteins is favored at disulfide bonds and other sites of high hydrogen atom affinity. J Am Chem Soc 121:2857–2862CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  1. 1.Merck Research LaboratoriesRahwayUSA
  2. 2.Department of BiochemistryDuke University Medical CenterDurhamUSA
  3. 3.Merck Research LaboratoriesWest PointUSA

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