Electron Capture Dissociation Studies of the Fragmentation Patterns of Doubly Protonated and Mixed Protonated-Sodiated Peptoids

  • Bogdan Bogdanov
  • Xiaoning Zhao
  • David B. Robinson
  • Jianhua RenEmail author
Research Article


The fragmentation patterns of a group of doubly protonated ([P + 2H]2+) and mixed protonated-sodiated ([P + H + Na]2+) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C′-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z′-series of ions in addition to the C′-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H]•+) and the sodiated peptoids ([P + H + Na]•+). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.


ECD Radical assisted fragmentation Odd-electron negative ion Peptide-mimicking oligomer Poly(N-substituted glycine) 



The authors thank Dr. Kiran Morishetti (University of the Pacific, currently at Abon Pharmaceuticals LLC) for helping to interpret some of the spectra data, and Dr. Ronald Zuckermann (The Molecular Foundry, Lawrence Berkeley National Laboratory) for providing peptoid-10. J.R. acknowledges the support from the National Science Foundation [CHE-0749737 (prior) and CHE-1301505 (current)]. D.R. acknowledges the support from the Laboratory-Directed Research and Development program at Sandia National Laboratories (DE-AC04-94AL85000). Peptoid synthesis at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences, US Department of Energy (DE-AC02-05CH11231). All ECD experiments were conducted at the Center for Regulatory and Environmental Analytical Metabolomics (CREAM) of the University of Louisville. The authors thank Dr. Shenheng Guan for assisting with the ETD experiments at the mass spectrometry facility of the University of California at San Francisco. They are also thankful for performing some of the ETD experiments in Dr. Joseph Loo’s laboratory at the University of California at Los Angeles.

Supplementary material

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  1. 1.
    Hill, D.J., Mio, M.J., Prince, R.B., Hughes, T.S., Moore, J.S.: A field guide to foldamers. Chem. Rev. 101, 3893–4011 (2001)CrossRefGoogle Scholar
  2. 2.
    Sun, J., Zuckermann, R.N.: Peptoid polymers: a highly designable bioinspired material. ACS Nano 7, 4715–4732 (2013)CrossRefGoogle Scholar
  3. 3.
    Simon, R.J., Kania, R.S., Zuckermann, R.N., Huebner, V.D., Jewell, D.A., Banville, S., Ng, S., Wang, L., Rosenberg, S., Marlowe, C.K., Spellmeyer, D.C., Tan, R., Frankel, A.D., Santi, D.V., Cohen, F.E., Bartlett, P.A.: Peptoids: a modular approach to drug discovery. Proc. Natl. Acad. Sci. U. S. A. 89, 9367–9371 (1992)Google Scholar
  4. 4.
    Farmer, P.S., Ariens, E.J.: Speculations on the design of nonpeptidic peptidomimetics. Trends Pharmacol. Sci. 3, 362–365 (1982)CrossRefGoogle Scholar
  5. 5.
    Paul, B., Butterfoss, G.L., Boswell, M.G., Renfrew, P.D., Yeung, F.G., Shah, N.H., Wolf, C., Bonneau, R., Kirshenbaum, K.: Peptoid atropisomers. J. Am. Chem. Soc. 133, 10910–10919 (2011)CrossRefGoogle Scholar
  6. 6.
    Burkoth, T.S., Beausoleil, E., Kaur, S., Tang, D., Cohen, F.E., Zuckermann, R.N.: Toward the synthesis of artificial proteins. The discovery of an amphiphilic helical peptoid assembly. Chem. Biol. 9, 647–654 (2002)CrossRefGoogle Scholar
  7. 7.
    Kirshenbaum, K., Barron, A.E., Goldsmith, R.A., Armand, P., Bradley, E.K., Truong, K.T.V., Dill, K.A., Cohen, F.E., Zuckermann, R.N.: Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proc. Natl. Acad. Sci. U. S. A. 95, 4303–4308 (1998)CrossRefGoogle Scholar
  8. 8.
    Wu, C.W., Sanborn, T.J., Huang, K., Zuckermann, R.N., Barron, A.E.: Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices. J. Am. Chem. Soc. 123, 6778–6784 (2001)CrossRefGoogle Scholar
  9. 9.
    Wu, C.W., Sanborn, T.J., Zuckermann, R.N., Barron, A.E.: Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure. J. Am. Chem. Soc. 123, 2958–2963 (2001)CrossRefGoogle Scholar
  10. 10.
    Wu, C.W., Kirshenbaum, K., Sanborn, T.J., Patch, J.A., Huang, K., Dill, K.A., Zuckermann, R.N., Barron, A.E.: Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J. Am. Chem. Soc. 125, 13525–13530 (2003)CrossRefGoogle Scholar
  11. 11.
    Lee, B.-C., Zuckermann, R.N., Dill, K.A.: Folding a nonbiological polymer into a compact multihelical structure. J. Am. Chem. Soc. 127, 10999–11009 (2005)CrossRefGoogle Scholar
  12. 12.
    Lee, B.-C., Chu, T.K., Dill, K.A., Zuckermann, R.N.: Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J. Am. Chem. Soc. 130, 8847–8855 (2008)CrossRefGoogle Scholar
  13. 13.
    Lee, J., Udugamasooriya, D.G., Lim, H.-S., Kodadek, T.: Potent and selective photo-inactivation of proteins with peptoid–ruthenium conjugates. Nat. Chem. Biol. 6, 258–260 (2010)CrossRefGoogle Scholar
  14. 14.
    Fowler, S.A., Blackwell, H.E.: Structure–function relationships in peptoids: recent advances toward deciphering the structural requirements for biological function. Org. Biomol. Chem. 7, 1508–1524 (2009)CrossRefGoogle Scholar
  15. 15.
    Miller, S.M., Simon, R.J., Ng, S., Zuckermann, R.N., Kerr, J.M., Moos, W.H.: Comparison of the proteolytic susceptibilities of homologous L-amino acid, D-amino acid, and N-substituted glycine peptide and peptoid oligomers. Drug Dev. Res. 35, 20–32 (1995)CrossRefGoogle Scholar
  16. 16.
    Miller, S.M., Simon, R.J., Ng, S., Zuckermann, R.N., Kerr, J.M., Moos, W.H.: Proteolytic studies of homologous peptide and N-substituted glycine peptoid oligomers. Bioorg. Med. Chem. Lett. 4, 2657–2662 (1994)CrossRefGoogle Scholar
  17. 17.
    Nguyen, J.T., Turck, C.W., Cohen, F.E., Zuckermann, R.N., Lim, W.A.: Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science 282, 2088–2092 (1998)CrossRefGoogle Scholar
  18. 18.
    Kruijtzer, J.A.W., Nijenhuis, W.A.J., Wanders, N., Gispen, W.H., Liskamp, R.M.J., Adan, R.A.H.: Peptoid–peptide hybrids as potent novel melanocortin receptor ligands. J. Med. Chem. 48, 4224–4230 (2005)CrossRefGoogle Scholar
  19. 19.
    Liu, B., Alluri, P.G., Yu, P., Kodadek, T.: A potent transactivation domain mimic with activity in living cells. J. Am. Chem. Soc. 127, 8254–8255 (2005)CrossRefGoogle Scholar
  20. 20.
    Ruijtenbeek, R., Kruijtzer, J.A.W., Van de Wiel, W., Fischer, M.J.E., Fluck, M., Redegeld, F.A.M., Liskamp, R.M.J., Nijkamp, F.P.: Peptoid–peptide hybrids that bind syk SH2 domains involved in signal transduction. Chem. Biochem. 2, 171–179 (2001)Google Scholar
  21. 21.
    Chongsiriwatana, N.P., Patch, J.A., Czyzewski, A.M., Dohm, M.T., Ivankin, A., Gidalevitz, D., Zuckermann, R.N., Barron, A.E.: Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides. Proc. Natl. Acad. Sci. U. S. A. 105, 2794–2799 (2008)CrossRefGoogle Scholar
  22. 22.
    Patch, J.A., Barron, A.E.: Helical peptoid mimics of magainin-2 amide. J. Am. Chem. Soc. 125, 12092–12093 (2003)CrossRefGoogle Scholar
  23. 23.
    Seurynck-Servoss, S.L., Dohm, M.T., Barron, A.E.: Effects of including an N-terminal insertion region and arginine-mimetic side chains in helical peptoid analogues of lung surfactant Protein B. Biochemistry 45, 11809–11818 (2006)CrossRefGoogle Scholar
  24. 24.
    Brown, N.J., Wu, C.W., Seurynck-Servoss, S.L., Barron, A.E.: Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C. Biochemistry 47, 1808–1818 (2008)CrossRefGoogle Scholar
  25. 25.
    Izzo, I., De Cola, C., De Riccardis, F.: Properties and bioactivities of peptoids tagged with heterocycles. Heterocycles 82, 981–1006 (2011)Google Scholar
  26. 26.
    Deane, S., Yao, N., Lam, K.S.: On arrows and traps: the use of the one-bead one-compound combinatorial library method to identify cell surface targeting ligands. In: Firer, M.A. (ed) Targeted Drug Delivery in Cancer Therapeutics, pp. 85-125. Research Signpost, Kerala, India (2010)Google Scholar
  27. 27.
    Lam, K.S., Lebl, M., Krchnak, V.: The "one-bead-one-compound" combinatorial library method. Chem. Rev. 97, 411–448 (1997)CrossRefGoogle Scholar
  28. 28.
    Zuckermann, R.N., Kerr, J.M., Kent, S.B.H., Moos, W.H.: Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis. J. Am. Chem. Soc. 114, 10646–10647 (1992)CrossRefGoogle Scholar
  29. 29.
    Alluri, P.G., Reddy, M.M., Bachhawat-Sikder, K., Olivos, H.J., Kodadek, T.: Isolation of protein ligands from large peptoid libraries. J. Am. Chem. Soc. 125, 13995–14004 (2003)CrossRefGoogle Scholar
  30. 30.
    Udugamasooriya, D.G., Dineen, S.P., Brekken, R.A., Kodadek, T.: A peptoid antibody surrogate that antagonizes VEGF receptor 2 activity. J. Am. Chem. Soc. 130, 5744–5752 (2008)CrossRefGoogle Scholar
  31. 31.
    Liu, R., Lam, K.S.: Automatic Edman microsequencing of peptides containing multiple unnatural amino acids. Anal. Biochem. 295, 9–16 (2001)CrossRefGoogle Scholar
  32. 32.
    Aebersold, R., Mann, M.: Mass spectrometry-based proteomics. Nature 422, 198–207 (2003)CrossRefGoogle Scholar
  33. 33.
    Paizs, B., Suhai, S.: Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508–548 (2005)CrossRefGoogle Scholar
  34. 34.
    Dodds, E.D.: Gas-phase dissociation of glycosylated peptide ions. Mass Spectrom. Rev. 31, 666–682 (2012)CrossRefGoogle Scholar
  35. 35.
    Konermann, L., Stocks, B.B., Pan, Y., Tong, X.: Mass spectrometry combined with oxidative labeling for exploring protein structure and folding. Mass Spectrom. Rev. 29, 651–667 (2010)Google Scholar
  36. 36.
    Thakkar, A., Cohen, A.S., Connolly, M.D., Zuckermann, R.N., Pei, D.: High-throughput sequencing of peptoids and peptide–peptoid hybrids by partial Edman degradation and mass spectrometry. J. Comb. Chem. 11, 294–302 (2009)CrossRefGoogle Scholar
  37. 37.
    Paulick, M.G., Hart, K.M., Brinner, K.M., Tjandra, M., Charych, D.H., Zuckermann, R.N.: Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry. J. Comb. Chem. 8, 417–426 (2006)CrossRefGoogle Scholar
  38. 38.
    Gibson, C., Sulyok, G.A.G., Hahn, D., Goodman, S.L., Holzemann, G., Kessler, H.: Nonpeptidic αv β3 integrin antagonist libraries: on-bead screening and mass spectrometric identification without tagging. Angew. Chem. Int. Ed. 40, 165–169 (2001)Google Scholar
  39. 39.
    Ruijtenbeek, R., Versluis, C., Heck, A.J.R., Redegeld, F.A.M., Nijkamp, F.P., Liskamp, R.M.J.: Characterization of a phosphorylated peptide and peptoid and peptoid–peptide hybrids by mass spectrometry. J. Mass Spectrom. 37, 47–55 (2002)CrossRefGoogle Scholar
  40. 40.
    Kruijtzer, J.A.W., Hofmeyer, L.J.F., Heerma, W., Versluis, C., Liskamp, R.M.J.: Solid-phase syntheses of peptoids using Fmoc-protected N-substituted glycines: the synthesis of (retro)peptoids of leu-enkephalin and Substance P. Chem. Eur. J. 4, 1570–1580 (1998)CrossRefGoogle Scholar
  41. 41.
    Heerma, W., Boon, J.-P.J.L., Versluis, C., Kruijtzer, J.A.W., Hofmeyer, L.J.F., Liskamp, R.M.J.: Comparing mass spectrometric characteristics of peptides and peptoids. 2. J. Mass Spectrom. 32, 697–704 (1997)CrossRefGoogle Scholar
  42. 42.
    Heerma, W., Versluis, C., de Koster, C.G., Kruijtzer, J.A.W., Zigrovic, I., Liskamp, R.M.J.: Comparing mass spectrometric characteristics of peptides and peptoids. Rapid Commun. Mass Spectrom. 10, 459–464 (1996)CrossRefGoogle Scholar
  43. 43.
    Sarma, B.K., Kodadek, T.: Submonomer synthesis of a hybrid peptoid-azapeptoid library. ACS Comb. Sci. 14, 558–564 (2012)CrossRefGoogle Scholar
  44. 44.
    Morishetti, K.K., Russell, S.C., Zhao, X., Robinson, D.B., Ren, J.: Tandem mass spectrometry studies of protonated and alkali metalated peptoids: enhanced sequence coverage by metal cation addition. Int. J. Mass Spectrom. 308, 98–108 (2011)CrossRefGoogle Scholar
  45. 45.
    Pitteri, S.J., McLuckey, S.A.: Recent developments in the ion/ion chemistry of high-mass multiply charged ions. Mass Spectrom. Rev. 24, 931–958 (2005)CrossRefGoogle Scholar
  46. 46.
    Zubarev, R.A., Kelleher, N.L., McLafferty, F.W.: Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120, 3265–3266 (1998)CrossRefGoogle Scholar
  47. 47.
    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. 101, 9528–9533 (2004)CrossRefGoogle Scholar
  48. 48.
    Li, W., Song, C., Bailey, D.J., Tseng, G.C., Coon, J.J., Wysocki, V.H.: Statistical analysis of electron transfer dissociation pairwise fragmentation patterns. Anal. Chem. 83, 9540–9545 (2011)CrossRefGoogle Scholar
  49. 49.
    Zhurov, K.O., Fornelli, L., Wodrich, M.D., Laskay, U.A., Tsybin, Y.O.: Principles of electron capture and transfer dissociation mass spectrometry applied to peptide and protein structure analysis. Chem. Soc. Rev. 42, 5014–5030 (2013)CrossRefGoogle Scholar
  50. 50.
    Wiesner, J., Premsler, T., Sickmann, A.: Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8, 4466–4483 (2008)CrossRefGoogle Scholar
  51. 51.
    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. U. S. A. 104, 2193–2198 (2007)CrossRefGoogle Scholar
  52. 52.
    Li, X., Lin, C., Han, L., Costello, C.E., O'Connor, P.B.: Charge remote fragmentation in electron capture and electron transfer dissociation. J. Am. Soc. Mass Spectrom. 21, 646–656 (2010)CrossRefGoogle Scholar
  53. 53.
    Coon, J.J., Shabanowitz, J., Hunt, D.F., Syka, J.E.P.: Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom. 16, 880–882 (2005)CrossRefGoogle Scholar
  54. 54.
    Cooper, H.J., Hakansson, K., Marshall, A.G.: The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev. 24, 201–222 (2005)CrossRefGoogle Scholar
  55. 55.
    Yoo, H.J., Wang, N., Zhuang, S., Song, H., Hakansson, K.: Negative-ion electron capture dissociation: radical-driven fragmentation of charge-increased gaseous peptide anions. J. Am. Chem. Soc. 133, 16790–16793 (2011)CrossRefGoogle Scholar
  56. 56.
    Turecek, F., Julian, R.R.: Peptide radicals and cation radicals in the gas phase. Chem. Rev. 113, 6691–6733 (2013)CrossRefGoogle Scholar
  57. 57.
    Zubarev, R.A.: Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 22, 57–77 (2003)CrossRefGoogle Scholar
  58. 58.
    Turecek, F., Chen, X., Hao, C.: Where does the electron go? Electron distribution and reactivity of peptide cation radicals formed by electron transfer in the gas phase. J. Am. Chem. Soc. 130, 8818–8833 (2008)CrossRefGoogle Scholar
  59. 59.
    Sawicka, A., Skurski, P., Hudgins, R.R., Simons, J.: Model calculations relevant to disulfide bond cleavage via electron capture influenced by positively charged groups. J. Phys. Chem. B 107, 13505–13511 (2003)CrossRefGoogle Scholar
  60. 60.
    Syrstad, E.A., Turecek, F.: Toward a general mechanism of electron capture dissociation. J. Am. Soc. Mass Spectrom. 16, 208–224 (2005)CrossRefGoogle Scholar
  61. 61.
    Simons, J.: Mechanisms for N–Cα bond cleavage in peptide ECD and ETD mass spectrometry. Chem. Phys. Lett. 484, 81–95 (2010)CrossRefGoogle Scholar
  62. 62.
    Chamot-Rooke, J., Malosse, C., Frison, G., Turecek, F.: Electron capture in charge-tagged peptides. Evidence for the role of excited electronic states. J. Am. Soc. Mass Spectrom. 18, 2146–2161 (2007)CrossRefGoogle Scholar
  63. 63.
    Neff, D., Sobczyk, M., Simons, J.: Through-space and through-bond electron transfer within positively charged peptides in the gas phase. Int. J. Mass Spectrom. 276, 91–101 (2008)CrossRefGoogle Scholar
  64. 64.
    Roepstorff, P., Fohlman, J.: Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601 (1984)CrossRefGoogle Scholar
  65. 65.
    Figliozzi, G.M., Goldsmith, R., Ng, S.C., Banville, S.C., Zuckermann, R.N.: Synthesis of N-substituted glycine peptoid libraries. Methods Enzymol. 267, 437–447 (1996)CrossRefGoogle Scholar
  66. 66.
    Han, H., Xia, Y., McLuckey, S.A.: Ion trap collisional activation of c and z ions formed via gas-phase ion/ion electron-transfer dissociation. J. Proteome Res. 6, 3062–3069 (2007)Google Scholar
  67. 67.
    Chung, T.W., Hui, R., Ledvina, A., Coon, J.J., Turecek, F.: Cascade dissociations of peptide cation-radicals. Part 1. Scope and effects of amino acid residues in penta-, nona-, and decapeptides. J. Am. Soc. Mass Spectrom. 23, 1336–1350 (2012)CrossRefGoogle Scholar
  68. 68.
    Ledvina, A.R., Chung, T.W., Hui, R., Coon, J.J., Turecek, F.: Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides. J. Am. Soc. Mass Spectrom. 23, 1351–1363 (2012)CrossRefGoogle Scholar
  69. 69.
    Cooper, H.J.: Investigation of the presence of b ions in electron capture dissociation mass spectra. J. Am. Soc. Mass Spectrom. 16, 1932–1940 (2005)CrossRefGoogle Scholar
  70. 70.
    Haselmann, K.F., Schmidt, M.: Do b-ions occur from vibrational excitation upon H-desorption in electron capture dissociation? Rapid Commun. Mass Spectrom. 21, 1003–1008 (2007)CrossRefGoogle Scholar
  71. 71.
    Turecek, F., Syrstad, E.A., Seymour, J.L., Chen, X., Yao, C.: Peptide cation-radicals. A computational study of the competition between peptide N–Cα bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+ cation radical. J. Mass Spectrom. 38, 1093–1104 (2003)CrossRefGoogle Scholar
  72. 72.
    Blanksby, S.J., Ellison, G.B.: Bond Dissociation energies of organic molecules. Acc. Chem. Res. 36, 255–263 (2003)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2014

Authors and Affiliations

  • Bogdan Bogdanov
    • 1
  • Xiaoning Zhao
    • 1
  • David B. Robinson
    • 2
  • Jianhua Ren
    • 1
    Email author
  1. 1.Department of ChemistryUniversity of the PacificStocktonUSA
  2. 2.Sandia National LaboratoriesLivermoreUSA

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