Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

Research Article

Abstract

It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-“like” ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

Keywords

Collision-induced dissociation (CID) Ion mobility spectrometry (IMS) Mass spectrometry (MS) Peptide fragmentation Sequence-scrambling y Fragment 

Notes

Acknowledgments

The authors thank Baylor University for financial support. They also thank Dr. Behrooz Zekavat for helpful discussions of IM-MS and MSn data reported in this manuscript.

Supplementary material

13361_2014_955_MOESM1_ESM.docx (313 kb)
ESM 1 (DOCX 312 kb)

References

  1. 1.
    Paizs, B., Suhai, S.: Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508–548 (2005)CrossRefGoogle Scholar
  2. 2.
    Zhurov, K.O., Fornelli, L., Wodrich, M.D., Laskay, Ü.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
  3. 3.
    Asakawa, D., Smargiasso, N., Quinton, L., Pauw, E.D.: Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrix-assisted laser desorption/ionization in-source decay mass spectrometry. J. Mass Spectrom. 48, 352–360 (2013)CrossRefGoogle Scholar
  4. 4.
    Roepstorff, P., Fohlman, J.: Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601–601 (1984)CrossRefGoogle Scholar
  5. 5.
    Tang, X.J., Boyd, R.K.: An investigation of fragmentation mechanisms of doubly protonated tryptic peptides. Rapid Commun. Mass Spectrom. 6, 651–657 (1992)CrossRefGoogle Scholar
  6. 6.
    Tang, X.J., Thibault, P., Boyd, R.K.: Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation. Anal. Chem. 65, 2824–2834 (1993)CrossRefGoogle Scholar
  7. 7.
    Tang, X.J., Boyd, R.K.: Rearrangements of doubly charged acylium ions from lysyl and ornithyl peptides. Rapid Commun. Mass Spectrom. 8, 678–686 (1994)CrossRefGoogle Scholar
  8. 8.
    Harrison, A.G., Young, A.B.., Bleiholder, C., Suhai, S., Paizs, B.: Scrambling of sequence information in collision-induced dissociation of peptides. J. Am. Chem. Soc. 128, 10364–10365 (2006)CrossRefGoogle Scholar
  9. 9.
    Polfer, N.C., Oomens, J., Suhai, S., Paizs, B.: Infrared spectroscopy and theoretical studies on gas-phase protonated leu-enkephalin and its fragments: direct experimental evidence for the mobile proton. J. Am. Chem. Soc. 129, 5887–5897 (2007)CrossRefGoogle Scholar
  10. 10.
    Polfer, N.C., Oomens, J.: Reaction products in mass spectrometry elucidated with infrared spectroscopy. Phys. Chem. Chem. Phys. 9, 3804–3817 (2007)CrossRefGoogle Scholar
  11. 11.
    Bleiholder, C., Osburn, S., Williams, T.D., Suhai, S., Van Stipdonk, M., Harrison, A.G.: Paizs, B.l.: Sequence-scrambling fragmentation pathways of protonated peptides. J. Am. Chem. Soc. 130, 17774–17789 (2008)CrossRefGoogle Scholar
  12. 12.
    Sadygov, R.G., Cociorva, D., Yates III, J.R.: Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat. Methods 1, 195–202 (2004)CrossRefGoogle Scholar
  13. 13.
    Fattahi, A., Solouki, T.: Conformational analysis of metal complexed model peptides and their fragment ions using FT-ICR MS and gas-phase H/D exchange reactions. Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, May (2001)Google Scholar
  14. 14.
    Somogyi, A.: Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments. J. Am. Soc. Mass Spectrom. 19, 1771–1775 (2008)CrossRefGoogle Scholar
  15. 15.
    Chen, X., Yu, L., Steill, J.D., Oomens, J., Polfer, N.C.: Effect of peptide fragment size on the propensity of cyclization in collision-induced dissociation: oligoglycine b2–b8. J. Am. Chem. Soc. 131, 18272–18282 (2009)CrossRefGoogle Scholar
  16. 16.
    Fattahi, A., Zekavat, B., Solouki, T.: H/D exchange kinetics: experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing. J. Am. Soc. Mass Spectrom. 21, 358–369 (2010)CrossRefGoogle Scholar
  17. 17.
    Chen, X., Steill, J.D., Oomens, J., Polfer, N.C.: Oxazolone versus macrocycle structures for leu-enkephalin b2–b4: insights from infrared multiple-photon dissociation spectroscopy and gas-phase hydrogen/deuterium exchange. J. Am. Soc. Mass Spectrom. 21, 1313–1321 (2010)CrossRefGoogle Scholar
  18. 18.
    Miladi, M., Zekavat, B., Munisamy, S.M., Solouki, T.: A systematic study on the effect of histidine position and fragment ion size on the formation of bn ions. Int. J. Mass Spectrom. 316/318, 164–173 (2012)CrossRefGoogle Scholar
  19. 19.
    Riba-Garcia, I., Giles, K., Bateman, R.H., Gaskell, S.J.: Evidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 609–613 (2008)CrossRefGoogle Scholar
  20. 20.
    Riba Garcia, I., Giles, K., Bateman, R.H., Gaskell, S.J.: Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 1781–1787 (2008)CrossRefGoogle Scholar
  21. 21.
    Polfer, N.C., Bohrer, B.C., Plasencia, M.D., Paizs, B., Clemmer, D.E.: On the dynamics of fragment isomerization in collision-induced dissociation of peptides. J. Phys. Chem. A 112, 1286–1293 (2008)CrossRefGoogle Scholar
  22. 22.
    Zekavat, B., Solouki, T.: Chemometric data analysis for deconvolution of overlapped ion mobility profiles. J. Am. Soc. Mass Spectrom. 23, 1873–1884 (2012)CrossRefGoogle Scholar
  23. 23.
    Yoon, S.H., Chamot-Rooke, J., Perkins, B.R., Hilderbrand, A.E., Poutsma, J.C., Wysocki, V.H.: IRMPD spectroscopy shows that AGG forms an oxazolone b2 + ion. J. Am. Chem. Soc. 130, 17644–17645 (2008)CrossRefGoogle Scholar
  24. 24.
    Perkins, B.R., Chamot-Rooke, J., Yoon, S.H., Gucinski, A.C., Somogyi, A., Wysocki, V.H.: Evidence of diketopiperazine and oxazolone structures for HA b2 + ion. J. Am. Chem. Soc. 131, 17528–17529 (2009)CrossRefGoogle Scholar
  25. 25.
    Erlekam, U., Bythell, B.J., Scuderi, D., Van Stipdonk, M., Paizs, B., Maitre, P.: Infrared spectroscopy of fragments of protonated peptides: direct evidence for macrocyclic structures of b5 ions. J. Am. Chem. Soc. 131, 11503–11508 (2009)CrossRefGoogle Scholar
  26. 26.
    Bianco, G., Labella, C., Pepe, A., Cataldi, T.I.: Scrambling of autoinducing precursor peptides investigated by infrared multiphoton dissociation with electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. Anal. Bioanal. Chem. 405, 1721–1732 (2013)CrossRefGoogle Scholar
  27. 27.
    Solouki, T., Zekavat, B., Miladi, M.: On the existence of structurally different isobaric bn fragment ions. Proceedings of the 58th ASMS Conference on Mass Spectrometry and Allied Topics, Salt Lake City, UT, May (2010)Google Scholar
  28. 28.
    Bythell, B.J., Somogyi, A., Paizs, B.: What is the structure of b2 ions generated from doubly protonated tryptic peptides? J. Am. Soc. Mass Spectrom. 20, 618–624 (2009)CrossRefGoogle Scholar
  29. 29.
    Bythell, B.J., Knapp-Mohammady, M., Paizs, B., Harrison, A.G.: Effect of the His residue on the cyclization of b ions. J. Am. Soc. Mass Spectrom. 21, 1352–1363 (2010)CrossRefGoogle Scholar
  30. 30.
    Bythell, B.J., Csonka, I.P., Suhai, S., Barofsky, D.F., Paizs, B.: Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine. J. Phys. Chem. B 114, 15092–15105 (2010)CrossRefGoogle Scholar
  31. 31.
    Yalcin, T., Khouw, C., Csizmadia, I.G., Peterson, M.R., Harrison, A.G.: Why are b ions stable species in peptide spectra? J. Am. Soc. Mass Spectrom. 6, 1165–1174 (1995)CrossRefGoogle Scholar
  32. 32.
    Yalcin, T., Csizmadia, I.G., Peterson, M.R., Harrison, A.G.: The structure and fragmentation of bn (n ≥ 3) ions in peptide spectra. J. Am. Soc. Mass Spectrom. 7, 233–242 (1996)CrossRefGoogle Scholar
  33. 33.
    Paizs, B., Simonyi, M.: Ring inversion barrier of diazepam and derivatives: an ab initio study. Chirality 11, 651–658 (1999)CrossRefGoogle Scholar
  34. 34.
    Polfer, N.C., Oomens, J., Suhai, S., Paizs, B.: Spectroscopic and theoretical evidence for oxazolone ring formation in collision-induced dissociation of peptides. J. Am. Chem. Soc. 127, 17154–17155 (2005)CrossRefGoogle Scholar
  35. 35.
    Bythell, B.J., Erlekam, U., Paizs, B., Maitre, P.: Infrared spectroscopy of fragments from doubly protonated tryptic peptides. Chem. Phys. Chem. 10, 883–885 (2009)Google Scholar
  36. 36.
    Oomens, J., Young, S., Molesworth, S., van Stipdonk, M.: Spectroscopic evidence for an oxazolone structure of the b2 fragment ion from protonated tri-alanine. J. Am. Soc. Mass Spectrom. 20, 334–339 (2009)CrossRefGoogle Scholar
  37. 37.
    Tirado, M., Polfer, N.C.: Defying entropy: forming large head-to-tail macrocycles in the gas phase. Angew. Chem. Int. Ed. Engl. 124, 1–4 (2012)CrossRefGoogle Scholar
  38. 38.
    Badman, E.R., Myung, S., Clemmer, D.E.: Gas-phase separations of protein and peptide ion fragments generated by collision-induced dissociation in an ion trap. Anal. Chem. 74, 4889–4894 (2002)CrossRefGoogle Scholar
  39. 39.
    Miladi, M., Harper, B., Solouki, T.: Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions. J. Am. Soc. Mass Spectrom. 24, 1755–1766 (2013)CrossRefGoogle Scholar
  40. 40.
    Badger, J.: Implication of basic amino acid residues on peptide fragmentation: an H/D exchange and SORI-CID study Undergraduate Honor’s Thesis. University of Maine, Orono (2011)Google Scholar
  41. 41.
    Amblard, M., Fehrentz, J.A., Martinez, J., Subra, G.: Methods and protocols of modern solid phase peptide synthesis. Mol. Biotechnol. 33, 239–254 (2006)CrossRefGoogle Scholar
  42. 42.
    Brandon, T.R., Justin, L.P.B., Alan, M.S., Suk-Joon, H., Carol, V.R.: Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 3, 1139–1152 (2008)CrossRefGoogle Scholar
  43. 43.
    Lopez, L.L., Tiller, P.R., Senko, M.W., Schwartz, J.C.: Automated strategies for obtaining standardized collisionally induced dissociation spectra on a benchtop ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 13, 663–668 (1999)CrossRefGoogle Scholar
  44. 44.
    Murray, K.K., Boyd, R.K., Eberlin, M.N., Langley, G.J., Li, L., Naito, Y.: Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013). Pure Appl. Chem. 85, 1515–1609 (2013)CrossRefGoogle Scholar
  45. 45.
    Makarov, A., Denisov, E., Kholomeev, A., Balschun, W., Lange, O., Strupat, K., Horning, S.: Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78, 2113–2120 (2006)CrossRefGoogle Scholar
  46. 46.
    Harrison, A., Tasoglu, C., Yalcin, T.: Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides—an energy-resolved study. J. Am. Soc. Mass Spectrom. 24, 1565–1572 (2013)CrossRefGoogle Scholar
  47. 47.
    Bythell, B.J., Maitre, P., Paizs, B.: Cyclization and rearrangement reactions of an fragment ions of protonated peptides. J. Am. Chem. Soc. 132, 14766–14779 (2010)CrossRefGoogle Scholar
  48. 48.
    Paizs, B., Bythell, B.J., Maitre, P.: Rearrangement pathways of the a4 ion of protonated YGGFL characterized by IR spectroscopy and modeling. J. Am. Soc. Mass Spectrom. 23, 664–675 (2012)CrossRefGoogle Scholar
  49. 49.
    Wassermann, T., Boyarkin, O., Paizs, B., Rizzo, T.: Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap. J. Am. Soc. Mass Spectrom. 23, 1029–1045 (2012)CrossRefGoogle Scholar
  50. 50.
    Ambihapathy, K., Yalcin, T., Leung, H.-W., Harrison, A.G.: Pathways to immonium ions in the fragmentation of protonated peptides. J. Mass Spectrom. 32, 209–215 (1997)CrossRefGoogle Scholar
  51. 51.
    Xia, Y., Liang, X., McLuckey, S.A.: Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions. Anal. Chem. 78, 1218–1227 (2006)CrossRefGoogle Scholar
  52. 52.
    Karpas, Z., Berant, Z., Stimac, R.: An ion mobility spectrometry/mass spectrometry (IMS/MS) study of the site of protonation in anilines. Struct. Chem. 1, 201–204 (1990)CrossRefGoogle Scholar
  53. 53.
    Lalli, P.M., Iglesias, B.A., Toma, H.E., de Sa, G.F., Daroda, R.J., Silva Filho, J.C., Szulejko, J.E., Araki, K., Eberlin, M.N.: Protomers: formation, separation, and characterization via traveling wave ion mobility mass spectrometry. J. Mass Spectrom. 47, 712–719 (2012)CrossRefGoogle Scholar
  54. 54.
    Student: Probable error of a correlation coefficient. Biometrika 6, 302–310 (1908)Google Scholar
  55. 55.
    Student: The probable error of a mean. Biometrika 6, 1–25 (1908)Google Scholar
  56. 56.
    Xuan, Y., Creese, A.J., Horner, J.A., Cooper, H.J.: High-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high-resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides. Rapid Commun. Mass Spectrom. 23, 1963–1969 (2009)CrossRefGoogle Scholar
  57. 57.
    Lee, S., Li, Z., Valentine, S.J., Zucker, S.M., Webber, N., Reilly, J.P., Clemmer, D.E.: Extracted fragment ion mobility distributions: a new method for complex mixture analysis. Int. J. Mass Spectrom. 309, 154–160 (2012)Google Scholar
  58. 58.
    Creese, A.J., Cooper, H.J.: Separation and identification of isomeric glycopeptides by high field asymmetric waveform ion mobility spectrometry. Anal. Chem. 84, 2597–2601 (2012)CrossRefGoogle Scholar
  59. 59.
    Pringle, S.D., Giles, K., Wildgoose, J.L., Williams, J.P., Slade, S.E., Thalassinos, K., Bateman, R.H., Bowers, M.T., Scrivens, J.H.: An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/traveling wave IMS/oa-ToF instrument. Int. J. Mass Spectrom. 261, 1–12 (2007)CrossRefGoogle Scholar
  60. 60.
    Giles, K., Williams, J.P., Campuzano, I.: Enhancements in traveling wave ion mobility resolution. Rapid Commun. Mass Spectrom. 25, 1559–1566 (2011)CrossRefGoogle Scholar
  61. 61.
    Tsaprailis, G., Nair, H., Zhong, W., Kuppannan, K., Futrell, J.H., Wysocki, V.H.: A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides. Anal. Chem. 76, 2083–2094 (2004)CrossRefGoogle Scholar
  62. 62.
    Breci, L.A., Tabb, D.L., Yates, J.R., Wysocki, V.H.: Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963–1971 (2003)CrossRefGoogle Scholar
  63. 63.
    Kish, M.M., Wesdemiotis, C.: Selective cleavage at internal lysine residues in protonated versus metalated peptides. Int. J. Mass Spectrom. 227, 191–203 (2003)CrossRefGoogle Scholar
  64. 64.
    Bythell, B.J., Suhai, S., Somogyi, A., Paizs, B.: Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons. J. Am. Chem. Soc. 131, 14057–14065 (2009)CrossRefGoogle Scholar
  65. 65.
    Chawner, R., Eyers, C.E., Gaskell, S.J.: The influence of a C-terminal basic residue on peptide fragmentation pathways. Int. J. Mass Spectrom. 316/318, 284–291 (2012)CrossRefGoogle Scholar
  66. 66.
    Zekavat, B., Miladi, M., Becker, C., Munisamy, S., Solouki, T.: Combined use of post-ion mobility/collision-induced dissociation and chemometrics for b fragment ion analysis. J. Am. Soc. Mass Spectrom. 24, 1355–1365 (2013)CrossRefGoogle Scholar
  67. 67.
    Paizs, B., Szlávik, Z., Lendvay, G., Vékey, K., Suhai, S.: Formation of a2+ ions of protonated peptides. An ab initio study. Rapid Commun. Mass Spectrom. 14, 746–755 (2000)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2014

Authors and Affiliations

  1. 1.Institute of Biomedical StudiesBaylor UniversityWacoUSA
  2. 2.Department of Chemistry and BiochemistryBaylor UniversityWacoUSA

Personalised recommendations