Probabilistic model applied to ion abundances in product-ion spectra: quantitative analysis of aspartic acid isomerization in peptides

  • Daniil G. Ivanov
  • Maria I. Indeykina
  • Stanislav I. Pekov
  • Adel E. Iusupov
  • Anna E. Bugrova
  • Alexey S. Kononikhin
  • Eugene N. NikolaevEmail author
  • Igor A. Popov
Research Paper


Evaluation of post-translational modifications of protein molecules is important for both basic and applied biomedical research. Mass spectrometric quantitative studies of modifications, which do not change the mass of the protein, such as isomerization of aspartic acid, do not necessarily require the use of isotope-labelled standards. However, the accurate solution of this problem requires a deep understanding of the relationship between the mole fractions of the isomers and the peak intensities in the mass spectra. In previous studies on the isomerization of aspartic acid in short beta-amyloid fragments, it has been shown that calibration curves used for such quantitative studies often have a non-linear form. The reason for the deviation in the shape of the calibration curves from linearity has not yet been established. Here, we propose an explanation for this phenomenon based on a probabilistic model of the fragmentation process and present a general approach for the selection of fragments that can be used for quantitative studies of the degree of isomerization.

Graphical Abstract


Mass spectrometry Label-free quantitation Isoaspartic acid Beta-amyloid peptides 


Funding information

The research was supported by the Russian Scientific Foundation Grant No. 16-14-00181.

Compliance with ethical standards

Conflict of interest

There authors declare that they have no conflicts of interest.

Supplementary material

216_2019_2174_MOESM1_ESM.pdf (635 kb)
ESM 1 (PDF 635 KB)


  1. 1.
    Tsvetkov PO, Popov IA, Nikolaev EN, Archakov AI, Makarov AA, Kozin SA. Isomerization of the Asp7 residue results in zinc-induced oligomerization of Alzheimer’s disease amyloid β(1–16) peptide. Chem Bio Chem. 2008;9(10):1564–7.CrossRefGoogle Scholar
  2. 2.
    Zirah S, Kozin SA, Mazur AK, Blond A, Cheminant M, Ségalas-Milazzo I, et al. J Biol Chem. 2006;281(4):2151–61.CrossRefGoogle Scholar
  3. 3.
    Kozin SA, Mitkevich VA, Makarov AA. Amyloid-β containing isoaspartate 7 as potential biomarker and drug target in Alzheimer’s disease. Mendeleev Commun. 2016;26(4):269–75.CrossRefGoogle Scholar
  4. 4.
    Moro ML, Phillips AS, Gaimster K, Paul C, Mudher A, Nicoll JAR, et al. Pyroglutamate and isoaspartate modified amyloid-beta in ageing and Alzheimer’s disease. Acta Neuropathol Commun. 2018;6(1):3.Google Scholar
  5. 5.
    Perez-Hurtado P, O’Connor PB. Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry. Mass Spectrom Rev. 2012;31(6):609–25.CrossRefGoogle Scholar
  6. 6.
    Jia C, Lietz CB, Yu Q, Li L. Site-specific characterization of D-amino acid containing peptide epimers by ion mobility spectrometry. Anal Chem. 2014;86(6):2972–81.CrossRefGoogle Scholar
  7. 7.
    Jeanne Dit Fouque K, Garabedian A, Porter J, Baird M, Pang X, Williams TD, et al. Fast and effective ion mobility–mass spectrometry separation of D-amino-acid-containing peptides. Anal Chem. 2017;89(21):11787–94.CrossRefGoogle Scholar
  8. 8.
    Zheng X, Deng L, Baker ES, Ibrahim YM, Petyuk VA, Smith RD. Distinguishing D- and L-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chem Commun. 2017;53(56):7913–6.CrossRefGoogle Scholar
  9. 9.
    Yang H, Zubarev RA. Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides. Electrophoresis. 2010;31(11):1764–72.CrossRefGoogle Scholar
  10. 10.
    O’Connor PB, Cournoyer JJ, Pitteri SJ, Chrisman PA, Mcluckey SA. Differentiation of aspartic and isoaspartic acids using electron transfer dissociation. J Am Soc Mass Spectrom. 2006;17(1):15–9.CrossRefGoogle Scholar
  11. 11.
    Pekov S, Indeykina M, Popov I, Kononikhin A, Bocharov K, Kozin S, et al. Application of MALDI-TOF/TOF-MS for relative quantitation of α- and β-Asp7 isoforms of amyloid-β peptide. Eur J Mass Spectrom. 2018;24(1):141–4.CrossRefGoogle Scholar
  12. 12.
    Degraan-Weber N, Zhang J, Reilly JP. Distinguishing aspartic and isoaspartic acids in peptides by several mass spectrometric fragmentation methods. J Am Soc Mass Spectrom. 2016;27(12):2041–53.CrossRefGoogle Scholar
  13. 13.
    Hamidane HB, Vorobyev A, Larregola M, Lukaszuk A, Tourwé D, Lavielle S, et al. Radical stability directs electron capture and transfer dissociation of β-amino acids in peptides. Chem A Eur J. 2010;16(15):4612–22.CrossRefGoogle Scholar
  14. 14.
    Yamazaki Y, Fujii N, Sadakane Y, Fujii N. Differentiation and semiquantitative analysis of an isoaspartic acid in human α-crystallin by postsource decay in a curved field reflectron. Anal Chem. 2010;82(15):6384–94.CrossRefGoogle Scholar
  15. 15.
    Ayrton ST, Chen X, Bain RM, Pulliam CJ, Achma-Towicz M, Flick TG, et al. Gas phase ion chemistry to determine isoaspartate in a peptide backbone. J Am Soc Mass Spectrom. 2018;29(7):1339–44.CrossRefGoogle Scholar
  16. 16.
    Riggs DL, Gomez SV, Julian RR. Sequence and solution effects on the prevalence of D-isomers produced by deamidation. ACS Chem Biol. 2017;12(11):2875–82.CrossRefGoogle Scholar
  17. 17.
    Tao Y, Julian R. Identification of amino acid epimerization and isomerization in crystallin proteins by tandem LC-MS. Anal Chem. 2014;86(19):9733–41.CrossRefGoogle Scholar
  18. 18.
    Cournoyer JJ, Lin C, Bowman MJ, O’Connor PB. Quantitating the relative abundance of isoaspartyl residues in deamidated proteins by electron capture dissociation. J Am Soc Mass Spectrom. 2007;18(1):48–56.CrossRefGoogle Scholar
  19. 19.
    Indeykina MI, Popov IA, Kozin SA, Kononikhin AS, Kharybin ON, Tsvetkov PO, et al. Capabilities of MS for analytical quantitative determination of the ratio of α- And βasp7 isoforms of the amyloid-β peptide in binary mixtures. Anal Chem. 2011;83(8):3205–10.CrossRefGoogle Scholar
  20. 20.
    Pekov SI, Ivanov DG, Bugrova AE, Indeykina MI, Zakharova NV, Popov IA, et al. Evaluation of MALDI-TOF/TOF mass spectrometry approach for quantitative determination of aspartate residue isomerization in the amyloid-β peptide. J Am Soc Mass Spectrom. 2019;30:1325–9.CrossRefGoogle Scholar
  21. 21.
    Suckau D, Resemann A, Schuerenberg M, et al. A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem. 2003;376:952.CrossRefGoogle Scholar
  22. 22.
    Paizs B, Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev. 2005;24(4):508–48.CrossRefGoogle Scholar
  23. 23.
    Zagorski MG, Barrow CJ. NMR studies of amyloid .beta.-peptides: proton assignments, secondary structure, and mechanism of an alpha-helix to beta-sheet conversion for a homologous, 28-residue, N-terminal fragment. Biochemistry. 1992;31(24):5621–31.CrossRefGoogle Scholar
  24. 24.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–12.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Daniil G. Ivanov
    • 1
    • 2
  • Maria I. Indeykina
    • 1
    • 2
  • Stanislav I. Pekov
    • 2
    • 3
  • Adel E. Iusupov
    • 1
    • 2
  • Anna E. Bugrova
    • 1
    • 4
  • Alexey S. Kononikhin
    • 2
    • 5
  • Eugene N. Nikolaev
    • 5
    Email author
  • Igor A. Popov
    • 2
    • 3
    • 4
  1. 1.Emanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscowRussia
  2. 2.Moscow Institute of Physics and TechnologyMoscow RegionRussia
  3. 3.V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical PhysicRussian Academy of SciencesMoscowRussia
  4. 4.V. I. Kulakov Research Center for Obstetrics, Gynecology and PerinatologyMinistry of Healthcare of the Russian FederationMoscowRussia
  5. 5.Skolkovo Institute of Science and TechnologyMoscow RegionRussia

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