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Analytical and Bioanalytical Chemistry

, Volume 411, Issue 24, pp 6275–6285 | Cite as

Detection and fragmentation of doubly charged peptide ions in MALDI-Q-TOF-MS by ion mobility spectrometry for improved protein identification

  • Jens SproßEmail author
  • Alexander Muck
  • Harald GrögerEmail author
Research Paper
Part of the following topical collections:
  1. Close-Up of Current Developments in Ion Mobility Spectrometry

Abstract

Today, bottom-up protein identification in MALDI-MS is based on employing singly charged peptide ions, which are predominantly formed in the ionization process. However, peptide mass fingerprinting (PMF) with subsequent tandem MS confirmation using these peptide ions is often hampered due to the lower quality of fragment ion mass spectra caused by the higher collision energy necessary for fragmenting singly protonated peptides. Accordingly, peptide ions of higher charge states would be of high interest for analytical purposes, but they are usually not detected in MALDI-MS experiments as they overlap with singly charged matrix clusters and peptide ions. However, when utilizing ion mobility spectrometry (IMS), doubly charged peptide ions can be actively used by separating them from the singly protonated peptides, visualized, and selectively targeted for tandem MS experiments. The generated peptide fragment ion spectra can be used for a more confident protein identification using PMF with tandem MS confirmation, as most doubly protonated peptide ions yield fragment ion mass spectra of higher quality compared to tandem mass spectra of the corresponding singly protonated precursor ions. Mascot protein scores can be increased by approximately 50% when using tandem mass spectra of doubly charged peptide ions, with ion scores up to six times higher compared with ion scores of tandem mass spectra from singly charged precursors.

Keywords

Doubly charged peptide ions Ion mobility spectrometry (IMS) MALDI-Q-TOF mass spectrometry Protein analysis Proteomics 

Notes

Acknowledgements

The authors thank T. Winkler for the preparation of ene reductase.

Funding information

J.S. and H.G. received generous support from the German Research Foundation (DFG; grant number: INST 215/484-1 FUGG).

Compliance with ethical standards

Conflict of interest

Jens Sproß and Harald Gröger declare no conflict of interest. Alexander Muck is an employee of Waters Corp.

Supplementary material

216_2019_1578_MOESM1_ESM.pdf (2 mb)
ESM 1 (PDF 2021 kb)

References

  1. 1.
    Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198–207.CrossRefGoogle Scholar
  2. 2.
    Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev. 2006;25:663–82.CrossRefGoogle Scholar
  3. 3.
    Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol. 2010;28:695–709.CrossRefGoogle Scholar
  4. 4.
    Shevchenko A, Tomas H, Havli J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2007;1:2856–60.CrossRefGoogle Scholar
  5. 5.
    Jaskolla TW, Karas M. Compelling evidence for lucky survivor and gas phase protonation: the unified MALDI analyte protonation mechanism. J Am Soc Mass Spectrom. 2011;22:976–88.CrossRefGoogle Scholar
  6. 6.
    Alves S, Fournier F, Afonso C, Wind F, Tabet JC. Gas-phase ionization/desolvation processes and their effect on protein charge state distribution under matrix-assisted laser desorption/ionization conditions. Eur J Mass Spectrom. 2006;12:369–83.Google Scholar
  7. 7.
    Kononikhin AS, Nikolaev EN, Frankevich V, Zenobi R. Letter: multiply charged ions in matrix-assisted laser desorption/ionization generated from electrosprayed sample layers. Eur J Mass Spectrom. 2005;11:257–9.CrossRefGoogle Scholar
  8. 8.
    Liu ZL, Schey KL. Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry. J Am Soc Mass Spectrom. 2008;19:231–8.CrossRefGoogle Scholar
  9. 9.
    Koch A, Schnapp A, Soltwisch J, Dreisewerd K. Generation of multiply charged peptides and proteins from glycerol-based matrices using lasers with ultraviolet, visible and near-infrared wavelengths and an atmospheric pressure ion source. Int J Mass Spectrom. 2017;416:61–70.CrossRefGoogle Scholar
  10. 10.
    König S, Kollas O, Dreisewerd K. Generation of highly charged peptide and protein ions by atmospheric pressure matrix-assisted infrared laser desorption/ionization ion trap mass spectrometry. Anal Chem. 2007;79:5484–8.CrossRefGoogle Scholar
  11. 11.
    Leisner A, Rohlfing A, Berkenkamp S, Hillenkamp F, Dreisewerd K. Infrared laser post-ionization of large biomolecules from an IR-MALD(I) plume. J Am Soc Mass Spectrom. 2004;15:934–41.CrossRefGoogle Scholar
  12. 12.
    Ryumin P, Brown J, Morris M, Cramer R. Investigation and optimization of parameters affecting the multiply charged ion yield in AP-MALDI MS. Methods. 2016;104:11–20.CrossRefGoogle Scholar
  13. 13.
    Ryumin P, Brown J, Morris M, Cramer R. Protein identification using a nanoUHPLC-AP-MALDI MS/MS workflow with CID of multiply charged proteolytic peptides. Int J Mass Spectrom. 2017;416:20–8.CrossRefGoogle Scholar
  14. 14.
    Cramer R, Pirkl A, Hillenkamp F, Dreisewerd K. Liquid AP-UV-MALDI enables stable ion yields of multiply charged peptide and protein ions for sensitive analysis by mass spectrometry. Angew Chem Int Ed. 2013;52:2364–7.CrossRefGoogle Scholar
  15. 15.
    Jaskolla TW, Lehmann W-D, Karas M. 4-Chloro-alpha-cyanocinnamic acid is an advanced, rationally designed MALDI matrix. PNAS. 2008;105:12200–5.CrossRefGoogle Scholar
  16. 16.
    Jaskolla TW, Papasotiriou DG, Karas M. Comparison between the matrices alpha-cyano-4-hydroxycinnamic acid and 4-chloro-alpha-cyanocinnamic acid for trypsin, chymotrypsin, and pepsin digestions by MALDI-TOF mass spectrometry. J Proteome Res. 2009;8:3588–97.CrossRefGoogle Scholar
  17. 17.
    Soltwisch J, Jaskolla TW, Hillenkamp F, Karas M, Dreisewerd K. Ion yields in UV-MALDI mass spectrometry as a function of excitation laser wavelength and optical and physico-chemical properties of classical and halogen-substituted MALDI matrixes. Anal Chem. 2012;84:6567–76.CrossRefGoogle Scholar
  18. 18.
    Wiegelmann M, Soltwisch J, Jaskolla TW, Dreisewerd K. Matching the laser wavelength to the absorption properties of matrices increases the ion yield in UV-MALDI mass spectrometry. Anal Bioanal Chem. 2013;405:6925–32.CrossRefGoogle Scholar
  19. 19.
    Cramer R, Corless S. The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics. Rapid Commun Mass Spectrom. 2001;15:2058–66.CrossRefGoogle Scholar
  20. 20.
    Paizs B, Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev. 2005;24:508–48.CrossRefGoogle Scholar
  21. 21.
    Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I. Review on ion mobility spectrometry. Part 1: current instrumentation. Analyst. 2015;140:1376–90.CrossRefGoogle Scholar
  22. 22.
    Bohrer BC, Merenbloom SI, Koeniger SL, Hilderbrand AE, Clemmer DE. Biomolecule analysis by ion mobility spectrometry. Annu Rev Anal Chem (Palo Alto, Calif). 2008;1:293–327.CrossRefGoogle Scholar
  23. 23.
    Seo J, Hoffmann W, Warnke S, Bowers MT, Pagel K, von Helden G. Retention of native protein structures in the absence of solvent: a coupled ion mobility and spectroscopic study. Angew Chem Int Ed. 2016;55:14173–6.CrossRefGoogle Scholar
  24. 24.
    Pagel K, Harvey DJ. Ion mobility-mass spectrometry of complex carbohydrates: collision cross sections of sodiated N-linked glycans. Anal Chem. 2013;85:5138–45.CrossRefGoogle Scholar
  25. 25.
    Hofmann J, Hahm HS, Seeberger PH, Pagel K. Identification of carbohydrate anomers using ion mobility–mass spectrometry. Nature. 2015;526:241–4.CrossRefGoogle Scholar
  26. 26.
    Stauber J, MacAleese L, Franck J, Claude E, Snel M, Kaletas BK, et al. On-tissue protein identification and imaging by MALDI-ion mobility mass spectrometry. J Am Soc Mass Spectrom. 2010;21:338–47.CrossRefGoogle Scholar
  27. 27.
    Inutan ED, Wager-Miller J, Narayan SB, Mackie K, Trimpin S. The potential for clinical applications using a new ionization method combined with ion mobility spectrometry-mass spectrometry. Int J Ion Mobil Spectrom. 2013;16:145–59.CrossRefGoogle Scholar
  28. 28.
    Distler U, Kuharev J, Navarro P, Tenzer S. Label-free quantification in ion mobility-enhanced data-independent acquisition proteomics. Nat Protoc. 2016;11:795–812.CrossRefGoogle Scholar
  29. 29.
    Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, et al. An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom. 2007;261:1–12.CrossRefGoogle Scholar
  30. 30.
    Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci U S A. 1993;90:5011–5.CrossRefGoogle Scholar
  31. 31.
    Mann M, Højrup P, Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom. 1993;22:338–45.CrossRefGoogle Scholar
  32. 32.
    Richter N, Gröger H, Hummel W. Asymmetric reduction of activated alkenes using an enoate reductase from Gluconobacter oxydans. Appl Microbiol Biotechnol. 2011;89:79–89.CrossRefGoogle Scholar
  33. 33.
    Sladkova K, Houska J, Havel J. Laser desorption ionization of red phosphorus clusters and their use for mass calibration in time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 2009;23:3114–8.CrossRefGoogle Scholar
  34. 34.
    Inutan ED, Wang BX, Trimpin S. Commercial intermediate pressure MALDI ion mobility spectrometry mass spectrometer capable of producing highly charged laserspray ionization ions. Anal Chem. 2011;83:678–84.CrossRefGoogle Scholar
  35. 35.
    Kraußer M, Winkler T, Richter N, Dommer S, Fingerhut A, Hummel W, et al. Combination of C=C bond formation by Wittig reaction and enzymatic C=C bond reduction in a one-pot process in water. ChemCatChem. 2011;3:293–6.CrossRefGoogle Scholar
  36. 36.
    Burda E, Reß T, Winkler T, Giese C, Kostrov X, Huber T, et al. Highly enantioselective reduction of α-methylated nitroalkenes. Angew Chem Int Ed. 2013;52:9323–6.CrossRefGoogle Scholar
  37. 37.
    Reß T, Hummel W, Hanlon SP, Iding H, Gröger H. The organic-synthetic potential of recombinant ene reductases: substrate-scope evaluation and process optimization. ChemCatChem. 2015;7:1302–11.CrossRefGoogle Scholar
  38. 38.
    Biermann M, Gruß H, Hummel W, Gröger H. Guerbet alcohols: from processes under harsh conditions to synthesis at room temperature under ambient pressure. ChemCatChem. 2016;8:895–9.CrossRefGoogle Scholar
  39. 39.
    Biermann M, Bakonyi D, Hummel W, Gröger H. Design of recombinant whole-cell catalysts for double reduction of C=C and C=O bonds in enals and application in the synthesis of Guerbet alcohols as industrial bulk chemicals for lubricants. Green Chem. 2017;19:405–10.CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Industrial Organic Chemistry and Biotechnology, Faculty of ChemistryBielefeld UniversityBielefeldGermany
  2. 2.Waters GmbHEschbornGermany

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