Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

  • Sasa Kazazic
  • Hui-Min Zhang
  • Tanner M. Schaub
  • Mark R. Emmett
  • Christopher L. Hendrickson
  • Gregory T. Blakney
  • Alan G. Marshall
Article

Abstract

Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins.

Supplementary material

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Supplementary material, approximately 49 KB.
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Supplementary material, approximately 25 KB.
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Supplementary material, approximately 15 KB.

References

  1. 1.
    Englander, J. J.; Del Mar, C.; Li, W.; Englander, S. W.; Englander, S. K. J.; Stranz, D. D.; Hamuro, Y.; Woods, V. L. J. Protein Structure Change Studied by Hydrogen-Deuterium Exchange, Functional Labeling, and Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7057–7062.CrossRefGoogle Scholar
  2. 2.
    Englander, S. W. Hydrogen Exchange and Mass Spectrometry: A Historical Perspective. J. Am. Soc. Mass Spectrom. 2006, 17, 1481–1489.CrossRefGoogle Scholar
  3. 3.
    Truhlar, S. M. E.; Droy, C. H.; Torpey, J. W.; Koeppe, J. R.; Komives, E. A. Solvent Accessibility of Protein Surfaces by Amide H/2H Exchange MALDI-TOF Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2006, 17, 1490–1497.CrossRefGoogle Scholar
  4. 4.
    Weis, D. D.; Wales, T. E.; Engen, J. R.; Hotchko, M.; Eyck, L. F. T. Identification and Characterization of EX1 Kinetics in H/D Exchange Mass Spectrometry by Peak Width Analysis. J. Am. Soc. Mass Spectrom. 2006, 17, 1498–1509.CrossRefGoogle Scholar
  5. 5.
    Wang, F.; Li, W.; Emmett, M. R.; Hendrickson, C. L.; Marshall, A. G.; Zhang, Y. L.; Wu, L.; Zhang, Z. Y. Conformational and Dynamic Changes of Yersinia Protein Tyrosine Phosphatase Induced by Ligand Binding and Active Site Mutation and Revealed by H/D Exchange and Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Biochemistry. 1998, 37, 15289–15299.CrossRefGoogle Scholar
  6. 6.
    Lam, T. T.; Lanman, J. K.; Emmett, M. R.; Hendrickson, C. L.; Marshall, A. G.; Prevelige, P. E. Mapping of Protein:Protein Contact Surfaces by Hydrogen/Deuterium Exchange, Followed by On-Line High-Performance Liquid Chromatography-Electrospray Ionization Fourier-Transform Ion-Cyclotron-Resonance Mass Analysis. J. Chromatogr. A. 2002, 982, 85–95.CrossRefGoogle Scholar
  7. 7.
    Lanman, J.; Lam, T. K. T.; Barnes, S.; Sakalian, M.; Emmett, M. R.; Marshall, A. G.; Prevelige, P. E. J. Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-Resolution Mass Spectrometry. J. Mol. Biol. 2003, 325, 759–772.CrossRefGoogle Scholar
  8. 8.
    Emmett, M. R.; Caprioli, R. M. Microelectrospray Mass Spectrometry: Ultra-High-Sensitivity Analysis of Peptides and Proteins. J. Am. Soc. Mass Spectrom. 1994, 5, 605–613.CrossRefGoogle Scholar
  9. 9.
    Kazazic, S.; Emmett, M. R.; Blakney, G. T.; Marshall, A. G. Automated Hydrogen Deuterium Exchange with High Resolution FT-ICR MS Analysis and Enhanced Automated Data Reduction. Proceedings of the 54th ASMS Annual Conference on Mass Spectrometry and Allied Topics, Seattle, WA, 27 May–2 June, 2006, TP394.Google Scholar
  10. 10.
    Chalmers, M. J.; Busby, S. A.; Pascal, B. D.; He, Y.; Hendrickson, C. L.; Marshall, A. G.; Griffin, P. R. Probing Protein Ligand Interactions by Automated Hydrogen/Deuterium Exchange Mass Spectrometry. Anal. Chem. 2006, 78, 1005–1014.CrossRefGoogle Scholar
  11. 11.
    Hotchko, M.; Anand, G. S.; Komives, E. A.; Eyck, L. F. T. Automated Extraction of Backbone Deuteration Levels from Amide H/2H Mass Spectrometry Experiments. Protein Sci. 2006, 15, 583–601.CrossRefGoogle Scholar
  12. 12.
    Weis, D. D.; Engen, J. R.; Kass, I. J. Semi-Automated Data Processing of Hydrogen Exchange Mass Spectra Using HX-Express. J. Am. Soc. Mass Spectrom. 2006, 17, 1700–1703.CrossRefGoogle Scholar
  13. 13.
    Buijs, J.; Hakansson, K.; Hagman, C.; Hakansson, P.; Oscarsson, S. A New Method for the Accurate Determination of the Isotopic State of Single Amide Hydrogens within Peptides using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom. 2000, 14, 1751–1756.CrossRefGoogle Scholar
  14. 14.
    Pascal, B. D.; Chalmers, M. J.; Busby, S. A.; Mader, C. C.; Southern, M. R.; Tsinoremas, N. F.; Griffin, P. R. The Deuterator: Software for the Determination of Backbone Amide Deuterium Levels from H/D Exchange MS Data. BMC Bioinformatics. 2007, 8, 156–168.CrossRefGoogle Scholar
  15. 15.
    Senko, M. W.; C., B. S.; McLafferty, F. W. Determination of Monoisotopic Masses and Ion Populations for Large Biomolecules from Resolved Isotopic Distributions. J. Am. Soc. Mass Spectrom. 1995, 6, 229–233.CrossRefGoogle Scholar
  16. 16.
    Horn, D. M.; A., Z. R.; McLafferty, F. W. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320–332.CrossRefGoogle Scholar
  17. 17.
    Zhang, Z.; Guan, S.; Marshall, A. G. Enhancement of the Effective Resolution of Mass Spectra of High-Mass Biomolecules by Maximum-Entropy Based Deconvolution to Eliminate the Isotopic Natural Abundance Distribution. J. Am. Soc. Mass Spectrom. 1997, 8, 659–670.CrossRefGoogle Scholar
  18. 18.
    Abzalimov, R. R.; Kaltashov, I. A. Extraction of Local Hydrogen Exchange Data from HDX CAD MS Measurements by Deconvolution of Isotopic Distributions of Fragment Ions. J. Am. Soc. Mass Spectrom. 2006, 17, 1543–1551.CrossRefGoogle Scholar
  19. 19.
    Marshall, A. G.; Hendrickson, C. L.; Jackson, G. S. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: A Primer. Mass Spectrom. Rev. 1998, 17, 1–35.CrossRefGoogle Scholar
  20. 20.
    Lanman, J.; Lam, T. K. T.; Emmett, M. R.; Marshall, A. G.; Sakalian, M.; Prevelige, P. E. Jr. Key Interactions in HIV-1 Maturation Identified by Mass Spectrometry Based H/D Exchange. Nat. Struct. Mol. Biol. 2004, 11, 676–677.CrossRefGoogle Scholar
  21. 21.
    Lisal, J.; Lam, T. K. T.; Kainov, D. E.; Emmett, M. R.; Marshall, A. G.; Tuma, R. Functional Visualization of a Viral Molecular Motor by Hydrogen-Deuterium Exchange Reveals Transient States During RNA Packaging. Nat. Struct. Mol. Biol. 2005, 2, 460–466.CrossRefGoogle Scholar
  22. 22.
    Lisal, J.; Kainov, D. E.; Lam, T. K. T.; Emmett, M. R.; Wei, H.; Gottlieb, P.; Marshall, A. G.; Tuma, R. Interaction of Packaging Motor with the Polymerase Complex of dsRNA Bacteriophage. Virology. 2006, 351, 73–79.CrossRefGoogle Scholar
  23. 23.
    Seyfried, N. T.; Atwood, J. A. I.; Yongye, A.; Almond, A.; Day, A. J.; Orlando, R.; Woods, R. J. Fourier Transform Mass Spectrometry to Monitor Hyaluronan-Protein Interactions: Use of Hydrogen/Deuterium Amide Exchange. Rapid Commun. Mass Spectrom. 2007, 21, 121–131.CrossRefGoogle Scholar
  24. 24.
    Woods, V. L. J.; Hamuro, Y. High Resolution, High-Throughput Amide Deuterium Exchange-Mass Spectrometry (DXMS) Determination of Protein Binding Site Structure and Dynamics: Utility in Pharmaceutical Design. J. Cellular Biochem. 2001, 37(Suppl.), 89–98.CrossRefGoogle Scholar
  25. 25.
    Hamuro, Y.; Coales, S. J.; Southern, M. R.; Nemeth-Cawley, J. J.; Stranz, D. D.; Griffin, P. R. Rapid Analysis of Protein Structure and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry. J. Biomol. Techniques. 2003, 14, 171–182.Google Scholar
  26. 26.
    Schaub, T. M.; Hendrickson, C. L.; Horning, S.; Quinn, J. P.; Senko, M. W.; Marshall, A. G. High-Performance Mass Spectrometry: Fourier Transform Ion Cyclotron Resonance at 14.5 Tesla. Anal. Chem. 2008, 80, 3985–3990.CrossRefGoogle Scholar
  27. 27.
    Schwartz, J. C.; Senko, M. W.; Syka, J. E. P. A Two-Dimensional Quadrupole Ion Trap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2002, 13, 659–669.CrossRefGoogle Scholar
  28. 28.
    Syka, J. E. P.; Marto, J. A.; Bai, D. L.; S., H.; Senko, M. W.; Schwartz, J. C.; Ueberheide, B.; Garcia, B.; Busby, S. A.; Muratore, T.; Shabanowitz, J.; Hunt, D. F. Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer: Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-Translational Modifications. J. Proteome. Res. 2004, 3, 621–626.CrossRefGoogle Scholar
  29. 29.
    Beu, S. C.; Laude, D. A. r. Elimination of Axial Ejection during Excitation with a Capacitively Coupled Open Trapped-Ion Cell for FTICRMS. Anal. Chem. 1992, 64, 177–180.CrossRefGoogle Scholar
  30. 30.
    Chen, L.; Sze, S. K.; Yang, H. Automated Intensity Descent Algorithm for Interpretation of Complex High-Resolution Mass Spectra. Anal. Chem. 2006, 78, 5006–5018.CrossRefGoogle Scholar
  31. 31.
    Gajiwala, K. S.; Wu, J. C.; Christensen, J.; Deshmukh, G. D.; Diehl, W.; DiNitto, J. P.; English, J. M.; Greig, M. J.; He, Y. A.; Jacques, S. L.; Lunney, E. A.; McTigue, M.; Molina, D.; Quenzer, T.; Wells, P. A.; Yu, X.; Zhang, Y.; Zou, A.; Emmett, M. R.; Marshall, A. G.; Zhang, H. M.; Demetri, G. D. KIT Kinase Mutants Show Unique Mechanisms of Drug Resistance to Imatinib and Sunitinib in Gastrointestinal Stromal Tumor Patients. Proc. Nat. Acad. Sci. U.S.A. 2009, 106, 1542–1547.CrossRefGoogle Scholar
  32. 32.
    Zhang, H. M.; Mcloughlin, S. M.; He, H.; Nilsson, C. L.; Emmett, M. R.; Marshall, A. G. Conformational and Functional Effect of Posttranslational Modifications on sRAGE Protein by Solution-Phase H/D Exchange FT-ICR Mass Spectrometry. Proceedings of the 57th ASMS. Annual Conference on Mass Spectrometry and Allied Topics, Philadelphia, PA, 31 May–5 June, 2007.Google Scholar
  33. 33.
    Chen, L.; Cottrell, C. E.; Marshall, A. G. Effect of Signal-to-Noise Ratio and Number of Data Points upon Precision in Measurement of Peak Amplitude, Position, and Width in Fourier Transform Spectrometry. Chemom. Intell. Lab. Syst. 1986, 1, 51–58.CrossRefGoogle Scholar
  34. 34.
    Yanofsky, C. M.; Bell, A. W.; Lesimple, S.; Morales, F.; Lam, T. K. T.; Blakney, G. T.; Marshall, A. G.; Carrillo, B.; Lekpor, K.; Boismenu, D.; Kearney, R. E. Multicomponent Internal Recalibration of an LC-FTICR-MS Analysis of a Partially Characterized Complex Peptide Mixture: Systematic and Random Errors. Anal. Chem. 2005, 77, 7246–7254.CrossRefGoogle Scholar
  35. 35.
    Zhang, Z.; Smith, D. L. Determination of Amide Hydrogen Exchange by Mass Spectrometry: A New Tool for Protein Structure Elucidation. Protein Sci. 1993, 2, 522–531.CrossRefGoogle Scholar
  36. 36.
    Zhang, H. M.; Bou-Assaf, G. M.; Emmett, M. R.; Marshall, A. G. Fast Reversed-Phase Liquid Chromatography to Reduce Back Exchange and Increase Throughput in H/D Exchange Monitored by FT-ICR Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2009, 20, 520–524.CrossRefGoogle Scholar
  37. 37.
    Frantom, P. A.; Zhang, H. M.; Emmett, M. R.; Marshall, A. G.; Blanchard, J. S. Mapping of the Allosteric Network in the Regulation of A-Isopropylmalate Synthase from Mycobacterium tuberculosis by the Feedback Inhibitor L-Leucine: Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry. Biochemistry. 2009, 48, 7457–7464.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2010

Authors and Affiliations

  • Sasa Kazazic
    • 1
  • Hui-Min Zhang
    • 2
  • Tanner M. Schaub
    • 1
  • Mark R. Emmett
    • 1
    • 3
  • Christopher L. Hendrickson
    • 1
    • 3
  • Gregory T. Blakney
    • 1
  • Alan G. Marshall
    • 1
    • 3
  1. 1.Ion Cyclotron Resonance Program, National High Magnetic Field LaboratoryFlorida State UniversityTallahasseeUSA
  2. 2.Molecular Biophysics ProgramFlorida State UniversityTallahasseeUSA
  3. 3.Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeUSA

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