Improved sequence resolution by global analysis of overlapped peptides in hydrogen/ deuterium exchange mass spectrometry

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 7, 2012, Pages 1202-1208

  Fajer, Piotr G ^a,b   Bou Assaf, George M ^a   Marshall, Alan G ^a,b  

^a FLORIDA STATE UNIVERSITY   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

FTMS; HDX; Ion cyclotron resonance mass spectrometry

Indexed keywords

AMIDE HYDROGENS; AUTOMATED DATA REDUCTION; DEUTERATIONS; DEUTERIUM EXCHANGE; FK506-BINDING PROTEINS; FTMS; GLOBAL ANALYSIS; HDX; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; N-TERMINALS; PEPTIDE FRAGMENTS; SOFTWARE ANALYSIS;

ALGORITHMS; AMIDES; AMINO ACIDS; DATA REDUCTION; DEUTERIUM; HYDROGEN; MASS SPECTROMETRY; RATE CONSTANTS;

PEPTIDES;

ALANINE; AMIDE; FK 506 BINDING PROTEIN; HYDROGEN; PEPSIN A; PEPTIDE FRAGMENT; PROTEINASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; COMPUTER PROGRAM; DEUTERIUM HYDROGEN EXCHANGE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INTERMETHOD COMPARISON; MASS SPECTROMETRY; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN DEGRADATION; SEQUENCE ANALYSIS; VALIDATION STUDY;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; DEUTERIUM EXCHANGE MEASUREMENT; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEOLYSIS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84865844741     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0373-3     Document Type: Article

References (25)

1. Englander, S.W.: Hydrogen exchange and mass spectrometry: A historical perspective. J. Am. Soc. Mass Spectrom. 17, 1481-1489 (2006) (Pubitemid 44635273)
2. Wales, T.E., Engen, J.R.: Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25, 158-170 (2006)
3. Zhang, Z.Q., Marshall, A.G.: A universal algorithm for fast and automated charge state deconvolution of electrospray mass-To-charge ratio spectra. J. Am. Soc. Mass Spectrom. 9, 225-233 (1998) (Pubitemid 128370213)
4. Palmblad, M., Buijs, J., Hakansson, P.: Automatic analysis of hydrogen/ deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. J. Am. Soc. Mass Spectrom. 12, 1153-1162 (2001) (Pubitemid 34552641)
5. Hotchko, M., Anand, G.S., Komives, E.A., Ten Eyck, L.F.: Automated extraction of backbone deuteration levels from amide H/(2) H mass spectrometry experiments. Protein Sci. 15, 583-601 (2006)
6. Chik, J.K., Van de Graaf, J.L., Schriemer, D.C.: Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78, 207-214 (2006) (Pubitemid 43050156)
7. 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. 17, 1543-1551 (2006) (Pubitemid 44635283)
8. 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. 17, 1700-1703 (2006) (Pubitemid 44809951)
9. Kazazic, S., Zhang, H.M., Schaub, T.M., Emmett, M.R., Hendrickson, C.L., Blakney, G.T., Marshall, A.G.: Automated Data Reduction for Hydrogen/Deuterium Exchange Experiments. Enabled by High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom. 21, 550-558 (2010)
10. Hamuro, Y., Coales, S.J., Southern, M.R., Nemeth-Cawley, J.F., Stranz, D.D., Griffin, P.R.: Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J. Biomol. Tech. 14, 171-182 (2003)
11. Slysz, G.W.; Baker, C.A.H.; Bozsa, B.M.; Dang, A.; Percy, A.J.; Bennett,M.; Schriemer, D.C. Hydra: Software for tailored processing of H/D exchange data fromMS or tandemMS analyses. BMC Bioinformatics 10, 162-175 (2009)
12. Nikamanon, P.; Pun, E.; Chou, W.; Koter, M.D.; Gershon, P.D. TOF2H: A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinformatics 9, 387-402 (2008)
13. 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. 8, 156-167 (2007)
14. Pascal, B.D., Chalmers, M.J., Busb, S.A., Griffin, P.R.: HD Desktop: An integrated platform for the analysis and visualization of H/D exchange data. J. Am. Soc. Mass Spectrom. 20, 601-610 (2009)
15. Zhang, H.M., Kazazic, S., Schaub, T.M., Tipton, J.D., Emmett, M.R., Marshall, A.G.: Enhanced digestion efficiency, peptide ionization efficiency, and sequence resolution for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 80, 9034-9041 (2008)
16. Althaus, E., Canzar, S., Ehrler, C., Emmett, M.R., Karrenbauer, A., Marshall, A.G., Meyer-Base, A., Tipton, J.D., Zhang, H.-M.: Computing H/D-exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics 11, 424 (2010)
17. Zhang, Z.Q., Li, W.Q., Logan, T.M., Li, M., Marshall, A.G.: Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 6, 2203-2217 (1997) (Pubitemid 27449300)
18. 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. 20, 520-524 (2009)
19. Emmett, M.R., White, F.M., Hendrickson, C.L., Shi, S.D.H., Marshall, A.G.: Application of micro-electrospray liquid chromatography techniques to FT-ICR MS to enable high-sensitivity biological analysis. J. Am. Soc. Mass Spectrom. 9, 333-340 (1998)
20. Zhang, Z.Q., Smith, D.L.: Determination of amide hydrogen-exchange by mass-spectrometry-a new tool for protein-structure elucidation. Protein Sci. 2, 522-531 (1993) (Pubitemid 23119303)
21. Beechem, J.M.: Global analysis of biochemical and biophysical data. Methods Enzymol. 210, 37-54 (1992)
22. Chetty, P.S., Mayne, L., Lund-Katz, S., Stranz, D., England, S.W., Phillips, M.C.: Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106, 19005-19010 (2009)
23. Press, W.H., Teukolsky, S.A., Vetterling,W.T., Flannery, B.P.: Numerical Recipes. Cambridge University Press, Cambridge, MA (2007)
24. Fajer, P.G., Bennett, R.L.H., Polnaszek, C.F., Fajer, E.A., Thomas, D.D.: General-method for multiparameter fitting of high-resolution Eprspectra using a simplex algorithm. J. Magn. Reson. 88, 111-125 (1990)
25. Khairy, K., Budil, D., Fajer, P.: Nonlinear-least-squares analysis of slow motional regime EPR spectra. J. Magn. Reson. 183, 152-159 (2006) (Pubitemid 44692525)