1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Analytical Chemistry
  4. Volume 8, 2015
  5. Article

Annual Review of Analytical Chemistry

Volume 8, 2015

Analytical Aspects of Hydrogen Exchange Mass Spectrometry

Abstract

This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.

Keyword(s): biopharmaceutical, deuterium, fragment separation method, protein conformation, protein dynamics
Loading

Article metrics loading...

/content/journals/10.1146/annurev-anchem-062011-143113
2015-07-22
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/anchem/8/1/annurev-anchem-062011-143113.html?itemId=/content/journals/10.1146/annurev-anchem-062011-143113&mimeType=html&fmt=ahah

Literature Cited

  1. Rosa JJ, Richards FM. 1.  1979. An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide. J. Mol. Biol. 133:399–416 [Google Scholar]
  2. Englander SW, Calhoun DB, Englander JJ, Kallenbach NR, Liem RK. 2.  et al. 1980. Individual breathing reactions measured in hemoglobin by hydrogen exchange methods. Biophys. J. 32:577–89 [Google Scholar]
  3. Rosa JJ, Richards FM. 3.  1981. Hydrogen exchange from identified regions of the S-protein component of ribonuclease as a function of temperature, pH, and the binding of S-peptide. J. Mol. Biol. 145:835–51 [Google Scholar]
  4. Rosa JJ, Richards FM. 4.  1982. Effects of binding of S-peptide and 2′-cytidine monophosphate on hydrogen exchange from the S-protein component of ribonuclease S. J. Mol. Biol. 160:517–30 [Google Scholar]
  5. Englander JJ, Rogero JR, Englander SW. 5.  1985. Protein hydrogen exchange studied by the fragment separation method. Anal. Biochem. 147:234–44 [Google Scholar]
  6. Katta V, Chait BT. 6.  1991. Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun. Mass Spectrom. 5:214–17 [Google Scholar]
  7. Katta V, Chait BT. 7.  1993. Hydrogen/deuterium exchange electrospray ionization mass spectrometry: a method for probing protein conformational changes in solution. J. Am. Chem. Soc. 115:6317–21 [Google Scholar]
  8. Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM. 8.  1993. Detection of transient protein folding populations by mass spectrometry. Science 262:896–900 [Google Scholar]
  9. Zhang Z, Smith DL. 9.  1993. Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2:522–31 [Google Scholar]
  10. Johnson RS, Walsh KA. 10.  1994. Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci. 3:2411–18 [Google Scholar]
  11. Maier CS, Deinzer ML. 11.  2005. Protein conformations, interactions, and H/D exchange. Methods Enzymol. 402:312–60 [Google Scholar]
  12. Hamuro Y, Weber PC, Griffin PR. 12.  2005. High-throughput analysis of protein structure by hydrogen/deuterium exchange mass spectrometry. Methods Biochem. Anal. 45:131–57 [Google Scholar]
  13. Wales TE, Engen JR. 13.  2006. Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25:158–70 [Google Scholar]
  14. Tsutsui Y, Wintrode PL. 14.  2007. Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr. Med. Chem. 14:2344–58 [Google Scholar]
  15. Brier S, Engen JR. 15.  2008. Hydrogen exchange mass spectrometry: principles and capabilities. Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics M Chance 11–43 New York: Wiley- Blackwell [Google Scholar]
  16. Yan X, Maier CS. 16.  2009. Hydrogen/deuterium exchange mass spectrometry. Methods Mol. Biol. 492:255–71 [Google Scholar]
  17. Marcsisin SR, Engen JR. 17.  2010. Hydrogen exchange mass spectrometry: What is it and what can it tell us?. Anal. Bioanal. Chem. 397:967–72 [Google Scholar]
  18. Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR. 18.  2011. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev. Proteomics 8:43–59 [Google Scholar]
  19. Konermann L, Pan J, Liu YH. 19.  2011. Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem. Soc. Rev. 40:1224–34 [Google Scholar]
  20. Engen JR, Wales TE, Shi X. 20.  2011. Hydrogen exchange mass spectrometry for conformational analysis of proteins. Encyclopedia of Analytical Chemistry RA Meyers 1–14 New York: Wiley [Google Scholar]
  21. Brock A. 21.  2012. Fragmentation hydrogen exchange mass spectrometry: a review of methodology and applications. Protein Expr. Purif. 84:19–37 [Google Scholar]
  22. Iacob RE, Engen JR. 22.  2012. Hydrogen exchange mass spectrometry: Are we out of the quicksand?. J. Am. Soc. Mass Spectrom. 23:1003–10 [Google Scholar]
  23. Percy AJ, Rey M, Burns KM, Schriemer DC. 23.  2012. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry—a review. Anal. Chim. Acta 721:7–21 [Google Scholar]
  24. Jaswal SS. 24.  2013. Biological insights from hydrogen exchange mass spectrometry. Biochim. Biophys. Acta 1834:1188–201 [Google Scholar]
  25. Cao J, Burke JE, Dennis EA. 25.  2013. Using hydrogen/deuterium exchange mass spectrometry to define the specific interactions of the phospholipase A2 superfamily with lipid substrates, inhibitors, and membranes. J. Biol. Chem. 288:1806–13 [Google Scholar]
  26. Wei H, Mo J, Tao L, Russell RJ, Tymiak AA. 26.  et al. 2014. Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications. Drug Discov. Today 19:95–102 [Google Scholar]
  27. Richards FM. 27.  1992. Linderstrøm-Lang and the Carlsberg Laboratory: the view of a postdoctoral fellow in 1954. Protein Sci. 1:1721–30 [Google Scholar]
  28. Schellman JA, Schellman CG. 28.  1997. Kaj Ulrick Linderstrøm-Lang (1896–1959). Protein Sci. 6:1092–100 [Google Scholar]
  29. Englander SW, Mayne L, Bai Y, Sosnick TR. 29.  1997. Hydrogen exchange: the modern legacy of Linderstrøm-Lang. Protein Sci. 6:1101–9 [Google Scholar]
  30. Baldwin RL. 30.  2009. In memoriam: reflections on Fred Richards (1925–2009). Protein Sci. 18:682–85 [Google Scholar]
  31. Baldwin RL. 31.  2011. Early days of protein hydrogen exchange: 1954–1972. Proteins 79:2021–26 [Google Scholar]
  32. Klotz IM, Frank BH. 32.  1965. Deuterium–Hydrogen Exchange in Amide N–H Groups. J. Am. Chem. Soc. 87:2721–8 [Google Scholar]
  33. Klotz IM. 33.  1968. Molecular aspects of hydrogen-deuterium exchange in macromolecules. J. Colloid Interface Sci. 27:804–17 [Google Scholar]
  34. Englander SW, Downer NW, Teitelbaum H. 34.  1972. Hydrogen exchange. Annu. Rev. Biochem. 41:903–24 [Google Scholar]
  35. Woodward CK, Hilton BD. 35.  1979. Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. Annu. Rev. Biophys. Bioeng. 8:99–127 [Google Scholar]
  36. Hvidt A, Linderstrøm-Lang K. 36.  1954. Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim. Biophys. Acta 14:574–5 [Google Scholar]
  37. Linderstrøm-Lang K. 37.  1955. Deuterium exchange between peptides and water. Symposium on Peptide Chemistry: Special Publication No. 2 1–20 London: Chem. Soc.
  38. Hvidt A, Nielsen SO. 38.  1966. Hydrogen exchange in proteins. Adv. Protein Chem. 21:287–386 [Google Scholar]
  39. Ottesen M. 39.  1971. Methods for measurement of hydrogen isotope exchange in globular proteins. Methods Biochem. Anal. 20:135–68 [Google Scholar]
  40. Englander SW, Kallenbach NR. 40.  1983. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16:521–655 [Google Scholar]
  41. Hvidt A, Johansen G, Linderstrøm-Lang K. 41.  1960. Deuterium and 18O exchange. A Laboratory Manual of Analytical Methods of Protein Chemistry (Including Polypeptides) 2 Composition, Structure and Reactivity of Proteins P Alenxander, RJ Block 101–30 Oxford, UK: Pergamon Press [Google Scholar]
  42. Leach SJ, Springell PH. 42.  1962. Tritium-hydrogen exchange in studies of protein structure. Aust. J. Chem. 15:350–64 [Google Scholar]
  43. Englander SW. 43.  1963. A hydrogen exchange method using tritium and Sephadex: its application to ribonuclease. Biochemistry 2:798–807 [Google Scholar]
  44. Englander SW, Poulsen A. 44.  1969. Hydrogen-tritium exchange of the random chain polypeptide. Biopolymers 7:379–93 [Google Scholar]
  45. Gregory RB, Carbo L, Percy AJ, Rosenberg A. 45.  1983. Water catalysis of peptide hydrogen isotope exchange. Biochemistry 22:910–17 [Google Scholar]
  46. Connelly GP, Bai Y, Jeng M-F, Englander SW. 46.  1993. Isotope effects in peptide group hydrogen exchange. Proteins: Struct. Funct. Genet. 17:87–92 [Google Scholar]
  47. Englander JJ, Calhoun DB, Englander SW. 47.  1979. Measurement and calibration of peptide group hydrogen-deuterium exchange by ultraviolet spectrophotometry. Anal. Biochem. 95:517–24 [Google Scholar]
  48. Blout ER, De Loze C, Asadourian A. 48.  1961. The deuterium exchange of water-soluble polypeptides and proteins as measured by infrared spectroscopy. J. Am. Chem. Soc. 83:1895–900 [Google Scholar]
  49. Parker FS, Bhaskar KR. 49.  1970. Infrared studies of hydrogen-deuterium exchange in biological molecules. Appl. Spectrosc. Rev. 3:91–142 [Google Scholar]
  50. Kossiakoff AA. 50.  1982. Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique. Nature 296:713–21 [Google Scholar]
  51. Woodward CK, Rosenberg A. 51.  1971. Studies of hydrogen exchange in proteins. VI. Urea effects on ribonuclease exchange kinetics leading to a general model for hydrogen exchange from folded proteins. J. Biol. Chem. 246:4114–21 [Google Scholar]
  52. Wagner G, Wuthrich K. 52.  1982. Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. J. Mol. Biol. 160:343–61 [Google Scholar]
  53. Barksdale AD, Rosenberg A. 53.  1982. Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. Methods Biochem. Anal. 28:1–113 [Google Scholar]
  54. Roder H, Wuthrich K. 54.  1986. Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons. Proteins 1:34–42 [Google Scholar]
  55. Englander SW, Mayne L. 55.  1992. Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu. Rev. Biophys. Biomol. Struct. 21:243–65 [Google Scholar]
  56. Paterson Y, Englander SW, Roder H. 56.  1990. An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science 249:755–59 [Google Scholar]
  57. Zhang YZ, Paterson Y, Roder H. 57.  1995. Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR. Protein Sci. 4:804–14 [Google Scholar]
  58. Nonnenmacher G, Coursaget J. 58.  1969. Utilizing deuterium in study of exchangeable hydrogen atoms of proteins and application to ribonuclease. J. Chim. Phys. 66:616–18 [Google Scholar]
  59. Nonnenmacher G, Viala E, Thiery JM, Calvet P. 59.  1971. A deuterium-hydrogen exchange study of inhibitor-induced conformational changes in ribonuclease A. Eur. J. Biochem. 21:393–99 [Google Scholar]
  60. Sethi SK, Smith DL, McCloskey JA. 60.  1983. Determination of active hydrogen content by fast atom bombardment mass spectrometry following hydrogen-deuterium exchange. Biochem. Biophys. Res. Commun. 112:126–31 [Google Scholar]
  61. Thévenon-Emeric G, Kozlowski J, Zhang Z, Smith DL. 61.  1992. Determination of amide hydrogen exchange rates in peptides by mass spectrometry. Anal. Chem. 64:2456–58 [Google Scholar]
  62. Engen JR, Smith DL. 62.  2000. Investigating the higher order structure of proteins. Hydrogen exchange, proteolytic fragmentation, and mass spectrometry. Methods Mol. Biol. 146:95–112 [Google Scholar]
  63. Hoofnagle AN, Resing KA, Ahn NG. 63.  2003. Protein analysis by hydrogen exchange mass spectrometry. Annu. Rev. Biophys. Biomol. Struct. 32:1–25 [Google Scholar]
  64. Hoofnagle AN, Resing KA, Ahn NG. 64.  2004. Practical methods for deuterium exchange/mass spectrometry. Meth. Mol. Biol. 250:283–98 [Google Scholar]
  65. Leichtling BH, Klotz IM. 65.  1966. Catalysis of hydrogen-deuterium exchange in polypeptides. Biochemistry 5:4026–37 [Google Scholar]
  66. Suckaw D, Shi Y, Beu SC, Senko MW, Quinn JP. 66.  et al. 1993. Coexisting stable conformations of gaseous protein ions. Proc. Natl. Acad. Sci. USA 90:790–93 [Google Scholar]
  67. Berger A, Linderstrøm-Lang K. 67.  1957. Deuterium exchange of poly-DL-alanine in aqueous solution. Arch. Biochem. Biophys. 69:106–18 [Google Scholar]
  68. Hvidt A. 68.  1964. A discussion of the pH dependence of the hydrogen-deuterium exchange of proteins. C. R. Trav. Lab. Carlsberg. 34:299–317 [Google Scholar]
  69. Eigen M. 69.  1964. Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Part I: elementary processes. Angew. Chem. 3:1–19 [Google Scholar]
  70. Klotz IM, Mueller DD. 70.  1969. Local environment effects on hydrogen–deuterium exchange. Biochemistry 8:12–16 [Google Scholar]
  71. Woodward CK, Rosenberg A. 71.  1970. Oxidized RNase as a protein model having no contribution to the hydrogen exchange rate from conformational restrictions. Proc. Natl. Acad. Sci. USA 66:1067–74 [Google Scholar]
  72. Molday RS, Englander SW, Kallen RG. 72.  1972. Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150–58 [Google Scholar]
  73. Bai Y, Milne JS, Mayne L, Englander SW. 73.  1993. Primary structure effects on peptide group hydrogen exchange. Proteins 17:75–86 [Google Scholar]
  74. Venable JD, Okach L, Agarwalla S, Brock A. 74.  2012. Subzero temperature chromatography for reduced back-exchange and improved dynamic range in amide hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 84:9601–8 [Google Scholar]
  75. Pan J, Zhang S, Parker CE, Borchers CH. 75.  2014. Subzero temperature chromatography and top-down mass spectrometry for protein higher-order structure characterization: method validation and application to therapeutic antibodies. J. Am. Chem. Soc. 136:13065–71 [Google Scholar]
  76. Cravello L, Lascoux D, Forest E. 76.  2003. Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins. Rapid Commun. Mass Spectrom. 17:2387–93 [Google Scholar]
  77. Englander JJ, Del Mar C, Li W, Englander SW, Kim JS. 77.  et al. 2003. Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Proc. Natl. Acad. Sci. USA 100:7057–62 [Google Scholar]
  78. Zhang HM, Kazazic S, Schaub TM, Tipton JD, Emmett MR, Marshall AG. 78.  2008. 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. 80:9034–41 [Google Scholar]
  79. Fukumoto J, Tsuru D, Yamamoto T. 79.  1967. Studies on mold proteases. Part I. Purification, crystallization and some enzymatic properties of acid protease of Rhizopus chinensis. Agr. Biol. Chem. 31:710–17 [Google Scholar]
  80. Rey M, Man P, Brandolin G, Forest E, Pelosi L. 80.  2009. Recombinant immobilized rhizopuspepsin as a new tool for protein digestion in hydrogen/deuterium exchange mass spectrometry. Rapid Commun. Mass Spectrom. 23:3431–38 [Google Scholar]
  81. Marcoux J, Thierry E, Vives C, Signor L, Fieschi F, Forest E. 81.  2010. Investigating alternative acidic proteases for H/D exchange coupled to mass spectrometry: Plasmepsin 2 but not plasmepsin 4 is active under quenching conditions. J. Am. Soc. Mass Spectrom. 21:76–79 [Google Scholar]
  82. Brier S, Maria G, Carginale V, Capasso A, Wu Y. 82.  et al. 2007. Purification and characterization of pepsins A1 and A2 from the Antarctic rock cod Trematomus bernacchii. FEBS J. 274:6152–66 [Google Scholar]
  83. Ahn J, Cao MJ, Yu YQ, Engen JR. 83.  2013. Accessing the reproducibility and specificity of pepsin and other aspartic proteases. Biochim. Biophys. Acta 1834:1222–29 [Google Scholar]
  84. Rey M, Yang M, Burns KM, Yu Y, Lees-Miller SP, Schriemer DC. 84.  2013. Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry. Mol. Cell Proteomics 12:464–72 [Google Scholar]
  85. Kadek A, Mrazek H, Halada P, Rey M, Schriemer DC, Man P. 85.  2014. Aspartic protease nepenthesin-1 as a tool for digestion in hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 86:4287–94 [Google Scholar]
  86. Ehring H. 86.  1999. Hydrogen exchange/electrospray ionization mass spectrometry studies of structural features of proteins and protein/protein interactions. Anal. Biochem. 267:252–59 [Google Scholar]
  87. Wang L, Pan H, Smith DL. 87.  2002. Hydrogen exchange-mass spectrometry: optimization of digestion conditions. Mol. Cell Proteomics 1:132–38 [Google Scholar]
  88. Busby SA, Chalmers MJ, Griffin PR. 88.  2007. Improving digestion efficiency under H/D exchange conditions with activated pepsinogen coupled columns. Int. J. Mass Spectrom. 259:130–39 [Google Scholar]
  89. Ahn J, Jung MC, Wyndham K, Yu YQ, Engen JR. 89.  2012. Pepsin immobilized on high-strength hybrid particles for continuous flow online digestion at 10,000 psi. Anal. Chem. 84:7256–62 [Google Scholar]
  90. Wang JL, Edelman GM. 90.  1971. Fluorescent probes for conformational states of proteins. IV. The pepsinogen-pepsin conversion. J. Biol. Chem. 246:1185–91 [Google Scholar]
  91. Fruton JS. 91.  2002. A history of pepsin and related enzymes. Q. Rev. Biol. 77:127–47 [Google Scholar]
  92. Powers JC, Harley AD, Myers DV. 92.  1977. Subsite specificity of porcine pepsin. Adv. Exp. Med. Biol. 95:141–57 [Google Scholar]
  93. Palashoff MH. 93.  2008. Determining the specificity of pepsin for proteolytic digestion MS thesis, Northeast. Univ., Boston.
  94. Hamuro Y, Coales SJ, Molnar KS, Tuske SJ, Morrow JA. 94.  2008. Specificity of immobilized porcine pepsin in H/D exchange compatible conditions. Rapid Commun. Mass Spectrom. 22:1041–46 [Google Scholar]
  95. Woods VL Jr. 95.  2001. Methods for the high-resolution identification of solvent-accessible amide hydrogens in polypeptides or proteins and for characterization of the fine structure of protein binding sites US Patent No. 6,291,189
  96. Yan X, Zhang H, Watson J, Schimerlik MI, Deinzer ML. 96.  2002. Hydrogen/deuterium exchange and mass spectrometric analysis of a protein containing multiple disulfide bonds: solution structure of recombinant macrophage colony stimulating factor-beta (rhM-CSFbeta). Protein Sci. 11:2113–24 [Google Scholar]
  97. Hamuro Y, Coales SJ, Southern MR, Nemeth-Cawley JF, Stranz DD, Griffin PR. 97.  2003. Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J. Biomol. Tech. 14:171–82 [Google Scholar]
  98. Houde D, Arndt J, Domeier W, Berkowitz S, Engen JR. 98.  2009. Characterization of IgG1 conformation and conformational dynamics by hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 81:2644–51 [Google Scholar]
  99. Zhang HM, McLoughlin SM, Frausto SD, Tang H, Emmett MR, Marshall AG. 99.  2010. Simultaneous reduction and digestion of proteins with disulfide bonds for hydrogen/deuterium exchange monitored by mass spectrometry. Anal. Chem. 82:1450–54 [Google Scholar]
  100. Abzalimov RR, Kaltashov IA. 100.  2006. Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions. J. Am. Soc. Mass Spectrom. 17:1543–51 [Google Scholar]
  101. Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A. 101.  et al. 2010. Computing H/D-exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics 11:424 [Google Scholar]
  102. Mayne L, Kan ZY, Chetty PS, Ricciuti A, Walters BT, Englander SW. 102.  2011. Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method. J. Am. Soc. Mass Spectrom. 22:1898–905 [Google Scholar]
  103. Fajer PG, Bou-Assaf GM, Marshall AG. 103.  2012. Improved sequence resolution by global analysis of overlapped peptides in hydrogen/deuterium exchange mass spectrometry. J. Am. Soc. Mass Spectrom. 23:1202–8 [Google Scholar]
  104. Lindner R, Lou X, Reinstein J, Shoeman RL, Hamprecht FA, Winkler A. 104.  2014. Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. J. Am. Soc. Mass Spectrom. 25:1018–28 [Google Scholar]
  105. Sheff JG, Rey M, Schriemer DC. 105.  2013. Peptide-column interactions and their influence on back exchange rates in hydrogen/deuterium exchange-MS. J. Am. Soc. Mass Spectrom. 24:1006–15 [Google Scholar]
  106. Wang L, Lane LC, Smith DL. 106.  2001. Detecting structural changes in viral capsids by hydrogen exchange and mass spectrometry. Protein Sci. 10:1234–43 [Google Scholar]
  107. Tuma R, Coward LU, Kirk MC, Barnes S, Prevelige PE Jr. 107.  2001. Hydrogen-deuterium exchange as a probe of folding and assembly in viral capsids. J. Mol. Biol. 306:389–96 [Google Scholar]
  108. Zhang Q, Chen J, Kuwajima K, Zhang HM, Xian F. 108.  et al. 2013. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry. Sci. Rep. 3:1247 [Google Scholar]
  109. Houde D, Demarest SJ. 109.  2011. Fine details of IGF-1R activation, inhibition, and asymmetry determined by associated hydrogen/deuterium-exchange and peptide mass mapping. Structure 19:890–900 [Google Scholar]
  110. Vadas O, Dbouk HA, Shymanets A, Perisic O, Burke JE. 110.  et al. 2013. Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors (GPCRs). Proc. Natl. Acad. Sci. USA 110:18862–67 [Google Scholar]
  111. Chen J, Walter S, Horwich AL, Smith DL. 111.  2001. Folding of malate dehydrogenase inside the GroEL-GroES cavity. Nat. Struct. Biol. 8:721–28 [Google Scholar]
  112. Georgescauld F, Popova K, Gupta AJ, Bracher A, Engen JR. 112.  et al. 2014. GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding. Cell 157:922–34 [Google Scholar]
  113. Hebling CM, Morgan CR, Stafford DW, Jorgenson JW, Rand KD, Engen JR. 113.  2010. Conformational analysis of membrane proteins in phospholipid bilayer nanodiscs by hydrogen exchange mass spectrometry. Anal. Chem. 82:5415–19 [Google Scholar]
  114. Rey M, Mrazek H, Pompach P, Novak P, Pelosi L. 114.  et al. 2010. Effective removal of nonionic detergents in protein mass spectrometry, hydrogen/deuterium exchange, and proteomics. Anal. Chem. 82:5107–16 [Google Scholar]
  115. Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA. 115.  2002. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci. 11:1300–8 [Google Scholar]
  116. Coales SJ, Tuske SJ, Tomasso JC, Hamuro Y. 116.  2009. Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry. Rapid Commun. Mass Spectrom. 23:639–47 [Google Scholar]
  117. Ling JM, Silva L, Schriemer DC, Schryvers AB. 117.  2012. Hydrogen-deuterium exchange coupled to mass spectrometry to investigate ligand-receptor interactions. Methods Mol. Biol. 799:237–52 [Google Scholar]
  118. Jensen PF, Jorgensen TJ, Koefoed K, Nygaard F, Sen JW. 118.  2013. Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes. Anal. Chem. 85:7052–59 [Google Scholar]
  119. Zhang Z, Li W, Logan TM, Li M, Marshall AG. 119.  1997. Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 6:2203–17 [Google Scholar]
  120. Palmblad M, Buijs J, Hakansson P. 120.  2001. Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. J. Am. Soc. Mass Spectrom. 12:1153–62 [Google Scholar]
  121. Chalmers MJ, Busby SA, Pascal BD, He Y, Hendrickson CL. 121.  et al. 2006. Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 78:1005–14 [Google Scholar]
  122. Zhang HM, Bou-Assaf GM, Emmett MR, Marshall AG. 122.  2009. 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. 20:520–24 [Google Scholar]
  123. Kazazic S, Zhang HM, Schaub TM, Emmett MR, Hendrickson CL. 123.  et al. 2010. Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 21:550–58 [Google Scholar]
  124. Hotchko M, Anand GS, Komives EA, Ten Eyck LF. 124.  2006. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 15:583–601 [Google Scholar]
  125. Chik JK, Vande Graaf JL, Schriemer DC. 125.  2006. Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78:207–14 [Google Scholar]
  126. Pascal BD, Willis S, Lauer JL, Landgraf RR, West GM. 126.  et al. 2012. HDX workbench: software for the analysis of H/D exchange MS data. J. Am. Soc. Mass Spectrom. 23:1512–21 [Google Scholar]
  127. Guttman M, Weis DD, Engen JR, Lee KK. 127.  2013. Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. J. Am. Soc. Mass Spectrom. 24:1906–12 [Google Scholar]
  128. Jorgenson JW. 128.  2010. Capillary liquid chromatography at ultrahigh pressures. Annu. Rev. Anal. Chem. 3:129–50 [Google Scholar]
  129. Wu Y, Engen JR, Hobbins WB. 129.  2006. Ultra performance liquid chromatography (UPLC) further improves hydrogen/deuterium exchange mass spectrometry. J. Am. Soc. Mass Spectrom. 17:163–67 [Google Scholar]
  130. Plumb R, Castro-Perez J, Granger J, Beattie I, Joncour K, Wright A. 130.  2004. Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 18:2331–37 [Google Scholar]
  131. Chalmers MJ, Busby SA, Pascal BD, Southern MR, Griffin PR. 131.  2007. A two-stage differential hydrogen deuterium exchange method for the rapid characterization of protein/ligand interactions. J. Biomol. Tech. 18:194–204 [Google Scholar]
  132. Wales TE, Fadgen KE, Gerhardt GC, Engen JR. 132.  2008. High-speed and high-resolution UPLC separation at zero degrees Celsius. Anal. Chem. 80:6815–20 [Google Scholar]
  133. Jones LM, Zhang H, Vidavsky I, Gross ML. 133.  2010. Online, high-pressure digestion system for protein characterization by hydrogen/deuterium exchange and mass spectrometry. Anal. Chem. 82:1171–74 [Google Scholar]
  134. Ruotolo BT, Gillig KJ, Stone EG, Russell DH. 134.  2002. Peak capacity of ion mobility mass spectrometry: separation of peptides in helium buffer gas. J. Chromatogr. B 782:385–92 [Google Scholar]
  135. Hilderbrand AE, Myung S, Barnes CA, Clemmer DE. 135.  2003. Development of LC-IMS-CID-TOFMS techniques: analysis of a 256 component tetrapeptide combinatorial library. J. Am. Soc. Mass Spectrom. 14:1424–36 [Google Scholar]
  136. Valentine SJ, Liu X, Plasencia MD, Hilderbrand AE, Kurulugama RT. 136.  et al. 2005. Developing liquid chromatography ion mobility mass spectometry techniques. Expert Rev. Proteomics 2:553–65 [Google Scholar]
  137. Iacob RE, Murphy JP 3rd, Engen JR. 137.  2008. Ion mobility adds an additional dimension to mass spectrometric analysis of solution-phase hydrogen/deuterium exchange. Rapid Commun. Mass Spectrom. 22:2898–904 [Google Scholar]
  138. Fadgen KE, Wales TE, Stapels M, Eggertson MJ, Engen JR. 138.  2011. Validation of an ion mobility hydrogen/deuterium exchange mass spectrometry system. J. Biomol. Tech. 22:SupplS63 [Google Scholar]
  139. Wales TE, Eggertson MJ, Engen JR. 139.  2013. Considerations in the analysis of hydrogen exchange mass spectrometry data. Methods Mol. Biol. 1007:263–88 [Google Scholar]
  140. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ. 140.  2006. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell Proteomics 5:144–56 [Google Scholar]
  141. Rand KD, Zehl M, Jorgensen TJ. 141.  2014. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling. Acc. Chem. Res. 47:3018–27 [Google Scholar]
  142. Pan J, Han J, Borchers CH, Konermann L. 142.  2009. Hydrogen/deuterium exchange mass spectrometry with top-down electron capture dissociation for characterizing structural transitions of a 17 kDa protein. J. Am. Chem. Soc. 131:12801–8 [Google Scholar]
  143. Huang RY, Garai K, Frieden C, Gross ML. 143.  2011. Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization. Biochemistry 50:9273–82 [Google Scholar]
  144. Landgraf RR, Chalmers MJ, Griffin PR. 144.  2012. Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution. J. Am. Soc. Mass Spectrom. 23:301–9 [Google Scholar]
  145. Bobst CE, Kaltashov IA. 145.  2014. Enhancing the quality of H/D exchange measurements with mass spectrometry detection in disulfide-rich proteins using electron capture dissociation. Anal. Chem. 86:5225–31 [Google Scholar]
  146. Wang G, Abzalimov RR, Bobst CE, Kaltashov IA. 146.  2013. Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry. Proc. Natl. Acad. Sci. USA 110:20087–92 [Google Scholar]
  147. Pan J, Borchers CH. 147.  2014. Top-down mass spectrometry and hydrogen/deuterium exchange for comprehensive structural characterization of interferons: implications for biosimilars. Proteomics 14:1249–58 [Google Scholar]
  148. Burkitt W, O'Connor G. 148.  2008. Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements. Rapid Commun. Mass Spectrom. 22:3893–901 [Google Scholar]
  149. Houde D, Berkowitz SA, Engen JR. 149.  2011. The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J. Pharm. Sci. 100:2071–86 [Google Scholar]
  150. Tiyanont K, Wales TE, Siebel CW, Engen JR, Blacklow SC. 150.  2013. Insights into Notch3 activation and inhibition mediated by antibodies directed against its negative regulatory region. J. Mol. Biol. 425:3192–204 [Google Scholar]
  151. Nakazawa S, Ahn J, Hashii N, Hirose K, Kawasaki N. 151.  2013. Analysis of the local dynamics of human insulin and a rapid-acting insulin analog by hydrogen/deuterium exchange mass spectrometry. Biochim. Biophys. Acta 1834:1210–14 [Google Scholar]
  152. Underbakke ES, Iavarone AT, Chalmers MJ, Pascal BD, Novick S. 152.  et al. 2014. Nitric oxide-induced conformational changes in soluble guanylate cyclase. Structure 22:602–11 [Google Scholar]
  153. Wei H, Ahn J, Yu YQ, Tymiak A, Engen JR, Chen G. 153.  2012. Using hydrogen/deuterium exchange mass spectrometry to study conformational changes in granulocyte colony stimulating factor upon PEGylation. J. Am. Soc. Mass Spectrom. 23:498–504 [Google Scholar]
  154. Creighton TE. 154.  1984. Pathways and mechanisms of protein folding. Adv. Biophys. 18:1–20 [Google Scholar]
  155. Chothia C. 155.  1984. Principles that determine the structure of proteins. Annu. Rev. Biochem. 53:537–72 [Google Scholar]
  156. Engen JR, Smithgall TE, Gmeiner WH, Smith DL. 156.  1997. Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry. Biochemistry 36:14384–91 [Google Scholar]
  157. Sivaraman T, Robertson AD. 157.  2001. Kinetics of conformational fluctuations by EX1 hydrogen exchange in native proteins. Methods Mol. Biol. 168:193–214 [Google Scholar]
  158. Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck LF. 158.  2006. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Am. Soc. Mass Spectrom. 17:1498–509 [Google Scholar]
  159. Zhang J, Ramachandran P, Kumar R, Gross ML. 159.  2013. H/D exchange centroid monitoring is insufficient to show differences in the behavior of protein states. J. Am. Soc. Mass Spectrom. 24:450–53 [Google Scholar]
  160. Fang J, Rand KD, Beuning PJ, Engen JR. 160.  2011. False EX1 signatures caused by sample carryover during HX MS analyses. Int. J. Mass Spectrom. 302:19–25 [Google Scholar]
  161. Majumdar R, Manikwar P, Hickey JM, Arora J, Middaugh CR. 161.  et al. 2012. Minimizing carry-over in an online pepsin digestion system used for the H/D exchange mass spectrometric analysis of an IgG1 monoclonal antibody. J. Am. Soc. Mass Spectrom. 23:2140–48 [Google Scholar]
  162. Yang H, Smith DL. 162.  1997. Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36:14992–99 [Google Scholar]
  163. Chen S, Brier S, Smithgall TE, Engen JR. 163.  2007. The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding. Protein Sci. 16:572–81 [Google Scholar]
  164. Engen JR, Wales TE, Chen S, Marzluff EM, Hassell KM. 164.  et al. 2013. Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. Int. Rev. Phys. Chem. 32:96–127 [Google Scholar]
/content/journals/10.1146/annurev-anchem-062011-143113
Loading
Analytical Aspects of Hydrogen Exchange Mass Spectrometry
Annual Review of Analytical Chemistry 8, 127 (2015); https://doi.org/10.1146/annurev-anchem-062011-143113
/content/journals/10.1146/annurev-anchem-062011-143113
/content/journals/10.1146/annurev-anchem-062011-143113
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error