Abstract
Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b +5 and b +4 fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H]+) and its b +5 and b +4 fragment ions (with ND3) were observed. Isolated 12Call isotopomers of both b +5 and b +4 fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b +5 and b +4 fragment ions exist as combination of slow-exchanging (“s”) and fast-exchanging (“f”) species. The calculated rate constant for the first labile hydrogen exchange of [M + H]+ (k[M + H] + = 3.80 ± 0.7 × 10−10 cm3 mol−1 s−1) was ∼30 and ∼5 times greater than those for the “s” and “f” species of b +5 , respectively. Data from H/D exchange of isolated “s” species at longer ND3 reaction times confirmed the existence of different conformers or isomers for b +5 fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that “s” and “f” species of b +5 and b +4 fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Loo, J. A.; Loo, R. R. O.; Udseth, H. R.; Edmonds, C. G.; Smith, R. D. Solvent-Induced Conformational Changes of Polypeptides Probed by Electrospray Ionization-Mass Spectrometry. Rapid Commun. Mass Spectrom. 1991, 5, 101–105.
Winger, B. E.; Light-Wahl, K. J.; Rockwood, A. L.; Smith, R. D. Probing Qualitative Conformation Differences of Multiply Protonated Gas-Phase Proteins via H/D Isotopic Exchange with D2O. J. Am. Chem. Soc. 1992, 114, 5897–5898.
Suckau, D.; Shi, Y.; Beu, S. C.; Senko, M. W.; Quinn, J. P.; Wampler-III, F. M.; McLafferty, F. W. Coexisting Stable Conformations of Gaseous Protein Ions. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 790–793.
Gard, E.; Willard, D.; Bregar, J.; Green, M. K.; Lebrilla, C. B. Site Specificity on the H-D Exchange Reactions of Gas-Phase Protonated Amino Acids with CH3OD. Org. Mass Spectrom. 1993, 28, 1632–1639.
Katta, V.; Chait, B. T. Hydrogen/Deuterium Exchange Electrospray Ionization Mass Spectrometry: A Method for Probing Protein Conformational Changes in Solution. J. Am. Chem. Soc. 1993, 115, 6317–6321.
Gross, D. S.; Schnier, P. D.; Rodrigues-Cruz, S. E.; Fagerquist, C. K.; Williams, E. R. Conformations and Folding of Lysozyme Ions In Vacuo. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 3143–3148.
Valentine, S. J.; Clemmer, D. E. H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase. J. Am. Chem. Soc. 1997, 119, 3558–3566.
McLafferty, F. W.; Guan, Z.; Haupts, U.; Wood, T. W.; Kelleher, N. L. Gaseous Conformational Structures of Cytochrome c. J. Am. Chem. Soc. 1998, 120, 4732–4740.
Veenstra, T. D.; Johnson, K. L.; Tomlinson, A. J.; Craig, T. A.; Kumar, R.; Naylor, S. Zinc-Induced Conformational Changes in the DNA-Binding Domain of the Vitamin D Receptor Determined by Electrospray Ionization Mass Spectrometry. J. Am. Soc. Mass Spectrom. 1998, 9, 8–14.
Eyles, S. J.; Speir, J. P.; Kruppa, G. H.; Gierasch, L. M.; Kaltashov, I. A. Protein Conformational Stability Probed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Chem. Soc. 2000, 122, 495–500.
Freitas, M. A.; Hendrickson, C. L.; Emmett, M. R.; Marshall, A. G. Gas-Phase Bovine Ubiquitin Cation Conformations Resolved by Gas-Phase Hydrogen/Deuterium Exchange Rate and Extent. Int. J. Mass Spectrom. 1999, 185/186/187, 565–575.
Solouki, T.; Fort, R.; Alomary, A.; Fattahi, A. Gas-Phase Hydrogen/Deuterium Exchange Reactions of a Model Meptide: FT-ICR and Computational Analyses of Metal Induced Conformational Mmutations. J. Am. Soc. Mass Spectrom. 2001, 12, 1272–1285.
Gauthier, J. W.; Trautman, T. R.; Jacobson, D. B. Sustained Off-Resonance Irradiation for Collision-Activated Dissociation Involving Fourier Transform Mass Spectrometry: Collision-Activated Dissociation Technique That Emulates Infrared Multiphoton Dissociation. Anal. Chim. Acta. 1991, 246, 211–225.
Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations: A Nonergodic Process. J. Am. Chem. Soc. 1998, 120, 3265–3266.
Roepstorff, P.; Fohlman, J. Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom. 1984, 11, 601.
Harrison, A. G.; Young, A. B.; Bleiholder, C.; Suhai, S.; Paizs, B. Scrambling of Sequence Information in Collision-Induced Dissociation of Peptides. J. Am. Chem. Soc. 2006, 128, 10364–10365.
Harrison, A. G. Peptide Sequence Scrambling Through Cyclization of b5 Ions. J. Am. Soc. Mass Spectrom. 2008, 19, 1776–1780.
Jia, C.; Qi, W.; He, Z. Cyclization Reaction of Peptide Fragment Ions During Multistage Collisionally Activated Decomposition: An Inducement to Lose Internal Amino-Acid Residues. J. Am. Soc. Mass Spectrom. 2007, 18, 663–678.
Arnott, D.; Kottmeier, D.; Yates, N.; Shabanovitz, J.; Hunt, D. F. Fragmentation of Multiply Protonated Peptides Under Low Energy Conditions. Proceedings of the 42nd ASMS Conference on Mass Spectrometry and Allied Topics; Chicago, IL, May 29–June 3, 1994; p. 470.
Yalcin, T.; Khouw, C.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. Why are b Ions Stable Species in Peptide Spectra?. J. Am. Soc. Mass Spectrom. 1995, 6, 1165–1174.
Yalcin, T.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. The Structure and Fragmentation of B n (n ≥ 3) Ions in Peptide Spectra. J. Am. Soc. Mass Spectrom. 1996, 7, 233–242.
Paizs, B.; Lendvay, G.; Vékey, K.; Suhai, S. Formation of b +2 Ions from Protonated Peptides: An Ab Initio Study. Rapid Commun. Mass Spectrom. 1999, 13, 525–533.
Schlosser, A.; Lehmann, W. D. Five-Membered Ring Formation in Unimolecular Reactions of Peptides: A Key Structural Element Controlling Low-Energy Collision-Induced Dissociation of Peptides. J. Mass Spectrom. 2000, 35, 1382–1390.
Paizs, B.; Suhai, S. Combined Quantum Chemical and RRKM Modeling of the Main Fragmentation Pathways of Protonated GGG: II. Formation of b2, y1, and y2 Ions. Rapid Commun. Mass Spectrom. 2002, 16, 375–389.
Ngoka, L. C. M.; Gross, M. L. Location of Alkali Metal Binding Sites in Endothelin A Selective Receptor Antagonists, Cyclo(D-Trp-D-Asp-Pro-D-Val-Leu) and Cyclo(D-Trp-D-Asp-Pro-D-Ile-Leu), from Multistep Collisionally Activated Decompositions. J. Mass Spectrom. 2000, 35, 265–276.
Klassen, J. S.; Kebarle, P. Collision-Induced Dissociation Threshold Energies of Protonated Glycine, Glycinamide, and Some Related Small Peptides and Peptide Amino Amides. J. Am. Chem. Soc. 1997, 119, 6552–6563.
Nold, M. J.; Cerda, B. A.; Wesdemiotis, C. Proton Affinities of the N- and C-Terminal Segments Arising Upon the Dissociation of the Amide Bond in Protonated Peptides. J. Am. Soc. Mass Spectrom. 1999, 10, 1–8.
Polce, M. J.; Ren, D.; Wesdemiotis, C. Dissociation of the Peptide Bond in Protonated Peptides. J. Mass Spectrom. 2000, 35, 1391–1398.
Paizs, B.; Suhai, S. Combined Quantum Chemical and RRKM Modeling of the Main Fragmentation Pathways of Protonated GGG. I. Cis-trans Isomerization Around Protonated Amide Bond. Rapid Commun. Mass Spectrom. 2001, 15, 2307–2323.
Paizs, B.; Suhai, S. Theoretical Study of the Main Fragmentation Pathways for Protonated Glycylglycine. Rapid Commun. Mass Spectrom. 2001, 15, 651–663.
Chen, X.; Powell, D. H.; Polfer, N. Fragment Structures in Collision-Induced Dissociation of Peptides Investigated by H/D Exchange. Proceedings of the 56th ASMS Conference on Mass Spectrometry and Allied Topics; May 31–June 4, 2008; NPMM 334.
Polfer, N. C.; Bohrer, B. C.; Plasencia, M. D.; Paizs, B.; Clemmer, D. E. On the Dynamics of Fragment Isomerization in Collision-Induced Dissociation of Peptides. J. Phys. Chem. A. 2008, 112, 1286–1293.
Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508–548.
Fattahi, A.; Solouki, T. Comparison of Conformational Variations Induced by Metal Complexation and b Type Fragmentation for Peptides with Acidic- and Basic-Side Chains: Gas-Phase H/D Exchange Kinetic Studies. Proceedings of the 51st ASMS Conference on Mass Spectrometry and Allied Topics; Montreal, QC, Canada, 2003; ThPK2 199.
Riba-Garcia, I.; Giles, K.; Bateman, R. H.; Gaskella, S. J. Evidence for Structural Variants of a- and b-Type Peptide Fragment Ions Using Combined Ion Mobility/Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2008, 19, 609–613.
Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. Infrared Spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-Enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton. J. Am. Chem. Soc. 2007, 129, 5887–5897.
Fattahi, A.; Solouki, T. Conformational Analysis of Metal Complexed Model Peptides and Their Fragment Ions Using FT-ICR MS and Gas-Phase H/D Exchange Reactions. Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics; Chicago, IL, May 27–31, 2001; WPE 102.
Arehart, E.; Fattahi, A.; Patterson, H.; Solouki, T. Fluorescence Quenching, Mass Spectral H/D Exchange, and Ion Fragmentation Studies of Trp-His-Trp-Leu-Gln-Leu Upon Metal Complexation. Proceedings of the 224th American Chemical Society (ACS) National Meeting; Boston, MA, 2002.
Bythell, B. J.; Somogyi, Á.; Paizs, B. What is the Structure of b 2 Ions Generated from Doubly Protonated Tryptic Peptides?. J. Am. Soc. Mass Spectrom. 2009, 20(4), 618–624.
Stemmler, E. A.; Yoshida, E.; Pacheco, J.; Brunton, J.; Woodbury, E.; Solouki, T. Reactions of O−. with Methyl Benzoate: A Negative Ion Chemical Ionization and Fourier Transform Ion Cyclotron Resonance Study. J. Am. Soc. Mass Spectrom. 2001, 12, 694–706.
Comisarow, M. B.; Marshall, A. G. Frequency-Sweep Fourier Transform Ion Cyclotron Resonance Spectroscopy. Chem. Phys. Lett. 1974, 26, 489–490.
Wang, T. C. L.; Ricca, T. L.; Marshall, A. G. Extension of Dynamic Range in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry via Stored Waveform Inverse Fourier Transform Excitation. Anal. Chem. 1986, 58, 2935–2938.
Jiao, C. Q.; Ranatunga, D. R. A.; Vaughn, W. E.; Freiser, B. S. A Pulsed-Leak Valve for Use with Ion Trapping Mass Spectrometers. J. Am. Soc. Mass Spectrom. 1996, 7, 118–122.
Solouki, T.; Szulejko, J. E. Bimolecular and Unimolecular Contributions to the Disparate Self-Chemical Ionizations of α-Pinene and Camphene Isomers. J. Am. Soc. Mass Spectrom. 2007, 18, 2026–2039.
Morris, M.; Thibault, P.; Boyd, R. K. Low-Energy Ion/Molecule Products from Collisions with Ammonia. Rapid Commun. Mass Spectrom. 1993, 7, 1136–1140.
Ausloos, P.; Lias, S. G. Thermoneutral Isotope Exchange Reactions of Cations in the Gas Phase. J. Am. Chem. Soc. 1981, 103, 3641–3645.
Campbell, S.; Rodgers, M. T.; Marzluff, E. M.; Beauchamp, J. L. Deuterium Exchange Reactions as a Probe of Biomolecule Structure: Fundamental Studies of Gas Phase H/D Exchange Reactions of Protonated Glycine Oligomers with D2O, CD3OD, CD3CO2D, and ND3. J. Am. Chem. Soc. 1995, 117, 12840–12854.
Solouki, T.; Freitas, M. A.; Alomary, A. Gas-Phase Hydrogen/Deuterium Exchange Reactions of Fulvic Acids: An Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectral Study. Anal. Chem. 1999, 71, 4719–4726.
Alomary, A.; Solouki, T.; Patterson, H. H.; Cronan, C. S. Elucidation of Aluminum-Fulvic Acid Interactions by Gas-Phase Hydrogen/Deuterium (H/D) Exchange and Electrospray Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ESI FT-ICR). Environ. Sci. Technol. 2000, 34, 2830–2838.
Zekavat, B.; Al-Fdeilat, A. H.; Solouki, T. Gas-Phase Basicity Measurements of Singly- and Doubly-Charged bn Fragment Ions Using ESI/FT-ICR MS. Proceedings of the 57th ASMS Conference on Mass Spectrometry and Allied Topics; Philadelphia, PA, 2009; TP 357.
He, F.; Marshall, A. G. Weighted Quasi-Newton and Variable-Order, Variable-Step Adams Algorithm for Determining Site-Specific Reaction Rate Constants. J. Phys. Chem. A. 2000, 104, 562–567.
Green, M. K.; Gard, E.; Bregar, J.; Lebrilla, C. B. H-D Exchange Kinetics of Alcohols and Protonated Peptides: Effects of Structure and Proton Affinity. J. Mass Spectrom. 1995, 30, 1103–1110.
Vaisar, T.; Urban, J. Low-Energy Collision Induced Dissociation of Protonated Peptides: Importance of an Oxazolone Formation for a Peptide Bond Cleavage. J. Eur. Mass Spectrom. 1998, 4, 359–364.
Clemmer, D. E.; Jarrold, M. F. Ion Mobility Measurements and Their Applications to Clusters and Biomolecules. J. Mass Spectrom. 1997, 32, 577–592.
Wyttenbach, T.; Batka, J. J., Jr.; Gidden, J.; Bowers, M. T. Host/Guest Conformations of Biological Systems: Valinomycin/Alkali Ions. Int. J. Mass Spectrom. 1999, 193, 143–152.
Ruotolo, B. T.; Verbeck, G. F.; Thomson, L. M.; Gillig, K. J.; Russell, D. H. Observation of Conserved Solution-Phase Secondary Structure in Gas-Phase Tryptic Peptides. J. Am. Chem. Soc. 2002, 124, 4214–4215.
Collins, D. C.; Lee, M. L. Developments in Ion Mobility Spectrometry-Mass Spectrometry. Anal. Bioanal. Chem. 2002, 372, 66–73.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published online October 29, 2009
Rights and permissions
About this article
Cite this article
Fattahi, A., Zekavat, B. & Solouki, T. H/D exchange kinetics: Experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing. J Am Soc Mass Spectrom 21, 358–369 (2010). https://doi.org/10.1016/j.jasms.2009.10.017
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1016/j.jasms.2009.10.017