Abstract
The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Wells, J. M.; McLuckey, S. A. Collision-Induced Dissociation (CID) of Peptides and Proteins. Methods Enzymol. 2005, 402, 148–185.
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.
Syka, J. E. P.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528–9533.
Mirgorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Localization of O-Glycosylation Sites in Peptides by Electron Capture Dissociation in a Fourier Transform Mass Spectrometer. Anal. Chem. 1999, 71, 4431–4436.
Stensballe, A.; Jensen, O. N.; Olsen, J. V.; Haselmann, K. F.; Zubarev, R. A. Electron Capture Dissociation of Singly and Multiply Phosphorylated Peptides. Rapid Commun. Mass Spectrom. 2000, 14, 1793–1800.
Hakansson, K.; Cooper, H. J.; Emmett, M. R.; Costello, C. E.; Marshall, A. G.; Nilsson, C. L. Electron Capture Dissociation and Infrared Multiphoton Dissociation MS/MS of an N-Glycosylated Tryptic Peptide to Yield Complementary Sequence Information. Anal. Chem. 2001, 73, 4530–4536.
Kleinnijenhuis, A. J.; Kjeldsen, F.; Kallipolitis, B.; Haselmann, K. F.; Jensen, O. N. Analysis of Histidine Phosphorylation Using Tandem MS and Ion-Electron Reactions. Anal. Chem. 2007, 79, 7450–7456.
Srikanth, R.; Wilson, J.; Bridgewater, J. D.; Numbers, J. R.; Lim, J.; Olbris, M. R.; Kettani, A.; Vachet, R. W. Improved Sequencing of Oxidized Cysteine and Methionine Containing Peptides Using Electron Transfer Dissociation. J. Am. Soc. Mass Spectrom. 2007, 18, 1499–1506.
Kjeldsen, F.; Giessing, A. M. B.; Ingrell, C. R.; Jensen, O. N. Peptide Sequencing and Characterization of Post-Translational Modifications by Enhanced Ion-Charging and Liquid Chromatography Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal. Chem. 2007, 79, 9243–9252.
Swaney, D. L.; McAlister, G. C.; Wirtala, M.; Schwartz, J. C.; Syka, J. E. P.; Coon, J. J. Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors. Anal. Chem. 2007, 79, 477–485.
Little, D. P.; Speir, J. P.; Senko, M. W.; O’Connor, P. B.; McLafferty, F. W. Infrared Multiphoton Dissociation of Large Multiply Charged Ions for Biomolecule Sequencing. Anal. Chem. 1994, 66, 2809–2815.
Li, W.; Hendrickson, C. L.; Emmett, M. R.; Marshall, A. G. Identification of Intact Proteins in Mixtures by Alternated Capillary Liquid Chromatography Electrospray Ionization and LC ESI Infrared Multiphoton Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 1999, 71, 4397–4402.
Hofstadler, S. A.; Sannes-Lowery, K. A.; Griffey, R. H. Infrared Multiphoton Dissociation in an External Ion Reservoir. Anal. Chem. 1999, 71, 2067–2070.
Flora, J. W.; Muddiman, D. C. Selective, Sensitive, and Rapid Phosphopeptide Identification in Enzymatic Digests Using ESI-FTICR-MS with Infrared Multiphoton Dissociation. Anal. Chem. 2001, 73, 3305–3311.
Flora, J. W.; Muddiman, D. C. Gas-Phase Ion Unimolecular Dissociation for Rapid Phosphopeptide Mapping by IRMPD in a Penning Ion Trap: An Energetically Favored Process. J. Am. Chem. Soc. 2002, 124, 6546–6547.
Drader, J. J.; Hannis, J. C.; Hofstadler, S. A. Infrared Multiphoton Dissociation with a Hollow Fiber Waveguide. Anal. Chem. 2003, 75, 3669–3674.
Hofstadler, S. A.; Drader, J. J.; Gaus, H.; Hannis, J. C.; Sannes-Lowery, K. A. Alternative Approaches to Infrared Multiphoton Dissociation in an External Ion Reservoir. J. Am. Soc. Mass Spectrom. 2003, 14, 1413–1423.
Chalmers, M. J.; Quinn, J. P.; Blakney, G. T.; Emmett, M. R.; Mischak, H.; Gaskell, S. J.; Marshall, A. G. Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance Mass Spectrometric Characterization of Protein Kinase C Phosphorylation. J. Proteome Res. 2003, 2, 373–382.
Flora, J. W.; Muddiman, D. C. Determination of the Relative Energies of Activation for the Dissociation of Aromatic versus Aliphatic Phosphopeptides by ESI-FTICR-MS and IRMPD. J. Am. Soc. Mass Spectrom. 2004, 15, 121–127.
Chalmers, M. J.; Hakansson, K.; Johnson, R.; Smith, R.; Shen, J.; Emmett, M. R.; Marshall, A. G. Protein Kinase A Phosphorylation Characterized by Tandem Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics 2004, 4, 970–981.
Tsybin, Y. O.; Ramstroem, M.; Witt, M.; Baykut, G.; Hakansson, P. Peptide and Protein Characterization by High-Rate Electron Capture Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Mass Spectrom. 2004, 39, 719–729.
Yamada, N.; Suzuki, E.-I.; Hirayama, K. Effective Novel Dissociation Methods for Intact Protein: Heat-Assisted Nozzle-Skimmer Collisionally Induced Dissociation and Infrared Multiphoton Dissociation Using a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Equipped with a Micrometal Electrospray Ionization Emitter. Anal. Biochem. 2006, 348, 139–147.
Mihalca, R.; van der Burgt, Y. E. M.; McDonnell, L. A.; Duursma, M.; Cerjak, I.; Heck, A. J. R.; Heeren, R. M. A. Combined Infrared Multiphoton Dissociation and Electron-Capture Dissociation Using Co-Linear and Overlapping Beams in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom. 2006, 20, 1838–1844.
Clowers, B. H.; Dodds, E. D.; Seipert, R. R.; Lebrilla, C. B. Site Determination of Protein Glycosylation Based on Digestion with Immobilized Nonspecific Proteases and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Proteome Res. 2007, 6, 4032–4040.
Payne, A. H.; Glish, G. L. Thermally Assisted Infrared Multiphoton Photodissociation in a Quadrupole Ion Trap. Anal. Chem. 2001, 73, 3542–3548.
Steen, H.; Fernandez, M.; Ghaffari, S.; Pandey, A.; Mann, M. Phosphotyrosine Mapping in Bcr/Abl Oncoprotein Using Phosphotyrosine-Specific Immonium Ion Scanning. Mol. Cell Proteomics 2003, 2, 138–145.
Trelle, M. B.; Jensen, O. N. Utility of Immonium Ions for Assignment of e-N-Acetyllysine-Containing Peptides by Tandem Mass Spectrometry. Anal. Chem. 2008, 80, 3422–3430.
Couttas, T. A.; Raftery, M. J.; Bernardini, G.; Wilkins, M. R. Immonium Ion Scanning for the Discovery of Post-Translational Modifications and Its Application to Histones. J. Proteome Res. 2008, 7, 2632–2641.
Crowe, M. C.; Brodbelt, J. S. Infrared Multiphoton Dissociation (IRMPD) and Collisionally Activated Dissociation of Peptides in a Quadrupole Ion Trap with Selective IRMPD of Phosphopeptides. J. Am. Soc. Mass Spectrom. 2004, 15, 1581–1592.
Wilson, J. J.; Brodbelt, J. S. Infrared Multiphoton Dissociation for Enhanced De Novo Sequence Interpretation of N-Terminal Sulfonated Peptides in a Quadrupole Ion Trap. Anal. Chem. 2006, 78, 6855–6862.
Pikulski, M.; Wilson, J. J.; Aguilar, A.; Brodbelt, J. S. Amplification of Infrared Multiphoton Dissociation Efficiency in a Quadruple Ion Trap Using IR-Active Ligands. Anal. Chem. 2006, 78, 8512–8517.
Pikulski, M.; Hargrove, A.; Shabbir, S. H.; Anslyn, E. V.; Brodbelt, J. S. Sequencing and Characterization of Oligosaccharides Using Infrared Multiphoton Dissociation and Boronic Acid Derivatization in a Quadrupole Ion Trap. J. Am. Soc. Mass Spectrom. 2007, 18, 2094–2106.
Gardner, M. W.; Vasicek, L. A.; Shabbir, S.; Anslyn, E. V.; Brodbelt, J. S. Chromogenic Cross-Linker for the Characterization of Protein Structure by Infrared Multiphoton Dissociation Mass Spectrometry. Anal. Chem. 2008, 80, 4807–4819.
Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation. J. Mass Spectrom. 2000, 35, 1399–1406.
Iavarone, A. T.; Jurchen, J. C.; Williams, E. R. Effects of Solvent on the Maximum Charge State and Charge State Distribution of Protein Ions Produced by Electrospray Ionization. J. Am. Soc. Mass Spectrom. 2000, 11, 976–985.
Iavarone, A. T.; Jurchen, J. C.; Williams, E. R. Supercharged Protein and Peptide Ions Formed by Electrospray Ionization. Anal. Chem. 2001, 73, 1455–1460.
Iavarone, A. T.; Williams, E. R. Supercharging in Electrospray Ionization: Effects on Signal and Charge. Int. J. Mass Spectrom. 2002, 219, 63–72.
Iavarone, A. T.; Williams, E. R. Collisionally Activated Dissociation of Supercharged Proteins Formed by Electrospray Ionization. Anal. Chem. 2003, 75, 4525–4533.
Iavarone, A. T.; Williams, E. R. Mechanism of Charging and Supercharging Molecules in Electrospray Ionization. J. Am. Chem. Soc. 2003, 125, 2319–2327.
Black, D. M.; Payne, A. H.; Glish, G. L. Determination of Cooling Rates in a Quadrupole Ion Trap. J. Am. Soc. Mass Spectrom. 2006, 17, 932–938.
Schwartz, J. C. High-Q pulsed fragmentation in ion traps. U.S. Patent 7 102 129, 2006.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published online November 5, 2008
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Madsen, J.A., Brodbelt, J.S. Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps. J Am Soc Mass Spectrom 20, 349–358 (2009). https://doi.org/10.1016/j.jasms.2008.10.018
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1016/j.jasms.2008.10.018