Abstract
The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with 15N and uniformly with 13C. The pattern of isotope labeling of second-generation fragment ions derived via a n and b n ions (where n=4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b n ions where n=8 or 9.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
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.
Riba-Garcia, I.; Giles, K.; Bateman, R. H.; Gaskell, 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.
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.
Yague, J.; Paradela, A.; Ramos, M.; Ogueta, S.; Marina, A.; Barahona, F.; Lopez de Castro, J. A.; Vazquez, J. Peptide Rearrangement During Quadrupole Ion Trap Fragmentation: Added Complexity to MS/MS Spectra. Anal. Chem. 2003, 75, 1524–1535.
Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508–548.
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.
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.
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.
Mouls, L.; Aubagnac, J. L.; Martinez, J.; Enjalbal, C. Low Energy Peptide Fragmentations in an ESI-Q-Tof Type Mass Spectrometer. J. Proteome Res. 2007, 6, 1378–1391.
Pringle, S. D.; Giles, K.; Wildgoose, J. L.; Slade, S. E.; Thalassinos, K.; Bateman, R. H.; Bowers, M. T.; Scrivens, J. H. An Investigation of the Mobility Separation of Some Peptide and Protein Ions Using a New Hybrid Quadrupole/Travelling Wave IMS/Oa-ToF Instrument. Int. J. Mass Spec. 2007, 261, 1–12.
Reid, G. E.; Simpson, R. J.; O’Hair, R. A. J. Probing the Fragmentation Reactions of Protonated Glycine Oligomers via Multistage Mass Spectrometry and Gas Phase Ion Molecule Hydrogen/Deuterium Exchange. Int. J. Mass Spectrom. 1999, 191, 209–230.
Vachet, R. W.; Bishop, B. M.; Erickson, B. W.; Glish, G. L. Novel Peptide Dissociation: Gas-Phase Intramolecular Rearrangement of Internal Amino Acid Residues. J. Am. Chem. Soc. 1997, 119, 5481–5488.
Cooper, T.; Talaty, E.; Grove, J.; Van Stipdonk, M.; Suhai, S.; Paizs, B. Isotope Labeling and Theoretical Study of the Formation of a*3 Ions from Protonated Tetraglycine. J. Am. Soc. Mass Spectrom. 2006, 17, 1654–1664.
Bythell, B. J.; Barofsky, D. F.; Pingitore, F.; Polce, M. J.; Wang, P.; Wesdemiotis, C.; Paizs, B. Backbone Cleavages of Carbon Monoxide and Sequential Loss and Ammonia from Protonated AGG: A Combined Tandem Mass Spectrometry, Isotope Labeling, and Theoretical Study. J. Am. Soc. Mass Spectrom. 2007, 18, 1291–1303.
Koeniger, S. L.; Merenbloom, S. I.; Valentine, S. J.; Jarrold, M. F.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. An IMS-IMS Analogue of MS-MS. Anal. Chem. 2006, 78, 4161–4174.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published online September 30, 2008
Rights and permissions
About this article
Cite this article
Garcia, I.R., Giles, K., Bateman, R.H. et al. Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry. J Am Soc Mass Spectrom 19, 1781–1787 (2008). https://doi.org/10.1016/j.jasms.2008.09.024
Received:
Revised:
Accepted:
Issue Date:
DOI: https://doi.org/10.1016/j.jasms.2008.09.024