Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides
Article first published online: 15 APR 2009
Copyright © 2009 John Wiley & Sons, Ltd.
Rapid Communications in Mass Spectrometry
Volume 23, Issue 10, pages 1508–1514, 30 May 2009
How to Cite
Lau, K. W., Hart, S. R., Lynch, J. A., Wong, S. C. C., Hubbard, S. J. and Gaskell, S. J. (2009), Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides. Rapid Commun. Mass Spectrom., 23: 1508–1514. doi: 10.1002/rcm.4032
- Issue published online: 15 APR 2009
- Article first published online: 15 APR 2009
- Manuscript Accepted: 15 MAR 2009
- Manuscript Revised: 11 MAR 2009
- Manuscript Received: 27 NOV 2008
- BBSRC. Grant Numbers: EGM17685, BB/C007735/1
- EPSRC. Grant Number: EP/D013615/1
Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument-specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole-time-of-flight and quadrupole ion trap instruments. Specifically, quadrupole-time-of-flight tandem mass spectra show a significant under-representation of N-terminal b-type fragments in comparison to quadrupole ion trap product ion spectra. Energy-resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b-type ions are significantly less stable than their y-type N-terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole-time-of-flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. Copyright © 2009 John Wiley & Sons, Ltd.