Article ID Journal Published Year Pages File Type
1195367 Journal of the American Society for Mass Spectrometry 2006 9 Pages PDF
Abstract

A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive α-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases.

Related Topics
Physical Sciences and Engineering Chemistry Analytical Chemistry
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