on 05-01-201210:38 AM - edited on 10-15-202110:48 AM by Closed Account
Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. Anal Chem. 2008 Apr 1;80(7):2499-505. Recent advances in mass spectrometry instrumentation, such as FTICR and OrbiTrap, have made it possible to generate high-resolution spectra of entire proteins. While these methods offer new opportunities for performing “top-down” studies of proteins, the computational tools for analyzing top-down data are still scarce. In this paper, we investigate the application of spectral alignment to the problem of identifying protein forms in top-down mass spectra (i.e., identifying the modifications, mutations, insertions, and deletions). We demonstrate how spectral alignment efficiently discovers protein forms even in the presence of numerous modifications and how the algorithm can be extended to discover positional isomers from spectra of mixtures of isobaric protein forms.