title: Interpreting top-down mass spectra using spectral alignment.
abstract: 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.
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093-0404, USA. arf@cs.ucsd.edu
authors.forename: Ari M
authors.initials: AM
authors.lastname: Frank
authors.forename: James J
authors.initials: JJ
authors.lastname: Pesavento
authors.forename: Craig A
authors.initials: CA
authors.lastname: Mizzen
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D006657:Histones / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D006657:Histones