Interpreting top-down mass spectra using spectral alignment

Ari M. Frank, James J. Pesavento, Craig A. Mizzen, Neil L. Kelleher, Pavel A. Pevzner

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)2499-2505
Number of pages7
JournalAnalytical Chemistry
Issue number7
StatePublished - Apr 1 2008

ASJC Scopus subject areas

  • Analytical Chemistry


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