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.