Peptide identification using both spectrum libraries and protein databases

Marshall Bern*

Palo Alto Research Center, 3333 Coyote Hill Rd., Palo Alto, CA 94304, USA. an_bern@parc.com

Proc LSS Comput Syst Bioinform Conf. August, 2009. Vol. 8, p. 117-126. Full-Text PDF

*To whom correspondence should be addressed.

The standard method for peptide identification by tandem mass spectrometry compares observed mass spectra to predicted mass spectra, computed from protein databases. Another approach, actively promoted in the last few years, compares observed mass spectra to previously observed, library spectra. In this paper we describe algorithms and software for combining the two methods in a way transparent to the user. The software applies the same dot-product scoring algorithm to theoretical and library spectra, so that results from the two types of searches are directly comparable. We show that combined database and library search out performs either method alone.