A parallel algorithm for de novo peptide sequencing

Abstract

Protein identification is a main problem in proteomics,the large-scale analysis of proteins. Tandem mass spec-trometry (MS/MS) provides an important tool to handleprotein identification problem. Indeed the spectrometeris capable of ionizing a mixture of peptides, essentiallyseveral copies of the same unknown peptide, dissociatingevery molecule into two fragments called complementaryions, and measuring the mass/charge ratios of the pep-tides and of their fragments. These measures are visualizedas mass peaks in a mass spectrum.There are two fundamental approaches to interpret thespectra. The first approach is to search in a database tofind the peptides that match the MS/MS spectra. This data-base search approach is effective for known proteins, butdoes not permit to detect novel proteins. This second taskcan be dealt with the de novo sequencing that computesthe amino acid sequence of the peptides directly fromtheir MS/MS spectra.In the de novo sequencing problem one knows the pep-tide mass