A new parameterized algorithm for rapid peptide sequencing

De novo sequencing is an important computational approach to determining the amino acid sequence of a peptide with tandem mass spectrometry (MS/MS). Most of the existing approaches use a graph model to describe a spectrum and the sequencing is performed by computing the longest antisymmetric path in the graph. The task is often computationally intensive since a given MS/MS spectrum often contains noisy data, missing mass peaks, or post translational modifications/mutations. This paper develops a new parameterized algorithm that can efficiently compute the longest antisymmetric partial path in an extended spectrum graph that is of bounded path width. Our testing results show that this algorithm can efficiently process experimental spectra and provide sequencing results of high accuracy.