An effective algorithm for peptide de novo sequencing from MS/MS spectra

The determination of the amino acid sequence of a peptide from its MS/MS spectrum is an important task in proteomics. The determination without the help of a protein database is called the de novo sequencing, which is especially useful in the identification of unknown proteins. Many studies on the de novo sequencing problem have been done. In this paper, we define a new model for this problem, and provide a sophisticated dynamic programming algorithm to solve it. Experiments on real MS/MS data demonstrated that the algorithm works superior to other methods on QTof MS/MS data.