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

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Abstract

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.

Keywords

De novo sequencing
MS/MS
Mass spectrometry

Cited by (0)

A preliminary version of this paper appeared in the Proceedings of CPM’03.

1

Supported by NSERC research Grant RGP0238748.

2

Supported by NSERC research Grant OGP0046373 and a SharcNet research fellowship.

3

Supported by Bioinformatics Solutions Inc.