Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry

Abstract

Determining glycan structures is vital to comprehend cell-matrix, cell-cell, and even intracellular biological events. Glycan structure sequencing, which is to determine the primary structure of a glycan using MS/MS spectrometry, remains one of the most important tasks in proteomics. Analogous to the peptide de novo sequencing, the glycan de novo sequencing is to determine the structure without the aid of a known glycan database. We show in this paper that glycan de novo sequencing is NP-hard. We then provide a heuristic algorithm and develop a software program to solve the problem in practical cases. Experiments on real MS/MS data of glycopeptides demonstrate that our heuristic algorithm gives satisfactory results on practical data.