1. Bioinformatics of glycosaminoglycans
- Author
-
Yu Huang, Yang Mao, Joseph Zaia, Han Hu, and Cheng Lin
- Subjects
0301 basic medicine ,Tandem mass spectrometry ,Cell ,Heparan sulfate ,Bioinformatics ,01 natural sciences ,Glycosaminoglycan ,03 medical and health sciences ,chemistry.chemical_compound ,Electron transfer dissociation ,Growth factor receptor ,medicine ,lcsh:Science ,lcsh:Science (General) ,Divide-and-conquer ,Chemistry ,010401 analytical chemistry ,0104 chemical sciences ,Electron-transfer dissociation ,030104 developmental biology ,medicine.anatomical_structure ,Sulfated polysaccharides ,lcsh:Q ,Signalling pathways ,lcsh:Q1-390 - Abstract
Summary Cell surface heparan sulfates modulate many signalling pathways by binding growth factors and growth factor receptors. Expressed in a spatially and temporally regulated manner, these highly sulfated polysaccharides play important roles in all aspects of animal physiology. To understand heparan sulfate-protein binding, it is necessary to develop instrumental sequencing methods. Towards this end, we and others have demonstrated the effectiveness of activated electron dissociation (ExD) tandem mass spectrometry. The value in the ExD approach is that extremely rich tandem mass spectra are produced. The challenge is that bioinformatics methods are needed to convert the raw data into HS saccharide sequences. In this article we describe HS–SEQ, an algorithm developed for this purpose.
- Published
- 2017