De novo glycan structural identification from mass spectra using tree merging strategy

doi:10.1016/j.compbiolchem.2019.03.015

	De novo glycan structural identification from mass spectra using tree merging strategy
	Ju, Fusong 1,3; Zhang, Jingwei 1,3; Bu, Dongbo 1,3; Li, Yan 2,3; Zhou, Jinyu 2,3; Wang, Hui 1,3; Wang, Yaojun 1,3; Huang, Chuncui 2,3; Sun, Shiwei 1,3
	2019-06-01
发表期刊	COMPUTATIONAL BIOLOGY AND CHEMISTRY
ISSN	1476-9271
卷号	80 页码:217-224
摘要	Motivation: Glycans are large molecules with specific tree structures. Glycans play important roles in a great variety of biological processes. These roles are primarily determined by the fine details of their structures, making glycan structural identification highly desirable. Mass spectrometry (MS) has become the major technology for elucidation of glycan structures. Most de novo approaches to glycan structural identification from mass spectra fall into three categories: enumerating followed by filtering approaches, heuristic and dynamic programming-based approaches. The former suffers from its low efficiency while the latter two suffer from the possibility of missing the actual glycan structures. Thus, how to reliably and efficiently identify glycan structures from mass spectra still remains challenging. Results: In this study we propose an efficient and reliable approach to glycan structure identification using tree merging strategy. Briefly, for each MS peak, our approach first calculated monosaccharide composition of its corresponding fragment ion, and then built a constraint that forces these monosaccharides to be directly connected in the underlying glycan tree structure. According to these connecting constraints, we next merged constituting monosaccharides of the glycan into a complete structure step by step. During this process, the intermediate structures were represented as subtrees, which were merged iteratively until a complete tree structure was generated. Finally the generated complete structures were ranked according to their compatibility to the input mass spectra. Unlike the traditional enumerating followed by filtering strategy, our approach performed deisomorphism to remove isomorphic subtrees, and ruled out invalid structures that violates the connection constraints at each tree merging step, thus significantly increasing efficiency. In addition, all complete structures satisfying the connection constraints were enumerated without any missing structure. Over a test set of 10 N-glycan standards, our approach accomplished structural identification in minutes and gave the manually-validated structure first three highest score. We further successfully applied our approach to profiling and subsequent structure assignment of glycans released from glycoprotein mAb, which was in perfect agreement with previous studies and CE analysis.
DOI	10.1016/j.compbiolchem.2019.03.015
收录类别	SCI
语种	英语
资助项目	National High-Tech Research and Development Project[2014AA021101] ; National Natural Science Foundation of China[31600650] ; National Natural Science Foundation of China[31671369] ; National Natural Science Foundation of China[31770775] ; National Key Research and Development program of China[FC2018YFC0910405]
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Computer Science
WOS类目	Biology ; Computer Science, Interdisciplinary Applications
WOS记录号	WOS:000474314000024
出版者	ELSEVIER SCI LTD
引用统计	被引频次：6[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4324
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Huang, Chuncui; Sun, Shiwei
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Beijing 100101, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Ju, Fusong,Zhang, Jingwei,Bu, Dongbo,et al. De novo glycan structural identification from mass spectra using tree merging strategy[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2019,80:217-224.
APA	Ju, Fusong.,Zhang, Jingwei.,Bu, Dongbo.,Li, Yan.,Zhou, Jinyu.,...&Sun, Shiwei.(2019).De novo glycan structural identification from mass spectra using tree merging strategy.COMPUTATIONAL BIOLOGY AND CHEMISTRY,80,217-224.
MLA	Ju, Fusong,et al."De novo glycan structural identification from mass spectra using tree merging strategy".COMPUTATIONAL BIOLOGY AND CHEMISTRY 80(2019):217-224.