Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP

作     者：Jiechen Shen Zexuan Chen Shisheng Sun Jiechen Shen;Zexuan Chen;Shisheng Sun

作者机构：College of Life Sciences Northwest University 

出 版 物：《Biophysics Reports》 (生物物理学报)

年 卷 期：2022年第8卷第Z1期

页      面：282-300页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 07[理学] 

基　　金：supported by the National Key Research and Development Program of China(2019YFA09005200) the National Natural Science Foundation of China (91853123, 81773180) 

主　　题：Protein glycosylation Glycoproteomics Mass spectrometry StrucGP Glycan structure 

摘      要：Protein glycosylation is of great importance in many biological processes. Glycosylation has been increasingly analyzed at the intact glycopeptide level using mass spectrometry to study site-specific glycosylation changes under different physiological and pathological conditions. StrucGP is a glycan database-independent search engine for the structural interpretation of N-glycoproteins at the site-specific level. To ensure the accuracy of results, two collision energies are implemented in instrument settings for each precursor to separate fragments of peptides and glycans. In addition, the false discovery rates(FDR) of peptides and glycans as well as probabilities of detailed structures are estimated. In this protocol, the use of StrucGP is demonstrated, including environment configuration,data preprocessing as well as result inspection and visualization using our in-house software“GlycoVisualTool . The described workflow should be able to be performed by anyone with basic proteomic knowledge.