Baker Margaret R, Ching Travers, Tabb David L, Li Qing X
Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, Cape Town, South Africa.
Methods Mol Biol. 2018;1789:205-220. doi: 10.1007/978-1-4939-7856-4_16.
plantGlycoMS is a set of tools, implemented in R, which is used to assess and validate glycopeptide spectrum matches (gPSMs). Validity of gPSMs is based on characteristic fragmentation patterns of glycopeptides (gPSMvalidator), adherence of the glycan moiety to the known N-glycan biosynthesis pathway in plants (pGlycoFilter), and elution of the glycopeptide within the observed retention time window of other glycopeptides sharing the same peptide backbone (rt.Restrict). plantGlycoMS also contains a tool for relative quantitation of glycoforms based on selected ion chromatograms of glycopeptide ion precursors in the mass spectrometry level 1 data (glycoRQ). This protocol walks the user through this workflow with example mass spectrometry data obtained for a plant glycoprotein.
plantGlycoMS是一组用R语言实现的工具，用于评估和验证糖肽谱匹配（gPSM）。gPSM的有效性基于糖肽的特征性裂解模式（gPSMvalidator）、聚糖部分与植物中已知的N-聚糖生物合成途径的一致性（pGlycoFilter）以及糖肽在与相同肽骨架的其他糖肽所观察到的保留时间窗口内的洗脱情况（rt.Restrict）。plantGlycoMS还包含一个基于质谱一级数据中糖肽离子前体的选择离子色谱图进行糖型相对定量的工具（glycoRQ）。本方案通过为一种植物糖蛋白获得的示例质谱数据，引导用户完成此工作流程。
