Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.

中文翻译：

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从自下而上的 LC-MS 数据提高定量糖蛋白覆盖率的方法

质谱仪器、方法开发和生物信息学的进步极大地提高了位点特异性定量糖蛋白组学分析的简便性和准确性。数据相关采集是最流行的糖肽鉴定和定量方法；然而，这种方法仍然难以完全覆盖糖基化位点糖型。有针对性的采集方法提高了量化的精度和准确性，但以吞吐量和可发现性为代价。数据独立采集 (DIA) 为更完整和高度定量的位点特异性糖蛋白组学分析带来了巨大希望，同时保持在没有先验知识的情况下发现新型糖肽的能力。我们回顾了可用于提高 DIA 工作流程的选择性和覆盖率的其他功能：保留时间建模，这将简化复杂串联质谱的解释，以及离子淌度分离，这将在给定的色谱保留时间最大化所有前体的采样。将这些特征纳入糖蛋白组学分析的仪器和生物信息学已经存在。这些定量、定点分析的改进将使研究人员能够评估相关生物系统中糖基化的相似性，回答有关糖基化状态和生物功能之间相互作用的新问题。将这些特征纳入糖蛋白组学分析的仪器和生物信息学已经存在。这些定量、定点分析的改进将使研究人员能够评估相关生物系统中糖基化的相似性，回答有关糖基化状态和生物功能之间相互作用的新问题。将这些特征纳入糖蛋白组学分析的仪器和生物信息学已经存在。这些定量、定点分析的改进将使研究人员能够评估相关生物系统中糖基化的相似性，回答有关糖基化状态和生物功能之间相互作用的新问题。