Abstract
Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.
Highlights
Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism
Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies
Hybrid dissociation techniques developed for an Orbitrap Fusion mass spectrometer, such as electron-transfer/collisioninduced dissociation [30, 31], electron-transfer/higher-energy collision dissociation [29, 32, 33], and activated ion electron transfer dissociation [34, 35], where a supplementary energy source is applied to all fragment ions formed by electron-transfer dissociation (ETD), have shown great potential in N-glycopeptide identification [11, 35,36,37,38,39]
Summary
In Brief This article provides a systematic review of the most recent MSbased strategies and corresponding software tools for the analysis of intact glycopeptides, intact N-glycopeptides, reported in the last decade, including the process of identifying Nglycopeptides from MS data, the existing methods of MS data acquisition and interpretation, the quality control methods, the display of results, and the software applications. This review will specify the most recent MS-based strategies and corresponding software tools for the analysis of intact glycopeptides, intact Nglycopeptides, reported in the last decade, while reviewing the process of identifying N-glycopeptides from MS data, the existing methods of MS data acquisition and interpretation, the quality control methods, the display of results, and the software applications (Table 1)
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