Reviews & Perspectives
Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis
In Brief This article provides a systematic review of the most recent MS-based strategies and corresponding software tools for the analysis of intact glycopeptides, particularly intact N-glycopeptides, reported in the last decade, including 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.Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation
In Brief Recent years have seen an explosion in novel strategies for quantitative glycomics and glycoproteomics. Whether through metabolic incorporation of stable isotopes, deposition of custom isotopic labels, or high-throughput isobaric chemical tags, these numerous novel strategies provide ease of access to glycomic and glycoproteomic investigation. This review highlights the recent innovations in labeling methods, label-free strategies, acquisition modes, and bioinformatic tools for glycan and glycopeptide quantitation, while providing critical evaluations and technical considerations to enable effective analysis.The Role of Data-Independent Acquisition for Glycoproteomics
In Brief As a highly abundant and diverse post-translational modification, protein glycosylation is challenging to characterize in various approaches including MS. In MS-based proteomics, data-independent acquisition (DIA) has been advanced rapidly and showed outstanding analytical performances. DIA now started to be applied in different facets of glycoproteomics, including deglycosylated and intact N-linked and O-linked glycopeptides, and screening of oxonium ions. We summarized current applications of DIA in glycoproteomics and discussed its limitations and perspectives.Calculating Glycoprotein Similarities From Mass Spectrometric Data
In Brief To understand the roles of glycoproteins in biological processes, it is necessary to quantify the changes that occur to glycosylation at individual sites and to the whole molecule. That glycoprotein glycosylation is inherently heterogeneous means that the distribution of glycoforms at each glycosite must be quantified in order to inform calculation of molecular similarities. We review analytical and statistical methods for determining glycoprotein molecular similarities from glycoproteomics data.Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review
In Brief Glycosaminoglycans (GAGs) participate in a variety of biological functions and have a multitude of medicinal properties. Due to their non template driven biosynthesis, GAGs are produced as nonuniform complex mixtures. Mass spectrometry paired with on-line separation techniques has been utilized to determine the composition of these complex mixtures. Advances in tandem mass spectrometry have also made determining sequence information such as sulfation location and C-5 epimerization possible. This review covers recent developments in the analysis of GAGs using mass spectrometry.Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites
In Brief This review article summarizes methods for O-GlcNAc enrichment and different mass spectrometric approaches for acquiring data on modified peptides and describes software strategies for analyzing data, including the challenges of reliably identifying modification sites and differentiating between other potential HexNAc modifications. It then presents a new dataset to exemplify what is currently achievable.A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics
In Brief Interest in mass spectrometry–based glycoproteomics analysis is increasing because of recent advances in instrumentation and data analysis tools. Such studies can provide a wealth of information across a wide spectrum of glycan classes and biological systems. However, many studies require the choice of an enrichment strategy for glycosylated species prior to analysis to obtain the maximum amount of analytical information. Here, common enrichment strategies are reviewed with strengths and weaknesses, and the practical considerations for various methods are discussed.Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein
In Brief Diversity in protein glycosylation can be described in terms of micro-heterogeneity and macro-heterogeneity, respectively, referring to the variation and occupancy of glycans at a given glycosylation site. However, these terms are not sufficient to describe a higher level of regulation when proteins are multiply glycosylated. For this, we propose the term meta-heterogeneity: variation in glycosylation across multiple sites of a given glycoprotein. In this review, we describe several remarkable examples of glycoprotein meta-heterogeneity and underline the need for its investigation.Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches
In Brief Histone post-translational modifications play essential roles in the epigenetic regulation of chromatin-related functions. Because of its high throughput, accuracy, and flexibility, mass spectrometry has emerged as a powerful tool in the epigenetic field. In this review, we describe the contributions of mass spectrometry–based proteomics in combination with distinct labeling strategies and various biological techniques to understand the roles of histone post-translational modifications and how they regulate chromatin function.
