key: cord-0756167-ni4drbe1 authors: Hart, Gerald W.; Wells, Lance title: Glycoproteomics: Making the Study of the Most Structurally Diverse and Most Abundant Post-Translational Modifications More Accessible to the Scientific Community date: 2021-06-03 journal: Mol Cell Proteomics DOI: 10.1016/j.mcpro.2021.100086 sha: 9a5518953b836913cf6132e29dc848168d20e01a doc_id: 756167 cord_uid: ni4drbe1 nan In 2013, we served as guest editors for the Glycomics special issue where the Athens guidelines for glycomic analyses were first revealed that have since been adopted by multiple journals (1) . At that moment in time, we could not have easily conceived of a special issue dedicated to glycoproteomics. However, just 8 years later, we find ourselves presenting a special issue of Molecular & Cellular Proteomics on Glycoproteomics that introduces the reader to the recent explosion in front-end enrichment methods, analytical approaches, and back-end software solutions dedicated to glycoproteomics. This special issue includes nine review articles and nine research articles that introduce the reader to the exciting, challenging, and rapidly evolving field of glycoproteomics, which is so highly dependent on MS. Glycoproteomics has been front and center this past year as scientists tackled the COVID-19 pandemic, given that the spike glycoprotein of SARS-CoV-2, which is often the basis for antibody and vaccine therapeutics, is a trimer glycoprotein consisting of 66 occupied N-linked glycosylation sites, and that the host receptor, ACE2, is also heavily glycosylated (2, 3). Thus, an issue devoted to understanding this heterogenous class of post-translational modifications seems very timely. The number of various glycan moieties that can modify proteins easily surpasses the sum of all other post-translational modifications combined, and the majority of all expressed mammalian proteins (secreted, membrane bound, and intracellular) are glycosylated (4). Thus, it is essential to be able to characterize these challenging biomolecules to better understand the fundamental roles that glycoconjugates play in nearly all aspects of physiology and pathophysiology. A review by West et al. (5) gives us an intertaxa evolutionary perspective on glycomics, glycoproteomics, and glycogenomics. Riley et al. (18), discuss recent advances in data analysis for glycans, intact glycopeptides, and quantification methods. The reviews by Caval et al. (19) , and by Hackett and Zaia (20) , tackle the challenging problem of describing the inherent heterogeneity of glycoproteins and in calculating the similarities between glycoproteins. Finally, Roushan et al. (21) illustrate the power of tools of multiple data analyses for glycoproteomics. In this special issue, we have attempted to capture many of the recent developments in enrichment and labeling strategies, MS-based interrogation approaches, and data analysis platforms for glycoproteins that have evolved over the last decade. Although multiple challenges still exist, the existing and continuing technological advancements in glycoproteomics are making the study of glycoproteins more amenable to the scientific community at large. of excellence in glycoproteomics. This work was supported in part by grants from the NIH (R01DK124366 (G. W. H.), R01GM116891 (G. W. H. and L. W.), U01CA233581 (L. W.), R01GM130915 (L. W.), and R01GM111939 (L. W.)). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Conflict of interest -The authors declare no competing interests. Glycomics: Building upon proteomics to advance glycosciences Site-specific glycan analysis of the SARS-CoV-2 spike Virusreceptor interactions of glycosylated SARS-CoV-2 spike and human ACE2 receptor Essentials of Glycobiology Glycomics, glycoproteomics, and glycogenomics: An inter-taxa evolutionary perspective A pragmatic guide to enrichment strategies for mass spectrometry-based glycoproteomics Methods for enrichment and assignment of N-acetylglucosamine modification sites Separation and identification of permethylated glycan isomers by reversed phase NanoLC-NSI-MS(n) Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development Imaging mass spectrometry and lectin analysis of N-linked glycans in carbohydrate antigen-defined pancreatic cancer tissues In-depth sitespecific analysis of N-glycoproteome in human cerebrospinal fluid (CSF) and glycosylation landscape changes Quantitative proteomics reveals that the OGT interactome is remodeled in response to oxidative stress The role of data-independent acquisition for glycoproteomics Quantitative data-independent acquisition glycoproteomics of sparkling wine Developments in mass spectrometry for glycosaminoglycan analysis: A review Domain mapping of chondroitin/dermatan sulfate glycosaminoglycans enables structural characterization of proteoglycans Recent advances in software tools for more generic and precise intact glycopeptide analysis Recent advances in analytical approaches for glycan and glycopeptide quantitation Meta-heterogeneity: Evaluating and describing the diversity in glycosylation between sites on the same glycoprotein Calculating glycoprotein similarities from mass spectrometric data 2021) Peak filtering, peak annotation, and wildcard search for glycoproteomics