Reviews & Perspectives
The Role of Data-Independent Acquisition for GlycoproteomicsIn 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 DataIn 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.
A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based GlycoproteomicsIn 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.
Proteomics, Glycomics, and Glycoproteomics of Matrisome MoleculesExtracellular networks of matrisome proteins and their binding partners give rise to dynamic cell and tissue-specific microenvironments. The extreme complexity of matrisome molecule glycosylation and other post-translational modifications belies the need for specialized omics methods. It is necessary to map the modifications of matrisome molecules in detail in order to understand their roles in normal and pathological physiology. We review proteomics, glycomics and glycoproteomics methods for matrisome molecules toward the goal of achieving detailed matrisome maps.