[Recent advances in glycopeptide enrichment and mass spectrometry data interpretation approaches for glycoproteomics analyses]

Glycosylation: mechanisms, biological functions and clinical implications

Protein post-translational modification (PTM) is a covalent process that occurs in proteins during or after translation through the addition or removal of one or more functional groups, and has a profound effect on protein function. Glycosylation is one of the most common PTMs, in which polysaccharides are transferred to specific amino acid residues in proteins by glycosyltransferases. A growing body of evidence suggests that glycosylation is essential for the unfolding of various functional activities in organisms, such as playing a key role in the regulation of protein function, cell adhesion and immune escape. Aberrant glycosylation is also closely associated with the development of various diseases. Abnormal glycosylation patterns are closely linked to the emergence of various health conditions, including cancer, inflammation, autoimmune disorders, and several other diseases. However, the underlying composition and structure of the glycosylated residues have not been determined. It is imperative to fully understand the internal structure and differential expression of glycosylation, and to incorporate advanced detection technologies to keep the knowledge advancing. Investigations on the clinical applications of glycosylation focused on sensitive and promising biomarkers, development of more effective small molecule targeted drugs and emerging vaccines. These studies provide a new area for novel therapeutic strategies based on glycosylation.

Identification and characterization of intact glycopeptides in human urine

Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of glycoproteins in human urine using LC-MS/MS-based intact glycopeptide analysis, providing both the identification of protein glycosites and characterization of the glycan composition at specific glycosites. Gene enrichment analysis reveals differences in biological processes, cellular components, and molecular functions in the urine glycoproteome versus the urine proteome, as well as differences based on the major glycan class observed on proteins. Meta-heterogeneity of glycosylation is examined on proteins to determine the variation in glycosylation across multiple sites of a given protein with specific examples of individual sites differing from the glycosylation trends in the overall protein. Taken together, this dataset represents a potentially valuable resource as a baseline characterization of glycoproteins in human urine for future urine glycoproteomics studies.

Hydrophilic Interaction Liquid Chromatography (HILIC) Enrichment of Glycopeptides Using PolyHYDROXYETHYL A

Glycosylation of proteins is an important post-translational modification that plays a role in a wide range of biological processes, including immune response, intercellular signaling, inflammation, and host-pathogen interaction. Abnormal protein glycosylation has been correlated with various diseases. However, the study of protein glycosylation remains challenging due to its low abundance, microheterogeneity of glycosylation sites, and low ionization efficiency. During the past decade, several methods for enrichment and for isolation of glycopeptides from biological samples have been developed and successfully employed in glycoproteomics research. In this chapter, we discuss the sample preparation protocol and the strategies for effectively isolating and enriching glycopeptides from biological samples, using PolyHYDROXYETHYL A as a hydrophilic interaction liquid chromatography (HILIC) enrichment technique.

Comprehensive Overview the Role of Glycosylation of Extracellular Vesicles in Cancers

Extracellular vesicles (EVs) are membranous structures secreted by various cells carrying diverse biomolecules. Recent advancements in EV glycosylation research have underscored their crucial role in cancer. This review provides a global overview of EV glycosylation research, covering aspects such as specialized techniques for isolating and characterizing EV glycosylation, advances on how glycosylation affects the biogenesis and uptake of EVs, and the involvement of EV glycosylation in intracellular protein expression, cellular metastasis, intercellular interactions, and potential applications in immunotherapy. Furthermore, through an extensive literature review, we explore recent advances in EV glycosylation research in the context of cancer, with a focus on lung, colorectal, liver, pancreatic, breast, ovarian, prostate, and melanoma cancers. The primary objective of this review is to provide a comprehensive update for researchers, whether they are seasoned experts in the field of EVs or newcomers, aiding them in exploring new avenues and gaining a deeper understanding of EV glycosylation mechanisms. This heightened comprehension not only enhances researchers' knowledge of the pathogenic mechanisms of EV glycosylation but also paves the way for innovative cancer diagnostic and therapeutic strategies.

Improved analysis ZIC-HILIC-HCD-Orbitrap method for mapping the glycopeptide by mass spectrometry

Glycosylation is one of the most common post-translational modifications (PTMs). Protein glycosylation analysis is the bottleneck to deeply understand their functions. At present, the LC-MS analysis of glycosylated post-translational modification is mainly focused on the analysis of glycopeptides. However, the factors affecting the identification of glycopeptides were not fully elucidated. In the paper, we have carefully studied the factors, e.g., HILIC materials, search engines, protein amount, gradient duration, extraction solution, etc. According to the results, HILIC materials were the most important factors affecting the glycopeptides identification, and the amphoteric sulfoalkyl betaine stationary phase enriched glycopeptides 6-fold more compared to the amphiphilic ion-bonded fully porous spherical silica stationary phase. We explored the influence of the extraction solutions on glycan identification. Comparing sodium dodecyl sulfate (SDS) and urea (UA), the results showed that N-glycolylneuraminic acid (NeuGc) type of glycan content was found to be increased 1.4-fold in the SDS compared to UA. Besides, we explored the influence of the search engine on glycopeptide identification. Comparing pGlyco3.0 and MSFragger-Glyco, it was observed that pGlyco3.0 outperformed MSFragger-Glyco in identifying glycopeptides. Then, using our optimized method we found that there was a significant difference in the distribution of monosaccharide types in plasma and brain tissue, e.g., the content of NeuAc in brain was 5-fold higher than that in plasma. To importantly, two glycoproteins (Neurexin-2 and SUN domain-containing protein 2) were also found for the first time by our method. In summary, we have comprehensively studied the factors influencing glycopeptide identification than any previous research, and the optimized method could be widely used for identifying the glycoproteins or glycolpeptides biomarkers for disease detection and therapeutic targets.

[Application of smart responsive materials in phosphopeptide and glycopeptide enrichment]

Phosphorylation and glycosylation of proteins, two of the most widely studied post-translational modifications (PTMs), have shown increasing potential in the early non-invasive diagnosis, prognosis, and therapeutic evaluation of diseases. Besides regulating the function of cell membranes and intracellular signal transduction, protein phosphorylation participates in mitochondrial function and cellular and transcriptional metabolism. Protein glycosylation plays an important role in both intracellular and extracellular signal transduction and intracellular endocytosis. Aberrant phosphorylation and glycosylation of proteins are frequently observed in clinical proteomic studies and in the discovery of disease-related biomarkers. There are generally three methods for detecting protein phosphorylation/glycosylation: isotope radiolabeling, western blotting, and mass spectrometry. Mass spectrometry has become the most important and advantageous detection method due to its high throughput and time- and labor-efficiency. However, phosphopeptides and glycopeptides have low stoichiometry and ionization efficiency, and a large number of non-phosphopeptides and -glycopeptides interference. These issues make it difficult to directly detect phosphopeptides and glycopeptides by mass spectrometry. Therefore, the enrichment of phosphopeptides and glycopeptides before mass spectrometry detection is a key step. At present, a variety of materials have been developed for enrichment studies of phosphopeptides and glycopeptides. For example, immobilized metal affinity (IMAC) and metal oxide affinity chromatography (MOAC) methods are mostly used for the enrichment of phosphopeptides. The IMAC mainly uses positively charged metal ions and negatively charged phosphate groups to attract each other for the purpose of enriching phosphopeptides. MOAC materials rely on the chelation of metal atoms and phosphate oxygens to capture phosphopeptides. IMAC and MOAC materials rely on strong interactions between metals and phosphate groups, which often lead to difficult elution. The enrichment method for glycopeptides is mainly based on the difference in hydrophilicity between glycopeptides and non-glycopeptides, which are mainly enriched by hydrophilic interaction chromatography (HILIC). In addition, materials containing compounds such as boronic acid and lectin materials are also widely used for the separation and enrichment of glycopeptides. Smart responsive materials have also been successively reported for the enrichment of phosphopeptides and glycopeptides due to their unique responsiveness and reversibility. Smart responsive materials can respond to external stimuli; undergo structural and property changes; and convert signals such as optical, electrical, thermal, and mechanical into biochemical signals. Responsive molecules are a prerequisite for determining the response properties of smart responsive materials, and their reversible isomerization under different stimuli (such as temperature, pH, light, mechanical stress, and electromagnetic field) will lead to dynamic changes in the physical and chemical properties of materials. Compared with traditional materials, smart responsive materials can be reversibly "turned on" and "off" with better controllability. Exogenous stimuli, including temperature, light, ultrasound, electromagnetic field, and mechanical stress, can be implemented in a specific time and space. Exogenous responsive materials do not depend on changes in the reaction system itself and are non-invasive. Enzymes, pH, redox, solution polarity, and ionic strength are endogenous stimuli. Endogenous responsive materials depend on changes in the reaction system itself, and sometimes the regulation process requires the introduction of other chemicals into the reaction system. The identification, capture, and release of phosphopeptides or glycopeptides can be achieved by modulating the interactions between smart responsive materials and phosphopeptides or glycopeptides (such as hydrogen bonds, and electrostatic and hydrophobic interactions). This review classifies smart responsive materials according to the types of stimuli, which are specifically divided into exogenous and endogenous responsive materials. The enrichment of phosphopeptides and glycopeptides of exogenous/endogenous responsive materials and endogenous/exogenous co-responsive materials are summarized. In addition, we discuss the development prospects of smart responsive materials in the enrichment of phosphopeptides and glycopeptides, and also raised the challenges existing in the application of smart responsive materials in other protein post-translational modifications.