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Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody‐based agents targeting CD22 or CD20 on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high‐affinity and specific CD22 ligands onto NK‐92MI and cytokine‐induced natural killer cells to achieve tumor‐specific CD22 targeting. These CD22‐ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo, we further functionalized CD22 ligand‐modified NK‐92MI cells with the E‐selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The dual‐functionalized cells resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that natural killer cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively. [ABSTRACT FROM AUTHOR]

PNGase F-catalyzed glycosylation site 18O-labeling is a widely used method for glycoprotein quantitation owing to its efficiency and simplicity. However, PNGase F-catalyzed glycan 18O-labeling, which offers advantages for glycomics, has not yet been developed. In this study, PNGase F-mediated incorporation of 18O into glycans during the N-glycan release from glycoproteins by PNGase F was finally realized, named as PCGOL (PNGase F-catalyzed glycan 18O-labeling), which offers a potential strategy for relative glycan quantitation. This new method showed good linearity and high reproducibility within at least 2 orders of magnitude in the dynamic range. Furthermore, PCGOL combined with our previously developed TOSIL method (tandem 18O stable isotope labeling for N-glycoproteome quantitation) can be used for comprehensive N-glycosylation quantification, achieving simultaneous quantification of glycans, glycopeptides and glycoproteins in a single workflow, which was also used to analyze glycosylation changes in immunoglobulin G (IgG) associated with hepatocellular carcinoma in the present work. [ABSTRACT FROM AUTHOR]

The influence of calcium-deficiency and cerium addition on the antioxidative defense system in spinach leaves was investigated. It was found that spinach cultivated in calcium-deficiency media developed distinct calcium deficiency symptoms and the plant growth was significantly inhibited as expected. While cerium-treated spinach remained green and expanded, and plant growth was improved. Calcium deprivation in spinach also increased the permeability of plasma membrane, malondialdehyde as a degradation product of lipid peroxidation, reactive oxygen species such as superoxide radicals, hydrogen peoxide, and decreased activities of the antioxidant enzymes such as superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase and glutathione content. However, cerium treatment cultivated in calcium-deficiency media decreased the permeability of plasma membrane, malondialdehyde and reactive oxygen species, and increased activities of the antioxidative defense system. This is viewed as evidence for cerium addition to calcium-deficiency media in the spinach plants could substitute calcium and enhance oxidative stress-resistance. [ABSTRACT FROM AUTHOR]

Abstract  Chloroplasts were isolated from spinach cultured in calcium-deficient, cerium-chloride-administered calcium-present Hoagland’s media or that of calcium-deficient Hoagland’s media and demonstrated the effects of cerium on distribution of light energy between photosystems II and I and photochemical activities of spinach chloroplast grown in calcium-deficient media. It was observed that calcium deprivation significantly inhibited light absorption, energy transfer from LHCII to photosystemII, excitation energy distribution from PSI to PSII, and transformation from light energy to electron energy and oxygen evolution of chloroplasts. However, cerium treatment to calcium-deficient chloroplasts could obviously improve light absorption and excitation energy distribution from photosystem I to photosystem II and increase activity of whole chain electron transport, photosystems II and I DCPIP photoreduction, and oxygen evolution of chloroplasts. The results suggested that cerium under calcium deficiency condition could substitute for calcium in chloroplasts, maintain the stability of chloroplast membrane, and improve photosynthesis of spinach chloroplast, but the mechanisms still need further study. [ABSTRACT FROM AUTHOR]

Abstract  The main aim of the study was to determine the role of cerium in the amelioration of calcium-deficiency effects in spinach plants. Spinach plants were cultivated in Hoagland’s solution. They were subjected to calcium-deficiency and to cerium chloride administered in the calcium-present Hoagland’s media and calcium-deficient Hoagland’s media. Within 3weeks, young leaves developed distinct calcium-deficient symptoms, and plant growth significantly inhibited to calcium deprivation as would be expected; cerium-treated groups grown in the same conditions did not develop calcium-deficient symptoms; fresh weight, dry weight and chlorophyll content of spinach plants were increased by 35.9, 45 and 64.05% compared to those of plants cultivated in calcium-deficient media. In addition, calcium deprivation in spinach plants caused the reduction of photosynthetic rate, oxygen evolution rate and ribulose-1,5-bisphosphate carboxylase/oxygenase activity. The reduction of activities of nitrate reductase, glutamate dehydrogenase, glutamate synthase and glutamic-pyruvic transaminase was observed under calcium-deficient media. However, cerium treatment under calcium-deficient media could significantly improve photosynthesis and nitrogen metabolism of spinach plants. This is viewed as evidence that cerium added to calcium-deficient media in the spinach plants could substitute for calcium and improve spinach growth. [ABSTRACT FROM AUTHOR]

Glycoproteome analysis at a site-specific level and proteome scale stands out as a highly promising approach for gaining insights into the intricate roles of glycans in biological systems. Recent years have witnessed an upsurge in the development of innovative methodologies tailored for precisely this purpose. Breakthroughs in mass spectrometry-based glycoproteomic techniques, enabling the identification, quantification, and systematic exploration of site-specific glycans, have significantly enhanced our capacity to comprehensively and thoroughly characterize glycoproteins. In this short review, we delve into novel tools in advancing site-specific glycoproteomic analysis and summarize pertinent studies published in the past two years. Lastly, we discuss the ongoing challenges and outline future prospects in the field, considering both the analytical strategies of mass spectrometry and the tools employed for data interpretation., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Weiqian Cao reports financial support and article publishing charges were provided by National Natural Science Foundation of China. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced natural killer cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo, we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The dual-functionalized cells resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that natural killer cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively., (© 2020 Wiley-VCH GmbH.)

PNGase F-catalyzed glycosylation site (18)O-labeling is a widely used method for glycoprotein quantitation owing to its efficiency and simplicity. However, PNGase F-catalyzed glycan (18)O-labeling, which offers advantages for glycomics, has not yet been developed. In this study, PNGase F-mediated incorporation of (18)O into glycans during the N-glycan release from glycoproteins by PNGase F was finally realized, named as PCGOL (PNGase F-catalyzed glycan (18)O-labeling), which offers a potential strategy for relative glycan quantitation. This new method showed good linearity and high reproducibility within at least 2 orders of magnitude in the dynamic range. Furthermore, PCGOL combined with our previously developed TOSIL method (tandem (18)O stable isotope labeling for N-glycoproteome quantitation) can be used for comprehensive N-glycosylation quantification, achieving simultaneous quantification of glycans, glycopeptides and glycoproteins in a single workflow, which was also used to analyze glycosylation changes in immunoglobulin G (IgG) associated with hepatocellular carcinoma in the present work.