Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural- and Site-specific N-glycosylation Characterization of COVID-19 Virus Spike with StrucGP

ABSTRACT: Spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycans compositions of S protein. Here, we further provide structure-clear N-glycosylation of S protein at site-specific level by using our recently developed structure- and site-specific N-glycoproteomics sequencing algorithm StrucGP. In addition to the common N-glycans as detected in previous studies, many uncommon glycosylation structures such as LacdiNAc structures, Lewis structures, Mannose 6-Phosphate (M6P) residues and bisected core structures were unambiguously mapped at a total of 20 glycosites in the S protein trimer and protomer. These data further supports the glycosylation structural-functional investigations of COVID-19 virus Spike.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Early Embryonic Cell

DISEASE(S): Influenza

SUBMITTER: Bojing Zhu

LAB HEAD: Shisheng Sun

PROVIDER: PXD034086 | Pride | 2022-10-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Structural- and Site-Specific N-Glycosylation Characterization of COVID-19 Virus Spike with StrucGP.

Zhu Bojing B Chen Zexuan Z Shen Jiechen J Xu Yintai Y Lan Rongxia R Sun Shisheng S

Analytical chemistry 20220829 36

The spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycan compositions as well as many important structural motifs of the S protein. Here, we further provide structural-clear N-glycosylation of the S protein at a site-specific level by using our recently developed structural- and site-specific N-glycoproteomics sequencing algorithm, StrucGP. In addition to the common N-gly ...[more]

PMID: 36036581

Similar Datasets

Precision Characterization of Site-specific O-Acetylated Sialic Acids on N-Glycoproteins

Project description:O-Acetylation is a common modification of sialic acid, playing a significant role in glycoprotein stability, immune response, and cell development. The lack of efficient methods for direct analysis of O-acetylated sialoglycopeptides (O-AcSGPs) made the majority of identified O-acetylated sialic acids (O-AcSia) till now had no glycosite/glycoprotein information. Herein, we introduced a new workflow for precise interpretation of O-AcSGPs with probability estimation by recognizing the characteristic B and Y ions of O-AcSias.

2023-01-13 | PXD037161 | Pride

Profiling of human spermatozoa glycoproteins by LC/MS/MS

Project description:N-linked glycoproteins are known to be important for spermatozoa development and gametes fusion. However, little is known about detailed information of these glycoproteins, particularly the glycosylation sites and its corresponding glycan structures in human spermatozoa. In present study, an in house software coupled with LC-MS/MS analysis of intact glycopeptides was employed to establish a large scale of site-specific N-glycoproteome map in human spermatozoa. The results mapped the large-scale N-glycoproteins in human spermatozoa and interpreted the precise glycan structures with the corresponding glycosites. These presented data laid the foundation for the exploration of biological function of glycosylation on human spermatozoa and glycan structure involved male infertility.

2023-03-04 | PXD020286 | Pride

A hinge glycan regulates spike bending and impacts coronavirus infectivity

Project description:Analysis of the structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectroscopy

2024-01-26 | PXD039247 | Pride

Hydrophobic-hydration hydrophilic interaction (H3I) capturing intact glycopeptides

Project description:H3I was adopted to idetify the glycosylation of bovine fetuin, human ACE2 and SARS-CoV-2 S1 proteins. Both N- and O-linked glycopeptides are successfully captured with significant enrichment rate improvements, especially for O-glycopeptides with relatively lower hydrophilicity. The majority of N- and O-glycosylation within SARS-CoV-2 S1 and hACE2 proteins are characterized simultaneously by H3I strategy, including 10 novel O-glycosylation regions with important functions in viral fusion and antibody evasion.

2023-04-06 | PXD033779 | Pride

Glycoproteomics of human THP-1-derived M0, M1 and M2 macrophages

Project description:In this study, we used human THP-1-derived macrophages as an immune cell model, and systematically performed glycoproteomics of three subtypes of macrophages by StrucGP.To study the N‑Glycoproteomic of them, the intact glycopeptides were first enriched and identified using triplicate mass spectrometry (MS)-based glycoproteomic approaches, then StrucGP was used for subsequent analysis. In total three subtypes of macrophages, these intact glycopeptides consist of 253 N-linked glycan structures at 652 unique glycosites from 372 N-glycoproteins, along with their PSM information. A total of 135, 163, and 201 N-glycan structures were identified from M0, M1, and M2 macrophages, respectively.

2023-10-19 | PXD030277 | Pride

Structural Interpretation of Glycosite-specific N-Glycans Using Tandem Mass Spectrometry

Project description:In this project we developed a new algorithm termed StrucGP, for large-scale interpretation of N-glycan structures on intact glycopeptides from tandem mass spectrometry data. StrucGP is able to reveal the glycan structure heterogeneity for individual glycosites. The StrucGP also has high performance in distinguishing various structure isoforms and identifying new and rare glycan structures from complex samples.

2021-07-07 | PXD025859 | Pride

Re-analysis of glycoproteomics data with Glyco-Decipher

Project description:Reanalysis of submissions PXD005411, PXD005413, PXD005412, PXD005553, PXD005555, PXD005565 and PXD019937 using Glyco-Decipher. Identification results of peptide-spectrum matches supporting Glyco-Decipher manuscript (Glyco-Decipher: glycan database-independent peptide matching enables discovery of new glycans and in-depth characterization of site-specific N-glycosylation). Recently, several elegant bioinformatics tools have been developed to identify glycopeptides from tandem mass spectra for site-specific glycoproteomics studies. These glycan database-dependent tools have substantially improved glycoproteomics analysis but fail to identify glycopeptides with unexpected glycans. We present a platform called Glyco-Decipher to interpret the glycoproteomics data of N-linked glycopeptides. It adopts a glycan database-independent peptide matching scheme that allows the unbiased profiling of glycans and the discovery of new glycans linked with modifications. Reanalysis of several large-scale datasets showed that Glyco-Decipher outperformed the open search method in glycan blind searching and the popular glycan database-dependent software tools in glycopeptide identification. Our glycan database-independent search also revealed that modified glycans are responsible for a large fraction of unassigned glycopeptide spectra in shotgun glycoproteomics.

2022-03-04 | PXD031032 | Pride

Origin of N-glycan site-specific heterogeneity glycopeptide analysis by LC-MSMS

Project description:LC-MS/MS analysis of glycopeptides of protein disulfide-isomerase (PDI1), etanercept, erythropoietin (EPO), low affinity immunoglobulin gamma Fc region receptor III-A (FCGR3A), and spike glycoprotein (S) from wild type and Lec1 (GnT1-/-) HEK293 cells

2022-10-14 | PXD032149 | Pride

Intact N-glycopeptides and proteomics from HCC tissue tumors with low and high AFP concentrations

Project description:Hepatocellular carcinoma (HCC) is still one of the malignant tumors with high morbidity and mortality in China and worldwide. Although AFP have been widely used as important biomarkers for HCC diagnosis and evaluation, the AFP level has a huge variation among HCC patient populations. Understanding the intrinsic heterogeneities of HCC associated with AFP levels is essential for the molecular mechanism studies of HCC with different AFP levels as well as for the potential early diagnosis and personalized treatment of HCC with AFP negative. Here, an integrated glycoproteomic and proteomic analysis of low and high AFP level of HCC tumors was performed to investigate the intrinsic heterogeneities of site-specific glycosylation associated with different AFP levels of HCC. we identified many commonly altered site-specific glycans from HCC tumors regardless of AFP levels, including decreased modifications by oligo-mannose and sialylated bi-antennary glycans, and increased modifications by bisecting glycans. By relative quantifying the intact glycopeptides between low and high AFP tumor groups, the great heterogeneities of site-specific N-glycans between two groups of HCC tumors were also uncovered. We found that several sialylated but not core fucosylated tri-antennary glycans were uniquely high-regulated in low AFP level of HCC tumors, while many core fucosylated bi-antennary or hybrid glycans as well as bisecting glycans were uniquely increased in high AFP tumors. The data provide a valuable resource for future HCC studies regarding the mechanism, heterogeneities and new biomarker discovery.

2020-03-19 | PXD016406 | Pride

A Combinatorial Enzymatic Approach for Identifying O-glycopeptides

Project description:Proteins glycosylation is primarily characterized as N-glycosylation or O-glycosylation. Recognition of the consensus N-glycosylation sequon (N-X-S/T/C) has enabled the mapping of the glycosite occupancy of intact glycopeptides, whereas O-glycosylation consensus sequons do not exit, making the characterization of O-glycosites challenging because of the different degrees of occupancy within a protein. Most O-glycosylation occurs via O-GalNAcylation, which is critical to diverse biological functions. However, only a small fraction of the O-glycosites and their glycan structures have been identified. We introduced a robust and reliable O-glycoproteomic workflow to achieve the long-standing goal of glycobiology—identifying novel O-glycosylation profiles on a large-scale. We developed and implemented a novel O-glycoproteomic workflow through the use of complementary digestion with O-glycoprotease (IMPa), trypsin, Asp-N, and Glu-C for enrichment of O-glycopeptides. The N-terminal of O-glycosylated serine or threonine residues cleaved using IMPa (95% of total PSMs) and over 99% of O-glycopeptides were enriched by the RAX column. Our O-glycoproteomic workflow involving peptide identification (using sceHCD-based MS/MS) and annotation (using FDR evaluation) enabled the identification of O-glycosylation of 189 O-glycosites carrying 379 glycan structures on 79 O-glycoproteins in human plasma. Of the O-glycan forms, 91.7% were distinctively and abundantly observed in core 1 and 2 structures. Importantly, we assessed five well-characterized native proteins purified from human plasma (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) to validate the identification of O-glycosites with high confidence and confirm the presence of numerous novel glycosites. We believe that this combinatorial approach is broadly applicable for comprehensive characterization of O-glycoproteomes in biomedical research.

2024-04-25 | PXD042701 | Pride