GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control DOI Creative Commons
Yi Yang,

Guoquan Yan,

Siyuan Kong

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Oct. 18, 2021

Abstract Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) an emerging technology with deep proteome coverage and accurate quantitative capability proteomics studies, still the early stage development field We propose GproDIA, a framework for proteome-wide characterization from DIA data comprehensive statistical control by 2-dimentional false discovery rate approach glycoform inference algorithm, enabling identification using wide isolation windows. further utilize semi-empirical spectrum prediction strategy to expand spectral libraries glycopeptides. benchmark our method N-glycopeptide on yeast human serum samples, demonstrating that GproDIA outperforms data-dependent acquisition-based methods glycoproteomics terms capacity completeness identification, as well accuracy precision quantification. expect this work can provide powerful tool glycoproteomic studies.

Language: Английский

The glycosylation in SARS-CoV-2 and its receptor ACE2 DOI Creative Commons
Yanqiu Gong,

Suideng Qin,

Lunzhi Dai

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2021, Volume and Issue: 6(1)

Published: Nov. 15, 2021

Coronavirus disease 2019 (COVID-19), a highly infectious caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to 4.8 deaths worldwide as of October 5 2021. Cryo-electron microscopy topology show that the SARS-CoV-2 genome encodes lots glycosylated proteins, such spike (S), envelope (E), membrane (M), ORF3a which are responsible for host recognition, penetration, binding, recycling pathogenesis. Here we reviewed detections, substrates, biological functions glycosylation in proteins well human receptor ACE2, also summarized approved undergoing therapeutics associated with glycosylation. This review may not only broad understanding viral glycobiology, but provide key clues development new preventive therapeutic methodologies against its variants.

Language: Английский

Citations

172
Glycoproteomics DOI Open Access
Ieva Bagdonaite, Stacy A. Malaker, Daniel A. Polasky

et al.

Nature Reviews Methods Primers, Journal Year: 2022, Volume and Issue: 2(1)

Published: June 23, 2022

Language: Английский

Citations

156
Glyco-Decipher enables glycan database-independent peptide matching and in-depth characterization of site-specific N-glycosylation DOI Creative Commons
Zheng Fang, Hongqiang Qin,

Jiawei Mao

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 7, 2022

Abstract Glycopeptides with unusual glycans or poor peptide backbone fragmentation in tandem mass spectrometry are unaccounted for typical site-specific glycoproteomics analysis and thus remain unidentified. Here, we develop a tool, Glyco-Decipher, to address these issues. Glyco-Decipher conducts glycan database-independent matching exploits the pattern of shared backbones glycopeptides improve spectrum interpretation. We benchmark on several large-scale datasets, demonstrating that it identifies more peptide-spectrum matches than Byonic, MSFragger-Glyco, StrucGP pGlyco 3.0, 33.5%-178.5% increase number identified glycopeptide spectra. The unbiased profiling attached enables discovery 164 modified mouse tissues, including chemical biological modifications. By enabling in-depth characterization protein glycosylation, is promising tool advancing research.

Language: Английский

Citations

79
Structural basis of Epstein-Barr virus gp350 receptor recognition and neutralization DOI Creative Commons
Cong Sun,

Xin‐Yan Fang,

Guo‐Long Bu

et al.

Cell Reports, Journal Year: 2025, Volume and Issue: 44(1), P. 115168 - 115168

Published: Jan. 1, 2025

Highlights•Cryo-EM structure of EBV gp350-CR2 complex at a resolution 3.29 Å•Depiction polar and glycan-free contacting interface•Key residue divergence in CR2 affects host tropism•Designed CR2-Fc neutralizes B cell infection by targeting 72A1 epitopeSummaryEpstein-Barr virus (EBV) is an oncogenic associated with multiple lymphoid malignancies autoimmune diseases. During cells, uses its major glycoprotein gp350 to recognize the receptor CR2, initiating viral attachment, process that has lacked direct structural evidence for decades. In this study, we resolved complex, elucidated their key interactions, determined site-specific N-glycosylation map gp350. Our findings reveal primarily binds through electrostatically complementary interface diversity residues across different species influences selectivity mediated With confirmed binding, constructed antibody analog targets vulnerable site gp350, demonstrating potent neutralization effect against cells. work provides essential insights into mechanism tropism, suggesting potential antiviral agent.Graphical abstract

Language: Английский

Citations

2
Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics DOI Creative Commons
Tomislav Čaval, Frederico Alisson‐Silva, Flavio Schwarz

et al.

Theranostics, Journal Year: 2023, Volume and Issue: 13(8), P. 2605 - 2615

Published: Jan. 1, 2023

Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis the evasion immune responses.Recently, number glycosyltransferases that lead altered have been linked reduced anti-tumor responses: B3GNT3, which is implicated PD-L1 triple negative breast cancer, FUT8, through fucosylation B7H3, B3GNT2, confers resistance T cell cytotoxicity.Given increased appreciation relevance protein glycosylation, there critical need for development methods allow an unbiased interrogation status.Here we provide overview broad changes at describe selected examples receptors with aberrant leading functional changes, emphasis on checkpoint inhibitors, growth-promoting growth-arresting receptors.Finally, posit field glycoproteomics matured extent where large-scale profiling intact glycopeptides from feasible poised discovery new actionable targets against cancer.

Language: Английский

Citations

42
Critical considerations in N-glycoproteomics DOI
The Huong Chau, Anastasia Chernykh, Rebeca Kawahara

et al.

Current Opinion in Chemical Biology, Journal Year: 2023, Volume and Issue: 73, P. 102272 - 102272

Published: Feb. 7, 2023

Language: Английский

Citations

38
Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides DOI Creative Commons
Daniel Geiszler, Daniel A. Polasky, Fengchao Yu

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 12, 2023

Abstract Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge methods to detect them recent years. However, post-translational can introduce complexity into proteomics searches by fragmenting unexpected ways, ultimately hindering the detection modified peptides. To address these deficiencies, we present fully automated method find diagnostic spectral features for any modification. The be incorporated search engines improve peptide recovery and localization. We show utility this approach interrogating fragmentation patterns cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, ADP-ribosylated also analyze interactions between ion’s intensity its statistical properties. This has been open-search annotation tool PTM-Shepherd FragPipe computational platform.

Language: Английский

Citations

23
Prediction of glycopeptide fragment mass spectra by deep learning DOI Creative Commons
Yi Yang, Qun Fang

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 19, 2024

Abstract Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging glycoproteomics. While various deep models can predict fragment spectra of peptides with good accuracy, they cannot cope the non-linear glycan structure an intact glycopeptide. Herein, we present DeepGlyco, learning-based approach for prediction glycopeptides. Our model adopts tree-structured long-short term memory networks to process moiety graph neural network architecture incorporate potential fragmentation pathways specific structure. This feature beneficial explainability differentiation ability structural isomers. We further demonstrate that predicted spectral libraries be used data-independent acquisition glycoproteomics as supplement library completeness. expect this work will provide valuable resource

Language: Английский

Citations

13
A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation DOI
Yang Zhao, Yong Zhang, Bo Meng

et al.

Phenomics, Journal Year: 2024, Volume and Issue: 4(3), P. 213 - 226

Published: April 10, 2024

Language: Английский

Citations

9
Liposome-encapsulated mannose-1-phosphate therapy improves global N-glycosylation in different congenital disorders of glycosylation DOI
Rohit Budhraja, Silvia Radenkovic,

Anu Jain

et al.

Molecular Genetics and Metabolism, Journal Year: 2024, Volume and Issue: 142(2), P. 108487 - 108487

Published: May 7, 2024

Language: Английский

Citations

9