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

Guoquan Yan,

Siyuan Kong

и другие.

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Окт. 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.

Язык: Английский

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

Suideng Qin,

Lunzhi Dai

и другие.

Signal Transduction and Targeted Therapy, Год журнала: 2021, Номер 6(1)

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

175
Glycoproteomics DOI Open Access
Ieva Bagdonaite, Stacy A. Malaker, Daniel A. Polasky

и другие.

Nature Reviews Methods Primers, Год журнала: 2022, Номер 2(1)

Опубликована: Июнь 23, 2022

Язык: Английский

Процитировано

159
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

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Апрель 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.

Язык: Английский

Процитировано

80
Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics DOI Creative Commons
Tomislav Čaval, Frederico Alisson‐Silva, Flavio Schwarz

и другие.

Theranostics, Год журнала: 2023, Номер 13(8), С. 2605 - 2615

Опубликована: Янв. 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.

Язык: Английский

Процитировано

43
Critical considerations in N-glycoproteomics DOI
The Huong Chau, Anastasia Chernykh, Rebeca Kawahara

и другие.

Current Opinion in Chemical Biology, Год журнала: 2023, Номер 73, С. 102272 - 102272

Опубликована: Фев. 7, 2023

Язык: Английский

Процитировано

38
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics DOI Creative Commons
Weiping Sun,

Qianqiu Zhang,

Xiyue Zhang

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июль 8, 2023

Abstract Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based glycan-based strategies to address challenge complex fragmentation glycopeptides. A deep learning model is designed capture glycan tree structures their fragment ions glycans that do not exist in database. We performed extensive analyses validate false discovery rates (FDRs) at both peptide levels evaluate based on comprehensive benchmarks previous community-based studies. Our results show achieved comparable performance other leading glycoproteomics softwares terms FDR control number identifications. Moreover, was also able identify found existing databases. Finally, conducted experiment antibody N-linked glycosylation profiling could distinguish isomeric peptides four immunoglobulin G subclasses, which had been challenging problem

Язык: Английский

Процитировано

24
Prediction of glycopeptide fragment mass spectra by deep learning DOI Creative Commons
Yi Yang, Qun Fang

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Март 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

Язык: Английский

Процитировано

13
Advancing mass spectrometry–based glycoproteomic software tools for comprehensive site-specific glycoproteome analysis DOI
Weiqian Cao

Current Opinion in Chemical Biology, Год журнала: 2024, Номер 80, С. 102442 - 102442

Опубликована: Март 8, 2024

Язык: Английский

Процитировано

10
A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation DOI
Yang Zhao, Yong Zhang, Bo Meng

и другие.

Phenomics, Год журнала: 2024, Номер 4(3), С. 213 - 226

Опубликована: Апрель 10, 2024

Язык: Английский

Процитировано

10
Structural basis of Epstein-Barr virus gp350 receptor recognition and neutralization DOI Creative Commons
Cong Sun,

Xin‐Yan Fang,

Guo‐Long Bu

и другие.

Cell Reports, Год журнала: 2025, Номер 44(1), С. 115168 - 115168

Опубликована: Янв. 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

Язык: Английский

Процитировано

2