ArticleNature communications2021
GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Article
- Glycan Sequencing, A Brief Primer.Glycoscience & therapy · 2026Article
- Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe.bioRxiv : the preprint server for biology · 2026Article
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Glycosylation in neuroinflammation: mechanisms, implications, and therapeutic strategies for neurodegenerative diseases.Translational neurodegeneration · 2025Review
- Development and application of GlycanDIA workflow for glycomic analysis.Nature communications · 2025Article
- Library-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification.Nature communications · 2025Article
- Temporal resolved multi-proteomic analysis enabled the systematic characterization of N-glycosylation pattern changes during Jurkat T cell activation.Analytical and bioanalytical chemistry · 2025Article
- In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer.Nature communications · 2025Article
- Optimization of glycopeptide enrichment techniques for the identification of clinical biomarkers.Expert review of proteomics · 2024Review
- Data Independent Acquisition Mass Spectrometry Enhanced Personalized Glycosylation Profiling of Haptoglobin in Hepatocellular Carcinoma.Journal of proteome research · 2024Article
- Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.Nature communications · 2024Article
- Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network.bioRxiv : the preprint server for biology · 2024Article
- Prediction of glycopeptide fragment mass spectra by deep learning.Nature communications · 2024Article
- Serum Proteomics Identified TAFI as a Potential Molecule Facilitating the Migration of Peripheral Monocytes to Damaged White Matter During Chronic Cerebral Hypoperfusion.Neurochemical research · 2024Article
- Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.Nature biomedical engineering · 2024Article
- Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts.Microbial cell (Graz, Austria) · 2024Article
- RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes.Bioinformatics advances · 2024Article
- Deciphering the Properties and Functions of Glycoproteins Using Quantitative Proteomics.Journal of proteome research · 2023Review
- pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level.Nature communications · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.
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