ArticleNature communications2023
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 47 citations in OpenAlex.
- Article
- High-accuracy glycan de novo prediction for N- and O-linked glycopeptides across multiple fragmentation techniques.Nature communications · 2026Article
- Site-specific and global glycan analysis of the human cytomegalovirus pentameric glycoprotein by high resolution mass spectrometry.Glycobiology · 2026Article
- GlycoDiveR: A Modular R Framework to Analyze and Visualize Highly Dimensional Glycoproteomics Data.ACS measurement science au · 2026Article
- Optimized Simultaneous N/O-Glycopeptide Enrichment Strategy Identifies Lung Cancer Diagnostic Biomarkers in Serum.Journal of proteome research · 2026Article
- Mass Spectrometry-Based Proteomics Methods for Systematic Identification and Quantification of Protein O-Glycosylation in Complex Biological Samples.Journal of the American Society for Mass Spectrometry · 2026Review
- StrucGAP: a modular, streamlined and traceable data mining platform for structural and site-specific glycoproteomics.Nature communications · 2026Article
- Glycan Sequencing, A Brief Primer.Glycoscience & therapy · 2026Article
- Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe.bioRxiv : the preprint server for biology · 2026Article
- Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides.Molecular & cellular proteomics : MCP · 2026Article
- A comprehensive N-glycoproteome atlas reveals tissue-specific glycan remodeling but non-random structural microheterogeneities.Nature communications · 2026Article
- Mass Spectrometry Analysis of Biotherapeutic Monoclonal Antibody Glycosylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- A Glycoproteome Data Mining Strategy for Characterizing Structural Features of Altered Glycans with Thymic Involution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Library-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification.Nature communications · 2025Article
- Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases.Nature communications · 2025Article
- A high-resolution N-glycoproteome landscape of aging mouse ovary.Redox biology · 2025Article
- Deep structure-level N-glycan identification using feature-induced structure diagnosis integrated with a deep learning model.Analytical and bioanalytical chemistry · 2025Article
- GP-Marker facilitates the analysis of intact glycopeptide quantitative data at different levels.Analytical and bioanalytical chemistry · 2025Article
- Mass Spectrometry-Based Glycomics and Proteomics Profiling of On-Slide Digested Tissue from Complex Biological Samples.Methods in molecular biology (Clifton, N.J.) · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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 and glycan-based search strategies to address the challenge of complex fragmentation of glycopeptides. A deep learning model is designed to capture glycan tree structures and their fragment ions for de novo sequencing of glycans that do not exist in the database. We performed extensive analyses to validate the false discovery rates (FDRs) at both peptide and glycan levels and to evaluate GlycanFinder based on comprehensive benchmarks from previous community-based studies. Our results show that GlycanFinder achieved comparable performance to other leading glycoproteomics softwares in terms of both FDR control and the number of identifications. Moreover, GlycanFinder was also able to identify glycopeptides not found in existing databases. Finally, we conducted a mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses, which had been a challenging problem to previous studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.