ArticleNature methods2024
Predicting glycan structure from tandem mass spectrometry via deep learning.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Single-monosaccharide resolution glycan profiling enabled by the nanopipette.Chemical science · 2026Article
- An engineered nanopore identifies saccharides, amino acids, peptides and ribonucleotides.Nature biotechnology · 2026Article
- Single-Cell Glycomics of the Pancreatic Tumor Microenvironment: Technologies, Glyco-Immune Checkpoints, and Tumor-Immune Communication.Advanced biology · 2026Review
- A single amino acid in the viral capsid makes a major contribution to the interaction between human norovirus GII.6 and the bacterial Psl exopolysaccharide.Applied and environmental microbiology · 2026Article
- A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Cryogenic Infrared Spectroscopy Unmasks Gas-Phase Charge Migration in Mucin-Type O-Glycans.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- GlyGen: a knowledgebase linking glycan data with protein and gene data to reveal novel biological connections.Research square · 2026Article
- The 'sugar' side of extracellular vesicle-glycome: a panorama from basic characteristics, deciphering technologies, functions, to applications.Journal of nanobiotechnology · 2026Review
- Optimization of LC-ExD methods for glycopeptides on an Omnitrap-Orbitrap platform.Analytical and bioanalytical chemistry · 2026Article
- Generating 3D models of complex carbohydrates with GLYCAM-Web.Nature methods · 2026Article
- The non-scaffold effects of natural polysaccharides in promoting organ regeneration: a review.Journal of biological engineering · 2026Review
- Glycan Sequencing, A Brief Primer.Glycoscience & therapy · 2026Article
- Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases.Nature methods · 2026Article
- Nanopore profiling and structure determination of oligosaccharides by fragmentation.Science advances · 2026Article
- Understanding glycan structure and function through artificial intelligence.BBA advances · 2026Review
- GlycoGenius: a streamlined high-throughput glycan composition identification tool.Nature communications · 2025Article
- Biochemical Applications of Microbial Rare Glycan Biosynthesis, Recognition, and Sequencing.Biochemistry · 2025Review
- Glycomics in Human Diseases and Its Emerging Role in Biomarker Discovery.Biomedicines · 2025Review
- Collision-Induced Fragmentation of Oligosaccharides: Mechanistic Insights for Mass Spectrometry-Based Glycomics.Angewandte Chemie (International ed. in English) · 2025Review
- Transformer-based Deep Learning for Glycan Structure Inference from Tandem Mass Spectrometry.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography-MS/MS data in seconds (top-1 accuracy: 90.3%). We developed an open-access Python-based workflow of raw data conversion and prediction, followed by automated curation and fragment annotation, with predictions recapitulating and extending expert annotation. We demonstrate that this can be used for de novo annotation, diagnostic fragment identification and high-throughput glycomics. For maximum impact, this entire pipeline is tightly interlaced with our glycowork platform and can be easily tested at https://colab.research.google.com/github/BojarLab/CandyCrunch/blob/main/CandyCrunch.ipynb . We envision CandyCrunch to democratize structural glycomics and the elucidation of biological roles of glycans.
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Registered trials
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.