Abstract
AbstractGlycans 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.
Funder
Knut och Alice Wallenbergs Stiftelse
Vetenskapsrådet
Science Foundation Ireland
Publisher
Springer Science and Business Media LLC
Reference60 articles.
1. Guo, Y., Jia, W., Yang, J. & Zhan, X. Cancer glycomics offers potential biomarkers and therapeutic targets in the framework of 3P medicine. Front. Endocrinol. 13, 970489 (2022).
2. Cvetko, A. et al. Plasma N-glycome shows continuous deterioration as the diagnosis of insulin resistance approaches. BMJ Open Diabetes Res. Care 9, e002263 (2021).
3. Varki, A. Biological roles of glycans. Glycobiology 27, 3–49 (2017).
4. Zhao, C. & Pu, J. Influence of host sialic acid receptors structure on the host specificity of influenza viruses. Viruses 14, 2141 (2022).
5. Rudd, P. M. et al. in Essentials of Glycobiology (eds Varki, A. et al.) Ch. 51 (Cold Spring Harbor Laboratory Press, 2022).
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