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Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species

Author

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  • Wen-Feng Zeng

    (CAS
    Westlake University)

  • Guoquan Yan

    (Fudan University
    Fudan University)

  • Huan-huan Zhao

    (Fudan University
    Fudan University)

  • Chao Liu

    (CAS
    Beihang University)

  • Weiqian Cao

    (Fudan University
    Fudan University)

Abstract

Precision mapping of site-specific glycans using mass spectrometry is vital in glycoproteomics. However, the diversity of glycan compositions across species often exceeds database capacity, hindering the identification of rare glycans. Here, we introduce pGlycoNovo, a software within the pGlyco3 software environment, which employs a glycan first-based full-range Y-ion dynamic searching strategy. pGlycoNovo enables de novo identification of intact glycopeptides with rare glycans by considering all possible monosaccharide combinations, expanding the glycan search space to 16~1000 times compared to non-open search methods, while maintaining accuracy, sensitivity and speed. Reanalysis of SARS Covid-2 spike protein glycosylation data revealed 230 additional site-specific N-glycans and 30 previously unreported O-glycans. pGlycoNovo demonstrated high complementarity to six other tools and superior search speed. It enables characterization of site-specific N-glycosylation across five evolutionarily distant species, contributing to a dataset of 32,549 site-specific glycans on 4602 proteins, including 2409 site-specific rare glycans, and uncovering unexpected glycan fragments.

Suggested Citation

  • Wen-Feng Zeng & Guoquan Yan & Huan-huan Zhao & Chao Liu & Weiqian Cao, 2024. "Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52099-7
    DOI: 10.1038/s41467-024-52099-7
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    References listed on IDEAS

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    1. Johannes Stadlmann & Jasmin Taubenschmid & Daniel Wenzel & Anna Gattinger & Gerhard Dürnberger & Frederico Dusberger & Ulrich Elling & Lukas Mach & Karl Mechtler & Josef M. Penninger, 2017. "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity," Nature, Nature, vol. 549(7673), pages 538-542, September.
    2. Weiping Sun & Qianqiu Zhang & Xiyue Zhang & Ngoc Hieu Tran & M. Ziaur Rahman & Zheng Chen & Chao Peng & Jun Ma & Ming Li & Lei Xin & Baozhen Shan, 2023. "Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
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