biostudies-literatureKlein JNIAID NIH HHSNIGMS NIH HHS6168https://www.ebi.ac.uk/biostudies/studies/S-EPMC11263600biostudies-literatureUnknown15(1)Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a challenging problem at scale. Recent innovation has been made in increasing the scope and accuracy of glycopeptide identifications, with more precise uncertainty estimates for each part of the structure. We present a dynamically adapting relative retention time model for detecting and correcting ambiguous glycan assignments that are difficult to detect from fragmentation alone, a layered approach to glycopeptide fragmentation modeling that improves N-glycopeptide identification in samples without compromising identification quality, and a site-specific method to increase the depth of the glycoproteome confidently identifiable even further. We demonstrate our techniques on a set of previously published dataNature communicationsExpanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.PMC11263600R01 AI155975R35 GM144090Carvalho LZaia JKlein JfalseExpanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a challenging problem at scale. Recent innovation has been made in increasing the scope and accuracy of glycopeptide identifications, with more precise uncertainty estimates for each part of the structure. We present a dynamically adapting relative retention time model for detecting and correcting ambiguous glycan assignments that are difficult to detect from fragmentation alone, a layered approach to glycopeptide fragmentation modeling that improves N-glycopeptide identification in samples without compromising identification quality, and a site-specific method to increase the depth of the glycoproteome confidently identifiable even further. We demonstrate our techniques on a set of previously published data2024-01-01T00:00:00Z2024 Jul2026-06-01T20:29:46.943Z2026-05-20T03:08:14.925ZS-EPMC112636003903906310.1038/s41467-024-50338-5