biostudies-literatureUnknown24(12)Kothlow KGlycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. While these fragment ions are often straightforward to observe by eye, few tools exist to systemically explore these common glycopeptide spectral features or explore their relationships with each other. Instead, most studies rely on manual inspection to understand glycan-informative ion content in their data, or they are restricted to evaluating the presence of these ions only in the small fraction of spectra that are identified by glycopeptide search algorithms. Here we introduce GlyCounter as a freely available, open-source tool to rapidly extract oxonium, Y-type, and custom ion information fromMolecular & cellular proteomics : MCP101085https://www.ebi.ac.uk/biostudies/studies/S-EPMC12701960biostudies-literatureExtracting Informative Glycan-Specific Ions From Glycopeptide MS/MS Spectra With GlyCounter.PMC12701960Drager LSSchramm HMRussell JHMarkuson KASutherland ERiley NMDuboff AGKothlow KTejus VRMcDermott LEZhang RVeth TSfalseExtracting Informative Glycan-Specific Ions From Glycopeptide MS/MS Spectra With GlyCounter.Glycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. While these fragment ions are often straightforward to observe by eye, few tools exist to systemically explore these common glycopeptide spectral features or explore their relationships with each other. Instead, most studies rely on manual inspection to understand glycan-informative ion content in their data, or they are restricted to evaluating the presence of these ions only in the small fraction of spectra that are identified by glycopeptide search algorithms. Here we introduce GlyCounter as a freely available, open-source tool to rapidly extract oxonium, Y-type, and custom ion information from2025-01-01T00:00:00Z2025 Dec2026-07-15T11:17:07.342Z2026-07-04T03:11:58.208ZS-EPMC127019604110647910.1016/j.mcpro.2025.101085