GlycoTraitR: an R package for characterizing structural heterogeneity in N-linked glycoproteomics data

Abstract Glycoproteomics data are rapidly accumulating due to advances in mass spectrometry instrumentation and the development of specialized search engines (e.g., pGlyco3, Glyco-Decipher) that enable identification of N-linked glycopeptide spectral matches (GPSMs) together with glycan structures. These advances have greatly expanded the scale and depth of N-linked glycopeptides; however, the intrinsic structural heterogeneity of glycosylation remains challenging to interpret. No existing tool provides a unified trait-based framework for analyzing N-linked GPSM data at both the glycosylation-site and protein levels. We developed glycoTraitR, an R package for trait-based analysis of structural heterogeneity in N-linked glycoproteomics data. GlycoTraitR provides a unified workflow to import GPSMs from search engine outputs, extract biologically interpretable glycan structural traits, and perform comparative analyses of micro- and macro-heterogeneity across experimental conditions using statistical testing. Implementation The R package and the source code of glycoTraitR are freely available on github at https://github.com/matsui-lab/glycoTraitR. A more detailed introduction and quick start guide are avaible at https://matsui-lab.github.io/glycoTraitR/. Competing Interest Statement The authors have declared no competing interest.