Nature Communications • Vol 16 • No 1
Library-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification
July 2025 • He Zhu, Zheng Fang, Lei Liu, Yan Wang, Hongqiang Qin, Yongzhan Nie, Mingming Dong, Mingliang Ye
Glycosylation changes are closely related to various diseases, including cancer. The quantitative analysis of site-specific glycans at proteomics scale remains challenging due to low glycopeptide spectra interpretation. Here, we present GlyPep-Quant, a tool for sensitive quantification and identification of site-specific glycans. Using a well-trained machine learning model, GlyPep-Quant quantified 25.1%-178.9% more site-specific glycans without missing values than pGlycoQuant, MSFragger-Glyco, and Skyline. To util…