Abstract
Protein N-glycosylation plays a vital role in diverse cellular processes, and dysregulated N-glycosylation is implicated in a variety of human diseases including neurodegenerative disorders and cancer. With recent advances in high-resolution mass spectrometry-based glycoproteomics technologies enabling large-scale N-glycoproteome profiling of disease and control samples, analysis of the large datasets has become a challenge. Here, we provide a protocol for the systems-level analysis of in vivo N-glycosylation sites on N-glycosylated proteins and their changes in human disease, such as Alzheimer's disease. The protocol includes quantitation and differential analysis of N-glycopeptide abundance, in addition to integrative N-glycoproteome and proteome data analyses, to determine disease-associated changes in N-glycosylation site occupancy and identify differentially N-glycosylated proteins in human disease versus control samples. This protocol can be modified and applied to study proteome-wide N-glycosylation alterations in response to different cellular stresses or pathophysiological states in other organisms or model systems.