HLA-Glyco

HLA-Glyco analyzes glycosylated Major Histocompatibility Complex (MHC)-associated peptides, focusing on MHC class II to characterize N-glycopeptides and their implications for antigen presentation.

Key Features:

• MSFragger-Glyco-based workflow: Uses the MSFragger-Glyco search algorithm with stringent false discovery rate control for glycopeptide identification from mass spectrometry-based immunopeptidome data.
• Extensive dataset: Contains over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides mapped to 1,049 distinct protein glycosylation sites derived from eight large-scale publicly available studies.
• Glycosylation pattern analysis: Reports high levels of truncated glycans, conserved HLA-binding cores, and variations in glycosylation positional specificity among different HLA allele groups.
• FragPipe integration: Implements the workflow within the FragPipe computational platform for processing immunopeptidomics data.

Scientific Applications:

• Immune recognition studies: Enables investigation of how glycosylated peptides contribute to antigen presentation and immune recognition.
• Peptide–MHC interaction analysis: Supports analysis of the effects of N-glycosylation on peptide-MHC binding and presentation.
• Therapeutic and vaccine research: Provides data and analyses relevant to targeted therapy and vaccine development focused on glyco-modified antigens.
• Autoimmune disease research: Facilitates study of mechanisms by which glycosylation may influence autoimmune responses.

Methodology:

Computational processing uses MSFragger-Glyco searches with stringent false discovery rate control on mass spectrometry-based immunopeptidome data, compiled from eight large-scale publicly available studies and executed within FragPipe.