gpAnnotate

gpAnnotate annotates MS/MS spectra of glycopeptides and generates Symbol Nomenclature For Glycans (SNFG) visualizations by converting IUPAC-condensed glycan inputs with DrawGlycan-SNFG v2 to support structural interpretation in glycoproteomics.

Key Features:

• Integration with DrawGlycan-SNFG v2: Converts IUPAC-condensed glycan strings into SNFG drawings using DrawGlycan-SNFG version 2.
• Modification display options: Supports local and global display options for glycan/peptide modifications including bond breakages, adducts, repeat structures, and ambiguous identifications.
• Fragmentation mode support: Scores and annotates individual MS/MS glycopeptide spectra across multiple established fragmentation modes.
• Implementation and portability: Originally developed in MATLAB and provided as compiled packages with Python and Java implementations.

Scientific Applications:

• Glycopeptide MS/MS interpretation: Enables detailed annotation of MS/MS spectra for assignment of glycopeptide fragments and composition.
• Structural elucidation: Facilitates visualization and interpretation of glycan structures via SNFG for structural characterization.
• Glycosylation pattern analysis: Supports analysis of glycosylation heterogeneity and pattern identification from experimental spectra.
• Translational research: Assists studies in biomarker discovery, disease diagnostics, and therapeutic development that require accurate glycopeptide structural information.

Methodology:

Converts IUPAC-condensed glycan inputs into SNFG sketches via DrawGlycan-SNFG v2 and scores/annotates individual MS/MS glycopeptide spectra across different fragmentation modes while accounting for modifications such as bond breakages, adducts, repeat structures, and ambiguous identifications; implemented originally in MATLAB with compiled Python and Java packages.