pGlyco3

pGlyco3 performs glycan-first identification and characterization of intact N- and O-glycopeptides to determine glycan compositions, modified saccharide units, and site-specific glycosylation.

Key Features:

• Glycan-First Search Approach: Prioritizes glycans in the search space to enable targeted identification of intact glycopeptides.
• Novel Glycan Ion-Indexing Algorithm: Uses a glycan ion-indexing algorithm to accelerate glycan fragment matching during database searches.
• Search Speed: Delivers 5 to 40 times faster searches than existing glycoproteomic search engines while maintaining accuracy and sensitivity.
• Integration with Electron-Based Dissociation Spectra: Incorporates electron-based dissociation spectra to improve glycopeptide identification.
• Dynamic Programming-Based Algorithm (pGlycoSite): Applies a dynamic programming algorithm (pGlycoSite) to compute site-specific glycan localization (SSGL) probabilities.
• Handling of Modified Saccharide Units: Supports identification of glycopeptides containing modified saccharide units.

Scientific Applications:

• Identification of Modified Saccharide Units: Identifies and characterizes glycopeptides containing modified saccharide units.
• Site-Specific Glycan Localization: Provides site-specific glycan localization (SSGL) with localization probabilities to map glycosylation sites.
• Verification of Glycopeptide Modifications: Enables verification of modifications such as ammonia adducts on Hex (aH) in yeast by corroborating intact glycopeptide identifications with released N-glycans and 15N/13C-labeled data.

Methodology:

Performance was evaluated using synthetic and natural glycopeptide samples and by comprehensive analysis of intact glycopeptides.