glycoTraitR

glycoTraitR analyzes glycoproteomics data, particularly glycopeptide-spectrum matches (GPSMs), by parsing glycan structures, computing monosaccharide compositions and structural traits, and performing differential analysis of glycan heterogeneity.

Key Features:

• Search Engine Compatibility: Supports results generated by the pGlyco3 and Glyco-Decipher search engines.
• Glycan Structure Parsing: Parses glycan structures and computes monosaccharide compositions.
• Structural Trait Computation: Computes structural traits from glycan structures.
• Differential Analysis: Performs differential analysis of glycan heterogeneity.
• Matrix Construction: Constructs trait-by-PSM matrices stored in a SummarizedExperiment object.
• Custom Motif Support: Supports user-defined structural motifs.
• Visualization: Provides visualization utilities for interpreting glycan trait changes.

Scientific Applications:

• Glycoproteomics Data Analysis: Analyzes glycopeptide-spectrum matches (GPSMs) from glycoproteomics experiments.
• Glycan Heterogeneity Profiling: Profiles and compares glycan structural heterogeneity across conditions.
• Glycan Trait Interpretation: Interprets changes in glycan structural traits through integrated visualization.

Methodology:

The package parses glycan structures, computes monosaccharide compositions and structural traits, constructs trait-by-PSM matrices stored in a SummarizedExperiment object, and performs differential analysis of glycan heterogeneity with support for user-defined structural motifs.