GlycoFragment

GlycoFragment computes theoretical glycan fragments and matches them to experimental mass spectra to identify carbohydrate structures.

Key Features:

• Fragment Calculation: Computes all theoretically possible fragments from input carbohydrate (glycan) sequences to predict potential mass-spectrometric fragmentation patterns.
• Integration with SweetDB: Interfaces with the SweetDB database to compare measured spectrum peaks against calculated fragments derived from repository carbohydrate structures.
• Spectrum Matching (GlycoSearchMS): Uses GlycoSearchMS to compare spectral data with theoretical fragments and rank candidate matches by similarity.
• Efficiency and Automation: Implements optimized fragment calculation and spectrum-matching algorithms for automated, high-throughput processing of series of mass spectra.

Scientific Applications:

• Structural Elucidation: Determine structures of unknown glycans by comparing experimental spectra with theoretical fragmentation predictions.
• Pathway Analysis: Support analysis of glycan biosynthesis pathways through accurate identification and characterization of carbohydrate molecules.
• Disease Biomarker Discovery: Aid identification of glycan biomarkers associated with diseases by matching experimental spectra to database-derived structures.

Methodology:

GlycoFragment generates comprehensive sets of theoretical fragments for given carbohydrate structures and uses GlycoSearchMS to compare each experimental peak against these fragments, ranking results by similarity.