Oligator

Oligator generates theoretical tandem mass spectrometry (MS/MS) spectra from candidate glycan and oligosaccharide structures to support interpretation of MS/MS experiments, including cases with unreferenced chemical substitutions.

Key Features:

• Structure construction: Constructs candidate glycan and oligosaccharide structures from user-provided representations for downstream spectral prediction.
• Theoretical spectrum generation: Generates theoretical tandem mass spectrometry (MS/MS) spectra from constructed glycan structures to aid interpretation of experimental data.
• Standard ion nomenclature: Applies standard ion nomenclature for fragment assignment in the generated spectra.
• Standard linear notations (text format): Saves structural information using standard linear notations in text format to support data exchange and further processing.
• Support for unreferenced substitutions: Handles oligosaccharides with unreferenced chemical substitutions to enable analysis of chemically modified glycans.

Scientific Applications:

• Glycomics research: Facilitates hypothesis generation and interpretation of glycan fragmentation patterns in glycomics studies.
• Oligosaccharide identification: Aids identification and characterization of oligosaccharides in biological samples by comparing theoretical and experimental MS/MS spectra.
• Biomarker discovery: Supports discovery of glycan-based biomarkers through structural characterization of oligosaccharides.
• Disease diagnostics: Contributes to diagnostics by enabling characterization of disease-associated glycan variants.
• Therapeutic development: Enables structural characterization of oligosaccharides relevant to therapeutic research and development.

Methodology:

Translates user-constructed glycan structures into theoretical MS/MS spectra using standard ion nomenclature and stores structural representations in standard linear notations (text format).