DecoyDeveloper

DecoyDeveloper generates decoy glycopeptide sequences for mass spectrometry (MS)-based glycoproteomics validation by producing biologically plausible peptide and glycan combinations with minimal mass differences to real targets.

Key Features:

• On-Demand Generation: Generates decoy glycopeptides on demand to supply negative controls for validation experiments.
• High Volume Production: Produces large numbers of decoy sequences to support robust statistical validation and false discovery estimation.
• Low Mass Differences: Creates decoys with minimal mass differences to real glycopeptides to challenge spectral matching algorithms.
• Biologically Relevant Sequences: Outputs decoys that include complete peptide and glycan components maintained as biologically plausible structures.

Scientific Applications:

• Glycoproteomics validation: Supplies decoy sequences for validating glycopeptide assignments from MS data.
• Algorithm assessment: Assesses specificity and accuracy of glycopeptide assignment algorithms using negative-control decoys.
• Automated workflow improvement: Aids evaluation and improvement of automated workflows that match experimental spectra to theoretical glycopeptide models.
• False discovery rate estimation and method refinement: Enables determination of false discovery rates and refinement of analytical methods for glycopeptide identification.

Methodology:

Generates decoys by manipulating peptide and glycan sequences to produce biologically plausible glycopeptides that are distinct from real targets yet have minimal mass differences, for use as negative controls in validation experiments.