TargetDecoy

TargetDecoy generates diagnostic plots to evaluate the quality of the target decoy approach for False Discovery Rate control in mass spectrometry-based proteomics.

Key Features:

• Diagnostic Plot Generation: Creates visualizations to assess whether decoy peptide-spectrum matches have similar properties to bad target hits.
• Target Decoy Approach Evaluation: Enables users to evaluate the crucial assumption that decoy PSM scores are a good simulation of target PSM scores.
• Score Distribution Assessment: Evaluates the characterization of score distributions for PSMs matched to wrong peptides.

Scientific Applications:

• Peptide-Spectrum Match Quality Control: Evaluates the reliability of PSMs identified by search engines comparing observed spectra to theoretical peptides from sequence databases.
• False Discovery Rate Validation: Supports FDR control in downstream analysis of MS-based proteomics data by validating target decoy method assumptions.
• Decoy Database Performance Assessment: Assesses the quality of decoy databases generated by reversing target databases for proteomics studies.

Methodology:

The tool generates diagnostic plots based on peptide-spectrum match scores from target and decoy databases, comparing score distributions of decoy PSMs to bad target PSMs to evaluate target decoy approach assumptions.