TIDD

TIDD improves confidence of peptide identification in shotgun proteomics by calculating universal peptide-spectrum match (PSM) features for post-processing database search results across diverse search engines.

Key Features:

• Universal Feature Calculation: TIDD calculates universal features that assess PSM quality independently of the database search engine.
• Compatibility with Additional Features: TIDD accepts and integrates additional search-engine-specific features provided by users or search engines alongside its universal features.
• Engine-agnostic Performance: TIDD demonstrated similar or superior peptide-identification performance to Percolator and PeptideProphet and identified 10.23-38.95% more PSMs than target-decoy estimation for MSFragger.
• Avoids engine-specific feature engineering: TIDD addresses limitations of existing post-processors that require per-engine feature optimization, enabling application across newly developed and varied search engines.

Scientific Applications:

• Shotgun proteomics: TIDD increases confidence of peptide identifications from tandem mass (MS/MS) spectra across diverse database search engines.
• Search-engine development and benchmarking: TIDD provides engine-independent post-processing to support validation and comparison of new or alternative database search engines.
• PSM quality assessment: TIDD provides robust post-processing to improve identification rates relative to target-decoy estimation and existing post-processors.

Methodology:

TIDD employs machine learning to combine multiple scores from database search engines with its universal PSM features to assess PSM quality.