Ursgal

Ursgal provides a Python framework for integrating bottom-up proteomics search engines, statistical postprocessing, and open modification search to improve peptide identification and post-translational modification characterization.

Key Features:

• Framework integration: Integrates database search engines X!Tandem, OMSSA, MS-GF+, Myrimatch, and MS Amanda within a Python framework.
• Statistical postprocessing: Supports qvality and Percolator for statistical scoring and false discovery rate estimation.
• Combined FDR algorithm: Implements a novel combined FDR approach to merge outputs from multiple search engines.
• Combined PEP algorithm: Implements a combined PEP method that merges search results using elements from combined FDR, PeptideShaker, and Bayes' theorem.
• Open modification search (OMS) integration: Incorporates OMS engines for comprehensive searches of post-translational modifications and peptidoform identification.
• Result unification and PTM mapping: Unifies search results from multiple OMS engines and supports mapping of candidate modifications to potential PTMs, with reported increases in peptide-spectrum matches by 8–18%.
• High-throughput analysis: Enables large-scale proteomics analyses with consistent parameters and results files within the Python framework.

Scientific Applications:

• Peptide identification: Improve peptide-spectrum matching by combining multiple search engines and statistical postprocessing.
• PTM characterization: Identify and quantify post-translational modifications and peptidoforms using OMS integration and PTM mapping.
• Large-scale proteomics studies: Support high-throughput, large-scale analyses requiring consistent parameterization and consolidated results.
• Consensus-based identification: Increase robustness and accuracy of identifications through combined FDR and combined PEP merging across search engines.
• Search optimization and cascaded searches: Facilitate optimization of search parameters and application of cascaded search strategies.

Methodology:

Performs database searches with X!Tandem, OMSSA, MS-GF+, Myrimatch, and MS Amanda; applies qvality and Percolator for statistical postprocessing; computes combined FDR and combined PEP (using elements of PeptideShaker and Bayes' theorem); integrates open modification search engines and unifies OMS outputs for mapping to potential PTMs.