ProteoAnnotator

ProteoAnnotator performs proteogenomic analysis by integrating mass spectrometry (MS) data with genomic information to validate and refine gene models.

Key Features:

• Comprehensive Pipeline: Provides a modular pipeline for proteogenomic analysis that integrates MS data with genomic information.
• Adherence to Standards: Implements the mzIdentML standard from the Proteomics Standards Initiative (PSI) at each stage of analysis.
• Standalone Modules: Exposes each pipeline step as standalone modules for reuse or integration into other workflows.
• Pre-processing and Database Integration: Includes modules for pre-processing MS data and combining multiple search databases.
• Peptide-Level Statistics: Performs peptide-level statistical analysis on mzIdentML files to validate protein identifications.
• Genomic Mapping: Maps identified proteins back onto the genome to support annotation and gene structure analysis.

Scientific Applications:

• Gene Structure Validation: Uses peptide-level evidence and genomic mapping to confirm, refine, and validate updates to official gene models.

Methodology:

Modular pipeline integrating MS data with genomic information; implements the mzIdentML standard; includes MS pre-processing, combining multiple search databases, peptide-level statistical analysis of mzIdentML files, and mapping identified proteins onto the genome.