psm_utils

psm_utils standardizes and interconverts peptide-spectrum match (PSM) files and associated data structures to enable integration and downstream analysis of PSMs and peptidoforms across diverse proteomics workflows.

Key Features:

• Format Agnosticism: Reads and writes multiple PSM file formats to ensure compatibility across search engines and heterogeneous outputs.
• Unified Data Structure: Represents peptidoforms, individual PSMs, and lists of PSMs in a single standardized data structure for consistent manipulation.
• Python API: Exposes a high-level Python API for programmatic access and integration into bioinformatics workflows.
• Interoperability and Extensibility: Leverages existing packages and community standards to interoperate with other tools and enable extensibility.

Scientific Applications:

• PSM Integration: Integrates PSM outputs from different search engines into cohesive datasets for comparative analysis.
• Statistical Analysis and Visualization: Enables statistical analysis and visualization of PSM and peptidoform data.
• Custom Workflow Development: Supports development of custom processing and analysis workflows via the Python API.

Methodology:

Builds on existing software libraries and adheres to community standards to provide a unified approach to PSM file handling.