ProXL

ProXL analyzes and visualizes protein cross-linking mass spectrometry (XL-MS) data to support structural analysis and quality control of protein interactions and conformations.

Key Features:

• Data Independence: Independent of specific software pipelines, enabling import and analysis of XL-MS results from multiple sources.
• ProXL XML data format: ProXL XML abstracts the relational database schema to simplify integration and compatibility with diverse XL-MS outputs.
• Comprehensive Visualization: Dynamic, structure-based visualizations of cross-links to support interpretation and quality control of mass spectrometry data.
• Data Sharing: Support for public and private data sharing and project-based organization to enable controlled dissemination and collaborative analysis.
• Collaborative Dataset Integration: Enables merging and comparison of datasets from disparate pipelines to integrate diverse XL-MS results for comparative analyses.

Scientific Applications:

• Protein–protein interaction mapping: Exploration and mapping of protein–protein interactions using XL-MS cross-links.
• Structural model validation: Validation of structural models by comparing observed cross-links with expected structural constraints.
• Quality control of XL-MS data: Assessment and quality control of cross-linking mass spectrometry datasets.
• Analysis of molecular architecture: Integration and visualization of diverse datasets to investigate protein and complex molecular architecture.

Methodology:

ProXL imports XL-MS data via the ProXL XML format, which abstracts the relational database schema, loads data into a database backend, and produces dynamic structure-based visualizations.