crisscrosslinkeR

crisscrosslinkeR maps and visualizes protein–protein and protein–RNA crosslinks from crosslinking mass spectrometry (XL-MS) to enable comprehensive analysis of ribonucleoprotein complexes.

Key Features:

• Integration of diverse crosslinking data: Integrates XL-MS outputs from different crosslinking methods and software packages to enable combined analysis of protein–protein and protein–RNA interactions.
• Crosslinking approach compatibility: Supports handling of multiple crosslinking approaches to reconcile heterogeneous XL-MS datasets.
• Visualization export: Generates output files compatible with external visualization software for creation of publication-quality figures.

Scientific Applications:

• Ribonucleoprotein interaction mapping: Enables unbiased detection and mapping of protein–protein and protein–RNA interactions within ribonucleoprotein complexes using XL-MS data.
• RNA biology and gene regulation studies: Supports analysis of interaction networks relevant to RNA processing, regulation, and function.
• Protein complex characterization: Facilitates structural and functional investigation of protein complex formation via detected crosslink sites.

Methodology:

Processes crosslinking mass spectrometry (XL-MS) data to identify crosslink sites where proteins interact with each other or with RNA, and reconciles datasets from different crosslinking methods and analysis software.