xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

Area of Science:

• Structural biology
• Proteomics
• Bioinformatics

Background:

• Mass spectrometry-based crosslinking is crucial for hybrid structural analysis of protein complexes.
• Interpreting topological data from crosslinking experiments is challenging due to tabular formats.
• A need exists for intuitive tools to visualize and analyze protein crosslinking data.

Purpose of the Study:

• To develop xVis, a web server for visualizing and interpreting protein crosslinking data.
• To facilitate the topological and functional analysis of protein complex architectures.
• To enable qualitative assessment and manual validation of crosslink identifications.

Main Methods:

• Development of xVis, a web-based tool employing interactive schematic representations (circular, bar, network diagrams).
• Integration of linkage site information, identification scores, and spatial proximity data.
• Implementation of filtering options based on identification scores or false discovery rates for data validation.

Main Results:

• xVis provides clear visualizations of crosslinks, including linkage sites and scores.
• The tool depicts spatial proximity of protein regions and evolutionary conservation of amino acids.
• xVis facilitates protein clustering into subcomplexes and allows manual validation via fragment ion spectra.

Conclusions:

• xVis offers an easy-to-use platform for rapid topological and functional interpretation of protein complex structures.
• The tool enhances the evaluation of crosslink mass spectrometry data.
• xVis supports the comprehensive analysis of distance information derived from crosslinking experiments.