Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data

Area of Science:

• Biochemistry
• Computational Biology
• Proteomics

Background:

• Protein-protein interactions (PPIs) are crucial for biological functions.
• Characterizing PPIs in complex biological samples is challenging.
• Chemical cross-linking coupled with mass spectrometry (MS) and computational modeling is an emerging technique for PPI studies.

Purpose of the Study:

• To introduce Cheetah-MS, a web server for predicting PPIs in complex mixtures.
• To integrate MS capabilities with protein-protein docking for enhanced PPI analysis.

Main Methods:

• Utilizes tandem MS/MS (MS2) data analysis.
• Combines mass spectrometry for sample analysis with protein-protein docking for structural resolution.
• Predicts the quaternary structure of protein-protein interactions.

Main Results:

• Cheetah-MS provides a method for predicting PPIs in complex biological samples.
• The integrated approach increases sensitivity in PPI detection.
• Facilitates the interpretation of complex PPI data.

Conclusions:

• Cheetah-MS offers a powerful web server tool for PPI prediction.
• The combination of MS and computational modeling improves the study of protein interactions.
• The tool is freely available at https://www.txms.org.