Khakzad H, Happonen L, Malmström J, Malmström L
Bioinformatics - (-) - [2021-06-15; online 2021-06-15]
Protein-protein interactions (PPI) are central in many biological processes but difficult to characterize, especially in complex, unfractionated samples. Chemical cross-linking combined with mass spectrometry (MS) and computational modeling is gaining recognition as a viable tool in protein interaction studies. Here, we introduce Cheetah-MS, a web server for predicting the PPIs in a complex mixture of samples. It combines the capability and sensitivity of MS to analyze complex samples with the power and resolution of protein-protein docking. It produces the quaternary structure of the PPI of interest by analyzing tandem MS/MS data (also called MS2). Combining MS analysis and modeling increases the sensitivity and, importantly, facilitates the interpretation of the results. Cheetah-MS is freely available as a web server at https://www.txms.org. Supplementary data are available at Bioinformatics online.