Xlink Mapping and AnalySis (XMAS) - Crosslinking study of commercial human Fibrinogen

Here, we introduce XMAS, a bundle that allows users to load results from several XL-MS search engines directly into ChimeraX and map the information onto protein structures. Besides automatically locating distance constraints on protein structures, XMAS offers the possibility to work with replicate experiments and/or different crosslinkers, and filter this data based on how many replicates for which a given distance constraint was detected, thereby increasing the data quality. Additionally, we introduce the concept of self-links, which allows easy modeling of homo-dimeric interactions. Core functionality is extended by the implementation of seamless connections to the HADDOCK suite to streamline otherwise time-consuming tasks in structural modeling pipelines. We then demonstrate these key elements of the XMAS bundle by modeling crosslinking data obtained from human fibrin clots. This software is freely available from the ChimeraX toolshed, with an extensive user manual and example datasets.