Innovation in Cross-Linking Mass Spectrometry Workflows: Toward a Comprehensive, Flexible, and Customizable Data Analysis Platform

Cross-linking mass spectrometry (XL-MS) is widely usedin the analysisof protein structure and protein-protein interactions (PPIs).Throughout the entire workflow, the utilization of cross-linkers andthe interpretation of cross-linking data are the core steps. In recentyears, the development of cross-linkers and analytical software mostlyfollow up on the classical models of non-cleavable cross-linkers suchas BS3/DSS and MS-cleavable cross-linkers such as DSSO. Although sucha paradigm promotes the maturity and robustness of the XL-MS field,it confines the innovation and flexibility of new cross-linkers andanalytical software. This critical insight will discuss the classification,advantages, and disadvantages of existing data analysis search engines.Take the new platinum-based metal cross-linker as an example, potentialpitfalls in characterization of cross-linked peptides using existingsoftware are discussed. Finally, ideas on developing more flexible,comprehensive, and user-friendly cross-linkers and software tools are proposed.