Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics

Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the performance of Scout and existing XL-MS software. We find that Scout offers an excellent combination of speed, sensitivity and false discovery rate control. The results illustrate how our large recombinant standard can support the development of XL-MS analysis tools and evaluation of XL-MS results. This Article reports cross-linking mass spectrometry (XL-MS) standard datasets with fully controlled protein interactions that are an order of magnitude more complex than existing ones. These datasets are used to benchmark XL-MS software and establish a fast, error-controlled search tool for XL-MS with cleavable reagents.