Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics
Milan Avila Clasen, Max Ruwolt, Cong Wang, Julia Ruta, Boris Bogdanow, Louise Ulrich Kurt, Zehong Zhang, Shuai Wang, Fábio C. Gozzo, Tao Chen, Paulo C. Carvalho, Diogo Borges Lima, Fan Liu
Abstract
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.