Exhaustive Cross-linking Search with Protein Feedback

Improving the sensitivity of protein-protein interaction detection and protein structure probing is a principal challenge in cross-linking mass spectrometry (XL-MS) data analysis. In this paper, we propose an exhaustive cross-linking search method with protein feedback (ECL-PF) for cleavable XL-MS data analysis. ECL-PF adopts an optimized /{beta} mass detection scheme and establishes protein-peptide association during the identification of cross-linked peptides. Existing major scoring functions can all benefit from the ECL-PF workflow to a great extent. In comparisons using synthetic datasets and hybrid simulated datasets, ECL-PF achieved three-fold higher sensitivity over standard techniques. In experiments using real datasets, it also identified 91.6% more cross-link spectrum matches and 52.6% more unique cross-links.