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bioRxiv · 10.1101/2022.03.03.482813

Exhaustive Cross-linking Search with Protein Feedback

Zhou, C.·Dai, S.·Lin, Y.·Li, N.·Yu, W.
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Abstract

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.

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Zhou, C., Dai, S., Lin, Y., Li, N., Yu, W.. 2022-03-04. Exhaustive Cross-linking Search with Protein Feedback. https://doi.org/10.1101/2022.03.03.482813

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