Extended Data Fig. 1: Expected fraction of false in-group ResPair cross-links in the XL-MS datasets derived from our recombinant analytical standard. | Nature Methods

Extended Data Fig. 1: Expected fraction of false in-group ResPair cross-links in the XL-MS datasets derived from our recombinant analytical standard.

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

Extended Data Fig. 1

The results are based on a mathematical simulation approach we recently developed19. We considered the 2 database sizes used for our comparison of XL-MS search engines and 3 FDR cut-offs (determined by target-decoy competition in Scout). The bars show the percentage of false ResPair intra-links and inter-links that are expected within the same interaction group, that is cross-links that would be wrongly annotated when defining true-positive hits based on our mixing scheme. Shown are the average +/− SD from 10 simulations with identical input parameters.

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