Extended Data Fig. 4: Search space-dependent performance of Scout. | Nature Methods

Extended Data Fig. 4: Search space-dependent performance of Scout.

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

Extended Data Fig. 4

(a) Number of inter-protein CSMs, ResPairs and PPIs identified by Scout using standard parameters and all-level 1% naïve FDR cutoff on the benchmarking dataset with increasing database size. True positives shown in blue, false positives in yellow. Empirical FDR is indicated above the bars. (b) Processing time of Scout when searching the benchmarking data against increasingly large databases.

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