Extended Data Fig. 3: Benchmarking of Scout against xiSEARCH/xiFDR. | Nature Methods

Extended Data Fig. 3: Benchmarking of Scout against xiSEARCH/xiFDR.

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

Extended Data Fig. 3

(a) Inter-protein CSM, ResPairs and PPI identifications at 5% naïve PPI-FDR and empirically determined FDR using Scout and xiSEARCH (both with default parameters, xiFDR with boost between proteins) on a subset of the benchmarking dataset using a 540-protein database and KSTY as possible reaction sites for the cross-linking reagent. (b) Processing time of Scout and xiSEARCH on four selected RAW files of the benchmarking dataset on the same computational setup using a 540-protein database.

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