Extended Data Fig. 2: Demonstration of the utility of our comprehensive set of validation metrics on a publicly available mouse mitochondrial XL-MS dataset. | Nature Methods

Extended Data Fig. 2: Demonstration of the utility of our comprehensive set of validation metrics on a publicly available mouse mitochondrial XL-MS dataset.

From: Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies

Extended Data Fig. 2

(a) Table showing the number of interprotein cross-links obtained at different filtering criteria, and upon mapping to representative 3D structures. (b) Conventional structure-based validation (n = 47 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 59 XLs for ‘1% FDR’; n = 63 XLs for ‘10% FDR’). (c) Fraction of structure-corroborating identifications (FSI) (n = 360 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 1402 XLs for ‘1% FDR’; n = 2097 XLs for ‘10% FDR’). (d) Fraction of mis-identifications (FMI) (n = 4814 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 15323 XLs for ‘1% FDR’; n = 24317 XLs for ‘10% FDR’). (e) Fraction of interprotein cross-links from known interactions (FKI) (n = 2368 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 11418 XLs for ‘1% FDR’; n = 19665 XLs for ‘10% FDR’). P values in (b-e) were calculated using a two-sided Z-test and the error bars indicate +/- SE of proportion.

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