Extended Data Fig. 1: Analysis of the human proteome-wide XL-MS dataset using MaXLinker software. | Nature Methods

Extended Data Fig. 1: Analysis of the human proteome-wide XL-MS dataset using MaXLinker software.

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

Extended Data Fig. 1

(a) Table showing the number of interprotein cross-links obtained at different filtering criteria, and upon mapping to a representative 3D structure of a human 26S proteasome (PDB id: 5GJQ). (b) Comparison of the fraction of validated cross-links using the conventional structure-based approach (n = 49 XLs for ‘1% FDR’; n = 65 XLs for ‘10% FDR). (c) Comparison using the fraction of structure-corroborating identifications (FSI) (n = 63 XLs for ‘1% FDR’; n = 125 XLs for ‘10% FDR). (d) Comparison using the fraction of mis-identifications (FMI) (n = 8127 XLs for ‘1% FDR’; n = 15110 XLs for ‘10% FDR). (e) Comparison using the fraction of interprotein cross-links from known interactions (FKI) (n = 1144 XLs for ‘1% FDR’; n = 5158 XLs for ‘10% FDR). for (b–e), the P values were calculated using a two-sided Z-test and the error bars indicate +/- SE of proportion.

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