Extended Data Fig. 5: Corrected FMI for the three datasets analyzed in the study (Utilizing Equation 3 from Methods section). | Nature Methods

Extended Data Fig. 5: Corrected FMI for the three datasets analyzed in the study (Utilizing Equation 3 from Methods section).

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

Extended Data Fig. 5

(a) Human proteome-wide XL-MS (n = 668 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 3029 XLs for ‘1% FDR’; n = 4957 XLs for ‘10% FDR). (b) E. coli proteome-wide XL-MS (n = 340 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 553 XLs for ‘1% FDR’; n = 755 XLs for ‘10% FDR). (c) Mouse mitochondrial XL-MS (n = 4814 XLs for ‘1% FDR with ΔXlinkX score≥50’; n = 15323 XLs for ‘1% FDR’; n = 24317 XLs for ‘10% FDR). P values in all the panels were calculated using a two-sided Z-test and the error bars indicate +/- SE of proportion.

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