Extended Data Fig. 4: EndoMAP.v1 extension by AlphaLink2 and XL-MS using DHSO/DMTMM cross-linkers.
From: EndoMAP.v1 charts the structural landscape of human early endosome complexes
a, Overlap of DSSO cross-linking data analyzed using XlinkX at 5% FDR compared to Scout at 1%FDR. b, Number of protein interactions based on DSSO cross-links identified with XlinkX and Scout for known interactions and across the selection criteria used in EndoMAP.v1 (i.e. filtering for AF-M score, endosomal protein and cross-link distance). c, ipTM scores for AF-M compared to AlphaLink2 predictions. Color gradient represents the score difference; higher in AlphaLink2 (red) or AF-M (blue). d, Distances between DSSO cross-linked lysines for AF-M compared to AlphaLink2 predictions. Green and orange dots represent interprotein and intraprotein cross-links, respectively. e-i, Individual and overlay AF-M and AlphaLink2 predictions for several protein pairs (see Supplementary Text). DSSO and DHSO/DMTMM interprotein cross-links are indicated with red and cyan lines and arrowheads, respectively. j, Mapping DHSO/DMTMM cross-linking data to the proteins and interactions identified with DSSO. k, Pie chart showing the number of protein pairs identified with both DMTMM and DSSO (top) or DHSO and DSSO (bottom). l, Identified DSSO (red) and DHSO/DMTMM (cyan) cross-links mapped into the endolysosomal V-ATPase (PDB:6WM2)59. m,n, Distribution of Cα-Cα distances (Å) for intraprotein (m) and interprotein (n) cross-linked residues in AlphaLink2 predictions. o, Distribution of Cα-Cα distances (Å) for interprotein cross-links reflecting predictions with SPOC > 0.33.
