Fig. 1: EEA1⁺ endosomal proteome analysis through dual complexomics strategies.

a, EndoMAP.v1 workflow schematic depicting integration of XL–MS, BN–MS, scoring method and structural predictions to create an endosomal protein complex structural interaction landscape. b, Endosomal scoring method; known (blue) and candidate (black) endosomal proteins ranked on the basis of combined scoring method, with higher values indicating higher probability of a protein being endosomal. The inset shows receiver operating characteristic curves for each individual metric and its combination for annotating endosomal proteins. Partial area under the curve values at 10% false-positive percentage: combined score, 6.9%; PPIs, 6.1%; dataset count, 4.0%; abundance, 2.1%. c, Correlation heat map of BN–MS co-fractionation data showing unsupervised clustering of well-known endosomal complexes. Number of proteins included in each complex is indicated in brackets. d, Co-fractionation profiles of selected protein complexes from BN–MS. e, Summary of DSSO crosslinks identified in Endo-IP samples, including intraprotein and interprotein crosslinks involving high-confidence endosomal proteins. f, Pie chart showing the number of DSSO crosslinks within and between topological compartments based on Uniprot. g, Density plots showing the distribution of Cα–Cα distances (Å) for intraprotein and interprotein DSSO crosslinks for all structures available in the PDB for the entire XL–MS dataset. The vertical dashed line indicates the maximum distance allowed by the crosslinker. h,i, Identified DSSO crosslinks (red lines) mapped into the endolysosomal V-ATPase (h, PDB 6WM2)⁵⁹ and the class II PI3P lipid kinase complex (i, PDB 7BL1)²⁷. Panel a adapted from ref. ⁴⁴, CC BY 4.0.

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