Extended Data Fig. 2: Application of correlation profiling and cross-linking proteomics to endosomes purified by Endo-IP.
From: EndoMAP.v1 charts the structural landscape of human early endosome complexes
a, Co-fractionation profiles of selected protein complexes from BN-MS. b, Number of Bioplex interactions identified by BN-MS compared to co-fractionation PCProphet scores. c, Number of Bioplex interactions identified using PCProphet in either 2 or 3 replicates of the Endo-IP BN-MS compared to the maximum number of proteins per complex allowed in the analysis. d, Box plot depicting the protein MS signal intensity in Endo-IP compared to the number of DSSO cross-links identified for each protein (n number of proteins in each category is indicated on top). e, Box plot depicting the minimum protein MS signal intensity for PPIs identified by BN and DSSO cross-linking compared to all proteins identified in Endo-IP (n number of interactions in each category is indicated on top). f, Distribution of protein copy number (log10)18 for cross-linked proteins compared to the whole proteome. g-i, Box plots depicting the protein copy number (g), number of interactors in BioPlex (h), and molecular weight (i) compared to the number of interprotein DSSO cross-links identified for each protein (n number of proteins in each category is indicated on top). j, Venn diagram showing the number of protein pairs identified by yeast two hybrid (YTH), Bioplex, and cross-linking proteomics for the same set of proteins. k, Boxplot showing co-fractionation SECAT p-values for cross-linked proteins identified by different number of DSSO cross-links (n number of interactions in each category is indicated on top). l,m, Number (panel l) and rank (panel m) of cross-linked protein interactions that have been previously reported (or not) compared to their co-fractionation SECAT p-value (Supplementary Table 2). SECAT was used for statistical analysis169,170. n, Overview of protein interactions within EndoMAP.v1 including the method, organelle and previous reports. o, Venn diagram showing the overlap of endosomal interactions between EndoMAP.v1 and Bioplex for interactions in which both proteins are present in both datasets. For all box plot panels, the middle line corresponds to the median, the lower and upper end of the box correspond respectively to the first and third quartiles, and the whiskers extend from the box to 1.5 times the inter-quartile range.
