Fig. 1: CLASP reveals localization information for most proteins in a XL-based mitochondrial PPI network. | Nature Communications

Fig. 1: CLASP reveals localization information for most proteins in a XL-based mitochondrial PPI network.

From: Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies

Fig. 1

A Workflow for the XL-MS analysis of human mitochondrial proteins. B All identified proteins ranked by the number of their interactions. The inset shows the top 10 and top 50 most-connected proteins. The top 10 proteins are HSPD1, MDH2, HSPE1, ATP5F1A, HSPA9, C1QBP, CYCS, ATP5F1B, PHB2, and SHMT2. C Network coverage achieved when considering the first-tier interactors of 31 LMs derived from the top 50 most-connected proteins (left bar) and all LMs (right bar). D The origins and sub-compartment localizations for all 244 LMs. Proteins were selected as LMs if (i) their sub-mitochondrial localization had been thoroughly established in previous work, (ii) they were part of the top 50 most-connected proteins, had a corresponding PDB structure, or were a component of a well-studied mitochondrial protein assembly, and (iii) there are no cross-links contradicting their sub-compartment localization. E Overview of the mitochondrial PPI network, showing that XL-MS achieves a high degree of interconnectivity. The majority of the network is covered by LMs (red) and their first-tier interactors (blue), i.e. the proteins considered in the CLASP analysis. Source data are provided as a Source Data file.

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