Combining\nQuantitative Proteomics and Interactomics\nfor a Deeper Insight into Molecular Differences between Human Cell\nLines

In modern biomedical research, cultivable cell lines\nare an indispensable\ntool, and the selection of cell lines that exhibit specific functional\nprofiles is often critical to success. Cellular functional pathways\nhave evolved through the selection of protein intra- and intermolecular\ninteractions collectively referred to as the interactome. In the present\nwork, quantitative in vivo protein cross-linking and mass spectrometry\nwere used to probe large-scale protein interactome differences among\nthree commonly employed human cell lines, namely, HEK293, MCF-7, and\nHeLa cells. These data illustrated highly reproducible quantitative\ninteractome levels with <i>R</i><sup>2</sup> values larger\nthan 0.8 for all biological replicates. Proteome abundance levels\nwere also measured using data-independent acquisition quantitative\nproteomics methods. Combining quantitative interactome and proteome\ninformation allowed the visualization of cell type-specific interactome\nchanges mediated by proteome level adaptations and independently regulated\ninteractome changes to gain deeper insight into possible drivers of\nthese changes. Among the largest detected alterations in protein interactions\nand conformations are changes in cytoskeletal proteins, RNA-binding\nproteins, chromatin remodeling complexes, mitochondrial proteins,\nand others. Overall, these data demonstrate the utility and reproducibility\nof quantitative cross-linking to study system-level interactome variations.\nMoreover, these results illustrate how combined quantitative interactomics\nand proteomics can provide unique insight into cellular functional\nlandscapes.