The study presents BioPlex 2.0, a comprehensive resource for understanding the human interactome. BioPlex 2.0 is the largest collection of human co-complex data to date, containing over 56,000 interactions from 10,961 proteins, with more than 29,000 previously unknown co-associations. The network was generated using robust affinity purification-mass spectrometry (AP-MS) methodology, targeting more than 25% of protein-coding genes from the human genome. The network identifies 1,320 protein communities representing diverse cellular activities and enriches in 53 communities essential for cell fitness. Additionally, 442 communities are associated with over 2,000 disease annotations, providing a cellular framework for candidate disease genes. The study also highlights the utility of BioPlex 2.0 for predicting subcellular localization, domain co-association, and functional modules of poorly characterized proteins. Overall, BioPlex 2.0 is a valuable resource for exploring the biology of incompletely characterized proteins and elucidating larger-scale patterns of proteome organization.The study presents BioPlex 2.0, a comprehensive resource for understanding the human interactome. BioPlex 2.0 is the largest collection of human co-complex data to date, containing over 56,000 interactions from 10,961 proteins, with more than 29,000 previously unknown co-associations. The network was generated using robust affinity purification-mass spectrometry (AP-MS) methodology, targeting more than 25% of protein-coding genes from the human genome. The network identifies 1,320 protein communities representing diverse cellular activities and enriches in 53 communities essential for cell fitness. Additionally, 442 communities are associated with over 2,000 disease annotations, providing a cellular framework for candidate disease genes. The study also highlights the utility of BioPlex 2.0 for predicting subcellular localization, domain co-association, and functional modules of poorly characterized proteins. Overall, BioPlex 2.0 is a valuable resource for exploring the biology of incompletely characterized proteins and elucidating larger-scale patterns of proteome organization.