Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein?protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein?protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein?protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein?protein interaction. In addition, we discuss the application of these tools in the investigation of protein?protein interaction networks involved in DNA damage response and DNA repair.