Updated project metadata. This work was made possible thanks to Prof. John LaCava, who co-directed and financed all the proteomics work (European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, The Netherlands AND Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA) and Dr. Wouter Huiting, who produced all the samples that were run in the MS (Department of BSCS, University Medical Center Groningen, University of Groningen, The Netherlands). This dataset consists of 2 independent experiments. The first research aim was to identify the proteins that aggregate in HEK293T cells treated with the chemotherapeutic agent camptothecin (CPT), the second to identify the proteins that aggregate in U2OS cells after a loss of the checkpoint kinase ATM. For the first experiment, cells were treated for 24 hours with vehicle (DMSO) or CPT, left to recover for 48 hours, and harvested. For the second experiment, wild-type and ATM KO cells were grown for 72 hours and harvested. For both experiments, aggregated proteins were isolated by a differential detergent fractionation protocol, which ultimately resulted in a 1% SDS insoluble protein fraction.