We performed abundance analysis of chromatin-residing proteins in BLaER1 cells during the early stages of B-cell-to-macrophage transdifferentiation. We employed protein aggregation capture (PAC) to analyze chromatin-residing protein abundances at 0, 6 and 24 h after induction of transdifferentiation in the absence and presence of the small-molecule SUMOylation inhibitor ML-792 (SUMOi). Mass spectrometry analyses were executed with high resolution mass spectrometry (LC-MS), using the Evosep One liquid chromatography system coupled to Orbitrap Astral mass spectrometer. Raw Orbitrap Astral data-independent acquisition (DIA) data were processed with DIA-NN. Data ouput from DIA-NN were further processed with ProteoGyver.