Updated project metadata. Here we present high resolution data from two cancer cell lines. A human cell line, A431 was treated with a drug at different time points and then fractionated into its different subcellular compartments (nuclear, organellar, soluble, whole cell). Protein extracts were trypsinized, peptides separated by HiRIEF (high resolution isoelectric focusing) and analysed by LC-MS. From the mouse cell line N2A proteins were extracted and subjected to the same HiRIEF-LC-MS procedure.