We present a targeted proteomic approach using parallel reaction monitoring (PRM) to assess the enrichment of cytosolic, mitochondrial, and nuclear fractions obtained from liver samples using commercial isolation kits. For mitochondrial fraction, CPS1 and ATP5F1 were chosen. For the cytosolic fraction, HSP90AB1 and AHCY were selected. For the nuclear fraction, LMNA and NPM1 were used as markers.