Despite the importance of studying nucleoprotein complexes, no appropriate method for quantifying them is available. Here, a UV absorbance method using the formula “C_mg/mL = 1.55A₂₈₀ – 0.76A₂₆₀” were applied to quantify nucleoprotein complexes. After modification using two paired A₂₆₀ and A₂₈₀ values, the UV-derived formula-based method could accurately quantify proteins in nucleoprotein complexes. Otherwise, by taking the target protein as a standard, the Bradford assay can accurately quantify proteins in nucleoprotein complexes without interference by nucleic acids. The above methods were successfully applied to measure the concentration of MtuP49-CTG complexes of Mycobacterium tuberculosis. In conclusion, both the Bradford assay and the UV-derived formula-based method were appropriate for quantifying proteins in nucleoprotein complexes, which may make contributions to explore the interactions between proteins and nucleic acids at the molecular level.