The MFI of the Ab-RPE conjugate before S300 purification is always better than after purification (even if the F/P ratio after purification is still correct), what may happen and improve?
Are you comparing like with like? Before purification, you will have unconjugated RPE which will be removed by chromatography. You will also have some volume expansion of the conjugate. For both reasons the fluorescence intensity of the pure conjugate will be lower than that of the more crude starting material.