Ultrafiltration can be used to rapidly and easily remove small molecules such as Tris, glycerol and glycine from antibody solutions, or to concentrate antibodies prior to conjugation. They also can be used to remove free dye or free biotin from antibodies after conjugation.

For ultrafiltration of proteins, it is recommended to use a MWCO 3 to 6× smaller than the protein to be retained. Ultrafiltration vials with an MWCO of 3 kD are recommended for ultrafiltration of proteins larger than 10 kD. Vials with an MWCO of 10 kD are more suitable for ultrafiltration of antibodies and other proteins larger than 30 kD. Ultrafiltration is not effective for fractionating proteins (separating one protein from another protein based on size) unless there is at least a 10-fold difference in the protein molecular weights.