Interfering Substances in 2D Gel Electrophoresis

Lipids: Lipids can bind to proteins changing both their isoelectric point and molecular weight.

Nucleic acids: It c an block gel pores and increase sample viscosity, they may also bind proteins, particularly nucleic acid binding proteins changing both their isoelectric point and molecular weight. Thus, sample before loading must be processed to remove nucleic acid. It can be removed by ultracentrifugation method. Higher density of nucleic acids ensures that they are removed without the loss of proteins. Other method include use of nucleases which can digest nucleic acids

Polysaccharides: Uncharged (starch, glycogen) polysaccharides can block gel pores and inhibit migration of sample proteins resulting in poor focusing. These can simply be removed by ultracentrifugation. However, charged (mucins, dextrans) polysaccharides, on the other hand, bind protein due to charge and change isoelectric point and molecular weight. They can also be very difficult to remove. Polysaccharides cause severe smearing in protein bands.

Salts: High concentrations of salt can pose problems in isoelectric focusing process.