In biotechnology, proteins (usually enzymes) are often produced using large-scale fermentation processes. If a purified enzyme is required for industrial or other (research, medical) use, it must be separated from the matrix of other proteins, live and dead cells and growth media. This often presents a challenge as the enzyme must be separated in such a way as to maintain it's maximal catalytic activity (measured as the specific activity). Some separation techniques are damaging to the target protein itself, therefore methods are often custom designed to suit the target protein. The basic, tradiationally used methods for protein purification in a laboratory environment are:

• Precipitation
• Ion exchange chromatography
• Antibody tags/ Affinity chromatography
• Gel filtration/ Size exclusion chromatography

Protocols for large-scale protein purification are generally based on the basic principles of filtration, affinity binding or separation by precipitation and dissolution, and represent variations of these basic techniques.