Immunoprecipitation can be done in two different ways - direct or indirect. In the direct method, the primary antibody is first bound to the Protein A, G or A/G beads. The beads and sample are then mixed and incubated at 2–8?C. The direct method gives better control of the antibody binding. Direct IP is preferred when the binding kinetics of protein to antibody is fast.

When the antibody has poor affinity for the target or when the target protein is in low abundance, indirect IP is preferred. The indirect method requires minimal co-incubation of Protein A, G or A/G beads with the sample. It has fewer steps and is very easy to use. Indrecit IP allows for optimal control of background binding.