During immunoprecipitation (IP), a protein of interest is pulled down with a specific antibody or Nanobody. The antibody is coupled to a matrix such as agarose or magnetic agarose and binds specifically to the protein of interest. Unbound sample content like proteins and lipids is washed away, while the precipitated protein is enriched on the matrix.

Immunoprecipitation is also a common and powerful technique for isolating a specific protein and its associated factors from cell or organelle extracts (see Co-Immunoprecipitation below).

Mass Spectrometry (MS) is a common method for identification of proteins.

MS is particularly helpful for protein-protein interaction assays or interactome studies, which aim to identify the interacting partners of a protein within a cell at a time point. Here, in so called affinity purification MS (AP/MS) or capture MS experiments, the protein of interest and its interaction partners are isolated by co-immunoprecipitation (Co-IP).

The subsequent identification of the interacting partners by MS is called bottom-up proteomics. The protein samples are specially prepared for MS analysis: the samples are denatured, reduced, alkylated, and digested. Then, the resulting peptides are cleaned-up and transferred to the MS instrument

Chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) and cross-linking immunoprecipitation (CLIP) are related techniques to investigate the interaction between proteins and nucleic acids.

A convenient way to analyze an enzyme reaction is an enzymatic assay, whereby either the consumption of a substrate or the making of a product is measured. Enzyme assays may serve to identify an enzyme or to determine the amount or activity of an enzyme. In an on-bead enzyme assay, the enzymatic activity can be determined while the enzyme is immobilized on a bead.