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.