Other methods

Sometimes it is necessary to use methods that can be performed in mammalian cell lines, providing a more physiological environment for studies using mammalian proteins. Here are some examples that can be used in medium- or high-throughput setups:

LUMIER: luminescence-based mammalian interactome mapping

MAPPIT: mammalian protein-protein interaction trap

FRET/BRET: fluorescence/bioluminescence-resonance energy transfer

For more information on these techniques, see Reference.¹²

One of the few ways of identifying transient interactions missed by other methods is the enzyme assay. These assays are based on taking enzyme-catalysed reactions as evidence that an enzyme interacts with its substrate, for example. However, these assays can only use in vitro data, requiring purified proteins, as there are too many unknowns if they are performed with a whole cell lysates. Moreover, many enzymes are promiscuous in vitro – most prominently kinases. This can lead to a large number of false positives.

There are many other methodologies we have not covered here, such as PLA, SPR or protein arrays, among others. You can have a look at the Proteomics Standards Initiative Molecular Interactions (PSI-MI) Controlled Vocabulary for a good list. Check the ‘interaction detection method’ branch for a hierarchically-organized collection of methods, with definitions and relevant publications.