The field of chemical proteomics is described by the utilization of chemical probes to study biological questions in a proteomics setup. The most commonly utilized approaches are affinity matrices which use immobilized chemical probes to enrich proteins from complex protein mixtures, and activity based protein profiling (ABPP) where a bifunctional chemical probe reacts covalently with the active site of an enzyme class. Coupling those technologies to gel-based shotgun proteomics facilitates identification and label-free or label-based quantification of all target proteins simultaneously.
Affinity matrices are used to enrich sub-proteomes (e.g. protein kinases, histone deacetylases) from complex samples such as cell or tissue lysates in order to obtain robust identification of low abundant proteins. This technology enables the unbiased investigation of native proteins including their posttranslational modifications, binding partners and differential formation of protein complexes and therefore offers great advantages over conventional methods using fusion proteins or recombinantly expressed domains. It can be used to profile relative differences across different samples, conditions, cell lines or tissues. In a competition setup, it enables the comprehensive and simultaneous determination of binding affinities of all bound target proteins. Pulldowns are usually performed in native conditions and co-enrichment of complex partners allow for the analysis of protein complexes and differential complex formation.
BayBioMS offers consulting for the development and testing of new chemical probes and mass spectrometry based read-out of pulldown eluates. Affinity matrices designed for protein kinases and other ATP binding proteins (Kinobeads technology) and histone deacetylases are available at BayBioMS.
The outcome of a chemical proteomics experiment using affinity matrices is a list of identified and quantified proteins. In a dose-dependent competition setup, a list of target proteins with their respective binding affinities and potential complex partners will be provided.