Targeted proteomics

Usually, proteomics is thought of as a technique for the identification and quantification of thousands of proteins. Most proteomics studies follow this credo and use discovery proteomics technologies for the measurement of proteins. Although discovery proteomics techniques are very powerful, they are limited in their ability to identify the same set of proteins in larger cohorts. Several isotope-based labeling techniques have been developed to overcome this. Targeted proteomics follows a different path by just focussing on a small set of proteins of interest. The proteins are selected prior to the measurement, and a specific method for the measurement of the protein set is implemented. By restricting the measurement to a set of proteins, the measurement gains sensitivity and is highly reproducible. These characteristics are making the method particularly interesting for the measurement of large cohorts, like clinical cohorts.

Targeted proteomics come mainly in two different flavors, selected reaction monitoring (SRM) and parallel reaction monitoring (PRM). While SRM is bound to be used with a triple-quadrupole type of mass spectrometer, the PRM method can be used on orbitrap-based machines. In an SRM experiment, the different key-fragment pairs, used for the quantification of the protein of interest, are addressed sequentially, while the PRM method allows the simultaneous acquisition of all pairs, which allows the selection of the best pairs in silico after the acquisition.

My group uses different PRM techniques for the measurement of protein sets, or biomarkers in clinical cohorts. A different application is the monitoring of ubiquitin signaling, selecting a specific set of ubiquitin peptides, unique for the different ubiquitin chains.