Functional insight from quantitative mass spectrometry based proteomics

Description

Mass spectrometry based proteomics has become one of the most popular proteomics tools because of its ability to acquire high-content quantitative information about biological samples of enormous complexity. Mass spectrometry based proteomics has already demonstrated its unique capability to provide insight into the molecular function of proteins and their role in biological processes by the characterization of protein complexes and pathways, and through the compositional analysis of subcellular structures. Such experiments have created valuable repositories of information about protein-protein interactions, regulatory post translational modifications, and the localization of proteins in cells.

More recently, quantitative proteomics based on stable isotope labeling by for example amino acids in cell culture (SILAC) has emerged as powerful methods to follow in time how localization, modifications and interaction partners of proteins changes under different physiological conditions. Furthermore, through a variation of these experimental strategies, protein synthesis and trafficking can be studied directly. Importantly, the dynamics of proteins can be assessed for a large variety of perturbations once the proteome of interest has been defined and the method has been established. In this way, quantitative mass spectrometry can be used as a functional assay similar to others that are routinely used in cell biology. These developments in proteomics will be described and illustrated with recent studies from the Center for Experimental Bioinformatics along with a discussion about future perspectives.