The proteomics toolbox applied to peroxisomes

Abstract

The full understanding of a cell's functionality and activity requires comprehensive knowledge about the properties and the individual contribution of all players involved, both as single entities and as parts of functional units such as membrane-enclosed organelles or larger multi-protein complexes. This comprises, among others, the gathering of information about the accurate subcellular localization of proteins and the interaction networks they form as well as dynamic alterations thereof upon metabolic, developmental, or environmental changes. The proteomics toolbox provides us here with a powerful means for the systematic, discovery-driven analysis of protein properties on a proteome-wide scale. In clever combination with classical biochemical or cell biological methods, state-of-the-art mass spectrometry (MS)-based proteomics has boosted the functional and quantitative analysis of proteins beyond the sheer generation of identification lists. In this chapter, we will highlight the potential of modern MS-based proteomics research for the in-depth analysis of different aspects of peroxisome biology. The focus will be on quantitative MS strategies based on label-free (e.g., protein correlation profiling) or stable isotope-labeling techniques. We will review the applicability of these powerful approaches to the virtually complete delineation of the peroxisomal proteome including the discovery of new peroxisomal constituents as well as the characterization of peroxisomal membrane protein complexes providing new insights into distinct aspects of biogenesis and functioning of peroxisomes.