Proteomic Analysis of Cellular Systems

The large-scale identification and quantification of proteins is an important foundation of systems biology. Here we focus on the particularly powerful technology of mass spectrometry (MS)-based proteomics, with an emphasis on recent high-resolution and quantitative approaches. MS-based proteomics is used to characterize proteins in complex mixtures and it is now possible to quantify nearly all the proteins in human cell lines. Subcellular localization and protein turnover can also be addressed comprehensively. In affinity purifications, quantitative proteomics distinguishes specific interacting proteins from background binders. Thousands of phosphorylation sites as well as other post-translational modifications can readily be quantified in vivo, providing direct access to cellular information processing events. Underlying the recent success of the field are developments in computational proteomics, which now allow highly sophisticated and completely automatic analysis of raw MS data and streamlined bioinformatic and systems-level interpretation of the results.