Proteomics: how to control highly dynamic patterns of millions of molecules and interpret changes correctly?

"Proteomics" is essentially protein analysis and, until recently, could be described as an umbrella for a set of technology and bioinformatic platforms aimed at the comprehensive molecular description of the actual protein complement of a given sample. Today, it is typically associated with systems biology. In this context, powerful new technologies for differential complexity reduction promise to solve some of the most pressing problems in drug development. The resulting analytical challenges of unprecedented complexity are emerging as one of the last frontiers of molecular biology. Considerable progress has been made in characterizing rapid post-translational protein modifications in highly complex molecular signatures as key disease-related biomarkers from experimental model systems or clinical samples.: Section Editors: Wolfgang Fischer, Rob Hooft, and Michael Walker Identifying a potential protein drug target within a cell is a major challenge in modern drug discovery; techniques for screening the proteome are, therefore, an important tool. Major difficulties for target identification include the separation of proteins and their detection. The latest developments in techniques that master these challenges, such as SDS-PAGE and liquid chromatography in combination with isotopic labeling and staining techniques, are highlighted in this review. The authors evaluate the applicability of these approaches for specific tasks.