Cover Picture: Proteomics 24'11

Might mighty switches small molecules make? Regulation of production of secondary metabolites is an important issue in the production of a variety of pharmaceuticals in Streptomyces coelicolor , a typical Actinomycete. Of particular interest is developing a switch operated by a metabolic change without a nutrient limitation. In this paper, Jankevics et al. explore the use of a non‐coding RNA as a switch. This requires large‐scale, untargeted metabolomics and thorough statistical analysis. And samples, lots of samples to get the noise out – biological, analytical and technical. Unique (97) samples found were putatively matched for very high concordance, 77 based on HILIC, 54 for C18 and 34 for high consistency. And surprise, GSI was found to be an unexpected switch element. Jankevics, A. et al., Proteomics 2011, 11 , 4622–4631. Split bead soup Funny how you begin to focus on basic issues when you get hungry or tired or pressed for time. Like the football game is about to start but I have not finished this note. To the meat of the matter: a bead “array” protocol described by Zhang et al. These researchers have developed a procedure that clarifies links between protein targets (phosphoproteins) and the regulatory network of protein kinases. Although chip technology has been proven for this type of data, it is expensive and difficult. In this case, the target protein to be analyzed is diluted to binding of <25:1 protein molecule per bead. Bound by cyanogen bromide, this is too little to measure by mass spec., instead, a quantitative measure of substrate can be determined (HeLa standard, Bradford assay). The results were closely parallel to previous studies. One remaining issue is accounting for the organelle proteomes in the samples. Let the games begin. Zhang, M. et al., Proteomics 2011, 11 , 4632–4637. Map‐making for matrix molecules Cartilage is central to the proper growth within the growth plate and in articulation of the joint. The cartilage tissue is composed of chondrocytes and a dense extracellular matrix, which is in turn, composed of water, proteoglycans and collagens. Over 200 of 2400 chondrocyte gene products are extracellular. Understanding these complex gene families will make major improvements in the quality of life for those dealing with a broad spectrum of arthritic syndromes. Brown et al. have begun exploring this territory with tools including LC/MS‐MS/1‐D electrophoresis and affinity chromatography. False discovery rates were determined using decoy searches. Interactions were identified using STRING, which integrates protein–protein data from gene fusion, co‐occurrence, experimental, ...surface plasmon resonance and solution equilibrium. Brown, R. J. et al., Proteomics 2011, 11 , 4660–4676.