Cover Picture: Proteomics 1'12

Tuning up your tools An old adage among woodworkers states that sharp tools cut fewer fingers than dull ones and they cut more accurate joints. Having few sharp tools, I can't really argue. In this note, Kalli et al. sharpen up their proteomic tools to improve the experimental reproducibility of their “shotgun” protocols. Parts of the shotgun methodology have been worked over by other labs, but given the expense and complexity of the equipment, the LC and MS/MS instruments have not been as thoroughly tested and evaluated. These workers elected to optimize a nanoflow liquid chromatography system, EASY‐nLC II, coupled to an LTQ‐Orbitrap (both Thermo Fisher Scientific). With appropriate statistical controls and repetitions, they developed a set of sample handling and loading routines that make the most of these expensive research instruments. Kalli, A. et al., Proteomics 2012, 12 , 21–31. Spreading the buzzzz to the surface: Interactomes and fluorescent surface proteins The spread of technology, like the spread of infection, requires that the substrate be present and ready whether it is a particular instrument or strain of mosquito. In the case presented here by Jiang et al., they extend work previously done on the instrumentation and biological tags required to study the detailed structure of the cell‐surface protein interactions. They used radicals formed by “enzyme‐mediated activation of radical sources” (EMARS) in the presence of horseradish peroxidase to label fluorescein‐conjugated aryl azide. Western blot results were cleanly detected with a standard fluorescence image analyzer. A second system used cholera toxin B as a target and reported finding 30 membrane proteins associated with lipid rafts and gangliocide GM1. Further development should make this a valuable diagnostic tool. Jiang, S. et al., Proteomics 2012, 12 , 54–62. At the top of our menu today: Roast oxide stew (ROS) of Cys The acquisition of knowledge tends to follow a sawtooth exponential decay – a new theory answers a bunch of questions, then the distance (or time) between “nuggets” grows longer. We get impatient and look for a sharper knife or bigger shovel. Here, Yang et al. pull out an ultra high‐resolution chromatograph (Nano‐UPLC‐MS E ; ACQUITY, Waters), a matched pair of Prdx −/− and +/+ mice strains, some newer reagents for labeling and detection of oxidized CYS (BIAM) and some good protocols for determining ROS (reactive oxygen species). Using a newer version of shotgun proteomics tools, quantitation of fragments is much easier and more reliable. Given all these features, the network determination with pathway analysis software (Ingenuity Systems) became a tool for the study of a wider range of diseases, including redox‐imbalanced diseases. Yang, H.‐Y. et al., Proteomics 2012, 12 , 101–112.