Cover Picture: Proteomics 9'11

Abstract Tugo' war: Jet turbine engine vs man‐stoked coal You have seen the cartoons, political, comic, and Wild West, and the outcome – whatever fits the story. Well, here (Wellberry Smith et al.) we have a case of thermodynamics driving multiple engines. A few small, high‐affinity units hang onto the rails while all sizes of low‐ and mixed‐affinity units wash past. The bulk of the work is done by quad in‐line diesel turbine antibodies that mean it when they say “for dear life” and “immunodepletion”. Built on a template more precise than a Japanese watch, they can distinguish fakes at ppb levels. Systematically removing 6, 14, or 20 targets vs the whole serum, followed by 2‐D DIGE (top‐down) or LC‐MS/MS (bottom‐up) reveals the levels of reproducibility, specificity, and depth of coverage when analyzed by 1‐D SDS‐PAGE and 2‐D methods. It takes a lot of energy to sort molecules. Wellberry Smith, M. P. et al., Proteomics 2011, 11 , 2222–2235. It is the neighborhood, dumbo The influence of neighboring molecules on transcription has been recognized for some time – like since the isolation of the E. coli lac repressor in the late 1960s – yeah, by hand, my hand. No, we did not know anything about tumor‐related diversity. That came later, just before Hatakeyama et al. demonstrated that neighboring genomic probes, constructed specifically to produce fragmented transcripts, showed cancer‐specific splicing variants that might be worth your time – if you are interested in biomarkers for diagnostic or prognostic applications. Say, is that your boss's ring tone? Hatakeyama, K. et al., Proteomics 2011, 11 , 2275–2282. Shotguns can shoot straight (if the shot does not get in the way) Or the shot pattern is wide enough to insure a hit. Cardiomyopathies are easy targets, a major cause of death, but a difficult etiology call, probably because there are a number of potential causes. So what to do? Call in the proteomics cavalry armed with shotguns (MudPIT‐style) and run analyses on mice heart chambers – left ventricles, right ventricles, and atria. Comunian et al. looked to validate their mastery of shotgun proteomic analysis as well as gather significant data on a critical medical problem. Their reproducibility for a spectral count method was ±5.6% for proteins ( n =302) and ±7.9% for peptides ( n =2848). This compares to ±8% in a previously published study. It is also a good, stable starting point for label‐free quantitative analysis. Differential analysis revealed six groups with interesting members worth further study. Comunian, C. et al., Proteomics 2011, 11 , 2320–2328.