Cover Picture: Proteomics 9'10

Soft‐headed proteome subject of a play For those of us who don't know our developmental anatomy, calavarial osteoblasts (CO) are the cells responsible for hardening that soft spot in your skull you were left with at birth. They normally do their job promptly and disappear. Kumar et al. were curious about the director and actors in this “one actor” so they applied proteomic tools to the problem. The play started with a course of kaempferol, a flavonol found by this group to promote mineralization of rat COs in vitro and in vivo . Samples of stimulated and unstimulated cell extracts were analyzed by 2‐DE, identified by MALDI‐TOF MS, and validated by Western blots, qPCR, and enzyme assay (aldose reductase). The proteins found thus far provide an interesting preface to a new show. Kumar, A. et al ., Proteomics 2010, 10 , 1730–1739. Cultured breast cancer cells behave properly Murphy et al. wanted to be sure that their analysis of changes over time in the proteome of MCF‐7 breast cancer cells, stimulated with insulin‐like growth factor‐1R (IGF‐1R), was done with the right tools, the right methods, and the right model. It had to be quantitative so they used iTRAQ chemistry and two independent statistical methods. Vesicle trafficking activity jumped and biologically relevant activities increased as judged by 2‐D LC‐MS/MS and by a targeted multiple reaction monitoring (MRM) system. Validated activities included pyruvate kinase (M2), alcohol dehydrogenase, and cytochrome P450 isoforms. With further work, one or more of these proteins may prove of value as a therapeutic target or biomarker for IGF‐1R in breast cancer. Murphy, J. P. and Pinto, D. M., Proteomics 2010, 10 , 1847–1860. Multi‐source mapping made manageable “Keeping up with the Jones's” in proteomics does not necessarily mean matching every new mass spec with one better – it also means having the analytical computing power required to extract the information in the results. Askenazi et al. describe in this Technical Brief their publicly available proteome analysis/protein–protein interaction pathway package, Pathway Palette . Input can be from a number of sources, ranging in form from simple text lists to Entrez gene lists, spreadsheets, GO, KEGG, or OMIM reports. Peptides remain linked to mass spectra so you can always “drill down” into underlying information. Result storage and output are done client‐side, calculations and analysis are done server‐side anonymously. The PPI network can be edited and extended as needed. All in all, it sounds like a Swiss army knife for protein pathway mapping. Askenazi, M. et al ., Proteomics 2010, 10 , 1880–1885.