Cover Picture: Proteomics 20'10

Proteomics on its head: Improvements to top‐down analysis of whole proteomes We no longer need a herd of “one‐trick ponies” to solve protein identification problems in a top‐down fashion. A new pony capable of doing multiple tricks, such as recognition of multiple post‐translational modification sites, is now available. Durbin et al. here describe an improved software system capable of high‐throughput, high‐resolution top‐down analysis and identification of proteins up to 70‐ to 90‐kDa. Identification at the high end of the range requires the GELFrEE device, kDecon software and expects its input from an ion trap MS. The low end of the range, under ∼30 kDa, is covered by PTMcrawler software coupled to a Fourier Transfer MS system. Also included are improved noise reduction, visualization of identified masses and mapping of particular Δ m values. Durbin, K. R. et al ., Proteomics 2010, 10 , 3589–3597. New‐ish gear for starting from the top puts users in orbit Selecting a liquid chromatography system and a compatible mass spec. platform must feel like judging a livestock or dog show — the competitors all have their good points but you can only choose one. Mohr et al. introduce a relatively new combination, the Orbitrap mass analyzer, introduced in 2000, and monolithic chromatography columns, introduced in the late '90s, both relatively young by HPLC standards. The tortuous path of a monolithic column is much more efficient than the path through loose beads, producing >130 peaks in 25 min with a 0.1 mm id×150 mm column. Column resolution was not lost by a slow detector, the Orbitrap could take 2.5 spectra per second. A drawback (not unique) is that recovery depended on the stationary phase material and the particular characteristics of the specific protein. Mohr, J. et al ., Proteomics 2010, 10 , 3598–3609. Malevolent microRNA behind hepatocellular carcinoma When a hepatocellular carcinoma turns up, chances are high (∼70%) that microRNA‐122a (miR‐122a) is in the vicinity. Often it is downregulated and its functional target is unknown. Diao et al. picked up their set of proteomics tools and went to work on the target question, applying 2‐DE, MALDI‐TOF, multiple liver cancer cell lines, and lentivirus miR‐122a over‐expression vector transformation, among others. They confirmed that over‐expression of miR‐122a caused under‐expression of cyclin G1 and induced apoptosis. In total, they found ten proteins responded to over‐expression of miR‐122a. One of particular interest was peroxiredoxin II (PRDX II), an antioxidant protein that is often seen over‐expressed in human cancers of the lung, breast, and pancreas. Diao, S. et al ., Proteomics 2010, 10 , 3723–3731.