Cover Picture: Proteomics 6/2008

Abstract In this issue of Proteomics you will find the following highlighted articles: Reversing dimensions for quantitation: chromatography and electrophoresis From somewhere in the deep fog of the past, remnants of my sophomore physics surface occasionally. This time it is part of a physics lecture on symmetry and the statement that even the dimension of time was reversible. Tribl et al. scrambled the order of chromatographic and electrophoretic separations and used both stable isotopic and fluorescent labels. They started by tagging proteins with DIGE system CyDyes (Cy3, Cy5) for sensitive fluorescent labeling and tagging with isotope coded 12C‐ or 13C‐N‐nicotinoyloxy‐succinimide for relative quantitation. The doubly‐labeled proteins were fractionated on strong anion exchange (ten fractions) followed by reverse phase chromatography (nine fractions) to reduce peptide complexity. They further separated proteins by 1‐D SDS‐PAGE. Differentially labeled proteins were excised, digested and analyzed by nano‐RPC‐ESI‐MS/MS for identification by mass fingerprint. The authors feel the new protocol is complementary to 2‐D DIGE. Tribl, F. et al., Proteomics 2008, 8 , 1204–1211. Tangles and tangled tangles: tauopathies, synucleinopathies and proteasomes Getting rid of the garbage in a cell is not a trivial matter: damaged or unneeded proteins are flagged with ubiquitin and transported to a proteasome, a complex structure of gates and rings where proteins are sorted out, chopped up and dumped out for further processing. Malfunctions of this system (tau‐types or synuclein‐type) can be serious – they are implicated in a number of progressive neurological syndromes, including Alzheimer's, Pick's disease, progressive supranuclear palsy (all taus), and Parkinson's (synuclein). To examine the proteasome proteins involved, Zouambia et al. tested antibodies raised against most of the subunits and subcomplexes as well as a set of overlapping peptides from protein MS73c. The antibodies were used in ELISA, molecular immunohistological and Western blot detection. The results were complicated and depended on whether the antigen target was native or denatured and tau‐ or synuclein‐defect dependent. Clearly, the proteasome proteome will be a very complex affair. Zouambia, M. et al., Proteomics 2008, 8 , 1221–1236. How much interest does a brain bank pay? It depends… How fresh is it? Did it have any interesting diseases? What was its IQ? Any special talents? Did it visit any labs, oops, farms in Transylvania? It would be convenient to have a pop‐up indicator that signals a brain is overcooked, but we don't, so Crecelius et al. used a proteomic approach to find appropriate markers of grey matter status. The critical factors are the postmortem interval (PMI, time between death and storage at –80°C) and storage temperature prior to freezing. Samples stored under various conditions of time (2–48 h) and temperature (4°C and RT) were analyzed by 2‐D DIGE (pH 4–7) and MALDI‐TOF/TOF for protein mass fingerprint identification. Interestingly, out of ∼2000 spots, only ∼6% showed a significant change in quantity at RT, and only 2.5% showed changes at 4°C after 48 h. Changes included both increases and decreases. Crecelius, A. et al., Proteomics 2008, 8 , 1276–1291.