In this issue: Proteomics 17/2008

In this issue of Proteomics you will find the following highlighted articles: Slidin' and slipin': Substrates for autoantibody antigen arrays Proteins do not have a reputation for being well‐behaved. Given the number of sequence permutations possible for a particular length, it is no wonder that protein arrays have a notorious history. Balboni et al. report here on a systematic survey of supports and application methods for autoantibody antigen arrays. These arrays are central to studies of autoimmune diseases such as juvenile‐onset (type I) diabetes, rheumatoid arthritis, multiple sclerosis, etc . Over 20 commercial and home‐made slides were tested for background, smearing, streaking, adherence, and intra‐ and inter‐slide variability (CVs). FAST® slides were ranked the best on the CV scores. Also acceptable were PATH® and SuperEpoxy2 slides. The authors note that other slide types may be better for specific antigens or detection methods. Balboni, I. et al, Proteomics 2008, 8 , 3443–3449. Cheesy target for high resolution proteomics We are what we eat and sometimes that includes the leftovers from other organisms. “Yecch!” you say, but these are the products of a fermentome (to coin a new name), those proteins and organisms that ferment our food – grapes to wine, milk to yogurt, etc. – processes that need to be well understood for food safety and quality. Soufi et al. explore the phosphoproteome of Lactococcus lactis, an important commercial strain of bacteria, used in making a variety of fermented food products. L. lactis exhibits site‐specific phosphorylation of serine, threonine and tryptophan residues similar to that found in eukaryotes. Unlike eukaryotes, bacteria usually have only one phosphorylation site per protein. The evidence presented suggests protein phosphorylation is a means to regulate gene expression in bacteria, albeit on a smaller scale than in higher organisms. Soufi, B. et al, Proteomics 2008, 8 , 3486–3493. To see or not to see: That is not a question One of the most frequent healing complications of surgical repair of a detached retina is the overgrowth of membranes on both surfaces of the retina and the back side of the vitreous body (PVR) which can contract and rip the underlying tissue loose, creating major vision problems. Yu et al. applied proteomic tools to the problem and found the explanation lay in misregulation of a number of cytoskeleton and metabolism genes. Normal, moderate and severe PVR vitreous and serum samples were treated with trypsin and analyzed by strong cation exchange‐ and reverse phase‐chromatography then nanoelectrospray‐double quadrupole MS. Identity of vitreous proteins was verified by Western blots. The combined total of proteins identified was 255 but only 35 were common to both PVR and control samples, 24 were common to moderate and severe PVR. The regulation model is still a bit murky but should clear soon. Yu, J. et al., Proteomics 2008, 8 , 3667–3678.