In this issue: Proteomics 9/2008

In this issue of Proteomics you will find the following highlighted articles: 2‐DE: Where do all the little errors come from? Two‐dimensional gel electrophoresis as described by O'Farrell and Klose has always had a reputation for “artsiness,” especially in inter‐lab reproducibility. 2‐D DIGE solves some of the problems but is limited in the number of samples per gel. Here, Fuxius et al. examine the spot density variance (“false significance”) caused by many of the non‐biological components and methods of analysis. Experiments address casting and running of gels: e.g. , in two independent runs, 42% of matched spots exhibited falsely significant differences when gels were compared 1–12 vs. 13–24 but 3% if gels were alternated (1, 3, 5, … vs. 2, 4, 6, …). In another example, first dimension gels that were run as one group, split for second dimension gave over 50% false results. Two batches of 12 second dimension gels from the same caster showed 16% error, 24 gels from one caster had a 5% error rate. Fuxius, S. et al., Proteomics 2008, 8 , 1780–1784. Leishmania: Dwellers from a different dimension? Leishmania species really are dwellers from another dimension, living as flagellated extracellular promastigotes in the stomach of sand flies and as unflagellated intracellular amastigotes in the human macrophages' phagolysosome. The differentiation can be simulated by shifting the promastigotes from an insect‐like environment (26°C, pH 7.0) to a human lysosomal environment (37°C, pH 5.5, 5% CO 2 ). Rosenzweig et al. examined the changes in post‐translational modifications during the transitional period after inducing the pro‐ to amastigote shift. Using iTRAQ/LC‐MS/MS they were able to follow changes over time in >12 000 peptides (1713 distinct proteins). They examined (i) phosphorylation and dephosphorylation: 10 out of 16 had unknown function, no kinases; (ii) methylation: 19 proteins, 20 peptides; (iii) acetylation: 26 peptides, 26 proteins; and (iv) glycosylation: 9 proteins including the first 4 fucosylations reported. The change of state was coordinated with changes in only a few post‐translational modifications, leaving a substantial puzzle for later. Rosenzweig, D. et al., Proteomics 2008, 8 , 1843–1850. Hearts and quads: Mouse proteome targets Our hearts grow and shrink in response to long term changes in oxygen demand, quadriceps volume responds to exercise load (as anyone knows who has had an arm in a cast for a long time). Inappropriate growth or atrophy is characteristic of a number of cardiac and muscular diseases. Although several labs have published proteomic analyses of these tissues, much remains to be discovered. In this manuscript Raddatz et al. identified proteins by 2‐DE‐MALDI‐TOF MS, ultimately detecting 1163 heart spots and 909 quadriceps spots in the pH range of 3–10 and masses between M r 1300 and M r 142 000 by silver staining. With Coomassie Blue for preparative runs, 351 spots/249 heart proteins and 284 spots/214 proteins from skeletal muscle were identified. Proteins could be assigned to seven compartments. These spots complement ∼1000 identified by a non‐gel method recently, with a 46% overlap. Raddatz, K. et al., Proteomics 2008, 8 , 1885–1897.