In this issue

Wh has the answer to the dreaded black spot disease ? This is not the black spot of Stevenson's Treasure Island , a piece of paper that only condemned one person to death, but an infectious fungus that condemns forests of poplar trees to massive defoliation and reduced photosynthesis. The fungus, Marssonina brunnea is well studied microscopically, but is molecularly poorly characterized. To address this lacuna, Cheng et al. characterized the fungal peptides and proteins secreted by the fungus in a free‐living state. Since no DNA or protein sequences were published, this required de novo peptide and protein sequencing (ESI‐MS/MS) after growth and isolation of secreted products from culture medium. Previous steps included 2‐DE, two rounds of an improved degenerate primer PCR (aka CODEHOP), 5′‐ and 3′‐ RACE cloning of mRNAs, and RT‐PCR. The presence of signal sequences on mRNA and proteins confirmed a secreted role for many of the proteins. pp. 2406–2417Double your pleasure, double your fun Double your protein IDs to make sure it's the one. (hmm, scans a bit rough). Platelets make an interesting proteome target because when mature, they are anucleate. Traditionally known for participating in hemostasis and clotting, new information points to many other platelet functions, including immune response, bone metastasis, and liver regeneration. Yu et al. wanted to explore this further in an appropriate animal model system. Rat was the preferred animal, with a strong resemblance to humans in cardiovascular problems. A problem at the time the work was done was no rat genome sequence. To carry out the research, the platelet proteomes were compared extensively: multi‐step protein purification, various modes of LC‐MS/MS, two different algorithms for MS/MS spectrum interpretation. Some 837 unique proteins were identified by at least two unique peptide matches each. pp. 2444–2457Mouse mammary tumor model marks more potential markers The growth of transformed cells into tumors and tumors into multi‐site metastases requires a consortium of cytokines, growth factors, Ras proteins, chemo‐attractants, and other molecules. Assuming that messenger molecules would have to be secreted to call for help, Xu et al. looked into quantitative changes in the levels of proteins secreted into conditioned medium (CM) using SILAC and MudPIT technologies. This required more than a simple proteomic analysis: potential for serum starvation effects required careful choice of controls; SILAC labeling cutoff points, differences in MS and immune (Western blot, ELISA) quantitation and specificity could all affect results. A total of 1786 proteins were identified at 95% and the potency of TGF‐β type II receptor in encouraging polyoma virus tumor growth was confirmed. CXCL10 was also an abundant secreted tumor growth factor of substantial interest. pp. 2458–2470