In this issue: Proteomics 11/2008

Abstract

AbstractIn this issue of Proteomics you will find the following highlighted articles:Pancreatic cancer signs autograph on micro antibody arrayPancreatic cancer has been one of the nastier members of the “Discovered‐too‐late‐to‐do‐anything‐about‐it” disease club. Its 5‐year survival rate is 3–5 % because of late diagnosis and no effective therapy for advanced disease cases. This paper by Ingvarsson et al. reports their encouraging findings on the use of recombinant antibody microarrays to survey serum for diagnostic and prognostic proteins. In these “proof‐of‐concept” experiments they found a signature of 19 unique scFv antibodies, specific for immunoregulatory proteins, that could distinguish pancreatic cancer from normal and from Helicobacter pylori (an indicator of inflammation, 3 out of 14 overlap). The test panel distinguished long and short survivors (with only one long survivor misclassified). Data was classified using a Support Vector Machine. The classifier was validated by multiple splits of the data and leave‐one‐out tests.Ingvarsson, J. et al., Proteomics 2008, 8, 2211–2219.Of cadmium and zinc: Brothers or not?Cadmium and zinc occupy the same column in the periodic table so you might expect some biological similarities. Not much luck – mercury is also in that column. Zinc, under tight control, is an essential mineral; cadmium is toxic and induces a variety of defensive responses. A highly zinc‐resistant cell line (HZR) has been derived from the human HeLa line. Rousselet et al. have compared the proteomes of HZR and HeLa cultured in Cd and Zn using a variety of proteomic and genomic tools. MALDI‐TOF MS after 2‐DE revealed examples of a co‐chaperone, a heat‐shock organizing protein (Hop), ubiquitin and a number of reactive oxygen species control proteins elevated in HZR. Of special interest was 4‐hydroxyphenyl‐pyruvate dioxygenase (HPPD), catalyst of one of the first breakdown steps of tyrosine. The complex relationships revealed will require a lot more than one paragraph for explanation.Rousselet, E. et al., Proteomics 2008, 8, 2244–2255.Grey box proteomics of salty speciesIn the classic black box experiment you know nothing about the contents of the box. I propose a grey box for experiments directed by homologous knowledge – like these. Pandhal et al. have developed a protocol for proteomic analysis of an unsequenced species by homology. The organism of interest is a halotolerant cyanobacterium, Euhalothece sp. which can grow in NaCl concentrations ranging from 0% to >9% NaCl. The nearest sequenced relative is a Synechocystis sp. By metabolic labeling with 15N/­14N, the researchers were able to use MS to match proteins from the two species and also quantitate changes in levels of proteins in response to salt levels. Three labelling experiments ([% NaCl], 0% +3%, 3% +6%, and 3% +9%) yielded 229, 212, and 96 proteins, respectively, by MASCOT search of proteins with two peptides of each isotope. MS BLAST found 32, 30, and 7 more proteins, respectively.Pandhal, J. et al., Proteomics 2008, 8, 2266–2284.