In this issue: Proteomics 15/2008

Abstract

AbstractIn this issue of Proteomics you will find the following highlighted articles:An old dog refines new tricksOld dogs are reputed to be slow learners but they can be subtle manipulators, able to induce younger dogs and gullible owners to share the food dish in their favor or choose the path they prefer. Two‐dimensional gel electrophoresis has been around for more than 25 years but “new and improved” versions continue to appear. Ericsson et al. scramble the order of several steps to get more information out of the combination of IPG/IEF and “shotgun” peptide analysis. Developed for studying mechanisms of drug resistance in small cell lung cancer, the modified protocol fractionates sonically disrupted cells into microsomes and soluble fractions before tryptic digestion and iTRAQ labeling for later quantitation. Digested samples were fractionated on narrow range immobilized pH gradient strips from which they were eluted for MALDI TOF or LC‐MS/MS analysis. Detection and identification of transmembrane proteins were dramatically improved.Ericsson, H. et al., Proteomics 2008, 8, 3008–3018.An evanescent view of a lectin micro‐array: through a glass faintlyLectins have the ability to distinguish closely‐related carbohydrate moieties attached (or not) to other molecules such as proteins, peptides, lipids, cells, etc. In some respects, they are much like antibodies, just not quite as specific. Using an array of 45 different lectins, the glycan portion of glycoproteins can be identified by its binding profile. Here, Uchiyama et al. report the improvements they have made to the reproducibility and sensitivity of the system. The binding of rhodamine‐labeled probes was detected in an evanescent field fluorescence‐based instrument that was capable of reaching, 10pM levels without having to wash off unbound probe. Depositing lectin spots with a non‐contact type printer, at the right humidity, and blocking with a non‐proteinaceous material greatly improved sensitivity.Uchiyama, N. et al., Proteomics 2008, 8, 3042–3050.The innate defense: multiplex proteomic probingThe body's first line of defense against pathogen infection is the innate response. In the case of bacterial infection, it is initiated by the sensing of the universal Gram‐positive cell wall lipopolysaccharide (LPS) component by macrophages primarily (but not solely) through the Toll‐like receptor 4 (TLR4). To understand the regulation of the LPS response, Gu et al. developed a multiplex quantitative proteomic analysis procedure to follow the response of TLR4+ and TLR4− cell lines. The method of choice was amino acid‐coded mass tagging (AACT, also referred to as SILAC). It showed high efficiency of labeling (95%) which eliminated interference with quantitation by the unlabeled fraction. Using triplex labeling of lysine (13C, 15N), the authors confirmed that TLR4− cells did show a response to LPS: 25 proteins were up‐regulated in TLR4+ cells, 5 in TLR4− cells. More than 500 proteins could be quantitated.Gu, S. et al., Proteomics 2008, 8, 3061–3070.