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Recent Research Papers of Note: Oct 30, 2009


Journal: Journal of Proteome Research, Oct. 21 [Epub ahead of print]
Title: An initial characterization of the serum phosphoproteome
Authors: Q Zhou; MM Ross; A Tessitore; D Ornstein; A Vanmeter; LA Liotta; EF Petricoin

Authors report "an initial attempt" to characterize the phosphoprotein content of serum using a method they developed in which phosphopeptides are enriched from digested serum proteins and analyzed by LC-MS/MS and LTQ-ETD mass spectrometers. They report the identification of about 100 unique phosphopeptides and a false discovery rate of lower than 1 percent.

Journal: Proceedings of the National Academy of Sciences of the United States of America, Oct. 21 [Epub ahead of print]
Title: Quantitative proteomic analysis of single pancreatic islets
Authors: LF Waanders; K Chwalek; M Monetti; C Kumar; E Lammert; M Mann

Described is a high-sensitivity chromatographic system for measuring nanogram protein mixtures for eight hours "with very high resolution," according to the abstract. The method extends the capability of mass spectrometry to extremely small, physiologically distinct cell types isolated from tissue. The technology is "based on splitting gradient effluents into a capture capillary and provides an inherent technical replicant," the authors said. Based on a single analysis, they were able to characterize kidney glomeruli isolated by laser capture microdissection to a depth of more than 2,400 proteins. From pooled pancreatic islets of Langerhans, they also achieved an in-depth proteome of 6,873 proteins, many involved in diabetes.

Journal: Biotechnology Journal, Oct. 20 [Epub ahead of print]
Title: A food safety control low mass-range proteomics platform for the detection of illicit treatments in veal calves by MALDI-TOF-MS serum profiling
Authors: L Della Donna; M Ronci; P Sacchetta; C Di Ilio; B Biolatti; G Federici; C Nebbia; A Urbani

In the abstract, the authors said that performance-enhancing agents are used in cattle and meat to increase food conversion and lean meat production, and that veal calves are the meat-producing bovine most subjected to such illicit treatments. The chemical agents are hard to detect by conventional analytical approaches "due to the employment of synergistic formulations at very low dosage … and the use of uncharacterized novel compounds." As a result, "strong interest" exists to discover functional biomarkers for the detection of growth-promoting agents. The article describes a multivariate MALDI-TOF-MS platform for use with bovine serum samples. The authors propose univariate and multivariate discrimination models that can identify calves that have been subjected to illicit treatments. "In particular, we found a strong discrimination power associated with a polypeptide fragment from beta2-glycoprotein-I," they said.

Journal: Nature Methods, Oct. 18 [Epub ahead of print]
Title: Visual proteomics of the human pathogen Leptospira interrogans
Authors: M Beck; JA Malmström; V Lange; A Schmidt; EW Deutsch; R Aebersold

In the abstract, the authors said that systems biology conceptualizes biological systems as "dynamic networks of interacting elements" where the structure of such networks bestows functionally important properties. Because of the ubiquitous role of complexes of interacting proteins in biological systems, "their subunit composition and temporal and spatial arrangement within the cell are of particular interest," they said. The article describes quantitative mass spectrometry coupled with cryo-electron tomography to detect, count, and localize specific protein complexes in the cytoplasm of Leptospira interrogans. They also describe a scoring function for visual proteomics and evaluate its performance and accuracy under "realistic conditions."

Journal: Molecular & Cellular Proteomics , Oct. 16 [Epub ahead of print]
Title: Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomic analyses and evaluation by the CPTAC network
Authors: PA Rudnick; KR Clauser; LE Kilpatrick, et al.

According to the abstract, a "major unmet need" in LC-MS proteomics analysis are tools for "the quantitative assessment of system performance and evaluation of technical variability." Described are 46 performance metrics for monitoring chromatography performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for tandem mass spectrometry, and peptide identification.

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Journal: Proteomics, Oct. 15 [Epub ahead of print]
Title: Improved reproducibility of reverse-phase protein microarrays using array microenvironment normalization
Authors: T Anderson; J Wulfkuhle; L Liotta; RL Winslow; E Petricoin

Introduced is a novel experimental method for the reverse phase protein microarray platform, "which reduces the typical measurement coefficient of variation as much as 70 percent," according to the abstract. The method, array microenvironment normalization, increases the statistical power of the platform, and in an experiment enabled the detection of a 1.1 fold shift in PSA concentration using approximately six replicates instead of 37 replicates, which had been previously required.

Journal:Proteomics Oct. 15 [Epub ahead of print]
Title: A highly sensitive near-infrared fluorescent detection method to analyze signaling pathways by reverse-phase protein array
Authors: L Dupuy; C Gauthier; G Durand; A Musnier; D Heitzler; A Herledan; V Sakanyan; P Crépieus; E Reiter

Authors describe an improved detection method for reverse-phase protein arrays that combines near-infrared with one or two rounds of tyramide-based signal amplification. "The limit of quantification was lowered from 6.84 attomoles with a direct detection protocol to 0.21 attomole with two amplification steps," according to the abstract. The authors report they consistently detected phosphorylated proteins in the sub-attomole range with less than 1 nanogram of total cell extracts. "Importantly, the method correlated with Western blot analysis of the same samples while displaying excellent intra- and inter-slide reproducibility," they said.

Journal: Proteomics, Oct. 15 [Epub ahead of print]
Title: The PSI semantic validator: a framework to check minimum information about a proteomics experiment compliance of proteomics data
Authors: L Montecchi-Palazzi; K Kerrien; F Reisinger; B Aranda; AR Jones; L Martens; H Hermjakob

Presented is a framework for checking that experimental data using a specific format, controlled vocabularies, and public bio-ontologies follow the Minimum Information About a Proteomics Experiment recommendations. "The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or [ controlled vocabulary] terms by checking that the terms exist in the resource and that they are used in the correct location of a document," according to the abstract. The framework is "extremely fast" and flexible, according to the authors, and provides a general solution for validating the correct usage of a data standard beyond simple XML schema definition validation.

Journal: Journal of Proteome Research, Oct. 12 [Epub ahead of print]
Title: Quantitative serum proteomics using dual stable isotope coding and nanoLC-MS-MS/MS
Authors: H Wang; CH Wong; A Chin; J Kennedy; Q Zhang; SM Hanash

The authors present a novel methodology "to increase the yield of quantified proteins while maintaining a high stable-isotopic labeling efficacy," according to the abstract. Intact proteins in complex biological samples are labeled with the designated dual stable isotope coding system. Intact proteins are coded sequentially with acrylamide to label cystein dyes and with succinic anhydrige to label lysine residues. These protein samples are subjected to an online 2D-HPLC fractionation. The resolved protein fractions are individually digested with trypsin and analyzed with nanoLC-MS-MS/MS

Journal:Proteomics, Oct. 12 [Epub ahead of print]
Title: Preserving the yeast proteome from sample degradation
Authors: J Grassl; JA Westbrook; A Robinson; M Borén; MJ Dunn; RK Clyne

The authors use Saccharomyces cerevisiae to evaluate the effects of trichloroacetic acid and thermal treatments prior to protein extraction as a method to minimize proteolysis. The methods were also compared to that of protease inhibitors and lyophilization. The results indicate that TCA or thermal treatment "significantly reduced the degree of degradation and that these pre-treatment protocols were more effective than treatment with either protease inhibitors or lyophilization," according to the abstract.

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Journal: Analytical and Bioanalytical Chemistry, Oct. 6 [Epub ahead of print]
Title: Proteomic strategies for the identification of proteinaceous binders in paintings
Authors: G Leo; L Cartechini; P Pucci; A Sgamellotti; G Marino L Birolo

According to the abstract, identifying proteinaceous components in paintings is challenging due to the minute amount of samples available, complex and variable chemical compositions of the paints, and possible simultaneous presence of several binders and contaminants, as well as the degradation of the original materials. They propose a strategy based on the direct tryptic cleavage of the sample without protein extraction and the use of microwave to enhance the enzymatic digestion yield. This was followed by the analysis of the peptide mixtures by nanoLC-MS/MS with ESI.

Journal: Proteomics Oct. 1 [Epub ahead of print]
Title: Attovial-based antibody arrays
Authors: P Ellmark; S Ghatnekar-Nilsson; A Meister; H Heinzelmann; L Montelius; C Wingren; CA Borrebaeck

Described is a first generation of a nanoarray platform based on attoliter sized vials, which were characterized and used for detecting complement factor C1q in human serum samples. The authors also demonstrated proof of concept for individual functionalization of the attovials with a recombinant antibody.

Journal: Journal of Proteome Research, October
Title: CLUE-TIPS, clustering methods for pattern analysis of LC-MS data
Authors: LM Akella; T Rejtar; C Orazine; M Hincapie; WS Hancock

Presented is an approach that compares complex proteomic samples for similarity/dissimilarity analysis. In the method, called CLUE-TIPS, for Clustering Using Euclidean Distance in Tanimoto Inter-Point Space, "an intersample distance feature map is generated from filtered, aligned and binarized raw LC-MS data by applying the Tanimoto distance metric to obtain normalized similarity scores between all sample pairs for each m/z value," according to the abstract. The authors developed clustering and visualization methods for the intersample distance map to interrogate samples for differences at the sample level and the individual m/z level.

Journal: Journal of Proteome Research, October
Title: High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
Authors: T Köcher; P Pichler; M Schutzbier; C Stingl; A Kaul; N Teucher; G Hasenfuss; JM Penninger; K Mechtler

In an effort to improve iTRAQ-based quantification on an LTQ-Orbitrap, authors developed an analytical strategy combining the advantages of CID and HCD, "allowing sensitive and accurate protein identification and quantitation at the same time," according to the abstract. The method described outperformed PQD and HCD in terms of the limit of detection, the number of identified peptides, and the analytical precision of quantitation, they said.

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Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.