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Recent Research Papers of Note: Apr 9, 2009


Journal: Journal of Proteome Research, April 1 [Epub ahead of print]
Title: An efficient organic solvent-based extraction method for the proteomic analysis of Arabidopsis plasma membranes
Authors: S Mitra; B Walters; S Clouse; M Goshe

In previous work, authors determined that methanol-assisted solubilization facilitates the identification of both hydrophobic and hydrophilic membrane proteins compared to Brij-58 solubilization. The method was particularly effective for leucine-rich repeat receptor-like kinases, they said. In the current article, they describe a chloroform extraction method to promote plasma membrane-protein identification. "The use of chloroform extraction over traditional solid-phase extraction prior to off-line strong cation exchange liquid chromatography and reversed-phase liquid chromatography-tandem mass spectrometry analysis facilitated the removal of chlorophylls, major contaminants of plant tissue preparations that can affect downstream analysis, in addition to the effective removal of trypsin used in the digestion," according to the paper's abstract.

Journal: Bioinformatics, March 31 [Epub ahead of print]
Title: StatQuant: A post-quantification analysis toolbox for improving quantitative mass spectrometry
Authors: B van Breukelen; HW van den Toorn; MM Drugan; AJ Heck

Presented is StatQuant, a software tool to process, filter, compare, and present data from several quantitative proteomics software packages such as MSQuant.

Journal: Journal of Proteome Research, March 27 [Epub ahead of print]
Title: Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development
Authors: A Prakash; D Tomazela; B Frewen; G Merrihew; B MacLean; S Peterman; M MacCoss

While selected reaction monitoring is a "powerful tandem mass-spectrometry method" for monitoring target peptides within a complex protein digest, "an underappreciated step in the development of an assay to measure many peptides in parallel is the time and effort necessary to establish a useable assay," the authors said in the abstract. Here, they report the use of shotgun proteomics data to speed up the selection of SRM transitions for target peptides of interest.

Journal: BMC Cancer, March 27 [Epub ahead of print]
Title: MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides
Authors: X Yang; IM Lazar

Authors analyzed MCF-7 breast cancer protein cellular extracts by 2D-strong cation exchange reversed-phase liquid chromatography separations interfaced to linear ion trap MS detection, then interpreted the data with the Sequest-based Bioworks software. Using Perl scripts developed in house, they calculated the spectral counts and the representative fragment ions for each peptide. They report generating a library of 9,677 peptides representing about 1,572 proteins from human breast cancer cells that can be used for MRM/MS-based biomarker screening studies.

Journal: Chemical Research in Toxicology, March 25 [Epub ahead of print]
Title: A targeted proteomics approach to the identification of peptides modified by reactive metabolites
Authors: M Tzouros; A Pahler
A "highly selective" proteomics workflow for the targeted identification of peptides modified by reactive metabolites is reported. According to the abstract, the approach is "generally suitable for the identification and characterization of modified proteins and metabolite structures involved in covalent binding and may serve as a valuable tool to link protein targets with clinically relevant toxicities."

Journal: Bioinformatics, March 24 [Epub ahead of print]
Title: Integrating shotgun proteomics and mRNA expression data to improve protein identification
Authors: SR Ramakrishnan; C Vogel; JT Prince; Z Li; LO Penalva; M Myers; EM Marcotte; DP Miranker

Described is a Bayesian score that estimates the "posterior probability of a protein's presence in the sample given its identification in an MS/Ms experiment and its mRNA concentration measured under similar experimental conditions," according to the abstract. The method, dubbed MSpresso, "substantially" increases the number of proteins identified in an MS/MS experiment at the same error rate, the authors said.

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Journal: Chembiochem : A European Journal of Chemical Biology, March 23
Title: Particle-based synthesis of peptide arrays
Authors: F Breitling; T Felgenhauer; A Nesterov; V Lindenstruth; V Stadler; FR Bischoff

In the abstract, the authors said that lithographic methods, which allow for the combinatorial synthesis of more than 50,000 oligonucleotides per square centimeter, have "revolutionized the field of genomics." While it holds the promise of advancing proteomics in a similar way, high-density peptide arrays currently lag behind. "This is mainly due to the monomer-by-monomer repeated consecutive coupling of 20 different amino acids associated with lithography, which adds up to an excessive number of coupling cycles," according to the abstract. "A combinatorial synthesis based on electrically charged solid amino acid particles resolves this problem."

Journal: Journal of Separation Science, March 19 [Epub ahead of print]
Title: Shotgun mass spectrometry analysis of the human thalamus proteome
Authors: D Martins de Souza; G Maccarrone; S Reckow; P Falkai; A Schmitt; CW Turck

Using a shotgun workflow consisting of IEF fractionation, RPLC, and MALDI-TOF/TOF MS, authors analyzed iTRAQ-labeled tryptic peptides of human mediodorsal thalamus protein extracts of two healthy males and two healthy females. They identified 542 proteins involved in different biological processes and from diverse cellular localizations. They said that a "considerable" fraction of these proteins had not been identified in traditional proteomics methods.

Journal: Proteomics, March 17 [Epub ahead of print]
Title: Analysis of low molecular weight plasma proteins using ultrafiltration and large gel two-dimensional electrophoresis
Authors: WW Jung; S Phark; S Oh; JY Khim; J Lee; MN Nam; JB Seo; SY Park; E Jo; S Choi; Z Zheng; JY Lee; M Lee; E Lee; D Sul

Various solvent systems were used to obtain a "high and consistent" recovery rate of low molecular weigh plasma proteins from human plasma. A buffer system containing 7 moles of urea, 2 moles of thiourea, 25 micromoles of NH4HCO3 and 20 percent ACN produced the highest recovery rate. The authors also conducted 2DE analysis to determine the relative intensity of each protein spot.

Journal: Proteomics, March 17 [Epub ahead of print]
Title: Benchmarking currently available SELDI-TOF MS preprocessing techniques
Authors: VA Emanuele; BM Gurbaxani

Authors conducted a large-scale evaluation of available signal processing techniques "to establish which are most effective," according to the abstract.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.