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Recent Research Papers of Note: Aug 13, 2009

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Journal: Journal of Proteome Research, Aug. 5 [Epub ahead of print]
Title:Isobaric peptide termini labeling for MS/MS-based quantitative proteomics
Authors:CJ Koehler; M Strozynski; F Kozielski; A Treumann; B Thiede

Described is a novel approach for identifying and quantifying two differentially labeled states using MS/MS spectra. The authors call the approach isobaric peptide termini labeling. "After endoproteinase Lys-C digestion, peptides were labeled at C-terminal lysine residues with either 2-methoxy-4,5-dihydro-1H-imidazole (MDHI) or with tetradeuterated MDHI-d4," according to the abstract. "Subsequently their N-termini were derivatized either with tetradeuterated succinic anhydride (SA-d4) or with SA." The mixed isotopic labeling resulted in isobaric masses. Several quantification data points for each peptide were also provided.


Journal: Proteomics, Aug. 5 [Epub ahead of print]
Title:A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization
Authors: : H Kuyama; C Nakajima; T Nakazawa; O Nishimura; S Tsunasawa

Describes a mass spec method for distinguishing "free modified forms of the C-terminal carboxyl group of peptides and proteins, in combination with chemical approaches for the isolation of C-terminal peptides and site-specific derivatization of the C-terminal carboxyl group," according to the abstract. The method "could be most advantageously exploited" for the discrimination of peptides with C-terminal carboxyl groups in the free and amide forms by "increasing their mass difference from 1 to 14 Daltons by selectively converting the free carboxyl group into methylamide."


Journal: : Journal of Proteome Research, Aug. 5 [Epub ahead of print]
Title: First insight into human liver proteome from PROTEOMESKY-LIVERHu 1.0, a publicly available database
Authors: Y Jiang, W Ying, S Wu, M Chen, W Guan, D Yang, et al

Authors report the proteome and transcriptome profiles of the human adult liver and report an initial analysis. Containing 6,788 identified proteins with at least two peptide matches at 95 percent confidence, including 3,721 newly identified liver proteins, and a dataset of 11,205 genes in the human liver transcriptome, the HLP is the largest proteome dataset for a human organ and the "first direct association between a proteome and its transcriptome derived from the same sample," according to the abstract.


Journal: Proteomics, Aug. 5 [Epub ahead of print]
Title: Carboxyl group derivatization for enhanced electron-transfer dissociation mass spectrometric analysis of phosphopeptides
Authors: L Zhang; Y Xu; H Lu; P Yang

Presented is a novel strategy for specific characterization of phosphopeptides. The strategy is based on carboxyl group derivatization. "By tagging the carboxy group with 1-(2-pyrimidyl) piperazine (PP), the ion charge states of phosphopeptides can be largely enhanced, showing great advantages for sequencing phosphorylated peptides with electron-transfer dissociation MS," according to the abstract. After PP-derivatization, most non-specific bindings can be avoided with the elimination of the interaction between the carboxy group and TiO2 "greatly improving the specificity of TiO2-based phosphopeptide enrichment strategy." Further, the enrichment time of phosphopeptides in RPLC can be prolonged, "overcoming the difficulty of separating phosphopeptides in [an] RPLC-based approach."


Journal: Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, Aug. 1 [Epub ahead of print]
Title: A Bayesian approach to protein inference problem in shotgun proteomics
Authors: YF Li; RJ Arnold; Y Li; P Radivojac; Q Sheng; H Tang

According to the authors, the protein inference problem is a "major challenge" in shotgun proteomics. To address this, they describe a novel Bayesian approach that incorporates the predicted peptide detectabilities as the prior probabilities of peptide identification. "We propose a rigorous probabilistic model for protein inference and provide practical algorithmic solutions to this problem," they said in the abstract.


Journal: Analytical Chemistry, July 30 [Epub ahead of print]
Title: Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes
Authors: F Yan, FY Che; D Rykunov; E Nieves; A Fiser; LM Weiss; R Hogue Angeletti

Advantages in cross-linking analysis of protein complexes and structures by MS/MS include speed, sensitivity, specificity, and the ability to handle complicated protein assemblies, but detection and accurate assignment of the cross-linked proteins are often challenging because of their low abundance and complicated fragmentation behavior in collision-induced dissociation, according to the authors. To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked proteins, they developed a novel peptide enrichment strategy "that utilizes a cross-linker with a cryptic thiol group and using beads modified with a photocleavable cross-linker," according to the abstract. The functional cross-linkers were designed to react with the primary amino groups in proteins and human serum albumin was used as a model protein in the detection of intra- and intermolecular cross-linkages.


Journal: Journal of Proteome Research, July 28 [Epub ahead of print]
Title: Proteomic expression profiling and identification of serum proteins using immobilized trypsin beads with MALDI-TOF/TOF
Author: ID Karbassi, JO Nyalwidhe; CE Wilkins; LH Cazares; RS Lance; OJ Semmes; RR Drake

In MALDI-TOF MS, many profiling strategies employ chemical affinity beads or surfaces, which decrease sample complexity of dynamic fluids such as serum and plasma, but which results in many proteins captured on a particular surface or bead not being resolved in the lower mass ranges where TOF MS is most effective, according to the authors. "Thus, a majority of reported protein expression profiling studies primarily interrogate the native low molecular mass constituents of the target sample," according to the abstract. Described is an expression profiling workflow that uses immobilized trypsin paramagnetic beads following an initial affinity bead fractionation step, "thereby reducing large mass proteins to peptides that are better suited to analysis and sequencing determinations." The authors report that their approach resulted in more efficient digestion of complex serum protein extracts at short incubation times.


Journal: Proteomics, July 28 [Epub ahead of print]
Title: Optimal analysis of complex protein mass spectra
Author: M Dijkstra; RC Jansen

Because of physical and chemical phenomena, a simple sample can result in a complex mass spectrum with "many more peaks than the number of molecular species present in the sample," according to the abstract. The authors link peaks within and between different spectra "and come up with an advanced analysis approach to produce reliable estimates of the molecule masses and abundances." In the paper, they model 29,952 peaks in 64 spectra, using 39 location parameters and one shape parameter. "This major reduction from many different molecules to a limited set of molecular species reduces the statistical test multiplicity for biomarker discovery and therefore we imply that the reduction should eventually increase the biomarker discovery power significantly, too," the authors said in the abstract.


Journal: Proteomics, July 27 [Epub ahead of print]
Title: Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues
Author: MF Addis; A Tanca; D Pagnozzi; S Crobu; G Fanciulli; P Cossu-Rocca; S Uzzau

According to the abstract, "a wealth of information on proteins" associated with many diseases can be found in formalin-fixed, paraffin-embedded tissue repositories stored in hospitals. Described is an optimized method for extracting full-length proteins from FFPE tissues. The method builds on the antigen retrieval method used for immunohistochemistry, "and allows generation of protein extracts with elevated and reproducible yields." The protein extracts generated with the technique can be used for the reproducible investigation of the proteome using a wide array of methods, and the paper presents results using SDS-PAGE, Western blotting, protein arrays, ELISA, and nanoHPLC-nanoESI-Q-TOF MS of FFPE proteins resolved by SDS-PAGE.


Journal: Bioinformatics, July 24 [Epub ahead of print]
Title: Mining gene functional networks to improve mass-spectrometry based proteins identification
Author: SR Ramakrishnan; C Vogel; T Kwon; LO Penalva; EM Marcotte; DP Miranker

Described is a method for MS/MS analysis of experiments "in the larger context of the biological processes active in a cell," according to the abstract. Called MSNet, the method improves protein identification in shotgun proteomics "by considering information on functional associations from a gene functional network." The authors report identifying 8 percent to 29 percent more proteins than the original MS experiment when applied to yeast grown in different experimental conditions analyzed on different MS platforms, and 37 percent more proteins in a human sample.

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