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Recent Research Papers of Note in Proteomics: Jan 10, 2008

Journal: Clinica Chimica Acta; International Journal of Clinical Chemistry, February [Epub ahead of print]
Title: Heparin chromatography to deplete high-abundance proteins for serum proteomics
Authors: T Lei; QY He; YL Wang; LS Si; JF Chiu
Authors couple traditional heparin chromatography with protein G sepharose to deplete high-abundance proteins. They report that their method leads to greater depletion than a multiple affinity removal system and leads to more proteins spots being visualized in 2D gel analysis.

Journal: BMC Bioinformatics, Jan. 7 [Epub ahead of print]
Title: An open-source representation of 2-DE-centric proteomics and support infrastructure for data storage and analysis
Authors: R Stanlislaus; JM Arthur; B Rajagopalan; R Moerschell; B McGlothlen; JS Almeida
Authors describe a data structure for the standardization of data generated by 2D gel work. A public repository is configured “with a suite of tools for the conversion from a variety of popular formats, web-based visualization, and interoperation with other tools and repositories, and is particularly mass-spectrometry oriented with I/O for annotation and data analysis,” according to the abstract.

Journal: Proteomics, Jan. 4 [Epub ahead of print]
Title: Evaluation of reproducibility of protein identification results after multidimensional human serum protein separation
Authors: D Stalder, A Haeberli; M Heller
A gel- and label-free method for the comparative studies of human serum is described. After the six most abundant proteins are depleted, protein fractionation is done by Off-Geltrade mark IEF and RP-HPLC, followed by tryptic digestion, LC-MS/MS, protein identification, and relative quantification using probabilistic peptide match score summation.

Journal: Molecular Microbiology, Jan. 2 [Epub ahead of print]
Title: A phage display system designed to detect and study protein-protein interactions
Authors: CL Bair; A Oppenheim; A Trostel; G Prag; S Adhya
Authors describe a bacteriophage 2-hybrid system for the in vitro study of protein-protein interactions. Bait and prey are displayed as fusions to the surface of the phage lambda, marked with different selectable drug-resistant markers. Interaction of phages in vitro through displayed proteins allows bacterial infection by two phages “resulting in double drug-resistant bacterial colonies at very low multiplicity of infections,” according to the abstract.

Journal: Journal of Proteome Research, January
Title: Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics
Authors: H Choi; AI Nesvizhskii
Authors present an algorithm for constructing a Bayes classifier for identifying peptides using the probability mixture model. The algorithm, they say, extends PeptideProphet to incorporate decoy peptide matches.

Journal: Proteomics, January
Title: Post alignment clustering procedure for comparative quantitative proteomics LC-MS data
Authors: JC de Groot; MW Fiers; RC van Ham; AH America
A procedure is described to address problems related to retention time shifts, saturation effects, limitations of experimental accuracy, and possible occurrence of split peaks that make it difficult for software to match all chromatograms. The authors further say that the aid of cluster analysis can enhance dataset quality.

Journal: Analytical Chemistry, Dec. 29, 2007 [Epub ahead of print]
Title: Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content
Authors: VA Petyuk; N Jaitly; RJ Moore; J Ding; TO Metz; K Tang; ME Monroe; AV Tolmachev; JN Adkins; ME Belov; AR Dabney; WJ Qian; DG Camp; RD Smith
To limit mass measurement errors, authors describe an approach by which calibration is provided through the use of a priori knowledge of a sample being analyzed. The approach has previously been demonstrated based on the dependence of systematic error on m/z alone. Authors employ multidimensional, nonparametric regression models to incorporate addition explanatory variables.

Journal: Carbohydrate Research, Dec. 23, 2007 [Epub ahead of print]
Title: Comparative RP-HPLC for rapid identification of glycopeptides and application in off-line LC-MALDI-MS analysis
Authors: Y kanie; A Enomoto; S Goto; O Kanie
Authors describe a method for structural analysis of glycoproteins. The method consists of a combination of rough fractionation using a reverse-phase cartridge column under acidic conditions and comparative RP-HPLC where two chromatograms obtained using phosphate and borate buffers under basic conditions are compared.

Journal: Journal of Proteome Research, Dec. 20, 2007 [Epub ahead of print]
Title: Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset
Authors: TO Metz; WJ Qian; JM Jacobs; MA Gritsenko; RJ Moore; AD Polpitiya; ME Monroe; DG Camp; PW Mueller; RD Smith
Authors evaluate LC-MS in a pilot proteomic analysis of human plasma and serum from a subset of control and type 1 diabetics in the Diabetes Autoantibody Standardization Program with the goal of identifying potential biomarkers for type 1 diabetes. High-resolution LC-MS/MS was done “to augment an existing plasma peptide database,” the authors say in the paper’s abstract. Subsequent LC-FTICR work identified quantitative differences in the abundance of plasma proteins. Five candidate biomarkers were identified.

Journal: BMC Bioinformatics, Dec. 19, 2007 [Epub ahead of print]
Title: PARPs Database: A LIMS systems for protein-protein interaction data mining or laboratory information management system
Authors: A Droit; JM Hunter; M Rouleau; C Ethier; A Picard-Cloutier; D Bourgais; GG Poirier
Authors describe the PARPs database, a data analysis and management pipeline for LC-MS/MS proteomics. The database is web based. Features include experiment annotation, protein database searching, protein sequence management, and data-mining of proteins and peptides that are identified.

Journal: Molecular & Cellular Proteomics, Dec. 18, 2007 [Epub ahead of print]
Title: Quantitative analysis of snake venoms using soluble polymer-based isotope labeling
Authors: JA Galan; M Guo; EE Sanchez; E Cantu; A Rodriguez-Acosta; JC Perez; WA Tao
Authors describe Soluble Polyer-based Isotope Labeling, or SoPIL, a new quantitative strategy for the identification and relative quantification of individual proteins in complex snake venoms. The authors say the method could be an efficient and widely applicable tool for quantitative proteomics.
The SoPIL reagent selectively captures and isolates cysteine-containig peptides. The subsequently tagged peptides are released and analyzed using nanoflow LC-MS/MS.

Journal: Molecular & Cellular Proteomics, Dec. 17 [Epub ahead of print]
Title: Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics
Authors: H Mirzaei; J McBee; J Watts; R Aebersold
Authors used sets of synthetic and biological peptides in parallel to evaluate the accuracy of peptides generated either by chemical stepwise synthesis or concatenation of nucleotide sequences coding for the respective peptides into a synthetic gene. They conclude that neither method proved superior to the other for the production of reference peptides for absolute quantification.

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