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Recent Research Papers of Note in Proteomics: Oct 11, 2007

Journal: Human Molecular Genetics, Oct. 15
Title: Fruit flies and the sperm proteome
Author: TL Karr
Author describes why sperm are ideal candidate cell types for proteomic analyses and the current state of the field, focusing on the recently described sperm proteome in the fruit fly Drosophila melanogaster.

Journal: BMC Biotechnology, Oct. 3, [Epub ahead of print]
Title: A systematic approach for testing expression of human full-length proteins in cell-free expression systems
Authors: C Langlais; B Guilleaume: N Wermke; T Scheuermann; L Ebert; J Labaer; B Korn
Authors describe a systematic approach to express a full-length protein of interest by using cell-free and cell-based expression systems.
They evaluated the expression of 960 human full-length open reading frames in Escherichia coli, in vivo and in vitro. After analyzing the protein expression rate and solubility, they chose 87 plasmids yielding no protein product in E. coli in vivo. The targets were then analyzed in greater detail, comparing a prokaryotic cell-free, E. coli system with a eukaryotic wheat germ system. They also determined the expression rate, yield, and solubility of those proteins. The authors say their success rate of cell-free protein expression reached 93 percent.

Journal: Molecular & Cellular Proteomics, Oct. 3 [Epub ahead of print]
Title: A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues
Authors: E. Bjorling; C Lindskog; P Oksvold; J Linne; C Kampf; S Hober; M Uhlen; F Ponten
The paper reports a publicly available web-based analysis tool for exploring proteins expressed in a tissue- or cancer-specific manner. The search tool enables the systematic exploration of the Human Protein Atlas to discover potential protein biomarkers including specific tissue-specific markers, cell type-specific markers, tumor type-specific markers, markers of malignancy, and prognostic or predictive markers of cancer.

Journal: Journal of Proteome Research, Oct. 2 [Epub ahead of print]
Title: Experimental approach for assessing the outcome accuracy of antibody microarray experiments
Authors: Q Gu; TM Sivanandam; J Haymore
Authors describe an experimental strategy for quality control of antibody microarray analyses. The method uses proteins prepared for regular antibody microarray experiments. Exogenous positive or negative reference markers are not needed, and the determination of absolute concentration of each individual protein in the sample is not necessary.

Journal: The Biochemical Journal, October 1
Title: Profiling constitutive proteolytic events in vivo
Authors: JC Timmer, M Enoksson; E Wildfang; Y Igarashi; JB Denault; Y Ma; B Dummitt; YH Chang; AE Mast; A Eroshkin; JW Smith; WA Tao; GS Salvesen
Authors describe a method to define the encoding of proteases that are crucial for constitutive proteolytic events in proteomes from Escherichia coli to humans. The method “takes advantage of specific N-terminal biotinylation of protein samples, followed by affinity enrichment and conventional LC analysis,” according to the abstract.

Journal: Molecular & Cellular Proteomics, October
Title: Proteomics identification of proteins in human cortex using multidimensional separations and MALDI tandem mass spectrometry
Authors: S Pan; M Shi; J Jin; RL Albin; A Lieberman; M Gearing; B Lin, C Pan; X Yan; DT Kashima; J Zhang
Authors report an in-depth proteomics identification of proteins extracted from the frontal cortex. The method consisted of biochemical fractionation, strong cation exchange chromatography, reverse phase LC, and MALDI-TOF/TOF MS analysis. They report the identification of 812 proteins with high confidence.

Journal: Analytical Chemistry, Sept. 29 [Epub ahead of print]
Title: Fast multiple electron capture dissociation in a linear radio frequency quadrupole ion trap
Authors: H Satake; H Hasegawa; A Hirabayashi; Y Hashimoto; T Baba; K Masuda
Authors developed a fast electron capture dissociation device using a linear radio frequency-quadrupole ion trap that dissociated peptides and proteins using a focused electron beam with an intensity of 0.5 muA and a diameter of 1 mm. They coupled the device to a TOF MS to apply multiple ECD.

Journal: Journal of Proteome Research, Sept. 29 [Epub ahead of print]
Title: ITRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer
Authors: TJ Griffin; H Xie; S Bandhakavi; J Popko; A Mohan; JV Carlis; L Higgins
Authors developed software to capture abundance ratios “via summing reporter ion intensities across spectra matching to each protein, thereby providing maximized accuracy,” according to the abstract. Tests found that results correspond closely between analysis using optimized LTQ-PDQ settings plus the software and using a QStar instrument.

Journal: Proteomics, Sept. 19 [Epub ahead of print]
Title: Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry
Authors: H Cho; DM Smalley; D Theodorescu; K Ley; JK Lee
Authors propose a novel statistical method for reliably identifying differentially expressed proteins while maintaining high sensitivity. The method is based on an advanced error pooling technique.

Journal: Analytical Chemistry, Sept. 15 [Epub ahead of print]
Title: Non-gel-based dual 18O labeling quantitative proteomics strategy
Authors: H Liu; Y Zhang; L Meng; P Qin; J Wei; W Jia; X Li; Y Cai; X Qian
Authors report on the development of a new strategy to improve the quantitation of target proteins in proteomic analysis. The method uses an acylating chemical reagent with two anhydride functional groups, bicyclic anhydride diethylenetriamine-N,N,N', N' ',N' '-pentaacetic acid dianhydride. In the first 18O method of the dual strategy, one functional group was covalently coupled to the primary amines of the peptides. 18O from H218O was incorporated by hydrolysis at the other functional group. In the second method, chemical 18O labeling and enzyme-catalyzed 18O labeling of the carboxyl-termini of the peptides were combined.

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