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Recent Research Papers of Note: Aug 31, 2006

Journal: Lab on a Chip, September
Title: An integrated digital microfluidic chip for multiplexed proteomic sample preparation and analysis by MALDI-MS
Authors: H. Moon, A.R. Wheeler; R.L. Garrell; J.A. Loo; C.J. Kim
Authors develop “two critical new functions in handling protein solutions and standard proteomic reagents with electrowetting-on-dielectric actuation, leading to an integrated chip for multiplexed sample preparation for MALDI-MS,” according to the abstract.

Journal: Chemical Research in Toxicology, Aug. 21
Title: Identification of early proteomic markers for hepatic steatosis
Authors: G. Meneses-Lorente; A. Watt; K. Salim; S.J. Gaskell; N. Muniappa; J. Lawrence; P.C. Guest
Authors identified proteomic markers associated with hepatocellular steatosis in rats by using 2D differential in-gel electrophoresis and MS.

Journal: Electrophoresis, Aug. 16 [Epub ahead of print]
Title: Online concentration and separation of basic proteins using a cationic polyelectrolyte in the presence of reversed electroosmotic flow
Authors: C.J. Yu and W.L. Tseng
Authors report an online concentration and separation method for basic proteins by using polydiallyldimethylammonium chloride (PDDA) solutions in the presence of reversed EOF.

Journal: Proteomics, Aug. 15 [Epub ahead of print]
Title: A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies
Authors: L. Martens; M. Muller; C. Stephan; M. Hamacher; K.A. Reidegeld; H.E. Meyer; M. Bluggel; J. Vandekerckhove; K. Gevaert; R. Apweiler
Authors compare protein identifications and project organization between the HUPO Brain Proteome Project and three other proteomic studies.

Journal: Proteomics, Aug. 15, [Epub ahead of print]
Title: Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study
Authors: L. Martens; M. Muller; C. Stephan; M. Hamacher; K.A. Reidegeld; H.E. Meyer; M. Bluggel; J. Vandekerckhove; K. Gevaert; R. Apweiler
“Proteins identified in human brain samples during the project's pilot phase were put into biological context through integration with various annotation sources followed by a bioinformatics analysis,” according to the study’s abstract. “The data set was related to the genome sequence via the genes encoding identified proteins including an assessment of splice variant identification as well as an analysis of tissue specificity of the respective transcripts. Proteins were furthermore categorized according to subcellular localization, molecular function and biological process, grouped into protein families and mapped to biological pathways they are known to act in.”

Journal: Analytical Chemistry, Aug. 15,
Title: Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries
Authors: B.E. Frewen; G.E. Merrihew; C.C. Wu; W.S. Noble; M.J. Maccoss
Authors propose a method for collecting previously identified tandem mass spectra into a reference library used for identification of new spectra.

Journal: Biochemical and Biophysical Research Communications, Aug. 7 [Epub ahead of print]
Title: A targeted proteomic approach for the identification of tumor-associated membrane antigens using Beckman Coulter’s ProteomeLab PF-2D in tandem with mass spectrometry
Authors: F.C. Chahal; J. Entwistle; N. Glover; G.C. Macdonald
Authors demonstrate a targeted proteomic approach to map differential expression of soluble proteins that can be used to identify tumor-associated membrane antigens. The approach employs immunoprecipitation, prior to 2D-LC separation in tandem with MS/MS.

Journal: Proteomics, Aug. 15 [Epub ahead of print]
Title: Gel-free analysis of the human brain proteome: Application of liquid chromatography and mass spectrometry on biopsy and autopsy samples
Authors: D. Dumont; J.P. Noben; P. Verhaert; P. Stinissen; J. Robben
Authors report on the findings of the Biomedical Research Institute, one of the participants in the HUPO Brain Proteome Project. “A biopsy and autopsy study sample derived from human brain was distributed among the participants for proteomic analysis,” said the study’s abstract. “In our laboratory, attention was focused on protein identification using the bottom-up shotgun approach. Protein extracts derived from both samples were trypsinized and analyzed separately by 2D LC and MS. In a complementary approach, the tryptic digests were analyzed directly by LC-ESI-MS/MS and gas-phase fractionation in the mass spectrometer.”

Journal: Omics: A journal of Integrative Biology, Summer 2006
Title: The Work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)
Authors: C.F. Taylor, H Hermjakob; R.K. Julian; J.S. Garavelli; R. Aebersold; R. Apweiler
Authors describe “the origins, working practices and various development projects of the Human Proteome Organization's Proteomics Standards Initiative, specifically, our work on reporting requirements, data exchange formats and controlled vocabulary terms. We also offer our view of the two functional genomics projects in which the PSI plays a role (FuGE and FuGO), discussing their impact on our process and laying out the benefits we see as accruing, both to the PSI and to biomedical science as a whole as a result of their widespread acceptance,” they said in the study’s abstract.

Journal: Biotechnology Progress, Aug. 4
Title: Photoimmobilization for Microarrays
Authors: Y. Ito
Author proposes method for developing the preparation of microarray chips. The method enables easy covalent immobilization of various types of organic molecules and cells on a chip. 

Journal: Proteomics, Aug. 8 [Epub ahead of print]
Title: High-coverage quantitative proteomics using amine-specific isotopic labeling
Authors: J.E. Melanson, S.L. Avery; D.M. Pinto
Authors evaluated peptide dimethylation with isotopically coded formaldehydes as a potential alternative to techniques such as iTRAQ method for comparative proteomics.

Journal: Journal of Proteome Research, Aug. 4
Title: ProteomIQ Blue, a Potent Post-stain for the Visualization and Subsequent Mass Spectrometry Based Identification of Fluorescent Stained Proteins on 2D-gels
Authors: D. Wijte; A.L. de Jong; M.A. Mol; B.L. van Baar; A.J. Heck
Authors explore the use of ProteomIQ Blue as a post-stain method for the visualization of fluorescent stained/labeled proteins.

Journal: Rapid Communications in Mass Spectrometry, Aug.4
Title: 'Information-Based-Acquisition' (IBA) technique with an ion-trap/time-of-flight mass spectrometer for high-throughput and reliable protein profiling
Authors: T. Yokosuka, K. Yoshinari; K. Kobayashi; A. Ohtake; A. Hirabayashi; Y. Hashimoto; I. Waki; T. Takao.
“Highly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS),” the authors said in the study’s abstract. “In an LC/MS run, intense peptide ions originating from high-abundance proteins are preferentially analyzed using tandem mass spectrometry (MS(2)), so obtaining the MS(2) spectra of peptide ions from low-abundance proteins is difficult even if such ions are detected. Furthermore, the MS(2) spectra may produce insufficient information to identify the peptides or proteins.” Authors developed a real-time optimization technique for MS(2), called the Information-Based-Acquisition (IBA) system to solve these problems.

Journal: Methods in Molecular Biology, 2006
Title: Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins
Authors: M.F. Berger; M.L. Bulyk
Authors have developed a DNA microarray-based technology that allows rapid, high-throughput characterization of the in vitro DNA binding site sequence specificities of transcription factors in a single day. “The resulting DNA binding site data can be used in a number of ways, including for the prediction of the genes regulated by a given transcription factor, annotation of transcription factor function, and functional annotation of the predicted target genes,” according to the study’s abstract.

Journal: Methods in Molecular Biology, 2006
Title: Isolation and mass spectrometry of specific DNA binding proteins
Authors: M. Yaneva; P. Tempts
Authors present a protocol allowing the certification of any specific DNA binding protein and its subsequent identification by MS.

Journal: Electrophoresis, Aug. 3 [Epub ahead of print]
Title: Dialysis-assisted two-dimensional gel electrophoresis
Authors: O. Danos; F. Svinartchouk
“[I]ntrinsic gel-to-gel variability of 2-DE often masks the biological differences between the samples and compromises quantitative comparison of protein expression levels,” the abstract of the study said. Authors describe a modification of 2-De that improves matching and quantification of proteins.

Journal: Molecular bioSystems, May 2006
Title:A novel peptide microarray for protein detection and analysis utilizing a dry peptide array system
Authors: K. Usui; K.Y. Tomizaki; T. Ohyama; K. Nokihara; H. Mihara
Authors constructed a dry peptide microarray system that affords practical solution for protein detection and analysis.

Journal: Biostatistics, Aug. 2 [Epub ahead of print]
Title: A statistical method for chromatographic alignment of LC-MS data.
Authors: P. Wang; M. Coram; H. Tang; M.P. Fitzgibbon; H. Zhang; E. Yi; R. Aebersold; M. McIntosh
Authors propose a new method, peptide element alignment, which uses raw spectrum data and detected peak to simultaneously align features from multiple LC-MS experiments.

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