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Recent Research Papers of Note in Proteomics: May 10, 2007

Journal: Journal of Biochemical and Biophysical Methods, June 10
Title: A DIGE-based approach to study interacting proteins
Authors: A Lyakhovich; F Canals; M Nosov; J Surralles
Authors apply different in-gel electrophoresis techniques on native gel electrophoresis to study protein-protein interactions. They conclude that the study “shows a good potential for investigating various interacting partners and benefits towards creation of interactome.”

Journal: Biochemical and Biophysical Research Communications, June 8
Title: A proteomics approach to identify the ubiquitinated proteins in mouse hearts
Authors: HB Jeon; ES Choi; JH Yoon; JH Hwang; JW Chang; EK Lee; HW Choi; ZY Park; YJ Yoo
Authors generated a transgenic mouse expressing a tagged ubiquitin in the heart and found that the majority of ubiquitinated proteins “are insoluble in detergent-free buffer and were chemically cleaved after methionine with CNBr.” The authors purified ubiquitin-conjugated polypeptides under denaturing conditions and digested them with Lys-C and trypsin. Using LC-MS, they identified 121 proteins ubiquitinated in mouse heart and detected 33 ubiquitinated sites in 21 of the proteins.

Journal: Biochemical and Biophysical Research Communications, June 1
Title: Alignment of two-dimensional electrophoresis gels
Authors: G Shi; T Jiang; W Zhu; B Liu; H Zhao
Authors propose a novel iterative closest point method for 2D gel electrophoresis image alignment, introducing an information theoretic measure as one part of the distance metric to gel image alignment. They combine intensity information of spots with geometric information of landmarks by applying information potential idea.

Journal: Biochemical and Biophysical Research Communications, June 1
Title: Prediction of subcellular protein localization based on functional domain composition
Authors: P Jia; Z Qian; Z Zeng; Y Cai; Y Li
Authors developed a prediction system for protein subcellular localization using the nearest neighbor algorithm approach. Their approach also incorporated a protein functional domain profile. The authors say that the overall accuracy achieved by their approach is 93.96 percent.

Journal: Journal of Chromatography: A, May 18
Title: Restricted-access material-based high molecular-weight protein depletion coupled on-line with nano-liquid chromatography-mass spectrometry for proteomics applications.
Authors: L Rieux; R Bischoff; E Verpoorte; HA Niederlander
Authors devised a novel setup for multidimensional nanoLC-MS with three columns coupled online for the analysis of low-abundance proteins. According to the authors, their approach removed up to 99.7 percent of albumin in samples and separations were highly reproducible.

Journal: Journal of the American Chemical Society, May 9
Title: Neutral fragment mass spectra via ambient thermal dissociation of peptide and protein ions
Authors: H Chen; LS Eberlin; RG Cooks
Authors describe a novel method for fragmenting peptide and protein ions at atmospheric pressure outside the mass spectrometer. Compared to the conventional method of using a vacuum, they say their approach is easier to perform outside the mass spectrometer and yields increased structural information from the resulting mass spectra in both the positive and negative ion modes.

Journal: Electrophoresis, May 8 [Epub ahead of print]
Title: Development of an integrated approach for evaluation of 2-D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel MALDI workflow
Authors: Y Yang; TW Thannhauser; L Li; S Zhang
Authors say they have developed an integrated approach to improve accuracy and reliability of comparative 2D electrophoresis by comparing protein identifications using direct MALDI/TOF/TOF and LC-ESI-MS/MS analysis of 2D gel separated proteins for cauliflower florets. The approach is proposed as an alternative to traditional gel-based quantitative proteomics studies.

Journal: Journal of Proteome Research, May 2 [Epub ahead of print]
Title: Comparing SILAC and two-dimensional gel electrophoresis image analysis for profiling urokinase plasminogen activator signaling in ovarian cancer cells
Authors: PM Uitto; BK Lance; GR Wood; J Sherman; MS Baker; MP Molloy
Authors investigate changes in protein expression using an ovarian cancer cell line, OVMZ6, 24 hours post-stimulation with urokinase-type plasminogen activator. MALDI/TOF/TOF was used to obtain quantitative protein profiles from stable isotope-labeled cells in culture. The results were compared to the quantitative ratios obtained by 2D gel image analysis. According to the authors, because of lower variances associated with the SILAC technique, smaller changes in expression of uPA-inducible proteins could be found with “greater clarity.”

Journal: Journal of the American Society for Mass Spectrometry, May
Title: Validated MALDI/TOF/TOF mass spectra for protein standards
Authors: JA Falkner; M Kachman; DM Veine; A Walker; JR Strahler; PC Andrews
Authors describe an openly accessible library of spectra generated on an Applied Biosystems 4700 MALDI/TOF/TOF from 246 known, individually purified and trypsin-digested protein systems. The initial release of the so-called Aurum dataset includes “gel images, peak lists, spectra, search result files, decoy database analysis files, FASTA file of protein sequences, manual curation, and summary pages describing protein coverage and peptides matched my MS/MS followed by decoy database analysis using Mascot, Sequest, and X!Tandem,” according to the abstract.

Journal: Journal of Proteome Research, May
Title: Estimating the statistical significance of peptide identifications from shotgun proteomics experiments
Authors: RE Higgs, MD Knierman; AB Freeman; LM Gelbert; ST Patil; JE Hale
Authors present a wrapper-based approach to estimate and control the false discovery rate for peptide identifications. Their approach allows users to combine output from multiple search engines with sequence and spectral derived features in a flexible classification model “to produce a score associated with correct peptide identifications,” according to the abstract.

Journal: Journal of the American Society for Mass Spectrometry, May
Title: Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID-MS/MS) for the identification of proteins
Authors: AJ Creese; HJ Cooper
Authors compared LC-ECD-MS/MS and LC-CID-MS/MS for the identification of proteins. A hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer was used and replicate analyses of a six-protein tryptic digest were performed. The results were analyzed for overall protein coverage and sequence tag lengths within individual peptides. According to the authors, LC-ECD-MS/MS provided lower protein coverage but longer peptide sequence tags, providing greater confidence in protein assignment.

Journal: Journal of Proteome Research, May
Title: Mining phosphopeptide signals in liquid chromatography-mass spectrometry data for protein phosphorylation analysis
Authors: HY Wu; VS Tseng; PC Liao
Authors propose an approach to mine phosphopeptide signals generated from a mixture of proteins when LC-MS/MS analysis is involved. The method combines dephosphorylation reaction, accurate mass measurements from a quadrupole/time-of-flight MS, and a computing algorithm.

Journal: Nature biotechnology, April 22 [Epub ahead of print]
Title: A high-quality catalog of Drosophila melanogaster proteome
Authors: E Brunner; CH Ahrens; S Mohanty; H Baetschmann; S Loevenich; F Potthast; EW Deutsch; C Panse; U de Lichtenberg; O Rinner; H Lee; PG Pedrioli; J Malmstrom; K Koehler; S Schrimpf; J Krijgsveld; F Kregenow; AJ heck; E Hafen; R Schlapbach; R Aebersold
Authors catalogued 63 percent of the predicted Drosphila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. “We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models,” the authors say. “We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.”

Journal: Journal of Proteome Research, April 19 [Epub ahead of print]
Title: A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS
Authors: VP Andreev; L Li; L Cao; Y Gu; T Reitar; SL Wu; BL Karger
Authors describe a new algorithm for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Their algorithm, Q-MEND, is based on MEND. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQ-FT MS instrument. In the new strategy, all MS/MS identifications for the set of analyzed sample are put into a master ID list. Each LC-MS run is then searched for the features that can be assigned to a specific identification from the master list.

Journal: Methods in Molecular Biology, 2007
Title: An isotope coding strategy for proteomics involving both amine and carboxyl group labeling
Authors: FE Regnier
A stable isotope coding strategy is described for analysis of all types of tryptic peptides, including those that are N-terminally blocked and from the C-terminus of proteins. The method “exploits differential derivatization of amine and carboxyl groups generated during proteolysis as a means of coding,” according to the abstract.

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