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Recent Research Papers of Note in Proteomics: Feb 21, 2008

Journal: Molecular & Cellular Proteomics, Feb. 18 [Epub ahead of print]
Title: A high-throughput proteomics screen identifies novel substrates of death associated protein kinase
Authors: S Bialik; H Berissi; A Kimchi
Authors developed an in vitro, unbiased assay to search for novel death-associated protein kinase substrates. Biochemical fractionation and MS analysis was used to purify and identify potential substrates from HeLA cell lysate. The authors report the identification of two candidate substrates, the ribosomal protein L5 and Mcm3, a replication licensing factor.

Journal: Analytical Chemistry, Feb. 15 [Epub ahead of print]
Title: Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data
Authors: B Lu; A Motoyama; C Ruse; J Venable; JR Iii
Described is an investigation and comparison of three approaches for shotgun protein identification by combining MS and MS/MS information using LTQ-Orbitrap high mass accuracy data. The first approach employed a unique mass identifier method “where MS peaks matched to peptides predicted from proteins identified from an MS/MS database search are first subtracted before using the MS peaks as unique mass identifiers for protein identification,” according to the abstract. The second approach used an accurate mass and time tag method by building a potential mass and retention time database from earlier MudPIT analyses. The last method combined a peptide mass fingerprinting-like approach with a randomized database for protein identification.

Journal: Bioconjugate Chemistry, Feb. 15 [Epub ahead of print]
Title: Efficient site-specific labeling of proteins via cysteines
Authors: Y Kim; SO Ho; NR Gassman; Y Korlann; EV Landorf; FR Collart; S Weiss
Authors describe an “efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state,” according to the abstract. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the 70 percent to 90 percent range and specificities are better than 95 percent.

Journal: Proteomics, Feb. 13 [Epub ahead of print]
Title: Towards multidimensional liquid chromatography separation of proteins using fluorescence and isotope-coded protein labeling for quantitative proteomics
Authors: F Tribl; C Lohaus; T Dombert; E Langenfeld; H Piechura; B Warscheid; HE Meyer; K Marcus
Authors developed a multidimensional LC-based approach followed by large gel 1D SDS-PAGE for the analysis of complex proteomes and quantitative changes of proteins therein. A novel strategy is presented that allows for identifying and quantifying differentially regulated proteins following three separation and fractionation steps.

Journal: Journal of Separation Science, Feb. 11 [Epub ahead of print]
Title: Bioaffinity magnetic reactor for peptide digestion followed by analysis using bottom-up shotgun proteomics strategy
Authors: L Korecká, B Jankovicová, J Krenková; L Hernychová; M Slováková; A LeNell; J Chemelík; F Foret; JL Viovy; Z Bílková
Authors say that using a shotgun proteomics method combined with bioaffinity purification they can “remove or minimize the interference contamination of a complex tryptic digest and so avoid the time-consuming separation steps before the final [mass spectrometry] analysis.”

Journal: Hepatology, Feb. 11 [Epub ahead of print]
Title: Comprehensive and quantitative proteome profiling of the mouse liver and plasma
Authors: KK Lai; D Kolippakkam; L Beretta
Authors report a comprehensive and quantitative analysis of the mouse liver and plasma proteomes that they say reaches a depth in proteomic profiling not previously reported for a mammalian tissue or a biological fluid.  The method is based on extensive fractionation of intact proteins, further separation based on protein size and abundance, and mass spectrometry. They report 7,099 proteins identified with high confidence in the liver and 4,727 proteins identified with high confidence in the corresponding plasma.

Journal: Journal of Proteome Research, Feb. 8 [Epub ahead of print]
Title: Phosphoproteome analysis of fission yeast
Authors: JT Wilson-Grady; J Villén; SP Gygi
Authors provide what they say is the first large-scale phosphorylation analysis of the fission yeast, Schizosaccharomyces pombe. They separated proteins from thiabendazole-treated cells by preparative SDS-PAGE and digested them with typsin. The resulting peptides were then subjected either to IMAC or TiO2 phosphopeptide enrichment methods and analyzed by LC-MS/MS. They identified 2,887 distinct phosphorylation sites from 1,194 proteins with an estimated false discovery rate of less than 0.5 percent at the peptide level.

Journal: Journal of Proteome Research, Feb. 8 [Epub ahead of print]
Title: Proteome profiling of breast tumors by gel electrophoresis and nanoscale electrospray ionization mass spectrometry
Authors: L Alldridge, G Metodieva; C Greenwood; K Al-Janabi; L Thwaites; P Sauven; M Metodiev
Authors used an approach integrating size-based intact protein fractionation, nanoscale liquid separation of peptides, electrospray ion trap MS, and bioinformatics to do a proteome-wide analysis of fresh surgery specimens derived from patients with breast cancer. They acquired a large amount of peptide fragmentation spectra from size-resolved fractions of the proteomes of several breast cancer tumor, tissue peripheral to the tumor, and samples from patient undergoing non-cancer surgery.
They performed label-free quantitation to generate protein abundance maps for each proteome and do a comparative analysis. MS data showed distinct qualitative and quantitative patterns distinguishing tumors from healthy tissue and differences between metastatic and non-metastatic breast cancers. Potential novel biomarkers were detected. Selected proteins were evaluated by Western blotting, and immunohistochemical analysis of a wide panel of tumors was used to assess expression in different types of breast cancers and the cellular distribution of the candidate proteins.

Journal: Journal of Proteome Research, Feb. 8 [Epub ahead of print]
Title: Novel microwave-assisted digestion by trypsin-immobilized magnetic nanoparticles for proteomic analysis
Authors: S Lin; D Yun; D Qi; C Deng; Y Li; X Zhang
Authors say in their abstract that the magnetic nanoparticles work as a substrate for enzyme immobilization and as an excellent microwave irradiation absorber, improving the efficiency of microwave-assisted digestion greatly. Bovine serum albumin, myoglobin, and cytochrome c were used to optimize the conditions of the novel digestion methods. Under optimized conditions, peptide fragments produced in a “very short time” of 15 seconds could be identified successfully by MALDI-TOF MS. Even at microgram levels, the authors say, the methods digested proteins successfully.

Journal: Journal of Proteome Research, Feb. 8 [Epub ahead of print]
Title: Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues
Authors: H Xu; L Yang; W Wang; SR Shi; C Liu; Y Liu; X Fang; CR Taylor; CS Lee; BM Balgley
Authors evaluate the effects of fixation time on antigen retrieval for shotgun proteomics and demonstrate for the first time, they say, the capability of a capillary isotachophoresis-based proteomic platform for a shotgun proteomic analysis of formalin-fixed and paraffin-embedded tissues. Results from three FFPE liver tissues yielded 4,098 distinct SwissProt identifications at a false discovery rate of 1 percent, according to the abstract.

Journal: BMC Bioinformatics, Feb. 7 [Epub ahead of print]
Title: Comparison of normalization methods for surface-enhanced laser desorption and ionization (SELDI) time-of-flight (TOF) mass spectrometry data
Authors: W Meuleman; JY Engwegen; MC Gast; JH Beijnen; MJ Reinders; LF Wessels
Described is a systematic comparison of a wide range of normalization methods using two objectives — the minimization of inter-spectra variance and the maximization of signal with respect to class separation. Minimization of inter-spectra variance was assessed using an estimation of the coefficient of variation, while the maximization of signal was assessed using “the classification performance of three types of classifiers on real-world datasets representing two-class diagnostic problems,” according to the abstract. Both objectives were evaluated over multiple datasets and multiple configurations of baseline correction and peak detection methods for a robust evaluation of the normalization method.

Journal: BMC Bioinformatics, Feb. 6 [Epub ahead of print]
Title: The annotations, mapping, expression and network (AMEN) suite of tools for molecular systems biology
Authors: F Chalmel; M Primig
AMEN was developed as a stand-alone, unified suite of tools enabling biological and medical researchers with basic bioinformatics training to manage and explore proteomics data, protein-protein interactions, genome annotation, chromosomal mapping, and expression profiling. The current version includes modules for uploading and pre-processing data from microarray expression in profiling experiments; detecting groups of significantly co-expressed genes; and searching for enrichment of functional annotations within those groups. The user interface is designed to simultaneously visualize several types of data, as well.

Journal: Journal of Proteome Research, Feb. 6 [Epub ahead of print]
Title: Mixed-effects statistical model for comparative LC-MS proteomics studies
Authors: DS Daly, KK Anderson; EA Panisko; SO Purvine; R Fang; ME Monroe; SE
Authors describe a mixed-statistical model for comparative LC-MS studies. They describe LC-MS peptide abundance “with a linear model featuring pivotal terms that account for unequal peptide LC-MS measurability,” according to the abstract. They “advance” fit the model to an often incomplete LC-MS dataset with restricted maximum likelihood estimation, “producing estimates of model goodness-of fit, treatment effects, standard errors, confidence intervals, and protein relative concentrations,” according to the abstract.

Journal: Journal of Proteome Research, Feb. 2 [Epub ahead of print]
Title: Evaluation of comprehensive multidimensional separations using reversed-phase, reversed phase liquid chromatography/mass spectrometry for shotgun proteomics
Authors: K Makamura; J Kuromitsu; Y Oda
Authors examine 2D LC separation followed by MS analysis for peptide identification as an alternative to 2D gel electrophoresis followed by MS. They did off-line coupling of a narrow-bore, polymer-based, reversed-phase column using an acetonitrile gradient in an alkaline mobile phase in the first dimension. In the second dimension, octadecylsilanized silica-based nano-LC-MS was used.
After the first separation, successive fractions were acidified and dried off-line then loaded on the column for second dimension separation. Both columns separate peptides based on hydrophobicity under different pH conditions.

Journal: Analytical Chemistry, Feb. 2 [Epub ahead of print]
Title: Surface-induced dissociation of peptides and protein complexes in a quadrupole/time-of-flight mass spectrometer
Authors: AS Galhena; S Dagan; CM Jones; RL Beardsley; VH Wysocki
Authors designed a novel in-line, surface-induced dissociation device and implemented it in a commercial Q-TOF. The setup allows efficient SID for a broad range of molecules, they say in the abstract, and allows a direct comparison with conventional collision-induced dissociation on the same instrument “taking advantage of the characteristics of QTOF instrumentation, including extended mass range, improved sensitivity, and better resolution compared with quadrupole analyzers and ion traps.”

Journal: Proteomics, Feb. 1 [Epub ahead of print]
Title: Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics
Authors: NA Karp; R Feret; DV Rubtsov; KS Lilley
The deep purple system was compared to DIGE using a traditional as well as a SameSpots approach to gel analysis. Missing values in the traditional approach was a significant issue with both systems. SameSpots tries to address the issue and was found to increase the proportion of low volume data for DP but not for DIGE, according to the abstract. Analysis of the same images gave “significantly lower noise” with SameSpots over the traditional approach for DP, but not for DIGE, the authors report.

Journal: Electrophoresis, February
Title: Microscale solution IEF combined with 2-D DIGE substantially enhances analysis depth of complex proteomes such as mammalian cell and tissue extracts
Authors: MJ Han; M Herlyn; AB Fisher; DW Speicher
Fluorescently tagging and mixing samples and controls before prefractionation eliminates complications from minor run-to-run variations during MicroSol-IEF, the authors say in the abstract, improving the reliability of quantitative comparisons. They used a 3D DIGE strategy to illustrate the utility of their method and applied it to an analysis of human melanoma cells and mouse lung tissue extracts. They report that about 1,000 reproducible spots could be obtained from narrow range 2D gels of individual MicroSol-IEF fractions, and about 6,000 spots could be obtained from entire proteomes.

Journal: Analytical Chemistry, Jan. 30 [Epub ahead of print]
Title: Automated proteomics of E. coli via top-down electron-transfer dissociation mass spectrometry
Authors: MK Bunger; BJ Cargile; A Ngunjiri; JL Bundy; JL Stephenson
The utility of ETD in high-throughput, top-down proteomics using soluble extracts of E. coli is demonstrated. Development of a multidimensional fractionation platform and a custom algorithm and scoring scheme designed specifically for this type of data is described. The robust identification of 322 different protein forms representing 174 proteins was achieved.

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