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Recent Research Papers of Note in Proteomics: Jan 31, 2008

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Journal: Proteins, Feb. 15
Title: Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab ignition simulation of Raman optical activity data
Authors: F Zhu; J Kapitan; GE Tranter; PD Pudney; NW Isaacs; L Hecht; LD Barron
 
According to the authors, vibrational Raman optical activity is “a powerful probe of the aqueous solution structure of proteins.” They previously used nonlinear mapping to map a large dataset of peptide, protein, and virs ROA spectra into “a readily visualizable two-dimensional space,” in which the position of points relative to each other represent similar or dissimilar structures. Their dataset contains folded proteins, ROA spectra from natively unfolded proteins, proteins containing both folded and unfolded domains, denatured partially structured molten globule and reduced protein states, and folded proteins with little or no alpha-helix or beta-sheet.
 
In the article, the relative positions of these systems in the NLM plot are used to gain knowledge about any residual structure they may contain.
 

 
Journal: Analytical Chemistry, Jan. 30 [Epub ahead of print]
Title: Gel-eluted liquid fraction entrapment electphoresis: An electrophoretic method for broad molecular weight range proteome separation
Authors: JC Tran; AA Doucette
 
Presented are techniques for continuous elution tube gel electrophoresis for broad mass range separation of proteins. The authors say their device enables rapid separation of a proteome into discrete mass range fractions in the solution phase. High recovery is achieved at submicrogram to milligram sample loadings. They demonstrate comprehensive, reproducible separations of protein mixtures and a proteome in as little as one hour, covering mass ranges from below 10 kilodaltons to 250 kilodaltons. They also identified proteins from a prefractionated standard protein mixture using LC-MS/MS analysis.
 

 
Journal: Analytical and Bioanalytical Chemistry, Jan. 28 [Epub ahead of print]
Title: Application of partial least squares discriminant analysis and variable selection procedures: a 2D PAGE proteomic study
Authors: E Marengo; E Robotti; M Bobba; A Milli; N Campostrini; SC Righetti; D Cecconi; PG Righetti
 
Authors applied partial least squares discriminant analysis to improve results from image analysis based on 2D gel electrophoresis and to identify the significant spots responsible for the differences between two datasets. They analyzed a human colon cancer HCT116 cell line, treated and untreated with a new histone deacetylase inhibitor, RC307. Proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles, and some regulated spots were identified by MS/MS.
 

 
Journal: Proteome Science, Jan. 28 [Epub ahead of print]
Title: Automated production of recombinant human proteins as resource for proteome research
Authors: T Kohl; C Schmidt; S Wiemann; A Poustka; U Korf
 
Authors present a strategy for fully automated protein production, covering all steps from DNA preparation to protein purification and analysis. They selected an arbitrary set of 96 human proteins for testing. Target proteins were encoded by functionally characterized open reading frames identified by the German cDNA consortium. Fusion proteins were produced in E. coli with four different fusion tags and tested in five different purification strategies.
 

 
Journal: Pharmaceutical Research, Jan. 25 [Epub ahead of print]
Title: Quantitative atlas of membrane transporter proteins: Development and application of highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria
Authors: J Kamiie; S Ohtsuki; R Iwase; K Ohmine; Y Katsukura; K Yanai; Y Sekine; Y Uchida; S Ito; T Terasaki
 
Authors sought to develop an absolute quantification method for membrane proteins and construct a quantitative atlas of membrane transporter proteins in the blood-brain barrier, liver and kidney of a mouse. They digest tissues with trypsin and mixed them with stable isotope labeled-peptide as a quantitative standard. The amounts of transporter proteins were determined by LC-MS/MS.
 

 
Journal: Proceedings of the National Academy of Sciences, Jan. 24 [Epub ahead of print]
Title: Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
Authors: ME Sardiu; Y Cai; J Jin; SK Swanson; RC Conaway; JW Conaway; L Florens; MP Washburn
 
Authors have develop a method for building local and focused protein interaction networks that couples vector algebra and statistical methods with normalized spectral counting derived from the analysis of affinity purifications via chromatography-based proteomics. After mathematically removing contaminant proteins, “the core components of multiprotein complexes are determined by singular value decomposition analysis and clustering” the authors say in the abstract. The probability of interactions within and between complexes is determined based upon normalized spectral counting using Bayes’ approach.
 

 
Journal: Journal of Proteome Research, Jan. 23 [Epub ahead of print]
Title: Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing
Authors: JM Chick; PA Haynes; MP Molloy: B Bjellqvist; MS Baker; AC Len
 
Authors compared different concentrations of methanol for membrane protein digestion with trypsin prior to analysis using a gel-based shotgun proteomics approach called immobilized pH gradient isolectric focusing. They demonstrate the utility of the approach on pH 3-10 IPG strips as the first dimension of two-dimensional shotgun proteomics for protein identifications from the membrane fraction of rat liver.
 

 
Journal: Analytical Chemistry, Jan. 23 [Epub ahead of print]
Title: Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides
Authors: A Scherl; SA Shaffer; GK Taylor; HD Kulasekara; SI Miller; DR Goodlett
 
Authors determined optimal m/z ranges based on genomic complexity and experimental data, and then calculated theoretical precursor ion densities in silico from various organism genomes. The densities were found to corroborate the empirical selection of m/z ranges based on ion density mapping. The calculations suggest the choice of m/z range for most efficient gas-phase fractionation coverage in the lower m/z range should be very narrow and increase as m/z value increases. A systematic LC-MS/MS analysis was done for confirmation. LTQ-Orbitrap MS analysis was done to observe the behavior of data-dependent precursor ion selection and the origin of observed variability. Gas-phase fractionation combined with data-dependent analysis was compared to a targeted, pseudo-MRM analysis of proteotypic peptides “that should be, based on empirical observation of LC-ESI-MS/MS data, detectable,” the authors say in the abstract.
 

 
Journal: Genome Biology, Jan. 23, [Epub ahead of print]
Title: Towards defining the nuclear proteome
Authors: JL Fink; S Karunaratne; A Mittal; DM Gardiner; N Hamilton; D Mahony; C Kai; H Suzuki; Y Hayashizaki; RD Teasdale
 
Authors report direct evidence for 2,568 mammalian proteins within the nuclear proteome, including the nuclear subcellular localization of 1,529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and 1,039 proteins “for which clear experiment evidence is document in published literature,” they say in the abstract. They conclude this indicates that the nuclear proteome consists of “at least 14 percent of the entire proteome.”
 

 
Journal: Molecular & Cellular Proteomics, Jan. 22 [Epub ahead of print]
Title: Hydrophilic-interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection
Authors: DE McNulty; RS Annan
 
Authors report on the use of hydrophilic-interaction chromatography as part of a multidimensional chromatography strategy for proteomics and demonstrate that it represents a “significant advance in phosphoproteomic analysis,” according to the abstract. Exploiting the strong hydrophilicity of the phosphate group, they selectively enriched and fractionated phosphopeptides based on their increased retention under HILIC conditions.
 

 
Journal: BMC Bioinformatics, Jan. 21 [Epub ahead of print]
Title: A nonparametric model for quality control of database search results in shotgun proteomics
Authors: J Zhang; J Li; X Liu; H Xie; Y Zhu; F He
 
Authors used a multivariate nonlinear discriminate function based on the multivariate nonparametric density estimation technique to filer out false-positive databases search results with a predictable false positive rate. Applying the method to control dataset of different instruments yield estimated FPR’s close to the actual FPR. It also proved to be more sensitive than two commonly used methods on three complex sample datasets and three control datasets.
 

 
Journal: Journal of Proteome Research, Jan. 17 [Epub ahead of print]
Title: Spectral index for assessment of differential protein expression in shotgun proteomics
Authors: X Fu; SA Gharib; PS Green; ML Aitken; DA Frazer; DR Park; T Vaisar; JW Heinecke
 
Described is a label-free method, the spectral index, for analyzing relative protein abundance in large-scale data sets derived from biological samples via shotgun proteomics. The spectral index comprises of relative protein abundance, assessed by spectral counts, and the number of samples within a group of detectable peptides.
 

 
Journal: Analytical Chemistry, Jan. 12 [Epub ahead of print]
Title: Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data
Authors: GL Finney; AR Blackler; MR Hoopmann; JD Canterbury; CC Wu; MJ MacCoss
 
Authors developed and applied an algorithm using chromatographic alignment of mu LC-MS runs for improved detection of differences between complex protein mixtures, then demonstrate the performance of their software by finding differences in E. coli protein abundance upon induction of the lac operon genes using isopropyl beta-d-thiogalactopyranoside. They report a 4-fold decrease in mean relative retention time error and a 6-fold increase in the number of statistically significant differences between samples using their alignment.
 

 
Journal: Journal of Proteome Research, Jan. 12 [Epub ahead of print]
Title: Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for quantitative proteomics
Authors: G Zhang; D Fenyö; TA Neubert
 
A new strategy was developed to overcome poor reproducibility of cutting gel slices in label-free and peptide-labeling quantitative proteomics methods. The new strategy combines a DNA ladder with the sample protein before PAGE separation. After PAGE separation, the DNA ladder is stained for “easy, precise, and reproducible gel cutting,” the authors say in the abstract. They evaluated the reproducibility of DNA-ladder-assisted gel cutting for quantitative protein fractionation by using SILAC, and show that quantitative errors associated with fractionation can be minimized using DNA-assisted fractionation and multiple replicates of gel cutting.
 

 
Journal: Journal of Proteome Research, Jan. 11 [Epub ahead of print]
Title: Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LCMALDI TOF/TOF) platform
Authors: S Pan; J Rush; ER Peskind; D Galasko; K Chung; J Quinn; J Jankovic; JB Leverenz; C Zabetian; C Pan; Y Wang; JH Oh; J Gao; J Zhang; T Montine; J Zhang
 
Authors use a MALDI TOF/TOF platform to demonstrate its use in targeted quantitative proteomics for searching, identifying, and quantifying selected peptides in human CSF. The approach involved the use of isotopic-labeled synthetic peptides and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The authors say the LC MALDI TOF/TOF platform and a complementary identification strategy, they were able to “selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins.”
 

 
Journal: Bioinformatics, Jan. 10 [Epub ahead of print]
Title: Incorporating sequence information in the scoring function: A hidden Markov model for improved peptide identification
Authors: J Khatun; E Hamlett; MC Giddings
 
Authors developed a machine-learning approach using a hidden Markov model to capture the complex and subtle links between peptide sequence and MS/MS spectrum, to improve the accuracy of peptide identification algorithms. Their model, HMM Score, represents ion types as HMM states “and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types, and the intensity dependence of ion types. “
 
They used the Viterbi algorithm to calculate the most probable assignment between ion types in a spectrum and peptide sequence and added a correction factor to account for the tendency of the model to favor longer peptides. They calculated an expectation value based on the model score to assess the significance of each peptide/spectrum match.
 

 
Journal: Bioinformatics, Jan. 10 [Epub ahead of print]
Title: OutlierD: An R package for outlier detection using quantile regression on mass spectrometry data
Authors: H Cho; YJ Kim; HJ Jung; SW Lee; JW Lee
 
An outlier detection software program was developed by the authors, accounting for the heterogeneous variability by using linear, nonlinear, and nonparametric quantile regression techniques. The program was developed using the R computer language, and so can be used interactively and conveniently in the R environment.
 

 
Journal: Journal of Proteome Research, Jan. 10 [Epub ahead of print]
Title: Strategy for comprehensive identification of post-translational modification in cellular proteins, including low abundant modifications: Applictions to glyceraldehydes-3-phosphae dehydrogenase
Authors: J Seo; J Jeong; YM Kim; N Hwang; E Paek; KJ Lee
 
Described is a strategy for the identification of PTMS I biological processes in vivo rapidly, efficiently, and comprehensively. The strategy involves a selectively excluded MS analysis of unmodified peptides during LC-ESI-q-TOF MS/MS analysis through replicated runs of a purified protein on 2D gel. The initial run resulted in a precursor ion list of unmodified peptides with high mass intensities. Exclusion of these unmodified peptides in subsequent runs followed.

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