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Recent Research Papers of Note: Jul 23, 2009

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Journal: Protein and Peptide Letters, Nov. 10 [Epub ahead of print]
Title: Evaluation of protein phosphorylation site predictors
Authors: S Oue; Y Wang; P Chen; Y Tang; Z Zhang; H He

The authors evaluated six recently published methods for phosphorylation-site prediction: DISPHOS, MetPhosK, PPSP, KinasePhos, Scansite, and PredPhospho. Three testing datasets containing experimentally verified phosphorylation sites for mammalian, Arabidopsis, and rice proteins were compiled. The authors then presented the prediction performance of the tested methods on the three datasets, concluding that current phosphorylation site predictors are not "effective for practical use and there is substantial need to improve phosphorylation site prediction," according to the abstract


Journal: Rapid Communications in Mass Spectrometry: RCM , August
Title: Data-dependent electron transfer dissociation of large peptides and medium-size proteins in a QTOF instrument on a liquid chromatography timescale
Authors: RG Hartmer; DA Kaplan; C Stoermer; M Lubeck; MA Park

Authors demonstrate liquid chromatography electron transfer dissociation tandem mass spectrometry of protein digests in a hybrid quadrupole hexapole orthogonal time-of-flight mass spectrometer. They also investigated the capability of the hybrid instrument for the analysis of small proteins.


Journal: Analytical Chemistry, July 15
Title: Preventing carryover of peptides and proteins in nanoLC-MS separations
Authors: G Mitulović; C Stingl; I Steinmacher; O Hudecz; JR Hutchins; JM Peters; K Mechtler

Presented is a method for eliminating carryover caused by the autosampler and trap column, which the authors call in the abstract a "significant" problem in HPLC analyses. The washing method uses an injection of trifluoroethanol into the injection path and onto the trap column to remove strongly bound peptides and proteins. Trifluoroethanal is used as an additional solvent in the chromatographic mobile phase "for enhanced cleaning of the separation column. By application of this method, a significant reduction in carryover was achieved without any loss in the amount of proteins and peptides identified by MS," the authors said.


Journal: Journal of Proteome Research , July 14 [Epub ahead of print]
Title: Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics
Authors: A Peterson; L Hohmann; L Huang; B Kim; JK Eng; DB Martin

While "substantial energy and resources" have been invested in improving mass spectrometry technology, upstream sample preparation protocols, and database searches, "the role of HPLC sample loading methods … has been largely overlooked, and there exists an immense heterogeneity in the methods employed in the proteomics literature," according to the abstract. To address this, authors sought to optimize loading methods by testing multiple loading conditions using tryptic digests of a mixture containing 18 proteins, and whole yeast lysate.


Journal: Molecular & Cellular Proteomics, July 13 [Epub ahead of print]
Title: Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution.
Authors: H Keshishian; T Addona; M Burgess; DR Mani; X Shi; E Kuhn; MS Sabatine; RE Gerszten; SA Carr

Authors used multiple reaction monitoring coupled with stable isotope dilution mass spectrometry to develop quantitative, multiplexed assays in plasma for six proteins of clinical relevance to cardiac injury. The method requires no immunoaffinity enrichment of either proteins or peptides, and the results are the "first demonstration of a multiplexed, MS-based assay for detection and quantification of changes in concentration of proteins associated with cardiac injury in the low nanogram/mL range," according to the abstract. "Our results also demonstrate that these assays retain the necessary precision, reproducibility, and sensitivity to be applied to novel and uncharacterized candidate biomarkers for verification of proteins in blood."


Journal: PLoS One, July 10
Title: Genome2Drugs: identifies target proteins and lead drugs from proteome data
Authors: D Toomey; HC Hoppe; MP Brennan; KB Nolan; AJ Chubb

Despite the increasing amount of data of target genes and proteins and the full hypothetical proteome of many pathogenic organisms being generated by protemics experiments, "the challenge remains to identify new targets for drug discovery from this wealth of information," according to the abstract. To address the many issues surrounding this, the authors have developed a free online resource called Genomes2Drugs. The tool ranks sequences to identify proteins that are homologous to previously crystallized proteins, or targets of known drugs, but are not homologous to human proteins.


Journal: Analytical Biochemistry, July 6 [Epub ahead of print]
Title: Characterization of cluster-assembled nanostructured titanium oxide coating as substrate for protein arrays
Authors: R Carbone; M de Marni; A Zanardi; S Vinati; E Barborini; L Fornasari; P Milani

According to the authors, nanostructured titanium oxide film synthesized by Supersonic Cluster Beam Deposition has recently emerged as a material for use as biocompatible substrate in biological assays. They present a systematic characterization of nanostructured titanium oxide coatings as protein binding surfaces and compare their performances with those of commonly used substrates in commercial protein and antibody microarray assays. "Through a robust statistical evaluation of repeatability in term of coefficient of variation analysis, we demonstrate that ns-TiO(x) can be used as reliable substrate for biochips in analytical protein microarray application," according to the abstract.

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Journal: Biotechnology and Applied Biochemistry, July 6
Title: Application of the SILAC (stable isotope labeling with amino acids in cell culture) technique in quantitative comparisons for tissue proteome expression
Authors: Y Xu; S Liang; G Shen; X Xu; Q Liu; Z Xu; F Gong; M Tang; Y Wei

Authors expand the application of SILAC to compare the relative protein expression levels between two different states of tissues based on cultured cells with leucine labeling as an internal standard in mass spectra.


Journal: Journal of Proteome Research, July 6 [Epub ahead of print]
Title: Proteome maps of the main human peripheral blood constituents
Authors: VJ Haudek; A Slany; NC Gundacker; H Wimmer; J Drach; C Gerner

Authors purified T cells, monocytes, neutrophils, erythrocytes, platelets, and plasma, then did a comparative proteome profile using 2D PAGE to detect proteins that may be indicative of the presence of major blood constituents. Using mass analysis, they identified 594 different proteins in the 2D gels, six displaying highly specific expression patterns. Shotgun proteomics led to the identification of 1,774 proteins, including 51 with highly specific expression patterns. The protein maps generated could serve as references for comparative analyses and aid in interpreting proteomic profiles of clinical materials, the authors said.


Journal: Journal of Proteome Research, July 6
Title: An iterative strategy for precursor ion selection for LC-MS/MS-based shotgun proteomics
Authors: A Zerck; E Nordhoff; A Resemann; E Mirgorodskaya; D Suckau; K Reinert; H Lehrach; J Gobom

Current precursor ion selection strategies in LC-MS is based on choosing the most prominent peptide signals for MS/MS analysis, the authors said in the study's abstract. As a result, high-abundance proteins may be identified at the expense of low-abundance proteins. Presented is a "novel, iterative, and result-driven approach" for precursor ion selection "that significantly increases the efficiency of an MS/MS analysis by decreasing data redundancy and analysis time."


Journal: Analytical Chemistry, July 2 [Epub ahed of print]
Title: Multiplexed size separation of intact proteins in solution phase for mass spectrometry
Authors: JC Tran; AA Doucette

Reliable size-based protein-separation techniques are invaluable but underutilized due to the poor resolution of conventional techniques, the authors said in the abstract. To address this, they developed an enhanced multiplexed gel-eluted liquid fraction entrapment electrophoresis device that incorporates eight independent separation channels, operating with high repeatability. "This enables simultaneous size separation of independent proteome samples, each into 16-well resolved liquid fractions, covering 10-150 kDa in 1.5 hours," according to the abstract. The authors also present a novel strategy for increasing sample loads while maintaining electrophoretic resolution.


Journal: Analytical Chemistry, July 2 [Epub ahead of print]
Title: Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean
Authors: A Panchaud; A Scherl; SA Shaffer; PD von Haller; HD Kulasekara; SI Miller; DR Goodlett

Data-dependent precursor ion selection is a popular technique in shotgun proteomics for profiling protein components in complex samples. However, this bottom-up approach presents "major drawbacks" in terms of detectable dynamic range. Presented is a data-independent method the authors call precursor acquisition independent from ion count, or PAcIFIC. Their results show that almost the entire, predicted soluble bacterial proteome can be analyzed by PAcIFIC "without the need for any sample fractionation other than the C18-based liquid chromatography used to introduce the peptide mixture into the mass spectrometer," according to the abstract.


Journal:Analytical Chemistry , July
Title: Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search
Authors: G Han; M Ye; X Jiang; R Chen; J Ren; Y Xue; F Wang; C Song; X Yao; H Zou

Described is a modified target-decoy search strategy for "confident phosphorylation site analysis of individual phosphoproteins without manual interpretation of spectra," according to the abstract. Instead of all the protein sequences in a proteome database or an organism, the strategy described includes only sequences of the individual target proteins and a decoy version of a small "inhomogeneous" protein database. The confidence in phosphopeptide identification could be controlled when the MS2 And MS3 spectra were searched against the composite database followed by data processing, the authors said.

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