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In Print: Recent Proteomics Papers of Note: May 3, 2013


In Print: Recent Proteomics Papers of Note

Journal: Proceedings of the National Academy of Sciences, March 4 [Epub ahead of print]

Title: Identification of genetic variants influencing the human plasma proteome.

Authors: Johansson Å; Enroth S; Palmblad M; Deelder AM; Bergquist J; Gyllensten U.

The authors combined high-resolution mass spec with genome-wide SNP data to identify genetic variants affecting the human plasma proteome. Of 163 proteins quantified, they found that the levels of 25 proteins were influenced by cis-acting SNPs.

Journal: Molecular & Cellular Proteomics, March 5 [Epub ahead of print]

Title: Extensive mass spectrometry-based analysis of the fission yeast proteome: The S. pombe PeptideAtlas.

Authors: Gunaratne J; Schmidt A; Quandt A; Neo SP; Sarac OS; Gracia T; Loguercio S; Ahrne E; Li Hai Xia R; Tan KH; Loessner C; Bahler J; Beyer A; Blackstock W; Aebersold R.

The authors present as a resource for targeted, quantitative proteomic studies a system-wide proteome catalogue covering 71 percent – 3,542 proteins – of the predicted genes of fission yeast.

Journal: Nature Methods, March 10 [Epub ahead of print]

Title: QuaNCAT: quantitating proteome dynamics in primary cells.

Authors: Howden AJ; Geoghegan V; Katsch K; Efstathiou G; Bhushan B; Boutureira O; Thomas B; Trudgian DC; Kessler BM; Dieterich DC; Davis BG; Acuto O.

The authors present a technique for quantitation of stimuli-induced proteomics dynamics that combines bio-orthogonal noncanonical amino acid tagging BONCAT and stable-isotope labeling of amino acids in cell culture followed by mass spec analysis.

Journal: Analytical Chemistry, March 12 [Epub ahead of print]

Title: Data-dependent middle-down nano-liquid chromatography-electron capture dissociation-tandem mass spectrometry: an application for the analysis of unfractionated histones.

Authors: Kalli A; Sweredoski MJ; Hess S.

The authors present a workflow coupling middle-down mass spec using electron capture dissociation to online nano-LC, using it to analyze large and heavily modified polypepdtides, specifically peptides derived from Asp-N and Glu-C digestions of histones from calf thymus and HeLa, MCF-7, and Jurkat cells. With this workflow they were able to identify several histone variants for all samples examined, including single, multiople, and positional isomeric PTM sites.

Journal: Journal of Proteomics, March 14 [Epub ahead of print]

Title: G protein-coupled receptor quantification using peptide group-specific enrichment combined with internal peptide standard reporter calibration.

Authors: Eisen D; Planatscher H; Hardie DB; Kraushaar U; Pynn CJ; Stoll D; Borchers C; Joos TO; Poetz O.

The authors designed an immunoaffinity and mass spec-based approach to analyze G-protein-coupled receptor specific peptides in rat tissue lysates, demonstrating the ability of mass spec-based methods to offer quantitative analysis of multi-membrane spanning receptor molecules.

Journal: Critical Care Medicine, March 15 [Epub ahead of print]

Title: Determination of burn patient outcome by large-scale quantitative discovery proteomics.

Authors: Finnerty CC; Jeschke MG; Qian WJ; Kaushal A; Xiao W; Liu T; Gritsenko MA; Moore RJ; Camp DG 2nd; Moldawer LL; Elson C; Schoenfeld D; Gamelli R; Gibran N; Klein M; Arnoldo B; Remick D; Smith RD; Davis R; Tompkins RG; Herndon DN; for the Investigators of the Inflammation and the Host Response Glue Grant.

The authors used mass spec and cytokine analysis to profile the plasma proteome of 16 burn survivors and 16 non-survivors. They identified differences in levels of 43 proteins, 32 of which were not known to play a role in burn response.

Journal: Journal of Proteome Research, March 20 [Epub ahead of print]

Title: The effects of travelling wave ion mobility separation on data independent acquisition in proteomics studies.

Authors: Shliaha PV; Bond NJ; Gatto L; Lilley KS.

The authors investigated the effects of TWIMS on data-independent acquisition on a Synapt G2 mass spec, finding that they were able to obtain up to 60 percent higher proteome coverage including many peptides and proteins in the low intensity range of the proteome. They also, however, observed signal loss that limited the instrument's linear range of quantitation.

Journal: PLoS One, March 22 [Epub ahead of print]

Title: Differential denaturation of serum proteome reveals a significant amount of hidden information in complex mixtures of proteins.

Authors: Verdoliva V; Senatore C; Polci ML; Rossi S; Cordella M; Carlucci G; Marchetti P; Antonini-Cappellini G; Facchiano A; D'Arcangelo D; Facchiano F.

The authors examined the effect of proteome denaturation processes on proteomic analysis, testing 69 different denaturation treatments and applying three to human sera. They found significant improvements in serum protein discrimination as measured by MALDI-TOF and LC-MS/MS depending on the type of denaturation used.