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In Print: Recent Proteomics Papers of Note: Aug 16, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Cellular & Molecular Life Sciences, June 6 [Epub ahead of print]

Title: Paleoproteomic study of the Iceman's brain tissue.

Authors: Maixner F; Overath T; Linke D; Janko M; Guerriero G; van den Berg BH; Stade B; Leidinger P; Backes C; Jaremek M; Kneissl B; Meder B; Franke A; Egarter-Vigl E; Meese E; Schwarz A; Tholey A; Zink A; Keller A.

The researchers performed a proteomic analysis of brain samples from the Tyrolean Iceman, a Copper-age ice mummy, identifying 502 proteins, including 10 related to blood and coagulation, as well as accumulation of proteins related to stress response and wound healing, reopening discussions about a possible injury of the Iceman's head.


Journal: Journal of Proteomics, June 7 [Epub ahead of print]

Title: Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring.

Authors: Di Girolamo F; Righetti PG; Soste M; Feng Y; Picotti P.

The authors used selected-reaction monitoring mass spec to assay a set of target protein in Saccharomyces cerevisiae to determine the reproducibility of protein capture using combinatorial hexapeptide ligand libraries, finding an average variability of around ten percent.


Journal: Journal of Proteome Research, June 13 [Epub ahead of print]

Title: Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion.

Authors: Shi T; Sun X; Gao Y; Fillmore TL; Schepmoes AA; Zhao R; He J; Moore RJ; Kagan J; Rodland KD; Liu T; Liu AY; Smith RD; Tang K; Camp DG 2nd; Qian WJ.

The authors use a previously presented antibody-free targeted protein quantification strategy called PRISM to quantify low abundance serum proteins, achieving limits of detection at low ng/mL levels with coefficients of variation of around 12 percent. They then used the technique to measure several serum proteins including prostate-specific antigen.


Journal: Mass Spectrometry Reviews, June 15 [Epub ahead of print]

Title: Getting intimate with trypsin, the leading protease in proteomics.

Authors: Vandermarliere E; Mueller M; Martens L.

The authors investigate the shortcomings in the proteomic's field's understanding of the behavior of trypsin and the downstream implications of these shortcomings for proteomics as an analytical tool.


Journal: Molecular & Cellular Proteomics, June 19 [Epub ahead of print]

Title: Comprehensive identification of proteins from MALDI imaging.

Authors: Maier SK; Hahne H; Moghaddas Gholami A; Balluff B; Meding S; Schoene C; Walch AK; Kuster B.

The authors present a method for identifying proteins visualized via MALDI imaging using a combination of bottom-up and top-down proteomics. Applying the method to ten human tissues, they identified 1,400 proteins.


Journal: Molecular & Cellular Proteomics, June 20 [Epub ahead of print]

Title: Global relative quantification with LC-MALDI - cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences.

Authors: Hessling B; Büttner K; Hecker M; Becher D.

The authors used LC-MALDI and an LTQ Orbitrap for a relative quantification analyses of the proteome of Staphylococcus aureus. A comparison of the analyses showed good correlation between the two methods suggesting that LC-MALDI is suitable for proteome-wide quantification. The study also revealed biases by both systems toward certain classes of peptides, suggesting the complementarity of the two methods.


Journal: Proteomics, June 21 [Epub ahead of print]

Title: Critical assessment of proteome-wide label-free absolute abundance estimation strategies.

Authors: Ahrné E; Molzahn L; Glatter T; Schmidt A

The authors evaluated five popular proteome quantification methods, comparing spectral count-based methods to MS1 peak intensity-based methods and looking at the impact of mis-cleaved, modified, and shared peptides as well as protein size and the number of reference proteins used.


Journal: Journal of Proteome Research, June 21 [Epub ahead of print]

Title:Characterization of molecules binding to the 70K N-terminal region of fibronectin by IFAST purification coupled with mass spectrometry.

Authors: Moussavi-Harami SF; Annis DS; Ma W; Berry SM; Coughlin EE; Strotman LN; Maurer LM; Westphall MS; Coon JJ; Mosher DF; Beebe DJ.

The authors present a novel affinity purification technique called immiscible phase filtration using a magnet to draw paramagnetic particle-bound analytes through an immiscible barrier to remove unbound proteins. Using the method, they identified 31 interactors of fibronectin, of which only seven were previously known as interactors.


Journal: Analytical Chemistry, June 27 [Epub ahead of print]

Title: Improved mass spectrometric analysis of membrane proteins based on rapid and versatile sample preparation on nanodiamond particles.

Authors: Pham MD; Yu SS; Han CC; Chan SI.

The authors present a mass spec sample prep method for membrane proteins using nanodiamond particles that allows for concentrating the proteins on the nanodiamonds and separating out the detergents, chaotropic agents, salts, and other impurities to generate mass spec-ready samples in minutes.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.