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In Print: Last Month’s Proteomics Papers of Note: Feb 3, 2012


In Print: Last Month’s Proteomics Papers of Note

Journal: Analytical Chemistry, Jan. 16 [Epub ahead of print]

Title: Opportunities for sensitive plasma proteome analysis.

Authors: Landegren U; Vänelid J; Hammond M; Nong RY; Wu D; Ullerås E; Kamali-Moghaddam M.

The authors cover techniques for identifying low-abundance protein biomarkers in plasma, suggesting that such low-abundance markers will prove most useful as markers.

Journal: Journal of Proteome Research, Jan. 18 [Epub ahead of print]

Title: A proteomic analysis of eccrine sweat: implications for the discovery of schizophrenia biomarker proteins.

Authors: Raiszadeh M; Ross M; Russo P; Schaepper MA; Zhou W; Deng J; Ng D; Dickson A; Dickson C; Strom M; Osorio C; Soeprono T; Wulfkuhle J; Kabbani N; Petricoin EF; Liotta LA; Kirsch WM.

The researchers used a combination of LC-MS/MS and MRM-MS proteomics to compare the sweat proteomes of schizophrenic and normal individuals, identifying 17 proteins that showed a differential abundance of two-fold or greater.

Journal: Molecular & Cellular Proteomics, Jan. 18 [Epub ahead of print]

Title: Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis.

Authors: Gillet LC; Navarro P; Tate S; Roest H; Selevsek N; Reiter L; Bonner R; Aebersold R.

The authors present a new mass spec strategy that used a high-resolution Qq-TOF instrument repeatedly cycling through 32 consecutive 25 Da precursor isolation windows to generate time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range. This data was sufficient to query peptides over a dynamic range of four orders of magnitude.

Journal: Journal of Proteome Research, Jan. 19 [Epub ahead of print]

Title: Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis.

Authors: Bislev SL; Kusebauch U; Codrea MC; Beynon RJ; Harman VM; Røntved CM; Aebersold R; Moritz RL; Bendixen E.

The researchers performed a targeted proteome analysis of a panel of 20 proteins believed to be key players and indicators of bovine host response to mastitis pathogens. They used the QconCAT method to obtain stable isotope labeled variants of two concordant proteotypic peptides for each of these 20 proteins, with which they were able to achieve robust monitoring of 17 of them.

Journal: Journal of the American Society of Nephrology, Jan. 19 [Epub ahead of print]

Title: Circulating TNF receptors 1 and 2 predict stage 3 CKD in type 1 diabetes.

Authors: Gohda T; Niewczas MA; Ficociello LH; Walker WH; Skupien J; Rosetti F; Cullere X; Johnson AC; Crabtree G; Smiles AM; Mayadas TN; Warram JH; Krolewski AS.

The authors investigated whether concentrations of TNFR1 and TNFR2 were linked to risk for early renal decline by following two cohorts consisting of 628 patients with type 1 diabetes, normal renal function, and no proteinuria. They determined that GFR loss is strongly associated with circulating TNF receptor levels.

Journal: PLoS One, Jan. 23 [Epub ahead of print]

Title: Polar electrophoresis: shape of two-dimensional maps is as important as size.

Authors: Millioni R; Polati R; Menini M; Puricelli L; Miuzzo M; Tessari P; Novelli E; Righetti PG; Cecconi D.

The researchers evaluate the performance of two-dimensional gel electrophoresis in Cartesian coordinates versus polar coordinates, finding that the polar coordinate method offered higher reproducibility and better resolution.

Journal: BMC Bioinformatics, Jan. 23 [Epub ahead of print]

Title: Developing a powerful in silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome.

Authors: Ayyash M; Tamimi H; Ashhab Y.

The authors developed a bioinformatic tool for identifying cellular targets of caspase-3 in hopes of gaining insights into various mechanisms implicated in cancer and neurodegenerative and immunodeficiency diseases.

Journal: Molecular & Cellular Proteomics, Jan. 25 [Epub ahead of print]

Title: Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.

Authors: Geiger T; Wehner A; Schaab C; Cox J; Mann M.

The authors analyzed 11 human cell lines using an LTQ-Orbitrap mass spec, identifying a total of 11,731 proteins, and an average of 10,361 proteins per cell line. They observed great similarly in the proteomes across the cell lines, but significant differences in expression for roughly two-thirds of the proteins, with much of this variability observed in metabolic pathways as opposed to basic cellular machinery.

Journal: Journal of Proteome Research, Jan. 30 [Epub ahead of print]

Title: Automated workflow for large-scale Selected Reaction Monitoring experiments.

Authors: Malmström L; Malmström J; Selevsek N; Rosenberger G; Aebersold R.

The authors present proof-of-principle software that automates most aspects of selected-reaction monitoring mass spectrometry workflows, including generation of the assay, generation of mass spec driver and methods files, and the import and analysis of the data. They apply the technology to a large-scale experiment on how S. pyogenes remodels its proteome in response to human plasma.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.