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In Print: Last Month's Proteomics Papers of Note: Apr 13, 2012


In Print: Last Month’s Proteomics Papers of Note

Journal: PLoS One, March 12 [Epub ahead of print]

Title: Unique proteomic signatures distinguish macrophages and dendritic cells.

Authors: Becker L; Liu NC; Averill MM; Yuan W; Pamir N; Peng Y; Irwin AD; Fu X; Bornfeldt KE; Heinecke JW.

The authors characterized the proteomes of several types of macrophages, developing specific protein signatures for each cell type, suggesting that proteomic analysis could be used to define immune cell phenotypes in vivo.

Journal: PLoS One, March 21 [Epub ahead of print]

Title: HDL proteome in hemodialysis patients: A quantitative nanoflow liquid chromatography-tandem mass spectrometry approach.

Authors: Mangé A; Goux A; Badiou S; Patrier L; Canaud B; Maudelonde T; Cristol JP; Solassol J.

The authors used iTRAQ labeling and nanoflow LC-MS to generate quantitative data on HDL-associated proteins, comparing the composition of these proteins between seven chronic hemodialysis patients and seven controls. They identified 40 differentially expressed proteins, involved across a range of HDL functions.

Journal: Molecular & Cellular Proteomics, March 21 [Epub ahead of print]

Title: Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles.

Authors: Deeb SJ; D'Souza R; Cox J; Schmidt-Supprian M; Mann M.

The authors used a super-SILAC mix developed from heavy stable isotope labeled lymphoma cell lines, which they then combined with cell lysates from two histologically indistinguishable subtypes of lymphoma. Using mass spec-based quantification they were able to distinguish between these subtypes via protein signatures.

Journal: Analytical Chemistry, March 21 [Epub ahead of print]

Title: Trypsin immobilization on hairy polymer chains hybrid magnetic nanoparticles for ultra fast, highly efficient proteome digestion, facile (18)O labeling and absolute protein quantification.

Authors: Qin W; Song Z; Fan C; Zhang W; Cai Y; Zhang Y; Qian X.

The authors present a new type of immobilized trypsin that uses hybrid nanoparticles synthesized by in situ growth of hairy polymer chains that is intended to offer fast, efficient proteomic digestion. Using this trypsin they achieved a 27 percent increase in proteins and 40 percent increase in peptides identified in complex proteomic samples.

Journal: Molecular & Cellular Proteomics, March 21 [Epub ahead of print]

Title: Quantitative proteomics reveals that only a subset of the endoplasmic reticulum contributes to the phagosome.

Authors: Campbell-Valois FX; Trost M; Chemali M; Dill BD; Laplante A; Duclos S; Sadeghi S; Rondeau C; Morrow IC; Bell C; Hatsuzawa K; Thibault P; Desjardins M.

The researchers developed a label-free mass spec approach to quantify the contribution of various organelles to the phagosome proteome and used this method to determine that the endoplasmic reticulum contributes significantly to the early phagosome proteome, offering potential new avenues of research into the mechanisms of various pathogens.

Journal: Analytical Chemistry, March 23 [Epub ahead of print]

Title: Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling.

Authors: Guan S; Price JC; Ghaemmaghami S; Prusiner SB; Burlingame AL.

The authors describe a connection between proteome-wide protein turnover data obtained via elemental isotope labeling experiments and compartment modeling experiments and demonstrate that the application of compartment modeling can help in fitting of experimental data.

Journal: Journal of Proteome Research, March 26 [Epub ahead of print]

Title: Standard guidelines for the chromosome-centric human proteome project.

Authors: Paik YK; Omenn GS; Uhlen M; Hanash S; Marko-Varga G; Aebersold R; Bairoch A; Yamamoto T; Legrain P; Lee HJ; Na K; Jeong SK; He F; Binz PA; Nishimura T; Keown P; Baker MS; Yoo JS; Garin J; Archakov A; Bergeron J; Salekdeh GH; Hancock WS.

The authors, members of the Human Proteome Organization's Chromosome-Centric Human Proteome Project, present the agreed upon guidelines for experiments within the project.

Journal: Journal of Proteomics, March 29 [Epub ahead of print]

Title: Detecting outlier peptides in quantitative high-throughput mass spectrometry data.

Authors: Erhard F; Zimmer R.

The researchers present a method of detecting outlier peptides in mass spec data that can distinguish between real outliers and outliers caused by imprecise measurement, which they suggest in the abstract could help reduce technical bias in mass spec experiments.

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.