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Recent Research Papers of Note: Jun 17, 2011


Proteomics research papers of note, May 2011

Journal: The Plant Cell, May 3 [Epub ahead of print]

Title: Extending SILAC to proteomics of plant cell lines.

Authors: Schütz W; Hausmann N; Krug K; Hampp R; Macek B.

The authors present a method for rendering SILAC labeling fully applicable to dark-grown plant cell lines by differential labeling using two different version of labeled amino acids. Incomplete incorporation of SILAC labels has prevented the technique from being used widely in plants, but, the authors said, the method presented enables similar accuracy and precision as conventional SILAC in animal cells.

Journal: Science Signaling, May 10

Title: A peptide-based target screen implicates the protein kinase CK2 in the global regulation of caspase signaling.

Authors: Duncan JS; Turowec JP; Duncan KE; Vilk G; Wu C; Lüscher B; Li SS; Gloor GB; Litchfield DW.

The authors designed a peptide match program to identify sequences of the human proteome containing overlapping recognition motifs for caspases and kinases in order to investigate the role of phosphorylation in caspase signaling. They identified the protein kinase CK2 as the most prominent kinase with a site overlapping with caspase recognition motifs and identified numerous shared targets between the kinase and caspases.

Journal: Molecular & Cellular Proteomics, May 17 [Epub ahead of print]

Title: Deep and highly sensitive proteome coverage by LC-MS/MS without pre-fractionation.

Authors: Thakur SS; Geiger T; Chatterjee B; Bandilla P; Froehlich F; Cox J; Mann M.

The authors used long LC runs with high resolution coupled to a mass spectrometer with fast sequencing speed to explore how much of the proteome is accessible via LC-MS/MS without pre-fractionation. They identified 68 percent of the total proteome in yeast and 5,376 proteins in a mammalian cell line.

Journal: Medicine and Science in Sports and Exercise, May 20 [Epub ahead of print]

Title: Human muscle proteome modifications following acute or repeated eccentric exercises.

Authors: Hody S; Leprince P; Sergeant K; Renaut J; Croisier JL; Wang F; Rogister B.

The study used 2D-DIGE coupled with MALDI-TOF-MS to examine human muscle proteome modifications caused by strenuous exercises with the aim of developing methods of preventing delayed-onset muscle soreness.

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

Title: A proteomics platform combining depletion, multi-lectin affinity chromatography (M-LAC), and isoelectric focusing to study the breast cancer proteome.

Authors: Zeng Z; Hincapie M; Pitteri SJ; Hanash S; Schalkwijk J; Hogan JM; Wang H; Hancock WS.

The authors devised a multidimensional fractionation platform consisting of immunoaffinity depletion, multi-lectin chromatography, HPLC, and isoelectric focusing followed by mass spec analysis to identify proteins and potential glycan changes associated with breast cancer.

Journal: PLoS One, May 26

Title: Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Authors: Chavez JD; Hoopmann MR; Weisbrod CR; Takara K; Bruce JE.

Using SILAC labeling coupled with mass spectrometry, the authors quantified changes in protein levels between cisplatin-resistant and cisplatin-sensitive HeLa cells in an unbiased fashion, finding 374 that displayed significantly altered expression levels between the cell lines. They then integrated this expression data with a network of protein-protein interactions to develop a systems view of proteome changes linked to cisplatin resistance.

Journal: PloS One, May 27

Title: Mitotic spindle proteomics in Chinese hamster ovary cells.

Authors: Bonner MK; Poole DS; Xu T; Sarkeshik A; Yates JR 3rd; Skop AR.

The authors used MudPIT analysis followed by tandem mass spectrometry to investigate four different isolations of metaphase mitotic spindles, identifying 1,155 proteins, providing the first characterization of the mitotic spindle proteome in CHO cells.

Journal: Analytical Chemistry, May 27 [Epud ahead of print]

Title: Performance characteristics of a new hybrid triple quadrupole time-of-flight tandem mass spectrometer.

Authors: Andrews GL; Simons BL; Young JB; Hawkridge AM; Muddiman DC.

Using a Saccharomysces cerevisiae tryptic digest, the researchers evaluated the key features of the AB Sciex TripleTOF 5600 including acquisition rates, data quality, proteome coverage, and biological depth, finding that of the system's various performance features, its speed contributed most to the resultant data.

Journal: Journal of Proteomics, May 30 [Epub ahead of print]

Title: Poppea's bath liquor: The secret proteome of she-donkey's milk.

Authors: Cunsolo V; Muccilli V; Fasoli E; Saletti R; Righetti PG; Foti S.

Donkey's milk is among the best mother's milk substitute for allergic newborns, according to the authors, but few of the proteins in the milk have been characterized. The authors identified 106 unique gene products in the milk, thus far the largest description of the substance.

The Scan

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Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

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Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.