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In Print: Last Month’s Proteomics Papers of Note: Jan 6, 2012

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In Print: Last Month’s Proteomics Papers of Note

Journal: PLoS One, Dec. 19 [Epub ahead of print]

Title: Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library.

Authors: Rivers J; Hughes C; McKenna T; Woolerton Y; Vissers JP; Langridge JI; Beynon RJ.

The authors used an immobilized combinatorial peptide library to reduce the dynamic range in tissue samples, specifically the soluble fraction of skeletal muscle. The approach managed some equalization of protein abundance, but formation of protein complex assemblies on the beads limited their effectiveness.


Journal: Journal of Proteomics, Dec. 20 [Epub ahead of print]

Title: Evaluation of the salivary proteome as a surrogate tissue for systems biology approaches to understanding appetite.

Authors:Harden CJ; Perez-Carrion K; Babakordi Z; Plummer SF; Hepburn N; Barker ME; Wright PC; Evans CA; Corfe BM.

Using an iTRAQ-based workflow, the researchers examined changes in the salivary proteome in response to isocaloric doses of long chain fatty acid emulsions to investigate proteomic changes associated with appetite response. Several proteins, including thioredoxin and serpin B4, showed changes.


Journal: Journal of Proteome Research, Dec. 22 [Epub ahead of print]

Title: Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos.

Authors: Li Z; Adams RM; Chourey K; Hurst GB; Hettich RL; Pan C.

The researchers compared label-free, metabolic, and isobaric labeling methods on a Thermo Scientific LTQ Orbitrap Velos, finding that iTRAQ and TMT labeling performed similarly in all aspects; spectra counting provided the deepest coverage but the poorest quantification; and that isobaric labeling surpassed metabolic labeling in terms of quantification precision and reproducibility.


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

Title: Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.

Authors: Swearingen KE; Hoopmann MR; Johnson RS; Saleem RA; Aitchison JD; Moritz RL.

The authors detailed a high-field asymmetric waveform ion mobility spectrometry, or FAIMS, platform, finding that coupling FAIMS to nanoLC more than doubled the effective dynamic range compared to a standard nanoLC-MS platform.


Journal: Molecular & Cellular Proteomics, Dec. 13 [Epub ahead of print]

Title: Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response.

Authors: Sharma K; Vabulas RM; Macek B; Pinkert S; Cox J; Mann M; Hartl FU.

Using high-resolution, quantitative mass spec, the researchers mapped protein expression changes in HeLa cells in response to the heat shock protein 90 inhibitor 17-DMAG. They found that proteins involved in DNA damage repair were particularly affected, and followed up this finding with a quantitative phosphoproteomic analysis of 4,000 sites that revealed Hsp90 inhibition leads to down-regulation of the phosphoproteome.


Journal: Molecular & Cellular Proteomics, Dec. 12 [Epub ahead of print]

Title: TraML: a standard format for exchange of selected reaction monitoring transition lists.

Authors: Deutsch EW; Chambers M; Neumann S; Levander F; Binz PA; Shofstahl J; Campbell DS; Mendoza L; Ovelleiro D; Helsens K; Martens L; Aebersold R; Moritz RL; Brusniak MY.

The authors present a new format for encoding selected-reaction monitoring mass spec transition lists and associated metadata that is intended to facilitate exchange of such information and accelerate adoption of SRM methods.


Journal: The Analyst, Dec. 8 [Epub ahead of print]

Title: A multiplex lectin-channel monitoring method for human serum glycoproteins by quantitative mass spectrometry.

Authors: Ahn YH; Ji ES; Shin PM; Kim KH; Kim YS; Ko JH; Yoo JS.

The authors used multiple-reaction monitoring mass spec to analyze multiple lectin-captured fractions of human serum, enabling them to quantitatively measure protein glycosylation on a proteome-wide scale.


Journal: Proceedings of the National Academy of Sciences, Dec. 13

Title: Investment in rapid growth shapes the evolutionary rates of essential proteins.

Authors: Vieira-Silva S; Touchon M; Abby SS; Rocha EP.

To investigate the relationship between growth rates and protein evolution, the authors analyzed 61 families of protein orthologs in 74 proteobacteria, finding that differences in evolutionary rates between low and highly expressed proteins depend on maximal growth rates.

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