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In Print: Recent Proteomics Papers of Note: Dec 14, 2012

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In Print: Recent Proteomics Papers of Note

Journal: Frontiers in Plant Science, Oct. 10 [Epub ahead of print]

Title: Seeds in Chernobyl: the database on proteome response on radioactive environment.

Authors: Klubicová K; Vesel M; Rashydov NM; Hajduch M.

The authors present a database containing proteomic data on seeds harvested from plants grown in the radioactive Chernobyl area, providing information on the seed proteome response to increased levels of radiation.


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

Title: Ultradepletion of human plasma using chicken antibodies: a proof of concept study.

Authors: Tan SH; Mohamedali A; Kapur A; Baker MS.

The researchers describe an approach to deplete high-abundance proteins from human plasma by fractionating the plasma on dual ion exchange columns, producing polyclonal IgY antibodies against each fraction, and then using the antibodies in an immunodepletion column. Using the technique, they identified 39 proteins not previously detected in the non-depleted plasma.


Journal: Proteomics. Clinical Applications, Oct. 23 [Epub ahead of print]

Title: Proteomic workflow for analysis of archival formalin fixed and paraffin embedded clinical samples to a depth of 10,000 proteins.

Authors: Wiśniewski JR; Duś K; Mann M.

The authors present a workflow for preparation and mass spec analysis of FFPE samples that enabled identification of up 10,000 proteins per sample.


Journal: Analytical Chemistry, Oct 24 [Epub ahead of print]

Title: Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion-trap mass spectrometer.

Authors: Vincent CE; Rensvold JW; Westphall MS; Pagliarini DJ; Coon JJ.

The authors present a method for eliminating precursor interference in isobaric tagging on a linear ion trap system, achieving significant improvements in quantitative accuracy.


Journal: Clinical Chemistry, Nov. 13 [Epub ahead of print]

Title: The riddle of protein diagnostics: future bleak or bright?

Authors: Anderson NL; Ptolemy AS; Rifai N.

The authors discuss the potential and challenges facing protein diagnostics.


Journal: Molecular Biosystems, Nov 13 [Epub ahead of print]

Title: A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

Authors: Ansong C; Schrimpe-Rutledge AC; Mitchell HD; Chauhan S; Jones MB; Kim YM; McAteer K; Deatherage Kaiser BL; Dubois JL; Brewer HM; Frank BC; McDermott JE; Metz TO; Peterson SN; Smith RD; Motin VL; Adkins JN.

The authors used genomics and proteomics to examine the differences between Yersinia pestis, which causes plague and has a high morality rate, and Yersinia pseudotuberculosis, which has a much lower mortality rate. They discovered higher hene and protein expression levels of conserved major virulence factors of YP compared to YPT.


Journal: Genome Medicine, Nov. 18 [Epub ahead of print]

Title: Comprehensive analysis of the genome, transcriptome, and proteome landscapes of three tumor cell lines.

Authors: Akan P Dr; Alexeyenko A Dr; Costea PI; Hedberg L; Solnestam BW; Lundin S; Hallman J; Lundberg E Dr; Uhlen M Prof; Lundeberg J Prof.

The authors presented a comparative genome, transcriptome, and proteome analysis of three tumor cell lines, finding that while gene copy number significantly influenced transcript levels it has less effect on protein levels.


Journal: Nature Methods, Nov. 18 [Epub ahead of print]

Title: Digestion and depletion of abundant proteins improves proteomic coverage.

Authors: Fonslow BR; Stein BD; Webb KJ; Xu T; Choi J; Park SK; Yates JR 3rd.

The authors present a depletion method that uses the kinetics of trypsin digestion to selectively digest and deplete high-abundance proteins to improve the coverage of mass spec analysis. They observed greater than threefold improvement in low-abundance protein identification and quantitation.


Journal: Journal of Proteomics, Nov. 23 [Epub ahead of print]

Title: Laser microdissection and two-dimensional difference gel electrophoresis reveal proteomic intra-tumor heterogeneity in colorectal cancer.

Authors: Sugihara Y; Taniguchi H; Kushima R; Tsuda H; Kubota D; Ichikawa H; Fujita S; Kondo T.

The authors used laser microdissection to obtain colorectal cancer tumor cells localized in the ulcer floor, the central area, and the invasive front, as well as normal colorectal epithelial cells and characterize their proteomes by mass spectrometry. When they distinguished the tumor cells based on tissue localization, they observed 88 proteins at different intensities in the tumor groups compared to normal cells.


Journal: Analytical Chemistry, Nov. 26 [Epub ahead of print]

Title: First signal from a broadband cryogenic preamplifier cooled by circulating liquid nitrogen in a 7 T Fourier transform ion cyclotron resonance mass spectrometer.

Authors: Choi MC; Lee JM; Lee SG; Choi SH; Choi YS; Lee KJ; Kim S; Kim HS; Stahl S.

The authors developed a liquid circulation cooling system in order to improve the sensitivity of their FTICR mass spec. Using it, they demonstrated a 130 percent improvement in signal-to-noise ratio compared to room temperature operation.


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

Title: Quantification of amyloid precursor protein isoforms using QconCAT internal standard.

Authors: Chen J; Wang M; Turko IV.

The researchers used QconCAT internal standards – artificial proteins that are concatamers of tryptic peptides for several proteins – for quantifying isoforms of amyloid precursor proteins in human frontal cortex samples from both controls and Alzheimer's patients.


Journal: Molecular & Cellular Proteomics, Nov. 29 [Epub ahead of print]

Title: In-depth proteomic characterization of endogenous nuclear receptors in mouse liver.

Authors: Liu Q; Ding C; Liu W; Song L; Liu M; Qi L; Fu T; Malovannaya A; Wang Y; Qin J; Zhen B.

The authors used DNA constructs of hormone response elements as affinity reagents to enrich nuclear receptor proteins from extracts of mouse liver and identify them via mass spectrometry. They detected proteins for 35 of the 41 NR families expressed in mouse liver at the mRNA level.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.