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In Print: Last Month’s Proteomics Papers of Note: Mar 9, 2012

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In Print: Last Month’s Proteomics Papers of Note

Journal: Molecular & Cellular Proteomics, Feb. 2 [Epub ahead of print]

Title: Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Authors: Schaab C; Geiger T; Stoehr G; Cox J; Mann M.
The authors present a database named MaxQB for storing and displaying large collections of proteomics data to support joint analysis and comparison. They demonstrated the database's analysis tools by comparing proteomic data from 11 different human cell lines and 28 mouse tissues.


Journal: Molecular & Cellular Proteomics, Feb. 3 [Epub ahead of print]

Title: Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.

Authors: Jeong JS; Jiang L; Albino E; Marrero J; Rho HS; Hu J; Hu S; Vera C; Bayron-Poueymiroy D; Rivera-Pacheco ZA; Ramos L; Torres-Castro C; Qian J; Bonaventura J; Boeke JD; Yap WY; Pino I; Eichinger DJ; Zhu H; Blackshaw S.

The researchers built a human proteome microarray from GST-His6 fusion proteins generated from a library of 16,368 full-length human ORFs that they then used to analyze the specificity of monospecific, monoclonal antibodies.


Journal: Molecular & Cellular Proteomics, Feb. 6 [Epub ahead of print]

Title: Advancing cell biology through proteomics in space and time (PROSPECTS).

Authors: Lamond AI; Uhlen M; Horning S; Makarov A; Robinson CV; Serrano L; Hartl FU; Baumeister W; Werenskiold AK; Andersen JS; Vorm O; Linial M; Aebersold R; Mann M.

The researchers provide updates on work ongoing under the EU-Funded Proteomics Specification in Time and Space program, a collaborative five-year initiative to develop new methods and applications for protein analysis.


Journal: Journal of Proteome Research, Feb. 10 [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 a proof-of-principle software suite that automates most steps of selected-reaction monitoring mass spec analysis, applying it to a large-scale experiment investigating the remodeling of the Streptococcus pyogenes proteome under stimulation of human plasma.


Journal: Molecular & Cellular Proteomics, Feb. 14 [Epub ahead of print]

Title: Systematic identification of the HSP90 regulated proteome.

Authors: Wu Z; Moghaddas Gholami A; Kuster B.

The researchers applied a global chemical proteomic approach to identifying all HSP90 and HSP90-regulated proteins via SILAC and quantitative mass spec. They identified more than 6,200 proteins in four different human cell lines, roughly 1,600 of which showed significant regulation upon treatment with geldanamycin. This included more than 50 kinases not previously known to be regulated by HSP90.


Journal: Journal of Proteomics, Feb. 22 [Epub ahead of print]

Title: An MRM-based workflow for quantifying cardiac mitochondrial protein phosphorylation in murine and human tissue.

Authors: Lam MP; Scruggs SB; Kim TY; Zong C; Lau E; Wang D; Ryan CM; Faull KF; Ping P.

The researchers used MRM-MS to quantify site-specific phosphorylation of mitochondrial proteins to investigate the regulatory effects of mitochondrial protein phosphorylation in cardiac physiology and disease.


Journal: Analytical Chemistry, Feb. 22

Title: Nano-LC FTICR tandem mass spectrometry for top-down proteomics: routine baseline unit mass resolution of whole cell lysate proteins up to 72 kDa.

Authors: Tipton JD; Tran JC; Catherman AD; Ahlf DR; Durbin KR; Lee JE; Kellie JF; Kelleher NL; Hendrickson CL; Marshall AG.

The researchers present a top-down proteomic analysis of whole cell lysate proteins up to 78 kDA using FTICR-MS. They were able to baseline mass resolve proteins up to 72 kDa on a nano-LC time scale and demonstrate improved throughput for identification of proteins up to 50 kDa.


Journal: Methods, Feb. 25 [Epub ahead of print]

Title: Duplexed iMALDI for the detection of angiotensin I and angiotensin II.

Authors: Mason DR; Reid JD; Camenzind AG; Holmes DT; Borchers CH.

The authors present an immunocapture-based MALDI-MS workflow for detecting and quantifying angiotensin I and II in human plasma for quantification of plasma renin and ACE activities.


Journal: PLoS One, Feb. 29

Title: Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

Authors: Totir M; Echols N; Nanao M; Gee CL; Moskaleva A; Gradia S; Iavarone AT; Berger JM; May AP; Zubieta C; Alber T.

Using high-throughput protein crystallography the researchers fractionated, purified, crystallized, and structurally characterized the Escherichia coli proteome. Applying macroscale fractionation, they subdivided the soluble proteome into 408 fractions, 295 of which yielded crystals. Of these 295, 152 were selected for optimization, screening, and data collection, and 23 protein structures were determined, four of which were novel.

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.