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In Print: Recent Proteomics Papers of Note: Apr 5, 2013

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In Print: Recent Proteomics Papers of Note

Journal: Clinical Proteomics, Feb. 8 [Epub ahead of print]

Title: Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome.

Authors: Cho CK; Drabovich AP; Karagiannis GS; Martínez-Morillo E; Dason S; Dimitromanolakis A; Diamandis EP

The authors used SILAC and mass spectrometry to compare the proteomes of Down syndrome and normal amniocytes, identifying 904 differentially expressed proteins involved in 25 molecular pathways.


Journal: Journal of Proteomics, Feb. 11 [Epub ahead of print]

Title: The "Vampirome": Transcriptome and proteome analysis of the submaxillary and accessory glands of the vampire bat Desmodus rotundus, a vector of human rabies.

Authors: Francischetti IM; Assumpção TC; Ma D; Li Y; Vicente EC; Uieda W; Ribeiro JM.

The authors performed a transcriptomic and proteomic analysis of the salivary glands of the vampire bat, finding that bat saliva is a source of antihemostatics that modulate several aspects of vascular biology.


Journal: Proteomics – Clinical Applications, Feb. 12 [Epub ahead of print]

Title: Proteomic profiling of the autoimmune response to breast cancer antigens uncovers a suppressive effect of hormone therapy.

Authors: Chao T; Ladd JJ; Qiu J; Johnson MM; Israel R; Chin A; Wang H; Prentice RL; Feng Z; Disis ML; Hanash S.

The authors used protein arrays to investigate the effect of hormone therapy on the immune response toward breast tumor antigens, finding a global altered immune response to breast cancer derived proteins associated with hormone therapy.


Journal: BMC Bioinformatics, Feb. 12

Title: MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

Authors: Lamarche BL; Crowell KL; Jaitly N; Petyuk VA; Shah AR; Polpitiya AD; Sandoval JD; Kiebel GR; Monroe ME; Callister SJ; Metz TO; Anderson GA; Smith RD.

The authors present MultiAlign, a software tool for aligning multiple liquid chromatography mass spectrometry datasets by clustering mass and chromatographic elution features across datasets.


Journal: Bioinformatics, Feb. 17 [Epub ahead of print]

Title: Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.

Authors: Chung C; Emili A; Frey BJ.

The authors present a new post-translational modification refinement algorithm, iPTMClust, which extends a recently introduced PTM refinement algorithm and uses a non-parametric Bayesian model to account for uncertainties in the quantity and identity of PTMs in the input data.


Journal: Proteomics, Feb. 19 [Epub ahead of print]

Title: Quantitative analysis of chaperone network throughput in budding yeast.

Authors: Brownridge P; Lawless C; Payapilly AB; Lanthaler K; Holman SW; Harman VM; Grant CM; Beynon RJ; Hubbard SJ.

The authors used the QconCAT methodology to quantify the set of yeast protein chaperones via SRM MS, characterizing the different workloads, efficiencies, and target preferences for these chaperones and finding that they mediate folding of roughly 62 percent of total proteins in a cell.


Journal: Journal of Proteome Research, Feb. 20 [Epub ahead of print]

Title: From cells to peptides: "one-stop" integrated proteomic processing using amphipols.

Authors: Ning Z; Seebun D; Hawley B; Chiang CK; Figeys D.

The authors present a protocol for total and membrane proteome preparation using amphipols, which they write provide a faster, simpler alternative to conventional detergent approaches.


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

Title: Deep proteome coverage based on ribosome profiling aids MS-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Authors: Menschaert G; Van Criekinge W; Notelaers T; Koch A; Crappe J; Gevaert K; Van Damme P.

The authors constructed a protein sequence search space for MS/MS spectrum identification using SwissProt and ribosome profiling-derived translation products, finding that it increased the overall protein identification rate as compared to only searching UniProtKB-SwissProt.


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

Title: Initial quantitative proteomic map of twenty-eight mouse tissues using the SILAC mouse.

Authors:Geiger T; Velic A; Macek B; Lundberg E; Kampf C; Nagaraj N; Uhlen M; Cox J; Mann M.

The authors performed a proteomic analysis of 28 mouse tissues using mass spec and SILAC mice specimens, quantifying 6,974 proteins across the different tissues, and identifying the tissue specialization reflected in their proteomics profiles. They found that while the number of strictly tissue specific proteins is small, even common proteins can have dramatic expression differences between tissues.


Journal: Nature Methods, Feb. 24 [Epub ahead of print]

Title: Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Authors: Stadler C; Rexhepaj E; Singan VR; Murphy RF; Pepperkok R; Uhlén M; Simpson JC; Lundberg E.

The authors report a systematic analysis of more than 500 proteins comparing their localizations in live versus fixed cells using fluorescent protein fusions and immunofluorescence, respectively. They found that for 80 percent of the proteins, both methods yielded the same subcellular distribution, and by using the overlap between the two methods they were able to localize 250 previously unlocalized proteins.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.