Proteomics research papers of note, December 2010
Journal: Phytochemistry, Dec. 6 [Epub ahead of print]
Title: Agricultural recovery of a formerly radioactive area: I. Establishment of high-resolution quantitative protein map of mature flax seeds harvested from the remediated Chernobyl area.
Authors: Klubicová K; Berčák M; Danchenko M; Skultety L; Rashydov NM; Berezhna VV; Miernyk JA; Hajduch M.
Using tandem mass spectrometry, the authors built a quantitative proteome map of mature flax seeds grown in a remediated plot of land in Chernobyl as part of a long-term study to characterize crop plants grown in the formerly radiation-contaminated area. They obtained information on 318 protein spots including seed storage proteins and 82 proteins tied to central metabolism.
Journal: European Journal of Heart Failure, Dec. 10 [Epub ahead of print]
Title: Proteomic analysis of myocardial tissue from the border zone during early stage post-infarct remodelling in rats.
Authors: Xiang F; Shi Z; Guo X; Qiu Z; Chen X; Huang F; Sha J; Chen X.
Because the long-term outcome of patients after myocardial infarction depends on the extent of post-infarction modeling, the authors undertook a comparative proteomic analysis to identify differential myocardial proteome profiles in the border zone of post-MI hearts. They identified 69 differentially expressed proteins possibly involved in post-infarction modeling.
Journal: Clinica Chimica Acta, Dec. 15 [Epub ahead of print]
Title: Prospective highlights of serum glycoproteins in spontaneous tolerance after orthotopic liver transplantation.
Authors: Pan TL; Wang PW; Chen ST; Fang JY; Hsu TK; Sintupisut N; Goto S; Chen CL.
Using mass spectrometry, the researchers performed a functional proteome analysis investigating differentially expressed proteins involved in overcoming major histocompatibility complex barriers, finding that IL-6 and glycoproteins may play critical roles in liver transplant tolerance.
Journal: Journal of Proteome Research, Dec 20. [Epub ahead of print]
Title: Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides.
Authors: Tran BQ; Hernandez C; Waridel P; Potts A; Barblan J; Lisacek F; Quadroni M.
Although trypsin is typically the best available enzyme for protein digestion in bottom-up proteomics studies, it rarely leads to complete sequence coverage as many peptides are either too short or too long to be identified by LC-MS/MS. The researchers found that secondary digestion of large post-trypsin peptides provided a 50 percent increase in coverage compared to the initial digest alone. Applying this strategy to the phosphoproteome of a human cell line, the authors identified a significant number of novel phosphosites.
Journal: Journal of Visualized Experiments, Dec. 20
Title: Profiling of Methyltransferases and other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS).
Authors: Lenz T; Poot P; Gräbner O; Glinski M; Weinhold E; Dreger M; Köster H.
Using the Capture Compound Mass Spectrometry technology owned by Caprotec Analytics, the company's scientists enriched for MTases and other SAH-binding proteins from a strain of E. coli.
Journal: Analytical Chemistry, Dec. 21 [Epub ahead of print]
Title: A novel multidimensional protein identification technology approach combining protein size exclusion prefractionation, peptide zwitterion-ion hydrophilic interaction chromatography, and nano-ultraperformance RP chromatography/nESI-MS(2) for the in-depth analysis of the serum proteome and phosphoproteome: application to clinical sera derived from humans with benign prostate hyperplasia.
Authors: Garbis SD; Roumeliotis TI; Tyritzis SI; Zorpas KM; Pavlakis K; Constantinides CA.
In this proof-of-principle, study the researchers used a MudPIT approach comprising three liquid chromatography chemistries for the deep proteome analysis of human serum derived from benign prostate hyperplasia. They were able to confidently identify more than 1,955 proteins, including 375 phosphoproteins and secreted, tissue-specific proteins spanning roughly 12 orders of magnitude.
Journal: Journal of Cellular Physiology, Dec. 28, [Epub ahead of print]
Title: The requirement for proteomics to unravel stem cell regulatory mechanisms.
Authors: Williamson AJ; Whetton AD.
The authors describe current research using proteomics and mass spec analysis to investigate stem cell regulatory mechanisms including post-translational regulation of protein levels and interactions.
Journal: Neuropharmacology, Dec. 31 [Epub ahead of print]
Title: Synaptoproteomics of learned helpless rats involve energy metabolism and cellular remodeling pathways in depressive-like behavior and antidepressant response.
Authors: Mallei A; Giambelli R; Gass P; Racagni G; Mathé AA; Vollmayr B; Popoli M.
The study compared the proteomes of synaptosomes from learned helpless and non-learned helpless rats, treated and untreated with the tricyclic antidepressant nortriptyline, discovering that proteins involved in energy metabolism and cellular remodeling were dysregulated and that several proteins were regulated in opposite directions by stress and drug treatment – suggesting putative drug targets.