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Recent Research Papers of Note: Jan 2, 2009

Journal: Methods in Molecular Biology, 2009
Title: Identification of SUMO target proteins by quantitative proteomics
Authors: JS Anderson; I Matic; AC Vertegaal
According to the abstract, the identification of target proteins for small ubiquitin-like modifiers, or SUMOs, is critical in understanding cellular functions of SUMOs, but substrate protein identification for SUMOs is hampered by the low abundance of SUMO targets. The authors said that quantitative proteomics is a “powerful tool” that allows discrimination between contaminating proteins in SUMO-enriched preparations and true protein targets. They detail the application of SILAC for the identification of protein targets for SUMOs.

Journal: Rapid Communications in Mass Spectrometry: RCM, January 2009
Title: Improving peptide identification using an empirical peptide retention time database
Authors: W Sun; L Zhang; R Yang; C Shao; Z Zhang; Y Gao
Authors combined peptide retention time with tandem-MS information for enhanced peptide identification. The approach resulted in the construction of an empirical peptide retention time database based on peptides showing a false-positive rate of about 1 percent detected in several LC-MS/MS analyses.

Journal: Molecular & Cellular Proteomics, Dec. 30 [Epub ahead of print]
Title: Elastase digests: new ammunition for shotgun membrane proteomics
Authors: B Rietschel; TN Arrey; B Meyer: S Bornemann; M Schuerken; M Karas; A Poetsch
Presented is a method for the nanoLC-based analysis of complex membrane proteomes “on the basis of methanolic porcine pancreatic elastase digest to increase transmembrane coverage,” according to the abstract. Using the method, the authors successfully analyzed salinarium purple and Corynebacterium glutamicum.

Journal: Analytical Chemistry, Dec. 23 [Epub ahead of print]
Title: Quadrupole time-of-flight mass spectrometer modified for higher-energy dissociation reduces protein assemblies to peptide fragments
Authors: JL Benesch; BT Ruotolo; F Sobott; J Wildgoose; A Gilbert; R Bateman; CV Robinson
Authors reported new insights into the collision-induced dissociation mechanism of protein assemblies. “By holding activation energy constant and varying the charge state of the precursor ion, we show that the total charge of the precursor ion dramatically influences the internal energy required to dissociate monomers from the protein assembly,” they said in the abstract. They added they have developed a modified quadrupole time-of-flight instrument that can access activation energies higher than previously possible.

Journal: Proteomics, Dec. 22 [Epub ahead of print]
Title: Investigation sample pooling strategies for DIGE experiments to address biological variability
Authors: NA Karp; KS Lilley
In the abstract the authors said that sample subpooling can be used to reduce the variance but still allow studies “to encompass biological variation.” Their study found no evidence of a systematic bias triggered by sample pooling for DIGE and that pooling can be useful in reducing biological variation.

Journal: Analytical and Bioanalytical Chemistry, Dec. 9 [Epub ahead of print]
Title: A 2D reversed-phase x ion-pair reversed-phase HPLC-MALDI TOF/TOF-MS approach for shotgun proteome analysis
Authors: M Lasaosa; N Delmotte; CG Huber; K Melchior; K Heinzle; A Tholey
An earlier study showed that a 2D separation scheme encompassing reversed-phase x ion-pair reversed-phase liquid chromatography coupled online to electrospray ion trap mass spectrometry is superior for separating complex peptide mixtures in shotgun proteome analysis compared to the classically used separation scheme using strong cation exchange x IP-RP-chromatography. Authors expand on the approach by coupling offline the novel separation scheme to MALDI TOF/TOF-MS for the analysis of a tryptic digestion of the cytosolic proteome of the bacterium Corynebacterium glutamicum. They said that their approach yielded a significant increase in the number of proteins and peptides. “The high proteome coverage, as well as the large number of low-abundant proteins identified with this improved analytical platform, pave the way for new biological studies,” according to the abstract.

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