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Recent Research Papers of Note: Dec 14, 2006

Journal: Proteomics, Dec. 7 [Epub ahead of print]
Title:Faster and easier chromatin immunoprecipitation assay with high sensitivity
Authors: H Kohzaki; Y Murakami
Authors have developed a rapid chromatin immunoprecipitation assay in which the immunoprecipitates “serve directly as PCR templates,” the authors say in the abstract. The assay eliminates the need to reverse the crosslinking, shortening the assay by one day, requires less immunoprecipitating antibody and permits many samples to be tested simultaneously.

Journal: Journal of Proteome Research, Dec. 5
Title: A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes
Authors: X Hanouelle; JV Damme; A Staes; L Martens; M Goethals; J Vandekerckhove; K Gevaert
Authors describe a functional, chemical, gel-free proteomics technology allowing the identification of protein adenine nucleotide-binding site in cell lystates. The technology uses a synthetic ATP analogue, 5’-p-fluorosulfonylbenzoyladenosine as an affinity/activity-based probe for nucleotide-binding sites, the authors say in the abstract.

Journal: Journal of Proteome Research, Dec. 5
Title: A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea
Authors: SC Kim; Y Chen; S Mirza; Y Xu; J Lee; P Liu; Y Zhao
Authors describe a method for digesting a complicated protein mixture in the absence of denaturants. “Proteins in the mixture are precipitated with trichloroacetic acid/acetone for denaturation and salt removal, and resuspended in NH4HCO3 buffer,” the authors say in the abstract. “After trypsinolysis, the resulting peptides are not contaminated by urea or other nonvolatile salts and can be dried in a SpeedVac to remove NH4HCO3.”

Journal: Nature Reviews. Molecular Cell Biology, Dec. 7
Title: Functional and quantitative proteomics using SILAC
Author: M Mann
“SILAC removes false positives in protein-interaction studies, reveals large-scale kinetics of proteomes and — as a quantitative phosphoproteomics technology — directly uncovers important points in the signaling pathways that control cellular decisions,” the author says in the abstract.

Journal: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, Dec. 4 [Epub ahead of print]
Title:A bifunctional monolithic column for combined protein preconcentration and digestion for high throughput proteomics research
Authors: K Zhang; S Wu; X Tang; NK Kaiser; JE Bruce
Authors explore solid phase digestion as a strategy to hasten protein digestion and eliminate autodigestion by immobilizing and isolating the enzyme moieties on solid supports. They “prepared immobilized trypsin monolithic capillaries for on-column protein digestion, analyzed the digested peptides through LC/FTICR tandem MS, and compared peptide mass fingerprinting by MALDI-TOF-MS,” they say in the abstract. To improve digestion of low abundance proteins, they introduced C4 functional groups onto the monolith surfaces to combine on-column protein enrichment and digestion.  

Journal: Rapid Communications in Mass Spectrometry: RCM, 2007
Title:Optimization of microfabricated nanoliter-scale solid-phase extraction device for detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization mass spectrometry
Authors: W Chen; J Shen; X Yin; Y Yu
Authors developed a nano-scale solid phase extraction device for detecting gel-separated proteins in low abundance by MALDI-TOF-MS with a simplified microfabrication technology. Authors say they were able to significantly reduce polymeric contaminant signals in MS analysis by using SU-8 photoresist instead of epoxy glue to connect the microchannel and transfer capillary.

Journal: Methods, December
Title: Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors
Authors: L Florens; MJ Carozza; SK Swanson; M Fournier; MK Coleman; JL Workman; MP Washburn
Authors describe an approach to visualize multiprotein complex datasets providing structure information that they say is superior to tabular lists of data.

Journal: Rapid Communications in Mass Spectrometry, Nov. 29 [Epub ahead of print]
Title: Evaluation of an on-target sample preparation system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in conjunction with normal-flow peptide high-performance liquid chromatography for peptide mass fingerprint analyses
Authors: ME McComb; DH Perlman; H Huang; CE Costello
To simplify and reduce the cost of sample preparation, authors investigate the use of a novel and inexpensive 96-well elastomeric array “that affixes to a MALDI target to create an on-target 96-well plate that accommodates a high resolution volume, thereby enabling the on-target processing of samples for MALDI-TOF/MS,” the authors say in the abstract.

Journal: Applied Microbiology Biotechnology, Nov. 23, [Epub ahead of print]
Title:Use of protein chip mass spectrometry to monitor biotinylation reactions
Authors: LL Blazer; MD Boyle
Authors describe a method using SELDI to monitor the kinetics and heterogeneity of product information during the biotinylation of model proteins and peptide targets. “The novelty of the method was in the ability to determine the molecular mass shift, without first separating the targeted molecule from the biotinylating reagent,” the authors say in the abstract.

Journal: Rapid Communications in Mass Spectrometry, Nov. 21 [Epub ahead of print]
Title: Quantitative analysis of amyloid beta peptides in cerebrospinal fluid of Alzheimer's disease patients by immunoaffinity purification and stable isotope dilution liquid chromatography/negative electrospray ionization tandem mass spectrometry
Authors: T Oe; BL Ackermann; K Inoue; MJ Berna; CO Garner; V Gelfanova; RA Dean; ER Siemers; DM Holtzman; MR Farlow; IA Blair
Authors describe a method for analyzing Abeta peptides in CSF that they say overcomes common challenges such as the ability of the peptides to self-aggregate or bind to other proteins and glassware, or the ability of the peptides to undergo post-translational modifications. The approach is LC/MS/MS-based.

Journal: Molecular & Cellular Proteomics, Nov. 17 [Epub ahead of print]
Title: Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations
Authors: RP Munton; R Tweedie-Cullen; M Livingstone-Zatchej; F Weinandy; M Waidelich; D Longo; P Gehrig; F Potthast; D Rutishauser; B Berrits; C Panse; R Schlapbach; IM Mansuy
Authors resolve “activity-dependent changes in phosphorylation stoichiometry at specific sites in distinct sub-cellular compartments of brain cells,” according to the study’s abstract.

Journal: The Analyst, Dec 2006 [Epub Oct. 11]
Title: Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
Authors: EL Hendrickson; Q Xia; T Wang; JA Leigh; M Hackett
Authors compare spectral counting to metabolic stable isotope labeling using (15)N (14) N “heavy/light” peptide pairs. The data were drawn mainly from a Methanococcus maripaludis experiment comparing a wild-type strain with a mutant lacking a key enzyme for energy metabolism. The dataset contained both proteome and transcriptome measurements.

Journal: Bioinformatics, Nov. 22 [Epub ahead of print]
Title: Apredictive model for identifying proteins by a single peptide match
Authors: R Higdon: E Kolker
Authors describe a method for distinguishing true identifications of peptides from false positives among single-hit proteins. The approach is based on randomized database searching and logistic regression models with cross validation.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.