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Recent Research Papers of Note: Oct 26, 2006

Journal: Electrophoresis, Oct. 19 [Epub ahead of print]
Title: Simultaneous electrophoretic analysis of proteins of very high and low molecular weights using low-percentage acrylamide gel and a gradient SDS-PAGE gel
Authors: E Casas-Terradellas; FR Garcia-Gonzalo; O Hadjebi; R Bartrons; F Ventura; JL Rosa
Authors show that a system they have devised, LAG, can be used in general applications of SDS-PAGE electrophoresis. The LAG gel is formed by combining a low-percentage acrylamide gel and a gradient SDS-PAGE gel. To get good resolution of proteins of more than 200 kDa, the authors used an acrylamide/bisacrylamide ratio of 80:1 in the low-percentage acrylamide gel. To successfully resolve proteins in the 5-200 kDa range, they used a conventional 6-15% SDS-PAGE gradient gel with the standard acrylamide/bisacrylamide ratio of 40:1.

Journal: Proteomics, Oct. 9 [Epub ahead of print]
Title: Minimum reporting requirements for proteomics: A MIAPE primer
Author: CF Taylor
The primer describes efforts by HUPO to create guidelines specifying appropriate levels of details to provide when describing various components of a proteomics experiment. “This primer describes the structure and scope of MIAPE, places it in context amongst reporting specifications for other domains, briefly discusses related informatics resources and closes by considering the ramifications for the proteomics,” the author said in the paper’s abstract.

Journal: Proteomics, Oct. 9 [Epub ahead of print]
Title: The HUPO proteomics standards initiative — overcoming the fragmentation of proteomic data
Authors: H. Hermjakob
The article provides an overview of the PSI organization structure, activities, and current results as well as ways to get involved in the PSI process.

Journal: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, Oct. 9 [Epub ahead of print]
Title: Solid phase proteomics: Dramatic reinforcement of very weak protein-protein interactions.
Authors: M. Fuentes; C. Mateo; BC Pessela; P Batalla; R Fernandez-Lafuente; JM Guisan
Authors devise a strategy to detect very weak protein-protein interactions in in vitro experiments.

Journal: Analytical Chemistry, Oct. 15
Title: Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics
Authors: C Pan; G Kora; DL Tabb; DA Pelletier; WH McDonald; GB Hurst; RL Hettich; NF Samatova
Authors describe a method to score the abundance ratio between light and heavy isotopologues of isotopically labeled peptides while also scoring each abundance ratio for the expected estimation bias and variability

Journal: Analytical Chemistry, Oct. 15
Title: Analysis of complex protein mixtures with improved sequence coverage using (CE-MS/MS) (n) ()
Authors: S Garza; M Moini
Authors describe the new technique as a way to identify proteins in a complex protein mixture without the problem of low sequence coverage typically found in methods using one-dimensional HPLC-MS/MS.

Journal: Journal of Proteome Research, Oct. 5
Title: Simple urinary sample preparation for proteomic analysis
Authors: A Khan; NH Packer
Authors describe a method using 2D gel electrophoresis involving precipitation of proteins with simultaneous desalting.

Journal: Journal of Proteome Research, Oct. 5
Title: A Proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability
Authors: V Prosinecki; HM Botelho; S Francese; G Mastrobuoni; G Moneti; T Urich; A Kletzin; CM Gomes
Authors describe a method to identify the subset of cytosolic hyperstable proteins using Sulfurispharea sp., a hyperthermophilic archaeon, able to grow between 70 and 97 degrees C, as a model organism.

Journal: Journal of Proteome Research, Oct. 5
Title: The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis
Authors: M Ethier; W Hou; HS Duewel; D Figeys
Authors report the development of a microfluidic proteomic reactor that greatly simplifies the processing of complex proteomic samples by combining multiple proteomic steps.

Journal: Journal of Proteome Research, Oct. 5
Title: Novel strategy of high-abundance protein depletion using multidimensional liquid chromatography
Authors: M Gao; J Zhang; C Deng; P Yang; X Zhang
“In this study, for the first time, a comprehensive two-dimensional (2D) liquid-phase separation system, coupling strong cation exchange chromatography (SCX) to reversed-phase high performance liquid chromatography (RPLC), instead of specificity depletion method, was developed at the intact protein level for depletion of high-abundance proteins from rat liver,” according to the paper’s abstract.

Journal: Science, Oct. 6
Title: Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons
Authors: X Han; M Jin; K Brueker; FW McLafferty
Authors describe a new technique that can increase by four times the size of proteins that can be analyzed, from those that contain about 500 amino acids to those containing more than 2,000 amino acids. Using a top-down approach, the researchers break up the protein into pieces and weigh the masses of the entire protein and of the individual pieces, then match them against those of known protein sequences in a database to identify the protein [See PM 10/12/06 for interview with McLafferty].

Journal: Molecular & Cellular Proteomics: MCP, Oct. 2 [Epub ahead of print]
Title: Improved validation of peptide MS/MS assignments using spectral intensity prediction
Authors: S Sun; K Meyer-Arendt; B Eichelberger; R Brown; CY Yen; WM Old; K Pierce; KJ Cios; NG Ahn; KA Resing
Authors report a program allowing for the identification of peptides from complex mixtures and assessing borderline identifications more accurately and timely than with manual analysis.

Journal: Rapid Communications in Mass Spectrometry: RCM, Oct. 2 [Epub ahead of print]
Title: Usefulness of an integrated microfluidic device (HPLC-Chip-MS) to enhance confidence in protein identification by proteomics
Authors: J Hardouin; M Duchateau; R Joubert-Caron; M Caron
Authors test a new integrated microfluidic device, HPLC-Chip, coupled to ion trap MS for the identification of proteins obtained from 2D gel electrophoresis or chromatography. “We conclude that this recently available microfluidic device can be a valuable tool during biomarker discovery programs, particularly identifying low-abundance proteins,” the authors said in the paper’s abstract.

Journal: BMC Bioinformatics, Oct. 4 [Epub ahead of print]
Title: Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
Authors: H Morisawa; M Hirota; T Toda
Authors developed an open source laboratory information system customized for 2D gel electrophoresis-based proteomics workflow.

Journal: Rapid Communications in Mass Spectrometry, Oct. 3, [Epub ahead of print]
Title: Guanidination chemistry for qualitative and quantitative proteomics
Authors: S Warwood; S Mohammed; IM Cristea; C Evans; AD Whetton; SJ Gaskell
Authors apply guanidination chemistry to illustrate several important considerations relating to the use of isotope labeling for relative quantification in proteomics. “This chemistry has been extended for relative quantification, applicable to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and also tandem mass spectrometry (MS/MS). It provides a robust method for the quantitative comparison of two samples that have been separated by 2DE,” the authors said in the paper’s abstract.

Journal: Proteomics, Sept. 27 [Epub ahead of print]
Title: MASCOT HTML and XML parser: An implementation of a novel object model for protein identification data
Authors: CG Yang; SJ Granite; JE Van Eyk; RL Winslow
Authors developed protein identification object model and a parser based on this model to facilitate the analysis and storage of proteomics data generated by using a mass spec.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.