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Recent Research Papers of Note: Feb 26, 2010


Journal: Electrophoresis, Feb. 17 [Epub ahead of print]
Title: Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis
Authors: G Han; M Ye; H Liu; C Song; D Sun; Y Wu; X Jiang; R Chen; C Wang; L Wang; H Zou

Researchers applied nanoflow reverse-phase liquid chromatography to reduce the complexity of phosphopeptides. Two approaches were used to improve the coverage of phosphoproteome analysis of human liver tissue. In one, 10 replicated long-gradient LC-MS/MS runs were performed to analyze the enriched phosphopeptides, resulting in the localization of 1,080 phosphorylation sites from 495 proteins. In another approach, liver tissue proteins were fractionated by SDS-PAGE, and then long-gradient LC-MS/MS analysis was done to analyze the phosphopeptides derived from each fraction, resulting in the localization of 1,786 phosphorylation sites from 911 proteins. "The two approaches showed the complementation in phosphoproteome analysis of human liver tissue," the authors said in the abstract. Combining the results of the two approaches led to the identification of 2,225 non-redundant phosphorylation sites from 1,023 proteins.

Journal: Analytical Chemistry, Feb. 17 [Epub ahead of print]
Title: Free-flow zone electrophoresis of peptides and proteins in PDMS microchip for narrow pI range sample prefractionation coupled with mass spectrometry
Authors: YA Song; M Chan; C Celio; SR Tannenbaum; JS Wishnok; J Han

Authors evaluated a strategy for sorting peptides and/or proteins based on the charge-to-mass ratio "without resorting to ampholytes and/or isoelectric focusing, using a single-[step] and two-step, free-flow zone electrophoresis," according to the abstract. They developed a simple fabrication method to create a salt bridge for free-flow zone electrophoresis in PDMS chips by surface-printing a hydrophobic layer on a glass substrate. "With this device, we demonstrated a separation of positive and negative peptides and proteins at a given pH in standard buffer systems and validated the sorting result with LC/MS," they said. "Furthermore, we coupled two sorting steps via off-chip titration and isolated peptides within specific pI ranges from sample mixtures, where the pI range was simply set by the pH values of the buffer solutions."

Journal: Proteomics, Feb. 16 [Epub ahead of print]
Title: Use of SELDI mass spectrometry to discover and identify potential biomarkers of toxicity in InnoMed PredTox: a multi-site, multi-compound study
Authors: BC Collins; A Sposny; D McCarthy; A Brandenburg; R Woodbury; SR Pennington; JC Gautier; P Hewitt; WM Gallagher

In the abstract, the authors said that a "serious bottleneck" in drug development is the inability of current preclinical toxicology evaluation methods to predict in the early stages and with accuracy whether a drug candidate may have toxicology and health issues that may result in it being dropped from further development. The InnoMed PredTox consortium attempted to address this by assessing techniques such as proteomics, transcriptomics, and metabonomics combined with traditional toxicology measurements in predicting the preclinical safety of drug candidates. In this study, the authors report on the SELDI-TOF-MS proteomics portion of the InnoMed PredTox project. They identified seven plasma proteins and four liver proteins that were modulated by treatment "and [that] correlated with histopathological evaluations and can be considered potential biomarker candidates for the given toxicology endpoints," according to the abstract.

Journal: Analytical Chemistry, Feb. 15
Title: Microfluidic preparative free-flow isoelectric focusing: system optimization for protein complex separation
Authors: J Wen; EW Wilker; MB Yaffe; KF Jensen

Authors present a microfluidic free-flow isoelectric focusing device to address limitations of traditional IEF. The device, they said, is for continuous protein separation into 24 fractions. It reproducibly establishes a "nearly linear pH gradient from four to 10," they said in the abstract. The authors used a protein complex of nine proteins and 13 isoforms and said that they demonstrated improved separation with their device over traditional 2D gel electrophoresis.

Journal: Journal of Proteome Research, Feb. 15 [Epub ahead of print]
Title: Application of an end-to-end biomarker discovery platform to identify target engagement markers in cerebrospinal fluid by high resolution differential mass spectrometry
Authors: CP Paweletz; MC Wiener; AY Bondarenko; NA Yates; Q Song; A Liaw; AY Lee; BT Hunt; ES Henle; F Meng; Sleph H Funk; M Holahan; S Sankaranarayanan; AJ Simon; RE Settlage; JR Sach; M Shearman; AB Sachs; JJ Cook; RC Hendrickson

Described is a general proteomic approach for discovering and identifying proteins that show a "statistically significant" difference in abundance in cerebrospinal fluid before and after drug intervention. The approach is based on an analysis of full-scan mass spec data. Complex mixing and pooling strategies and isotope-labeling techniques are not needed. Clinical samples can be analyzed individually, "allowing the use of longitudinal designs and with-subject data analysis in which each subject acts as its own control," according to the abstract.

Journal: Analytical Chemistry, Feb. 10 [Epub ahead of print]
Title: Integration of protein processing steps on a droplet microfluidics platform for MALDI-MS analysis
Authors: D Chatterjee; AJ Ytterberg; SU Son; JA Loo; RL Garrell

Described is a microfluidic platform to prepare and purify protein samples for measurement by MALDI-MS. "Liquid droplets are moved in air by sequentially applying an electric potential to an array of electrodes patterned beneath a hydrophobic dielectric layer," according to the abstract. They show that a complete integrated sequence of protein processing steps can be done on the platform.

Journal: Journal of Proteome Research, Feb. 5
Title: Single-step procedure for the isolation of proteins at near-native conditions from mammalian tissue for proteomic analysis on antibody microarrays
Authors: MS Alhamdani; C Schröder; J Werner; N Giese; A Bauer; JK Hoheisel

Describes a single-step extraction buffer for isolating proteins from mammalian tissues under native conditions in "an effective and reproducible manner," according to the abstract.

Journal: Journal of Proteome Research, Feb. 3 [Epub ahead of print]
Title: Combinatorial peptide libraries facilitate development of multiple reaction monitoring assays for low-abundance proteins
Authors: AP Drabovich; EP Diamandis

Describes a strategy that facilitates the development of MRM assays for "large numbers of unpurified low-abundance proteins," according to the abstract. The strategy is based on reducing the dynamic range of protein concentration in biological fluids "by means of one-bead, one-compound combinatorial peptide libraries. The approach led to the identification of 484 unique proteins in ovarian cancer ascites, with 216 proteins assigned as low-abundance. The authors also confirmed that MRM assays worked for 30 low-abundance proteins in the unfractionated ascites digest.

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.