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In Print: Last Month’s Proteomics Papers of Note: Dec 9, 2011


In Print: Last Month’s Proteomics Papers of Note

Journal: Proteomics, Nov. 4 [Epub ahead of print]

Title: Comprehensive proteomic analysis of human bile.

Authors: Barbhuiya MA; Sahasrabuddhe NA; Pinto SM; Muthusamy B; Singh TD; Nanjappa V; Keerthikumar S; Delanghe B; Harsha HC; Chaerkady R; Jalaj V; Gupta S; Shrivastav BR; Tiwari PK; Pandey A.

Using a separations approach combining SDS-PAGE, strong cation exchange chromatography, and off-gel electrophoresis along with high-resolution MS analysis, the researchers identified 2,552 proteins in human bile, the most reported in human bile to date. The protein catalog generated can serve as a baseline for future biomarker studies, they suggested.

Journal: Analytical Chemistry, Nov. 21 [Epub ahead of print]

Title: Robust analysis of the yeast proteome under 50 kDa by molecular weight-based fractionation and top-down mass spectrometry.

Authors: Kellie JF; Catherman AD; Durbin KR; Tran JC; Tipton JD; Norris JL; Witkowski CE; Thomas PM; Kelleher NL.

The researchers describe a high-throughput workflow for top-down proteomics incorporating a tube-gel electrophoresis device to separate intact proteins by molecular weight with a nanocapillary LC-MS/MS platform. In the study they identified 530 unique yeast proteins and 1103 distinct protein species.

Journal: Proteomics, Nov. 22 [Epub ahead of print]

Title: The 2011 Human Liver Proteome Project (HLPP) workshop September 5, 2011, Geneva, Switzerland.

Authors: Elortza F; Beretta L; Zhang X; He F; Mato JM.

The researchers present the latest results from various projects going on under the Human Liver Proteome Project and a discussion of the initiative’s possible next steps.

Journal: The Journal of Biological Chemistry, Nov. 23 [Epub ahead of print]

Title: Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics.

Authors: Malmstrom J; Karlsson C; Nordenfelt P; Ossola R; Weisser H; Quandt A; Hansson K; Aebersold R; Malmstrom L; Bjorck L.

The researchers used a combination of label-free quantitative proteomics approaches to analyze the affect of human plasma on the intracellular proteome homeostasis of S. pyogenes, identifying and quantifying 842 proteins and identifying several changes in expression – down-regulation of proteins involved in fatty acid synthesis, in particular.

Journal: New Biotechnology, Nov. 23 [Epub ahead of print]

Title: Validation of affinity reagents using antigen microarrays.

Authors: Sjöberg R; Sundberg M; Gundberg A; Sivertsson A; Schwenk JM; Uhlén M; Nilsson P.

The researchers describe an antigen microarray-based method of validating affinity reagents. They used the array to screen roughly 400 different affinity reagents to SH2-domain containing human proteins, demonstrating its ability to provide detailed specificity profiles and detect off-target interactions

Journal: The American Journal of Pathology, Nov. 25 [Epub ahead of print]

Title: Age-dependent changes in the cerebrospinal fluid proteome by slow off-rate modified aptamer array.

Authors: Baird GS; Nelson SK; Keeney TR; Stewart A; Williams S; Kraemer S; Peskind ER; Montine TJ.

Using Somalogic’s proprietary Somamer reagents, the researchers screened cerebrospinal fluid samples from 90 cognitively normal adults 21 to 85 years of age to study age-related changes in the CSF proteome. They detected 248 proteins possessing signals greater than twofold over the background, including proteins related to inflammation and response to injury in the central nervous system.

Journal: Molecular Biosystems, Nov. 28 [Epub ahead of print]

Title: Comparative proteomics to evaluate multi drug resistance in Escherichia coli.

Authors: Piras C; Soggiu A; Bonizzi L; Gaviraghi A; Deriu F; De Martino L; Iovane G; Amoresano A; Roncada P.

The researchers analyzed the proteomes of drug-resistant E. coli isolated from young never-vaccinated water buffalo, identifying proteins differentially expressed under drug resistance conditions in order to gain insights about mechanisms involved in resistance.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.