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Recent Research Papers of Note: Jul 23, 2010

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Proteomics research papers of note, July 2010

Journal: Journal of Proteome Research, Jul 6 [Epub ahead of print]

Title: Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics

Authors: Azimzadeh O; Barjaktarovic Z; Aubele M; Calzada-Wack J; Sarioglu H; Atkinson M; Tapio S.

Formalin-fixed paraffin embedded tissue has received interest lately as a sample source for retrospective protein biomarker discovery. There are large stocks of such tissue around the world. However, during the fixing process proteins undergo degradation and cross-linking, making conventional protein extraction difficult. The authors investigated several extraction and separation methods for the analysis of proteins in FFPE tissues.


Journal: Proteomics, July 9 [Epub ahead of print]

Title: The minotaur proteome: Avoiding cross-species identifications deriving from bovine serum in cell culture models

Authors: Bunkenborg J; García GE; Paz MI; Andersen JS; Molina H.

Because cell culture growth media used in proteomics work is often supplemented with fetal bovine serum, contamination by bovine proteins can be difficult to avoid. The researchers generated peptides from bovine serum and analyzed them by LC-MS/MS, seeking strategies to distinguish between bovine and human peptides.


Journal: Geriatrics & Gerontology International, July 10

Title: Proteomic approaches to oxidative protein modifications implicated in the mechanism of aging

Authors: Toda T; Nakamura M; Morisawa H; Hirota M; Nishigaki R; Yoshimi Y.

The authors examined proteomic approaches for observing accumulation of oxidatively modified proteins in aged tissue including immunochemical techniques and biotin tagging for carbonylated protein detection, biotin tagging for protein s-thiolation, and peptide mass fingerprinting for methionine oxidation.


Journal: Molecular & Cellular Proteomics, Jul 13 [Epub ahead of print]

Title: A quantitative proteomics design for systematic identification of protease cleavage events

Authors: Impens F; Colaert N; Helsens K; Ghesquiere B; Timmerman E; De Bock PJ; Chain BM; Vandekerckhove J; Gevaert K.

The authors used differential isotopic proteome labeling to systematically identify protease cleavage events by quantitative N-terminal proteomics. The labeling was done such that the substrate reporter peptides were readily distinguishable from all other N-terminal peptides, eliminating the problem of singleton detection. Validating the approach using the human caspase-3 protease, the researchers identified the largest set of protein protease substrates ever reported, according to the study.


Journal: Amino Acids, Jul 13 [Epub ahead of print]

Title: 100% protein sequence coverage: a modern form of surrealism in proteomics

Authors: Meyer B; Papasotiriou DG; Karas M.

This review discusses the difficulties of achieving 100 percent sequence coverage for proteins and suggests that, in addition to bottom-up shotgun approaches, top-down proteomic analysis is necessary to account for proteins' many variant forms.


Journal: Bioinformatics, Jul 13 [Epub ahead of print]

Title: A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data

Authors: Wang P; Yang P; Arthur J; Yee Hwa Yang J.

The authors developed a new pre-processing algorithm for mass spectrometry proteomics analysis based on wavelet theory that, according to the paper, resulted in the identification of significantly more peptides and proteins in downstream analysis.


Journal: Molecular & Cellular Proteomics, Jul 14 [Epub ahead of print]

Title: PTMScout: A web resource for analysis of high-throughput post-translational proteomic studies

Authors: Naegle KM; Gymrek M; Joughin BA; Wagner JP; Welsch RE; Yaffe MB; Lauffenburger DA; White FM.

The paper details PTMScout, a web-based interface for viewing, manipulating, and analyzing high-throughput experimental measurements of protein post-translational modifications, the discovery of which, the authors say, is "significantly outpacing our biological understanding of [their] function and regulation."


Journal: Structure, July 14

Title: Thermophilic adaptation of protein complexes inferred from proteomic homology modeling

Authors: Ma BG; Goncearenco A; Berezovsky IN.

Using sets of structural templates and sequences of 127 complete prokaryotic proteomes, the authors performed proteomic homology modeling of protein complexes, analyzing traits related to thermostability. They demonstrated the importance of positively charged amino acids in stabilizing protein complexes.


Journal: Molecular & Cellular Proteomics, July 20 [Epub ahead of print]

Title: Quantitative proteomic analysis of A549 cells infected with human respiratory syncytial virus

Authors: Munday D; Emmott E; Surtees R; Lardeau CH; Wu W; Duprex WP; Dove BK; Barr JN; Hiscox JA.

The authors used SILAC coupled to LC-MS/MS to examine changes in human alveolar basal epithelial cells infected with human respiratory syncytial virus, validating and expanding upon known RSV-host interactions and demonstrating the broader usefulness of SILAC with LC-MS/MS for analysis of virus-host interactions.

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