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Recent Research Papers of Note: Mar 4, 2011

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Proteomics research papers of note, January 2011

Journal: Proteomics, Jan 31 [Epub ahead of print]

Title: Application of 2-D DIGE to formalin-fixed, paraffin-embedded tissues.

Authors: Tanca A; Pagnozzi D; Falchi G; Tonelli R; Rocca S; Roggio T; Uzzau S; Addis MF.

The authors investigated using 2-D DIGE technology for the study of proteins in formalin-fixed, paraffin-embedded tissue, checking for internal reproducibility among replicate FFPE extracts and comparability between FFPE and fresh-frozen tissues. According to the abstract they obtained highly reproducible results with satisfactory resolution and complexity, suggesting that 2-D DIGE might be used for the differential proteomic study of archival tissues.


Journal: Clinical and Vaccine Immunology, Jan. 26 [Epub ahead of print]

Title: Antibody recognition of the dengue virus proteome and implications for development of vaccines.

Authors: Fernandez S; Cisney ED; Tikhonov AP; Schweitzer B; Putnak RJ; Simmons M; Ulrich RG.

The authors describe a protein microarray technique for measuring antibody responses to the viral proteome of the four dengue virus serotypes. Using the method they identified differences in antibody response at the proteome level that, they said, could prove useful in vaccine development.


Journal: BMC Systems Biology, Jan. 26

Title: Initial characterization of the human central proteome.

Authors: Burkard TR; Planyavsky M; Kaupe I; Breitwieser FP; Bürckstümmer T; Bennett KL; Superti-Furga G; Colinge J.

Using mass spectrometry, the authors experimentally identified a central proteome consisting of 1,124 proteins that are ubiquitously and abundantly expressed in all human cells. The main functions represented by the identified proteins include proteostasis, primary metabolism, and proliferation. At least 10 percent of this proteome, however, had no or very limited functional annotation.


Journal: PLoS One, Jan. 12

Title: Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer's disease.

Authors: Perrin RJ; Craig-Schapiro R; Malone JP; Shah AR; Gilmore P; Davis AE; Roe CM; Peskind ER; Li G; Galasko DR; Clark CM; Quinn JF; Kaye JA; Morris JC; Holtzman DM; Townsend RR; Fagan AM.

The researchers identified four new CSF biomarkers for Alzheimer's disease – NrCAM, YKL-40, chromogranin A, and carnosinase I – that can improve the diagnostic accuracy of the conventional Alzheimer's biomarkers Aβ42 and tau.


Journal: Bioinformatics, Jan. 22 [Epub ahead of print]

Title: Computational refinement of post-translational modifications predicted from tandem mass spectrometry.

Authors: Chung C; Liu J; Emili A; Frey B.

The authors present a machine learning algorithm, PTMClust, that suppresses noise in mass spec data and clusters peptides into groups based on post-translational modifications to improve the prediction quality of blind PTM searches. According to the abstract, the researchers were able to identify numerous known and novel PTMs when applying the algorithm to a large-scale yeast MS/MS dataset.


Journal: Journal of Cancer Research and Clinical Oncology, Jan. 21 [Epub ahead of print]

Title: Identification of vitronectin as a novel serum marker for early breast cancer detection using a new proteomic approach.

Authors: Kadowaki M; Sangai T; Nagashima T; Sakakibara M; Yoshitomi H; Takano S; Sogawa K; Umemura H; Fushimi K; Nakatani Y; Nomura F; Miyazaki M.

Using a new three-step proteome analysis technique, the researchers identified vitronectin as a potential serum biomarker for primary breast cancer. The method consists of immunodepletion of abundant proteins followed by fractionation using reverse-phase HPLC and separation using 2-DE.


Journal: Proteomics, Jan. 18 [Epub ahead of print]

Title: Targeted large-scale analysis of protein acetylation.

Authors: Mischerikow N; Heck AJ.

The authors review several technologies developed in recent years for the targeted analysis of protein acetylation – both N-terminal acetylation and lysine side chain acetylation – by high-throughput mass spectrometry.


Journal: Science, Jan. 13 [Epub ahead of print]

Title: Proteome half-life dynamics in living human cells.

Authors: Eden E; Geva-Zatorsky N; Issaeva I; Cohen A; Dekel E; Danon T; Cohen L; Mayo A; Alon U.

The authors developed a technique called "bleach-chase" to measure protein half-lives and used it to assay 100 proteins in human cancer cells, observing that under stresses that stop cell division long-lived proteins became longer-lived while short-lived proteins remained largely unaffected, suggesting a mechanism for differentially killing of rapidly growing cells by growth-arresting drugs.


Journal: Nature Protocols, Jan. 6 [Epub ahead of print]

Title: Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry.

Authors: Schilling O; Huesgen PF; Barré O; Auf dem Keller U; Overall CM.

The authors present a method for characterizing the prime- and non-prime-side specificities of individual proteases by identifying individual cleavage sequences from proteome-derived peptide libraries.


Journal: Molecular & Cellular Proteomics, Jan. 5 [Epub ahead of print]

Title: An informatics-assisted label-free approach for personalized tissue membrane proteomics: case study on colorectal cancer.

Authors: Han CL; Chen JS; Chan EC; Wu CP; Yu KH; Chen KT; Tsou CC; Tsai CF; Chien CW; Kuo YB; Lin PY; Yu JS; Hsueh C; Chen MC; Chan CC; Chang YS; Chen YJ.

Using a multiplexed label-free quantification technique, the researchers characterized the proteomes of paired tumor and adjacent normal tissues from 28 patients with various stages of colorectal cancer, identifying STOML2 as a potential protein biomarker tied to decreased survival.

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