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Recent Research Papers of Note: Jun 18, 2010


Proteomics research papers of note, June 2010

Journal: Journal of Proteome Research, June 4 [Epub ahead of print]

Title: Mass Spectrometric Discovery and Selective Reaction Monitoring (SRM) of Putative Protein Biomarker Candidates in First Trimester Trisomy 21 Maternal Serum

Authors: Lopez MF; Kuppusamy R; Sarracino DA; Prakash A; Athanas M; Krastins B; Rezai T; Sutton JN; Peterman S; Nicolaides K

The study applied proteomics and mass spectrometry to the discovery of new putative biomarkers for trisomy 21, identifying a series of differentially expressed proteins and developing a multiplexed, high-throughput SRM assay for verification of 12 of these putative markers selected as particularly promising through the use of receiver operating curve algorithms.

Journal: PLoS One, June 9

Title: Proteome-wide profiling of the MCF10AT breast cancer progression model.

Authors: Choong LY; Lim S; Chong PK; Wong CY; Shah N; Lim YP

Using iTRAQ-based tandem mass spectrometry, the authors conducted a proteomic study of the MCF10AT breast cancer model, which mimics various stages of the disease's progression. The study identified 98 proteins showing significant expression changes across the model and validated aberrant expression of three novel breast cancer-associated proteins.

Journal: Proteomics, June 10 [Epub ahead of print]

Title: Proteome analysis of brain in murine experimental autoimmune encephalomyelitis

Authors: Fazeli AS; Nasrabadi D; Sanati MH; Pouya A; Ibrahim SM; Baharvand H; Salekdeh GH

The authors used a 2D gel electrophoresis-based proteomics approach to analyze brain protein expression in healthy samples and those affected by experimental autoimmune encephalomyelitis – one of the best characterized models of multiple sclerosis. Of the more than 1,000 proteins analyzed, 70 showed reproducible and significant changes in EAE and of these 42 could be identified using MALDI TOF-TOF mass spectrometry.

Journal: PLoS One, June 11

Title: Establishing the proteome of normal human cerebrospinal fluid

Authors: Schutzer SE; Liu T; Natelson BH; Angel TE; Schepmoes AA; Purvine SO; Hixson KK; Lipton MS; Camp DG; Coyle PK; Smith RD; Bergquist J

The authors analyzed cerebrospinal fluid from groups of subjects identified as neurologically normal using immunoaffinity separation and high-sensitivity and -resolution LC-MS in order to build a proteomic profile for normal CSF that can be used as a comparative standard and basis for the study of a variety of neurological diseases.

Journal: Proceedings of the National Academy of Sciences, June 14 [Epub ahead of print]

Title: Proteomic identification of phosphatidylinositol (3,4,5) triphosphate-binding proteins in Dictyostelium discoideum

Authors: Zhang P; Wang Y; Sesaki H; Iijima M

Phosphatidylinositol (3,4,5) triphosphate (PtdlinsP(3)) mediates intracellular signaling for directional sensing and pseudopod extension at the leading edge of migrating cells during chemotaxis, but how this signal translates into remodeling of the actin cytoskeleton is poorly understood. The authors used a proteomics approach to identify multiple PtdlinsP(3)-binding proteins in order to study its role in chemotaxis.

Journal: Molecular & Cellular Proteomics, June 15 [Epub ahead of print]

Title: Proteomic characterization of extracellular space components in the human aorta

Authors: Didangelos A; Yin X; Mandal K; Baumert M; Jahangiri M; Mayr M

Few proteomics studies have specifically targeted the vascular extracellular matrix, which is key to the structural integrity of vessel walls and binds secreted products from vascular cells and molecules from circulation. Using a novel protein extraction approach, the authors identified 103 extracellular vascular proteins, one-third of which have never before been reported.

Journal: BMC Bioinformatics, June 15 [Epub ahead of print]

Title: Pripper: prediction of caspase cleavage sites from whole proteomes

Authors: Piippo M; Lietzen N; Nevalainen OS; Salmi J; Nyman TA

Caspases have key roles in apoptosis and inflammation, but there are currently no methods to predict caspase cleavage sites across multiple proteins or entire proteomes. The authors developed a new bioinformatic tool, Pripper, capable of predicting caspase cut sites, which they used to build a database to identify caspase products from tandem mass spectrometry data. This technique should be broadly applicable to many other proteases, the authors said.

Journal: Oncology Reports, July

Title: Identification of a 17-protein signature in the serum of lung cancer patients

Authors: Sreseli RT; Binder H; Kuhn M; Digel W; Veelken H; Sienel W; Passlick B; Schumacher M; Martens UM; Zimmermann S

Early detection of lung cancer could improve survival rates of the disease, but currently there are no satisfactory laboratory tests to screen for it. The study aimed to discover serum biomarkers for lung cancer using SELDI-TOF MS. A total of 17 differential predictive protein mass clusters were identified, providing a potential risk prediction model, the authors said.

Journal: European Journal of Mass Spectrometry, 2010 (Volume 3)

Title: Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides

Authors: Darula Z; Chalkley RJ; Baker P; Burlingame AL; Medzihradszky KF

Complex mixtures containing O-linked glycopeptides were analyzed via collision-induced dissociation and electron transfer dissociation on a linear ion trap-Orbitrap. The authors provide an overview of the structural information provided by the different fragmentation methods.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.