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Recent Research Papers of Note: May 6, 2011

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Proteomics research papers of note, April 2011

Journal: Genes & Development, April 1

Title: Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.

Authors: Fasolo J; Sboner A; Sun MG; Yu H; Chen R; Sharon D; Kim PM; Gerstein M; Snyder M.

The authors used protein microarrays to globally investigate proteins interacting with 85 yeast protein kinases, identifying 1,023 interactions including several novel links of kinases to previously distinct cellular pathways — for instance, between the Kss1 filamentous pathway and the stress response pathway.


Journal: PLoS One, April 12

Title: A comprehensive peptidome profiling technology for the identification of early detection biomarkers for lung adenocarcinoma.

Authors: Ueda K; Saichi N; Takami S; Kang D; Toyama A; Daigo Y; Ishikawa N; Kohno N; Tamura K; Shuin T; Nakayama M; Sato TA; Nakamura Y; Nakagawa H.

The authors describe an integrative peptidomic approach for the identification of lung cancer-specific serum peptide biomarkers using one-step effective enrichment of peptidome fractions followed by label-free quantification by nano-LC/MS/MS analysis. The approach, they said, provides a simple, high-throughput quantification method suitable for validation studies involving a large number of clinical samples.


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

Title: High-resolution mapping of the cardiac transmural proteome using reverse phase protein microarrays.

Authors: Anderson T; Wulfkuhle J; Petricoin E; Winslow RL.

The authors used reverse phase protein microarrays to map the left ventricular transmural proteome in order to better understand the structure-function relationships within the heart in health and disease. Using the technique they mapped the transmural expression of Serca2a in the left ventricle of 12 canine hearts in three states: normal, dyssynchronous heart failure, and dyssynchronous heart failure followed by cardiac re-synchronization therapy.


Journal: Journal of Proteome Research, April 18 [Epub ahead of print]

Title: A comprehensive map of the human urinary proteome.

Authors: Marimuthu A; Meally RO; Chaerkady R; Subbannayya Y; Nanjappa V; Kumar P; Kelkar DS; Pinto SM; Sharma R; Renuse S; Goel R; Christopher R; Delanghe B; Cole RN; Harsha HC; Pandey A.

The authors characterized the human urinary proteome using high resolution Fourier transform mass spectrometry, identifying 1,823 proteins, of which 671 had not been previously reported in human urine. The dataset could serve as a reference list for future studies of disease biomarkers in urine.


Journal: International Orthopaedics, April 21 [Epub ahead of print]

Title: Analysis of synovial fluid in knee joint of osteoarthritis:5 proteome patterns of joint inflammation based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Authors: Pan X; Huang L; Chen J; Dai Y; Chen X.

The authors used MALDI-TOF-MS to find differentially expressed disease-related and condition-specific peptides in synovial fluid in the knee joint of patients suffering from osteoarthritis and to develop a model using these peptides for OA diagnosis. They identified four significant peptide peaks that could represent biomarkers for the condition.


Journal: Molecular & Cellular Proteomics, April 29 [Epub ahead of print]

Title: The human proteome project: Current state and future direction.

Authors: Legrain P; Aebersold R; Archakov A; Bairoch A; Bala K; Beretta L; Bergeron J; Borchers C; Corthals GL; Costello CE; Deutsch EW; Domon B; Hancock W; He F; Hochstrasser D; Marko-Varga G; Salekdeh GH; Sechi S; Snyder M; Srivastava S; Uhlen M; Hu CH; Yamamoto T; Paik YK; Omenn GS.

The authors describe the recently officially launched Human Proteome Project, designed to map the entire human proteome. The article covers the general experimental strategy of the project and the three primary techniques it employs: mass spectrometry, antibody capture, and bioinformatics.


Journal: Methods in Molecular Biology, 2011; 725:315-31

Title: Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach.

Authors: Ebner OA; Selbach M.

The authors used pulsed stable isotope labeling by amino acids in conjunction with shotgun mass spectrometry to assess the differences in protein expression in cells transfected with microRNA and non-transfected cells in order to better understand the effect of microRNA on gene expression.


Journal: Methods in Molecular Biology, 2011;731:395-405

Title: Proteomic evaluation of cancer cells: identification of cell surface proteins.

Authors: Larkin S; Aukim-Hastie C.

Using biotin labeling followed by avidin chromatography, the authors obtained membrane protein-enriched cell lysates, which they then analyzed by SDS-PAGE, Coomassie staining, and mass spectrometry to analyze the differential expression of membrane proteins in various types of cancer.

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