A novel preparation technique of red (sparkling) wine for protein analysis
Publication date: Available online 4 March 2016 Source:EuPA Open Proteomics Author(s): Elisabeth I. Vogt, Veronika M. Kupfer, Rudi F. Vogel, Ludwig Niessen Despite their low concentration, proteins can influence several key enological parameters such as foam stability or haze formation in (sparkling) wine. Most studies focus on white (sparkling) wine since the higher content of phenolic compounds in red wines impairs proteomic research. The aim of the study was the development of a method for the preparation of red (sparkling) wine proteins for proteomic analysis. Three methods of sample preparation were assess...
Source: EuPA Open Proteomics - March 5, 2016 Category: Bioinformatics Source Type: research
Experimental setup for the identification of mitochondrial protease substrates by shotgun and top-down proteomics
Publication date: Available online 22 February 2016 Source:EuPA Open Proteomics Author(s): Alice Di Pierro, Heather Bondi, Chiara Monti, Luisa Pieroni, Enrico Cilio, Andrea Urbani, Tiziana Alberio, Mauro Fasanoab, Maurizio Ronci Mitochondria possess a proteolytic system that contributes to the regulation of mitochondrial dynamics, mitochondrial biogenesis and mitophagy. We aimed at the identification by bottom-up proteomics of altered protein processing due to the activation of mitochondrial proteases in a cellular model of impaired dopamine homeostasis. Moreover, we optimized the conditions for top-d...
Source: EuPA Open Proteomics - February 23, 2016 Category: Bioinformatics Source Type: research
Peptide-mediated ‘miniprep’ isolation of extracellular vesicles is suitable for high-throughput proteomics
Publication date: Available online 22 February 2016 Source:EuPA Open Proteomics Author(s): Jaco C. Knol, Inge de Reus, Tim Schelfhorst, Robin Beekhof, Meike de Wit, Sander R. Piersma, Thang V. Pham, Egbert F. Smit, Henk M.W. Verheul, Connie R. Jiménez Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since EVs are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, they represent a rich source for disease biomarkers. However, standard ultracentrifugation meth...
Source: EuPA Open Proteomics - February 23, 2016 Category: Bioinformatics Source Type: research
Systemic amyloidoses and proteomics: The state of the art
Publication date: Available online 23 February 2016 Source:EuPA Open Proteomics Author(s): Francesca Lavatelli, Andrea di Fonzo, Giovanni Palladini, Giampaolo Merlini Systemic amyloidoses are caused by misfolding-prone proteins that polymerize in tissues, causing organ dysfunction. Since proteins are etiological agents of these diseases, proteomics was soon recognized as a privileged instrument for their investigation. Mass spectrometry-based proteomics has acquired a fundamental role in management of systemic amyloidoses, being now considered a gold standard approach for amyloid typing. In parallel, approaches...
Source: EuPA Open Proteomics - February 23, 2016 Category: Bioinformatics Source Type: research
The identification of FERM domain protein in serum infected with Plasmodium berghei
In this study, we compared the protein profile of uninfected and Plasmodium berghei-infected serum samples by one dimensional SDS-PAGE analysis, MALDI-TOF/TOF mass spectrometry and confirmed by semi-quantitative RT-PCR. Also the protein interacting networks were established using STRING protein–protein interaction analysis. We observed for the first time the upregulation of FERM domain during P. berghei infection. We predict that FRMD5 along with the other protein partners (identified by STRING analysis) are involved in the merozoites entry or protein trafficking where cell to cell interaction happens with the host eryth...
Source: EuPA Open Proteomics - January 30, 2016 Category: Bioinformatics Source Type: research
Lysine acetylation of major Chlamydia trachomatis antigens
Publication date: Available online 28 January 2016 Source:EuPA Open Proteomics Author(s): Jelena Mihailovic, Aleksandra Inic-Kanada, Katarina Smiljanic, Elisabeth Stein, Talin Barisani-Asenbauer, Tanja Cirkovic Velickovic Chlamydia trachomatis (Ct) is a human pathogen causing trachoma and infertility. We investigated acetylation at lysine residues of chlamydial antigenic proteins: major outer membrane protein (MOMP), 60kDa chaperonin (chlamydial HSP60), elongation factor G (EF–G), enolase and the polymorphic membrane proteins PmpB, PmpE and PmpF. 60kDa chaperonin, EF–G, and PmpB showed the highest degr...
Source: EuPA Open Proteomics - January 30, 2016 Category: Bioinformatics Source Type: research
Introducing the Affinity Binder Knockdown Initiative—A public–private partnership for validation of affinity reagents
Publication date: March 2016 Source:EuPA Open Proteomics, Volume 10 Author(s): Tove Alm, Emma Lundberg, Mathias Uhlén The newly launched Affinity Binder Knockdown Initiative encourages antibody suppliers and users to join this public–private partnership, which uses crowdsourcing to collect characterization data on antibodies. Researchers are asked to share validation data from experiments where gene-editing techniques (such as siRNA or CRISPR) have been used to verify antibody binding. The initiative is launched under the aegis of Antibodypedia, a database designed to allow comparisons and scoring of publicly ...
Source: EuPA Open Proteomics - January 30, 2016 Category: Bioinformatics Source Type: research
Comparative proteomic analysis of malignant pleural mesothelioma: Focusing on the biphasic subtype
Publication date: Available online 16 January 2016 Source:EuPA Open Proteomics Author(s): Laura Giusti, Federica Ciregia, Alessandra Bonotti, Ylenia Da Valle, Elena Donadio, Claudia Boldrini, Rudy Foddis, Gino Giannaccini, Maria R. Mazzoni, Pier Aldo Canessa, Alfonso Cristaudo, Antonio Lucacchini Malignant pleural mesothelioma (MPM) is a rare cancer originated from pleural mesothelial cells. MPM has been associated with long-term exposure to asbestos. In this work we performed a comparative proteomic analysis of biphasic pleural mesothelioma (B-PM). Tissue biopsies were obtained from 61 patients...
Source: EuPA Open Proteomics - January 17, 2016 Category: Bioinformatics Source Type: research
Translating epithelial mesenchymal transition markers into the clinic: novel insights from proteomics
Publication date: Available online 6 January 2016 Source:EuPA Open Proteomics Author(s): Vergara Daniele, Simeone Pasquale, Julien Frank, Trerotola Marco, Giudetti Anna, Capobianco Loredana, Tinelli Andrea, Bellomo Claudia, Fournier Isabelle, Antonio Gaballo, Alberti Saverio, Salzet Michel, Maffia Michele The growing understanding of the molecular mechanisms underlying epithelial-to-mesenchymal transition (EMT) may represent a potential source of clinical markers. Despite EMT drivers have not yet emerged as candidate markers in the clinical setting, their association with established clinical ...
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Developmental origins of metabolic disorders: The need for biomarker candidates and therapeutic targets from adequate preclinical models
Publication date: Available online 7 January 2016 Source:EuPA Open Proteomics Author(s): Antonio Gonzalez-Bulnes, Susana Astiz, Marta Vazquez-Gomez, Consolación Garcia-Contreras The investigation on obesity and associated disorders have changed from an scenario in which genome drove the phenotype to a dynamic setup in which prenatal and early-postnatal conditions are determinant. However, research in human beings is difficult due to confounding factors (lifestyle and socioeconomic heterogeneity), plus ethical issues. Hence, there is currently an intensive effort for developing adequate preclinical models, aimi...
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Towards a functional definition of the mitochondrial human proteome
Publication date: Available online 7 January 2016 Source:EuPA Open Proteomics Author(s): Mauro Fasano, Tiziana Alberio, Mohan Babu, Emma Lundberg, Andrea UrbaniGraphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Introducing the Affinity Binder Knockdown Initiative - a public–private partnership for validation of affinity reagents
Publication date: Available online 7 January 2016 Source:EuPA Open Proteomics Author(s): Tove Alm, Emma Lundberg, Mathias Uhlén The newly launched Affinity Binder Knockdown Initiative encourages antibody suppliers and users to join this public-private partnership, which uses crowdsourcing to collect characterization data on antibodies. Researchers are asked to share validation data from experiments where gene-editing techniques (such as siRNA or CRISPR) have been used to verify antibody binding. The initiative is launched under the aegis of Antibodypedia, a database designed to allow comparisons and scoring of p...
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Effect of Fetal Bovine Serum in culture media on MS analysis of mesenchymal stromal cells secretome
Publication date: Available online 7 January 2016 Source:EuPA Open Proteomics Author(s): Simona Nonnis, Elisa Maffioli, Lucia Zanotti, Fabiana Santagata, Armando Negri, Antonella Viola, Stephen Elliman, Gabriella Tedeschi The analysis of mesenchymal stromal cells secretome is fundamental to identify key players of processes involving these cells. Truly secreted proteins may be difficult to detect in MS based analysis of conditioned media (CM) due to proteins supplemented with fetal bovine serum (FBS). We compared different growth conditions to determine the effect of varying FBS concentration on the num...
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LC–MS—A technical report
Publication date: March 2016 Source:EuPA Open Proteomics, Volume 10 Author(s): L. Staunton, C. Tonry, R. Lis, S. Finn, J. O’Leary, M. Loda, M. Bowden, S.R. Pennington Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections. Here, we present an optimized workflow for coupling LCM to LC–MS/MS including: sectioning of tissue, a standard LCM workflow, protein digestion and advanced LC–MS/MS. Soluble proteins extracted from benign epithelial cells, their associated stroma, tumor epithelial cells and their associated stromal cells from a single pati...
Source: EuPA Open Proteomics - January 11, 2016 Category: Bioinformatics Source Type: research
Novel product development and future directions in support of proteomics standardization, biobanking, and binder validation using CRISPR knockout technology
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Kevin Ray (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
