Independent validation initiative
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Stefan Pellenz (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
Improving productivity and quality in Biobanking: The need for synergy between industry, academia, and the public sector
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Åsa Wheelock (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
Affinity Binder Knock-Down Initiative
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Tove Alm, Emma Lundberg, Mathias Uhlén (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
Standardization initiative. Integrating proteomic strengths across Europe
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Fernando J. Corrales (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
Flagship program for EuPA Initiatives: Opportunities for the EuPA Company Club
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Andrey Lisitsa (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 22, 2015 Category: Bioinformatics Source Type: research
Proteomic comparison of the EWS-FLI1 expressing cells EF with NIH-3T3 and actin remodeling effect of (R/W)9 cell-penetrating peptide
Publication date: Available online 30 October 2015 Source:EuPA Open Proteomics Author(s): Séverine Clavier, Françoise Illien, Sandrine Sagan, Gérard Bolbach, Emmanuelle Sachon EWS-FLI1 expression in NIH-3T3 fibroblasts has a profound impact on the phenotype, resulting in the cytoskeleton and adhesive capacity disorganization (EF cells). Besides this, (R/W)9, a cell-penetrating peptide (CPP), has an intrinsic actin remodeling activity in EF cells. To evaluate the impact of the oncogenic protein EWS-FLI1 on proteins expression levels, a quantitative comparison of tumoral EF and non-tumoral 3T3 proteomes was ...
Source: EuPA Open Proteomics - November 8, 2015 Category: Bioinformatics Source Type: research
☆Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples
Publication date: Available online 2 November 2015 Source:EuPA Open Proteomics Author(s): Tue Bjerg Bennike, Kenneth Kastaniegaard, Simona Padurariu, Michael Gaihede, Svend Birkelund, Vibeke Andersen, Allan Stensballe Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one...
Source: EuPA Open Proteomics - November 8, 2015 Category: Bioinformatics Source Type: research
Enhancing Cognate Target Elution Efficiency in Gel-Free Chemical Proteomics
Publication date: Available online 30 September 2015 Source:EuPA Open Proteomics Author(s): Branka Radic-Sarikas, Uwe Rix, Alexey Stukalov, Manuela Gridling, André C. Müller, Jacques Colinge, Giulio Superti-Furga, Keiryn L. Bennett Gel-free liquid chromatography mass spectrometry coupled to chemical proteomics is a powerful approach for characterizing cellular target profiles of small molecules. We have previously described a fast and efficient elution protocol; however, altered target profiles were observed. We hypothesised that elution conditions critically impact the effectiveness of disrupting dru...
Source: EuPA Open Proteomics - October 1, 2015 Category: Bioinformatics Source Type: research
Changes in the repertoire of bovine milk proteins during mammary involution
Publication date: Available online 28 September 2015 Source:EuPA Open Proteomics Author(s): Irina Boggs, Brad Hine, Grant Smolenski, Kasper Hettinga, Lina Zhang, Thomas T. Wheeler Changes of abundance that occur in the repertoire of low abundance milk proteins after cessation of milk removal have not been characterised. Skimmed milk and whey from cows sampled at day 0 and either day 3 or day 8 after drying off were subjected to three untargeted proteomics techniques; 2-D gel electrophoresis, GeLC-MS, and dimethyl isotopic labelling of tryptic peptides. The changes observed included 45 fragments of abundant ...
Source: EuPA Open Proteomics - September 30, 2015 Category: Bioinformatics Source Type: research
The EuPA Company Club: Emphasis on the synergy with EuPA’s Initiatives beyond education—Towards further integration with EuPA’s goals and objectives
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Andrea Urbani, Andrey Lisitsa, Peter Verhaert (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 28, 2015 Category: Bioinformatics Source Type: research
Assessment of global proteome in LNCaP cells by 2D-RP/RP LC–MS/MS following sulforaphane exposure
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Gregory W. Watson, Samanthi Wickramasekara, Claudia S. Maier, David E. Williams, Roderick H. Dashwood, Emily Ho The phytochemical sulforaphane can induce cell cycle arrest and apoptosis in metastatic prostate cancer cells, though the mechanism of action is not fully known. We conducted a global proteome analysis in LNCaP metastatic prostate cancer cells to characterize how global protein signature responds to sulforaphane. We conducted parallel analyses to evaluate semi-quantitative 1-dimensional versus 2-dimensional liquid chr...
Source: EuPA Open Proteomics - August 16, 2015 Category: Bioinformatics Source Type: research
Assessment of global proteome in LNCaP cells by 2D-RP/RP LC-MS/MS following sulforaphane exposure
Publication date: Available online 10 August 2015 Source:EuPA Open Proteomics Author(s): Gregory W Watson, Samanthi Wickramasekara, Claudia S. Maier, David E. Williams, Roderick H. Dashwood, Emily Ho The phytochemical sulforaphane can induce cell cycle arrest and apoptosis in metastatic prostate cancer cells, though the mechanism of action is not fully known. We conducted a global proteome analysis in LNCaP metastatic prostate cancer cells to characterize how global protein signature responds to sulforaphane. We conducted parallel analyses to evaluate semi-quantitative 1-dimensional versus 2-dimensional liq...
Source: EuPA Open Proteomics - August 11, 2015 Category: Bioinformatics Source Type: research
Bayesian Methods for Proteomic Biomarker Development
Publication date: Available online 10 August 2015 Source:EuPA Open Proteomics Author(s): Belinda Hernández, Stephen R Pennington, Andrew C Parnell The advent of liquid chromatography mass spectrometry has seen a dramatic increase in the amount of data derived from proteomic biomarker discovery. These experiments have seemingly identified many potential candidate biomarkers. Frustratingly, very few of these candidates have been evaluated and validated sufficiently such that that they have progressed to the stage of routine clinical use. It is becoming apparent that the statistical methods used to evaluate the per...
Source: EuPA Open Proteomics - August 11, 2015 Category: Bioinformatics Source Type: research
Quantification of total apolipoprotein E and its specific isoforms in cerebrospinal fluid and blood in alzheimer’s disease and other neurodegenerative diseases
Publication date: Available online 7 August 2015 Source:EuPA Open Proteomics Author(s): Melinda Rezeli, Henrik Zetterberg, Kaj Blennow, Ann Brinkmalm, Thomas Laurell, Oskar Hansson, György Marko-Varga A targeted mass spectrometric assay was developed for identification and quantification of apoE isoforms (apoE2, E3 and E4), and it was utilized for screening of samples from AD patients (n =39) and patients with other neurodegenerative disorders (n =38). The assay showed good linearity with LOQ corresponds to total apoE concentration of 0.8 and 40ng/mL in CSF and plasma/serum, respectively. We identified a...
Source: EuPA Open Proteomics - August 9, 2015 Category: Bioinformatics Source Type: research
Proteomic Profiling of Hyperplasia/Atypia and Adenoma-induced by NNK in Mouse Lung identified Multiple Proteins as Potential Biomarkers for Early Detection
Publication date: Available online 3 August 2015 Source:EuPA Open Proteomics Author(s): Arunangshu Das, James D. Bortner, Cesar Aliaga, Timothy Cooper, Anne Stanley, Bruce A. Stanley, Chandra P. Belani, Karam El-Bayoumy We used a proteomics approach (iTRAQ) to identify differentially expressed lung proteins during early stages of the tobacco carcinogen, NNK-induced lung tumorigenesis (hyperplasia/atypia, 4-10 weeks and adenoma, 25 week) prior to the detection of adenocarcinoma in A/J mice. We identified 790 proteins at week 4 and 710 proteins at weeks 10 and 25 with >95% confidence and a Local Fa...
Source: EuPA Open Proteomics - August 5, 2015 Category: Bioinformatics Source Type: research
