⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples
Publication date: March 2016 Source:EuPA Open Proteomics, Volume 10 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 set of biopsies, fo...
Source: EuPA Open Proteomics - February 2, 2017 Category: Bioinformatics Source Type: research
Comprehensive mass spectrometry based biomarker discovery and validation platform as applied to diabetic kidney disease
Publication date: Available online 5 January 2017 Source:EuPA Open Proteomics Author(s): Scott D. Bringans, Jun Ito, Thomas Stoll, Kaye Winfield, Michael Phillips, Kirsten Peters, Wendy A. Davis, Timothy M.E. Davis, Richard J. Lipscombe A protein biomarker discovery workflow was applied to plasma samples from patients at different stages of diabetic kidney disease, a chronic complication of diabetes mellitus. The proteomics platform used for this study produced a panel of significant biomarkers specific for diabetic kidney disease that were statistically scrutinised against the current gold standard tests. The r...
Source: EuPA Open Proteomics - January 4, 2017 Category: Bioinformatics Source Type: research
Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data
Publication date: Available online 15 September 2016 Source:EuPA Open Proteomics Author(s): Yu. Kondrakhin, T. Valeev, R. Sharipov, I. Yevshin, F. Kolpakov, A. Kel We compared positional weight matrix-based prediction methods for transcription factor (TF) binding sites using selected fraction of ChIP-seq data with the help of partial AUC measure (limited to false positive rate 0.1, that is the most relevant for the application of the TF search in the genome scale). Comparison of three prediction methods—additive, multiplicative and information-vector based (MATCH) showed an advantage of the MATCH method for major...
Source: EuPA Open Proteomics - September 15, 2016 Category: Bioinformatics Source Type: research
Multi-omics “Upstream Analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer
We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemic...
Source: EuPA Open Proteomics - September 9, 2016 Category: Bioinformatics Source Type: research
EuPA ’s tribute to Juan Pablo Albar
Publication date: September 2015 Source:EuPA Open Proteomics, Volume 8 Author(s): Concha Gil, Fernando Corrales, Garry Corthals, György Marko-Varga, Peter Verhaert (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - June 17, 2016 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 - June 17, 2016 Category: Bioinformatics Source Type: research
Bottom –up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance.
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Peter Raus, Bharath Raghuraman Kumar, Martijn Pinkse, Peter Verhaert A relatively simple combination of Schirmer strip sampling with straightforward sensitive nanoLC quadrupole-Orbitrap tandem mass spectrometry after a minimum of sample processing steps allows for replicate proteomic analysis of single human tears, i.e., without the requirement for sample pooling. This opens the way to clinical applications of the analytical workflow, e.g., to monitor disease progression or treatment efficacy within individual patients. Proof of co...
Source: EuPA Open Proteomics - June 17, 2016 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 - June 17, 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 - June 17, 2016 Category: Bioinformatics Source Type: research
The EuPA2015 Congress. Proteomics: Back to the Future
Publication date: June 2016 Source:EuPA Open Proteomics, Volume 11 (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - May 21, 2016 Category: Bioinformatics Source Type: research
Call for Candidates for the 2016 EuPA Young Investigator Prize (PhD)
Publication date: June 2016 Source:EuPA Open Proteomics, Volume 11 (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - May 2, 2016 Category: Bioinformatics Source Type: research
Proteomics: Back to the Future
Publication date: Available online 27 April 2016 Source:EuPA Open Proteomics Author(s): Paola Roncada, Gabriella Tedeschi, Peter Verhaert, Mauro Fasano (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - April 27, 2016 Category: Bioinformatics Source Type: research
The EuPA2015 Congress.Proteomics: Back to the Future
Publication date: Available online 8 April 2016 Source:EuPA Open Proteomics Author(s): Paola Roncada, Andrea Urbani, Concha Gil (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - April 7, 2016 Category: Bioinformatics Source Type: research
EuPACa: An Opportunity for EuPA to co-ordinate and promote Prostate Cancer Proteomics in Europe as part of Global Initiatives
Publication date: Available online 8 April 2016 Source:EuPA Open Proteomics Author(s): Corinna Henkel, Stephen R. Pennington, Andrea Urbani (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - April 7, 2016 Category: Bioinformatics Source Type: research
Creation of the EuPA Young Proteomics Investigators Club, YPIC
Publication date: Available online 7 April 2016 Source:EuPA Open Proteomics Author(s): Fernando Corrales (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - April 6, 2016 Category: Bioinformatics Source Type: research
