Proteomics

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Toward a better analysis of secreted proteins: the example of the myeloid cells secretome
Proteomics - Tập 7 Số 11 - Trang 1757-1770 - 2007
Mireille Chevallet, Hélène Diemer, Alain Van Dorssealer, Christian Villiers, Thierry Rabilloud
AbstractThe analysis of secreted proteins represents a challenge for current proteomics techniques. Proteins are usually secreted at low concentrations in the culture media, which makes their recovery difficult. In addition, culture media are rich in salts and other compounds interfering with most proteomics techniques, which makes selective precipitation of protei...... hiện toàn bộ
ATR inhibition rewires cellular signaling networks induced by replication stress
Proteomics - Tập 16 Số 3 - Trang 402-416 - 2016
Sebastian Wagner, Hannah Oehler, Andrea Voigt, Denis Dalic, Anja Freiwald, Hubert Serve, Petra Beli
The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA‐DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3‐related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy ...... hiện toàn bộ
Modulation of gene expression by extracellular pH variations in human fibroblasts: A transcriptomic and proteomic study
Proteomics - Tập 3 Số 5 - Trang 675-688 - 2003
Maja A. Bumke, Dario Neri, Giuliano Elia
AbstractHomeostasis of the intracellular ionic concentration, in particular that of hydrogen ions, is pivotal to the maintenance of cell function and viability. Nonetheless, pH fluctuations in both the intracellular and the extracellular compartments can occurr during development, in physiological processes and in disease. The influence of pH variations on gene exp...... hiện toàn bộ
XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search results
Proteomics - Tập 10 Số 7 - Trang 1522-1524 - 2010
Thilo Muth, Marc Vaudel, Harald Barsnes, Lennart Martens, Albert Sickmann
AbstractIdentification of proteins by MS plays an important role in proteomics. A crucial step concerns the identification of peptides from MS/MS spectra. The X!Tandem Project (http://www.thegpm.org/tandem) supplies an open‐source search engine for this purpose. In this study, we present an open‐source Java library called XTandem Parser that parses X!Tandem XML result files into an easily accessible and fully functional object model ( hiện toàn bộ
A posteriori quality control for the curation and reuse of public proteomics data
Proteomics - Tập 11 Số 11 - Trang 2182-2194 - 2011
Joseph Foster, Sven Degroeve, Laurent Gatto, Matthieu Visser, Rui Wang, Johannes Griss, Rolf Apweiler, Lennart Martens
AbstractProteomics is a rapidly expanding field encompassing a multitude of complex techniques and data types. To date much effort has been devoted to achieving the highest possible coverage of proteomes with the aim to inform future developments in basic biology as well as in clinical settings. As a result, growing amounts of data have been deposited in publicly a...... hiện toàn bộ
Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two‐dimensional electrophoresis
Proteomics - Tập 3 Số 3 - Trang 249-253 - 2003
Sylvie Luche, Véronique Santoni, Thierry Rabilloud
AbstractThe solubilizing power of various nonionic and zwitterionic detergents as membrane protein solubilizers for two‐dimensional electrophoresis was investigated. Human red blood cell ghosts and Arabidopsis thaliana leaf membrane proteins were used as model systems. Efficient detergents could be found in each class, i.e.... hiện toàn bộ
Plasticity demonstrated in the proteome of a parasitic nematode within the intestine of different host strains
Proteomics - Tập 6 Số 16 - Trang 4633-4645 - 2006
Charly Morgan, E. James LaCourse, Benjamin J. Rushbrook, Darren Greetham, Joanne V. Hamilton, J. Barrett, Kevin Bailey, Peter M. Brophy
Plasma membrane proteome in Arabidopsis and rice
Proteomics - Tập 8 Số 19 - Trang 4137-4145 - 2008
Setsuko Komatsu
AbstractPlant cells contain many membrane systems that are specially adapted to perform particular functions. In plant cells, the processing of signals that are involved in responses to biotic and abiotic stressors occurs in the plasma membrane. Therefore, characterization of the plasma membrane proteome can provide new insights into the functions of various plant ...... hiện toàn bộ
Proteomic analysis of mouse liver plasma membrane: Use of differential extraction to enrich hydrophobic membrane proteins
Proteomics - Tập 5 Số 17 - Trang 4510-4524
Lijun Zhang, Jinyun Xie, Wang Xie, Xiaohui Liu, Xinke Tang, Rui Cao, Weijun Hu, Song Nie, Chunming Fan, Songping Liang
COMPASS: A suite of pre‐ and post‐search proteomics software tools for OMSSA
Proteomics - Tập 11 Số 6 - Trang 1064-1074 - 2011
Craig D. Wenger, Douglas H. Phanstiel, M. Violet Lee, Derek J. Bailey, Joshua J. Coon
AbstractHere we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open‐source software pipeline for high‐throughput analysis of proteomics data, designed around the Open Mass S...... hiện toàn bộ
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