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
Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition
Proteomics - Tập 9 Số 2 - Trang 254-271 - 2009
Michaël Bourgeois, Françoise Jacquin, Vincent Savois, Nicolas Sommerer, Valérie Labas, Céline Henry, Judith Burstin
AbstractPea (Pisum sativum L.) is the most cultivated European pulse crop and the pea seeds mainly serve as a protein source for monogastric animals. Because the seed protein composition impacts on seed nutritional value, we aimed at identifying the determinants of its variability. This paper presents the first pea mature seed proteome re...... hiện toàn bộ
Proteomic investigation of natural variation between Arabidopsis ecotypes
Proteomics - Tập 4 Số 5 - Trang 1372-1381 - 2004
François Chevalier, Martin Olivier, Valérie Rofidal, Anne-Dominique Devauchelle, Samuel Barteau, Nicolas Sommerer, Michel Galinier
AbstractTwo‐dimensional (2‐D) gel electrophoresis and peptide mass fingerprinting were used to investigate the natural variation in the proteome among 8 Arabidopsis thaliana ecotypes, of which 3 were previously shown to display atypical responses to environmental stress. Comparison of 2‐D maps demonstrated that only one‐quarter of spots w...... hiện toàn bộ
The Holm Oak leaf proteome: Analytical and biological variability in the protein expression level assessed by 2‐DE and protein identification tandem mass spectrometry de novo sequencing and sequence similarity searching
Proteomics - Tập 5 Số 1 - Trang 222-234 - 2005
Inmaculada Jorge, Rafael M. Navarro, Christof Lenz, David Ariza, Carlos Porras, Jesús V. Jorrín–Novo
AbstractAs a first approach in establishing the holm oak leaf proteome, we have optimised a protocol for this plant and tissue which includes the following steps: trichloroacetic acid‐acetone extraction, two‐dimensional gel electrophoresis (2‐DE) on pH 5 to 8 linear gradient immobilised pH gradient strips as the first dimension, and sodium dodecyl sulfate‐polyacryl...... hiện toàn bộ
Variation in the holm oak leaf proteome at different plant developmental stages, between provenances and in response to drought stress
Proteomics - Tập 6 Số S1 - Trang S207-S214
Inmaculada Jorge, Rafael M. Navarro, Christof Lenz, David Ariza, Jesús V. Jorrín–Novo
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
PRIDE: The proteomics identifications database
Proteomics - Tập 5 Số 13 - Trang 3537-3545 - 2005
Lennart Martens, Henning Hermjakob, Philip Jones, Marcin Adamski, Chris Taylor, David J. States, Kris Gevaert, Joël Vandekerckhove, Rolf Apweiler
AbstractThe advent of high‐throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large‐scale proteomics projects about to dis...... 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
OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results
Proteomics - Tập 9 Số 14 - Trang 3772-3774 - 2009
Harald Barsnes, Steffen Huber, Albert Sickmann, Ingvar Eidhammer, Lennart Martens
AbstractProtein identification by MS is an important technique in both gel‐based and gel‐free proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) (http://pubchem.ncbi.nlm.nih.gov/omssa) is an open‐source search engine that can be used to identify MS/MS spectra acquired in these experiments. We here present a lightweight, open‐source Java software library, OMSSA Parser ( hiện toàn bộ
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