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
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 proteins almost mandatory for
a correct...
Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition
Proteomics - Tập 9 Số 2 - Trang 254-271 - 2009
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 reference map, which includes 156 identified proteins
(http://...
Proteomic investigation of natural variation between Arabidopsis ecotypes
Proteomics - Tập 4 Số 5 - Trang 1372-1381 - 2004
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 was shared by all accessions. On the
other hand, only 15% of ...
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
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
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‐polyacrylamide gel
electrophoresis on 13% ...
ATR inhibition rewires cellular signaling networks induced by replication stress
Proteomics - Tập 16 Số 3 - Trang 402-416 - 2016
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 for the ...
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
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 expression has been studied in
diffe...
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
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
accessib...
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
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
(http://cod...
A posteriori quality control for the curation and reuse of public proteomics data
Proteomics - Tập 11 Số 11 - Trang 2182-2194 - 2011
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 available
proteomics databases. Th...
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