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Eddy Esmans

Publications and source records attributed to Eddy Esmans.

6 recordsLinked to original sources

Integration of gel-based proteome data with pProRep.

UNLABELLED: pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. AVAILABILITY: The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

Computational Biology↗

Tissue distribution of perfluorinated chemicals in harbor seals (Phoca vitulina) from the Dutch Wadden Sea.

Perfluorinated acids (PFAs) are today widely distributed in the environment, even in remote arctic areas. Recently, perfluorooctane sulfonate (PFOS) has been identified in marine mammals all over the world, but information on the compound-specific tissue distribution remains scarce. Furthermore, although longer perfluorinated carboxylic acids (PFCAs) are used in industry and were shown to cause severe toxic effects, still little is known on potential sources or their widespread distribution. In this study, we report for the first time on levels of longer chain PFCAs, together with some short chain PFAs, perfluorobutane sulfonate (PFBS) and perfluorobutanoate (PFBA), in liver, kidney, blubber, muscle, and spleen tissues of harbor seals (Phoca vitulina) from the Dutch Wadden Sea. PFOS was the predominant compound in all seal samples measured (ranging from 89 to 2724 ng/g wet weight); however, large variations between tissues were monitored. Although these are preliminary results, it is, to our knowledge, the first time that PFBS could be found at detectable concentrations (2.3 +/- 0.7 ng/g w wt) in environmental samples. PFBS was only detected in spleen tissue. PFCA levels were much lower than PFOS concentrations. The dominant PFCA in all tissues was PFNA (perfluorononanoic acid), and concentrations generally decreased in tissues for all other PFCA homologues with increasing chain length. No clear relationship between PFOS levels in liver and kidney was observed. Furthermore, hepatic PFDA (perfluorodecanoic acid) levels increased with increasing body length, but in kidney tissue, PFDA levels showed an inverse relationship with increasing body length. These data suggest large differences in tissue distribution and accumulation patterns of perfluorinated compounds in marine organisms.

Alkanesulfonic Acids↗

Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture.

Using two-dimensional gel electrophoresis (2-DE) and electrospray-tandem mass spectrometry (ESI-MS/MS), we have started the proteome analysis of the cell line Nicotiana tabacum cv. Bright Yellow-2 (tobacco BY-2). The BY-2 cell suspension culture is widely used as a model system to study the growth and development of plant cells. We present a protocol describing the sample preparation and 2-DE, enabling us to separate and display more than 1000 proteins from this cell culture. A reference gel was generated, using immobilized pH gradient isoelectric focusing in a linear gradient from pH 3 to 10 and 12% Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Although the tobacco genome is not sequenced yet, a range of protein spots from this reference map was identified by means of a semi-automated liquid chromatography-ESI-quadrupole time of flight-tandem MS (LC-ESI-QTOF-MS-MS) setup and cross-species matching. These data were integrated in a database, which can be accessed at http://tby2-www.uia.ac.be/tby2/. On the on-line reference map, the identified protein spots are hyperlinked to individual protein entries. Each protein entry contains all identification information, as well as links to relevant entries in other on-line databases. Comprehensive search functions are implemented. Especially for an unsequenced but widespread model organism like tobacco BY-2, such a reference database is a convenient source for protein information that brings protein identification within reach without the need for extensive MS. This publicly accessible database provides a solid basis for tobacco BY-2 proteomics in the future.

Databases as Topic↗

Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification.

Using a parallel microcolumn switching liquid chromatography set-up coupled to a quadrupole time-of-flight mass spectrometer, a rapid liquid chromatography/mass spectrometric (LC/MS) protein identification method is presented. Without prior sample clean-up up to 300 protein digest samples a day can be processed. Using data-directed acquisition, up to 10 fragmentation analyses for each protein sample can be acquired in the same chromatographic run that can be used for database searching. Using internal peptide sequence information, protein databases and the various nucleic acid databases can both be queried for cross-species identification of the protein sample. The method was evaluated and put into force to generate data for a tobacco cell culture protein database.

Cell Line↗