Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction
Identifieur interne : 000333 ( Istex/Checkpoint ); précédent : 000332; suivant : 000334Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction
Auteurs : Olivier Langella [France] ; Benoît Valot [France] ; Daniel Jacob [France] ; Thierry Balliau [France] ; Raphaël Flores [France] ; Christine Hoogland [Suisse, Australie] ; Johann Joets [France] ; Michel Zivy [France]Source :
- PROTEOMICS [ 1615-9853 ] ; 2013-05.
Descripteurs français
- Wicri :
- topic : Base de données, Ontologie, Moteur de recherche, Logiciel.
English descriptors
- KwdEn :
- Annotation, Bioinformatics, Correlated, Correlation circle, Current address, Database, Database software, Database structure, Different peptides, Different tools, External portals, Extraction, Fresh matter, Genetique vegetale, Gmbh, Information table, Intrinsic membrane proteins, Kgaa, Langella, Large part, Mass spectrometry proteomics, Nucleic acids, Ontology, Ontology terms, Other methods, Particular species, Peak area, Pellet, Peptide, Positive side, Project name, Protein, Protein data, Protein extraction, Protein quantities, Protein sequences, Protein solubilization, Proteomic, Proteomic data, Proteomics, Proteomics data, Proticdb, Proticdb database, Quantitative data, Quantitative proteomics data, Quantitative variations, Query, Query builder, Retention time, Ribosomal, Ribosomal subunit, Ribosomal subunits, Sample description, Sample descriptions, Sample names, Sdsr, Search engine, Software, Solubilization, Solubilization buffer, Sophisticated queries, Subunit, Tcaa, Tcaa method, Third party software, User, Verlag, Verlag gmbh, Weinheim.
- Teeft :
- Annotation, Bioinformatics, Correlated, Correlation circle, Current address, Database, Database software, Database structure, Different peptides, Different tools, External portals, Extraction, Fresh matter, Genetique vegetale, Gmbh, Information table, Intrinsic membrane proteins, Kgaa, Langella, Large part, Mass spectrometry proteomics, Nucleic acids, Ontology, Ontology terms, Other methods, Particular species, Peak area, Pellet, Peptide, Positive side, Project name, Protein, Protein data, Protein extraction, Protein quantities, Protein sequences, Protein solubilization, Proteomic, Proteomic data, Proteomics, Proteomics data, Proticdb, Proticdb database, Quantitative data, Quantitative proteomics data, Quantitative variations, Query, Query builder, Retention time, Ribosomal, Ribosomal subunit, Ribosomal subunits, Sample description, Sample descriptions, Sample names, Sdsr, Search engine, Software, Solubilization, Solubilization buffer, Sophisticated queries, Subunit, Tcaa, Tcaa method, Third party software, User, Verlag, Verlag gmbh, Weinheim.
Abstract
High throughput MS‐based proteomic experiments generate large volumes of complex data and necessitate bioinformatics tools to facilitate their handling. Needs include means to archive data, to disseminate them to the scientific communities, and to organize and annotate them to facilitate their interpretation. We present here an evolution of PROTICdb, a database software that now handles MS data, including quantification. PROTICdb has been developed to be as independent as possible from tools used to produce the data. Biological samples and proteomics data are described using ontology terms. A Taverna workflow is embedded, thus permitting to automatically retrieve information related to identified proteins by querying external databases. Stored data can be displayed graphically and a “Query Builder” allows users to make sophisticated queries without knowledge on the underlying database structure. All resources can be accessed programmatically using a Java client API or RESTful web services, allowing the integration of PROTICdb in any portal. An example of application is presented, where proteins extracted from a maize leaf sample by four different methods were compared using a label‐free shotgun method. Data are available at http://moulon.inra.fr/protic/public. PROTICdb thus provides means for data storage, enrichment, and dissemination of proteomics data.
Url:
DOI: 10.1002/pmic.201200564
Affiliations:
- Australie, France, Suisse
- Aquitaine, Nouvelle-Aquitaine, Île-de-France
- Bordeaux, Évry (Essonne)
- Université de Bordeaux
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gmbh</term><term>Weinheim</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Annotation</term><term>Bioinformatics</term><term>Correlated</term><term>Correlation circle</term><term>Current address</term><term>Database</term><term>Database software</term><term>Database structure</term><term>Different peptides</term><term>Different tools</term><term>External portals</term><term>Extraction</term><term>Fresh matter</term><term>Genetique vegetale</term><term>Gmbh</term><term>Information table</term><term>Intrinsic membrane proteins</term><term>Kgaa</term><term>Langella</term><term>Large part</term><term>Mass spectrometry proteomics</term><term>Nucleic acids</term><term>Ontology</term><term>Ontology terms</term><term>Other methods</term><term>Particular species</term><term>Peak area</term><term>Pellet</term><term>Peptide</term><term>Positive side</term><term>Project name</term><term>Protein</term><term>Protein data</term><term>Protein extraction</term><term>Protein 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données</term><term>Ontologie</term><term>Moteur de recherche</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">High throughput MS‐based proteomic experiments generate large volumes of complex data and necessitate bioinformatics tools to facilitate their handling. Needs include means to archive data, to disseminate them to the scientific communities, and to organize and annotate them to facilitate their interpretation. We present here an evolution of PROTICdb, a database software that now handles MS data, including quantification. PROTICdb has been developed to be as independent as possible from tools used to produce the data. Biological samples and proteomics data are described using ontology terms. A Taverna workflow is embedded, thus permitting to automatically retrieve information related to identified proteins by querying external databases. Stored data can be displayed graphically and a “Query Builder” allows users to make sophisticated queries without knowledge on the underlying database structure. All resources can be accessed programmatically using a Java client API or RESTful web services, allowing the integration of PROTICdb in any portal. An example of application is presented, where proteins extracted from a maize leaf sample by four different methods were compared using a label‐free shotgun method. Data are available at http://moulon.inra.fr/protic/public. PROTICdb thus provides means for data storage, enrichment, and dissemination of proteomics data.</div></front></TEI><affiliations><list><country><li>Australie</li><li>France</li><li>Suisse</li></country><region><li>Aquitaine</li><li>Nouvelle-Aquitaine</li><li>Île-de-France</li></region><settlement><li>Bordeaux</li><li>Évry (Essonne)</li></settlement><orgName><li>Université de Bordeaux</li></orgName></list><tree><country name="France"><noRegion><name sortKey="Langella, Olivier" sort="Langella, Olivier" uniqKey="Langella O" first="Olivier" last="Langella">Olivier Langella</name></noRegion><name sortKey="Balliau, Thierry" sort="Balliau, Thierry" uniqKey="Balliau T" first="Thierry" last="Balliau">Thierry Balliau</name><name sortKey="Flores, Raphael" sort="Flores, Raphael" uniqKey="Flores R" first="Raphaël" last="Flores">Raphaël Flores</name><name sortKey="Flores, Raphael" sort="Flores, Raphael" uniqKey="Flores R" first="Raphaël" last="Flores">Raphaël Flores</name><name sortKey="Jacob, Daniel" sort="Jacob, Daniel" uniqKey="Jacob D" first="Daniel" last="Jacob">Daniel Jacob</name><name sortKey="Joets, Johann" sort="Joets, Johann" uniqKey="Joets J" first="Johann" last="Joets">Johann Joets</name><name sortKey="Valot, Benoit" sort="Valot, Benoit" uniqKey="Valot B" first="Benoît" last="Valot">Benoît Valot</name><name sortKey="Zivy, Michel" sort="Zivy, Michel" uniqKey="Zivy M" first="Michel" last="Zivy">Michel Zivy</name><name sortKey="Zivy, Michel" sort="Zivy, Michel" uniqKey="Zivy M" first="Michel" last="Zivy">Michel Zivy</name></country><country name="Suisse"><noRegion><name sortKey="Hoogland, Christine" sort="Hoogland, Christine" uniqKey="Hoogland C" first="Christine" last="Hoogland">Christine Hoogland</name></noRegion></country><country name="Australie"><noRegion><name sortKey="Hoogland, Christine" sort="Hoogland, Christine" uniqKey="Hoogland C" first="Christine" last="Hoogland">Christine Hoogland</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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