A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development
Identifieur interne : 001B59 ( Main/Merge ); précédent : 001B58; suivant : 001B60A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development
Auteurs : Ehud Katz [États-Unis] ; Mario Fon [États-Unis] ; Richard A. Eigenheer [États-Unis] ; Brett S. Phinney [États-Unis] ; Joseph N. Fass [États-Unis] ; Dawei Lin [États-Unis] ; Avi Sadka [Israël] ; Eduardo Blumwald [États-Unis]Source :
- Proteome Science [ 1477-5956 ] ; 2010.
Abstract
Citrus is one of the most important and widely grown commodity fruit crops. In this study a label-free LC-MS/MS based shot-gun proteomics approach was taken to explore three main stages of citrus fruit development. These approaches were used to identify and evaluate changes occurring in juice sac cells in various metabolic pathways affecting citrus fruit development and quality.
Protein changes in citrus juice sac cells were identified and quantified using label-free shotgun methodologies. Two alternative methods, differential mass-spectrometry (dMS) and spectral counting (SC) were used to analyze protein changes occurring during earlier and late stages of fruit development. Both methods were compared in order to develop a proteomics workflow that could be used in a non-model plant lacking a sequenced genome. In order to resolve the bioinformatics limitations of EST databases from species that lack a full sequenced genome, we established iCitrus. iCitrus is a comprehensive sequence database created by merging three major sources of sequences (HarvEST:citrus, NCBI/citrus/unigenes, NCBI/citrus/proteins) and improving the annotation of existing unigenes. iCitrus provided a useful bioinformatics tool for the high-throughput identification of citrus proteins. We have identified approximately 1500 citrus proteins expressed in fruit juice sac cells and quantified the changes of their expression during fruit development. Our results showed that both dMS and SC provided significant information on protein changes, with dMS providing a higher accuracy.
Our data supports the notion of the complementary use of dMS and SC for label-free comparative proteomics, broadening the identification spectrum and strengthening the identification of trends in protein expression changes during the particular processes being compared.
Url:
DOI: 10.1186/1477-5956-8-68
PubMed: 21162737
PubMed Central: 3017515
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Eigenheer</name><affiliation wicri:level="1"><nlm:aff id="I2">Genome Center, Proteomics Core Facility, University of California, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, Proteomics Core Facility, University of California, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Phinney, Brett S" sort="Phinney, Brett S" uniqKey="Phinney B" first="Brett S" last="Phinney">Brett S. Phinney</name><affiliation wicri:level="1"><nlm:aff id="I2">Genome Center, Proteomics Core Facility, University of California, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, Proteomics Core Facility, University of California, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Fass, Joseph N" sort="Fass, Joseph N" uniqKey="Fass J" first="Joseph N" last="Fass">Joseph N. Fass</name><affiliation wicri:level="1"><nlm:aff id="I3">Genome Center, Bioinformatics Core Facility, University of California, Davis, CA 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, Bioinformatics Core Facility, University of California, Davis, CA 95616</wicri:regionArea><wicri:noRegion>CA 95616</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Dawei" sort="Lin, Dawei" uniqKey="Lin D" first="Dawei" last="Lin">Dawei Lin</name><affiliation wicri:level="1"><nlm:aff id="I3">Genome Center, Bioinformatics Core Facility, University of California, Davis, CA 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, Bioinformatics Core Facility, University of California, Davis, CA 95616</wicri:regionArea><wicri:noRegion>CA 95616</wicri:noRegion></affiliation></author><author><name sortKey="Sadka, Avi" sort="Sadka, Avi" uniqKey="Sadka A" first="Avi" last="Sadka">Avi Sadka</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Fruit Tree Species, ARO, The Volcani Center, 50250 Bet Dagan, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Tree Species, ARO, The Volcani Center, 50250 Bet Dagan</wicri:regionArea><wicri:noRegion>50250 Bet Dagan</wicri:noRegion></affiliation></author><author><name sortKey="Blumwald, Eduardo" sort="Blumwald, Eduardo" uniqKey="Blumwald E" first="Eduardo" last="Blumwald">Eduardo Blumwald</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Plant Sciences, University of California, Davis, CA, 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Sciences, University of California, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author></analytic><series><title level="j">Proteome Science</title><idno type="eISSN">1477-5956</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Citrus is one of the most important and widely grown commodity fruit crops. In this study a label-free LC-MS/MS based shot-gun proteomics approach was taken to explore three main stages of citrus fruit development. These approaches were used to identify and evaluate changes occurring in juice sac cells in various metabolic pathways affecting citrus fruit development and quality.</p></sec><sec><title>Results</title><p>Protein changes in citrus juice sac cells were identified and quantified using label-free shotgun methodologies. Two alternative methods, differential mass-spectrometry (dMS) and spectral counting (SC) were used to analyze protein changes occurring during earlier and late stages of fruit development. Both methods were compared in order to develop a proteomics workflow that could be used in a non-model plant lacking a sequenced genome. In order to resolve the bioinformatics limitations of EST databases from species that lack a full sequenced genome, we established iCitrus. iCitrus is a comprehensive sequence database created by merging three major sources of sequences (HarvEST:citrus, NCBI/citrus/unigenes, NCBI/citrus/proteins) and improving the annotation of existing unigenes. iCitrus provided a useful bioinformatics tool for the high-throughput identification of citrus proteins. We have identified approximately 1500 citrus proteins expressed in fruit juice sac cells and quantified the changes of their expression during fruit development. Our results showed that both dMS and SC provided significant information on protein changes, with dMS providing a higher accuracy.</p></sec><sec><title>Conclusion</title><p>Our data supports the notion of the complementary use of dMS and SC for label-free comparative proteomics, broadening the identification spectrum and strengthening the identification of trends in protein expression changes during the particular processes being compared.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Sarry, Je" uniqKey="Sarry J">JE Sarry</name></author><author><name sortKey="Sommerer, N" uniqKey="Sommerer N">N Sommerer</name></author><author><name sortKey="Sauvage, Fx" uniqKey="Sauvage F">FX Sauvage</name></author><author><name sortKey="Bergoin, A" uniqKey="Bergoin A">A Bergoin</name></author><author><name sortKey="Rossignol, M" uniqKey="Rossignol M">M Rossignol</name></author><author><name sortKey="Albagnac, G" uniqKey="Albagnac G">G 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uniqKey="Rosenfeld J">J Rosenfeld</name></author><author><name sortKey="Capdevielle, J" uniqKey="Capdevielle J">J Capdevielle</name></author><author><name sortKey="Guillemot, Jc" uniqKey="Guillemot J">JC Guillemot</name></author><author><name sortKey="Ferrara, P" uniqKey="Ferrara P">P Ferrara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nesvizhskii, Ai" uniqKey="Nesvizhskii A">AI Nesvizhskii</name></author><author><name sortKey="Keller, A" uniqKey="Keller A">A Keller</name></author><author><name sortKey="Kolker, E" uniqKey="Kolker E">E Kolker</name></author><author><name sortKey="Aebersold, R" uniqKey="Aebersold R">R Aebersold</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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