A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development

Proteome Science

Research

Avi Sadka¹  Eduardo Blumwald²  Ehud Katz²  Mario Fon²  Joseph N Fass³  Dawei Lin³  Richard A Eigenheer⁴  Brett S Phinney⁴ 

[1] Department of Fruit Tree Species, ARO, The Volcani Center, 50250, Bet Dagan, Israel;Department of Plant Sciences, University of California, 95616, Davis, CA, USA;Genome Center, Bioinformatics Core Facility, University of California, 95616, Davis, CA, USA;Genome Center, Proteomics Core Facility, University of California, 95616, Davis, CA, USA;

关键词: Fruit Development;    Protein Change;    Vesicular Trafficking;    Spectral Counting;    Shotgun Proteomics;   

DOI  :  10.1186/1477-5956-8-68

 received in 2010-10-20, accepted in 2010-12-16,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundCitrus 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.ResultsProtein 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.ConclusionOur 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.

【 授权许可】

Unknown   
© Katz et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.