A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development.
A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development.
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DOI：
10.1186/1477-5956-8-68
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发表时间：
2010-12-16
期刊：
影响因子：
2
通讯作者：
Blumwald E
中科院分区：
文献类型：
--
作者：
Katz E;Fon M;Eigenheer RA;Phinney BS;Fass JN;Lin D;Sadka A;Blumwald E
柑橘是我国最重要、最广泛种植的商品性果树作物之一。本研究采用基于无标记LC-MS/MS的蛋白质组学方法，对柑橘果实发育的三个主要阶段进行了研究。这些方法被用来识别和评估影响柑橘果实发育和品质的各种代谢途径中汁囊细胞的变化。用无标记猎枪方法鉴定和定量了柑橘汁囊细胞中蛋白质的变化。采用差示质谱(DMS)和光谱计数(SC)两种方法分析了果实发育前期和后期蛋白质的变化。对这两种方法进行了比较，以开发一种蛋白质组学工作流程，该工作流程可以用于缺乏测序基因组的非模式植物。为了解决缺乏全序列基因组的物种EST数据库的生物信息学局限性，我们建立了iCitrus。ICitrus是一个综合的序列数据库，通过合并三个主要的序列来源(收获：柑橘、NCBI/Citrus/Uniges、NCBI/Citrus/Proteins)并改进现有Uniges的注释而创建。ICitrus为柑橘蛋白质的高通量鉴定提供了一个有用的生物信息学工具。我们已经鉴定了大约1500个在果汁囊细胞中表达的柑橘蛋白，并对它们在果实发育过程中的表达变化进行了量化。我们的结果表明，DMS和SC都提供了关于蛋白质变化的重要信息，其中DMS提供了更高的准确性。我们的数据支持将DMS和SC互补用于无标记比较蛋白质组学的概念，拓宽了识别谱并加强了对被比较的特定过程中蛋白质表达变化趋势的识别。
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.
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影响因子：
4.4
作者：
Deluc LG;Grimplet J;Wheatley MD;Tillett RL;Quilici DR;Osborne C;Schooley DA;Schlauch KA;Cushman JC;Cramer GR
通讯作者：
Cramer GR
影响因子：
4.3
作者：
Katz, E;Lagunes, PM;Goldschmidt, EE
通讯作者：
Goldschmidt, EE
影响因子：
5.2
作者：
Etxeberria, Ed;Gonzalez, Pedro;Pozueta, Javier
通讯作者：
Pozueta, Javier
影响因子：
3.3
作者：
Bianco, Linda;Lopez, Loredana;Perrotta, Gaetano
通讯作者：
Perrotta, Gaetano
DOI：
10.1071/bt9580001
发表时间：
1958-01-01
期刊：
AUSTRALIAN JOUR BOT
影响因子：
--
作者：
BAIN, JOAN M.
通讯作者：
BAIN, JOAN M.