Identification of proteins from non-model organisms using mass spectrometry: application to a hibernating mammal.
Identification of proteins from non-model organisms using mass spectrometry: application to a hibernating mammal.
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使用质谱法鉴定非模式生物中的蛋白质：应用于冬眠哺乳动物。
DOI：
10.1021/pr050306a
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
Andrews,MatthewT
中科院分区：
文献类型：
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作者：
Russeth,KevinP;Higgins,LeeAnn;Andrews,MatthewT
生命科学中的一个主要挑战是从植物和动物中提取详细的分子信息，这些植物和动物不属于少数经过详尽研究的“模式生物”。因此，由于缺乏可搜索的数据库、易处理的遗传学、库存中心以及最近的测序基因组，某些具有新表型的物种经常被忽视。在分子水平上表征表型通常依赖于通过将数据库搜索与来自蛋白质片段化的肽的串联质谱（MS）相结合来鉴定差异表达的蛋白质。然而，从非模式生物中识别短肽可能会受到缺乏足够的氨基酸序列同源性与现有数据库中的蛋白质的阻碍，因此，数据库搜索策略，包括身份和同源性可以提供更强的证据比一个单一的搜索。使用多种算法进行数据库搜索还可以增加正确蛋白质鉴定的概率，因为每个程序不太可能对相同肽产生假阴性或阳性命中。在这项研究中，四个软件包，吉祥物，临ID，Sequest和临BLAST，在他们的能力进行比较，以确定蛋白质的十三线地松鼠（Spermophilus tridecemlineatus），冬眠的哺乳动物，缺乏一个完整的测序基因组。我们的研究结果显示了相似性，以及不同的软件包之间的变化程度时，相同的蛋白质数据库进行搜索。在这项研究的过程中，我们确定了琥珀酰CoA-转移酶（SCOT）在冬眠动物的心脏上调。SCOT是酮体分解的限速酶，是冬眠期间重要的替代燃料来源.关键词：冬眠·非模型· MS/MS ·Spermophilus tridecemlineatus·算法·蛋白质鉴定
A major challenge in the life sciences is the extraction of detailed molecular information from plants and animals that are not among the handful of exhaustively studied “model organisms.” As a consequence, certain species with novel phenotypes are often ignored due to the lack of searchable databases, tractable genetics, stock centers, and more recently, a sequenced genome. Characterization of phenotype at the molecular level commonly relies on the identification of differentially expressed proteins by combining database searching with tandem mass spectrometry (MS) of peptides derived from protein fragmentation. However, the identification of short peptides from nonmodel organisms can be hampered by the lack of sufficient amino acid sequence homology with proteins in existing databases; therefore, a database search strategy that encompasses both identity and homology can provide stronger evidence than a single search alone. The use of multiple algorithms for database searches may also increase the probability of correct protein identification since it is unlikely that each program would produce false negative or positive hits for the same peptides. In this study, four software packages, Mascot, Pro ID, Sequest, and Pro BLAST, were compared in their ability to identify proteins from the thirteen-lined ground squirrel (Spermophilus tridecemlineatus), a hibernating mammal that lacks a completely sequenced genome. Our results show similarities as well as the degree of variability among different software packages when the identical protein database is searched. In the process of this study, we identified the up-regulation of succinyl CoA-transferase (SCOT) in the heart of hibernators. SCOT is the rate-limiting enzyme in the catabolism of ketone bodies, an important alternative fuel source during hibernation.Keywords: hibernation • nonmodel • MS/MS •Spermophilus tridecemlineatus• algorithm • protein identification