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《MOL CELL PROTEOMICS》发表翻译后修饰研究平台
    蛋白质翻译后修饰,是蛋白质发挥正常生物学功能的关键步骤,在生命体中具有十分重要的作用。近年来,高灵敏性、高准确性和高通量的质谱实验实现了蛋白质翻译后修饰的大规模鉴定,使其成为蛋白组学研究领域的一个热点。
    在中科院系统生物学重点实验室李亦学研究员、曾嵘研究员和上海生物信息技术研究中心谢鹭副研究员的共同指导下,博士生李虹和邢晓斌等开发了一个系统的翻译后修饰研究平台SysPTM(http://www.sysbio.ac.cn/SysPTM)。该平台首先将分散在公共数据库和文献中的实验鉴定的翻译后修饰信息整合,建立了一个目前最完整的翻译后修饰数据库。它包括近50种修饰类型,33421个蛋白质上的117349个修饰位点。在此数据基础上,SysPTM又开发了四个在线工具(PTMBlast,PTMPathway,PTMPhylog,PTMCluster),以探索翻译后修饰的生物学功能。这一平台的建立是生物信息学与蛋白组学紧密结合的研究成果,适应了翻译后修饰蛋白质组学的发展需求。该数据库为生物信息学者深入分析翻译后修饰奠定了基础,在线工具也对蛋白组学研究者分析高通量数据有具有意义。国际著名学术刊物《Molecular and Cellular Proteomics》于2009年4月14日在线发表该研究成果。
 
SysPTM - a systematic resource for proteomic research of post-translational modifications
H Li, X Xing, G Ding, Q Li, C Wang, L Xie*, R Zeng*, Y Li*
    With the rapid expansion of protein post-translational modification (PTM) research based on large-scale proteomic work, there is an increasing demand for a suitable repository to analyze PTM data. Here we present a curated, web-accessible PTM database-SysPTM. SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools. Currently, SysPTM contains data detailing 117349 experimentally determined PTM sites on 33421 proteins involving nearly 50 PTM types, curated from public resources including five databases and four webservers and more than one hundred peer-reviewed mass spectrometry papers. Protein annotations including Pfam domains, KEGG pathways, GO functional classification, and ortholog groups are integrated into the database. Four online tools have been developed and incorporated, including: PTMBlast, to compare a user’s PTM dataset with PTM data in SysPTM; PTMPathway, to map PTM proteins to KEGG pathways; PTMPhylog, to discover potentially conserved PTM sites; and PTMCluster, to find clusters of multi-site modifications. The workflow of SysPTM was demonstrated by analyzing an in-house phosphorylation dataset identified by MS/MS. It is shown that, in SysPTM, the roles of single-type and multi-type modifications can be systematically investigated in a full biological context. SysPTM could be an important contribution to modificomics research. SysPTM is freely available at: http://www.sysbio.ac.cn/SysPTM.
   
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