8月12日, 國際知名學(xué)術(shù)期刊Molecular and Cellular Proteomics在線發(fā)表了中國科學(xué)院上海生命科學(xué)研究院生物化學(xué)與細胞生物學(xué)研究所/系統(tǒng)生物學(xué)重點實驗室曾嶸研究組的工作：運用陰陽多維液相色譜-質(zhì)譜系統(tǒng)和穩(wěn)定同位素標記的方法,，同步定量細胞蛋白質(zhì)組及磷酸化蛋白質(zhì)組,，從而系統(tǒng)地揭示了蛋白質(zhì)磷酸化和基因表達間的關(guān)系。
磷酸化是蛋白質(zhì)最重要的翻譯后修飾之一,磷酸化肽段和非磷酸化肽段的不同特性,，使得磷酸化肽段和非磷酸化肽段的同步鑒定及定量成為蛋白質(zhì)組學(xué)研究中的難點,。生化與細胞所博士生伍一博等人在曾嶸研究員指導(dǎo)下,，運用該實驗室發(fā)明的陰陽多維液相色譜-質(zhì)譜系統(tǒng)(Yin-Yang-MDLC-MS/MS)及在線pH梯度洗脫對細胞內(nèi)蛋白質(zhì)酶解肽段進行分級分離，實現(xiàn)了一次實驗中對磷酸化肽段和非磷酸化肽段的同步鑒定,。進一步結(jié)合穩(wěn)定同位素標記 (SILAC)的方法,，可以同步定量細胞內(nèi)蛋白質(zhì)表達及其磷酸化水平。對于單個蛋白質(zhì)而言,，這一方法有助于區(qū)分兩種不同的磷酸化水平改變方式,，即直接受激酶調(diào)控，或者通過蛋白質(zhì)表達量的變化而變化,。從系統(tǒng)水平上看,，這一方法可以揭示轉(zhuǎn)錄因子磷酸化對其下游靶基因的調(diào)控關(guān)系。該工作以脂肪細胞為研究對象,，鑒定到了一些在分化早期磷酸化水平或表達量發(fā)生顯著變化的蛋白質(zhì),，進一步的生物信息學(xué)分析揭示了一些轉(zhuǎn)錄因子磷酸化水平與下游靶基因表達水平的關(guān)系。這一工作為系統(tǒng)水平上詮釋脂肪細胞分化早期分子事件提供了研究策略和實驗依據(jù),，發(fā)展的技術(shù)方法也可以廣泛應(yīng)用于信號轉(zhuǎn)導(dǎo)分子機制研究,。
該項工作是與吳家睿研究組和李亦學(xué)研究員領(lǐng)導(dǎo)的生物信息中心合作完成的，并得到了科技部,，基金委和中科院經(jīng)費支持,。（生物谷Bioon.com）
生物谷推薦原始出處：
Molecular & Cellular Proteomics 8:1839-1849, 2009.
SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications*
Hong Li,,?,||, Xiaobin Xing,,?,||, Guohui Ding, Qingrun Li,?, Chuan Wang, Lu Xie,**, Rong Zeng,** and Yixue Li,,**
1 From the Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China,
2 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China, and
Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
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 data base, 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 117,349 experimentally determined PTM sites on 33,421 proteins involving nearly 50 PTM types, curated from public resources including five data bases and four web servers 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 data base. 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 role 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.
