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Molecular & Cellular Proteomics 8:1839-1849, 2009.
© 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

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^,,**

From the Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China,
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. SysPTM is freely available online at www.sysbio.ac.cn/SysPTM.

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