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  Frequently Asked Questions :
1. What is SysPTM ?
2. How to use SysPTM ?
3. How many items are included in the database ?
4. What information can I obtain from the database ?
5. How do I cite SysPTM ?
6. Who are we ?
  What is SysPTM ?
PTMs of proteins play essential roles in almost all cellular processes, and are closely related to physiological activity and disease development of living organisms. The collection of these data will provide invaluable source to understand the cellular processes and the signaling pathways regulated by PTMs. While many databases have been established to collect information of protein PTM sites, there is no such resource providing a searchable platform for quick and in-depth analysis of user PTM datasets by comparing to the known PTMs. SysPTM was thus designed to incorporates the existing features of numerous previous databases and modification datasets from MS/MS experiments reported in the literature, presented in a user-friendly browser with a suit of analysis tools to support high-throughput annotation of proteomics PTMs. The database is publicly available at http://lifecenter.sgst.cn/SysPTM/.
  How to use SysPTM ?
SysPTM is a user-friendly web tool and service to help you explore PTM-related information in peptides and proteins. You can access the database as follows:
  • Search
    The "Search" page may be the most frequently used service. "Text search" is a powerful engine to search keyword through the database, such as protein name (eg, cellular tumor antigen TP53), protein identifier (eg, P53_HUMAN), or protein accession number (eg, P04637). ”Sequence search” is a Blast based engine to find similar proteins by sequence, which is complementary to “Text search”. In principle, you can input any FASTA protein sequence in the input box. Click “example” button to get an example demo.
    -----Details about the Search help
  • Browse
    The Browse page allows users to scan PTM proteins based on given PTM type, Data source or Kegg Pathway. For the Kegg Pathway, a pathway map marked with PTM proteins will also be displayed by clicking the pathway ID. The yellow items on the map contain PTM information, click and find it. The green ones belong to the selected species.
    -----Details about the Browse help
  • Statistics
    This page gives the data increase in SysPTM with each updated version. The PTM protein numbers, PTM site numbers, and peptide numbers (if available) of each data source in the most current version are given.
  • Download
    To protect the license of other databases, we do not provide download of SysPTM-A data; users can download them via the original websites. SysPTM-B data can be downloaded for research use only but should not be distributed to a third party without prior consent.
  • FAQ
    The FAQ page is a help document for SysPTM database. You can find solutions to almost all your questions here, so try to read it carefully. Further questions or advices can be sent to: sysptm2.0@gmail.com .
  • Links
    The Links list many web tools based on different algorithms to predict potential PTM sites, types, and motifs, et.al.
  • PTMBlast
    SysPTM has large PTM site collection from public databases and MS experiments(see statistics for detail). You can evaluate your data and affirm novel PTM sites by comparing your own data with SysPTM repository. PTMBlast provides three candidate comparison methods:
    1. Query protein sequence must be entirely identical with entries in SysPTM, then compare the overlapped PTM sites.
    2. Query protein sequence has given similarity with entries of SysPTM by Blast, then compare the overlapped PTM sites.
    3. Directly map query peptide to protein sequence, and compare the overlapped PTM sites.
    -----Details about the PTMBlast help
  • PTMPathway
    PTMpathway can be browsed to find PTM information in a given KEGG pathway, or find PTM information for a particular protein or a protein list in all related KEGG pathways.
    -----Details about the PTMPathway help
  • PTMPhylog
    PTMPhylog tool can help you explore the relation between different species in terms of protein conserved regions as well as PTM information, as the example indicates.
    -----Details about the PTMPhylog help
  • PTMCluster
    PTMCluster is used to detect PTM sites that tend to form “clusters” on a protein sequence, which locate in a physically close space.
    -----Details about the PTMCluster help

  • PTMGO
    PTMGO is used to support functional annotation and enrichment analysis of PTM proteins, which could facilitate a better understanding of PTM events in complex biological processes.
    -----Details about the PTMGO help

  How many items are included in the database ?
  • SysPTM-A
    Database Version PMID Protein_Number Site_Number
    Phosphositeplus Version 1.0 (20131004) 22135298 34688 365293
    SwissProt Version 2012.12 (20121101) 15174124 23919 95213
    HPRD Release 9 (20121101) 14681466 12571 85576
    LysAcet Version 1.1 (20081027) 384 1022
    MeMo Version 2.0 (20060421) 16845004 142 397
    SUMOsp Version 1.0 (20051210) 16845005 143 239
    ubiprot Version 1.0 (20071026) 17442109 120 179
    NetAcet Version 1.0 (20071013) 15539450 57 57

    -----Details about PTMs types

  • SysPTM-B
    PMID Protein_Number Peptide_Number Site_Number
    23312004 4623 19580 19569
    23266961 4524 28355 28298
    23186163 3882 23274 18115
    20068231 3865 18024 18137
    22199227 3733 17029 17260
    20873877 3591 21410 18967
    21715320 3445 13528 11765
    21890473 3285 9339 9253
    23090842 3104 13441 13842
    18669648 2852 10144 9707

    -----Details about these papers

  What information can I obtain from the database ?
  • Protein annotation information
  • 1 Sequence
    2.Pfam Domain
    3.KEGG Pathway
    4.Gene Onthology
    5.OMIM Disease
  • Homolog and conservation information of PTM Site and Type
  • Source of different PTMs
  • Three types of map for PTM sites and clusters

-----Click for more detailed information

  How do I cite SysPTM ?
  • http://lifecenter.sgst.cn/SysPTM
  • Hong Li, Xiaobin Xing, Guohui Ding, Qingrun Li, Chuan Wang, Lu Xie, Rong Zeng, Yixue Li. (2008)
    "SysPTM – a Systematic Resource for Proteomic Research of Post-translational Modifications"

  Who are we ?
  • Institute :

    Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P. R. China, 430074

    Shanghai Center for Bioinformation Technology, Shanghai, P. R. China, 201203

    Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, P.R. China, 430074

    Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, P. R. China, 200031

    Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, P. R. China, 200240

  • Authors :
    Jing Li - sysptm2.0@gmail.com
    Jia Jia - jiajia@scbit.org
    Lu Xie - xielu@scbit.org
    Qian Liu - qianliu@mail.hust.edu.cn
    Guoqing Zhang - gqzhang@scbit.org
    Yixue Li - yxli@sibs.ac.cn