SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

Yixue Li,Rong Zeng,Hong Li,Xiaobin Xing,Qingrun Li,Lu Xie,Chuan Wang,Guohui Ding

doi:10.1074/mcp.m900030-mcp200

Abstract

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.

Highlights

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 Post-translational modifications (PTMs) data
More recent MS/MS experiments have led to the discovery of thousands try; GO, Gene Ontology; SysPTM-A, PTM sites culled from public resources; SysPTM-B, PTM sites culled from peer-reviewed tandem mass spectrometry literature; PTMBlast, a tool for comparing user PTM datasets with data in SysPTM; PTMPathway, a tool for mapping PTM proteins to KEGG pathways; PTMPhylog, a tool for analyzing potentially conserved PTM sites; PTMCluster, a tool for finding clusters of multi-site modifications; mES, mouse embryonic stem; E3, ubiquitin-protein isopeptide ligase; Focal adhesion kinase (FAK), focal adhesion kinase; KEGG, Kyoto encyclopedia of genes and genomes; HPRD, human protein reference database
The progress of post-translational modification research has accelerated since the introduction of mass spectrometry as a primary technology in the field of proteomics

Summary

EXPERIMENTAL PROCEDURES

SysPTM consists of a relational data base and a dynamic web interface. A simplified entity-relationship diagram of the SysPTM data base is shown in supplemental Fig. S1. In the current version of SysPTM, modification information was automatically retrieved from five data bases (Swiss-Prot version 56.2 [21], Phospho.ELM version 8.0 [19], HPRD release 7 [22], O-GLYCBASE version 6.0 [20], and Ubiprot version 1.0 [25]) and four web servers (SUMOsp version 1.0 [26], Memo version 2.0 [27], NetAcet version 1.0 [28], and LysAcet version 1.1 [55]) These data were integrated and stored as SysPTM-A (see Supplemental Methods). The spectra of phosphopeptides used for the case study were manually checked (Supplemental Methods)

RESULTS

Data Accessibility

DISCUSSION AND CONCLUSION