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Nucleic Acids Research Advance Access published online on November 26, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn848
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry

Hong Xi1, Jongsun Park2,3,4, Guohui Ding5, Yong-Hwan Lee2,3,4 and Yixue Li1,5,6,*

1Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, 2Fungal Bioinformatics Laboratory, 3Department of Agricultural Biotechnology, 4Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, 5Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and 6Shanghai Center for Bioinformation Technology, Shanghai, China

*To whom correspondence should be addressed. Tel: +86 21 54065001; Fax: +86 21 54065058; Email: yxli{at}sibs.ac.cn

Received August 12, 2008. Revised September 29, 2008. Accepted October 16, 2008.

Some mutations resulting in protein sequence change might be tightly related to certain human diseases by affecting its roles, such as sickle cell anemia. Until now several databases, such as PMD, OMIM and HGMD, have been developed, providing useful information about human disease-related mutation. Tandem mass spectrometry (MS) has been used for characterizing proteins in various conditions; however, there is no system in place for finding disease-related mutated proteins within the MS results. Here, a Systematical Platform for Identifying Mutated Proteins (SysPIMP; http://pimp.starflr.info/) was developed to efficiently identify human disease-related mutated proteins within MS results. SysPIMP comprises of three layers: (i) a standardized data warehouse, (ii) a pipeline layer for maintaining human disease databases and X!Tandem and BLAST and (iii) a web-based interface. From OMIM AV part, PMD and SwissProt databases, 35 497 non-redundant human disease-related mutated sequences were collected with disease information described by OMIM terms. With the interfaces to browse sequences archived in SysPIMP, X!Tandem, an open source database-search engine used to identify proteins within MS data, was integrated into SysPIMP to help support the detection of potential human disease-related mutants in MS results. In addition, together with non-redundant disease-related mutated sequences, original non-mutated sequences are also provided in SysPIMP for comparative research. Based on this system, SysPIMP will be the platform for efficiently and intensively studying human diseases caused by mutation.


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