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

Abstract

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.