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

Area of Science:

• Biochemistry
• Bioinformatics
• Genomics

Background:

• Protein sequence mutations can cause human diseases like sickle cell anemia.
• Existing databases (PMD, OMIM, HGMD) catalog disease-related mutations.
• Mass spectrometry (MS) is used for protein characterization, but lacks tools for identifying disease-related mutations within results.

Purpose of the Study:

• To develop a system for efficiently identifying human disease-related mutated proteins within mass spectrometry (MS) results.
• To create a platform that integrates disease mutation databases and analysis tools for comprehensive mutation research.

Main Methods:

• Developed SysPIMP (Systematical Platform for Identifying Mutated Proteins), a three-layered system.
• Integrated data from OMIM, PMD, and SwissProt databases, collecting 35,497 non-redundant human disease-related mutated sequences.
• Incorporated X!Tandem, an open-source search engine, into SysPIMP for detecting mutated proteins in MS data.

Main Results:

• SysPIMP provides a standardized data warehouse, a pipeline layer with disease databases and search engines (X!Tandem, BLAST), and a web interface.
• The platform successfully integrates disease-related mutated sequences with disease information from OMIM terms.
• SysPIMP offers original non-mutated sequences for comparative analysis alongside mutated sequences.

Conclusions:

• SysPIMP serves as a crucial platform for the efficient and intensive study of human diseases caused by protein mutations.
• The system facilitates the detection of potential human disease-related mutants within MS results.
• SysPIMP enhances research into the roles of mutations in human diseases.