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YPED: a proteomics database for protein expression analysis.

Mark A Shifman1, Kexin Sun, Christopher M Colangelo

  • 1Center for Medical Informatics, Yale University, New Haven, CT, USA.

AMIA ... Annual Symposium Proceedings. AMIA Symposium
|June 17, 2006
PubMed
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The Yale Protein Expression Database (YPED) offers integrated proteomics data analysis. It supports sample management and data retrieval for researchers, enhancing scientific discovery.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Proteomics

Background:

  • Proteomics research generates vast amounts of data requiring specialized management.
  • Existing systems may lack integrated analysis capabilities for diverse experimental workflows.

Purpose of the Study:

  • To develop a comprehensive database for storing, retrieving, and analyzing proteomics data.
  • To provide a web-accessible platform for managing sample information and experimental results.

Main Methods:

  • Developed the Yale Protein Expression Database (YPED) with web accessibility.
  • Integrated data processing for ICAT, DIGE, and MUDPIT sample types.
  • Utilized Sequest, Mascot, and Trans-Proteomic Pipeline for peptide and protein identification and validation.
  • Stored validated data in XML format within the database.

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Main Results:

  • YPED is operational and handles sample requisition, result reporting, and sample comparison.
  • Sample descriptions adhere to evolving Minimum Information About a Proteomics Experiment (MIAPE) standards.
  • Researchers can securely access, subset, and download their proteomics data via a web interface.

Conclusions:

  • YPED provides a robust solution for proteomics data management and analysis.
  • The database facilitates efficient data sharing and utilization for the research community.
  • YPED supports standardized data reporting, improving reproducibility in proteomics studies.