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Related Experiment Videos

Global proteome discovery using an online three-dimensional LC-MS/MS.

Jing Wei1, Jun Sun, Wen Yu

  • 1Diversa Corporation, 4955 Directors Place, San Diego, California 92121, USA. jwei@diversa.com

Journal of Proteome Research
|June 15, 2005
PubMed
Summary

We developed a novel three-dimensional liquid chromatography coupled to tandem mass spectrometry (3D LC-MS/MS) proteomics technology. This method significantly enhances yeast protein identification, including membrane proteins, for comprehensive proteome discovery.

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Proteome analysis is crucial for understanding cellular functions.
  • Identifying and quantifying proteins, especially membrane proteins, presents significant challenges.
  • Existing proteomics technologies have limitations in resolving complex protein mixtures.

Purpose of the Study:

  • To develop and validate a novel proteomics technology for enhanced protein identification.
  • To improve the analysis of both soluble and membrane-bound proteins.
  • To facilitate comprehensive yeast proteome discovery and pathway mapping.

Main Methods:

  • Development of an on-line three-dimensional liquid chromatography coupled to tandem mass spectrometry (3D LC-MS/MS) system.
  • Application of 3D LC-MS/MS to yeast-soluble, urea-solubilized peripheral membrane, and SDS-solubilized membrane protein samples.

Related Experiment Videos

  • Utilizing SEQUEST search algorithm against the Saccharomyces Genome Database for protein identification.

    • Main Results:

    • Achieved 3019 unique yeast protein identifications from combined samples.
    • A single run of urea-solubilized sample yielded 2255 unique protein identifications, demonstrating high resolving power.
    • Successfully identified 495 membrane proteins with two or more predicted transmembrane domains.

    Conclusions:

    • The 3D LC-MS/MS technology offers high peak capacity and resolving power for complex proteome analysis.
    • This technology enables efficient identification of challenging membrane proteins.
    • The developed 3D LC-MS/MS method is a powerful tool for global proteome discovery and functional pathway mapping.