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Related Experiment Videos

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

Michael J MacCoss1, Christine C Wu, Hongbin Liu

  • 1Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Analytical Chemistry
|December 13, 2003
PubMed
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RelEx is a new software tool that automatically quantifies protein levels from mass spectrometry data. This automated approach improves quantitative proteomic accuracy and was validated in yeast.

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Quantitative shotgun proteomics relies on chemical tags and stable isotope labeling.
  • High-throughput proteomic data requires automated software for analysis.
  • Converting mass spectrometry data into relative protein abundances is crucial.

Purpose of the Study:

  • To develop an automated software tool for quantitative shotgun proteomics.
  • To accurately calculate peptide ion current ratios from mass spectrometry data.
  • To validate the software's performance on known mixtures and biological samples.

Main Methods:

  • Developed RelEx software using least-squares regression.
  • Utilized mass spectrometry-derived ion chromatograms for peptide quantification.

Related Experiment Videos

  • Applied a correction for systematic errors to improve accuracy.

    • Main Results:

    • RelEx automatically converts peptide data into relative protein abundances.
    • The software is tolerant of poor signal-to-noise data and discards unusable chromatograms.
    • A systematic error correction improved quantitative measurement accuracy by 32 +/- 4%.

    Conclusions:

    • RelEx provides an automated and accurate method for quantitative shotgun proteomics.
    • The software facilitates high-throughput analysis of proteomic data.
    • Demonstrated utility in measuring protein expression changes under osmotic stress in yeast.