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Related Experiment Videos

Interrogating the human genome using uninterpreted mass spectrometry data.

J S Choudhary1, W P Blackstock, D M Creasy

  • 1Cell Mapping Project, Glaxo Wellcome R&D, Stevenage, Hertfordshire, UK.

Proteomics
|October 27, 2001
PubMed
Summary

Researchers demonstrated searching the human genome with mass spectrometry data. This technique verifies predicted genes and may discover new ones, advancing proteogenomic analysis.

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Area of Science:

  • Proteomics
  • Genomics
  • Bioinformatics

Background:

  • The human genome project has made draft sequences publicly available.
  • Mass spectrometry is a powerful tool for protein identification.

Purpose of the Study:

  • To demonstrate the feasibility of searching a complete eukaryotic genome using uninterpreted mass spectrometry data.
  • To compare the effectiveness of different databases for this application.

Main Methods:

  • A complex liquid chromatography-tandem mass spectrometry (LC-MS/MS) dataset was used.
  • The data was searched against a protein database, an expressed sequence tag (EST) database, and the human genome draft assembly.

Main Results:

  • The search against the human genome draft assembly successfully identified peptides.

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  • Introns in the genomic DNA prevented matching approximately 25% of spectra.
  • The expressed sequence tag (EST) database, summarized by the UniGene index, simplified search results.

    • Conclusions:

    • Searching a complete genome with mass spectrometry data is feasible.
    • This approach can experimentally verify predicted coding sequences.
    • The technique holds potential for identifying novel coding sequences.