Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Theoretical Peptide Mass Distribution in the Non-Redundant Protein Database of the NCBI

  • Lim Da-Jeong (Department of Food and Animal Biotechnology, Seoul National University) ;
  • Oh Hee-Seok (Department of Statistics, Seoul National University) ;
  • Kim Hee-Bal (Department of Food and Animal Biotechnology, Seoul National University)
  • Published : 2006.06.01
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Abstract

Peptide mass mapping is the matching of experimentally generated peptides masses with the predicted masses of digested proteins contained in a database. To identify proteins by matching their constituent fragment masses to the theoretical peptide masses generated from a protein database, the peptide mass fingerprinting technique is used for the protein identification. Thus, it is important to know the theoretical mass distribution of the database. However, few researches have reported the peptide mass distribution of a database. We analyzed the peptide mass distribution of non-redundant protein sequence database in the NCBI after digestion with 15 different types of enzymes. In order to characterize the peptide mass distribution with different digestion enzymes, a power law distribution (Zipfs law) was applied to the distribution. After constructing simulated digestion of a protein database, rank-frequency plot of peptide fragments was applied to generalize a Zipfs law curve for all enzymes. As a result, our data appear to fit Zipfs law with statistically significant parameter values.

Keywords

References

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