Genomics Inform Search

CLOSE


Genomics Inform > Volume 4(2); 2006 > Article
Theoretical Peptide Mass Distribution in the Non-Redundant Protein Database of the NCBI.
Da Jeong Lim, Hee Seok Oh, Hee Bal Kim
1Department of Food and Animal Biotechnology, Seoul National University, Korea. heebal@snu.ac.kr
2Department of Statistics, Seoul National University, Korea.
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: peptide mass; non-redundant protein database; Zipfs law
TOOLS
Share :
Facebook Twitter Linked In Google+
METRICS Graph View
  • 1,656 View
  • 14 Download
Related articles in GNI


ABOUT
ARTICLE CATEGORY

Browse all articles >

BROWSE ARTICLES
FOR CONTRIBUTORS
Editorial Office
Room No. 806, 193 Mallijae-ro, Jung-gu, Seoul 04501, Korea
Tel: +82-2-558-9394    Fax: +82-2-558-9434    E-mail: kogo3@kogo.or.kr                

Copyright © 2024 by Korea Genome Organization.

Developed in M2PI

Close layer
prev next