Genomics Inform.
2006 Jun;4(2):65-70.
Theoretical Peptide Mass Distribution in the Non-Redundant Protein Database of the NCBI
- Affiliations
-
- 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.
- Full Text Links
-
- Actions
-
Cited
- CITED
-
- Close
- Share
-
- Similar articles
-
- Patome: Database of Patented Bio-sequences
- Screening of Peptide Libraries to Investigate the Substrate Specificity of UL97 Protein Kinase from Human Cytomegalovirus
- Improved Algorithms for the Identification of Yeast Proteins and Significant Transcription Factor and Motif Analysis
- The Comparison between FSGS and MCNS Using Proteomic Method in Childhood Nephrotic Syndrome; Preliminary Study
- A Case of the Redundant Nerve Root Syndrome Mimicking Intradural Spinal Tumor
