Conference proceeding
MS2DB: A mass-based hashing algorithm for the identification of disulfide linkage patterns in protein utilizing mass spectrometric data
TWENTIETH IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, PROCEEDINGS, pp.397-402
IEEE International Symposium on Computer-Based Medical Systems
01/01/2007
DOI: 10.1109/CBMS.2007.72
Abstract
The tertiary structure and biological function of a protein can be better understood given knowledge of the number and location of its disulfide bonds. By utilizing mass spectrometric (MS) experimental procedures that produce spectra of the protein's peptides joined by a disulfide bond, we can make initial identifications of these bonded cysteine pairings. The algorithmic problem then becomes how to match a theoretical mass space of all possible bonded peptides against the MS data. Our solution, MSHashID, utilizes the Expected Amino Acid Mass in combination with a hash structure to improve the time complexity of making an identification from worse than O(n(2)) to approximately O(n), where n is the size of the mass space. We have developed a software package, MS2DB, which includes an implementation of this algorithm. Experiments using published data show that the MSHashID algorithm efficiently makes the correct initial identifications, which can then be confirmed using tandem mass spectrometry (MS/MS).
Details
- Title: Subtitle
- MS2DB: A mass-based hashing algorithm for the identification of disulfide linkage patterns in protein utilizing mass spectrometric data
- Creators
- Timothy Lee - San Francisco State UniversityRahul Singh - San Francisco State UniversityTen-Yang Yen - San Francisco State UniversityBruce Macher - San Francisco State University
- Contributors
- P Kokol (Editor)V Podgorelec (Editor)D MiceticTurk (Editor)M Zorman (Editor)M Verlic (Editor)
- Resource Type
- Conference proceeding
- Publication Details
- TWENTIETH IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, PROCEEDINGS, pp.397-402
- Publisher
- IEEE
- Series
- IEEE International Symposium on Computer-Based Medical Systems
- DOI
- 10.1109/CBMS.2007.72
- ISSN
- 2372-9198
- eISSN
- 2372-9198
- Number of pages
- 3
- Grant note
- National Center on Minority Health and Health Disparities (NCMHD); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Minority Health & Health Disparities (NIMHD) NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA IIS-0644418; CHE-0619163 / NSF; National Science Foundation (NSF) P20 MD000262 / Research Infrastructure in Minority Institutions Program Center for Computing for Life Sciences at San Francisco State University
- Language
- English
- Date published
- 01/01/2007
- Academic Unit
- Computer Science
- Record Identifier
- 9984446274502771
Metrics
4 Record Views