Exact string matching for MS/MS protein identification using the cell broadband engine

Journal of Medical and Biological Engineering

Volumn 31, Issue 2, 2011, Pages 99-104

  Peace, Robert James ^a   Mahmoud, Hanan Akram ^a   Green, James Robert ^a  

^a CARLETON UNIVERSITY   (Canada)

Author keywords

Bioinformatics; Cell broadband engine (Cell B E); Exact string matching; High performance computing; Proteomics; Tandem mass spectrometry (MS MS)

Indexed keywords

CELL BROADBAND ENGINE (CELL B/E); EXACT STRING MATCHING; HIGH-PERFORMANCE COMPUTING; PROTEOMICS; TANDEM MASS SPECTROMETRY (MS/MS);

ALGORITHMS; BIOINFORMATICS; CELLS; COMPUTER SOFTWARE SELECTION AND EVALUATION; DATA REDUCTION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; MULTICORE PROGRAMMING; PARALLEL PROGRAMMING; PEPTIDES;

SEARCH ENGINES;

ALGORITHM; ARTICLE; COMPUTER; DATA BASE; DIRECTED TANDEM MASS SPECTROMETRY; MASS SPECTROMETRY; MICROPROCESSOR; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS;

EID: 79959665447     PISSN: 16090985     EISSN: None     Source Type: Journal    
DOI: 10.5405/jmbe.824     Document Type: Article

References (22)

1. A. Zerck, E. Nordho, A. Resemann, E. Mirgorodskaya, D. Suckau, K. Reinert, H. Lehrach and J. Gobom, "An iterative strategy for precursor ion selection for lc-ms/ms based shotgun proteomics," J. Proteome Res., 8: 3239-3251, 2009.
2. R. Aebersold and M. Mann, "Mass spectrometry-based proteomics," Nature, 422: 198-207, 2003.
3. A. Nesvizhskii and R. Aebersold, "Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem ms," Drug Discov. Today, 9: 173-181, 2004.
4. R. Johnson, M. Davis, J. Taylor and S. Patterson, "Informatics for protein identification by mass spectrometry," Nat. Methods, 35: 223-236, 2005.
5. A. Nesvizhskii, O. Vitek and R. Aebersold, "Analysis and validation of proteomic data generated by tandem mass spectrometry," Nat. Methods, 4: 787-797, 2007.
6. R. Sadygov, D. Cociorva and J. Yates III, "Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book," Nat. Methods, 1: 195-202, 2004.
7. E. Deutsch, H. Lam and R. Aebersold, "Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics," Physiol. Genomics, 33: 18-25, 2008.
8. E. Kapp, F. Schütz, L. Connolly, J. Chakel, J. Meza, C. Miller, D. Fenyo, J. Eng, J. Adkins, G. Omenn and R. Simpson, "An evaluation, comparison, and accurate benchmarking of several publicly available ms/ms search algorithms: sensitivity and specificity analysis," Proteomics, 5: 3475-3490, 2005.
9. L. Mueller, M. Brusniak, D. Mani and R. Aebersold, "An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data," J. Proteome Res., 7: 51-61, 2008.
10. M. Sturm and O. Kohlbacher, "TOPPView: an open-source viewer for mass spectrometry data," J. Proteome Res., 8: 3760-3763, 2009.
11. A. T. Alex, M. Dumontier, J. S. Rose and C. W. Hogue, "Hardware-accelerated protein identification for mass spectrometry," Rapid Commun. Mass Spectrom., 19: 833-837, 2005.
12. A. Scherl, P. Francois, V. Converset, M. Bento, J. A. Burgess, J. C. Sanchez, D. F. Hochstrasser, J. Schrenzel and G. L. Corthals, "Non-redundant mass spectrometry: a strategy to integrate mass spectrometry acquisition and analysis," Proteomics, 4: 917-927, 2004.
13. S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands and K. Yelick, "The potential of the cell processor for scientific computing," Proc. 3rd Conf. on Computing Frontiers, 9-20, 2006.
14. A. Aho and M. Corasick, "Efficient string matching: an aid to bibliographic search," Commun. ACM, 18: 333-340, 1975.
15. D. P. Scarpazza, O. Villa and F. Petrini, "Peak-performance DFA-based string matching on the cell processor," Proc. Parallel and Distributed Processing Symposium, 1-8, 2007.
16. D. P. Scarpazza, O. Villa and F. Petrini, "Exact multi-pattern string matching on the cell/b.e. processor," Proc. 5th Conf. on Computing Frontiers, 33-42, 2008.
17. M. Schatz and C. Trapnell, "Fast exact string matching on the GPU," Center for Bioinformatics and Computational Biology, Technical report, 2007.
18. G. Vasiliadis, M. Polychronakis, S. Antonatos, E. Markatos and S. Ioannidis, "Regular expression matching on graphics hardware for intrusion detection," Lect. Notes Comput. Sci., 5758: 265-283, 2009.
19. D. P. Scarpazza and G. Russell, "High-performance regular expression scanning on the Cell/B.E. processor," Proc. 23rd Int. Conf. on Supercomputing, 14-25, 2009.
20. R. Cameron, K. Herdy and D. Lin, "High performance xml parsing using parallel bit stream technology," Proc. Conf. of the Center for Advanced Studies on Collaborative Research: Meeting of Minds (CASCON), 2008.
21. R. S. Boyer and J. S. Moore, "A fast string searching algorithm," Commun. ACM, 20: 762-772, 1977.
22. R. M. Karp and M. O. Rabin, "Efficient randomized pattern-matching algorithms," IBM J. Res. Dev., 31: 249-260, 1987.