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BioMed Research International
Volume 2013 (2013), Article ID 414069, 7 pages
Method for Rapid Protein Identification in a Large Database
1Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
2State Key Laboratory of Computer Architecture, ICT, CAS, Beijing 100190, China
3Graduate University of Chinese Academy of Sciences, Beijing 100049, China
Received 17 May 2013; Revised 10 July 2013; Accepted 14 July 2013
Academic Editor: Lei Chen
Copyright © 2013 Wenli Zhang and Xiaofang Zhao. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. S. Cottrell, “Protein identification using MS/MS data,” Journal of Proteomics, vol. 74, no. 10, pp. 1842–1851, 2011.
- R. S. Johnson, M. T. Davis, J. A. Taylor, and S. D. Patterson, “Informatics for protein identification by mass spectrometry,” Methods, vol. 35, no. 3, pp. 223–236, 2005.
- N. J. Edwards, “Protein identification from tandem mass spectra by database searching,” Methods in Molecular Biology, vol. 694, pp. 119–138, 2011.
- D. N. Perkins, D. J. C. Pappin, D. M. Creasy, and J. S. Cottrell, “Probability-based protein identification by searching sequence databases using mass spectrometry data,” Electrophoresis, vol. 20, no. 18, pp. 3551–3567, 1999.
- J. K. Eng, A. L. McCormack, and J. R. Yates III, “An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database,” Journal of the American Society for Mass Spectrometry, vol. 5, no. 11, pp. 976–989, 1994.
- R. Craig and R. C. Beavis, “TANDEM: matching proteins with tandem mass spectra,” Bioinformatics, vol. 20, no. 9, pp. 1466–1467, 2004.
- L. Y. Geer, S. P. Markey, J. A. Kowalak et al., “Open mass spectrometry search algorithm,” Journal of Proteome Research, vol. 3, no. 5, pp. 958–964, 2004.
- L. Y. Geer, et al., “Reducing false positive rates in MS/MS sequence searching and incorporating intensity into match based statistics,” ftp://ftp.ncbi.nih.gov/pub/lewisg/presentations/asms06poster.pdf.
- D. Li, Y. Fu, R. Sun et al., “pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry,” Bioinformatics, vol. 21, no. 13, pp. 3049–3050, 2005.
- L. Wang, D. Li, Y. Fu et al., “pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry,” Rapid Communications in Mass Spectrometry, vol. 21, no. 18, pp. 2985–2991, 2007.
- EBI, http://www.ebi.ac.uk/uniprot/TrEMBLstats/.
- R. D. Bjornson, N. J. Carriero, C. Colangelo et al., “X!!Tandem, an improved method for running X!Tandem in parallel on collections of commodity computers,” Journal of Proteome Research, vol. 7, no. 1, pp. 293–299, 2008.
- D. T. Duncan, R. Craig, and A. J. Link, “Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem,” Journal of Proteome Research, vol. 4, no. 5, pp. 1842–1847, 2005.
- A. Quandt, P. Hernandez, P. Kunzst et al., “Grid-based analysis of tandem mass spectrometry data in clinical proteomics,” Studies in health technology and informatics, vol. 126, pp. 13–22, 2007.
- D. Zosso, M. Podvinec, M. Müller, R. Aebersold, M. C. Peitsch, and T. Schwede, “Tandem mass spectrometry protein identification on a PC grid,” Studies in Health Technology and Informatics, vol. 126, pp. 3–12, 2007.
- B. D. Halligan, J. F. Geiger, A. K. Vallejos, A. S. Greene, and S. N. Twigger, “Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms,” Journal of Proteome Research, vol. 8, no. 6, pp. 3148–3153, 2009.
- B. Pratt, J. J. Howbert, N. I. Tasman, and E. J. Nilsson, “Mr-tandem: parallel x!Tandem using hadoop MapReduce on Amazon web services,” Bioinformatics, vol. 28, no. 1, Article ID btr615, pp. 136–137, 2012.
- Unimod, http://www.unimod.org/.
- E. Ahrné, M. Müller, and F. Lisacek, “Unrestricted identification of modified proteins using MS/MS,” Proteomics, vol. 10, no. 4, pp. 671–686, 2010.
- P. Wilmes and P. L. Bond, “Metaproteomics: Studying functional gene expression in microbial ecosystems,” Trends in Microbiology, vol. 14, no. 2, pp. 92–97, 2006.
- S. D. Patterson, “Data analysis—the Achilles heel of proteomics,” Nature Biotechnology, vol. 21, no. 3, pp. 221–222, 2003.
- Y. Fu, L. Xiu, W. Jia et al., “DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data,” Molecular and Cellular Proteomics, vol. 10, no. 5, 2011.
- W. Jia, Z. Lu, Y. Fu et al., “A strategy for precise and large scale identification of core fucosylated glycoproteins,” Molecular and Cellular Proteomics, vol. 8, no. 5, pp. 913–923, 2009.
- W. Zhang, H. Chi, Y. Lu, Y. Huang, X. Zhao, and S. He, “Preliminary search engine for open protein identification,” in Proceeding of the 13th International Conference on Parallel and Distributed Computing, Applications and Technologies, pp. 410–415, 2012.
- L. Wang, S. He, R. Sun et al., “An efficient parallelization of phosphorylated peptide and protein identification,” Rapid Communications in Mass Spectrometry, vol. 24, no. 12, pp. 1791–1798, 2010.