An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data

Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Volumn , Issue , 2012, Pages 618-625

  Saeed, Fahad ^a   Pisitkun, Trairak ^a   Hoffert, Jason D ^a   Wang, Guanghui ^b   Gucek, Marjan ^b   Knepper, Mark A ^a  

^a Epithelial Systems Biology Laboratory   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEGREE OF SENSITIVITY; DYNAMIC PROGRAMMING ALGORITHM; FUNCTIONAL INTERPRETATIONS; MASS SPECTROMETRY DATA; OBJECTIVE FUNCTIONS; PHOSPHOPEPTIDE FRAGMENTATIONS; PHOSPHORYLATION SITES; TANDEM MASS SPECTROMETRY;

BIOINFORMATICS; DYNAMIC PROGRAMMING; MASS SPECTROMETRY; PEPTIDES; PHOSPHORYLATION;

ALGORITHMS;

EID: 84875575749     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2012.6470210     Document Type: Conference Paper

References (34)

1. J. D. Hoffert, T. Pisitkun, G. Wang, R.-F. Shen, and M. A. Knepper, "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: Regulation of aquaporin-2 phosphorylation at two sites.," Proc Natl Acad Sci USA, vol. 103, no. 18, pp. 7159-7164, 2006.
2. J. P. Whitelegge, "Hplc and mass spectrometry of intrinsic membrane proteins," in HPLC ofPeptides and Proteins (M.-I. Aguilar, ed.), vol. 251 of Methods in Molecular Biology, pp. 323-339, Humana Press, 2004. 10.1385/1-59259-742-4:323.
3. ] S. Tanner, H. Shu, A. Frank, L. C. Wang, E. Zandi, M. Mumby, P. A. Pevz.ner, and y. Bafna, "InsPecT: identification of post translationally modified peptides from tandem mass spectra.," Analytical Chemistry, vol. 77, pp. 4626-4639, July 2005.
4. J. K. Eng, B. Fischer, J. Grossmann, and M. J. MacCoss, "A fast sequest cross correlation algorithm," Journal ofProteome Research, vol. 7, no. 10, pp. 4598-4602, 2008.
5. N. Musbacher, T. B. Schreiber, and H. Daub, "Glycoprotein Capture and Qu~ntit~tive Phosphoproteomics Indicate Coordinated Regulation of Cell Migration upon Lysophosphatidic Acid Stimulation," Molecular &Cellular Proteomics, vol. 9, no. 11, pp. 2337-2353, 2010.
6. D. B. Solit and I. K. Mellinghoff, "Tracing cancer networks with phosphoproteomics," Nat Biotech, vol. 28, pp. 1028-1029, 10 2010.
7. A. Gruhler, J. V. Olsen, S. Mohammed, P. Mortensen, N. J. Frgeman, M. Mann, and O. N. Jensen, "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway," Mo!' Cell. Proteomics, vol. 4, p. 310, 2005.
8. A. Wolf-Yadlin, S. Hautaniemi, D. A. Lauffenburger, and F. M. White, "Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks," Proc. Nat!' Acad. Sci. U.S.A., vol. 104, p. 5860, 2007.
9. G. T. Cantin, 1. D. Venable, D. Cociorva, and J. R. Yates, "Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway," J. Proteome Res., vol. 5, p. 127, 2006.
10. J. D. Hoffert, T. Pisitkun, G. Wang, R.-F. Shen, and M. A. Knepper, "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites," Proc. Nat!' Acad. Sci. U.S.A., vol. 103, p. 7159, 2006.
11. X. Jiang, . Ye, G. Han, X. Dong, and H. Zou, "Classification filtering strategy to Improve the coverage and sensitivity of phosphoproteome analysis," Analytical Chemistry, vol. 82, no. 14, pp. 6168-6175, 2010.
12. X. Du, F. Yang, N. P. Manes, D. L. Stenoien, M. E. Monroe, J. N. Adkins, D. J. States, S. O. Purvine, D. G. Camp, II, and R. D. Smith, "Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications," Journal ofProteome Research, vol. 7, no. 6, pp. 2195-2203, 2008.
13. B. E. Ruttenberg, T. Pisitkun, M. A. Knepper, and J. D. Hoffert, "PhosphoScore: an open-source phosphorylation site assignment tool for MSn data.," Journal of Proteome Research, vol. 7, pp. 3054-3059, July 2008. 625
14. A. Ritz, G. Shakhnarovich, A. R. Salomon, and B. J. Raphael, "Discovery of phosphorylation motif mixtures in phosphoproteomics data," Bioinformatics, vol. 25, no.T, pp. 14-21, 2009.
15. S. A. Beausoleil, J. Villen, S. A. Gerber, J. Rush, and S. P. Gygi, "A probability-based approach for high-throughput protein phosphorylation analysis and site localization," Nature Biotechnology, vol. 24, pp. 12851292, September 2006.
16. M. M. Savitski, S. Lemeer, M. Boesche, M. Lang, T. Mathieson, M. Bantscheff, and B. Kuster, "Confident phosphorylation site localization using the mascot delta score," Molecular and Cellular Proteomics vol. 10, no. 2, 2011. '
17. J. Cox and M. Mann, "Maxquant enables high peptide identification rates, individualized p.p.h.-range mass accuracies and proteome-wide protein quantification," Nat Biotech, vol. 26, pp. 1367-1372, 12 2008.
18. D. Li, Y. Fu, R. Sun, C. X. Ling, Y. Wei, H. Zhou, R. Zeng, Q. Yang, S. He, and W. Gao, "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.
19. D. L. Swaney, C. D. Wenger, J. A. Thomson, and J. J. Coon, "Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry," Proceedings of the National Academy of Sciences, vol. 106, no. 4, pp. 995-1000, 2009.
20. S. H. Payne, M. Yau, M. B. Smolka, S. Tanner, H. Zhou, and V. Bafna, "Phosphorylation-specific mslms scoring for rapid and accurate phosphoproteome analysis," Journal of Proteome Research, vol. 7, no. 8, pp. 3373-3381, 2008.
21. T. Taus, T. Kocher, P. Pichler, C. Paschke, A. Schmidt, C. Henrich, and K. Mechtler, "Universal and confident phosphorylation site localization using phosphors," Journal of Proteome Research, vol. 10, no. 12, pp. 5354-5362, 2011.
22. H. Barsnes, S. Huber, A. Sickmann, I. Eidhammer, and L. Martens, "OMSSA parser: an open-source library to parse and extract data from MS/MS search results.," Proteomics, vol. 9, no. 14, pp. 3772-4, 2009.
23. J. Kleinberg and E. Tardos, Algorithm Design. Boston, MA, USA: Addison-Wesley Longman Publishing Co., Inc., 2005.
24. J. K. Eng, A. L. McCormack, and J. R. Y. III, "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database," Journal ofthe American Society for Mass Spectrometry, vol. 5, no. 11, pp. 976-989, 1994.
25. S. Tanner, P. A. Pevzner, and V. Bafna, "Unrestrictive identification of post-translational modifications through peptide mass spectrometry," Nat. Protocols, vol. 1, pp. 67-72, 06 2006.
26. D. L. Tabb, M. J. MacCoss, C. C. Wu, S. D. Anderson, and J. R. Yates, "Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility," Analytical Chemistry, vol. 75, no. 10, pp. 2470-2477, 2003. PMID: 12918992.
27. A. M. Frank, N. Bandeira, Z. Shen, S. Tanner, S. P. Briggs, R. D. Smith, and P.A. Pevzner, "Clustering Millions of Tandem Mass Spectra," Journal of Proteome Research, vol. 7, pp. 113-122, January 2008.
28. N. Bandeira, D. Tsur, A. Frank, and P.A. Pevzner, "Protein identification by spectral networks analysis," Proceedings of the National Academy of Sciences, vol. 104, no. 15, pp. 6140-6145, 2007.
29. M. M. Rinschen, M.-J. Yu, G. Wang, E. S. Boja, J. D. Hoffert, T. Pisitkun, and M. A. Knepper, "Quantitative phosphoproteomic analysis reveals vasopressin v2-receptordependent signaling pathways in renal collecting duct cells," Proceedings of the National Academy of Sciences, vol. 107, no. 8, pp. 3882-3887, 2010.
30. Hoffert, Jason D. and Pisitkun, Trairak and Saeed, Fahad and Song, Jae H. and Chou, Chung-Lin and Knepper, Mark A., "Dynamics of the G Protein-coupled Vasopressin V2 Receptor Signaling Network Revealed by Quantitative Phosphoproteornics," Molecular &Cellular Proteomics, vol. 11, no. 2, 2012.
31. Schulz-Trieglaff, Ole and Pfeifer, Nico and Gropl, Clemens and Kohlbacher, Oliver and Reinert, Knut, "LC-MSsim-a simulation software for liquid chromatography mass spectrometry data," BMC Bioinformatics, vol. 9, no. 1, 2008.
32. Bielow, Chris and Aiche, Stephan and Andreotti, Sandro and Reinert, Knut, "MSSimulator: Simulation of Mass Spectrometry Data," Journal of Proteome Research, vol. 10, no. 7, 2011.
33. Saeed, Fahad and Pisitkun, Trairak and Hoffert, Jason D. and Knepper, Mark A., "High Performance Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data using Multicore Systems," Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 2012.
34. Saeed, Fahad and Pisitkun, Trairak and Knepper, Mark A. and Hoffert, Jason D., "An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data," Proc. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2012.