Mediator-lipidomics: Databases and search algorithms for PUFA-derived mediators

Journal of Lipid Research

Volumn 46, Issue 4, 2005, Pages 790-802

  Lu, Yan ^a   Hong, Song ^a   Tjonahen, Eric ^a   Serhan, Charles N ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Cognoscitive contrast angle algorithm and database; Docosatrienes; Eicosanoids; Inflammation; Neuroprotectins; Polyunsaturated fatty acid; Resolution; Resolvins; Theoretical database and algorithm

Indexed keywords

OMEGA 3 FATTY ACID; UNSATURATED FATTY ACID;

ALGORITHM; ANIMAL TISSUE; ARTICLE; FRAGMENTATION REACTION; LIQUID CHROMATOGRAPHY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; TANDEM MASS SPECTROMETRY; ULTRAVIOLET RADIATION; ANIMAL; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE; ISOLATION AND PURIFICATION; LIPID METABOLISM; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; RABBIT;

ALGORITHMS; ANIMALS; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; FATTY ACIDS, UNSATURATED; LIPID METABOLISM; MASS SPECTROMETRY; MICE; MOLECULAR STRUCTURE; RABBITS;

EID: 21744442925     PISSN: 00222275     EISSN: 15397262     Source Type: Journal    
DOI: 10.1194/jlr.D400020-JLR200     Document Type: Article

References (27)

1. Serhan, C. N. 2002. Endogenous chemical mediators in anti-inflammation and pro-resolution. Curr. Med. Chem. 1: 177-192.
2. Serhan, C. N., C. B. Clish, J. Brannon, S. P. Colgan, N. Chiang, and K. Gronert. 2000. Novel functional sets of lipid-derived mediators with antiinflammatory actions generated from omega-3 fatty acids via cyclooxygenase 2-nonsteroidal antiinflammatory drugs and transcellular processing. J. Exp. Med. 192: 1197-1204.
3. Serhan, C. N., S. Hong, K. Gronert, S. P. Colgan, P. R. Devchand, G. Mirick, and R. L. Moussignac. 2002. Resolvins: a family of bioactive products of omega-3 fatty acid transformation circuits initiated by aspirin treatment that counter proinflammation signals. J. Exp. Med. 196: 1025-1037.
4. Hong, S., K. Gronert, P. R. Devchand, R. L. Moussignac, and C. N. Serhan. 2003. Novel docosatrienes and 17S-resolvins generated from docosahexaenoic acid in murine brain, human blood and glial cells: autocoids in anti-inflammation. J. Biol. Chem. 278: 14677-14687.
5. Balazy, M. 2004. Eicosanomics: targeted lipidomics of eicosanoids in biological systems. Prostaglandins Other Lipid Mediat. 73: 173-180.
6. Serhan, C. N. 2005. Mediator lipidomics. Prostaglandins Other Lipid Mediat. In press.
7. Murphy, R. C., J. Fiedler, and J. Hevko. 2001. Analysis of nonvolatile lipids by mass spectrometry. Chem. Rev. 101: 479-526.
8. Griffiths, W. J., Y. Yang, J. Sjoevall, and J. Lindgren. 1996. Electrospray/collision-induced dissociation mass spectrometry of mono-, di- and tri-hydroxylated lipoxygenase products, including leukotrienes of the B-series and lipoxins. Rapid Commun. Mass Spectrom. 10: 183-196.
9. Wenk, M. R., L. Lucast, G. D. Paolo, A. J. Romanelli, S. F. Suchy, R. L. Nussbaum, G. W. Cline, G. I. Shulman, W. McMurray, and P. D. Camilli. 2003. Phosphoinositide profiling in complex, lipid mixtures using electrospray ionization mass spectrometry. Nat. Biotechnol. 21: 813-817.
10. Lee, S. H., M. V. Williams, R. N. DuBois, and L. A. Blair 2003. Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry. Rapid Commun. Mass Spectrom. 17: 2168-2176.
11. 4 ELISA. J. Pharmacol. Exp. Ther. 287: 779-790.
12. th Winter Eicosanoid Conference. Baltimore, MD, March 9-12, 2003).
13. Stein, S. E., and D. R. Scott. 1994. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5: 859-866.
14. Stein, S. E. 1995. Chemical substructure identification by mass spectral library searching. J. Am. Soc. Mass Spectrom. 6: 644-655.
15. Ausloos, P., C. L. Clifton, S. G. Lias, A. I. Mikaya, S. E. Stein, D. V. Tchekhovskoi, O. D. Sparkman, V. Zaikin, and D. Zhu. 1999. The critical evaluation of a comprehensive mass spectral library. J. Am. Soc. Mass Spectrom. 10: 287-299.
16. Mallard, G. W., and J. Reed. 1997. Automated mass spectral deconvolution and identification system. U. S. Department of Commerce, Technology, Administration, National Institute of Standards and Technology, Gaithersburg, MD.
17. Serhan, C. N. 1989. On the relationship between leukotriene and lipoxin production by human neutrophils: evidence for differential metabolism of 15-HETE and 5-HETE. Biochim. Biophys. Acta. 1004: 158-168.
18. Kiss, L., E. Bieniek, N. Weissmann, H. Schütte, U. Sibelius, A. Günther, J. Bier, K. Mayer, K. Henneking, W. Padberg, H. Grimm, W. Seeger, and F. Grimminger. 1998. Simultaneous analysis of 4- and 5-series lipoxygenase and cytochrome P450 products from different biological sources by reversed-phase high-performance liquid chromatographic technique. Anal. Biochem. 261: 16-28.
19. Serhan, C. N., A. Jain, S. Marleau, C. Clish, A. Kantarci, B. Behbehani, S. P. Colgan, G. L. Stahl, A. Merched, N. A. Petasis, L. Chan, and T. E. Van Dyke. 2003. Reduced inflammation and tissue damage in transgenic rabbits overexpressing 15-lipoxygenase and endogenous anti-inflammatory lipid mediators. J. Immunol. 171: 6856-6865.
20. Aliberti, J., S. Hieny, C. R. Sousa, C. N. Serhan, and A. Sher. 2002. Lipoxin-mediated inhibition of IL-12 production by DCs: a mechanism for regulation of microbial immunity. Nat. Immunol. 3: 76-82.
21. Levy, B. D., K. Gronert, C. B. Clish, and C. N. Serhan. 1999. Leukotriene and lipoxin biosynthesis. In Lipid Second Messengers. S. G. Laychock and R. P. Rubin, editors. CRC Press, Roca Raton, FL. 83-111.
22. MassFrontier™ version 2.0 user manual. 1998-2000. HighChem, Ltd., Finnigan Mat, San Jose, CA.
23. McLafferry, F. W., and F. Turecek. 1993. Elemental composition. In Interpretation of Mass Spectra. 4th edition. I. Imfeld and A. Kelly, editors. University Science Books, Mill Valley, CA. 19-34.
24. Wan, K. X., I. Vidavsky, and M. L. Gross. 2002. Comparing similar spectra: from similarity index to spectral contrast angle. J. Am. Soc. Mass Spectrom. 13: 85-88.
25. LCQ™ user manual. 1996. Finnigan Mat, San Jose, CA.
26. McLafferty, F. W., D. A. Stauffer, S. Y. Loh, and C. Wesdemiotis. 1999. Unknown identification using reference mass spectra: quality evaluation of databases. J. Am. Soc. Mass Spectrom. 10: 1229-1240.
27. Wheelan, P., J. A. Zirrolli, and R. C. Murphy. 1996. Electrospray ionization and low energy tandem mass spectrometrv of polyhydroxy unsaturated fatty acids. J. Am. Soc. Mass Spectrom. 7: 140-149.