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Journal of Lipid Research, Vol. 46, 790-802, April 2005
Copyright © 2005 by American Society for Biochemistry and Molecular Biology

Methods

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

Yan Lu¹, Song Hong¹, Eric Tjonahen and Charles N. Serhan²

Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115

Published, JLR Papers in Press, February 1, 2005. DOI 10.1194/jlr.D400020-JLR200

The online version of this article (available at http://www.jlr.org) contains supplemental data.

¹ Y. Lu and S. Hong contributed equally to this work.

² To whom correspondence should be addressed. e-mail: cnserhan{at}zeus.bwh.harvard.edu

Lipid mediators (LMs) derived from PUFAs play important roles in health and disease. Databases and search algorithms are crucial, but currently unavailable, for accurate and prompt analysis of LMs via liquid chromatography-ultraviolet-tandem mass spectrometry (LC-UV-MS/MS). A novel algorithm and databases, cognoscitive-contrast-angle algorithm and databases (COCAD), were developed for the identification of LMs based on the integration of standard MS/MS spectra with chromatograms and UV spectra. Segment naming and empirical fragmentation rules were introduced to determine MS/MS ion identities, along with ion intensities used by COCAD in matching the unknown to those of authentic standards. The structures of potential LMs without synthetic and/or authentic products as standards were identified by developing theoretical databases and algorithms based on virtual LC-UV-MS/MS spectra and chromatograms. The performance of these databases and algorithms was tested by identifying LMs in murine tissues.

These results indicate that COCAD has many advantages for profiling and identification of LMs compared with the conventional dot-product algorithm.

Abbreviations: COCAD, cognoscitive-contrast-angle algorithm and databases; CRT, chromatographic retention time; ESI, electrospray ionization; HETE, hydroxy-eicosatetraenoic acid; LC-UV-MS/MS, liquid chromatography-ultraviolet-tandem mass spectrometry; LM, lipid mediator; LTB₄, 5S,12R-dihydroxy-6Z,8E,10E,14Z-eicosatetraenoic acid; LXA₄, 5S,6R,15S-trihydroxy-7E,9E,11Z,13E-trans-11-cis-eicosatetraenoic acid; LXB₄, 5S,14R,15S-trihydroxy-6E,8Z,10E,12E-eicosatetraenoic acid; PGE₂, 11,15S- dihydroxy-9-oxo-prosta-5Z,13E-dien-1-oic acid; PGF₂, 9,11,15S-trihydroxy-prosta-5Z,13E-dien-1-oic acid

Supplementary key words cognoscitive-contrast-angle algorithm and database • theoretical database and algorithm • inflammation • resolution • eicosanoids • resolvins • neuroprotectins • docosatrienes • polyunsaturated fatty acid

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