Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014, Article ID 818670, 8 pages
http://dx.doi.org/10.1155/2014/818670
Research Article

Predicting Glycerophosphoinositol Identities in Lipidomic Datasets Using VaLID (Visualization and Phospholipid Identification)—An Online Bioinformatic Search Engine

1Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5
2Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5
3CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5
4Carleton Immersive Media Studio, Azrieli School of Architecture and Urbanism, Carleton University, ON, Canada K1S 5B6

Received 6 November 2013; Accepted 23 December 2013; Published 20 February 2014

Academic Editor: Tao Huang

Copyright © 2014 Graeme S. V. McDowell et al. 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.

Linked References

  1. S. A. L. Bennett, N. Valenzuela, H. Xu et al., “Using neurolipidomics to identify phospholipid mediators of synaptic (dys)function in Alzheimer's Disease,” Frontiers in Physiology, vol. 4, p. 168, 2013. View at Google Scholar
  2. C. Le Roy and J. L. Wrana, “Clathrin- and non-clathrin-mediated endocytic regulation of cell signalling,” Nature Reviews Molecular Cell Biology, vol. 6, no. 2, pp. 112–126, 2005. View at Publisher · View at Google Scholar · View at Scopus
  3. L. C. Skwarek and G. L. Boulianne, “Great Expectations for PIP: phosphoinositides as regulators of signaling during development and disease,” Developmental Cell, vol. 16, no. 1, pp. 12–20, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Piomelli, G. Astarita, and R. Rapaka, “A neuroscientist's guide to lipidomics,” Nature Reviews Neuroscience, vol. 8, no. 10, pp. 743–754, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. H. A. Brown and R. C. Murphy, “Working towards an exegesis for lipids in biology,” Nature Chemical Biology, vol. 5, no. 9, pp. 602–606, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. M. Bou Khalil, W. Hou, H. Zhou et al., “Lipidomics era: accomplishments and challenges,” Mass Spectrometry Reviews, vol. 29, no. 6, pp. 877–929, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. H. Xu, N. Valenzuela, S. Fai et al., “Targeted lipidomics—advances in profiling lysophosphocholine and platelet-activating factor second messengers,” FEBS Journal, vol. 280, pp. 5652–5667, 2013. View at Google Scholar
  8. X. Han, K. Yang, and R. W. Gross, “Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses,” Mass Spectrometry Reviews, vol. 31, no. 1, pp. 134–178, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. P. S. Niemelä, S. Castillo, M. Sysi-Aho, and M. Orešič, “Bioinformatics and computational methods for lipidomics,” Journal of Chromatography B, vol. 877, no. 26, pp. 2855–2862, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. W. Hou, H. Zhou, M. B. Khalil, D. Seebun, S. A. L. Bennett, and D. Figeys, “Lyso-form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids,” Rapid Communications in Mass Spectrometry, vol. 25, no. 1, pp. 205–217, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. J. C. Smith, W. Hou, S. N. Whitehead, M. Ethier, S. A. L. Bennett, and D. Figeys, “Identification of lysophosphatidylcholine (LPC) and platelet activating factor (PAF) from PC12 cells and mouse cortex using liquid chromatography/multi-stage mass spectrometry (LC/MS3),” Rapid Communications in Mass Spectrometry, vol. 22, no. 22, pp. 3579–3587, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. S. N. Whitehead, W. Hou, M. Ethier et al., “Identification and quantitation of changes in the platelet activating factor family of glycerophospholipids over the course of neuronal differentiation by high-performance liquid chromatography electrospray ionization tandem mass spectrometry,” Analytical Chemistry, vol. 79, no. 22, pp. 8539–8548, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. C.-H. Tang, P.-N. Tsao, C.-Y. Chen, M.-S. Shiao, W.-H. Wang, and C.-Y. Lin, “Glycerophosphocholine molecular species profiling in the biological tissue using UPLC/MS/MS,” Journal of Chromatography B, vol. 879, no. 22, pp. 2095–2106, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. E. Fahy, D. Cotter, M. Sud, and S. Subramaniam, “Lipid classification, structures and tools,” Biochimica et Biophysica Acta, vol. 1811, no. 11, pp. 637–647, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. U. Igbavboa, J. Hamilton, H.-Y. Kim, G. Y. Sun, and W. G. Wood, “A new role for apolipoprotein E: modulating transport of polyunsaturated phospholipid molecular species in synaptic plasma membranes,” Journal of Neurochemistry, vol. 80, no. 2, pp. 255–261, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. M. J. Sharman, G. Shui, A. Z. Fernandis et al., “Profiling brain and plasma lipids in human apoe ε2, ε3, and ε4 knock-in mice using electrospray ionization mass spectrometry,” Journal of Alzheimer's Disease, vol. 20, no. 1, pp. 105–111, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. R. B. Chan, T. G. Oliveira, E. P. Cortes et al., “Comparative lipidomic analysis of mouse and human brain with Alzheimer disease,” The Journal of Biological Chemistry, vol. 287, no. 4, pp. 2678–2688, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. P. H. Axelsen and R. C. Murphy, “Quantitative analysis of phospholipids containing arachidonate and docosahexaenoate chains in microdissected regions of mouse brain,” Journal of Lipid Research, vol. 51, no. 3, pp. 660–671, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Osawa, S. Funamoto, M. Nobuhara et al., “Phosphoinositides suppress γ-secretase in both the detergent-soluble and -insoluble states,” The Journal of Biological Chemistry, vol. 283, no. 28, pp. 19283–19292, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. E. Fahy, D. Cotter, R. Byrnes et al., “Bioinformatics for Lipidomics,” Methods in Enzymology, vol. 432, pp. 247–273, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. T. Kind, K. H. Liu, Y. Lee do et al., “LipidBlast in silico tandem mass spectrometry database for lipid identification,” Nature Methods, vol. 10, no. 8, pp. 755–758, 2013. View at Google Scholar
  22. A. P. Blanchard, G. S. McDowell, N. Valenzuela et al., “Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass,” Bioinformatics, vol. 29, no. 2, pp. 284–285, 2013. View at Google Scholar
  23. J. R. De Laeter, J. K. Böhlke, P. De Bièvre et al., “Atomic weights of the elements: review 2000,” Pure and Applied Chemistry, vol. 75, no. 6, pp. 683–800, 2003. View at Google Scholar
  24. G. Di Paolo and P. De Camilli, “Phosphoinositides in cell regulation and membrane dynamics,” Nature, vol. 443, no. 7112, pp. 651–657, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Miyazaki and J. M. Ntambi, “Fatty acid desaturation and chain elongation in mammals,” in Biochemistry of Lipids, Lipoproteins and Membranes, D. E. Vance and J. E. Vance, Eds., pp. 191–211, Elsevier, 2008. View at Google Scholar
  26. E. Fahy, S. Subramaniam, R. C. Murphy et al., “Update of the LIPID MAPS comprehensive classification system for lipids,” Journal of Lipid Research, vol. 50, pp. S9–S14, 2009. View at Publisher · View at Google Scholar · View at Scopus