LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets

JCI Insight

Volumn 2, Issue 7, 2017, Pages

  O’connor, Anne ^a   Brasher, Christopher J ^a   Slatter, David A ^a   Meckelmann, Sven W ^a   Hawksworth, Jade I ^a   Allen, Stuart M ^b   O’donnell, Valerie B ^a  

^a CARDIFF UNIVERSITY SCHOOL OF MEDICINE   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85033583658     PISSN: None     EISSN: 23793708     Source Type: Journal    
DOI: 10.1172/jci.insight.91634     Document Type: Article

References (42)

1. Hinterwirth H, Stegemann C, Mayr M. Lipidomics: quest for molecular lipid biomarkers in cardiovascular disease. Circ Cardiovasc Genet. 2014;7(6):941–954.
2. Wenk MR. The emerging field of lipidomics. Nat Rev Drug Discov. 2005;4(7):594–610.
3. Oresic M, Hänninen VA, Vidal-Puig A. Lipidomics: a new window to biomedical frontiers. Trends Biotechnol. 2008;26(12):647–652.
4. Han X. Neurolipidomics: challenges and developments. Front Biosci. 2007;12:2601–2615.
5. Kind T, Liu KH, Lee DY, DeFelice B, Meissen JK, Fiehn O. LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat Methods. 2013;10(8):755–758.
6. Kochen MA, et al. Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification. Anal Chem. 2016;88(11):5733–5741.
7. Wenk MR. Lipidomics: new tools and applications. Cell. 2010;143(6):888–895.
8. Shevchenko A, Simons K. Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol. 2010;11(8):593–598.
9. Slatter DA, et al. Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation. Cell Metab. 2016;23(5):930–944.
10. Tsugawa H, et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015;12(6):523–526.
11. Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006;78(3):779–787.
12. Pluskal T, Castillo S, Villar-Briones A, Oresic M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics. 2010;11:395.
13. Lommen A, Kools HJ. MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware. Metabolomics. 2012;8(4):719–726.
14. Sturm M, et al. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008;9:163.
15. Orešič M. Informatics and computational strategies for the study of lipids. Biochim Biophys Acta. 2011;1811(11):991–999.
16. Codrea MC, Jiménez CR, Heringa J, Marchiori E. Tools for computational processing of LC-MS datasets: a user’s perspective. Comput Methods Programs Biomed. 2007;86(3):281–290.
17. Pietiläinen KH, et al. Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects-a monozygotic twin study. PLoS ONE. 2007;2(2):e218.
18. Hilvo M, et al. Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression. Cancer Res. 2011;71(9):3236–3245.
19. Layre E, et al. A comparative lipidomics platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem Biol. 2011;18(12):1537–1549.
20. de Grauw JC, van de Lest CH, van Weeren PR. A targeted lipidomics approach to the study of eicosanoid release in synovial joints. Arthritis Res Ther. 2011;13(4):R123.
21. Paglia G, et al. Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem. 2015;87(2):1137–1144.
22. Haoula Z, et al. Lipidomic analysis of plasma samples from women with polycystic ovary syndrome. Metabolomics. 2015;11(3):657–666.
23. Keller BO, Sui J, Young AB, Whittal RM. Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta. 2008;627(1):71–81.
24. Tong H, Bell D, Tabei K, Siegel MM. Automated data massaging, interpretation, and e-mailing modules for high throughput open access mass spectrometry. J Am Soc Mass Spectrom. 1999;10(11):1174–1187.
25. ESI+ Common Background Ions. Waters Web site. http://www.waters.com/webassets/cms/support/docs/bckgrnd_ion_mstr_lst_4_13_2010.pdf. Accessed March 21, 2017.
26. Barwick V, Langley J, Mallet T, Stein B, Webb K. Best Practice Guide for Generating Mass Spectra. LGC Limited; 2006.
27. Foster JM, et al. LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PLoS ONE. 2013;8(5):e61951.
28. Wishart DS, et al. HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res. 2013;41(Database issue):D801–D807.
29. Fahy E, Sud M, Cotter D, Subramaniam S. LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007;35(Web Server issue):W606–W612.
30. Fahy E, et al. Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res. 2009;50 Suppl:S9–14.
31. Keich U, Kertesz-Farkas A, Noble WS. Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics. J Proteome Res. 2015;14(8):3148–3161.
32. Jeong K, Kim S, Bandeira N. False discovery rates in spectral identification. BMC Bioinformatics. 2012;13 Suppl 16:S2.
33. Elias JE, Gygi SP. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol. 2010;604:55–71.
34. Quehenberger O, et al. Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010;51(11):3299–3305.
35. Caesar R, Nygren H, Orešič M, Bäckhed F. Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism. J Lipid Res. 2016;57(3):474–481.
36. Thomas CP, et al. Phospholipid-esterified eicosanoids are generated in agonist-activated human platelets and enhance tissue factor-dependent thrombin generation. J Biol Chem. 2010;285(10):6891–6903.
37. Jackson SP, Yap CL, Anderson KE. Phosphoinositide 3-kinases and the regulation of platelet function. Biochem Soc Trans. 2004;32(Pt 2):387–392.
38. Min SH, Abrams CS. Regulation of platelet plug formation by phosphoinositide metabolism. Blood. 2013;122(8):1358–1365.
39. Purvis JE, Chatterjee MS, Brass LF, Diamond SL. A molecular signaling model of platelet phosphoinositide and calcium regulation during homeostasis and P2Y1 activation. Blood. 2008;112(10):4069–4079.
40. Mayor S, Riezman H. Sorting GPI-anchored proteins. Nat Rev Mol Cell Biol. 2004;5(2):110–120.
41. Hurley S, Smith DH, Thiel SU. FASoft: A system for discrete channel frequency assignment. Radio Sci. 1997;32:1921–1939.
42. Tautenhahn R, Böttcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 2008;9:504.