Prince:BYU Lipidomics Team: Difference between revisions
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Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/] | Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/] | ||
Basics of ESI and intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full] | Basics of ESI and ESI intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full] | ||
Factors influencing ESI intrasource separation. [http://www.sciencedirect.com/science/article/pii/S1044030505009591] | |||
*Sample preparation for intrasource separation.** [http://www.sciencedirect.com/science/article/pii/S0003269704003112] [http://pubs.acs.org/doi/full/10.1021/bi051908a] | *Sample preparation for intrasource separation.** [http://www.sciencedirect.com/science/article/pii/S0003269704003112] [http://pubs.acs.org/doi/full/10.1021/bi051908a] | ||
Revision as of 10:11, 29 June 2011
Basic Protocol
- Get sample from almost any source
- Extraction (both methods use Folch reagent [2:1 chloroform:methanol])
- use Kaluzne method
- trying to implement Bligh & Dyer (gold standard)
- MTBE Extraction [1]
- Mass Spectrometry
- ESI-Agilent TOF
- Tandem MS-Q-Star (8-10am)
- Analysis
- Matlab (particular toolbox?) PCA analysis
Main analytes are phosphatidylcholine and phosphatidylethanolamine. Analytes in (-) mode would be phosphatidylserines and phosphatidylethanolamines (which are expected to have stronger signal in - mode). Typical number of analytes?
FAME-GC associated with Craig Thulin and UVU.
Literature
Lipidomics
Lipidomics and lipid profiling in metabolomics [2]
Lipidomics: coming to grips with lipid diversity, Nature Reviews Molecular Cell Biology, 11, 593–598 (1 August 2010)
Mass Spectrometry
Practical essentials of ESI.* [3]
Solid tutorial review on mass spec "-omics."* [4]
General approaches to lipidomics. [5]
Recent advances (2011) in MS lipidomics. [6]
Basics of ESI and ESI intrasource separation shotgun lipidomics.** [7]
Factors influencing ESI intrasource separation. [8]
Multiple precursor ion and neutral loss scanning with data-dependent acquisition. [11]
Top-down lipidomic strategy.** [12]
Top-down lipidomic analysis of blood plasma.* [13]
Yeast quantitative shotgun lipidomics. [14] [15]
Bioinformatics
Informatics and computational strategies for the study of lipids. [16]
Computational lipidomics. [17]
Chemometrics for Metabonomics. [18] [19]
LipidXplorer: open-source lipid identification and quantification software. [20]
PCA package. [21]
K-OPLS package. [22]
S-plot. [23]
Special Journal Issues on Lipidomics
Journal of Chromatography B, Volume 877, Issue 26, [24]
Prostaglandins and Other Lipid Mediators, Volume 77 [25]
European Journal of Lipid Science and Technology, Volume 111, Issue 1 [26]
Frontiers in Bioscience, Volume 12, January 2007
Methods in Enzymology, Volume 432, 2007
Signalling Lipids and Lipidomics
Sphingolipid signalling. [27]
Lipid mediators in health and disease. [28]
Lipid mediators for inflammation resolution. [29]
Eicosanoid lipidomics. [30]
Bioactive lipidomics. [31]
Lipid mediator informatics-lipidomics. [32]
Mediator lipidomics. [33]
Group Members
Current
- Mary Blackburn
- Mackay Merrill
- Dean Flanders
- Landon Weist
- Rob Roden
- Greg Jackson
- Daniel Edmondson
- Matthew Linford
- Craig Thulin
- Steven Wood
- John Prince
Former or Associated
- Jennifer MacDonald
- Jonathan Lee
- Vinod Chaudhary
- Steven Herron
Relevant Publications
- Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, Fantin VR, Jang HG, Jin S, Keenan MC, Marks KM, Prins RM, Ward PS, Yen KE, Liau LM, Rabinowitz JD, Cantley LC, Thompson CB, Vander Heiden MG, and Su SM. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2009 Dec 10;462(7274):739-44. DOI:10.1038/nature08617 |
This has a great protocol for negative ion mode extraction and analysis on the Orbitrap.
