Prince:BYU Lipidomics Team: Difference between revisions
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AMDMS-SL. [http://pubs.acs.org/doi/abs/10.1021/ac900241u] | AMDMS-SL. [http://pubs.acs.org/doi/abs/10.1021/ac900241u] | ||
Top-down lipidomic strategy.** [http://pubs.acs.org/doi/ | Top-down lipidomic strategy.** [http://pubs.acs.org/doi/full/10.1021/ac062455y] | ||
Blood plasma and top-down lipidomics.* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006261] | Blood plasma and top-down lipidomics.* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006261] | ||
Revision as of 15:11, 17 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
Lipid Mediator Biochemistry
Sphingolipid signalling. [2]
Lipid mediators in health and disease. [3]
Lipid mediators for inflammation resolution. [4]
Mass Spectrometry
Practical essentials of ESI.* [5]
Solid tutorial review on mass spec "-omics."* [6]
Recent advances (2011) in MS lipidomics. [7]
General aspects of lipidomics. [8]
Basics of ESI and intrasource separation shotgun lipidomics.** [9]
Tissue sample preparation for intrasource separation.** [10]
AMDMS-SL. [11]
Top-down lipidomic strategy.** [12]
Blood plasma and top-down lipidomics.* [13]
Yeast quantitative shotgun lipidomics. [14] [15]
Eicosanoid lipidomics. [16]
Bioactive lipidomics. [17]
Lipid mediator informatics-lipidomics. [18]
Mediator lipidomics. [19]
Bioinformatics
S-plot. [22]
PCA package. [23]
K-OPLS package. [24]
Molecular fragmentation query language. [25]
Miscellaneous
Special issue of Journal of Chromatography B on lipidomics. [26]
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.
