Prince:BYU Lipidomics Team: Difference between revisions
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==Literature== | ==Literature== | ||
===Lipid Mediator Biochemistry=== | |||
Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html] | Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html] | ||
| Line 26: | Line 28: | ||
Inflammation resolution lipid mediators. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2796.2010.02235.x/full] | Inflammation resolution lipid mediators. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2796.2010.02235.x/full] | ||
===Mass Spectrometry Lipidomics=== | |||
Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/] | Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/] | ||
| Line 44: | Line 48: | ||
Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120] | Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120] | ||
===Bioinformatics=== | |||
Lipidomics and molecular fragmentation query language. [http://genomebiology.com/2011/12/1/R8/ref] | Lipidomics and molecular fragmentation query language. [http://genomebiology.com/2011/12/1/R8/ref] | ||
===Miscellaneous=== | |||
Special issue of ''Journal of Chromatography B'' on lipidomics. [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%237220%232009%23991229973%231383050%23FLA%23&_cdi=7220&_pubType=J&_auth=y&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=fceed4eb1611cde1e48a2b25f4ff62d4] | Special issue of ''Journal of Chromatography B'' on lipidomics. [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%237220%232009%23991229973%231383050%23FLA%23&_cdi=7220&_pubType=J&_auth=y&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=fceed4eb1611cde1e48a2b25f4ff62d4] | ||
Revision as of 12:53, 8 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]
Inflammation resolution lipid mediators. [4]
Mass Spectrometry Lipidomics
Recent advances (2011) in MS lipidomics. [5]
Review covering general aspects of lipidomics. [6]
Review on the basics of ESI and intrasource separation shotgun lipidomics. [7]
AMDMS-SL. [8]
Practical essentials of ESI. [9]
Eicosanoid lipidomics. [10]
Bioactive lipidomics. [11]
Lipid mediator informatics-lipidomics. [12]
Mediator lipidomics. [13]
Bioinformatics
Lipidomics and molecular fragmentation query language. [14]
Miscellaneous
Special issue of Journal of Chromatography B on lipidomics. [15]
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.
