Prince:BYU Lipidomics Team: Difference between revisions
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==Notes== | ==Notes== | ||
Mackay, 12/28/2011, with PE standard is solvent with ammonium acetate using positive-ion mode: | |||
*CID produced only ammonia losses for any normalized collision energy. | *CID produced only ammonia losses for any normalized collision energy. | ||
*HCD produced ethanolamine losses; nCE at 35% was sufficient. At an isolation window of 1 amu, no fragments were isolated; at 1.5 amu fragments were isolated but spectra were noisy; at 2 amu, fragments were isolated with little noise; at 3 amu, fragments were isolated with no noise. | *HCD produced ethanolamine losses; nCE at 35% was sufficient. At an isolation window of 1 amu, no fragments were isolated; at 1.5 amu fragments were isolated but spectra were noisy; at 2 amu, fragments were isolated with little noise; at 3 amu, fragments were isolated with no noise. | ||
Revision as of 10:36, 4 January 2012
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
- LipidXplorer
- PCA analysis in R
- Latest is to use the intensities reported by LipidXplorer in R.
For Running Standards:
- SOLVENT: chloroform:methanol:2-propanol (2:1:1, v/v/v)
- IONIZATION AID: 18 mM ammonium acetate
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
Background
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).
Membrane lipid composition. [3]
Lipid rafts. [4]
Mass Spectrometry
Practical essentials of ESI.* [5]
Solid tutorial review on mass spec "-omics."* [6]
General approaches to lipidomics. [7]
Recent advances (2011) in MS lipidomics. [8]
Advances is mass spectrometry lipidomics. [9]
Specific lipid classes and MS. [10]
Basics of ESI and ESI intrasource separation shotgun lipidomics.** [11] [12]
Factors influencing ESI intrasource separation. [13]
Multiple precursor ion and neutral loss scanning with data-dependent acquisition. [16]
Top-down lipidomic strategy.** [17]
Top-down lipidomic analysis of blood plasma.* [18]
Quantitative shotgun yeast lipidomics. [19] [20]
Quantitative shotgun membrane lipidomics, including glycosphingolipids. [21]
LTQ Orbitrap shotgun lipidomics. [22]
Tandem Mass Spectrometry
Membrane lipids. [23]
Sphingolipids [26]
Glycosphingolipids [27]
Bioinformatics
Informatics and computational strategies for the study of lipids. [28]
Computational lipidomics. [29]
Chemometrics for Metabonomics. [30] [31]
LipidXplorer: open-source lipid identification and quantification software. [32]
- LipidXplorer wiki. [33]
PCA package. [34]
K-OPLS package. [35]
S-plot. [36]
Special Journal Issues on Lipidomics
Journal of Chromatography B, Volume 877, Issue 26. [37]
Prostaglandins and Other Lipid Mediators, Volume 77. [38]
European Journal of Lipid Science and Technology, Volume 111, Issue 1. [39]
Frontiers in Bioscience, Volume 12, January 2007.
Methods in Enzymology, Volume 432, 2007.
Signalling Lipids and Lipidomics
Lipid rafts and GPCRs. [40]
Eicosanoid biology. [41]
Sphingolipid signalling. [42]
Lipid mediators in health and disease. [43]
Lipid mediators for inflammation resolution. [44]
Eicosanoid lipidomics. [45]
Bioactive lipidomics. [46]
Lipid mediator informatics-lipidomics. [47]
Mediator lipidomics. [48]
LC/MS Lipidomics
HPLC/MS of complex lipidomes. [49]
UPLC/MS of complex lipidomes. [50]
Notes
Mackay, 12/28/2011, with PE standard is solvent with ammonium acetate using positive-ion mode:
- CID produced only ammonia losses for any normalized collision energy.
- HCD produced ethanolamine losses; nCE at 35% was sufficient. At an isolation window of 1 amu, no fragments were isolated; at 1.5 amu fragments were isolated but spectra were noisy; at 2 amu, fragments were isolated with little noise; at 3 amu, fragments were isolated with no noise.
Group Members
Current
- Mackay Merrill
- Landon Weist
- Rob Roden
- Greg Jackson
- Matthew Linford
- Craig Thulin
- Steven Wood
- John Prince
Former or Associated
- Jennifer MacDonald
- Jonathan Lee
- Vinod Chaudhary
- Steven Herron
- Mary Blackburn
- Daniel Edmondson
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.
