Prince:BYU Lipidomics Team
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*** Latest is to use the intensities reported by LipidXplorer in R. | *** Latest is to use the intensities reported by LipidXplorer in R. | ||
| - | For Running Standards: | + | For Running Lipid Standards: |
*SOLVENT: chloroform:methanol:2-propanol (2:1:1, v/v/v) | *SOLVENT: chloroform:methanol:2-propanol (2:1:1, v/v/v) | ||
*IONIZATION AID: 18 mM ammonium acetate | *IONIZATION AID: 18 mM ammonium acetate | ||
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UPLC/MS of complex lipidomes. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000097] | UPLC/MS of complex lipidomes. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000097] | ||
| + | |||
| + | ==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== | ==Group Members== | ||
Current revision
Contents |
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 Lipid 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
- Error fetching PMID 19935646:
This has a great protocol for negative ion mode extraction and analysis on the Orbitrap.
