Prince:BYU Lipidomics Team

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(Bioinformatics)
(Mass Spectrometry)
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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/]
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Basics of ESI and intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full]
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Basics of ESI and ESI intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full]
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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 12:11, 29 June 2011

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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
    • 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]

  • Sample preparation for intrasource separation.** [9] [10]

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

Error fetching PMID 19935646:
  1. Error fetching PMID 19935646: [P1]
    This has a great protocol for negative ion mode extraction and analysis on the Orbitrap.

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