Prince:BYU Lipidomics Team: Difference between revisions

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** Tandem MS-Q-Star (8-10am)
** Tandem MS-Q-Star (8-10am)
* Analysis
* Analysis
** Matlab (particular toolbox?) PCA 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).
Main analytes are phosphatidylcholine and phosphatidylethanolamine.  Analytes in (-) mode would be phosphatidylserines and phosphatidylethanolamines (which are expected to have stronger signal in - mode).
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==Literature==
==Literature==


===Lipid Mediator Biochemistry===
===Background===
 
Lipidomics and lipid profiling in metabolomics. [http://ovidsp.tx.ovid.com/sp-3.4.1b/ovidweb.cgi?&S=ONCGFPGADMDDHPLMNCBLLEJCFILIAA00&Link+Set=S.sh.15.16.21.26|14|sl_10]
 
Lipidomics: coming to grips with lipid diversity, ''Nature Reviews Molecular Cell Biology'', 11, 593–598 (1 August 2010).
 
Membrane lipid composition. [http://www.jlr.org/content/26/9/1015.short]


Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html]
Lipid rafts. [http://www.sciencemag.org/content/327/5961/46.full]
 
===Mass Spectrometry===


Lipid mediators in health and disease. [http://www.annualreviews.org/doi/full/10.1146/annurev.pharmtox.011008.145616]
Practical essentials of ESI.* [http://onlinelibrary.wiley.com/doi/10.1002/mas.10008/full]


Inflammation resolution lipid mediators. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2796.2010.02235.x/full]
Solid tutorial review on mass spec "-omics."* [http://pubs.rsc.org/en/Content/ArticleLanding/2009/CS/b618553n]


===Mass Spectrometry Lipidomics===
General approaches to lipidomics. [http://www.annualreviews.org/doi/pdf/10.1146/annurev-biochem-060409-092612]


Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/]
Recent advances (2011) in MS lipidomics. [http://www.springerlink.com/content/630081030520180w/]


Review covering general aspects of lipidomics. [http://www.annualreviews.org/doi/pdf/10.1146/annurev-biochem-060409-092612]
Advances is mass spectrometry lipidomics. [http://www.annualreviews.org/doi/full/10.1146/annurev.anchem.111808.073705]
 
Specific lipid classes and MS. [http://pubs.acs.org/doi/full/10.1021/cr9900883]
 
Basics of ESI and ESI intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full] [http://www.jlr.org/content/44/6/1071.full]
 
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]
 
Multiple precursor ion and neutral loss scanning with data-dependent acquisition. [http://pubs.acs.org/doi/full/10.1021/ac051605m]
 
Top-down lipidomic strategy.** [http://pubs.acs.org/doi/full/10.1021/ac062455y]
 
Top-down lipidomic analysis of blood plasma.* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006261]
 
Quantitative shotgun yeast lipidomics. [http://www.pnas.org/content/106/7/2136.full] [http://www.pnas.org/content/106/7/2089.full]
 
Quantitative shotgun membrane lipidomics, including glycosphingolipids. [http://www.pnas.org/content/108/5/1903.full]
 
LTQ Orbitrap shotgun lipidomics. [http://pubs.acs.org/doi/full/10.1021/ac102505f]
 
===Tandem Mass Spectrometry===
 
Membrane lipids. [http://www.pnas.org/content/94/6/2339.full]
 
Phospholipids [http://onlinelibrary.wiley.com/doi/10.1002/mas.10061/full] [http://www.sciencedirect.com/science/article/pii/S1570023209001172]
 
Sphingolipids [http://www.sciencedirect.com/science/article/pii/S1044030599001506]
 
Glycosphingolipids [http://www.sciencedirect.com/science/article/pii/S104403050000194X]
 
===Bioinformatics===
 
Informatics and computational strategies for the study of lipids. [http://pubs.rsc.org/en/Content/ArticleLanding/2008/MB/b715468b]
 
Computational lipidomics. [http://molpharm.aspetjournals.org/content/65/4/813.full]
 
Chemometrics for Metabonomics. [http://www.springerlink.com/content/rfxn289vnfanw957/] [http://pubs.acs.org/doi/abs/10.1021/pr060594q]
 
LipidXplorer: open-source lipid identification and quantification software. [http://genomebiology.com/2011/12/1/R8/ref]
*LipidXplorer wiki. [https://wiki.mpi-cbg.de/wiki/lipidx/index.php/Main_Page]
 
PCA package. [http://bioinformatics.oxfordjournals.org/content/23/9/1164.short]
 
K-OPLS package. [http://www.biomedcentral.com/1471-2105/9/106]
 
S-plot. [http://pubs.acs.org/doi/abs/10.1021/ac0713510]
 
===Special Journal Issues on Lipidomics===
 
''Journal of Chromatography B'', Volume 877, Issue 26.  [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]
 
''Prostaglandins and Other Lipid Mediators'', Volume 77. [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=4947&_pubType=J&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=8cad50d7658cd70048a44f088a20f87e&jchunk=77#77]
 
''European Journal of Lipid Science and Technology'', Volume 111, Issue 1. [http://onlinelibrary.wiley.com/doi/10.1002/ejlt.v111:1/issuetoc]
 
''Frontiers in Bioscience'', Volume 12, January 2007.
 
''Methods in Enzymology'', Volume 432, 2007.
 
===Signalling Lipids and Lipidomics===
 
Lipid rafts and GPCRs. [http://onlinelibrary.wiley.com/doi/10.1038/sj.bjp.0705930/full]
 
Eicosanoid biology. [http://www.sciencemag.org/content/294/5548/1871.full]


Review on the basics of ESI and intrasource separation shotgun lipidomics. [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full]
Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html]


AMDMS-SL. [http://pubs.acs.org/doi/abs/10.1021/ac900241u]
Lipid mediators in health and disease. [http://www.annualreviews.org/doi/full/10.1146/annurev.pharmtox.011008.145616]


Practical essentials of ESI. [http://onlinelibrary.wiley.com/doi/10.1002/mas.10008/full]
Lipid mediators for inflammation resolution. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2796.2010.02235.x/full]


Eicosanoid lipidomics. [http://www.sciencedirect.com/science/article/pii/S0003269705003386]
Eicosanoid lipidomics. [http://www.sciencedirect.com/science/article/pii/S0003269705003386]
Line 49: Line 128:
Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120]
Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120]


===Bioinformatics===
===LC/MS Lipidomics===


Lipidomics and molecular fragmentation query language. [http://genomebiology.com/2011/12/1/R8/ref]
HPLC/MS of complex lipidomes. [http://pubs.acs.org/doi/full/10.1021/ac048489s]


===Miscellaneous===
UPLC/MS of complex lipidomes. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000097]


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]
==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==
Line 61: Line 143:
===Current===
===Current===


* Mary Blackburn
 
* Mackay Merrill
* Mackay Merrill
* Dean Flanders
* Landon Weist
* Landon Weist
* Rob Roden
* Rob Roden
* Greg Jackson
* Greg Jackson
* Daniel Edmondson
* Matthew Linford
* Matthew Linford
* Craig Thulin
* Craig Thulin
Line 79: Line 159:
* Vinod Chaudhary
* Vinod Chaudhary
* Steven Herron
* Steven Herron
* Mary Blackburn
* Daniel Edmondson


==Relevant Publications==
==Relevant Publications==

Latest revision as of 10:37, 4 January 2012

Home        Lab Members         Research         Publications         Internal         Mass Spec         Contact        


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]

  • Sample preparation for intrasource separation.** [14] [15]

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]

Phospholipids [24] [25]

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

  1. 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 | PubMed ID:19935646 | HubMed [P1]

    This has a great protocol for negative ion mode extraction and analysis on the Orbitrap.

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