Prince:BYU Lipidomics Team

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(Special Journal Issues on Lipidomics)
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(Basic Protocol)
 
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Line 12: Line 12:
** 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).
Line 21: Line 27:
==Literature==
==Literature==
-
===Lipid Signalling===
+
===Background===
-
Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html]
+
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]
-
Lipid mediators in health and disease. [http://www.annualreviews.org/doi/full/10.1146/annurev.pharmtox.011008.145616]
+
Lipidomics: coming to grips with lipid diversity, ''Nature Reviews Molecular Cell Biology'', 11, 593–598 (1 August 2010).
-
Lipid mediators for inflammation resolution. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2796.2010.02235.x/full]
+
Membrane lipid composition. [http://www.jlr.org/content/26/9/1015.short]
 +
 
 +
Lipid rafts. [http://www.sciencemag.org/content/327/5961/46.full]
===Mass Spectrometry===
===Mass Spectrometry===
Line 34: Line 42:
Solid tutorial review on mass spec "-omics."* [http://pubs.rsc.org/en/Content/ArticleLanding/2009/CS/b618553n]
Solid tutorial review on mass spec "-omics."* [http://pubs.rsc.org/en/Content/ArticleLanding/2009/CS/b618553n]
 +
 +
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/]
-
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]
-
Basics of ESI and intrasource separation shotgun lipidomics.** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20023/full]
+
Factors influencing ESI intrasource separation. [http://www.sciencedirect.com/science/article/pii/S1044030505009591]
-
Tissue sample preparation for intrasource separation.** [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]
-
AMDMS-SL. [http://pubs.acs.org/doi/abs/10.1021/ac900241u]
+
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 strategy.** [http://pubs.acs.org/doi/full/10.1021/ac062455y]
-
Blood plasma and top-down lipidomics.* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006261]
+
Top-down lipidomic analysis of blood plasma.* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006261]
-
Yeast quantitative shotgun lipidomics. [http://www.pnas.org/content/106/7/2136.full] [http://www.pnas.org/content/106/7/2089.full]
+
Quantitative shotgun yeast lipidomics. [http://www.pnas.org/content/106/7/2136.full] [http://www.pnas.org/content/106/7/2089.full]
-
Eicosanoid lipidomics. [http://www.sciencedirect.com/science/article/pii/S0003269705003386]
+
Quantitative shotgun membrane lipidomics, including glycosphingolipids. [http://www.pnas.org/content/108/5/1903.full]
-
Bioactive lipidomics. [http://pubs.acs.org/doi/abs/10.1021/ac1015563]
+
LTQ Orbitrap shotgun lipidomics. [http://pubs.acs.org/doi/full/10.1021/ac102505f]
-
Lipid mediator informatics-lipidomics. [http://www.springerlink.com/content/d322jt33q4j38282/]
+
===Tandem Mass Spectrometry===
-
Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120]
+
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===
===Bioinformatics===
-
Chemometrics. [http://www.springerlink.com/content/rfxn289vnfanw957/] [http://pubs.acs.org/doi/abs/10.1021/pr060594q]
+
Informatics and computational strategies for the study of lipids. [http://pubs.rsc.org/en/Content/ArticleLanding/2008/MB/b715468b]
-
S-plot. [http://pubs.acs.org/doi/abs/10.1021/ac0713510]
+
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]
PCA package. [http://bioinformatics.oxfordjournals.org/content/23/9/1164.short]
Line 69: Line 94:
K-OPLS package. [http://www.biomedcentral.com/1471-2105/9/106]
K-OPLS package. [http://www.biomedcentral.com/1471-2105/9/106]
-
Molecular fragmentation query language. [http://genomebiology.com/2011/12/1/R8/ref]
+
S-plot. [http://pubs.acs.org/doi/abs/10.1021/ac0713510]
===Special Journal Issues on Lipidomics===
===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]
+
''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]
 +
 
 +
Sphingolipid signalling. [http://www.nature.com/nrm/journal/v9/n2/full/nrm2329.html]
 +
 
 +
Lipid mediators in health and disease. [http://www.annualreviews.org/doi/full/10.1146/annurev.pharmtox.011008.145616]
 +
 
 +
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]
 +
 
 +
Bioactive lipidomics. [http://pubs.acs.org/doi/abs/10.1021/ac1015563]
 +
 
 +
Lipid mediator informatics-lipidomics. [http://www.springerlink.com/content/d322jt33q4j38282/]
 +
 
 +
Mediator lipidomics. [http://www.sciencedirect.com/science/article/pii/S0076687907320120]
 +
 
 +
===LC/MS Lipidomics===
 +
 
 +
HPLC/MS of complex lipidomes. [http://pubs.acs.org/doi/full/10.1021/ac048489s]
-
''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]
+
UPLC/MS of complex lipidomes. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000097]
-
''European Journal of Lipid Science and Technology'', Volume 111, Issue 1 [http://onlinelibrary.wiley.com/doi/10.1002/ejlt.v111:1/issuetoc]
+
==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 83: 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 101: Line 159:
* Vinod Chaudhary
* Vinod Chaudhary
* Steven Herron
* Steven Herron
 +
* Mary Blackburn
 +
* Daniel Edmondson
==Relevant Publications==
==Relevant Publications==

Current revision

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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
    • 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

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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