Lipidomics: Methods and Protocols

283 Pages·2017·10.101 MB·English

by  Sanjoy K. Bhattacharya (eds.)

Methods in
Molecular Biology 1609
Sanjoy K. Bhattacharya Editor
Lipidomics
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
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Lipidomics
Methods and Protocols
Edited by
Sanjoy K. Bhattacharya
University of Miami, Miami, FL, USA
Editor
Sanjoy K. Bhattacharya
University of Miami
Miami, FL, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6995-1 ISBN 978-1-4939-6996-8 (eBook)
DOI 10.1007/978-1-4939-6996-8
Library of Congress Control Number: 2017939352
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Preface
The history of lipids spans almost four centuries, ever since Techenius Otto suggested the
presence of acidic compound in fat in 1673 (fatty acids: Otto found that the alkali is neu-
tralized by animal fat in the process of making soap). Lipids are the biomolecules that pro-
vide boundary to cells. They are also highly efficient signaling molecules. Every fragment
generated from a lipid can be used for differential signaling in a living cell. Indeed, all major
journals with biological chemistry mandate have a dedicated section for lipid biochemistry
and signaling. Despite a rich history of lipid research that includes perspectives from funda-
mental biology and synthetic organic chemistry, the lipids are not a dominant theme in
most biological laboratories. Only about a 10th or less of the laboratories engaged in bio-
medical research focus on lipid biochemistry. This is also partly due to the lack of easily
available reagents and otherwise due to the lack of awareness about tools, techniques, and
knowledge of protocols. For example, antibodies to most lipids are neither available nor
could be easily generated. However, in the last five years alone, there have been tremendous
advancements in lipid identification and quantification methods. This includes major
advancements in mass spectrometric and bioinformatic methods towards identification and
quantification of lipids. There have also been tremendous advancements in other tech-
niques as well as in generating mice models with specific alterations in lipid metabolizing
enzymes. A wealth of clones of different enzymes and lipid handling proteins also have been
accumulated over a number of years. This book presents an account of areas of utility, tech-
niques, and bioinformatic advancements. We expect this issue of the Methods in Molecular
Biology series to be useful to Biochemists, Molecular Biologists, and Neuroscientists with
interest in Neurology, Ophthalmology, and Vision Science as well as Mass spectrometrists
with interest in disease discovery. This issue includes protocols for lipid isolation for extrac-
tive as well as imaging mass spectrometry. The latter helps in localization of lipids in tissues
and is expected to address issues such as pathologic deposits and fluorescence in correct
cellular layers within the tissue. The protocols also include isolation of specific membranes
and specialized fractionation of subcellular compartments. A number of different high-
throughput mass spectrometric approaches, databases, and bioinformatic analyses methods
are included in protocols. These protocols have been complemented by utilization of meth-
ods in specific problems from fractionated organelles, cells to whole organism. A few pro-
tocols have dealt with computational and functional analysis of lipid metabolizing enzymes
while others about their interaction with proteins including an electrochemical method. It
is hoped that these protocols will come handy in the investigation of biological questions in
many biomedical research laboratories in ensuing future.
Miami, FL, USA Sanjoy K. Bhattacharya
v
Contents
Preface.......................................................... v
Contributors...................................................... ix
1 Lipid Sample Preparation for Biomedical Research ..................... 1
Ravin Sajnani and Katyayini Aribindi
2 Lipid Extraction Techniques for Stable Isotope Analysis
and Ecological Assays ........................................... 9
Kyle H. Elliott, James D. Roth, and Kevin Crook
3 Isolation of Lipid Raft Proteins from CD133+ Cancer Stem Cells . . . . . . . . . . 25
Vineet K. Gupta and Sulagna Banerjee
4 Isolation of Neuronal Synaptic Membranes by Sucrose
Gradient Centrifugation ......................................... 33
Blake R. Hopiavuori, Dustin R. Masser, Joseph L. Wilkerson,
Richard S. Brush, Nawajes A. Mandal, Robert E. Anderson,
and Willard M. Freeman
5 Sample Preparation and Analysis for Imaging Mass Spectrometry .......... 43
Genea Edwards, Annia Mesa, Robert I. Vazquez-Padron,
Jane-Marie Kowalski, and Sanjoy K. Bhattacharya
6 Direct Measurement of Free and Esterified Cholesterol Mass
in Differentiated Human Podocytes: A TLC and Enzymatic
Assay-Based Method............................................ 51
Christopher E. Pedigo, Sandra M. Merscher, and Alessia Fornoni
7 High-Performance Chromatographic Separation of Cerebrosides .......... 57
Renaud Sicard and Ralf Landgraf
8 Lipid Identification by Untargeted Tandem Mass Spectrometry
Coupled with Ultra-High-Pressure Liquid Chromatography.............. 65
Gabriel B. Gugiu
9 Utility of Moderate and High-Resolution Mass Spectrometry
for Class-Specific Lipid Identification and Quantification................. 83
Maria del Carmen Piqueras
10 A Robust Lipidomics Workflow for Mammalian Cells, Plasma,
and Tissue Using Liquid-Chromatography High- Resolution Tandem
Mass Spectrometry ............................................. 91
Candice Z. Ulmer, Rainey E. Patterson, Jeremy P. Koelmel,
Timothy J. Garrett, and Richard A. Yost
11 Combined Use of MALDI-TOF Mass Spectrometry
and 31P NMR Spectroscopy for Analysis of Phospholipids ................ 107
Jenny Schröter, Yulia Popkova, Rosmarie Süß, and Jürgen Schiller
vii
viii Contents
12 Global Monitoring of the Mammalian Lipidome by Quantitative
Shotgun Lipidomics ............................................ 123
Inger Ødum Nielsen, Kenji Maeda, and Mesut Bilgin
13 Bioinformatics Pertinent to Lipid Analysis in Biological Samples ........... 141
Justin Ma, Ulises Arbelo, Yenifer Guerra, Katyayini Aribindi,
Sanjoy K. Bhattacharya, and Daniel Pelaez
14 LC–MS-Based Lipidomics and Automated Identification
of Lipids Using the LipidBlast In-Silico MS/MS Library................. 149
Tomas Cajka and Oliver Fiehn
15 Single-Step Capture and Targeted Metabolomics of Alkyl-Q uinolones
in Outer Membrane Vesicles of Pseudomonas aeruginosa ................. 171
Pallavi Lahiri and Dipankar Ghosh
16 Analysis of Fatty Acid and Cholesterol Content from Detergent-Resistant
and Detergent-Free Membrane Microdomains ........................ 185
Mark E. McClellan and Michael H. Elliott
17 Computational Functional Analysis of Lipid Metabolic Enzymes........... 195
Carolina Bagnato, Arjen Ten Have, María B. Prados,
and María V. Beligni
18 Isoprenylation of Monomeric GTPases in Human Trabecular
Meshwork Cells ............................................... 217
Evan B. Stubbs Jr.
19 Purification and Validation of Lipid Transfer Proteins ................... 231
Matti A. Kjellberg, Anders P.E. Backman, Anna Möuts, and Peter Mattjus
20 Incorporation of Artificial Lipid-Anchored Proteins into Cultured
Mammalian Cells .............................................. 241
Rania Leventis and John R. Silvius
21 Sonication-Based Basic Protocol for Liposome Synthesis................. 255
Roberto Mendez and Santanu Banerjee
22 On Electrochemical Methods for Determination
of Protein- Lipid Interaction ...................................... 261
Zhiping Hu and Yanli Mao
23 Angiogenesis Model of Cornea to Understand the Role of Sphingosine
1-Phosphate .................................................. 267
Joseph L. Wilkerson and Nawajes A. Mandal
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Contributors
RobeRt e. AndeRson • Oklahoma Center for Neuroscience, University of Oklahoma Health
Sciences Center, Oklahoma City, OK, USA; Department of Ophthalmology, Dean McGee
Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA;
Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma
City, OK, USA
Ulises ARbelo • Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
KAtyAyini ARibindi • Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
AndeRs P.e. bAcKmAn • Department of Biochemistry, Faculty of Science and Engineering,
Åbo Akademi University, Turku, Finland
cARolinA bAgnAto • Instituto de Energía y Desarrollo Sustentable – Comisión Nacional de
Energía Atómica, Centro Atómico Bariloche, S .C . de Bariloche, Río Negro, Argentina
sAntAnU bAneRjee • Division of Surgical Oncology, Department of Surgery, Sylvester
Comprehensive Cancer Center, Miller School of Medicine, University of Miami,
Miami, FL, USA
sUlAgnA bAneRjee • Division of Surgical Oncology, Department of Surgery, Miller School of
Medicine, University of Miami, Miami, FL, USA
mARíA V. beligni • Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP),
Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata,
Mar del Plata, Argentina
sAnjoy K. bhAttAchARyA • Bascom Palmer Eye Institute, University of Miami, Miami, FL,
USA; Department of Biochemistry and Molecular Biology, University of Miami, Miami,
FL, USA
mesUt bilgin • Cell Death and Metabolism Unit, Center for Autophagy, Recycling and
Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
RichARd s. bRUsh • Department of Ophthalmology, Dean McGee Eye Institute,
University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
tomAs cAjKA • UC Davis Genome Center—Metabolomics, University of California-D avis,
Davis, CA, USA
KeVin cRooK • Department of Biological Sciences, University of Manitoba, Winnipeg,
Manitoba, Canada
geneA edwARds • Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA;
Department of Biochemistry and Molecular Biology, University of Miami, Miami,
FL, USA
Kyle h. elliott • Department of Natural Resource Sciences, McGill University,
Ste . Anne-de-Bellevue, Quebec, Canada
michAel h. elliott • Department of Ophthalmology, Dean McGee Eye Institute,
University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA;
Department of Physiology, University of Oklahoma Health Sciences Center,
Oklahoma City, OK, USA; Oklahoma Center for Neuroscience, University of Oklahoma
Health Sciences Center, Oklahoma City, OK, USA
ix
x Contributors
oliVeR Fiehn • UC Davis Genome Center—Metabolomics, University of California-D avis,
Davis, CA, USA; Biochemistry Department, King Abdulaziz University, Jeddah,
Saudi Arabia
AlessiA FoRnoni • Division of Nephrology and Hypertension and Peggy and Harold Katz
Drug Discovery Center, Miller School of Medicine, University of Miami, Miami, FL, USA
willARd m. FReemAn • Oklahoma Center for Neuroscience, University of Oklahoma
Health Sciences Center, Oklahoma City, OK, USA; Department of Physiology,
University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA;
Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center,
Oklahoma City, OK, USA
timothy j. gARRett • Department of Pathology, Immunology and Laboratory Medicine,
College of Medicine, University of Florida, Gainesville, FL, USA
diPAnKAR ghosh • Special Center for Molecular Medicine, Jawaharlal Nehru University,
New Delhi, India
yeniFeR gUeRRA • Orbital Vision Research Center, Bascom Palmer Eye Institute, University
of Miami, Miami, FL, USA
gAbRiel b. gUgiU • Beckman Research Institute of the City of Hope, Duarte, CA, USA
Vineet K. gUPtA • Division of Surgical Oncology, Department of Surgery, University of
Miami, Miami, FL, USA
ARjen ten hAVe • Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP),
Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar
del Plata, Argentina
blAKe R. hoPiAVUoRi • Oklahoma Center for Neuroscience, University of Oklahoma
Health Sciences Center, Oklahoma City, OK, USA; Department of Ophthalmology,
Dean McGee Eye Institute, University of Oklahoma Health Sciences Center,
Oklahoma City, OK, USA
ZhiPing hU • School of Physics and Electronics, Henan University, Kaifeng, China
mAtti A. KjellbeRg • Biochemistry, Faculty of Science and Engineering, Åbo Akademi
University, Turku, Finland
jeRemy Koelmel • Department of Chemistry, University of Florida, Gainesville, FL, USA
PAUl KowAlsKi • Bruker Daltonics Inc ., Billerica, MA, USA
PAllAVi lAhiRi • Special Center for Molecular Medicine, Jawaharlal Nehru University,
New Delhi, India
RAlF lAndgRAF • Department of Biochemistry and Molecular Biology, Sylvester
Comprehensive Cancer Center, Miller School of Medicine, University of Miami,
Miami, FL, USA
RAniA leVentis • Department of Biochemistry, McGill University, Montreal, Quebec,
Canada
jUstin mA • Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
Kenji mAedA • Cell Death and metabolism Unit, Center for Autophagy, Recycling and
Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
nAwAjes A. mAndAl • Department of Cell Biology, University of Oklahoma Health Sciences
Center, Oklahoma City, OK, USA; Dean McGee Eye Institute, Oklahoma City, OK,
USA; Department of Ophthalmology, University of Tennessee Health Sciences Center,
Memphis, TN, USA; Department of Anatomy and Neurobiology, University of Tennessee
Health Sciences Center, Memphis, TN, USA
yAnli mAo • School of Physics and Electronics, Henan University, Kaifeng, China
Contributors xi
dUstin R. mAsseR • Department of Physiology, University of Oklahoma Health Sciences
Center, Oklahoma City, OK, USA; Reynolds Oklahoma Center on Aging, University of
Oklahoma Health Sciences Center, Oklahoma City, OK, USA
PeteR mAttjUs • Department of Biochemistry, Åbo Akademi University, Turku, Finland
mARK e. mcclellAn • Department of Ophthalmology, Dean McGee Eye Institute,
University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
RobeRto mendeZ • Division of Surgical Oncology, Department of Surgery, Sylvester
Comprehensive Cancer Center, Miller School of Medicine, University of Miami,
Miami, FL, USA
sAndRA m. meRscheR • Division of Nephrology and Hypertension and Peggy and Harold
Katz Drug Discovery Center, Miller School of Medicine, University of Miami, Miami,
FL, USA
AnniA mesA • Department of Surgery and Vascular Biology Institute, University of Miami,
Miami, FL, USA
AnnA möUts • Department of Biochemistry, Faculty of Science and Engineering, Åbo
Akademi University, Turku, Finland
ingeR ØdUm nielsen • Cell Death and Metabolism Unit, Center for Autophagy, Recycling
and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
RAiney PAtteRson • Department of Chemistry, University of Florida, Gainesville, FL, USA
chRistoPheR e. Pedigo • Division of Nephrology and Hypertension and Peggy and Harold
Katz Drug Discovery Center, Miller School of Medicine, University of Miami, Miami,
FL, USA
dAniel PelAeZ • Orbital Vision Research Center, Bascom Palmer Eye Institute, University
of Miami, Miami, FL, USA
mARiA del cARmen PiqUeRAs • Bascom Palmer Eye Institute, University of Miami, Miami,
FL, USA
yUliA PoPKoVA • Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig,
Germany
mARíA b. PRAdos • Instituto de Energía y Desarrollo Sustentable - Comisión Nacional de
Energía Atómica, Centro Atómico Bariloche, S . C . de Bariloche, Río Negro, Argentina
jAmes d. Roth • Department of Biological Sciences, University of Manitoba, Winnipeg,
Manitoba, Canada
RAVin sAjnAni • Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
jüRgen schilleR • Institute of Medical Physics and Biophysics, University of Leipzig,
Leipzig, Germany
jenny schRöteR • Institute of Medical Physics and Biophysics, University of Leipzig,
Leipzig, Germany
RenAUd sicARd • Department of Biochemistry and Molecular Biology, Sylvester
Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami,
FL, USA
john R. silViUs • Department of Biochemistry, McGill University, Montréal, Quebec,
Canada; McIntyre Medical Sciences, Montréal, QC, Canada
eVAn b. stUbbs jR. • Research Service, Department of Veterans Affairs, Edward Hines Jr .
VA Hospital, Hines, IL, USA; Department of Ophthalmology, Stritch School of Medicine,
Loyola University Chicago, Maywood, IL, USA
RosmARie süss • Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig,
Germany