Special Issue "Lipidomics"

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A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (25 December 2011)

Special Issue Editor

Guest Editor
Prof. Dr. Dietrich A. Volmer (Website)

Institute for Bioanalytical Chemistry, Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
Phone: +49 681 302 3433
Interests: metabolomics; lipidomics; proteomics; analytical method development; structure elucidation; quantitative mass spectrometry; ionization mechanisms and gas-phase ion chemistry

Special Issue Information

Dear Colleagues,

Lipids play essential roles in biological systems and many diseases involve changes in lipid metabolism and perturbed lipid pathways. Even though lipid analysis is widely applied in the biological sciences, lipidomics, the detailed and comprehensive analysis of lipids in a cell or tissue, is just at the beginning of its evolution. The chemical complexity of lipids, the difficulties of studying lipids in their biological framework, and the requirement to relate identity and modulation of bioactive lipids with function of genes and proteins require sophisticated high resolution analytical tools for their structural and quantitative analysis. Importantly, lipidomics techniques are increasingly used in studies of biological function, and for diagnostic and prognostic purposes (biomarkers). A considerable amount of research effort goes into data crunching and data mining of lipidomics datasets, which is a key to successful comprehensive exploration of lipidomics data as a function of treatment, genotype or phenotype.

Therefore, this special issue of Metabolites will be dedicated to publishing current advances on bioanalytical techniques, discovery and characterization of novel lipid biomarkers, functional lipidomics, clinical applications of lipidomics, and biocomputational approaches to data-mining and databases of lipidomics datasets.

Prof. Dr. Dietrich Volmer
Guest Editor

Keywords

  • lipidomics
  • lipid metabolism
  • lipid profiling
  • lipid fingerprints
  • global profiling of lipids
  • metabolic phenotype
  • lipid biomarkers
  • mass spectrometry
  • untargeted lipidomics
  • targeted lipidomics
  • data mining
  • databases
  • clinical lipidomics

Published Papers (8 papers)

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Research

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Open AccessArticle Metabolomic and Lipidomic Analysis of the Heart of Peroxisome Proliferator-Activated Receptor-γ Coactivator 1-β Knock Out Mice on a High Fat Diet
Metabolites 2012, 2(2), 366-381; doi:10.3390/metabo2020366
Received: 5 April 2012 / Revised: 21 May 2012 / Accepted: 4 June 2012 / Published: 18 June 2012
Cited by 1 | PDF Full-text (441 KB) | HTML Full-text | XML Full-text
Abstract
The peroxisome proliferator-activated receptor-γ coactivators (PGC-1) are transcriptional coactivators with an important role in mitochondrial biogenesis and regulation of genes involved in the electron transport chain and oxidative phosphorylation in oxidative tissues including cardiac tissue. These coactivators are thought to play a [...] Read more.
The peroxisome proliferator-activated receptor-γ coactivators (PGC-1) are transcriptional coactivators with an important role in mitochondrial biogenesis and regulation of genes involved in the electron transport chain and oxidative phosphorylation in oxidative tissues including cardiac tissue. These coactivators are thought to play a key role in the development of obesity, type 2 diabetes and the metabolic syndrome. In this study we have used a combined metabolomic and lipidomic analysis of cardiac tissue from the PGC-1β null mouse to examine the effects of a high fat diet on this organ. Multivariate statistics readily separated tissue from PGC-1β null mice from their wild type controls either in gender specific models or in combined datasets. This was associated with an increase in creatine and a decrease in taurine in the null mouse, and an increase in myristic acid and a reduction in long chain polyunsaturated fatty acids for both genders. The most profound changes were detected by liquid chromatography mass spectrometry analysis of intact lipids with the tissue from the null mouse having a profound increase in a number of triglycerides. The metabolomic and lipodomic changes indicate PGC-1β has a profound influence on cardiac metabolism. Full article
(This article belongs to the Special Issue Lipidomics)
Open AccessArticle Comparative Lipidomic Profiling of S. cerevisiae and Four Other Hemiascomycetous Yeasts
Metabolites 2012, 2(1), 254-267; doi:10.3390/metabo2010254
Received: 19 January 2012 / Revised: 23 February 2012 / Accepted: 24 February 2012 / Published: 2 March 2012
Cited by 2 | PDF Full-text (528 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Glycerophospholipids (GP) are the building blocks of cellular membranes and play essential roles in cell compartmentation, membrane fluidity or apoptosis. In addition, GPs are sources for multifunctional second messengers. Whereas the genome and proteome of the most intensively studied eukaryotic model organism, [...] Read more.
Glycerophospholipids (GP) are the building blocks of cellular membranes and play essential roles in cell compartmentation, membrane fluidity or apoptosis. In addition, GPs are sources for multifunctional second messengers. Whereas the genome and proteome of the most intensively studied eukaryotic model organism, the baker’s yeast (Saccharomyces cerevisiae), are well characterized, the analysis of its lipid composition is still at the beginning. Moreover, different yeast species can be distinguished on the DNA, RNA and protein level, but it is currently unknown if they can also be differentiated by determination of their GP pattern. Therefore, the GP compositions of five different yeast strains, grown under identical environmental conditions, were elucidated using high performance liquid chromatography coupled to negative electrospray ionization-hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry in single and multistage mode. Using this approach, relative quantification of more than 100 molecular species belonging to nine GP classes was achieved. The comparative lipidomic profiling of Saccharomyces cerevisiae, Saccharomyces bayanus, Kluyveromyces thermotolerans, Pichia angusta, and Yarrowia lipolytica revealed characteristic GP profiles for each strain. However, genetically related yeast strains show similarities in their GP compositions, e.g., Saccharomyces cerevisiae and Saccharomyces bayanus. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessArticle Shotgun Lipidomics by Sequential Precursor Ion Fragmentation on a Hybrid Quadrupole Time-of-Flight Mass Spectrometer
Metabolites 2012, 2(1), 195-213; doi:10.3390/metabo2010195
Received: 24 December 2011 / Revised: 10 February 2012 / Accepted: 13 February 2012 / Published: 20 February 2012
Cited by 25 | PDF Full-text (3041 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Shotgun lipidomics has evolved into a myriad of multi-dimensional strategies for molecular lipid characterization, including bioinformatics tools for mass spectrum interpretation and quantitative measurements to study systems-lipidomics in complex biological extracts. Taking advantage of spectral mass accuracy, scan speed and sensitivity of [...] Read more.
Shotgun lipidomics has evolved into a myriad of multi-dimensional strategies for molecular lipid characterization, including bioinformatics tools for mass spectrum interpretation and quantitative measurements to study systems-lipidomics in complex biological extracts. Taking advantage of spectral mass accuracy, scan speed and sensitivity of improved quadrupole linked time-of-flight mass analyzers, we developed a bias-free global lipid profiling acquisition technique of sequential precursor ion fragmentation called MS/MSALL. This generic information-independent tandem mass spectrometry (MS) technique consists of a Q1 stepped mass isolation window through a set mass range in small increments, fragmenting and recording all product ions and neutral losses. Through the accurate MS and MS/MS information, the molecular lipid species are resolved, including distinction of isobaric and isomeric species, and composed into more precise lipidomic outputs. The method demonstrates good reproducibility and at least 3 orders of dynamic quantification range for isomeric ceramides in human plasma. More than 400 molecular lipids in human plasma were uncovered and quantified in less than 12 min, including acquisitions in both positive and negative polarity modes. We anticipate that the performance of sequential precursor ion fragmentation both in quality and throughput will lead to the uncovering of new avenues throughout the biomedical research community, enhance biomarker discovery and provide novel information target discovery programs as it will prospectively shed new insight into affected metabolic and signaling pathways. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessArticle Quantification of Signaling Lipids by Nano-Electrospray Ionization Tandem Mass Spectrometry (Nano-ESI MS/MS)
Metabolites 2012, 2(1), 57-76; doi:10.3390/metabo2010057
Received: 29 November 2011 / Revised: 4 January 2012 / Accepted: 6 January 2012 / Published: 16 January 2012
Cited by 11 | PDF Full-text (947 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Lipids, such as phosphoinositides (PIPs) and diacylglycerol (DAG), are important signaling intermediates involved in cellular processes such as T cell receptor (TCR)-mediated signal transduction. Here we report identification and quantification of PIP, PIP2 and DAG from crude lipid extracts. Capitalizing on [...] Read more.
Lipids, such as phosphoinositides (PIPs) and diacylglycerol (DAG), are important signaling intermediates involved in cellular processes such as T cell receptor (TCR)-mediated signal transduction. Here we report identification and quantification of PIP, PIP2 and DAG from crude lipid extracts. Capitalizing on the different extraction properties of PIPs and DAGs allowed us to efficiently recover both lipid classes from one sample. Rapid analysis of endogenous signaling molecules was performed by nano-electrospray ionization tandem mass spectrometry (nano-ESI MS/MS), employing lipid class-specific neutral loss and multiple precursor ion scanning for their identification and quantification. Profiling of DAG, PIP and PIP2 molecular species in primary human T cells before and after TCR stimulation resulted in a two-fold increase in DAG levels with a shift towards 1-stearoyl-2-arachidonoyl-DAG in stimulated cells. PIP2 levels were slightly reduced, while PIP levels remained unchanged. Full article
(This article belongs to the Special Issue Lipidomics)

Review

Jump to: Research

Open AccessReview Lipidomics of Glycosphingolipids
Metabolites 2012, 2(1), 134-164; doi:10.3390/metabo2010134
Received: 28 November 2011 / Revised: 27 January 2012 / Accepted: 30 January 2012 / Published: 2 February 2012
Cited by 7 | PDF Full-text (484 KB) | HTML Full-text | XML Full-text
Abstract
Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of [...] Read more.
Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessReview Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms
Metabolites 2012, 2(1), 19-38; doi:10.3390/metabo2010019
Received: 23 November 2011 / Revised: 22 December 2011 / Accepted: 24 December 2011 / Published: 5 January 2012
Cited by 30 | PDF Full-text (411 KB) | HTML Full-text | XML Full-text
Abstract
One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble [...] Read more.
One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble subdivision. Within recent years, lipids are more and more regarded not only as energy storage compounds but also as interactive players in various cellular regulation cycles and thus attain rising interest in the bio-medical community. The field of lipidomics is, on one hand, fuelled by analytical technology advances, particularly mass spectrometry and chromatography, but on the other hand new biological questions also drive analytical technology developments. Compared to fairly standardized genomic or proteomic high-throughput protocols, the high degree of molecular heterogeneity adds a special analytical challenge to lipidomic analysis. In this review, we will take a closer look at various mass spectrometric platforms for lipidomic analysis. We will focus on the advantages and limitations of various experimental setups like ‘shotgun lipidomics’, liquid chromatography—Mass spectrometry (LC-MS) and matrix assisted laser desorption ionization-time of flight (MALDI-TOF) based approaches. We will also examine available software packages for data analysis, which nowadays is in fact the rate limiting step for most ‘omics’ workflows. Full article
(This article belongs to the Special Issue Lipidomics)
Open AccessReview Perturbations of Lipid Metabolism Indexed by Lipidomic Biomarkers
Metabolites 2012, 2(1), 1-18; doi:10.3390/metabo2010001
Received: 28 November 2011 / Revised: 21 December 2011 / Accepted: 22 December 2011 / Published: 4 January 2012
Cited by 3 | PDF Full-text (509 KB) | HTML Full-text | XML Full-text
Abstract
The lipidome of the liver and the secreted circulating lipoproteins can now be interrogated conveniently by automated mass spectrometric methods. Multivariate analysis of the liver and serum lipid composition in various animal modes or in human patients has pointed to specific molecular [...] Read more.
The lipidome of the liver and the secreted circulating lipoproteins can now be interrogated conveniently by automated mass spectrometric methods. Multivariate analysis of the liver and serum lipid composition in various animal modes or in human patients has pointed to specific molecular species markers. The perturbations of lipid metabolism can be categorized on the basis of three basic pathological mechanisms: (1) an accelerated rate of de novo lipogenesis; (2) perturbation of the peroxisome pathway of ether-lipid and very-long-chain fatty acid biosynthesis; (3) a change in the rate of interconversion of essential omega-3 and -6 polyunsaturated fatty acids. This review provides examples to illustrate the practicalities of lipidomic studies in biomedicine. Full article
(This article belongs to the Special Issue Lipidomics)
Open AccessReview Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics
Metabolites 2011, 1(1), 21-40; doi:10.3390/metabo1010021
Received: 8 October 2011 / Revised: 2 November 2011 / Accepted: 4 November 2011 / Published: 11 November 2011
Cited by 35 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges [...] Read more.
Electrospray ionization mass spectrometry (ESI-MS) has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of lipidomics. Herein, we discuss the principles, advantages, and possible limitations of different mass spectrometry-based methodologies for lipid quantification, as well as a few practical issues important for accurate quantification of individual lipid species. Accordingly, accurate quantification of individual lipid species, one of the key challenges in lipidomics, can be practically met. Full article
(This article belongs to the Special Issue Lipidomics)
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