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Mass Spectrometry-Based Lipidomics

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 41728

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Special Issue Editors

Dr. Amaury Cazenave Gassiot

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Guest Editor

1. Department of Biochemistry, Yong Loo Lin School of Medicine, Singapore 117596, Singapore
2. Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
Interests: lipidomics; chromatography; mass spectrometry; lipid biochemistry; harmonisation
Special Issues, Collections and Topics in MDPI journals

Dr. Federico Tesio Torta

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Guest Editor

Department of Biochemistry, Yong Loo Lin School of Medicine, and Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
Interests: lipidomics; protein and lipid biochemistry; metabolic diseases; harmonisation
Special Issues, Collections and Topics in MDPI journals

Dr. Bo Johannes Burla

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Guest Editor

Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
Interests: lipidomics; MS data processing; glycosphingolipids; platelets; reproducible data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last few years, it has become increasingly apparent that explaining complex biochemical pathways cannot rely solely on the study of genetic background and genetic variation. A better understanding of proteins, peptides, metabolites, and lipids at the molecular level is required. However, these components and their natural variations are still poorly characterized, be it in model organisms or human populations.

Of particular interest, the implication of lipids in many biological processes, such as plant growth, viral infection mechanisms, neuronal pathologies, autoimmune diseases, diabetes, obesity, or cancer, has only recently emerged. These developments have been made possible by advances in mass-spectrometry-based lipidomics and associated techniques, which have made it easier to grasp the lipidome’s complexity.

Mass-spectrometry-based lipidomic workflows have considerably improved over the years, yielding ever more comprehensive coverage, structural resolution, and better quantification of the lipidome and its variations. The field has now reached a point where translation to clinical applications is within reach. In this context, the lipidomics community must work towards developing ever-better analytics and establishing widely accepted guidelines for validation and reproducibility.

In this Special Issue, we would like to invite manuscripts on all aspects of mass-spectrometry-based lipidomic workflows: sample preparation, chromatographic separation, MS and MS/MS, quality control, data processing and statistical analysis, harmonization efforts, and clinical translation. Both review articles and original studies are welcome.

Dr. Amaury Cazenave Gassiot
Dr. Federico Tesio Torta
Dr. Bo Johannes Burla
Guest Editors

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Keywords

Lipidomics
Mass spectrometry
Targeted and untargeted lipidomics
Workflows

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Published Papers (10 papers)

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Research

14 pages, 2009 KiB

Open AccessArticle

Tailored Polymer-Based Selective Extraction of Lipid Mediators from Biological Samples

by Yohannes Abere Ambaw, Sandra Rinne Dahl, Yan Chen, Tyge Greibrokk, Elsa Lundanes, Issam Lazraq, Sudhirkumar Shinde, Jayashree Selvalatchmanan, Markus R. Wenk, Börje Sellergren and Federico Torta

Metabolites 2021, 11(8), 539; https://doi.org/10.3390/metabo11080539 - 13 Aug 2021

Cited by 1 | Viewed by 3009

Abstract

Lipid mediators, small molecules involved in regulating inflammation and its resolution, are a class of lipids of wide interest as their levels in blood and tissues may be used to monitor health and disease states or the effect of new treatments. These molecules are present at low levels in biological samples, and an enrichment step is often needed for their detection. We describe a rapid and selective method that uses new low-cost molecularly imprinted (MIP) and non-imprinted (NIP) polymeric sorbents for the extraction of lipid mediators from plasma and tissue samples. The extraction process was carried out in solid-phase extraction (SPE) cartridges, manually packed with the sorbents. After extraction, lipid mediators were quantified by liquid chromatography–tandem mass spectrometry (LC–MSMS). Various parameters affecting the extraction efficiency were evaluated to achieve optimal recovery and to reduce non-specific interactions. Preliminary tests showed that MIPs, designed using the prostaglandin biosynthetic precursor arachidonic acid, could effectively enrich prostaglandins and structurally related molecules. However, for other lipid mediators, MIP and NIP displayed comparable recoveries. Under optimized conditions, the recoveries of synthetic standards ranged from 62% to 100%. This new extraction method was applied to the determination of the lipid mediators concentration in human plasma and mouse tissues and compared to other methods based on commercially available cartridges. In general, the methods showed comparable performances. In terms of structural specificity, our newly synthesized materials accomplished better retention of prostaglandins (PGs), hydroxydocosahexaenoic acid (HDoHE), HEPE, hydroxyeicosatetraenoic acids (HETE), hydroxyeicosatrienoic acid (HETrE), and polyunsaturated fatty acid (PUFA) compounds, while the commercially available Strata-X showed a higher recovery for dihydroxyeicosatetraenoic acid (diHETrEs). In summary, our results suggest that this new material can be successfully implemented for the extraction of lipid mediators from biological samples. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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13 pages, 2875 KiB

Open AccessArticle

Accurate Lipid Quantification of Tissue Homogenates Requires Suitable Sample Concentration, Solvent Composition, and Homogenization Procedure—A Case Study in Murine Liver

by Marcus Höring, Sabrina Krautbauer, Louisa Hiltl, Verena Babl, Alexander Sigruener, Ralph Burkhardt and Gerhard Liebisch

Metabolites 2021, 11(6), 365; https://doi.org/10.3390/metabo11060365 - 8 Jun 2021

Cited by 17 | Viewed by 6770

Abstract

Lipidomics aim to quantify lipid species in all kinds of samples, including tissues. To subject a fixed amount of sample to various workflows, tissue homogenates were frequently prepared at defined concentrations in water or by addition of organic solvents. Here, we investigated this first step of tissue lipidomics by quantitative flow injection analysis coupled to Fourier-Transform mass spectrometry (FTMS). The influence of sample concentration, solvent composition, and homogenization procedure on the recovery of lipids was studied in murine liver. Liver homogenates were prepared either by grinding tissue in liquid nitrogen or by bead-based homogenization. Ground samples were dissolved at different concentrations in water, methanol, and water/methanol = 1/1 (v/v). Here, lipid recovery depends on solvent composition and sample concentration. The recovery of nonpolar lipid classes, including triglycerides and cholesteryl ester, was decreased in methanolic homogenates. In contrast, due to superior dispersion of precipitates, bead-based homogenization resulted in efficient lipid recovery independent of the solvent composition. However, lipid distribution within samples, i.e., lipid content of supernatant and pellet following centrifugation, was altered substantially by solvent composition. In conclusion, accurate lipid quantification of tissue homogenates requires evaluation of solvent composition, sample concentration, as well as the homogenization method to guarantee efficient lipid recovery. Due to a potential loss of lipids, removal of precipitates by centrifugation prior to lipid extraction should be avoided. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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16 pages, 1754 KiB

Open AccessEditor’s ChoiceArticle

Untargeted Lipidomic Profiling of Dry Blood Spots Using SFC-HRMS

by Pauline Le Faouder, Julia Soullier, Marie Tremblay-Franco, Anthony Tournadre, Jean-François Martin, Yann Guitton, Caroline Carlé, Sylvie Caspar-Bauguil, Pierre-Damien Denechaud and Justine Bertrand-Michel

Metabolites 2021, 11(5), 305; https://doi.org/10.3390/metabo11050305 - 11 May 2021

Cited by 13 | Viewed by 3740

Abstract

Lipids are essential cellular constituents that have many critical roles in physiological functions. They are notably involved in energy storage and cell signaling as second messengers, and they are major constituents of cell membranes, including lipid rafts. As a consequence, they are implicated in a large number of heterogeneous diseases, such as cancer, diabetes, neurological disorders, and inherited metabolic diseases. Due to the high structural diversity and complexity of lipid species, the presence of isomeric and isobaric lipid species, and their occurrence at a large concentration scale, a complete lipidomic profiling of biological matrices remains challenging, especially in clinical contexts. Using supercritical fluid chromatography coupled with high-resolution mass spectrometry, we have developed and validated an untargeted lipidomic approach to the profiling of plasma and blood. Moreover, we have tested the technique using the Dry Blood Spot (DBS) method and found that it allows for the easy collection of blood for analysis. To develop the method, we performed the optimization of the separation and detection of lipid species on pure standards, reference human plasma (SRM1950), whole blood, and DBS. These analyses allowed an in-house lipid data bank to be built. Using the MS-Dial software, we developed an automatic process for the relative quantification of around 500 lipids species belonging to the 6 main classes of lipids (including phospholipids, sphingolipids, free fatty acids, sterols, and fatty acyl-carnitines). Then, we compared the method using the published data for SRM 1950 and a mouse blood sample, along with another sample of the same blood collected using the DBS method. In this study, we provided a method for blood lipidomic profiling that can be used for the easy sampling of dry blood spots. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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19 pages, 4200 KiB

Open AccessArticle

A Novel Solid Phase Extraction Sample Preparation Method for Lipidomic Analysis of Human Plasma Using Liquid Chromatography/Mass Spectrometry

by Alex Apffel, Limian Zhao and Mark J. Sartain

Metabolites 2021, 11(5), 294; https://doi.org/10.3390/metabo11050294 - 4 May 2021

Cited by 12 | Viewed by 4588

Abstract

Lipidomic approaches are widely used to investigate the relationship between lipids, human health, and disease. Conventional sample preparation techniques for the extraction of lipids from biological matrices like human plasma are based on liquid-liquid extraction (LLE). However, these methods are labor-intensive, time-consuming, and can show poor reproducibility and selectivity on lipid extraction. A novel, solid-phase extraction (SPE) approach was demonstrated to extract lipids from human plasma using a lipid extraction SPE in both cartridge and 96-well-plate formats, followed by analysis using a combination of targeted and untargeted liquid chromatography/mass spectrometry. The Lipid Extraction SPE method was compared to traditional LLE methods for lipid class recovery, lipidome coverage, and reproducibility. The novel SPE method used a simplified protocol with significant time and labor savings and provided equivalent or better qualitative and quantitative results than traditional LLE methods with respect to several critical performance metrics; recovery, reproducibility, and lipidome coverage. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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14 pages, 2583 KiB

Open AccessArticle

Control of n-Butanol Induced Lipidome Adaptations in E. coli

by Aike Jeucken, Miaomiao Zhou, Marc M. S. M. Wösten and Jos F. Brouwers

Metabolites 2021, 11(5), 286; https://doi.org/10.3390/metabo11050286 - 29 Apr 2021

Cited by 2 | Viewed by 2616

Abstract

The versatile compound n-butanol is one of the most promising biofuels for use in existing internal combustion engines, contributing to a smooth transition towards a clean energy society. Furthermore, n-butanol is a valuable resource to produce more complex molecules such as bioplastics. Microbial production of n-butanol from waste materials is hampered by the biotoxicity of n-butanol as it interferes with the proper functioning of lipid membranes. In this study we perform a large-scale investigation of the complete lipid-related enzyme machinery and its response to exposure to a sublethal concentration of n-butanol. We profiled, in triplicate, the growth characteristics and phospholipidomes of 116 different genetic constructs of E. coli, both in the presence and absence of 0.5% n-butanol (v/v). This led to the identification of 230 lipid species and subsequently to the reconstruction of the network of metabolites, enzymes and lipid properties driving the homeostasis of the E. coli lipidome. We were able to identify key lipids and biochemical pathways leading to altered n-butanol tolerance. The data led to new conceptual insights into the bacterial lipid metabolism which are discussed. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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9 pages, 1318 KiB

Open AccessArticle

Application of Lipid Class Ratios for Sample Stability Monitoring—Evaluation of Murine Tissue Homogenates and SDS as a Stabilizer

by Sabrina Krautbauer, Raquel Blazquez, Gerhard Liebisch, Marcus Hoering, Philip Neubert, Tobias Pukrop, Ralph Burkhardt and Alexander Sigruener

Metabolites 2021, 11(5), 277; https://doi.org/10.3390/metabo11050277 - 27 Apr 2021

Cited by 6 | Viewed by 3023

Abstract

Lipids are a ubiquitous class of structurally complex molecules involved in various biological processes. In the fast-growing field of lipidomics, preanalytical issues are frequently neglected. Here, we investigated the stability of lipid profiles of murine liver, brain, lung, heart, and spleen homogenates by quantitative flow injection analysis using tandem mass spectrometry and high-resolution mass spectrometry. Storage of tissue homogenates at room temperature showed substantial alterations of the lipid profiles reflecting lipolytic action. Therefore, ratios of ceramide to sphingomyelin, lysophosphatidylethanolamine to phosphatidylethanolamine, lysophosphatidylcholine to phosphatidylcholine, and diglyceride to triglyceride were applied to monitor sample stability and the effect of sodium dodecyl sulfate (SDS) as a potential stabilizing agent. The addition of SDS led to a concentration-dependent stabilization of lipid profiles in liver, brain, and heart homogenates, while in lung and spleen homogenates, in particular, the lysophosphatidylethanolamine to phosphatidylethanolamine ratio increased upon addition of SDS. In conclusion, we demonstrated that lipid class ratios reflecting lipolytic activity could be applied to evaluate both the stability of samples and the influence of stabilizers. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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14 pages, 5489 KiB

Open AccessArticle

Plasma Metabolome and Lipidome Associations with Type 2 Diabetes and Diabetic Nephropathy

by Yan Ming Tan, Yan Gao, Guoshou Teo, Hiromi W.L. Koh, E Shyong Tai, Chin Meng Khoo, Kwok Pui Choi, Lei Zhou and Hyungwon Choi

Metabolites 2021, 11(4), 228; https://doi.org/10.3390/metabo11040228 - 8 Apr 2021

Cited by 24 | Viewed by 4638

Abstract

We conducted untargeted metabolomics analysis of plasma samples from a cross-sectional case–control study with 30 healthy controls, 30 patients with diabetes mellitus and normal renal function (DM-N), and 30 early diabetic nephropathy (DKD) patients using liquid chromatography-mass spectrometry (LC-MS). We employed two different modes of MS acquisition on a high-resolution MS instrument for identification and semi-quantification, and analyzed data using an advanced multivariate method for prioritizing differentially abundant metabolites. We obtained semi-quantification data for 1088 unique compounds (~55% lipids), excluding compounds that may be either exogenous compounds or treated as medication. Supervised classification analysis over a confounding-free partial correlation network shows that prostaglandins, phospholipids, nucleotides, sugars, and glycans are elevated in the DM-N and DKD patients, whereas glutamine, phenylacetylglutamine, 3-indoxyl sulfate, acetylphenylalanine, xanthine, dimethyluric acid, and asymmetric dimethylarginine are increased in DKD compared to DM-N. The data recapitulate the well-established plasma metabolome changes associated with DM-N and suggest uremic solutes and oxidative stress markers as the compounds indicating early renal function decline in DM patients. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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15 pages, 2080 KiB

Open AccessArticle

Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry

by Nobuyuki Okahashi, Masahiro Ueda, Fumio Matsuda and Makoto Arita

Metabolites 2021, 11(4), 197; https://doi.org/10.3390/metabo11040197 - 26 Mar 2021

Cited by 13 | Viewed by 3583

Abstract

Lipid A is a characteristic molecule of Gram-negative bacteria that elicits an immune response in mammalian cells. The presence of structurally diverse lipid A types in the human gut bacteria has been suggested before, and this appears associated with the immune response. However, lipid A structures and their quantitative heterogeneity have not been well characterized. In this study, a method of analysis for lipid A using liquid chromatography–quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) was developed and applied to the analyses of Escherichia coli and Bacteroidetes strains. In general, phosphate compounds adsorb on stainless-steel piping and cause peak tailing, but the use of an ammonia-containing alkaline solvent produced sharp lipid A peaks with high sensitivity. The method was applied to E. coli strains, and revealed the accumulation of lipid A with abnormal acyl side chains in knockout strains as well as known diphosphoryl hexa-acylated lipid A in a wild-type strain. The analysis of nine representative strains of Bacteroidetes showed the presence of monophosphoryl penta-acylated lipid A characterized by a highly heterogeneous main acyl chain length. Comparison of the structures and amounts of lipid A among the strains suggested a relationship between lipid A profiles and the phylogenetic classification of the strains. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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24 pages, 4287 KiB

Open AccessArticle

Comprehensive Identification of Glycosphingolipids in Human Plasma Using Hydrophilic Interaction Liquid Chromatography—Electrospray Ionization Mass Spectrometry

by Karel Hořejší, Robert Jirásko, Michaela Chocholoušková, Denise Wolrab, David Kahoun and Michal Holčapek

Metabolites 2021, 11(3), 140; https://doi.org/10.3390/metabo11030140 - 26 Feb 2021

Cited by 19 | Viewed by 4613

Abstract

Glycosphingolipids (GSL) represent a highly heterogeneous class of lipids with many cellular functions, implicated in a wide spectrum of human diseases. Their isolation, detection, and comprehensive structural analysis is a challenging task due to the structural diversity of GSL molecules. In this work, GSL subclasses are isolated from human plasma using an optimized monophasic ethanol–water solvent system capable to recover a broad range of GSL species. Obtained deproteinized plasma is subsequently purified and concentrated by C18-based solid-phase extraction (SPE). The hydrophilic interaction liquid chromatography coupled to electrospray ionization linear ion trap tandem mass spectrometry (HILIC-ESI-LIT-MS/MS) is used for GSL analysis in the human plasma extract. Our results provide an in-depth profiling and structural characterization of glycosphingolipid and some phospholipid subclasses identified in the human plasma based on their retention times and the interpretation of tandem mass spectra. The structural composition of particular lipid species is readily characterized based on the detailed interpretation of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) spectra and further confirmed by specific fragmentation behavior following predictable patterns, which yields to the unambiguous identification of 154 GSL species within 7 lipid subclasses and 77 phospholipids representing the highest number of GSL species ever reported in the human plasma. The developed HILIC-ESI-MS/MS method can be used for further clinical and biological research of GSL in the human blood or other biological samples. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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13 pages, 2864 KiB

Open AccessArticle

Free Saturated Oxo Fatty Acids (SOFAs) and Ricinoleic Acid in Milk Determined by a Liquid Chromatography-High-Resolution Mass Spectrometry (LC-HRMS) Method

by Maroula G. Kokotou, Charikleia S. Batsika, Christiana Mantzourani and George Kokotos

Metabolites 2021, 11(1), 46; https://doi.org/10.3390/metabo11010046 - 11 Jan 2021

Cited by 10 | Viewed by 3390

Abstract

Oxidized saturated fatty acids, containing a hydroxyl or an oxo functionality, have attracted little attention so far. Recent studies have shown that saturated hydroxy fatty acids, which exhibit cancer cell growth inhibition and may suppress β-cell apoptosis, are present in milk. Herein, we present the application of a liquid chromatography-high-resolution mass spectrometry (LC-HRMS) method for the detection and quantification of various saturated oxo fatty acids (SOFAs) previously unrecognized in milk. This robust and rapid analytical method, which involves simple sample preparation and a single 10-min run, revealed the presence of families of oxostearic acids (OSAs) and oxopalmitic acids (OPAs) in milk. 8OSA, 9OSA, 7OSA, 10OSA and 10OPA were found to be the most abundant SOFAs in both cow and goat milk. Higher contents of SOFAs were found in cow milk in comparison to goat milk. Together with SOFAs, ricinoleic acid, which is isobaric to OSA, was detected and quantified in all milk samples, following a “suspect” HRMS analysis approach. This unique natural fatty acid, which is the main component (>90%) of castor oil triglycerides, was estimated at mean content values of 534.3 ± 6.0 μg/mL and 460 ± 8.1 μg/mL in cow and goat milk samples, respectively. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Lipidomics)

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