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Mass Spectrometry Based Lipidomics

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 32766

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Dr. Maria do Rosário Domingues

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CESAM—Centre for Environmental and Marine Studies & Department of Chemistry, University of Aveiro, Aveiro, Portugal
Interests: mass spectrometry lipidomics; marine lipidomics; lipidomics in health and disease; food lipidomics; microbial lipidomics glycomics; biomolecules modification associated with oxidative stress monitored by mass spectrometry
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Prof. Dr. Pedro Domingues

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Mass Spectrometry Centre, Chemistry Department &QOPNA, University of Aveiro, 3810-193 Aveiro, Portugal
Interests: mass spectrometry; liquid chromatography-mass spectrometry; lipidomics; proteomics; oxidative stress
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Lipidomics is an emerging field of research that aims at the large scale mapping and quantification of lipids in living systems, their interactions with other lipids and proteins, and the elucidation of lipid metabolism at the cellular level. It is used as a tool to understand lipid function in biological systems and its physiological and pathophysiological roles in a wide variety of disease states. Liquid chromatography–mass spectrometry (LC-MS) is the base technology used in lipidomics and allows high throughput analysis for the detection and determination of molecular structures, and the quantification of thousands of lipid species in tissues and body fluids. Alterations in the lipidome of cells, tissues or biofluids has been correlated with the onset, development and severity of several human disorders, and are considered of significant importance for the diagnosis, prognosis and therapeutics of several chronic and non-communicable diseases. The aim of this Special Issue is to:

Review the recent methodological advances, applications and key findings of lipidomics;
Present advances in lipidomics technologies;
Report the use of lipidomics technologies to lipid research;
Increase our understanding of the role of lipids in health and disease.

Prof. Dr. Rosário Domingues
Prof. Dr. Pedro Domingues
Guest Editors

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Keywords

lipidomics
mass spectrometry
liquid chromatography–mass spectrometry
phospholipid
oxidative lipidomics
lipidomics in health and disease

Published Papers (7 papers)

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Research

16 pages, 3230 KiB

Open AccessArticle

HILIC-ESI-FTMS with All Ion Fragmentation (AIF) Scans as a Tool for Fast Lipidome Investigations

by Giovanni Ventura, Mariachiara Bianco, Cosima Damiana Calvano, Ilario Losito and Tommaso R. I. Cataldi

Molecules 2020, 25(10), 2310; https://doi.org/10.3390/molecules25102310 - 14 May 2020

Cited by 20 | Viewed by 3334

Abstract

Lipidomics suffers from the lack of fast and reproducible tools to obtain both structural information on intact phospholipids (PL) and fatty acyl chain composition. Hydrophilic interaction liquid chromatography with electrospray ionization coupled to an orbital-trap Fourier-transform analyzer operating using all ion fragmentation mode (HILIC-ESI-FTMS-AIF MS) is seemingly a valuable resource in this respect. Here, accurate m/z values, HILIC retention times and AIF MS scan data were combined for PL assignment in standard mixtures or real lipid extracts. AIF scans in both positive and negative ESI mode, achieved using collisional induced dissociation for fragmentation, were applied to identify both the head-group of each PL class and the fatty acyl chains, respectively. An advantage of the AIF approach was the concurrent collection of tandem MS-like data, enabling the identification of linked fatty acyl chains of precursor phospholipids through the corresponding carboxylate anions. To illustrate the ability of AIF in the field of lipidomics, two different types of real samples, i.e., the lipid extracts obtained from human plasma and dermal fibroblasts, were examined. Using AIF scans, a total of 253 intact lipid species and 18 fatty acids across 4 lipid classes were recognized in plasma samples, while FA C20:3 was confirmed as the fatty acyl chain belonging to phosphatidylinositol, PI 38:3, which was found to be down-regulated in fibroblast samples of Parkinson’s disease patients. Full article

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

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19 pages, 2177 KiB

Open AccessArticle

Advancing Target Identification of Nitrated Phospholipids in Biological Systems by HCD Specific Fragmentation Fingerprinting in Orbitrap Platforms

by Bruna Neves, Sofia Duarte, Pedro Domingues, Dolores Pérez-Sala, Maria Manuel Oliveira, Maria do Rosário Domingues and Tânia Melo

Molecules 2020, 25(9), 2120; https://doi.org/10.3390/molecules25092120 - 01 May 2020

Cited by 10 | Viewed by 4020

Abstract

Nitrated phospholipids have recently been detected in vitro and in vivo and associated with beneficial health effects. They were identified and quantified in biological samples by lipidomics methodologies using liquid chromatography-collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) acquired with the linear ion trap mass spectrometer. Only a few studies have used higher-energy collision dissociation (HCD)-MS/MS in high-resolution Orbitraps to characterize nitrated phosphatidylserines and nitrated cardiolipins, highlighting the marked differences in the fragmentation patterns when using CID or HCD fragmentation methods. In this study, we aimed to evaluate the fragmentation of nitrated phosphatidylcholine and nitrated phosphatidylethanolamine species under HCD-MS/MS. We studied the effect of normalized collision energy (NCE) in the fragmentation pattern to identify the best acquisition conditions and reporter ions to detect nitrated phospholipids. The results showed that the intensity of the typical neutral loss of nitrous acid (HNO₂) diminishes with increasing NCE, becoming non-detectable for a higher NCE. Thus, the loss of HNO₂ could not be the most suitable ion/fragment for the characterization of nitrated phospholipids under HCD. In HCD-MS/MS new fragment ions were identified, corresponding to the nitrated fatty acyl chains, NO₂-RCOO⁻, (NO₂-RCOOH-H₂O + H)⁺, and (NO₂-RCOOH + H)⁺, suggested as potential reporter ions to detect nitrated phospholipids when using the HCD-MS/MS lipidomics analysis. Full article

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

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12 pages, 2436 KiB

Open AccessFeature PaperArticle

Sphingomyelins Prevent Propagation of Lipid Peroxidation—LC-MS/MS Evaluation of Inhibition Mechanisms

by Giulia Coliva, Mike Lange, Simone Colombo, Jean-Pierre Chervet, M. Rosario Domingues and Maria Fedorova

Molecules 2020, 25(8), 1925; https://doi.org/10.3390/molecules25081925 - 21 Apr 2020

Cited by 16 | Viewed by 3511

Abstract

Free radical driven lipid peroxidation is a chain reaction which can lead to oxidative degradation of biological membranes. Propagation vs. termination rates of peroxidation in biological membranes are determined by a variety of factors including fatty acyl chain composition, presence of antioxidants, as well as biophysical properties of mono- or bilayers. Sphingomyelins (SMs), a class of sphingophospholipids, were previously described to inhibit lipid oxidation most probably via the formation of H-bond network within membranes. To address the “antioxidant” potential of SMs, we performed LC-MS/MS analysis of model SM/glycerophosphatidylcholine (PC) liposomes with different SM fraction after induction of radical driven lipid peroxidation. Increasing SM fraction led to a strong suppression of lipid peroxidation. Electrochemical oxidation of non-liposomal SMs eliminated the observed effect, indicating the importance of membrane structure for inhibition of peroxidation propagation. High resolution MS analysis of lipid peroxidation products (LPPs) observed in in vitro oxidized SM/PC liposomes allowed to identify and relatively quantify SM- and PC-derived LPPs. Moreover, mapping quantified LPPs to the known pathways of lipid peroxidation allowed to demonstrate significant decrease in mono-hydroxy(epoxy) LPPs relative to mono-keto derivatives in SM-rich liposomes. The results presented here illustrate an important property of SMs in biological membranes, acting as “biophysical antioxidant”. Furthermore, a ratio between mono-keto/mono-hydroxy(epoxy) oxidized species can be used as a marker of lipid peroxidation propagation in the presence of different antioxidants. Full article

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

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14 pages, 2514 KiB

Open AccessArticle

Lipidomic Analysis Reveals Specific Differences between Fibroblast and Keratinocyte Ceramide Profile of Patients with Psoriasis Vulgaris

by Wojciech Łuczaj, Adam Wroński, Pedro Domingues, M Rosário Domingues and Elżbieta Skrzydlewska

Molecules 2020, 25(3), 630; https://doi.org/10.3390/molecules25030630 - 31 Jan 2020

Cited by 32 | Viewed by 4065

Abstract

Ceramides are important lipid metabolites for primal skin functions. There is increasing evidence that alteration of the profile and metabolism of ceramides is associated with skin diseases, such as psoriasis vulgaris. Most studies have reported alteration in ceramide content in the stratum corneum, but these have been scarcely reported for other skin layers. In the present work, we aimed to explore changes in the ceramide profile of fibroblasts and keratinocytes in patients with psoriasis vulgaris and healthy subjects. Using the reversed-phase liquid chromatography-quadrupole-time-of-flight-tandem-mass spectrometry (RPLC-QTOF-MS/MS) platform, we identified ceramide containing non-hydroxy fatty acid ([N]), α-hydroxy fatty acid ([A]), and esterified ω-hydroxy fatty acid ([EO]) and 3 sphingoid bases, dihydrosphingosine ([DS]), sphingosine ([S]), and phytosphingosine ([P]). We found that in the keratinocytes of patients with psoriasis, CER[NS], CER[NP], CER[AS], CER[ADS], CER[AP] and CER[EOS] tended to be expressed at higher relative levels, whereas CER[NDS] tended to be expressed with lower levels than in healthy subjects. In the case of fibroblasts, significant differences were observed, mainly in the three ceramide classes (CER[AS], CER[ADS] and CER[EOS]), which were expressed at significantly higher levels in patients with psoriasis. The most significant alteration in the fibroblasts involved elevated levels of CER[EOS] that contained ester-linked fatty acids. Our findings provide insights into the ceramide profile in the dermis and epidermis of patients with psoriasis and contribute for the research in this field, focusing on the role of keratinocyte-fibroblast crosstalk in the development of psoriasis vulgaris. Full article

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

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13 pages, 3767 KiB

Open AccessArticle

Quantitative Analysis of Cold Stress Inducing Lipidomic Changes in Shewanella putrefaciens Using UHPLC-ESI-MS/MS

by Xin Gao, Wenru Liu, Jun Mei and Jing Xie

Molecules 2019, 24(24), 4609; https://doi.org/10.3390/molecules24244609 - 16 Dec 2019

Cited by 15 | Viewed by 3017

Abstract

Shewanella putrefaciens is a well-known specific spoilage organism (SSO) and cold-tolerant microorganism in refrigerated fresh marine fish. Cold-adapted mechanism includes increased fluidity of lipid membranes by the ability to finely adjust lipids composition. In the present study, the lipid profile of S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C was explored using ultra-high-pressure liquid chromatography/electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) to discuss the effect of lipid composition on cold-adapted tolerance. Lipidomic analysis detected a total of 27 lipid classes and 606 lipid molecular species in S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C. S. putrefaciens cultivated at 30 °C (SP-30) had significantly higher content of glycerolipids, sphingolipids, saccharolipids, and fatty acids compared with that at 0 °C (SP-0); however, the lower content of phospholipids (13.97%) was also found in SP-30. PE (30:0), PE (15:0/15:0), PE (31:0), PA (33:1), PE (32:1), PE (33:1), PE (25:0), PC (22:0), PE (29:0), PE (34:1), dMePE (15:0/16:1), PE (31:1), dMePE (15:1/15:0), PG (34:2), and PC (11:0/11:0) were identified as the most abundant lipid molecular species in S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C. The increase of PG content contributes to the construction of membrane lipid bilayer and successfully maintains membrane integrity under cold stress. S. putrefaciens cultivated at low temperature significantly increased the total unsaturated liquid contents but decreased the content of saturated liquid contents. Full article

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

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19 pages, 5601 KiB

Open AccessFeature PaperArticle

The Power of LC-MS Based Multiomics: Exploring Adipogenic Differentiation of Human Mesenchymal Stem/Stromal Cells

by Evelyn Rampler, Dominik Egger, Harald Schoeny, Mate Rusz, Maria Pires Pacheco, Giada Marino, Cornelia Kasper, Thomas Naegele and Gunda Koellensperger

Molecules 2019, 24(19), 3615; https://doi.org/10.3390/molecules24193615 - 08 Oct 2019

Cited by 22 | Viewed by 5860

Abstract

The molecular study of fat cell development in the human body is essential for our understanding of obesity and related diseases. Mesenchymal stem/stromal cells (MSC) are the ideal source to study fat formation as they are the progenitors of adipocytes. In this work, we used human MSCs, received from surgery waste, and differentiated them into fat adipocytes. The combination of several layers of information coming from lipidomics, metabolomics and proteomics enabled network analysis of the biochemical pathways in adipogenesis. Simultaneous analysis of metabolites, lipids, and proteins in cell culture is challenging due to the compound’s chemical difference, so most studies involve separate analysis with unimolecular strategies. In this study, we employed a multimolecular approach using a two–phase extraction to monitor the crosstalk between lipid metabolism and protein-based signaling in a single sample (~10⁵ cells). We developed an innovative analytical workflow including standardization with in-house produced ¹³C isotopically labeled compounds, hyphenated high-end mass spectrometry (high-resolution Orbitrap MS), and chromatography (HILIC, RP) for simultaneous untargeted screening and targeted quantification. Metabolite and lipid concentrations ranged over three to four orders of magnitude and were detected down to the low fmol (absolute on column) level. Biological validation and data interpretation of the multiomics workflow was performed based on proteomics network reconstruction, metabolic modelling (MetaboAnalyst 4.0), and pathway analysis (OmicsNet). Comparing MSCs and adipocytes, we observed significant regulation of different metabolites and lipids such as triglycerides, gangliosides, and carnitine with 113 fully reprogrammed pathways. The observed changes are in accordance with literature findings dealing with adipogenic differentiation of MSC. These results are a proof of principle for the power of multimolecular extraction combined with orthogonal LC-MS assays and network construction. Considering the analytical and biological validation performed in this study, we conclude that the proposed multiomics workflow is ideally suited for comprehensive follow-up studies on adipogenesis and is fit for purpose for different applications with a high potential to understand the complex pathophysiology of diseases. Full article

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

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31 pages, 7068 KiB

Open AccessArticle

Non-Targeted LC-MS/MS Assay for Screening Over 100 Lipid Mediators from ARA, EPA, and DHA in Biological Samples Based on Mass Spectral Fragmentations

by Gabriel Dasilva, Silvia Muñoz, Salomé Lois and Isabel Medina

Molecules 2019, 24(12), 2276; https://doi.org/10.3390/molecules24122276 - 19 Jun 2019

Cited by 14 | Viewed by 8163

Abstract

A non-targeted strategy to simultaneously screen for over 100 lipid mediators from ω-6 ARA and ω-3 EPA and DHA fatty acids is presented. The method based on an extensive study of fragmentation patterns obtained by SPE-LC-MS/MS analysis-provided fingerprints to comprehensively elucidate and identify lipid mediators in biological samples. Many of these metabolites are associated to metabolic disorders, inflammatory, immune and oxidative stress. The methodology consisted of a three-step procedure. (1) SPE extraction of compounds from plasma and adipose tissue was followed by LC-MS/MS analysis operating in full scan mode. The methodology was validated for a group of 65 metabolites using standards. SPE recoveries ranged from 29–134% and matrix effect from 10–580%. LOD and LOQ ranged from 0.01 to 1765 ng/mL and 0.03 to 5884 ng/mL respectively, similarly than current analytical strategies based on MRM mode. (2) An extensive study of the mass spectra of a wide range of compounds was done to stablish a specific fragmentation pattern. Interestingly, illustrative fragmentations and new specific transitions to identify EPA and DHA lipid mediators have been innovatively established. (3) After analysis, 30 lipid mediators were tentatively identified in plasma and 35 in adipose tissue of rats according to the pre stablished fragmentation patterns. The hypothetical identification of compounds was validated by using reference standards. Around 85–90% of proposed identifications were correctly assigned and only 4 and 3 identifications failed in adipose tissue and plasma, respectively. The method allowed the identification of these metabolites without losing information by the use of predefined ions list. Therefore, the use of full scan mode together with the study of fragmentation patterns provided a novel and stronger analytical tool to study the complete profile of lipid mediators in biological samples than the analysis through MRM based methods. Importantly, no analytical standards were required at this qualitative screening stage and the performance and sensitivity of the assay were very similar to that of a MRM method. Full article

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

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