Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Phospholipids and Sphingolipids in Osteoarthritis

Many studies now emphasize the intricate relationship between lipid metabolism and osteoarthritis (OA), a leading cause of disability. This narrative review examines alterations in the levels of phospholipids (PLs) and sphingolipids (SLs) in synovial fluid (SF), plasma, serum, and articular tissues; discusses their role in joint lubrication, inflammation, and cartilage degradation; and describes their potential as diagnostic markers and therapeutic targets. Key findings include stage-dependent elevated levels of specific PLs and SLs in the SF, blood, and tissue of OA patients, implicating them as possible biomarkers of disease severity and progression. Studies suggest that beyond the involvement of these lipids in joint lubrication, individual species, such as lysophosphatidylcholine (LPC) 16:0, lysophosphatidic acid (LPA), ceramide-1-phosphate (C1P), and sphingosine-1-phosphate (S1P), contribute to pain, inflammation, and degradation of joints through various signaling pathways. Cross-species comparisons suggest that dogs and mice experience similar lipidomic changes during OA as humans, rendering them valuable models for studying lipid-related mechanisms. PLs and SLs in SF appear to originate primarily from the synovial blood capillaries through diffusion. In addition, lipids that are produced locally by fibroblast-like synoviocytes (FLSs) are influenced by cytokines and growth factors that regulate the biosynthesis of PLs for joint lubrication. Emerging research has identified genes such as UGCG and ESYT1 as regulators of lipid metabolism in OA. Further, we examine the suitability of lipids as biomarkers of OA and the potential of targeting the PL and SL pathways to treat OA, emphasizing the need for further research to translate these findings into clinical applications.

Analysis of triacylglycerol regioisomers in plant oils using direct inlet negative ion chemical ionization tandem mass spectrometry

Triacylglycerols (TGs) are the primary lipids of plant oils and the positional distribution of fatty acids (FAs) is essential to physicochemical, functional, and nutritional qualities of oils. Most studies have reported TG species in plant oils. In some studies, FA combinations in each TG species have been reported still neglecting the regioisomer composition of TGs. In this study, a fast direct inlet negative ion chemical ionization tandem mass spectrometric (NICI-MS/MS) method and optimization algorithm were applied to study the regioisomerism of TGs in 18 different plant oils. According to FA composition results, oleic, FA 18:1(9); linoleic, FA 18:2(9,12); palmitic, FA 16:0 and stearic acid, FA 18:0 were the most abundant FAs, composing mainly TG species having acyl carbon numbers 50, 52 and 54 and 1-4 double bonds. Based on 35 detected TG species, oils were classified into five groups using clustering analysis. Each group had a different dominant TG species of which the most abundant were triunsaturated ones. In regioisomeric pairs or triplets, FA 16:0, FA 16:1(9), FA 18:0, and FA 18:2(9,12) were more commonly in the sn-1/3 position, while FA 18:1 slightly preferred sn-2. The most abundant TG regioisomers were: TG 16:0_18:1(sn-2)_18:1 (52:2, mainly 18:1 in sn-2) especially in avocado, macadamia nut, olive, and palm oils; TG 18:2_18:2(sn-2)_18:1 and TG 18:2_18:1(sn-2)_18:2 (TG 54:5, mainly 18:2 in sn-2) in corn, pumpkin seed, sesame, and sunflower oils. The use of high-throughput NICI-MS/MS method to study regioisomers in commercial plant oils contributes to further studies on profiling lipid structure and developing products with specific TG compositions to meet dietary needs. The regiospecific information of TGs in edible oils is crucial for understanding their health benefits and functional properties, which are in turn needed in selecting oils for various applications.

Assessment of the effects of cadmium, samarium and gadolinium on the blue mussel (Mytilus edulis): A biochemical, transcriptomic and metabolomic approach

Improving the understanding of how chemicals affect on organisms and assessing the associated environmental risks is of major interest in environmental studies. This can be achieved by using complementary approaches based on the study of the molecular responses of organisms. Because of the known chemical pressures on the environment, regulations on the content of some chemicals, such as cadmium, have been mostly completed. In contrast, the environmental toxicity of rare earth elements (REEs), which are widely used in industry, has only recently begun to receive attention. Here, we investigated the effects of cadmium, and two REEs, samarium and gadolinium, on marine mussels under laboratory exposures. We found that after an 8-day exposure at 500 µg/L, the metals were bioaccumulated by the mussels. Furthermore, samarium and gadolinium affected two oxidative stress biomarkers, GST and SOD. Lipidomic analysis showed that lipid content was modulated by the REEs, but not by cadmium. Interestingly, several compounds belonging to the phosphoinositide metabolism were more abundant, suggesting a pro-mitotic or cell survival response, while a higher abundance of cardiolipins after samarium exposure suggested an alteration of mitochondrial activity. Moreover, depending on the tissue and the metal considered, transcriptional analyses revealed an effect on metallothionein, hsp70/90, energy metabolism enzymes, as well as pro-mitotic transcript accumulation. Thus, this study sheds a new light on metal toxicity and in particularl REEs by highlighting the accumulation and toxicity of cadmium, samarium and gadolinium at 500 µg/L at different molecular levels, from gene expression to the lipidome of blue mussels.

Temperature adaptation of yeast phospholipid molecular species at the acyl chain positional level

Yeast is a poikilothermic organism and adapts its lipid composition to the environmental temperature to maintain membrane physical properties. Studies addressing temperature-dependent adaptation of the lipidome have described changes in the phospholipid composition at the level of sum composition (e.g. PC 32:1) and molecular composition (e.g. PC 16:0_16:1). However, there is little information at the level of positional isomers (e.g. PC 16:0/16:1 versus PC 16:1/16:0). Here, we used collision- and ozone-induced dissociation (CID/OzID) mass spectrometry to investigate homeoviscous adaptation of PC, PE and PS to determine the phospholipid acyl chains at the sn-1 and sn-2 position. Our data establish the sn-molecular species composition of PC, PE and PS in the lipidome of yeast cultured at different temperatures.

The developmental lipidome of Nippostrongylus brasiliensis

BACKGROUND

Nippostrongylus brasiliensis-a nematode of rodents-is commonly used as a model to study the immunobiology of parasitic nematodes. It is a member of the Strongylida-a large order of socioeconomically important parasitic nematodes of animals. Lipids are known to play essential roles in nematode biology, influencing cellular membranes, energy storage and/or signalling.

METHODS

The present investigation provides a comprehensive, untargeted lipidomic analysis of four developmental stages/sexes (i.e. egg, L3, adult female and adult male stages) of N. brasiliensis utilising liquid chromatography coupled to mass spectrometry.

RESULTS

We identified 464 lipid species representing 18 lipid classes and revealed distinct stage-specific changes in lipid composition throughout nematode development. Triacylglycerols (TGs) dominated the lipid profile in the egg stage, suggesting a key role for them in energy storage at this early developmental stage. As N. brasiliensis develops, there was a conspicuous transition toward membrane-associated lipids, including glycerophospholipids (e.g. PE and PC) and ether-linked lipids, particularly in adult stages, indicating a shift toward host adaptation and membrane stabilisation.

CONCLUSIONS

We provide a comprehensive insight into the lipid composition and abundance of key free-living and parasitic stages of N. brasiliensis. This study provides lipidomic resources to underpin the detailed exploration of lipid biology in this model parasitic nematode.

Unveiling cellular changes in leukaemia cell lines after cannabidiol treatment through lipidomics

The present study was aimed at revealing the metabolic changes that occurred in the cellular lipid pattern of acute and chronic myeloid leukaemia cells following treatment with cannabidiol (CBD). CBD is a non-psychoactive compound present in Cannabis sativa L., which has shown an antiproliferative action in these type of cancer cells. CBD treatment reduced cell viability and initiated apoptotic and necrotic processes in both cancer cell lines in a time and dose-dependent manner, showing acute myeloid leukaemia (HL-60) cells greater sensitivity than chronic myeloid leukaemia ones (K-562), without differences in the activation of caspases 3/7. Then, control and treated cells of HL-60 and K-562 cell lines were studied through an untargeted lipidomic approach. The treatment was carried out with CBD at a concentration of 10 μM for HL-60 cells and 23 µM CBD for K-562 cells for 48 h. After the extraction of the lipid content from cell lysates, the samples were analysed by UHPLC-QTOF-MS/MS both in the positive and the negative ionization modes. The comprehensive characterization of cellular lipids unveiled several classes significantly affected by CBD treatment. Most of the differences correspond to phospholipids, including cardiolipins (CL), phosphatidylcholines (PC) and phosphosphingolipids (SM), and also triacylglycerols (TG), being many TG species increased after CBD treatment in the acute and chronic models, whereas phospholipids were found to be decreased. The results highlight some important lipid alterations related to CBD treatment, plausibly connected with different metabolic mechanisms involved in the process of cell death by apoptosis in cancer cell lines.

Enhancing Biomedicine: Proteomics and Metabolomics in Action

The rapid and substantial advancements in proteomic and metabolomic technologies have revolutionized our ability to investigate biological systems [...].

Securing food authenticity by translating triacylglycerol profiles of edible oils into a versatile identification method for pumpkin seed oil adulteration

Edible plant oils provide a crucial source of lipids for human nutrition. Owing to the complex processing of some high-quality variants, including Styrian pumpkin seed oil, edible plant oils have become susceptible to food fraud by adulteration with cheaper vegetable oils, compromising both authenticity and quality. To address this issue, a workflow was developed utilizing QTOF-MS/MS to search for triacylglycerol markers indicative of adulteration and subsequently adapted them for routine analysis using triple quadrupole MS/MS. By developing a transparent classification system utilizing a multi-feature triacylglycerol panel, reliable detection of adulteration down to 3 % (w/w) is possible. Calculating ratios of selected markers and establishing intervals derived from pure oils further enables easy scalability to adjust marker ratios and ensure robustness against permanent or seasonal changes. Our work aims to make advances towards a rapid and accurate detection of oil adulteration in food industry, crucial for maintaining customer trust and safety.

Comprehensive lipidomic profiling of human milk from lactating women across varying lactation stages and gestational ages

An untargeted lipidomic analysis was conducted to investigate the lipid composition of human milk across different lactation stages and gestational ages systematically. A total of 25 lipid subclasses and 934 lipid species as well as 90 free fatty acids were identified. Dynamic changes of the lipids throughout lactation and gestational phases were highlighted. In general, lactation stages introduced more variations in the lipid composition of human milk than gestational ages. Most lipids decreased as the milk progressed from the colostral stage to the mature stage, with some reaching a peak at the transitional stage. Significant variations in lipid composition across gestational ages were predominantly evident during early lactation period. In mature milks, most of the lipids exhibited no discernible statistical differences among gestational ages. This elucidation offers valuable insights and guidance for tailoring precise nutritional strategies for infants with diverse health needs.

LipoCLEAN: A Machine Learning Filter to Improve Untargeted Lipid Identification Confidence

In untargeted lipidomics experiments, putative lipid identifications generated by automated analysis software require substantial manual filtering to arrive at usable high-confidence data. However, identification software tools do not make full use of the available data to assess the quality of lipid identifications. Here, we present a machine-learning-based model to provide coherent, holistic quality scores based on multiple lines of evidence. Underutilized metrics such as isotope ratios and chromatographic behavior allow for much higher accuracy of identification confidence. We find that approximately 50% of tandem mass spectrometry-based automated lipid identifications are incorrect but that multidimensional rescoring reduces false discoveries to only 7% while retaining 80% of true positives. Our method works with most chromatography methods and generalizes across a family of MS instruments. LipoCLEAN is available at https://github.com/stavis1/LipoCLEAN.

Don't Be Surprised When These Surprise You: Some Infrequently Studied Sphingoid Bases, Metabolites, and Factors That Should Be Kept in Mind During Sphingolipidomic Studies

Sphingolipidomic mass spectrometry has provided valuable information-and surprises-about sphingolipid structures, metabolism, and functions in normal biological processes and disease. Nonetheless, many noteworthy compounds are not routinely determined, such as the following: most of the sphingoid bases that mammals biosynthesize de novo other than sphingosine (and sometimes sphinganine) or acquire from exogenous sources; infrequently considered metabolites of sphingoid bases, such as N-(methyl)n-derivatives; "ceramides" other than the most common N-acylsphingosines; and complex sphingolipids other than sphingomyelins and simple glycosphingolipids, including glucosyl- and galactosylceramides, which are usually reported as "monohexosylceramides". These and other subspecies are discussed, as well as some of the circumstances when they are likely to be seen (or present and missed) due to experimental conditions that can influence sphingolipid metabolism, uptake from the diet or from the microbiome, or as artifacts produced during extraction and analysis. If these compounds and factors are kept in mind during the design and interpretation of lipidomic studies, investigators are likely to be surprised by how often they appear and thereby advance knowledge about them.

Lipidomics of Huntington's Disease: A Comprehensive Review of Current Status and Future Directions

BACKGROUND

Huntington's disease (HD) is a multifaceted neurological disorder characterized by the progressive deterioration of motor, cognitive, and psychiatric functions. Despite a limited understanding of its pathogenesis, research has implicated abnormal trinucleotide cytosine-adenine-guanine CAG repeat expansion in the huntingtin gene (HTT) as a critical factor. The development of innovative strategies is imperative for the early detection of predictive biomarkers, enabling timely intervention and mitigating irreversible cellular damage. Lipidomics, a comprehensive analytical approach, has emerged as an indispensable tool for systematically characterizing lipid profiles and elucidating their role in disease pathology.

METHOD

A MedLine search was performed to identify studies that use lipidomics for the characterization of HD. Search terms included "Huntington disease"; "lipidomics"; "biomarker discovery"; "NMR"; and "Mass spectrometry".

RESULTS

This review highlights the significance of lipidomics in HD diagnosis and treatment, exploring changes in brain lipids and their functions. Recent breakthroughs in analytical techniques, particularly mass spectrometry and NMR spectroscopy, have revolutionized brain lipidomics research, enabling researchers to gain deeper insights into the complex lipidome of the brain.

CONCLUSIONS

A comprehensive understanding of the broad spectrum of lipidomics alterations in HD is vital for precise diagnostic evaluation and effective disease management. The integration of lipidomics with artificial intelligence and interdisciplinary collaboration holds promise for addressing the clinical variability of HD.

To image or not to image: Use of imaging mass spectrometry in biomedical lipidomics

Lipid imaging mass spectrometry (LIMS) allows for establishing the bidimensional distribution of lipid species within a tissue section. One of the main advantages is the generation of spatial information on lipid species distribution at a spatial (lateral) resolution bordering on single-cell resolution with no need to isolate cells. Thus, LIMS images demonstrate, with a level of detail never described before, that lipid profiles are highly sensitive to cell type and pathophysiological state. The wealth and relevance of the information conveyed by LIMS makes up for the lack of a separation stage before sample injection into the mass analyzer, which can somehow be circumvented by other means. Hence, the possibility of describing the lipidome at the cellular level while preserving the microenvironment offers an incomparable opportunity to investigate physiological and pathological contexts. However, to fully grasp the biological implications of the lipid profiles, it is essential to contextualize LIMS data within the broader multiscale 'omic' landscape, entailing genomics, epigenomics, and proteomics, each offering a unique window into the regulatory layers of the cell. In this line, the number of techniques that can be combined with LIMS to delve into the molecular mechanisms underlying differential lipid profiles is continuously increasing. Herein, we aim to describe the key features of LIMS analyses, from sample preparation to data interpretation, as well as the current methodologies to enrich and complete the final outcome. While the field is rapidly advancing, we consider there is solid evidence to foresee the incorporation of LIMS into clinical environments.

Spatial lipidomic profiles of atherosclerotic plaques: A mass spectrometry imaging study

Lipids contribute to atherosclerotic cardiovascular disease but their roles are not fully understood. Spatial lipid composition of atherosclerotic plaques was compared between species focusing on aortic plaques from New Zealand White rabbits and carotid plaques from humans (n = 3), using matrix-assisted laser desorption/ionization mass spectrometry imaging. Histologically discriminant lipids within plaque features (neointima and media in rabbits, and lipid-necrotic core and fibrous cap/tissue in humans) included sphingomyelins, phosphatidylcholines, and cholesteryl esters. There were 67 differential lipids between rabbit plaque features and 199 differential lipids in human, each with variable importance in projection score ≥1.0 and p < 0.05. The lipid profile of plaques in the rabbit model closely mimicked that of human plaques and two key pathways (impact value ≥ 0.1), sphingolipid and glycerophospholipid metabolism, were disrupted by atherosclerosis in both species. Thus, mass spectrometry imaging of spatial biomarkers offers valuable insights into atherosclerosis.

Absolute quantitative lipidomics reveals the disturbance of lipid metabolism induced by oral exposure of titanium dioxide nanoparticles

The widespread use of titanium dioxide nanoparticles (TiO2 NPs) as a white pigment in consumer goods increases the possibility of its release into the environment, which poses a great health risk to human beings. Many studies have proved the liver damage caused by TiO2 NPs, but the research about the potential effects of TiO2 NPs on liver lipid metabolism has been limited. Therefore, we selected Sprague-Dawley (SD) rats to explore the effects of long-term exposure to TiO2 NPs on lipid metabolism. Rats were exposed to TiO2 NPs at 0, 2, 10, 50 mg/kg body weight daily for 90 consecutive days. Subsequently, absolute quantitative lipidomics was used to ascertain variation of differential lipid metabolites in rat liver and serum. The results showed that TiO2 NPs (50 mg/kg) changed 22 lipid metabolites such as DAG (18:2/20:5) and TAG (58:10/FA18:2) in rat liver. In the serum, the alteration of 119 lipid metabolites such as DAG (18:0/18:2) were more significant. There was a significant correlation between the different lipid metabolites in liver and serum. At the same time, it was observed that the relative expression levels of oxidative stress-related genes Nrf-2 and Ho-1 changed significantly, and they were closely related to differential metabolites. In conclusion, oral exposure of TiO2 NPs has changed the lipid metabolomics of liver and serum, and the strong induction of oxidative stress may be related to it. TAG and DAG are key metabolites and metabolic pathways in two distinct biological samples, serving as potential indicators of liver injury to a certain extent.

Growth of Staphylococcus aureus in the presence of oleic acid shifts the glycolipid fatty acid profile and increases resistance to antimicrobial peptides

Staphylococcus aureus readily adapts to various environments and quickly develops antibiotic resistance, which has led to an increase in multidrug-resistant infections. Hence, S. aureus presents a significant global health issue and its adaptations to the host environment are crucial for understanding pathogenesis and antibiotic susceptibility. When S. aureus is grown conventionally, its membrane lipids contain a mix of branched-chain and straight-chain saturated fatty acids. However, when unsaturated fatty acids are present in the growth medium, they become a major part of the total fatty acid composition. This study explores the biophysical effects of incorporating straight-chain unsaturated fatty acids into S. aureus membrane lipids. Membrane preparations from cultures supplemented with oleic acid showed more complex differential scanning calorimetry scans than those grown in tryptic soy broth alone. When grown in the presence of oleic acid, the cultures exhibited a transition significantly above the growth temperature, attributed to the presence of glycolipids with long-chain fatty acids causing acyl chain packing frustration within the bilayer. Functional aspects of the membrane were assessed by studying the kinetics of dye release from unilamellar vesicles induced by the antimicrobial peptide mastoparan X. Dye release was slower from liposomes prepared from cells grown in oleic acid-supplemented cultures, suggesting that changes in membrane lipid composition and biophysics protect the cell membrane against peptide-induced lysis. These findings underscore the intricate relationship between the growth environment, membrane lipid composition, and the physical properties of the bacterial membrane, which should be considered when developing new strategies against S. aureus infections.

Unsaturated Fatty Acids Are Decreased in Aβ Plaques in Alzheimer's Disease

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-beta (Aβ) plaques in the brain, contributing to neurodegeneration. This study investigates lipid alterations within these plaques using a novel, label-free, multimodal approach. Combining infrared (IR) imaging, machine learning, laser microdissection (LMD), and flow injection analysis mass spectrometry (FIA-MS), we provide the first comprehensive lipidomic analysis of chemically unaltered Aβ plaques in post-mortem human AD brain tissue. IR imaging revealed decreased lipid unsaturation within plaques, evidenced by a reduction in the alkene (=C-H) stretching vibration band. The high spatial resolution of IR imaging, coupled with machine learning-based plaque detection, enabled precise and label-free extraction of plaques via LMD. Subsequent FIA-MS analysis confirmed a significant increase in short-chain saturated lipids and a concomitant decrease in long-chain unsaturated lipids within plaques compared to the surrounding tissue. These findings highlight a substantial depletion of unsaturated fatty acids (UFAs) in Aβ plaques, suggesting a pivotal role for lipid dysregulation and oxidative stress in AD pathology. This study advances our understanding of the molecular landscape of Aβ plaques and underscores the potential of lipid-based therapeutic strategies in AD.

Cold-induced phosphatidylethanolamine synthesis in liver and brown adipose tissue of mice

Increasing energy expenditure in brown adipose (BAT) tissue by cold-induced lipolysis is discussed as a potential strategy to counteract imbalanced lipid homeostasis caused through unhealthy lifestyle and cardiometabolic disease. Yet, it is largely unclear how liberated fatty acids (FA) are metabolized. We investigated the liver and BAT lipidome of mice housed for 1 week at thermoneutrality, 23 °C and 4 °C using quantitative mass spectrometry-based lipidomics. Housing at temperatures below thermoneutrality triggered the generation of phosphatidylethanolamine (PE) in both tissues. Particularly, the concentrations of PE containing polyunsaturated fatty acids (PUFA) in their acyl chains like PE 18:0_20:4 were increased at cold. Investigation of the plasma's FA profile using gas chromatography coupled to mass spectrometry revealed a negative correlation of PUFA with unsaturated PE in liver and BAT indicating a flux of FA from the circulation into these tissues. Beta-adrenergic stimulation elevated intracellular levels of PE 38:4 and PE 40:6 in beige wildtype adipocytes, but not in adipose triglyceride lipase (ATGL)-deficient cells. These results imply an induction of PE synthesis in liver, BAT and thermogenic adipocytes after activation of the beta-adrenergic signaling cascade.

Lipidomics of coconut, almond and soybean milks - Detailed analysis of polar lipids and comparison with bovine milk

In this work, the lipidomic analysis on polar components of almond, coconut, and soy beverages was performed by liquid chromatography quadrupole time-of-flight mass spectrometry. A comparison with bovine milk was also performed. A total of 30 subclasses of polar lipids, belonging mainly to glycerophospholipids and sphingolipids, and a total of 572 molecular species were identified. Coconut showed various kinds of sphingolipids, belonging to hexosylceramides and sulfatides. Soy is particularly rich in molecular species of phospholipids. Fatty acids with chain length from 16 to 18 were the most common in almond. Numerous species of sphingomyelins were found in bovine milk, differently from plant-based beverages. Furthermore, a principal component analysis based on the polar lipid data was applied to discriminate samples, with 21 molecular species identified as biomarkers. This research opens interesting perspectives on vegetable beverages as bovine milk alternatives, especially in vegetarian and vegan diets.

Sex-specific response of the human plasma lipidome to short-term cold exposure

Cold-induced lipolysis is widely studied as a potential therapeutic strategy to combat metabolic disease, but its effect on lipid homeostasis in humans remains largely unclear. Blood plasma comprises an enormous repertoire in lipids allowing insights into whole body lipid homeostasis. So far, reported results originate from studies carried out with small numbers of male participants. Here, the blood plasma's lipidome of 78 male and 93 female volunteers, who were exposed to cold below the shivering threshold for 2 h, was quantified by comprehensive lipidomics using high-resolution mass spectrometry. Short-term cold exposure increased the concentrations in 147 of 177 quantified circulating lipids and the response of the plasma's lipidome was sex-specific. In particular, the amounts of generated glycerophospholipid and sphingolipid species differed between the sexes. In women, the BMI could be related with the lipidome's response. A logistic regression model predicted with high sensitivity and specificity whether plasma samples were from male or female subjects based on the cold-induced response of phosphatidylcholine (PC), lysophosphatidylcholine (LPC), and sphingomyelin (SM) species. In summary, cold exposure promotes lipid synthesis by supplying fatty acids generated after lipolysis for all lipid classes. The plasma lipidome, i.e. PC, LPC and SM, shows a sex-specific response, indicating a different regulation of its metabolism in men and women. This supports the need for sex-specific research and avoidance of sex bias in clinical trials.

A Method for Analysis of Oxidized Phospholipids from Biological Samples Using Mass Spectrometry

Oxidized phospholipids (oxPLs) are generated during innate immunity and inflammation, where they play a variety of biological roles, including regulation of autoimmunity and coagulation. Some are generated by enzymatic reactions, leading to stereo- and regiospecificity, while many others can be formed through nonenzymatic oxidation and truncation and can be used as biomarkers of oxidative stress. Mass spectrometry methods have been developed over many years for oxPL analysis, which can provide robust estimations of molecular species and amounts, where standards are available. Here we present a method used for the analysis of enzymatically-generated oxPL (eoxPL), which allows quantification of mono-hydroxy oxylipin-containing species. We also show profiling of many other partially characterized structures in tissue samples and provide typical chromatograms obtained.

Analysis of the Mammalian Lipidome by DMS Shotgun Lipidomics

Shotgun Lipidomics is a robust methodology for the characterization of the lipidome of complex biological samples. This assay is among the most quantitative lipidomics methods and is capable of surveying a wide breadth of lipid subclasses, both neutral and polar. The shortfalls of the technique include limitations in lipid species characterization and computationally demanding data analysis requiring isotopic and isobaric overlap correction. Differential Mobility Spectrometry (DMS) has demonstrated its utility in enabling acyl tail characterization within a Shotgun Lipidomics experiment. Here, we present a workflow for DMS Shotgun Lipidomics that measures 1400 possible lipid species. It utilizes the Shotgun Lipidomics Assistant (SLA) application, an open-source application that supervises the data analysis for an expansive Shotgun Lipidomics experiment.

Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipdiomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

[Progress in applications of ambient ionization mass spectrometry for lipids identification]

Lipids are indispensable components of living organisms and play pivotal roles in cell-membrane fluidity, energy provision, and neurotransmitter transmission and transport. Lipids can act as potential biomarkers of diseases given their abilities to indicate cell-growth status. For example, the lipid-metabolism processes of cancer cells are distinct from those of normal cells owing to their rapid proliferation and adaptation to ever-changing biological environments. As a result, the ability to rapidly detect, identify, and monitor lipid components is critical for tracking life-related processes and may enhance cancer diagnosis and treatment efficacy. Mass spectrometry (MS) is regarded to be among the most efficient methods for directly obtaining molecular-structural information, and is distinctly advantageous for identifying lipids. Recent years have witnessed the emergence of ambient mass spectrometry (AMS), which enables direct analyte sampling and ionization without the need for sample preprocessing. These characteristics endow AMS with special advantages for identifying and monitoring lipids. Furthermore, the ongoing development of soft ionization technologies has led to the widespread use of AMS for the detection of complex and diverse lipid molecules. Electrospray ionization (ESI) is a gentle ionization method that can be used to detect medium-to-high-polarity compounds and provide detailed chemical information for lipids by producing a fine mist of charged droplets from a liquid sample. Consequently, a series of ESI-based ionization methods have been developed for fabricating different AMS systems capable of rapidly detecting lipids in a simple manner. For example, desorption electrospray ionization (DESI) is among the most extensively employed ambient ionization techniques, and has been used to detect a wide range of samples, including solids, liquids, and gases. DESI involves spraying a charged solvent onto the surface of a sample, after which the solvent is desorbed, the analyte is ionized, and the generated ions are transferred to the detector of the mass spectrometer via a gas plume. DESI can easily and precisely regulate the sampling space, thereby offering a highly effective approach for the in-situ detection of lipids from tissue samples. Additionally, single-cell lipid analysis is limited by small cell volumes, complex cellular matrices, and minimal absolute amounts of analyte. Common detection methods for single cells include flow cytometry and fluorescence microscopy, both of which require fluorescent labeling to detect specific target molecules, which limits detection selectivity and reproducibility to some extent. ESI-based single-cell mass spectrometry has emerged as a more-effective method for detecting cellular lipids owing to advantages that include high sensitivity, low sample consumption, high throughput, and multiple-detection capabilities. Moreover, lipid chemical diversity poses a significant challenge for determining structural details. Therefore, AMS-based lipid detection has been augmented with a series of chemical-treatment methods that provide more-comprehensive structural information for lipids. For example, diverse gas-phase dissociation techniques have been used to discriminate between lipid C=C-bond isomers and their sn-positions. Strategies that involve chemically modifying specific target C=C bonds prior to MS detection have also been employed. For example, the Paternò-Büchi (P-B) photochemical reaction oxidizes C=C bonds in unsaturated lipids to form oxetane structures, C=C bonds can be epoxidized to form the corresponding oxaziridines, the N-H aziridination reaction converts C=C bonds into aziridines, and the 1ΔO2 ene reaction adds an OOH group to a C=C bond. In this review, we discuss various environmental ionization techniques for lipid AMS developed over the past five years, with an emphasis on typical chemical strategies used to analyze lipid fine structures. Obtaining a high-coverage, high-sensitivity lipid-detection platform based on AMS remains challenging and requires further in-depth studies despite significant improvements in lipid MS-based detection techniques.

(Pre)Clinical Metabolomics Analysis

Metabolomics is the scientific field with the eager goal to comprehensively analyze the entirety of all small molecules of a biological system, i.e., the metabolome. Over the last few years, metabolomics has matured to become an analytical cornerstone of life science research across diverse fields, from fundamental biochemical applications to preclinical studies, including biomarker discovery and drug development. In this chapter, we provide an introduction to (pre)clinical metabolomics. We define key metabolomics aspects and provide the basis to thoroughly understand the relevance of this field in a biological and clinical context. We present and explain state-of-the-art analytical technologies devoted to metabolomic analysis as well as emerging technologies, discussing both strengths and weaknesses. Given the ever-increasing demand for handling complex datasets, the role of bioinformatics approaches in the context of metabolomic analysis is also illustrated.

Lipid imaging mass spectrometry: Towards a new molecular histology

Lipid research is attracting greater attention, as these molecules are key components to understand cell metabolism and the connection between genotype and phenotype. The study of lipids has also been fueled by the development of new and powerful technologies, able to identify an increasing number of species in a single run and at decreasing concentrations. One of such key developments has been the image techniques that enable the visualization of lipid distribution over a tissue with cell resolution. Thanks to the spatial information reported by such techniques, it is possible to associate a lipidome trait to individual cells, in fixed metabolic stages, which greatly facilitates understanding the metabolic changes associated to diverse pathological conditions, such as cancer. Furthermore, the image of lipids is becoming a kind of new molecular histology that has great chances to make an impact in the diagnostic units of the hospitals. Here, we examine the current state of the technology and analyze what the next steps to bring it into the diagnosis units should be. To illustrate the potential and challenges of this technology, we present a case study on clear cell renal cell carcinoma, a good model for analyzing malignant tumors due to their significant cellular and molecular heterogeneity.

Recommendations for Accurate Lipid Annotation and Semi-absolute Quantification from LC-MS/MS Datasets

Recent developments in LC-MS instrumentation and analytical technologies together with bioinformatics tools supporting high-throughput processing of large omics datasets significantly enhanced our capabilities and efficiency of identification and quantification of lipids in diverse biological materials. However, each biological matrix is characterized by its unique lipid composition, thus requiring optimization of analytical and bioinformatics workflows for each studied lipidome. Here, we describe an integrated workflow for deep lipidome profiling, accurate annotation, and semi-absolute quantification of complex lipidomes based on reversed phase chromatography and high resolution mass spectrometry. This chapter provides details on selection of the optimal extraction protocol, acquisition of LC-MS/MS data for accurate annotation of lipid molecular species, and design of lipidome-specific mixtures of internal standards to assist quantitative analysis of complex, native lipidomes.

Quantitative Lipidomics of Biological Samples Using Supercritical Fluid Chromatography Mass Spectrometry

Lipidomics has attracted attention in the discovery of unknown biomolecules and for capturing the changes in metabolism caused by genetic and environmental factors in an unbiased manner. However, obtaining reliable lipidomics data, including structural diversity and quantification data, is still challenging. Supercritical fluid chromatography (SFC) is a suitable technique for separating lipid molecules with high throughput and separation efficiency. Here, we describe a quantitative lipidomics method using SFC coupled with mass spectrometry. This technique is suitable for characterizing the structural diversity of lipids (e.g., phospholipids, sphingolipids, glycolipids, and glycerolipids) with high quantitative accuracy to understand their biological functions.

Copepod Lipidomics: Fatty Acid Substituents of Structural Lipids in Labidocerca aestiva, a Dominant Species in the Food Chain of the Apalachicola Estuary of the Gulf of Mexico

Zooplanktonic copepods represent a major biological mass in the marine food chain that can be affected by climate change. Monitoring the health of this critical biomass is essential for increasing our understanding of the impact of environmental changes on marine environments. Since the lipidomes of marine organisms are known to adapt to alterations in pH, temperature, and availability of metabolic precursors, lipidomics is one technology that can be used for monitoring copepod adaptations. Among the key lipid parameters that can be monitored are the fatty acid substituents of glycerolipids and glycerophospholipids. We utilized high-resolution tandem mass spectrometry (≤2 ppm mass error) to characterize the fatty acid substituents of triacylglycerols, glycerophosphocholines, ceramides, and sphingomyelins of Labidocerca aestiva. This included monitoring for furan fatty acid substituents, a family of fatty acids unique to marine organisms. These data will contribute to establishing a lipid database of the fatty acid substituents of essential structural lipids. The key findings were that polyunsaturated fatty acids (PUFAs) were only major substituents in glycerophosphocholines with 36 to 44 carbons. Triacylglycerols, ceramides, and sphingomyelins contained minimal PUFA substituents. Furan fatty acids were limited to mono- and di-acylglycerols. In summary, we have built a baseline database of the fatty acid substituents of key structural lipids in Labidocerca aestiva. With this database, we will next evaluate potential seasonal changes in these lipid substituents and long-term effects of climate change.

Parallel single-cell metabolic analysis and extracellular vesicle profiling reveal vulnerabilities with prognostic significance in acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive disease with a high relapse rate. In this study, we map the metabolic profile of CD34+(CD38low/-) AML cells and the extracellular vesicle signatures in circulation from AML patients at diagnosis. CD34+ AML cells display high antioxidant glutathione levels and enhanced mitochondrial functionality, both associated with poor clinical outcomes. Although CD34+ AML cells are highly dependent on glucose oxidation and glycolysis for energy, those from intermediate- and adverse-risk patients reveal increased mitochondrial dependence. Extracellular vesicles from AML are mainly enriched in stem cell markers and express antioxidant GPX3, with their profiles showing potential prognostic value. Extracellular vesicles enhance mitochondrial functionality and dependence on CD34+ AML cells via the glutathione/GPX4 axis. Notably, extracellular vesicles from adverse-risk patients enhance leukemia cell engraftment in vivo. Here, we show a potential noninvasive approach based on liquid 'cell-extracellular vesicle' biopsy toward a redefined metabolic stratification in AML.

Follicular fluid and plasma lipidome profiling and associations towards embryonic development outcomes during ART treatment

Introduction

It is well acknowledged that lipids assume a critical role in oocyte maturation and early embryonic metabolism, this study aimed to evaluate the relationship between the lipid composition of plasma and follicular fluid (FF), and the consequences of embryonic development. This study compared the lipidomic profiles of paired plasma and FF samples obtained from sixty-five Chinese women who underwent assisted reproductive technology (ART) treatments.

Methods

Non-targeted lipidomics analysis.

Result

Results not only indicated similarities in lipid composition between these biofluids, but also revealed a number of unique differences. The biomatrix distinction was found to be primarily driven by lipids belonging to the lysophosphatidylcholines (LPC), phosphatidylethanolamines (PE), ether PE, and triglyceride (TG) classes. In addition, specific species from these subclasses were discovered to be correlated with embryo development outcomes during ART. Notably, the composition of the fatty acyl chains appeared to play a crucial role in these associations. Furthermore, thirteen plasma lipid variables were identified, represented by Phosphatidylcholine 18:014:0 and PE P-18:020:1, which correlated with successful blastocyst formation (BF).

Discussion

The present study demonstrated that FF has a distinctive lipid composition, setting it apart from plasma; and the association observed with embryonic development underscored an important role of lipid composition in the healthy development of oocytes.

Combined Association of Plasma Metabolites with Body Mass Index and Physical Activity Level

Metabolomic analysis of the changes in plasma metabolites in obesity along with physical activity interaction may contribute to disease diagnosis and treatment. We sought to make a comprehensive assessment of the plasma metabolite profile of subjects with a lean (n = 20, BMI = 22.3) or overweight/obese (n = 29, BMI = 29) body mass index (BMI) and low (n = 33, IPAQ = 842) or high (n = 16, IPAQ = 6935) index of physical activity questionnaire (IPAQ), using an untargeted metabolomic approach. Two-way analysis of variance was applied to the data obtained from liquid chromatography-mass spectrometry analyses and resulted in 64 metabolites, mainly responsible for the data variance among the different groups. Finally, a complex network approach reveals the most relevant metabolites. The majority of the relevant metabolites are oxidized species of phospholipids. Most species of phosphatidylcholine and a species of phosphatidylglycerol were found to be decreased in obese subjects, while most species of phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol were increased. Only a single species each of prostaglandin, phosphatidylglycerol, and phosphatidylinositol were modulated by IPAQ, but interaction effects between BMI and IPAQ were found for most of the metabolites in the combination of obese BMI with low IPAQ.

The Multifaceted Impact of Bioactive Lipids on Gut Health and Disease

Bioactive lipids have a multifaceted role in health and disease and are recognized to play an important part in gut immunity and disease conditions such as inflammatory bowel disease and colon cancer. Advancements in lipidomics, enabled by mass spectrometry and chromatographic techniques, have enhanced our understanding of lipid diversity and functionality. Bioactive lipids, including short-chain fatty acids, saturated fatty acids, omega-3 fatty acids, and sphingolipids, exhibit diverse effects on inflammation and immune regulation. Short-chain fatty acids like butyrate demonstrate anti-inflammatory properties, enhancing regulatory T cell function, gut barrier integrity, and epigenetic regulation, making them promising therapeutic targets for inflammatory bowel disease and colon cancer. Conversely, saturated fatty acids promote inflammation by disrupting gut homeostasis, triggering oxidative stress, and impairing immune regulation. Omega-3 lipids counteract these effects, reducing inflammation and supporting immune balance. Sphingolipids exhibit complex roles, modulating immune cell trafficking and inflammation. They can exert protective effects or exacerbate colitis depending on their source and context. Additionally, eicosanoids can also prevent pathology through prostaglandin defense against damage to epithelial barriers. This review underscores the importance of dietary lipids in shaping gut health and immunity and also highlights the potential use of lipids as therapeutic strategies for managing inflammatory conditions and cancer.

Glycolipidomics of Liver Flukes and Host Tissues during Fascioliasis: Insights from Mass Spectrometry Imaging

Fascioliasis, a zoonotic disease caused by liver flukes of the genus Fasciola, poses significant health threats to both humans and livestock. While some infections remain asymptomatic, others can lead to fatal outcomes, particularly during the acute phase characterized by the migration of immature parasites causing severe liver damage. Through the combination of data acquired via high-spatial-resolution atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) and nanohydrophilic interaction chromatography tandem mass spectrometry, we investigated glycosphingolipids (GSLs) in both adult and immature parasite stages as well as the host liver and bile duct to unravel the intricacies of the host-pathogen interplay and associated pathology. Several GSLs showed characteristic distribution patterns within the parasite depending on the fatty acid composition of their ceramides, notably including GSLs carrying very long-chain fatty acids. Additionally, GSL compositions within the tegument of immature versus adult parasites varied, suggestive of tissue remodeling upon maturation. AP-SMALDI MSI further enabled the identification of GSLs potentially involved in in vivo interactions between the host and immature parasites. Moreover, our experiments unveiled alterations in other lipid classes during Fasciola infection, providing a broader understanding of lipidomic changes associated with the disease. Collectively, our findings contribute to a deeper comprehension of the molecular intricacies underlying fascioliasis, with a specific focus on GSLs.

Effects of Dietary Medium-Chain Triglyceride Supplementation on the Serum Metabolome of Young Adult and Senior Canines

In dogs, brain aging may lead to cognitive decline and cognitive dysfunction syndrome (CDS) [...].

Four-Dimensional Lipidomic Analysis Using Comprehensive Online UHPLC × UHPSFC/Tandem Mass Spectrometry

Multidimensional chromatography offers enhanced chromatographic resolution and peak capacity, which are crucial for analyzing complex samples. This study presents a novel comprehensive online multidimensional chromatography method for the lipidomic analysis of biological samples, combining lipid class and lipid species separation approaches. The method combines optimized reversed-phase ultrahigh-performance liquid chromatography (RP-UHPLC) in the first dimension, utilizing a 150 mm long C18 column, with ultrahigh-performance supercritical fluid chromatography (UHPSFC) in the second dimension, using a 10 mm long silica column, both with sub-2 μm particles. A key advantage of employing UHPSFC in the second dimension is its ability to perform ultrafast analysis using gradient elution with a sampling time of 0.55 min. This approach offers a significant increase in the peak capacity. Compared to our routinely used 1D methods, the peak capacity of the 4D system is 10 times higher than RP-UHPLC and 18 times higher than UHPSFC. The entire chromatographic system is coupled with a high-resolution quadrupole-time-of-flight (QTOF) mass analyzer using electrospray ionization (ESI) in both full-scan and tandem mass spectrometry (MS/MS) and with positive- and negative-ion polarities, enabling the detailed characterization of the lipidome. The confident identification of lipid species is achieved through characteristic ions in both polarity modes, information from MS elevated energy (MSE) and fast data-dependent analysis scans, and mass accuracy below 5 ppm. This analytical method has been used to characterize the lipidomic profile of the total lipid extract from human plasma, which has led to the identification of 298 lipid species from 16 lipid subclasses.

Microbial Metabolomics' Latest SICRIT: Soft Ionization by Chemical Reaction In-Transfer Mass Spectrometry

Microbial metabolomics studies are a common approach for identifying microbial strains that have a capacity to produce new chemistries both in vitro and in situ. A limitation to applying microbial metabolomics to the discovery of new chemical entities is the rediscovery of known compounds, or "known unknowns." One factor contributing to this rediscovery is that the majority of laboratories use one ionization source─electrospray ionization (ESI)─to conduct metabolomics studies. Although ESI is an efficient, widely adopted ionization method, its widespread use may contribute to the reidentification of known metabolites. Here, we present the use of a dielectric barrier discharge ionization (DBDI) for microbial metabolomics applications through the use of soft ionization chemical reaction in-transfer (SICRIT). Additionally, we compared SICRIT to ESI using two different Vibrio species: Vibrio fischeri, a symbiotic marine bacterium, and Vibrio cholerae, a pathogenic bacterium. Overall, we found that the SICRIT source ionizes a different set of metabolites than ESI, and it has the ability to ionize lipids more efficiently than ESI in the positive mode. This work highlights the value of using more than one ionization source for the detection of metabolites.

Oxysterol sulfates in fluids, cells and tissues: how much do we know about their clinical significance, biological relevance and biophysical implications?

Oxysterol sulfates are emerging as key players in lipid homeostasis, inflammation and immunity. Despite this, knowledge on their basal levels in fluids, cells and tissues and any changes associated with age, gender and diet in health and disease; as well as their spatio-temporal distribution in cell membranes and organelles have been greatly hampered by the lack of commercially available pure synthetic standards. Expansion of the panel of pure oxysterol sulfates standards is pivotal to improve our understanding on the impact of oxysterol sulfates at the membrane level and their role in cellular events. While the clinical significance, biophysical implications and biological relevance of oxysterol sulfates in fluids, cells and tissues remains largely unknown, knowledge already gathered on the precursors of oxysterol sulfates (e.g. oxysterols and cholesterol sulfate) can be used to guide researchers on the most relevant aspects to search for when screening for oxysterol sulfates bioavailability in (patho)physiological conditions which are crucial in the design of biophysical and of cell-based assays. Herein, we provide a review on the brief knowledge involving oxysterol sulfate and an overview on the biophysical implications and biological relevance of oxysterols and cholesterol sulfate useful to redirect further investigations on the role of oxysterol sulfates in health and disease.

Lipidomics in forensic science: a comprehensive review of applications in drugs, alcohol, latent fingermarks, fire debris, and seafood authentication

Forensic science, an interdisciplinary field encompassing the collection, examination, and presentation of evidence in legal proceedings, has recently embraced lipidomics as a valuable tool. Lipidomics, a subfield of metabolomics, specializes in the analysis of lipid structures and functions, offering insights into biological processes that can aid forensic investigations. While not a substitute for DNA analysis in personal identification, lipidomics complements this technique by focusing on small biological molecules, with distinct sample requirements. This review comprehensively explores the current applications of lipidomics in forensic science. The review commences with an introduction to the concept and historical background of lipidomics, subsequently delving into its utilization in diverse areas such as drug analysis, ethyl alcohol and substitute assessment, latent fingermark detection, fire debris analysis, and seafood authentication. By showcasing the various biological materials and methods employed, this review underscores the potential of lipidomics as a powerful adjunct in forensic investigations.

Behind the stoNE wall: A fervent activity for nuclear lipids

The four main types of biomolecules are nucleic acids, proteins, carbohydrates and lipids. The knowledge about their respective interactions is as important as the individual understanding of each of them. However, while, for example, the interaction of proteins with the other three groups is extensively studied, that of nucleic acids and lipids is, in comparison, very poorly explored. An iconic paradigm of physical (and likely functional) proximity between DNA and lipids is the case of the genomic DNA in eukaryotes: enclosed within the nucleus by two concentric lipid bilayers, the wealth of implications of this interaction, for example in genome stability, remains underassessed. Nuclear lipid-related phenotypes have been observed for 50 years, yet in most cases kept as mere anecdotical descriptions. In this review, we will bring together the evidence connecting lipids with both the nuclear envelope and the nucleoplasm, and will make critical analyses of these descriptions. Our exploration establishes a scenario in which lipids irrefutably play a role in nuclear homeostasis.

Radical-directed dissociation mass spectrometry for differentiation and relative quantitation of isomeric ether-linked phosphatidylcholines

BACKGROUND

Ether-linked phosphatidylcholines (PCs) include both plasmanyl and plasmenyl PCs, which contain an ether or a vinyl ether bond at the sn-1 linkage position, respectively. Profiling and quantifying ether PCs with accurate structural information is challenging because of the common presence of isomeric and isobaric species in a lipidome.

RESULTS

In the present study, radical directed dissociation (RDD) from collision-induced dissociation (CID) of the bicarbonate anion adduct of ether PCs has been investigated to differentiate and relatively quantify ether PCs. Alkyl- and alkenyl- PCs give diagnostic characteristic fragment patterns that enable their confident identification and isomer differentiation. Additionally, the sn-position specific product ions have proven effective for relative quantitation among isomers in ether PCs and their isobaric PC species. Using this methodology, we successfully identified a total of 30 PC-O species, 21 PC-P species at the chain composition level, and 22 species of isobaric PC at the sn-position level in the human plasma lipid extract. The quantitative analysis revealed that ether PCs with a 20:4 fatty acyl chain are relatively more abundant in human plasma. Finally, the profile of ether PCs in type 2 diabetic (T2D) groups compared to normal control groups revealed a significant decrease in PC-O 18:1/20:5. We also found it is the PC species containing a 17-carbon fatty acyl chain, rather than their isobaric ether PCs, that shows a decreasing trend in the T2D groups.

SIGNIFICANCE

ether-linked PCs are firstly investigated by RDD mass spectrometry.

Quantifying acyl-chain diversity in isobaric compound lipids containing monomethyl branched-chain fatty acids

Compound lipids comprise a diverse group of metabolites present in living systems, and metabolic- and environmentally-driven structural distinctions across this family are increasingly linked to biological function. However, methods for deconvoluting these often isobaric lipid species are lacking or require specialized instrumentation. Notably, acyl-chain diversity within cells may be influenced by nutritional states, metabolic dysregulation, or genetic alterations. Therefore, a reliable, validated method of quantifying structurally similar even-, odd-, and branched-chain acyl groups within intact compound lipids will be invaluable for gaining molecular insights into their biological functions. Here we demonstrate the chromatographic resolution of isobaric lipids containing distinct combinations of straight-chain and branched-chain acyl groups via ultra-high-pressure liquid chromatography (UHPLC)-mass spectrometry (MS) using a C30 liquid chromatography column. Using metabolically engineered adipocytes lacking branched-keto acid dehydrogenase A (Bckdha), we validate this approach through a combination of fatty acid supplementation and metabolic tracing using monomethyl branched-chain fatty acids and valine. We observe the resolution of numerous isobaric triacylglycerols and other compound lipids, demonstrating the resolving utility of this method. This approach adds to the toolbox for laboratories to quantify and characterize acyl chain diversity across the lipidome.

Unraveling the neutral and polar lipidome of Nordic brown macroalgae: A sustainable source of functional lipids

Brown macroalgae represent a sustainable and abundant source of lipids with acknowledged functional and health benefits. Nonetheless, macroalgae lipidome has been poorly unraveled due to lipids complex structural and chemical diversity. In this study, a comprehensive lipidomic analysis was performed in four macroalgae: Saccharina latissima, Fucus vesiculosus, Fucus serratus and the invasive Sargassum muticum, using HILIC-C30RP-HRMS. Neutral lipids (tri-, di-glycerides) comprised 72-82% of total lipids (TL) with a highly unsaturation profile (27-49% depending on species). The polar lipidome comprised glycolipids, phospholipids, betaine lipids and sphingolipids with varied content among macroalgae. S. latissima displayed the greatest level of glycolipids (23% of TL), by contrast with the dominance of long-chain polyunsaturated betaine lipids (10-18% of TL) in the other species, particularly in S. muticum. Phospholipids and sphingolipids were detected in low abundance (<1.7% of TL). This study elevated the potential of brown macroalgae as an emerging reservoir of bioactive lipids with nutritional relevance.

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs handling multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 for in-depth lipidome structural elucidation through electron-activated dissociation (EAD)-based tandem MS and determining their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section values. With the optimized EAD settings using 14 eV kinetic energy, the program correctly delineated lipid structures for 96.4% of authentic standards, among which 78.0% had the sn-, OH-, and/or C = C positions correctly assigned at concentrations exceeding 1 μM. We showcased our workflow by annotating the sn- and double-bond positions of eye-specific phosphatidylcholines containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and n-3-VLC-PUFA-supplemented HeLa cells, we identified glycerol 3-phosphate acyltransferase as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn1 position of phospholipids in mammalian cells, which was confirmed using EAD-MS/MS and recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering insights into lipid biology.

Gut microbiota analysis and LC-MS-based metabolomics to investigate AMPK/NF-κB regulated by Clostridium butyricum in the treatment of acute pancreatitis

BACKGROUND

Acute pancreatitis (AP) is an inflammatory condition with potentially life-threatening complications. This study investigates the therapeutic potential of Clostridium butyricum for modulating the inflammatory cascade through the AMPK/NF-κB signaling pathway, focusing on inflammation induced by AP. LC-MS analysis of serum samples from AP patients highlighted the regulation of lipid metabolism and inflammation, and found that metabolites involved in the inhibition of NF-κB phosphorylation and the AMPK activation pathway were downregulated. We hypothesized that pre-administration of Clostridium butyricum and its culture supernatant could mitigate AP-induced damage by modulating the AMPK/NF-κB pathway.

METHODS

Lipopolysaccharide (LPS)-induced cell inflammation models. LPS combined with CAE induced acute pancreatitis in mice. We divided mice into four groups: Con, AP, AP + C.Buty (AP with Clostridium butyricum treatment), and AP + CFS (AP with culture supernatant treatment). Analyses were performed using WB, RT-qPCR, Elisa, flow cytometry, IHC, and HE, respectively.

RESULTS

Our study shows that CFS can reduce the apoptosis of LPS-induced cellular inflammation and reduce the release of LPS-induced cytoinflammatory factors through the AMPK/NF-κB pathway in vitro. In vivo, Clostridium butyricum and its supernatant significantly reduced inflammatory markers, and corrected histopathological alterations in AP mice. Gut microbiota analysis further supported these results, showing that Clostridium butyricum and its supernatant could restore the balance of intestinal flora disrupted by AP.

CONCLUSIONS

Mechanistically, our results indicated that the therapeutic effects of Clostridium butyricum are mediated through the activation of AMPK, leading to the inhibition of the NF-κB pathway, thereby reducing the production of pro-inflammatory cytokines. Clostridium butyricum and its culture supernatant exert a protective effect against AP-induced damage by modulating the AMPK/NF-κB signaling pathway. Future studies will further elucidate the molecular mechanisms underlying the beneficial effects of Clostridium butyricum in AP and explore its clinical applicability in human subjects.

Nondestructive determination of canola oil oxidation causes: A near-infrared spectroscopy coupled with liquid chromatography-mass spectrometry for analyzing triacylglycerol hydroperoxide isomers

Monitoring oxidation causes (i.e. radical and/or photo-oxidation) of vegetable oil gives very important information for its quality control. This study aimed to develop a rapid and simple near infrared (NIR) spectroscopy method to explore the oxidation causes in vegetable oil by quantifying triacylglycerol hydroperoxide (TGOOH) positional isomers proceeded by different oxidation causes. First, the concentrations of TGOOH isomers were determined by liquid chromatography-mass spectrometry. Partial least square regression for concentrations of TGOOH isomers (R2: 0.994-0.998) using NIR spectra in the regions of 7500-6000 cm-1 and 5500-4500 cm-1 as explanatory variables. Principal component analysis revealed that those models were created because NIR spectra capture trace changes of the peak around 6980 cm-1(-CH2-) and 5260 cm-1 (H2O) derived by different oxidation causes (i.e. radical and/or photo-oxidation). The application of this method to various kinds of vegetable oil is expected to lead to a simple and rapid quality evaluation of vegetable oil.

Lipidomic Profiling of Common Wheat Flours from 1891-2010

Wheat lipids are a minor constituent of wheat, with an important influence on its processing properties. While breeding aimed to improve the protein composition of wheat flour, its influence on the lipid composition remains unknown. We therefore analyzed the lipidome of 60 different common wheat (Triticum aestivum) flours representing cultivars registered and grown in Germany from 1891 to 2010. Four different extraction techniques were tested before the application of a semiquantitative, untargeted UHPLC-MS/MS method. The measurements included 16 different lipid classes and 102 different lipid species. Based on the lipid profile, discrimination between old (registered between 1891 to 1950) and modern (1951 to 2010) cultivars was possible. While the lipid class composition remained constant, differences were due to variations within the class of triacylglycerols, with modern cultivars containing less unsaturated fatty acids than the older ones. Our results imply that improving the lipid class composition of common wheat is a promising target for further breeding.

Interlaboratory comparison of standardised metabolomics and lipidomics analyses in human and rodent blood using the MxP® Quant 500 kit

Metabolomics and lipidomics are pivotal in understanding phenotypic variations beyond genomics. However, quantification and comparability of mass spectrometry (MS)-derived data are challenging. Standardised assays can enhance data comparability, enabling applications in multi-center epidemiological and clinical studies. Here we evaluated the performance and reproducibility of the MxP® Quant 500 kit across 14 laboratories. The kit allows quantification of 634 different metabolites from 26 compound classes using triple quadrupole MS. Each laboratory analysed twelve samples, including human plasma and serum, lipaemic plasma, NIST SRM 1950, and mouse and rat plasma, in triplicates. 505 out of the 634 metabolites were measurable above the limit of detection in all laboratories, while eight metabolites were undetectable in our study. Out of the 505 metabolites, 412 were observed in both human and rodent samples. Overall, the kit exhibited high reproducibility with a median coefficient of variation (CV) of 14.3 %. CVs in NIST SRM 1950 reference plasma were below 25 % and 10 % for 494 and 138 metabolites, respectively. To facilitate further inspection of reproducibility for any compound, we provide detailed results from the in-depth evaluation of reproducibility across concentration ranges using Deming regression. Interlaboratory reproducibility was similar across sample types, with some species-, matrix-, and phenotype-specific differences due to variations in concentration ranges. Comparisons with previous studies on the performance of MS-based kits (including the AbsoluteIDQ p180 and the Lipidyzer) revealed good concordance of reproducibility results and measured absolute concentrations in NIST SRM 1950 for most metabolites, making the MxP® Quant 500 kit a relevant tool to apply metabolomics and lipidomics in multi-center studies.

Acid Sphingomyelinase Activation and ROS Generation Potentiate Antiproliferative Effects of Mitomycin in HCC

Sphingolipids play a major role in the regulation of hepatocellular apoptosis and proliferation. We have previously identified sphingolipid metabolites as biomarkers of chronic liver disease and hepatocellular carcinoma. Human hepatocellular carcinoma cell lines were transfected with a plasmid vector encoding for acid sphingomyelinase. Overexpressing cells were subsequently treated with mitomycin and cell proliferation, acid sphingomyelinase activity, sphingolipid concentrations, and generation of reactive oxygen species were assessed. The stimulation of acid sphingomyelinase-overexpressing cell lines with mitomycin showed a significant activation of the enzyme (p < 0.001) followed by an accumulation of various ceramide species (p < 0.001) and reactive oxygen radicals (p < 0.001) as compared to control transfected cells. Consequently, a significant reduction in cell proliferation was observed in acid sphingomyelinase-overexpressing cells (p < 0.05) which could be diminished by the simultaneous application of antioxidant agents. Moreover, the application of mitomycin induced significant alterations in mRNA expression levels of ceramidases and sphingosine kinases (p < 0.05). Our data suggest that the overexpression of the acid sphingomyelinase in human hepatoma cell lines enhances the in vitro antiproliferative potential of mitomycin via accumulation of ceramide and reactive oxygen species. The selective activation of acid sphingomyelinase might offer a novel therapeutic approach in the treatment of hepatocellular carcinoma.

Loss of Sterol Biosynthesis in Economically Important Plant Pests and Pathogens: A Review of a Potential Target for Pest Control

Sterol biosynthesis is a crucial metabolic pathway in plants and various plant pathogens. Their vital physiological role in multicellular organisms and their effects on growth and reproduction underline their importance as membrane compounds, hormone precursors, and signaling molecules. Insects, nematodes, and oomycetes of the Peronosporales group, which harbor important agricultural pests and pathogens, have lost the ability to synthesize their own sterols. These organisms rely on the acquisition of sterols from their host and are dependent on the sterol composition of the host. It is thought that sterol-synthesizing enzymes were lost during co-evolution with the hosts, which provided the organisms with sufficient amounts of the required sterols. To meet the essential requirements of these organisms, some sterol auxotrophs retained a few remaining sterol-modifying enzymes. Several molecular and biochemical investigations have suggested promising avenues for pest and pathogen control by targeting host sterol composition, sterol uptake, or sterol modification in organisms that have lost the ability to biosynthesize sterol de novo. This review examines the loss of sterol biosynthesis de novo in insects, nematodes, and oomycetes with the aim of investigating the sterol metabolic constraints and sterol acquisition of these organisms. This will shed light on its potential as a control target for the management of sterol-dependent organisms in a comprehensive agronomic approach.