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Members of Brassica seed oil are important sources of nutritionally superior edible oil. There are no comprehensive reports on complete lipidomic profile of these oilseed crops. In this study, the lipidomic profiling of edible oil from 7 different cultivated species of Brassica seed oils was performed by shotgun approach using electrospray High Resolution Time of Flight-Mass Spectrometry (ESI-ToF-MS). The mass spectrum under positive polarity revealed 1098 lipids under different lipid classes including sphingolipids, phospholipids and different storage lipids. Under negative polarity, 70 lipids including free fatty acids (FFA), cardiolipins and phospholipids were detected. Erucic acid in FFA form was found to be most abundant in both Yellow and Brown sarson. Brassica napus contains almost all forms of cardiolipins (CL). Out of 26 different species of cardiolipins detected in negative ion mode, CL 56:1 (FA 18:1) and CL 56:1 (FA 22:1) were present only in brown sarson. Similarly, CL 56:2 (FA 18:2) and CL 56:1 (FA 22:1) were present only in Yellow and Brown sarson. These findings enhance our understanding of the nutritional diversity in Brassica seed oils, emphasizing the significance of lipidomic analysis for elucidating the molecular composition of edible oils. [ABSTRACT FROM AUTHOR]

Lipid droplets (LDs) are intracellular storage vesicles composed of a neutral lipid core surrounded by a glycerophospholipid membrane. LD accumulation is associated with different stages of cancer progression and stress responses resulting from chemotherapy. In previous work, a novel dual nano-electrospray ionization source and data-dependent acquisition method for measuring the relative abundances of lipid species between two extracts were described and validated. Here, this same source and method were used to determine if oxaliplatin-sensitive and resistant cells undergo similar lipid profile changes, with the goal of identifying potential signatures that could predict the effectiveness of an oxaliplatin-containing treatment. Oxaliplatin is commonly used in the treatment of colorectal cancer. When compared to a no-drug control, oxaliplatin dosing caused significant increases in triglyceride (TG) and cholesterol ester (CE) species. These increases were more pronounced in the oxaliplatin-sensitive cells than in oxaliplatin-resistant cells. The increased neutral lipid abundance correlated with LD formation, as confirmed by confocal micrographs of Nile Red–stained cells. Untargeted proteomic analyses also support LD formation after oxaliplatin treatment, with an increased abundance of LD-associated proteins in both the sensitive and resistant cells. [ABSTRACT FROM AUTHOR]

Differential mobility spectrometry (DMS) is highly useful for shotgun lipidomic analysis because it overcomes difficulties in measuring isobaric species within a complex lipid sample and allows for acyl tail characterization of phospholipid species. Despite these advantages, the resulting workflow presents technical challenges, including the need to tune the DMS before every batch to update compensative voltages settings within the method. The Sciex Lipidyzer platform uses a Sciex 5500 QTRAP with a DMS (SelexION), an LC system configured for direction infusion experiments, an extensive set of standards designed for quantitative lipidomics, and a software package (Lipidyzer Workflow Manager) that facilitates the workflow and rapidly analyzes the data. Although the Lipidyzer platform remains very useful for DMS-based shotgun lipidomics, the software is no longer updated for current versions of Analyst and Windows. Furthermore, the software is fixed to a single workflow and cannot take advantage of new lipidomics standards or analyze additional lipid species. To address this multitude of issues, we developed Shotgun Lipidomics Assistant (SLA), a Python-based application that facilitates DMS-based lipidomics workflows. SLA provides the user with flexibility in adding and subtracting lipid and standard MRMs. It can report quantitative lipidomics results from raw data in minutes, comparable to the Lipidyzer software. We show that SLA facilitates an expanded lipidomics analysis that measures over 1450 lipid species across 17 (sub)classes. Lastly, we demonstrate that the SLA performs isotope correction, a feature that was absent from the original software.

Objective: To study the plasma lipidome of patients with anorexia nervosa (AN) before and after weight restoration treatment and report associations with AN subtypes and oral contraceptive pill (OCP) usage. Methods: Quantitative shotgun lipidomics analysis was used to study plasma lipids of 50 female patients with AN before and after weight restoration treatment and 50 healthy female controls (HC). The AN group was assessed with blood samples and questionnaires before and after weight restoration. Results: In total we quantified 260 lipid species representing 26 lipid classes of which 13 lipid class concentrations were elevated in patients with AN at admission compared with HC. Lipid classes remained elevated after weight restoration treatment of 84 days (median; interquartile range 28), and only the concentration of the ceramide lipid class increased between pre‐ and post‐treatment (p =.03), whereas lysophosphatidylcholine (LPC, p =.02), ether‐linked Phosphatidylcholine (LPCO, p =.02), and lysophosphatidylethanolamine (LPE, p =.009) decreased. Conclusion: In AN, 13 out of 26 lipid class concentrations were elevated at admission and remained elevated post‐treatment. Ceramides increased further between pre‐ and post‐weight restoration treatment, which could be related to the rapid weight gain during re‐nutrition. Further research is needed to elucidate the effects of weight restoration treatment on short‐ and long‐term lipid profiles in individuals with AN. Public Significance Statement: Lipidomics research can increase the understanding of AN, a complex and potentially life‐threatening eating disorder. By analyzing lipids, or fats, in the body, we can identify biological markers that may inform diagnosis and develop more effective treatments. This research can also shed light on the underlying mechanisms of the disorder, leading to a better understanding of the processes involved in eating behavior. [ABSTRACT FROM AUTHOR]

Specific biomarker molecules are increasingly being used for detection and quantification in plant and soil samples of arbuscular mycorrhizal (AM) fungi, an important and widespread microbial guild heavily implicated in transfers of nutrients and carbon between plants and soils and in the maintenance of soil physico-chemical properties. Yet, concerns have previously been raised as to the validity of a range of previously used approaches (e.g., microscopy, AM-specific fatty acids, sterols, glomalin-like molecules, ribosomal DNA sequences), justifying further research into novel biomarkers for AM fungal abundance and/or functioning. Here, we focused on complex polar lipids contained in pure biomass of Rhizophagus irregularis and in nonmycorrhizal and mycorrhizal roots of chicory (Cichorium intybus), leek (Allium porrum), and big bluestem (Andropogon gerardii). The lipids were analyzed by shotgun lipidomics using a high-resolution hybrid mass spectrometer. Size range between 1350 and 1550 Da was chosen for the detection of potential biomarkers among cardiolipins (1,3-bis(sn-3′-phosphatidyl)-sn-glycerols), a specific class of phospholipids. The analysis revealed a variety of molecular species, including cardiolipins containing one or two polyunsaturated fatty acids with 20 carbon atoms each, i.e., arachidonic and/or eicosapentaenoic acids, some of them apparently specific for the mycorrhizal samples. Although further verification using a greater variety of AM fungal species and samples from various soils/ecosystems/environmental conditions is needed, current results suggest the possibility to identify novel biochemical signatures specific for AM fungi within mycorrhizal roots. Whether they could be used for quantification of both root and soil colonization by the AM fungi merits further scrutiny. [ABSTRACT FROM AUTHOR]

Lipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5 years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches. [ABSTRACT FROM AUTHOR]

Interactions between macrophages and adipocytes are early molecular factors influencing adipose tissue (AT) dysfunction, resulting in high leptin, low adiponectin circulating levels and low-grade metaflammation, leading to insulin resistance (IR) with increased cardiovascular risk. We report the characterization of AT dysfunction through measurements of the adiponectin/leptin ratio (ALR), the adipo-insulin resistance index (Adipo-IRi), fasting/postprandial (F/P) immunometabolic phenotyping and direct F/P differential gene expression in AT biopsies obtained from symptom-free adults from the GEMM family study. AT dysfunction was evaluated through associations of the ALR with F/P insulin-glucose axis, lipid-lipoprotein metabolism, and inflammatory markers. A relevant pattern of negative associations between decreased ALR and markers of systemic low-grade metaflammation, HOMA, and postprandial cardiovascular risk hyperinsulinemic, triglyceride and GLP-1 curves was found. We also analysed their plasma non-coding microRNAs and shotgun lipidomics profiles finding trends that may reflect a pattern of adipose tissue dysfunction in the fed and fasted state. Direct gene differential expression data showed initial patterns of AT molecular signatures of key immunometabolic genes involved in AT expansion, angiogenic remodelling and immune cell migration. These data reinforce the central, early role of AT dysfunction at the molecular and systemic level in the pathogenesis of IR and immunometabolic disorders.

Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI‐MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI‐MS/MS, with the aid of collision‐induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbon–carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas‐phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GP − H]−, generates FA anions, [FA − H]−. The fatty acid anions can then react with doubly charged cationic magnesium tris‐phenanthroline complex, [Mg(Phen)3]2+, to form charge inverted complex cations of the form [FA − H + MgPhen2]+. CID of the complex generates product ion spectral patterns that allow for the identification of carbon–carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli. [ABSTRACT FROM AUTHOR]

The objective of this exploratory study was to assess the changes on lipidome and metabolome profiling of Longissimus lumborum bull muscle with different ultimate pH (pHu) and aging periods. The bull muscles classified as normal, intermediate, or high pHu were collected from a Brazilian commercial slaughterhouse, cut into steaks, individually vacuum-packaged, and aged for 3 days (3-d) or 21 days (21-d) at 2 °C. Muscle extracts were analyzed for the profiles of both lipids, by mass spectrometry (via direct flow-injection), and metabolites, by nuclear magnetic resonance, with downstream multivariate data analysis. As major results, pairwise comparisons identified C12:0 and C14:0 acylcarnitines as potential biomarkers of the intermediate pHu-muscle, which are related to lipid catabolism for alternative energy metabolism and indicate less protein breakage postmortem. Interestingly, the concentration of arginine at early postmortem aging (3-d) may influence the previously reported improved tenderness in normal and high pHu-muscles. Moreover, upregulation of fumarate, formate, and acetate with increased pHu muscle at 21-d aging indicate more intense tricarboxylic acid cycle, amino acid degradation, and pyruvate oxidation by reactive oxygen species, respectively. These three compounds (fumarate, formate, and acetate) discriminated statistically the muscle with high pHu at 21-d aging. The normal pHu-muscle showed higher concentrations of glycogenolysis and glycolysis metabolites, including glucose, mannose, and pyruvate. Hence, our results enhance knowledge of postmortem biochemical changes of beef within different pHu groups aged up to 21 days, which is essential to understand the mechanisms underpinning bull meat quality changes. • Lipidome and metabolome to assess beef with distinct ultimate pH and aging time. • Acylcarnitines identified as potential biomarkers of aged intermediate pHu-muscle. • Fumarate, formate and acetate as potential biomarkers of high pHu-muscle at 21-d aging. • Arginine found in higher concentrations in normal and high pHu-muscles at 3-d aging. [ABSTRACT FROM AUTHOR]

Objective: Acute myeloid leukemia (AML) is a vigorous type of leukemia requiring effective treatment. Myeloid cell leukemia-1 (Mcl-1) is an anti-apoptotic molecule that is upregulated in AML and is studied as a target for treatment. The specific Mcl-1 inhibitor, S63845, has antiproliferative effects on AML cells. Bioactive sphingolipids have crucial roles in cells and regulate Mcl-1 stability. This study aimed to elucidate the changes in lipid profiles of AML cell lines in response to Mcl-1 inhibitor S63845 treatment, with a special focus on sphingolipids. Materials and Methods: The cytotoxic effects of S63845 were identified in the AML cell lines MV4-11, HL60, and KG1 using the MTT cell proliferation assay. Lipidome analysis was conducted by quantitative shotgun lipidomics covering 378 individual lipid species in 26 classes within the major lipid categories. Results: The IC50 values of S63845 have been calculated as 7 nM for MV4-11, 53 nM for HL60, and 479 nM for KG1. The lipidome results reveal the S63845 treatment to increase ceramide (Cer) levels in the MV4-11 and KG1 cell lines at the expense of downstream sphingolipids while increasing the hexosylceramide (HexCer) levels in the HL60 cell line at the expense of the Cer and sphingomyelin (SM). Conclusion: This study showed S63845 to be able to suppress cell proliferation by altering lipid compositions in AML cell lines. More importantly, the study suggested S63845 to differentially affect the lipid profiles of AML cell lines. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease, and the dysregulation of lipid metabolism has been found to play an important role in the pathogenesis of RA and is related to the severity and prognosis of patients. Tripterygium wilfordii glycosides (TWG) is extracted from the roots of Tripterygium wilfordii Hook F. with anti-inflammatory and immunosuppressive effects, and numerous clinical trials have supported its efficacy in the treatment of RA. Some evidence suggested that TWG can modulate the formation of lipid mediators in various innate immune cells; however whether it can improve RA-related lipid disorders has not been systematically studied. In the study, type II collagen-induced arthritis (CIA) model was used to investigate the efficacy of TWG in the treatment of RA and its effect on lipid metabolism. Paw volume, arthritis score, pathological changes of ankle joint, serum autoantibodies and inflammatory cytokines were detected to assess the therapeutic effect on arthritis in CIA rats. Then, shotgun lipidomics based on multi-dimensional mass spectrometry platform was performed to explore the alterations in serum lipidome caused by TWG. The study showed that TWG could effectively ameliorate arthritis in CIA rats, such as reducing paw volume and arthritis score, alleviating the pathological damages of joint, and preventing the production of anti-CII autoantibodies and IL-1β cytokine. Significant increase in ceramide and decrease in lysophosphatidylcholine were observed in CIA rats, and were highly correlated with arthritis score and IL-1β level. After TWG treatment, these lipid abnormalities can be corrected to a great extent. These data demonstrate that TWG exerts a beneficial therapeutic effect on aberrant lipid metabolism which may provide new insights for further exploring the role and mechanism of TWG in the treatment of RA. [ABSTRACT FROM AUTHOR]

CD1d is an atypical MHC class I molecule which binds endogenous and exogenous lipids and can activate natural killer T (NKT) cells through the presentation of lipid antigens. CD1d surveys different cellular compartments including the secretory and the endolysosomal pathway and broadly binds lipids through its two hydrophobic pockets. Purification of the transmembrane protein CD1d for the analysis of bound lipids is technically challenging as the use of detergents releases CD1d-bound lipids. To address these challenges, we have developed a novel approach based on Sortase Adependent enzymatic release of CD1d at the cell surface of live mammalian cells, which allows for single step release and affinity tagging of CD1d for shotgun lipidomics. Using this system, we demonstrate that CD1d carrying the Sortase A recognition motif shows unimpaired subcellular trafficking through the secretory and endolysosomal pathway and is able to load lipids in these compartments and present them to NKT cells. Comprehensive shotgun lipidomics demonstrated that the spectrum and abundance of CD1d-associated lipids is not representative of the total cellular lipidome but rather characterized by preferential binding to long chain sphingolipids and glycerophospholipids. As such, sphingomyelin species recently identified as critical negative regulators of NKT cell activation, represented the vast majority of endogenous CD1d-associated lipids. Moreover, we observed that inhibition of endolysosomal trafficking of CD1d surprisingly did not affect the spectrum of CD1d-bound lipids, suggesting that the majority of endogenous CD1d-associated lipids load onto CD1d in the secretory rather than the endolysosomal pathway. In conclusion, we present a novel system for the analysis of CD1d-bound lipids in mammalian cells and provide new insight into the spectrum of CD1d-associated lipids, with important functional implications for NKT cell activation. [ABSTRACT FROM AUTHOR]

CD1d is an atypical MHC class I molecule which binds endogenous and exogenous lipids and can activate natural killer T (NKT) cells through the presentation of lipid antigens. CD1d surveys different cellular compartments including the secretory and the endolysosomal pathway and broadly binds lipids through its two hydrophobic pockets. Purification of the transmembrane protein CD1d for the analysis of bound lipids is technically challenging as the use of detergents releases CD1d-bound lipids. To address these challenges, we have developed a novel approach based on Sortase A-dependent enzymatic release of CD1d at the cell surface of live mammalian cells, which allows for single step release and affinity tagging of CD1d for shotgun lipidomics. Using this system, we demonstrate that CD1d carrying the Sortase A recognition motif shows unimpaired subcellular trafficking through the secretory and endolysosomal pathway and is able to load lipids in these compartments and present them to NKT cells. Comprehensive shotgun lipidomics demonstrated that the spectrum and abundance of CD1d-associated lipids is not representative of the total cellular lipidome but rather characterized by preferential binding to long chain sphingolipids and glycerophospholipids. As such, sphingomyelin species recently identified as critical negative regulators of NKT cell activation, represented the vast majority of endogenous CD1d-associated lipids. Moreover, we observed that inhibition of endolysosomal trafficking of CD1d surprisingly did not affect the spectrum of CD1d-bound lipids, suggesting that the majority of endogenous CD1d-associated lipids load onto CD1d in the secretory rather than the endolysosomal pathway. In conclusion, we present a novel system for the analysis of CD1d-bound lipids in mammalian cells and provide new insight into the spectrum of CD1d-associated lipids, with important functional implications for NKT cell activation.

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., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Lipidomics is a research area that investigates lipidomes that refer to the complete lipid profile within a cell, tissue, organism, or ecosystem by focusing on the interactions with neighboring molecules at the inter- or intracellular spaces of organisms. In recent decades, lipidomics has greatly evolved along with developments in mass spectrometric analysis (i.e., ionization approaches, the types of analyzers, and the data processing tools), leading to a rapid and accurate performance in the identification and quantification of individual lipid species. In this contribution, the identification and quantification of triacylglycerol (TAG) and phospholipid (PL) species in marine sources using mass spectrometry analysis are comprehensively discussed along with their physiological roles and health-beneficial effects on the human body. Moreover, this review emphasizes the importance of the isotopic deconvolution and instrument responses caused by the difference in the carbon number and the unsaturation of TAG and PL species in quantitative analysis. Most TAG and PL detected in marine taxa possess a high proportion of polyunsaturated ω3 long-chain polyunsaturated fatty acids (LCPUFA, ≥C20) in particular eicosapentaenoic acid (EPA, 20:5ω3) and docosahexaenoic acid (DHA, 22:6ω3), indicating the large number and structural diversity of glycerolipid species containing EPA and DHA. This review also discusses the health effects of TAG and PL species esterified with ω3 LCPUFA. Given that most fisheries science and aquaculture research during recent decades has mainly focused on ω3 LCPUFA after release from parent molecules, discussion of the health effects of ω3 LCPUFA in the form of TAG and PL extends understanding of the bioactivities of ω3 fatty acids as they occur naturally. [ABSTRACT FROM AUTHOR]

Pesticide formulations typically contain adjuvants added to enhance the performance of the active ingredient. Adjuvants may modify the bioavailability and toxicity of pesticides. In this study, the aim was to examine to which degree nonylphenol (NP) may interfere with the toxicity of two organophosphorus pesticides found in aquafeeds, chlorpyrifos-methyl (CPM) and pirimiphos-methyl (PPM). Atlantic salmon liver cells were exposed to these compounds singly or in combinations for 48 h using 3D cell cultures. Cytotoxicity, gene expression (RT-qPCR), and lipidomics endpoints were used to assess toxicity. The dose-response assessment showed that NP was the most toxic compound at equimolar concentrations (100 μM). Shotgun lipidomics pointed to a general pattern of elevated levels of saturated 18:0 fatty acids and declined levels of 18:1 monounsaturated fatty acids by the combined treatment. All three compounds had a distinct effect on membrane phospholipids, in particular on phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Lipid species patterns predicted inhibited stearoyl CoA desaturase (SCD) activity and increased Δ6 desaturase (D6D) activity in co-treated cells. While all three compounds alone mitigated increased triacylglycerol (TAG) accumulation, combined treatment resulted in lower total TAG in the cells. Multivariate analysis with PLS regression showed significant combined effects for nine genes (d5d, d6d, scd, srebf2, vtg, esr1, cyp1, ugt1a, and cat) and four lipid species (FFA 22:5, LPC 18:0, TAG52:1-FA16:0, and TAG52:1-FA18:0). In summary, this study demonstrates that the adjuvant can be the main contributor to the toxicity of a mixture of two organophosphorus pesticides with relatively low toxicity in fish cells.

Interactions between macrophages and adipocytes are early molecular factors influencing adipose tissue (AT) dysfunction, resulting in high leptin, low adiponectin circulating levels and low-grade metaflammation, leading to insulin resistance (IR) with increased cardiovascular risk. We report the characterization of AT dysfunction through measurements of the adiponectin/leptin ratio (ALR), the adipo-insulin resistance index (Adipo-IRi), fasting/postprandial (F/P) immunometabolic phenotyping and direct F/P differential gene expression in AT biopsies obtained from symptom-free adults from the GEMM family study. AT dysfunction was evaluated through associations of the ALR with F/P insulin-glucose axis, lipid-lipoprotein metabolism, and inflammatory markers. A relevant pattern of negative associations between decreased ALR and markers of systemic low-grade metaflammation, HOMA, and postprandial cardiovascular risk hyperinsulinemic, triglyceride and GLP-1 curves was found. We also analysed their plasma non-coding microRNAs and shotgun lipidomics profiles finding trends that may reflect a pattern of adipose tissue dysfunction in the fed and fasted state. Direct gene differential expression data showed initial patterns of AT molecular signatures of key immunometabolic genes involved in AT expansion, angiogenic remodelling and immune cell migration. These data reinforce the central, early role of AT dysfunction at the molecular and systemic level in the pathogenesis of IR and immunometabolic disorders.

Lipidomic data often exhibit missing data points, which can be categorized as missing completely at random (MCAR), missing at random, or missing not at random (MNAR). In order to utilize statistical methods that require complete datasets or to improve the identification of potential effects in statistical comparisons, imputation techniques can be employed. In this study, we investigate commonly used methods such as zero, half-minimum, mean, and median imputation, as well as more advanced techniques such as k-nearest neighbor and random forest imputation. We employ a combination of simulation-based approaches and application to real datasets to assess the performance and effectiveness of these methods. Shotgun lipidomics datasets exhibit high correlations and missing values, often due to low analyte abundance, characterized as MNAR. In this context, k-nearest neighbor approaches based on correlation and truncated normal distributions demonstrate best performance. Importantly, both methods can effectively impute missing values independent of the type of missingness, the determination of which is nearly impossible in practice. The imputation methods still control the type I error rate., (© 2024 The Authors. Proteomics published by Wiley‐VCH GmbH.)

Differential mobility spectrometry (DMS) is highly useful for shotgun lipidomic analysis because it overcomes difficulties in measuring isobaric species within a complex lipid sample and allows for acyl tail characterization of phospholipid species. Despite these advantages, the resulting workflow presents technical challenges, including the need to tune the DMS before every batch to update compensative voltages settings within the method. The Sciex Lipidyzer platform uses a Sciex 5500 QTRAP with a DMS (SelexION), an LC system configured for direction infusion experiments, an extensive set of standards designed for quantitative lipidomics, and a software package (Lipidyzer Workflow Manager) that facilitates the workflow and rapidly analyzes the data. Although the Lipidyzer platform remains very useful for DMS-based shotgun lipidomics, the software is no longer updated for current versions of Analyst and Windows. Furthermore, the software is fixed to a single workflow and cannot take advantage of new lipidomics standards or analyze additional lipid species. To address this multitude of issues, we developed Shotgun Lipidomics Assistant (SLA), a Python-based application that facilitates DMS-based lipidomics workflows. SLA provides the user with flexibility in adding and subtracting lipid and standard MRMs. It can report quantitative lipidomics results from raw data in minutes, comparable to the Lipidyzer software. We show that SLA facilitates an expanded lipidomics analysis that measures over 1450 lipid species across 17 (sub)-classes. Lastly, we demonstrate that the SLA performs isotope correction, a feature that was absent from the original software. [ABSTRACT FROM AUTHOR]

To investigate alterations of lipidomes in the progress of photoreceptor degeneration induced by N‐methyl‐N‐nitrosourea (MNU) in a rat model, retinal lipid molecular species in adult Sprague–Dawley (SD) rats at 1, 3, and 7 days after MNU administration and age‐matched controls were analyzed by the shotgun lipidomics technology. Moreover, total fatty acid levels in retinal, liver, and plasma samples of different groups were determined with gas chromatography. Generally, at day 1, the levels of ethanolamine plasmalogen species in retinas were markedly elevated after treatment with MNU, while the contents of other phospholipids and sphingolipids in the retina were not significantly changed than those of the control group. The compositions of almost all of unsaturated fatty acids in the retina increased significantly at day 1 after MNU administration. At day 7, the MNU treatment group has significant increases in lipid species in the retina. However, the majority of lipids containing docosahexaenoic acid (DHA, 22:6n‐3) and docosapentaenoic acid (22:5n‐6) declined, especially di‐DHA phospholipids were dramatically reduced in the retina. In contrast, similar alterations did not occur in plasma or the liver after MNU treatment. These results suggested that at the early stage of photoreceptor degeneration, lipidome remodeling in the retina might involve protection of photoreceptor from apoptosis and continue their transduction of light. However, at the late stage of photoreceptor apoptosis, increases in comprehensive lipid species occurred, likely due to the myelination of the retina. Finally, the deficiency of DHA in photoreceptor degeneration could exacerbate the influence of myelination on retinal function. We further investigated the effects of unsaturated fatty acids on neuronal apoptosis. The preliminary experiments confirmed our observation from lipidomics analysis that unsaturated fatty acids can protect neurons from apoptosis. Collectively, our study suggests that increased levels of DHA should be protective from photoreceptor degeneration. [ABSTRACT FROM AUTHOR]

Abstract Background The application of advanced sequencing technologies and improved mass-spectrometry platforms revealed significant changes in gene expression and lipids in Alzheimer’s disease (AD) brain. The results so far have prompted further research using “multi-omics” approaches. These approaches become particularly relevant, considering the inheritance of APOEε4 allele as a major genetic risk factor of AD, disease protective effect of APOEε2 allele, and a major role of APOE in brain lipid metabolism. Methods Postmortem brain samples from inferior parietal lobule genotyped as APOEε2/c (APOEε2/carriers), APOEε3/3, and APOEε4/c (APOEε4/carriers), age- and gender-matched, were used to reveal APOE allele-associated changes in transcriptomes and lipidomes. Differential gene expression and co-expression network analyses were applied to identify up- and downregulated Gene Ontology (GO) terms and pathways for correlation to lipidomics data. Results Significantly affected GO terms and pathways were determined based on the comparisons of APOEε2/c datasets to those of APOEε3/3 and APOEε4/c brain samples. The analysis of lists of genes in highly correlated network modules and of those differentially expressed demonstrated significant enrichment in GO terms associated with genes involved in intracellular proteasomal and lysosomal degradation of proteins, protein aggregates and organelles, ER stress, and response to unfolded protein, as well as mitochondrial function, electron transport, and ATP synthesis. Small nucleolar RNA coding units important for posttranscriptional modification of mRNA and therefore translation and protein synthesis were upregulated in APOEε2/c brain samples compared to both APOEε3/3 and APOEε4/c. The analysis of lipidomics datasets revealed significant changes in ten major lipid classes (exclusively a decrease in APOEε4/c samples), most notably non-bilayer-forming phosphatidylethanolamine and phosphatidic acid, as well as mitochondrial membrane-forming lipids. Conclusions The results of this study, despite the advanced stage of AD, point to the significant differences in postmortem brain transcriptomes and lipidomes, suggesting APOE allele associated differences in pathogenic mechanisms. Correlations within and between lipidomes and transcriptomes indicate coordinated effects of changes in the proteasomal system and autophagy—canonical and selective, facilitating intracellular degradation, protein entry into ER, response to ER stress, nucleolar modifications of mRNA, and likely myelination in APOEε2/c brains. Additional research and a better knowledge of the molecular mechanisms of proteostasis in the early stages of AD are required to develop more effective diagnostic approaches and eventually efficient therapeutic strategies.

Nonalcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including nonsteatotic patients with normal or excessive weight, patients diagnosed with NAFL (nonalcoholic fatty liver) or NASH (nonalcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and triacylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of nonsteatotic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.

The synthetic fatty acid 2-hydroxyoleic acid (2OHOA) has been extensively investigated as a cancer therapy mainly based on its regulation of membrane lipid composition and structure, activating various cell fate pathways. We discovered, additionally, that 2OHOA can uncouple oxidative phosphorylation, but this has never been demonstrated mechanistically. Here, we explored the effect of 2OHOA on mitochondria isolated by ultracentrifugation from U118MG glioblastoma cells. Mitochondria were analyzed by shotgun lipidomics, molecular dynamic simulations, spectrophotometric assays for determining respiratory complex activity, mass spectrometry for assessing beta oxidation and Seahorse technology for bioenergetic profiling. We showed that the main impact of 2OHOA on mitochondrial lipids is their hydroxylation, demonstrated by simulations to decrease co-enzyme Q diffusion in the liquid disordered membranes embedding respiratory complexes. This decreased co-enzyme Q diffusion can explain the inhibition of disjointly measured complexes I–III activity. However, it doesn’t explain how 2OHOA increases complex IV and state 3 respiration in intact mitochondria. This increased respiration probably allows mitochondrial oxidative phosphorylation to maintain ATP production against the 2OHOA-mediated inhibition of glycolytic ATP production. This work correlates 2OHOA function with its modulation of mitochondrial lipid composition, reflecting both 2OHOA anticancer activity and adaptation to it by enhancement of state 3 respiration.

Lipid species possess very different structures, leading to their very diversified cellular functions in biological systems. Lipidomics represents a powerful technology for deep analysis of hundreds to thousands of intact lipid molecular species. In the current study, a cluster of unknown ion peaks was displayed when we profiled cerebroside species in rat spinal cord samples by neutral loss scan of 162 Da in the positive ion mode using a multi-dimensional mass spectrometry-based shotgun lipidomics strategy. In order to identify the structural identities of these unknown ion peaks, MS2 and MS3 analyses of these ions were performed by high mass resolution mass spectrometry. Extensive lines of evidence allowed us to identify that these unknown ion peaks were monohexosyl alkyl-acyl glycerol (HAAG) species, including their sn -positional isomers and alkyl-acyl compositional isomers. We also applied the developed method to identify and quantify HAAG species present in a variety of mouse nerve tissues. We believe that the first kind of lipidomics study on HAAG species present in mammalian nerve tissue samples provided the foundation for future biological research in this unknown area. • Extensive characterization and profiling of monohexosyl alkyl-acyl glycerol species from nerve samples at the first time. • Determination of the positional isomers of these species via tandem MS analysis. • Validation of the minimal co-existence of vinyl ether-containing isomers with alkyl analogs in nerve samples. [ABSTRACT FROM AUTHOR]

Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of endogenous bioactive lipids with anti-diabetic and anti-inflammatory effects. Identification of FAHFAs is challenging due to both the relatively low abundance of these metabolites in most biological samples and the significant structural diversity arising from the co-occurrence of numerous regioisomers. Ultimately, development of sensitive analytical techniques that enable rapid and unambiguous identification of FAHFAs is integral to understanding their diverse physiological functions in health and disease. While a battery of mass spectrometry (MS) based methods for complex lipid analysis has been developed, FAHFA identification presents specific challenges to conventional approaches. Notably, while the MS2 product ion spectra of [FAHFA – H]¯ anions afford the assignment of fatty acid (FA) and hydroxy fatty acid (HFA) constituents, FAHFA regioisomers are usually indistinguishable by this approach. Here, we report the development of a novel MS-based technique employing charge inversion ion/ion reactions with tris-phenanthroline magnesium complex dications, Mg(Phen) 3 2+, to selectively and efficiently derivatize [FAHFA – H]¯ anions in the gas phase, yielding fixed-charge cations. Subsequent activation of [FAHFA – H + MgPhen 2 ]+ cations yield product ions that facilitate the assignment of FA and HFA constituents, pinpoints unsaturation sites within the FA moiety, and elucidates ester linkage regiochemistry. Collectively, the presented approach represents a rapid, entirely gas-phase method for near-complete FAHFA structural elucidation and confident isomer discrimination without the requirement for authentic FAHFA standards. Image 1 • Selective gas-phase charge switching of anions of fatty acid esters of hydroxyl fatty acids (FAHFAs). • Charge switching and CID enables the elucidation of ester linkage regiochemistry. • Charge switching and CID enables the elucidation of site(s) of unsaturation in the FA moiety. • Charge switching and CID facilitates the assignment of the FA and HFA consituents of a given FAHFA. [ABSTRACT FROM AUTHOR]

This study aimed to identify potential lipid biomarkers in women with polycystic ovary syndrome (PCOS) and determine their predictive value for PCOS. Eighteen women with PCOS and 17 healthy controls were enrolled. A multi-dimensional mass spectrometry-based shotgun lipidomics approach was employed to analyze serum lipid profiles. Shotgun lipidomics revealed that the concentrations of ceramide (Cer) and phosphatidylcholine (PC) were higher (PC: 831.6 ± 217.4 vs. 605.2 ± 164.2 μmol/l; Cer: 3,387.6 ± 829.9 vs. 2,552.2 ± 679.4 nmol/l, respectively), whereas that of lysophosphatidylcholine was lower, in PCOS women than in healthy controls (82.02 ± 39.49 vs. 133.62 ± 65.36 μmol/l, respectively). Receiver operating characteristic analysis showed that the combination of Cer (OH_N16:0/N18:0) and Cer (N22:0) had the greatest discriminatory power to differentiate between women with and without PCOS (area under the curve: 0.889, 95% confidence interval: 0.784–0.994). These results indicate that the combination of Cer (OH_N16:0/N18:0) and Cer (N22:0) may represent a novel lipid predictor of PCOS. [ABSTRACT FROM AUTHOR]

Lipidomics plays an essential role in the development of an improved understanding of lipids metabolism and the identification of new biomarkers or therapeutic targets of related diseases. The strong analytical power of mass spectrometry and its rapid developments in the respect of instruments and techniques have significantly accelerated the emerging lipidomics and related application fields in biology, medicine, and pharmacy. The strategy of chemical derivatization can remarkably improve the shortcomings of mass spectrometric analytical technologies of shotgun lipidomics and liquid chromatography mass spectrometry, and in the past decade many related studies have been reported for fatty acids, glycerophospholipids, sphingomyelins, monoglycerides, diacylglycerols, long‐chain bases, steroids, and so on. Therefore, this review will focus on new chemical derivatization approaches about the research progresses of shotgun‐based and liquid chromatography mass spectrometry–based targeted lipidomics (from 2005 to July 2019, most of reports emerged in the past 5 years), and put forward the problems and prospects in this field. It is expected to be helpful for the design and synthesis of new derivatization reagents, especially the outstanding stable isotope labeling derivatization reagents, and the development and application of new chemical derivatization strategies and matched mass spectrometric analysis methods. [ABSTRACT FROM AUTHOR]

Lipids are amongst the most important organic compounds in living organisms, where they serve as building blocks for cellular membranes as well as energy storage and signaling molecules. Lipidomics is the science of the large-scale determination of individual lipid species, and the underlying analytical technology that is used to identify and quantify the lipidome is generally mass spectrometry (MS). This review article provides an overview of the crucial steps in MS-based lipidomics workflows, including sample preparation, either liquid–liquid or solid-phase extraction, derivatization, chromatography, ion-mobility spectrometry, MS, and data processing by various software packages. The associated concepts are discussed from a technical perspective as well as in terms of their application. Furthermore, this article sheds light on recent advances in the technology used in this field and its current limitations. Particular emphasis is placed on data quality assurance and adequate data reporting; some of the most common pitfalls in lipidomics are discussed, along with how to circumvent them. [ABSTRACT FROM AUTHOR]

Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are an important family of endogenous lipids, possessing antidiabetic and anti-inflammatory functions. Therefore, analysis of FAHFAs in biological samples obtained under healthy and disease states can uncover underlying mechanisms of various relevant disorders (e.g., diabetes and autoimmune diseases). Up to now, due to their extremely low abundance, the determination of the changed levels of these species is still a huge challenge, even though great efforts have been made by utilizing liquid chromatography-tandem mass spectrometry with or without derivatization. Herein, we described a novel method for analysis of FAHFAs present in lipid extracts of biological examples after solid-phase extraction and chemical derivatization with one authentic FAHFA specie as an internal standard based on the principles of multi-dimensional mass spectrometry-based shotgun lipidomics. The approach possessed marked sensitivity, high specificity, and broad linear dynamic range of over 3 orders without obvious matrix effects. Moreover, after chemical derivatization, the molecular masses of FAHFAs shift from an overlapped region with ceramide species to a new region without overlaps, removing these contaminating signals from ceramides, and thereby reducing the false results of FAHFAs. Finally, this novel method was successfully applied for determining FAHFAs levels in varieties of representative biological samples, including plasma from lean and overweight/obese individuals of normoglycemia, and tissue samples (such as liver and white adipose tissue from diabetic (db/db) mice). We revealed significant alterations of FAHFAs in samples under patho(physio)logical conditions compared to their respective controls. Taken together, the developed method could greatly contribute to studying altered FAHFA levels under a variety of biological/biomedical conditions, and facilitate the understanding of these lipid species in the patho(physio)logical process. Image 1 • Developed a shotgun lipidomics approach with solid-phase extraction and chemical derivatization for quantitative analysis of FAHFA species. • Compared to previous methods, a smaller amount of biological sample is used. • Successfully applied the developed method for determining FAHFA in representative biological samples. [ABSTRACT FROM AUTHOR]

Vitamin D3 hypovitaminosis is associated with several neurological diseases such as Alzheimer’s disease, Parkinson’s disease or multiple sclerosis but also with other diseases such as cancer, diabetes or diseases linked to inflammatory processes. Importantly, in all of these diseases lipids have at least a disease modifying effect. Besides its well-known property to modulate gene-expression via the VDR-receptor, less is known if vitamin D hypovitaminosis influences lipid homeostasis and if these potential changes contribute to the pathology of the diseases themselves. Therefore, we analyzed mouse brain with a mild vitamin D hypovitaminosis via a targeted shotgun lipidomic approach, including phosphatidylcholine, plasmalogens, lyso-phosphatidylcholine, (acyl-/acetyl-) carnitines and triglycerides. Alterations were compared with neuroblastoma cells cultivated in the presence and with decreased levels of vitamin D. Both in cell culture and in vivo, decreased vitamin D level resulted in changed lipid levels. While triglycerides were decreased, carnitines were increased under vitamin D hypovitaminosis suggesting an impact of vitamin D on energy metabolism. Additionally, lyso-phosphatidylcholines in particular saturated phosphatidylcholine (e.g., PC aa 48:0) and plasmalogen species (e.g., PC ae 42:0) tended to be increased. Our results suggest that vitamin D hypovitaminosis not only may affect gene expression but also may directly influence cellular lipid homeostasis and affect lipid turnover in disease states that are known for vitamin D hypovitaminosis.

Background: The application of advanced sequencing technologies and improved mass-spectrometry platforms revealed significant changes in gene expression and lipids in Alzheimer's disease (AD) brain. The results so far have prompted further research using "multi-omics" approaches. These approaches become particularly relevant, considering the inheritance of APOEε4 allele as a major genetic risk factor of AD, disease protective effect of APOEε2 allele, and a major role of APOE in brain lipid metabolism. Methods: Postmortem brain samples from inferior parietal lobule genotyped as APOEε2/c (APOEε2/carriers), APOEε3/3, and APOEε4/c (APOEε4/carriers), age- and gender-matched, were used to reveal APOE allele-associated changes in transcriptomes and lipidomes. Differential gene expression and co-expression network analyses were applied to identify up- and downregulated Gene Ontology (GO) terms and pathways for correlation to lipidomics data. Results: Significantly affected GO terms and pathways were determined based on the comparisons of APOEε2/c datasets to those of APOEε3/3 and APOEε4/c brain samples. The analysis of lists of genes in highly correlated network modules and of those differentially expressed demonstrated significant enrichment in GO terms associated with genes involved in intracellular proteasomal and lysosomal degradation of proteins, protein aggregates and organelles, ER stress, and response to unfolded protein, as well as mitochondrial function, electron transport, and ATP synthesis. Small nucleolar RNA coding units important for posttranscriptional modification of mRNA and therefore translation and protein synthesis were upregulated in APOEε2/c brain samples compared to both APOEε3/3 and APOEε4/c. The analysis of lipidomics datasets revealed significant changes in ten major lipid classes (exclusively a decrease in APOEε4/c samples), most notably non-bilayer-forming phosphatidylethanolamine and phosphatidic acid, as well as mitochondrial membrane-forming lipids. Conclusions: The results of this study, despite the advanced stage of AD, point to the significant differences in postmortem brain transcriptomes and lipidomes, suggesting APOE allele associated differences in pathogenic mechanisms. Correlations within and between lipidomes and transcriptomes indicate coordinated effects of changes in the proteasomal system and autophagy—canonical and selective, facilitating intracellular degradation, protein entry into ER, response to ER stress, nucleolar modifications of mRNA, and likely myelination in APOEε2/c brains. Additional research and a better knowledge of the molecular mechanisms of proteostasis in the early stages of AD are required to develop more effective diagnostic approaches and eventually efficient therapeutic strategies. [ABSTRACT FROM AUTHOR]

Abstract The mainstream of lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about lipidomics and to provide readers with some core ideas and the most important approaches for studying the field. Graphical abstract Image 1 Highlights • Introductory knowledge of mass spectrometry-based lipidomics approaches. • Principles and the technical aspects of quantitative lipidomics. • Basic bioinformatics for lipidomics. [ABSTRACT FROM AUTHOR]

Phosphatidylcholine (PC) species in human plasma are used as biomarkers of disease. PC biomarkers are often limited by the inability to separate isobaric PCs. In this work, we developed a targeted shotgun approach for analysis of isobaric and isomeric PCs. This approach is comprised of two MS methods: a precursor ion scanning (PIS) of mass m/z 184 in positive mode (PIS m/z +184) and MS3 fragmentation in negative mode, both performed on the same instrument, a hybrid triple quadrupole ion-trap mass spectrometer. The MS3 experiment identified the FA composition and the relative abundance of isobaric and sn-1, sn-2 positional isomeric PC species, which were subsequently combined with absolute quantitative data obtained by PIS m/z +184 scan. This approach was applied to the analysis of a National Institute of Standards and Technology human blood plasma standard reference material (SRM 1950). We quantified more than 70 PCs and confirmed that a majority are present in isobaric and isomeric mixtures. The FA content determined by this method was comparable to that obtained using GC with flame ionization detection, supporting the quantitative nature of this MS method. This methodology will provide more in-depth biomarker information for clinical and mechanistic studies.

The lipidome of femoral gland secretions of the marine iguana (Amblyrhynchus cristatus) was studied. The main aim of this work was to identify and quantify the lipids present in femoral secretions using mass spectrometry-based shotgun lipidomics. Lipids belonging to seven lipid classes were identified: ceramides (43.41%), triacylglycerols (42.15%), cholesteryl esters (4.18%), sphingomyelins (3.61%), phosphatidylcholines (2.67%), phosphatidylinositols (2.50%) and phosphatidylethanolamines (1.48%). The second aim of the study was to explore whether lipid composition matches the different subspecies or populations of marine iguanas. The different subspecies of iguanas did not group together in relation to their lipidome. The authors’ findings are discussed in an ecological context and compared with the results of a previous study that characterized volatile lipids in marine iguana secretions using gas chromatography. Given the high diversity of lipid structures in femoral secretions discovered in this study, it is likely that some of these could be involved in intraspecific communication. Certain lipids could have other functions, such as building a barrier to avoid water loss. More data needs to be added to explore this hypothesis. This study is the first to use a lipidomics-based approach to characterize lipid composition in lizard femoral secretions. The application of shotgun lipidomics to reptilian glandular secretions will shed new light on the potential function of lipids in intraspecific chemical communication. [ABSTRACT FROM AUTHOR]

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MS technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. [ABSTRACT FROM AUTHOR]

Abstract: Cardiolipin (Ptd2Gro) is a complex, doubly charged phospholipid located in the inner mitochondrial membrane where it plays an essential role in regulating bioenergetics. Abnormalities in Ptd2Gro content or composition have been associated with mitochondrial dysfunction in a variety of disease states. Here, we report the development of an adapted high‐resolution data‐independent acquisition (DIA) MS/MSALL shotgun lipidomic method to enhance the accuracy and reproducibility of Ptd2Gro molecular species quantitation from biological samples. Utilizing the doubly charged molecular ions and the isotopic pattern with negative mode electrospray ionization mass spectrometry (ESI‐MS) using an adapted MS/MSALL approach, we profiled more than 150 individual Ptd2Gro species, including monolysocardiolipin (MLPtd2Gro). The method described in this study demonstrated high reproducibility, sensitivity, and throughput with a wide dynamic range. This high‐resolution MS/MSALL shotgun lipidomics approach could be extended to screening aberrations of Ptd2Gro metabolism involved in mitochondrial dysfunction in various pathological conditions and diseases. [ABSTRACT FROM AUTHOR]

[Display omitted] • Shotgun lipidomic approach was employed. • 64 phospholipid molecular species were identified. • Different changes in phospholipids of indica and japonica rice during accelerated storage. • Potential PL markers were identified and verified for distinguish between fresh and aged brown rice. Brown rice exhibits higher nutritional value and attracts more and more attentions; however, the change in phospholipid molecular species in brown rice during aging is poorly understood. In this study, shotgun lipidomics was employed to investigate the changes in phospholipid molecular species in four brown rice varieties (two japonica rice and two indica rice) during accelerated aging. A total of 64 phospholipid molecular species were identified, and most of them were rich in polyunsaturated fatty acids. For japonica rice, phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG) gradually decreased during accelerated aging. However, the content of PC, PE, and PG in indica rice showed no difference during accelerated aging. Significantly different phospholipid molecular species from four brown rice were screened during accelerated aging. Based on these significantly different phospholipids, the metabolic pathways including glycerophospholipid metabolism and linoleic acid metabolism during accelerated aging were depicted. The findings from this study could be helpful in explaining the impact of accelerated aging on phospholipids of brown rice, and offer an understanding on relationships between phospholipids degradation and brown rice deterioration. [ABSTRACT FROM AUTHOR]

A fast and efficient shotgun lipidomics strategy was applied to analyze phospholipids (PL) in the oyster Crassostrea plicatula, including 29 species of phosphatidylcholine (PtdCho), 23 species of phosphatidylethanolamine (PtdEtn), 11 species of phosphatidylserine (PtdSer), 6 species of phosphatidylinositol (PtdIns), and 17 species of lysophospholipids (Lyso-PL). During storage at 4 °C for 7 days, the PL content decreased by 68.08%, but a significant increase in the FFA content was observed (from 63.11 to 318.72 μg/g). PtdCho and PtdIns decreased relatively by 64.97 and 67.49%, and PtdSer decreased most markedly by 74.15%. However, the PtdEtn content increased slightly during the early stages of storage but subsequently began to decrease. Moreover, PL with eicosapentaenoic acid (EPA-PL) and docosahexaenoic acid (DHA-PL) decreased by 51.77 and 50.61%, whereas plasmalogens were relatively stable showing only a 25.46% decrease. In particular, through enzyme activity analysis of lipase, phospholipase A (PLA), phospholipase A (PLA), phospholipase C (PLC), and phospholipase D (PLD), it was observed that the activities of all these enzymes increased at the early stage at 4 °C, but their activities were at lower levels when the oysters were stored at −20 °C. During the storage period at 4 °C, correlation analysis suggests that the degradation of PtdCho was mostly correlated to PLA ( p < 0.05), whereas PtdEtn and PtdSer were more markedly correlated to lipase and PLD, respectively. The above result indicates that the hydrolysis mechanism of PL during seafood storage was correlated to the lipid hydrolytic enzyme activities under different storage temperatures. [ABSTRACT FROM AUTHOR]