Advances in Liquid Chromatography–Mass Spectrometry-Based Lipidomics: A Look Ahead

Multi-Pass Arrival Time Correction in Cyclic Ion Mobility Mass Spectrometry for Imaging and Shotgun Lipidomics

Direct-infusion mass spectrometry (DI-MS) and mass spectrometry imaging (MSI) are powerful techniques for lipidomics research. However, annotating isomeric and isobaric lipids with these methods is challenging due to the absence of chromatographic separation. Recently, cyclic ion mobility mass spectrometry (cIM-MS) has been proposed to overcome this limitation. However, fluctuations in room conditions can affect ion mobility multipass arrival times, potentially reducing annotation confidence. In this study, we developed a multipass arrival time correction method that proved effective across various dates, room temperatures, ion mobility settings, and laboratories using mixtures of reference standards. We observed slight variations in the linear correction lines between lipid and nonlipid molecules, underscoring the importance of choosing appropriate reference molecules. Based on these results, we demonstrated that an accurate multipass arrival time database can be constructed from corrected t 0 and t p for interlaboratory use and can effectively identify isomeric lipids in MSI using only a single measurement. This approach significantly simplifies the identification process compared to determining multipass collision cross-section, which requires multiple measurements that are both sample- and time-intensive for MSI. Additionally, we validated our multipass drift time correction method in shotgun lipidomics analyses of human and mouse serum samples and observed no matrix effect for the analysis. Despite variations in dates, room temperatures, instruments, and ion mobility settings, our approach reduced the mean drift time differences from over 2% to below 0.2%.

ALISTER - Application for lipid stability evaluation and research

BACKGROUND AND AIMS

In lipidomic and metabolomic studies, pre-analytical pitfalls enhance the risk of misusing resources such as time and money, as samples that are analyzed may not yield accurate or reliable data due to poor sample handling. Guidance and pre-analytic know-how are necessary for translation of omics technologies into routine clinical testing. The present work aims to enable decision making regarding sample stability in every phase of lipidomics- and metabolomics-centered studies.

MATERIALS AND METHODS

Data of multiple pre-analytic studies were aggregated into a database. Flexible approaches for evaluating these data were implemented in an RShiny-based web-application, tailored towards broad applicability in clinical and bioanalytic research.

RESULTS

Our "Application for lipid stability evaluation & research" - ALISTER facilitates decision making on blood sample stability during lipidomic and metabolomic studies, such as biomarker research, analysis of biobank samples and clinical testing. The interactive tool gives sampling recommendations when planning sample collection or aids in the assessment of sample quality of experiments retrospectively.

CONCLUSION

ALISTER is available for use under https://itmp.shinyapps.io/alister/. The application enables and simplifies data-driven decision making concerning pre-analytic blood sample handling and fits the needs of clinical investigations from multiple perspectives.

Effect of high NEFA concentration on lipid metabolism disorders in hepatocytes based on lipidomics

Introduction: High concentrations of nonesterified fatty acids (NEFA) is the key of characteristic of fatty liver in dairy cows. Therefore, the aim of this study was to investigate the effect of high concentration of NEFA on lipid metabolism in hepatocytes through the lipidomic approach and molecular biology techniques. Methods: Stimulate AML-12 cells with different concentrations of NEFA, observe the cellular lipid accumulation, and select 0.6 mM NEFA stimulation concentration for subsequent experiments. Collect cells for lipidomics analysis. Results: High concentration of NEFA (0.6-2.4 mM) significantly reduced the cell viability in a concentration-dependent manner, indicating that high concentrations of NEFA have lipotoxicity on hepatocytes. In addition, NEFA promoted triglycerides (TAG) accumulation, increased the mRNA expression of the lipogenic molecules SREBP1c and FASN, and decreased the mRNA expression of lipolytic molecules CPT1A and HSL in hepatocytes. Mechanistically, high concentration of NEFA induced lipid metabolism disorders in hepatocytes by regulating metabolic pathways such as glycerol phospholipid metabolism, glycosyl phosphatidylinositol anchored biosynthesis, triglyceride metabolism, sphingolipid metabolism, and inositol phosphate metabolism. Discussion: High concentration of NEFA is lipotoxic to cells, promoting lipid accumulation. LPE (18:2), LPE (18:3), LPE (18:1) via glycerophospholipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, glycerolipid metabolism, sphingolipid metabolism, and inositol phosphate metabolism, indicating their potential regulation role in the pathogenesis of fatty liver.

Recent Analytical Methodologies in Lipid Analysis

Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.

Lipid class-dependent alterations of Caenorhabditis elegans under harmane exposure

Altered lipid patterns in Caenorhabditis elegans (C. elegans) resulting from exposure to harmane remain to be explored. In this study, untargeted lipidomics was carried out to elucidate the effects of acute exposure to harmane on the lipidome of C. elegans. Exposure to the compound was evaluated based on the reproduction ability of the worms at 0.1 and 1 μg/mL. No significant effects of harmane were observed at these concentrations. Furthermore, we found that the modulatory effects of harmane on the lipidome of C. elegans at 1 μg/mL were lipid class dependent. In particular, harmane-treated worms were enriched in triglycerides and fatty acids, regardless of the degree of saturation. Glycerophospholipids were generally down-regulated. Furthermore, functional analyses suggested that there was a reduction in lipid membrane bilayer-related terms, and in some related to the mitochondria, and endoplasmic reticulum of C. elegans when treated with harmane. Lipid droplets and storage appeared to be up-regulated. In conclusion, our findings suggest that harmane exposure affects the lipidome of C. elegans in a sophisticated manner. Further investigations are required to elucidate the molecular mechanisms underlying these lipid pattern changes.

Rapid, sensitive, and high-throughput quantification of broad serological ceramides by using isotope dilution liquid chromatography-negative ion electrospray tandem mass spectrometry

Ceramides are important intermediates in the metabolism of sphingolipids. High-throughput liquid chromatography-mass spectrometry has been used extensively for monitoring the levels of serological ceramides, but is still limited by inadequate coverage or lack of sensitivity. Herein, a rapid, sensitive, and high-throughput isotope dilution liquid chromatography-negative ion electrospray tandem mass spectrometry (IDLC-nESI-MS/MS) method was developed and verified for accurate quantification of 41 ceramides, involving ceramides with C16-20 sphingosine, dihydro-ceramide, and dehydro-ceramide. This method was validated with excellent linearity (R² > 0.99) and good recovery in the range of 90-110%. Intra- and inter-day imprecision were below 5.57% and 7.83% respectively. The improved high-throughput quantitative method developed in this study may aid in the accurate characterization of ceramides for understanding ceramide biology and application in disease diagnosis.

Comprehensive lipidomic profiling by plasma separation cards

Large-scale lipidomic analyses have been limited by the cost and accessibility of traditional venipuncture sampling. Microsampling techniques offer a less-invasive and more accessible alternative. From a single drop of blood, plasma separation cards (PSC) deliver two volumetric dried plasma samples which are studied here for profiling endogenous blood lipids. Six lots of EDTA-treated human whole blood were used to compare PSC, dried blood spot analyses (DBS), and classic wet plasma extractions. Six replicate extractions were performed for each lot. Nontargeted lipidomics was performed by liquid chromatography-high resolution tandem mass spectrometry. Lipids were annotated by accurate mass/retention time matching and MS/MS spectral library matching using peak intensities for quantitation. Four hundred ninety-eight compounds covering 24 lipid subclasses were annotated. Inter-lot repeatability was evaluated by the percent relative standard deviation (%RSD) for each lot, giving median %RSD values across the lots at 14.6% for PSC, 9.3% for DBS, and 8.6% for wet plasma. Strong correlations of lipid peak intensities between wet plasma and PSCs were observed, but less for DBS. Lipid recovery and stability were comparable between the PSC and DBS samples, with roughly 60% of annotated lipids stable at room temperature after 28 days. Overall, PSCs provide a better alternative for quantitative blood lipidomic analyses compared to dried blood spots. However, problems with lipid stability for samples handled and shipped at room temperature are currently unavoidable outside of a clinical setting. Data transferability and comparability to standard plasma is lipid and lipid class dependent.

Human serum lipidomics analysis revealed glyphosate may lead to lipid metabolism disorders and health risks

Glyphosate-based herbicides (GBH) are one of the most widely used pesticides worldwide. Industrial workers in glyphosate-based herbicides manufacture are the populations who experience long-term exposure to high glyphosate levels. The impacts of glyphosate on human health are the important public health problem of great concern. Up to date, the potential adverse effects of glyphosate on humans or other mammals have been reported in multiple studies. However, limited research is available on lipid alternations related to human exposure to glyphosate. In fact, the perturbations in some lipid metabolisms have been found in industrial workers in previous work. This study aims to explore the serum lipidomic characterization and to understand the underlying mechanisms of health risks associated with glyphosate exposure. A nontargeted lipidomics study was conducted to investigate the 391 serum samples from the general population and chemical factory workers. It was demonstrated that glyphosate caused significant perturbations of 115 differentially expressed lipids. The main manifestations were the elevation of circulating diacylglycerols (DG), cholesteryl esters (CE), ceramides (Cer), sphingomyelins (SM), lysophosphatidylethanolamines (LPE) and phosphatidylcholines (PC), and the decrease of ysophosphatidylcholines (LPC), triacylglycerols (TG), fatty acids (FA) and phosphatidylethanolamines (PE). A total of 88 lipids were further screened as potential lipid biomarkers associated closely with glyphosate using partial correlation analysis, and five of which (including PC 16:0/18:2; O, PC 18:0/18:2; O, PC 18:0/20:4; O, PC O-40:9 and CE 18:3) showed excellent superior performance (AUC = 1) to evaluate and monitor health risks due to glyphosate exposure. The present work discovered glyphosate-induced potential health risks, including chronic hepatic and renal dysfunction, atherosclerosis, cardiovascular disease and neurodegenerative diseases from a lipidomic perspective, and could inform the identification of early indicators and interpretation of biological mechanisms to detect health risks of the glyphosate-exposed populations as early as possible.

Screening and characterization estrogen receptor ligands from Arnebia euchroma (Royle) Johnst. via affinity ultrafiltration LC-MS and molecular docking

Arnebiae Radix (dried root of Arnebia euchroma (Royle) Johnst.) is a traditional Chinese medicine (TCM) used to treat macular eruptions, measles, sore throat, carbuncles, burns, skin ulcers, and inflammations. The Arnebiae Radix extract can exert anti-breast cancer effects through various mechanisms of action. This study aimed to rapidly screen potential estrogen receptor (estrogen receptor α and estrogen receptor β) ligands from the Arnebiae Radix extract. In this study, an analytical method based on affinity ultrafiltration coupled with UHPLC-Q-Exactive Orbitrap mass spectrometry was established for rapidly screening and identifying estrogen receptor ligands. Then, bindings of the components to the active site of estrogen receptor (estrogen receptor α and estrogen receptor β) were investigated via molecular docking. Moreover, surface plasmon resonance (SPR) experiments with six compounds were performed to verify the affinity. As a result, a total of 21 ligands were screened from Arnebiae Radix using affinity ultrafiltration. Among them, 14 and 10 compounds from Arnebiae Radix showed affinity with estrogen receptor α and estrogen receptor β, respectively. All of those ligands could have a good affinity for the multiple amino acid residues of the estrogen receptor based on molecular docking. In addition, six compounds display the great affinity by SPR. The method established in the study could be used to rapidly screen estrogen receptor ligands in Traditional Chinese medicine. The results demonstrated that the affinity ultrafiltration-UHPLC-Q-Exactive Orbitrap mass spectrometry method not only aids in the interpretation of the potential bioactive components and possible mechanisms of action of Arnebiae Radix but also provides a further effective basis for the quality control of this valuable herb medicine.

Impurity Profiling of Dinotefuran by High Resolution Mass Spectrometry and SIRIUS Tool

Dinotefuran (DNT) is a neonicotinoid insecticide widely used in pest control. Identification of structurally related impurities is indispensable during material purification and pesticide registration and certified reference material development, and therefore needs to be carefully characterized. In this study, a combined strategy with liquid chromatography high-resolution mass spectrometry and SIRIUS has been developed to elucidate impurities from DNT material. MS and MS/MS spectra were used to score the impurity candidates by isotope score and fragment tree in the computer assisted tool, SIRIUS. DNT, the main component, worked as an anchor for formula identification and impurity structure elucidation. With this strategy, two by-product impurities and one stereoisomer were identified. Their fragmentation pathways were concluded, and the mechanism for impurity formation was also proposed. This result showed a successful application for combined human intelligence and machine learning, in the identification of pesticide impurities.

Impurity identification in thiamethoxam by high resolution mass spectrometry and computer assisted elucidation

Thiamethoxam (TMX) is a widely used neonicotinoid insecticide in pest control. Identification of structurally related impurities is very important during certified reference material development and pesticide registration, thus it needs to be carefully characterized. In this study, a combined strategy with liquid chromatography-high resolution mass spectrometry and computer assisted elucidation (SIRIUS) has been developed for the impurity elucidation in TMX material. MS and MS/MS spectra were used to score the impurity candidates by isotope score and fragment tree in SIRIUS. TMX, the main component, worked as an anchor for formula identification and structure elucidation of impurity. With this strategy, four impurities were identified, including two byproducts (TMX-OCH₃ and TMX-Cl) and two metabolites (clothianidin and TMX-urea). Their fragmentation pathways were concluded, and mechanism of impurity formation was also proposed. This result showed successful application of combining human intelligence with machine learning in impurity identification from chemicals.

Spatial metabolomics shows contrasting phosphonolipid distributions in tissues of marine bivalves

Lipids are an integral part of cellular membranes that allow cells to alter stiffness, permeability, and curvature. Among the diversity of lipids, phosphonolipids uniquely contain a phosphonate bond between carbon and phosphorous. Despite this distinctive biochemical characteristic, few studies have explored the biological role of phosphonolipids, although a protective function has been inferred based on chemical and biological stability. We analyzed two species of marine mollusks, the blue mussel Mytilus edulis and pacific oyster Crassostrea gigas, and determined the diversity of phosphonolipids and their distribution in different organs. High-resolution spatial metabolomics revealed that the lipidome varies significantly between tissues within one organ. Despite their chemical similarity, we observed a high heterogeneity of phosphonolipid distributions that originated from minor structural differences. Some phosphonolipids are ubiquitously distributed, while others are present almost exclusively in the layer of ciliated epithelial cells. This distinct localization of certain phosphonolipids in tissues exposed to the environment could support the hypothesis of a protective function in mollusks. This study highlights that the tissue specific distribution of an individual metabolite can be a valuable tool for inferring its function and guiding functional analyses.

Coenzyme Q10 in the eye isomerizes by sunlight irradiation

Photoisomerization of lipids has been well studied. As for the eyes, photoisomerization from 11-cis isomer to all-trans-retinal is well-known as the first step of the visual transduction in the photoreceptors. In addition to that, there would be other ocular lipids that undergo photoisomerization, which may be involved in ocular health and function. To explore any photoisomerizable lipids in the eyes, the nonirradiated and sunlight-irradiated eyeball extracts were subjected to liquid chromatography-mass spectrometry analysis, followed by the identification of the decreased lipid species in the irradiated extracts. Surprisingly, more than nine hundred lipid species were decreased in the irradiated extracts. Three lipid species, coenzyme Q10 (CoQ10), triglyceride(58:4), and coenzyme Q9, were decreased both significantly (p < 0.05) and by more than two-fold, where CoQ10 showed the most significant decrease. Later, photoisomerization was identified as the prominent cause underlying the decrease of CoQ10. Interestingly, CoQ10 in the sunlight-irradiated fresh eyeballs was also isomerized. Both the visible light and ultraviolet radiation were capable of producing CoQ10 isomer, while the latter showed rapid action. This study is believed to enhance our understanding of the biochemistry and photodamage of the eye and can potentially contribute to the advancement of opto-lipidomics.

Systematic Screening of Chemical Constituents in the Traditional Chinese Medicine Arnebiae Radix by UHPLC-Q-Exactive Orbitrap Mass Spectrometry

Arnebiae Radix (dried root of Arnebia euchroma (Royle) Johnst.) has been used in traditional Chinese medicine (TCM) to treat macular eruptions, measles, sore throat, carbuncles, burns, skin ulcers, and inflammation. Previous studies have shown that shikonins and shikonofurans are two of their main bioactive ingredients. However, systematic investigations of their constituents have rarely been conducted. It is necessary to establish a rapid and effective method to identify the chemical constituents of Arnebiae Radix. This will help to further improve the effective resource utilization rate of this plant. In this study, a rapid and effective UHPLC-Q-Exactive Orbitrap mass spectrometry method was established to simultaneously analyze chemical ingredients in Arnebiae Radix within a short period of time. Based on the results of a full scan MS, the MS2 database (mzVault and mzCloud), the diagnostic fragment ions, the retention time, and the bibliography, a total of 188 compounds were identified, with 114 of those being reported from Arnebiae Radix for the first time. The results of this study lay the foundation for obtaining a thorough understanding of the active ingredients in Arnebiae Radix and its quality control. This method may be widely used for the chemical characterization of different samples.

Diagnostic Fragment-Ion-Based for Rapid Identification of Chlorogenic Acids Derivatives in Inula cappa Using UHPLC-Q-Exactive Orbitrap Mass Spectrometry

Inula cappa (Buch.-Ham. ex D. Don) DC has been used in traditional Chinese medicine to treat malaria, dysentery, and hepatitis. Previous studies have shown that chlorogenic acid is the effective ingredient of plants in this family. And the research of the chlorogenic acid in Inula cappa will help to further improve the effective resource utilization rate of this plant. Therefore, it is necessary to establish an accurate method to characterize the chlorogenic acid components in Inula cappa. In this study, a simple, fast, and sensitive UHPLC-Q-Exactive Orbitrap mass spectrometry method was established, which can simultaneously analyze known and unknown ingredients in a short time (within 30 minutes) in Inula cappa. According to the diagnosis fragmentation ions, retention time, and bibliography, 68 chlorogenic acid derivatives were identified in Inula cappa. The results of this experiment lay the foundation for the active substances and quality control of Inula cappa and provide a theoretical basis for whether Inula cappa can be an alternative to the endangered wild medicinal materials of the same family.

Mass spectrometry-based phospholipid imaging: methods and findings

Introduction: Imaging is a technique used for direct visualization of the internal structure or distribution of biomolecules of a living system in a two-dimensional or three-dimensional fashion. Phospholipids are important structural components of biological membranes and have been reported to be associated with various human diseases. Therefore, the visualization of phospholipids is crucial to understand the underlying mechanism of cellular and molecular processes in normal and diseased conditions. Areas covered: Mass spectrometry imaging (MSI) has enabled the label-free imaging of individual phospholipids in biological tissues and cells. The commonly used MSI techniques include matrix-assisted laser desorption ionization-MSI (MALDI-MSI), desorption electrospray ionization-MSI (DESI-MSI), and secondary ion mass spectrometry (SIMS) imaging. This special report described those methods, summarized the findings, and discussed the future development for the imaging of phospholipids. Expert opinion: Phospholipids imaging in complex biological samples has been significantly benefited from the development of MSI methods. In MALDI-MSI, novel matrix that produces homogenous crystals exclusively with polar lipids is important for phospholipids imaging with greater efficiency and higher spatial resolution. DESI-MSI has the potential of live imaging of the biological surface while SIMS is expected to image at the subcellular level in the near future.