Using precursor ion scan of 184 with liquid chromatography-electrospray ionization-tandem mass spectrometry for concentration normalization in cellular lipidomic studies

Recent Advances in Gas-phase Ion/Ion Chemistry for Lipid Analysis

Gas-phase ion/ion reactions can be used to alter analyte ion-types for subsequent dissociation both quickly and efficiently without the need for altering analyte ionization conditions. This capability can be particularly useful when the ion-type that is most efficiently generated by the ionization method at hand does not provide the structural information of interest using available dissociation methods. This situation often arises in the analysis of lipids, which constitute a diverse array of chemical species with many possibilities for isomers. Gas-phase ion/ion reactions have been demonstrated to be capable of enhancing the ability of tandem mass spectrometry to characterize the structures of various lipid classes. This review summarizes progress to date in the application of gas-phase ion/ion reactions to lipid structural characterization.

Optimization of the Sulfo-Phospho-Vanillin Assay for Total Lipid Normalization in Untargeted Quantitative Lipidomic LC-MS/MS Applications

Liquid chromatography (LC)-mass spectrometry (MS)/MS lipidomic normalization is generally performed by equalizing pre-extraction sample materials or via DNA or protein pre-quantitation methods, which have known measurement inaccuracies. We propose the use of the sulfo-phospho-vanillin assay (SPVA), a total lipid colorimetric analysis, as a pre-quantitation method to normalize lipids in lipidomic LC-MS/MS applications. The assay has been applied to a 300 μL well volume in a 96-well plate and tested using Avanti total lipid standards of porcine brain and E. coli. Assay parameters for lipid sample volume, sulfuric acid, vanillin/phosphoric acid, post-reaction incubation time, and wavelength are optimized for robust application to biologically sourced lipid samples. Standard test samples were prepared using three concentrations covering approximately 100 μg/mL range. The optimized assay yielded test sample errors less than 10%, indicating a precise and accurate assay performance. The test samples were then analyzed by LC-MS/MS and normalized using SPVA pre-quantitation and pseudo-mass normalization. The detected lipids showed smaller standard deviations and greater relative concentration differences compared to the pseudo-mass normalized lipids, showing promise as a normalization method.

Differentiating ether phosphatidylcholines with a collision energy-optimized MRM method by RPLC-MS/MS and its application to studying ischemia-neuronal injury

The identification of ether-phosphatidylcholine (ether-PC) isomers, including alkyl-PC (PC(O-)) and plasmalogen-PC (PC(P-)), is technically challenging in MS/MS analysis, which hinders scientists from gaining a deeper understanding of such important lipids. In this study, we developed a sensitive and specific LC-MS/MS-MRM method to accurately identify PC(O-) and PC(P-). We first deciphered the specific fragmentation rules from LPC(O-) and LPC(P-) isomers, in which the product ion of LPC(P-) would be dominated by alkenyl ions (A). In contrast, LPC(O-) only provided a ring-structure fragment (R) without further fragmentation to the alkyl ion, showing completely different characteristics between LPC(O-) and LPC(P-) in negative ion mode. Next, to overcome the sensitivity issue, the MRM approach based on fragmentation rules was used to differentiate PC(O-) and PC(P-). The CE-optimized MRM method increased the alkenyl-to-ring ratio (A/R) between PC(O-) and PC(P-), in which A/R was almost equal to zero for PC(O-) but A/R ≥ 3 for PC(P-). This highly selective property of the CE-optimized MRM method provides accurate identification of PC(O-) and PC(P-) in whole blood samples. The proposed method was applied in primary neuronal cultures with oxygen-glucose deprivation (OGD) treatment to investigate the regulation of PCs under hypoxic stress. The results showed that the regulation of ether-PCs was mainly related to the sn-1 chain length, and the concentration changes of diacyl-PCs were highly dependent on the degree of unsaturation. In summary, the CE-optimized MRM method enables users to distinguish between PC(O-) and PC(P-) in a simple way.

Fast and Specific Screening of EPA/DHA-Enriched Phospholipids in Fish Oil Extracted from Different Species by HILIC-MS

Eicosapentaenoic acid- and docosahexaenoic acid-enriched phospholipids (PL_EPA/DHA) have versatile health-beneficial functions and can be well absorbed in the intestine. Herein, a precursor ion scan-driven hydrophilic interaction chromatography mass spectrometry (PreIS-HILIC-MS) method with the fatty acyl moieties of m/z 301.6 and 327.6 locked was established to specifically and selectively screen PL_EPA/DHA in different fish oil samples, including saury, grass carp, hairtail, and yellow croaker. Taking saury oil as an example, a total of 24 PL_EPA/DHA were successfully identified and quantified, including 20 PC_EPA/DHA and 4 PE_EPA/DHA. Finally, this method was validated in terms of sensitivity (limit of detection ≤ 4.15 μg·mL^-1), linearity (≥0.9979), precision (RSD_intraday ≤ 4.65%), and recovery (≥78.6%). The performance of the PreIS-HILIC-MS method was also compared with that of the traditional full-scan mode, and the former demonstrated its unique superiority in targeted screening of PL_EPA/DHA in fish oils.

Insight into chemical basis of traditional Chinese medicine based on the state-of-the-art techniques of liquid chromatography-mass spectrometry

Traditional Chinese medicine (TCM) has been an indispensable source of drugs for curing various human diseases. However, the inherent chemical diversity and complexity of TCM restricted the safety and efficacy of its usage. Over the past few decades, the combination of liquid chromatography with mass spectrometry has contributed greatly to the TCM qualitative analysis. And novel approaches have been continuously introduced to improve the analytical performance, including both the data acquisition methods to generate a large and informative dataset, and the data post-processing tools to extract the structure-related MS information. Furthermore, the fast-developing computer techniques and big data analytics have markedly enriched the data processing tools, bringing benefits of high efficiency and accuracy. To provide an up-to-date review of the latest techniques on the TCM qualitative analysis, multiple data-independent acquisition methods and data-dependent acquisition methods (precursor ion list, dynamic exclusion, mass tag, precursor ion scan, neutral loss scan, and multiple reaction monitoring) and post-processing techniques (mass defect filtering, diagnostic ion filtering, neutral loss filtering, mass spectral trees similarity filter, molecular networking, statistical analysis, database matching, etc.) were summarized and categorized. Applications of each technique and integrated analytical strategies were highlighted, discussion and future perspectives were proposed as well.

In vitro generation of oxidized standards for lipidomics. Application to major membrane lipid components

Membrane lipids (sphingolipids, glycerophospholipids, cardiolipins, and cholesteryl esters) are critical in cellular functions. Alterations in the levels of oxidized counterparts of some of these lipids have been linked to the onset and development of many pathologies. Unfortunately, the scarce commercial availability of chemically defined oxidized lipids is a limitation for accurate quantitative analysis, characterization of oxidized composition, or testing their biological effects in lipidomic studies. To address this dearth of standards, several approaches rely on in-house prepared mixtures of oxidized species generated under in vitro conditions from different sources - non-oxidized commercial standards, liposomes, micelles, cells, yeasts, and human preparations - and using different oxidant systems - UVA radiation, air exposure, enzymatic or chemical oxidant systems, among others. Moreover, high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-MS) have provided evidence of their capabilities to study oxidized lipids both in in vitro models and complex biological samples. In this review, we describe the commercial resources currently available, the in vitro strategies carried out for obtaining oxidized lipids as standards for LC-MS analysis, and their applications in lipidomics studies, specifically for lipids found in cell and mitochondria membranes.

Cell metabolomics analyses revealed a role of altered fatty acid oxidation in neurotoxicity pattern difference between nab-paclitaxel and solvent-based paclitaxel

Peripheral neuropathy (PN) is a dose-limiting, painful adverse reaction associated with the use of paclitaxel. This common side effect was often partially attributed to the solvent used for solubilization of the highly hydrophobic drug substance. Therefore, the development of alternative formulations thrived, which included that of Abraxane® containing nanoparticle albumin-bound paclitaxel (nab-paclitaxel). However, studies demonstrated inconsistent conclusions regarding the mitigation of PN in comparison with the traditional formulation. The mass spectrometry-based cell metabolomics approach was used in the present study to explore the potentially associated mechanisms. Although no significant difference in the effects on cell viability was observed, fold changes in carnitine, several acylcarnitines and long-chain fatty acid(s) were significantly different between treatment groups in differentiated and undifferentiated SH-SY5Y cells. The most prominent difference observed was the significant increase of octanoylcarnitine in cells treated with solvent-based paclitaxel, which was found to be associated with significant decrease of medium-chain acyl-CoA dehydrogenase (MCAD). The findings suggested the potential role of altered fatty acid oxidation in the different neurotoxicity patterns observed, which may be a possible target for therapeutic interventions worth further investigation.

Differences in Fatty Acid Oxidation between Nab-Paclitaxel- and Solvent-Based Paclitaxel-Treated A549 Cells Based on Metabolomics

The pharmacokinetics, safety, and anticancer efficacy profiles of nanoparticle albumin-bound (nab)-paclitaxel formulations are superior to those of solvent-based paclitaxel formulations. The aims of the present study were to study the effects of nab-paclitaxel and solvent-based paclitaxel formulations on the metabolic profiles of the model cell line (A549) and attempt to elucidate the associated metabolic pathways. A mass spectrometry-based cell metabolomics approach and viability evaluation were used to explore the potential difference. Western blotting was utilized to measure the levels of relevant proteins, and carnitine palmitoyltransferase 1 (CPT1) activities were quantified. Fold changes normalized to controls in levels of carnitine and several acylcarnitines were significantly different (p < 0.05) between A549 cells treated with nab-paclitaxel and those treated with solvent-based paclitaxel. Relative to the controls, there were also significant fold change differences in palmitic and linoleic acid levels in the cell lysates, mitochondrial CPT1 activities, and mitochondrial medium-chain acyl-CoA dehydrogenase (MCAD) protein levels in the A549 cells subjected to the nab-paclitaxel and solvent-based paclitaxel formulations. Results suggested that the two formulations differentially modulated fatty acid oxidation in the A549 cells. While cell viability results did not reveal significant differences, the findings implied that a mass spectrometry-based cell metabolomics approach could be a sensitive tool to explore the differences caused by formulation changes without using animals. Since uncertainties of products containing nanomaterials warrant holistic screening to address safety concerns, the aforementioned approach may be of regulatory importance and is worth further investigation.

Resolving Modifications on Sphingoid Base and N-Acyl Chain of Sphingomyelin Lipids in Complex Lipid Extracts

Sphingomyelins (SMs) are an essential class of lipids widely existing in different organisms. The sphingoid base and N-acyl chain are two building blocks which can undergo different types of modifications during lipogenesis, including desaturation, hydroxylation, and methyl branching. Current lipidomic analysis methods cannot provide detailed information on these structural motifs. Herein, we developed a tandem mass spectrometric method by harnessing radical-directed dissociation (RDD) from collision-induced dissociation (CID) of the bicarbonate anion adduct of SM ([M + HCO₃]^-). A major RDD channel produced a high-abundance fragment carrying the intact N-acyl chain, termed as "N-acyl fragment", allowing the assignment of the sphingoid base/N-acyl composition and relative quantitation of compositional isomers of SM at high sensitivity. RDD also produced intrachain fragments in lower abundances, which helped localization of methyl branching and hydroxylation in SM. The acetone Paternò-Büchi (PB) reaction was found to be capable of derivatizing the Δ4 carbon-carbon double bond (C═C) in sphingosine (SPH) base and producing C═C diagnostic ions upon CID, albeit at much lower efficiencies than those of the isolated C═C in alkyl chains. A liquid chromatography-mass spectrometry workflow was developed by incorporating MS² CID of SM via [M + HCO₃]^- and PB-MS² CID. The capability of profiling SM with detailed structural information was demonstrated by analyzing complex lipid extracts from porcine brain and Caenorhabditis elegans. These results provided visualization of the sphingoid base/N-acyl compositional isomers of SM lipids and revealed large structural diversity from each sample. These included identification of the sphingadiene base [d18:1(Δ4,14)], C═C location isomers in N-acyls, C-2 hydroxylation of N-acyls, and iso-methyl branched SPH base.

Differences in lipidomics may be potential biomarkers for early diagnosis of pancreatic cancer

Purpose

To analyze the plasma lipid spectrum between healthy control and patients with pancreatic cancer and to select differentially expressed tumor markers for early diagnosis.

Methods

In total, 20 patents were divided into case group and healthy control group according to surgical pathology. Of almost 1206 plasma lipid molecules harvested from 20 patients were measured by HILIC using the normal phase LC/MS. Heat map presented the relative levels of metabolites and lipids in the healthy control group and patients with pancreatic cancer. The PCA model was constructed to find out the difference in lipid metabolites. The principal components were drawn in a score plot and any clustering tendency could be observed. PLS-DA were performed to distinguish the healthy control group and pancreatic cancer according to the identified lipid profiling datasets. The volcano plot was used to visualize all variables with VIP>1 and presented the important variables with P<0.01 and |FC|>2.

Results

The upregulated lipid metabolites in patients with pancreatic cancer contained 9 lipids; however, the downregulated lipid metabolites contained 79 lipids.

Conclusion

There were lipid metabolomic differences in patients with pancreatic cancer, which could serve as potential tumor markers for pancreatic cancer.

Advances in lipidomics

The present article examines recently published literature on lipids, mainly focusing on research involving glycero-, glycerophospho- and sphingo-lipids. The primary aim is identification of distinct profiles in biologic lipidomic systems by ultra-high-performance liquid chromatography (UHPLC) coupled with mass spectrometry (MS, tandem MS) with multivariate data analysis. This review specifically targets lipid biomarkers and disease pathway mechanisms in humans and artificial targets. Different specimen matrices such as primary blood derivatives (plasma, serum, erythrocytes, and blood platelets), faecal matter, urine, as well as biologic tissues (liver, lung and kidney) are highlighted.

Sphingolipidomics Investigation of the Temporal Dynamics after Ischemic Brain Injury

Sphingolipids (SPLs) have been proposed as potential therapeutic targets for strokes, but no reports have ever profiled the changes of the entire range of SPLs after a stroke. This study applied sphingolipidomic methods to investigate the temporal and individual changes in the sphingolipidome including the effect of atorvastatin after ischemic brain injury. We conducted sphingolipidomic profiling of mouse brain tissue by liquid chromatography-electrospray ionization tandem mass spectrometry at 3 h and 24 h after 1 h of middle cerebral artery occlusion (MCAO), and SPL levels were compared with those of the Sham control group. At 3 h post-MCAO, ceramides (Cers) exhibited an increase in levels of long-chain Cers but a decrease in very-long-chain Cers. Moreover, sphingosine, the precursor of sphingosine-1-phosphate (S1P), decreased and S1P increased at 3 h after MCAO. In contrast to 3 h, both long-chain and very-long-chain Cers showed an increased trend at 24 h post-MCAO. Most important, the administration of atorvastatin improved the neurological function of the mice and significantly reversed the SPL changes resulting from the ischemic injury. Furthermore, we used plasma samples from nonstroke control and stroke patients at time points of 72 h after a stroke, and found a similar trend of Cers as in the MCAO model. This study successfully elucidated the overall effect of ischemic injury on SPL metabolism with and without atorvastatin treatment. The network of SPL components that change upon ischemic damage may provide novel therapeutic targets for ischemic stroke.

Differential Isotope Labeling by Permethylation and Reversed-Phase Liquid Chromatography-Mass Spectrometry for Relative Quantification of Intact Neutral Glycolipids in Mammalian Cells

Probing the role of glycolipids in health and disease warrants development of practical strategies to determine these molecules at the intact structural level, namely to simultaneously characterize and quantify the glycan and lipid moieties without breaking the linkage between them. Herein we present such an approach utilizing differential isotope labeling and reversed phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) for structural characterization and relative quantification of intact neutral glycolipids. In this approach, each individual sample and a pooled aliquot of each sample were permethylated using ¹²CH₃I and ¹³CH₃I, respectively, with the latter one serving as internal reference standard. The individual ¹²C-permethylated samples were spiked with equal amounts of the ¹³C-permethylated pooled sample and analyzed by RPLC-MS/MS. Permethylation not only increased the ionization efficiency of glycolipids but also facilitated structural characterization of both moieties. The ratio of the peak areas between the ¹²C- and ¹³C-labeled glycolipids served as surrogate measure of their relative concentrations. The coefficient of variation of the method was <6% measured across four representative glycolipids in five different ratios and triplicate experiments, after correction of natural isotopic distribution. When analyzing the low abundant glycolipids in total lipid extract, permethylation can dramatically reduce the analytical background by depleting most of the highly abundant ester-linked lipids. Application to conduritol B epoxide-, a β-glucocerebrosidase inhibitor, treated RAW 264.7 cells demonstrated the practical utility of this method in profiling the temporal accumulation of different glycolipids. Overall, this methodology offers a practical LC-MS based identification and quantification strategy to advance intact glycolipids analysis in mammalian cells.

Comparative study on metabolite level in tissue-specific human mesenchymal stem cells by an ultra-performance liquid chromatography quadrupole time of flight mass spectrometry

Mesenchymal stem cells (MSCs) are a promising therapeutic option for cell-based therapy due to their immunomodulatory and regenerative properties. They can be isolated from various adult tissues, including bone marrow, fat, dental tissue, and glandular tissue. Although they share common characteristics, little is known about the biological differences between MSC populations derived from different tissues. In this study, we used MS to compare the endogenous metabolite level in the human MSCs originating from the bone marrow, adipose tissue, periodontal ligaments, and salivary glands. Using an optimized metabolomics technique, we verified that human MSCs exhibit differences in the endogenous metabolite level depending on their source material, while the multivariate analysis showed that 5 lysophosphatidylcholines and 3 lysophosphatidylethanolamines can serve as markers for the discrimination between MSC sources and may be related to differences in their differentiation capacity. These results may significantly contribute to further mechanistic studies on the MSCs and provide novel insights into the properties and optimal usage of MSCs from different tissues.