Unsaturation Elements and Other Modifications of Phospholipids in Bacteria: New Insight from Ultraviolet Photodissociation Mass Spectrometry

Isomer-resolved characterization of acylcarnitines reveals alterations in type 2 diabetes

BACKGROUND

Acylcarnitines (CARs) are metabolites of fatty acids that play crucial roles in various cellular energy metabolism pathways. The structural diversity of CAR species arises from several modifications localized on the fatty acyl chain and there is currently a lack of reports characterizing these detailed structures. High-performance liquid chromatography (HPLC)-electrospray mass spectrometry (ESI-MS) is the common tool for CARs analysis.

RESULTS

In this study, we improved the MS detection signals of CARs by adding NH4HCO3 as buffer in the mobile phase of LC system. We demonstrated that electron activated dissociation (EAD) on the ZenoTOF 7600 system is capable of localizing the hydroxyl group and methyl branching position in CARs. The benzophenone Paternò-Büchi (PB) reaction was used for derivatizing the carbon-carbon double bond (CC). The capability of profiling CARs with detailed structural information was demonstrated by analyzing complex lipid extracts from mouse plasma. Our results also provided visualization of isomers composition, including branched chain isomers of CAR 4:0 and CAR 5:0 and CC location isomers of unsaturated CARs. Notably, we observed significant changes in the relative compositions of branched-chain isomers of CAR 5:0 and CC location isomers of several unsaturated CARs in mouse plasma samples from type 2 diabetes (T2D) compared to normal controls, suggesting their potential as diagnostic indicators for T2D.

SIGNIFICANCE

In this work, we enhanced the limit of detection for acylcarnitine species by incorporating ammonium bicarbonate into the LC system. The CC positions in the acyl chain of CARs were identified using Paternò-Büchi (PB) derivatization coupled with tandem mass spectrometry. Modifications such as methyl branching and hydroxyl groups along the acyl chain were localized through Electron-Activated Dissociation (EAD) on the Zeno-TOF 7600 system.

Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating baijiu fermentation through multi-omics analysis

Lactic acid bacteria (LAB) are pivotal in constructing the intricate bio-catalytic networks underlying traditional fermented foods such as Baijiu. However, LAB and their metabolic mechanisms are partially understood in Moutai flavor Baijiu fermentation. Here, we found that Acetilactobacillus jinshanensis became the· dominant species with relative abundance reaching 92%, where the acid accumulated rapidly and peaked at almost 30 g/kg in Moutai flavor Baijiu. After separation, purification, and cultivation, A. jinshanensis exhibited pronounced acidophilia and higher acid resistance compared to other LAB. Further integrated multi-omics analysis revealed that fatty acid synthesis, cell membrane integrity, pHi and redox homeostasis maintenance, protein and amide syntheses were possibly crucial acid-resistant mechanisms in A. jinshanensis. Structural proteomics indicated that the surfaces of A. jinshanensis proteases contained more positively charged amino acid residues to maintain protein stability in acidic environments. The genes HSP20 and acpP were identified as acid-resistant genes for A. jinshanensis by heterologous expression analysis. These findings not only enhance our understanding of LAB in Baijiu, providing a scientific basis for acid regulation for production process, but also offer valuable insights for studying core species in other fermentation systems.

Investigating Lipid Transporter Protein and Lipid Interactions Using Variable Temperature Electrospray Ionization, Ultraviolet Photodissociation Mass Spectrometry, and Collision Cross Section Analysis

Gram-negative bacteria develop and exhibit resistance to antibiotics, owing to their highly asymmetric outer membrane maintained by a group of six proteins comprising the Mla (maintenance of lipid asymmetry) pathway. Here, we investigate the lipid binding preferences of one Mla protein, MlaC, which transports lipids through the periplasm. We used ultraviolet photodissociation (UVPD) to identify and characterize modifications of lipids endogenously bound to MlaC expressed in three different bacteria strains. UVPD was also used to localize lipid binding to MlaC residues 130-140, consistent with the crystal structure reported for lipid-bound MlaC. The impact of removing the bound lipid from MlaC on its structure was monitored based on collision cross section measurements, revealing that the protein unfolded prior to release of the lipid. The lipid selectivity of MlaC was evaluated based on titrimetric experiments, indicating that MlaC-bound lipids in various classes (sphingolipids, glycerophospholipids, and fatty acids) as long as they possessed no more than two acyl chains.

Nano-Reactors Based on Ovotransferrin Organic Skeleton through a Ferroptosis-like Strategy Efficiently Enhance Antibacterial Activity

The issue of bacterial resistance is an escalating problem due to the misuse of antibiotics worldwide. This study introduces a new antibacterial mechanism, the ferroptosis-like death (FLD) of bacteria, and an approach to creating green antibacterial nano-reactors. This innovative method leverages natural iron-containing ovotransferrin (OVT) assembled into an organic skeleton to encapsulate low-concentration adriamycin (ADM) for synthesizing eco-friendly nano-reactors. FLD utilizes the Fenton reaction of reactive oxygen species and ferrous ions to continuously produce ·OH, which can attack the bacterial cell membrane and destroy the cell structure to achieve bacteriostasis. The OVT@ADM nano-reactors are nearly spherical, with an average diameter of 247.23 nm and uniform particle sizing. Vitro simulations showed that Fe3+ in OVT@ADM was reduced to Fe2+ by glutathione in the bacterial periplasmic space, which made the structure of OVT loose, leading to a sustained slow release of ADM from OVT@ADM. The H2O2 continuously produced by ADM oxidized Fe2+ through the Fenton reaction to produce ·OH and Fe3+. The results of the antibacterial assay showed that OVT@ADM had a satisfactory antibacterial effect against S. aureus, and the inhibition rate was as high as 99.3%. The cytotoxicity results showed that the mitigation strategy significantly reduced the cytotoxicity caused by ADM. Based on the FLD mechanism, OVT@ADM nano-reactors were evaluated and applied to bacteriostasis. Therefore, the novel antibacterial mechanism and OVT@ADM by the green synthesis method have good application prospects.

Carbon Dioxide Microbubble Bursting Ionization Mass Spectrometry

Aerosols generated by bubble bursting have been proved to promote the extraction of analytes and have ultrahigh electric fields at their water-air interfaces. This study presented a simple and efficient ionization method, carbon dioxide microbubble bursting ionization (CDMBI), without the presence of an exogenous electric field (namely, zero voltage), by simulating the interfacial chemistries of sea spray aerosols. In CDMBI, microbubbles are generated in situ by continuous input of carbon dioxide into an aqueous solution containing low-concentration analytes. The microbubbles extract low- and high-polarity analytes as they pass through the aqueous solution. Upon reaching the water-air interface, these microbubbles burst to produce charged aerosol microdroplets with an average diameter of 260 μm (8.1-10.4 nL in volume), which are immediately transferred to a mass spectrometer for the detection and identification of extracted analytes. The above analytical process occurs every 4.2 s with a stable total ion chromatogram (relative standard deviation: 9.4%) recorded. CDMBI mass spectrometry (CDMBI-MS) can detect surface-active organic compounds in aerosol microdroplets, such as perfluorooctanoic acid, free fatty acids epoxidized by bubble bursting, sterols, and lecithins in soybean and egg, with the limit of detection reaching the level of fg/mL. In addition, coupling CDMBI-MS with an exogenous voltage yields relatively weak gains in ionization efficiency and sensitivity of analysis. The results suggested that CDMBI can simultaneously accomplish both bubbling extraction and microbubble bursting ionization. The mechanism of CDMBI involves bubbling extraction, proton transfer, inlet ionization, and electrospray-like ionization. Overall, CDMBI-MS can work in both positive and negative ion modes without necessarily needing an exogenous high electric field for ionization and quickly detect trace surface-active analytes in aqueous solutions.

Computational mass spectrometry accelerates C = C position-resolved untargeted lipidomics using oxygen attachment dissociation

Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C = C) position being a crucial factor in biological system, the C = C defined structures have not yet been characterized comprehensively. Here, we present an approach for C = C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the annotation rate. We validated the accuracy of our platform as per the authentic standards of 85 lipids and the biogenic standards of 52 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived samples, we characterized 648 unique lipids with the C = C position-resolved level encompassing 24 lipid subclasses defined by LIPIDMAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon [Formula: see text] 28 and double bonds [Formula: see text] 4) in the eye, testis, and brain of the mouse.

Identification of Monomethyl Branched-Chain Lipids by a Combination of Liquid Chromatography Tandem Mass Spectrometry and Charge-Switching Chemistries

While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions. Subsequent activation of these charge inverted anions yields mass spectra that differentiate anteiso-branched- from straight-chain and iso-branched-chain FA isomers with the predictable fragmentation enabling de novo assignment of anteiso branch points. The application of these charge-inversion chemistries in both gas- and solution-phase modalities is demonstrated to assign the position of anteiso-methyl branch-points in FAs and, with the aid of liquid chromatography, can be extended to de novo assignment of additional branching sites via predictable fragmentation patterns as methyl branching site(s) move closer to the carboxyl carbon. The gas-phase approach is shown to be compatible with top-down structure elucidation of complex lipids such as phosphatidylcholines, while the integration of solution-phase charge-inversion with reversed phase liquid chromatography enables separation and unambiguous identification of FA structures within isomeric mixtures. Taken together, the presented charge-switching MS-based technique, in combination with liquid chromatography, enables the structural identification of branched-chain FA without the requirement of authentic methyl-branched FA reference standards.

Structural Characterization and Quantitation of Ether-Linked Glycerophospholipids in Peroxisome Biogenesis Disorder Tissue by Ultraviolet Photodissociation Mass Spectrometry

The biological impact of ether glycerophospholipids (GP) in peroxisomal disorders and other diseases makes them significant targets as biomarkers for diagnostic assays or deciphering pathology of the disorders. Ether lipids include both plasmanyl and plasmenyl lipids, which each contain an ether or a vinyl ether bond at the sn-1 linkage position, respectively. This linkage, in contrast to traditional diacyl GPs, precludes their detailed characterization by mass spectrometry via traditional collisional-based MS/MS techniques. Additionally, the isomeric nature of plasmanyl and plasmenyl pairs of ether lipids introduces a further level of complexity that impedes analysis of these species. Here, we utilize 213 nm ultraviolet photodissociation mass spectrometry (UVPD-MS) for detailed characterization of phosphatidylethanolamine (PE) and phosphatidylcholine (PC) plasmenyl and plasmanyl lipids in mouse brain tissue. 213 nm UVPD-MS enables the successful differentiation of these four ether lipid subtypes for the first time. We couple this UVPD-MS methodology to reversed-phase liquid chromatography (RPLC) for characterization and relative quantitation of ether lipids from normal and diseased (Pex7 deficiency modeling the peroxisome biogenesis disorder, RCDP) mouse brain tissue, highlighting the ability to pinpoint specific structural features of ether lipids that are important for monitoring aberrant lipid metabolism in peroxisomal disorders.

Enhancing the Signal-to-Noise of Diagnostic Fragment Ions of Unsaturated Glycerophospholipids via Precursor Exclusion Ultraviolet Photodissociation Mass Spectrometry (PEx-UVPD-MS)

Understanding and elucidating the diverse structures and functions of lipids has motivated the development of many innovative tandem mass spectrometry (MS/MS) strategies. Higher-energy activation methods, such as ultraviolet photodissociation (UVPD), generate unique fragment ions from glycerophospholipids that can be used to perform in-depth structural analysis and facilitate the deconvolution of isomeric lipid structures in complex samples. Although detailed characterization is central to the correlation of lipid structure to biological function, it is often impeded by the lack of sufficient instrument sensitivity for highly bioactive but low-abundance phospholipids. Here, we present precursor exclusion (PEx) UVPD, a simple yet powerful technique to enhance the signal-to-noise (S/N) of informative low-abundance fragment ions produced from UVPD of glycerophospholipids. Through the exclusion of the large population of undissociated precursor ions with an MS3 strategy, the S/N of diagnostic fragment ions from PC 18:0/18:2(9Z, 12Z) increased up to an average of 13x for PEx-UVPD compared to UVPD alone. These enhancements were extended to complex mixtures of lipids from bovine liver extract to confidently identify 35 unique structures using liquid chromatography PEx-UVPD. This methodology has the potential to advance lipidomics research by offering deeper structure elucidation and confident identification of biologically active lipids.

Localization of Intrachain Modifications in Bacterial Lipids Via Radical-Directed Dissociation

Intrachain modifications of membrane glycerophospholipids (GPLs) due to formation of the carbon-carbon double bond (C═C), cyclopropane ring, and methyl branching are crucial for bacterial membrane homeostasis. Conventional collision-induced dissociation (CID) of even-electron ions of GPL favors charge-directed fragmentation channels, and thus little structurally informative fragments can be detected for locating intrachain modifications. In this study, we report a radical-directed dissociation (RDD) approach for characterization of the intrachain modifications within phosphoethanolamines (PEs), a major lipid component in bacterial membrane. In this method, a radical precursor that can produce benzyl or pyridine methyl radical upon low-energy CID at high efficiency is conjugated onto the amine group of PEs. The carbon-centered radical ions subsequently initiate RDD along the fatty acyl chain, producing fragment patterns key to the assignment and localization of intrachain modifications including C═C, cyclopropane rings, and methyl branching. Besides intrachain fragmentation, RDD on the glycerol backbone produces fatty acyl loss as radicals, allowing one to identify the fatty acyl chain composition of PE. Moreover, RDD of lyso-PEs produces radical losses for distinguishing the sn-isomers. The above RDD approach has been incorporated onto a liquid chromatography-mass spectrometry workflow and applied for the analysis of lipid extracts from Escherichia coli and Bacillus subtilis.

Bacterial growth monitored by two-dimensional tandem mass spectrometry

The growth of the bacterium E. coli was monitored by targeting the phospholipid constituents through desorption electrospray ionization and characterizing individual sets of isomers by recording the full 2D MS/MS data domain in a single scan of a modified quadrupole ion trap mass spectrometer. The experiments tested the applicability of the new instrumental capabilities which include sample interrogation at the molecular level for multiple components at speeds of <10 seconds/sample. The major lipids observed were phosphatidylethanolamines and phosphatidylglycerols and the growth experiment showed fatty acid chain modification from alkene to cyclopropyl groups over time. Notably, these novel MS scans were also performed using desorption electrospray ionization (DESI) to quickly sample complex mixtures without pre-separation. This demonstration experiment has implications for the value of ambient ionization mass spectrometry for monitoring biological systems on physiologically relevant timescales.

Relative Quantitation of Unsaturated Phosphatidylcholines Using 193 nm Ultraviolet Photodissociation Parallel Reaction Monitoring Mass Spectrometry

Structural characterization of glycerophospholipids beyond the fatty acid level has become a major endeavor in lipidomics, presenting an opportunity to advance the understanding of the intricate relationship between lipid metabolism and disease state. Distinguishing subtle lipid structural features, however, remains a major challenge for high-throughput workflows that implement traditional tandem mass spectrometry (MS/MS) techniques, stunting the molecular depth of quantitative strategies. Here, reversed phase liquid chromatography is coupled to parallel reaction mass spectrometry utilizing the double bond localization capabilities of ultraviolet photodissociation (UVPD) mass spectrometry to produce double bond isomer specific responses that are leveraged for relative quantitation. The strategy provides lipidomic characterization at the double bond level for phosphatidylcholine phospholipids from biological extracts. In addition to quantifying monounsaturated lipids, quantitation of phospholipids incorporating isomeric polyunsaturated fatty acids is also achieved. Using this technique, phosphatidylcholine isomer ratios are compared across human normal and tumor breast tissue to reveal significant structural alterations related to disease state.

Revealing Fatty Acid Heterogeneity in Staphylococcal Lipids with Isotope Labeling and RPLC-IM-MS

Up to 80% of the fatty acids in Staphylococcus aureus membrane lipids are branched, rather than straight-chain, fatty acids. The branched fatty acids (BCFAs) may have either an even or odd number of carbons, and the branch position may be at the penultimate carbon (iso) or the antepenultimate (anteiso) carbon of the tail. This results in two sets of isomeric fatty acid species with the same number of carbons that cannot be resolved by mass spectrometry. The isomer/isobar challenge is further complicated when the mixture of BCFAs and straight-chain fatty acids (SCFAs) are esterified into diacylated lipids such as the phosphatidylglycerol (PG) species of the S. aureus membrane. No conventional chromatographic method has been able to resolve diacylated lipids containing mixtures of SCFAs, anteiso-odd, iso-odd, and iso-even BCFAs. A major hurdle to method development in this area is the lack of relevant analytical standards for lipids containing BCFA isomers. The diversity of the S. aureus lipidome and its naturally high levels of BCFAs present an opportunity to explore the potential of resolving diacylated lipids containing BCFAs and SFCAs. Using our knowledge of lipid and fatty acid biosynthesis in S. aureus, we have used a stable-isotope-labeling strategy to develop and validate a 30 min C18 reversed-phase liquid chromatography method combined with traveling-wave ion mobility-mass spectrometry to provide resolution of diacylated lipids based on the number of BCFAs that they contain.

Pseudotargeted Lipidomics Strategy Enabling Comprehensive Profiling and Precise Lipid Structural Elucidation of Polyunsaturated Lipid-Rich Echium Oil

Echium oil has great nutritional value as a result of its high content of α-linolenic acid (ALA, 18:3ω-3) and stearidonic acid (SDA, 18:4ω-3). However, the comprehensive lipid profiling and exact structural characterization of bioactive polyunsaturated lipids in echium oil have not yet been obtained. In this study, we developed a novel pseudotargeted lipidomics strategy for comprehensive profiling and lipid structural elucidation of polyunsaturated lipid-rich echium oil. Our approach integrated untargeted lipidomics analysis with a targeted lipidomics strategy based on Paternò-Büchi (PB)-tandem mass spectrometry (MS/MS) using 2-acetylpyridine (2-AP) as the reaction reagent, allowing for high-coverage lipid profiling and simultaneous determination of C═C locations in triacylglycerols (TGs), diacylglycerols (DGs), free fatty acids (FFAs), and sterol esters (SEs) in echium oil. A total of 209 lipid species were profiled, among which 162 unsaturated lipids were identified with C═C location assignment and 42 groups of ω-3 and ω-6 C═C location isomers were discovered. In addition, relative isomer ratios of certain groups of lipid C═C location isomers were revealed. This pseudotargeted lipidomics strategy described in this study is expected to provide new insight into structural characterization of distinctive bioactive lipids in food.

Mapping the distribution of double bond location isomers in lipids across mouse tissues

Lipids are highly diverse and essential biomolecules in all living systems. As lipid homeostasis is often perturbed in metabolic diseases, these molecules can serve as both biomarkers and drug targets. The development of modern mass spectrometry (MS) provided the platform for large-scale lipidomic studies at the level of molecular species. Traditionally, more detailed structural information, such as the C[double bond, length as m-dash]C location, was mostly assumed instead of properly measured, though the specific isomers were indicated as potential biomarkers of cancers or cardiovascular diseases. Recent C[double bond, length as m-dash]C localization methods, including the Paternò-Büchi (PB) reaction, have shown the prevalent and heterogeneous distribution of C[double bond, length as m-dash]C location in lipids across tissues. Mapping the lipidome of model animals at the level of C[double bond, length as m-dash]C position would increase the understanding of the metabolism and function of lipid isomers, facilitating clinical research. In this study, we employed an online PB reaction on a liquid chromatography-high resolution MS platform to map C[double bond, length as m-dash]C location isomers in five different murine tissues. We analyzed phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins; we relatively quantified and mapped the distribution of ∼30 groups of co-existing isomers, characterized by different chain lengths and degrees of unsaturation. More specifically, we performed relative quantitation of four isomers of the C16:1 fatty acyl, which included rarely reported n-10 and n-5 species besides n-9 and n-7 isomers. We showed a small variation of the isomers' relative composition among individual animals (<20%) but significant differences across different lipid species and mouse tissues. Our results provided an initial database to map alternative lipid metabolic pathways at the tissue level.

Characterization of Fatty Acyl Modifications in Phosphatidylcholines and Lysophosphatidylcholines via Radical-Directed Dissociation

Phosphatidylcholines (PCs) are the major structural components of the plasma membrane of mammalian cells, while lysophosphatidylcholines (LPCs) are critical intermediates in lipid remodeling. Conventional tandem mass spectrometric (MSⁿ) methods via collision-induced dissociation (CID) are blind to intrachain modifications such as the location of the carbon-carbon double bond (C═C) and methyl branching point. In this study, we demonstrate that almost complete structural information can be inferred from a single MS² CID spectrum of the bicarbonate anion adducts of PC or LPC ([M + HCO₃]^-), including the identity of the headgroup, composition of fatty acyl chains, their sn-positions, the location of C═C, and the point of methyl branching in fatty acyls. We have integrated this MS² CID method onto liquid chromatography for the analysis LPCs in human plasma, revealing the existence of multiple sn-isomers, branched chain isomers, and C═C location isomers of LPC.

Next-generation derivatization reagents optimized for enhanced product ion formation in photodissociation-mass spectrometry of fatty acids

Next-generation derivatives for photodissociation-mass spectrometry for fatty acids generating photoproduct yields of up to 97% at 266 nm.

Multifunctional Reactive MALDI Matrix Enabling High-Lateral Resolution Dual Polarity MS Imaging and Lipid C═C Position-Resolved MS2 Imaging

Local lipid variations in tissues are readily revealed with mass spectrometry imaging (MSI) methods, and the resulting lipid distributions serve as bioanalytical signatures to reveal cell- or tissue-specific lipids. Comprehensive MSI lipid mapping requires measurements in both ion polarities. Additionally, structural lipid characterization is necessary to link the lipid structure to lipid function. Whereas some structural elements of lipids are readily derived from high-resolution mass spectrometry (MS) and tandem-MS (MSⁿ), the localization of C═C double bonds (DBs) requires specialized fragmentation and/or functionalization methods. In this work, we identify a multifunctional matrix-assisted laser desorption/ionization (MALDI) matrix for spatially resolved lipidomics investigations that reacts with lipids in Paternò-Büchi (PB) reactions during laser irradiation facilitating DB-position assignment and allows dual-polarity high-resolution MALDI-MSI and MALDI MS²I studies. By screening 12 compounds for improved ionization efficiency in positive-/negative-ion mode and the functionalization yield compared to the previously introduced reactive MALDI matrix benzophenone, 2-benzoylpyridine (BzPy) is identified as the best candidate. The new matrix enables DB localization of authentic standards belonging to 12 lipid classes and helps to assign 133/58 lipid features in positive-/negative-ion mode from mouse cerebellum tissue. The analytical capabilities of BzPy as a multifunctional MALDI-MSI matrix are demonstrated by imaging endogenous and PB-functionalized lipids in mouse kidney sections with 7 μm lateral resolution in both ion modes. Tracking diagnostic lipid DB-position fragment ions in mouse pancreatic tissue with down to 10 μm pixel size allows us to identify the islets of Langerhans associated with lipid isomer upregulation and depletion.