Rapid differentiation of isomeric lipids by photodissociation mass spectrometry of fatty acid derivatives

LC-MS/MS-based phospholipid profiling of plant-pathogenic bacteria with tailored separation of methyl-branched species

Plant-pathogenic bacteria are one of the major constraints on agricultural yield. In order to selectively treat these bacteria, it is essential to understand the molecular structure of their cell membrane. Previous studies have focused on analyzing hydrolyzed fatty acids (FA) due to the complexity of bacterial membrane lipids. These studies have highlighted the occurrence of branched-chain fatty acids (BCFA) alongside normal-chain fatty acids (NCFA) in many bacteria. As several FA are bound in the intact phospholipids of the bacterial membrane, the presence of isomeric FA complicates lipid analysis. Furthermore, commercially available reference standards do not fully cover potential lipid isomers. To address this issue, we have developed a reversed-phase high-performance liquid chromatography (RP-HPLC) method with tandem mass spectrometry (MS/MS) to analyze the phospholipids of various plant-pathogenic bacteria with a focus on BCFA containing phospholipids. The study revealed the separation of three isomeric phosphatidylethanolamines (PE) depending on the number of bound BCFA to NCFA. The validation of the retention order was based on available reference standards in combination with the analysis of hydrolyzed fatty acids through gas chromatography with mass spectrometry (GC/MS) after fractionation. Additionally, the transferability of the retention order to other major lipid classes, such as phosphatidylglycerols (PG) and cardiolipins (CL), was thoroughly examined. Using the information regarding the retention behavior, the phospholipid profile of six plant-pathogenic bacteria was structurally elucidated. Furthermore, the developed LC-MS/MS method was used to classify the plant-pathogenic bacteria based on the number of bound BCFA in the phospholipidome.

Structural characterization of fatty acid anions via gas-phase charge inversion using Mg(tri-butyl-terpyridine)2 2+ reagent ions

RATIONALE

Free fatty acids and lipid classes containing fatty acid esters are major components of lipidome. In the absence of a chemical derivatization step, FA anions do not yield all of the structural information that may be of interest under commonly used collision-induced dissociation (CID) conditions. A line of work that avoids condensed-phase derivatization takes advantage of gas-phase ion/ion chemistry to charge invert FA anions to an ion type that provides the structural information of interest using conventional CID. This work was motivated by the potential for significant improvement in overall efficiency for obtaining FA chain structural information.

METHODS

A hybrid triple quadrupole/linear ion-trap tandem mass spectrometer that has been modified to enable the execution of ion/ion reaction experiments was used to evaluate the use of 4,4',4″-tri-tert-butyl-2,2':6',2″-terpyridine (ttb-Terpy) as the ligand in divalent magnesium complexes for charge inversion of FA anions.

RESULTS

Mg(ttb-Terpy)2 2+ complexes provide significantly improved efficiency in producing structurally informative products from FA ions relative to Mg(Terpy)2 2+ complexes, as demonstrated for straight-chain FAs, branched-chain FAs, unsaturated FAs, and cyclopropane-containing FAs. It was discovered that most of the structurally informative fragmentation from [FA-H + Mg(ttb-Terpy)]+ results from the loss of a methyl radical from the ligand followed by radical-directed dissociation (RDD), which stands in contrast to the charge-remote fragmentation (CRF) believed to be operative with the [FA-H + Mg(Terpy)]+ ions.

CONCLUSIONS

This work demonstrates that a large fraction of product ions from the CID of ions of the form [FA-H + Mg(ttb-Terpy)]+ are derived from RDD of the FA backbone, with a very minor fraction arising from structurally uninformative dissociation channels. This ligand provides an alternative to previously used ligands for the structural characterization of FAs via CRF.

Gas-Phase Ion/Ion Reactions to Enable Radical-Directed Dissociation of Fatty Acid Ions: Application to Localization of Methyl Branching

Methyl branching on the carbon chains of fatty acids and fatty esters is among the structural variations encountered with fatty acids and fatty esters. Branching in fatty acid/ester chains is particularly prominent in bacterial species and, for example, in vernix caseosa and sebum. The distinction of branched chains from isomeric straight-chain species and the localization of branching can be challenging to determine by mass spectrometry (MS). Condensed-phase derivatization strategies, often used in conjunction with separations, are most commonly used to address the identification and characterization of branched fatty acids. In this work, a gas-phase ion/ion strategy is presented that obviates condensed-phase derivatization and introduces a radical site into fatty acid ions to facilitate radical-directed dissociation (RDD). The gas-phase approach is also directly amenable to fatty acid anions generated via collision-induced dissociation from lipid classes that contain fatty esters. Specifically, divalent magnesium complexes bound to two terpyridine ligands that each incorporate a ((2,2,6,6-tetramethyl-1-piperidine-1-yl)oxy) (TEMPO) moiety are used to charge-invert fatty acid anions. Following the facile loss of one of the ligands and the TEMPO group of the remaining ligand, a radical site is introduced into the complex. Subsequent collision-induced dissociation (CID) of the complex exhibits preferred cleavages that localize the site(s) of branching. The approach is illustrated with iso-, anteiso-, and isoprenoid branched-chain fatty acids and an intact glycerophospholipid and is applied to a mixture of branched- and straight-chain fatty acids derived from Bacillus subtilis.

Permethylation and Metal Adduction: A Toolbox for the Improved Characterization of Glycolipids with Cyclic Ion Mobility Separations Coupled to Mass Spectrometry

Lipids are an important class of molecules involved in various biological functions but remain difficult to characterize through mass-spectrometry-based methods because of their many possible isomers. Glycolipids, specifically, play important roles in cell signaling but display an even greater level of isomeric heterogeneity as compared to other lipid classes stemming from the introduction of a carbohydrate and its corresponding linkage position and α/β anomericity at the headgroup. While liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidomics, it is still unable to characterize all isomeric species, thus presenting the need for new, orthogonal, methodologies. Ion mobility spectrometry-mass spectrometry (IMS-MS) can provide an additional dimension of information that supplements LC-MS/MS workflows, but has seen little use for glycolipid analyses. Herein, we present an analytical toolbox that enables the characterization of various glycolipid isomer sets using high-resolution cyclic ion mobility separations coupled with mass spectrometry (cIMS-MS). Specifically, we utilized a combination of both permethylation and metal adduction to fully resolve isomeric sphingolipids and ceramides with our cIMS-MS platform. We also introduce a new metric that can enable comparing peak-to-peak resolution across varying cIMS-MS pathlengths. Overall, we envision that our presented methodologies are highly amenable to existing LC-MS/MS-based workflows and can also have broad utility toward other omics-based analyses.

Formation and Tandem Mass Spectrometry of Doubly Charged Lipid-Metal Ion Complexes

Phospholipids are major components of most eukaryotic cell membranes. Changes in metabolic states are often accompanied by phospholipid structure variations. The structural changes of phospholipids are the hallmark of disease states, or specific lipid structures have been associated with distinct organisms. Prime examples are microorganisms that synthesize phospholipids with, for example, different branched chain fatty acids. Assignment and relative quantitation of structural isomers of phospholipids that arise from attachment of different fatty acids to the glycerophospholipid backbone are difficult with routine tandem mass spectrometry or with liquid chromatography without authentic standards. In this work, we report on the observation that all investigated phospholipid classes form doubly charged lipid-metal ion complexes during electrospray ionization (ESI) and show that these complexes can be used to assign lipid classes and fatty acid moieties, distinguish isomers of branched chain fatty acids, and relatively quantify these isomers in positive-ion mode. Use of water free methanol and addition of divalent metal salts (100 mol %) to ESI spray solutions afford highly abundant doubly charged lipid-metal ion complexes (up to 70 times of protonated compounds). Higher-energy collisional dissociation and collision-induced dissociation of doubly charged complexes yield a diverse set of lipid class-dependent fragment ions. In common for all lipid classes is the liberation of fatty acid-metal adducts that yield fragment ions from the fatty acid hydrocarbon chain upon activation. This ability is used to pinpoint sites of branching in saturated fatty acids and is showcased for free fatty acids as well as glycerophospholipids. The analytical utility of doubly charged phospholipid-metal ion complexes is demonstrated by distinguishing fatty acid branching-site isomers in phospholipid mixtures and relatively quantifying the corresponding isomeric compounds.

Establishing carbon-carbon double bond position and configuration in unsaturated fatty acids by gas-phase infrared spectroscopy

Fatty acids are an abundant class of lipids that are characterised by wide structural variation including isomeric diversity arising from the position and configuration of functional groups. Traditional approaches to fatty acid characterisation have combined chromatography and mass spectrometry for a description of the composition of individual fatty acids while infrared (IR) spectroscopy has provided insights into the functional groups and bond configurations at the bulk level. Here we exploit universal 3-pyridylcarbinol ester derivatization of fatty acids to acquire IR spectra of individual lipids as mass-selected gas-phase ions. Intramolecular interactions between the protonated pyridine moiety and carbon-carbon double bonds present highly sensitive probes for regiochemistry and configuration through promotion of strong and predictable shifts in IR resonances. Gas-phase IR spectra obtained from unsaturated fatty acids are shown to discriminate between isomers and enable the first unambiguous structural assignment of 6Z-octadecenoic acid in human-derived cell lines. Compatibility of 3-pyridylcarbinol ester derivatization with conventional chromatography-mass spectrometry and now gas-phase IR spectroscopy paves the way for comprehensive structure elucidation of fatty acids that is sensitive to regio- and stereochemical variations and with the potential to uncover new pathways in lipid metabolism.

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.

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.

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.

Structures and functions of the gut microbial lipidome

Microbial lipids provide signals that are responsible for maintaining host health and controlling disease. The differences in the structures of microbial lipids have been shown to alter receptor selectivity and agonist/antagonist activity. Advanced lipidomics is an emerging field that helps to elucidate the complex bacterial lipid diversity. The use of cutting-edge technologies is expected to lead to the discovery of new functional metabolites involved in host homeostasis. This review aims to describe recent updates on functional lipid metabolites derived from gut microbiota, their structure-activity relationships, and advanced lipidomics technologies.

Enhanced Characterization of Cardiolipins via Hybrid 193 nm Ultraviolet Photodissociation Mass Spectrometry

Cardiolipins (CLs) constitute a structurally complex class of glycerophospholipids with a unique tetraacylated structure accompanied by distinctive functional roles. Aberrations in the composition of this lipid class have been associated with disease states, spurring interest in the development of new approaches to differentiate the structures of diverse CLs in complex mixtures. The structural characterization of these complex lipids using conventional methods, however, suffers from limited resolution and frequently proves unable to discern subtle yet biologically significant features such as unsaturation sites or acyl chain position assignments. Here, we describe the synergistic use of chemical derivatization and hybrid dissociation techniques to characterize CL from complex biological mixtures with both double bond and sn positional isomer resolution in a shotgun mass spectrometry strategy. Utilizing (trimethylsilyl)diazomethane (TMSD), CL phosphate groups were methylated to promote positive-mode ionization by the production of metal-cationized lipids, enabling structural interrogation via hybrid higher-energy collisional activation/ultraviolet photodissociation (HCD/UVPD). This combination of TMSD derivatization and HCD/UVPD fragmentation results in diagnostic product ions that permit distinction and relative quantitation of sn-stereoisomers and the localization of double bonds. Applying this strategy to a total lipid extract from a thyroid carcinoma revealed a previously unreported 18:2/18:1 motif, elucidating a structural feature unique to the lipid class.

Profiling of branched-chain fatty acids via nitroxide radical-directed dissociation integrated on an LC-MS/MS workflow

By coupling O-benzylhydroxylamine derivatization and tandem mass spectrometry, nitroxide radical-induced dissociation can be initiated via collisional activation which enables the analysis of methyl branching(s) in fatty acids.

Enabling High Structural Specificity to Lipidomics by Coupling Photochemical Derivatization with Tandem Mass Spectrometry

Lipids have pivotal roles in many biological processes, including energy storage, signal transduction, and plasma membrane formation. A disruption of lipid homeostasis is found to be associated with a range of diseases, such as cardiovascular diseases, diabetes, and cancer. Fundamental lipid biology and disease diagnostics can benefit from monitoring lipid changes in cells, tissues, organs, or the whole biological system. Therefore, it is important to develop lipid analysis tools to achieve comprehensive lipid characterization and quantitation. Over the past two decades, mass spectrometry (MS) has become the method of choice for qualitative and quantitative analyses of lipids, owing to its high sensitivity, multiplexed analysis, and soft ionization features. With the rapid development and adoption of ultrahigh-resolution MS, isobaric lipids can now be routinely resolved. By contrast, the structural characterization and quantitation of isomeric lipids remain an analytical challenge. Although some lipid C═C location or sn-isomers can be resolved by chromatography, ion mobility, or selective ionization approaches, a detailed structural characterization on the lipidome-wide level needs to be achieved.Over the past six years, we have successfully combined the Paternò-Büchi (PB) reaction, which is a UV-promoted photocycloaddition reaction specific to the C═C, with tandem MS (MS/MS) to locate the C═C in lipids and quantify lipid C═C location isomers. The PB reactions have analytical advantages such as a simple experimental setup, rapid lipid C═C derivatization, and highly specific C═C cleavage during PB-MS/MS to produce abundant diagnostic ions. More importantly, without a need of isomer separation or a comparison to authentic standards, PB-MS/MS can be directly applied to identify and quantify a mixture of lipid C═C location isomers, often coexisting with molar ratios sensitive to the biological state of the system. The PB-MS/MS method is compatible with conventional shotgun lipidomics employing a nanoelectrospray ionization or a large-sale lipid structural analysis via liquid chromatography (LC) coupled to any mass spectrometer with tandem MS capability. The PB-MS/MS method is highly versatile, as a variety of PB reagents can be tailored to a broad range of applications. Besides UV-promoted PB reactions, visible-light PB reactions have also been developed to offer more flexibility for a lipid analysis. By using selected PB reagents, the sn-positions of fatty acyls can be resolved together with C═C locations in phospholipids. This method has been used in lipidomic analyses of tissue, blood, and plasma from animal models and clinical samples, demonstrating the potential of using lipid C═C or sn-location isomer ratios for phenotyping and disease diagnostics. Lipid isomer-resolving MS imagings of tissues and single-cell lipid analysis have also been demonstrated by a proper implementation of PB-MS/MS.

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.

Investigation of the Experimental Parameters of Ultraviolet Photodissociation for the Structural Characterization of Chondroitin Sulfate Glycosaminoglycan Isomers

Glycosaminoglycans (GAGs) are linear polysaccharides that participate in a broad range of biological functions. Their incomplete biosynthesis pathway leads to nonuniform chains and complex mixtures. For this reason, the characterization of GAGs has been a difficult hurdle for the analytical community. Recently, ultraviolet photodissociation (UVPD) has emerged as a useful tool for determining sites of modification within a GAG chain. Here, we investigate the ability for UVPD to distinguish chondroitin sulfate epimers and the effects of UVPD experimental parameters on fragmentation efficiency. Chondroitin sulfate A (CS-A) and chondroitin sulfate B (CS-B), commonly referred to as dermatan sulfate (DS), differ only in C-5 uronic acid stereochemistry. This uronic acid difference can influence GAG-protein binding and therefore can alter the specific biological function of a GAG chain. Prior tandem mass spectrometry methods investigated for the elucidation of GAG structures also have difficulty differentiating 4-O from 6-O sulfation in chondroitin sulfate GAGs. Preliminary data using UVPD to characterize GAGs showed a promising ability to characterize 4-O sulfation in CS-A GAGs. Here, we look in depth at the capability of UVPD to distinguish chondroitin sulfate C-5 diastereomers and the role of key experimental parameters in making this distinction. Results using a 193 nm excimer laser and a 213 nm solid-state laser are compared for this study. The effect of precursor ionization state, the number of laser pulses (193 or 213 nm UVPD), and the use of the low-pressure versus high-pressure trap are investigated.

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.

Enhancing detection and characterization of lipids using charge manipulation in electrospray ionization-tandem mass spectrometry

Heightened awareness regarding the implication of disturbances in lipid metabolism with respect to prevalent human-related pathologies demands analytical techniques that provide unambiguous structural characterization and accurate quantitation of lipids in complex biological samples. The diversity in molecular structures of lipids along with their wide range of concentrations in biological matrices present formidable analytical challenges. Modern mass spectrometry (MS) offers an unprecedented level of analytical power in lipid analysis, as many advancements in the field of lipidomics have been facilitated through novel applications of and developments in electrospray ionization tandem mass spectrometry (ESI-MS/MS). ESI allows for the formation of intact lipid ions with little to no fragmentation and has become widely used in contemporary lipidomics experiments due to its sensitivity, reproducibility, and compatibility with condensed-phase modes of separation, such as liquid chromatography (LC). Owing to variations in lipid functional groups, ESI enables partial chemical separation of the lipidome, yet the preferred ion-type is not always formed, impacting lipid detection, characterization, and quantitation. Moreover, conventional ESI-MS/MS approaches often fail to expose diverse subtle structural features like the sites of unsaturation in fatty acyl constituents or acyl chain regiochemistry along the glycerol backbone, representing a significant challenge for ESI-MS/MS. To overcome these shortcomings, various charge manipulation strategies, including charge-switching, have been developed to transform ion-type and charge state, with aims of increasing sensitivity and selectivity of ESI-MS/MS approaches. Importantly, charge manipulation approaches afford enhanced ionization efficiency, improved mixture analysis performance, and access to informative fragmentation channels. Herein, we present a critical review of the current suite of solution-based and gas-phase strategies for the manipulation of lipid ion charge and type relevant to ESI-MS/MS.

Structural elucidation of hydroxy fatty acids by photodissociation mass spectrometry with photolabile derivatives

RATIONALE

Eicosanoids are short-lived bio-responsive lipids produced locally from oxidation of polyunsaturated fatty acids (FAs) via a cascade of enzymatic or free radical reactions. Alterations in the composition and concentration of eicosanoids are indicative of inflammation responses and there is strong interest in developing analytical methods for the sensitive and selective detection of these lipids in biological mixtures. Most eicosanoids are hydroxy FAs (HFAs), which present a particular analytical challenge due to the presence of regioisomers arising from differing locations of hydroxylation and unsaturation within their structures.

METHODS

In this study, the recently developed derivatization reagent 1-(3-(aminomethyl)-4-iodophenyl)pyridin-1-ium (4-I-AMPP⁺ ) was applied to a representative set of HFAs including bioactive eicosanoids. Photodissociation (PD) mass spectra obtained at 266 nm of 4-I-AMPP⁺ -modified HFAs exhibit abundant product ions arising from photolysis of the aryl-iodide bond within the derivative with subsequent migration of the radical to the hydroxyl group promoting fragmentation of the FA chain and facilitating structural assignment.

RESULTS

Representative polyunsaturated HFAs (from the hydroxyeicosatetraenoic acid and hydroxyeicosapentaenoic acid families) were derivatized with 4-I-AMPP⁺ and subjected to a reversed-phase liquid chromatography workflow that afforded chromatographic resolution of isomers in conjunction with structurally diagnostic PD mass spectra.

CONCLUSIONS

PD of these complex HFAs was found to be sensitive to the locations of hydroxyl groups and carbon-carbon double bonds, which are structural properties strongly associated with the biosynthetic origins of these lipid mediators.

Localization of Double Bonds in Bacterial Glycerophospholipids Using 193 nm Ultraviolet Photodissociation in the Negative Mode

The need for detailed structural characterization of glycerophospholipids (GPLs) for many types of biologically motivated applications has led to the development of novel mass spectrometry-based methodologies that utilize alternative ion activation methods. Ultraviolet photodissociation (UVPD) has shown great utility for localizing sites of unsaturation within acyl chains and to date has predominantly been used for positive mode analysis of GPLs. In the present work, UVPD is used to localize sites of unsaturation in GPL anions. Similar to UVPD mass spectra of GPL cations, UVPD of deprotonated or formate-adducted GPLs yields diagnostic fragment ions spaced 24 Da apart. This method was integrated into a liquid chromatography workflow and used to evaluate profiles of sites of unsaturation of lipids in Escherichia coli (E. coli) and Acinetobacter baumannii (A. baumannii). When assigning sites of unsaturation, E. coli was found to contain all unsaturation elements at the same position relative to the terminal methyl carbon of the acyl chain; the first carbon participating in a site of unsaturation was consistently seven carbons along the acyl chain when counting carbons from the terminal methyl carbon. GPLs from A. baumannii exhibited more variability in locations of unsaturation. For GPLs containing sites of unsaturation in both acyl chains, an MS3 method was devised to assign sites to specific acyl chains.

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.

Coupling Headgroup and Alkene Specific Solution Modifications with Gas-Phase Ion/Ion Reactions for Sensitive Glycerophospholipid Identification and Characterization

Shotgun lipidomics provides sensitive and fast lipid identification without the need for chromatographic separation. Challenges faced by shotgun analysis of glycerophospholipids (GPs) include the lack of signal uniformity across GP classes and the inability to determine the carbon-carbon double bond (C═C) location within the fatty acyl chains of an unsaturated species. Two distinct derivatization strategies were employed to both enhance the ionization of GPs, via trimethylation enhancement using ¹³C-diazomethane (¹³C-TrEnDi), as well as determine location of double bonds within fatty acyl chains, employing an in-solution photochemical reaction with acetone (via the Paternò-Büchi reaction). The modified GPs were then subjected to positive ion mode ionization via electrospray ionization, producing uniform ionization efficiencies for different classes of GP species. The GPs were charge inverted via gas-phase ion/ion reactions and sequentially fragmented using ion trap collision-induced dissociation (CID). The CID of the species led to fragmentation producing diagnostic ions indicative of C═C bond location. The approach enabled enhanced ionization and the identification of phosphatidylcholine and phosphatidylethanolamine species at the C═C level in a bovine lipid extract.

Strategy for Global Profiling and Identification of 2- and 3-Hydroxy Fatty Acids in Plasma by UPLC-MS/MS

2-Hydroxy fatty acids (2-OHFAs) and 3-hydroxy fatty acids (3-OHFAs) with the same carbon backbone are isomers, both of which are closely related to diseases involving fatty acid oxidation disorder. However, the comprehensive profiling of 2- and 3-OHFAs remains an ongoing challenge due to their high structure similarity, few structure-informative product ions, and limited availability of standards. Here, we developed a new strategy to profile and identify 2- and 3-OHFAs according to structure-dependent retention time prediction models using ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Both accurate MS and MS/MS spectra were collected for peak annotation by comparison with an in-house database of theoretically possible 2- and 3-OHFAs. The structures were further confirmed by the validated structure-dependent retention time prediction models, taking advantage of the correlation between the retention time, carbon chain length and number of double bonds, as well as the hydroxyl position-induced isomeric retention time shift rule. With the use of this strategy, 18 2-OHFAs and 32 3-OHFAs were identified in the pooled plasma, of which 7 2-OHFAs and 20 3-OHFAs were identified for the first time in this work, furthering our understanding of OHFA metabolism. Subsequent quantitation method was developed by scheduled multiple reaction monitoring (MRM) and then applied to investigate the alteration of 2- and 3-OHFAs in esophageal squamous cell carcinoma (ESCC) patients. Finally, a potential biomarker panel consisting of six OHFAs with good diagnostic performance was achieved. Our study provides a new strategy for isomer identification and analysis, showing great potential for targeted metabolomics in clinical biomarker discovery.

Evaluation of ultraviolet photodissociation tandem mass spectrometry for the structural assignment of unsaturated fatty acid double bond positional isomers

Fatty acids are a major source of structural diversity within the lipidome due to variations in their acyl chain lengths, branching, and cyclization, as well as the number, position, and stereochemistry of double bonds within their mono- and poly-unsaturated species. Here, the utility of 193 nm UltraViolet PhotoDissociation tandem mass spectrometry (UVPD-MS/MS) has been evaluated for the detailed structural characterization of a series of unsaturated fatty acid lipid species. UVPD-MS/MS of unsaturated fatty acids is shown to yield pairs of unique diagnostic product ions resulting from cleavages adjacent to their C=C double bonds, enabling unambiguous localization of the site(s) of unsaturation within these lipids. The effect of several experimental variables on the observed fragmentation behaviour and UVPD-MS/MS efficiency, including the position and number of double bonds, the effect of conjugated versus non-conjugated double bonds, the number of laser pulses, and the influence of alkali metal cations (Li, Na, K) as the ionizing adducts, has been evaluated. Importantly, the abundance of the diagnostic ions is shown to enable relative quantitation of mixtures of fatty acid isomers across a range of molar ratios. Finally, the practical application of 193 nm UVPD-MS/MS is demonstrated via characterization of changes in the ratios of fatty acid double bond positional isomers in isogenic colorectal cancer cell lines. This study therefore demonstrates the practicality of UVPD-MS/MS for the structural characterization of fatty acid isomers in lipidome analysis workflows.

Hybrid 193 nm Ultraviolet Photodissociation Mass Spectrometry Localizes Cardiolipin Unsaturations

Developing alternative MS/MS strategies to distinguish isomeric lipids has become a high impact goal in shotgun lipidomics. Novel approaches have been developed to resolve structural features that are not discernible by traditional shotgun methods and have consequently promoted the discovery of new disease biomarkers. However, these methods have largely been limited to characterizing lipids with low structural complexity. Here, ultraviolet photodissociation (UVPD) strategies for phospholipid characterization are expanded for analysis of cardiolipins (CL), a class of phospholipids that exhibits a higher degree of structural complexity. A hybrid collision induced dissociation/193 nm UVPD (CID/UVPD) approach was implemented to pinpoint the location of both double bond and cyclopropyl unsaturations on the four acyl chains of CLs. This strategy was complemented with CID for the de novo elucidation of unknown CLs in biological extracts.

Determination and quantification of fatty acid C=C isomers by epoxidation reaction and liquid chromatography-mass spectrometry

The location of double bond in unsaturated fatty acids (FAs) plays a critical role in their physiological properties. However, structural identification and quantification of unsaturated FAs by mass spectrometry are still challenging. In this work, we reported the coupling of epoxidation reaction of the C=C in unsaturated FAs and liquid chromatography-mass spectrometry (LC-MS) with multiple reaction monitoring (MRM) mode for accurate identification and quantification of C=C isomers of FAs. Epoxidation of the C=C in unsaturated FAs was induced by a dioxide of ketone, tetrahydrothiopyran-4-one 1,1-dioxide, as a catalyst and Oxone as an oxidant in less than 5 min with nearly 100% yield. All the C=C bonds were epoxidized to obtain a single product, simplifying the chromatographic separation of epoxidation products to enable more accurate quantification analysis. The epoxidation products were stable at room temperature and can produce highly abundant diagnostic ions indicative of C=C locations by tandem mass spectrometry using collision-induced association (CID). The application of this approach for the analysis of FAs isomers in human plasma demonstrated the potential of our method for the qualitative and quantitative analysis of unsaturated FAs in complex biological samples, which is valuable in biological and medical analysis.

In-depth structural characterization of phospholipids by pairing solution photochemical reaction with charge inversion ion/ion chemistry

Shotgun lipid analysis based on electrospray ionization-tandem mass spectrometry (ESI-MS/MS) is increasingly used in lipidomic studies. One challenge for the shotgun approach is the discrimination of lipid isomers and isobars. Gas-phase charge inversion via ion/ion reactions has been used as an effective method to identify multiple isomeric/isobaric components in a single MS peak by exploiting the distinctive functionality of different lipid classes. In doing so, fatty acyl chain information can be obtained without recourse to condensed-phase separations or derivatization. This method alone, however, cannot provide carbon-carbon double bond (C=C) location information from fatty acyl chains. Herein, we provide an enhanced method pairing photochemical derivatization of C=C via the Paternò-Büchi reaction with charge inversion ion/ion tandem mass spectrometry. This method was able to provide gas-phase separation of phosphatidylcholines and phosphatidylethanolamines, the fatty acyl compositions, and the C=C location within each fatty acyl chain. We have successfully applied this method to bovine liver lipid extracts and identified 40 molecular species of glycerophospholipids with detailed structural information including head group, fatty acyl composition, and C=C location. Graphical Abstract ᅟ.

Desorption Electrospray Ionization Coupled with Ultraviolet Photodissociation for Characterization of Phospholipid Isomers in Tissue Sections

Desorption electrospray ionization (DESI) mass spectrometry imaging has become a powerful strategy for analysis of tissue sections, enabling differentiation of normal and diseased tissue based on changes in the lipid profiles. The most common DESI workflow involves collection of MS1 spectra as the DESI spray is rastered over a tissue section. Relying on MS1 spectra inherently limits the ability to differentiate isobaric and isomeric species or evaluate variations in the relative abundances of key isomeric lipids, such as double-bond positional isomers which may distinguish normal and diseased tissues. Here, 193 nm ultraviolet photodissociation (UVPD), a technique capable of differentiating double-bond positional isomers, is coupled with DESI to map differences in the double-bond isomer composition in tissue sections in a fast, high throughput manner compatible with imaging applications.

Mass spectrometry-directed structure elucidation and total synthesis of ultra-long chain (O-acyl)-ω-hydroxy fatty acids

The (O-acyl)-ω-hydroxy FAs (OAHFAs) comprise an unusual lipid subclass present in the skin, vernix caseosa, and meibomian gland secretions. Although they are structurally related to the general class of FA esters of hydroxy FAs (FAHFAs), the ultra-long chain (30-34 carbons) and the putative ω-substitution of the backbone hydroxy FA suggest that OAHFAs have unique biochemistry. Complete structural elucidation of OAHFAs has been challenging because of their low abundance within complex lipid matrices. Furthermore, because these compounds occur as a mixture of closely related isomers, insufficient spectroscopic data have been obtained to guide structure confirmation by total synthesis. Here, we describe the full molecular structure of ultra-long chain OAHFAs extracted from human meibum by exploiting the gas-phase purification of lipids through multi-stage MS and novel multidimensional ion activation methods. The analysis elucidated sites of unsaturation, the stereochemical configuration of carbon-carbon double bonds, and ester linkage regiochemistry. Such isomer-resolved MS guided the first total synthesis of an ultra-long chain OAHFA, which, in turn, confirmed the structure of the most abundant OAHFA found in human meibum, OAHFA 50:2. The availability of a synthetic OAHFA opens new territory for future investigations into the unique biophysical and biochemical properties of these lipids.

Benzophenone used as the photochemical reagent for pinpointing C=C locations in unsaturated lipids through shotgun and liquid chromatography-mass spectrometry approaches

Unsaturated lipids exhibit different physiological significances due to the different locations of the carbon-carbon double bond (C=C). Identifying lipid isomers with mass-based methods remains challenging. Xia's group has been successfully employed Paternò-Büchi (PB) reaction, a photochemical reaction with UV irradiation, coupled with tandem mass spectrometry (MS/MS) to identify and quantify unsaturated lipids in complex mixtures. However, the existing PB reagents possess certain demerits. In this regard, a new PB reagent that is compatible with various lipidomic analysis platforms must be screened. In this study, we comprehensively evaluated the conditions of the PB reaction and screened benzophenone as a new PB reagent. Benzophenone possesses unique advantages, such as a relative high PB yield; the PB products could be readily distinguished from the reacted lipids based on the added high molecular weight (182 Da); and the benzophenone does not affect the lipids appearance interval for reversed-phase column separation. Furthermore, we optimized the reaction conditions by using benzophenone as a PB reagent and summarized the molecular formulas of the diagnostic ions according to the fragment rules. The proposed PB method has been implemented in shotgun and LC-MS lipidomics. To our best knowledge, this work is the first to report the integrated PB reaction with LC-MS lipidomics for identification of lipid isomers.

Uncovering Structural Diversity of Unsaturated Fatty Acyls in Cholesteryl Esters via Photochemical Reaction and Tandem Mass Spectrometry

Mass spectrometry analysis of cholesteryl esters (CEs) faces several challenges, with one of them being the determination of the carbon-carbon double bond (C=C) locations within unsaturated fatty acyl chains. Paternὸ-Büchi (PB) reaction, a photochemical reaction based on the addition of acetone to C=C, is capable of C=C location determination when coupled with tandem mass spectrometry (MS/MS). In this study, the PB reaction conditions were tailored for CEs and subsequent nanoelectrospray ionization (nanoESI). A solvent system containing acetone/methanol/dichloromethane/water (40/30/20/10, volume ratios) and 100 μM LiOH was determined to be optimal, resulting in reasonable PB reaction yield (~30%) and good ionization efficiency (forming lithium adduct of CEs). Collision-induced dissociation (CID) of the PB reaction products produced characteristic fragment ions of CE together with those modified by the PB reactions, such as lithiated fatty acyl ([FA + Li]+) and its PB product ([FA - PB + Li]+). MS3 CID of [FA - PB + Li]+ led to abundant C=C diagnostic ion formation, which was used for C=C location determination and isomer quantitation. A PB-MS3 CID approach was developed and applied for CE analysis from human plasma. A series of unsaturated CEs was identified with specific C=C locations within fatty acyl chains. Absolute quantitation for each CE species was achieved including coexisting C=C location isomers, such as Δ9 and Δ11 isomers of CE 18:1 and ω-6 and ω-3 isomers of CE 18:3. These results show that PB-MS/MS is useful in uncovering structural diversity of CEs due to unsaturation in fatty acyls, which is often undetected from current lipid analysis approach. Graphical Abstract ᅟ.

Charge transfer dissociation of phosphocholines: gas-phase ion/ion reactions between helium cations and phospholipid cations

Phospholipid cations formed by electrospray ionization were subjected to excitation and fragmentation by a beam of 6 keV helium cations in a process termed charge transfer dissociation (CTD). The resulting fragmentation pattern in CTD is different from that of conventional collision-induced dissociation, but analogous to that of metastable atom-activated dissociation and electron-induced dissociation. Like collision-induced dissociation, CTD yields product ions indicative of acyl chain lengths and degrees of unsaturation in the fatty acyl moieties but also provides additional structural diagnostic information, such as double bond position. Although CTD has not been tested on a larger lipid sample pool, the extent of structural information obtained demonstrates that CTD is a useful tool for lipid structure characterization, and a potentially useful tool in future lipidomics workflows. CTD is relatively unique in that it can produce a relatively strong series of 2+ product ions with enhanced abundance at the double bond position. The generally low signal-to-noise ratios and spectral complexity of CTD make it less appealing than OzID or other radical-induced methods for the lipids studies here, but improvements in CTD efficiency could make CTD more appealing in the future. Copyright © 2017 John Wiley & Sons, Ltd.

Lipidomics, en route to accurate quantitation

Accurate quantitation is prerequisite for the sustainable development of lipidomics via enabling its applications in various biological and biomedical settings. In this review, the technical considerations and limitations of existent lipidomics technologies, particularly in terms of accurate quantitation; as well as the potential sources of errors along a typical lipidomic workflow that could ultimately give rise to quantitative inaccuracies will be addressed. Furthermore, the pressing need to exercise stricter definitions of terms and protocol standardization pertaining to quantitative lipidomics will be critically discussed, as quantitative accuracy may substantially impact upon the persevering development of lipidomics in the long run. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.

Structural Characterization of Phosphatidylcholines Using 193 nm Ultraviolet Photodissociation Mass Spectrometry

Advances in mass spectrometry have made it a preferred tool for structural characterization of glycerophospholipids. Collisional activation methods commonly implemented on commercial instruments do not provide fragmentation patterns that allow elucidation of certain structural features, including acyl chain positions on the glycerol backbone and double bond positions within acyl chains. In the present work, 193 nm ultraviolet photodissociation (UVPD) implemented on an Orbitrap mass spectrometer is used to localize double bond positions within phosphatidylcholine (PC) acyl chains. Cleavage of the carbon-carbon bonds adjacent to the double bond provides a diagnostic mass difference of 24 Da and enables differentiation of double-bond positional isomers. The UVPD method was extended to the characterization of PCs in a bovine liver extract via a shotgun strategy. Positive mode higher energy collisional dissociation (HCD) and UVPD, and negative mode HCD were undertaken in a complementary manner to identify species as PCs and to localize double bonds, respectively.

Determination of ester position in isomeric (O-acyl)-hydroxy fatty acids by ion trap mass spectrometry

RATIONALE

(O-acyl)-hydroxy fatty acids (OAHFAs) are a recently discovered class of endogenous lipids, generating significant interest for their correlation with enhanced glucose tolerance. Structural variants that differ in the position of the ester linkage have been described, including the ω-OAHFA sub-class, that plays a key role in stabilizing the human tear film. Developing analytical tools for rapid and unambiguous structural elucidation of OAHFAs is essential to understanding their diverse physiological functions.

METHODS

Commercially available and synthesized OAHFA standards were dissolved in chloroform and subsequently diluted into methanol with 1.5 mM ammonium acetate. Negative ion collision-induced dissociation (CID) MSⁿ spectra were acquired using chip-based nano-electrospray ionization (Advion TriVersa NanoMate) coupled to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific).

RESULTS

Major product ions observed during CID of [OAHFA - H]^- ions readily identify the constituent fatty acid and hydroxy fatty acid; however, isomers are not easily distinguished. Interrogation of the hydroxy fatty acid and dehydrated hydroxy fatty acid product ions by MSⁿ and ion-molecule reactions yielded diagnostic ions that readily pinpoint hydroxylation position and, thus, the OAHFA ester location. Conversely, these ions are characteristically absent in the MS³ spectra of ω-OAHFAs. Unimolecular dissociation mechanisms are proposed, which are shown to be consistent with prior isotopic labelling experiments.

CONCLUSIONS

A mechanistic rationale is provided to explain the unimolecular dissociation of [OAHFA - H]^- ions in an ion trap mass spectrometer, thus enabling near-complete de novo structural elucidation of OAHFAs in shotgun lipidomics workflows, even if synthetic standards are unavailable for comparison. Copyright © 2016 John Wiley & Sons, Ltd.

Multistage Mass Spectrometry of Phospholipids using Collision-Induced Dissociation (CID) and Metastable Atom-Activated Dissociation (MAD)

We herein demonstrate an approach to gas phase ion manipulation that provides MS3-level CID spectra of phospholipid radical cations that are almost independent of the original charging adduct ions. In the MS2 He-MAD spectra of the protonated, sodiated and potassiated adducts of POPC, the different adducts induce different primary fragmentation pathways and provide significantly different spectra, as is commonly observed by other activation methods. In separate experiments, the even-electron adduct ions ([M+H]+, [M+Na]+, [M+K]+) of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) were first converted to radical cations [POPC]+• by using helium metastable atom-activated dissociation (He-MAD) to eject the charging adduct ions, then exposed to low-energy collision induced dissociation (CID) to induce extensive fragmentation along the acyl chains. Such charge-remote fragmentation is generally inaccessible through low-energy CID of the even-electron precursor ions. The combination of He-MAD and CID provides radical-induced spectra that show very major similarities and only minor differences, and therefore overcomes major differences in chemistry that are otherwise observed by the original adducting species. Collisional activation of even-electron [POPC+H]+ required higher CID amplitudes than odd-electron [POPC]+• to effect fragmentation-as expected-and the latter provided fragments within the acyl chains that were influenced by the double bond position.

Preferential alkali metal adduct formation by cis geometrical isomers of dicaffeoylquinic acids allows for efficient discrimination from their trans isomers during ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry

RATIONALE

Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemicals that have attracted attention due to their many health benefits. The structural diversity of these molecules is due in part to the presence of regio- and geometrical isomerism. This structural diversity hampers the accurate annotation of these molecules in plant extracts. Mass spectrometry (MS) is successfully used to differentiate between the different regioisomers of the CQA derivatives; however, the accurate discrimination of the geometrical isomers of these molecules has proven to be an elusive task.

METHODS

UV-irradiated methanolic solutions of diCQA were analyzed using an ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UHPLC/QTOFMS) method in negative ionisation mode. An in-source collision-induced dissociation (ISCID) method was optimized by varying both the capillary and cone voltages to achieve differential fragmentation patterns between UV-generated geometrical isomers of the diCQAs during MS analyses.

RESULTS

Changes in the capillary voltage did not cause a significant difference to the fragmentation patterns of the four geometrical isomers, while changes in the cone voltage resulted in significant differences in the fragmentation patterns. The results also show, for the first time, the preferential formation of alkali metal (Li(+), Na(+) and K(+)) adducts by the cis geometrical isomers of diCQAs, compared to their trans counterparts.

CONCLUSIONS

Optimized QTOFMS-based methods may be used to differentiate the geometrical isomers of diCQAs. Finally, additives such as metal salts to induce adduct formation can be applied as an alternative method to differentiate closely related isomers which could have been difficult to differentiate under normal MS settings.

Bioanalytical techniques in nontargeted clinical lipidomics

Lipidomic analysis aims at comprehensive characterization of molecular lipids in biological systems. Due to the central role of lipid metabolism in many devastating diseases, lipidomics is being increasingly applied in biomedical research. Over the past years, advances in analytical techniques and bioinformatics enabled increasingly comprehensive and accurate coverage of lipids both in tissues and biofluids, yet many challenges remain. This review highlights recent progress in the domain of analytical lipidomics, with main emphasis on non-targeted methodologies for large scale clinical applications, as well as discusses some of the key challenges and opportunities in this field.

Characterization of glycosphingolipid epimers by radical-directed dissociation mass spectrometry

Radical chemistry can efficiently distinguish isomers varying in position at a single alcohol.

Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins

Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense.