Structural Analysis of Phospholipid Using Hydrogen Abstraction Dissociation and Oxygen Attachment Dissociation in Tandem Mass Spectrometry

Aza-Prilezhaev Aziridination-Enabled Multidimensional Analysis of Isomeric Lipids via High-Resolution U-Shaped Mobility Analyzer-Mass Spectrometry

Unsaturated lipids constitute a significant portion of the lipidome, serving as players of multifaceted functions involving cellular signaling, membrane structure, and bioenergetics. While derivatization-assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidome, it mainly faces challenges in efficiently labeling the carbon-carbon double bond (C═C) and differentiating isomeric lipids in full dimension. This presents a need for new orthogonal methodologies. Herein, a metal- and additive-free aza-Prilezhaev aziridination (APA)-enabled ion mobility mass spectrometric method is developed for probing multiple levels of unsaturated lipid isomerization with high sensitivity. Both unsaturated polar and nonpolar lipids can be efficiently labeled in the form of N-H aziridine without significant side reactions. The signal intensity can be increased by up to 3 orders of magnitude, achieving the nM detection limit. Abundant site-specific fragmentation ions indicate C═C location and sn-position in MS/MS spectra. Better yet, a stable monoaziridination product is dominant, simplifying the spectrum for lipids with multiple double bonds. Coupled with a U-shaped mobility analyzer, identification of geometric isomers and separation of different lipid classes can be achieved. Additionally, a unique pseudo MS3 mode with UMA-QTOF MS boosts the sensitivity for generating diagnostic fragments. Overall, the current method provides a comprehensive solution for deep-profiling lipidomics, which is valuable for lipid marker discovery in disease monitoring and diagnosis.

Ion-molecule reactions of mass-selected ions

Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.

Analysis of Metabolic Changes in Endogenous Metabolites and Diagnostic Biomarkers for Various Diseases Using Liquid Chromatography and Mass Spectrometry

Analysis of endogenous metabolites in various diseases is useful for searching diagnostic biomarkers and elucidating the molecular mechanisms of pathophysiology. The author and collaborators have developed some LC/tandem mass spectrometry (LC/MS/MS) methods for metabolites and applied them to disease-related samples. First, we identified urinary conjugated cholesterol metabolites and serum N-palmitoyl-O-phosphocholine serine as useful biomarkers for Niemann-Pick disease type C (NPC). For the purpose of intraoperative diagnosis of glioma patients, we developed the LC/MS/MS analysis methods for 2-hydroxyglutaric acid or cystine and found that they could be good differential biomarkers. For renal cell carcinoma, we searched for various biomarkers for early diagnosis, malignancy evaluation and recurrence prediction by global metabolome analysis and targeted LC/MS/MS analysis. In pathological analysis, we developed a simultaneous LC/MS/MS analysis method for 13 steroid hormones and applied it to NPC cells, we found 6 types of reductions in NPC model cells. For non-alcoholic steatohepatitis (NASH), model mice were prepared with special diet and plasma bile acids were measured, and as a result, hydrophilic bile acids were significantly increased. In addition, we developed an LC/MS/MS method for 17 sterols and analyzed liver cholesterol metabolites and found a decrease in phytosterols and cholesterol synthetic markers and an increase in non-enzymatic oxidative sterols in the pre-onset stage of NASH. We will continue to challenge themselves to add value to clinical practice based on cutting-edge analytical chemistry methodology.

Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species

Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.

Deep-profiling of phospholipidome via rapid orthogonal separations and isomer-resolved mass spectrometry

A lipidome comprises thousands of lipid species, many of which are isomers and isobars. Liquid chromatography-tandem mass spectrometry (LC-MS/MS), although widely used for lipidomic profiling, faces challenges in differentiating lipid isomers. Herein, we address this issue by leveraging the orthogonal separation capabilities of hydrophilic interaction liquid chromatography (HILIC) and trapped ion mobility spectrometry (TIMS). We further integrate isomer-resolved MS/MS methods onto HILIC-TIMS, which enable pinpointing double bond locations in phospholipids and sn-positions in phosphatidylcholine. This system profiles phospholipids at multiple structural levels with short analysis time (<10 min per LC run), high sensitivity (nM detection limit), and wide coverage, while data analysis is streamlined using a home-developed software, LipidNovelist. Notably, compared to our previous report, the system doubles the coverage of phospholipids in bovine liver and reveals uncanonical desaturation pathways in RAW 264.7 macrophages. Relative quantitation of the double bond location isomers of phospholipids and the sn-position isomers of phosphatidylcholine enables the phenotyping of human bladder cancer tissue relative to normal control, which would be otherwise indistinguishable by traditional profiling methods. Our research offers a comprehensive solution for lipidomic profiling and highlights the critical role of isomer analysis in studying lipid metabolism in both healthy and diseased states.

Identification of Negative Ion at m/z 20 Produced by Atmospheric Pressure Corona Discharge Ionization under Ambient Air

The negative ion at m/z 20 observed at atmospheric pressure corona discharge ionization mass spectra has been identified by supplying the vapors of deuterium oxide (D₂O) and H₂¹⁸O. From the mass shifts of the ion at m/z 20 observed with D₂O and H₂¹⁸O, it was suggested that the chemical composition of the ion at m/z 20 is to be H₄O. Further mass shift from m/z 20 to 22 was observed by supplying the vapor of perfluorokerocene, suggesting the chemical composition of H₃F. The chemical compositions of the negative ions H₄O^- and H₃F^- were consistence with the dipole-bound complex states between hydrogen H₂ and polar molecules such as H₂O and hydrogen fluoride (HF) having dipole moments beyond a critical dipole moment of 1.625 D, theoretically proposed by Skurski and Simons. The ionic chemical compositions and structures of H₄O^- and H₃F^- obtained with density functional theory calculations implied that both dipole-bound complex H₂O^-…H₂ and HF^-…H₂ can be formed by exothermic reactions by which H₂ molecule is complexing with negative ions H₂O^- and HF^-, respectively.

MS-RIDD paves the way toward routine double bond localization in mass spectrometry-based lipidomics

Pinpointing double bond (C=C) positions in native lipid extracts is beyond the capabilities of standard mass spectrometry-based approaches. This article highlights a novel untargeted workflow supported by the open-source software MS-RIDD, that allows for semi-automated annotation of C=C locations with high confidence.

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.

The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry

Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.

Bioinformatics in bioscience and bioengineering: Recent advances, applications, and perspectives

Recent advances have led to the emergence of highly comprehensive and analytical approaches, such as omics analysis and high-resolution, time-resolved bioimaging analysis. These technologies have made it possible to obtain vast data from a single measurement. Subsequently, large datasets have pioneered the data-driven approach, an alternative to the traditional hypothesis-testing system, for researchers. However, processing, interpreting, and elucidating enormous datasets is no longer possible without computation. Bioinformatics is a field that has developed over long periods, intending to understand biological phenomena using methods collected from information science and statistics, thus solving this proposed research challenge. This review presents the latest methodologies and applications in sequencing, imaging, and mass spectrometry that were developed using bioinformatics. We presented the features of individual techniques and outlines in each part, avoiding the use of complex algorithms and formulas to allow beginning researchers to understand an overview. In the section on sequencing, we focused on comparative genomic, transcriptomic, and bacterial microbiome analyses, which are frequently used as applications of next-generation sequencing. Bioinformatic methods for handling sequence data and case studies were described. In the section on imaging, we introduced the analytical methods and microscopy imaging informatics techniques used in animal cell biology and plant physiology. We introduce informatics technologies for maximizing the value of measured data, including predicting the structure of unknown molecules and untargeted analysis in the section on mass spectrometry. Finally, we discuss the future outlook of this field. We anticipate that this review will assist biologists in using bioinformatics more effectively.

Dual-resolving of positional and geometric isomers of C=C bonds via bifunctional photocycloaddition-photoisomerization reaction system

The biological functions of lipids largely depend on their chemical structures. The position and configuration of C=C bonds are two of the essential attributes that determine the structures of unsaturated lipids. However, simultaneous identification of both attributes remains challenging. Here, we develop a bifunctional visible-light-activated photocycloaddition-photoisomerization reaction system, which enables the dual-resolving of the positional and geometric isomerism of C=C bonds in lipids when combines with liquid chromatography-mass spectrometry. The dual-pathway reaction mechanism is demonstrated by experiments and density functional theory calculations. Based on this bifunctional reaction system, a workflow of deep structural lipidomics is established, and allows the revealing of unique patterns of cis-trans-isomers in bacteria, as well as the tracking of C=C positional isomers changes in mouse brain ischemia. This study not only offers a powerful tool for deep lipid structural biology, but also provides a paradigm for developing the multifunctional visible-light-induced reaction.

The simultaneous identification of position and configuration of double bonds in unsaturated lipids is challenging. Here, the authors develop a workflow for deep structural lipidomics to address this issue using a bifunctional reaction system combined with liquid chromatography-mass spectrometry, revealing double bond patterns in bacteria and in mouse brain ischemia.

Deep-lipidotyping by mass spectrometry: recent technical advances and applications

In-depth structural characterization of lipids is an essential component of lipidomics. There has been a rapid expansion of mass spectrometry methods that are capable of resolving lipid isomers at various structural levels over the past decade. These developments finally make deep-lipidotyping possible, which provides new means to study lipid metabolism and discover new lipid biomarkers. In this review, we discuss recent advancements in tandem mass spectrometry (MS/MS) methods for identification of complex lipids beyond the species (known headgroup information) and molecular species (known chain composition) levels. These include identification at the levels of carbon-carbon double bond (C=C) location and sn-position as well as characterization of acyl chain modifications. We also discuss the integration of isomer-resolving MS/MS methods with different lipid analysis workflows and their applications in lipidomics. The results showcase the distinct capabilities of deep-lipidotyping in untangling the metabolism of individual isomers and sensitive phenotyping by using relative fractional quantitation of the isomers.

Structural characterization of phospholipids and sphingolipids by in-source fragmentation MALDI/TOF mass spectrometry

Phospholipids (PLs) and sphingolipids (SLs) perform critical structural and biological functions in cells. The structure of these lipids, including the stereospecificity and double-bond position of fatty acyl (FA) chains, is critical in decoding lipid biology. In this study, we presented a simple in-source fragmentation (ISF) MALDI/TOF mass spectrometry method that affords complete structural characterization of PL and SL molecules. We analyzed several representative unsaturated lipid species including phosphatidylcholine (PC), plasmalogen PC (pPC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), cardiolipin (CL), sphingomyelin (SM), and ceramide (Cer). Fragment ions reflecting the FA chains at sn-1 and sn-2 position, and those characteristics of the head groups of different PL classes, are readily identified. Specific fragment ions from cleavages of the C-C bond immediately adjacent to the cis C=C double-bond position(s) of FA chains and the trans C=C double bond of the sphingosine constituents allow precise localization of double bonds. The identities of the exemplary product ions from vinylic, allylic, and double-bond cleavages were also verified by LIFT-TOF/TOF. Identification of individual PL species in the lipid mixture was also carried out with ISF-MALDI/TOF. Together, this approach provides a simple yet effective method for structural characterization of PLs and SLs without the additional modification on the instrument hardware, and serves as a simple tool for the identification of lipids.

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.

Searching, Structural Determination, and Diagnostic Performance Evaluation of Biomarker Molecules for Niemann-Pick Disease Type C Using Liquid Chromatography/Tandem Mass Spectrometry

Niemann-Pick disease type C (NPC) is an autosomal recessive disorder that is characterized by progressive neuronal degeneration. Patients with NPC have a wide age of onset and various clinical symptoms. Therefore, the discovery and diagnosis of NPC are very difficult. Conventional laboratory tests are complicated and time consuming. In this context, biomarker searches have recently been performed. Our research group has previously also investigated NPC biomarkers based on liquid chromatography/tandem mass spectrometry (LC/MS/MS) and related techniques. To identify biomarker candidates, nontargeted analysis with high-resolution MS and MS/MS scanning is commonly used. Structural speculation has been performed using LC/MS/MS fragmentation and chemical derivatization, while identification is performed by matching authentic standards and sample specimens. Diagnostic performance evaluation was performed using the validated LC/MS/MS method and analysis of samples from patients and control subjects. NPC biomarkers, which have been identified and evaluated in terms of performance, are various classes of lipid molecules. Oxysterols, cholenoic acids, and conjugates are cholesterol-derived molecules detected in the blood or urine. Plasma lyso-sphingolipids are biomarkers for both NPC and other lysosomal diseases. N-palmitoyl-O-phosphocholine-serine is a novel class of lipid biomarkers for NPC. This article reviews biomarkers for NPC and the analysis methods employed to that end.

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos

Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.

Advanced tandem mass spectrometry in metabolomics and lipidomics-methods and applications

Metabolomics and lipidomics are new drivers of the omics era as molecular signatures and selected analytes allow phenotypic characterization and serve as biomarkers, respectively. The growing capabilities of untargeted and targeted workflows, which primarily rely on mass spectrometric platforms, enable extensive charting or identification of bioactive metabolites and lipids. Structural annotation of these compounds is key in order to link specific molecular entities to defined biochemical functions or phenotypes. Tandem mass spectrometry (MS), first and foremost collision-induced dissociation (CID), is the method of choice to unveil structural details of metabolites and lipids. But CID fragment ions are often not sufficient to fully characterize analytes. Therefore, recent years have seen a surge in alternative tandem MS methodologies that aim to offer full structural characterization of metabolites and lipids. In this article, principles, capabilities, drawbacks, and first applications of these "advanced tandem mass spectrometry" strategies will be critically reviewed. This includes tandem MS methods that are based on electrons, photons, and ion/molecule, as well as ion/ion reactions, combining tandem MS with concepts from optical spectroscopy and making use of derivatization strategies. In the final sections of this review, the first applications of these methodologies in combination with liquid chromatography or mass spectrometry imaging are highlighted and future perspectives for research in metabolomics and lipidomics are discussed.

Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer

We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 μA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.

Gas-Phase Peptide Fragmentation Induced by Hydrogen Attachment, from Principle to Sequencing of Amide Nitrogen-Methylated Peptides

Tandem mass spectrometry (MS/MS) with radical-based fragmentation was developed recently, which involves the reaction of hydrogen atoms and peptides in a process called hydrogen attachment/abstraction dissociation (HAD). HAD mainly produces [c_n + 2H]⁺ and [z_m + 2H]⁺ via hydrogen attachment to the carbonyl oxygen on the peptide backbone. In addition, HAD often generates [a_n + 2H]⁺ and [x_m + 2H]⁺. To explain the formation of [a_n + 2H]⁺ and [x_m + 2H]⁺, hydrogen attachment to the carbonyl carbon atom on the peptide backbone is proposed to initiate C_α-C bond cleavage. The resultant hydrogen-abundant oxygen-centered radical intermediate undergoes radical-induced dissociation to give [a_n + H]^+• and [x_m + 2H]⁺. Subsequently, [a_n + 2H]⁺ was produced by the reaction of [a_n + H]^+• and a hydrogen atom. The fragment ions formed by the cleavage of N-C_α and C_α-C bonds are observed in the HAD-MS/MS spectra, and the mass differences of these fragment ions correspond to the mass of peptide bonds. Consequently, HAD-MS/MS allows the identification of post-translational modifications on the peptide backbone. In addition, HAD-MS/MS provides a consecutive series of [c_n + 2H]⁺ and [a_n + 2H]⁺ as the N-terminal fragments, as well as [z_m + 2H]⁺ and [x_m + 2H]⁺, which enables the sequencing of peptides with post-translational modification, including the discrimination of modifications on the side chain and backbone.

Systems biology approaches to study lipidomes in health and disease

Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.

Biomarker analysis of Niemann-Pick disease type C using chromatography and mass spectrometry

Niemann-Pick disease type C (NPC) is an autosomal recessive disorder with progressive degradation of central nervous system. The age of the onset varies from perinatal to adulthood. Patients with NPC are affected in the central nervous system, peripheral nerves, and systemic organs. From these background, it is extremely difficult to discover NPC clinically and diagnose it correctly. The procedure of the conventional laboratory methods are complicated and it takes long time to obtain the result. Because of the importance of early treatments and the shortcomings of conventional diagnostic methods for NPC, remarkable attention has been paid to biomarkers and chemical diagnoses. In the last decade, many NPC biomarkers have been reported. They are classified as cholesterol-related metabolites, sphingolipid metabolites, and novel phospholipid metabolites, respectively. Therefore, these are all lipid metabolites. Various chemical analysis methods have been used for their identification. In addition, chromatography and mass spectrometry are mainly used for their quantification. This review article outlines NPC biomarkers reported in the last decade and their analytical methods.

Acyltransferase that catalyses the condensation of polyketide and peptide moieties of goadvionin hybrid lipopeptides

Fusions of fatty acids and peptides expand the structural diversity of natural products; however, polyketide/ribosomally synthesized and post-translationally modified peptides (PK/RiPPs) hybrid lipopeptides are relatively rare. Here we report a family of PK/RiPPs called goadvionins, which inhibit the growth of Gram-positive bacteria, and an acyltransferase, GdvG, which catalyses the condensation of the PK and RiPP moieties. Goadvionin comprises a trimethylammonio 32-carbon acyl chain and an eight-residue RiPP with an avionin structure. The positions of six hydroxyl groups and one double bond in the very-long acyl chain were determined by radical-induced dissociation tandem mass spectrometry, which collides radical ion species to generate C-C bond cleavage fragments. GdvG belongs to the Gcn5-related N-acetyltransferase superfamily. Unlike conventional acyltransferases, GdvG transfers a very long acyl chain that is tethered to an acyl carrier protein to the N-terminal amino group of the RiPP moiety. gdvG homologues flanked by PK/fatty acid and RiPP biosynthesis genes are widely distributed in microbial species, suggesting that acyltransferase-catalysed condensation of PKs and RiPPs is a general strategy in biosynthesis of similar lipopeptides.

A visible-light activated [2 + 2] cycloaddition reaction enables pinpointing carbon-carbon double bonds in lipids

The precise location of C[double bond, length as m-dash]C bonds in bioactive molecules is critical for a deep understanding of the relationship between their structures and biological roles. However, the traditional ultraviolet light-based approaches exhibited great limitations. Here, we discovered a new type of visible-light activated [2 + 2] cycloaddition of carbonyl with C[double bond, length as m-dash]C bonds. We found that carbonyl in anthraquinone showed great reactivities towards C[double bond, length as m-dash]C bonds in lipids to form oxetanes under the irradiation of visible-light. Combined with tandem mass spectrometry, this site-specific dissociation of oxetane enabled precisely locating the C[double bond, length as m-dash]C bonds in various kinds of monounsaturated and polyunsaturated lipids. The proof-of-concept applicability of this new type of [2 + 2] photocycloaddition was validated in the global identification of unsaturated lipids in a complex human serum sample. 86 monounsaturated and polyunsaturated lipids were identified with definitive positions of C[double bond, length as m-dash]C bonds, including phospholipids and fatty acids even with up to 6 C[double bond, length as m-dash]C bonds. This study provides new insights into both the photocycloaddition reactions and the structural lipidomics.

Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide

Graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory calculations were performed to shed light on the mechanisms for the production of [a_n + H]⁺, x_n⁺, y_n⁺, z_n⁺, and [y_n + 2H]⁺ fragments formed in free radical-initiated peptide sequencing (FRIPS) mass spectrometry measurements of a small model system of glycine-glycine-arginine (GGR). In particular, the graph theory-based searches, which are rarely applied to gas-phase reaction studies, allowed us to investigate reaction mechanisms in an exhaustive manner without resorting to chemical intuition. As expected, radical-driven reaction pathways were favorable over charge-driven reaction pathways in terms of kinetics and thermodynamics. Charge- and radical-driven pathways for the formation of [y_n + 2H]⁺ fragments were carefully compared, and it was revealed that the [y_n + 2H]⁺ fragments observed in our FRIPS MS spectra originated from the radical-driven pathway, which is in contrast to the general expectation. The acquired understanding of the FRIPS fragmentation mechanism is expected to aid in the interpretation of FRIPS MS spectra. It should be emphasized that graph theory-based searches are powerful and effective methods for studying reaction mechanisms, including gas-phase reactions in mass spectrometry.

Characterization of Polyethers Using Tandem Mass Spectrometry with Hydrogen Abstraction Dissociation and Thermal Activation

The recently developed hydrogen radical-mediated fragmentation technique using an ion trap involving hydrogen attachment/abstraction dissociation-tandem mass spectrometry (HAD-MS/MS) was applied to the analysis of polyethylene glycol (PEG) and its derivatives. HAD was found to be initiated by hydrogen abstraction from carbon atoms in the polyether. Subsequently, the produced carbon-centered radical intermediates underwent radical-induced cleavage of their C-O bonds, with this process being facilitated by heating of the ion trap. The bond cleavage resulted in the formation of b fragments containing double bonds between carbon atoms. A counterpart c^• alkoxy radical was discovered to be a fragile radical species. Consequently, c^• underwent further radical-induced dissociation to produce small fragments during HAD-MS/MS with thermal activation. As a result, HAD-MS/MS with thermal activation through ion trap heating preferentially provided b fragments, facilitating identification of repeating units and individual end groups of the polyether analytes.

Large-scale lipid analysis with C=C location and sn-position isomer resolving power

Lipids play a pivotal role in biological processes and lipid analysis by mass spectrometry (MS) has significantly advanced lipidomic studies. While the structure specificity of lipid analysis proves to be critical for studying the biological functions of lipids, current mainstream methods for large-scale lipid analysis can only identify the lipid classes and fatty acyl chains, leaving the C=C location and sn-position unidentified. In this study, combining photochemistry and tandem MS we develop a simple but effective workflow to enable large-scale and near-complete lipid structure characterization with a powerful capability of identifying C=C location(s) and sn-position(s) simultaneously. Quantitation of lipid structure isomers at multiple levels of specificity is achieved and different subtypes of human breast cancer cells are successfully discriminated. Remarkably, human lung cancer tissues can only be distinguished from adjacent normal tissues using quantitative results of both lipid C=C location and sn-position isomers.

Structural Determination of Lysosphingomyelin-509 and Discovery of Novel Class Lipids from Patients with Niemann-Pick Disease Type C

Niemann-Pick disease type C (NPC) is an autosomal recessive disorder caused by the mutation of cholesterol-transporting proteins. In addition, early treatment is important for good prognosis of this disease because of the progressive neurodegeneration. However, the diagnosis of this disease is difficult due to a variety of clinical spectrum. Lysosphingomyelin-509, which is one of the most useful biomarkers for NPC, was applied for the rapid and easy detection of NPC. The fact that its chemical structure was unknown until recently implicates the unrevealed pathophysiology and molecular mechanisms of NPC. In this study, we aimed to elucidate the structure of lysosphingomyelin-509 by various mass spectrometric techniques. As our identification strategy, we adopted analytical and organic chemistry approaches to the serum of patients with NPC. Chemical derivatization and hydrogen abstraction dissociation-tandem mass spectrometry were used for the determination of function groups and partial structure, respectively. As a result, we revealed the exact structure of lysosphingomyelin-509 as N-acylated and O-phosphocholine adducted serine. Additionally, we found that a group of metabolites with N-acyl groups were increased considerably in the serum/plasma of patients with NPC as compared to that of other groups using targeted lipidomics analysis. Our techniques were useful for the identification of lysosphingomyelin-509.

A lipidomic workflow capable of resolving sn- and C[double bond, length as m-dash]C location isomers of phosphatidylcholines

As a major class of mammalian lipids, phosphatidylcholines (PCs) often contain mixtures of structural isomers, resulting from different lipogenesis pathways. Profiling PCs at the isomer level, however, remains challenging in lipidomic settings, especially for characterizing the positions of fatty acyls on the glycerol backbone (sn-positions) and the locations of carbon-carbon double bonds (C[double bond, length as m-dash]Cs) in unsaturated acyl chains. In this work, we have developed a workflow for profiling PCs down to sn- and C[double bond, length as m-dash]C locations at high coverage and sensitivity. This capability is enabled by radical-directed fragmentation, forming sn-1 specific fragment ions upon collision-induced dissociation (CID) of bicarbonate anion adducts of PCs ([M + HCO₃]^-) inside a mass spectrometer. This new tandem mass spectrometry (MS/MS) method can be simply incorporated into liquid chromatography by employing ammonium bicarbonate in the mobile phase without any instrument modification needed. It is also compatible with the online Paternò-Büchì reaction and subsequent MS/MS for the assignment of C[double bond, length as m-dash]C locations in sn-1 fatty acyl chains of unsaturated PCs. The analytical performance of the workflow is manifested by identification of 82 distinct PC molecular species from the polar extract of bovine liver, including quantification of 19 pairs of sn-isomers. Finally, we demonstrate that five pairs of PC sn-isomers show significant compositional changes in tissue samples of human breast cancer relative to controls, suggesting a potential for monitoring PC sn-isomers for biomedical applications.

Carbon-carbon double bond position elucidation in fatty acids using ozone-coupled direct analysis in real time mass spectrometry

The carbon-carbon double bond positions of unsaturated fatty acids can have markedly different effects on biological function and also serve as biomarkers of disease pathology, dietary history, and species identity. As such, there is great interest in developing methods for the facile determination of double bond position for natural product chemistry, the pharmaceutical industry, and forensics. We paired ozonolysis with direct analysis in real time mass spectrometry (DART MS) to cleave and rapidly identify carbon-carbon double bond position in fatty acids, fatty alcohols, wax esters, and crude fatty acid extracts. In addition, ozone exposure time and DART ion source temperature were investigated to identify optimal conditions. Our results reveal that brief, offline exposure to ozone-generated aldehyde and carboxylate products that are indicative of carbon-carbon double bond position. The relative abundance of diagnostic fragments quantitatively reflects the ratios of isobaric fatty acid positional isomers in a mixture with a correlation coefficient of 0.99. Lastly, the unsaturation profile generated from unfractionated, fatty acid extracts can be used to differentiate insect species and populations. The ability to rapidly elucidate lipid double bond position by combining ozonolysis with DART MS will be useful for lipid structural elucidation, assessing isobaric purity, and potentially distinguishing between animals fed on different diets or belonging to different ecological populations.

Identifying Double Bond Positions in Phospholipids Using Liquid Chromatography-Triple Quadrupole Tandem Mass Spectrometry Based on Oxygen Attachment Dissociation

Lipids, a class of biomolecules, play a significant role in the physiological system. In this study, gas-phase hydroxyl radicals (OH·) and atomic oxygens (O) were introduced into the collision cell of a triple quadruple mass spectrometer (TQ-MS) to determine the positions of the double bond in unsaturated phospholipids. A microwave-driven compact plasma generator was used as the OH·/O source. The reaction between OH·/O and the precursor ions passing through the collision cell generates product ions that correspond to the double bond positions in the fatty acyl chain. This double bond position specific fragmentation process initiated by the attachment of OH·/O to the double bond of a fatty acyl chain is a characteristic of oxygen attachment dissociation (OAD). A TQ-MS incorporating OAD, in combination with liquid chromatography, permitted a high throughput analysis of the double bond positions in complex biomolecules. It is important to know the precise position of double bonds in lipids, since these molecules can have widely different functionalities based on the position of the double bonds. The assignment of double bond positions in a mixture of eight standard samples of phosphatidylcholines (phospholipids with choline head groups) with multiple saturated fatty acyl chains attached was successfully demonstrated.