Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis.     

Recent advances of chromatography and mass spectrometry in lipidomics

Lipidomics, as a novel branch of metabolomics, which is aimed at comprehensive analysis of lipids and their biological roles with respect to health and diseases, has attracted increased attention from biological and analytical scientists. As a result of the complexity and diversity of lipids, accurate identification and efficient separation are required for lipidomics analysis. Mass spectrometry (MS) and chromatography have been extensively developed in the past few decades and hold a distinguished position in qualification and separation science. They are powerful and indispensable tools for lipidomics. Herein, we present the recent advancement of MS, chromatography, and their hyphenation technologies in lipidomics.     

Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry

There is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed-phase chromatography. Normal-phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI- and APCI-MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non-esterified bioactive lipids are present. The use of electron capture APCI-MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal-phase chiral chromatography and electron capture APCI-MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non-selective lipoxygenase inhibitor to be assessed.     

Mobility-Modulated Sequential Dissociation Analysis Enables Structural Lipidomics in Mass Spectrometry Imaging

Spatial lipidomics based on mass spectrometry imaging (MSI) is a powerful tool for fundamental biology studies and biomarker discovery. But the structure-resolving capability of MSI is limited because of the lack of multiplexed tandem mass spectrometry (MS/MS) method, primarily due to the small sample amount available from each pixel and the poor ion usage in MS/MS analysis. Here, we report a mobility-modulated sequential dissociation (MMSD) strategy for multiplex MS/MS imaging of distinct lipids from biological tissues. With ion mobility-enabled data-independent acquisition and automated spectrum deconvolution, MS/MS spectra of a large number of lipid species from each tissue pixel are acquired, at no expense of imaging speed. MMSD imaging is highlighted by MS/MS imaging of 24 structurally distinct lipids in the mouse brain and the revealing of the correlation of a structurally distinct phosphatidylethanolamine isomer (PE 18 : 1_18 : 1) from a human hepatocellular carcinoma (HCC) tissue. Mapping of structurally distinct lipid isomers is now enabled and spatial lipidomics becomes feasible for MSI.     

“Polymeromics”: Mass spectrometry based strategies in polymer science toward complete sequencing approaches: A review

Mass spectrometry (MS) is the most versatile and comprehensive method in “OMICS” sciences (i.e. in proteomics, genomics, metabolomics and lipidomics). The applications of MS and tandem MS (MS/MS or MSⁿ) provide sequence information of the full complement of biological samples in order to understand the importance of the sequences on their precise and specific functions. Nowadays, the control of polymer sequences and their accurate characterization is one of the significant challenges of current polymer science. Therefore, a similar approach can be very beneficial for characterizing and understanding the complex structures of synthetic macromolecules. MS-based strategies allow a relatively precise examination of polymeric structures (e.g. their molar mass distributions, monomer units, side chain substituents, end-group functionalities, and copolymer compositions). Moreover, tandem MS offer accurate structural information from intricate macromolecular structures; however, it produces vast amount of data to interpret. In “OMICS” sciences, the software application to interpret the obtained data has developed satisfyingly (e.g. in proteomics), because it is not possible to handle the amount of data acquired via (tandem) MS studies on the biological samples manually. It can be expected that special software tools will improve the interpretation of (tandem) MS output from the investigations of synthetic polymers as well. Eventually, the MS/MS field will also open up for polymer scientists who are not MS-specialists. In this review, we dissect the overall framework of the MS and MS/MS analysis of synthetic polymers into its key components. We discuss the fundamentals of polymer analyses as well as recent advances in the areas of tandem mass spectrometry, software developments, and the overall future perspectives on the way to polymer sequencing, one of the last Holy Grail in polymer science.     

Paternò-Büchi(PB)反应与串联质谱结合实现不饱和脂质精确结构解析

脂质在一系列关键生命过程中发挥着重要作用。结构决定功能,因此脂质结构解析与功能研究一直受到研究者的关注。尽管质谱已成为脂质分析的最常用技术之一,但脂质的精细结构解析仍面临诸多挑战。为解决上述问题,将Paternò-Büchi(PB)光化学反应与串联质谱相结合,实现了不饱和脂质中碳碳双键■的定位以及不饱和脂质■位置异构体的定量分析。此外,该技术可与鸟枪法、液相色谱-质谱和质谱成像等技术联用,用于复杂生物样品中脂质的分析。     

Fiber optic lifetime pH sensing based on ruthenium(II) complexes with dicarboxybipyridine

This review will focus on the role of mass spectrometry in the emerging field of lipidomics. Particular emphasis will be placed on recent developments in the use of tandem mass spectrometry methods in lipid analysis using low-energy collision induced dissociation (CID). After a brief discussion on ionization techniques, novel ion-activation methods that allow for increased sensitivity and selectivity will be critically discussed. Examples will be drawn from the analysis of higher order lipids, specifically triacylglycerols (TAGs) and glycerophospholipids, as the numerous positional isomers and head groups present in these classes of lipids continue to pose a significant analytical challenge to the field of lipidomics. The role of bioinformatics in the development of lipidomics will also be discussed.     

Supercritical fluid chromatography coupled to mass spectrometry for lipidomics

Supercritical fluid chromatography (SFC) has experienced a particular revival in recent years thanks to the development of robust and efficient commercial systems. Because of its physico‐chemical properties, supercritical carbon dioxide (CO₂) mixed with cosolvents and additives is particularly suitable for SFC to allow the elution of compounds of different polarities and more particularly complex lipids. Hyphenation with mass spectrometry (MS) is increasingly described in the literature but still requires many further developments in order to be as user‐friendly as coupling with liquid chromatography. The basic concepts of SFC and MS hyphenation will be first considered. Then a representative example of method development in lipidomics will be introduced. In conclusion, the challenges and future needs in this field of research will be discussed.     

MALDIMSI在脂质组学研究中的应用

脂质组学概念自2003年被提出以来,其已成为研究生物体、组织或细胞中脂质的结构、功能及代谢途径的一门学科。脂质的种类众多,同时结构非常复杂,脂质的分析充满了困难和挑战。基质辅助激光解吸电离质谱成像(MALDI MSI)分析技术不仅可以进行物质鉴定,而且可对被分析物进行空间分布成像,近年来,该技术广泛地应用于脂质组学的研究。该文介绍了MALDI MSI在脂质组学研究中的样品处理、基质喷涂及应用方面的研究进展,并就目前存在的问题及解决方案进行了探讨,以期扩展MALDI MSI的应用范围。     

基于衍生化技术的甘油磷脂分析方法研究进展

磷脂是所有生物细胞膜的主要成分,在许多生命活动过程中具有重要的功能。但由于生物样本中的磷脂种类繁多,含量极低,存在基质抑制效应,且结构中缺少易电离的官能团,从而导致对磷脂的定性和定量分析较困难。利用化学衍生化技术对其进行结构修饰可以提高离子化效率、改善色谱分离度且提高质谱(MS)检测的灵敏度和选择性。MS与衍生化方法结合已被广泛用于蛋白组学、糖组学、代谢物等的分析。近年来,这一策略逐渐被应用于脂质组学的分析研究。该文综述了国内外近10年基于衍生化技术的甘油磷脂分析方法及其应用研究进展,以激发衍生化技术在脂质组学分析中的应用潜能。     

表面修饰探针纳升电喷雾质谱脂质组学对大型溞和蚤状溞的快速鉴别

采用表面修饰探针敞开式纳升电喷雾质谱技术建立了脂质组学方法,以实现溞属(Daphnia)生物大型溞和蚤状溞的快速鉴别.采用微尺度表面修饰探针直接从Daphnia体内萃取和富集出脂质化合物,然后在常压敞开条件下进行纳升电喷雾质谱分析,利用高分辨率质谱仪获得脂质指纹图谱并进行脂质种类和结构鉴定.采用该方法获得了大型溞和蚤状溞的脂质指纹图谱,并研究了大型溞和蚤状溞体内的脂质组成特征.通过结合化学计量学手段实现了大型溞和蚤状溞的快速区分,并鉴定了相关的生物标志物.结果表明,所建立的微萃取探针纳升电喷雾质谱脂质组学方法具有分析速度快、灵敏度高的优点,可用于Daphnia属生物的快速鉴定和识别.     

Towards Non-Targeted Screening of Lipid Biomarkers for Improved Equine Anti-Doping

The current approach to equine anti-doping is focused on the targeted detection of prohibited substances. However, as new substances are rapidly being developed, the need for complimentary methods for monitoring is crucial to ensure the integrity of the racing industry is upheld. Lipidomics is a growing field involved in the characterisation of lipids, their function and metabolism in a biological system. Different lipids have various biological effects throughout the equine system including platelet aggregation and inflammation. A certain class of lipids that are being reviewed are the eicosanoids (inflammatory markers). The use of eicosanoids as a complementary method for monitoring has become increasingly popular with various studies completed to highlight their potential. Studies including various corticosteroids, non-steroidal anti-inflammatories and cannabidiol have been reviewed to highlight the progress lipidomics has had in contributing to the equine anti-doping industry. This review has explored the techniques used to prepare and analyse samples for lipidomic investigations in addition to the statistical analysis and potential for lipidomics to be used for a longitudinal assessment in the equine anti-doping industry.     

In situ structural characterization of glycerophospholipids and sulfatides in brain tissue using MALDI-MS/MS

Lipids are major structural components of biomembranes. Negatively charged species such as phosphatidylinositol, phosphatidylserine, sulfatides, and the zwitterionic phosphatidylethanolamines are major components of the cytoplasmic surface of the cellular membrane lipid bilayer and play a key role in several receptors signaling functions. Lipids are not just involved in metabolic and neurological diseases; negatively charged lipids in particular play crucial roles in physiological events such as signal transduction, receptors, and enzymatic activation, as well as storage and release of therapeutic drugs and toxic chemicals in the body. Due to the importance of their role in signaling, the field of lipidomics has rapidly expanded in recent years. In the present study, direct probing of tissue slices with negative ion mode matrix assisted laser desorption/ionization mass spectrometry was employed to profile the distribution of lipids in the brain. In total, 32 lipid species consisting of phosphatidylethanolamines, phosphatidylglycerol, phosphatidylinositols, phosphatidylserines, and sulfatides were assigned. To confirm the structure of lipid species, MALDI-MS/MS analysis was conducted. Product-ion spectra obtained in negative ion mode allow for the assignment of the head groups and the fatty acid chains for the lipid species.     

Computer-assisted interpretation of atmospheric pressure chemical ionization mass spectra of triacylglycerols

Current lipidomics approaches require simple and rapid algorithms enabling the interpretation of mass spectra of lipids. Most lipids are complex mixtures of related components in which the composition of the aliphatic fatty acid chains varies from one molecule to the next. Triacylglycerols (TAGs) are an example of such a lipid class. Fatty acid chains are the only parts of the molecule to change from one species to another. Fatty acids, and consequently also TAGs, can be characterized by two parameters; the number of carbon atoms and the number of double bonds. All calculations reflecting relations among ions in the spectra can be easily made using these parameters. An algorithm for the automated interpretation of TAGs from atmospheric pressure chemical ionization mass spectra (TriglyAPCI) is presented in this paper. The algorithm first identifies diacylglycerol fragments and molecular adducts. In the next step, relations among the ions are searched and possible TAG structures are suggested. Individual features of the algorithm are described in detail and the software performance is demonstrated for the liquid chromatography/mass spectrometric (LC/MS) analysis of TAGs isolated from the termite Prorhinotermes canalifrons.     

Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry

Correlations between the dimensions of a 2-D separation create trend lines that depend on structural or chemical characteristics of the compound class and thus facilitate classification of unknowns. This broadly applies to conventional ion mobility spectrometry (IMS)/mass spectrometry (MS), where the major biomolecular classes (e.g., lipids, peptides, nucleotides) occupy different trend line domains. However, strong correlation between the IMS and MS separations for ions of same charge has impeded finer distinctions. Differential IMS (or FAIMS) is generally less correlated to MS and thus could separate those domains better. We report the first observation of chemical class separation by trend lines using FAIMS, here for lipids. For lipids, FAIMS is indeed more independent of MS than conventional IMS, and subclasses (such as phospho-, glycero-, or sphingolipids) form distinct, often non-overlapping domains. Even finer categories with different functional groups or degrees of unsaturation are often separated. As expected, resolution improves in He-rich gases: at 70% He, glycerolipid isomers with different fatty acid positions can be resolved. These results open the door for application of FAIMS to lipids, particularly in shotgun lipidomics and targeted analyses of bioactive lipids.     

Recent Advances in Mass Spectrometry-Based Structural Elucidation Techniques

Mass spectrometry (MS) has become the central technique that is extensively used for the analysis of molecular structures of unknown compounds in the gas phase. It manipulates the molecules by converting them into ions using various ionization sources. With high-resolution MS, accurate molecular weights (MW) of the intact molecular ions can be measured so that they can be assigned a molecular formula with high confidence. Furthermore, the application of tandem MS has enabled detailed structural characterization by breaking the intact molecular ions and protonated or deprotonated molecules into key fragment ions. This approach is not only used for the structural elucidation of small molecules (MW < 2000 Da), but also crucial biopolymers such as proteins and polypeptides; therefore, MS has been extensively used in multiomics studies for revealing the structures and functions of important biomolecules and their interactions with each other. The high sensitivity of MS has enabled the analysis of low-level analytes in complex matrices. It is also a versatile technique that can be coupled with separation techniques, including chromatography and ion mobility, and many other analytical instruments such as NMR. In this review, we aim to focus on the technical advances of MS-based structural elucidation methods over the past five years, and provide an overview of their applications in complex mixture analysis. We hope this review can be of interest for a wide range of audiences who may not have extensive experience in MS-based techniques.     

Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high‐resolution shotgun lipidomics

The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high‐resolution shotgun lipidomics to characterize, for the first time, the lipid complement of the archaeon Sulfolobus islandicus. To support the identification of lipids in S. islandicus, we first compiled a database of ether lipid species previously ascribed to Archaea. Next, we analyzed the lipid complement of S. islandicus by high‐resolution Fourier transform mass spectrometry using an ion trap‐orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub‐ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we performed structural analysis using multistage activation on the ion trap‐orbitrap instrument as well as tandem mass analysis using a quadrupole time‐of‐flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described before. This uncharacterized lipid species features two head group structures composed of a trisaccharide residue carrying an uncommon sulfono group (?SO₃) and an inositol phosphate group. Both head groups are linked to a glycerol dialkyl glycerol tetraether core structure having isoprenoid chains with a total of 80 carbon atoms and 4 cyclopentane moieties. The shotgun lipidomics approach deployed here defines a novel workflow for exploratory lipid profiling of Archaea. Copyright © 2015 John Wiley & Sons, Ltd.     

Identification and relative quantification of fatty acids in Escherichia coli membranes by gas chromatography/mass spectrometry

The lipids that are essential to the functioning of the bacterial membrane exist in hundreds of different forms. The reasons for this diversity are far from clear but are presumably related to the roles of these lipids in both facilitating enzymic activities and generating proteolipid domains. A full understanding of bacterial physiology therefore requires characterization of lipids in different strains in a variety of environmental conditions. This characterization then becomes the basis for lipidomics, the lipid aspect of the growing field of metabolomics. To exploit the power of derivatization chemistry and of gas chromatography/mass spectrometry (GC/MS) and tandem mass spectrometry (MS/MS) for metabolomics studies, we report here the development of various GC/MS electron ionization (EI) and negative and positive chemical ionization (CI) methods for the identification and, for the first time, the relative quantification of fatty acids present in extracts from membranes of a laboratory strain of Escherichia coli. They consist of seven saturated fatty acids (C10:0, C12:0, C14:0, C15:0, C16:0, C17:0 and C18:0) and six unsaturated fatty acids (C16:1, cyC17:0 plus two isomers of C18:1, C18:2 and cyC19:0).     

Enantioselectivity Effects in Clinical Metabolomics and Lipidomics

Metabolomics and lipidomics have demonstrated increasing importance in underlying biochemical mechanisms involved in the pathogenesis of diseases to identify novel drug targets and/or biomarkers for establishing therapeutic approaches for human health. Particularly, bioactive metabolites and lipids have biological activity and have been implicated in various biological processes in physiological conditions. Thus, comprehensive metabolites, and lipids profiling are required to obtain further advances in understanding pathophysiological changes that occur in cells and tissues. Chirality is one of the most important phenomena in living organisms and has attracted long-term interest in medical and natural science. Enantioselective separation plays a pivotal role in understanding the distribution and physiological function of a diversity of chiral bioactive molecules. In this context, it has been the goal of method development for targeted and untargeted metabolomics and lipidomic assays. Herein we will highlight the benefits and challenges involved in these stereoselective analyses for clinical samples.     

结构蛋白质组学研究进展

蛋白质结构与其生物学功能直接相关，蛋白质功能的调控也主要依赖于其构象和相互作用的动态调节。对蛋白质结构和功能的研究一直是生命科学领域的研究热点，也是当前蛋白质组学研究的重要发展方向。该综述重点讨论了近年来基于质谱的结构蛋白质组学主要分析方法的原理、进展和应用，主要包括非变性质谱法、限制性蛋白质酶切法、化学交联法、氢氘交换法、共价化学标记法、热稳定性分析法等；最后对结构蛋白质组学的发展进行了总结与展望。