化学计量学方法在脂质组学数据解析中的应用

脂质组学是依赖于分析技术而发展的一门新兴学科,用于全面表征与基因调控、蛋白表达、脂质代谢密切相关的脂质分子,揭示脂质在各种生命活动中的作用机制和代谢途径网络。随着质谱及其联用技术进一步发展和完善,脂质组学逐渐向快速、自动化和高通量的方向发展,而大规模的脂质组数据分析已成为脂质组学研究领域的一大难点。化学计量学主要应用于脂质组学中的基线校正和背景扣除、信号峰识别、同位素分布解析、统计分析等过程,因此,基于化学计量学方法的脂质组学数据自动化解析策略成为研究者关心的热点。该文对近年来化学计量学在脂质组学数据解析中的应用进行了综述,并对基于化学计量学的脂质组学数据解析的未来发展进行了展望。     

Recent progresses of derivatization approaches in the targeted lipidomics analysis by mass spectrometry

Lipidomics plays an essential role in the development of an improved understanding of lipids metabolism and the identification of new biomarkers or therapeutic targets of related diseases. The strong analytical power of mass spectrometry and its rapid developments in the respect of instruments and techniques have significantly accelerated the emerging lipidomics and related application fields in biology, medicine, and pharmacy. The strategy of chemical derivatization can remarkably improve the shortcomings of mass spectrometric analytical technologies of shotgun lipidomics and liquid chromatography mass spectrometry, and in the past decade many related studies have been reported for fatty acids, glycerophospholipids, sphingomyelins, monoglycerides, diacylglycerols, long‐chain bases, steroids, and so on. Therefore, this review will focus on new chemical derivatization approaches about the research progresses of shotgun‐based and liquid chromatography mass spectrometry–based targeted lipidomics (from 2005 to July 2019, most of reports emerged in the past 5 years), and put forward the problems and prospects in this field. It is expected to be helpful for the design and synthesis of new derivatization reagents, especially the outstanding stable isotope labeling derivatization reagents, and the development and application of new chemical derivatization strategies and matched mass spectrometric analysis methods.     

Reshaping Lipid Biochemistry by Pushing Barriers in Structural Lipidomics

Lipidomics is a rapidly growing field with numerous examples showing the importance of lipid molecules throughout biology. It has also shed light onto the vast and complex functions performed by many lipids that possess an immense diversity in molecular structures. Mass spectrometry (MS) is the tool of choice for analyzing lipids and has been the key catalyst driving the field forward. However, MS does not yet permit true molecular lipidomics wherein the identification and quantification of lipids having defined molecular structures can be routinely achieved. Here we describe recent advances in MS‐based lipidomics that allow access to higher levels of molecular information in lipidomics experiments. These advances will form a key piece of the puzzle as the field moves towards systems characterization of lipids at the molecular level.     

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.     

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.     

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.     

Ultra performance liquid chromatography – mass spectrometry studies of formalin‐induced alterations of human brain lipidome

The development of ‘omics’ sciences offers new opportunities for the study of neurodegenerative diseases but increases at the same time the sample demand on brain banks that collect and store valuable human post‐mortem tissue. Our study aims to evaluate in lipidomics the potential of formalin‐fixed tissue compared with the cryopreservation method, considered as the gold standard for biochemical research. Two complementary liquid chromatography/mass spectrometry analytical platforms were used on the basis of hybrid quadrupole time‐of‐flight and triple quadrupole mass spectrometers. Untargeted fingerprinting, semitargeted profiling of specific lipid classes and targeted monitoring of lipid species were performed in formalin‐fixed and cryopreserved samples to provide detailed information at the molecular level on the formalin‐induced alterations of the brain tissue. In vitro incubations of lipid standards were also performed to further describe the degradation processes induced by formaldehyde. Phospholipid compounds were found to be extensively hydrolysed, whilst the sphingolipid ones were preserved. N‐methylation and N‐formylation of amine‐containing phospholipids have also been evidenced. These findings show that the potential detrimental effect of formalin on the analytes of interest must be taken into account when analysing formalin‐fixed samples. Copyright © 2014 John Wiley & Sons, Ltd.     

Mass spectrometry based cellular phosphoinositides profiling and phospholipid analysis: A brief review

Phospholipids are key components of cellular membrane and signaling. Among cellular phospholipids, phosphoinositides, phosphorylated derivatives of phosphatidylinositol are important as a participant in essential metabolic processes in animals. However, due to its low abundance in cells and tissues, it is difficult to identify the composition of phosphoinositides. Recent advances in mass spectrometric techniques, combined with established separation methods, have allowed the rapid and sensitive detection and quantification of a variety of lipid species including phosphoinositides. In this mini review, we briefly introduce progress in profiling of cellular phosphoinositides using mass spectrometry. We also summarize current progress of matrices development for the analysis of cellular phospholipids using matrix-assisted laser desorption/ionization mass spectrometry. The phosphoinositides profiling and phospholipids imaging will help us to understand how they function in a biological system and will provide a powerful tool for elucidating the mechanism of diseases such as diabetes, cancer and neurodegenerative diseases. The investigation of cellular phospholipids including phosphoinositides using electrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry will suggest new insights on human diseases, and on clinical application through drug development of lipid related diseases.     

Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry?

Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high‐performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).     

Plasma phospholipid metabolic profiling and biomarkers of rats following radiation exposure based on liquid chromatography–mass spectrometry technique

Lipidomics, a prominent area of metabolomics, utilizes novel analytical methodologies to study the extensive classes of lipid molecules, changes in lipid metabolism and lipid‐mediated signaling processes. In this paper, the phospholipid metabolic profiles changes and potential biomarker identification in the rats plasma after γ‐irradiation exposure were investigated by coupling high performance liquid chromatography–mass spectrometry technology to multivariate statistical analysis. Orthogonal partial least‐squares to latent structures discriminate analysis (OPLS‐DA) was used to find the potential plasma phospholipids biomarkers of rats for radiation exposure. According to the corresponding tandem mass spectrometric results, potential biomarkers were identified. After exposure to γ‐rays, phosphatidylethanolamine and phosphatidylserine showed a marked increase, and phosphatidylcholine, sphingomyelin and lysophosphatidylcholine followed the same trend, although their rise was not significant. The results suggested that radiated rats had a phospholipid metabolic abnormality, which could be an alternative way to assess the radiaton exposure. The biomarkers may involve a radiation‐induced apoptosis pathway and represent a promising target for discovery new radioprotective drugs and radiosensitizers. Copyright © 2009 John Wiley & Sons, Ltd.     

A review of chromatographic methods for the assessment of phospholipids in biological samples

Phospholipids are important constituents of all living cell membranes. Lipidomics is a rapidly growing field that provides insight as to how specific phospholipids play roles in normal physiological and disease states. There are many analytical methods available for the qualitative and quantitative determination of phospholipids. This review provides a summary of the methods that were historically used such as thin layer chromatography, gas chromatography and high-performance liquid chromatography. In addition, an introduction to applications of interfacing these traditional chromatographic techniques with mass spectrometry is provided.     

脂质组学及其分析方法

脂质组学的研究属于生命科学的范畴,与人类的健康密切相关。目前,脂质组学已成为代谢组学最重要的分支之一,且是一个非常活跃的研究领域,尤其在研究疾病方面的重要性已经引起了科学界的广泛关注。该文简要介绍了脂质组学的研究内容,重点评述了脂质组学分析方法,包括样品处理、轮廓分析、目标分析、成像分析以及数据处理。最后提出了脂质组学分析技术和方法的展望。     

High‐resolution extracted ion chromatography,a new tool for metabolomics and lipidomics using a second‐generation orbitrap mass spectrometer

Most analytical methods in metabolomics are based on one of two strategies. The first strategy is aimed at specifically analysing a limited number of known metabolites or compound classes. Alternatively, an unbiased approach can be used for profiling as many features as possible in a given metabolome without prior knowledge of the identity of these features. Using high‐resolution mass spectrometry with instruments capable of measuring m/z ratios with sufficiently low mass measurement uncertainties and simultaneous high scan speeds, it is possible to combine these two strategies, allowing unbiased profiling of biological samples and targeted analysis of specific compounds at the same time without compromises. Such high mass accuracy and mass resolving power reduces the number of candidate metabolites occupying the same retention time and m/z ratio space to a minimum. In this study, we demonstrate how targeted analysis of phospholipids as well as unbiased profiling is achievable using a benchtop orbitrap instrument after high‐speed reversed‐phase chromatography. The ability to apply both strategies in one experiment is an important step forward in comprehensive analysis of the metabolome. Copyright © 2009 John Wiley & Sons, Ltd.     

Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks

Protein post‐translational modifications and protein interactions are the central research areas in mass‐spectrometry‐based proteomics. Protein post‐translational modifications affect protein structures, stabilities, activities, and all cellular processes are achieved by interactions among proteins and protein complexes. With the continuing advancements of mass spectrometry instrumentations of better sensitivity, speed, and performance, selective enrichment of modifications/interactions of interest from complex cellular matrices during the sample preparation has become the overwhelming bottleneck in the proteomics workflow. Therefore, many strategies have been developed to address this issue by targeting specific modifications/interactions based on their physical properties or chemical reactivities, but only a few have been successfully applied for systematic proteome‐wide study. In this review, we summarized the highlights of recent developments in the affinity enrichment methods focusing mainly on low stoichiometric protein lipidations. Besides, to identify potential glyoxal modified arginines, a small part was added for profiling reactive arginine sites using an enrichment reagent. A detailed section was provided for the enrichment of protein interactions by affinity purification and chemical cross‐linking, to shed light on the potentials of different enrichment strategies, along with the unique challenges in investigating individual protein post‐translational modification or protein interaction network.     

Software tool for mining liquid chromatography/multi‐stage mass spectrometry data for comprehensive glycerophospholipid profiling

Electrospray ionization mass spectrometry (ESI‐MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler‐Merger‐Viewer tool is a software package for automatic processing of raw‐data from data‐dependent experiments, measured by high‐performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR‐MS and Orbitrap) in single and multi‐stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black‐box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso‐glycerophospholipids and free fatty acids. Copyright © 2010 John Wiley & Sons, Ltd.     

Profiling eicosanoids and phospholipids using LC-MS/MS: principles and recent applications

Eicosanoids are potent lipid mediators involved in numerous physiological and pathophysiological processes. Precursors are polyunsaturated fatty acids liberated from membrane phospholipids. Thus, profiling and quantification of these molecules has gained a lot of attention during last years. Eicosanoids and phospholipids are commonly profiled by LC-MS/MSbecause this technique allows accurate quantification within acceptable run-times. This article therefore focuses on liquid chromatography and the ESI-MS/MS analysis of proinflammatory lipid mediators, particularly arachidonic acid (C20:4) derived eicosanoids and their precursors phospholipids. Recent analytical developments for quantification of these compounds are highlighted and analytical challenges are discussed. Furthermore, applications such as the use of these molecules as biomarkers are presented.     

Recent applications of chemometrics in one‐ and two‐dimensional chromatography

The proliferation of increasingly more sophisticated analytical separation systems, often incorporating increasingly more powerful detection techniques, such as high‐resolution mass spectrometry, causes an urgent need for highly efficient data‐analysis and optimization strategies. This is especially true for comprehensive two‐dimensional chromatography applied to the separation of very complex samples. In this contribution, the requirement for chemometric tools is explained and the latest developments in approaches for (pre‐)processing and analyzing data arising from one‐ and two‐dimensional chromatography systems are reviewed. The final part of this review focuses on the application of chemometrics for method development and optimization.     

Applications of Activity‐Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery

Activity‐based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high‐throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity‐based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.     

Investigating aroma diversity combining purge‐and‐trap,comprehensive two‐dimensional gas chromatography,and mass spectrometry

Headspace gas chromatography is frequently used for aroma profiling thanks to its ability to naturally exploit the volatility of aroma compounds, and also to provide chemical information on sample composition. Its main advantages rely on simplicity, no use of solvent, amenability to automation, and the cleanliness of the extract. In the present contribution, the most effective sampling (dynamic extraction), separation (multidimensional gas chromatography), and detection (mass spectrometry) techniques for untargeted analysis are exploited in combination, showing their potential in unraveling aroma profiles in fruit beers. To complete the overall analytical process, a neat workflow for data analysis is discussed and used for the successful characterization and identification of five different beer flavors (berries, cherry, banana, apple, and peach). From the technical viewpoint, the coupling of purge‐and‐trap, comprehensive two‐dimensional gas chromatography, and mass spectrometry makes the global methodology unique, and it is for the first time discussed. A (low‐)flow modulation approach allowed for the full transfer into the second dimension with mass‐spectrometry compatible flow (< 7 mL/min), avoiding the need of splitting before detection and making the overall method sensitive (1.2–5.2‐fold higher signal to noise ratio compared to unmodulated gas chromatography conditions) and selective.