血浆代谢组同时定性定量分析方法研究

数据非依赖的质谱采集是近年来发展的一种新型多级质谱分析方法，只需一次进样便可同时快速获取所有母离子及其子离子信息。本研究以肺癌血浆样本为研究对象，采用数据非依赖的SWATH（sequential windowed acquisition of all theoretical fragment ions）采集技术，建立了液相色谱-串联质谱法（LC-MS/MS）同时定性定量分析血浆代谢组。基于代谢物数据库识别比对，成功识别了93个代谢物，实现了代谢物的定性分析。对成功识别的代谢物建立定量分析方法并进行方法学考察。结果表明，其中90个代谢物的线性相关系数大于0.99，定量限在1.25~12 000 μg/L之间；其中有86个代谢物可以满足生物样本定量分析的要求，其连续4天的日内精密度和日间精密度均小于20%；在4 ℃下，96 h内的放置稳定性在0.62%~19.35%之间。该方法的覆盖率高，能同时快速准确地对肺癌血浆中癌症相关代谢物进行定性定量分析，也适用于其他生物样品，可以为定量代谢组学分析提供重要的方法学平台。     

基于高分辨质谱的代谢组学分析技术研究进展

代谢组学研究的目标是对生物体系中所有内源小分子代谢物进行全面的定性和定量表征.由于代谢物组成复杂、种类繁多、理化性质各异、且浓度差异大,给分析工作带来了极大的挑战.高分辨质谱因具有高灵敏度、高质量分辨率和质量精度、宽动态范围等优势,已成为代谢组学研究的主流分析工具.本文综述了近5年来基于高分辨质谱的代谢组学分析技术和方...     

Mass spectrometry‐based holistic analytical approaches for metabolite profiling in systems biology studies

Metabonomics and metabolomics represent one of the three major platforms in systems biology. To perform metabolomics it is necessary to generate comprehensive “global” metabolite profiles from complex samples, for example, biological fluids or tissue extracts. Analytical technologies based on mass spectrometry (MS), and in particular on liquid chromatography–MS (LC–MS), have become a major tool providing a significant source of global metabolite profiling data. In the present review we describe and compare the utility of the different analytical strategies and technologies used for MS‐based metabolomics with a particular focus on LC–MS. Both the advantages offered by the technology and also the challenges and limitations that need to be addressed for the successful application of LC–MS in metabolite analysis are described. Data treatment and approaches resulting in the detection and identification of biomarkers are considered. Special emphasis is given to validation issues, instrument stability, and QA/quality control (QC) procedures. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:884–906, 2011     

Mass spectrometry-based metabolomics

This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed.     

Evaluating and minimizing batch effects in metabolomics

Determining metabolomic differences among samples of different phenotypes is a critical component of metabolomics research. With the rapid advances in analytical tools such as ultrahigh-resolution chromatography and mass spectrometry, an increasing number of metabolites can now be profiled with high quantification accuracy. The increased detectability and accuracy raise the level of stringiness required to reduce or control any experimental artifacts that can interfere with the measurement of phenotype-related metabolome changes. One of the artifacts is the batch effect that can be caused by multiple sources. In this review, we discuss the origins of batch effects, approaches to detect interbatch variations, and methods to correct unwanted data variability due to batch effects. We recognize that minimizing batch effects is currently an active research area, yet a very challenging task from both experimental and data processing perspectives. Thus, we try to be critical in describing the performance of a reported method with the hope of stimulating further studies for improving existing methods or developing new methods.     

Mass spectrometric based approaches in urine metabolomics and biomarker discovery

Urine metabolomics has recently emerged as a prominent field for the discovery of non‐invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non‐biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid‐liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze‐thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high‐performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)‐MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC‐MS, other MS‐based technologies have been utilized in urine metabolomics. These include direct injection (infusion)‐MS, capillary electrophoresis‐MS and gas chromatography‐MS. In this article, the current progresses of different MS‐based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115–134, 2017.     

Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research

Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis‐mass spectrometry (CE‐MS) in the past few years. This review provides highlights of recent advances in CE‐MS for proteomics research, including a short introduction to top‐down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE‐MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1–16, 2019.     

Current mass spectrometry strategies for the analysis of pesticides and their metabolites in food and water matrices

Analysis of pesticides and their metabolites in food and water matrices continues to be an active research area closely related to food safety and environmental issues. This review discusses the most widely applied mass spectrometric (MS) approaches to pesticide residues analysis over the last few years. The main techniques for sample preparation remain solvent extraction and solid‐phase extraction. The QuEChERS (Quick, Easy, Cheap, Effective, Rugged, Safe) approach is being increasingly used for the development of multi‐class pesticide residues methods in various sample matrices. MS detectors—triple quadrupole (QqQ), ion‐trap (IT), quadrupole linear ion trap (QqLIT), time‐of‐flight (TOF), and quadrupole time‐of‐flight (QqTOF)—have been established as powerful analytical tools sharing a primary role in the detection/quantification and/or identification/confirmation of pesticides and their metabolites. Recent developments in analytical instrumentation have enabled coupling of ultra‐performance liquid chromatography (UPLC) and fast gas chromatography (GC) with MS detectors, and faster analysis for a greater number of pesticides. The newly developed “ambient‐ionization” MS techniques (e.g., desorption electrospray ionization, DESI, and direct analysis in real time, DART) hyphenated with high‐resolution MS platforms without liquid chromatography separation, and sometimes with minimum pre‐treatment, have shown potential for pesticide residue screening. The recently introduced Orbitrap mass spectrometers can provide high resolving power and mass accuracy, to tackle complex analytical problems involved in pesticide residue analysis. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:907–939, 2011     

Structure elucidation of native N- and O-linked glycans by tandem mass spectrometry (tutorial)

Oligosaccharides play important roles in many biological processes. However, the structural elucidation of oligosaccharides remains a major challenge due to the complexities of their structures. Mass spectrometry provides a powerful method for determining oligosaccharide composition. Tandem mass spectrometry (MS) provides structural information with high sensitivity. Oligosaccharide structures differ from other polymers such as peptides because of the large number of linkage combinations and branching. This complexity makes the analysis of oligosaccharide unique from that of peptides. This tutorial addresses the issue of spectral interpretation of tandem MS under conditions of collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). The proper interpretation of tandem MS data can provide important structural information on different types of oligosaccharides including O- and N-linked.     

液相色谱-串联质谱生物分析方法的基质效应和对策

液相色谱-串联质谱（LC-MS/MS）法具有高灵敏度、高选择性、高通量等特点,已经成为生物分析的主流方法,广泛应用于新药发现和开发过程中新化学实体及其代谢物的定量分析。然而,由于生物样品基质成分复杂,共洗脱物质会影响分析物的离子化,使分析物的质谱响应增加或降低,从而影响LC-MS/MS分析方法的准确度和精密度。一般而言,离子抑制较离子增强更为常见。因此,在建立LC-MS/MS法时,需要对离子抑制进行评估和校正,并采用不同的策略消除或减少基质效应的影响。本文综述了生物样品分析中基质效应的来源和评估方法,重点介绍了克服基质效应的策略。引起基质效应的物质包括磷脂、盐类、尿素、代谢物等内源性物质和赋形剂、抗凝剂、固定相释放物质及降解产物等外源性物质。目前基质效应的评价方法主要有提取后加入法和柱后灌注法。克服基质效应的策略主要有使用稳定同位素内标,将极性药物衍生化,沉淀蛋白后稀释上清液,优化样品预处理方法、色谱和质谱条件等。结合本课题组的应用实例,重点阐述了建立LC-MS/MS生物分析方法时,为减少基质效应遇到的困难及解决方法。     

Development of LC/MS Techniques for Comprehensive Metabolome Analysis

Metabolomics is a rapidly evolving field for studying biological systems and discovering potential disease biomarkers. For any metabolomics application, metabolome analysis with adequate sensitivity and specificity is essential in defining the metabolome. Ideally, all metabolites present in a biological system are qualitatively and quantitatively profiled. Unfortunately, due to technical limitations, only a fraction of metabolites are currently analyzed by using techniques such as NMR and mass spectrometry (MS). Due to limited metabolome coverage, many important metabolome networks and some subdue changes in the metabolome may not be revealed with current techniques. In this presentation, several technical issues related to the development of LC/MS for enabling metabolome analysis will be discussed. Because of great diversity of chemical and physical properties of metabolites, we have been developing an isotope labeling LC/MS workflow with a goal of improving the metabolome coverage in analyzing biological samples such as human biofluids and tissue samples. Several labeling chemistries will be described to provide isotope tags to the metabolites for sensitive detection and accurate quantification. LC methods including multi-dimensional separation to separate the labeled metabolites with high efficiency will be discussed. New protocols for MS analysis, metabolite identification and quantitative data processing will be presented.     

FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM

Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.     

Chemical derivatization strategy for mass spectrometry-based lipidomics

Lipids, serving as the structural components of cellular membranes, energy storage, and signaling molecules, play the essential and multiple roles in biological functions of mammals. Mass spectrometry (MS) is widely accepted as the first choice for lipid analysis, offering good performance in sensitivity, accuracy, and structural characterization. However, the untargeted qualitative profiling and absolute quantitation of lipids are still challenged by great structural diversity and high structural similarity. In recent decade, chemical derivatization mainly targeting carboxyl group and carbon-carbon double bond of lipids have been developed for lipidomic analysis with diverse advantages: (i) offering more characteristic structural information; (ii) improving the analytical performance, including chromatographic separation and MS sensitivity; (iii) providing one-to-one chemical isotope labeling internal standards based on the isotope derivatization regent in quantitative analysis. Moreover, the chemical derivatization strategy has shown great potential in combination with ion mobility mass spectrometry and ambient mass spectrometry. Herein, we summarized the current states and advances in chemical derivatization-assisted MS techniques for lipidomic analysis, and their strengths and challenges are also given. In summary, the chemical derivatization-based lipidomic approach has become a promising and reliable technique for the analysis of lipidome in complex biological samples.     

基于信号放大策略的超灵敏质谱新方法及其应用

生物分子的超灵敏分析为精确理解生命活动内在机制提供了基础.质谱作为一种快速、高灵敏、高通量、定性能力强的分析技术,在生物大分子及小分子代谢物的检测中发挥着重要作用.但由于仪器分析灵敏度有限、样本基质干扰等多方面因素的影响,仅依靠直接质谱分析很难实现微量生物样本甚至单细胞中生物标志物的准确检测.引入信号放大或者增敏策略有...     

Radio-LC-MS及其在放射性药物研究中的应用

Radio-LC-MS是由高效液相色谱仪（HPLC）,紫外检测器（UV）,放射活性在线监测分析仪（radioactivity monitor, RAM）和质谱仪（MS）构成的完整在线检测体系,专门用于放射性药物的分析。根据实验目的,放射性检测器的种类和对放射性防护要求的不同,Radio-LC-MS采用两种不同的连接模式,即串联模式和并联模式。本工作综述了Radio-LC-MS在放射性药物的结构鉴定,代谢物分析和质量控制等方面的应用进展。     

The role of mass spectrometry in plant systems biology

Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.