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.     

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.     

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.     

Application of mass spectrometry in the analysis of polybrominated diphenyl ethers

This review summarized the applications of mass spectrometric techniques for the analysis of the important flame retardants polybrominated diphenyl ethers (PBDEs) to understand the environmental sources, fate and toxicity of PBDEs that were briefly discussed to give a general idea for the need of analytical methodologies. Specific performance of various mass spectrometers hyphenated with, for example, gas chromatograph, liquid chromatograph, and inductively coupled plasma (GC/MS, LC/MS, and ICP/MS, respectively) for the analysis of PBDEs was compared with an objective to present the information on the evolution of MS techniques for determining PBDEs in environmental and human samples. GC/electron capture negative ionization quadrupole MS (GC/NCI qMS), GC/high resolution MS (GC/HRMS) and GC ion trap MS (GC/ITMS) are most commonly used MS techniques for the determination of PBDEs. New analytical technologies such as fast tandem GC/MS and LC/MS become available to improve analyses of higher PBDEs. The development and application of the tandem MS techniques have helped to understand environmental fate and transformations of PBDEs of which abiotic and biotic degradation of decaBDE is thought to be one major source of Br_1‐9BDEs present in the environment in addition to direct loading from commercial mixtures. MS‐based proteomics will offer an insight into the molecular mechanisms of toxicity and potential developmental and neurotoxicity of PBDEs. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:737–775, 2010     

Advances in analysis of microbial metabolic fluxes via 13C isotopic labeling

Metabolic flux analysis via ¹³C labeling (¹³C MFA) quantitatively tracks metabolic pathway activity and determines overall enzymatic function in cells. Three core techniques are necessary for ¹³C MFA: (1) a steady state cell culture in a defined medium with labeled‐carbon substrates; (2) precise measurements of the labeling pattern of targeted metabolites; and (3) evaluation of the data sets obtained from mass spectrometry measurements with a computer model to calculate the metabolic fluxes. In this review, we summarize recent advances in the ¹³C‐flux analysis technologies, including mini‐bioreactor usage for tracer experiments, isotopomer analysis of metabolites via high resolution mass spectrometry (such as GC‐MS, LC‐MS, or FT‐ICR), high performance and large‐scale isotopomer modeling programs for flux analysis, and the integration of fluxomics with other functional genomics studies. It will be shown that there is a significant value for ¹³C‐based metabolic flux analysis in many biological research fields. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:362–375, 2009     

Mass spectrometry for small molecule pharmaceutical product development: a review

Developing a pharmaceutical product has become increasingly difficult and expensive. With an emphasis on developing project knowledge at an earlier stage in development, the use of information-rich technologies (particularly MS) has continued to expand throughout product development. Continued improvements in LC/MS technology have widened the scope of utilizing MS methods for performing both qualitative and quantitative applications within product development. This review describes a multi-tiered MS strategy designed to enhance and accelerate the identification and profiling of both process- and degradation-related impurities in either the active pharmaceutical ingredient (API) or formulated product. Such impurities can be formed either during chemical synthesis, formulation, or during storage. This review provides an overview of a variety of orthogonal-mass spectrometric methodologies, namely GC/MS, LC/MS, and ICP-MS, in support of product development. This review is not meant to be all inclusive; however, it has been written to highlight the increasing use of hyphenated MS techniques within the pharmaceutical development area.     

Tandem mass spectrometry in the study of fatty acids,bile acids,and steroids

Over the last 50 years, the mass spectrometry of lipids has evolved to become one of the most mature techniques in biomolecule analysis. Many volatile and non-polar lipids are directly amenable to analysis by gas-chromatography-mass spectrometry (GC-MS), a technique that combines the unsurpassed separation properties of gas-chromatography with the sensitivity and selectivity of electron ionization mass spectrometry. Less volatile and/or thermally labile lipids can be analyzed by GC-MS, following appropriate sample derivatization. However, many complex lipids are not readily analyzed by GC-MS, and it is these molecules that are the subject of the current review. Since the early 1970s, there have been three outstanding developments in mass spectrometry that are particularly appropriate in lipid analysis; i.e., the introduction of (i) fast atom bombardment (FAB); (ii) electrospray (ES); and (iii) tandem mass spectrometry (MS/MS). The FAB and ES ionization techniques will be discussed in relation to MS/MS, and examples of their application in biochemical studies will be presented. The review will concentrate on the analysis of fatty acids, bile acids, steroid conjugates, and neutral steroids.     

LC/MS applications in drug development

The combination of high-performance liquid chromatography and mass spectrometry (LC/MS) has had a significant impact on drug development over the past decade. Continual improvements in LC/MS interface technologies combined with powerful features for structure analysis, qualitative and quantitative, have resulted in a widened scope of application. These improvements coincided with breakthroughs in combinatorial chemistry, molecular biology, and an overall industry trend of accelerated development. New technologies have created a situation where the rate of sample generation far exceeds the rate of sample analysis. As a result, new paradigms for the analysis of drugs and related substances have been developed. The growth in LC/MS applications has been extensive, with retention time and molecular weight emerging as essential analytical features from drug target to product. LC/MS-based methodologies that involve automation, predictive or surrogate models, and open access systems have become a permanent fixture in the drug development landscape. An iterative cycle of "what is it?" and "how much is there?" continues to fuel the tremendous growth of LC/MS in the pharmaceutical industry. During this time, LC/MS has become widely accepted as an integral part of the drug development process. This review describes the utility of LC/MS techniques for accelerated drug development and provides a perspective on the significant changes in strategies for pharmaceutical analysis. Future applications of LC/MS technologies for accelerated drug development and emerging industry trends are also discussed.     

Advances in mass spectrometry for the identification of pathogens

Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.     

Recent advances in mass spectrometry analysis of phenolic endocrine disruptors and related compounds

This article reviews recent literature on current methodologies based on chromatography coupled to mass spectrometry to analyze phenolic compounds with endocrine‐disrupting capabilities. For this review we chose alkylphenol ethoxylates, bisphenol A, bisphenol F, and their degradation products and halogenated derivatives, which are considered important environmental contaminants. Additionally, some related compounds such as bisphenol diglycidylethers were included. Growing attention has been paid to the mass spectrometric characterization of these compounds and the instrumentation and strategies used for their quantification and confirmation. The current use of gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS) methodologies with different mass spectrometers and ionization and monitoring modes is discussed. Practical aspects with regards to the use of these analytical techniques, such as derivatizing reagents in GC–MS, ion suppression in LC–MS, and the most problematic aspects of quantification, are included in the discussion. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:776–805, 2010     

Top‐down mass spectrometry for the analysis of combinatorial post‐translational modifications

Protein post‐translational modifications (PTMs) are critically important in regulating both protein structure and function, often in a rapid and reversible manner. Due to its sensitivity and vast applicability, mass spectrometry (MS) has become the technique of choice for analyzing PTMs. Whilst the “bottom‐up' analytical approach, in which proteins are proteolyzed generating peptides for analysis by MS, is routinely applied and offers some advantages in terms of ease of analysis and lower limit of detection, “top‐down” MS, describing the analysis of intact proteins, yields unique and highly valuable information on the connectivity and therefore combinatorial effect of multiple PTMs in the same polypeptide chain. In this review, the state of the art in top‐down MS will be discussed, covering the main instrumental platforms and ion activation techniques. Moreover, the way that this approach can be used to gain insights on the combinatorial effect of multiple post‐translational modifications and how this information can assist in studying physiologically relevant systems at the molecular level will also be addressed. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:27–42, 2013     

Mass spectrometry for structural characterization of therapeutic antibodies

Antibodies, also known as immunoglobulins, have emerged as one of the most promising classes of therapeutics in the biopharmaceutical industry. The need for complete characterization of the quality attributes of these molecules requires sophisticated techniques. Mass spectrometry (MS) has become an essential analytical tool for the structural characterization of therapeutic antibodies, due to its superior resolution over other analytical techniques. It has been widely used in virtually all phases of antibody development. Structural features determined by MS include amino acid sequence, disulfide linkages, carbohydrate structure and profile, and many different post-translational, in-process, and in-storage modifications. In this review, we will discuss various MS-based techniques for the structural characterization of monoclonal antibodies. These techniques are categorized as mass determination of intact antibodies, and as middle-up, bottom-up, top-down, and middle-down structural characterizations. Each of these techniques has its advantages and disadvantages in terms of structural resolution, sequence coverage, sample consumption, and effort required for analyses. The role of MS in glycan structural characterization and profiling will also be discussed.     

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...     

质谱法在药物立体异构体区分中的应用及发展

质谱法广泛应用于化学、生命科学、药学等领域,能够提供分子质量信息,有助于未知物结构的解析,具有分辨率高、信息量大、样品用量少、灵敏快速等优点,在测定有机化合物精确分子质量、结构解析、反应机理等方面发挥着重要的作用。手性药物是药学领域的一个研究热点,近年来质谱法逐渐被用于药物手性杂质区分中,而且随着质谱技术的不断发展和改进,其在手性区分和分析中越来越受关注。本工作主要介绍了质谱法在手性药物立体异构体杂质分析中的应用及发展历程,阐述了各类质谱技术用于手性异构体分析的原理和特点,其中详细举例介绍了质谱动力学方法和离子淌度质谱方法在手性杂质分析中的应用。通过对比分析目前已有的各类手性分析方法的优缺点,说明利用质谱法实现手性异构体的区分和定量测定具有明显的优势。质谱法用于药物手性异构体的分离具有快速、不需要复杂的样品前处理和昂贵的手性柱等特点,极大地提高了手性药物分析的效率和准确度。随着质谱分析技术的迅速发展,质谱法将在多手性中心药物的手性杂质分离和生物大分子分析（如多糖、多肽）等领域发挥巨大潜能。     

Proteomic tools for quantitation by mass spectrometry

Techniques for the quantitation of proteins and peptides by mass spectrometry (MS) are reviewed. A range of labeling processes is discussed, including metabolic, enzymatic, and chemical labeling, and techniques that can be employed for comparative and absolute quantitation are presented. Advantages and drawbacks of the techniques are discussed, and suggestions for the appropriate uses of the methodologies are explained. Overall, the metabolic incorporation of isotopic labels provides the most accurate labeling strategy, and is most useful when an internal standard for comparative quantitation is needed. However, that technique is limited to research that uses cultured cells.     

Analytical strategies for identifying drug metabolites

With the dramatic increase in the number of new chemical entities (NCEs) arising from combinatorial chemistry and modern high-throughput bioassays, novel bioanalytical techniques are required for the rapid determination of the metabolic stability and metabolites of these NCEs. Knowledge of the metabolic site(s) of the NCEs in early drug discovery is essential for selecting compounds with favorable pharmacokinetic credentials and aiding medicinal chemists in modifying metabolic "soft spots". In development, elucidation of biotransformation pathways of a drug candidate by identifying its circulatory and excretory metabolites is vitally important to understand its physiological effects. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have played an invaluable role in the structural characterization and quantification of drug metabolites. Indeed, liquid chromatography (LC) coupled with atmospheric pressure ionization (API) MS has now become the most powerful tool for the rapid detection, structure elucidation, and quantification of drug-derived material within various biological fluids. Often, however, MS alone is insufficient to identify the exact position of oxidation, to differentiate isomers, or to provide the precise structure of unusual and/or unstable metabolites. In addition, an excess of endogenous material in biological samples often suppress the ionization of drug-related material complicating metabolite identification by MS. In these cases, multiple analytical and wet chemistry techniques, such as LC-NMR, enzymatic hydrolysis, chemical derivatization, and hydrogen/deuterium-exchange (H/D-exchange) combined with MS are used to characterize the novel and isomeric metabolites of drug candidates. This review describes sample preparation and introduction strategies to minimize ion suppression by biological matrices for metabolite identification studies, the application of various LC-tandem MS (LC-MS/MS) techniques for the rapid quantification and identification of drug metabolites, and future trends in this field.     

质谱技术在农药残留分析中的研究进展

现代农用化学品与农产品的数量和质量安全密切相关,农药残留问题一直是大众关注的焦点.采用灵敏、准确、可靠的质谱技术能够准确地对残留农药进行定性和定量分析,从而为农药登记、农药残留摄入风险评估、环境有益生物安全、食品及其加工品中农药残留监测与监管等方面提供有力的技术支撑,保障环境安全和人类健康.本文综述了各种质谱及其联用技...     

Comparative proteomics analysis of human pituitary adenomas: current status and future perspectives

This article will review the published research on the elucidation of the mechanisms of pituitary adenoma formation. Mass spectrometry (MS) plays a key role in those studies. Comparative proteomics has been used with the long-term goal to locate, detect, and characterize the differentially expressed proteins (DEPs) in human pituitary adenomas; to identify tumor-related and -specific biomarkers; and to clarify the basic molecular mechanisms of pituitary adenoma formation. The methodology used for comparative proteomics, the current status of human pituitary proteomics studies, and future perspectives are reviewed. The methodologies that are used in comparative proteomics studies of human pituitary adenomas are readily exportable to other different areas of cancer research.     

烟气暴露对大鼠代谢轮廓谱的影响

运用基于液相色谱-质谱联用技术的代谢组学方法研究了不同卷烟烟气暴露对大鼠内源小分子代谢物组的影响。分别建立了大鼠血清和尿液的代谢轮廓谱,分析了烟气暴露7天、14天和30天时对照组大鼠、普通卷烟暴露组大鼠及含有天然本草添加剂的某品牌卷烟暴露组大鼠的血浆和尿液样本,采用偏最小二乘判别分析（PLS-DA）对数据进行模式识别。结果表明,普通卷烟和天然本草添加卷烟均会影响大鼠整体代谢状态,干扰大鼠磷脂、能量代谢,并对其造成氧化损伤,但天然本草添加卷烟对大鼠的损伤程度低于普通卷烟。在烟气暴露30天时,一些重要标志物在各组相对含量的变化进一步证实了天然本草添加卷烟可降低烟气对大鼠整体代谢的影响,减轻烟气造成的损伤。因此,在烟草中加入天然本草添加剂可在一定程度上减少烟气对机体的伤害,改善体内因烟气干扰而紊乱的磷脂和能量代谢。