基于质谱分析的代谢组学研究进展

质谱分析技术是代谢组学研究的重要技术之一。该文通过近5年来的文献分析,对基于质谱分析的代谢组学研究方法的新进展,包括样品前处理方法、分析检测方法、数据处理方法等,以及近年来代谢组学在疾病诊断、药物研发、营养学、毒理学、运动医学等领域的应用进展,进行了较全面的综述,并对未来的发展趋势进行了展望。     

Data-Independent Microbial Metabolomics with Ambient Ionization Mass Spectrometry

Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry.

Metabolomics Research in Periodontal Disease by Mass Spectrometry

Periodontology is a newer field relative to other areas of dentistry. Remarkable progress has been made in recent years in periodontology in terms of both research and clinical applications, with researchers worldwide now focusing on periodontology. With recent advances in mass spectrometry technology, metabolomics research is now widely conducted in various research fields. Metabolomics, which is also termed metabolomic analysis, is a technology that enables the comprehensive analysis of small-molecule metabolites in living organisms. With the development of metabolite analysis, methods using gas chromatography–mass spectrometry, liquid chromatography–mass spectrometry, capillary electrophoresis–mass spectrometry, etc. have progressed, making it possible to analyze a wider range of metabolites and to detect metabolites at lower concentrations. Metabolomics is widely used for research in the food, plant, microbial, and medical fields. This paper provides an introduction to metabolomic analysis and a review of the increasing applications of metabolomic analysis in periodontal disease research using mass spectrometry technology.     

Preparative Mass Spectrometry Using a Rotating-Wall Mass Analyzer

The design of functional interfaces is central to both fundamental and applied research in materials science and energy technology. We introduce a new, broadly applicable technique for the precisely controlled high-throughput preparation of well-defined interfaces containing polyatomic species ranging from small ions to nanocrystals and large protein complexes. The mass-dispersive deposition of ions onto surfaces is achieved using a rotating-wall mass analyzer, a compact device which enables the separation of ions using low voltages and has a theoretically unlimited mass range. We demonstrate an efficient deposition of singly charged Au₁₄₄(SC₄H₉)₆₀ ions (33.7 kDa), which opens up exciting opportunities for the structural characterization of nanocrystals and their assemblies using transmission electron microscopy. Our approach also enables the high-throughput deposition of mass-selected ions from multicomponent mixtures, which is of interest to the controlled preparation of surface gradients and rapid screening of molecules in mixtures for a specific property.     

Hyphenated Mass Spectrometry versus Real-Time Mass Spectrometry Techniques for the Detection of Volatile Compounds from the Human Body

Mass spectrometry (MS) is an analytical technique that can be used for various applications in a number of scientific areas including environmental, security, forensic science, space exploration, agri-food, and numerous others. MS is also continuing to offer new insights into the proteomic and metabolomic fields. MS techniques are frequently used for the analysis of volatile compounds (VCs). The detection of VCs from human samples has the potential to aid in the diagnosis of diseases, in monitoring drug metabolites, and in providing insight into metabolic processes. The broad usage of MS has resulted in numerous variations of the technique being developed over the years, which can be divided into hyphenated and real-time MS techniques. Hyphenated chromatographic techniques coupled with MS offer unparalleled qualitative analysis and high accuracy and sensitivity, even when analysing complex matrices (breath, urine, stool, etc.). However, these benefits are traded for a significantly longer analysis time and a greater need for sample preparation and method development. On the other hand, real-time MS techniques offer highly sensitive quantitative data. Additionally, real-time techniques can provide results in a matter of minutes or even seconds, without altering the sample in any way. However, real-time MS can only offer tentative qualitative data and suffers from molecular weight overlap in complex matrices. This review compares hyphenated and real-time MS methods and provides examples of applications for each technique for the detection of VCs from humans.     

Analysis of Serum Metabolomics in Rats with Osteoarthritis by Mass Spectrometry

Osteoarthritis is a common multifactorial chronic disease that occurs in articular cartilage, subchondral bone, and periarticular tissue. The pathogenesis of OA is still unclear. To investigate the differences in serum metabolites between OA and the control group, liquid chromatography/mass spectrometry (LC/MS)-based metabolomics was used. To reveal the pathogenesis of OA, 12 SD male rats were randomly divided into control and OA groups using collagenase to induce OA for modeling, and serum was collected 7 days after modeling for testing. The OA group was distinguished from the control group by principal component analysis and orthogonal partial least squares-discriminant analysis, and six biomarkers were finally identified. These biomarkers were metabolized through tryptophan metabolism, glutamate metabolism, nitrogen metabolism, spermidine metabolism, and fatty acid metabolism pathways. The study identified metabolites that may be altered in OA, suggesting a role in OA through relevant metabolic pathways. Metabolomics, as an important tool for studying disease mechanisms, provides useful information for studying the metabolic mechanisms of OA.     

NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data

In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data.     

Preparative Mass Spectrometry Using a Rotating‐Wall Mass Analyzer

The design of functional interfaces is central to both fundamental and applied research in materials science and energy technology. We introduce a new, broadly applicable technique for the precisely controlled high‐throughput preparation of well‐defined interfaces containing polyatomic species ranging from small ions to nanocrystals and large protein complexes. The mass‐dispersive deposition of ions onto surfaces is achieved using a rotating‐wall mass analyzer, a compact device which enables the separation of ions using low voltages and has a theoretically unlimited mass range. We demonstrate an efficient deposition of singly charged Au₁₄₄(SC₄H₉)₆₀ ions (33.7 kDa), which opens up exciting opportunities for the structural characterization of nanocrystals and their assemblies using transmission electron microscopy. Our approach also enables the high‐throughput deposition of mass‐selected ions from multicomponent mixtures, which is of interest to the controlled preparation of surface gradients and rapid screening of molecules in mixtures for a specific property.     

二氢黄酮的电喷雾质谱研究

随着研究方法和技术的不断提高,人们发现生物类黄酮有很多新的种类和生理作用[1].中药苦参是豆科槐属植物苦参(Sophora Flavaescens Ait)的干燥根,含有丰富的黄酮类化合物,具有抗心率不齐等药理作用,特别是Kushenol A、Kurainone、Kuraridin为CAMP磷酸二酯酶的抑制剂[2].本文首次利用电喷雾多级串联质谱(ESI-MSn)的先进技术对苦参总黄酮中的2种二氢黄酮类化合物(kushenol A和nor-kurarinol)进行了多级串联质谱研究,得出了其在电喷雾条件下的碎片信息,为研究化合物在电喷雾条件下的裂解规律提供了一定的证据.     

Determination of Rosiglitazone by Direct Analysis in Real-Time Mass Spectrometry

The determination of rosiglitazone in dietary supplements by direct analysis in real-time mass spectrometry normally provides low repeatability. The [M+H]⁺ signal sharply decreased in the presence of strong-base and weak-acid ionic compounds because rosiglitazone decomposition occurred due to the hydrolysis of strong-base and weak-acid anions. The repeatability was improved and the influence of ionic compounds was minimized by the use of pioglitazone as an internal standard. Orbitrap mass spectrometry was used to provide high resolution in which isotopic interferences from M?+?1 of pioglitazone upon M of rosiglitazone were eliminated. This approach was used to determine rosiglitazone in tablet and dietary supplements in 1?min per sample.     

Comparison of Phytochemical Profiles of Wild and Cultivated American Ginseng Using Metabolomics by Ultra-High Performance Liquid Chromatography-High-Resolution Mass Spectrometry

American ginseng (Panax quinquefolius L.) has been recognized as a valuable herb medicine, and ginsenosides are the most important components responsible for the health-beneficial effects. This study investigated the secondary metabolites responsible for the differentiation of wild and cultivated American ginsengs with ultrahigh-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS)-based metabolomic approach. An in-house ginsenoside library was developed to facilitate data processing and metabolite identification. Data visualization methods, such as heatmaps and volcano plots, were utilized to extract discriminated ion features. The results suggested that the ginsenoside profiles of wild and cultivated ginsengs were significantly different. The octillol (OT)-type ginsenosides were present in greater abundance and diversity in wild American ginsengs; however, a wider distribution of the protopanaxadiol (PPD)-and oleanolic acid (OA)-type ginsenosides were found in cultivated American ginseng. Based on the tentative identification and semi-quantification, the amounts of five ginsenosides (i.e., notoginsenoside H, glucoginsenoside Rf, notoginsenoside R1, pseudoginsenoside RT2, and ginsenoside Rc) were 2.3–54.5 fold greater in wild ginseng in comparison to those in their cultivated counterparts, and the content of six ginsenosides (chicusetsusaponin IVa, malonylginsenoside Rd, pseudoginsenoside Rc1, malonylfloralginsenoside Rd6, Ginsenoside Rd, and malonylginsenoside Rb1) was 2.6–14.4 fold greater in cultivated ginseng compared to wild ginseng. The results suggested that the in-house metabolite library can significantly reduce the complexity of the data processing for ginseng samples, and UHPLC-HRMS is effective and robust for identifying characteristic components (marker compounds) for distinguishing wild and cultivated American ginseng.     

Real-Time Distinguishing of the Xylene Isomers Using Photoionization and Dissociation Mass Spectra Obtained by Femtosecond Laser Mass Spectrometry (FLMS)

Abstract

Distinguishing chemicals and improvement on analytical methods has a direct impact on modern chemical analysis. In this work, the dissociative ionization of xylene isomers was investigated using a femtosecond laser mass spectrometry (FLMS) method with a custom-built linear time-of-flight (TOF) instrument. Laser beams at 800?nm and 400?nm were used and intensity-dependent analysis of the obtained mass spectra was performed using principal component analysis (PCA) to distinguish the xylene isomers, which give identical mass spectra in appearance that cannot be distinguished using normal mass spectrometry methods. The results show that there is a statistically highly significant difference between the xylene isomers for two principal components (1 ? α?>?99.99%) and minimal information loss (<5%) took place during the PCA procedure. Also, the use of the k-medoid clustering method showed that the isomers may be distinguished in real-time for a wide range of ionization laser pulse powers with approximately 99% accuracy. The results suggest that real-time isomer analysis by the FLMS method is suitable for mass spectral identification applications. The FLMS method has been shown to be an important alternative to other mass spectrometric methods that use different ionization mechanisms.     

Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms

Targeted proteomic assays are becoming increasingly popular because of their robust quantitative applications enabled by internal standardization, and they can be routinely executed on high performance mass spectrometry instrumentation. However, these assays are typically limited to 100s of analytes per experiment. Considerable time and effort are often expended in obtaining and preparing samples prior to targeted analyses. It would be highly desirable to detect and quantify 1000s of analytes in such samples using comprehensive mass spectrometry techniques (e.g., SWATH and DIA) while retaining a high degree of quantitative rigor for analytes with matched internal standards. Experimentally, it is facile to port a targeted assay to a comprehensive data acquisition technique. However, data analysis challenges arise from this strategy concerning agreement of results from the targeted and comprehensive approaches. Here, we present the use of genetic algorithms to overcome these challenges in order to configure hybrid targeted/comprehensive MS assays. The genetic algorithms are used to select precursor-to-fragment transitions that maximize the agreement in quantification between the targeted and the comprehensive methods. We find that the algorithm we used provided across-the-board improvement in the quantitative agreement between the targeted assay data and the hybrid comprehensive/targeted assay that we developed, as measured by parameters of linear models fitted to the results. We also found that the algorithm could perform at least as well as an independently-trained mass spectrometrist in accomplishing this task. We hope that this approach will be a useful tool in the development of quantitative approaches for comprehensive proteomics techniques.

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Microanalysis Using Secondary Ion Mass Spectrometry

Secondary ion mass spectrometry (SIMS) has inherent features of high sensitivity, great dynamic range, and capability to provide spatially resolved chemical information making it well suited for trace and microanalysis of diverse materials. The various SIMS methods used to derive the boron distribution in hepatoma cells, to investigate the intcr-iayer reactions in multi-layer ceramic structural materials, and to evaluate the effects of fabrication on microstructural and functional properties in semiconductor devices, are presented to illustrate possible roles of SIMS in microanalysis.     

选择离子流动管质谱对汽车尾气成分的分析

运用选择离子流动管质谱(SIFT／MS)装置,以H3O^ 、NO^ 、O2^ 为初始离子对安装有催化转换装置的汽油车引擎启动5min后的尾气进行了取样分析,结果表明,尾气中含有大量的C—H化合物(包括烷烃、烯烃、炔烃、二烯烃以及芳香烃),含氧有机物(包括醛、酮、醇)以及NH3和NOx等污染成分。其中,NO的含量最高,它的浓度比其它所有SIFT／MS装置所能测量到的各种物质的总和还多;在C—H化合物中以芳香烃的含量最高,约占整个C—H化合物含量的一半以上;在含氧有机物中以醛类物质的含量最高。初步讨论了这些成分的形成动力学过程,对引擎冷启动和热启动时的尾气成分进行了分析,结果表明：冷启动尾气中C—H化合物和NOx的含量是热启动的3—5倍,而含氧有机物的含量没有很大的变化,此结果也证明了尾气的催化转化装置是一种减少尾气中C—H化合物和NOx污染物的一种有效的控制方法。这也证明了SIFT／MS技术是一种有效的分析痕量有机污染物的方法。     

Mass Determination of Entire Amyloid Fibrils by Using Mass Spectrometry

Amyloid fibrils are self‐assembled protein structures with important roles in biology (either pathogenic or physiological), and are attracting increasing interest in nanotechnology. However, because of their high aspect ratio and the presence of some polymorphism, that is, the possibility to adopt various structures, their characterization is challenging and basic information such as their mass is unknown. Here we show that charge‐detection mass spectrometry, recently developed for large self‐assembled systems such as viruses, provides such information in a straightforward manner.     

Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry

Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides. Multiple fragmentation techniques, namely HCD, CID, ETD, ETciD, and EThcD, have been used to compare the different fragmentation behaviors between peptides modified with these species. Sulfotyrosine undergoes neutral loss using HCD and CID, but the sulfuryl moiety is largely stable under ETD. In contrast, phosphotyrosine is stable during fragmentation using all these methods. This differential stability provides a mechanism to distinguish sulfopeptides from phosphopeptides. Based on the rigorous characterization presented herein, this work serves as a model for accurate identification of phosphotyrosine and, more challenging, sulfotyrosine, in complex proteomic samples.

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Identification of Nitro Explosives by Direct Analysis in Real-Time Time-of-Flight Mass Spectrometry

Nitro compounds such as 2,4,6-trinitrotoluene, cyclotrimethylene trinitramine, and pentaerythritol tetranitrate are common ingredients of high explosives found in homeland security threats, minefields, and industrial materials. This study aims at developing a convenient surface analysis method for rapid identification of these compounds by direct analysis in real time coupled with time-of-flight mass spectrometry. The possible ionization mechanisms and fragmentation pathways using the direct analysis in real-time ionization source were developed for each compound based on the ions produced by in-source collision-induced dissociation and acquired by a time-of-flight mass spectrometer. These compounds release nitro groups and form nitroless characteristic fragments with other nitro adducts during in-source collision-induced dissociation processes. The characteristic ion [M?+?C₂H₄N₃O₂]^? produced by cyclotrimethylene trinitramine was observed for the first time to our best knowledge. Direct analysis in real-time time-of-flight mass spectrometry has provided rapid identification of residues from various samples from explosion scenes and, therefore, is a potential powerful screening tool for criminal evidence.     

Mass Spectrometry-Based Metabolomics of Phytocannabinoids from Non-Cannabis Plant Origins

Phytocannabinoids are isoprenylated resorcinyl polyketides produced mostly in glandular trichomes of Cannabis sativa L. These discoveries led to the identification of cannabinoid receptors, which modulate psychotropic and pharmacological reactions and are found primarily in the human central nervous system. As a result of the biogenetic process, aliphatic ketide phytocannabinoids are exclusively found in the cannabis species and have a limited natural distribution, whereas phenethyl-type phytocannabinoids are present in higher plants, liverworts, and fungi. The development of cannabinomics has uncovered evidence of new sources containing various phytocannabinoid derivatives. Phytocannabinoids have been isolated as artifacts from their carboxylated forms (pre-cannabinoids or acidic cannabinoids) from plant sources. In this review, the overview of the phytocannabinoid biosynthesis is presented. Different non-cannabis plant sources are described either from those belonging to the angiosperm species and bryophytes, together with their metabolomic structures. Lastly, we discuss the legal framework for the ingestion of these biological materials which currently receive the attention as a legal high.