CE-MS for metabolomics: Developments and applications in the period 2018–2020

Capillary electrophoresis-mass spectrometry (CE-MS) is now a mature analytical technique in metabolomics, notably for the efficient profiling of polar and charged metabolites. Over the past few years, (further) progress has been made in the design of improved interfacing techniques for coupling CE to MS; also, in the development of CE-MS approaches for profiling metabolites in volume-restricted samples, and in strategies that further enhance the metabolic coverage. In this article, which is a follow-up of a previous review article covering the years 2016–2018 (Electrophoresis 2019, 40, 165–179), the main (technological) developments in CE-MS methods and strategies for metabolomics are discussed covering the literature from July 2018 to June 2020. Representative examples highlight the utility of CE-MS in the fields of biomedical, clinical, microbial, plant and food metabolomics. A complete overview of recent CE-MS-based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings, and MS detection mode. Finally, some general conclusions and perspectives are given.     

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid-2018–2022)

This review gives a wide overview of recent advances and applications of capillary electrophoresis and microchip capillary electrophoresis methods in the fields of proteomics and peptidomics in the period from mid-2018 up to the end of 2022. The methodological topics covering sample preparation and concentration techniques, hyphenation of capillary electrophoresis methods with mass spectrometry, and multidimensional separations by on-line or off-line coupled different capillary electrophoresis and liquid chromatography techniques are described and new developments in both bottom-up and top-down approaches in proteomics are presented. In addition, various applications of capillary electrophoresis methods in proteomic and peptidomic studies are demonstrated. They include monitoring of protein posttranslational modifications and applications in biological and biochemical research, clinical peptidomics and proteomics, and food analysis.     

Recent advances in the application of capillary electromigration methods for food analysis and Foodomics

The analysis of food components using capillary electromigration methods is reviewed in this work. Papers that were published from February 2009 to February 2011 are included following the previous review by Herrero et al. (Electrophoresis, 2010, 31, 205-228). The analysis of amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions and other compounds found in foods and beverages are reviewed, as well as those applications of CE for monitoring food interactions and food processing. The use of microchips, CE-MS and chiral-CE in food analysis is also discussed as well as other current and foreseen trends in this area of research including new developments in Foodomics.     

Capillary electrophoresis-electrospray-mass spectrometry in peptide analysis and peptidomics

In the present work, an exhaustive review of the main developments and applications of CE-MS for peptide analysis is given. This review includes the use of different CE separation modes, MS analyzers, capillary coatings, preconcentration techniques, on-chip applications as well as other different multidimensional strategies for peptide analysis. Key applications are critically discussed and relevant works published from January 2000 to May 2007 are summarized including information concerning the type of sample, CE-MS parameters as well as some figures of merit of the different CE-MS procedures developed for peptide analysis and peptidomics.     

CE-MS for metabolomics: Developments and applications in the period 2008-2010

This review provides an update of the state-of-the-art of CE-MS for metabolomic purposes, covering the scientific literature from July 2008 to June 2010. This review describes the different analytical aspects with respect to non-targeted and targeted metabolomics and the new technological developments used in CE-MS for metabolomics. The applicability of CE-MS in metabolomics research is illustrated by examples of the analysis of biomedical and clinical samples, and for bacterial and plant extracts. The relevant papers on CE-MS for metabolomics are comprehensively summarized in a table, including, e.g. information on sample type and pretreatment, and MS detection mode. Future considerations such as challenges for large-scale and (quantitative) clinical metabolomics studies and the use of sheathless interfacing and different ionization techniques are discussed.     

Metabolome analysis by capillary electrophoresis-mass spectrometry

Capillary electrophoresis (CE)-mass spectrometry (MS), as an analytical platform, has made significant contributions in advancing metabolomics research, if still limited up to this time. This review, covering reports published between 1998 and 2006, describes how CE-MS has been used thus far in this field, with the majority of the works dealing with targeted metabolite analyses and only a small fraction using it in the comprehensive context. It also discusses how some of the key features of CE-MS were exploited in selected metabolomic applications.     

Monolithic columns in plant proteomics and metabolomics

Since “omics” techniques emerged, plant studies, from biochemistry to ecology, have become more comprehensive. Plant proteomics and metabolomics enable the construction of databases that, with the help of genomics and informatics, show the data obtained as a system. Thus, all the constituents of the system can be seen with their interactions in both space and time. For instance, perturbations in a plant ecosystem as a consequence of application of herbicides or exposure to pollutants can be predicted by using information gathered from these databases. Analytical chemistry has been involved in this scientific evolution. Proteomics and metabolomics are emerging fields that require separation, identification, and quantification of proteins, peptides, and small molecules of metabolites in complex biological samples. The success of this work relies on efficient chromatographic and electrophoretic techniques, and on mass spectrometric detection. This paper reviews recent developments in the use of monolithic columns, focusing on their applications in “top-down” and “bottom-up” approaches, including their use as supports for immobilization of proteolytic enzymes and their use in two-dimensional and multidimensional chromatography. Whereas polymeric columns have been predominantly used for separation of proteins and polypeptides, silica-based monoliths have been more extensively used for separation of small molecules of metabolites. Representative applications in proteomics and in analysis of plant metabolites are given and summarized in tables.     

Capillary electrophoresis coupled to mass spectrometry for clinical diagnostic purposes

The introduction of fast, sensitive, and robust techniques for proteomic analysis into clinical practice represents a major step toward a new diagnostic approach of body fluids. In addition, proteomics emerges as a key technology for the discovery of disease biomarkers in various body fluids. However, even in relatively protein-deprived body fluids such as urine, the complexity and wide dynamic range of protein expression pose a considerable challenge to both separation and identification technologies. In the present review we discuss from a clinical point-of-view recent advances of the use of proteomics in clinical diagnosis as well as therapy evaluation. We focus on capillary electrophoresis coupled to mass spectrometry (CE-MS) and discuss CE-MS from an application point of view evaluating its merits and vices with regard to biomarker discovery. This review further presents examples of clinical applications of CE-MS for detection and identification of biomarkers in urine.     

Review of a current role of mass spectrometry for proteome research

This review is intended to give readers a snapshot of current mass spectrometry for proteomics research. It covers a brief history of mass spectrometry proteomic research, peptidomics and proteomics for biomarker search, quantitative proteomics, proteomics with post-translational modification and future perspective of proteomics.     

Advances in the analysis of proteins and peptides by capillary electrophoresis with matrix-assisted laser desorption/ionization and electrospray-mass spectrometry detection

High throughput, outstanding certainty in peptide/protein identification, exceptional resolution, and quantitative information are essential pillars in proteome research. Capillary electrophoresis (CE) coupled to mass spectrometry (MS) has proven to meet these requirements. Soft ionization techniques, such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), have paved the way for the story of success of CE-MS in the analysis of biomolecules and both approaches are subject of discussion in this article. Meanwhile, CE-MS is far away from representing a homogeneous field. Therefore the review will cover a vast area including the coupling of different modes of CE (capillary zone electrophoresis, capillary isoelectric foscusing, capillary electrochromatography, micellar electrokinetic chromatography, nonaqueous capillary electrophoresis) to MS as well as on-line preconcentration techniques (transient capillary isotachophoresis, solid-phase extraction, membrane preconcentration) applied to compensate for restricted detection sensitivity. Special attention is given to improvements in interfacing, namely addressing nanospray and coaxial sheath liquid design. Peptide mapping, collision-induced dissociation with subsequent tandem MS, and amendments in mass accuracy of instruments improve information validity gained from MS data. With 2-D on-line coupling of liquid chromatography (LC) and CE a further topic will be discussed. A special section is dedicated to recent attempts in establishing CE-ESI-MS in proteomics, in the clinical and diagnostic field, and in the food sector.     

Review: multistage mass spectrometry in quality, safety and origin of foods

Quality and safety control and the validation of origin are hot issues in the production of food and its distribution, and are of primary concern to food and agriculture organization. Modern mass spectrometry (MS) provides unique, reliable and affordable methodologies to approach with a high degree of scientificity any problem which may be posed in this field. In this review the contribution of mass spectrometry to food analysis is presented aiming at providing clues on the fundamental role of the basic principles of gas-phase ion chemistry in applied research fields. Applications in proteomics, allergonomics, glycomics, metabolomics, lipidomics, food safety and traceability have been surveyed. The high level of specificity and sensitivity of the MS approach allows the characterization of food components and contaminants present at ultra-trace levels, providing a distinctive and safe validation of the products.     

毛细管电泳-质谱联用技术及其在蛋白质组学中的应用

蛋白质组学研究在生物学、精准医学等方面发挥着重要的作用。然而研究面临的巨大挑战来自生物样品的复杂性,因此在质谱（MS）鉴定技术不断革新的同时,发展分离技术以降低样品复杂度尤为重要。毛细管电泳（CE）技术具有上样体积小、分离效率高、分离速度快等优势,其与质谱的联用在蛋白质组学研究中越来越受到关注。低流速鞘流液和无鞘流液接口的发展及商品化推动了CE-MS技术的发展。目前毛细管区带电泳（CZE）、毛细管等电聚焦（CIEF）、毛细管电色谱（CEC）等分离模式已与质谱联用,其中CZE-MS应用最广泛。目前被广泛采用的蛋白质组学研究策略主要是基于酶解肽段分离鉴定的"自下而上（bottom-up）"策略。首先,CE-MS技术对酶解肽段的检测灵敏度高达1 zmol,已成功应用于单细胞蛋白质组学;其次,毛细管电泳技术与反相液相色谱互补,为疏水性质相近的肽段（尤其是翻译后修饰肽段）的分离鉴定提供了新的途径。基于整体蛋白质分离鉴定的自上而下"top-down"策略可以直接获得更精准、更完整的蛋白质信息。CE技术在蛋白质大分子的分离方面具有分离效率高、回收率高的优势,其与质谱的联用提高了整体蛋白质的鉴定灵敏度和覆盖度。非变性质谱（native MS）是一种在近生理条件下从完整蛋白质复合物水平上进行分析的质谱技术。CE与非变性质谱联用已被尝试用于蛋白质复合体的分离鉴定。该文引用了与CE-MS和蛋白质组学应用相关的93篇文献,综述了以上介绍的CE-MS的研究进展以及在蛋白质组学分析中的应用优势,并总结和展望了其应用前景。     

Is metabolomics reachable? Different purification strategies of human colon cancer cells provide different CE-MS metabolite profiles

In this work, four different metabolite purification approaches are investigated prior to metabolomics of human HT29 colon cancer cells. Namely, methanol deproteinization, ultrafiltration and two SPE methods using C18 and polymer-based cartridges were studied. The extracts were characterized via a metabolomic approach based on the application of CE TOF MS (CE-MS). CE-MS analysis time was less than 20 min per sample and allowed the simultaneous and reproducible analysis of more than 80 metabolites in a single run with a minimum consumption of sample and reagents. Metabolome analysis revealed in some cases important differences among the studied metabolite purification procedures. No significant differences were observed in the metabolite profile using C18 and polymer-based cartridges, or between ultrafiltration and methanol deproteinization. However, important differences were observed in the metabolomic profiles obtained from SPE and methanol deproteinization samples. These results demonstrate the crucial role of the metabolite purification strategy in metabolomics since it can bias (and in some cases mislead) the conclusions achieved by the metabolomic study.     

毛细管电泳-质谱联用技术的新进展

毛细管电泳-质谱(CE-MS)联用技术综合了CE的高效分离能力、广泛的样品适应性和MS的高灵敏度、可提供结构信息等优势,已发展成为一种重要的分离分析手段。本文对近几年来CE-MS联用接口技术的发展作一简单介绍,并对CE-MS在生命分析、食品药品分析等领域的一些应用进展予以综述。     

微生物代谢物组学的研究方法与进展*

代谢物组学、基因组学、转录组学和蛋白质组学是系统生物学研究的重要组成部分。近年来,在代谢物组学领域,微生物代谢物组学的研究受到人们的重视,成为研究的热点。本文综述了微生物代谢物组学的研究方法,包括样品处理、分析平台、数据处理和生物学解释等,并讨论了微生物代谢物组学在代谢工程方面的应用潜力,以及微生物代谢物组学的研究前景和所面临的挑战。