Current applications of capillary electrophoresis-mass spectrometry for the analysis of biologically important analytes in urine (2017 to mid-2021): A review.

Capillary electrophoresis coupled online with mass detection is a modern tool for analyzing wide ranges of compounds in complex samples, including urine. Capillary electrophoresis with mass spectrometry allows the separation and identification of various analytes spanning from small ions to high molecular weight protein complexes. Similarly to the much more common liquid chromatography-mass spectrometry techniques, the capillary electrophoresis separation reduces the complexity of the mixture of analytes entering the mass spectrometer resulting in reduced ion suppression and a more straightforward interpretation of the mass spectrometry data. This review summarizes capillary electrophoresis with mass spectrometry studies published between the years 2017 and 2021, aiming at the determination of various compounds excreted in urine. The properties of the urine, including its diagnostical and analytical features and chemical composition, are also discussed including general protocols for the urine sample preparation. The mechanism of the electrophoretic separation and the instrumentation for capillary electrophoresis with mass spectrometry coupling is also included. This review shows the potential of the capillary electrophoresis with mass spectrometry technique for the analyses of different kinds of analytes in a complex biological matrix. The discussed applications are divided into two main groups (capillary electrophoresis with mass spectrometry for the determination of drugs and drugs of abuse in urine and capillary electrophoresis with mass spectrometry for the studies of urinary metabolome).

Mass spectrometry-based characterization of histones in clinical samples: applications, progress, and challenges.

In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post-translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody-based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS-based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS-based approaches currently available for histone PTM profiling, we will focus on the 'bottom-up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples.

Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics.

Metabolomics deals with the large-scale analysis of metabolites, belonging to numerous compound classes and showing an extremely high chemical diversity and complexity. Lipidomics, being a subcategory of metabolomics, analyzes the cellular lipid species. Both require state-of-the-art analytical methods capable of accessing the underlying chemical complexity. One of the major techniques used for the analysis of metabolites and lipids is Liquid Chromatography-Mass Spectrometry (LC-MS), offering both different selectivities in LC separation and high sensitivity in MS detection. Chromatography can be divided into different modes, based on the properties of the employed separation system. The most popular ones are Reversed-Phase (RP) separation for non- to mid-polar molecules and Hydrophilic Interaction Liquid Chromatography (HILIC) for polar molecules. So far, no single analysis method exists that can cover the entire range of metabolites or lipids, due to the huge chemical diversity. Consequently, different separation methods have been used for different applications and research questions. In this review, we explore the current use of LC-MS in metabolomics and lipidomics. As a proxy, we examined the use of chromatographic methods in the public repositories EBI MetaboLights and NIH Metabolomics Workbench. We extracted 1484 method descriptions, collected separation metadata and generated an overview on the current use of columns, eluents, etc. Based on this overview, we reviewed current practices and identified potential future trends as well as required improvements that may allow us to increase metabolite coverage, throughput or both simultaneously.

Editor Profile: Albert Heck.

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research and perspectives on the journal and more. Albert Heck is Professor of Chemistry and Pharmaceutical Sciences at Utrecht University, Scientific Director of the Netherlands Proteomics Center, and Head of the Biomolecular Mass Spectrometry and Proteomics group in Utrecht University since September 1998. He has served as Editorial Board Member of The FEBS Journal since 2020.

Mass Spectrometry-Based Steroid Profiling: Meeting Unmet Clinical Needs.

Despite ongoing concerns regarding its clinical application, mass spectrometry (MS)-based steroid assay represents a promising tool in endocrine research. Recent studies indicate that monitoring the blood levels of individual sterols provides improved diagnostic insight into hyperlipidemia compared with immunoassays routinely used in clinical practice. Hypercortisolism and hyperaldosteronism can also be easily evaluated along with successful subtyping of adrenal diseases using MS-based methods, while metabolic signatures of sex steroids provide experimental evidence of abnormal puberty and male infertility. Many MS-based biological and clinical studies are based on liquid chromatography-mass spectrometry (LC-MS) coupled to electrospray ionization and tandem MS scan modes. However, gas chromatography-mass spectrometry (GC-MS) provides better chromatographic separation. Improved chromatographic resolution enables large-scale steroid profiling to allow a bird-eye view and increase the chances of identifying potent biomarkers in endocrine research. In addition to the technical advantages of MS-based assays over immunoassays, minimizing the sample amounts with acceptable analytical sensitivity and standardization of surrogate materials provides cutting-edge tools for precision and personalized medicine.

Analysis of steroid profiles by mass spectrometry: A new tool for exploring adrenal tumors?

The assay of multiple steroids by mass spectrometry coupled with chromatography, combined with data analysis using an artificial intelligence approach, has become more widely accessible in recent years. Multiple applications for this technology exist for the study of adrenocortical tumors. Taking advantage of the capacity of malignant cortical tumor secretion of non-bioactive precursors, it provides an additional diagnostic approach that can point to the nature of a tumor. These encouraging perspectives have been based to date only on pilot retrospective studies. However, this has changed in 2020 with the publication of data from the EURINE-ACT study. This very large prospective European study provided more nuanced evidence for the benefit of combining the measurement of a panel of steroids with essential imaging tools. This study also facilitated our understanding and provided more precise characterisation of autonomous steroid secretion, particularly in the case of sublinical cortisol-secreting adrenocortical adenomas. This article will focus on our current knowledge on the potential utility of mass spectrometry for diagnosis of both the nature of an adrenal tumors and their secretion.

Mass cytometry and type 1 diabetes research in the age of single-cell data science.

PURPOSE OF REVIEW: New single-cell tec. hnologies developed over the past decade have considerably reshaped the biomedical research landscape, and more recently have found their way into studies probing the pathogenesis of type 1 diabetes (T1D). In this context, the emergence of mass cytometry in 2009 revolutionized immunological research in two fundamental ways that also affect the T1D world: first, its ready embrace by the community and rapid dissemination across academic and private science centers alike established a new standard of analytical complexity for the high-dimensional proteomic stratification of single-cell populations; and second, the somewhat unexpected arrival of mass cytometry awoke the flow cytometry field from its seeming sleeping beauty stupor and precipitated substantial technological advances that by now approach a degree of analytical dimensionality comparable to mass cytometry. RECENT FINDINGS: Here, we summarize in detail how mass cytometry has thus far been harnessed for the pursuit of discovery studies in T1D science; we provide a succinct overview of other single-cell analysis platforms that already have been or soon will be integrated into various T1D investigations; and we briefly consider how effective adoption of these technologies requires an adjusted model for expense allocation, prioritization of experimental questions, division of labor, and recognition of scientific contributions. SUMMARY: The introduction of contemporary single-cell technologies in general, and of mass cytometry, in particular, provides important new opportunities for current and future T1D research; the necessary reconfiguration of research strategies to accommodate implementation of these technologies, however, may both broaden research endeavors by fostering genuine team science, and constrain their actual practice because of the need for considerable investments into infrastructure and technical expertise.

Mass spectrometric analysis to unravel the venom proteome composition of Indian snakes: opening new avenues in clinical research.

INTRODUCTION: The 'Big Four' venomous snakes - Daboia russelii, Naja naja, Bungarus caeruleus, and Echis carinatus - are primarily responsible for the majority of snake envenomation in India. Several other lesser-known venomous snake species also inflict severe envenomation in the country. AREAS COVERED: A comprehensive analysis of the venom proteome composition of the 'Big Four' and other medically important venomous snakes of India and the effect of regional variation in venom composition on immunorecognition and/or neutralization by commercial antivenom was undertaken by searching the literature (from 1985 to date) available in large public databases. Further, mass spectrometric identification of poorly immunogenic toxins of snake venom (against which commercial polyvalent antivenom contains a significantly lower proportion of antibodies) and its impact on antivenom therapy against snakebite are discussed. The application of mass spectrometry to identify protein (toxin) complexes as well as drug prototypes from Indian snake venoms and the clinical importance of such studies are also highlighted. EXPERT OPINION: Further detailed clinical and proteomic research is warranted to better understand the effects of regional snake venom composition on the clinical manifestation of envenomation and antivenom therapy and to improve the production of antibodies against poorly immunogenic venom components.

High-resolution mass spectrometry for bioanalytical applications: Is this the new gold standard?

Liquid chromatography coupled to quadrupole-based tandem mass spectrometry (QqQ) is termed the "gold standard" for bioanalytical applications because of its unpreceded selectivity, sensitivity, and the ruggedness of the technology. More recently, however, high-resolution mass spectrometry (HRMS) has become increasingly popular for bioanalytical applications. Nonetheless, this technique is still viewed, either as a screening technology or as a research tool. Although HRMS is actively discussed during scientific conferences, it is yet to be widely utilised in routine laboratory settings and there remains a reluctance to use HRMS for quantitative measurements in regulated environments. This paper does not aim to comprehensively describe the potential of the latest HRMS technology, but rather, it focuses on what results can be obtained and outlines the author's experiences over a period of many years of the routine application of various forms of HRMS instrumentation. Fifteen years ago, some nine different QqQ methods were used in the author's laboratory to analyse a variety of different veterinary drug resides. Today, many more analytes are quantified by seven HRMS methods and just three QqQ methods remain in use for the analysis of a small set of compounds yet to be upgraded to HRMS analysis. This continual upgrading and migration of analytical methods were accompanied by regularly participating in laboratory proficiency tests (PTs). The PT reports (covering a range of analytes and analytical methods) were used to compare the accuracy of HRMS- versus QqQ-based measurements. In the second part of this paper, the particular strengths and limitations of HRMS for both method development and routine measurements are critically discussed. This also includes some anecdotal experiences encountered when replacing QqQ assays with HRMS methods.

Recent advances in LC-MS based characterization of protein-based bio-therapeutics - mastering analytical challenges posed by the increasing format complexity.

Alongside the success of protein-based bio-therapeutics over the last decades and facilitated by advances both in protein engineering and manufacturing, new product formats progressively enter into the biopharmaceutical industry's pipelines with major implications on the analytical methods used for their characterization. While conventional approaches have proved sufficient for standard (IgG-like) molecules, the increased complexity of novel formats requires proper adjustments of the employed methodologies, in particular with regard to separation-based techniques coupled to UV/FLD detection. After introducing the status quo for the characterization of biopharmaceuticals in quality control settings, this review provides a comprehensive portrayal of emerging LC-MS based technologies, which have already demonstrated their potential to complement the existing analytical toolbox. In this context, the benefits of native LC-MS and two-/multidimensional LC-MS applications to assess product attributes while preserving the higher-order structure are discussed based on challenges arising from the analysis of complex product formats.

[Advances in development and application of liquid chromatography coupled with isotope ratio mass spectrometry].

The first commercial interface for hyphenating liquid chromatography with isotope ratio mass spectrometry (LC-IRMS) was not available until 2004, and it was commercialized under the name LC IsoLink by Thermo Finnigan. LC-IRMS, a method of compound-specific isotope analysis, has enabled the detection of stable carbon isotope ratios (δ13C) in targeted substances in order to determine their origin and authenticity. This paper provides an overview of IRMS and LC-IRMS techniques, the history and detailed classification of the latter over the past twenty years. The application of LC-IRMS to the fields of food safety, environment and ecology, life sciences, and archeology are reviewed. Finally, the technical limitations, current challenges, and future development trends of LC-IRMS are outlined.

[Analysis of metabolomics and proteomics based on capillary electrophoresis-mass spectrometry].

Capillary electrophoresis-mass spectrometry (CE-MS) has the advantages of higher sensitivity, higher efficiency, and less sample consumption. Moreover, it possesses obvious advantages during the analysis of strongly charged and highly polar samples. CE-MS has been widely applied in life sciences, medicine, and pharmacology. In the past ten years, the main factors affecting its application were system stability, reproducibility, and data accuracy. In order to solve the existing problems of CE-MS, researchers have invested significant effort in technology innovation to further expand CE-MS application. In the fields of medicine and analytical chemistry, substantial research indicates that CE-MS is superior compared to other metabolomic and proteomic approaches. This study aims at reviewing the latest methods and applications developed in the fields of medicine and analytical chemistry since 2015. Furthermore, it also aims at enhancing the technology development-related application value of CE-MS and serving as a reference for future development. Further development of the CE-MS technology is discussed from the aspects of coating-sample interaction, interface types, and data processing methods. Concerning the coating types, neutral coatings had been applied extensively in CE-MS and there should be no limitation to the charge of the analyte. The coating decreased sample adsorption on the inner wall by covering the surface charge, greatly reducing the electroosmotic flow (EOF). A charged capillary coating could modify such an EOF direction. The cationic coating could reduce the hydrophobic interaction between the sample and the capillary column, resulting in higher EOF. If it is applied to the sheathless interface, the resolution could be improved by extending the capillary length. Anionic coatings are predominant among the anionic compounds, shortening the separation time by reducing the interaction between the anionic compounds and the capillary. The coating type should be chosen relative to the analyte characteristics. Concerning the interface technology, all interfaces should be simple, practical, and non-dependent on sheath liquid and background electrolytes. As far as data processing methods are concerned, it is necessary to design and develop a practical method for span space data comparison and processing. The optimized experimental conditions have effectively improved separation efficiency and data comparison analysis. Furthermore, they established a solid foundation for its application development. CE-MS analysis of complex samples in the fields of metabolomics and proteomics (e. g., of tissues, cells, body fluids, etc.) could provide a visualization method for future clinical analysis. It contributes to the development of cancer pathological analysis, drug development, disease surveillance, etc. The characteristic analysis of small molecule metabolites and protein biomarkers directly reflects on enzymatic activity in the biological systems. It could be associated with the development of various diseases/complications. Omics analysis also has an important directive to disease detection and surveillance with obvious advantages in disease diagnosis, staged treatment, drug development, and patient treatment progress. CE-MS is useful in detecting complications and promoting personalized medicine. It provides technical support for future clinical developments. In addition to a comprehensive review of the recent advances of CE-MS research, this paper also indicates the development directions of CE-MS. In order to avoid the problem of omics analysis and obtain the optimized analysis results, future analysis should be improved from the following three aspects:(i) The analysis conditions should be optimized concerning sample preparation methods and separation techniques. (ii) The analytic techniques should be supported to adjust to capillary coating and interface technology. (iii) New ideas should be developed in the fields of clinical research and statistical analysis.

Current trends in isotope-coded derivatization liquid chromatographic-mass spectrometric analyses with special emphasis on their biomedical application.

Currently, LC-MS has various applications in different areas such as metabolomics, pharmacokinetics, and pathological studies. Yet, matrix effects resulting from co-existing constituents remain a major problem for LC-MS [or LC-tandem mass spectrometry (LC-MS/MS)]. Moreover, technical problems and instrumental drifts may lead to ion abundance variance. Thus, an internal standard (IS) is required to guarantee the accuracy and precision of the method. Because of their limited number, isotope-coded derivatization (ICD) has been recently introduced to overcome this problem. For ICD, a stable heavy isotope-coded moiety is used for labeling the standard or the control sample and the formed products can act as ISs. A light form of the reagent is used for labeling the sample. Then, both are mixed and analyzed by LC-MS(/MS). This strategy permits the identification of different unknown analytes including potential metabolites and disease biomarkers. All these attributes lead to persistent growth in the applications of ICD LC-MS(/MS) in various biomedical branches. In this article we review the ICD methods published in the last eight years for biomedical applications as well as briefly summarize other applications for environmental and food analyses as some of their used ICD reagents were further applied for analyzing biological specimens or have the potential for that.

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.

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics.

Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.

Trends in mass spectrometry imaging for cardiovascular diseases.

Mass spectrometry imaging (MSI) is a widely established technology; however, in the cardiovascular research field, its use is still emerging. The technique has the advantage of analyzing multiple molecules without prior knowledge while maintaining the relation with tissue morphology. Particularly, MALDI-based approaches have been applied to obtain in-depth knowledge of cardiac (dys)function. Here, we discuss the different aspects of the MSI protocols, from sample handling to instrumentation used in cardiovascular research, and critically evaluate these methods. The trend towards structural lipid analysis, identification, and "top-down" protein MSI shows the potential for implementation in (pre)clinical research and complementing the diagnostic tests. Moreover, new insights into disease progression are expected and thereby contribute to the understanding of underlying mechanisms related to cardiovascular diseases.

Mass spectrometry in emergency toxicology: Current state and future applications.

This manuscript offers a broad overview of the state of emergency toxicology testing in clinical laboratories. We summarize the specific challenges of performing emergency toxicology testing, introduce a variety of currently used methods including mass spectrometry, and compare and contrast the utility of different types of mass spectrometers for this purpose. Finally, we examine evidence on the utility of toxicological testing in the treatment of poisoned patients, with special emphasis on the demonstrated utility of mass spectrometry-based tests. This review included primary literature indexed in the NCBI PubMed Database. Search terms included "emergency toxicology", "emergency mass spectrometry", "mass spectrometry toxicology", "utility of toxicology testing", and "toxicology surveillance". There are relatively few clinical trials on the utility of toxicology testing in overdosed or poisoned patients, and those studies that exist have a number of limitations. One of the most significant is that nearly all were conducted with immunoassay-based tests, which can only detect a limited number of compounds and are known to have a high false-positive rate. In addition, few are prospective. The overwhelming majority of studies of immunoassay-based tests concluded that results rarely changed patient management, regardless of the patient's clinical presentation. Many of these studies suggest that results could still be useful in other contexts, including identification of opportunities to refer a patient to substance abuse treatment or avoidance of drug-drug interactions. Mass spectrometry-based testing has several advantages over immunoassays, including the breadth of compounds that can be detected and substantially higher specificity, yet many questions remain about utility in emergency toxicology. The utility of mass spectrometry-based testing has not been assessed in a prospective clinical trial, rather the literature is overwhelmingly case-based, and a small number of laboratories are responsible for the majority of the case reports. The limited evidence that exists suggests that mass spectrometry can be useful in emergency situations, provided that results are available rapidly, interpreted by a knowledgeable physician, and that the scope of the method includes the compound implicated in the poisoning. Like results from immunoassays, many authors report using mass spectrometry-based testing for purposes other than direct patient care, namely surveillance of emerging drugs and trends in local drug use. A number of case reports and larger case series present evidence in support of this use. Despite the potential advantages of mass spectrometry, the quantity and quality of published evidence are not sufficient to adequately assess the utility of mass spectrometry-based emergency toxicology results. This is a field that is ripe for investigation, particularly as mass spectrometers become less expensive and the technology is adopted by an increasing number of clinical laboratories. There is a strong need for prospective studies on implementation of STAT mass spectrometry-based tests in emergency toxicology and larger scale assessments of impact on acute patient care as well as public health.

Mass spectrometry: From plasma proteins to mitochondrial membranes.

In this Inaugural Article, I trace some key steps that have enabled the development of mass spectrometry for the study of intact protein complexes from a variety of cellular environments. Beginning with the preservation of the first soluble complexes from plasma, I describe our early experiments that capitalize on the heterogeneity of subunit composition during assembly and exchange reactions. During these investigations, we observed many assemblies and intermediates with different subunit stoichiometries, and were keen to ascertain whether or not their overall topology was preserved in the mass spectrometer. Adapting ion mobility and soft-landing methodologies, we showed how ring-shaped complexes could survive the phase transition. The next logical progression from soluble complexes was to membrane protein assemblies but this was not straightforward. We encountered many pitfalls along the way, largely due to the use of detergent micelles to protect and stabilize complexes. Further obstacles presented when we attempted to distinguish lipids that copurify from those that are important for function. Developing new experimental protocols, we have subsequently defined lipids that change protein conformation, mediate oligomeric states, and facilitate downstream coupling of G protein-coupled receptors. Very recently, using a radical method-ejecting protein complexes directly from native membranes into mass spectrometers-we provided insights into associations within membranes and mitochondria. Together, these developments suggest the beginnings of mass spectrometry meeting with cell biology.