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Marín-Sáez J, Hernández-Mesa M, Cano-Sancho G, García-Campaña AM. Analytical challenges and opportunities in the study of endocrine disrupting chemicals within an exposomics framework. Talanta 2024; 279:126616. [PMID: 39067205 DOI: 10.1016/j.talanta.2024.126616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Exposomics aims to measure human exposures throughout the lifespan and the changes they produce in the human body. Exposome-scale studies have significant potential to understand the interplay of environmental factors with complex multifactorial diseases widespread in our society and whose origin remain unclear. In this framework, the study of the chemical exposome aims to cover all chemical exposures and their effects in human health but, today, this goal still seems unfeasible or at least very challenging, which makes the exposome for now only a concept. Furthermore, the study of the chemical exposome faces several methodological challenges such as moving from specific targeted methodologies towards high-throughput multitargeted and non-targeted approaches, guaranteeing the availability and quality of biological samples to obtain quality analytical data, standardization of applied analytical methodologies, as well as the statistical assignment of increasingly complex datasets, or the identification of (un)known analytes. This review discusses the various steps involved in applying the exposome concept from an analytical perspective. It provides an overview of the wide variety of existing analytical methods and instruments, highlighting their complementarity to develop combined analytical strategies to advance towards the chemical exposome characterization. In addition, this review focuses on endocrine disrupting chemicals (EDCs) to show how studying even a minor part of the chemical exposome represents a great challenge. Analytical strategies applied in an exposomics context have shown great potential to elucidate the role of EDCs in health outcomes. However, translating innovative methods into etiological research and chemical risk assessment will require a multidisciplinary effort. Unlike other review articles focused on exposomics, this review offers a holistic view from the perspective of analytical chemistry and discuss the entire analytical workflow to finally obtain valuable results.
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Affiliation(s)
- Jesús Marín-Sáez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain; Research Group "Analytical Chemistry of Contaminants", Department of Chemistry and Physics, Research Centre for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almeria, Agrifood Campus of International Excellence, ceiA3, E-04120, Almeria, Spain.
| | - Maykel Hernández-Mesa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain.
| | | | - Ana M García-Campaña
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain
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Kiuchi S, Otoguro Y, Nitta T, Chung MH, Nakaya T, Matsuzawa Y, Ohbuchi K, Sasaki K, Yamamoto H, Tsugawa H. Using Variable Data-Independent Acquisition for Capillary Electrophoresis-Based Untargeted Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2118-2127. [PMID: 39136275 DOI: 10.1021/jasms.4c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Capillary electrophoresis coupled with tandem mass spectrometry (CE-MS/MS) offers advantages in peak capacity and sensitivity for metabolic profiling owing to the electroosmotic flow-based separation. However, the utilization of data-independent MS/MS acquisition (DIA) is restricted due to the absence of an optimal procedure for analytical chemistry and its related informatics framework. We assessed the mass spectral quality using two DIA techniques, namely, all-ion fragmentation (AIF) and variable DIA (vDIA), to isolate 60-800 Da precursor ions with respect to annotation rates. Our findings indicate that vDIA, coupled with the updated MS-DIAL chromatogram deconvolution algorithm, yields higher spectral matching scores and annotation rates compared to AIF. Additionally, we evaluated a linear migration time (MT) correction method using internal standards to accurately align chromatographic peaks in a data set. Postcorrection, the data set exhibited less than 0.1 min MT drifts, a difference mostly equivalent to that of conventional reverse-phase liquid chromatography techniques. Moreover, we conducted MT prediction for metabolites recorded in mass spectral libraries and metabolite structure databases containing a total of 469,870 compounds, achieving an accuracy of less than 1.5 min root mean squares. Our platform provides a peak annotation platform utilizing MT information, accurate precursor m/z, and the MS/MS spectrum recommended by the metabolomics standards initiative. Applying this procedure, we investigated metabolic alterations in lipopolysaccharide (LPS)-induced macrophages, characterizing 170 metabolites. Furthermore, we assigned metabolite information to unannotated peaks using an in silico structure elucidation tool, MS-FINDER. The results were integrated into the nodes in the molecular spectrum network based on the MS/MS similarity score. Consequently, we identified significantly altered metabolites in the LPS-administration group, where glycinamide ribonucleotide, not present in any spectral libraries, was newly characterized. Additionally, we retrieved metabolites of false-negative hits during the initial spectral annotation procedure. Overall, our study underscores the potential of CE-MS/MS with DIA and computational mass spectrometry techniques for metabolic profiling.
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Affiliation(s)
- Saki Kiuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuhiro Otoguro
- Human Metabolome Technologies Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoaki Nitta
- Human Metabolome Technologies Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Mi Hwa Chung
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | - Yuki Matsuzawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | - Kazunori Sasaki
- Human Metabolome Technologies Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Hiroyuki Yamamoto
- Human Metabolome Technologies Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Li Y, Han S. Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases. Gastroenterol Clin North Am 2024; 53:383-397. [PMID: 39068001 DOI: 10.1016/j.gtc.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The human gut microbiota, consisting of trillions of microorganisms, encodes diverse metabolic pathways that impact numerous aspects of host physiology. One key way in which gut bacteria interact with the host is through the production of small metabolites. Several of these microbiota-dependent metabolites, such as short-chain fatty acids, have been shown to modulate host diseases. In this review, we examine how disease-associated metabolic signatures are identified using metabolomic platforms, and where metabolomics is applied in gut microbiota-disease interactions. We further explore how integration of metagenomic and metabolomic data in human studies can facilitate biomarkers discoveries in precision medicine.
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Affiliation(s)
- Yuxin Li
- Biochemistry Graduate Program, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shuo Han
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.
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Sukwattananipaat P, Kuroda H, Yamano-Adachi N, Omasa T. Metabolomic characterization of monoclonal antibody-producing Chinese hamster lung (CHL)-YN cells in glucose-controlled serum-free fed-batch operation. Biotechnol Bioeng 2024; 121:2848-2867. [PMID: 39138873 DOI: 10.1002/bit.28777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 08/15/2024]
Abstract
The fast-growing Chinese hamster lung (CHL)-YN cell line was recently developed for monoclonal antibody production. In this study, we applied a serum-free fed-batch cultivation process to immunoglobulin (Ig)G1-producing CHL-YN cells, which were then used to design a dynamic glucose supply system to stabilize the extracellular glucose concentration based on glucose consumption. Glucose consumption of the cultures rapidly oscillated following three phases of glutamine metabolism: consumption, production, and re-consumption. Use of the dynamic glucose supply prolonged the viability of the CHL-YN-IgG1 cell cultures and increased IgG1 production. Liquid chromatography with tandem mass spectrometry-based target metabolomics analysis of the extracellular metabolites during the first glutamine shift was conducted to search for depleted compounds. The results suggest that the levels of four amino acids, namely arginine, aspartate, methionine, and serine, were sharply decreased in CHL-YN cells during glutamine production. Supporting evidence from metabolic and gene expression analyses also suggest that CHL-YN cells acquired ornithine- and cystathionine-production abilities that differed from those in Chinese hamster ovary-K1 cells, potentially leading to proline and cysteine biosynthesis.
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Affiliation(s)
| | - Hirotaka Kuroda
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Shimadzu Corp., Kyoto, Japan
- Shimadzu Analytical Innovation Research Laboratories, Osaka, Japan
| | - Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
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Luo Y, Zhang W, Qin G. Metabolomics in diabetic nephropathy: Unveiling novel biomarkers for diagnosis (Review). Mol Med Rep 2024; 30:156. [PMID: 38963028 PMCID: PMC11258608 DOI: 10.3892/mmr.2024.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
Diabetic nephropathy (DN) also known as diabetic kidney disease, is a major microvascular complication of diabetes and a leading cause of end‑stage renal disease (ESRD), which affects the morbidity and mortality of patients with diabetes. Despite advancements in diabetes care, current diagnostic methods, such as the determination of albuminuria and the estimated glomerular filtration rate, are limited in sensitivity and specificity, often only identifying kidney damage after considerable morphological changes. The present review discusses the potential of metabolomics as an approach for the early detection and management of DN. Metabolomics is the study of metabolites, the small molecules produced by cellular processes, and may provide a more sensitive and specific diagnostic tool compared with traditional methods. For the purposes of this review, a systematic search was conducted on PubMed and Google Scholar for recent human studies published between 2011 and 2023 that used metabolomics in the diagnosis of DN. Metabolomics has demonstrated potential in identifying metabolic biomarkers specific to DN. The ability to detect a broad spectrum of metabolites with high sensitivity and specificity may allow for earlier diagnosis and better management of patients with DN, potentially reducing the progression to ESRD. Furthermore, metabolomics pathway analysis assesses the pathophysiological mechanisms underlying DN. On the whole, metabolomics is a potential tool in the diagnosis and management of DN. By providing a more in‑depth understanding of metabolic alterations associated with DN, metabolomics could significantly improve early detection, enable timely interventions and reduce the healthcare burdens associated with this condition.
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Affiliation(s)
- Yuanyuan Luo
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Wei Zhang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Guijun Qin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Fejfarová V, Jarošíková R, Antalová S, Husáková J, Wosková V, Beca P, Mrázek J, Tůma P, Polák J, Dubský M, Sojáková D, Lánská V, Petrlík M. Does PAD and microcirculation status impact the tissue availability of intravenously administered antibiotics in patients with infected diabetic foot? Results of the DFIATIM substudy. Front Endocrinol (Lausanne) 2024; 15:1326179. [PMID: 38774229 PMCID: PMC11106387 DOI: 10.3389/fendo.2024.1326179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 04/16/2024] [Indexed: 05/24/2024] Open
Abstract
Aims/hypothesis The aim of this substudy (Eudra CT No:2019-001997-27)was to assess ATB availability in patients with infected diabetic foot ulcers(IDFUs)in the context of microcirculation and macrocirculation status. Methods For this substudy, we enrolled 23 patients with IDFU. Patients were treated with boluses of amoxicillin/clavulanic acid(AMC)(12patients) or ceftazidime(CTZ)(11patients). After induction of a steady ATB state, microdialysis was performed near the IDFU. Tissue fluid samples from the foot and blood samples from peripheral blood were taken within 6 hours. ATB potential efficacy was assessed by evaluating the maximum serum and tissue ATB concentrations(Cmax and Cmax-tissue)and the percentage of time the unbound drug tissue concentration exceeds the minimum inhibitory concentration (MIC)(≥100% tissue and ≥50%/60% tissue fT>MIC). Vascular status was assessed by triplex ultrasound, ankle-brachial and toe-brachial index tests, occlusive plethysmography comprising two arterial flow phases, and transcutaneous oxygen pressure(TcPO2). Results Following bolus administration, the Cmax of AMC was 91.8 ± 52.5 μgmL-1 and the Cmax-tissue of AMC was 7.25 ± 4.5 μgmL-1(P<0.001). The Cmax for CTZ was 186.8 ± 44.1 μgmL-1 and the Cmax-tissue of CTZ was 18.6 ± 7.4 μgmL-1(P<0.0001). Additionally, 67% of patients treated with AMC and 55% of those treated with CTZ achieved tissue fT>MIC levels exceeding 50% and 60%, respectively. We observed positive correlations between both Cmax-tissue and AUCtissue and arterial flow. Specifically, the correlation coefficient for the first phase was r=0.42; (P=0.045), and for the second phase, it was r=0.55(P=0.01)and r=0.5(P=0.021). Conclusions Bactericidal activity proved satisfactory in only half to two-thirds of patients with IDFUs, an outcome that appears to correlate primarily with arterial flow.
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Affiliation(s)
- Vladimíra Fejfarová
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
- Department of Internal Medicine, Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Radka Jarošíková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
- Department of Internal Medicine, Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Simona Antalová
- Department of Clinical Pharmacy and Drug Information Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Jitka Husáková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Veronika Wosková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Pavol Beca
- Department of Clinical Pharmacy and Drug Information Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia
| | - Petr Tůma
- Department of Hygiene, Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Jan Polák
- Department of Pathophysiology, Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Michal Dubský
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Dominika Sojáková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Věra Lánská
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Martin Petrlík
- Vascular and Internal Medicine Outpatient Clinic, Prague, Czechia
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Di Poto C, Tian X, Mellors S, Rosengren S, Issop S, Bonvini SJ, Hess S, Allman EL. A microfluidic chip-based capillary zone electrophoresis-mass spectrometry method for measuring adenosine 5'-Triphosphate and its similar nucleotide analogues. Anal Chim Acta 2024; 1298:342400. [PMID: 38462348 DOI: 10.1016/j.aca.2024.342400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Extracellular ATP is involved in disorders that cause inflammation of the airways and cough, thus limiting its release has therapeutic benefits. Standard luminescence-based ATP assays measure levels indirectly through enzyme degradation and do not provide a simultaneous readout for other nucleotide analogues. Conversely, mass spectrometry can provide direct ATP measurements, however, common RPLC and HILIC methods face issues because these molecules are unstable, metal-sensitive analytes which are often poorly retained. These difficulties have traditionally been overcome using passivation or ion-pairing chromatography, but these approaches can be problematic for LC systems. As a result, more effective analytical methods are needed. RESULTS Here, we introduce a new application that uses microfluidic chip-based capillary zone electrophoresis-mass spectrometry (μCZE-MS) to measure ATP and its analogues simultaneously in biofluids. The commercially available ZipChip Interface and a High-Resolution Bare-glass microchip (ZipChip, HRB, 908 Devices Inc.) coupled to a Thermo Scientific Tribrid Orbitrap, were successfully used to separate and detect various nucleotide standards, as well as ATP, ADP, AMP, and adenosine in plasma and BALF obtained from naïve Brown Norway rats. The findings demonstrate that this approach can rapidly and directly detect ATP and its related nucleotide analogues, while also highlighting the need to preserve these molecules in biofluids with chelators like EDTA. In addition, we demonstrate that this μCZE-MS method is also suitable for detecting a variety of metabolites, revealing additional potential future applications. SIGNIFICANCE This innovative μCZE-MS approach provides a robust new tool to directly measure ATP and other nucleotide analogues in biofluids. This can enable the study of eATP in human disease and potentially contribute to the creation of ATP-targeting therapies for airway illnesses.
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Affiliation(s)
- Cristina Di Poto
- Dynamic Omics, Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Xiang Tian
- Dynamic Omics, Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | | | - Sanna Rosengren
- Translational Science and Experimental Medicine, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sabina Issop
- Division of Airway Disease, Respiratory Pharmacology Group, NHLI, Imperial College London, London, SW7 2AZ, UK
| | - Sara J Bonvini
- In Vivo Bioscience, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, London, SW7 2AZ, UK
| | - Sonja Hess
- Dynamic Omics, Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Erik L Allman
- Dynamic Omics, Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA.
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Schairer J, Plathe F, Hudelmaier S, Belau E, Pengelley S, Kruse L, Neusüß C. Ion mobility in gas and liquid phases: How much orthogonality is obtained in capillary electrophoresis-ion mobility-mass spectrometry? Electrophoresis 2024; 45:735-742. [PMID: 38085142 DOI: 10.1002/elps.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 04/28/2024]
Abstract
Ion mobility-mass spectrometry (IM-MS) is an ever-evolving tool to separate ions in the gas phase according to electrophoretic mobility with subsequent mass determination. CE is rarely coupled to IM-MS, possibly due to similar separation mechanisms based on electrophoretic mobility. Here, we investigate the orthogonality of CE and ion mobility (IM) by analyzing a complex peptide mixture (tryptic digest of HeLa proteins) with trapped ion mobility mass spectrometry (TIMS-MS). Using the nanoCEasy interface, excellent sensitivity was achieved by identifying thousands of peptides and achieving a peak capacity of 7500 (CE: 203-323 in a 150 cm long capillary, IM: 27-31). Plotting CE versus mass and CE versus (inverse) mobility, a clear grouping in curved striped patterns is observed according to the charge-to-size and mass-to-charge ratios. The peptide charge in the acidic background electrolyte can be estimated from the number of basic amino acids, with a few exceptions where neighboring effects reduce the positive charge. A surprisingly high orthogonality of CE and IM is observed, which is obviously caused by solvation effects leading to different charges and sizes in the liquid phase compared to the gas phase. A high orthogonality of CE and ion mobility is expected to be observed for other peptide samples as well as other substance classes, making CE-IM-MS a promising tool for various applications.
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Affiliation(s)
- Jasmin Schairer
- Faculty of Chemistry, Aalen University, Aalen, Germany
- Faculty of Science, University of Tübingen, Tübingen, Germany
| | | | | | | | | | - Lena Kruse
- Faculty of Chemistry, Aalen University, Aalen, Germany
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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Elbashir AA, Osman A, Elawad M, Ziyada AK, Aboul-Enein HY. Application of capillary electrophoresis with capacitively contactless conductivity detection for biomedical analysis. Electrophoresis 2024; 45:400-410. [PMID: 38100198 DOI: 10.1002/elps.202300216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 03/20/2024]
Abstract
The coupling of capillary electrophoresis (CE) with capacitively coupled contactless conductivity detection (C4 D) has become convenient analytical method for determination of small molecules that do not possess chromogenic or fluorogenic group. The implementations of CE with C4 D in the determination of inorganic and organic ions and amino acids in biomedical field are demonstrated. Attention on background electrolyte composition, sample treatment procedures, and the utilize of multi-detection systems are described. A number of tables summarizing highly developed CE-C4 D methods and the figures of merit attained are involved. Lastly, concluding remarks and perspectives are argued.
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Affiliation(s)
- Abdalla A Elbashir
- Department, of Chemistry, College of Science, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Chemistry, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Abdelbagi Osman
- Department of Chemical Engineering, College of Engineering, Najran University, Najran, Saudi Arabia
| | - Mohammed Elawad
- Department of Chemistry, Faculty of Science, Omdurman Islamic University, Omdurman, Sudan
| | - Abobakr K Ziyada
- Department of General Studies, Jubail Industrial College, Jubail Industrial City, Saudi Arabia
| | - Hassan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, Division of Pharmaceutical and Drug Industries Research Division, National Research Centre, Cairo, Egypt
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Ren Y, Liu Y, Zhang W, Ran J, Li L, Zhang Z. Sheathless CESI-MS versus LC-MS: Results of qualitative and quantitative analyses of the primary and secondary metabolites of Pleioblastus amarus bamboo shoots. Electrophoresis 2024; 45:266-274. [PMID: 37817363 DOI: 10.1002/elps.202300030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023]
Abstract
The bamboo shoot of Pleioblastus amarus (Keng) Keng f. is a medicinal and edible resource in China. In this study, three separation techniques were applied to identify the primary and secondary metabolites component of P. amarus bamboo shoots, including sheathless capillary electrophoresis electrospray ionization-mass spectrometry (CESI-MS), reverse-phase liquid chromatography-MS (RPLC-MS), and hydrophilic interaction liquid chromatography-MS (HILIC-MS). A total of 201 metabolites were identified by the three methods. Among those metabolites, 146 were identified by RPLC-MS, 85 were identified by HILIC-MS, and 46 were identified by sheathless CESI-MS. These methods were complementary and had a linear coefficient. CESI-MS presented advantages in the identification of isomers, high sensitivity, very low sample usage, and good detection of polar and nonpolar metabolites, showing its unique applications in food analysis and prospects in metabolic research.
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Affiliation(s)
- Yan Ren
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wenming Zhang
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Junfeng Ran
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Li Li
- The Sixth People's Hospital of Hengshui, Hengshui, Hebei, P. R. China
| | - Zhidan Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, P. R. China
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12
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2021-mid-2023). Electrophoresis 2024; 45:165-198. [PMID: 37670208 DOI: 10.1002/elps.202300152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023]
Abstract
This review article brings a comprehensive survey of developments and applications of high-performance capillary and microchip electromigration methods (zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical characterization of peptides in the period from 2021 up to ca. the middle of 2023. Progress in the study of electromigration properties of peptides and various aspects of their analysis, such as sample preparation, adsorption suppression, electroosmotic flow regulation, and detection, are presented. New developments in the particular capillary electromigration methods are demonstrated, and several types of their applications are reported. They cover qualitative and quantitative analysis of synthetic or isolated peptides and determination of peptides in complex biomatrices, peptide profiling of biofluids and tissues, and monitoring of chemical and enzymatic reactions and physicochemical changes of peptides. They include also amino acid and sequence analysis of peptides, peptide mapping of proteins, separation of stereoisomers of peptides, and their chiral analyses. In addition, micropreparative separations and physicochemical characterization of peptides and their interactions with other (bio)molecules by the above CE methods are described.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
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13
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Domínguez-Rodríguez G, Montero L, Herrero M, Cifuentes A, Castro-Puyana M. Capillary electromigration methods for food analysis and Foodomics: Advances and applications in the period March 2021 to March 2023. Electrophoresis 2024; 45:8-34. [PMID: 37603373 DOI: 10.1002/elps.202300126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
This work presents a revision of the main applications of capillary electromigration (CE) methods in food analysis and Foodomics. Papers that were published during the period March 2021 to March 2023 are included. The work shows the multiple CE methods that have been developed and applied to analyze different types of molecules in foods and beverages. Namely, CE methods have been applied to analyze amino acids, biogenic amines, heterocyclic amines, peptides, proteins, phenols, polyphenols, pigments, lipids, carbohydrates, vitamins, DNAs, contaminants, toxins, pesticides, additives, residues, small organic and inorganic compounds, and other minor compounds. In addition, new CE procedures to perform chiral separation and for evaluating the effects of food processing as well as the last developments of microchip CE and new applications in Foodomics will be also discussed. The new procedures of CE to investigate food quality and safety, nutritional value, storage, and bioactivity are also included in the present review work.
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Affiliation(s)
- Gloria Domínguez-Rodríguez
- Laboratory of Foodomics, CIAL, CSIC, Madrid, Spain
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Madrid, Spain
| | | | | | | | - María Castro-Puyana
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Madrid, Spain
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14
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Fukuyama Y, Shimamura S, Sakai S, Michimori Y, Sumida T, Chikaraishi Y, Atomi H, Nunoura T. Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen. ISME COMMUNICATIONS 2024; 4:ycad006. [PMID: 38282645 PMCID: PMC10809761 DOI: 10.1093/ismeco/ycad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/30/2024]
Abstract
Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 [Formula: see text] 104-105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.
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Affiliation(s)
- Yuto Fukuyama
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Sanae Sakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshito Chikaraishi
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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15
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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16
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Jariyasopit N, Khoomrung S. Mass spectrometry-based analysis of gut microbial metabolites of aromatic amino acids. Comput Struct Biotechnol J 2023; 21:4777-4789. [PMID: 37841334 PMCID: PMC10570628 DOI: 10.1016/j.csbj.2023.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023] Open
Abstract
Small molecules derived from gut microbiota have been increasingly investigated to better understand the functional roles of the human gut microbiome. Microbial metabolites of aromatic amino acids (AAA) have been linked to many diseases, such as metabolic disorders, chronic kidney diseases, inflammatory bowel disease, diabetes, and cancer. Important microbial AAA metabolites are often discovered via global metabolite profiling of biological specimens collected from humans or animal models. Subsequent metabolite identity confirmation and absolute quantification using targeted analysis enable comparisons across different studies, which can lead to the establishment of threshold concentrations of potential metabolite biomarkers. Owing to their excellent selectivity and sensitivity, hyphenated mass spectrometry (MS) techniques are often employed to identify and quantify AAA metabolites in various biological matrices. Here, we summarize the developments over the past five years in MS-based methodology for analyzing gut microbiota-derived AAA. Sample preparation, method validation, analytical performance, and statistical methods for correlation analysis are discussed, along with future perspectives.
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Affiliation(s)
- Narumol Jariyasopit
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
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17
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Krebs F, Zagst H, Stein M, Ratih R, Minkner R, Olabi M, Hartung S, Scheller C, Lapizco-Encinas BH, Sänger-van de Griend C, García CD, Wätzig H. Strategies for capillary electrophoresis: Method development and validation for pharmaceutical and biological applications-Updated and completely revised edition. Electrophoresis 2023; 44:1279-1341. [PMID: 37537327 DOI: 10.1002/elps.202300158] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
This review is in support of the development of selective, precise, fast, and validated capillary electrophoresis (CE) methods. It follows up a similar article from 1998, Wätzig H, Degenhardt M, Kunkel A. "Strategies for capillary electrophoresis: method development and validation for pharmaceutical and biological applications," pointing out which fundamentals are still valid and at the same time showing the enormous achievements in the last 25 years. The structures of both reviews are widely similar, in order to facilitate their simultaneous use. Focusing on pharmaceutical and biological applications, the successful use of CE is now demonstrated by more than 600 carefully selected references. Many of those are recent reviews; therefore, a significant overview about the field is provided. There are extra sections about sample pretreatment related to CE and microchip CE, and a completely revised section about method development for protein analytes and biomolecules in general. The general strategies for method development are summed up with regard to selectivity, efficiency, precision, analysis time, limit of detection, sample pretreatment requirements, and validation.
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Affiliation(s)
- Finja Krebs
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Holger Zagst
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Matthias Stein
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Ratih Ratih
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Surabaya, Surabaya, East Java, Indonesia
| | - Robert Minkner
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Mais Olabi
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Sophie Hartung
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Christin Scheller
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Blanca H Lapizco-Encinas
- Department of Biomedical Engineering, Kate Gleason College of Engineering, Rochester Institute of Technology, Rochester, New York, USA
| | - Cari Sänger-van de Griend
- Kantisto BV, Baarn, The Netherlands
- Department of Medicinal Chemistry, Faculty of Pharmacy, Uppsala Universitet, Uppsala, Sweden
| | - Carlos D García
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Hermann Wätzig
- Institute, of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany
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18
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Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
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Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
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19
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Thangavelu MU, Wouters B, Kindt A, Reiss IKM, Hankemeier T. Blood microsampling technologies: Innovations and applications in 2022. ANALYTICAL SCIENCE ADVANCES 2023; 4:154-180. [PMID: 38716066 PMCID: PMC10989553 DOI: 10.1002/ansa.202300011] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 06/23/2024]
Abstract
With the development of highly sensitive bioanalytical techniques, the volume of samples necessary for accurate analysis has reduced. Microsampling, the process of obtaining small amounts of blood, has thus gained popularity as it offers minimal-invasiveness, reduced logistical costs and biohazard risks while simultaneously showing increased sample stability and a potential for the decentralization of the approach and at-home self-sampling. Although the benefits of microsampling have been recognised, its adoption in clinical practice has been slow. Several microsampling technologies and devices are currently available and employed in research studies for various biomedical applications. This review provides an overview of the state-of-the-art in microsampling technology with a focus on the latest developments and advancements in the field of microsampling. Research published in the year 2022, including studies (i) developing strategies for the quantitation of analytes in microsamples and (ii) bridging and comparing the interchangeability between matrices and choice of technology for a given application, is reviewed to assess the advantages, challenges and limitations of the current state of microsampling. Successful implementation of microsampling in routine clinical care requires continued efforts for standardization and harmonization. Microsampling has been shown to facilitate data-rich studies and a patient-centric approach to healthcare and is foreseen to play a central role in the future digital revolution of healthcare through continuous monitoring to improve the quality of life.
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Affiliation(s)
| | - Bert Wouters
- Metabolomics and Analytics CentreLeiden UniversityLeidenThe Netherlands
| | - Alida Kindt
- Metabolomics and Analytics CentreLeiden UniversityLeidenThe Netherlands
| | - Irwin K. M. Reiss
- Department of Neonatal and Pediatric Intensive CareDivision of NeonatologyErasmus MCRotterdamThe Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics CentreLeiden UniversityLeidenThe Netherlands
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20
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Chalova P, Tazky A, Skultety L, Minichova L, Chovanec M, Ciernikova S, Mikus P, Piestansky J. Determination of short-chain fatty acids as putative biomarkers of cancer diseases by modern analytical strategies and tools: a review. Front Oncol 2023; 13:1110235. [PMID: 37441422 PMCID: PMC10334191 DOI: 10.3389/fonc.2023.1110235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of non-digestible carbohydrates in the gastrointestinal tract. They can be seen as the major flow of carbon from the diet, through the microbiome to the host. SCFAs have been reported as important molecules responsible for the regulation of intestinal homeostasis. Moreover, these molecules have a significant impact on the immune system and are able to affect inflammation, cardiovascular diseases, diabetes type II, or oncological diseases. For this purpose, SCFAs could be used as putative biomarkers of various diseases, including cancer. A potential diagnostic value may be offered by analyzing SCFAs with the use of advanced analytical approaches such as gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) coupled with mass spectrometry (MS). The presented review summarizes the importance of analyzing SCFAs from clinical and analytical perspective. Current advances in the analysis of SCFAs focused on sample pretreatment, separation strategy, and detection methods are highlighted. Additionally, it also shows potential areas for the development of future diagnostic tools in oncology and other varieties of diseases based on targeted metabolite profiling.
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Affiliation(s)
- Petra Chalova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
| | - Anton Tazky
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Ludovit Skultety
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Lenka Minichova
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
| | - Michal Chovanec
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia
| | - Sona Ciernikova
- Biomedical Research Center of the Slovak Academy of Sciences, Cancer Research Institute, Bratislava, Slovakia
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Juraj Piestansky
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
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21
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Tůma P. Progress in on-line, at-line, and in-line coupling of sample treatment with capillary and microchip electrophoresis over the past 10 years: A review. Anal Chim Acta 2023; 1261:341249. [PMID: 37147053 DOI: 10.1016/j.aca.2023.341249] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
The review presents an evaluation of the development of on-line, at-line and in-line sample treatment coupled with capillary and microchip electrophoresis over the last 10 years. In the first part, it describes different types of flow-gating interfaces (FGI) such as cross-FGI, coaxial-FGI, sheet-flow-FGI, and air-assisted-FGI and their fabrication using molding into polydimethylsiloxane and commercially available fittings. The second part deals with the coupling of capillary and microchip electrophoresis with microdialysis, solid-phase, liquid-phase, and membrane based extraction techniques. It mainly focuses on modern techniques such as extraction across supported liquid membrane, electroextraction, single drop microextraction, head space microextraction, and microdialysis with high spatial and temporal resolution. Finally, the design of sequential electrophoretic analysers and fabrication of SPE microcartridges with monolithic and molecularly imprinted polymeric sorbents are discussed. Applications include the monitoring of metabolites, neurotransmitters, peptides and proteins in body fluids and tissues to study processes in living organisms, as well as the monitoring of nutrients, minerals and waste compounds in food, natural and wastewater.
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Affiliation(s)
- Petr Tůma
- Department of Hygiene, Third Faculty of Medicine, Charles University, Ruská 87, 100 00, Prague 10, Czech Republic.
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22
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Recent applications and chiral separation developments based on stationary phases in open tubular capillary electrochromatography (2019–2022). J Pharm Anal 2023; 13:323-339. [PMID: 37181297 PMCID: PMC10173184 DOI: 10.1016/j.jpha.2023.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Capillary electrochromatography (CEC) plays a significant role in chiral separation via the double separation principle, partition coefficient difference between the two phases, and electroosmotic flow-driven separation. Given the distinct properties of the inner wall stationary phase (SP), the separation ability of each SP differs from one another. Particularly, it provides large room for promising applications of open tubular capillary electrochromatography (OT-CEC). We divided the OT-CEC SPs developed over the past four years into six types: ionic liquids, nanoparticle materials, microporous materials, biomaterials, non-nanopolymers, and others, to mainly introduce their characteristics in chiral drug separation. There also added a few classic SPs that occurred within ten years as supplements to enrich the features of each SP. Additionally, we discuss their applications in metabolomics, food, cosmetics, environment, and biology as analytes in addition to chiral drugs. OT-CEC plays an increasingly significant role in chiral separation and may promote the development of capillary electrophoresis (CE) combined with other instruments in recent years, such as CE with mass spectrometry (CE/MS) and CE with ultraviolet light detector (CE/UV).
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23
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Tůma P, Sommerová B, Koval D, Šiklová M, Koc M. Plasma levels of creatine, 2-aminobutyric acid, acetyl-carnitine and amino acids during fasting measured by counter-current electrophoresis in PAMAPTAC capillary. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Sugimoto M, Aizawa Y, Tomita A. Data Processing and Analysis in Liquid Chromatography-Mass Spectrometry-Based Targeted Metabolomics. Methods Mol Biol 2023; 2571:241-255. [PMID: 36152165 DOI: 10.1007/978-1-0716-2699-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry (MS)-based metabolomics provides high-dimensional datasets; that is, the data include various metabolite features. Data analysis begins by converting the raw data obtained from the MS to produce a data matrix (metabolite × concentrations). This is followed by several steps, such as peak integration, alignment of multiple data, metabolite identification, and calculation of metabolite concentrations. Each step yields the analytical results and the accompanying information used for the quality assessment of the anterior steps. Thus, the measurement quality can be analyzed through data processing. Here, we introduce a typical data processing procedure and describe a method to utilize the intermediate data as quality control. Subsequently, commonly used data analysis methods for metabolomics data, such as statistical analyses, are also introduced.
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Affiliation(s)
- Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Institute for Advanced Biosciences, Yamagata, Japan.
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Atsumi Tomita
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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25
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Abstract
Metabolomics is a continuously dynamic field of research that is driven by demanding research questions and technological advances alike. In this review we highlight selected recent and ongoing developments in the area of mass spectrometry-based metabolomics. The field of view that can be seen through the metabolomics lens can be broadened by adoption of separation techniques such as hydrophilic interaction chromatography and ion mobility mass spectrometry (going broader). For a given biospecimen, deeper metabolomic analysis can be achieved by resolving smaller entities such as rare cell populations or even single cells using nano-LC and spatially resolved metabolomics or by extracting more useful information through improved metabolite identification in untargeted metabolomic experiments (going deeper). Integration of metabolomics with other (omics) data allows researchers to further advance in the understanding of the complex metabolic and regulatory networks in cells and model organisms (going further). Taken together, diverse fields of research from mechanistic studies to clinics to biotechnology applications profit from these technological developments.
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Affiliation(s)
- Sofia Moco
- Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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26
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van Mever M, Ramautar R. Capillary Electrophoresis-Mass Spectrometry for the Direct Analysis of Metabolites in Highly Saline Samples Using In-Capillary Preconcentration. Methods Mol Biol 2023; 2571:95-103. [PMID: 36152153 DOI: 10.1007/978-1-0716-2699-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is gaining interest for metabolomics studies because of its high separation efficiency, selectivity, and versatility. The ability to inject nanoliters from only a few microliters of sample in the injection vial makes this approach very suited for volume-limited applications. However, the low injection volumes could compromise the detection sensitivity of CE-MS, thereby potentially limiting its scope in metabolomics. To overcome this issue, online sample preconcentration methods have been developed to increase sample-loading volumes without hampering the intrinsic high separation efficiency of CE. In this protocol, online preconcentration with sample stacking based on pH junction was assessed for the direct profiling of endogenous metabolites in rat brain microdialysates. Sample stacking was realized by a pre-injection of ammonium hydroxide, followed by a large sample injection (i.e., about 17% of the total capillary volume). It is shown that this relatively simple and fast preconcentration procedure is fully compatible with the high-salt concentration in microdialysates and significantly improves the detection sensitivity of the CE-MS method.
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Affiliation(s)
- Marlien van Mever
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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27
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Fejfarová V, Jarošíková R, Polák J, Sommerová B, Husáková J, Wosková V, Dubský M, Tůma P. Microdialysis as a tool for antibiotic assessment in patients with diabetic foot: a review. Front Endocrinol (Lausanne) 2023; 14:1141086. [PMID: 37139338 PMCID: PMC10150051 DOI: 10.3389/fendo.2023.1141086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/17/2023] [Indexed: 05/05/2023] Open
Abstract
Diabetic foot is a serious late complication frequently caused by infection and ischaemia. Both require prompt and aggressive treatment to avoid lower limb amputation. The effectiveness of peripheral arterial disease therapy can be easily verified using triplex ultrasound, ankle-brachial/toe-brachial index examination, or transcutaneous oxygen pressure. However, the success of infection treatment is difficult to establish in patients with diabetic foot. Intravenous systemic antibiotics are recommended for the treatment of infectious complications in patients with moderate or serious stages of infection. Antibiotic therapy should be initiated promptly and aggressively to achieve sufficient serum and peripheral antibiotic concentrations. Antibiotic serum levels are easily evaluated by pharmacokinetic assessment. However, antibiotic concentrations in peripheral tissues, especially in diabetic foot, are not routinely detectable. This review describes microdialysis techniques that have shown promise in determining antibiotic levels in the surroundings of diabetic foot lesions.
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Affiliation(s)
- Vladimíra Fejfarová
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
- *Correspondence: Vladimíra Fejfarová,
| | - Radka Jarošíková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Jan Polák
- Department of Pathophysiology, Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Blanka Sommerová
- Department of Hygiene, Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Jitka Husáková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Veronika Wosková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Michal Dubský
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petr Tůma
- Department of Hygiene, Third Faculty of Medicine, Charles University, Prague, Czechia
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28
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Chemotherapy-Induced Peripheral Neuropathy. Handb Exp Pharmacol 2023; 277:299-337. [PMID: 36253554 DOI: 10.1007/164_2022_609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side effect of many common anti-cancer agents that can lead to dose reduction or treatment discontinuation, which decrease chemotherapy efficacy. Long-term CIPN can interfere with activities of daily living and diminish the quality of life. The mechanism of CIPN is not yet fully understood, and biomarkers are needed to identify patients at high risk and potential treatment targets. Metabolomics can capture the complex behavioral and pathophysiological processes involved in CIPN. This chapter is to review the CIPN metabolomics studies to find metabolic pathways potentially involved in CIPN. These potential CIPN metabolites are then investigated to determine whether there is evidence from studies of other neuropathy etiologies such as diabetic neuropathy and Leber hereditary optic neuropathy to support the importance of these pathways in peripheral neuropathy. Six potential biomarkers and their putative mechanisms in peripheral neuropathy were reviewed. Among these biomarkers, histidine and phenylalanine have clear roles in neurotransmission or neuroinflammation in peripheral neuropathy. Further research is needed to discover and validate CIPN metabolomics biomarkers in large clinical studies.
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29
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Sugimoto M, Aizawa Y. Metabolomics Analysis of Blood, Urine, and Saliva Samples Based on Capillary Electrophoresis-Mass Spectrometry. Methods Mol Biol 2023; 2571:83-94. [PMID: 36152152 DOI: 10.1007/978-1-0716-2699-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is an ideal method for analyzing various metabolites in biological samples. CE-MS can simultaneously identify and quantify hundreds of charged metabolites using only two acquisition methods for positively and negatively charged metabolites. Furthermore, CE-MS is commonly used for analyzing biological samples to understand the pathology of diseases at the metabolic level and biofluid samples, such as blood and urine, to explore biomarkers. Here, we introduce a protocol that delineates the handling of clinical samples to ensure that the CE-MS analysis yields reproducible quantified data. We have focused on sample collection, storage, processing, and measurement. Although the implementation of rigorous standard operating protocols is preferred for enhancing the quality of the samples, various limitations in an actual clinical setting make it difficult to adhere to strict rules. Therefore, the effect of each process on the quantified metabolites needs to be evaluated to design a protocol with acceptable tolerances. Furthermore, quality controls and assessments to handle clinical samples are introduced.
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Affiliation(s)
- Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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30
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Zhang W, Xiang Y, Xu W. Probing protein higher-order structures by native capillary electrophoresis-mass spectrometry. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Recent advances in the hyphenation of electromigration techniques with mass spectrometry. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Advances in capillary electrophoresis mass spectrometry for metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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Creydt M, Fischer M. Food metabolomics: Latest hardware-developments for nontargeted food authenticity and food safety testing. Electrophoresis 2022; 43:2334-2350. [PMID: 36104152 DOI: 10.1002/elps.202200126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022]
Abstract
The analytical requirements for food testing have increased significantly in recent years. On the one hand, because food fraud is becoming an ever-greater challenge worldwide, and on the other hand because food safety is often difficult to monitor due to the far-reaching trade chains. In addition, the expectations of consumers on the quality of food have increased, and they are demanding extensive information. Cutting-edge analytical methods are required to meet these demands. In this context, non-targeted metabolomics strategies using mass and nuclear magnetic resonance spectrometers (mass spectrometry [MS]) have proven to be very suitable. MS-based approaches are of particular importance as they provide a comparatively high analytical coverage of the metabolome. Accordingly, the efficiency to address even challenging issues is high. A variety of hardware developments, which are explained in this review, have contributed to these advances. In addition, the potential of future developments is highlighted, some of which are currently not yet commercially available or only used to a comparatively small extent but are expected to gain in importance in the coming years.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
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34
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López-López Á, Ciborowski M, Niklinski J, Barbas C, López-Gonzálvez Á. Optimization of capillary electrophoresis coupled to negative mode electrospray ionization-mass spectrometry using polyvinyl alcohol coated capillaries. Application to a study on non-small cell lung cancer. Anal Chim Acta 2022; 1226:340259. [DOI: 10.1016/j.aca.2022.340259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/13/2022] [Accepted: 08/11/2022] [Indexed: 11/01/2022]
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35
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Mora MF, Kok MGM, Noell A, Willis PA. Detection of Biosignatures by Capillary Electrophoresis Mass Spectrometry in the Presence of Salts Relevant to Ocean Worlds Missions. ASTROBIOLOGY 2022; 22:914-925. [PMID: 35913998 DOI: 10.1089/ast.2021.0091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Capillary electrophoresis (CE) is a promising liquid-based technique for in situ chemical analysis on ocean worlds that allows the detection of a wide range of organic molecules relevant to the search for life. CE coupled with mass spectrometry (MS) is particularly valuable as it also enables the discovery of unknown compounds. Here we demonstrate that CE coupled to MS via electrospray ionization (ESI) can readily analyze samples containing up to half the saturation levels of salts relevant to ocean worlds when using 5 M acetic acid as the separation media. A mixture containing amino acids, peptides, nucleobases, and nucleosides was analyzed in the presence of two salts, NaCl and MgSO4, based on their relevance to Europa and Enceladus. We demonstrate here CE-MS limits of detection for these organics ranging from 0.05 to 1 μM (8 to 89 ppb) in the absence of salts. More importantly, we demonstrate here for the first time that organics in the low micromolar range (1-50 μM) are detected by CE-MS in the presence of 3 M NaCl without desalting, preconcentration, or derivatization. This demonstration highlights how CE-MS is uniquely suited for organic analysis on future missions to ocean worlds.
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Affiliation(s)
- Maria F Mora
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Miranda G M Kok
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Aaron Noell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Peter A Willis
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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36
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Huang Z, Tan J, Li Y, Miao S, Scotland KB, Chew BH, Lange D, Chen DDY. Migration time correction for dual pressure capillary electrophoresis in semi‐targeted metabolomics study. Electrophoresis 2022; 43:1626-1637. [DOI: 10.1002/elps.202100365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/23/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Zi‐Ao Huang
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Jiahua Tan
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Yueyang Li
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Siyu Miao
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Kymora B. Scotland
- Department of Urology University of California, Los Angeles Los Angeles California USA
| | - Ben H. Chew
- Department of Urologic Sciences The Stone Centre at Vancouver General Hospital University of British Columbia Vancouver British Columbia Canada
| | - Dirk Lange
- Department of Urologic Sciences The Stone Centre at Vancouver General Hospital University of British Columbia Vancouver British Columbia Canada
| | - David D. Y. Chen
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
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37
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Lima MF, Amaral AG, Moretto IA, Paiva-Silva FJTN, Pereira FOB, Barbas C, dos Santos AM, Simionato AVC, Rupérez FJ. Untargeted Metabolomics Studies of H9c2 Cardiac Cells Submitted to Oxidative Stress, β-Adrenergic Stimulation and Doxorubicin Treatment: Investigation of Cardiac Biomarkers. Front Mol Biosci 2022; 9:898742. [PMID: 35847971 PMCID: PMC9277393 DOI: 10.3389/fmolb.2022.898742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
One of the biggest challenges in the search for more effective treatments for diseases is understanding their etiology. Cardiovascular diseases (CVD) are an important example of this, given the high number of deaths annually. Oxidative stress (the imbalance between oxidant and antioxidant species in biological system) is one of the factors responsible for CVD occurrence, demanding extensive investigation. Excess of reactive oxygen species (ROS) are primarily responsible for this condition, and clinical and scientific literature have reported a significant increase in ROS when therapeutic drugs, such as doxorubicin and isoproterenol, are administered. In this context, the aim of this study is the investigation of potential biomarkers that might be associated with oxidative stress in cardiomyocytes. For this purpose, H9c2 cardiomyocytes were submitted to oxidative stress conditions by treatment with doxorubicin (DOX), isoproterenol (ISO) and hydrogen peroxide (PER). Metabolomics analyses of the cell extract and the supernatant obtained from the culture medium were then evaluated by CE-ESI(+)-TOF-MS. Following signal processing, statistical analyses, and molecular features annotations, the results indicate changes in the aspartate, serine, pantothenic acid, glycerophosphocholine and glutathione metabolism in the cell extract.
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Affiliation(s)
- Monica Força Lima
- Center for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alan Gonçalves Amaral
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabela Aparecida Moretto
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Flávia Oliveira Borges Pereira
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Aline Mara dos Santos
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Aline Mara dos Santos, ; Francisco Javier Rupérez,
| | - Ana Valéria Colnaghi Simionato
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
- National Institute of Science and Technology in Bioanalytics (INCTBio), Campinas, Brazil
| | - Francisco Javier Rupérez
- Center for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
- *Correspondence: Aline Mara dos Santos, ; Francisco Javier Rupérez,
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38
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Zhang W, Chetwynd AJ, Thorn JA, Lynch I, Ramautar R. Understanding the Significance of Sample Preparation in Studies of the Nanoparticle Metabolite Corona. ACS MEASUREMENT SCIENCE AU 2022; 2:251-260. [PMID: 35726252 PMCID: PMC9204816 DOI: 10.1021/acsmeasuresciau.2c00003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 05/28/2023]
Abstract
The adsorption of metabolites to the surface of nanomaterials is a growing area of interest in the field of bionanointeractions. Like its more-established protein counterpart, it is thought that the metabolite corona has a key role in the uptake, distribution, and toxicity of nanomaterials in organisms. Previous research has demonstrated that nanomaterials obtain a unique metabolite fingerprint when exposed to biological matrices; however, there have been some concerns raised over the reproducibility of bionanointeraction research due to challenges in dispersion of nanomaterials and their stability. As such, this work investigates a much-overlooked aspect of this field, i.e., sample preparation, which is vital to the accurate, reproducible, and informative analysis of the metabolite corona. The impact of elution buffer pH, volume, and ionic strength on the metabolite corona composition acquired by uncapped and polyvinylpyrrolidone (PVP)-capped TiO2 from mixtures of cationic and anionic metabolites was studied. We demonstrate the temporal evolution of the TiO2 metabolite corona and the recovery of the metabolite corona, which resulted from a complex biological matrix, in this case human plasma. This work also demonstrates that it is vital to optimize sample preparation for each nanomaterial being investigated, as the metabolite recovery from Fe3O4 and Dispex-capped TiO2 nanomaterials is significantly reduced compared to the aforementioned uncapped and PVP-capped TiO2 nanomaterials. These are important findings for future bionanointeraction studies, which is a rapidly emerging area of research in nanoscience.
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Affiliation(s)
- Wei Zhang
- Leiden
Academic Centre for Drug Research, Leiden
University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Andrew J. Chetwynd
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
- Department
of Women’s and Children’s Health, Institute of Life
Course and Medical Sciences, University
of Liverpool, Liverpool L12 2AP, U.K.
| | - James A. Thorn
- AB
SCIEX UK Ltd., SCIEX UK Centre of Innovation, Suite 21F18, 21 Mereside, Alderley
Park, Macclesfield, Cheshire SK10 4TG, U.K.
| | - Iseult Lynch
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Rawi Ramautar
- Leiden
Academic Centre for Drug Research, Leiden
University, Einsteinweg 55, 2333CC Leiden, The Netherlands
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39
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Sah S, Yun SR, Gaul DA, Botros A, Park EY, Kim O, Kim J, Fernández FM. Targeted Microchip Capillary Electrophoresis-Orbitrap Mass Spectrometry Metabolomics to Monitor Ovarian Cancer Progression. Metabolites 2022; 12:metabo12060532. [PMID: 35736465 PMCID: PMC9230880 DOI: 10.3390/metabo12060532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
The lack of effective screening strategies for high-grade serous carcinoma (HGSC), a subtype of ovarian cancer (OC) responsible for 70–80% of OC related deaths, emphasizes the need for new diagnostic markers and a better understanding of disease pathogenesis. Capillary electrophoresis (CE) coupled with high-resolution mass spectrometry (HRMS) offers high selectivity and sensitivity for ionic compounds, thereby enhancing biomarker discovery. Recent advances in CE-MS include small, chip-based CE systems coupled with nanoelectrospray ionization (nanoESI) to provide rapid, high-resolution analysis of biological specimens. Here, we describe the development of a targeted microchip (µ) CE-HRMS method, with an acquisition time of only 3 min and sample injection volume of 4nL, to analyze 40 target metabolites in serum samples from a triple-mutant (TKO) mouse model of HGSC. Extracted ion electropherograms showed sharp, baseline resolved peak shapes, even for structural isomers such as leucine and isoleucine. All calibration curves of the analytes maintained good linearity with an average R2 of 0.994, while detection limits were in the nM range. Thirty metabolites were detected in mouse serum with recoveries ranging from 78 to 120%, indicating minimal ionization suppression and good accuracy. We applied the µCE-HRMS method to biweekly-collected serum samples from TKO and TKO control mice. A time-resolved analysis revealed characteristic temporal trends for amino acids, nucleosides, and amino acid derivatives. These metabolic alterations are indicative of altered nucleotide biosynthesis and amino acid metabolism in HGSC development and progression. A comparison of the µCE-HRMS dataset with non-targeted ultra-high performance liquid chromatography (UHPLC)–MS results showed identical temporal trends for the five metabolites detected with both platforms, indicating the µCE-HRMS method performed satisfactorily in terms of capturing metabolic reprogramming due to HGSC progression while reducing the total data collection time three-fold.
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Affiliation(s)
- Samyukta Sah
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (S.S.); (D.A.G.)
| | - Sylvia R. Yun
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.R.Y.); (A.B.); (E.Y.P.); (O.K.)
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (S.S.); (D.A.G.)
| | - Andro Botros
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.R.Y.); (A.B.); (E.Y.P.); (O.K.)
| | - Eun Young Park
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.R.Y.); (A.B.); (E.Y.P.); (O.K.)
| | - Olga Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.R.Y.); (A.B.); (E.Y.P.); (O.K.)
| | - Jaeyeon Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.R.Y.); (A.B.); (E.Y.P.); (O.K.)
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Correspondence: (J.K.); (F.M.F.); Tel.: +1-317-278-9740 (ext. 274-4648) (J.K.); +1-404-385-4432 (ext. 894-7452) (F.M.F.)
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (S.S.); (D.A.G.)
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Correspondence: (J.K.); (F.M.F.); Tel.: +1-317-278-9740 (ext. 274-4648) (J.K.); +1-404-385-4432 (ext. 894-7452) (F.M.F.)
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40
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CHI Z, YANG L. Advances in chiral separation and analysis by capillary electrophoresis-mass spectrometry. Se Pu 2022; 40:509-519. [PMID: 35616196 PMCID: PMC9404244 DOI: 10.3724/sp.j.1123.2021.11006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
目前使用的绝大多数药物为手性化合物,它们具有相似的物理和化学性质,但药理活性不同,且常以外消旋混合物的形式存在,因此对手性化合物的分离在生物、环境、食品和医药等领域一直备受关注。与广泛使用的液相色谱-质谱(LC-MS)相比,毛细管电泳-质谱(CE-MS)作为一种新型分离分析技术,具有分离效率高、样品和试剂消耗量低、选择性高和分离模式多样化等诸多优势,已经发展成为手性分析领域中有广阔应用前景的分析方法之一。CE-MS结合了CE的高分离效率和低样品消耗以及MS的高灵敏度和强结构解析能力,在蛋白质组学和代谢组学等领域发挥了重要作用。CE杰出的手性拆分能力与MS优势的结合,亦使CE-MS成为实现手性化合物高效分离分析的完美组合。在过去的十几年里,基于不同CE-MS分离模式的高性能手性分析体系层出不穷,如电动色谱-质谱(EKC-MS)、胶束电动色谱-质谱(MEKC-MS)和毛细管电色谱-质谱(CEC-MS)等,并成功应用于医药、生物、食品和环境科学等领域的手性化合物分析。该文主要综述了2011~2021年,CE-MS在手性化合物分析领域的技术、手性选择剂(如改性环糊精和聚合物表面活性剂等)的使用以及在医药等领域应用方面的研究进展,并讨论了不同手性分析模式的局限性,为未来的CE-MS手性分离分析技术发展及应用提供借鉴。
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41
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Wang M, Gong Q, Liu W, Tan S, Xiao J, Chen C. Applications of capillary electrophoresis in the fields of environmental, pharmaceutical, clinical and food analysis (2019-2021). J Sep Sci 2022; 45:1918-1941. [PMID: 35325510 DOI: 10.1002/jssc.202100727] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/09/2022]
Abstract
So far, the potential of capillary electrophoresis (CE) in the application fields has been increasingly excavated due to the advantages of simple operation, short analysis time, high-resolution, less sample consumption and low cost. This review examines the implementations and advancements of CE in different application fields (environmental, pharmaceutical, clinical and food analysis) covering the literature from 2019 to 2021. In addition, ultrasmall sample injection volume (nanoliter range) and short optical path lead to relatively low concentration sensitivity of the most frequently used UV-absorption spectrophotometric detection, so the pretreatment technology being developed has been gradually utilized to overcome this problem. Despite the review is focused on the development of CE in the fields of environmental, pharmaceutical, clinical and food analysis, the new sample pretreatment techniques of microextraction and enrichment which fit excellently to CE in recent three years are also described briefly. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengyao Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Qian Gong
- Department of Pharmacy, Hunan Cancer Hospital/ The Affiliated Cancer Hospital of School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Wenfang Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Jian Xiao
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
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42
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Sun Y, Kong L, Zhang AH, Han Y, Sun H, Yan GL, Wang XJ. A Hypothesis From Metabolomics Analysis of Diabetic Retinopathy: Arginine-Creatine Metabolic Pathway May Be a New Treatment Strategy for Diabetic Retinopathy. Front Endocrinol (Lausanne) 2022; 13:858012. [PMID: 35399942 PMCID: PMC8987289 DOI: 10.3389/fendo.2022.858012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/01/2022] [Indexed: 12/31/2022] Open
Abstract
Diabetic retinopathy is one of the serious complications of diabetes, which the leading causes of blindness worldwide, and its irreversibility renders the existing treatment methods unsatisfactory. Early detection and timely intervention can effectively reduce the damage caused by diabetic retinopathy. Metabolomics is a branch of systems biology and a powerful tool for studying pathophysiological processes, which can help identify the characteristic metabolic changes marking the progression of diabetic retinopathy, discover potential biomarkers to inform clinical diagnosis and treatment. This review provides an update on the known metabolomics biomarkers of diabetic retinopathy. Through comprehensive analysis of biomarkers, we found that the arginine biosynthesis is closely related to diabetic retinopathy. Meanwhile, creatine, a metabolite with arginine as a precursor, has attracted our attention due to its important correlation with diabetic retinopathy. We discuss the possibility of the arginine-creatine metabolic pathway as a therapeutic strategy for diabetic retinopathy.
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Affiliation(s)
- Ye Sun
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ling Kong
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ai-Hua Zhang
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Han
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hui Sun
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Guang-Li Yan
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xi-Jun Wang
- National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant, Nanning, China
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43
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Sakurai N. Recent applications of metabolomics in plant breeding. BREEDING SCIENCE 2022; 72:56-65. [PMID: 36045891 PMCID: PMC8987846 DOI: 10.1270/jsbbs.21065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/19/2021] [Indexed: 05/27/2023]
Abstract
Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the 'omes' in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.
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Affiliation(s)
- Nozomu Sakurai
- Bioinformation and DDBJ Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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44
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Albóniga OE, Jiménez D, Sánchez-Conde M, Vizcarra P, Ron R, Herrera S, Martínez-Sanz J, Moreno E, Moreno S, Barbas C, Serrano-Villar S. Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis. J Proteome Res 2022; 21:623-634. [PMID: 35133846 DOI: 10.1021/acs.jproteome.1c00786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ("nonsusceptible"). We found a total of 42 metabolites of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citric acid, and 3-aminoisobutyric acid (BAIBA)), energy production and amino acid catabolism (phenylalanine and histidine), and endothelial dysfunction and thrombosis (citrulline, asymmetric dimethylarginine (ADMA), and 2-aminobutyric acid (2-AB)), and we found interconnections between these pathways. In summary, in this first report several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression were found by CE-MS based metabolomics that could be developed as biomarkers of COVID-19.
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Affiliation(s)
- Oihane E Albóniga
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Daniel Jiménez
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Matilde Sánchez-Conde
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Pilar Vizcarra
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Raquel Ron
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Sabina Herrera
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Javier Martínez-Sanz
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Elena Moreno
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Santiago Moreno
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Sergio Serrano-Villar
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
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45
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Skrutková Langmajerová M, Pelcová M, Vedrová P, Celá A, Glatz Z. Capillary electrophoresis-mass spectrometry as a tool for the noninvasive target metabolomic analysis of underivatized amino acids for evaluating embryo viability in assisted reproduction. Electrophoresis 2021; 43:679-687. [PMID: 34897743 DOI: 10.1002/elps.202100328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/06/2022]
Abstract
Monitoring metabolite uptake and excretion in the culture medium is a noninvasive technique that is used for the metabolic study of cleaving embryos after in vitro fertilization. Low sample consumption, the versatility of the detection, and optimal sensitivity and selectivity are essential elements for extracellular metabolome analyses, and can be conveniently achieved by combining CE with mass spectrometric detection. This paper reports a method for amino acid determination in a limited volume sample (8 μL) of spent culture media collected after the cultivation of in vitro fertilized embryos. Special attention was focused on the sample preparation procedure. The sample was processed with acetonitrile, which facilitates online sample preconcentration via field-amplified sample stacking, and undesired sample evaporation was significantly reduced by the simultaneous addition of dimethyl sulfoxide. Key parameters that affected electrophoretic separation and mass spectrometric detection were investigated, including the type of buffers and organic solvent, optimization of their concentrations, and finally the settings for their ionization. The separation and quantification of 19 amino acids were achieved using 15% acetic acid as the background electrolyte with a sheath liquid consisting of an equimolar mixture of methanol and water. The applicability of the optimized system was demonstrated by determining the amino acid profile in 40 samples of spent cultivation medium in this pilot study. This developed method also has great potential for amino acid analyses in minute sample volumes of other biological matrices.
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Affiliation(s)
| | - Marta Pelcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavla Vedrová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Andrea Celá
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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46
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Ornelas-González A, Ortiz-Martínez M, González-González M, Rito-Palomares M. Enzymatic Methods for Salivary Biomarkers Detection: Overview and Current Challenges. Molecules 2021; 26:7026. [PMID: 34834116 PMCID: PMC8624596 DOI: 10.3390/molecules26227026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 12/12/2022] Open
Abstract
Early detection is a key factor in patient fate. Currently, multiple biomolecules have been recognized as biomarkers. Nevertheless, their identification is only the starting line on the way to their implementation in disease diagnosis. Although blood is the biofluid par excellence for the quantification of biomarkers, its extraction is uncomfortable and painful for many patients. In this sense, there is a gap in which saliva emerges as a non-invasive and valuable source of information, as it contains many of the biomarkers found in blood. Recent technological advances have made it possible to detect and quantify biomarkers in saliva samples. However, there are opportunity areas in terms of cost and complexity, which could be solved using simpler methodologies such as those based on enzymes. Many reviews have focused on presenting the state-of-the-art in identifying biomarkers in saliva samples. However, just a few of them provide critical analysis of technical elements for biomarker quantification in enzymatic methods for large-scale clinical applications. Thus, this review proposes enzymatic assays as a cost-effective alternative to overcome the limitations of current methods for the quantification of biomarkers in saliva, highlighting the technical and operational considerations necessary for sampling, method development, optimization, and validation.
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Affiliation(s)
| | | | - Mirna González-González
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Monterrey 64710, N.L., Mexico; (A.O.-G.); (M.O.-M.)
| | - Marco Rito-Palomares
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Monterrey 64710, N.L., Mexico; (A.O.-G.); (M.O.-M.)
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47
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David A, Chaker J, Price EJ, Bessonneau V, Chetwynd AJ, Vitale CM, Klánová J, Walker DI, Antignac JP, Barouki R, Miller GW. Towards a comprehensive characterisation of the human internal chemical exposome: Challenges and perspectives. ENVIRONMENT INTERNATIONAL 2021; 156:106630. [PMID: 34004450 DOI: 10.1016/j.envint.2021.106630] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/15/2021] [Accepted: 05/03/2021] [Indexed: 05/18/2023]
Abstract
The holistic characterisation of the human internal chemical exposome using high-resolution mass spectrometry (HRMS) would be a step forward to investigate the environmental ætiology of chronic diseases with an unprecedented precision. HRMS-based methods are currently operational to reproducibly profile thousands of endogenous metabolites as well as externally-derived chemicals and their biotransformation products in a large number of biological samples from human cohorts. These approaches provide a solid ground for the discovery of unrecognised biomarkers of exposure and metabolic effects associated with many chronic diseases. Nevertheless, some limitations remain and have to be overcome so that chemical exposomics can provide unbiased detection of chemical exposures affecting disease susceptibility in epidemiological studies. Some of these limitations include (i) the lack of versatility of analytical techniques to capture the wide diversity of chemicals; (ii) the lack of analytical sensitivity that prevents the detection of exogenous (and endogenous) chemicals occurring at (ultra) trace levels from restricted sample amounts, and (iii) the lack of automation of the annotation/identification process. In this article, we discuss a number of technological and methodological limitations hindering applications of HRMS-based methods and propose initial steps to push towards a more comprehensive characterisation of the internal chemical exposome. We also discuss other challenges including the need for harmonisation and the difficulty inherent in assessing the dynamic nature of the internal chemical exposome, as well as the need for establishing a strong international collaboration, high level networking, and sustainable research infrastructure. A great amount of research, technological development and innovative bio-informatics tools are still needed to profile and characterise the "invisible" (not profiled), "hidden" (not detected) and "dark" (not annotated) components of the internal chemical exposome and concerted efforts across numerous research fields are paramount.
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Affiliation(s)
- Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Jade Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Elliott J Price
- Faculty of Sports Studies, Masaryk University, Brno, Czech Republic; RECETOX Centre, Masaryk University, Brno, Czech Republic
| | - Vincent Bessonneau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Andrew J Chetwynd
- School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Jana Klánová
- RECETOX Centre, Masaryk University, Brno, Czech Republic
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Robert Barouki
- Unité UMR-S 1124 Inserm-Université Paris Descartes "Toxicologie Pharmacologie et Signalisation Cellulaire", Paris, France
| | - Gary W Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
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48
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2019-mid 2021). Electrophoresis 2021; 43:82-108. [PMID: 34632606 DOI: 10.1002/elps.202100243] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/19/2022]
Abstract
The review provides a comprehensive overview of developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, microscale isolation, and physicochemical characterization of peptides from 2019 up to approximately the middle of 2021. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis, such as sample preparation, sorption suppression, EOF control, and detection, are presented. New developments in the individual CE and CEC methods are demonstrated and several types of their applications are shown. They include qualitative and quantitative analysis, determination in complex biomatrices, monitoring of chemical and enzymatic reactions and physicochemical changes, amino acid, sequence, and chiral analyses, and peptide mapping of proteins. In addition, micropreparative separations and determination of significant physicochemical parameters of peptides by CE and CEC methods are described.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague 6, Czechia
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49
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Codesido S, Drouin N, Ferré S, Schappler J, Rudaz S, González‐Ruiz V. New insights into the conversion of electropherograms to the effective electrophoretic mobility scale. Electrophoresis 2021; 42:1875-1884. [PMID: 34216494 PMCID: PMC8518790 DOI: 10.1002/elps.202000333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 11/20/2022]
Abstract
CE-MS is increasingly gaining momentum as an analytical tool in metabolomics, due to its ability to obtain information about the most polar elements in biological samples. This has been helped by improvements of robustness in peak identification by means of mobility-scale representations of the electropherograms (mobilograms). As a necessary step toward facilitating the use of CE-MS for untargeted metabolomics data, the authors previously developed and introduced ROMANCE, a software automating mobilogram generation for large untargeted datasets through a simple and self-contained user interface. Herein, we introduce a new version of ROMANCE including new features such as compatibility with other types of data (targeted MS data and 2D UV-Vis absorption-like electropherograms), and the much needed additional flexibility in the transformation parameters (including field ramping and the use of secondary markers), more measurement conditions (depending on detection and integration modes), and most importantly tackling the issue of quantitative peak conversion. First, we present a review of the current theoretical framework with regard to peak characterization, and we develop new formulas for multiple marker peak area corrections, for anticipating peak position precision, and for assessing peak shape distortion. Then, the new version of the software is presented and validated experimentally. We contrast the multiple marker mobility transformations with previous results, finding increased peak position precision, and finally we showcase an application to actual untargeted metabolomics data.
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Affiliation(s)
- Santiago Codesido
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
| | - Nicolas Drouin
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
| | - Sabrina Ferré
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
| | - Julie Schappler
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
| | - Serge Rudaz
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
- Swiss Centre for Applied Human ToxicologyBaselSwitzerland
| | - Víctor González‐Ruiz
- Department of Analytical SciencesInstitute of Pharmaceutical Sciences of Western SwitzerlandUniversity of GenevaGenevaSwitzerland
- School of Pharmaceutical SciencesUniversity of GenevaGenevaSwitzerland
- Swiss Centre for Applied Human ToxicologyBaselSwitzerland
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50
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Wei Y, Ding J, Li J, Cai S, Liu S, Hong L, Yin T, Zhang Y, Diao L. Metabolic Reprogramming of Immune Cells at the Maternal-Fetal Interface and the Development of Techniques for Immunometabolism. Front Immunol 2021; 12:717014. [PMID: 34566973 PMCID: PMC8458575 DOI: 10.3389/fimmu.2021.717014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Immunity and metabolism are interdependent and coordinated, which are the core mechanisms for the body to maintain homeostasis. In tumor immunology research, immunometabolism has been a research hotspot and has achieved groundbreaking changes in recent years. However, in the field of maternal-fetal medicine, research on immunometabolism is still lagging. Reports directly investigating the roles of immunometabolism in the endometrial microenvironment and regulation of maternal-fetal immune tolerance are relatively few. This review highlights the leading techniques used to study immunometabolism and their development, the immune cells at the maternal-fetal interface and their metabolic features required for the implementation of their functions, explores the interaction between immunometabolism and pregnancy regulation based on little evidence and clues, and attempts to propose some new research directions and perspectives.
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Affiliation(s)
- Yiqiu Wei
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinli Ding
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jianan Li
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Songchen Cai
- Shenzhen Key Laboratory for Reproductive Immunology of Peri-Implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Su Liu
- Shenzhen Key Laboratory for Reproductive Immunology of Peri-Implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China.,Shenzhen Jinxin Medical Technology Innovation Center, Co., Ltd., Shenzhen, China
| | - Ling Hong
- Shenzhen Key Laboratory for Reproductive Immunology of Peri-Implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China.,Shenzhen Jinxin Medical Technology Innovation Center, Co., Ltd., Shenzhen, China
| | - Tailang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lianghui Diao
- Shenzhen Key Laboratory for Reproductive Immunology of Peri-Implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China.,Shenzhen Jinxin Medical Technology Innovation Center, Co., Ltd., Shenzhen, China
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