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Hemmer S, Manier SK, Wagmann L, Meyer MR. Impact of four different extraction methods and three different reconstitution solvents on the untargeted metabolomics analysis of human and rat urine samples. J Chromatogr A 2024; 1725:464930. [PMID: 38696889 DOI: 10.1016/j.chroma.2024.464930] [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: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/21/2024] [Indexed: 05/04/2024]
Abstract
Unsuitable sample preparation may result in loss of important analytes and consequently affect the outcome of untargeted metabolomics. Due to species differences, different sample preparations may be required within the same biological matrix. The study aimed to compare the in-house sample preparation method for urine with methods from literature and to investigate the transferability of sample preparation from human urine to rat urine. A total of 12 different conditions for protein precipitation were tested, combining four different extraction solvents and three different reconstitution solvents using an untargeted liquid-chromatography high resolution mass spectrometry (LC-HRMS) metabolomics analysis. Evaluation was done based on the impact on feature count, their detectability, as well as the reproducibility of selected compounds. Results showed that a combination of methanol as extraction and acetonitrile/water (75/25) as reconstitution solvent provided improved results at least regarding the total feature count. Additionally, it was found that a higher amount of methanol was most suitable for extraction of rat urine among the tested conditions. In comparison, human urine requires significantly less volume of extraction solvent. Overall, it is recommended to systematically optimize both, the extraction method, and the reconstitution solvent for the used biofluid and the individual analytical settings.
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Affiliation(s)
- Selina Hemmer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Lea Wagmann
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany.
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2
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Benito S, Unceta N, Maciejczyk M, Sánchez-Ortega A, Taranta-Janusz K, Szulimowska J, Zalewska A, Andrade F, Gómez-Caballero A, Dubiela P, Barrio RJ. Revealing novel biomarkers for diagnosing chronic kidney disease in pediatric patients. Sci Rep 2024; 14:11549. [PMID: 38773318 PMCID: PMC11109104 DOI: 10.1038/s41598-024-62518-w] [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: 01/24/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Pediatric chronic kidney disease (CKD) is a clinical condition characterized by progressive renal function deterioration. CKD diagnosis is based on glomerular filtration rate, but its reliability is limited, especially at the early stages. New potential biomarkers (citrulline (CIT), symmetric dimethylarginine (SDMA), S-adenosylmethionine (SAM), n-butyrylcarnitine (nC4), cis-4-decenoylcarnitine, sphingosine-1-phosphate and bilirubin) in addition to creatinine (CNN) have been proposed for early diagnosis. To verify the clinical value of these biomarkers we performed a comprehensive targeted metabolomics study on a representative cohort of CKD and healthy pediatric patients. Sixty-seven children with CKD and forty-five healthy children have been enrolled in the study. Targeted metabolomics based on liquid chromatography-triple quadrupole mass spectrometry has been used for serum and plasma samples analysis. Univariate data analysis showed statistically significant differences (p < 0.05) in the concentration of CNN, CIT, SDMA, and nC4 among healthy and CKD pediatric patients. The predictive ability of the proposed biomarkers was also confirmed through specificity and sensitivity expressed in Receiver Operating Characteristic curves (AUC = 0.909). In the group of early CKD pediatric patients, AUC of 0.831 was obtained, improving the diagnostic reliability of CNN alone. Moreover, the models built on combined CIT, nC4, SDMA, and CNN allowed to distinguish CKD patients from healthy control regardless of blood matrix type (serum or plasma). Our data demonstrate potential biomarkers in the diagnosis of early CKD stages.
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Affiliation(s)
- Sandra Benito
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, 01006, Vitoria-Gasteiz, Spain
- i+Med, S.Coop Parque Tecnológico de Alava, Albert Einstein 15, 01510, Vitoria-Gasteiz, Álava, Spain
| | - Nora Unceta
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Mateusz Maciejczyk
- Department of Hygiene, Medical University of Bialystok, 15-233, Białystok, Poland
| | - Alicia Sánchez-Ortega
- Central Service of Analysis (Sgiker), University of the Basque Country (UPV/EHU), Laskaray Ikergunea, Miguel de Unamuno 3, 01006, Vitoria-Gasteiz, Spain
| | | | - Julita Szulimowska
- Department of Pedodontics, Medical University of Bialystok, 15-274, Białystok, Poland
| | - Anna Zalewska
- Department of Conservative Dentistry, Medical University of Bialystok, 15-274, Białystok, Poland
| | - Fernando Andrade
- Metabolomics and Proteomics Platform, Biobizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Alberto Gómez-Caballero
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Pawel Dubiela
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, 15-269, Białystok, Poland.
| | - Ramón J Barrio
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, 01006, Vitoria-Gasteiz, Spain
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3
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Ovbude ST, Sharmeen S, Kyei I, Olupathage H, Jones J, Bell RJ, Powers R, Hage DS. Applications of chromatographic methods in metabolomics: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1239:124124. [PMID: 38640794 DOI: 10.1016/j.jchromb.2024.124124] [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: 10/03/2023] [Revised: 03/11/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.
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Affiliation(s)
- Susan T Ovbude
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Harshana Olupathage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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Wang Z, Wu J, Kong W, Zhou Y, Ye C, Yuan Q, Zhang Y, Li P. The Integration of Transcriptome and Metabolome Analyses Provides Insights into the Determinants of the Wood Properties in Toona ciliata. Int J Mol Sci 2024; 25:4541. [PMID: 38674126 PMCID: PMC11050501 DOI: 10.3390/ijms25084541] [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: 02/23/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Toona ciliata, also known as Chinese mahogany, is a high-quality and fast-growing wood species with a high economic value. The wood properties of T. ciliata of different provenances vary significantly. In this study, we conducted comprehensive transcriptome and metabolome analyses of red and non-red T. ciliata wood cores of different provenances to compare their wood properties and explore the differential metabolites and genes that govern the variation in their wood properties. Through combined analyses, three differential genes and two metabolites were identified that are possibly related to lignin synthesis. The lignin content in wood cores from T. ciliata of different provenances shows significant variation following systematic measurement and comparisons. The gene Tci09G002190, one of the three differential genes, was identified as a member of the CAD (Cinnamyl alcohol dehydrogenase) gene family of T. ciliata, which is associated with lignin synthesis. Our data provide insights into the determinants of the wood properties in T. ciliata, providing a solid foundation for research into the subsequent mechanisms of the formation of T. ciliata wood.
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Affiliation(s)
- Zhi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Jinsong Wu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Weijia Kong
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Chunyi Ye
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Qianyun Yuan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yongjia Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (J.W.); (W.K.); (Y.Z.); (C.Y.); (Q.Y.); (Y.Z.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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Zhu P, Dubbelman AC, Hunter C, Genangeli M, Karu N, Harms A, Hankemeier T. Development of an Untargeted LC-MS Metabolomics Method with Postcolumn Infusion for Matrix Effect Monitoring in Plasma and Feces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:590-602. [PMID: 38379502 PMCID: PMC10921459 DOI: 10.1021/jasms.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Untargeted metabolomics based on reverse phase LC-MS (RPLC-MS) plays a crucial role in biomarker discovery across physiological and disease states. Standardizing the development process of untargeted methods requires paying attention to critical factors that are under discussed or easily overlooked, such as injection parameters, performance assessment, and matrix effect evaluation. In this study, we developed an untargeted metabolomics method for plasma and fecal samples with the optimization and evaluation of these factors. Our results showed that optimizing the reconstitution solvent and sample injection amount was critical for achieving the balance between metabolites coverage and signal linearity. Method validation with representative stable isotopically labeled standards (SILs) provided insights into the analytical performance evaluation of our method. To tackle the issue of the matrix effect, we implemented a postcolumn infusion (PCI) approach to monitor the overall absolute matrix effect (AME) and relative matrix effect (RME). The monitoring revealed distinct AME and RME profiles in plasma and feces. Comparing RME data obtained for SILs through postextraction spiking with those monitored using PCI compounds demonstrated the comparability of these two methods for RME assessment. Therefore, we applied the PCI approach to predict the RME of 305 target compounds covered in our in-house library and found that targets detected in the negative polarity were more vulnerable to the RME, regardless of the sample matrix. Given the value of this PCI approach in identifying the strengths and weaknesses of our method in terms of the matrix effect, we recommend implementing a PCI approach during method development and applying it routinely in untargeted metabolomics.
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Affiliation(s)
- Pingping Zhu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Anne-Charlotte Dubbelman
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | | | - Michele Genangeli
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
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6
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Xiong W, Anthony DC, Anthony S, Ho TBT, Louis E, Satsangi J, Radford-Smith DE. Sodium fluoride preserves blood metabolite integrity for biomarker discovery in large-scale, multi-site metabolomics investigations. Analyst 2024; 149:1238-1249. [PMID: 38224241 DOI: 10.1039/d3an01359f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Background: Metabolite profiling of blood by nuclear magnetic resonance (NMR) is invaluable to clinical biomarker discovery. To ensure robustness, biomarkers require validation in large cohorts and across multiple centres. However, collection procedures are known to impact on the stability of biofluids that may, in turn, degrade biomarker signals. We trialled three blood collection tubes with the aim of solving technical challenges due to preanalytical variation in blood metabolite levels that are common in cohort studies. Methods: We first investigated global NMR-based metabolite variability between biobanks, including the large-scale UK Biobank and TwinsUK biobank of the general UK population, and more targeted biobanks derived from multicentre clinical trials relating to inflammatory bowel disease. We then compared the blood metabolome of 12 healthy adult volunteers when collected into either sodium fluoride/potassium oxalate, lithium heparin, or serum blood tubes using different pre-processing parameters. Results: Preanalytical variation in the method of blood collection strongly influences metabolite composition within and between biobanks. This variability can largely be attributed to glucose and lactate. In the healthy control cohort, the fluoride oxalate collection tube prevented fluctuation in glucose and lactate levels for 24 hours at either 4 °C or room temperature (20 °C). Conclusions: Blood collection into a fluoride oxalate collection tube appears to preserve the blood metabolome with delayed processing up to 24 hours at 4 °C. This method may be considered as an alternative when rapid processing is not feasible.
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Affiliation(s)
- Wenzheng Xiong
- Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Daniel C Anthony
- Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Suzie Anthony
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Thi Bao Tien Ho
- Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Edouard Louis
- Department of Gastroenterology, University Hospital CHU of Liège, Liège, Belgium
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK
| | - Daniel E Radford-Smith
- Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK
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7
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Mosley JD, Schock TB, Beecher CW, Dunn WB, Kuligowski J, Lewis MR, Theodoridis G, Ulmer Holland CZ, Vuckovic D, Wilson ID, Zanetti KA. Establishing a framework for best practices for quality assurance and quality control in untargeted metabolomics. Metabolomics 2024; 20:20. [PMID: 38345679 PMCID: PMC10861687 DOI: 10.1007/s11306-023-02080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Quality assurance (QA) and quality control (QC) practices are key tenets that facilitate study and data quality across all applications of untargeted metabolomics. These important practices will strengthen this field and accelerate its success. The Best Practices Working Group (WG) within the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) focuses on community use of QA/QC practices and protocols and aims to identify, catalogue, harmonize, and disseminate current best practices in untargeted metabolomics through community-driven activities. AIM OF REVIEW A present goal of the Best Practices WG is to develop a working strategy, or roadmap, that guides the actions of practitioners and progress in the field. The framework in which mQACC operates promotes the harmonization and dissemination of current best QA/QC practice guidance and encourages widespread adoption of these essential QA/QC activities for liquid chromatography-mass spectrometry. KEY SCIENTIFIC CONCEPTS OF REVIEW Community engagement and QA/QC information gathering activities have been occurring through conference workshops, virtual and in-person interactive forum discussions, and community surveys. Seven principal QC stages prioritized by internal discussions of the Best Practices WG have received participant input, feedback and discussion. We outline these stages, each involving a multitude of activities, as the framework for identifying QA/QC best practices. The ultimate planned product of these endeavors is a "living guidance" document of current QA/QC best practices for untargeted metabolomics that will grow and change with the evolution of the field.
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Affiliation(s)
- Jonathan D Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA.
| | - Tracey B Schock
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | | | - Warwick B Dunn
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe, 46026, Valencia, Spain
| | - Matthew R Lewis
- Life Sciences Mass Spectrometry Division, Bruker UK Limited, Coventry, CV4 8HZ, UK
- National Phenome Centre & Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, W12 0NN, UK
| | - Georgios Theodoridis
- BIOMIC_Auth, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Aristotle University Thessaloniki, 57001, Thermi, Greece
| | - Candice Z Ulmer Holland
- Eastern Laboratory, Office of Public Health Science (OPHS), Food Safety and Inspection Service (FSIS), Department of Agriculture (USDA), Athens, GA, 30605, USA
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Ian D Wilson
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Division of Systems Medicine, Department of Metabolism Department of Metabolism, Digestion and Reproduction, Imperial College, London, W12 0NN, UK
| | - Krista A Zanetti
- Office of Nutrition Research, Office of the Director, Division of Program Coordination, Planning, and Strategic Initiatives, National Institutes of Health, Bethesda, MD, USA
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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Koussiouris J, Looby N, Kotlyar M, Kulasingam V, Jurisica I, Chandran V. Classifying patients with psoriatic arthritis according to their disease activity status using serum metabolites and machine learning. Metabolomics 2024; 20:17. [PMID: 38267619 PMCID: PMC10810020 DOI: 10.1007/s11306-023-02079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Psoriatic arthritis (PsA) is a heterogeneous inflammatory arthritis, affecting approximately a quarter of patients with psoriasis. Accurate assessment of disease activity is difficult. There are currently no clinically validated biomarkers to stratify PsA patients based on their disease activity, which is important for improving clinical management. OBJECTIVES To identify metabolites capable of classifying patients with PsA according to their disease activity. METHODS An in-house solid-phase microextraction (SPME)-liquid chromatography-high resolution mass spectrometry (LC-HRMS) method for lipid analysis was used to analyze serum samples obtained from patients classified as having low (n = 134), moderate (n = 134) or high (n = 104) disease activity, based on psoriatic arthritis disease activity scores (PASDAS). Metabolite data were analyzed using eight machine learning methods to predict disease activity levels. Top performing methods were selected based on area under the curve (AUC) and significance. RESULTS The best model for predicting high disease activity from low disease activity achieved AUC 0.818. The best model for predicting high disease activity from moderate disease activity achieved AUC 0.74. The best model for classifying low disease activity from moderate and high disease activity achieved AUC 0.765. Compounds confirmed by MS/MS validation included metabolites from diverse compound classes such as sphingolipids, phosphatidylcholines and carboxylic acids. CONCLUSION Several lipids and other metabolites when combined in classifying models predict high disease activity from both low and moderate disease activity. Lipids of key interest included lysophosphatidylcholine and sphingomyelin. Quantitative MS assays based on selected reaction monitoring, are required to quantify the candidate biomarkers identified.
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Affiliation(s)
- John Koussiouris
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Krembil Research Institute, University Health Network, Toronto, Canada.
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10
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González-Domínguez Á, Estanyol-Torres N, Brunius C, Landberg R, González-Domínguez R. QC omics: Recommendations and Guidelines for Robust, Easily Implementable and Reportable Quality Control of Metabolomics Data. Anal Chem 2024; 96:1064-1072. [PMID: 38179935 PMCID: PMC10809278 DOI: 10.1021/acs.analchem.3c03660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/03/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
The implementation of quality control strategies is crucial to ensure the reproducibility, accuracy, and meaningfulness of metabolomics data. However, this pivotal step is often overlooked within the metabolomics workflow and frequently relies on the use of nonstandardized and poorly reported protocols. To address current limitations in this respect, we have developed QComics, a robust, easily implementable and reportable method for monitoring and controlling data quality. The protocol operates in various sequential steps aimed to (i) correct for background noise and carryover, (ii) detect signal drifts and "out-of-control" observations, (iii) deal with missing data, (iv) remove outliers, (v) monitor quality markers to identify samples affected by improper collection, preprocessing, or storage, and (vi) assess overall data quality in terms of precision and accuracy. Notably, this tool considers important issues often neglected along quality control, such as the need of separately handling missing values and truly absent data to avoid losing relevant biological information, as well as the large impact that preanalytical factors may elicit on metabolomics results. Altogether, the guidelines compiled in QComics might contribute to establishing gold standard recommendations and best practices for quality control within the metabolomics community.
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Affiliation(s)
- Álvaro González-Domínguez
- Instituto
de Investigación e Innovación Biomédica de Cádiz
(INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz 11009, Spain
| | - Núria Estanyol-Torres
- Division
of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology,SE-412 96Gothenburg ,Sweden
| | - Carl Brunius
- Division
of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology,SE-412 96Gothenburg ,Sweden
| | - Rikard Landberg
- Division
of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology,SE-412 96Gothenburg ,Sweden
| | - Raúl González-Domínguez
- Instituto
de Investigación e Innovación Biomédica de Cádiz
(INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz 11009, Spain
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11
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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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12
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Chen CJ, Lee DY, Yu J, Lin YN, Lin TM. Recent advances in LC-MS-based metabolomics for clinical biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:2349-2378. [PMID: 35645144 DOI: 10.1002/mas.21785] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 06/15/2023]
Abstract
The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
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Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ning Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Min Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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13
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He D, Yan Q, Uppal K, Walker DI, Jones DP, Ritz B, Heck JE. Metabolite Stability in Archived Neonatal Dried Blood Spots Used for Epidemiologic Research. Am J Epidemiol 2023; 192:1720-1730. [PMID: 37218607 PMCID: PMC11004922 DOI: 10.1093/aje/kwad122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 09/01/2022] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
Epidemiologic studies of low-frequency exposures or outcomes using metabolomics analyses of neonatal dried blood spots (DBS) often require assembly of samples with substantial differences in duration of storage. Independent assessment of stability of metabolites in archived DBS will enable improved design and interpretation of epidemiologic research utilizing DBS. Neonatal DBS routinely collected and stored as part of the California Genetic Disease Screening Program between 1983 and 2011 were used. The study population included 899 children without cancer before age 6 years, born in California. High-resolution metabolomics with liquid-chromatography mass spectrometry was performed, and the relative ion intensities of common metabolites and selected xenobiotic metabolites of nicotine (cotinine and hydroxycotinine) were evaluated. In total, we detected 26,235 mass spectral features across 2 separate chromatography methods (C18 hydrophobic reversed-phase chromatography and hydrophilic-interaction liquid chromatography). For most of the 39 metabolites related to nutrition and health status, we found no statistically significant annual trends across the years of storage. Nicotine metabolites were captured in the DBS with relatively stable intensities. This study supports the usefulness of DBS stored long-term for epidemiologic studies of the metabolome. -Omics-based information gained from DBS may also provide a valuable tool for assessing prenatal environmental exposures in child health research.
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Affiliation(s)
| | | | | | | | | | | | - Julia E Heck
- Correspondence to Dr. Julia E. Heck, College of Health and Public Service, UNT 1155 Union Circle #311340, Denton, TX 76203-5017 (e-mail: )
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14
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Bertić M, Zimmer I, Andrés-Montaner D, Rosenkranz M, Kangasjärvi J, Schnitzler JP, Ghirardo A. Automatization of metabolite extraction for high-throughput metabolomics: case study on transgenic isoprene-emitting birch. TREE PHYSIOLOGY 2023; 43:1855-1869. [PMID: 37418159 DOI: 10.1093/treephys/tpad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Metabolomics studies are becoming increasingly common for understanding how plant metabolism responds to changes in environmental conditions, genetic manipulations and treatments. Despite the recent advances in metabolomics workflow, the sample preparation process still limits the high-throughput analysis in large-scale studies. Here, we present a highly flexible robotic system that integrates liquid handling, sonication, centrifugation, solvent evaporation and sample transfer processed in 96-well plates to automatize the metabolite extraction from leaf samples. We transferred an established manual extraction protocol performed to a robotic system, and with this, we show the optimization steps required to improve reproducibility and obtain comparable results in terms of extraction efficiency and accuracy. We then tested the robotic system to analyze the metabolomes of wild-type and four transgenic silver birch (Betula pendula Roth) lines under unstressed conditions. Birch trees were engineered to overexpress the poplar (Populus × canescens) isoprene synthase and to emit various amounts of isoprene. By fitting the different isoprene emission capacities of the transgenic trees with their leaf metabolomes, we observed an isoprene-dependent upregulation of some flavonoids and other secondary metabolites as well as carbohydrates, amino acid and lipid metabolites. By contrast, the disaccharide sucrose was found to be strongly negatively correlated to isoprene emission. The presented study illustrates the power of integrating robotics to increase the sample throughput, reduce human errors and labor time, and to ensure a fully controlled, monitored and standardized sample preparation procedure. Due to its modular and flexible structure, the robotic system can be easily adapted to other extraction protocols for the analysis of various tissues or plant species to achieve high-throughput metabolomics in plant research.
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Affiliation(s)
- Marko Bertić
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Ina Zimmer
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - David Andrés-Montaner
- Atmospheric Environmental Research, Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology, Kreuzeckbahnstr. 19, Garmisch-Partenkirchen 82467, Germany
- Corteva Agriscience Spain S.L.U, Carreño, Spain
| | - Maaria Rosenkranz
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
- Institute of Plant Sciences, Ecology and Conservation Biology, University of Regensburg, Regensburg 93053, Germany
| | - Jaakko Kangasjärvi
- Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O Box 65, FI-00014, Finland
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
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15
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Tang HS, Gates CR, Schultz MC. Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus. PLoS One 2023; 18:e0290892. [PMID: 37651389 PMCID: PMC10470895 DOI: 10.1371/journal.pone.0290892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
Some metabolic enzymes normally occur in the nucleus and cytoplasm. These compartments differ in molecular composition. Since post-translational modification and interaction with allosteric effectors can tune enzyme activity, it follows that the behavior of an enzyme as a catalyst may differ between the cytoplasm and nucleus. We explored this possibility for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Homogenates of pristine nuclei and cytoplasms isolated from Xenopus laevis oocytes were used for whole compartment activity profiling in a near-physiological buffer. Titrations of NAD+ revealed similar whole compartment activity profiles for GAPDH in nuclear and cytoplasmic homogenates. Surprisingly however GAPDH in these compartments did not have the same behavior in assays of the dependence of initial velocity (v0) on G3P concentration. First, the peak v0 for nuclear GAPDH was up to 2.5-fold higher than the peak for cytoplasmic GAPDH. Second, while Michaelis Menten-like behavior was observed in all assays of cytoplasm, the v0 versus [G3P] plots for nuclear GAPDH typically exhibited a non-Michaelis Menten (sigmoidal) profile. Apparent Km and Vmax (G3P) values for nuclear GAPDH activity were highly variable, even between replicates of the same sample. Possible sources of this variability include in vitro processing of a metabolite that allosterically regulates GAPDH, turnover of a post-translational modification of the enzyme, and fluctuation of the state of interaction of GAPDH with other proteins. Collectively these findings are consistent with the hypothesis that the environment of the nucleus is distinct from the environment of the cytoplasm with regard to GAPDH activity and its modulation. This finding warrants further comparison of the regulation of nuclear and cytoplasmic GAPDH, as well as whole compartment activity profiling of other enzymes of metabolism with cytosolic and nuclear pools.
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Affiliation(s)
- Helen S. Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chelsea R. Gates
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael C. Schultz
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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16
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Koussiouris J, Looby N, Kulasingam V, Chandran V. A Solid-Phase Microextraction-Liquid Chromatography-Mass Spectrometry Method for Analyzing Serum Lipids in Psoriatic Disease. Metabolites 2023; 13:963. [PMID: 37623906 PMCID: PMC10456752 DOI: 10.3390/metabo13080963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Approximately 25% of psoriasis patients have an inflammatory arthritis termed psoriatic arthritis (PsA). There is strong interest in identifying and validating biomarkers that can accurately and reliably predict conversion from psoriasis to PsA using novel technologies such as metabolomics. Lipids, in particular, are of key interest in psoriatic disease. We sought to develop a liquid chromatography-mass spectrometry (LC-MS) method to be used in conjunction with solid-phase microextraction (SPME) for analyzing fatty acids and similar molecules. A total of 25 chromatographic methods based on published lipid studies were tested on two LC columns. As a proof of concept, serum samples from psoriatic disease patients (n = 27 psoriasis and n = 26 PsA) were processed using SPME and run on the selected LC-MS method. The method that was best for analyzing fatty acids and fatty acid-like molecules was optimized and applied to serum samples. A total of 18 tentatively annotated features classified as fatty acids and other lipid compounds were statistically significant between psoriasis and PsA groups using both multivariate and univariate approaches. The SPME-LC-MS method developed and optimized was capable of detecting fatty acids and similar lipids that may aid in differentiating psoriasis and PsA patients.
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Affiliation(s)
- John Koussiouris
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Nikita Looby
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Vinod Chandran
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
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17
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Selegato DM, Zanatta AC, Pilon AC, Veloso JH, Castro-Gamboa I. Application of feature-based molecular networking and MassQL for the MS/MS fragmentation study of depsipeptides. Front Mol Biosci 2023; 10:1238475. [PMID: 37593127 PMCID: PMC10427501 DOI: 10.3389/fmolb.2023.1238475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023] Open
Abstract
The Feature-based Molecular Networking (FBMN) is a well-known approach for mapping and identifying structures and analogues. However, in the absence of prior knowledge about the molecular class, assessing specific fragments and clusters requires time-consuming manual validation. This study demonstrates that combining FBMN and Mass Spec Query Language (MassQL) is an effective strategy for accelerating the decoding mass fragmentation pathways and identifying molecules with comparable fragmentation patterns, such as beauvericin and its analogues. To accomplish this objective, a spectral similarity network was built from ESI-MS/MS experiments of Fusarium oxysporum at various collision energies (CIDs) and paired with a MassQL search query for conserved beauvericin ions. FBMN analysis revealed that sodiated and protonated ions clustered differently, with sodiated adducts needing more collision energy and exhibiting a distinct fragmentation pattern. Based on this distinction, two sets of particular fragments were discovered for the identification of these hexadepsipeptides: ([M + H]+) m/z 134, 244, 262, and 362 and ([M + Na]+) m/z 266, 284 and 384. By using these fragments, MassQL accurately found other analogues of the same molecular class and annotated beauvericins that were not classified by FBMN alone. Furthermore, FBMN analysis of sodiated beauvericins at 70 eV revealed subclasses with distinct amino acid residues, allowing distinction between beauvericins (beauvericin and beauvericin D) and two previously unknown structural isomers with an unusual methionine sulfoxide residue. In summary, our integrated method revealed correlations between adduct types and fragmentation patterns, facilitated the detection of beauvericin clusters, including known and novel analogues, and allowed for the differentiation between structural isomers.
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Affiliation(s)
- Denise M. Selegato
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Ana C. Zanatta
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas, São Paulo University (USP), São Paulo, Brazil
| | - Alan C. Pilon
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Juvenal H. Veloso
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Ian Castro-Gamboa
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
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18
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Yin J, Guo W, Li X, Ding H, Han L, Yang X, Zhu L, Li F, Bie S, Song X, Yu H, Li Z. Extensive evaluation of plasma metabolic sample preparation process based on liquid chromatography-mass spectrometry and its application in the in vivo metabolism of Shuang-Huang-Lian powder injection. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123808. [PMID: 37453388 DOI: 10.1016/j.jchromb.2023.123808] [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: 03/11/2023] [Revised: 06/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Shuang-Huang-Lian powder injection (SHLPI) is a natural drug injection made of honeysuckle, scutellaria baicalensis and forsythia suspensa. It has the characteristics of complex chemical composition and difficult metabolism research in vivo. LC-MS platform has been proven to be an important analytical technology in plasma metabolomics. Unfortunately, the lack of an effective sample preparation strategy before analysis often significantly impacts experimental results. In this work, twenty-one extraction protocols including eight protein precipitation (PPT), eight liquid-liquid extractions (LLE), four solid-phase extractions (SPE), and one ultrafiltration (U) were simultaneously evaluated using plasma metabolism of SHLPI in vivo. In addition, a strategy of "feature ion extraction of the multi-component metabolic platform of traditional Chinese medicine" (FMM strategy) was proposed for the in-depth characterization of metabolites after intravenous injection of SHLPI in rats. The results showed that the LLE-3 protocol (Pentanol:Tetrahydrofuran:H2O, 1:4:35, v:v:v) was the most effective strategy in the in vivo metabolic detection of SHLPI. Furthermore, we used the FMM strategy to elaborate the in vivo metabolic pathways of six representative substances in SHLPI components. This research was completed by ion migration quadrupole time of flight mass spectrometer combined with ultra high performance liquid chromatography (UPLC/Vion™-IMS-QTof-MS) and UNIFI™ metabolic platform. The results showed that 114 metabolites were identified or preliminarily identified in rat plasma. This work provides relevant data and information for further research on the pharmacodynamic substances and in vivo mechanisms of SHLPI. Meanwhile, it also proves that LLE-3 and FMM strategies could achieve the in-depth characterization of complex natural drug metabolites related to Shuang-Huang-Lian in vivo.
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Affiliation(s)
- Jiaxin Yin
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Wen Guo
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Xuejuan Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Hui Ding
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China
| | - Lifeng Han
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Xiangdong Yang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Limin Zhu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Fangyi Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Songtao Bie
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Xinbo Song
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China
| | - Heshui Yu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, West Tuanbo New Town, Jinghai District, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China.
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19
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Yang C, Pan Y, Yu H, Hu X, Li X, Deng C. Hollow Crystallization COF Capsuled MOF Hybrids Depict Serum Metabolic Profiling for Precise Early Diagnosis and Risk Stratification of Acute Coronary Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302109. [PMID: 37340584 PMCID: PMC10460873 DOI: 10.1002/advs.202302109] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 06/22/2023]
Abstract
Acute coronary syndrome (ACS), comprising unstable angina (UA) and acute myocardial infarction (AMI), is the leading cause of death worldwide. Currently, lacking effective strategies for classifying ACS hinders the prognosis improvement of ACS patients. Disclosing the nature of metabolic disorders holds the potential to reflect disease progress and high-throughput mass spectrometry-based metabolic analysis is a promising tool for large-scale screening. Herein, a hollow crystallization COF capsuled MOF hybrids (UiO-66@HCOF) assisted serum metabolic analysis is developed for the early diagnosis and risk stratification of ACS. UiO-66@HCOF exhibits unrivaled chemical and structural stability as well as endowing satisfying desorption/ionization efficiency in the detection of metabolites. Paired with machine learning algorithms, early diagnosis of ACS is achieved with the area under the curve (AUC) value of 0.945 for validation sets. Besides, a comprehensive ACS risk stratification method is established, and the AUC value for the discrimination of ACS from healthy controls, and AMI from UA are 0.890, and 0.928. Moreover, the AUC value of the subtyping of AMI is 0.964. Finally, the potential biomarkers exhibit high sensitivity and specificity. This study makes metabolic molecular diagnosis a reality and provided new insight into the progress of ACS.
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Affiliation(s)
- Chenjie Yang
- Department of ChemistryFudan UniversityShanghai200433China
| | - Yilong Pan
- Department of CardiologyShengjing Hospital of China Medical UniversityNO.36 Sanhao Street, Heping DistrictShenyang110004China
| | - Hailong Yu
- Department of ChemistryFudan UniversityShanghai200433China
| | - Xufang Hu
- School of Chemical Science and TechnologyYunnan UniversityNo. 2 North Cuihu RoadKunming650091P. R. China
| | - Xiaodong Li
- Department of CardiologyShengjing Hospital of China Medical UniversityNO.36 Sanhao Street, Heping DistrictShenyang110004China
| | - Chunhui Deng
- Department of ChemistryFudan UniversityShanghai200433China
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20
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Yuan X, Wang H, Song S, Qiu L, Lan X, Dong P, Zhang J. Stepwise Targeted Matching Strategy for Comprehensive Profiling of Xanthohumol Metabolites In Vivo and In Vitro Using UHPLC-Q-Exactive Orbitrap Mass Spectrometer. Molecules 2023; 28:5168. [PMID: 37446828 DOI: 10.3390/molecules28135168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Xanthohumol (XN), a natural prenylated flavonoid extracted and isolated from the hop plant (Humulus lupulus), possesses diverse pharmacological activities. Although the metabolites of XN have been investigated in the previous study, a comprehensive metabolic profile has been insufficient in vivo or in vitro until now. The current study was aimed at systematically elucidating the metabolic pathways of XN after oral administration to rats. Herein, a UHPLC-Q-Exactive Orbitrap MS was adopted for the potential metabolites detection. A stepwise targeted matching strategy for the overall identification of XN metabolites was proposed. A metabolic net (53 metabolites included) on XN in vivo and in vitro, as well as the metabolic profile investigation, were designed, preferably characterizing XN metabolites in rat plasma, urine, liver, liver microsomes, and feces. On the basis of a stepwise targeted matching strategy, the net showed that major in vivo metabolic pathways of XN in rats include glucuronidation, sulfation, methylation, demethylation, hydrogenation, dehydrogenation, hydroxylation, and so on. The proposed metabolic pathways in this research will provide essential data for further pharmaceutical studies of prenylated flavonoids and lay the foundation for further toxicity and safety studies.
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Affiliation(s)
- Xiaoqing Yuan
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Hong Wang
- College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Shuyi Song
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Lili Qiu
- Department of Medicine, Binzhou Polytechnic College, Binzhou 256600, China
| | - Xianming Lan
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Pingping Dong
- State Key Laboratory for Quality Research of Chinese Medicines, College of Pharmacy, Macau University of Science and Technology, Macao 999078, China
| | - Jiayu Zhang
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
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21
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Chowdhury CR, Kavitake D, Jaiswal KK, Jaiswal KS, Reddy GB, Agarwal V, Shetty PH. NMR-based metabolomics as a significant tool for human nutritional research and health applications. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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22
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Liu Y, Wu Z, Armstrong DW, Wolosker H, Zheng Y. Detection and analysis of chiral molecules as disease biomarkers. Nat Rev Chem 2023; 7:355-373. [PMID: 37117811 PMCID: PMC10175202 DOI: 10.1038/s41570-023-00476-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 04/30/2023]
Abstract
The chirality of small metabolic molecules is important in controlling physiological processes and indicating the health status of humans. Abnormal enantiomeric ratios of chiral molecules in biofluids and tissues occur in many diseases, including cancers and kidney and brain diseases. Thus, chiral small molecules are promising biomarkers for disease diagnosis, prognosis, adverse drug-effect monitoring, pharmacodynamic studies and personalized medicine. However, it remains difficult to achieve cost-effective and reliable analysis of small chiral molecules in clinical procedures, in part owing to their large variety and low concentration. In this Review, we describe current and emerging techniques that detect and quantify small-molecule enantiomers and their biological importance.
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Affiliation(s)
- Yaoran Liu
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Zilong Wu
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA.
| | - Daniel W Armstrong
- Department of Chemistry & Biochemistry, University of Texas at Arlington, Arlington, TX, USA.
| | - Herman Wolosker
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Yuebing Zheng
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA.
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
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23
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Guo H, Zhu Q, Gao H, Lyu Q, Chai W, Wu L, Li B. Metabolomics analysis of follicular fluid in ovarian endometriosis women receiving progestin-primed ovary stimulation protocol for in vitro fertilization. Sci Rep 2023; 13:5747. [PMID: 37029234 PMCID: PMC10082198 DOI: 10.1038/s41598-023-32797-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/03/2023] [Indexed: 04/09/2023] Open
Abstract
This study aimed to investigate the metabolite profile and inflammatory state of follicular fluid (FF) in women with stage III-IV ovarian endometriosis (OE) who underwent in vitro fertilization (IVF). A cohort of 20 consecutive patients with OE were recruited and received progestin-primed ovary stimulation (PPOS) protocol (study group), while another 20 OE patients received one-month ultra-long term protocol (control group) for IVF in this prospective, nonrandomized study. FF samples were obtained from dominant follicles during oocyte retrieval, and liquid chromatography-mass spectrometry (LC-MS) was used to investigate the metabolites profile of FF. Results showed that significant increases in the levels of proline, arginine, threonine, and glycine in patients who received PPOS protocol compared to the control group (P < 0.05). A panel of three metabolites (proline, arginine, and threonine) was identified as specific biomarkers of OE patients using PPOS protocol. Additionally, levels of interleukin-1β, regulated on activation, normal T cell expressed and secreted, and tumor necrosis factor-α markedly decreased in women who received PPOS protocol compared to the control group (P < 0.05). In conclusion, PPOS protocol regulates the metabolism of several amino acids in the FF, which may play critical roles in the oocyte development and blastocyst formation, and their specific mechanism should be further elucidated.
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Affiliation(s)
- Haiyan Guo
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Qianqian Zhu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Hongyuan Gao
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Qifeng Lyu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Weiran Chai
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Ling Wu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China
| | - Bin Li
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, 200011, China.
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24
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Rischke S, Hahnefeld L, Burla B, Behrens F, Gurke R, Garrett TJ. Small molecule biomarker discovery: Proposed workflow for LC-MS-based clinical research projects. J Mass Spectrom Adv Clin Lab 2023; 28:47-55. [PMID: 36872952 PMCID: PMC9982001 DOI: 10.1016/j.jmsacl.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry focusing on small endogenous molecules has become an integral part of biomarker discovery in the pursuit of an in-depth understanding of the pathophysiology of various diseases, ultimately enabling the application of personalized medicine. While LC-MS methods allow researchers to gather vast amounts of data from hundreds or thousands of samples, the successful execution of a study as part of clinical research also requires knowledge transfer with clinicians, involvement of data scientists, and interactions with various stakeholders. The initial planning phase of a clinical research project involves specifying the scope and design, and engaging relevant experts from different fields. Enrolling subjects and designing trials rely largely on the overall objective of the study and epidemiological considerations, while proper pre-analytical sample handling has immediate implications on the quality of analytical data. Subsequent LC-MS measurements may be conducted in a targeted, semi-targeted, or non-targeted manner, resulting in datasets of varying size and accuracy. Data processing further enhances the quality of data and is a prerequisite for in-silico analysis. Nowadays, the evaluation of such complex datasets relies on a mix of classical statistics and machine learning applications, in combination with other tools, such as pathway analysis and gene set enrichment. Finally, results must be validated before biomarkers can be used as prognostic or diagnostic decision-making tools. Throughout the study, quality control measures should be employed to enhance the reliability of data and increase confidence in the results. The aim of this graphical review is to provide an overview of the steps to be taken when conducting an LC-MS-based clinical research project to search for small molecule biomarkers.
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Key Words
- (U)HPLC (Ultra-), High pressure liquid chromatography
- Biomarker Discovery Study
- HILIC, Hydrophilic interaction liquid chromatography
- HRMS, High resolution mass spectrometry
- LC-MS, Liquid chromatography – mass spectrometry
- LC-MS-Based Clinical Research
- Lipidomics
- MRM, Multiple reaction monitoring
- Metabolomics
- PCA, Principal component analysis
- QA, Quality assurance
- QC, Quality control
- RF, Random Forest
- RP, Reversed phase
- SVA, Support vector machine
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Affiliation(s)
- S Rischke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - L Hahnefeld
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - B Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - F Behrens
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.,Division of Rheumatology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - R Gurke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - T J Garrett
- Department of Pathology, Immunology and Laboratory Medicine and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32611, USA
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25
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Fabrile MP, Ghidini S, Conter M, Varrà MO, Ianieri A, Zanardi E. Filling gaps in animal welfare assessment through metabolomics. Front Vet Sci 2023; 10:1129741. [PMID: 36925610 PMCID: PMC10011658 DOI: 10.3389/fvets.2023.1129741] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Sustainability has become a central issue in Italian livestock systems driving food business operators to adopt high standards of production concerning animal husbandry conditions. Meat sector is largely involved in this ecological transition with the introduction of new label claims concerning the defense of animal welfare (AW). These new guarantees referred to AW provision require new tools for the purpose of authenticity and traceability to assure meat supply chain integrity. Over the years, European Union (EU) Regulations, national, and international initiatives proposed provisions and guidelines for assuring AW introducing requirements to be complied with and providing tools based on scoring systems for a proper animal status assessment. However, the comprehensive and objective assessment of the AW status remains challenging. In this regard, phenotypic insights at molecular level may be investigated by metabolomics, one of the most recent high-throughput omics techniques. Recent advances in analytical and bioinformatic technologies have led to the identification of relevant biomarkers involved in complex clinical phenotypes of diverse biological systems suggesting that metabolomics is a key tool for biomarker discovery. In the present review, the Five Domains model has been employed as a vademecum describing AW. Starting from the individual Domains-nutrition (I), environment (II), health (III), behavior (IV), and mental state (V)-applications and advances of metabolomics related to AW setting aimed at investigating phenotypic outcomes on molecular scale and elucidating the biological routes most perturbed from external solicitations, are reviewed. Strengths and weaknesses of the current state-of-art are highlighted, and new frontiers to be explored for AW assessment throughout the metabolomics approach are argued. Moreover, a detailed description of metabolomics workflow is provided to understand dos and don'ts at experimental level to pursue effective results. Combining the demand for new assessment tools and meat market trends, a new cross-strategy is proposed as the promising combo for the future of AW assessment.
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Affiliation(s)
| | - Sergio Ghidini
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Mauro Conter
- Department of Veterinary Science, University of Parma, Parma, Italy
| | | | - Adriana Ianieri
- Department of Food and Drug, University of Parma, Parma, Italy
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26
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Quantitative challenges and their bioinformatic solutions in mass spectrometry-based metabolomics. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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27
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Optimized Fast Filtration-Based Sampling and Extraction Enables Precise and Absolute Quantification of the Escherichia coli Central Carbon Metabolome. Metabolites 2023; 13:metabo13020150. [PMID: 36837769 PMCID: PMC9965072 DOI: 10.3390/metabo13020150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/07/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have also been proven highly dependent on species-specific properties. For Escherichia coli, unspecific leakage has been demonstrated for conventional microbial metabolomics sampling protocols. We herein present a fast filtration-based sampling protocol for this widely applied model organism, focusing on pitfalls such as inefficient filtration, selective loss of biomass, matrix contamination, and membrane permeabilization and leakage. We evaluate the effect of and need for removal of extracellular components and demonstrate how residual salts can challenge analytical accuracy of hyphenated mass spectrometric analyses, even when sophisticated correction strategies are applied. Laborious extraction procedures are bypassed by direct extraction in cold acetonitrile:water:methanol (3:5:2, v/v%), ensuring compatibility with sample concentration and thus, any downstream analysis. By applying this protocol, we achieve and demonstrate high precision and low metabolite turnover, and, followingly, minimal perturbation of the inherent metabolic state. This allows us to herein report absolute intracellular concentrations in E. coli and explore its central carbon metabolome at several commonly applied cultivation conditions.
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28
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Chandran M, S S, Abhirami, Chandran A, Jaleel A, Plakkal Ayyappan J. Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches. Mol Omics 2023; 19:6-26. [PMID: 36426765 DOI: 10.1039/d2mo00260d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Atherosclerosis is the principal cause of vascular diseases and one of the leading causes of worldwide death. Even though several insights into its natural course, risk factors and interventions have been identified, it is still an ongoing global pandemic. Since the structure and biochemical composition of the plaques show high heterogeneity, a comprehensive understanding of the intraplaque composition, its microenvironment, and the mechanisms of the progression and instability across different vascular beds at their progression stages is crucial for better risk stratification and treatment modalities. Even though several cell-based studies, animal studies, and extensive multicentric population studies have been conducted concerning cardiovascular diseases for assessing the risk factors and plaque biology, the studies on human clinical samples are very limited. New novel approaches utilize samples from percutaneous coronary interventions, which could possibly gain more access to clinical samples at different stages of the diseases without complex invasive resections. As an emerging technological platform in disease discovery research, mass spectrometry-based omics technologies offer capabilities for a comprehensive understanding of the mechanisms linked to several vascular diseases. Here, we discuss the cellular and molecular processes of atherosclerosis, different mass spectrometry-based omics approaches, and the studies mostly done on clinical samples of atheroma plaque using mass spectrometry-based proteomics, metabolomics and lipidomics approaches.
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Affiliation(s)
- Mahesh Chandran
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Sudhina S
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Abhirami
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Akash Chandran
- Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India
| | - Abdul Jaleel
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Janeesh Plakkal Ayyappan
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India.,Centre for Advanced Cancer Research, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India
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29
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Gao Z, Zhou W, Lv X, Wang X. Metabolomics as a Critical Tool for Studying Clinical Surgery. Crit Rev Anal Chem 2023:1-14. [PMID: 36592066 DOI: 10.1080/10408347.2022.2162810] [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: 01/03/2023]
Abstract
Metabolomics enables the analysis of metabolites within an organism, which offers the closest direct measurement of the physiological activity of the organism, and has advanced efforts to characterize metabolic states, identify biomarkers, and investigate metabolic pathways. A high degree of innovation in analytical techniques has promoted the application of metabolomics, especially in the study of clinical surgery. Metabolomics can be employed as a clinical testing method to maximize therapeutic outcomes, and has been applied in rapid diagnosis of diseases, timely postoperative monitoring, prognostic assessment, and personalized medicine. This review focuses on the use of mass spectrometry and nuclear magnetic resonance-based metabolomics in clinical surgery, including identifying metabolic changes before and after surgery, finding disease-associated biomarkers, and exploring the potential of personalized therapy. Challenges and opportunities of metabolomics in organ transplantation are also discussed, with a particular emphasis on metabolomics in donor organ evaluation and protection, prognostic outcome prediction, as well as postoperative adverse reaction monitoring. In the end, current limitations of metabolomics in clinical surgery and future research directions are presented.
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Affiliation(s)
- Zhenye Gao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenxiu Zhou
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xiaoyuan Lv
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xin Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
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30
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Boness HVM, de Sá HC, Dos Santos EKP, Canuto GAB. Sample Preparation in Microbial Metabolomics: Advances and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:149-183. [PMID: 37843809 DOI: 10.1007/978-3-031-41741-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.
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Affiliation(s)
- Heiter V M Boness
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Hanna C de Sá
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Emile K P Dos Santos
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.
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31
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Wishart DS, Rout M, Lee BL, Berjanskii M, LeVatte M, Lipfert M. Practical Aspects of NMR-Based Metabolomics. Handb Exp Pharmacol 2023; 277:1-41. [PMID: 36271165 DOI: 10.1007/164_2022_613] [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
While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada.
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Matthias Lipfert
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Reference Standard Management & NMR QC, Lonza Group AG, Visp, Switzerland
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32
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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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33
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Tan Y, Liu X, Yang Y, Li B, Yu F, Zhao W, Fu C, Yu X, Han Z, Cheng M. Metabolomics analysis reveals serum biomarkers in patients with diabetic sarcopenia. Front Endocrinol (Lausanne) 2023; 14:1119782. [PMID: 37033246 PMCID: PMC10073735 DOI: 10.3389/fendo.2023.1119782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
INTRODUCTION Diabetic sarcopenia (DS) is characterized by muscle atrophy, slower nerve conduction, reduced maximum tension generated by skeletal muscle contraction, and slower contraction rate. Hence, DS can cause limb movement degeneration, slow movement, reduced balance, reduced metabolic rate, falls, fractures, etc. Moreover, the relevant early biological metabolites and their pathophysiological mechanism have yet to be characterized. METHOD The current cross-sectional study employed serum metabolomics analysis to screen potential noninvasive biomarkers in patients with diabetic sarcopenia. A total of 280 diabetic patients were enrolled in the study (n = 39 sarcopenia [DS], n = 241 without sarcopenia [DM]). Ten patients were randomly selected from both groups. Non-targeted metabolomic analysis was performed by ultra-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. RESULTS A total of 632 differential metabolites were identified, including 82 that were significantly differentially abundant (P < 0.05, VIP > 1, FC > 1.2 or FC < 0.8). Compared with the DM group, the contents of pentadecanoic acid, 5'-methylthioadenosine (5'-MTA), N,N-dimethylarginine (asymmetric dimethylarginine, ADMA), and glutamine in the DS group were significantly increased, while that of isoxanthohumol was decreased. DISCUSSION Based on receiver operating characteristic curve analysis, pentadecanoic acid, 5'-MTA, ADMA, and glutamine may serve as potential biomarkers of DS. Moreover, ATP-binding cassette (ABC) transporters and the mammalian target of the rapamycin signaling pathway were found to potentially have important regulatory roles in the occurrence and development of DS (P < 0.05). Collectively, the differential metabolites identified in this study provide new insights into the underlying pathophysiology of DS and serve as a basis for therapeutic interventions.
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Affiliation(s)
- Yuwei Tan
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Xiaosong Liu
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Yinping Yang
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Baoying Li
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Aixinzhuoer Medical Laboratory, Jinan, China
| | - Fei Yu
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Wenqian Zhao
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Chunli Fu
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Xin Yu
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Zhenxia Han
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
| | - Mei Cheng
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine (202132001), Jinan, China
- *Correspondence: Mei Cheng,
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He Y, Miggiels P, Drouin N, Lindenburg PW, Wouters B, Hankemeier T. An automated online three-phase electro-extraction setup with machine-vision process monitoring hyphenated to LC-MS analysis. Anal Chim Acta 2022; 1235:340521. [DOI: 10.1016/j.aca.2022.340521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
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35
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Kelly PE, Ng HJ, Farrell G, McKirdy S, Russell RK, Hansen R, Rattray Z, Gerasimidis K, Rattray NJW. An Optimised Monophasic Faecal Extraction Method for LC-MS Analysis and Its Application in Gastrointestinal Disease. Metabolites 2022; 12:1110. [PMID: 36422250 PMCID: PMC9698041 DOI: 10.3390/metabo12111110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 12/28/2023] Open
Abstract
Liquid chromatography coupled with mass spectrometry (LC-MS) metabolomic approaches are widely used to investigate underlying pathogenesis of gastrointestinal disease and mechanism of action of treatments. However, there is an unmet requirement to assess faecal metabolite extraction methods for large-scale metabolomics studies. Current methods often rely on biphasic extractions using harmful halogenated solvents, making automation and large-scale studies challenging. The present study reports an optimised monophasic faecal extraction protocol that is suitable for untargeted and targeted LC-MS analyses. The impact of several experimental parameters, including sample weight, extraction solvent, cellular disruption method, and sample-to-solvent ratio, were investigated. It is suggested that a 50 mg freeze-dried faecal sample should be used in a methanol extraction (1:20) using bead beating as the means of cell disruption. This is revealed by a significant increase in number of metabolites detected, improved signal intensity, and wide metabolic coverage given by each of the above extraction parameters. Finally, we addressed the applicability of the method on faecal samples from patients with Crohn's disease (CD) and coeliac disease (CoD), two distinct chronic gastrointestinal diseases involving metabolic perturbations. Untargeted and targeted metabolomic analysis demonstrated the ability of the developed method to detect and stratify metabolites extracted from patient groups and healthy controls (HC), highlighting characteristic changes in the faecal metabolome according to disease. The method developed is, therefore, suitable for the analysis of patients with gastrointestinal disease and can be used to detect and distinguish differences in the metabolomes of CD, CoD, and HC.
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Affiliation(s)
- Patricia E. Kelly
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
| | - H Jene Ng
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Gillian Farrell
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
| | - Shona McKirdy
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Richard K. Russell
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- Royal Hospital for Children and Young People, 50 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard Hansen
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- Royal Hospital for Children, 1345 Govan Road, Glasgow G52 4TF, UK
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
| | - Konstantinos Gerasimidis
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Nicholas J. W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
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36
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Current analytical methods to monitor type 2 diabetes medication in biological samples. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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38
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Rincón Remolina MC, Peleato NM. Augmentation of field fluorescence measures for improved in situ contaminant detection. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:34. [PMID: 36287271 DOI: 10.1007/s10661-022-10652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
This research proposes a new method that fuses data from the field and lab-based optical measures coupled with machine learning algorithms to quantify the concentrations of toxic contaminants found in fuels and oil sands process-affected water. Selected pairs of excitation/emission intensities at key wavelengths are inputs to an augmentation neural network (NN), trained using lab-based measurements, that generates synthetic high-resolution spectra. Then, an image processing NN is used to estimate the contaminant concentrations from the spectra generated from a few key wavelengths. The presented approach is tested using naphthenic acids, phenol, fluoranthene and pyrene spiked into natural waters. The spills or loss of containment of these contaminants represent a significant risk to the environment and public health, requiring accurate and rapid detection methods to protect the surrounding aquatic environment. Results were compared with models based on only the corresponding peak intensities of each contaminant and with an image processing NN using the original spectra. Naphthenic acids, fluoranthene and pyrene were easy to detect by all methods; however, performance for more challenging signals to identify, such as phenol, was optimized by the proposed method (peak picking with mean absolute error (MAE) of 30.48 µg/L, generated excitation-emission matrix with MAE of 8.30 µg/L). Results suggested that data fusion and machine learning techniques can improve the detection of contaminants in the aquatic environment at environmentally relevant concentrations.
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Affiliation(s)
| | - Nicolás M Peleato
- School of Engineering, The University of British Columbia Okanagan, 1137 Alumni Ave., Kelowna, BC, Canada, V1V 1V7
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39
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Bonicelli A, Cheung W, Hughes S, Wescott DJ, Procopio N. Preliminary Investigation of the Effect of Maceration Procedures on Bone Metabolome and Lipidome. Metabolites 2022; 12:1020. [PMID: 36355103 PMCID: PMC9693520 DOI: 10.3390/metabo12111020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
The study of post-mortem changes is a crucial component of forensic investigation. Human forensic taphonomic facilities (HFTFs) are the only institutions allowing the design and execution of controlled human decomposition experiments. When bodies are skeletonized, bones are normally stored in skeletal collections and used for anthropological studies. However, HFTFs apply chemical and/or thermal treatments to the remains prior bone long-term storage. These treatments are believed to alter heavily the original biochemical and molecular signature of bone material. The present study aims to evaluate the effect of these procedures on the bone metabolome and lipidome by using an animal bone model. Three intact bovine tibiae were processed using three protocols routinely applied at HFTFs, and their three counterparts were used as non-treated controls. Bone powder samples were subjected to biphasic extraction and both metabolites and lipids were analysed via liquid chromatography tandem mass-spectrometry. Results showed severe reductions in the abundances of both metabolites and lipids, and the presence of contamination introduced by cleaning agents. Despite the preliminary nature of the study, we demonstrated that the biochemical profile of bone is heavily affected by the maceration procedures. Ideally, these treatments should be avoided, or replaced by minimally invasive procedures agreed across HFTFs.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX 773402525, USA
| | - Daniel J. Wescott
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
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Baesu A, Bayen S. Application of Nontarget Analysis and High-Resolution Mass Spectrometry for the Identification of Thermal Transformation Products of Oxytetracycline in Pacific White Shrimp. J Food Prot 2022; 85:1469-1478. [PMID: 35723565 DOI: 10.4315/jfp-22-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/03/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Oxytetracycline (OTC) is an antibiotic authorized for use in aquaculture; it is often detected in seafood products, especially shrimp. Previous studies investigating the fate of OTC in shrimp tissues after cooking were limited to quantification of parent compound residues and did not describe any potential transformation products formed. Hence, the main objective of this study was to apply a nontarget analysis workflow to study the fate of OTC in shrimp muscle. Furthermore, "water" and "spiked" models were evaluated for their suitability to track the transformation of OTC in incurred muscle and to determine whether the matrix plays a role in the transformation pathway. First, four different extraction methods were compared for the determination of OTC in muscle. Second, raw and cooked samples were then extracted using a suitable method (acidified water-methanol-acetonitrile, with cleanup of samples achieved using freezing) and were analyzed by high-performance liquid chromatography quadrupole time-of-flight mass spectrometry. OTC levels were reduced by 75 and 87% in muscle and water, respectively. Identification of thermal transformation products was limited to formula generation, but results showed that different compounds were identified in spiked and incurred muscle. HIGHLIGHTS
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Affiliation(s)
- Anca Baesu
- Department of Food Science and Agricultural Chemistry, McGill University, 21111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, Canada H9X 3V9
| | - Stéphane Bayen
- Department of Food Science and Agricultural Chemistry, McGill University, 21111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, Canada H9X 3V9
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41
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Ma X. Recent Advances in Mass Spectrometry-Based Structural Elucidation Techniques. Molecules 2022; 27:molecules27196466. [PMID: 36235003 PMCID: PMC9572214 DOI: 10.3390/molecules27196466] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Mass spectrometry (MS) has become the central technique that is extensively used for the analysis of molecular structures of unknown compounds in the gas phase. It manipulates the molecules by converting them into ions using various ionization sources. With high-resolution MS, accurate molecular weights (MW) of the intact molecular ions can be measured so that they can be assigned a molecular formula with high confidence. Furthermore, the application of tandem MS has enabled detailed structural characterization by breaking the intact molecular ions and protonated or deprotonated molecules into key fragment ions. This approach is not only used for the structural elucidation of small molecules (MW < 2000 Da), but also crucial biopolymers such as proteins and polypeptides; therefore, MS has been extensively used in multiomics studies for revealing the structures and functions of important biomolecules and their interactions with each other. The high sensitivity of MS has enabled the analysis of low-level analytes in complex matrices. It is also a versatile technique that can be coupled with separation techniques, including chromatography and ion mobility, and many other analytical instruments such as NMR. In this review, we aim to focus on the technical advances of MS-based structural elucidation methods over the past five years, and provide an overview of their applications in complex mixture analysis. We hope this review can be of interest for a wide range of audiences who may not have extensive experience in MS-based techniques.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr NW, Atlanta, GA 30332, USA
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42
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Decker C, Krapf R, Kuballa T, Bunzel M. Differentiation of meat species of raw and processed meat based on polar metabolites using 1H NMR spectroscopy combined with multivariate data analysis. Front Nutr 2022; 9:985797. [PMID: 36245505 PMCID: PMC9566576 DOI: 10.3389/fnut.2022.985797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Meat species of raw meat and processed meat products were investigated by 1H NMR spectroscopy with subsequent multivariate data analysis. Sample preparation was based on aqueous extraction combined with ultrafiltration in order to reduce macromolecular components in the extracts. 1H NMR data was analyzed by using a non-targeted approach followed by principal component analysis (PCA), linear discrimination analysis (LDA), and cross-validation (CV) embedded in a Monte Carlo (MC) resampling approach. A total of 379 raw meat samples (pork, beef, poultry, and lamb) and 81 processed meat samples (pork, beef, poultry) were collected between the years 2018 and 2021. A 99% correct prediction rate was achieved if the raw meat samples were classified according to meat species. Predicting processed meat products was slightly less successful (93 %) with this approach. Furthermore, identification of spectral regions that are relevant for the classification via polar chemical markers was performed. Finally, data on polar metabolites were fused with previously published 1H NMR data on non-polar metabolites in order to build a broader classification model and to improve prediction accuracy.
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Affiliation(s)
- Christina Decker
- Karlsruhe Institute of Technology (KIT), Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
- Chemisches und Veterinäruntersuchungsamt Karlsruhe, Karlsruhe, Germany
| | - Reiner Krapf
- Bosch Power Tools, Leinfelden-Echterdingen, Germany
| | - Thomas Kuballa
- Chemisches und Veterinäruntersuchungsamt Karlsruhe, Karlsruhe, Germany
| | - Mirko Bunzel
- Karlsruhe Institute of Technology (KIT), Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
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Stability of Metabolomic Content during Sample Preparation: Blood and Brain Tissues. Metabolites 2022; 12:metabo12090811. [PMID: 36144215 PMCID: PMC9505456 DOI: 10.3390/metabo12090811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Thermal and enzymatic reactions can significantly change the tissue metabolomic content during the sample preparation. In this work, we evaluated the stability of metabolites in human whole blood, serum, and rat brain, as well as in metabolomic extracts from these tissues. We measured the concentrations of 63 metabolites in brain and 52 metabolites in blood. We have shown that metabolites in the extracts from biological tissues are stable within 24 h at 4 °C. Serum and whole blood metabolomes are also rather stable, changes in metabolomic content of the whole blood homogenate become apparent only after 1–2 h of incubation at 4 °C, and become strong after 24 h. The most significant changes correspond to energy metabolites: the concentrations of ATP and ADP decrease fivefold, and the concentrations of NAD, NADH, and NADPH decrease below the detectable level. A statistically significant increase was observed for AMP, IMP, hypoxanthine, and nicotinamide. The brain tissue is much more metabolically active than human blood, and significant metabolomic changes occur already within the first several minutes during the brain harvest and sample homogenization. At a longer timescale (hours), noticeable changes were observed for all classes of compounds, including amino acids, organic acids, alcohols, amines, sugars, nitrogenous bases, nucleotides, and nucleosides.
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44
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Eylem CC, Nemutlu E, Dogan A, Acik V, Matyar S, Gezercan Y, Altintas S, Okten AI, Basci Akduman NE. High-Throughput Single-Step plasma sample extraction optimization strategies with experimental design for LC-MS and GC–MS integrated metabolomics and lipidomics analysis. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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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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Doppler M, Bueschl C, Ertl F, Woischitzschlaeger J, Parich A, Schuhmacher R. Towards a broader view of the metabolome: untargeted profiling of soluble and bound polyphenols in plants. Anal Bioanal Chem 2022; 414:7421-7433. [PMID: 35678834 PMCID: PMC9482910 DOI: 10.1007/s00216-022-04134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/28/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
Phenylalanine (Phe) is a central precursor for numerous secondary plant metabolites with a multitude of biological functions. Recent studies on the fungal disease Fusarium head blight in wheat showed numerous Phe-derived defence metabolites to be induced in the presence of the pathogen. These studies also suggest a partial incorporation of Phe-derived secondary metabolites into the cell wall. To broaden the view of the metabolome to bound Phe derivatives, an existing approach using 13C-labelled Phe as tracer was extended. The developed workflow consists of three successive extractions with an acidified acetonitrile-methanol-water mixture to remove the soluble plant metabolites, followed by cell wall hydrolysis with 4M aqueous NaOH, acidification with aqueous HCl, and liquid-liquid extraction of the hydrolysate with ethyl acetate. The untargeted screening of Phe-derived metabolites revealed 156 soluble compounds and 90 compounds in the hydrolysed samples including known cell wall constituents like ferulic acid, coumaric acid, and tricin. Forty-nine metabolites were found exclusively in the hydrolysate. The average cumulative extraction yield of the soluble metabolites was 99.6%, with a range of 91.8 to 100%. Repeatability coefficients of variation of the protocol ranged from 10.5 to 25.9%, with a median of 16.3%. To demonstrate the suitability of the proposed method for a typical metabolomics application, mock-treated and Fusarium graminearum-treated wheat samples were compared. The study revealed differences between the hydrolysates of the two sample types, confirming the differential incorporation of Phe-derived metabolites into the cell wall under infection conditions.
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Affiliation(s)
- Maria Doppler
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria. .,Core Facility Bioactive Molecules: Screening and Analysis, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria.
| | - Christoph Bueschl
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Florian Ertl
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Jakob Woischitzschlaeger
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Alexandra Parich
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Rainer Schuhmacher
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria.
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Popov RS, Ivanchina NV, Dmitrenok PS. Application of MS-Based Metabolomic Approaches in Analysis of Starfish and Sea Cucumber Bioactive Compounds. Mar Drugs 2022; 20:md20050320. [PMID: 35621972 PMCID: PMC9147407 DOI: 10.3390/md20050320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Today, marine natural products are considered one of the main sources of compounds for drug development. Starfish and sea cucumbers are potential sources of natural products of pharmaceutical interest. Among their metabolites, polar steroids, triterpene glycosides, and polar lipids have attracted a great deal of attention; however, studying these compounds by conventional methods is challenging. The application of modern MS-based approaches can help to obtain valuable information about such compounds. This review provides an up-to-date overview of MS-based applications for starfish and sea cucumber bioactive compounds analysis. While describing most characteristic features of MS-based approaches in the context of starfish and sea cucumber metabolites, including sample preparation and MS analysis steps, the present paper mainly focuses on the application of MS-based metabolic profiling of polar steroid compounds, triterpene glycosides, and lipids. The application of MS in metabolomics studies is also outlined.
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Affiliation(s)
- Roman S. Popov
- Correspondence: (R.S.P.); (P.S.D.); Tel.: +7-423-231-1132 (P.S.D.)
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48
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Analytical strategies to profile the internal chemical exposome and the metabolome of human placenta. Anal Chim Acta 2022; 1219:339983. [DOI: 10.1016/j.aca.2022.339983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/02/2022] [Accepted: 05/22/2022] [Indexed: 11/20/2022]
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Frigerio G, Moruzzi C, Mercadante R, Schymanski EL, Fustinoni S. Development and Application of an LC-MS/MS Untargeted Exposomics Method with a Separated Pooled Quality Control Strategy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082580. [PMID: 35458780 PMCID: PMC9031529 DOI: 10.3390/molecules27082580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/31/2022] [Accepted: 04/15/2022] [Indexed: 11/16/2022]
Abstract
Pooled quality controls (QCs) are usually implemented within untargeted methods to improve the quality of datasets by removing features either not detected or not reproducible. However, this approach can be limiting in exposomics studies conducted on groups of exposed and nonexposed subjects, as compounds present at low levels only in exposed subjects can be diluted and thus not detected in the pooled QC. The aim of this work is to develop and apply an untargeted workflow for human biomonitoring in urine samples, implementing a novel separated approach for preparing pooled quality controls. An LC-MS/MS workflow was developed and applied to a case study of smoking and non-smoking subjects. Three different pooled quality controls were prepared: mixing an aliquot from every sample (QC-T), only from non-smokers (QC-NS), and only from smokers (QC-S). The feature tables were filtered using QC-T (T-feature list), QC-S, and QC-NS, separately. The last two feature lists were merged (SNS-feature list). A higher number of features was obtained with the SNS-feature list than the T-feature list, resulting in identification of a higher number of biologically significant compounds. The separated pooled QC strategy implemented can improve the nontargeted human biomonitoring for groups of exposed and nonexposed subjects.
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Affiliation(s)
- Gianfranco Frigerio
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg; (G.F.); (E.L.S.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (C.M.); (R.M.)
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Camilla Moruzzi
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (C.M.); (R.M.)
| | - Rosa Mercadante
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (C.M.); (R.M.)
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg; (G.F.); (E.L.S.)
| | - Silvia Fustinoni
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (C.M.); (R.M.)
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence:
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50
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Mohd Kamal K, Mahamad Maifiah MH, Abdul Rahim N, Hashim YZHY, Abdullah Sani MS, Azizan KA. Bacterial Metabolomics: Sample Preparation Methods. Biochem Res Int 2022; 2022:9186536. [PMID: 35465444 PMCID: PMC9019480 DOI: 10.1155/2022/9186536] [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: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 12/03/2022] Open
Abstract
Metabolomics is a comprehensive analysis of metabolites existing in biological systems. As one of the important "omics" tools, the approach has been widely employed in various fields in helping to better understand the complex cellular metabolic states and changes. Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. The approach in metabolomics is categorized into untargeted and targeted which serves different paradigms of interest. Nevertheless, the bottleneck in metabolomics has been the sample or metabolite preparation method. A custom-made method and design for a particular species or strain of bacteria might be necessary as most studies generally refer to other bacteria or even yeast and fungi that may lead to unreliable analysis. The paramount aspect of metabolomics design comprises sample harvesting, quenching, and metabolite extraction procedures. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, the existing and current developments of sample preparation methods of bacterial metabolomics used in both approaches are reviewed. The review also highlights previous literature of optimized conditions used to propose the most ideal methods for metabolite preparation, particularly for bacterial cells. Advantages and limitations of methods are discussed for future improvement of bacterial metabolomics.
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Affiliation(s)
- Khairunnisa Mohd Kamal
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | | | - Yumi Zuhanis Has-Yun Hashim
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Muhamad Shirwan Abdullah Sani
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, Bangi, Selangor 43600, Malaysia
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