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Tkalec Ž, Antignac JP, Bandow N, Béen FM, Belova L, Bessems J, Le Bizec B, Brack W, Cano-Sancho G, Chaker J, Covaci A, Creusot N, David A, Debrauwer L, Dervilly G, Duca RC, Fessard V, Grimalt JO, Guerin T, Habchi B, Hecht H, Hollender J, Jamin EL, Klánová J, Kosjek T, Krauss M, Lamoree M, Lavison-Bompard G, Meijer J, Moeller R, Mol H, Mompelat S, Van Nieuwenhuyse A, Oberacher H, Parinet J, Van Poucke C, Roškar R, Togola A, Trontelj J, Price EJ. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment. ENVIRONMENT INTERNATIONAL 2024; 186:108585. [PMID: 38521044 DOI: 10.1016/j.envint.2024.108585] [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: 08/18/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.
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Affiliation(s)
- Žiga Tkalec
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | | | - Nicole Bandow
- German Environment Agency, Laboratory for Water Analysis, Colditzstraße 34, 12099 Berlin, Germany.
| | - Frederic M Béen
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; KWR Water Research Institute, Nieuwegein, The Netherlands.
| | - Lidia Belova
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Jos Bessems
- Flemish Institute for Technological Research (VITO), Mol, Belgium.
| | | | - Werner Brack
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany; Goethe University Frankfurt, Department of Evolutionary Ecology and Environmental Toxicology, Max-von-Laue-Strasse 13, 60438 Frankfurt, Germany.
| | | | - Jade Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Nicolas Creusot
- INRAE, French National Research Institute For Agriculture, Food & Environment, UR1454 EABX, Bordeaux Metabolome, MetaboHub, Gazinet Cestas, France.
| | - Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | | | - Radu Corneliu Duca
- Unit Environmental Hygiene and Human Biological Monitoring, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg; Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium.
| | - Valérie Fessard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalonia, Spain.
| | - Thierry Guerin
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Strategy and Programs Department, F-94701 Maisons-Alfort, France.
| | - Baninia Habchi
- INRS, Département Toxicologie et Biométrologie Laboratoire Biométrologie 1, rue du Morvan - CS 60027 - 54519, Vandoeuvre Cedex, France.
| | - Helge Hecht
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Juliane Hollender
- Swiss Federal Institute of Aquatic Science and Technology - Eawag, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | - Jana Klánová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Tina Kosjek
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | - Martin Krauss
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Marja Lamoree
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Gwenaelle Lavison-Bompard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Jeroen Meijer
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Ruth Moeller
- Unit Medical Expertise and Data Intelligence, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Hans Mol
- Wageningen Food Safety Research - Part of Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands.
| | - Sophie Mompelat
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - An Van Nieuwenhuyse
- Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium; Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Insbruck, 6020 Innsbruck, Austria.
| | - Julien Parinet
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Christof Van Poucke
- Flanders Research Institute for Agriculture, Fisheries And Food (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Robert Roškar
- University of Ljubljana, Faculty of Pharmacy, Slovenia.
| | - Anne Togola
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France.
| | | | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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2
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Pego AMF, Knaven EJ, van de Plas APC, Brouwers JF, Cuypers E, Flinders B, Heeren RMA, van Asten AC, de Rooij BM. Untargeted metabolomics for lifestyle biomarker discovery in human hair. Forensic Sci Int 2024; 356:111938. [PMID: 38301432 DOI: 10.1016/j.forsciint.2024.111938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/30/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
There is a risk of crimes remaining unsolved when no matching DNA profiles or fingermarks are found. If this is the case, forensic investigations are faced with a significant shortage of evidence and information regarding the unknown perpetrator and/or victim as well as any missing persons. However, a rather commonly found biological trace encountered at crime scenes is human hair. As hair acts as a biochemical reservoir, it may contain valuable information regarding one's characteristics and habits. This study aimed to build an analytical method capable of determining a marker set of relevant metabolites in hair, eventually building up a profile of its donor. To find potential markers, an untargeted metabolomics approach was developed to select and identify statistically significant features. For that purpose, a total of 68 hair samples were collected at several hairdresser shops in varying neighbourhoods. Compound extraction was achieved via methanolic incubation overnight and analysis performed using a high-resolution mass spectrometry (HRMS) Orbitrap Q Exactive Focus. The acquired data was uploaded and statistically evaluated using two free online software/libraries, where a total of eight compounds have given a match on both tools. Their presumptive identity was confirmed using reference standards and consequently added to a dynamic target donor profiling list. These results show the potential of using untargeted metabolomics for the search for lifestyle biomarkers capable of differentiating individuals. Such tools are of paramount importance in a forensic setting with little or no evidence available and no clear tactical leads.
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Affiliation(s)
- Ana M F Pego
- Research group Analysis Techniques in the Life Sciences, Avans University of Applied Sciences, Breda, the Netherlands; Department of Sciences, John Jay College of Criminal Justice, City University of New York, NY, USA.
| | - Edward J Knaven
- Research group Analysis Techniques in the Life Sciences, Avans University of Applied Sciences, Breda, the Netherlands
| | - Anke P C van de Plas
- Research group Analysis Techniques in the Life Sciences, Avans University of Applied Sciences, Breda, the Netherlands
| | - Jos F Brouwers
- Research group Analysis Techniques in the Life Sciences, Avans University of Applied Sciences, Breda, the Netherlands
| | - Eva Cuypers
- Toxicology and Pharmacology, KU Leuven, Belgium; M4I, The Maastricht MultiModal Molecular Imaging institute, University Maastricht, the Netherlands
| | - Bryn Flinders
- M4I, The Maastricht MultiModal Molecular Imaging institute, University Maastricht, the Netherlands
| | - Ron M A Heeren
- M4I, The Maastricht MultiModal Molecular Imaging institute, University Maastricht, the Netherlands
| | - Arian C van Asten
- van 't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands; Co van Ledden Hulsebosch Center, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben M de Rooij
- Research group Analysis Techniques in the Life Sciences, Avans University of Applied Sciences, Breda, the Netherlands
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3
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Carapito Â, Roque ACA, Carvalho F, Pinto J, Guedes de Pinho P. Exploiting volatile fingerprints for bladder cancer diagnosis: A scoping review of metabolomics and sensor-based approaches. Talanta 2024; 268:125296. [PMID: 37839328 DOI: 10.1016/j.talanta.2023.125296] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
Bladder cancer (BC) represents a significant global health concern, for which early detection is essential to improve patient outcomes. This review evaluates the potential of the urinary volatile organic compounds (VOCs) as biomarkers for detecting and staging BC. The methods used include gas chromatography-mass spectrometry (GC-MS)-based metabolomics and electronic-nose (e-nose) sensors. The GC-MS studies that have been published reveal diverse results in terms of diagnostic performance. The sensitivities range from 27 % to an impressive 97 %, while specificities vary between 43 % and 94 %. Furthermore, the accuracies reported in these studies range from 80 to 89 %. In the urine of BC patients, a total of 80 VOCs were discovered to be significantly altered when compared to controls. These VOCs encompassed a variety of chemical classes such as alcohols, aldehydes, alkanes, aromatic compounds, fatty acids, ketones, and terpenoids, among others. Conversely, e-nose-based studies displayed sensitivities from 60 to 100 %, specificities from 53 to 96 %, and accuracies from 65 to 97 %. Interestingly, conductive polymer-based sensors performed better, followed by metal oxide semiconductor and optical sensors. GC-MS studies have shown improved performance in detecting early stages and low-grade tumors, providing valuable insights into staging. Based on these findings, VOC-based diagnostic tools hold great promise for early BC detection and staging. Further studies are needed to validate biomarkers and their classification performance. In the future, advancements in VOC profiling technologies may significantly contribute to improving the overall survival and quality of life for BC patients.
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Affiliation(s)
- Ângela Carapito
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
| | - Ana Cecília A Roque
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Félix Carvalho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Joana Pinto
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
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4
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Mik V, Pospíšil T, Brunoni F, Grúz J, Nožková V, Wasternack C, Miersch O, Strnad M, Floková K, Novák O, Široká J. Synthetic and analytical routes to the L-amino acid conjugates of cis-OPDA and their identification and quantification in plants. PHYTOCHEMISTRY 2023; 215:113855. [PMID: 37690699 DOI: 10.1016/j.phytochem.2023.113855] [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: 06/11/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Cis-(+)-12-oxophytodienoic acid (cis-(+)-OPDA) is a bioactive jasmonate, a precursor of jasmonic acid, which also displays signaling activity on its own. Modulation of cis-(+)-OPDA actions may be carried out via biotransformation leading to metabolites of various functions. This work introduces a methodology for the synthesis of racemic cis-OPDA conjugates with amino acids (OPDA-aa) and their deuterium-labeled analogs, which enables the unambiguous identification and accurate quantification of these compounds in plants. We have developed a highly sensitive liquid chromatography-tandem mass spectrometry-based method for the reliable determination of seven OPDA-aa (OPDA-Alanine, OPDA-Aspartate, OPDA-Glutamate, OPDA-Glycine, OPDA-Isoleucine, OPDA-Phenylalanine, and OPDA-Valine) from minute amount of plant material. The extraction from 10 mg of fresh plant tissue by 10% aqueous methanol followed by single-step sample clean-up on hydrophilic-lipophilic balanced columns prior to final analysis was optimized. The method was validated in terms of accuracy and precision, and the method parameters such as process efficiency, recovery and matrix effects were evaluated. In mechanically wounded 30-day-old Arabidopsis thaliana leaves, five endogenous (+)-OPDA-aa were identified and their endogenous levels were estimated. The time-course accumulation revealed a peak 60 min after the wounding, roughly corresponding to the accumulation of cis-(+)-OPDA. Our synthetic and analytical methodologies will support studies on cis-(+)-OPDA conjugation with amino acids and research into the biological significance of these metabolites in plants.
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Affiliation(s)
- Václav Mik
- Department of Experimental Biology, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Tomáš Pospíšil
- Department of Chemical Biology, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Federica Brunoni
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Jiří Grúz
- Department of Experimental Biology, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Vladimíra Nožková
- Department of Chemical Biology, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Claus Wasternack
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Otto Miersch
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Kristýna Floková
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Ondřej Novák
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Jitka Široká
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
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Shah R, Nguyen TV, Marcora A, Ruffell A, Hulthen A, Pham K, Wijffels G, Paull C, Beale DJ. Exposure to polylactic acid induces oxidative stress and reduces the ceramide levels in larvae of greater wax moth (Galleria mellonella). ENVIRONMENTAL RESEARCH 2023; 220:115137. [PMID: 36563977 DOI: 10.1016/j.envres.2022.115137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Plastic biodegradation by insects has made significant progress, opening up new avenues for the treatment of plastic waste. Wax moth larvae, for example, have attracted the attention of the scientific community because they are known to chew, ingest, and biodegrade natural polymer bee waxes. Despite this, we know very little about how these insects perform on manufactured plastics or how manufactured plastics affect insect metabolism. As a result, we studied the metabolism of greater wax moths (Galleria mellonella) fed on molasses-supplemented polylactic acid plastic (PLA) blocks. An analysis of the central carbon metabolism (CCM) metabolites was performed using liquid chromatography triple quadrupole mass spectrometry (LC-QQQ-MS), while an analysis of untargeted metabolites and lipids was conducted using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS). In total, 169 targeted CCM metabolites, 222 untargeted polar metabolites, and 196 untargeted nonpolar lipids were identified within the insect samples. In contrast, compared to control larvae, PLA-fed larvae displayed significantly different levels of 97 CCM metabolites, 75 polar metabolites, and 57 lipids. Purine and pyrimidine metabolisms were affected by PLA feeding, as well as amino acid metabolism, carbohydrates, cofactors, vitamins, and related metabolisms. Additionally, PLA exposure disrupted insect energy metabolism and oxidative stress, among other metabolic disturbances. The larvae fed PLA have lower levels of several lipids, suggesting a reduction in lipid reserves, and ceramide levels are likely to have changed due to apoptosis and inflammation. The study indicates that G. mellonella larvae could ingest PLA but this process causes some metabolic stress for the host. Future studies of the molecular pathways of this biodegradation process might help to provide strategies for stress reduction that would speed up insect digestion of plastic.
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Affiliation(s)
- Rohan Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Thao V Nguyen
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Anna Marcora
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Angela Ruffell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Andrew Hulthen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Khoa Pham
- CSIRO Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton VIC 4067, Australia
| | - Gene Wijffels
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Cate Paull
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia.
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Diamantidou D, Sampsonidis I, Liapikos T, Gika H, Theodoridis G. Liquid chromatography-mass spectrometry metabolite library for metabolomics: Evaluating column suitability using a scoring approach. J Chromatogr A 2023; 1690:463779. [PMID: 36681007 DOI: 10.1016/j.chroma.2023.463779] [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: 10/27/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023]
Abstract
Untargeted metabolomic studies require an extensive set of analyte (metabolic) information to be obtained from each analyzed sample. Thus, highly selective, and efficient analytical methodologies together with reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) are usually applied in these approaches. Here, we present a performance comparison of five different chromatographic columns (C18, C8, RP Amide, zicHILIC, OH5 HILIC phases) to evaluate their sufficiency of analysis for a large analyte library, consisting of 817 authentic standards. By taking into account experimental chromatographic parameters (i.e. retention time, peak tailing and asymmetry, FWHM, signal-to-noise ratio and peak area and intensity), the proposed column scoring approach provides a simple criterion that may assist analysis in the select of a stationary phase for those metabolites of interest. RPLC methods offered better results regarding metabolic library coverage, while the zicHILIC stationary phase delivered a bigger number of properly eluted compounds. This study demonstrates the importance of choosing the most suitable configuration for the analysis of different metabolic classes.
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Affiliation(s)
- Dimitra Diamantidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece; Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001; FoodOmicsGR Research Infrastructure, AUTh node, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001
| | - Ioannis Sampsonidis
- FoodOmicsGR Research Infrastructure, AUTh node, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001; Laboratory of Chemical Biology, Department of Nutritional Sciences and Dietetics, International Hellenic University, Thessaloniki, GR, 574 00, Greece.
| | - Theodoros Liapikos
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece; Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001
| | - Helen Gika
- Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001; FoodOmicsGR Research Infrastructure, AUTh node, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001; School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
| | - Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece; Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001; FoodOmicsGR Research Infrastructure, AUTh node, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001
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Fabio Turco J, Benhur Mokochinski J, Reyes Torres Y. Lipidomic Analysis of Geopropolis of Brazilian Stingless Bees by LC-HRMS. Food Res Int 2023; 167:112640. [PMID: 37087233 DOI: 10.1016/j.foodres.2023.112640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Stingless bees (Meliponini) represent over than 500 species, found in tropical and sub-tropical regions of the world. They produce geopropolis, a resinous natural product containing bioactive compounds, which is commonly used in folk medicine. In the current study, LC-HRMS and bioinformatic tools were used to carry out for the first time the lipidomic analysis of geopropolis from indigenous Brazilian stingless bees. As a result, 61 compounds of several lipid classes were identified with elevated degree of confidence. Then, we demonstrated that lipids in geopropolis are not restricted to waxes and fatty acids; but fatty amides and amines, phenolic lipids, resorcinols, retinoids, abietanoids, diterpenoids, pentacyclic triterpenoids, prostaglandins, retinoids, and steroids were found. In addition, multivariate analysis, based on the lipidomic profile of extracts, reinforces the assumption that the species of stingless bees, as well as the geographical origin are relevant factors to affect geopropolis composition once that the lipidic profile allowed the discrimination of geopropolis in groups related to the geographical origin, bee specie or bee genus. The lipidic profile also suggest a selective forage habits of T. angustula, which seems to collect resins from more specific vegetal sources regardless geographic origin, while other stingless bees, such as M. marginata and M. quadrifasciata, are less selective and may adapt to collect resins from a wider variety of plants.
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Affiliation(s)
- João Fabio Turco
- Department of Chemistry, State University of Midwest (UNICENTRO), Guarapuava, Parana, Brazil
| | - João Benhur Mokochinski
- Proteomics and Metabolomics Facility, Faculty of Medicine, Hammersmith Hospital Campus, Imperial College London, United Kingdom
| | - Yohandra Reyes Torres
- Department of Chemistry, State University of Midwest (UNICENTRO), Guarapuava, Parana, Brazil.
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [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
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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9
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Paglia G, Smith AJ, Astarita G. Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics. MASS SPECTROMETRY REVIEWS 2022; 41:722-765. [PMID: 33522625 DOI: 10.1002/mas.21686] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.
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Affiliation(s)
- Giuseppe Paglia
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Andrew J Smith
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
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10
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HPLC–(Q)-TOF-MS-Based Study of Plasma Metabolic Profile Differences Associated with Age in Pediatric Population Using an Animal Model. Metabolites 2022; 12:metabo12080739. [PMID: 36005611 PMCID: PMC9413543 DOI: 10.3390/metabo12080739] [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: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
A deep knowledge about the biological development of children is essential for appropriate drug administration and dosage in pediatrics. In this sense, the best approximation to study organ maturation is the analysis of tissue samples, but it requires invasive methods. For this reason, surrogate matrices should be explored. Among them, plasma emerges as a potential alternative since it represents a snapshot of global organ metabolism. In this work, plasma metabolic profiles from piglets of different ages (newborns, infants, and children) obtained by HPLC–(Q)-TOF-MS at positive and negative ionization modes were studied. Improved clustering within groups was achieved using multiblock principal component analysis compared to classical principal component analysis. Furthermore, the separation observed among groups was better resolved by using partial least squares-discriminant analysis, which was validated by bootstrapping and permutation testing. Thanks to univariate analysis, 13 metabolites in positive and 21 in negative ionization modes were found to be significant to discriminate the three groups of piglets. From these features, an acylcarnitine and eight glycerophospholipids were annotated and identified as metabolites of interest. The findings indicate that there is a relevant change with age in lipid metabolism in which lysophosphatidylcholines and lysophoshatidylethanolamines play an important role.
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11
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Milman BL, Zhurkovich IK. Present-Day Practice of Non-Target Chemical Analysis. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822050070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
We review the main techniques, procedures, and information products used in non-target analysis (NTA) to reveal the composition of substances. Sampling and sample preparation methods are preferable that ensure the extraction of analytes from test samples in a wide range of analyte properties with the most negligible loss. The necessary techniques of analysis are versions of chromatography–high-resolution tandem mass spectrometry (HRMS), yielding individual characteristics of analytes (mass spectra, retention properties) to accurately identify them. The prioritization of the analytical strategy discards unnecessary measurements and thereby increases the performance of the NTA. Chemical databases, collections of reference mass spectra and retention characteristics, algorithms, and software for processing HRMS data are indispensable in NTA.
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12
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Application of Liquid Chromatography Coupled to Mass Spectrometry in Quality Assessment of Dietary Supplements—A Case Study of Tryptophan Supplements: Release Assay, Targeted and Untargeted Studies. Pharmaceuticals (Basel) 2022; 15:ph15040448. [PMID: 35455446 PMCID: PMC9031539 DOI: 10.3390/ph15040448] [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: 02/17/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/27/2022] Open
Abstract
Dietary supplements are widely consumed in the EU and the USA. Based on their similarity to pharmaceuticals, consumers mistakenly believe that dietary supplements have also been approved for safety and efficacy. However, in the absence of mandatory testing, data on supplement quality is scarce. Thus, we applied liquid chromatography coupled with tandem mass spectrometry to analyse the quality of dietary supplements containing tryptophan (Trp). We examined 22 supplements in tablets or capsules, produced in the USA, Great Britain, Germany, France, Czech Republic, and Poland. Trp release, crucial for bioavailability and efficiency, was assessed. Additionally, we performed a qualitative analysis of the main ingredient and screened for contaminants. Among the contaminants, we detected Trp’s metabolites, condensation products of Trp and carbonyl compounds, Trp degradation products, degradation products of kynurenine, and other contaminants such as glucosamine and melatonin. The main ingredient content was in the range of 55–100% in capsules and 69–87% in tablets. Surprisingly, almost no Trp release was noted from some supplements. Our study confirms the need to advance research on supplements. We believe that the high-quality analysis of supplements based on reliable analytical techniques will be an important contribution to the discussion on the regulatory framework of these products.
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Sussman EM, Oktem B, Isayeva IS, Liu J, Wickramasekara S, Chandrasekar V, Nahan K, Shin HY, Zheng J. Chemical Characterization and Non-targeted Analysis of Medical Device Extracts: A Review of Current Approaches, Gaps, and Emerging Practices. ACS Biomater Sci Eng 2022; 8:939-963. [PMID: 35171560 DOI: 10.1021/acsbiomaterials.1c01119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The developers of medical devices evaluate the biocompatibility of their device prior to FDA's review and subsequent introduction to the market. Chemical characterization, described in ISO 10993-18:2020, can generate information for toxicological risk assessment and is an alternative approach for addressing some biocompatibility end points (e.g., systemic toxicity, genotoxicity, carcinogenicity, reproductive/developmental toxicity) that can reduce the time and cost of testing and the need for animal testing. Additionally, chemical characterization can be used to determine whether modifications to the materials and manufacturing processes alter the chemistry of a patient-contacting device to an extent that could impact device safety. Extractables testing is one approach to chemical characterization that employs combinations of non-targeted analysis, non-targeted screening, and/or targeted analysis to establish the identities and quantities of the various chemical constituents that can be released from a device. Due to the difficulty in obtaining a priori information on all the constituents in finished devices, information generation strategies in the form of analytical chemistry testing are often used. Identified and quantified extractables are then assessed using toxicological risk assessment approaches to determine if reported quantities are sufficiently low to overcome the need for further chemical analysis, biological evaluation of select end points, or risk control. For extractables studies to be useful as a screening tool, comprehensive and reliable non-targeted methods are needed. Although non-targeted methods have been adopted by many laboratories, they are laboratory-specific and require expensive analytical instruments and advanced technical expertise to perform. In this Perspective, we describe the elements of extractables studies and provide an overview of the current practices, identified gaps, and emerging practices that may be adopted on a wider scale in the future. This Perspective is outlined according to the steps of an extractables study: information gathering, extraction, extract sample processing, system selection, qualification, quantification, and identification.
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Affiliation(s)
- Eric M Sussman
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Berk Oktem
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Irada S Isayeva
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Jinrong Liu
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Samanthi Wickramasekara
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Vaishnavi Chandrasekar
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Keaton Nahan
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Hainsworth Y Shin
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Jiwen Zheng
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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14
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Morilla I, Chan P, Caffin F, Svilar L, Selbonne S, Ladaigue S, Buard V, Tarlet G, Micheau B, Paget V, François A, Souidi M, Martin JC, Vaudry D, Benadjaoud MA, Milliat F, Guipaud O. Deep models of integrated multiscale molecular data decipher the endothelial cell response to ionizing radiation. iScience 2022; 25:103685. [PMID: 35106469 PMCID: PMC8786676 DOI: 10.1016/j.isci.2021.103685] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/04/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
The vascular endothelium is a hot spot in the response to radiation therapy for both tumors and normal tissues. To improve patient outcomes, interpretable systemic hypotheses are needed to help radiobiologists and radiation oncologists propose endothelial targets that could protect normal tissues from the adverse effects of radiation therapy and/or enhance its antitumor potential. To this end, we captured the kinetics of multi-omics layers-i.e. miRNome, targeted transcriptome, proteome, and metabolome-in irradiated primary human endothelial cells cultured in vitro. We then designed a strategy of deep learning as in convolutional graph networks that facilitates unsupervised high-level feature extraction of important omics data to learn how ionizing radiation-induced endothelial dysfunction may evolve over time. Last, we present experimental data showing that some of the features identified using our approach are involved in the alteration of angiogenesis by ionizing radiation.
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Affiliation(s)
- Ian Morilla
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
- Corresponding author
| | - Philippe Chan
- Normandie Univ, UNIROUEN, PISSARO Proteomic Platform, 76821 Mont Saint-Aignan, France
| | - Fanny Caffin
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Ljubica Svilar
- Aix Marseille Univ, INSERM, INRA, C2VN, 13007 Marseille, France
- CriBioM, Criblage Biologique Marseille, Faculté de Médecine de la Timone, 13205 Marseille Cedex 01, France
| | - Sonia Selbonne
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Ségolène Ladaigue
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
- Sorbonne University, Doctoral College, 75005 Paris, France
| | - Valérie Buard
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Georges Tarlet
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Béatrice Micheau
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Vincent Paget
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Agnès François
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Maâmar Souidi
- IRSN, Radiobiology of Accidental Exposure Laboratory (LRAcc), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Jean-Charles Martin
- Aix Marseille Univ, INSERM, INRA, C2VN, 13007 Marseille, France
- CriBioM, Criblage Biologique Marseille, Faculté de Médecine de la Timone, 13205 Marseille Cedex 01, France
| | - David Vaudry
- Normandie Univ, UNIROUEN, PISSARO Proteomic Platform, 76821 Mont Saint-Aignan, France
| | - Mohamed-Amine Benadjaoud
- IRSN, Radiobiology and Regenerative Medicine Research Service (SERAMED), 92260 Fontenay-Aux-Roses, France
| | - Fabien Milliat
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
| | - Olivier Guipaud
- IRSN, Radiobiology of Medical Exposure Laboratory (LRMed), Human Health Radiation Protection Unit, 92260 Fontenay-Aux-Roses, France
- Corresponding author
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15
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Matsuda F, Komori S, Yamada Y, Hara D, Okahashi N. Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules. Mass Spectrom (Tokyo) 2022; 11:A0106. [PMID: 36713802 PMCID: PMC9853114 DOI: 10.5702/massspectrometry.a0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.
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Affiliation(s)
- Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan,Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, Japan,Correspondence to: Fumio Matsuda, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan, e-mail:
| | - Shuka Komori
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yuki Yamada
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Daiki Hara
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan,Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, Japan
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16
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Mendonça SC, Simas RC, Reis Simas DL, Leitão SG, Leitão GG. Mass spectrometry as a tool for the dereplication of saponins from Ampelozizyphus amazonicus Ducke bark and wood. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:262-282. [PMID: 32681766 DOI: 10.1002/pca.2972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Mass spectrometry in natural products research has been used as a first step to identify possible chemical structures and to guide subsequent efforts to isolate novel compounds. Preparations of Ampelozizyphus amazonicus Ducke (AA) are known for their high content of saponins, especially dammarane-type triterpenoid aglycones. In the Amazon, where it is known as "saracura-mirá", roots and bark are widely used for the treatment and prevention of malaria, while the wood is discarded. The extract prepared from the wood is also saponin-rich, but its exact chemical composition has not been described. OBJECTIVE This study provides information on the chemical profiling and tentative structural identification of the major compounds (saponins) present in aqueous and ethanol extracts of bark and wood of AA by mass spectrometry. METHODS The strategy used to identify compounds present in all samples was ultra-high-performance liquid chromatography with an ultraviolet detector coupled to tandem mass spectrometry (UHPLC-UV-MS/MS) for the analysis of fragmentation patterns through product ion scan using MZmine 2 software. Also, direct sample injection and electrospray ionisation combined with high-resolution mass spectrometry (DI-ESI-HRMS) measurements were performed. RESULTS The extracts showed chemical similarity, and 95 saponins were tentatively identified in AA wood and bark, including 73 which are described for the first time as tentative structures for this plant species. CONCLUSION This research describes a useful method for the fast and simultaneous tentative identification of major saponins in AA, contributing to the study of the chemical properties of this genus and family. Furthermore, it demonstrates the importance of the qualitative dereplication process, allowing a straightforward way to propose the tentative identification of compounds.
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Affiliation(s)
- Simony C Mendonça
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosineide C Simas
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Suzana G Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gilda G Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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17
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Data processing strategies for non-targeted analysis of foods using liquid chromatography/high-resolution mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116188] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Capillary Electrophoresis-Mass Spectrometry for Metabolomics: Possibilities and Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:159-178. [PMID: 34628632 DOI: 10.1007/978-3-030-77252-9_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is a very useful analytical technique for the selective and highly efficient profiling of polar and charged metabolites in a wide range of biological samples. Compared to other analytical techniques, the use of CE-MS in metabolomics is relatively low as the approach is still regarded as technically challenging and not reproducible. In this chapter, the possibilities of CE-MS for metabolomics are highlighted with special emphasis on the use of recently developed interfacing designs. The utility of CE-MS for targeted and untargeted metabolomics studies is demonstrated by discussing representative and recent examples in the biomedical and clinical fields. The potential of CE-MS for large-scale and quantitative metabolomics studies is also addressed. Finally, some general conclusions and perspectives are given on this strong analytical separation technique for probing the polar metabolome.
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19
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An assessment of quality assurance/quality control efforts in high resolution mass spectrometry non-target workflows for analysis of environmental samples. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116063] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Celma A, Sancho JV, Schymanski EL, Fabregat-Safont D, Ibáñez M, Goshawk J, Barknowitz G, Hernández F, Bijlsma L. Improving Target and Suspect Screening High-Resolution Mass Spectrometry Workflows in Environmental Analysis by Ion Mobility Separation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15120-15131. [PMID: 33207875 DOI: 10.1021/acs.est.0c05713] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Currently, the most powerful approach to monitor organic micropollutants (OMPs) in environmental samples is the combination of target, suspect, and nontarget screening strategies using high-resolution mass spectrometry (HRMS). However, the high complexity of sample matrices and the huge number of OMPs potentially present in samples at low concentrations pose an analytical challenge. Ion mobility separation (IMS) combined with HRMS instruments (IMS-HRMS) introduces an additional analytical dimension, providing extra information, which facilitates the identification of OMPs. The collision cross-section (CCS) value provided by IMS is unaffected by the matrix or chromatographic separation. Consequently, the creation of CCS databases and the inclusion of ion mobility within identification criteria are of high interest for an enhanced and robust screening strategy. In this work, a CCS library for IMS-HRMS, which is online and freely available, was developed for 556 OMPs in both positive and negative ionization modes using electrospray ionization. The inclusion of ion mobility data in widely adopted confidence levels for identification in environmental reporting is discussed. Illustrative examples of OMPs found in environmental samples are presented to highlight the potential of IMS-HRMS and to demonstrate the additional value of CCS data in various screening strategies.
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Affiliation(s)
- Alberto Celma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
| | - Juan V Sancho
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - David Fabregat-Safont
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
| | - María Ibáñez
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
| | - Jeff Goshawk
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Gitte Barknowitz
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Félix Hernández
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
| | - Lubertus Bijlsma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat s/n, E-12071 Castellón, Spain
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Pezzatti J, González-Ruiz V, Boccard J, Guillarme D, Rudaz S. Evaluation of Different Tandem MS Acquisition Modes to Support Metabolite Annotation in Human Plasma Using Ultra High-Performance Liquid Chromatography High-Resolution Mass Spectrometry for Untargeted Metabolomics. Metabolites 2020; 10:metabo10110464. [PMID: 33203160 PMCID: PMC7697060 DOI: 10.3390/metabo10110464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) is a powerful and essential technique for metabolite annotation in untargeted metabolomic applications. The aim of this study was to evaluate the performance of diverse tandem MS (MS/MS) acquisition modes, i.e., all ion fragmentation (AIF) and data-dependent analysis (DDA), with and without ion mobility spectrometry (IM), to annotate metabolites in human plasma. The influence of the LC separation was also evaluated by comparing the performance of MS/MS acquisition in combination with three complementary chromatographic separation modes: reversed-phase chromatography (RPLC) and hydrophilic interaction chromatography (HILIC) with either an amide (aHILIC) or a zwitterionic (zHILIC) stationary phase. RPLC conditions were first chosen to investigate all the tandem MS modes, and we found out that DDA did not provide a significant additional amount of chemical coverage and that cleaner MS/MS spectra can be obtained by performing AIF acquisitions in combination with IM. Finally, we were able to annotate 338 unique metabolites and demonstrated that zHILIC was a powerful complementary approach to both the RPLC and aHILIC chromatographic modes. Moreover, a better analytical throughput was reached for an almost negligible loss of metabolite coverage when IM-AIF and AIF using ramped instead of fixed collision energies were used.
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Affiliation(s)
- Julian Pezzatti
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; (J.P.); (V.G.-R.); (J.B.); (D.G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva 4, Switzerland
| | - Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; (J.P.); (V.G.-R.); (J.B.); (D.G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva 4, Switzerland
- Swiss Centre for Applied Human Toxicology (SCATH), 4055 Basel, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; (J.P.); (V.G.-R.); (J.B.); (D.G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva 4, Switzerland
- Swiss Centre for Applied Human Toxicology (SCATH), 4055 Basel, Switzerland
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; (J.P.); (V.G.-R.); (J.B.); (D.G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva 4, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; (J.P.); (V.G.-R.); (J.B.); (D.G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva 4, Switzerland
- Swiss Centre for Applied Human Toxicology (SCATH), 4055 Basel, Switzerland
- Correspondence: ; Tel.: +41-2‐2379-6572
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22
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Yeshi K, Creek DJ, Anderson D, Ritmejerytė E, Becker L, Loukas A, Wangchuk P. Metabolomes and Lipidomes of the Infective Stages of the Gastrointestinal nematodes, Nippostrongylus brasiliensis and Trichuris muris. Metabolites 2020; 10:metabo10110446. [PMID: 33171998 PMCID: PMC7694664 DOI: 10.3390/metabo10110446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023] Open
Abstract
Soil-transmitted helminths, including hookworms and whipworms, infect billions of people worldwide. Their capacity to penetrate and migrate through their hosts’ tissues is influenced by the suite of molecules produced by the infective developmental stages. To facilitate a better understanding of the immunobiology and pathogenicity of human hookworms and whipworms, we investigated the metabolomes of the infective stage of Nippostrongylus brasiliensis third-stage larvae (L3) which penetrate the skin and Trichuris muris eggs which are orally ingested, using untargeted liquid chromatography-mass spectrometry (LC-MS). We identified 55 polar metabolites through Metabolomics Standard Initiative level-1 (MSI-I) identification from N. brasiliensis and T. muris infective stages, out of which seven were unique to excretory/secretory products (ESPs) of N. brasiliensis L3. Amino acids were a principal constituent (33 amino acids). Additionally, we identified 350 putative lipids, out of which 28 (all known lipids) were unique to N. brasiliensis L3 somatic extract and four to T. muris embryonated egg somatic extract. Glycerophospholipids and glycerolipids were the major lipid groups. The catalogue of metabolites identified in this study shed light on the biology, and possible therapeutic and diagnostic targets for the treatment of these critical infectious pathogens. Moreover, with the growing body of literature on the therapeutic utility of helminth ESPs for treating inflammatory diseases, a role for metabolites is likely but has received little attention thus far.
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Affiliation(s)
- Karma Yeshi
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
- Correspondence: (K.Y.); (P.W.)
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; (D.J.C.); (D.A.)
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; (D.J.C.); (D.A.)
| | - Edita Ritmejerytė
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Luke Becker
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Phurpa Wangchuk
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
- Correspondence: (K.Y.); (P.W.)
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23
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Drouin N, van Mever M, Zhang W, Tobolkina E, Ferre S, Servais AC, Gou MJ, Nyssen L, Fillet M, Lageveen-Kammeijer GS, Nouta J, Chetwynd AJ, Lynch I, Thorn JA, Meixner J, Lößner C, Taverna M, Liu S, Tran NT, Francois Y, Lechner A, Nehmé R, Al Hamoui Dit Banni G, Nasreddine R, Colas C, Lindner HH, Faserl K, Neusüß C, Nelke M, Lämmerer S, Perrin C, Bich-Muracciole C, Barbas C, Gonzálvez Á, Guttman A, Szigeti M, Britz-McKibbin P, Kroezen Z, Shanmuganathan M, Nemes P, Portero EP, Hankemeier T, Codesido S, González-Ruiz V, Rudaz S, Ramautar R. Capillary Electrophoresis-Mass Spectrometry at Trial by Metabo-Ring: Effective Electrophoretic Mobility for Reproducible and Robust Compound Annotation. Anal Chem 2020; 92:14103-14112. [PMID: 32961048 PMCID: PMC7581015 DOI: 10.1021/acs.analchem.0c03129] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022]
Abstract
Capillary zone electrophoresis-mass spectrometry (CE-MS) is a mature analytical tool for the efficient profiling of (highly) polar and ionizable compounds. However, the use of CE-MS in comparison to other separation techniques remains underrepresented in metabolomics, as this analytical approach is still perceived as technically challenging and less reproducible, notably for migration time. The latter is key for a reliable comparison of metabolic profiles and for unknown biomarker identification that is complementary to high resolution MS/MS. In this work, we present the results of a Metabo-ring trial involving 16 CE-MS platforms among 13 different laboratories spanning two continents. The goal was to assess the reproducibility and identification capability of CE-MS by employing effective electrophoretic mobility (μeff) as the key parameter in comparison to the relative migration time (RMT) approach. For this purpose, a representative cationic metabolite mixture in water, pretreated human plasma, and urine samples spiked with the same metabolite mixture were used and distributed for analysis by all laboratories. The μeff was determined for all metabolites spiked into each sample. The background electrolyte (BGE) was prepared and employed by each participating lab following the same protocol. All other parameters (capillary, interface, injection volume, voltage ramp, temperature, capillary conditioning, and rinsing procedure, etc.) were left to the discretion of the contributing laboratories. The results revealed that the reproducibility of the μeff for 20 out of the 21 model compounds was below 3.1% vs 10.9% for RMT, regardless of the huge heterogeneity in experimental conditions and platforms across the 13 laboratories. Overall, this Metabo-ring trial demonstrated that CE-MS is a viable and reproducible approach for metabolomics.
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Affiliation(s)
- Nicolas Drouin
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic Centre for
Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Marlien van Mever
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic Centre for
Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Wei Zhang
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic Centre for
Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Elena Tobolkina
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
| | - Sabrina Ferre
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
| | - Anne-Catherine Servais
- Laboratory
for the Analysis of Medicines, Center for Interdisciplinary Research
on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, B-4000 Liège, Belgium
| | - Marie-Jia Gou
- Laboratory
for the Analysis of Medicines, Center for Interdisciplinary Research
on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, B-4000 Liège, Belgium
| | - Laurent Nyssen
- Laboratory
for the Analysis of Medicines, Center for Interdisciplinary Research
on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, B-4000 Liège, Belgium
- Department
of Clinical Chemistry, Center for Interdisciplinary Research on Medicines
(CIRM), University of Liège, Avenue Hippocrate 15, B-4000 Liège, Belgium
| | - Marianne Fillet
- Laboratory
for the Analysis of Medicines, Center for Interdisciplinary Research
on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, B-4000 Liège, Belgium
| | | | - Jan Nouta
- Leiden University
Medical Center, Center for Proteomics
and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Andrew J. Chetwynd
- School
of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Iseult Lynch
- School
of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - James A. Thorn
- AB
Sciex UK Ltd, Phoenix House, Lakeside Drive, Warrington, Cheshire WA1 1RX, U.K.
| | - Jens Meixner
- Agilent
Technologies R&D and Marketing GmbH & Co. KG, Hewlett-Packard-Straße 8, 76337 Waldbronn, Germany
| | | | - Myriam Taverna
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296 Châtenay-Malabry, France
- Institut Universitaire de France, 1 Rue Descartes, 75231 CEDEX 05 Paris, France
| | - Sylvie Liu
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296 Châtenay-Malabry, France
| | - N. Thuy Tran
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Yannis Francois
- Laboratoire
de Spectromètrie de Masse des Interactions et des Systémes
(LSMIS) UMR 7140 (Unistra-CNRS), Université
de Strasbourg, 4 Rue Blaise Pascal, 67081 CEDEX Strasbourg, France
| | - Antony Lechner
- Laboratoire
de Spectromètrie de Masse des Interactions et des Systémes
(LSMIS) UMR 7140 (Unistra-CNRS), Université
de Strasbourg, 4 Rue Blaise Pascal, 67081 CEDEX Strasbourg, France
| | - Reine Nehmé
- Institut
de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d’Orléans, 45067 Orléans, France
| | - Ghassan Al Hamoui Dit Banni
- Institut
de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d’Orléans, 45067 Orléans, France
| | - Rouba Nasreddine
- Institut
de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d’Orléans, 45067 Orléans, France
| | - Cyril Colas
- Institut
de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d’Orléans, 45067 Orléans, France
- Centre de Biophysique Moléculaire,
CNRS-Université
d’Orléans, UPR 4311, 45071 CEDEX 2 Orléans, France
| | - Herbert H. Lindner
- Institute
of Clinical Biochemistry, Innsbruck Medical
University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus Faserl
- Institute
of Clinical Biochemistry, Innsbruck Medical
University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Christian Neusüß
- Faculty
of Chemistry, Aalen University, Beethovenstraße 1, 73430 Aalen, Germany
| | - Manuel Nelke
- Faculty
of Chemistry, Aalen University, Beethovenstraße 1, 73430 Aalen, Germany
| | - Stefan Lämmerer
- Faculty
of Chemistry, Aalen University, Beethovenstraße 1, 73430 Aalen, Germany
| | - Catherine Perrin
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247-CNRS-UM-ENSCM, Université de Montpellier, 34093 CEDEX 5 Montpellier, France
| | - Claudia Bich-Muracciole
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247-CNRS-UM-ENSCM, Université de Montpellier, 34093 CEDEX 5 Montpellier, France
| | - Coral Barbas
- Centre
for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry
and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización
Montepríncipe, Boadilladel
Monte 28660, Madrid, Spain
| | - Ángeles
López Gonzálvez
- Centre
for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry
and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización
Montepríncipe, Boadilladel
Monte 28660, Madrid, Spain
| | - Andras Guttman
- Horváth
Csaba Memorial Laboratory of Bioseparation Sciences, Research Center
for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular
Medicine, University of Debrecen, 98 Nagyerdei Road, H-4032 Debrecen, Hungary
- Translation
Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem H-8200, Hungary
- Sciex, 250 South Kraemer Boulevard, Brea, California 92821, United States
| | - Marton Szigeti
- Horváth
Csaba Memorial Laboratory of Bioseparation Sciences, Research Center
for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular
Medicine, University of Debrecen, 98 Nagyerdei Road, H-4032 Debrecen, Hungary
- Translation
Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem H-8200, Hungary
| | - Philip Britz-McKibbin
- Department
of Chemistry and Chemical Biology, McMaster
University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
| | - Zachary Kroezen
- Department
of Chemistry and Chemical Biology, McMaster
University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
| | - Meera Shanmuganathan
- Department
of Chemistry and Chemical Biology, McMaster
University, 1280 Main St. W., Hamilton, Ontario L8S 4M1, Canada
| | - Peter Nemes
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Erika P. Portero
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Thomas Hankemeier
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic Centre for
Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Santiago Codesido
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
| | - Víctor González-Ruiz
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology
(SCAHT), Missionsstrasse
64, 4055 Bâle, Switzerland
| | - Serge Rudaz
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel Servet 1, 1211 4 Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology
(SCAHT), Missionsstrasse
64, 4055 Bâle, Switzerland
| | - Rawi Ramautar
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic Centre for
Drug Research, Leiden University, 2311 G Leiden, The Netherlands
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24
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Zhu Y, Wancewicz B, Schaid M, Tiambeng TN, Wenger K, Jin Y, Heyman H, Thompson CJ, Barsch A, Cox ED, Davis DB, Brasier AR, Kimple ME, Ge Y. Ultrahigh-Resolution Mass Spectrometry-Based Platform for Plasma Metabolomics Applied to Type 2 Diabetes Research. J Proteome Res 2020; 20:463-473. [PMID: 33054244 DOI: 10.1021/acs.jproteome.0c00510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Metabolomics-the endpoint of the omics cascade-is increasingly recognized as a preferred method for understanding the ultimate responses of biological systems to stress. Flow injection electrospray (FIE) mass spectrometry (MS) has advantages for untargeted metabolic fingerprinting due to its simplicity and capability for high-throughput screening but requires a high-resolution mass spectrometer to resolve metabolite features. In this study, we developed and validated a high-throughput and highly reproducible metabolomics platform integrating FIE with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS for analysis of both polar and nonpolar metabolite features from plasma samples. FIE-FTICR MS enables high-throughput detection of hundreds of metabolite features in a single mass spectrum without a front-end separation step. Using plasma samples from genetically identical obese mice with or without type 2 diabetes (T2D), we validated the intra and intersample reproducibility of our method and its robustness for simultaneously detecting alterations in both polar and nonpolar metabolite features. Only 5 min is needed to acquire an ultra-high resolution mass spectrum in either a positive or negative ionization mode. Approximately 1000 metabolic features were reproducibly detected and annotated in each mouse plasma group. For significantly altered and highly abundant metabolite features, targeted tandem MS (MS/MS) analyses can be applied to confirm their identity. With this integrated platform, we successfully detected over 300 statistically significant metabolic features in T2D mouse plasma as compared to controls and identified new T2D biomarker candidates. This FIE-FTICR MS-based method is of high throughput and highly reproducible with great promise for metabolomics studies toward a better understanding and diagnosis of human diseases.
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Affiliation(s)
- Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Benjamin Wancewicz
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Michael Schaid
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Research Service, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kent Wenger
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Heino Heyman
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | | | | | - Elizabeth D Cox
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53792, United States
| | - Dawn B Davis
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Research Service, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Allan R Brasier
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Michelle E Kimple
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Research Service, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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25
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Mass spectrometry-based metabolomics for an in-depth questioning of human health. Adv Clin Chem 2020; 99:147-191. [PMID: 32951636 DOI: 10.1016/bs.acc.2020.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Today, metabolomics is becoming an indispensable tool to get a more comprehensive analysis of complex living systems, providing insights on multiple aspects of physiology. Although its application in large scale population-based studies is very challenging due to the processing of large sample sets as well as the complexity of data information, its potential to characterize human health is well recognized. Technological advances in metabolomics pave the way for the efficient biomarker discovery of disease etiology, diagnosis and prognosis. Here, different steps of the metabolomics workflow, particularly mass spectrometry-based approaches, are discussed to demonstrate the potential of metabolomics to address biological questioning in human health. First an overview of metabolomics is provided with its interest in human health studies. Analytical development and advances in mass spectrometry instrumentation and computational tools are discussed regarding their application limits. Advancing metabolomics for applicability in human health and large-scale studies is presented and discussed in conclusion.
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26
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Drouin N, Mielcarek A, Wenz C, Rudaz S. Evaluation of ion mobility in capillary electrophoresis coupled to mass spectrometry for the identification in metabolomics. Electrophoresis 2020; 42:342-349. [PMID: 32744343 DOI: 10.1002/elps.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023]
Abstract
Currently, feature annotation remains one of the main challenges in untargeted metabolomics. In this context, the information provided by high-resolution mass spectrometry (HRMS) in addition to accurate mass can improve the quality of metabolite annotation, and MS/MS fragmentation patterns are widely used. Accurate mass and a separation index, such as retention time or effective mobility (μeff ), in chromatographic and electrophoretic approaches, respectively, must be used for unequivocal metabolite identification. The possibility of measuring collision cross-section (CCS) values by using ion mobility (IM) is becoming increasingly popular in metabolomic studies thanks to the new generation of IM mass spectrometers. Based on their similar separation mechanisms involving electric field and the size of the compounds, the complementarity of DT CCSN2 and μeff needs to be evaluated. In this study, a comparison of DT CCSN2 and μeff was achieved in the context of feature identification ability in untargeted metabolomics by capillary zone electrophoresis (CZE) coupled with HRMS. This study confirms the high correlation of DT CCSN2 with the mass of the studied metabolites as well as the orthogonality between accurate mass and μeff , making this combination particularly interesting for the identification of several endogenous metabolites. The use of IM-MS remains of great interest for facilitating the annotation of neutral metabolites present in the electroosmotic flow (EOF) that are poorly or not separated by CZE.
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Affiliation(s)
- Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, The Netherlands.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | | | - Christian Wenz
- Agilent Technologies, Hewlett-Packard, Waldbronn, Germany
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
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27
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Sabbioni G, Berset JD, Day BW. Is It Realistic to Propose Determination of a Lifetime Internal Exposome? Chem Res Toxicol 2020; 33:2010-2021. [PMID: 32672951 DOI: 10.1021/acs.chemrestox.0c00092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biomonitoring of xenobiotics has been performed for many years in occupational and environmental medicine. It has revealed hidden exposures and the exposure of workers could be reduced. Although most of the toxic effects of chemicals on humans were discovered in workers, the scientific community has more recently focused on environmental samples. In several countries, urinary and blood samples have been collected and analyzed for xenobiotics. Health, biochemical, and clinical parameters were measured in the biomonitoring program of the Unites States. The data were collected and evaluated as group values, comparing races, ages, and gender. The term exposome was created in order to relate chemical exposure to health effects together with the terms genome, proteome, and transcriptome. Internal exposures were mostly established with snapshot measurements, which can lead to an obvious misclassification of the individual exposures. Albumin and hemoglobin adducts of xenobiotics reflect the exposure of a larger time frame, up to 120 days. It is likely that only a small fraction of xenobiotics form such adducts. In addition, adduct analyses are more work intensive than the measurement of xenobiotics and metabolites in urine and/or blood. New technology, such as high-resolution mass spectrometry, will enable the discovery of new compounds that have been overlooked in the past, since over 300,000 chemicals are commercially available and most likely also present in the environment. Yet, quantification will be challenging, as it was for the older methods. At this stage, determination of a lifetime internal exposome is very unrealistic. Instead of an experimental approach with a large number of people, which is economically and scientifically not feasible, in silico methods should be developed further to predict exposure, toxicity, and potential health effects of mixtures. The computer models will help to focus internal exposure investigations on smaller groups of people and smaller number of chemicals.
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Affiliation(s)
- Gabriele Sabbioni
- Institute of Environmental and Occupational Toxicology, CH-6780 Airolo, Switzerland.,Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, D-80336 München, Germany
| | - Jean-Daniel Berset
- Institute of Environmental and Occupational Toxicology, CH-6780 Airolo, Switzerland
| | - Billy W Day
- Medantox LLC, Pittsburgh, Pennsylvania 15241, United States.,ReNeuroGen LLC, Elm Grove, Wisconsin 53122, United States
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Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 2020; 15:1954-1991. [PMID: 32405051 DOI: 10.1038/s41596-020-0317-5] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Christine M Aceves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Irina Koester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Catherine Roullier
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Kunyang Sun
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard M Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Martin H Christian
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | | | | | - Randy Mojica-Flores
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama
| | - Johant Lakey-Beitia
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Victor Vásquez-Chaves
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Yilue Zhang
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nicole Tayler
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa
| | - Nombuso Ndlovu
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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Pourchet M, Debrauwer L, Klanova J, Price EJ, Covaci A, Caballero-Casero N, Oberacher H, Lamoree M, Damont A, Fenaille F, Vlaanderen J, Meijer J, Krauss M, Sarigiannis D, Barouki R, Le Bizec B, Antignac JP. Suspect and non-targeted screening of chemicals of emerging concern for human biomonitoring, environmental health studies and support to risk assessment: From promises to challenges and harmonisation issues. ENVIRONMENT INTERNATIONAL 2020; 139:105545. [PMID: 32361063 DOI: 10.1016/j.envint.2020.105545] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 05/07/2023]
Abstract
Large-scale suspect and non-targeted screening approaches based on high-resolution mass spectrometry (HRMS) are today available for chemical profiling and holistic characterisation of biological samples. These advanced techniques allow the simultaneous detection of a large number of chemical features, including markers of human chemical exposure. Such markers are of interest for biomonitoring, environmental health studies and support to risk assessment. Furthermore, these screening approaches have the promising capability to detect chemicals of emerging concern (CECs), document the extent of human chemical exposure, generate new research hypotheses and provide early warning support to policy. Whilst of growing importance in the environment and food safety areas, respectively, CECs remain poorly addressed in the field of human biomonitoring. This shortfall is due to several scientific and methodological reasons, including a global lack of harmonisation. In this context, the main aim of this paper is to present an overview of the basic principles, promises and challenges of suspect and non-targeted screening approaches applied to human samples as this specific field introduce major specificities compared to other fields. Focused on liquid chromatography coupled to HRMS-based data acquisition methods, this overview addresses all steps of these new analytical workflows. Beyond this general picture, the main activities carried out on this topic within the particular framework of the European Human Biomonitoring initiative (project HBM4EU, 2017-2021) are described, with an emphasis on harmonisation measures.
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Affiliation(s)
| | - Laurent Debrauwer
- TOXALIM (Research Centre in Food Toxicology), Toulouse University, INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University, 31027 Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, F-31027 Toulouse, France
| | - Jana Klanova
- RECETOX Centre, Masaryk University, Brno, Czech Republic
| | - Elliott J Price
- RECETOX Centre, Masaryk University, Brno, Czech Republic; Faculty of Sports Studies, Masaryk University, Brno, Czech Republic
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Belgium
| | | | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Austria
| | - Marja Lamoree
- Vrije Universiteit, Department Environment & Health, Amsterdam, the Netherlands
| | - Annelaure Damont
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Jeroen Meijer
- Vrije Universiteit, Department Environment & Health, Amsterdam, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Martin Krauss
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Denis Sarigiannis
- HERACLES Research Center on the Exposome and Health, Aristotle University of Thessaloniki, Greece
| | - Robert Barouki
- Unité UMR-S 1124 Inserm-Université Paris Descartes "Toxicologie Pharmacologie et Signalisation Cellulaire", Paris, France
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30
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Santacruz L, Hurtado DX, Doohan R, Thomas OP, Puyana M, Tello E. Metabolomic study of soft corals from the Colombian Caribbean: PSYCHE and 1H-NMR comparative analysis. Sci Rep 2020; 10:5417. [PMID: 32214197 PMCID: PMC7096504 DOI: 10.1038/s41598-020-62413-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms have evolved to survive against predators in complex marine ecosystems via the production of chemical compounds. Soft corals (Cnidaria, Anthozoa, Octocorallia) are an important source of chemically diverse metabolites with a broad spectrum of biological activities. Herein, we perform a comparative study between high-resolution proton nuclear magnetic resonance (1H-NMR) and pure shift yielded by chirp excitation (PSYCHE) experiments to analyze the metabolic profile of 24 soft corals from the Colombian Caribbean to correlate chemical fingerprints with their cytotoxic activity against three cancer cell lines (human cervical carcinoma (SiHa), human prostatic carcinoma (PC3) and human lung adenocarcinoma (A549)). All data obtained were explored using multivariate analysis using principal components analysis (PCA) and orthogonal partial least squares (OPLS) analysis. The results did not show a significant correlation between clusters using 1H-NMR data in the PCA and OPLS-DA models and therefore did not provide conclusive evidence; on the other hand, a metabolomic analysis of PSYCHE data obtained under the same parameters revealed that when a decoupled experiment is performed, it was possible to establish a statistically valid correlation between the chemical composition of soft corals and their cytotoxic activity against the PC3 cancer cell line, where the asperdiol and plexaurolone markers were putatively identified and related to the cytotoxic activity presented by extracts of Plexaurella sp. and Plexaura kukenthali, respectively. These results increase the speed, effectiveness and reliability of analyses for the study of this type of complex matrices.
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Affiliation(s)
- Liliana Santacruz
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia
| | - Diana X Hurtado
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia
| | - Roisin Doohan
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
| | - Mónica Puyana
- Departamento de Ciencias Biológicas y Ambientales, Universidad Jorge Tadeo Lozano, Carrera 4 # 22-61, 110311, Bogotá, Colombia
| | - Edisson Tello
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia.
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31
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Pezzatti J, Boccard J, Codesido S, Gagnebin Y, Joshi A, Picard D, González-Ruiz V, Rudaz S. Implementation of liquid chromatography-high resolution mass spectrometry methods for untargeted metabolomic analyses of biological samples: A tutorial. Anal Chim Acta 2020; 1105:28-44. [PMID: 32138924 DOI: 10.1016/j.aca.2019.12.062] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Untargeted metabolomics is now widely recognized as a useful tool for exploring metabolic changes taking place in biological systems under different conditions. By its nature, this is a highly interdisciplinary field of research, and mastering all of the steps comprised in the pipeline can be a challenging task, especially for those researchers new to the topic. In this tutorial, we aim to provide an overview of the most widely adopted methods of performing LC-HRMS-based untargeted metabolomics of biological samples. A detailed protocol is provided in the Supplementary Information for rapidly implementing a basic screening workflow in a laboratory setting. This tutorial covers experimental design, sample preparation and analysis, signal processing and data treatment, and, finally, data analysis and its biological interpretation. Each section is accompanied by up-to-date literature to guide readers through the preparation and optimization of such a workflow, as well as practical information for avoiding or fixing some of the most frequently encountered pitfalls.
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Affiliation(s)
- Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Julien Boccard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Santiago Codesido
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Yoric Gagnebin
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Abhinav Joshi
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland.
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32
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Beccaria M, Cabooter D. Current developments in LC-MS for pharmaceutical analysis. Analyst 2020; 145:1129-1157. [DOI: 10.1039/c9an02145k] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid chromatography (LC) based techniques in combination with mass spectrometry (MS) detection have had a large impact on the development of new pharmaceuticals in the past decades.
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Affiliation(s)
- Marco Beccaria
- KU Leuven
- Department for Pharmaceutical and Pharmacological Sciences
- Pharmaceutical Analysis
- Leuven
- Belgium
| | - Deirdre Cabooter
- KU Leuven
- Department for Pharmaceutical and Pharmacological Sciences
- Pharmaceutical Analysis
- Leuven
- Belgium
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33
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Doppler M, Bueschl C, Kluger B, Koutnik A, Lemmens M, Buerstmayr H, Rechthaler J, Krska R, Adam G, Schuhmacher R. Stable Isotope-Assisted Plant Metabolomics: Combination of Global and Tracer-Based Labeling for Enhanced Untargeted Profiling and Compound Annotation. FRONTIERS IN PLANT SCIENCE 2019; 10:1366. [PMID: 31708958 PMCID: PMC6824187 DOI: 10.3389/fpls.2019.01366] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/04/2019] [Indexed: 05/10/2023]
Abstract
Untargeted approaches and thus biological interpretation of metabolomics results are still hampered by the reliable assignment of the global metabolome as well as classification and (putative) identification of metabolites. In this work we present an liquid chromatography-mass spectrometry (LC-MS)-based stable isotope assisted approach that combines global metabolome and tracer based isotope labeling for improved characterization of (unknown) metabolites and their classification into tracer derived submetabolomes. To this end, wheat plants were cultivated in a customized growth chamber, which was kept at 400 ± 50 ppm 13CO2 to produce highly enriched uniformly 13C-labeled sample material. Additionally, native plants were grown in the greenhouse and treated with either 13C9-labeled phenylalanine (Phe) or 13C11-labeled tryptophan (Trp) to study their metabolism and biochemical pathways. After sample preparation, liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis and automated data evaluation, the results of the global metabolome- and tracer-labeling approaches were combined. A total of 1,729 plant metabolites were detected out of which 122 respective 58 metabolites account for the Phe- and Trp-derived submetabolomes. Besides m/z and retention time, also the total number of carbon atoms as well as those of the incorporated tracer moieties were obtained for the detected metabolite ions. With this information at hand characterization of unknown compounds was improved as the additional knowledge from the tracer approaches considerably reduced the number of plausible sum formulas and structures of the detected metabolites. Finally, the number of putative structure formulas was further reduced by isotope-assisted annotation tandem mass spectrometry (MS/MS) derived product ion spectra of the detected metabolites. A major innovation of this paper is the classification of the metabolites into submetabolomes which turned out to be valuable information for effective filtering of database hits based on characteristic structural subparts. This allows the generation of a final list of true plant metabolites, which can be characterized at different levels of specificity.
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Affiliation(s)
- Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Bueschl
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Andrea Koutnik
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Marc Lemmens
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Justyna Rechthaler
- University of Applied Sciences Wr. Neustadt, Degree Programme Biotechnical Processes (FHWN-Tulln), Tulln, Austria
| | - Rudolf Krska
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
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Choosing an Optimal Sample Preparation in Caulobacter crescentus for Untargeted Metabolomics Approaches. Metabolites 2019; 9:metabo9100193. [PMID: 31547088 PMCID: PMC6836107 DOI: 10.3390/metabo9100193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/16/2022] Open
Abstract
Untargeted metabolomics aims to provide a global picture of the metabolites present in the system under study. To this end, making a careful choice of sample preparation is mandatory to obtain reliable and reproducible biological information. In this study, eight different sample preparation techniques were evaluated using Caulobacter crescentus as a model for Gram-negative bacteria. Two cell retrieval systems, two quenching and extraction solvents, and two cell disruption procedures were combined in a full factorial experimental design. To fully exploit the multivariate structure of the generated data, the ANOVA multiblock orthogonal partial least squares (AMOPLS) algorithm was employed to decompose the contribution of each factor studied and their potential interactions for a set of annotated metabolites. All main effects of the factors studied were found to have a significant contribution on the total observed variability. Cell retrieval, quenching and extraction solvent, and cell disrupting mechanism accounted respectively for 27.6%, 8.4%, and 7.0% of the total variability. The reproducibility and metabolome coverage of the sample preparation procedures were then compared and evaluated in terms of relative standard deviation (RSD) on the area for the detected metabolites. The protocol showing the best performance in terms of recovery, versatility, and variability was centrifugation for cell retrieval, using MeOH:H2O (8:2) as quenching and extraction solvent, and freeze-thaw cycles as the cell disrupting mechanism.
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Screening 89 Pesticides in Fishery Drugs by Ultrahigh Performance Liquid Chromatography Tandem Quadrupole-Orbitrap Mass Spectrometer. Molecules 2019; 24:molecules24183375. [PMID: 31533222 PMCID: PMC6767809 DOI: 10.3390/molecules24183375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Multiclass screening of drugs with high resolution mass spectrometry is of great interest due to its high time-efficiency and excellent accuracy. A high-scale, fast screening method for pesticides in fishery drugs was established based on ultrahigh performance liquid chromatography tandem quadrupole-Orbitrap high-resolution mass spectrometer. The target compounds - were diluted in methanol and extracted by ultrasonic treatment, and the extracts were diluted with MeOH-water (1:1, v/v) and centrifuged to remove impurities. The chromatographic separation was performed on an Accucore aQ-MS column (100 mm × 2.1 mm, 2.6 μm) with gradient elution using 0.1% formic acid in water (containing 5 mmol/L ammonium formate) and 0.1% formic acid in methanol (containing 5 mmol/L ammonium formate) in Full Scan/dd-MS2 (TopN) scan mode. A screening database, including mass spectrometric and chromatographic information, was established for identification of compounds. The screening detection limits of methods ranged between 1–500 mg/kg, the recoveries of real samples spiked with the concentration of 10 mg/kg and 100 mg/kg standard mixture ranged from 70% to 110% for more than sixty compounds, and the relative standard deviations (RSDs) were less than 20%. The application of this method showed that target pesticides were screened out in 10 samples out of 21 practical samples, in which the banned pesticide chlorpyrifos were detected in 3 out of the 10 samples.
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Bell M, Blais JM. "-Omics" workflow for paleolimnological and geological archives: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:438-455. [PMID: 30965259 DOI: 10.1016/j.scitotenv.2019.03.477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
"-Omics" is a powerful screening method with applications in molecular biology, toxicology, wildlife biology, natural product discovery, and many other fields. Genomics, proteomics, metabolomics, and lipidomics are common examples included under the "-omics" umbrella. This screening method uses combinations of untargeted, semi-targeted, and targeted analyses paired with data mining to facilitate researchers' understanding of the genome, proteins, and small organic molecules in biological systems. Recently, however, the use of "-omics" has expanded into the fields of geology, specifically petrology, and paleolimnology. Specifically, untargeted analyses stand to transform these fields as petroleomics, and sediment-"omics" become more prevalent. "-Omics" facilitates the visualization of small molecule profiles from environmental matrices (i.e. oil and sediment). Small molecule profiles can provide improved understanding of small molecules distributions throughout the environment, and how those compositions can change depending on conditions (i.e. climate change, weathering, etc.). "-Omics" also facilities discovery of next-generation biomarkers that can be used for oil source identification and as proxies for reconstructing past environmental changes. Untargeted analyses paired with data mining and multivariate statistical analyses represents a powerful suite of tools for hypothesis generation, and new method development for environmental reconstructions. Here we present an introduction to "-omics" methodology, technical terms, and examples of applications to paleolimnology and petrology. The purpose of this review is to highlight the important considerations at each step in the "-omics" workflow to produce high quality and statistically powerful data for petrological and paleolimnological applications.
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Affiliation(s)
- Madison Bell
- Laboratory for the Analysis of Natural and Synthetic Environmental Toxicants, Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jules M Blais
- Laboratory for the Analysis of Natural and Synthetic Environmental Toxicants, Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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Codesido S, Randazzo GM, Lehmann F, González-Ruiz V, García A, Xenarios I, Liechti R, Bridge A, Boccard J, Rudaz S. DynaStI: A Dynamic Retention Time Database for Steroidomics. Metabolites 2019; 9:E85. [PMID: 31052310 PMCID: PMC6572260 DOI: 10.3390/metabo9050085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/12/2019] [Accepted: 04/24/2019] [Indexed: 12/11/2022] Open
Abstract
: Steroidomics studies face the challenge of separating analytical compounds with very similar structures (i.e., isomers). Liquid chromatography (LC) is commonly used to this end, but the shared core structure of this family of compounds compromises effective separations among the numerous chemical analytes with comparable physico-chemical properties. Careful tuning of the mobile phase gradient and an appropriate choice of the stationary phase can be used to overcome this problem, in turn modifying the retention times in different ways for each compound. In the usual workflow, this approach is suboptimal for the annotation of features based on retention times since it requires characterizing a library of known compounds for every fine-tuned configuration. We introduce a software solution, DynaStI, that is capable of annotating liquid chromatography-mass spectrometry (LC-MS) features by dynamically generating the retention times from a database containing intrinsic properties of a library of metabolites. DynaStI uses the well-established linear solvent strength (LSS) model for reversed-phase LC. Given a list of LC-MS features and some characteristics of the LC setup, this software computes the corresponding retention times for the internal database and then annotates the features using the exact masses with predicted retention times at the working conditions. DynaStI (https://dynasti.vital-it.ch) is able to automatically calibrate its predictions to compensate for deviations in the input parameters. The database also includes identification and structural information for each annotation, such as IUPAC name, CAS number, SMILES string, metabolic pathways, and links to external metabolomic or lipidomic databases.
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Affiliation(s)
- Santiago Codesido
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
| | - Giuseppe Marco Randazzo
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
- Dalle Molle Institute for Artificial Intelligence, 6928 Manno, Switzerland.
| | - Fabio Lehmann
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
- Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland.
| | - Arnaud García
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
| | - Ioannis Xenarios
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Robin Liechti
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Alan Bridge
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
- Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland.
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland.
- Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland.
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Plante PL, Francovic-Fontaine É, May JC, McLean JA, Baker ES, Laviolette F, Marchand M, Corbeil J. Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS. Anal Chem 2019; 91:5191-5199. [PMID: 30932474 PMCID: PMC6628689 DOI: 10.1021/acs.analchem.8b05821] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Untargeted metabolomic measurements using mass spectrometry are a powerful tool for uncovering new small molecules with environmental and biological importance. The small molecule identification step, however, still remains an enormous challenge due to fragmentation difficulties or unspecific fragment ion information. Current methods to address this challenge are often dependent on databases or require the use of nuclear magnetic resonance (NMR), which have their own difficulties. The use of the gas-phase collision cross section (CCS) values obtained from ion mobility spectrometry (IMS) measurements were recently demonstrated to reduce the number of false positive metabolite identifications. While promising, the amount of empirical CCS information currently available is limited, thus predictive CCS methods need to be developed. In this article, we expand upon current experimental IMS capabilities by predicting the CCS values using a deep learning algorithm. We successfully developed and trained a prediction model for CCS values requiring only information about a compound's SMILES notation and ion type. The use of data from five different laboratories using different instruments allowed the algorithm to be trained and tested on more than 2400 molecules. The resulting CCS predictions were found to achieve a coefficient of determination of 0.97 and median relative error of 2.7% for a wide range of molecules. Furthermore, the method requires only a small amount of processing power to predict CCS values. Considering the performance, time, and resources necessary, as well as its applicability to a variety of molecules, this model was able to outperform all currently available CCS prediction algorithms.
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Affiliation(s)
- Pier-Luc Plante
- Big Data Research Centre, Université Laval, Québec City G1 V 0A6, Canada
- Centre de Recherche en Infectiologie de I’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City G1 V 4G2, Canada
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec City, G1 V 0A6, Canada
| | - Élina Francovic-Fontaine
- Big Data Research Centre, Université Laval, Québec City G1 V 0A6, Canada
- Centre de Recherche en Infectiologie de I’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City G1 V 4G2, Canada
| | - Jody C. May
- Départment of Chemistry, Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Départment of Chemistry, Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Erin S. Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - Mario Marchand
- Big Data Research Centre, Université Laval, Québec City G1 V 0A6, Canada
| | - Jacques Corbeil
- Big Data Research Centre, Université Laval, Québec City G1 V 0A6, Canada
- Centre de Recherche en Infectiologie de I’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City G1 V 4G2, Canada
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec City, G1 V 0A6, Canada
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Gagnebin Y, Pezzatti J, Lescuyer P, Boccard J, Ponte B, Rudaz S. Toward a better understanding of chronic kidney disease with complementary chromatographic methods hyphenated with mass spectrometry for improved polar metabolome coverage. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1116:9-18. [PMID: 30951967 DOI: 10.1016/j.jchromb.2019.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
The prevalence of chronic kidney disease (CKD) is increasing worldwide. New technical approaches are needed to improve early diagnosis, disease understanding and patient monitoring, and to evaluate new therapies. Metabolomics, as a prime candidate in the field of CKD research, aims to comprehensively analyze the metabolic complexity of biological systems. An extensive analysis of the metabolites contained in biofluids is therefore needed, and the combination of data obtained from multiple analytical platforms constitutes a promising methodological approach. This study presents an original workflow based on complementary chromatographic conditions, reversed-phase and hydrophilic interaction chromatography hyphenated to mass spectrometry to improve the polar metabolome coverage coupled with a univocal metabolite annotation strategy enabling a rapid access to the biological interpretation. This multiplatform workflow was applied in a CKD cohort study to assess plasma metabolic profile modifications related to renal disease. Multivariate analysis of 278 endogenous annotated metabolites enabled patient stratification with respect to CKD stages and helped to generate new biological insights, while also confirming the relevance of tryptophan metabolism pathway in this condition.
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Affiliation(s)
- Yoric Gagnebin
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Julian Pezzatti
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland; Swiss Center of Human Applied Toxicology, University of Basel, Switzerland
| | - Belén Ponte
- Service of Nephrology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland; Swiss Center of Human Applied Toxicology, University of Basel, Switzerland.
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Pezzatti J, González-Ruiz V, Codesido S, Gagnebin Y, Joshi A, Guillarme D, Schappler J, Picard D, Boccard J, Rudaz S. A scoring approach for multi-platform acquisition in metabolomics. J Chromatogr A 2019; 1592:47-54. [PMID: 30685186 DOI: 10.1016/j.chroma.2019.01.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/19/2018] [Accepted: 01/09/2019] [Indexed: 12/31/2022]
Abstract
Since the ultimate goal of untargeted metabolomics is the analysis of the broadest possible range of metabolites, some new metrics have to be used by researchers to evaluate and select different analytical strategies when multi-platform analyses are considered. In this context, we aimed at developing a scoring approach allowing to compare the performance of different LC-MS conditions for metabolomics studies. By taking into account both chromatographic and MS attributes of the analytes' peaks (i.e. retention, signal-to-noise ratio, peak intensity and shape), the newly proposed score reflects the potential of a set of LC-MS operating conditions to provide useful analytical information for a given compound. A chemical library containing 597 metabolites was used as a benchmark to apply this approach on two RPLC and three HILIC methods hyphenated to high resolution mass spectrometry (HRMS) in positive and negative ionization modes. The scores not only allowed to evaluate each analytical platform, but also to optimize the number of analytical methods needed for the analysis of metabolomics samples. As a result, the most informative combination of three LC methods and ionization modes was found, leading to a coverage of nearly 95% of the detected compounds. It was therefore demonstrated that the overall performance reached with three selected methods was almost equivalent to the performance reached when five LC-MS conditions were used.
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Affiliation(s)
- Julian Pezzatti
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Santiago Codesido
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Yoric Gagnebin
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Abhinav Joshi
- Department of Cell Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Julie Schappler
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Didier Picard
- Department of Cell Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU - Rue Michel Servet 1, 1211 Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland.
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Drouin N, Pezzatti J, Gagnebin Y, González-Ruiz V, Schappler J, Rudaz S. Effective mobility as a robust criterion for compound annotation and identification in metabolomics: Toward a mobility-based library. Anal Chim Acta 2018; 1032:178-187. [DOI: 10.1016/j.aca.2018.05.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/04/2018] [Accepted: 05/23/2018] [Indexed: 12/20/2022]
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Rochat B, Mohamed R, Sottas PE. LC-HRMS Metabolomics for Untargeted Diagnostic Screening in Clinical Laboratories: A Feasibility Study. Metabolites 2018; 8:metabo8020039. [PMID: 29914076 PMCID: PMC6027396 DOI: 10.3390/metabo8020039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022] Open
Abstract
Today’s high-resolution mass spectrometers (HRMS) allow bioanalysts to perform untargeted/global determinations that can reveal unexpected compounds or concentrations in a patient’s sample. This could be performed for preliminary diagnosis attempts when usual diagnostic processes and targeted determinations fail. We have evaluated an untargeted diagnostic screening (UDS) procedure. UDS is a metabolome analysis that compares one sample (e.g., a patient) with control samples (a healthy population). Using liquid chromatography (LC)-HRMS full-scan analysis of human serum extracts and unsupervised data treatment, we have compared individual samples that were spiked with one xenobiotic or a higher level of one endogenous compound with control samples. After the use of different filters that drastically reduced the number of metabolites detected, the spiked compound was eventually revealed in each test sample and ranked. The proposed UDS procedure appears feasible and reliable to reveal unexpected xenobiotics (toxicology) or higher concentrations of endogenous metabolites. HRMS-based untargeted approaches could be useful as preliminary diagnostic screening when canonical processes do not reveal disease etiology nor establish a clear diagnosis and could reduce misdiagnosis. On the other hand, the risk of overdiagnosis of this approach should be reduced with mandatory biomedical interpretation of the patient’s UDS results and with confirmatory targeted and quantitative determinations.
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Affiliation(s)
- Bertrand Rochat
- Protein Analysis Facility, Center for Integrative Genomics (CIG), University of Lausanne, CH-1015 Lausanne, Switzerland.
| | - Rayane Mohamed
- Département Formation Recherche, Centre Hospitalier Universitaire Vaudois (CHUV), CH-1011 Lausanne, Switzerland.
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Multiclass screening of >200 pharmaceutical and other residues in aquatic foods by ultrahigh-performance liquid chromatography-quadrupole-Orbitrap mass spectrometry. Anal Bioanal Chem 2018; 410:5545-5553. [PMID: 29748759 DOI: 10.1007/s00216-018-1124-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 01/21/2023]
Abstract
A quick screening method of more than 200 pharmaceutical and other residues in aquatic foods based on ultrahigh-performance liquid chromatography-quadrupole-Orbitrap mass spectrometry (UHPLC-Q/Orbitrap MS) was established. In this method, after the addition of 200 μL of 1 M EDTA-Na2, 2 g of each sample homogenate was extracted successively with 10 mL of acetonitrile and 10 mL of ethyl acetate. The extracts were combined, dried under nitrogen flow, and redissolved in 0.1% formic acid in acetonitrile/water (4:6, v/v) for analysis. The prepared samples were analyzed by UHPLC- Q/Orbitrap MS system in Full MS/ddMS2 (full-scan data-dependent MS/MS) mode. Compound identification was performed through comparison of the sample data with the database for standard chemicals, including the retention time, precursor ion, product ions, and isotope pattern for all 206 compounds. Five different aquatic food matrices (carp, shrimp, crab, eel, and mussel) spiked with the analytes at 1, 10, and 50 ng/g were evaluated to assess recoveries, precision, matrix effects, stability, and detection limits using the method. UHPLC analyses required 25 min, and 178-200 analytes met identification criteria at 50 ng/g depending on the matrix. Furthermore, practical application of this method for real samples displayed strong screening capability. Graphical abstract A quick screening method of >200 pharmaceutical and other residues in aquatic foods based on ultrahighperformance liquid chromatography-quadrupole-Orbitrap mass spectrometer was established. Fivedifferent aquatic food matrices, including carp, shrimp, crab, eel and mussel, were studied to evaluatescreen limit at 1, 10 and 50 μg·kg-1 level. Results suggest the high reliability, high time-efficiency and goodsimplicity of the method.
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Blaženović I, Kind T, Ji J, Fiehn O. Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites 2018; 8:E31. [PMID: 29748461 PMCID: PMC6027441 DOI: 10.3390/metabo8020031] [Citation(s) in RCA: 392] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/26/2018] [Accepted: 05/06/2018] [Indexed: 01/17/2023] Open
Abstract
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.
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Affiliation(s)
- Ivana Blaženović
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Tobias Kind
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science of Jiangnan University, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Vallarino JG, Erban A, Fehrle I, Fernie AR, Kopka J, Osorio S. Acquisition of Volatile Compounds by Gas Chromatography-Mass Spectrometry (GC-MS). Methods Mol Biol 2018; 1778:225-239. [PMID: 29761442 DOI: 10.1007/978-1-4939-7819-9_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plants synthesize and emit a large range of volatile organic compounds (VOCs) that play important roles in their interactions with the environment, from attracting pollinators and seed dispersers to protectants such as repellants and pathogen inhibitors. As such, the development of techniques for headspace collection of volatiles in combination with gas chromatography-mass spectrometry (GC-MS) has an important impact on our understanding of the biosynthesis of plant VOCs. Furthermore, knowledge of the plant VOCs can be valuable in relation to plant breeding for improving fruit flavor or enhancing resistance to insects or pathogens. This chapter describes a reliable method for extracting volatile compounds by headspace solid-phase microextraction (HS-SPME), and separate and detect them by GC-MS.
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Affiliation(s)
- José G Vallarino
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ines Fehrle
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterranea (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain.
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Godzien J, Gil de la Fuente A, Otero A, Barbas C. Metabolite Annotation and Identification. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Benito S, Sánchez-Ortega A, Unceta N, Andrade F, Aldámiz-Echevarria L, Goicolea MA, Barrio RJ. Untargeted metabolomics for plasma biomarker discovery for early chronic kidney disease diagnosis in pediatric patients using LC-QTOF-MS. Analyst 2018; 143:4448-4458. [DOI: 10.1039/c8an00864g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Pediatric chronic kidney disease (CKD) is a clinical syndrome characterized by renal hypofunction occurring due to gradual and irreversible kidney damage that can further progress over time.
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Affiliation(s)
- S. Benito
- Department of Analytical Chemistry
- University of the Basque Country (UPV/EHU)
- Faculty of Pharmacy
- Paseo de la Universidad 7
- 01006 Vitoria-Gasteiz
| | - A. Sánchez-Ortega
- Central Service of Analysis (SGiker)
- University of the Basque Country (UPV/EHU)
- 01006 Vitoria-Gasteiz
- Spain
| | - N. Unceta
- Department of Analytical Chemistry
- University of the Basque Country (UPV/EHU)
- Faculty of Pharmacy
- Paseo de la Universidad 7
- 01006 Vitoria-Gasteiz
| | - F. Andrade
- Group of Metabolism
- BioCruces Health Research Institute
- CIBER de Enfermedades Raras (CIBERER)
- 48903 Barakaldo
- Spain
| | - L. Aldámiz-Echevarria
- Group of Metabolism
- BioCruces Health Research Institute
- CIBER de Enfermedades Raras (CIBERER)
- 48903 Barakaldo
- Spain
| | - M. A. Goicolea
- Department of Analytical Chemistry
- University of the Basque Country (UPV/EHU)
- Faculty of Pharmacy
- Paseo de la Universidad 7
- 01006 Vitoria-Gasteiz
| | - R. J. Barrio
- Department of Analytical Chemistry
- University of the Basque Country (UPV/EHU)
- Faculty of Pharmacy
- Paseo de la Universidad 7
- 01006 Vitoria-Gasteiz
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