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Cafarella C, Mangraviti D, Rigano F, Dugo P, Mondello L. Rapid evaporative ionization mass spectrometry: A survey through 15 years of applications. J Sep Sci 2024; 47:e2400155. [PMID: 38772742 DOI: 10.1002/jssc.202400155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
Rapid evaporative ionization mass spectrometry (REIMS) is a relatively recent MS technique explored in many application fields, demonstrating high versatility in the detection of a wide range of chemicals, from small molecules (phenols, amino acids, di- and tripeptides, organic acids, and sugars) to larger biomolecules, that is, phospholipids and triacylglycerols. Different sampling devices were used depending on the analyzed matrix (liquid or solid), resulting in distinct performances in terms of automation, reproducibility, and sensitivity. The absence of laborious and time-consuming sample preparation procedures and chromatographic separations was highlighted as a major advantage compared to chromatographic methods. REIMS was successfully used to achieve a comprehensive sample profiling according to a metabolomics untargeted analysis. Moreover, when a multitude of samples were available, the combination with chemometrics allowed rapid sample differentiation and the identification of discriminant features. The present review aims to provide a survey of literature reports based on the use of such analytical technology, highlighting its mode of operation in different application areas, ranging from clinical research, mostly focused on cancer diagnosis for the accurate identification of tumor margins, to the agri-food sector aiming at the safeguard of food quality and security.
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Affiliation(s)
- Cinzia Cafarella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Domenica Mangraviti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Paola Dugo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont s.r.l., former Veterinary School, University of Messina, Messina, Italy
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont s.r.l., former Veterinary School, University of Messina, Messina, Italy
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Bradley R, Simon D, Spiga L, Xiang Y, Takats Z, Williams H. Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa. mSystems 2024; 9:e0116523. [PMID: 38530056 PMCID: PMC11019781 DOI: 10.1128/msystems.01165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors. IMPORTANCE This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the identification of specific oxidative stress biomarkers, and demonstrated that hypochlorous acid, an oxidant specifically produced by human neutrophils during infection, affects quorum sensing and reduces production of the virulence factors pyocyanin and elastase. No pyocyanin was detectable and elastase levels were reduced by more than 75% in bacteria grown in the presence of hypochlorous acid. This approach has the potential to be widely applicable to the characterization of the stress responses of bacteria.
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Affiliation(s)
- Rob Bradley
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Daniel Simon
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
- The Rosalind Franklin Institute, Didcot, United Kingdom
| | - Livia Spiga
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Huw Williams
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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Carpenter JM, Hynds HM, Bimpeh K, Hines KM. HILIC-IM-MS for Simultaneous Lipid and Metabolite Profiling of Bacteria. ACS MEASUREMENT SCIENCE AU 2024; 4:104-116. [PMID: 38404491 PMCID: PMC10885331 DOI: 10.1021/acsmeasuresciau.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 02/27/2024]
Abstract
Although MALDI-ToF platforms for microbial identifications have found great success in clinical microbiology, the sole use of protein fingerprints for the discrimination of closely related species, strain-level identifications, and detection of antimicrobial resistance remains a challenge for the technology. Several alternative mass spectrometry-based methods have been proposed to address the shortcomings of the protein-centric approach, including MALDI-ToF methods for fatty acid/lipid profiling and LC-MS profiling of metabolites. However, the molecular diversity of microbial pathogens suggests that no single "ome" will be sufficient for the accurate and sensitive identification of strain- and susceptibility-level profiling of bacteria. Here, we describe the development of an alternative approach to microorganism profiling that relies upon both metabolites and lipids rather than a single class of biomolecule. Single-phase extractions based on butanol, acetonitrile, and water (the BAW method) were evaluated for the recovery of lipids and metabolites from Gram-positive and -negative microorganisms. We found that BAW extraction solutions containing 45% butanol provided optimal recovery of both molecular classes in a single extraction. The single-phase extraction method was coupled to hydrophilic interaction liquid chromatography (HILIC) and ion mobility-mass spectrometry (IM-MS) to resolve similar-mass metabolites and lipids in three dimensions and provide multiple points of evidence for feature annotation in the absence of tandem mass spectrometry. We demonstrate that the combined use of metabolites and lipids can be used to differentiate microorganisms to the species- and strain-level for four of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa) using data from a single ionization mode. These results present promising, early stage evidence for the use of multiomic signatures for the identification of microorganisms by liquid chromatography, ion mobility, and mass spectrometry that, upon further development, may improve upon the level of identification provided by current methods.
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Affiliation(s)
- Jana M. Carpenter
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Hannah M. Hynds
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kingsley Bimpeh
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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Wagner I, Grigoraki L, Enevoldson P, Clarkson M, Jones S, Hurst JL, Beynon RJ, Ranson H. Rapid identification of mosquito species and age by mass spectrometric analysis. BMC Biol 2023; 21:10. [PMID: 36690979 PMCID: PMC9872345 DOI: 10.1186/s12915-022-01508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND A rapid, accurate method to identify and to age-grade mosquito populations would be a major advance in predicting the risk of pathogen transmission and evaluating the public health impact of vector control interventions. Whilst other spectrometric or transcriptomic methods show promise, current approaches rely on challenging morphological techniques or simple binary classifications that cannot identify the subset of the population old enough to be infectious. In this study, the ability of rapid evaporative ionisation mass spectrometry (REIMS) to identify the species and age of mosquitoes reared in the laboratory and derived from the wild was investigated. RESULTS The accuracy of REIMS in identifying morphologically identical species of the Anopheles gambiae complex exceeded 97% using principal component/linear discriminant analysis (PC-LDA) and 84% based on random forest analysis. Age separation into 3 different age categories (1 day, 5-6 days, 14-15 days) was achieved with 99% (PC-LDA) and 91% (random forest) accuracy. When tested on wild mosquitoes from the UK, REIMS data could determine the species and age of the specimens with accuracies of 91 and 90% respectively. CONCLUSIONS The accuracy of REIMS to resolve the species and age of Anopheles mosquitoes is comparable to that achieved by infrared spectroscopy approaches. The processing time and ease of use represent significant advantages over current, dissection-based methods. Importantly, the accuracy was maintained when using wild mosquitoes reared under differing environmental conditions, and when mosquitoes were stored frozen or desiccated. This high throughput approach thus has potential to conduct rapid, real-time monitoring of vector populations, providing entomological evidence of the impact of alternative interventions.
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Affiliation(s)
- Iris Wagner
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Linda Grigoraki
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
| | - Peter Enevoldson
- Walton Centre NHS Foundation Trust, Lower Lane, Liverpool, L9 7LJ UK
- Department of Livestock and One Health, University of Liverpool, Institute of Infection, Veterinary and Ecological Sciences, Leahurst Campus, Neston, CH64 7TE UK
| | - Michael Clarkson
- Department of Livestock and One Health, University of Liverpool, Institute of Infection, Veterinary and Ecological Sciences, Leahurst Campus, Neston, CH64 7TE UK
| | - Sam Jones
- International Pheromone Systems Ltd, Evolution House, Long Acres Road, Clayhill Industrial Estate, Neston, CH64 3RL Cheshire UK
| | - Jane L. Hurst
- Mammalian Behaviour and Evolution Group, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE UK
| | - Robert J. Beynon
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Hilary Ranson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
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Kaufmann M, Vaysse PM, Savage A, Amgheib A, Marton A, Manoli E, Fichtinger G, Pringle SD, Rudan JF, Heeren RMA, Takáts Z, Balog J, Porta Siegel T. Harmonization of Rapid Evaporative Ionization Mass Spectrometry Workflows across Four Sites and Testing Using Reference Material and Local Food-Grade Meats. Metabolites 2022; 12:1130. [PMID: 36422272 PMCID: PMC9699633 DOI: 10.3390/metabo12111130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid evaporative ionization mass spectrometry (REIMS) is a direct tissue metabolic profiling technique used to accurately classify tissues using pre-built mass spectral databases. The reproducibility of the analytical equipment, methodology and tissue classification algorithms has yet to be evaluated over multiple sites, which is an essential step for developing this technique for future clinical applications. In this study, we harmonized REIMS methodology using single-source reference material across four sites with identical equipment: Imperial College London (UK); Waters Research Centre (Hungary); Maastricht University (The Netherlands); and Queen's University (Canada). We observed that method harmonization resulted in reduced spectral variability across sites. Each site then analyzed four different types of locally-sourced food-grade animal tissue. Tissue recognition models were created at each site using multivariate statistical analysis based on the different metabolic profiles observed in the m/z range of 600-1000, and these models were tested against data obtained at the other sites. Cross-validation by site resulted in 100% correct classification of two reference tissues and 69-100% correct classification for food-grade meat samples. While we were able to successfully minimize between-site variability in REIMS signals, differences in animal tissue from local sources led to significant variability in the accuracy of an individual site's model. Our results inform future multi-site REIMS studies applied to clinical samples and emphasize the importance of carefully-annotated samples that encompass sufficient population diversity.
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Affiliation(s)
- Martin Kaufmann
- Department of Surgery, Queen’s University, Kingston, ON K7L 2V7, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center + (MUMC+), 6229 HX Maastricht, The Netherlands
- Department of Otorhinolaryngology, Head & Neck Surgery, MUMC+, 6229 HX Maastricht, The Netherlands
| | - Adele Savage
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
| | - Ala Amgheib
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
| | | | - Eftychios Manoli
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
| | - Gabor Fichtinger
- School of Computing, Queen’s University, Kingston, ON K7L 2N8, Canada
| | | | - John F. Rudan
- Department of Surgery, Queen’s University, Kingston, ON K7L 2V7, Canada
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Zoltán Takáts
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
| | - Júlia Balog
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
- Waters Research Center, 1031 Budapest, Hungary
| | - Tiffany Porta Siegel
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
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Morgan J, Salcedo-Sora JE, Wagner I, Beynon RJ, Triana-Chavez O, Strode C. Rapid Evaporative Ionization Mass Spectrometry (REIMS): a Potential and Rapid Tool for the Identification of Insecticide Resistance in Mosquito Larvae. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:5. [PMID: 36082679 PMCID: PMC9459442 DOI: 10.1093/jisesa/ieac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 06/15/2023]
Abstract
Insecticide resistance is a significant challenge facing the successful control of mosquito vectors globally. Bioassays are currently the only method for phenotyping resistance. They require large numbers of mosquitoes for testing, the availability of a susceptible comparator strain, and often insectary facilities. This study aimed to trial the novel use of rapid evaporative ionization mass spectrometry (REIMS) for the identification of insecticide resistance in mosquitoes. No sample preparation is required for REIMS and analysis can be rapidly conducted within hours. Temephos resistant Aedes aegypti (Linnaeus) larvae from Cúcuta, Colombia and temephos susceptible larvae from two origins (Bello, Colombia, and the lab reference strain New Orleans) were analyzed using REIMS. We tested the ability of REIMS to differentiate three relevant variants: population source, lab versus field origin, and response to insecticide. The classification of these data was undertaken using linear discriminant analysis (LDA) and random forest. Classification models built using REIMS data were able to differentiate between Ae. aegypti larvae from different populations with 82% (±0.01) accuracy, between mosquitoes of field and lab origin with 89% (±0.01) accuracy and between susceptible and resistant larvae with 85% (±0.01) accuracy. LDA classifiers had higher efficiency than random forest with this data set. The high accuracy observed here identifies REIMS as a potential new tool for rapid identification of resistance in mosquitoes. We argue that REIMS and similar modern phenotyping alternatives should complement existing insecticide resistance management tools.
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Affiliation(s)
- Jasmine Morgan
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, L39 4QP, UK
| | | | - Iris Wagner
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Omar Triana-Chavez
- Instituto de Biología, Facultad de Ciencias Exactas y Naturales (FCEN), University of Antioquia, Medellín, Colombia
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Das S, Bhatia R. Liquid extraction surface analysis-mass spectrometry: An advanced and environment-friendly analytical tool in modern analysis. J Sep Sci 2022; 45:2746-2765. [PMID: 35579471 DOI: 10.1002/jssc.202100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/23/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022]
Abstract
The Liquid Extraction Surface Analysis technique is a new high-throughput instrument for ambient mass spectrometry. The benefits of the Liquid Extraction Surface Analysis-Mass Spectrometry approach are the high throughput screening of samples and the absence of sample preparation. Liquid Extraction Surface Analysis-Mass Spectrometry also consumes less solvent for extraction, making it more environmentally friendly and there is no substrate restriction. It utilizes advanced instrumentation like the use of robotic pipettes, nanoelectrospray systems, electronspray ionization chips which makes it highly efficient. In recent years, Liquid Extraction Surface Analysis-Mass Spectrometry has seen widespread use in a variety of analytical fields including drug metabolite analysis, mapping drug distribution in tissues, protein and lipid characterization etc. In this review, we have summarized the basic working principles of the Liquid Extraction Surface Analysis-Mass Spectrometry approach in detail along with a detailed description of the recently reported applications in the analysis of proteins, lipids, drugs and foods. The investigated analytes along with detection methodologies and significant outcomes of various research reports have been presented with the help of tables. This tool has also been utilized in clinical investigations of biological fluids, fingerprint analysis and authentication of agarwood. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shibam Das
- Department of Pharmaceutical Chemistry & Analysis, ISF College of Pharmacy Moga, Punjab, 142001, India
| | - Rohit Bhatia
- Department of Pharmaceutical Chemistry & Analysis, ISF College of Pharmacy Moga, Punjab, 142001, India
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8
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Su H, Jiang ZH, Chiou SF, Shiea J, Wu DC, Tseng SP, Jain SH, Chang CY, Lu PL. Rapid Characterization of Bacterial Lipids with Ambient Ionization Mass Spectrometry for Species Differentiation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092772. [PMID: 35566120 PMCID: PMC9104219 DOI: 10.3390/molecules27092772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022]
Abstract
Ambient ionization mass spectrometry (AIMS) is both labor and time saving and has been proven to be useful for the rapid delineation of trace organic and biological compounds with minimal sample pretreatment. Herein, an analytical platform of probe sampling combined with a thermal desorption–electrospray ionization/mass spectrometry (TD-ESI/MS) and multivariate statistical analysis was developed to rapidly differentiate bacterial species based on the differences in their lipid profiles. For comparison, protein fingerprinting was also performed with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) to distinguish these bacterial species. Ten bacterial species, including five Gram-negative and five Gram-positive bacteria, were cultured, and the lipids in the colonies were characterized with TD-ESI/MS. As sample pretreatment was unnecessary, the analysis of the lipids in a bacterial colony growing on a Petri dish was completed within 1 min. The TD-ESI/MS results were further performed by principal component analysis (PCA) and hierarchical cluster analysis (HCA) to assist the classification of the bacteria, and a low relative standard deviation (5.2%) of the total ion current was obtained from repeated analyses of the lipids in a single bacterial colony. The PCA and HCA results indicated that different bacterial species were successfully distinguished by the differences in their lipid profiles as validated by the differences in their protein profiles recorded from the MALDI-TOF analysis. In addition, real-time monitoring of the changes in the specific lipids of a colony with growth time was also achieved with probe sampling and TD-ESI/MS. The developed analytical platform is promising as a useful diagnostic tool by which to rapidly distinguish bacterial species in clinical practice.
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Affiliation(s)
- Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Zong-Han Jiang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Shu-Fen Chiou
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Correspondence: (J.S.); (P.-L.L.)
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
- Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Shu-Huei Jain
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
| | - Chung-Yu Chang
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Po-Liang Lu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- College of Medicine, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- Correspondence: (J.S.); (P.-L.L.)
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9
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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10
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Zhou X, Zhang W, Ouyang Z. Recent advances in on-site mass spectrometry analysis for clinical applications. Trends Analyt Chem 2022; 149:116548. [PMID: 35125564 PMCID: PMC8802081 DOI: 10.1016/j.trac.2022.116548] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, mass spectrometry (MS) is increasingly attracting interests for clinical applications, which also calls for technical innovations to make a transfer of MS from conventional analytical laboratories to clinics. The system design and analysis procedure should be friendly for novice users and appliable for on-site clinical diagnosis. In addition, the analysis result should be auto-interpreted and reported in formats much simpler than mass spectra. This motivates new ideas for developments in all the aspects of MS. In this review, we report recent advances of direct sampling ionization and miniature MS system, which have been developed targeting clinical and even point-of-care analysis. We also discuss the trend of the development and provide perspective on the technical challenges raised by diseases such as coronavirus SARS-CoV-2.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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Havlikova J, May RC, Styles IB, Cooper HJ. Liquid Extraction Surface Analysis Mass Spectrometry of ESKAPE Pathogens. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1345-1351. [PMID: 33647207 PMCID: PMC8176453 DOI: 10.1021/jasms.0c00466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) represent clinically important bacterial species that are responsible for most hospital-acquired drug-resistant infections; hence, the need for rapid identification is of high importance. Previous work has demonstrated the suitability of liquid extraction surface analysis mass spectrometry (LESA MS) for the direct analysis of colonies of two of the ESKAPE pathogens (Staphylococcus aureus and Pseudomonas aeruginosa) growing on agar. Here, we apply LESA MS to the remaining four ESKAPE species (E. faecium E745, K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11) as well as E. faecalis V583 (a close relative of E. faecium) and a clinical isolate of A. baumannii AC02 using an optimized solvent sampling system. In each case, top-down LESA MS/MS was employed for protein identification. In total, 24 proteins were identified from 37 MS/MS spectra by searching against protein databases for the individual species. The MS/MS spectra for the identified proteins were subsequently searched against multiple databases from multiple species in an automated data analysis workflow with a view to determining the accuracy of identification of unknowns. Out of 24 proteins, 19 were correctly assigned at the protein and species level, corresponding to an identification success rate of 79%.
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Affiliation(s)
- Jana Havlikova
- EPSRC
Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Robin C. May
- Institute
of Microbiology and Infection, University
of Birmingham, Edgbaston, Birmingham B15 2TT, United
Kingdom
| | - Iain B. Styles
- EPSRC
Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Phone: +44 (0)121 414 7527; . (H.J.C.)
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12
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Cameron SJS, Perdones-Montero A, Van Meulebroek L, Burke A, Alexander-Hardiman K, Simon D, Schaffer R, Balog J, Karancsi T, Rickards T, Rebec M, Stead S, Vanhaecke L, Takáts Z. Sample Preparation Free Mass Spectrometry Using Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry: Applications to Microbiology, Metabolic Biofluid Phenotyping, and Food Authenticity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1393-1401. [PMID: 33980015 DOI: 10.1021/jasms.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mass spectrometry has established itself as a powerful tool in the chemical, biological, medical, environmental, and agricultural fields. However, experimental approaches and potential application areas have been limited by a traditional reliance on sample preparation, extraction, and chromatographic separation. Ambient ionization mass spectrometry methods have addressed this challenge but are still somewhat restricted in requirements for sample manipulation to make it suitable for analysis. These limitations are particularly restrictive in view of the move toward high-throughput and automated analytical workflows. To address this, we present what we consider to be the first automated sample-preparation-free mass spectrometry platform utilizing a carbon dioxide (CO2) laser for sample thermal desorption linked to the rapid evaporative ionization mass spectrometry (LA-REIMS) methodology. We show that the pulsatile operation of the CO2 laser is the primary factor in achieving high signal-to-noise ratios. We further show that the LA-REIMS automated platform is suited to the analysis of three diverse biological materials within different application areas. First, clinical microbiology isolates were classified to species level with an accuracy of 97.2%, the highest accuracy reported in current literature. Second, fecal samples from a type 2 diabetes mellitus cohort were analyzed with LA-REIMS, which allowed tentative identification of biomarkers which are potentially associated with disease pathogenesis and a disease classification accuracy of 94%. Finally, we showed the ability of the LA-REIMS system to detect instances of adulteration of cooking oil and determine the geographical area of production of three protected olive oil products with 100% classification accuracy.
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Affiliation(s)
- Simon J S Cameron
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Adam Burke
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Kate Alexander-Hardiman
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Daniel Simon
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Waters Research Center, Budapest 1031, Hungary
| | | | - Julia Balog
- Waters Research Center, Budapest 1031, Hungary
| | | | - Tony Rickards
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Sara Stead
- Waters Corporation, Wilmslow SK9 4AX, U.K
| | - Lynn Vanhaecke
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Zoltán Takáts
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
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13
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Gao H, Lin J, Jia X, Zhao Y, Wang S, Bai H, Ma Q. Real-time authentication of animal species origin of leather products using rapid evaporative ionization mass spectrometry and chemometric analysis. Talanta 2021; 225:122069. [PMID: 33592787 DOI: 10.1016/j.talanta.2020.122069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/22/2020] [Accepted: 12/25/2020] [Indexed: 12/18/2022]
Abstract
Increasing accounts of fraud and persistent labeling problems have brought the authenticity of leather products into question. In this study, we developed an extremely simplified workflow for real-time, in situ, and unambiguous authentication of leather samples using rapid evaporative ionization mass spectrometry (REIMS) coupled with an electric soldering iron. Initially, authentic leather samples from cattle, sheep, pig, deer, ostrich, crocodile, and snake were used to create a chemometric model based on principal component analysis and linear discriminant analysis algorithms. The validated multivariate statistical model was then used to analyze and generate live classifications of commercial leather samples. In addition to REIMS analysis, the microstructures of leathers were characterized by scanning electron microscopy to provide complementary information. The current study is expected to provide a high-throughput tool with superior efficiency and accuracy for authenticating the identity of leathers and other consumer products of biogenic origin.
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Affiliation(s)
- Haiyan Gao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China; Inner Mongolia Autonomous Region Institute of Product Quality Inspection, Huhhot 010070, China
| | - Jihong Lin
- Waters Corporation, Beijing 100176, China
| | | | - Yang Zhao
- National Quality Supervision and Testing Center for Leather Products, Beijing 100015, China
| | - Songying Wang
- Inner Mongolia Autonomous Region Institute of Product Quality Inspection, Huhhot 010070, China
| | - Hua Bai
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Qiang Ma
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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14
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Manoli E, Mason S, Ford L, Adebesin A, Bodai Z, Darzi A, Kinross J, Takats Z. Validation of Ultrasonic Harmonic Scalpel for Real-Time Tissue Identification Using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2021; 93:5906-5916. [PMID: 33787247 PMCID: PMC8153397 DOI: 10.1021/acs.analchem.1c00270] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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In this study, we integrate rapid
evaporative ionization mass spectrometry
(REIMS) with the Harmonic scalpel, an advanced laparoscopic surgical
instrument that utilizes ultrasound energy to dissect and coagulate
tissues. It provides unparalleled manipulation capability to surgeons
and has superseded traditional electrosurgical tools particularly
in abdominal surgery, but is yet to be validated with REIMS. The REIMS
platform coupled with the Harmonic device was shown to produce tissue-specific
lipid profiles through the analysis of porcine tissues in both negative
and positive ionization modes. Comparison with other methods of electrosurgical
dissection, such as monopolar electrosurgery and CO2 laser,
showed spectral differences in the profile dependent on the energy
device used. The Harmonic device demonstrated major spectral differences
in the phospholipid region of m/z 600–1000 compared with the monopolar electrosurgical and
CO2 laser-generated spectra. Within the Harmonic REIMS
spectra, high intensities of diglycerides and triglycerides were observed.
In contrast, monopolar electrosurgical and laser spectra demonstrated
high abundances of glycerophospholipids. The Harmonic scalpel was
able to differentiate between the liver, muscle, colon, and small
intestine, demonstrating 100% diagnostic accuracy. The validation
of the Harmonic device–mass spectrometry combination will allow
the platform to be used safely and robustly for real-time in vivo surgical tissue identification in a variety of clinical
applications.
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Affiliation(s)
- Eftychios Manoli
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - Sam Mason
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - Lauren Ford
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - Afeez Adebesin
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - Zsolt Bodai
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ara Darzi
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - James Kinross
- Department of Surgery and Cancer, Imperial College London, St Marys Hospital, London W2 1NY, United Kingdom
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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15
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Barlow RS, Fitzgerald AG, Hughes JM, McMillan KE, Moore SC, Sikes AL, Tobin AB, Watkins PJ. Rapid Evaporative Ionization Mass Spectrometry: A Review on Its Application to the Red Meat Industry with an Australian Context. Metabolites 2021; 11:171. [PMID: 33804276 PMCID: PMC8000567 DOI: 10.3390/metabo11030171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 01/01/2023] Open
Abstract
The red meat supply chain is a complex network transferring product from producers to consumers in a safe and secure way. There can be times when fragmentation can arise within the supply chain, which could be exploited. This risk needs reduction so that meat products enter the market with the desired attributes. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) is a novel ambient mass spectrometry technique originally developed for rapid and accurate classification of biological tissue which is now being considered for use in a range of additional applications. It has subsequently shown promise for a range of food provenance, quality and safety applications with its ability to conduct ex vivo and in situ analysis. These are regarded as critical characteristics for technologies which can enable real-time decision making in meat processing plants and more broadly throughout the sector. This review presents an overview of the REIMS technology, and its application to the areas of provenance, quality and safety to the red meat industry, particularly in an Australian context.
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Affiliation(s)
- Robert S. Barlow
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Adam G. Fitzgerald
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Joanne M. Hughes
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Kate E. McMillan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Sean C. Moore
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Werribee, VIC 3030, Australia; (S.C.M.); (P.J.W.)
| | - Anita L. Sikes
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Aarti B. Tobin
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, QLD 4108, Australia; (A.G.F.); (J.M.H.); (K.E.M.); (A.L.S.); (A.B.T.)
| | - Peter J. Watkins
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Werribee, VIC 3030, Australia; (S.C.M.); (P.J.W.)
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16
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Electrocautery, Diathermy, and Surgical Energy Devices: Are Surgical Teams at Risk During the COVID-19 Pandemic? Ann Surg 2021; 272:e257-e262. [PMID: 32541232 PMCID: PMC7467049 DOI: 10.1097/sla.0000000000004112] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Supplemental Digital Content is available in the text Objective: The aim of the study was to provide a rapid synthesis of available data to identify the risk posed by utilizing surgical energy devices intraoperatively due to the generation of surgical smoke, an aerosol. Secondarily it aims to summarize methods to minimize potential risk to operating room staff. Summary Background Data: Continuing operative practice during the coronavirus disease-19 (COVID-19) pandemic places the health of operating theatre staff at potential risk. SARS-CoV2 is transmitted through inhaled droplets and aerosol particles, thus posing an inhalation threat even at considerable distance. Surgical energy devices generate an aerosol of biological particular matter during use. The risk to healthcare staff through use of surgical energy devices is unknown. Methods: This review was conducted utilizing a rapid review methodology to enable efficient generation and dissemination of information useful for concurrent clinical practice. Results: There are conflicting stances on the use of energy devices and laparoscopy by different surgical governing bodies and societies. There is no definitive evidence that aerosol generated by energy devices may carry active SARS-CoV2 virus. However, investigations of other viruses have demonstrated aerosolization through energy devise use. Measures to reduce potential transmission include appropriate personal protective equipment, evacuation and filtration of surgical plume, limiting energy device use if appropriate, and adjusting endoscopic and laparoscopic practice (low CO2 pressures, evacuation through ultrafiltration systems). Conclusions: The risk of transmission of SARS-CoV2 through aerosolized surgical smoke associated with energy device use is not fully understood, however transmission is biologically plausible. Caution and appropriate measures to reduce risk to healthcare staff should be implemented when considering intraoperative use of energy devices.
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17
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Freeman Weiss Z, Leon A, Koo S. The Evolving Landscape of Fungal Diagnostics, Current and Emerging Microbiological Approaches. J Fungi (Basel) 2021; 7:jof7020127. [PMID: 33572400 PMCID: PMC7916227 DOI: 10.3390/jof7020127] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Invasive fungal infections are increasingly recognized in immunocompromised hosts. Current diagnostic techniques are limited by low sensitivity and prolonged turnaround times. We review emerging diagnostic technologies and platforms for diagnosing the clinically invasive disease caused by Candida, Aspergillus, and Mucorales.
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Affiliation(s)
- Zoe Freeman Weiss
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA 02115, USA
- Correspondence:
| | - Armando Leon
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
| | - Sophia Koo
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
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18
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Wang J, Xu L, Xu Z, Wang Y, Niu C, Yang S. Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry and Rapid Evaporative Ionization Mass Spectrometry Were Used to Develop a Lamb Authentication Method: A Preliminary Study. Foods 2020; 9:foods9121723. [PMID: 33255201 PMCID: PMC7761048 DOI: 10.3390/foods9121723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
A untargeted metabolomics approach was proposed in this study based on ultra-high performance liquid chromatography quadrupole time-of-flight (UHPLC-QTOF) and rapid evaporative ionization mass spectrometry (REIMS) to discriminate lamb and mutton meat and investigate their subtle metabolic differences, considering the higher popularity of lamb meat than mutton in the market. Multivariate statistical analysis was performed for data processing in order to distinguish between the two sample types. A total of 42 potential metabolites (20 in positive and 22 in negative ion mode) were defined for UHPLC-QTOF analysis, which provided references for discriminating the two kinds of meat. Furthermore, three potential markers were tentatively identified using LC/MS data against chemical databases. In addition, 14 potential metabolites were putatively identified in negative ion mode using the LipidMaps database. Meanwhile, the data-driven soft independent modeling of class analogy (DD-SIMCA) model was established, which could rapidly differentiate non-pretreated lamb meat and mutton with 92% specificity, rendering REIMS a promising technique for meat identification.
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Affiliation(s)
- Jishi Wang
- Key Laboratory of Agro-food Safety and Quality, Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.W.); (L.X.); (Y.W.); (S.Y.)
| | - Lei Xu
- Key Laboratory of Agro-food Safety and Quality, Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.W.); (L.X.); (Y.W.); (S.Y.)
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhenzhen Xu
- Key Laboratory of Agro-food Safety and Quality, Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.W.); (L.X.); (Y.W.); (S.Y.)
- Correspondence: ; Tel.: +86-10-8210-6560
| | - Yanyun Wang
- Key Laboratory of Agro-food Safety and Quality, Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.W.); (L.X.); (Y.W.); (S.Y.)
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Shuming Yang
- Key Laboratory of Agro-food Safety and Quality, Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.W.); (L.X.); (Y.W.); (S.Y.)
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19
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Integrating untargeted metabolomics and targeted analysis for not from concentrate and from concentrate orange juices discrimination and authentication. Food Chem 2020; 329:127130. [DOI: 10.1016/j.foodchem.2020.127130] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/10/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022]
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20
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Havlikova J, May RC, Styles IB, Cooper HJ. Direct identification of bacterial and human proteins from infected wounds in living 3D skin models. Sci Rep 2020; 10:11900. [PMID: 32681099 PMCID: PMC7368034 DOI: 10.1038/s41598-020-68233-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Trauma is one of the leading causes of death in people under the age of 49 and complications due to wound infection are the primary cause of death in the first few days after injury. The ESKAPE pathogens are a group of bacteria that are a leading cause of hospital-acquired infections and a major concern in terms of antibiotic resistance. Here, we demonstrate a novel and highly accurate approach for the rapid identification of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) directly from infected wounds in 3D in vitro skin models. Wounded skin models were inoculated with bacteria and left to incubate. Bacterial proteins were identified within minutes, directly from the wound, by liquid extraction surface analysis mass spectrometry. This approach was able to distinguish closely related strains and, unlike genomic approaches, can be modified to provide dynamic information about pathogen behaviour at the wound site. In addition, since human skin proteins were also identified, this method offers the opportunity to analyse both host and pathogen biomarkers during wound infection in near real-time.
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Affiliation(s)
- Jana Havlikova
- EPSRC Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Iain B Styles
- EPSRC Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Computer Science, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, The Midlands, Birmingham, UK.,Alan Turing Institute, 96 Euston Road, London, NW1 2DB, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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21
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Song G, Li L, Wang H, Zhang M, Yu X, Wang J, Xue J, Shen Q. Real-time assessing the lipid oxidation of prawn (Litopenaeus vannamei) during air-frying by iKnife coupling rapid evaporative ionization mass spectrometry. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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The intelligent knife (iKnife) and its intraoperative diagnostic advantage for the treatment of cervical disease. Proc Natl Acad Sci U S A 2020; 117:7338-7346. [PMID: 32179675 PMCID: PMC7132269 DOI: 10.1073/pnas.1916960117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clearance of surgical margins in early cervical cancer prevents the need for adjuvant chemoradiation and associated morbidity and allows fertility preservation. Clearance of disease is also crucial in the surgical management of local recurrence of cervical tumors with exenterative surgery. In this study intelligent knife technology was able to discriminate healthy from abnormal lesions on the cervix with high accuracy, highlighting the potential to improve intraoperative management of women treated surgically for cervical cancer and, as a result, patient outcomes. While pilot experiments in vivo are encouraging, accuracy remains to be validated in larger patient cohorts. Future studies could also explore whether this technology could be used for management of cervical preinvasive disease. Clearance of surgical margins in cervical cancer prevents the need for adjuvant chemoradiation and allows fertility preservation. In this study, we determined the capacity of the rapid evaporative ionization mass spectrometry (REIMS), also known as intelligent knife (iKnife), to discriminate between healthy, preinvasive, and invasive cervical tissue. Cervical tissue samples were collected from women with healthy, human papilloma virus (HPV) ± cervical intraepithelial neoplasia (CIN), or cervical cancer. A handheld diathermy device generated surgical aerosol, which was transferred into a mass spectrometer for subsequent chemical analysis. Combination of principal component and linear discriminant analysis and least absolute shrinkage and selection operator was employed to study the spectral differences between groups. Significance of discriminatory m/z features was tested using univariate statistics and tandem MS performed to elucidate the structure of the significant peaks allowing separation of the two classes. We analyzed 87 samples (normal = 16, HPV ± CIN = 50, cancer = 21 patients). The iKnife discriminated with 100% accuracy normal (100%) vs. HPV ± CIN (100%) vs. cancer (100%) when compared to histology as the gold standard. When comparing normal vs. cancer samples, the accuracy was 100% with a sensitivity of 100% (95% CI 83.9 to 100) and specificity 100% (79.4 to 100). Univariate analysis revealed significant MS peaks in the cancer-to-normal separation belonging to various classes of complex lipids. The iKnife discriminates healthy from premalignant and invasive cervical lesions with high accuracy and can improve oncological outcomes and fertility preservation of women treated surgically for cervical cancer. Larger in vivo research cohorts are required to validate these findings.
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23
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Hokkinen L, Kesti A, Lepomäki J, Anttalainen O, Kontunen A, Karjalainen M, Aittoniemi J, Vuento R, Lehtimäki T, Oksala N, Roine A. Differential mobility spectrometry classification of bacteria. Future Microbiol 2020; 15:233-240. [DOI: 10.2217/fmb-2019-0192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: Rapid identification of bacteria would facilitate timely initiation of therapy and improve cost–effectiveness of treatment. Traditional methods (culture, PCR) require reagents, consumables and hours to days to complete the identification. In this study, we examined whether differential mobility spectrometry could classify most common bacterial species, genera and between Gram status within minutes. Materials & methods: Cultured bacterial sample gaseous headspaces were measured with differential mobility spectrometry and data analyzed using k-nearest-neighbor and leave-one-out cross-validation. Results: Differential mobility spectrometry achieved a correct classification rate 70.7% for all bacterial species. For bacterial genera, the rate was 77.6% and between Gram status, 89.1%. Conclusion: Largest difficulties arose in distinguishing bacteria of the same genus. Future improvement of the sensor characteristics may improve the classification accuracy.
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Affiliation(s)
- Lauri Hokkinen
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | - Artturi Kesti
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | - Jaakko Lepomäki
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | - Osmo Anttalainen
- Vascular & interventional Center, Tampere University Hospital, Tampere, Finland
| | - Anton Kontunen
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | - Markus Karjalainen
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | | | | | - Terho Lehtimäki
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center – Tampere, Tampere University, Tampere, Finland
| | - Niku Oksala
- Vascular & interventional Center, Tampere University Hospital, Tampere, Finland
- Department of Surgery, Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
| | - Antti Roine
- Faculty of Medicine & Health Technology, Tampere University, Tampere, Finland
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24
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Arena K, Rigano F, Mangraviti D, Cacciola F, Occhiuto F, Dugo L, Dugo P, Mondello L. Exploration of Rapid Evaporative-Ionization Mass Spectrometry as a Shotgun Approach for the Comprehensive Characterization of Kigelia Africana (Lam) Benth. Fruit. Molecules 2020; 25:molecules25040962. [PMID: 32093421 PMCID: PMC7070896 DOI: 10.3390/molecules25040962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022] Open
Abstract
Rapid evaporative-ionization mass spectrometry (REIMS) coupled with an electroknife as a sampling device was recently employed in many application fields to obtain a rapid characterization of different samples without any need for extraction or cleanup procedures. In the present research, REIMS was used to obtain a metabolic profiling of the Kigelia africana fruit, thus extending the applicability of such a technique to the investigation of phytochemical constituents. In particular, the advantages of REIMS linked to a typical electrosurgical handpiece were applied for a comprehensive screening of this botanical species, by exploiting the mass accuracy and tandem MS capabilities of a quadrupole-time of flight analyzer. Then, 78 biomolecules were positively identified, including phenols, fatty acids and phospholipids. In the last decade, Kigelia africana (Lam.) Benth. fruit has attracted special interest for its drug-like properties, e.g., its use for infertility treatments and as anti-tumor agent, as well as against fungal and bacterial infections, diabetes, and inflammatory processes. Many of these properties are currently correlated to the presence of phenolic compounds, also detected in the present study, while the native lipid composition is here reported for the first time and could open new directions in the evaluation of therapeutic activity.
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Affiliation(s)
- Katia Arena
- Foundation A. Imbesi c/o University of Messina, I-98168 Messina, Italy;
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
- Correspondence:
| | - Domenica Mangraviti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
| | - Francesco Cacciola
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, I-98168 Messina, Italy;
| | - Francesco Occhiuto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
| | - Laura Dugo
- Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, I-00128 Rome, Italy;
| | - Paola Dugo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy; (D.M.); (F.O.); (P.D.); (L.M.)
- Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, I-00128 Rome, Italy;
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy
- BeSep s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, I-98168 Messina, Italy
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Lellman SE, Cramer R. Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. ACTA ACUST UNITED AC 2019; 58:930-938. [DOI: 10.1515/cclm-2019-0908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Abstract
Background
In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.
Methods
Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.
Results
Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.
Conclusions
Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.
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Affiliation(s)
- Sophie E. Lellman
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
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26
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Wang H, Cao X, Han T, Pei H, Ren H, Stead S. A novel methodology for real-time identification of the botanical origins and adulteration of honey by rapid evaporative ionization mass spectrometry. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.106753] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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27
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Sarsby J, McLean L, Harman VM, Beynon RJ. Monitoring recombinant protein expression in bacteria by rapid evaporative ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 35 Suppl 2:e8670. [PMID: 31760669 PMCID: PMC8047878 DOI: 10.1002/rcm.8670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/06/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE There is increasing interest in methods of direct analysis mass spectrometry that bypass complex sample preparation steps. METHODS One of the most interesting new ionisation methods is rapid evaporative ionisation mass spectrometry (REIMS) in which samples are vapourised and the combustion products are subsequently ionised and analysed by mass spectrometry (Synapt G2si). The only sample preparation required is the recovery of a cell pellet from a culture that can be analysed immediately. RESULTS We demonstrate that REIMS can be used to monitor the expression of heterologous recombinant proteins in Escherichia coli. Clear segregation was achievable between bacteria harvesting plasmids that were strongly expressed and other cultures in which the plasmid did not result in the expression of large amounts of recombinant product. CONCLUSIONS REIMS has considerable potential as a near-instantaneous monitoring tool for protein production in a biotechnology environment.
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Affiliation(s)
- Joscelyn Sarsby
- Centre for Proteome Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUK
| | - Lynn McLean
- Centre for Proteome Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUK
| | - Victoria M. Harman
- Centre for Proteome Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUK
| | - Robert J. Beynon
- Centre for Proteome Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUK
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28
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Cameron SJS, Alexander JL, Bolt F, Burke A, Ashrafian H, Teare J, Marchesi JR, Kinross J, Li JV, Takáts Z. Evaluation of Direct from Sample Metabolomics of Human Feces Using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2019; 91:13448-13457. [DOI: 10.1021/acs.analchem.9b02358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Simon J. S. Cameron
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - James L. Alexander
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Frances Bolt
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Adam Burke
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Hutan Ashrafian
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Julian Teare
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Julian R. Marchesi
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, U.K
| | - James Kinross
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Jia V. Li
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Zoltán Takáts
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
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29
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Davidson NB, Koch NI, Sarsby J, Jones E, Hurst JL, Beynon RJ. Rapid identification of species, sex and maturity by mass spectrometric analysis of animal faeces. BMC Biol 2019; 17:66. [PMID: 31412863 PMCID: PMC6693146 DOI: 10.1186/s12915-019-0686-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/26/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND We describe a new approach to the recovery of information from faecal samples, based on the analysis of the molecular signature generated by rapid evaporative ionisation mass spectrometry (REIMS). RESULTS Faecal pellets from five different rodent species were analysed by REIMS, and complex mass spectra were acquired rapidly (typically a few seconds per sample). The uninterpreted mass spectra (signatures) were then used to seed linear discriminant analysis and classification models based on random forests. It was possible to classify each species of origin with a high rate of accuracy, whether faeces were from animals maintained under standard laboratory conditions or wild-caught. REIMS signatures were stable to prior storage of the faecal material under a range of different conditions and were not altered rapidly or radically by changes in diet. Further, within species, REIMS signatures could be used to discriminate faeces from adult versus juvenile mice, male versus female mice and those from three different laboratory strains. CONCLUSIONS REIMS offers a completely novel method for the rapid analysis of faecal samples, extending faecal analysis (previously focused on DNA) to an assessment of phenotype, and has considerable potential as a new tool in the armamentarium of the field biologist.
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Affiliation(s)
- Nicola B Davidson
- Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Natalie I Koch
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Joscelyn Sarsby
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Emrys Jones
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK.
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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30
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Jones EA, Simon D, Karancsi T, Balog J, Pringle SD, Takats Z. Matrix Assisted Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2019; 91:9784-9791. [PMID: 31194519 DOI: 10.1021/acs.analchem.9b01441] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rapid evaporative ionization mass spectrometry (REIMS) is a highly versatile technique allowing the sampling of a range of biological solid or liquid samples with no sample preparation. The cost of such a direct approach is that certain sample types provide only moderate amounts of chemical information. Here, we introduce a matrix assisted version of the technique (MA-REIMS), where an aerosol of a pure solvent, such as isopropanol, is mixed with the sample aerosol generated by rapid evaporation of the sample, and it is shown to enhance the signal intensity obtained from a REIMS sampling event by over 2 orders of magnitude. Such an increase greatly expands the scope of the technique, while providing additional benefits such as reducing the fouling of the REIMS source and allowing for a simple method of constant introduction of a calibration correction compound for accurate mass measurements. A range of experiments are presented in order to investigate the processes that occur within this modified approach, and applications where such enhancements are critical, such as intrasurgical tissue identification, are discussed.
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Affiliation(s)
- Emrys A Jones
- Waters Corporation , Altrincham Road , Wilmslow SK9 4AX , United Kingdom
| | - Daniel Simon
- Waters Research Center , Graphisoft Park, 7 Zahony Street , Budapest 1031 , Hungary
| | - Tamas Karancsi
- Waters Research Center , Graphisoft Park, 7 Zahony Street , Budapest 1031 , Hungary
| | - Julia Balog
- Waters Research Center , Graphisoft Park, 7 Zahony Street , Budapest 1031 , Hungary
| | - Steven D Pringle
- Waters Corporation , Altrincham Road , Wilmslow SK9 4AX , United Kingdom
| | - Zoltan Takats
- Imperial College London , South Kensington, London SW7 2AZ , United Kingdom
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31
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Abu-Rabie P, Sheelan D, Laures A, Spaull J, Dowell S. Increasing the discrimination power of rapid evaporative ionisation mass spectrometry (REIMS) in analytical control tissue quality screening and cell line sample identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 35. [PMID: 31295371 DOI: 10.1002/rcm.8525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/31/2019] [Accepted: 07/04/2019] [Indexed: 05/15/2023]
Abstract
RATIONALE Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has been evaluated as a tool to improve analytical efficiency and add capability in areas within Pharmaceutical Research and Development (Pharma R&D). This article reports the comparison of single MS, and tandem MS/MS REIMS (REIMS and REIMS/MS) methodologies to investigate which mode produces maximum discrimination power for screening applications. METHODS Control tissue samples and cell line suspension samples were analysed using optimised REIMS and REIMS/MS to evaluate which technique produced optimal discrimination power for control tissue and cell line identification. The iKnife sampling tool and a prototype 'cell sampler' were utilised for tissue and cell analysis, respectively. The REIMS source was coupled to a hybrid Quadrupole-Time Of Flight (QTOF) mass spectrometer. Multivariate Analysis (MVA) was utilised to evaluate the resulting Mass Spectrometry (MS) data and discriminate between sample types. RESULTS Proof of concept investigations demonstrating that REIMS/MS offered increased MVA discrimination for sample identification, compared with REIMS, is presented for the first time. Control tissue data showed discrimination by timepoint classification over 0-144 h storage after removal from the host. Timepoint discrimination was optimised using REIMS/MS with a collision energy that effectively maximised ion fragmentation. Similar optimisation was observed when REIMS/MS was applied to the identification of cell lines. CONCLUSIONS The proof of concept results demonstrate that REIMS/MS can offer advantages over REIMS for control tissue quality screening, and cell line identification applications in Pharma R&D. Further work following this proof of concept investigation is being undertaken to implement the technology for these applications, utilising the optimised REIMS/MS methodology. REIMS/MS will also be used as an optimised tool for other applications.
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Affiliation(s)
- Paul Abu-Rabie
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Denver Sheelan
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Alice Laures
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - John Spaull
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Simon Dowell
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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32
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Pu F, Chiang S, Zhang W, Ouyang Z. Direct sampling mass spectrometry for clinical analysis. Analyst 2019; 144:1034-1051. [PMID: 30520890 DOI: 10.1039/c8an01722k] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Direct sampling mass spectrometry (MS) has been advancing aggressively, showing immense potential in translating MS into the clinical field. Unlike traditional MS analysis involving extensive sample preparation and chromatographic separation, quick and simple procedures with minimal sample pretreatment or purification became available with direct sampling. An overview of the development in this field is provided, including some representative ambient ionization and fast extraction methods. Quantitative applications of these methods are emphasized and their efficacy are highlighted from a clinical aspect; non-quantitative applications in clinical analysis are also discussed. This review also discusses the integration of direct sampling MS with miniature mass spectrometers and its future outlook as an emerging clinical tool for point-of-care analysis.
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Affiliation(s)
- Fan Pu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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33
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Rapid detection and specific identification of offals within minced beef samples utilising ambient mass spectrometry. Sci Rep 2019; 9:6295. [PMID: 31000779 PMCID: PMC6472348 DOI: 10.1038/s41598-019-42796-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The morphological transformation of beef tissues after various processing treatments facilitates the addition of cheap offal products. Undetectable to the naked eye, analytical techniques are required to identify such scenarios within minced and processed products. DNA methodologies are ill-equipped to detect adulteration of offal cuts from the same species and vibrational spectroscopic studies, although rapid and non-destructive, have proved inconclusive as to whether the specific adulterant can be identified. For the first time we present a mass spectrometric approach employing an ambient ionisation process to eliminate sample preparation and provide near-instantaneous results. Rapid evaporative ionisation mass spectrometry (REIMS) was used to assess its capabilities of detecting minced beef adulteration with beef brain, heart, kidney, large intestine and liver tissues and chemometric analysis enabled unique or significant markers to be identified. The adulteration levels detected with the REIMS technology when analysing raw adulterated beef burgers were; brain (5%); heart (1–10%); kidney (1–5%); large intestine (1–10%) and liver (5–10%). For boiled adulterated samples; brain (5–10%); heart (1–10%); kidney (1–5%); large intestine (1–10%) and liver (5–10%). REIMS allows rapid and specific identification of offal cuts within adulterated beef burgers and could provide a paradigm shift across many authenticity applications.
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Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification. Sci Rep 2019; 9:3006. [PMID: 30816263 PMCID: PMC6395639 DOI: 10.1038/s41598-019-39815-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/30/2019] [Indexed: 02/08/2023] Open
Abstract
The accurate and timely identification of the causative organism of infection is important in ensuring the optimum treatment regimen is prescribed for a patient. Rapid evaporative ionisation mass spectrometry (REIMS), using electrical diathermy for the thermal disruption of a sample, has been shown to provide fast and accurate identification of microorganisms directly from culture. However, this method requires contact to be made between the REIMS probe and microbial biomass; resulting in the necessity to clean or replace the probes between analyses. Here, optimisation and utilisation of ambient laser desorption ionisation (ALDI) for improved speciation accuracy and analytical throughput is shown. Optimisation was completed on 15 isolates of Escherichia coli, showing 5 W in pulsatile mode produced the highest signal-to-noise ratio. These parameters were used in the analysis of 150 clinical isolates from ten microbial species, resulting in a speciation accuracy of 99.4% - higher than all previously reported REIMS modalities. Comparison of spectral data showed high levels of similarity between previously published electrical diathermy REIMS data. ALDI does not require contact to be made with the sample during analysis, meaning analytical throughput can be substantially improved, and further, increases the range of sample types which can be analysed in potential direct-from-sample pathogen detection.
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35
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Kailasa SK, Koduru JR, Park TJ, Wu HF, Lin YC. Progress of electrospray ionization and rapid evaporative ionization mass spectrometric techniques for the broad-range identification of microorganisms. Analyst 2019; 144:1073-1103. [DOI: 10.1039/c8an02034e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrospray ionization and rapid evaporative ionization mass spectrometric techniques have attracted much attention in the identification of microorganisms, and in the diagnosis of bacterial infections from clinical samples.
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Affiliation(s)
- Suresh Kumar Kailasa
- Department of Applied Chemistry
- S. V. National Institute of Technology
- Surat – 395007
- India
- Department of Chemistry
| | | | - Tae Jung Park
- Department of Chemistry
- Institute of Interdisciplinary Convergence Research
- Research Institute of Halal Industrialization Technology
- Chung-Ang University
- Seoul 06974
| | - Hui-Fen Wu
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- Center for Nanoscience and Nanotechnology
| | - Ying-Chi Lin
- School of Pharmacy
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
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36
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Burckhardt I. Laboratory Automation in Clinical Microbiology. Bioengineering (Basel) 2018; 5:bioengineering5040102. [PMID: 30467275 PMCID: PMC6315553 DOI: 10.3390/bioengineering5040102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 01/21/2023] Open
Abstract
Laboratory automation is currently the main organizational challenge for microbiologists. Automating classic workflows is a strenuous process for the laboratory personnel and a huge and long-lasting financial investment. The investments are rewarded through increases in quality and shortened time to report. However, the benefits for an individual laboratory can only be estimated after the implementation and depending on the classic workflows currently performed. The two main components of automation are hardware and workflow. This review focusses on the workflow aspects of automation and describes some of the main developments during recent years. Additionally, it tries to define some terms which are related to automation and specifies some developments which would further improve automated systems.
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Affiliation(s)
- Irene Burckhardt
- Department for Infectious Diseases, Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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37
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Use of an “Intelligent Knife” (iknife), Based on the Rapid Evaporative Ionization Mass Spectrometry Technology, for Authenticity Assessment of Pistachio Samples. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1386-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Cameron SJ, Takáts Z. Mass spectrometry approaches to metabolic profiling of microbial communities within the human gastrointestinal tract. Methods 2018; 149:13-24. [DOI: 10.1016/j.ymeth.2018.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022] Open
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39
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Ghosh PN, Fisher MC, Bates KA. Diagnosing Emerging Fungal Threats: A One Health Perspective. Front Genet 2018; 9:376. [PMID: 30254662 PMCID: PMC6141620 DOI: 10.3389/fgene.2018.00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022] Open
Abstract
Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Kieran A. Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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40
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Bardin EE, Cameron SJS, Perdones-Montero A, Hardiman K, Bolt F, Alton EWFW, Bush A, Davies JC, Takáts Z. Metabolic Phenotyping and Strain Characterisation of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients Using Rapid Evaporative Ionisation Mass Spectrometry. Sci Rep 2018; 8:10952. [PMID: 30026575 PMCID: PMC6053451 DOI: 10.1038/s41598-018-28665-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/22/2018] [Indexed: 01/16/2023] Open
Abstract
Rapid evaporative ionisation mass spectrometry (REIMS) is a novel technique for the real-time analysis of biological material. It works by conducting an electrical current through a sample, causing it to rapidly heat and evaporate, with the analyte containing vapour channelled to a mass spectrometer. It was used to characterise the metabolome of 45 Pseudomonas aeruginosa (P. aeruginosa) isolates from cystic fibrosis (CF) patients and compared to 80 non-CF P. aeruginosa. Phospholipids gave the highest signal intensity; 17 rhamnolipids and 18 quorum sensing molecules were detected, demonstrating that REIMS has potential for the study of virulence-related metabolites. P. aeruginosa isolates obtained from respiratory samples showed a higher diversity, which was attributed to the chronic nature of most respiratory infections. The analytical sensitivity of REIMS allowed the detection of a metabolome that could be used to classify individual P. aeruginosa isolates after repeated culturing with 81% accuracy, and an average 83% concordance with multilocus sequence typing. This study underpins the capacities of REIMS as a tool with clinical applications, such as metabolic phenotyping of the important CF pathogen P. aeruginosa, and highlights the potential of metabolic fingerprinting for fine scale characterisation at a sub-species level.
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Affiliation(s)
- Emmanuelle E Bardin
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Simon J S Cameron
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | - Kate Hardiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Frances Bolt
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Eric W F W Alton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Zoltan Takáts
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
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41
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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Bodai Z, Cameron S, Bolt F, Simon D, Schaffer R, Karancsi T, Balog J, Rickards T, Burke A, Hardiman K, Abda J, Rebec M, Takats Z. Effect of Electrode Geometry on the Classification Performance of Rapid Evaporative Ionization Mass Spectrometric (REIMS) Bacterial Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:26-33. [PMID: 29038998 PMCID: PMC5785610 DOI: 10.1007/s13361-017-1818-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/31/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
The recently developed automated, high-throughput monopolar REIMS platform is suited for the identification of clinically important microorganisms. Although already comparable to the previously reported bipolar forceps method, optimization of the geometry of monopolar electrodes, at the heart of the system, holds the most scope for further improvements to be made. For this, sharp tip and round shaped electrodes were optimized to maximize species-level classification accuracy. Following optimization of the distance between the sample contact point and tube inlet with the sharp tip electrodes, the overall cross-validation accuracy improved from 77% to 93% in negative and from 33% to 63% in positive ion detection modes, compared with the original 4 mm distance electrode. As an alternative geometry, round tube shaped electrodes were developed. Geometry optimization of these included hole size, number, and position, which were also required to prevent plate pick-up due to vacuum formation. Additional features, namely a metal "X"-shaped insert and a pin in the middle were included to increase the contact surface with a microbial biomass to maximize aerosol production. Following optimization, cross-validation scores showed improvement in classification accuracy from 77% to 93% in negative and from 33% to 91% in positive ion detection modes. Supervised models were also built, and after the leave 20% out cross-validation, the overall classification accuracy was 98.5% in negative and 99% in positive ion detection modes. This suggests that the new generation of monopolar REIMS electrodes could provide substantially improved species level identification accuracies in both polarity detection modes. Graphical abstract.
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Affiliation(s)
- Zsolt Bodai
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK.
| | - Simon Cameron
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Frances Bolt
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Daniel Simon
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Richard Schaffer
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tamas Karancsi
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Julia Balog
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tony Rickards
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, W6 8RF, UK
| | - Adam Burke
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Kate Hardiman
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Julia Abda
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, W6 8RF, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
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Galea D, Inglese P, Cammack L, Strittmatter N, Rebec M, Mirnezami R, Laponogov I, Kinross J, Nicholson J, Takats Z, Veselkov KA. Translational utility of a hierarchical classification strategy in biomolecular data analytics. Sci Rep 2017; 7:14981. [PMID: 29101330 PMCID: PMC5670129 DOI: 10.1038/s41598-017-14092-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 01/10/2023] Open
Abstract
Hierarchical classification (HC) stratifies and classifies data from broad classes into more specific classes. Unlike commonly used data classification strategies, this enables the probabilistic prediction of unknown classes at different levels, minimizing the burden of incomplete databases. Despite these advantages, its translational application in biomedical sciences has been limited. We describe and demonstrate the implementation of a HC approach for "omics-driven" classification of 15 bacterial species at various taxonomic levels achieving 90-100% accuracy, and 9 cancer types into morphological types and 35 subtypes with 99% and 76% accuracy, respectively. Unknown bacterial species were probabilistically assigned with 100% accuracy to their respective genus or family using mass spectra (n = 284). Cancer types were predicted by mRNA data (n = 1960) for most subtypes with 95-100% accuracy. This has high relevance in clinical practice where complete datasets are difficult to compile with the continuous evolution of diseases and emergence of new strains, yet prediction of unknown classes, such as bacterial species, at upper hierarchy levels may be sufficient to initiate antimicrobial therapy. The algorithms presented here can be directly translated into clinical-use with any quantitative data, and have broad application potential, from unlabeled sample identification, to hierarchical feature selection, and discovery of new taxonomic variants.
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Affiliation(s)
- Dieter Galea
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Paolo Inglese
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Lidia Cammack
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Nicole Strittmatter
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Monica Rebec
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Reza Mirnezami
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ivan Laponogov
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - James Kinross
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jeremy Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Zoltan Takats
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kirill A Veselkov
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom.
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Kocurek KI, Stones L, Bunch J, May RC, Cooper HJ. Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2066-2077. [PMID: 28681361 PMCID: PMC5594050 DOI: 10.1007/s13361-017-1718-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/21/2023]
Abstract
We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. Graphical Abstract ᅟ.
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Affiliation(s)
- Klaudia I Kocurek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Leanne Stones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Abstract
Since the introduction of desorption electrospray ionization (DESI) mass spectrometry (MS), ambient MS methods have seen increased use in a variety of fields from health to food science. Increasing its popularity in metabolomics, ambient MS offers limited sample preparation, rapid and direct analysis of liquids, solids, and gases, in situ and in vivo analysis, and imaging. The metabolome consists of a constantly changing collection of small (<1.5 kDa) molecules. These include endogenous molecules that are part of primary metabolism pathways, secondary metabolites with specific functions such as signaling, chemicals incorporated in the diet or resulting from environmental exposures, and metabolites associated with the microbiome. Characterization of the responsive changes of this molecule cohort is the principal goal of any metabolomics study. With adjustments to experimental parameters, metabolites with a range of chemical and physical properties can be selectively desorbed and ionized and subsequently analyzed with increased speed and sensitivity. This review covers the broad applications of a variety of ambient MS techniques in four primary fields in which metabolomics is commonly employed.
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Affiliation(s)
- Chaevien S. Clendinen
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
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Identification of the ESKAPE pathogens by mass spectrometric analysis of microbial membrane glycolipids. Sci Rep 2017; 7:6403. [PMID: 28743946 PMCID: PMC5526941 DOI: 10.1038/s41598-017-04793-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/19/2017] [Indexed: 12/16/2022] Open
Abstract
Rapid diagnostics that enable identification of infectious agents improve patient outcomes, antimicrobial stewardship, and length of hospital stay. Current methods for pathogen detection in the clinical laboratory include biological culture, nucleic acid amplification, ribosomal protein characterization, and genome sequencing. Pathogen identification from single colonies by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of high abundance proteins is gaining popularity in clinical laboratories. Here, we present a novel and complementary approach that utilizes essential microbial glycolipids as chemical fingerprints for identification of individual bacterial species. Gram-positive and negative bacterial glycolipids were extracted using a single optimized protocol. Extracts of the clinically significant ESKAPE pathogens: E nterococcus faecium, S taphylococcus aureus, K lebsiella pneumoniae, A cinetobacter baumannii, P seudomonas aeruginosa, and E nterobacter spp. were analyzed by MALDI-TOF-MS in negative ion mode to obtain glycolipid mass spectra. A library of glycolipid mass spectra from 50 microbial entries was developed that allowed bacterial speciation of the ESKAPE pathogens, as well as identification of pathogens directly from blood bottles without culture on solid medium and determination of antimicrobial peptide resistance. These results demonstrate that bacterial glycolipid mass spectra represent chemical barcodes that identify pathogens, potentially providing a useful alternative to existing diagnostics.
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Verplanken K, Stead S, Jandova R, Poucke CV, Claereboudt J, Bussche JV, Saeger SD, Takats Z, Wauters J, Vanhaecke L. Rapid evaporative ionization mass spectrometry for high-throughput screening in food analysis: The case of boar taint. Talanta 2017; 169:30-36. [DOI: 10.1016/j.talanta.2017.03.056] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 11/25/2022]
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Bandyopadhyay A, Cambray S, Gao J. Fast Diazaborine Formation of Semicarbazide Enables Facile Labeling of Bacterial Pathogens. J Am Chem Soc 2017; 139:871-878. [PMID: 27992180 PMCID: PMC6191850 DOI: 10.1021/jacs.6b11115] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bioorthogonal conjugation chemistry has enabled the development of tools for the interrogation of complex biological systems. Although a number of bioorthogonal reactions have been documented in literature, they are less ideal for one or several reasons including slow kinetics, low stability of the conjugated product, requirement of toxic catalysts, and side reactions with unintended biomolecules. Herein we report a fast (>103 M-1 s-1) and bioorthogonal conjugation reaction that joins semicarbazide to an aryl ketone or aldehyde with an ortho-boronic acid substituent. The boronic acid moiety greatly accelerates the initial formation of a semicarbazone conjugate, which rearranges into a stable diazaborine. The diazaborine formation can be performed in blood serum or cell lysates with minimal interference from biomolecules. We further demonstrate that application of this conjugation chemistry enables facile labeling of bacteria. A synthetic amino acid D-AB3, which presents a 2-acetylphenylboronic acid moiety as its side chain, was found to incorporate into several bacterial species through cell wall remodeling, with particularly high efficiency for Escherichia coli. Subsequent D-AB3 conjugation to a fluorophore-labeled semicarbazide allows robust detection of this bacterial pathogen in blood serum.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Samantha Cambray
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Jianmin Gao
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
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Ambient Desorption/Ionization. Mass Spectrom (Tokyo) 2017. [DOI: 10.1007/978-3-319-54398-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Black C, Chevallier OP, Haughey SA, Balog J, Stead S, Pringle SD, Riina MV, Martucci F, Acutis PL, Morris M, Nikolopoulos DS, Takats Z, Elliott CT. A real time metabolomic profiling approach to detecting fish fraud using rapid evaporative ionisation mass spectrometry. Metabolomics 2017; 13:153. [PMID: 29151824 PMCID: PMC5668337 DOI: 10.1007/s11306-017-1291-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Fish fraud detection is mainly carried out using a genomic profiling approach requiring long and complex sample preparations and assay running times. Rapid evaporative ionisation mass spectrometry (REIMS) can circumvent these issues without sacrificing a loss in the quality of results. OBJECTIVES To demonstrate that REIMS can be used as a fast profiling technique capable of achieving accurate species identification without the need for any sample preparation. Additionally, we wanted to demonstrate that other aspects of fish fraud other than speciation are detectable using REIMS. METHODS 478 samples of five different white fish species were subjected to REIMS analysis using an electrosurgical knife. Each sample was cut 8-12 times with each one lasting 3-5 s and chemometric models were generated based on the mass range m/z 600-950 of each sample. RESULTS The identification of 99 validation samples provided a 98.99% correct classification in which species identification was obtained near-instantaneously (≈ 2 s) unlike any other form of food fraud analysis. Significant time comparisons between REIMS and polymerase chain reaction (PCR) were observed when analysing 6 mislabelled samples demonstrating how REIMS can be used as a complimentary technique to detect fish fraud. Additionally, we have demonstrated that the catch method of fish products is capable of detection using REIMS, a concept never previously reported. CONCLUSIONS REIMS has been proven to be an innovative technique to help aid the detection of fish fraud and has the potential to be utilised by fisheries to conduct their own quality control (QC) checks for fast accurate results.
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Affiliation(s)
- Connor Black
- 0000 0004 0374 7521grid.4777.3Institute for Global Food Security, Advanced ASSET Centre, School of Biological Sciences, Queen’s University Belfast, 18-30 Malone Road, Belfast, BT9 5BN Northern Ireland, UK
| | - Olivier P. Chevallier
- 0000 0004 0374 7521grid.4777.3Institute for Global Food Security, Advanced ASSET Centre, School of Biological Sciences, Queen’s University Belfast, 18-30 Malone Road, Belfast, BT9 5BN Northern Ireland, UK
| | - Simon A. Haughey
- 0000 0004 0374 7521grid.4777.3Institute for Global Food Security, Advanced ASSET Centre, School of Biological Sciences, Queen’s University Belfast, 18-30 Malone Road, Belfast, BT9 5BN Northern Ireland, UK
| | - Julia Balog
- Waters Research Centre, 7 Zahony Street, Budapest, 1031 Hungary
- 0000 0001 2113 8111grid.7445.2Imperial College London, South Kensington Campus, Sir Alexander Fleming Building, London, SW7 2AZ UK
| | - Sara Stead
- Waters Corporation, Altrincham Road, Wilmslow, SK9 4AX UK
| | | | - Maria V. Riina
- 0000 0004 1759 3180grid.425427.2Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Francesca Martucci
- 0000 0004 1759 3180grid.425427.2Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Pier L. Acutis
- 0000 0004 1759 3180grid.425427.2Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Mike Morris
- Waters Corporation, Altrincham Road, Wilmslow, SK9 4AX UK
| | - Dimitrios S. Nikolopoulos
- 0000 0004 0374 7521grid.4777.3School of Electronics, Electrical Engineering and Computer Science, Queen’s University Belfast, Belfast, UK
| | - Zoltan Takats
- 0000 0001 2113 8111grid.7445.2Imperial College London, South Kensington Campus, Sir Alexander Fleming Building, London, SW7 2AZ UK
| | - Christopher T. Elliott
- 0000 0004 0374 7521grid.4777.3Institute for Global Food Security, Advanced ASSET Centre, School of Biological Sciences, Queen’s University Belfast, 18-30 Malone Road, Belfast, BT9 5BN Northern Ireland, UK
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