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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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2
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Trimpin S, Inutan ED, Pagnotti VS, Karki S, Marshall DD, Hoang K, Wang B, Lietz CB, Richards AL, Yenchick FS, Lee C, Lu IC, Fenner M, Madarshahian S, Saylor S, Chubatyi ND, Zimmerman T, Moreno-Pedraza A, Wang T, Adeniji-Adele A, Meher AK, Madagedara H, Owczarzak Z, Musavi A, Hendrickson TL, Peacock PM, Tomsho JW, Larsen BS, Prokai L, Shulaev V, Pophristic M, McEwen CN. Direct sub-atmospheric pressure ionization mass spectrometry: Evaporation/sublimation-driven ionization is amazing, fundamentally, and practically. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5018. [PMID: 38736378 DOI: 10.1002/jms.5018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/08/2023] [Accepted: 03/04/2024] [Indexed: 05/14/2024]
Abstract
This paper covers direct sub-atmospheric pressure ionization mass spectrometry (MS). The discovery, applications, and mechanistic aspects of novel ionization processes for use in MS that are not based on the high-energy input from voltage, laser, and/or high temperature but on sublimation/evaporation within a region linking a higher to lower pressure and modulated by heat and collisions, are discussed, including how this new reality has guided a series of discoveries, instrument developments, and commercialization. A research focus, inter alia, is on how best to understand, improve, and use these novel ionization processes, which convert volatile and nonvolatile compounds from solids (sublimation) or liquids (evaporation) into gas-phase ions for analysis by MS providing reproducible, accurate, sensitive, and prompt results. Our perception on how these unprecedented versus traditional ionization processes/methods relate to each other, how they can be made to coexist on the same mass spectrometer, and an outlook on new and expanded applications (e.g., clinical, portable, fast, safe, and autonomous) is presented, and is based on ST's Opening lecture presentation at the Nordic Mass spectrometry Conference, Geilo, Norway, January 2023. Focus will be on matrix-assisted ionization (MAI) and solvent-assisted ionization (SAI) MS covering the period from 2010 to 2023; a potential paradigm shift in the making.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Vincent S Pagnotti
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Darrell D Marshall
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Khoa Hoang
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Beixi Wang
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | - Alicia L Richards
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Frank S Yenchick
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Chuping Lee
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - I-Chung Lu
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Madeleine Fenner
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Sara Madarshahian
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Sarah Saylor
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Nicolas D Chubatyi
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Teresa Zimmerman
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | - Tongwen Wang
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Adetoun Adeniji-Adele
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Hasini Madagedara
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Zachary Owczarzak
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Ahmed Musavi
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | | | - John W Tomsho
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | | | - Laszlo Prokai
- Department of Pharmacology and Neuroscience, The University of North Texas Health Science Center at Forth Worth, Fort Worth, Texas, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, Texas, USA
| | - Milan Pophristic
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Charles N McEwen
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Wang Y, Ma W, Qu Y, Jia K, Liu J, Li Y, Jiang L, Xiong C, Nie Z. Desorption Separation Ionization Mass Spectrometry (DSI-MS) for Rapid Analysis of COVID-19. Anal Chem 2024; 96:7360-7366. [PMID: 38697955 DOI: 10.1021/acs.analchem.4c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, which has witnessed over 772 million confirmed cases and over 6 million deaths globally, the outbreak of COVID-19 has emerged as a significant medical challenge affecting both affluent and impoverished nations. Therefore, there is an urgent need to explore the disease mechanism and to implement rapid detection methods. To address this, we employed the desorption separation ionization (DSI) device in conjunction with a mass spectrometer for the efficient detection and screening of COVID-19 urine samples. The study encompassed patients with COVID-19, healthy controls (HC), and patients with other types of pneumonia (OP) to evaluate their urine metabolomic profiles. Subsequently, we identified the differentially expressed metabolites in the COVID-19 patients and recognized amino acid metabolism as the predominant metabolic pathway involved. Furthermore, multiple established machine learning algorithms validated the exceptional performance of the metabolites in discriminating the COVID-19 group from healthy subjects, with an area under the curve of 0.932 in the blind test set. This study collectively suggests that the small-molecule metabolites detected from urine using the DSI device allow for rapid screening of COVID-19, taking just three minutes per sample. This approach has the potential to expand our understanding of the pathophysiological mechanisms of COVID-19 and offers a way to rapidly screen patients with COVID-19 through the utilization of machine learning algorithms.
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Affiliation(s)
- Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Ma
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Yijiao Qu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Liu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province 341000, China
- Ganzhou Key Laboratory of Neuroinflammation Research, Gannan Medical University, Ganzhou, Jiangxi Province 341000, China
| | - Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Lixia Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province 341000, China
- Ganzhou Key Laboratory of Neuroinflammation Research, Gannan Medical University, Ganzhou, Jiangxi Province 341000, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Lawlor K, Clausen J, Johnston A, Edge A, Wolff K, Castrignanò E, Couchman L. A review of analytical parameters in 'rapid' liquid chromatographic methods for bioanalysis: Can we do better? J Chromatogr A 2024; 1721:464803. [PMID: 38547680 DOI: 10.1016/j.chroma.2024.464803] [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: 07/03/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Rapid bioanalysis is beneficial to many applications. However, how 'rapid' a method is, or could be, is often an unanswered question. In this statistical review, the authors have assessed multiple pre-analytical (i.e. sample preparation), and analytical method parameters specifically for liquid chromatography to assist researchers in developing and validating 'rapid' bioanalytical methods. We restricted the search to urine and plasma matrices only. Data were extracted from over 2,000 recent studies and evaluated to assess how these parameters affected the 'on-instrument' analysis time. In addition to methods using ultra-violet (UV) detection, there were a large number of mass spectrometric (MS) methods, allowing additional review of the differences between high- and low-resolution MS on analysis time. We observed that most (N = 922, 70 %) methods used 5 or 10 cm columns, and that whilst uptake of ultra-high performance (U)HPLC columns was good, the use of sub-5 cm columns and/or flow rates in excess of 1 mL/min was incredibly rare (N = 25, 3 %). The detector of choice for quantitative (U)HPLC-MS remains the triple quadrupole, although a number of groups report the use of high-resolution MS for such methods.
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Affiliation(s)
- K Lawlor
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - J Clausen
- Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - A Johnston
- Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - A Edge
- Avantor Sciences, The Markham Centre, Station Road, Theale, Reading, RG7 4PE
| | - K Wolff
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Drug Control Centre, King's College London, London, SE1 9NH, UK
| | - E Castrignanò
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Drug Control Centre, King's College London, London, SE1 9NH, UK
| | - L Couchman
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
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6
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Henderson A, Heaney LM, Rankin-Turner S. Ambient ionisation mass spectrometry for drug and toxin analysis: A review of the recent literature. Drug Test Anal 2024. [PMID: 38326879 DOI: 10.1002/dta.3644] [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: 08/31/2023] [Revised: 11/17/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024]
Abstract
Ambient ionisation mass spectrometry (AIMS) is a form of mass spectrometry whereby analyte ionisation occurs outside of a vacuum source under ambient conditions. This enables the direct analysis of samples in their native state, with little or no sample preparation and without chromatographic separation. The removal of these steps facilitates a much faster analytical process, enabling the direct analysis of samples within minutes if not seconds. Consequently, AIMS has gained rapid popularity across a diverse range of applications, in particular the analysis of drugs and toxins. Numerous fields rely upon mass spectrometry for the detection and identification of drugs, including clinical diagnostics, forensic chemistry, and food safety. However, all of these fields are hindered by the time-consuming and laboratory-confined nature of traditional techniques. As such, the potential for AIMS to resolve these challenges has resulted in a growing interest in ambient ionisation for drug and toxin analysis. Since the early 2000s, forensic science, diagnostic testing, anti-doping, pharmaceuticals, environmental analysis and food safety have all seen a marked increase in AIMS applications, foreshadowing a new future for drug testing. In this review, some of the most promising AIMS techniques for drug analysis will be discussed, alongside different applications of AIMS published over a 5-year period, to provide a summary of the recent research activity for ambient ionisation for drug and toxin analysis.
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Affiliation(s)
- Alisha Henderson
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Liam M Heaney
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Stephanie Rankin-Turner
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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7
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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8
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Wong TF, So PK, Yao ZP. Advances in rapid detection of SARS-CoV-2 by mass spectrometry. Trends Analyt Chem 2022; 157:116759. [PMID: 36035092 PMCID: PMC9391230 DOI: 10.1016/j.trac.2022.116759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/01/2022] [Accepted: 08/14/2022] [Indexed: 12/25/2022]
Abstract
COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.
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Affiliation(s)
- Tsz-Fung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
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9
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Moura AV, de Oliveira DC, Silva AAR, da Rosa JR, Garcia PHD, Sanches PHG, Garza KY, Mendes FMM, Lambert M, Gutierrez JM, Granado NM, dos Santos AC, de Lima IL, Negrini LDDO, Antonio MA, Eberlin MN, Eberlin LS, Porcari AM. Urine Metabolites Enable Fast Detection of COVID-19 Using Mass Spectrometry. Metabolites 2022; 12:1056. [PMID: 36355139 PMCID: PMC9697918 DOI: 10.3390/metabo12111056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic boosted the development of diagnostic tests to meet patient needs and provide accurate, sensitive, and fast disease detection. Despite rapid advancements, limitations related to turnaround time, varying performance metrics due to different sampling sites, illness duration, co-infections, and the need for particular reagents still exist. As an alternative diagnostic test, we present urine analysis through flow-injection-tandem mass spectrometry (FIA-MS/MS) as a powerful approach for COVID-19 diagnosis, targeting the detection of amino acids and acylcarnitines. We adapted a method that is widely used for newborn screening tests on dried blood for urine samples in order to detect metabolites related to COVID-19 infection. We analyzed samples from 246 volunteers with diagnostic confirmation via PCR. Urine samples were self-collected, diluted, and analyzed with a run time of 4 min. A Lasso statistical classifier was built using 75/25% data for training/validation sets and achieved high diagnostic performances: 97/90% sensitivity, 95/100% specificity, and 95/97.2% accuracy. Additionally, we predicted on two withheld sets composed of suspected hospitalized/symptomatic COVID-19-PCR negative patients and patients out of the optimal time-frame collection for PCR diagnosis, with promising results. Altogether, we show that the benchmarked FIA-MS/MS method is promising for COVID-19 screening and diagnosis, and is also potentially useful after the peak viral load has passed.
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Affiliation(s)
- Alexandre Varao Moura
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Danilo Cardoso de Oliveira
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alex Ap. R. Silva
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Jonas Ribeiro da Rosa
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Dias Garcia
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Godoy Sanches
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Kyana Y. Garza
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Flavio Marcio Macedo Mendes
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Mayara Lambert
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Junier Marrero Gutierrez
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Nicole Marino Granado
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alicia Camacho dos Santos
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Iasmim Lopes de Lima
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | | | - Marcia Aparecida Antonio
- Integrated Unit of Pharmacology and Gastroenterology, UNIFAG, Bragança Paulista 12916-900, SP, Brazil
| | - Marcos N. Eberlin
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andreia M. Porcari
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
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10
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Rankin‐Turner S, Reynolds JC, Turner MA, Heaney LM. Applications of ambient ionization mass spectrometry in 2021: An annual review. ANALYTICAL SCIENCE ADVANCES 2022; 3:67-89. [PMID: 38715637 PMCID: PMC10989594 DOI: 10.1002/ansa.202100067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/17/2022] [Accepted: 02/27/2022] [Indexed: 06/26/2024]
Abstract
Ambient ionization mass spectrometry (AIMS) has revolutionized the field of analytical chemistry, enabling the rapid, direct analysis of samples in their native state. Since the inception of AIMS almost 20 years ago, the analytical community has driven the further development of this suite of techniques, motivated by the plentiful advantages offered in addition to traditional mass spectrometry. Workflows can be simplified through the elimination of sample preparation, analysis times can be significantly reduced and analysis remote from the traditional laboratory space has become a real possibility. As such, the interest in AIMS has rapidly spread through analytical communities worldwide, and AIMS techniques are increasingly being integrated with standard laboratory operations. This annual review covers applications of AIMS techniques throughout 2021, with a specific focus on AIMS applications in a number of key fields of research including disease diagnostics, forensics and security, food safety testing and environmental sciences. While some new techniques are introduced, the focus in AIMS research is increasingly shifting from the development of novel techniques toward efforts to improve existing AIMS techniques, particularly in terms of reproducibility, quantification and ease-of-use.
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Affiliation(s)
- Stephanie Rankin‐Turner
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - James C. Reynolds
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Matthew A. Turner
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Liam M. Heaney
- School of SportExercise and Health SciencesLoughborough UniversityLoughboroughLeicestershireUK
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Spick M, Lewis HM, Wilde MJ, Hopley C, Huggett J, Bailey MJ. Systematic review with meta-analysis of diagnostic test accuracy for COVID-19 by mass spectrometry. Metabolism 2022; 126:154922. [PMID: 34715115 PMCID: PMC8548837 DOI: 10.1016/j.metabol.2021.154922] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND The global COVID-19 pandemic has led to extensive development in many fields, including the diagnosis of COVID-19 infection by mass spectrometry. The aim of this systematic review and meta-analysis was to assess the accuracy of mass spectrometry diagnostic tests developed so far, across a wide range of biological matrices, and additionally to assess risks of bias and applicability in studies published to date. METHOD 23 retrospective observational cohort studies were included in the systematic review using the PRISMA-DTA framework, with a total of 2858 COVID-19 positive participants and 2544 controls. Risks of bias and applicability were assessed via a QUADAS-2 questionnaire. A meta-analysis was also performed focusing on sensitivity, specificity, diagnostic accuracy and Youden's Index, in addition to assessing heterogeneity. FINDINGS Sensitivity averaged 0.87 in the studies reviewed herein (interquartile range 0.81-0.96) and specificity 0.88 (interquartile range 0.82-0.98), with an area under the receiver operating characteristic summary curve of 0.93. By subgroup, the best diagnostic results were achieved by viral proteomic analyses of nasopharyngeal swabs and metabolomic analyses of plasma and serum. The performance of other sampling matrices (breath, sebum, saliva) was less good, indicating that these protocols are currently insufficiently mature for clinical application. CONCLUSIONS This systematic review and meta-analysis demonstrates the potential for mass spectrometry and 'omics in achieving accurate test results for COVID-19 diagnosis, but also highlights the need for further work to optimize and harmonize practice across laboratories before these methods can be translated to clinical applications.
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Affiliation(s)
- Matt Spick
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Holly M Lewis
- Surrey Ion Beam Centre, University of Surrey, Guildford GU2 7XH, UK
| | - Michael J Wilde
- School of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Christopher Hopley
- National Measurement Laboratory, LGC, Queens Road, Teddington TW11 0LY, UK
| | - Jim Huggett
- National Measurement Laboratory, LGC, Queens Road, Teddington TW11 0LY, UK; School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Melanie J Bailey
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK; Surrey Ion Beam Centre, University of Surrey, Guildford GU2 7XH, UK.
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Yaari Z, Horoszko CP, Antman-Passig M, Kim M, Nguyen FT, Heller DA. Emerging technologies in cancer detection. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00011-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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: 19] [Impact Index Per Article: 9.5] [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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