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Lima NM, Fernandes BL, Alves GF, de Souza JC, Siqueira MM, Patrícia do Nascimento M, Moreira OB, Sussulini A, de Oliveira MA. Mass spectrometry applied to diagnosis, prognosis, and therapeutic targets identification for the novel coronavirus SARS-CoV-2: A review. Anal Chim Acta 2021; 1195:339385. [PMID: 35090661 PMCID: PMC8687343 DOI: 10.1016/j.aca.2021.339385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/27/2022]
Abstract
Mass spectrometry (MS) has found numerous applications in medicine and has been widely used in the detection and characterization of biomolecules associated with viral infections such as COVID-19. COVID-19 is a multisystem disease and, therefore, the need arises to carry out a careful and conclusive assessment of the pathophysiological parameters involved in the infection, to develop an effective therapeutic approach, assess the prognosis of the disease, and especially the early diagnosis of the infected population. Thus, the urgent need for highly accurate methods of diagnosis and prognosis of this infection presents new challenges for the development of laboratory medicine, whose methods require sensitivity, speed, and accuracy of the techniques for analyzing the biological markers involved in the infection. In this context, MS stands out as a robust analytical tool, with high sensitivity and selectivity, accuracy, low turnaround time, and versatility for the analysis of biological samples. However, it has not yet been adopted as a frontline clinical laboratory technique. Therefore, this review explores the potential and trends of current MS methods and their contribution to the development of new strategies to COVID-19 diagnosis and prognosis and how this tool can assist in the discovery of new therapeutic targets, in addition, to comment what could be the future of MS in medicine.
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Bhardwaj J, Hong S, Jang J, Han CH, Lee J, Jang J. Recent advancements in the measurement of pathogenic airborne viruses. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126574. [PMID: 34252679 PMCID: PMC8256664 DOI: 10.1016/j.jhazmat.2021.126574] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 05/11/2023]
Abstract
Air-transmissible pathogenic viruses, such as influenza viruses and coronaviruses, are some of the most fatal strains and spread rapidly by air, necessitating quick and stable measurements from sample air volumes to prevent further spread of diseases and to take appropriate steps rapidly. Measurements of airborne viruses generally require their collection into liquids or onto solid surfaces, with subsequent hydrosolization and then analysis using the growth method, nucleic-acid-based techniques, or immunoassays. Measurements can also be performed in real time without sampling, where species-specific determination is generally disabled. In this review, we introduce some recent advancements in the measurement of pathogenic airborne viruses. Air sampling and measurement technologies for viral aerosols are reviewed, with special focus on the effects of air sampling on damage to the sampled viruses and their measurements. Measurement of pathogenic airborne viruses is an interdisciplinary research area that requires understanding of both aerosol technology and biotechnology to effectively address the issues. Hence, this review is expected to provide some useful guidelines regarding appropriate air sampling and virus detection methods for particular applications.
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Affiliation(s)
- Jyoti Bhardwaj
- Sensors and Aerosols Laboratory, Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | | | - Junbeom Jang
- Sensors and Aerosols Laboratory, Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chang-Ho Han
- Sensors and Aerosols Laboratory, Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaegil Lee
- Sensors and Aerosols Laboratory, Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaesung Jang
- Sensors and Aerosols Laboratory, Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering & Department of Urban and Environmental Engineering, UNIST, Ulsan 44919, Republic of Korea.
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Garza KY, Silva AAR, Rosa JR, Keating MF, Povilaitis SC, Spradlin M, Sanches PHG, Varão Moura A, Marrero Gutierrez J, Lin JQ, Zhang J, DeHoog RJ, Bensussan A, Badal S, Cardoso de Oliveira D, Dias Garcia PH, Dias de Oliveira Negrini L, Antonio MA, Canevari TC, Eberlin MN, Tibshirani R, Eberlin LS, Porcari AM. Rapid Screening of COVID-19 Directly from Clinical Nasopharyngeal Swabs Using the MasSpec Pen. Anal Chem 2021; 93:12582-12593. [PMID: 34432430 PMCID: PMC8409149 DOI: 10.1021/acs.analchem.1c01937] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/06/2021] [Indexed: 12/25/2022]
Abstract
The outbreak of COVID-19 has created an unprecedent global crisis. While the polymerase chain reaction (PCR) is the gold standard method for detecting active SARS-CoV-2 infection, alternative high-throughput diagnostic tests are of a significant value to meet universal testing demands. Here, we describe a new design of the MasSpec Pen technology integrated to electrospray ionization (ESI) for direct analysis of clinical swabs and investigate its use for COVID-19 screening. The redesigned MasSpec Pen system incorporates a disposable sampling device refined for uniform and efficient analysis of swab tips via liquid extraction directly coupled to an ESI source. Using this system, we analyzed nasopharyngeal swabs from 244 individuals including symptomatic COVID-19 positive, symptomatic negative, and asymptomatic negative individuals, enabling rapid detection of rich lipid profiles. Two statistical classifiers were generated based on the lipid information acquired. Classifier 1 was built to distinguish symptomatic PCR-positive from asymptomatic PCR-negative individuals, yielding a cross-validation accuracy of 83.5%, sensitivity of 76.6%, and specificity of 86.6%, and validation set accuracy of 89.6%, sensitivity of 100%, and specificity of 85.3%. Classifier 2 was built to distinguish symptomatic PCR-positive patients from negative individuals including symptomatic PCR-negative patients with moderate to severe symptoms and asymptomatic individuals, yielding a cross-validation accuracy of 78.4%, specificity of 77.21%, and sensitivity of 81.8%. Collectively, this study suggests that the lipid profiles detected directly from nasopharyngeal swabs using MasSpec Pen-ESI mass spectrometry (MS) allow fast (under a minute) screening of the COVID-19 disease using minimal operating steps and no specialized reagents, thus representing a promising alternative high-throughput method for screening of COVID-19.
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Affiliation(s)
- Kyana Y. Garza
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Alex Ap. Rosini Silva
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - Jonas R. Rosa
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - Michael F. Keating
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Sydney C. Povilaitis
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Meredith Spradlin
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Pedro H. Godoy Sanches
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - Alexandre Varão Moura
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - Junier Marrero Gutierrez
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - John Q. Lin
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Jialing Zhang
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Rachel J. DeHoog
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Alena Bensussan
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Sunil Badal
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Danilo Cardoso de Oliveira
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | - Pedro Henrique Dias Garcia
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
| | | | - Marcia Ap. Antonio
- Integrated Unit of Pharmacology and
Gastroenterology, UNIFAG, Bragança Paulista, Sao Paulo 12916-900,
Brazil
| | - Thiago C. Canevari
- School of Material Engineering and Nanotechnology,
MackMass Laboratory, Mackenzie Presbyterian University,
São Paulo, SP 01302-907, Brazil
| | - Marcos N. Eberlin
- School of Material Engineering and Nanotechnology,
MackMass Laboratory, Mackenzie Presbyterian University,
São Paulo, SP 01302-907, Brazil
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford
University, Stanford, California 94305, United
States
| | - Livia S. Eberlin
- Department of Chemistry, The University
of Texas at Austin, Austin, Texas 78712, United
States
| | - Andreia M. Porcari
- MS4Life Laboratory of Mass Spectrometry, Health
Sciences Postgraduate Program, São Francisco University,
Bragança Paulista, São Paulo 12916-900, Brazil
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Abstract
This article reviews the many and varied mass spectrometry based responses to the SARS-CoV2 coronavirus amidst a continuing global healthcare crisis. Although RT-PCR is the most prevalent molecular based surveillance approach, improvements in the detection sensitivities with mass spectrometry coupled to the rapid nature of analysis, the high molecular precision of measurements, opportunities for high sample throughput, and the potential for in-field testing, offer advantages for characterising the virus and studying the molecular pathways by which it infects host cells. The detection of biomarkers by MALDI-TOF mass spectrometry, studies of viral peptides using proteotyping strategies, targeted LC-MS analyses to identify abundant peptides in clinical specimens, the analysis of viral protein glycoforms, proteomics approaches to understand impacts of infection on host cells, and examinations of point-of-care breath analysis have all been explored. This review organises and illustrates these applications with reference to the many studies that have appeared in the literature since the outbreak. In this respect, those studies in which mass spectrometry has a major role are the focus, and only those which have peer-reviewed have been cited.
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Affiliation(s)
- Justin H Griffin
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia
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Jing R, Kudinha T, Zhou ML, Xiao M, Wang H, Yang WH, Xu YC, Hsueh PR. Laboratory diagnosis of COVID-19 in China: A review of challenging cases and analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:17-26. [PMID: 33153907 PMCID: PMC7568515 DOI: 10.1016/j.jmii.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/10/2020] [Indexed: 12/24/2022]
Abstract
Since the initial emergence of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei province, China, a rapid spread of the disease occurred around the world, rising to become an international global health concern at pandemic level. In the face of this medical challenge threatening humans, the development of rapid and accurate methods for early screening and diagnosis of COVID-19 became crucial to containing the emerging public health threat, and prevent further spread within the population. Despite the large number of COVID-19 confirmed cases in China, some problematic cases with inconsistent laboratory testing results, were reported. Specifically, a high false-negative rate of 41% on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription-polymerase chain reaction (qRT-PCR) assays was observed in China. Although serological testing has been applied worldwide as a complementary method to help identify SARS-CoV-2, several limitations on its use have been reported in China. Therefore, the use of both qRT-PCR and serological testing in the diagnosis of COVID-19 in China and elsewhere, presented considerable challenges, but when used in combination, can be valuable tools in the fight against COVID-19. In this review, we give an overview of the advantages and disadvantages of different molecular techniques for SARS-CoV-2 detection that are currently used in several labs, including qRT-PCR, gene sequencing, loop-mediated isothermal amplification (LAMP), nucleic acid mass spectrometry (MS), and gene editing technique based on clustered regularly interspaced short palindromic repeats (CRISPR/Cas13) system. Then we mainly review and analyze some causes of false-negative qRT-PCR results, and how to resolve some of the diagnostic dilemma.
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Affiliation(s)
- Ran Jing
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Leeds Parade, Orange, NSW, 2800, Australia; NSW Health Pathology, Orange Pathology Lab, Orange, NSW, 2800, Australia.
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - He Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Hang Yang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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Laser-assisted rapid evaporative ionisation mass spectrometry (LA-REIMS) as a metabolomics platform in cervical cancer screening. EBioMedicine 2020; 60:103017. [PMID: 32980699 PMCID: PMC7522750 DOI: 10.1016/j.ebiom.2020.103017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background The introduction of high-risk human papillomavirus (hrHPV) testing as part of primary cervical screening is anticipated to improve sensitivity, but also the number of women who will screen positive. Reflex cytology is the preferred triage test in most settings but has limitations including moderate diagnostic accuracy, lack of automation, inter-observer variability and the need for clinician-collected sample. Novel, objective and cost-effective approaches are needed. Methods In this study, we assessed the potential use of an automated metabolomic robotic platform, employing the principle of laser-assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) in cervical cancer screening. Findings In a population of 130 women, LA-REIMS achieved 94% sensitivity and 83% specificity (AUC: 91.6%) in distinguishing women testing positive (n = 65) or negative (n = 65) for hrHPV. We performed further analysis according to disease severity with LA-REIMS achieving sensitivity and specificity of 91% and 73% respectively (AUC: 86.7%) in discriminating normal from high-grade pre-invasive disease. Interpretation This automated high-throughput technology holds promise as a low-cost and rapid test for cervical cancer screening and triage. The use of platforms like LA-REIMS has the potential to further improve the accuracy and efficiency of the current national screening programme. Funding Work was funded by the MRC Imperial Confidence in Concept Scheme, Imperial College Healthcare Charity, British Society for Colposcopy and Cervical Pathology, National Research Development and Innovation Office of Hungary, Waters corporation and NIHR BRC.
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After another decade: LC-MS/MS became routine in clinical diagnostics. Clin Biochem 2020; 82:2-11. [PMID: 32188572 DOI: 10.1016/j.clinbiochem.2020.03.004] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 01/01/2023]
Abstract
Tandem mass spectrometry - especially in combination with liquid chromatography (LC-MS/MS) - is applied in a multitude of important diagnostic niches of laboratory medicine. It is unquestioned in its routine use and is often unreplaceable by alternative technologies. This overview illustrates the development in the past decade (2009-2019) and intends to provide insight into the current standing and future directions of the field. The instrumentation matured significantly, the applications are well understood, and the in vitro diagnostics (IVD) industry is shaping the market by providing assay kits, certified instruments, and the first laboratory automated LC-MS/MS instruments as an analytical core. In many settings the application of LC-MS/MS is still burdensome with locally lab developed test (LDT) designs relying on highly specialized staff. The current routine applications cover a wide range of analytes in therapeutic drug monitoring, endocrinology including newborn screening, and toxicology. The tasks that remain to be mastered are, for example, the quantification of proteins by means of LC-MS/MS and the transition from targeted to untargeted omics approaches relying on pattern recognition/pattern discrimination as a key technology for the establishment of diagnostic decisions.
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Lee AYS, Chataway T, Colella AD, Gordon TP, Wang JJ. Quantitative Mass Spectrometric Analysis of Autoantibodies as a Paradigm Shift in Autoimmune Serology. Front Immunol 2019; 10:2845. [PMID: 31867009 PMCID: PMC6904311 DOI: 10.3389/fimmu.2019.02845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Adrian Y S Lee
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tim Chataway
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Alex D Colella
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tom P Gordon
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Jing J Wang
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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Challenges and opportunities of using liquid chromatography and mass spectrometry methods to develop complex vaccine antigens as pharmaceutical dosage forms. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:23-38. [PMID: 27071526 DOI: 10.1016/j.jchromb.2016.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Liquid chromatographic methods, combined with mass spectrometry, offer exciting and important opportunities to better characterize complex vaccine antigens including recombinant proteins, virus-like particles, inactivated viruses, polysaccharides, and protein-polysaccharide conjugates. The current abilities and limitations of these physicochemical methods to complement traditional in vitro and in vivo vaccine potency assays are explored in this review through the use of illustrative case studies. Various applications of these state-of-the art techniques are illustrated that include the analysis of influenza vaccines (inactivated whole virus and recombinant hemagglutinin), virus-like particle vaccines (human papillomavirus and hepatitis B), and polysaccharide linked to protein carrier vaccines (pneumococcal). Examples of utilizing these analytical methods to characterize vaccine antigens in the presence of adjuvants, which are often included to boost immune responses as part of the final vaccine dosage form, are also presented. Some of the challenges of using chromatographic and LC-MS as physicochemical assays to routinely test complex vaccine antigens are also discussed.
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10
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Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:194-210. [PMID: 26510657 PMCID: PMC4723618 DOI: 10.1007/s13361-015-1271-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 05/13/2023]
Abstract
Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple 'fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Guanghui Wang
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anthony F Suffredini
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Sacks
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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11
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Bustin S. Transparency of reporting in molecular diagnostics. Int J Mol Sci 2013; 14:15878-84. [PMID: 23903047 PMCID: PMC3759891 DOI: 10.3390/ijms140815878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 12/12/2022] Open
Affiliation(s)
- Stephen Bustin
- Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK; E-Mail: ; Tel.: +44-0-845-196-4845
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