1
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Ghimire ML, Cox BD, Winn CA, Rockett TW, Schifano NP, Slagle HM, Gonzalez F, Bertino MF, Caputo GA, Reiner JE. Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing. ACS NANO 2022; 16:17229-17241. [PMID: 36214366 DOI: 10.1021/acsnano.2c07842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Cole A Winn
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Thomas W Rockett
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nicholas P Schifano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Hannah M Slagle
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Frank Gonzalez
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Massimo F Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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2
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Evans-Nguyen K, Stelmack AR, Clowser PC, Holtz JM, Mulligan CC. FIELDABLE MASS SPECTROMETRY FOR FORENSIC SCIENCE, HOMELAND SECURITY, AND DEFENSE APPLICATIONS. MASS SPECTROMETRY REVIEWS 2021; 40:628-646. [PMID: 32722885 DOI: 10.1002/mas.21646] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 02/24/2020] [Indexed: 05/26/2023]
Abstract
Mass spectrometry is commonly used in forensic chemistry laboratories for sensitive, definitive analysis. There have been significant efforts to bring mass spectrometry analysis on-site through the development of ruggedized, fieldable instruments. Testing samples in the field is of particular interest in forensic science, homeland security, and defense applications. In forensic chemistry, testing seized drugs in the field can significantly improve efficiencies in processing of related criminal cases. The screening of passengers and luggage at transportation hubs is a critical need for homeland security for which mass spectrometry is well suited to provide definitive answers with low false positive rates. Mass spectrometry can yield reliable data for military personnel testing sites for potential chemical weapons release. To meet the needs of the forensic and security communities fieldable mass spectrometers based on membrane inlet systems and hybrid gas chromatography systems have been developed and commercialized. More recently developed ambient ionization mass spectrometry methods can eliminate the time, equipment, and expertise associated with sample preparation, and so are especially appealing for on-site analysis. We describe the development of fieldable mass spectrometry systems, with emphasis on commercially available systems that have been deployed for on-site analysis of seized drugs, chemical warfare agents, explosives, and other analytes of interest to the forensic and security communities. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Kenyon Evans-Nguyen
- Department of Chemistry, Biochemistry and Physics, University of Tampa, Tampa, FL
| | | | | | - Jessica M Holtz
- Department of Chemistry, Illinois State University, Normal, IL
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3
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Petukhova VZ, Young AN, Wang J, Wang M, Ladanyi A, Kothari R, Burdette JE, Sanchez LM. Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:344-354. [PMID: 30353292 PMCID: PMC6347503 DOI: 10.1007/s13361-018-2088-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 05/09/2023]
Abstract
MALDI fingerprinting was first described two decades ago as a technique to identify microbial cell lines. Microbial fingerprinting has since evolved into an automated platform for microorganism identification and classification, which is now routinely used in clinical and environmental sectors. The extension of fingerprinting to mammalian cells has yet to progress partly due to compartmentalization of eukaryotic cells and overall higher cellular complexity. A number of publications on mammalian whole cell fingerprinting suggest that the method could be useful for classification of different cell types, cell states, and monitoring cell differentiation. We report the optimization of MALDI fingerprinting workflow parameters for mammalian cells and its application for differential profiling of mammalian cell lines and two-component cell line mixtures. Murine fallopian tube cells and high-grade ovarian carcinoma cell lines and their mixtures are used as model mammalian cell lines. Two-component cell mixtures serve to determine the method's feasibility for complex biological samples as the ability to detect cancer cells in a mixed cell population. The level of detection of cancer cells in the two-component mixture by principle component analysis (PCA) starts to deteriorate at 5% but with application of a different statistical approach, Wilcoxon rank sum test, the level of detection was determined to be 1%. The ability to differentiate heterogeneous cell mixtures will help further extend whole cell MALDI fingerprinting to complex biological systems. Graphical Abstract.
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Affiliation(s)
- Valentina Z Petukhova
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St., MC 781, Room 539, Chicago, IL, 60612, USA
| | - Alexandria N Young
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St., MC 781, Room 539, Chicago, IL, 60612, USA
| | - Jian Wang
- Ometa Labs, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Mingxun Wang
- Ometa Labs, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Andras Ladanyi
- Department of Obstetrics & Gynecology, Rush University Medical Center, 1653 W Congress Pkwy, Chicago, IL, 60612, USA
| | - Rajul Kothari
- Department of Obstetrics & Gynecology-Division of Gynecologic Oncology, University of Illinois at Chicago, 820 S Wood St., Chicago, IL, 60612, USA
| | - Joanna E Burdette
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St., MC 781, Room 539, Chicago, IL, 60612, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St., MC 781, Room 539, Chicago, IL, 60612, USA.
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4
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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5
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Lasch P, Stämmler M, Zhang M, Baranska M, Bosch A, Majzner K. FT-IR Hyperspectral Imaging and Artificial Neural Network Analysis for Identification of Pathogenic Bacteria. Anal Chem 2018; 90:8896-8904. [DOI: 10.1021/acs.analchem.8b01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Lasch
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Maren Stämmler
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Miao Zhang
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| | - Alejandra Bosch
- CINDEFI,
CONICET-CCT
La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Buenos Aires, Argentina
| | - Katarzyna Majzner
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
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6
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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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7
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Duracova M, Klimentova J, Fucikova A, Dresler J. Proteomic Methods of Detection and Quantification of Protein Toxins. Toxins (Basel) 2018; 10:toxins10030099. [PMID: 29495560 PMCID: PMC5869387 DOI: 10.3390/toxins10030099] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/11/2022] Open
Abstract
Biological toxins are a heterogeneous group of compounds that share commonalities with biological and chemical agents. Among them, protein toxins represent a considerable, diverse set. They cover a broad range of molecular weights from less than 1000 Da to more than 150 kDa. This review aims to compare conventional detection methods of protein toxins such as in vitro bioassays with proteomic methods, including immunoassays and mass spectrometry-based techniques and their combination. Special emphasis is given to toxins falling into a group of selected agents, according to the Centers for Disease Control and Prevention, such as Staphylococcal enterotoxins, Bacillus anthracis toxins, Clostridium botulinum toxins, Clostridium perfringens epsilon toxin, ricin from Ricinus communis, Abrin from Abrus precatorius or control of trade in dual-use items in the European Union, including lesser known protein toxins such as Viscumin from Viscum album. The analysis of protein toxins and monitoring for biological threats, i.e., the deliberate spread of infectious microorganisms or toxins through water, food, or the air, requires rapid and reliable methods for the early identification of these agents.
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Affiliation(s)
- Miloslava Duracova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Jana Klimentova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Alena Fucikova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, CZ-160 00 Prague 6, Czech Republic.
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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9
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Pfrunder S, Grossmann J, Hunziker P, Brunisholz R, Gekenidis MT, Drissner D. Bacillus cereus Group-Type Strain-Specific Diagnostic Peptides. J Proteome Res 2016; 15:3098-107. [DOI: 10.1021/acs.jproteome.6b00216] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefanie Pfrunder
- Agroscope, Institute
for Food Sciences, Schloss
1, 8820 Waedenswil, Switzerland
| | - Jonas Grossmann
- Functional
Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstraße
190, 8057 Zurich, Switzerland
| | - Peter Hunziker
- Functional
Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstraße
190, 8057 Zurich, Switzerland
| | - René Brunisholz
- Functional
Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstraße
190, 8057 Zurich, Switzerland
| | - Maria-Theresia Gekenidis
- Agroscope, Institute
for Food Sciences, Schloss
1, 8820 Waedenswil, Switzerland
- ETH Zurich, Institute of Food, Nutrition and
Health, Schmelzbergstraße
7, 8092 Zurich, Switzerland
| | - David Drissner
- Agroscope, Institute
for Food Sciences, Schloss
1, 8820 Waedenswil, Switzerland
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10
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Duriez E, Armengaud J, Fenaille F, Ezan E. Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:183-199. [PMID: 26956386 DOI: 10.1002/jms.3747] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.
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Affiliation(s)
| | - Jean Armengaud
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunologie, 30207, Bagnols sur-Cèze, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191, Gif-sur-Yvette cedex, France
| | - Eric Ezan
- CEA, Programme Transversal Technologies pour la Santé, 91191, Gif sur Yvette, France
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11
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Niyompanich S, Srisanga K, Jaresitthikunchai J, Roytrakul S, Tungpradabkul S. Utilization of Whole-Cell MALDI-TOF Mass Spectrometry to Differentiate Burkholderia pseudomallei Wild-Type and Constructed Mutants. PLoS One 2015; 10:e0144128. [PMID: 26656930 PMCID: PMC4685992 DOI: 10.1371/journal.pone.0144128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/14/2015] [Indexed: 01/19/2023] Open
Abstract
Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has been widely adopted as a useful technology in the identification and typing of microorganisms. This study employed the whole-cell MALDI-TOF MS to identify and differentiate wild-type and mutants containing constructed single gene mutations of Burkholderia pseudomallei, a pathogenic bacterium causing melioidosis disease in both humans and animals. Candidate biomarkers for the B. pseudomallei mutants, including rpoS, ppk, and bpsI isolates, were determined. Taxon-specific and clinical isolate-specific biomarkers of B. pseudomallei were consistently found and conserved across all average mass spectra. Cluster analysis of MALDI spectra of all isolates exhibited separate distribution. A total of twelve potential mass peaks discriminating between wild-type and mutant isolates were identified using ClinProTools analysis. Two peaks (m/z 2721 and 2748 Da) were specific for the rpoS isolate, three (m/z 3150, 3378, and 7994 Da) for ppk, and seven (m/z 3420, 3520, 3587, 3688, 4623, 4708, and 5450 Da) for bpsI. Our findings demonstrated that the rapid, accurate, and reproducible mass profiling technology could have new implications in laboratory-based rapid differentiation of extensive libraries of genetically altered bacteria.
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Affiliation(s)
- Suthamat Niyompanich
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kitima Srisanga
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand
| | - Sumalee Tungpradabkul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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12
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Dupré M, Gilquin B, Fenaille F, Feraudet-Tarisse C, Dano J, Ferro M, Simon S, Junot C, Brun V, Becher F. Multiplex Quantification of Protein Toxins in Human Biofluids and Food Matrices Using Immunoextraction and High-Resolution Targeted Mass Spectrometry. Anal Chem 2015; 87:8473-80. [DOI: 10.1021/acs.analchem.5b01900] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mathieu Dupré
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Benoit Gilquin
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - François Fenaille
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Cécile Feraudet-Tarisse
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Julie Dano
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Myriam Ferro
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Stéphanie Simon
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Christophe Junot
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Virginie Brun
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - François Becher
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
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13
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Abstract
Developments in forensic mass spectrometry tend to follow, rather than lead, the developments in other disciplines. Examples of techniques having forensic potential born independently of forensic applications include ambient ionization, imaging mass spectrometry, isotope ratio mass spectrometry, portable mass spectrometers, and hyphenated chromatography-mass spectrometry instruments, to name a few. Forensic science has the potential to benefit enormously from developments that are funded by other means, if only the infrastructure and personnel existed to adopt, validate, and implement the new technologies into casework. Perhaps one unique area in which forensic science is at the cutting edge is in the area of chemometrics and the determination of likelihood ratios for the evaluation of the weight of evidence. Such statistical techniques have been developed most extensively for ignitable-liquid residue analyses and isotope ratio analysis. This review attempts to capture the trends, motivating forces, and likely impact of developing areas of forensic mass spectrometry, with the caveat that none of this research is likely to have any real impact in the forensic community unless: (a) The instruments developed are turned into robust black boxes with red and green lights for positives and negatives, respectively, or (b) there are PhD graduates in the workforce who can help adopt these sophisticated techniques.
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Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial. J Clin Microbiol 2015; 53:2632-40. [PMID: 26063856 DOI: 10.1128/jcm.00813-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/01/2015] [Indexed: 02/02/2023] Open
Abstract
In the case of a release of highly pathogenic bacteria (HPB), there is an urgent need for rapid, accurate, and reliable diagnostics. MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive technique that is becoming increasingly important in microbiological diagnostics to complement classical microbiology, PCR, and genotyping of HPB. In the present study, the results of a joint exercise with 11 partner institutions from nine European countries are presented. In this exercise, 10 distinct microbial samples, among them five HPB, Bacillus anthracis, Brucella canis, Burkholderia mallei, Burkholderia pseudomallei, and Yersinia pestis, were characterized under blinded conditions. Microbial strains were inactivated by high-dose gamma irradiation before shipment. Preparatory investigations ensured that this type of inactivation induced only subtle spectral changes with negligible influence on the quality of the diagnosis. Furthermore, pilot tests on nonpathogenic strains were systematically conducted to ensure the suitability of sample preparation and to optimize and standardize the workflow for microbial identification. The analysis of the microbial mass spectra was carried out by the individual laboratories on the basis of spectral libraries available on site. All mass spectra were also tested against an in-house HPB library at the Robert Koch Institute (RKI). The averaged identification accuracy was 77% in the first case and improved to >93% when the spectral diagnoses were obtained on the basis of the RKI library. The compilation of complete and comprehensive databases with spectra from a broad strain collection is therefore considered of paramount importance for accurate microbial identification.
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15
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Kryazhevskikh NA, Loiko NG, Demkina EV, Mulyukin AL, Lebedev AT, Gaponov AM, Tutel’yan AV, Nikolaev YA, El’-Registan GI. Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715030121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Li J, Yue L, Li C, Pan Y, Yang L. Enantioselectivity and catalysis improvements of Pseudomonas cepacia lipase with Tyr and Asp modification. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00110b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A concise strategy to improve the p-nitrophenyl palmitate catalytic activity and enantioselectivity towards secondary alcohols of PcL is described.
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Affiliation(s)
- Jing Li
- Institute of Biological Engineering
- Department of Chemical & Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Lei Yue
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Chang Li
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Yuanjiang Pan
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Lirong Yang
- Institute of Biological Engineering
- Department of Chemical & Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
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17
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Labas V, Spina L, Belleannee C, Teixeira-Gomes AP, Gargaros A, Dacheux F, Dacheux JL. Analysis of epididymal sperm maturation by MALDI profiling and top-down mass spectrometry. J Proteomics 2015; 113:226-43. [DOI: 10.1016/j.jprot.2014.09.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/17/2014] [Accepted: 09/30/2014] [Indexed: 12/27/2022]
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Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard N, Blesbois E. Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen. J Proteomics 2014; 112:313-35. [PMID: 25086240 DOI: 10.1016/j.jprot.2014.07.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/03/2014] [Accepted: 07/17/2014] [Indexed: 01/21/2023]
Abstract
UNLABELLED Understanding of the avian male gamete biology is essential to improve the conservation of genetic resources and performance in farming. In this study, the chicken semen peptidome/proteome and the molecular phenotype related to sperm quality were investigated. Spermatozoa (SPZ) and corresponding seminal plasma (SP) from 11 males with different fertilizing capacity were analyzed using three quantitative strategies (fluid and intact cells MALDI-MS, SDS-PAGE combined to LC-MS/MS with spectral counting and XIC methods). Individual MALDI profiling in combination with top-down MS allowed to characterize specific profiles per male and to identify 16 biomolecules (e.g.VMO1, AvBD10 and AvBD9 including polymorphism). Qualitative analysis identified 1165 proteins mainly involved in oxidoreduction mechanisms, energy processes, proteolysis and protein localization. Comparative analyses between the most and the least fertile males were performed. The enzymes involved in energy metabolism, respiratory chain or oxido-reduction activity were over-represented in SPZ of the most fertile males. The SP of the most and the least fertile males differed also on many proteins (e.g. ACE, AvBD10 and AvBD9, NEL precursor, acrosin). Thus proteomic is a "phenomic molecular tool" that may help to discriminate avian males on their reproductive capacity. The data have been deposited with ProteomeXchange (identifiers PXD000287 and PXD001254). BIOLOGICAL SIGNIFICANCE This peptidomic and proteomic study i) characterized for the first time the semen protein composition of the main domestic avian species (Gallus gallus) by analysis of ejaculated spermatozoa and corresponding seminal plasma; ii) established a characteristic molecular phenotype distinguishing semen and males at an individual level; and iii) proposedthe first evidence of biomarkers related to fertility.
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Affiliation(s)
- Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France; INRA, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | - Isabelle Grasseau
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Karine Cahier
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Audrey Gargaros
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Grégoire Harichaux
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France; INRA, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | - Ana-Paula Teixeira-Gomes
- INRA, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France; INRA, UMR 1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France; Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
| | - Sabine Alves
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Marie Bourin
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Nadine Gérard
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Elisabeth Blesbois
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France.
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19
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Niyompanich S, Jaresitthikunchai J, Srisanga K, Roytrakul S, Tungpradabkul S. Source-identifying biomarker ions between environmental and clinical Burkholderia pseudomallei using whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). PLoS One 2014; 9:e99160. [PMID: 24914956 PMCID: PMC4051666 DOI: 10.1371/journal.pone.0099160] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, which is an endemic disease in Northeast Thailand and Northern Australia. Environmental reservoirs, including wet soils and muddy water, serve as the major sources for contributing bacterial infection to both humans and animals. The whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has recently been applied as a rapid, accurate, and high-throughput tool for clinical diagnosis and microbiological research. In this present study, we employed a whole-cell MALDI-TOF MS approach for assessing its potency in clustering a total of 11 different B. pseudomallei isolates (consisting of 5 environmental and 6 clinical isolates) with respect to their origins and to further investigate the source-identifying biomarker ions belonging to each bacterial group. The cluster analysis demonstrated that six out of eleven isolates were grouped correctly to their sources. Our results revealed a total of ten source-identifying biomarker ions, which exhibited statistically significant differences in peak intensity between average environmental and clinical mass spectra using ClinProTools software. Six out of ten mass ions were assigned as environmental-identifying biomarker ions (EIBIs), including, m/z 4,056, 4,214, 5,814, 7,545, 7,895, and 8,112, whereas the remaining four mass ions were defined as clinical-identifying biomarker ions (CIBIs) consisting of m/z 3,658, 6,322, 7,035, and 7,984. Hence, our findings represented, for the first time, the source-specific biomarkers of environmental and clinical B. pseudomallei.
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Affiliation(s)
- Suthamat Niyompanich
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Kitima Srisanga
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Sumalee Tungpradabkul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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20
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Chenau J, Fenaille F, Simon S, Filali S, Volland H, Junot C, Carniel E, Becher F. Detection of Yersinia pestis in environmental and food samples by intact cell immunocapture and liquid chromatography-tandem mass spectrometry. Anal Chem 2014; 86:6144-52. [PMID: 24847944 DOI: 10.1021/ac501371r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Yersinia pestis is the causative agent of bubonic and pneumonic plague, an acute and often fatal disease in humans. In addition to the risk of natural exposure to plague, there is also the threat of a bioterrorist act, leading to the deliberate spread of the bacteria in the environment or food. We report here an immuno-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) method for the direct (i.e., without prior culture), sensitive, and specific detection of Y. pestis in such complex samples. In the first step, a bottom-up proteomics approach highlighted three relevant protein markers encoded by the Y. pestis-specific plasmids pFra (murine toxin) and pPla (plasminogen activator and pesticin). Suitable proteotypic peptides were thoroughly selected to monitor the three protein markers by targeted MS using the selected reaction monitoring (SRM) mode. Immunocapture conditions were optimized for the isolation and concentration of intact bacterial cells from complex samples. The immuno-LC-SRM assay has a limit of detection of 2 × 10(4) CFU/mL in milk or tap water, which compares well with those of state-of-the-art immunoassays. Moreover, we report the first direct detection of Y. pestis in soil, which could be extremely useful in confirming Y. pestis persistence in the ground.
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Affiliation(s)
- Jérôme Chenau
- Service de Pharmacologie et d'Immunoanalyse, Institut de Biologie et de Technologies de Saclay (iBiTec-S), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) , 91191 Gif-sur-Yvette, France
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21
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Tevell Åberg A, Björnstad K, Hedeland M. Mass Spectrometric Detection of Protein-Based Toxins. Biosecur Bioterror 2013; 11 Suppl 1:S215-26. [DOI: 10.1089/bsp.2012.0072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Annica Tevell Åberg
- Annica Tevell Åberg, PhD, is a Senior Researcher; Kristian Björnstad, PhD, is a Senior Researcher; and Mikael Hedeland, PhD, is an Associate Professor and Deputy Head of Department; all at the Department of Chemistry, Environment and Feed Hygiene, National Veterinary Institute (SVA), Uppsala, Sweden. Dr. Åberg and Dr. Hedeland are also affiliated with the Division of Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
| | - Kristian Björnstad
- Annica Tevell Åberg, PhD, is a Senior Researcher; Kristian Björnstad, PhD, is a Senior Researcher; and Mikael Hedeland, PhD, is an Associate Professor and Deputy Head of Department; all at the Department of Chemistry, Environment and Feed Hygiene, National Veterinary Institute (SVA), Uppsala, Sweden. Dr. Åberg and Dr. Hedeland are also affiliated with the Division of Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
| | - Mikael Hedeland
- Annica Tevell Åberg, PhD, is a Senior Researcher; Kristian Björnstad, PhD, is a Senior Researcher; and Mikael Hedeland, PhD, is an Associate Professor and Deputy Head of Department; all at the Department of Chemistry, Environment and Feed Hygiene, National Veterinary Institute (SVA), Uppsala, Sweden. Dr. Åberg and Dr. Hedeland are also affiliated with the Division of Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
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22
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Fenselau CC. Rapid characterization of microorganisms by mass spectrometry--what can be learned and how? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1161-6. [PMID: 23722726 PMCID: PMC3715556 DOI: 10.1007/s13361-013-0660-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/08/2013] [Accepted: 02/08/2013] [Indexed: 05/11/2023]
Abstract
Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.
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Affiliation(s)
- Catherine C Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA,
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23
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Demirev PA, Hagan NS, Antoine MD, Lin JS, Feldman AB. Establishing drug resistance in microorganisms by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1194-1201. [PMID: 23568030 DOI: 10.1007/s13361-013-0609-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 06/02/2023]
Abstract
A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and (13)C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.
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Affiliation(s)
- Plamen A Demirev
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD 20723, USA.
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24
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Rapid identification of Bacillus anthracis spores in suspicious powder samples by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Appl Environ Microbiol 2013; 79:5372-83. [PMID: 23811517 DOI: 10.1128/aem.01724-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory-based matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis method for identifying B. anthracis spores in suspicious powder samples. A reference library containing 22 different Bacillus sp. strains or hoax materials was constructed and coupled with a novel classification algorithm and standardized processing protocol for various powder samples. The method's limit of B. anthracis detection was determined to be 2.5 × 10(6) spores, equivalent to a 55-μg sample size of the crudest B. anthracis-containing powder discovered during the 2001 Amerithrax incidents. The end-to-end analysis method was able to successfully discriminate among samples containing B. anthracis spores, closely related Bacillus sp. spores, and commonly encountered hoax materials. No false-positive or -negative classifications of B. anthracis spores were observed, even when the analysis method was challenged with a wide range of other bacterial agents. The robustness of the method was demonstrated by analyzing samples (i) at an external facility using a different MALDI-TOF MS instrument, (ii) using an untrained operator, and (iii) using mixtures of Bacillus sp. spores and hoax materials. Taken together, the observed performance of the analysis method developed demonstrates its potential applicability as a rapid, specific, sensitive, robust, and cost-effective laboratory-based analysis tool for resolving incidents involving suspicious powders in less than 30 min.
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Sandrin TR, Goldstein JE, Schumaker S. MALDI TOF MS profiling of bacteria at the strain level: a review. MASS SPECTROMETRY REVIEWS 2013; 32:188-217. [PMID: 22996584 DOI: 10.1002/mas.21359] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 05/16/2023]
Abstract
Since the advent of the use of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) as a tool for microbial characterization, efforts to increase the taxonomic resolution of the approach have been made. The rapidity and efficacy of the approach have suggested applications in counter-bioterrorism, prevention of food contamination, and monitoring the spread of antibiotic-resistant bacteria. Strain-level resolution has been reported with diverse bacteria, using library-based and bioinformatics-enabled approaches. Three types of characterization at the strain level have been reported: strain categorization, strain differentiation, and strain identification. Efforts to enhance the library-based approach have involved sample pre-treatment and data reduction strategies. Bioinformatics approaches have leveraged the ever-increasing amount of publicly available genomic and proteomic data to attain strain-level characterization. Bioinformatics-enabled strategies have facilitated strain characterization via intact biomarker identification, bottom-up, and top-down approaches. Rigorous quantitative and advanced statistical analyses have fostered success at the strain level with both approaches. Library-based approaches can be limited by effects of sample preparation and culture conditions on reproducibility, whereas bioinformatics-enabled approaches are typically limited to bacteria, for which genetic and/or proteomic data are available. Biological molecules other than proteins produced in strain-specific manners, including lipids and lipopeptides, might represent other avenues by which strain-level resolution might be attained. Immunological and lectin-based chemistries have shown promise to enhance sensitivity and specificity. Whereas the limits of the taxonomic resolution of MALDI TOF MS profiling of bacteria appears bacterium-specific, recent data suggest that these limits might not yet have been reached.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona 85069, USA.
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26
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Emergence of whole-cell MALDI-MS biotyping for high-throughput bioanalysis of mammalian cells? Bioanalysis 2013; 5:885-93. [DOI: 10.4155/bio.13.47] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since their inception in the 1970s, methods for classification of microorganisms based on mass spectral fingerprints obtained by MALDI-TOF MS have become a mainstay in environmental as well as in clinical microbiology. Recently, related whole-cell MALDI-TOF fingerprinting workflows have been adopted for the classification of mammalian cells. In this report we summarize this work and discuss the challenges of adapting whole-cell MS fingerprinting methods for the successful classification of mammalian cells. We highlight current limitations as well as opportunities and emerging applications of this technology in industrial and clinical settings, such as cell-line authentication, clinical diagnostics, and quality and productivity control in bioprocesses.
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27
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Fagerquist CK, Sultan O, Carter MQ. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2102-2114. [PMID: 23055076 DOI: 10.1007/s13361-012-0490-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/29/2012] [Accepted: 09/03/2012] [Indexed: 06/01/2023]
Abstract
We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, Hde, and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight tandem mass spectrometry (TOF-TOF-MS/MS) and post-source decay (PSD). We also reported the absence of adduct formation when using α-cyano-4-hydroxycinnamic acid (CHCA) matrix. Further mass spectrometric analysis of disulfide-intact and disulfide-reduced over-expressed HdeA and HdeB proteins from lysates of gene-inserted E. coli plasmids suggests covalent attachment of SA occurs not at cysteine residues but at lysine residues. In this revised hypothesis, the attachment of SA is preceded by formation of a solid phase ammonium carboxylate salt between SA and accessible lysine residues of the protein during sample preparation under acidic conditions. Laser irradiation at 355 nm of the dried sample spot results in equilibrium retrogradation followed by nucleophilic attack by the amine group of lysine at the carbonyl group of SA and subsequent amide bond formation and loss of water. The absence of CHCA adducts suggests that the electron-withdrawing effect of the α-cyano group of this matrix may inhibit salt formation and/or amide bond formation. This revised hypothesis is supported by dissociative loss of SA (-224 Da) and the amide-bound SA (-206 Da) from SA-adducted HdeA and HdeB ions by MS/MS (PSD). It is proposed that cleavage of the amide-bound SA from the lysine side-chain occurs via rearrangement involving a pentacyclic transition state followed by hydrogen abstraction/migration and loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal (-206 Da).
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Affiliation(s)
- Clifton K Fagerquist
- Agricultural Research Service, US Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
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Havlicek V, Lemr K, Schug KA. Current Trends in Microbial Diagnostics Based on Mass Spectrometry. Anal Chem 2012; 85:790-7. [DOI: 10.1021/ac3031866] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Havlicek
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Karel Lemr
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Kevin A. Schug
- The University of Texas at Arlington,
Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065,
United States
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30
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Toh-Boyo GM, Wulff SS, Basile F. Comparison of Sample Preparation Methods and Evaluation of Intra- and Intersample Reproducibility in Bacteria MALDI-MS Profiling. Anal Chem 2012; 84:9971-80. [DOI: 10.1021/ac302375e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gwendoline M. Toh-Boyo
- Department
of Chemistry and ‡Department of Statistics, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming 82072,
United States
| | - Shaun S. Wulff
- Department
of Chemistry and ‡Department of Statistics, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming 82072,
United States
| | - Franco Basile
- Department
of Chemistry and ‡Department of Statistics, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming 82072,
United States
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31
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Translational plant proteomics: a perspective. J Proteomics 2012; 75:4588-601. [PMID: 22516432 DOI: 10.1016/j.jprot.2012.03.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/25/2012] [Accepted: 03/25/2012] [Indexed: 11/21/2022]
Abstract
Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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32
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Li D, Truong TV, Bills TM, Holt BC, VanDerwerken DN, Williams JR, Acharya A, Robison RA, Tolley HD, Lee ML. GC/MS Method for Positive Detection of Bacillus anthracis Endospores. Anal Chem 2012; 84:1637-44. [DOI: 10.1021/ac202606x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dan Li
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Tai V. Truong
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Teri M. Bills
- Department of Microbiology and
Molecular Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Brian C. Holt
- Department of Statistics, Brigham Young University, Provo, Utah 84602, United
States
| | | | - John R. Williams
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Abhilasha Acharya
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Richard A. Robison
- Department of Microbiology and
Molecular Biology, Brigham Young University, Provo, Utah 84602, United States
| | - H. Dennis Tolley
- Department of Statistics, Brigham Young University, Provo, Utah 84602, United
States
| | - Milton L. Lee
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
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33
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Pratt KA, Prather KA. Mass spectrometry of atmospheric aerosols--recent developments and applications. Part II: On-line mass spectrometry techniques. MASS SPECTROMETRY REVIEWS 2012; 31:17-48. [PMID: 21449003 DOI: 10.1002/mas.20330] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 08/19/2010] [Accepted: 08/19/2010] [Indexed: 05/30/2023]
Abstract
Many of the significant advances in our understanding of atmospheric particles can be attributed to the application of mass spectrometry. Mass spectrometry provides high sensitivity with fast response time to probe chemically complex particles. This review focuses on recent developments and applications in the field of mass spectrometry of atmospheric aerosols. In Part II of this two-part review, we concentrate on real-time mass spectrometry techniques, which provide high time resolution for insight into brief events and diurnal changes while eliminating the potential artifacts acquired during long-term filter sampling. In particular, real-time mass spectrometry has been shown recently to provide the ability to probe the chemical composition of ambient individual particles <30 nm in diameter to further our understanding of how particles are formed through nucleation in the atmosphere. Further, transportable real-time mass spectrometry techniques are now used frequently on ground-, ship-, and aircraft-based studies around the globe to further our understanding of the spatial distribution of atmospheric aerosols. In addition, coupling aerosol mass spectrometry techniques with other measurements in series has allowed the in situ determination of chemically resolved particle effective density, refractive index, volatility, and cloud activation properties.
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Affiliation(s)
- Kerri A Pratt
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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34
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Misra RV, Ahmod NZ, Parker R, Fang M, Shah H, Gharbia S. Developing an integrated proteo-genomic approach for the characterisation of biomarkers for the identification of Bacillus anthracis. J Microbiol Methods 2011; 88:237-47. [PMID: 22178189 DOI: 10.1016/j.mimet.2011.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis is the causative agent of anthrax, an acute and often fatal disease in humans. Due to the high genomic relatedness within the Bacillus cereus group of species it is a challenge to identify B. anthracis consistently. Alternative strategies such as proteomics coupled with mass spectrometry (MS) provide a powerful approach for biomarker discovery. However, validating and evaluating these markers, particularly for genetically homogeneous species such as B. anthracis are challenging. The objective of this study is to develop a robust biomarker discovery and validation pipeline, using proteomic methodology combined with in silico and molecular approaches, to determine a biomarker list, using B. anthracis as a model. In this exploratory study we profiled the proteome of B. anthracis and genetically related species using GeLC-Liquid Chromatography MS/MS (GeLC-LC MS/MS), identifying peptides that could be used to detect B. anthracis. Peptides were filtered to remove low quality identifications. Using comparative bioinformatic approaches, matching and searching against genomic sequence data a shortlist of peptide biomarkers was determined and validated using DNA sequencing, against a panel of closely related strains, to determine marker specificity. Further validation was performed using MS quantitation methods to assess sensitivity and specificity. A biomarker discovery pipeline was successfully developed in this study, comprising four distinct stages: proteome profiling, comparative bioinformatic validation, DNA sequencing and MS validation. Using the pipeline, 5379 peptides specific for Bacillus species and 36 peptides specific for B. anthracis were identified and validated. The 36 peptides, representing 30 proteins were derived from over 15 different clusters of orthologous group categories, including proteins involved in transcription, energy production/conservation as well as multifunctional proteins. We demonstrated that the peptide biomarkers identified in this study could be detected in a complex background, in which 0.1 μg of protein extract from B. anthracis was spiked into 9.90 μg of B. cereus protein extracts. The integration of both stable non-redundant peptides with molecular methodology for marker discovery and validation, improves the robustness of identifying and characterising candidate biomarkers for the identification of bacteria such as B. anthracis.
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Affiliation(s)
- Raju V Misra
- Department for Bioanalysis and Horizon Technologies, Health Protection Agency, 61 Colindale Avenue, London NW95EQ, United Kingdom.
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35
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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36
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Chenau J, Fenaille F, Ezan E, Morel N, Lamourette P, Goossens PL, Becher F. Sensitive detection of Bacillus anthracis spores by immunocapture and liquid chromatography-tandem mass spectrometry. Anal Chem 2011; 83:8675-82. [PMID: 21961787 DOI: 10.1021/ac2020992] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacillus anthracis is one of the most dangerous agents of the bioterrorism threat. We present here a sensitive immuno-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) approach to spore detection in complex environmental samples. It is based on the combined specificity and sensitivity of two techniques: immunocapture and targeted mass spectrometry. The immunocapture step, realized directly on the intact spores, is essential for their selective isolation and concentration from complex environmental samples. After parallel trypsin and Glu-C digestions, proteotypic peptides corresponding to small acid-soluble spore protein-B (SASP-B) are specifically monitored in the multiple reaction monitoring (MRM) mass spectrometry mode. Peptide ratio is carefully monitored and provides an additional level of specificity, which is shown to be highly useful for distinguishing closely related samples and avoiding false-positive/negative results. Sensitivity at the level of the infectious dose is demonstrated, with limits of detection of 7 × 10(3) spores/mL of milk or 10 mg of soil. This mass spectrometry approach is thus complementary to polymerase chain reaction (PCR) techniques.
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Affiliation(s)
- Jérôme Chenau
- Service de Pharmacologie et d'Immunoanalyse, iBiTec-S, CEA, Gif-sur-Yvette Cedex, France
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37
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Abstract
ABSTRACT
Rapid identification of microorganisms in the clinical microbiology laboratory can be of great value for selection of optimal patient management strategies for infections caused by bacteria, viruses, fungi, mycobacteria, and parasites. Rapid identification of microorganisms in clinical samples enables expedient de-escalation from broad-spectrum agents to targeted antimicrobial therapy. The switch to tailored therapy minimizes risks of antibiotics, namely, disruption of normal flora, toxic side effects, and selective pressure. There is a critical need for new technologies in clinical microbiology, particularly for bloodstream infections, in which associated mortality is among the highest of all infections. Just as importantly, there is a need for the clinical laboratory community to embrace the practices of evidence-based interventional laboratory medicine and collaborate in translational research projects to establish the clinical utility, cost benefit, and impact of new technologies.
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38
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39
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Tipton JD, Tran JC, Catherman AD, Ahlf DR, Durbin KR, Kelleher NL. Analysis of intact protein isoforms by mass spectrometry. J Biol Chem 2011; 286:25451-8. [PMID: 21632550 DOI: 10.1074/jbc.r111.239442] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The diverse proteome of an organism arises from such events as single nucleotide substitutions at the DNA level, different RNA processing, and dynamic enzymatic post-translational modifications. This minireview focuses on the measurement of intact proteins to describe the diversity found in proteomes. The field of biological mass spectrometry has steadily advanced, enabling improvements in the characterization of single proteins to proteins derived from cells or tissues. In this minireview, we discuss the basic technology for "top-down" intact protein analysis. Furthermore, examples of studies involved with the qualitative and quantitative analysis of full-length polypeptides are provided.
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Affiliation(s)
- Jeremiah D Tipton
- Departmen of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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40
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Šedo O, Sedláček I, Zdráhal Z. Sample preparation methods for MALDI-MS profiling of bacteria. MASS SPECTROMETRY REVIEWS 2011; 30:417-434. [PMID: 21500244 DOI: 10.1002/mas.20287] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 11/15/2009] [Accepted: 11/15/2009] [Indexed: 05/30/2023]
Abstract
Direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) bacterial cell or lysate analysis appears to meet all the criteria required for a rapid and reliable analytical microorganism identification and taxonomical classification tool. Few-minute analytical procedure providing information extending up to sub-species level underlines the potential of the MALDI-MS profiling in comparison with other methods employed in the field. However, the quality of MALDI-MS profiles and consequently the performance of the method are influenced by numerous factors, which involve particular steps of the sample preparation procedure. This review is aimed at advances in development and optimization of the MALDI-MS profiling methodology. Approaches improving the quality of the MALDI-MS profiles and universal feasibility of the method are discussed.
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Affiliation(s)
- Ondrej Šedo
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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41
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Pierce CL, Rees JC, Fernández FM, Barr JR. Detection of Staphylococcus aureus using 15N-labeled bacteriophage amplification coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Anal Chem 2011; 83:2286-93. [PMID: 21341703 DOI: 10.1021/ac103024m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel approach to rapid bacterial detection using an isotopically labeled (15)N bacteriophage and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is introduced. Current phage amplification detection (PAD) via mass spectrometric analysis is limited because host bacteria must be inoculated with low phage titers in such a way that initial infecting phage concentrations must be below the detection limit of the instrument, thus lengthening incubation times. Additionally, PAD techniques cannot distinguish inoculate input phage from output phage which can increase the possibility of false positive results. Here, we report a rapid and accurate PAD approach for identification of Staphylococcus aureus via detection of bacteriophage capsid proteins. This approach uses both a wild-type (14)N and a (15)N-isotopically labeled S. aureus-specific bacteriophage. High (15)N phage titers, above our instrument's detection limits, were used to inoculate S. aureus. MALDI-TOF MS detection of the (14)N progeny capsid proteins in the phage-amplified culture indicated the presence of the host bacteria. Successful phage amplification was observed after 90 min of incubation. The amplification was observed by both MALDI-TOF MS analysis and by standard plaque assay measurements. This method overcomes current limitations by improving analysis times while increasing selectivity when compared to previously reported PAD methodologies.
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Affiliation(s)
- Carrie L Pierce
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F-50, Atlanta, Georgia 30341, United States
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42
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Microorganism Identification Based On MALDI-TOF-MS Fingerprints. NATO SCIENCE FOR PEACE AND SECURITY SERIES A: CHEMISTRY AND BIOLOGY 2011. [DOI: 10.1007/978-90-481-9815-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Hagan NA, Lin JS, Antoine MD, Cornish TJ, Quizon RS, Collins BF, Feldman AB, Demirev PA. MALDI Mass Spectrometry for Rapid Detection and Characterization of Biological Threats. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1065.ch012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Nathan A. Hagan
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Jeffrey S. Lin
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Miquel D. Antoine
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Timothy J. Cornish
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Rachel S. Quizon
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Bernard F. Collins
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Andrew B. Feldman
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
| | - Plamen A. Demirev
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- C&E Research, Columbia, MD 21045
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44
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Askenazi M, Marto JA, Linial M. The complete peptide dictionary - A meta-proteomics resource. Proteomics 2010; 10:4306-10. [DOI: 10.1002/pmic.201000270] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Seng P, Rolain JM, Fournier PE, La Scola B, Drancourt M, Raoult D. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733-54. [DOI: 10.2217/fmb.10.127] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost–effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.
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Affiliation(s)
- Piseth Seng
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Jean-Marc Rolain
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Pierre Edouard Fournier
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Bernard La Scola
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Michel Drancourt
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
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46
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Johnson EM, Ellis WR, Powers LS, Wysocki VH. Affinity capture mass spectrometry of biomarker proteins using peptide ligands from biopanning. Anal Chem 2010; 81:5999-6005. [PMID: 19572565 DOI: 10.1021/ac900868q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Affinity capture mass spectrometry was used to isolate and ionize protein A from Staphylococcus aureus from both a commercial source and cell culture lysate using matrix assisted laser desorption/ionization (MALDI) mass spectrometry. Two surfaces are compared: gold surfaces with immunoglobulin G covalently immobilized and silica surfaces with a covalently bound small peptide discovered via biopanning. A detection limit of 2.22 bacterial cells/mL of culture fluid was determined for the immobilized peptide surfaces. This study emphasizes the ability to use peptide ligands to effectively capture a biomarker protein out of a complex mixture. This demonstrates the potential to use biopanning to generate capture ligands for a large variety of target proteins and subsequently detect the captured protein using MALDI mass spectrometry.
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Affiliation(s)
- Erin M Johnson
- Departments of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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47
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Fagerquist CK, Garbus BR, Miller WG, Williams KE, Yee E, Bates AH, Boyle S, Harden LA, Cooley MB, Mandrell RE. Rapid identification of protein biomarkers of Escherichia coli O157:H7 by matrix-assisted laser desorption ionization-time-of-flight-time-of-flight mass spectrometry and top-down proteomics. Anal Chem 2010; 82:2717-25. [PMID: 20232878 DOI: 10.1021/ac902455d] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Six protein biomarkers from two strains of Escherichia coli O157:H7 and one non-O157:H7, nonpathogenic strain of E. coli have been identified by matrix-assisted laser desorption ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-MS/MS) and top-down proteomics. Proteins were extracted from bacterial cell lysates, ionized by MALDI, and analyzed by MS/MS. Protein biomarker ions were identified from their sequence-specific fragment ions by comparison to a database of in silico fragment ions derived from bacterial protein sequences. Web-based software, developed in-house, was used to rapidly compare the mass-to-charge (m/z) of MS/MS fragment ions to the m/z of in silico fragment ions derived from hundreds of bacterial protein sequences. A peak matching algorithm and a p-value algorithm were used to independently score and rank identifications on the basis of the number of MS/MS-in silico matches. The six proteins identified were the acid stress chaperone-like proteins, HdeA and HdeB; the cold shock protein, CspC; the YbgS (or homeobox protein); the putative stress-response protein YjbJ (or CsbD family protein); and a protein of unknown function, YahO. HdeA, HdeB, YbgS, and YahO proteins were found to be modified post-translationally with removal of an N-terminal signal peptide. Gene sequencing of hdeA, hdeB, cspC, ybgS, yahO, and yjbJ for 11 strains of E. coli O157:H7 and 7 strains of the "near-neighbor" serotype O55:H7 revealed a high degree sequence homology between these two serotypes. Although it was not possible to distinguish O157:H7 from O55:H7 from these six biomarkers, it was possible to distinguish E. coli O157:H7 from a nonpathogenic E. coli by top-down proteomics of the YahO and YbgS. In the case of the YahO protein, a single amino acid residue substitution in its sequence (resulting in a molecular weight difference of only 1 Da) was sufficient to distinguish E. coli O157:H7 from a non-O157:H7, nonpathogenic E. coli by MALDI-TOF-TOF-MS/MS, whereas this would be difficult to distinguish by MALDI-TOF-MS. Finally, a protein biomarker ion at m/z approximately 9060 observed in the MS spectra of non-O157:H7 E. coli strains but absent from MS spectra of E. coli O157:H7 strains was identified by top-down analysis to be the HdeB acid stress chaperone-like protein consistent with previous identifications by gene sequencing and bottom-up proteomics.
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Affiliation(s)
- Clifton K Fagerquist
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, California 94710, USA.
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48
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Jabbour RE, Wade MM, Deshpande SV, Stanford MF, Wick CH, Zulich AW, Snyder AP. Identification of Yersinia pestis and Escherichia coli Strains by Whole Cell and Outer Membrane Protein Extracts with Mass Spectrometry-Based Proteomics. J Proteome Res 2010; 9:3647-55. [DOI: 10.1021/pr100402y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rabih E. Jabbour
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Mary Margaret Wade
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Samir V. Deshpande
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Michael F. Stanford
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Charles H. Wick
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Alan W. Zulich
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - A. Peter Snyder
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
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Fagerquist CK, Garbus BR, Williams KE, Bates AH, Harden LA. Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:819-832. [PMID: 20188588 DOI: 10.1016/j.jasms.2010.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 01/12/2010] [Accepted: 01/14/2010] [Indexed: 05/28/2023]
Abstract
We report covalent attachment via a thiol ester linkage of 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid or SA) to cysteine-containing protein biomarkers from bacterial cell lysates of E. coli analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry when using SA as the matrix. Evidence to support this conclusion is the appearance of additional peaks in the MS spectra when using SA, which are absent when using alpha-cyano-4-hydroxycinnamic acid (HCCA). The additional peaks appear at a mass-to-charge (m/z) approximately 208 greater to the m/z of a more abundant protein ion peak. Protein biomarkers were identified by tandem mass spectrometry (MS/MS) using a MALDI time-of-flight/time-of-flight (TOF-TOF) mass spectrometer and top-down proteomics. Three protein biomarkers, HdeA, HdeB, and homeobox or YbgS (each containing two cysteine residues) were identified as having reactivity to SA. Non-cysteine-containing protein biomarkers showed no evidence of reactivity to SA. MS ions and MS/MS fragment ions were consistent with covalent attachment of SA via a thiol ester linkage to the side-chain of cysteine residues. MS/MS of a protein biomarker ion with a covalently attached SA revealed fragment ion peaks suggesting dissociative loss SA. We propose dissociative loss of SA is facilitated by a pentacyclic transition-state followed by proton abstraction of the beta-hydrogen of the bound SA by a sulfur lone pair followed by dissociative loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal. The apparent reactivity of SA to cysteine/disulfide-containing proteins may complicate identification of such proteins, however the apparent differential reactivity of SA and HCCA toward cysteine/disulfide-containing proteins may be exploited for identification of unknown cysteine-containing proteins.
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Affiliation(s)
- Clifton K Fagerquist
- Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, California 94710, USA.
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Abstract
BACKGROUND Mass spectrometry (MS) is a suitable technology for microorganism identification and characterization. CONTENT This review summarizes the MS-based methods currently used for the analyses of pathogens. Direct analysis of whole pathogenic microbial cells using MS without sample fractionation reveals specific biomarkers for taxonomy and provides rapid and high-throughput capabilities. MS coupled with various chromatography- and affinity-based techniques simplifies the complexity of the signals of the microbial biomarkers and provides more accurate results. Affinity-based methods, including those employing nanotechnology, can be used to concentrate traces of target microorganisms from sample solutions and, thereby, improve detection limits. Approaches combining amplification of nucleic acid targets from pathogens with MS-based detection are alternatives to biomarker analyses. Many data analysis methods, including multivariate analysis and bioinformatics approaches, have been developed for microbial identification. The review concludes with some current clinical applications of MS in the identification and typing of infectious microorganisms, as well as some perspectives. SUMMARY Advances in instrumentation (separation and mass analysis), ionization techniques, and biological methodologies will all enhance the capabilities of MS for the analysis of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan.
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