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Du Y, May RC, Cooper HJ. Native ambient mass spectrometry of intact protein assemblies directly from Escherichia coli colonies. Chem Commun (Camb) 2022; 58:6857-6860. [PMID: 35617055 PMCID: PMC9196203 DOI: 10.1039/d2cc02085h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we demonstrate that by combining electroporation with native ambient mass spectrometry, it is possible to detect intact non-covalent protein complexes directly from bacterial colonies growing on agar. Homodimers HdeA and HdeB were identified, together with the 50 kDa Mn-bound superoxide dismutase homodimer, in addition to some previously undetected monomeric proteins.
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Affiliation(s)
- Yuying Du
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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2
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Armengaud J. Defining Diagnostic Biomarkers Using Shotgun Proteomics and MALDI-TOF Mass Spectrometry. Methods Mol Biol 2017; 1616:107-120. [PMID: 28600764 DOI: 10.1007/978-1-4939-7037-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted. The proteins which contribute to these peaks are deduced from label-free shotgun proteomics measurements carried out on the same sample. Quantitative information based on the spectral count approach allows ranking the most probable candidates. Proteogenomic approaches help to define whether these proteins give the same m/z values along the whole taxon under consideration or result in heterogeneous lists. These specific biomarkers nicely complement conventional profiling approaches and may help to better define groups of organisms, for example at the subspecies level.
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Affiliation(s)
- Jean Armengaud
- CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, 30200, Bagnols-sur-Cèze, France.
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Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: A New Guide to Infectious Disease. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2016. [DOI: 10.5812/pedinfect.31816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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4
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Kuang H, Yang L, Shah NP, Aguilar ZP, Wang L, Xu H, Wei H. Synergistic in vitro and in vivo antimicrobial effect of a mixture of ZnO nanoparticles and Lactobacillus fermentation liquor. Appl Microbiol Biotechnol 2015; 100:3757-66. [PMID: 26695158 DOI: 10.1007/s00253-015-7221-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/25/2015] [Accepted: 11/28/2015] [Indexed: 10/22/2022]
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5
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MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species. Int J Med Microbiol 2014; 304:669-77. [PMID: 24877727 DOI: 10.1016/j.ijmm.2014.04.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/07/2014] [Accepted: 04/27/2014] [Indexed: 11/21/2022] Open
Abstract
MALDI-TOF MS is becoming the technique of choice for rapid bacterial identification at species level in routine diagnostics. However, some drawbacks concerning the identification of closely related species such as those belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex lead to high rates of misidentifications. In this work we successfully developed an approach that combines MALDI-TOF MS and chemometric tools to discriminate the six Acb complex species (A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, A. calcoaceticus, genomic species "Close to 13TU" and genomic species "Between 1 and 3"). Mass spectra of 83 taxonomically well characterized clinical strains, reflecting the breadth of currently known phenetic diversity within the Acb complex, were achieved from intact cells and cell extracts and analyzed with hierarchical cluster analysis (HCA) and partial least squares discriminant analysis (PLSDA). This combined approach lead to 100% of correct species identification using mass spectra obtained from intact cells. Moreover, it was possible to discriminate two Acb complex species (genomic species "Close to 13TU" and genomic species "Between 1 and 3") not included in the MALDI Biotyper database.
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Napoli A, Aiello D, Aiello G, Cappello MS, Di Donna L, Mazzotti F, Materazzi S, Fiorillo M, Sindona G. Mass Spectrometry-Based Proteomic Approach in Oenococcus oeni Enological Starter. J Proteome Res 2014; 13:2856-66. [DOI: 10.1021/pr4012798] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anna Napoli
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | - Donatella Aiello
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | - Gilda Aiello
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | | | - Leonardo Di Donna
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | - Fabio Mazzotti
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | | | - Marco Fiorillo
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
| | - Giovanni Sindona
- Department
of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12/D, 87036 Arcavacata di Rende (CS), Italy
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7
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 522] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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Biswas S, Rolain JM. Use of MALDI-TOF mass spectrometry for identification of bacteria that are difficult to culture. J Microbiol Methods 2013; 92:14-24. [DOI: 10.1016/j.mimet.2012.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/25/2012] [Accepted: 10/29/2012] [Indexed: 01/22/2023]
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9
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Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36:380-407. [DOI: 10.1111/j.1574-6976.2011.00298.x] [Citation(s) in RCA: 581] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 11/30/2022] Open
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10
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Lindenstrauß AG, Pavlovic M, Bringmann A, Behr J, Ehrmann MA, Vogel RF. Comparison of genotypic and phenotypic cluster analyses of virulence determinants and possible role of CRISPR elements towards their incidence in Enterococcus faecalis and Enterococcus faecium. Syst Appl Microbiol 2011; 34:553-60. [DOI: 10.1016/j.syapm.2011.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/10/2011] [Accepted: 05/12/2011] [Indexed: 10/17/2022]
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11
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Welker M. Proteomics for routine identification of microorganisms. Proteomics 2011; 11:3143-53. [DOI: 10.1002/pmic.201100049] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/31/2011] [Accepted: 04/20/2011] [Indexed: 11/10/2022]
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12
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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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13
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Wynne C, Edwards NJ, Fenselau C. Phyloproteomic classification of unsequenced organisms by top-down identification of bacterial proteins using capLC-MS/MS on an Orbitrap. Proteomics 2010; 10:3631-43. [DOI: 10.1002/pmic.201000172] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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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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Microbial fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) applications and challenges. ADVANCES IN APPLIED MICROBIOLOGY 2010; 71:149-84. [PMID: 20378054 DOI: 10.1016/s0065-2164(10)71006-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent threats posed by pathogenic microorganisms in food, recreational waters, and as agents of bioterror have underscored the need for the development of more rapid, accurate, and cost-effective methods of microbial characterization and identification. This chapter focuses on the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to rapidly characterize and identify microorganisms through generation of characteristic fingerprints of intact cells. While most efforts have focused on bacteria, this technology has also been applied to fungi and viruses. Results of most studies suggest that MALDI-TOF MS can be used to rapidly and accurately characterize microorganisms. A variety of quantitative approaches have been employed in the analysis of MALDI-TOF MS fingerprints of microorganisms. The reproducibility of fingerprints of intact cells remains a primary concern and limitation associated with this approach. Protocols and instrumentation used have varied considerably and likely account for much of the variability in reproducibility reported. Key first steps to overcoming this limitation will be the development of standard approaches to quantifying reproducibility and the development of standard protocols for sample preparation and analysis.
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Sariyar-Akbulut B. Rapid differentiation of new isolates with MALDI-TOF mass spectrometry via discriminant function analysis based on principal components. KOREAN J CHEM ENG 2010. [DOI: 10.1007/s11814-009-0243-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Chen WJ, Tsai PJ, Chen YC. Functional nanoparticle-based proteomic strategies for characterization of pathogenic bacteria. Anal Chem 2009; 80:9612-21. [PMID: 19007241 DOI: 10.1021/ac802042x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) can be employed to rapidly characterize pathogenic bacteria, bacterial cultures are generally required to obtain sufficient quantities of the bacterial cells prior to MALDI MS analysis. If this time-consuming step could be eliminated, the length of time required for identification of bacterial strains would be greatly reduced. In this paper, we propose an effective means of rapidly identifying bacteria--one that does not require bacterial culturing--using functional nanoparticle-based proteomic strategies that are characterized by extremely short analysis time. In this approach, we used titania-coated magnetic iron oxide nanoparticles (Fe(3)O(4)@TiO(2) NPs) as affinity probes to concentrate the target bacteria. The magnetic properties of the Fe(3)O(4)@TiO(2) NPs allow the conjugated target species to be rapidly isolated from the sample solutions under a magnetic field. Taking advantage of the absorption of the magnetic Fe(3)O(4) NPs in the microwave region of the electromagnetic spectrum, we performed the tryptic digestion of the captured bacteria under microwave heating for only 1-1.5 min prior to MALDI MS analysis. We identified the resulting biomarker ions by combining their MS/MS analysis results with protein database searches. Using this technique, we identified potential biomarker ions representing five gram-negative bacteria: Escherichia coli O157:H7, uropathogenic E. coli, Shigella sonnei, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Finally, we demonstrated the practical feasibility of using this approach to rapidly characterize bacteria in clinical samples.
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Affiliation(s)
- Wei-Jen Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan
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Vanlaere E, Sergeant K, Dawyndt P, Kallow W, Erhard M, Sutton H, Dare D, Devreese B, Samyn B, Vandamme P. Matrix-assisted laser desorption ionisation-time-of of-flight mass spectrometry of intact cells allows rapid identification of Burkholderia cepacia complex. J Microbiol Methods 2008; 75:279-86. [DOI: 10.1016/j.mimet.2008.06.016] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 06/17/2008] [Accepted: 06/20/2008] [Indexed: 11/27/2022]
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Differentiation of Streptococcus pneumoniae conjunctivitis outbreak isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2008; 74:5891-7. [PMID: 18708515 DOI: 10.1128/aem.00791-08] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus [Pnc]) is a causative agent of many infectious diseases, including pneumonia, septicemia, otitis media, and conjunctivitis. There have been documented conjunctivitis outbreaks in which nontypeable (NT), nonencapsulated Pnc has been identified as the etiological agent. The use of mass spectrometry to comparatively and differentially analyze protein and peptide profiles of whole-cell microorganisms remains somewhat uncharted. In this report, we discuss a comparative proteomic analysis between NT S. pneumoniae conjunctivitis outbreak strains (cPnc) and other known typeable or NT pneumococcal and streptococcal isolates (including Pnc TIGR4 and R6, Streptococcus oralis, Streptococcus mitis, Streptococcus pseudopneumoniae, and Streptococcus pyogenes) and nonstreptococcal isolates (including Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus) as controls. cPnc cells and controls were grown to mid-log phase, harvested, and subsequently treated with a 10% trifluoroacetic acid-sinapinic acid matrix mixture. Protein and peptide fragments of the whole-cell bacterial isolate-matrix combinations ranging in size from 2 to 14 kDa were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Additionally Random Forest analytical tools and dendrogramic representations (Genesis) suggested similarities and clustered the isolates into distinct clonal groups, respectively. Also, a peak list of protein and peptide masses was obtained and compared to a known Pnc protein mass library, in which a peptide common and unique to cPnc isolates was tentatively identified. Information gained from this study will lead to the identification and validation of proteins that are commonly and exclusively expressed in cPnc strains which could potentially be used as a biomarker in the rapid diagnosis of pneumococcal conjunctivitis.
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Moura H, Woolfitt AR, Carvalho MG, Pavlopoulos A, Teixeira LM, Satten GA, Barr JR. MALDI-TOF mass spectrometry as a tool for differentiation of invasive and noninvasive Streptococcus pyogenes isolates. ACTA ACUST UNITED AC 2008; 53:333-42. [PMID: 18537829 PMCID: PMC2658026 DOI: 10.1111/j.1574-695x.2008.00428.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel mass spectral fingerprinting and proteomics approach using MALDI-TOF MS was applied to detect and identify protein biomarkers of group A Streptococcus (GAS) strains. Streptococcus pyogenes ATCC 700294 genome strain was compared with eight GAS clinical isolates to explore the ability of MALDI-TOF MS to differentiate isolates. Reference strains of other bacterial species were also analyzed and compared with the GAS isolates. MALDI preparations were optimized by varying solvents, matrices, plating techniques, and mass ranges for S. pyogenes ATCC 700294. Spectral variability was tested. A subset of common, characteristic, and reproducible biomarkers in the range of 2000–14 000 Da were detected, and they appeared to be independent of the culture media. Statistical analysis confirmed method reproducibility. Random Forest analysis of all selected GAS isolates revealed differences among most of them, and summed spectra were used for hierarchical cluster analysis. Specific biomarkers were found for each strain, and invasive GAS isolates could be differentiated. GAS isolates from cases of necrotizing fasciitis were clustered together and were distinct from isolates associated with noninvasive infections, despite their sharing the same emm type. Almost 30% of the biomarkers detected were tentatively identified as ribosomal proteins.
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Affiliation(s)
- Hercules Moura
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway NE, Atlanta, GA 30341, USA
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Nedvěd J, Sulc M, Jegorov A, Giannakopulos A, Havlicek V. Application of Fungal Cyclic Peptides and Metabolites. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Russell SC, Edwards N, Fenselau C. Detection of Plasmid Insertion inEscherichia coliby MALDI-TOF Mass Spectrometry. Anal Chem 2007; 79:5399-406. [PMID: 17579482 DOI: 10.1021/ac0705061] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proteomics approach is reported for the rapid recognition of genetically modified Escherichia coli bacteria. The approach targets a class of proteins required for genetic manipulation of bacteria with plasmids and alleviates the need to construct extensive libraries of toxins and other predicted payload proteins. Detection was performed using MALDI-TOF MS to monitor peptide products after an on-probe enzymatic digestion. Digestion products were identified by searching their postsource decay spectra using MASCOT. A 5 min digestion time was required to observe peptide products from the genetic insert as well as the host bacterium. This proteomics approach enables rapid detection of genetic manipulation along with information about the host organism, both of which have forensic applications.
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Affiliation(s)
- Scott C Russell
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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23
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Pierce CY, Barr JR, Woolfitt AR, Moura H, Shaw EI, Thompson HA, Massung RF, Fernandez FM. Strain and phase identification of the U.S. category B agent Coxiella burnetii by matrix assisted laser desorption/ionization time-of-flight mass spectrometry and multivariate pattern recognition. Anal Chim Acta 2007; 583:23-31. [PMID: 17386522 DOI: 10.1016/j.aca.2006.09.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 09/22/2006] [Accepted: 09/25/2006] [Indexed: 10/24/2022]
Abstract
Accurate bacterial identification is important in diagnosing disease and in microbial forensics. Coxiella burnetii, a highly infective microorganism causative of the human disease Q fever, is now considered a U.S. category B potential bioterrorism agent. We report here an approach for the confirmatory identification of C. burnetii at the strain level which involves the combined use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and supervised pattern recognition via Partial Least Squares-Discriminant Analysis (PLS-DA). C. burnetii isolates investigated in this study included the following prototype strains from different geographical and/or historical origins and with different antigenic properties: Nine Mile I, Australian QD, M44, KAV, PAV, Henzerling, and Ohio. After culture and purification following standard protocols, linear MALDI-TOF mass spectra of pure bacterial cultures were acquired in positive ion mode. Mass spectral data were normalized, baseline-corrected, denoised, binarized and modeled by PLS-DA under crossvalidation conditions. Robustness with respect to uncontrolled variations in the sample preparation and MALDI analysis protocol was assessed by repeating the experiment on five different days spanning a period of 6 months. The method was validated by the prediction of unknown C. burnetii samples in an independent test set with 100% sensitivity and specificity for five out of six strain classes.
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Affiliation(s)
- Carrie Y Pierce
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
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Loo RRO, Loo JA. Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry of Hydrophobic Proteins in Mixtures Using Formic Acid, Perfluorooctanoic Acid, and Sorbitol. Anal Chem 2006; 79:1115-25. [PMID: 17263344 DOI: 10.1021/ac061916c] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Three MALDI-MS sample/matrix preparation approaches were evaluated for their ability to enhance hydrophobic protein detection from complex mixtures: (1) formic acid-based formulations, (2) perfluorooctanoic acid (PFOA) surfactant addition, and (3) sorbitol addition. While MALDI-MS of Escherichia coli cells desorbed from a standard sinapinic acid matrix displayed 94 (M + H)+ ions, 119 were observed from a formic acid-based matrix with no more than 10 common to both. Formic acid matrix revealed many lipoproteins and an 8282 m/z ion proposed to be the abundant, water-insoluble ATPase proteolipid. Among the formic acid-based cocktails examined, the slowest rate of serine/threonine formylation was found for 50% H2O/33% 2-propanol/17% formic acid. Faster formylation was observed from cocktails containing more formic acid and from mixtures including CH3CN. Sinapinic, ferulic, DHB, 4-hydroxybenzylidene malononitrile, and 2-mercaptobenzothiazole matrixes performed well in formic acid formulations. Dramatic differences in mixture spectra were also observed from PFOA/sinapinic acid, at detergent concentrations exceeding the critical micelle concentration, although these matrix cocktails proved difficult to crystallize. E. coli ions observed from these matrix conditions are listed in Tables S-1 and S-3 (Supporting Information). Similar complementarity was observed for M. acetivorans whole-cell mixtures. Including sorbitol in the sinapinic acid matrix was found to promote homogeneous crystallization and to enhance medium and higher m/z ion detection from dilute E. coli cellular mixtures.
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry and Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA-DOE Institute for Genomics & Proteomics, University of California-Los Angeles, Los Angeles, California 90095, USA.
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Richardson SD. Environmental Mass Spectrometry: Emerging Contaminants and Current Issues. Anal Chem 2006; 78:4021-46. [PMID: 16771539 DOI: 10.1021/ac060682u] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susan D Richardson
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Athens, Georgia 30605, USA
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Jegorov A, Hajduch M, Sulc M, Havlicek V. Nonribosomal cyclic peptides: specific markers of fungal infections. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:563-76. [PMID: 16770826 DOI: 10.1002/jms.1042] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Some cyclic peptides and depsipeptides are synthesized in microorganisms by large multienzymes called nonribosomal peptide synthetases. The structures of peptide products originating in this way are complex and diverse and are microorganism-specific. This work proposes the use of fungal cyclic peptides and depsipeptides as extremely specific markers of fungal infections. Since a reliable molecular tool for diagnosing fungal infections at an early stage is still missing, we present mass spectrometry as a new, modern, broadband (with respect to fungal strain) and specific tool for clinical mycologists. More than 40 different fungal species can be rapidly characterized according to specific families of cyclic peptides, and in some cases, a particular fungal strain can be identified on the basis of its cyclopeptide profile. This paper is also aimed at initiating discussion on the biological role of these secondary metabolites, especially of those synthesized by medically important strains. Proven cytotoxic, anti-inflammatory or immunosuppressive activities of some cyclic peptides indicate that these molecules may contribute to the synergistic array of fungal virulence factors and support microbial invasion during fungal infection. In addition to an overview on recent mass spectrometric protocols for cyclic peptide sequencing, the structures of new peptides from Paecilomyces and Pseudallescheria are presented.
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Affiliation(s)
- Alexandr Jegorov
- IVAX Pharmaceuticals, Branisovska 31, CZ-370 05 Ceske Budejovice, Czech Republic
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