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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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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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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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El Rassi Z. Electrophoretic and electrochromatographic separation of proteins in capillaries: an update covering 2007-2009. Electrophoresis 2010; 31:174-91. [PMID: 20039288 DOI: 10.1002/elps.200900576] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This review article covers 3-year period from 2007 to 2009 and is a continuation of the review article by V. Dolnik, [Electrophoresis 2008, 29, 143-156]. This article with 125 references describes recent developments in CE and CEC of proteins in capillary format and does not cover the developments of CE and CEC in microchip format, since Tran et al. review the microchip subject in this special issue. The present review article has four major topics including (i) the separation media, (ii) multidimensional separations, (iii) detection, and (iv) applications.
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Affiliation(s)
- Ziad El Rassi
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071, USA.
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Dworzanski JP, Dickinson DN, Deshpande SV, Snyder AP, Eckenrode BA. Discrimination and Phylogenomic Classification of Bacillus anthracis-cereus-thuringiensis Strains Based on LC-MS/MS Analysis of Whole Cell Protein Digests. Anal Chem 2009; 82:145-55. [DOI: 10.1021/ac9015648] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacek P. Dworzanski
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Danielle N. Dickinson
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Samir V. Deshpande
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - A. Peter Snyder
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Brian A. Eckenrode
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
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