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Chen D, Bryden WA, Fenselau C, McLoughlin M, Haddaway CR, Devin AP, Caton ER, Bradrick SS, Miller JM, Tacheny EA, Lemmon MM, Bogan J. MALDI-TOF Mass Spectrometric Detection of SARS-CoV-2 Using Cellulose Sulfate Ester Enrichment and Hot Acid Treatment. J Proteome Res 2022; 21:2055-2062. [PMID: 35787094 PMCID: PMC9305670 DOI: 10.1021/acs.jproteome.2c00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Indexed: 11/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. Here we report a novel strategy for the rapid detection of SARS-CoV-2 based on an enrichment approach exploiting the affinity between the virus and cellulose sulfate ester functional groups, hot acid hydrolysis, and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Virus samples were enriched using cellulose sulfate ester microcolumns. Virus peptides were prepared using the hot acid aspartate-selective hydrolysis and characterized by MALDI-TOF MS. Collected spectra were processed with a peptide fingerprint algorithm, and searching parameters were optimized for the detection of SARS-CoV-2. These peptides provide high sequence coverage for nucleocapsid (N protein) and allow confident identification of SARS-CoV-2. Peptide markers contributing to the detection were rigorously identified using bottom-up proteomics. The approach demonstrated in this study holds the potential for developing a rapid assay for COVID-19 diagnosis and detecting virus variants from a variety of sources, such as sewage and nasal swabs.
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Affiliation(s)
- Dapeng Chen
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | | | - Catherine Fenselau
- Department of Chemistry and Biochemistry,
University of Maryland, College Park, Maryland 20742,
United States
| | | | | | - Alese P. Devin
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | - Emily R. Caton
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | | | - Joy M. Miller
- MRIGlobal, Kansas City,
Missouri 64110, United States
| | | | | | - Joseph Bogan
- MRIGlobal, Gaithersburg,
Maryland 20878, United States
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2
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Yuan K, Jiang Z, Jurado-Sánchez B, Escarpa A. Nano/Micromotors for Diagnosis and Therapy of Cancer and Infectious Diseases. Chemistry 2019; 26:2309-2326. [PMID: 31682040 DOI: 10.1002/chem.201903475] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Indexed: 12/23/2022]
Abstract
Micromotors are man-made nano/microscale devices capable of transforming energy into mechanical motion. The accessibility and force offered by micromotors hold great promise to solve complex biomedical challenges. This Review highlights current progress and prospects in the use of nano and micromotors for diagnosis and treatment of infectious diseases and cancer. Motion-based sensing and fluorescence switching detection strategies along with therapeutic approaches based on direct cell capture; killing by direct contact or specific drug delivery to the affected site, will be comprehensively covered. Future challenges to translate the potential of nano/micromotors into practical applications will be described in the conclusions.
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Affiliation(s)
- Kaisong Yuan
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, 28805, Madrid, Spain.,Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, P. R. China
| | - Zhengjin Jiang
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, 28805, Madrid, Spain.,Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, P. R. China
| | - Beatriz Jurado-Sánchez
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, 28805, Madrid, Spain.,Chemical Research Institute "Andres M. Del Rio", University of Alcala, 28805, Madrid, Spain
| | - Alberto Escarpa
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, 28805, Madrid, Spain.,Chemical Research Institute "Andres M. Del Rio", University of Alcala, 28805, Madrid, Spain
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3
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Abstract
Detecting and identifying infectious agents and potential pathogens in complex environments and characterizing their mode of action is a critical need. Traditional diagnostics have targeted a single characteristic (e.g., spectral response, surface receptor, mass, intrinsic conductivity, etc.). However, advances in detection technologies have identified emerging approaches in which multiple modes of action are combined to obtain enhanced performance characteristics. Particularly appealing in this regard, electrophotonic devices capable of coupling light to electron translocation have experienced rapid recent growth and offer significant advantages for diagnostics. In this review, we explore three specific promising approaches that combine electronics and photonics: (1) assays based on closed bipolar electrochemistry coupling electron transfer to color or fluorescence, (2) sensors based on localized surface plasmon resonances, and (3) emerging nanophotonics approaches, such as those based on zero-mode waveguides and metamaterials.
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Affiliation(s)
- Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Wei Xu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jiayun Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Arielle Lopez
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
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4
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Wang C, Cui Q, Wang X, Li L. Preparation of Hybrid Gold/Polymer Nanocomposites and Their Application in a Controlled Antibacterial Assay. ACS Appl Mater Interfaces 2016; 8:29101-29109. [PMID: 27700040 DOI: 10.1021/acsami.6b12487] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, we report a photosensitizer-loaded hybrid nanostructure that shows high antibacterial efficiency after surface interaction with a lectin protein. Gold nanoparticles were generated on the polymer nanoparticle surface through an in situ reduction method and behaved as a plasmonic amplifier. After conjugation of the photosensitizer rose bengal onto the hybrid nanoparticles, higher phosphorescence intensity and generation of reactive oxygen species (ROS) were observed. The nanocomposites showed high antibacterial efficiency toward Gram-negative Escherichia coli treated with a lectin protein concanavalin A, which caused self-assembly of the bacteria and nanoparticles. Therefore, the as-prepared nanostructure considerably improved the effectiveness of ROS toward bacteria and provides an alternative strategy for controlled antibacterial assays.
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Affiliation(s)
- Chun Wang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Qianling Cui
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Xiaoyu Wang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P.R. China
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5
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Zhong D, Zhuo Y, Feng Y, Yang X. Employing carbon dots modified with vancomycin for assaying Gram-positive bacteria like Staphylococcus aureus. Biosens Bioelectron 2015; 74:546-53. [DOI: 10.1016/j.bios.2015.07.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/14/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
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6
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Hong SA, Kwon J, Kim D, Yang S. A rapid, sensitive and selective electrochemical biosensor with concanavalin A for the preemptive detection of norovirus. Biosens Bioelectron 2015; 64:338-44. [DOI: 10.1016/j.bios.2014.09.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/11/2014] [Accepted: 09/11/2014] [Indexed: 01/28/2023]
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7
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Hansen RR, Shubert KR, Morrell-Falvey JL, Lokitz BS, Doktycz MJ, Retterer ST. Microstructured block copolymer surfaces for control of microbe adhesion and aggregation. Biosensors (Basel) 2014; 4:63-75. [PMID: 25587410 DOI: 10.3390/bios4010063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 01/26/2023]
Abstract
The attachment and arrangement of microbes onto a substrate is influenced by both the biochemical and physical surface properties. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe immobilization. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line arrays or square grid patterns with 5 μm wide features and varied pitch. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates immobilized was dependent on the pattern dimensions. Films patterned as parallel lines or square grids with a pitch of 10 μm or less led to the immobilization of individual microbes with minimal formation of aggregates. Both geometries allowed for incremental increases in aggregate size distribution with each increase in pitch. These engineered surfaces combine spatial confinement with affinity-based capture to control the extent of microbe adhesion and aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.
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Titov DV, Gening ML, Tsvetkov YE, Nifantiev NE. Conjugates of cyclooligosaccharide scaffolds and carbohydrate ligands: Methods for synthesis and the interaction with lectins. Russ J Bioorg Chem 2013; 39:509-46. [DOI: 10.1134/s1068162013050142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Sandrin TR, Goldstein JE, Schumaker S. MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev 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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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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] [What about the content of this article? (0)] [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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11
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Gopal J, Manikandan M, Hasan N, Lee CH, Wu HF. A comparative study on the mode of interaction of different nanoparticles during MALDI-MS of bacterial cells. J Mass Spectrom 2013; 48:119-127. [PMID: 23303755 DOI: 10.1002/jms.3135] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/26/2012] [Indexed: 06/01/2023]
Abstract
We propose the benefits of preincubation during nanoparticle-assisted bacterial analysis, where the bacteria are grown along with the nanoparticles. We were able to obtain a two to ten fold enhancement of bacterial signals in 3 h compared to the generally used methodology followed in previous literature. The previous literature method required a long time (18 h) to obtain such an enhancement. We probe the interactions of two bacteria, Staphylococcus aureus and Pseudomonas aeruginosa, with Ag, NiO, Pt TiO(2) and ZnO nanoparticles via transmission electron microscopy, ultraviolet spectroscopy and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Based on these results, we propose a mechanism for interaction of these five nanoparticles with bacteria. Two mechanisms were observed for the interactions: (1) Mechanism A is proposed for the Pt and NiO NPs which functioned based on affinity for bacterial cells. (2) Mechanism B was proposed for the bactericidal NPs such as TiO(2), ZnO and Ag NPs. The results indicate that the success of the unmodified NPs in MALDI-MS bacterial studies lies in following the ideal protocol for incubation at the ideal concentrations.
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Affiliation(s)
- Judy Gopal
- Department of Chemistry, National Sun Yat - Sen University, Kaohsiung, 70, Lien-Hai Road, 80424, Taiwan
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12
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Chen R, Chen S, Xiong C, Ding X, Wu CC, Chang HC, Xiong S, Nie Z. N-(1-naphthyl) ethylenediamine dinitrate: a new matrix for negative ion MALDI-TOF MS analysis of small molecules. J Am Soc Mass Spectrom 2012; 23:1454-1460. [PMID: 22711516 DOI: 10.1007/s13361-012-0421-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/13/2012] [Accepted: 05/15/2012] [Indexed: 06/01/2023]
Abstract
An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules (m/z < 1000) such as oligosaccharides, peptides, metabolites and explosives using negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range (m/z < 200) consist of only nitrate and nitric acid cluster ions, making the matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.
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Affiliation(s)
- Rui Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, China
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13
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Wu HF, Gopal J, Manikandan M. Future perspective of nanoparticle interaction-assisted laser desorption/ionization mass spectrometry for rapid, simple, direct and sensitive detection of microorganisms. J Mass Spectrom 2012; 47:355-363. [PMID: 22431463 DOI: 10.1002/jms.2962] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The introduction of nanoparticles into mass spectrometric research greatly influenced the applicability of this technique into various omics. Surface-modified or functionalized nanoparticles (NPs) have recently extended the use of mass spectrometry into microorganism research. We survey the application of unmodified NPs, for microorganism research, on the basis of our expertise in this area within the recent years in this decade. The use of unmodified NPs in mass spectrometry, especially with respect to microorganisms, is an untreaded research area, which we have ventured to probe and have been fruitful. On the basis of our experience, we provide an insight into the principle behind the use of unmodified NPs and provide guidelines to be followed to obtain significant results. We also brief the current scenario of nanoparticle interaction-assisted laser desorption/ionization mass spectrometry (NPILDI-MS) for rapid, simple, direct and sensitive detection of microorganisms on the basis of our past and present reports, quoting examples of successful application of this technique. Finally, we address the future of the NPILDI-MS technique and the tools needed to reach those visions.
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Affiliation(s)
- Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan.
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14
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Wang ZF, Cheng S, Ge SL, Zhu JK, Wang H, Chen QM, Wang QJ, He PG, Fang YZ. Microchip electrophoresis of bacteria using lipid-based liquid crystalline nanoparticles. J Chromatogr A 2011; 1218:8281-8. [DOI: 10.1016/j.chroma.2011.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/10/2011] [Accepted: 09/12/2011] [Indexed: 01/10/2023]
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15
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. Mass Spectrom Rev 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Šedo O, Sedláček I, Zdráhal Z. Sample preparation methods for MALDI-MS profiling of bacteria. Mass Spectrom Rev 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
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Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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Tai Y, Wang L, Yan G, Gao J, Yu H, Zhang L. Recent research progress on the preparation and application of magnetic nanospheres. POLYM INT 2011; 60:976-94. [DOI: 10.1002/pi.3078] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Jonker N, Kool J, Irth H, Niessen WMA. Recent developments in protein-ligand affinity mass spectrometry. Anal Bioanal Chem 2010; 399:2669-81. [PMID: 21058031 PMCID: PMC3043251 DOI: 10.1007/s00216-010-4350-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/16/2010] [Accepted: 10/17/2010] [Indexed: 11/27/2022]
Abstract
This review provides an overview of direct and indirect technologies to screen protein–ligand interactions with mass spectrometry. These technologies have as a key feature the selection or affinity purification of ligands in mixtures prior to detection. Specific fields of interest for these technologies are metabolic profiling of bioactive metabolites, natural extract screening, and the screening of libraries for bioactives, such as parallel synthesis libraries and small combichem libraries. The review addresses the principles of each of the methods discussed, with a focus on developments in recent years, and the applicability of the methods to lead generation and development in drug discovery. Schematic view of the principle of filtration based 96-well affinity selection MS binding assays ![]()
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Affiliation(s)
- Niels Jonker
- BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, The Netherlands
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Li S, Guo Z, Wu HF, Liu Y, Yang Z, Woo CH. Rapid analysis of Gram-positive bacteria in water via membrane filtration coupled with nanoprobe-based MALDI-MS. Anal Bioanal Chem 2010; 397:2465-76. [PMID: 20512317 DOI: 10.1007/s00216-010-3777-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/19/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is challenging when it is directly applied to identify bacteria in water. This study demonstrates a rapid, sensitive, and selective technique for detection of Gram-positive bacteria in water. It involves a combination of membrane filtration (MF) and vancomycin-conjugated magnetite nanoparticles (VNPs) to selectively separate and concentrate Gram-positive bacteria in tap water and reservoir water, followed by rapid analysis of the isolates using whole-cell MALDI-MS. VNPs specifically recognize cells of Gram-positive bacteria, which serves as a basis for affinity capture of target Gram-positive bacteria. A two-step procedure of surface modification of bare magnetite nanoparticles was applied to synthesize VNPs. MF prior to VNP-based magnetic separation can effectively increase the enrichment factor and detection sensitivity and reduce time-consuming culture steps and the matrix effect for analysis of bacteria in MALDI-MS. The enrichment factor for the MF-VNP technique is about 6 x 10(4). A variety of bacteria, including Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, and Enterococcus faecium, were successfully analyzed from aqueous solutions and their mixtures with Gram-negative bacteria. The optimal conditions of the VNP/MALDI-MS technique, including selection of the MALDI matrix, the choice of cell-washing solution, and the VNP concentration, were also investigated. The capture efficiencies of Gram-positive bacteria with VNPs were 26.7-33.3%. The mass variations of characteristic peaks of the captured bacteria were within +/-5 Da, which indicated good reproducibility of the proposed technique. The technique was applied to detect Gram-positive bacteria in tap water and reservoir water with an analysis time of around 2 h. The detection limit for Bacillus cereus, Enterococcus faecium, and Staphylococcus aureus was 5 x 10(2) cfu/ml for 2.0-l water samples.
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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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22
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Zhang L, Lu H, Yang P. Specific enrichment methods for glycoproteome research. Anal Bioanal Chem 2009; 396:199-203. [DOI: 10.1007/s00216-009-3086-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 08/17/2009] [Accepted: 08/19/2009] [Indexed: 11/30/2022]
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23
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Hida RY, Ohashi Y, Takano Y, Dogru M, Goto E, Fujishima H, Saito I, Saito K, Fukase Y, Tsubota K. Elevated Levels of Human α -Defensin in Tears of Patients with Allergic Conjunctival Disease Complicated by Corneal Lesions: Detection by SELDI ProteinChip System and Quantification. Curr Eye Res 2009; 30:723-30. [PMID: 16123017 DOI: 10.1080/02713680591005986] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PURPOSE To analyze levels of alpha -defensin in the tears of allergic patients (with/without corneal lesions) comparing the results with those of normal control subjects. METHODS Screening of the protein profiles of the tears of allergic patients with corneal epithelial lesions and normal controls was performed by surface enhanced laser desorption/ionization (SELDI) ProteinChip array initially. ELISA was then performed to quantify the levels of alpha -defensin in the tears of allergic patients (with/without corneal epithelial lesions) and normal control patients. RESULTS Proteins expressing significant differences between patients and controls by SELDI analysis were examined. Several peptides with molecular weights similar to alpha -defensins were found to be expressed to a greater extent in allergic patients. ELISA was performed in tears of allergic patients and control subjects to ascertain the presence and increased expression of alpha -defensins in allergic patients. Concentrations of alpha -defensins in allergic patients with corneal epithelial lesions were significantly higher than those of allergic patients without epithelial lesions or normal controls. CONCLUSIONS Alpha-defensins were found in greater concentrations in tears of allergic patients with corneal lesions. The antimicrobial effects of alpha -defensins may play a role in the prevention of secondary infection of corneal lesions in allergic patients. SELDI ProteinChip technology is a useful and effective tool in profiling the differential expression of proteins in tears.
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Affiliation(s)
- Richard Y Hida
- Department of Ophthalmology, Tokyo Dental College, Chiba, Japan
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24
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Affiliation(s)
- Todd A. Morris
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899
| | - Alexander W. Peterson
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899
| | - Michael J. Tarlov
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899
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25
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Zhong H, El Rassi Z. Monolithic silica capillary columns having immobilized lectins and surface bound polar functionalities for lectin affinity and normal phase nano-LC and CEC of glycoconjugates, respectively. J Sep Sci 2009; 32:1642-53. [DOI: 10.1002/jssc.200900127] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Song Y, Talaty N, Datsenko K, Wanner BL, Cooks RG. In vivo recognition of Bacillus subtilis by desorption electrospray ionization mass spectrometry (DESI-MS). Analyst 2009; 134:838-41. [DOI: 10.1039/b900069k] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Liu JC, Chen WJ, Li CW, Mong KKT, Tsai PJ, Tsai TL, Lee YC, Chen YC. Identification of Pseudomonas aeruginosa using functional magnetic nanoparticle-based affinity capture combined with MALDI MS analysis. Analyst 2009; 134:2087-94. [DOI: 10.1039/b908069d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Shrivas K, Wu H. Oxidized multiwalled carbon nanotubes for quantitative determination of cationic surfactants in water samples using atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2008; 628:198-203. [DOI: 10.1016/j.aca.2008.09.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 09/02/2008] [Accepted: 09/05/2008] [Indexed: 11/22/2022]
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29
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Abstract
Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS-based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top-down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom-up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides.
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Affiliation(s)
- Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723, USA.
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30
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Huang CZ, Chen SF. Quantitation and Differentiation of Bioparticles Based on the Measurements of Light-Scattering Signals with a Common Spectrofluorometer. J Phys Chem B 2008; 112:11785-93. [DOI: 10.1021/jp802895b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cheng Zhi Huang
- College of Chemistry and Chemical Engineering, MOE Key Laboratory for Luminescence and Real-Time Analysis, CQKL-LTRA, Southwest University, Chongqing 400715, China
| | - Shao Fen Chen
- College of Chemistry and Chemical Engineering, MOE Key Laboratory for Luminescence and Real-Time Analysis, CQKL-LTRA, Southwest University, Chongqing 400715, China
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31
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Abstract
Reproducible and efficient affinity enrichment is increasingly viewed as an essential step in many investigations leading to the discovery of new biomarkers. In this work, we have evaluated the repeatability of lectin enrichment of glycoproteins from human blood serum through both qualitative and quantitative proteomic approaches. In a comprehensive evaluation of lectin binding, we have performed 30 separate microscale lectin affinity chromatography experiments, followed by a conventional sample purification, and LC-MS/MS analysis of the enriched glycoproteins. Two lectin affinity matrixes, both with Con A lectin, immobilized to the same solid support but differing in the amount of immobilized lectin, were investigated to characterize their binding properties. Both qualitative and quantitative data indicate acceptable repeatability and binding efficiency for the lectin materials received from two different commercial sources.
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Affiliation(s)
- Milan Madera
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, 47405
| | - Benjamin Mann
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, 47405
| | - Yehia Mechref
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, 47405
| | - Milos V. Novotny
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, 47405
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32
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Liu JC, Tsai PJ, Lee YC, Chen YC. Affinity Capture of Uropathogenic Escherichia coli Using Pigeon Ovalbumin-Bound Fe3O4@Al2O3 Magnetic Nanoparticles. Anal Chem 2008; 80:5425-32. [DOI: 10.1021/ac800487v] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jr-Chi Liu
- Department of Applied Chemistry, National Chiao Tung University Hsinchu 300, Taiwan, National Laboratory Animal Center, National Applied Research Laboratories, Tainan County, Taiwan, and Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
| | - Pei-Jane Tsai
- Department of Applied Chemistry, National Chiao Tung University Hsinchu 300, Taiwan, National Laboratory Animal Center, National Applied Research Laboratories, Tainan County, Taiwan, and Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
| | - Yuan C. Lee
- Department of Applied Chemistry, National Chiao Tung University Hsinchu 300, Taiwan, National Laboratory Animal Center, National Applied Research Laboratories, Tainan County, Taiwan, and Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University Hsinchu 300, Taiwan, National Laboratory Animal Center, National Applied Research Laboratories, Tainan County, Taiwan, and Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
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33
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Abstract
Advances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed.
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34
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García-Cañas V, Cifuentes A. Detection of microbial food contaminants and their products by capillary electromigration techniques. Electrophoresis 2007; 28:4013-30. [DOI: 10.1002/elps.200700253] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Abstract
In this work, the potential of PDMS-based microchip electrophoresis in the identifications and characterizations of microorganism was evaluated. Enteropathogenic E. coli (EPEC) was selected as the model microorganism. In this study, separation parameters such as applied voltage, concentrations of buffer and buffer modifier, injection voltage, and duration of injection had been investigated and optimized. Determination of EPEC bacteria could be completed within 2 min with good reproducibility. RSDs were less than 0.5 and 5% in migration time and peak area, respectively. Separation efficiency corresponding to plate number of more than 100,000 was achieved. In order to obtain reproducible separations, sample pretreatment was found to be essential. Microchip electrophoresis with LIF detection could potentially revolutionize certain aspects of microbiology involving diagnosis, profiling of pathogens, environmental analysis, and many other areas of study.
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Affiliation(s)
- Wai Siang Law
- Department of Chemistry, National University of Singapore, Republic of Singapore
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36
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Sugawara K, Kamiya N, Hirabayashi G, Kuramitz H. Voltammetric evaluation for the binding of wheat germ agglutinin to glucosamine-modified magnetic microbead. Talanta 2007; 72:1123-8. [DOI: 10.1016/j.talanta.2007.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 01/06/2007] [Accepted: 01/06/2007] [Indexed: 11/25/2022]
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37
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Abstract
Surface modification of MALDI probes is an attractive approach for combining bioaffinity isolation of targeted biomolecules with mass spectrometric analysis of the captured species. In this work, we demonstrate that a polymer thin film, produced by pulsed rf plasma polymerization of allylamine and deposited directly on a MALDI probe, can be subsequently biotinylated to develop a bioaffinity capture MALDI probe. The synthesis and characterization of the probe by XPS, FT-IR, and AFM is described, and the selective isolation of avidin from a three-component mixture of avidin, lysozyme, and cytochrome c is presented. These initial results offer encouragement for the further exploration of rf plasma polymer deposition as a novel approach for the development of on-probe affinity capture MALDI probes.
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Affiliation(s)
- Meiling Li
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019-0065, USA
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38
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Buszewski B, Kłodzińska E, Dahm H, Rózycki H, Szeliga J, Jackowski M. Rapid identification ofHelicobacter pylori by capillary electrophoresis: an overview. Biomed Chromatogr 2007; 21:116-22. [PMID: 17221910 DOI: 10.1002/bmc.733] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Helicobacter pylori can cause gastritis and peptic ulcers and is directly associated with the development of gastric cancer. There are many types of diagnostic methods used to identification H. pylori (invasive and non-invasive), but these methods usually require time-consuming and laborious procedures and therefore are not capable of fast diagnosis in cases of emergency. This contribution describes the new achievements, interdisciplinary significance and some future directions in the application of capillary electrophoresis for determination of H. pylori.
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Affiliation(s)
- B Buszewski
- Department of Environmental Chemistry and Ecoanalytics, Faculty of Chemistry, Nicolaus Copernicus University ul. Gagarin 7, 87-100 Toruń, Poland.
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39
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Song Y, Talaty N, Tao WA, Pan Z, Cooks RG. Rapid ambient mass spectrometric profiling of intact, untreated bacteria using desorption electrospray ionization. Chem Commun (Camb) 2006:61-3. [PMID: 17279261 DOI: 10.1039/b615724f] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Desorption electrospray ionization (DESI) allows the rapid acquisition of highly reproducible mass spectra from intact microorganisms under ambient conditions; application of principal component analysis to the data allows sub-species differentiation.
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Affiliation(s)
- Yishu Song
- Department of Chemistry, 560 Oval Drive, Purdue University, West Lafayette, IN 47906, USA
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40
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Abstract
Revolutionary advances in biological mass spectrometry (MS) have provided a basic tool to make possible comprehensive proteomic analysis. Traditionally, two-dimensional gel electrophoresis has been used as a separation method coupled with MS to facilitate analysis of complex protein mixtures. Despite the utility of this method, the many challenges of comprehensive proteomic analysis has motivated the development of gel-free MS-based strategies to obtain information not accessible using two-dimensional gel separations. These advanced strategies have enabled researchers to dig deeper into complex proteomes, gaining insights into the composition, quantitative response, covalent modifications and macromolecular interactions of proteins that collectively drive cellular function. This review describes the current state of gel-free, high throughput proteomic strategies using MS, including (i) the separation approaches commonly used for complex mixture analysis; (ii) strategies for large-scale quantitative analysis; (iii) analysis of post-translational modifications; and (iv) recent advances and future directions. The use of these strategies to make new discoveries at the proteome level into the effects of disease or other cellular perturbations is discussed in a variety of contexts, providing information on the potential of these tools in electromagnetic field research.
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Affiliation(s)
- Mikel R Roe
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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41
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Harvey SD, Mong GM, Ozanich RM, McLean JS, Goodwin SM, Valentine NB, Fredrickson JK. Preparation and evaluation of spore-specific affinity-augmented bio-imprinted beads. Anal Bioanal Chem 2006; 386:211-9. [PMID: 16865337 DOI: 10.1007/s00216-006-0622-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 06/02/2006] [Accepted: 06/13/2006] [Indexed: 10/24/2022]
Abstract
A novel, affinity-augmented, bacterial spore-imprinted, bead material was synthesized, based on a procedure developed for vegetative bacteria. The imprinted beads were intended as a front-end spore capture/concentration stage of an integrated biological detection system. Our approach involved embedding bead surfaces with Bacillus thuringiensis kurstaki (Bt) spores (as a surrogate for Bacillus anthracis) during synthesis. Subsequent steps involved lithographic deactivation using a perfluoroether; spore removal to create imprint sites; and coating imprints with the lectin, concanavalin A, to provide general affinity. The synthesis of the intended material with the desired imprints was verified by scanning electron and confocal laser-scanning microscopy. The material was evaluated using spore-binding assays with either Bt or Bacillus subtilis (Bs) spores. The binding assays indicated strong spore-binding capability and a robust imprinting effect that accounted for 25% additional binding over non-imprinted controls. The binding assay results also indicated that further refinement of the surface deactivation procedure would enhance the performance of the imprinted substrate.
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Affiliation(s)
- Scott D Harvey
- Pacific Northwest National Laboratory, P.O. Box 999/MSIN P8-50, Richland, WA 99352, USA.
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42
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000. Mass Spectrom Rev 2006; 25:595-662. [PMID: 16642463 DOI: 10.1002/mas.20080] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This review describes the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates and continues coverage of the field from the previous review published in 1999 (D. J. Harvey, Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates, 1999, Mass Spectrom Rev, 18:349-451) for the period 1999-2000. As MALDI mass spectrometry is acquiring the status of a mature technique in this field, there has been a greater emphasis on applications rather than to method development as opposed to the previous review. The present review covers applications to plant-derived carbohydrates, N- and O-linked glycans from glycoproteins, glycated proteins, mucins, glycosaminoglycans, bacterial glycolipids, glycosphingolipids, glycoglycerolipids and related compounds, and glycosides. Applications of MALDI mass spectrometry to the study of enzymes acting on carbohydrates (glycosyltransferases and glycosidases) and to the synthesis of carbohydrates, are also covered.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, United Kingdom.
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43
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Abstract
Bioaffinity mass spectrometry is a novel technology for analysis of binding proteins and their ligands. In this review, we introduce the concepts and principles of bioaffinity surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS). Various preactivated chip types and several approaches for binding of ligands or their binders to the chips are discussed. We also provide specific examples for the use of this technology for screening antibodies, analyzing ligands, glycoconjugates, protein-protein inter-actions, and DNA (RNA) binding proteins. In pursuit of developing new tests or studies of mechanism of drug action in therapeutic drug monitoring practice, this technology may provide a more rapid approach for ligand-binder studies.
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Affiliation(s)
- Yusheng Zhu
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, KY 40202, USA
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44
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Kłodzińiska E, Dahm H, Rózycki H, Szeliga J, Jackowski M, Buszewski B. Rapid identification ofEscherichia coli andHelicobacter pylori in biological samples by capillary zone electrophoresis. J Sep Sci 2006; 29:1180-7. [PMID: 16830734 DOI: 10.1002/jssc.200500351] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The differences in surface charge of different bacteria can be exploited for their separation by capillary electrophoresis. However, this method of separation of microorganisms is beset with various drawbacks such as adhesion of bacteria to the fused silica surface or cluster formation. To overcome these phenomena we investigated the addition of poly(ethylene oxide) as a focusing agent to the running buffer and used calcium and myoinositol hexakisphosphate as specific ions that interact with the bacterial surface, changing its electrical properties and electrophoretic mobilities. In the present work, we applied CZE to identification of E. coli in infected urine (direct injection) from patients with urinary tract infections and to identification of Helicobacter pylori, which is a gram-negative bacillus responsible for one of the most common infections found in humans worldwide. Helicobacter pylori colonize the stomach and are responsible for severe diseases of the gastric tract, ranging from chronic gastric ulcer to gastric cancer.
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Affiliation(s)
- Ewa Kłodzińiska
- Department of Environmental Chemistry and Ecoanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland
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45
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Deng G, Sanyal G. Applications of mass spectrometry in early stages of target based drug discovery. J Pharm Biomed Anal 2006; 40:528-38. [PMID: 16256286 DOI: 10.1016/j.jpba.2005.08.038] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/30/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022]
Abstract
Mass spectrometry (MS) has been applied to drug discovery for many years. With the advent of new ionization techniques, MS has emerged as an important analytical tool in identification and characterization of protein targets, structure elucidation of synthetic compounds, and early drug metabolism and pharmacokinetics studies. Two MS-based strategies, function-based and affinity-based, have been employed in recent years for screening and evaluation of compounds. In the function-based approach, the effects of compounds on the biological activity of a target molecule are measured. In the affinity-based approach, compounds are screened based on their binding affinities to target molecules. The interaction between targets and compounds can be directly evaluated by monitoring the formation of non-covalent target-ligand complexes (direct detection) or indirectly evaluated by detecting the compounds after separating bound compounds from unbound (indirect detection). Various techniques including high performance liquid chromatography (HPLC)-MS, size exclusion chromatography (SEC)-MS, frontal affinity chromatography (FAC)-MS and desorption/ionization on silicon (DIOS)-MS can be applied. The recent advances, relative advantages, and limitations of each MS-based method as a tool in compound screening and compound evaluation in the early stages of drug discovery are discussed in this review.
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Affiliation(s)
- Gejing Deng
- Department of Biochemistry, Infection Drug Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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46
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Zuo C, Yu W, Zhou X, Zhao D, Yang P. Highly efficient enrichment and subsequent digestion of proteins in the mesoporous molecular sieve silicate SBA-15 for matrix-assisted laser desorption/ionization mass spectrometry with time-of-flight/time-of-flight analyzer peptide mapping. Rapid Commun Mass Spectrom 2006; 20:3139-44. [PMID: 16986211 DOI: 10.1002/rcm.2709] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Based on a previous study of protein digestion inside the nanoreactor channels of the mesoporous molecular sieve silicate SBA-15 (Chem. Eur. J. 2005, 11: 5391), we have developed a highly efficient enrichment and subsequent tryptic digestion of proteins in SBA-15 for matrix-assisted laser desorption/ionization mass spectrometry with time-of-flight/time-of-flight analyzer (MALDI-TOF/TOF) peptide mapping. The performance of the method is exemplified with myoglobin and cytochrome c. First, protein adsorption isotherms for two standard proteins with a range of initial concentration of proteins were investigated at room temperature. The results revealed that the kinetic adsorption rate of a protein within SBA-15 was independent of initial protein concentration, and a 15-min protein enrichment within SBA-15 could be enough for protein identification in biological samples. It was noticed that no washing steps were needed to avoid protein loss due to desorption from the mesochannels into solution. Second, protein digestion inside the channels of SBA-15 was also optimized. After adsorption of proteins into SBA-15 in 15 min, the trypsin solution (pH 8) was directly added to the SBA-15 beads with immobilized proteins by centrifugation, and then the digestion was performed for 15 min at 37 degrees C. It was observed that a higher peptide sequence covering of 98% for myoglobin was obtained by MALDI-TOF/TOF analysis, compared to in-solution digestion. So the protein digestion inside SBA-15 was proved to be significantly faster and yielded a better sequence coverage. The new procedure allows for rapid protein enrichment and digestion inside SBA-15, and has great potential for protein analysis.
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Affiliation(s)
- Chao Zuo
- Department of Chemistry, Fudan University, Shanghai 200433, China
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47
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Stump MJ, Black G, Fox A, Fox KF, Turick CE, Matthews M. Identification of marker proteins forBacillus anthracis using MALDI-TOF MS and ion trap MS/MS after direct extraction or electrophoretic separation. J Sep Sci 2005; 28:1642-7. [PMID: 16224957 DOI: 10.1002/jssc.200500143] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Direct extraction of bacterial vegetative cells or spores followed by matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI TOF MS) has become popular for bacterial identification, since it is simple to perform and mass spectra are readily interpreted. However, only high-abundance proteins that are of low mass and ionize readily are observed. In the case of B. anthracis spores, small acid-soluble spore proteins (SASPs) have been the most widely studied. Additional information can be obtained using tandem mass spectrometry (MS-MS) to confirm the identity of proteins by sequencing. This is most readily accomplished using ion trap (IT) MS-MS. However, enzymatic digestion of these proteins is needed to generate peptides that are within the mass range of the ion trap. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), or other forms of electrophoresis, allows one to focus on specific proteins of interest (e.g. the high mass exosporium glycoproteins BcIA and BcIB) that provide additional species- and strain-specific discrimination.
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Affiliation(s)
- Michael J Stump
- Department of Pathology & Microbiology, Chemical Engineering, University of South Carolina, Columbia, SC, USA
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48
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Straub TM, Dockendorff BP, Quiñonez-Díaz MD, Valdez CO, Shutthanandan JI, Tarasevich BJ, Grate JW, Bruckner-Lea CJ. Automated methods for multiplexed pathogen detection. J Microbiol Methods 2005; 62:303-16. [PMID: 15979746 DOI: 10.1016/j.mimet.2005.04.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 03/03/2005] [Accepted: 04/04/2005] [Indexed: 01/31/2023]
Abstract
Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cycler where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides "live vs. dead" capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.
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Affiliation(s)
- Timothy M Straub
- Interfacial Chemistry and Engineering Group, Pacific Northwest National Laboratory, 902 Battelle Blvd., P.O. Box 999, Mail stop K4-12 Richland, WA 99352, USA.
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Abstract
Like other colloidal particles bacteria have a surface charge that originates from the ionization of surface molecules and of the adsorption of ions from solution. Bacterial cell wall and membranes containing numerous proteins, lipid molecules, teichoic acids, lipopolisaccharides which give them characteristic charge. Therefore, bacterial cells undergo electrophoresis in a free solution with their own mobility depending on ionic strength and pH of buffer solution. Various electromigration techniques can be used to separate and determine the intact cells. Successful separation of five species of bacteria was obtained using a trimethylchlorosilane-modified capillary and a divinylbenzene-modified with suppressed EOF over a short distance (8.5 cm). The utilization of coated capillaries prevents adsorption of bacteria to the capillary wall. Another approach is utilization of a dilute dissolved polymer, polyethylene oxide (PEO) in the running buffer as a non-bonded coating for the purpose of altering the EOE These experiment have proved the possibility of diagnosing a variety of diseases and the ability to separate and identify viable cells.
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Affiliation(s)
- Michał Szumski
- Department of Environmental Chemistry and Ecoanalytics, Faculty of Chemistry, Nicolas Copernicus University, ul. Gagarina 7, 87-100 Toruń, Poland
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Madera M, Mechref Y, Novotny MV. Combining lectin microcolumns with high-resolution separation techniques for enrichment of glycoproteins and glycopeptides. Anal Chem 2005; 77:4081-90. [PMID: 15987113 PMCID: PMC1472620 DOI: 10.1021/ac050222l] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Silica-based lectin microcolumns are described in this study together with the chemical procedures necessary for their preparation. The analytical merits of Canavalia ensiformis and Sambucus nigra lectins, [immobilized on activated macroporous silica], such as binding capacity, trapping reproducibility, and substrate selectivity, have been evaluated using model glycoproteins. The described microcolumns are applicable to high-pressure analytical schemes utilizing microvalving procedures, washing steps, and quantitative desorption for LC/MS analysis. The described analytical systems are amenable to the applications aiming at fractionation of complex glycopeptide mixtures and determination of the sites of glycosylation.
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Affiliation(s)
- Milan Madera
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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