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Liu H, Gao W, Cui T, Wang S, Song X, Wang Z, Zhang H, Li S, Yu YL, Cui Q. A high-throughput platform enables in situ screening of fatty acid-producing strains using laser ablation electrospray ionization mass spectrometry and a Python package. Talanta 2024; 268:125234. [PMID: 37839326 DOI: 10.1016/j.talanta.2023.125234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023]
Abstract
Microbial fatty acid-producing strains are commonly engineered to improve their performance for industrial applications. However, it is challenging to efficiently and rapidly screen target strains for engineering. This study reported an in situ analytical platform using laser ablation electrospray ionization mass spectrometry (LAESI-MS) for fast profiling of triacylglycerols in cellular lipid droplets of Aurantiochytrium sp. colonies cultured on agar plates. LAESI-MS approach allowed for the direct acquisition of a colony cell's characteristic fingerprint mass spectrum and MS/MS facilitated the identification of triacylglycerol species containing three fatty acyl groups. The fatty acid contents of colony cells were calculated based on the intensities of triacylglycerols from their characteristic fingerprint mass spectrum. A Python package called TAFA-LEMS (Triacylglycerol to Fatty Acid by LAESI-MS) was also developed to process the high-throughput MS data and extract fatty acid contents in colony cells. The results demonstrated that the LAESI-MS platform is fast, stable, and reproducible, with a data acquisition rate of ≤2 s per sampling point and ≤13.69% RSDs of the relative contents of fatty acids. In addition, LAESI-MS was successfully performed on the analysis of P. tricornutum and Y lipolytica strains. This in situ MS platform has the potential to become a common biotechnology platform for microbial strain engineering.
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Affiliation(s)
- Huan Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
| | - Wei Gao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Tianlun Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Sen Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Xiaojin Song
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Zhuojun Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Huidan Zhang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Shiming Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, Shandong, 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
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Olajide OE, Yi Y, Zheng J, Hamid AM. Strain-Level Discrimination of Bacteria by Liquid Chromatography and Paper Spray Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1125-1135. [PMID: 37249401 PMCID: PMC10407911 DOI: 10.1021/jasms.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Determining bacterial identity at the strain level is critical for public health to enable proper medical treatments and reduce antibiotic resistance. Herein, we used liquid chromatography, ion mobility, and tandem MS (LC-IM-MS/MS) to distinguish Escherichia coli (E. coli) strains. Numerical multivariate statistics (principal component analysis, followed by linear discriminant analysis) showed the capability of this method to perform strain-level discrimination with prediction rates of 96.1% and 100% utilizing the negative and positive ion information, respectively. The tandem MS and LC separation proved effective in discriminating diagnostic lipid isomers in the negative mode, while IM separation was more effective in resolving lipid conformational biomarkers in the positive ion mode. Because of the clinical importance of early detection for rapid medical intervention, a faster technique, paper spray (PS)-IM-MS/MS, was used to discriminate the E. coli strains. The achieved prediction rates of the analysis of E. coli strains by PS-IM-MS/MS were 62.5% and 73.5% in the negative and positive ion modes, respectively. The strategy of numerical data fusion of negative and positive ion data increased the classification rates of PS-IM-MS/MS to 80.5%. Lipid isomers and conformers were detected, which served as strain-indicating biomarkers. The two complementary multidimensional techniques revealed biochemical differences between the E. coli strains confirming the results obtained from comparative genomic analysis. Moreover, the results suggest that PS-IM-MS/MS is a rapid, highly selective, and sensitive method for discriminating bacterial strains in environmental and food samples.
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Affiliation(s)
- Orobola E. Olajide
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849, United States
| | - Yuyan Yi
- Department of Mathematics and Statistics, Auburn University, 221 Roosevelt Concourse, Auburn, AL 36849, United States
| | - Jingyi Zheng
- Department of Mathematics and Statistics, Auburn University, 221 Roosevelt Concourse, Auburn, AL 36849, United States
| | - Ahmed M. Hamid
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849, United States
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3
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Szalwinski LJ, Gonzalez LE, Morato NM, Marsh BM, Cooks RG. Bacterial growth monitored by two-dimensional tandem mass spectrometry. Analyst 2022; 147:940-946. [PMID: 35166732 DOI: 10.1039/d1an01901e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growth of the bacterium E. coli was monitored by targeting the phospholipid constituents through desorption electrospray ionization and characterizing individual sets of isomers by recording the full 2D MS/MS data domain in a single scan of a modified quadrupole ion trap mass spectrometer. The experiments tested the applicability of the new instrumental capabilities which include sample interrogation at the molecular level for multiple components at speeds of <10 seconds/sample. The major lipids observed were phosphatidylethanolamines and phosphatidylglycerols and the growth experiment showed fatty acid chain modification from alkene to cyclopropyl groups over time. Notably, these novel MS scans were also performed using desorption electrospray ionization (DESI) to quickly sample complex mixtures without pre-separation. This demonstration experiment has implications for the value of ambient ionization mass spectrometry for monitoring biological systems on physiologically relevant timescales.
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Affiliation(s)
- Lucas J Szalwinski
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - L Edwin Gonzalez
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Nicolás M Morato
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Brett M Marsh
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
| | - R Graham Cooks
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
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4
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Havlikova J, May RC, Styles IB, Cooper HJ. Liquid Extraction Surface Analysis Mass Spectrometry of ESKAPE Pathogens. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1345-1351. [PMID: 33647207 PMCID: PMC8176453 DOI: 10.1021/jasms.0c00466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) represent clinically important bacterial species that are responsible for most hospital-acquired drug-resistant infections; hence, the need for rapid identification is of high importance. Previous work has demonstrated the suitability of liquid extraction surface analysis mass spectrometry (LESA MS) for the direct analysis of colonies of two of the ESKAPE pathogens (Staphylococcus aureus and Pseudomonas aeruginosa) growing on agar. Here, we apply LESA MS to the remaining four ESKAPE species (E. faecium E745, K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11) as well as E. faecalis V583 (a close relative of E. faecium) and a clinical isolate of A. baumannii AC02 using an optimized solvent sampling system. In each case, top-down LESA MS/MS was employed for protein identification. In total, 24 proteins were identified from 37 MS/MS spectra by searching against protein databases for the individual species. The MS/MS spectra for the identified proteins were subsequently searched against multiple databases from multiple species in an automated data analysis workflow with a view to determining the accuracy of identification of unknowns. Out of 24 proteins, 19 were correctly assigned at the protein and species level, corresponding to an identification success rate of 79%.
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Affiliation(s)
- Jana Havlikova
- EPSRC
Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Robin C. May
- Institute
of Microbiology and Infection, University
of Birmingham, Edgbaston, Birmingham B15 2TT, United
Kingdom
| | - Iain B. Styles
- EPSRC
Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Phone: +44 (0)121 414 7527; . (H.J.C.)
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5
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Havlikova J, May RC, Styles IB, Cooper HJ. Direct identification of bacterial and human proteins from infected wounds in living 3D skin models. Sci Rep 2020; 10:11900. [PMID: 32681099 PMCID: PMC7368034 DOI: 10.1038/s41598-020-68233-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Trauma is one of the leading causes of death in people under the age of 49 and complications due to wound infection are the primary cause of death in the first few days after injury. The ESKAPE pathogens are a group of bacteria that are a leading cause of hospital-acquired infections and a major concern in terms of antibiotic resistance. Here, we demonstrate a novel and highly accurate approach for the rapid identification of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) directly from infected wounds in 3D in vitro skin models. Wounded skin models were inoculated with bacteria and left to incubate. Bacterial proteins were identified within minutes, directly from the wound, by liquid extraction surface analysis mass spectrometry. This approach was able to distinguish closely related strains and, unlike genomic approaches, can be modified to provide dynamic information about pathogen behaviour at the wound site. In addition, since human skin proteins were also identified, this method offers the opportunity to analyse both host and pathogen biomarkers during wound infection in near real-time.
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Affiliation(s)
- Jana Havlikova
- EPSRC Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,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.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Iain B Styles
- EPSRC Centre for Doctoral Training in Physical Sciences for Health, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Computer Science, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, The Midlands, Birmingham, UK.,Alan Turing Institute, 96 Euston Road, London, NW1 2DB, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Fresnais M, Haefeli WE, Burhenne J, Longuespée R. Rapid drug detection in whole blood droplets using a desorption electrospray ionization static profiling approach - a proof-of-concept. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8614. [PMID: 31657865 DOI: 10.1002/rcm.8614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/19/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE The introduction of desorption electrospray ionization (DESI) - and ambient desorption/ionization (ADI) ion sources in general - in the 2000s has opened new possibilities for mass spectrometric (MS) analyses of biological sample surfaces. DESI allows for a rapid screening of solid samples because no sample preparation is needed and the analysis is performed at atmospheric pressure. In the present study, we used DESI as an ion source for the rapid detection of a small molecule in blood droplets deposited on glass slides. METHODS Blood was spiked with different concentrations of a model drug, mebendazole. One microliter blood droplets of each preparation were deposited on the surface of a glass slide and analyzed by DESI, either in imaging or profiling mode. RESULTS The results suggested that DESI imaging mode was not appropriate for the detection of mebendazole in blood droplets as an initial solvation time was necessary before the obtention of signal. A profiling approach consisting of analyzing a single position of the blood droplet was used for further analysis and allowed mebendazole to be detected in the fg range and to monitor the volume of sample analyzed. CONCLUSIONS The study suggests that profiling mode at a single position is adequate for DESI analyses in whole blood droplets. This proof-of-concept study illustrates the potential of DESI profiling as a possible alternative to liquid chromatography/MS analyses of whole blood, when analyses are needed within a restricted time. Rapid detection methods in blood at atmospheric pressure may find interesting applications in the fields of toxicology and pharmacology.
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Affiliation(s)
- Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
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Gowers GOF, Cameron SJS, Perdones-Montero A, Bell D, Chee SM, Kern M, Tew D, Ellis T, Takáts Z. Off-Colony Screening of Biosynthetic Libraries by Rapid Laser-Enabled Mass Spectrometry. ACS Synth Biol 2019; 8:2566-2575. [PMID: 31622554 DOI: 10.1021/acssynbio.9b00243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By leveraging advances in DNA synthesis and molecular cloning techniques, synthetic biology increasingly makes use of large construct libraries to explore large design spaces. For biosynthetic pathway engineering, the ability to screen these libraries for a variety of metabolites of interest is essential. If the metabolite of interest or the metabolic phenotype is not easily measurable, screening soon becomes a major bottleneck involving time-consuming culturing, sample preparation, and extraction. To address this, we demonstrate the use of automated laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS)-a form of ambient laser desorption ionization mass spectrometry-to perform rapid mass spectrometry analysis direct from agar plate yeast colonies without sample preparation or extraction. We use LA-REIMS to assess production levels of violacein and betulinic acid directly from yeast colonies at a rate of 6 colonies per minute. We then demonstrate the throughput enabled by LA-REIMS by screening over 450 yeast colonies within <4 h, while simultaneously generating recoverable glycerol stocks of each colony in real time. This showcases LA-REIMS as a prescreening tool to complement downstream quantification methods such as liquid chromatography-mass spectroscopy (LCMS). By prescreening several hundred colonies with LA-REIMS, we successfully isolate and verify a strain with a 2.5-fold improvement in betulinic acid production. Finally, we show that LA-REIMS can detect 20 out of a panel of 27 diverse biological molecules, demonstrating the broad applicability of LA-REIMS to metabolite detection. The rapid and automated nature of LA-REIMS makes this a valuable new technology to complement existing screening technologies currently employed in academic and industrial workflows.
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Affiliation(s)
- Glen-Oliver F. Gowers
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - David Bell
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Soo Mei Chee
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Marcelo Kern
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - David Tew
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zoltan Takáts
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
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8
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Mavroudakis L, Valsami EA, Grafanaki S, Andreadaki TP, Ghanotakis DF, Pergantis SA. The effect of nitrogen starvation on membrane lipids of Synechocystis sp. PCC 6803 investigated by using easy ambient sonic-spray ionization mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183027. [DOI: 10.1016/j.bbamem.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 01/30/2023]
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9
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Mavrakis E, Mavroudakis L, Lydakis-Simantiris N, Pergantis SA. Investigating the Uptake of Arsenate by Chlamydomonas reinhardtii Cells and its Effect on their Lipid Profile using Single Cell ICP–MS and Easy Ambient Sonic-Spray Ionization–MS. Anal Chem 2019; 91:9590-9598. [DOI: 10.1021/acs.analchem.9b00917] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Emmanouil Mavrakis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion 70013, Greece
| | - Leonidas Mavroudakis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion 70013, Greece
| | - Nikos Lydakis-Simantiris
- Laboratory of Environmental Chemistry and of Biochemical Processes, Department of Agriculture, Hellenic Mediterranean University, Chania 73133, Greece
| | - Spiros A. Pergantis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion 70013, Greece
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10
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Javanshad R, Honarvar E, Venter AR. Addition of Serine Enhances Protein Analysis by DESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:694-703. [PMID: 30771107 DOI: 10.1007/s13361-018-02129-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 05/18/2023]
Abstract
Previous studies have suggested that the loss in sensitivity of DESI-MS for large molecules such as proteins is due to the poor dissolution during the short time scale of desorption and ionization. An investigation into the effect of serine as a solvent additive leads to the interesting observation that there is a concentration-dependent improvement in protein signal intensity when micromolar to low millimolar concentrations of serine is combined with a suitable co-additive in DESI spray. This effect, however, was not observed during similar ESI-MS experiments, where the same solvents and proteins were sprayed directly into the MS inlet. This suggests that the mechanism of signal improvement in DESI is associated with the desorption step of proteins, possibly by facilitating dissolution or improving solubility of proteins on the surface in the solvent micro-layer formed during DESI. Other than poor dissolution, cation adduction such as by sodium ions is also a major contributing factor to the mass-dependent loss in sensitivity in both ESI and DESI, leading to an increase in limits of detection for larger proteins. The adduction becomes a more pressing issue in native-state studies of proteins, as lower charge states are more susceptible to adduction. Previous studies have shown that addition of amino acids to the working spray solution during ESI-MS reduces sodium adduction and can help in stabilization of native-state proteins. Similar to the observed reduction in sodium adducts during native-state ESI-MS, when serine is added to the desorbing spray in DESI-MS, the removal of up to 10 mM NaCl is shown. A selection of proteins with high and low pI and molecular weights was analyzed to investigate the effects of serine on signal intensity by improvements in protein solubility and adduct removal. Graphical Abstract.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA.
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Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification. Sci Rep 2019; 9:3006. [PMID: 30816263 PMCID: PMC6395639 DOI: 10.1038/s41598-019-39815-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/30/2019] [Indexed: 02/08/2023] Open
Abstract
The accurate and timely identification of the causative organism of infection is important in ensuring the optimum treatment regimen is prescribed for a patient. Rapid evaporative ionisation mass spectrometry (REIMS), using electrical diathermy for the thermal disruption of a sample, has been shown to provide fast and accurate identification of microorganisms directly from culture. However, this method requires contact to be made between the REIMS probe and microbial biomass; resulting in the necessity to clean or replace the probes between analyses. Here, optimisation and utilisation of ambient laser desorption ionisation (ALDI) for improved speciation accuracy and analytical throughput is shown. Optimisation was completed on 15 isolates of Escherichia coli, showing 5 W in pulsatile mode produced the highest signal-to-noise ratio. These parameters were used in the analysis of 150 clinical isolates from ten microbial species, resulting in a speciation accuracy of 99.4% - higher than all previously reported REIMS modalities. Comparison of spectral data showed high levels of similarity between previously published electrical diathermy REIMS data. ALDI does not require contact to be made with the sample during analysis, meaning analytical throughput can be substantially improved, and further, increases the range of sample types which can be analysed in potential direct-from-sample pathogen detection.
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Liu S, Zuo J, Lu Y, Gao L, Zhai Y, Xu W. Direct bacteria analysis using laserspray ionization miniature mass spectrometry. Anal Bioanal Chem 2018; 411:4031-4040. [DOI: 10.1007/s00216-018-1385-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 01/29/2023]
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13
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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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14
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Uwakweh AO, Mwangi JN, Todd D, Jia Z, Chiu NHL. Nanospray desorption electrospray ionization mass spectrometry of untreated and treated probiotic Lactobacillus reuteri cells. Anal Bioanal Chem 2018; 410:4237-4245. [PMID: 29704030 DOI: 10.1007/s00216-018-1071-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/24/2018] [Accepted: 04/09/2018] [Indexed: 01/13/2023]
Abstract
Mass spectrometry has proven to be a useful technique for rapid identification of bacterial cells. Among various ionization techniques in mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) has been commonly used for the identification of bacterial cells. Recently, MALDI mass spectrometry has also been utilized to distinguish cellular responses. Ambient ionization techniques do support whole bacterial cell analysis, which include desorption electrospray ionization (DESI). Nanospray DESI (nDESI) is a new variant of DESI, and its application to whole-cell mass spectrometry is limited. In this project, the use of nDESI mass spectrometry to measure probiotic Lactobacillus reuteri (LR) cells is explored. A unique and reproducible mass spectral pattern of untreated LR cells was obtained by using 50% methanol/water as nDESI solvent. The use of nDESI mass spectrometry is further extended to distinguish untreated LR cells from treated LR cells that have been exposed to low pH. These findings demonstrate the feasibility of using nDESI in whole-cell mass spectrometry. Graphical abstract ᅟ.
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Affiliation(s)
- Agbo-Oma Uwakweh
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Joseph N Mwangi
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Daniel Todd
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Zhenquan Jia
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Norman H L Chiu
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA. .,The Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
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15
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Kocurek KI, Stones L, Bunch J, May RC, Cooper HJ. Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2066-2077. [PMID: 28681361 PMCID: PMC5594050 DOI: 10.1007/s13361-017-1718-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/21/2023]
Abstract
We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. Graphical Abstract ᅟ.
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Affiliation(s)
- Klaudia I Kocurek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Leanne Stones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, 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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16
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Si T, Li B, Comi TJ, Wu Y, Hu P, Wu Y, Min Y, Mitchell DA, Zhao H, Sweedler JV. Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. J Am Chem Soc 2017; 139:12466-12473. [PMID: 28792758 PMCID: PMC5600186 DOI: 10.1021/jacs.7b04641] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multistep biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling. MALDI-ToF MS profiling was utilized to screen both substrate and enzyme libraries for natural product biosynthesis. Computational algorithms were developed to process and visualize the resulting mass spectral data sets. For analogues of the peptidic antibiotic plantazolicin, multivariate analyses by t-distributed stochastic neighbor embedding were used to group similar spectra for rapid identification of nonisobaric variants. After MALDI-ToF MS screening, follow-up analyses using high-resolution MS and tandem MS were readily performed on the same sample target. Separately, relative ion intensities of rhamnolipid congeners with various lipid moieties were evaluated to engineer enzymatic specificity. The glycolipid profiles of each colony were overlaid with optical images to facilitate the recovery of desirable mutants. For both the antibiotic and rhamnolipid cases, large populations of colonies were rapidly surveyed at the molecular level, providing information-rich insights not easily obtained with traditional screening assays. Utilizing standard microbiological techniques with routine microscopy and MALDI-ToF MS instruments, this simple yet effective workflow is applicable for a wide range of screening campaigns targeting multistep enzymatic reactions.
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Affiliation(s)
| | - Bin Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing 210009, China
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17
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Abstract
Since the introduction of desorption electrospray ionization (DESI) mass spectrometry (MS), ambient MS methods have seen increased use in a variety of fields from health to food science. Increasing its popularity in metabolomics, ambient MS offers limited sample preparation, rapid and direct analysis of liquids, solids, and gases, in situ and in vivo analysis, and imaging. The metabolome consists of a constantly changing collection of small (<1.5 kDa) molecules. These include endogenous molecules that are part of primary metabolism pathways, secondary metabolites with specific functions such as signaling, chemicals incorporated in the diet or resulting from environmental exposures, and metabolites associated with the microbiome. Characterization of the responsive changes of this molecule cohort is the principal goal of any metabolomics study. With adjustments to experimental parameters, metabolites with a range of chemical and physical properties can be selectively desorbed and ionized and subsequently analyzed with increased speed and sensitivity. This review covers the broad applications of a variety of ambient MS techniques in four primary fields in which metabolomics is commonly employed.
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Affiliation(s)
- Chaevien S. Clendinen
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
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18
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Honarvar E, Venter AR. Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1109-1117. [PMID: 28315234 DOI: 10.1007/s13361-017-1628-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 05/11/2023]
Abstract
The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents. Three methods for ammonium bicarbonate addition during DESI-MS were investigated. The additive delivered improvements in S/N whether it was mixed with the analyte prior to sample deposition, applied over pre-prepared samples, or simply added to the desorption spray solvent. The improvement correlated well with protein pI but not with protein size. Other ammonium or bicarbonate salts did not produce similar improvements in S/N, nor was this improvement in S/N observed for ESI of the same samples. As was previously described for ESI, DESI also caused extensive protein unfolding upon the addition of ammonium bicarbonate. Graphical Abstract ᅟ.
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Affiliation(s)
- Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA.
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19
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Yan C, Parmeggiani F, Jones EA, Claude E, Hussain SA, Turner NJ, Flitsch SL, Barran PE. Real-Time Screening of Biocatalysts in Live Bacterial Colonies. J Am Chem Soc 2017; 139:1408-1411. [DOI: 10.1021/jacs.6b12165] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cunyu Yan
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Fabio Parmeggiani
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Emrys A. Jones
- Waters Corp., Stamford
Avenue, Altrincham Road, SK9 4AX, Wilmslow, United Kingdom
| | - Emmanuelle Claude
- Waters Corp., Stamford
Avenue, Altrincham Road, SK9 4AX, Wilmslow, United Kingdom
| | - Shaneela A. Hussain
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Perdita E. Barran
- Manchester
Synthetic Biology Research Centre for Fine and Speciality Chemicals
(SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
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20
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Pruski P, MacIntyre DA, Lewis HV, Inglese P, Correia GDS, Hansel TT, Bennett PR, Holmes E, Takats Z. Medical Swab Analysis Using Desorption Electrospray Ionization Mass Spectrometry: A Noninvasive Approach for Mucosal Diagnostics. Anal Chem 2017; 89:1540-1550. [PMID: 28208268 DOI: 10.1021/acs.analchem.6b03405] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Medical swabs are routinely used worldwide to sample human mucosa for microbiological screening with culture methods. These are usually time-consuming and have a narrow focus on screening for particular microorganism species. As an alternative, direct mass spectrometric profiling of the mucosal metabolome provides a broader window into the mucosal ecosystem. We present for the first time a minimal effort/minimal-disruption technique for augmenting the information obtained from clinical swab analysis with mucosal metabolome profiling using desorption electrospray ionization mass spectrometry (DESI-MS) analysis. Ionization of mucosal biomass occurs directly from a standard rayon swab mounted on a rotating device and analyzed by DESI MS using an optimized protocol considering swab-inlet geometry, tip-sample angles and distances, rotation speeds, and reproducibility. Multivariate modeling of mass spectral fingerprints obtained in this way readily discriminate between different mucosal surfaces and display the ability to characterize biochemical alterations induced by pregnancy and bacterial vaginosis (BV). The method was also applied directly to bacterial biomass to confirm the ability to detect intact bacterial species from a swab. These results highlight the potential of direct swab analysis by DESI-MS for a wide range of clinical applications including rapid mucosal diagnostics for microbiology, immune responses, and biochemistry.
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Affiliation(s)
- Pamela Pruski
- Computational and Systems Medicine, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London , London, W12 0NN, United Kingdom
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London , London, W12 0NN, United Kingdom
| | - Paolo Inglese
- Computational and Systems Medicine, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Gonçalo D S Correia
- Computational and Systems Medicine, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Trevor T Hansel
- Imperial Clinical Respiratory Research Unit (ICRRU), St Mary's Hospital, Mint Wing, Imperial College London , London, W2 INY, United Kingdom
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London , London, W12 0NN, United Kingdom
| | - Elaine Holmes
- Computational and Systems Medicine, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Zoltan Takats
- Computational and Systems Medicine, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
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21
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Pulliam CJ, Wei P, Snyder DT, Wang X, Ouyang Z, Pielak RM, Graham Cooks R. Rapid discrimination of bacteria using a miniature mass spectrometer. Analyst 2017; 141:1633-6. [PMID: 26844973 DOI: 10.1039/c5an02575c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer.
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Affiliation(s)
| | - Pu Wei
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Dalton T Snyder
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiao Wang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Zheng Ouyang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Rafal M Pielak
- L'Oreal California Research Center, San Francisco, CA, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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22
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23
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Bolt F, Cameron SJS, Karancsi T, Simon D, Schaffer R, Rickards T, Hardiman K, Burke A, Bodai Z, Perdones-Montero A, Rebec M, Balog J, Takats Z. Automated High-Throughput Identification and Characterization of Clinically Important Bacteria and Fungi using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2016; 88:9419-9426. [DOI: 10.1021/acs.analchem.6b01016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Frances Bolt
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tamas Karancsi
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Daniel Simon
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Richard Schaffer
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tony Rickards
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Kate Hardiman
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Adam Burke
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Zsolt Bodai
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Monica Rebec
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Julia Balog
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Zoltan Takats
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
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24
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Correa DN, Santos JM, Eberlin LS, Eberlin MN, Teunissen SF. Forensic Chemistry and Ambient Mass Spectrometry: A Perfect Couple Destined for a Happy Marriage? Anal Chem 2016; 88:2515-26. [DOI: 10.1021/acs.analchem.5b02397] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deleon N. Correa
- ThoMSon
Mass Spectrometry Laboratory, University of Campinas—UNICAMP, Campinas, São Paulo 13083-970, Brazil
- Technical-Scientific Police Superintendence—IC-SPTC-SP, São Paulo, São Paulo 05507-06, Brazil
| | - Jandyson M. Santos
- ThoMSon
Mass Spectrometry Laboratory, University of Campinas—UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Livia S. Eberlin
- Department
of Chemistry, The University of Texas at Austin, Austin, Texas 78712 United States
| | - Marcos N. Eberlin
- ThoMSon
Mass Spectrometry Laboratory, University of Campinas—UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Sebastiaan F. Teunissen
- ThoMSon
Mass Spectrometry Laboratory, University of Campinas—UNICAMP, Campinas, São Paulo 13083-970, Brazil
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25
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Tata A, Perez C, Campos ML, Bayfield MA, Eberlin MN, Ifa DR. Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging for Monitoring Secondary Metabolites Production during Antagonistic Interaction of Fungi. Anal Chem 2015; 87:12298-305. [PMID: 26637047 DOI: 10.1021/acs.analchem.5b03614] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Direct analysis of microbial cocultures grown on agar media by desorption electrospray ionization mass spectrometry (DESI-MS) is quite challenging. Due to the high gas pressure upon impact with the surface, the desorption mechanism does not allow direct imaging of soft or irregular surfaces. The divots in the agar, created by the high-pressure gas and spray, dramatically change the geometry of the system decreasing the intensity of the signal. In order to overcome this limitation, an imprinting step, in which the chemicals are initially transferred to flat hard surfaces, was coupled to DESI-MS and applied for the first time to fungal cocultures. Note that fungal cocultures are often disadvantageous in direct imaging mass spectrometry. Agar plates of fungi present a complex topography due to the simultaneous presence of dynamic mycelia and spores. One of the most devastating diseases of cocoa trees is caused by fungal phytopathogen Moniliophthora roreri. Strategies for pest management include the application of endophytic fungi, such as Trichoderma harzianum, that act as biocontrol agents by antagonizing M. roreri. However, the complex chemical communication underlying the basis for this phytopathogen-dependent biocontrol is still unknown. In this study, we investigated the metabolic exchange that takes place during the antagonistic interaction between M. roreri and T. harzianum. Using imprint-DESI-MS imaging we annotated the secondary metabolites released when T. harzianum and M. roreri were cultured in isolation and compared these to those produced after 3 weeks of coculture. We identified and localized four phytopathogen-dependent secondary metabolites, including T39 butenolide, harzianolide, and sorbicillinol. In order to verify the reliability of the imprint-DESI-MS imaging data and evaluate the capability of tape imprints to extract fungal metabolites while maintaining their localization, six representative plugs along the entire M. roreri/T. harzianum coculture plate were removed, weighed, extracted, and analyzed by liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Our results not only provide a better understanding of M. roreri-dependent metabolic induction in T. harzianum, but may seed novel directions for the advancement of phytopathogen-dependent biocontrol, including the generation of optimized Trichoderma strains against M. roreri, new biopesticides, and biofertilizers.
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Affiliation(s)
- Alessandra Tata
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada.,ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Rua Josué Castro, s/n Cidade Universitária, CEP 13083-970 Campinas, São Paulo, Brazil
| | - Consuelo Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
| | - Michel L Campos
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada.,Department of Natural Active Principles and Toxicology, School of Pharmaceutical Sciences, São Paulo State University , Rodovia Araraquara-Jaú, km 1, CEP 14 801-902 Araraquara, São Paulo, Brazil
| | - Mark A Bayfield
- Department of Biology, York University , 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
| | - Marcos N Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Rua Josué Castro, s/n Cidade Universitária, CEP 13083-970 Campinas, São Paulo, Brazil
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
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26
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass spectrometry tools and workflows for revealing microbial chemistry. Analyst 2015; 140:4949-66. [PMID: 25996313 PMCID: PMC5444374 DOI: 10.1039/c5an00171d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.
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27
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Tata A, Perez CJ, Ore MO, Lostun D, Passas A, Morin S, Ifa DR. Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites. RSC Adv 2015. [DOI: 10.1039/c5ra12805f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Optimized in situ screening, characterization and imaging of fungal metabolites by imprint DESI-MS.
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Affiliation(s)
| | | | | | | | | | - Sylvie Morin
- Department of Chemistry
- York University
- Toronto
- Canada
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28
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Hayes JM, Murray KK. Ambient laser ablation sample transfer with nanostructure-assisted laser desorption ionization mass spectrometry for bacteria analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2382-2384. [PMID: 25279752 DOI: 10.1002/rcm.7023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/19/2014] [Accepted: 08/19/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Juaneka M Hayes
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
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29
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Hamid AM, Jarmusch AK, Pirro V, Pincus DH, Clay BG, Gervasi G, Cooks RG. Rapid discrimination of bacteria by paper spray mass spectrometry. Anal Chem 2014; 86:7500-7. [PMID: 25014713 DOI: 10.1021/ac501254b] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Paper spray mass spectrometry ambient ionization is utilized for rapid discrimination of bacteria without sample preparation. Bacterial colonies were smeared onto filter paper precut to a sharp point, then wetted with solvent and held at a high potential. Charged droplets released by field emission were sucked into the mass spectrometer inlet and mass spectra were recorded. Sixteen different species representing eight different genera from Gram-positive and Gram-negative bacteria were investigated. Phospholipids were the predominant species observed in the mass spectra in both the negative and positive ion modes. Multivariate data analysis based on principal component analysis, followed by linear discriminant analysis, allowed bacterial discrimination. The lipid information in the negative ion mass spectra proved useful for species level differentiation of the investigated Gram-positive bacteria. Gram-negative bacteria were differentiated at the species level by using a numerical data fusion strategy of positive and negative ion mass spectra.
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Affiliation(s)
- Ahmed M Hamid
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University , West Lafayette, Indiana 47907, United States
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30
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Liu Y, Zhang J, Nie H, Dong C, Li Z, Zheng Z, Bai Y, Liu H, Zhao J. Study on Variation of Lipids during Different Growth Phases of Living Cyanobacteria Using Easy Ambient Sonic-Spray Ionization Mass Spectrometry. Anal Chem 2014; 86:7096-102. [DOI: 10.1021/ac501596v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yiqun Liu
- State
Key Lab of Protein and Plant Sciences, School of Life Science, Peking University, Beijing, 100871, P. R. China
| | - Jialing Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Institute
of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Honggang Nie
- Analytical
Instrumentation Center, Peking University, Beijing, 100871, P. R. China
| | - Chunxia Dong
- State
Key Lab of Protein and Plant Sciences, School of Life Science, Peking University, Beijing, 100871, P. R. China
| | - Ze Li
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Institute
of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zhenggao Zheng
- State
Key Lab of Protein and Plant Sciences, School of Life Science, Peking University, Beijing, 100871, P. R. China
| | - Yu Bai
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Institute
of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Huwei Liu
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Institute
of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jindong Zhao
- State
Key Lab of Protein and Plant Sciences, School of Life Science, Peking University, Beijing, 100871, P. R. China
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31
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Strittmatter N, Rebec M, Jones EA, Golf O, Abdolrasouli A, Balog J, Behrends V, Veselkov KA, Takats Z. Characterization and Identification of Clinically Relevant Microorganisms Using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2014; 86:6555-62. [DOI: 10.1021/ac501075f] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole Strittmatter
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Monica Rebec
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London W6 8RF, United Kingdom
| | - Emrys A. Jones
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ottmar Golf
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alireza Abdolrasouli
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London W6 8RF, United Kingdom
| | - Julia Balog
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Volker Behrends
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kirill A. Veselkov
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zoltan Takats
- Section of Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
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32
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Chingin K, Liang J, Chen H. Direct analysis of in vitro grown microorganisms and mammalian cells by ambient mass spectrometry. RSC Adv 2014. [DOI: 10.1039/c3ra46327c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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33
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Shih CJ, Chen PY, Liaw CC, Lai YM, Yang YL. Bringing microbial interactions to light using imaging mass spectrometry. Nat Prod Rep 2014; 31:739-55. [DOI: 10.1039/c3np70091g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Hsu CC, ElNaggar MS, Peng Y, Fang J, Sanchez LM, Mascuch SJ, Møller A, Alazzeh EK, Pikula J, Quinn RA, Zeng Y, Wolfe BE, Dutton RJ, Gerwick L, Zhang L, Liu X, Månsson M, Dorrestein PC. Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Anal Chem 2013; 85:7014-8. [PMID: 23819546 PMCID: PMC3890442 DOI: 10.1021/ac401613x] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microorganisms such as bacteria and fungi produce a variety of specialized metabolites that are invaluable for agriculture, biological research, and drug discovery. However, the screening of microbial metabolic output is usually a time-intensive task. Here, we utilize a liquid microjunction surface sampling probe for electrospray ionization-mass spectrometry to extract and ionize metabolite mixtures directly from living microbial colonies grown on soft nutrient agar in Petri-dishes without any sample pretreatment. To demonstrate the robustness of the method, this technique was applied to observe the metabolic output of more than 30 microorganisms, including yeast, filamentous fungi, pathogens, and marine-derived bacteria, that were collected worldwide. Diverse natural products produced from different microbes, including Streptomyces coelicolor , Bacillus subtilis , and Pseudomonas aeruginosa are further characterized.
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Affiliation(s)
- Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Yao Peng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jinshu Fang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laura M. Sanchez
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Amalie Møller
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | - Jiri Pikula
- University of Veterinary and Pharmaceutical Sciences, Palackeho 1/3, 612 42 Brno, Czech Republic
| | - Robert A. Quinn
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Yi Zeng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin E. Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachel J. Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lena Gerwick
- Scripps Institute of Oceanography, La Jolla, CA 92037, USA
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Maria Månsson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Pieter C. Dorrestein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA 92093, USA
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35
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Rath CM, Yang JY, Alexandrov T, Dorrestein PC. Data-independent microbial metabolomics with ambient ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1167-1176. [PMID: 23568029 PMCID: PMC3715584 DOI: 10.1007/s13361-013-0608-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/29/2013] [Accepted: 02/05/2013] [Indexed: 05/29/2023]
Abstract
Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry.
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Affiliation(s)
- Christopher M Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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36
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Abstract
The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779(T). The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family-gene cluster families of hundreds or more diverse organisms in one single MS/MS network.
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37
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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38
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Ferreira CR, Pirro V, Eberlin LS, Hallett JE, Cooks RG. Developmental phases of individual mouse preimplantation embryos characterized by lipid signatures using desorption electrospray ionization mass spectrometry. Anal Bioanal Chem 2012; 404:2915-26. [DOI: 10.1007/s00216-012-6426-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 08/26/2012] [Accepted: 09/13/2012] [Indexed: 11/30/2022]
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39
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Abstract
Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a "holy grail" in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097-1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.
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40
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Shrestha B, Sripadi P, Walsh CM, Razunguzwa TT, Powell MJ, Kehn-Hall K, Kashanchi F, Vertes A. Rapid, non-targeted discovery of biochemical transformation and biomarker candidates in oncovirus-infected cell lines using LAESI mass spectrometry. Chem Commun (Camb) 2011; 48:3700-2. [PMID: 22167302 DOI: 10.1039/c2cc17225a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Finding insights into how viruses hijack metabolic processes and biomarkers for viral diseases often require hypotheses about target compounds and/or labelling techniques. Here we present a method based on laser ablation electrospray ionization mass spectrometry to rapidly identify potential protein and metabolite biomarkers of oncovirus infection in B lymphocytes.
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Affiliation(s)
- Bindesh Shrestha
- Department of Chemistry, W. M. Keck Institute of Proteomics Technology and Applications, The George Washington University, Washington DC, USA
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41
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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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42
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Suni NM, Lindfors P, Laine O, Östman P, Ojanperä I, Kotiaho T, Kauppila TJ, Kostiainen R. Matrix effect in the analysis of drugs of abuse from urine with desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS) and desorption electrospray ionization-mass spectrometry (DESI-MS). Anal Chim Acta 2011; 699:73-80. [DOI: 10.1016/j.aca.2011.05.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 11/16/2022]
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43
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MALDI-ToF mass spectrometry-multivariate data analysis as a tool for classification of reactivation and non-culturable states of bacteria. Anal Bioanal Chem 2011; 401:1593-600. [PMID: 21769553 DOI: 10.1007/s00216-011-5227-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/09/2011] [Accepted: 06/30/2011] [Indexed: 10/18/2022]
Abstract
Some bacterial life states are only difficult to describe and to detect because they are on the border of active metabolism. A prominent example is the so-called viable but non-culturable state, which is mainly characterized by the inability of bacteria to grow on synthetic media. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF/MS) in combination with multivariate data analysis represents a powerful tool for mass-spectrometric pattern recognition of biological samples. This method is already used for differentiation of bacterial strains. In this study we present a rapid readout method based on MALDI-ToF/MS in combination with principal component analysis to classify the bacterial non-culturable state using Enterococcus faecalis as a model organism. By applying this technique to samples of different physiological states, distinct clusters were calculated and all mass spectra were classified correctly into groups of similar type concerning their physiological state.
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44
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Müller T, Oradu S, Ifa DR, Cooks RG, Kräutler B. Direct plant tissue analysis and imprint imaging by desorption electrospray ionization mass spectrometry. Anal Chem 2011; 83:5754-61. [PMID: 21675752 PMCID: PMC3137229 DOI: 10.1021/ac201123t] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 06/15/2011] [Indexed: 12/11/2022]
Abstract
The ambient mass spectrometry technique, desorption electrospray ionization mass spectrometry (DESI-MS), is applied for the rapid identification and spatially resolved relative quantification of chlorophyll degradation products in complex senescent plant tissue matrixes. Polyfunctionalized nonfluorescent chlorophyll catabolites (NCCs), the "final" products of the chlorophyll degradation pathway, are detected directly from leaf tissues within seconds and structurally characterized by tandem mass spectrometry (MS/MS) and reactive-DESI experiments performed in situ. The sensitivity of DESI-MS analysis of these compounds from degreening leaves is enhanced by the introduction of an imprinting technique. Porous polytetrafluoroethylene (PTFE) is used as a substrate for imprinting the leaves, resulting in increased signal intensities compared with those obtained from direct leaf tissue analysis. This imprinting technique is used further to perform two-dimensional (2D) imaging mass spectrometry by DESI, producing well-resolved images of the spatial distribution of NCCs in senescent leaf tissues.
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Affiliation(s)
- Thomas Müller
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020 Innsbruck, (Austria)
| | - Sheran Oradu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Demian R. Ifa
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020 Innsbruck, (Austria)
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45
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Desorption electrospray ionization mass spectrometry for lipid characterization and biological tissue imaging. Biochim Biophys Acta Mol Cell Biol Lipids 2011; 1811:946-60. [PMID: 21645635 DOI: 10.1016/j.bbalip.2011.05.006] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/29/2011] [Accepted: 05/13/2011] [Indexed: 01/08/2023]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) imaging of biological samples allows untargeted analysis and structural characterization of lipids ionized from the near-surface region of a sample under ambient conditions. DESI is a powerful and sensitive MS ionization method for 2D and 3D imaging of lipids from direct and unmodified complex biological samples. This review describes the strengths and limitations of DESI-MS for lipid characterization and imaging together with the technical workflow and a survey of applications. Included are discussions of lipid mapping and biomarker discovery as well as a perspective on the future of DESI imaging.
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46
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Zhou N, Wang N, Xu B, Wang J, Fang J, Dong F, He K, Yang X. Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of bacteria cultured in liquid media. SCIENCE CHINA-LIFE SCIENCES 2011; 54:48-53. [PMID: 21253870 DOI: 10.1007/s11427-010-4119-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/13/2010] [Indexed: 12/15/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used for many years to rapidly identify whole bacteria. However, no consistent methodology exists for the rapid identification of bacteria cultured in liquid media. Thus, in this study we explored the use of MALDI-TOF MS analysis for rapid identification of cells cultured in liquid media. We determined that 2,5-dihydroxybenzoic acid (50 mg mL(-1), 50% acetonitrile, 0.1% trifluoroacetic acid) was the best matrix solution for MALDI-TOF MS for this type of study. Moreover, the tested strains were successfully differentiated by principal component analysis, and the main characteristics of the mass peaks for each species were found in mixed culture samples. In addition, we found that the minimum number of cells for detection was 1.8 × 10(3). In conclusion, our findings suggest that MS-based techniques can be developed as an auxiliary method for rapidly and accurately identifying bacteria cultured in liquid media.
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Affiliation(s)
- Na Zhou
- Pharmaceutical Department of Jilin University, Changchun, 130021, China
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47
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Zhang JI, Costa AB, Tao WA, Cooks RG. Direct detection of fatty acid ethyl esters using low temperature plasma (LTP) ambient ionization mass spectrometry for rapid bacterial differentiation. Analyst 2011; 136:3091-7. [DOI: 10.1039/c0an00940g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Xu G, Chen B, Guo B, He D, Yao S. Detection of intermediates for the Eschweiler–Clarke reaction by liquid-phase reactive desorption electrospray ionization mass spectrometry. Analyst 2011; 136:2385-90. [DOI: 10.1039/c0an00879f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Direct detection of Salmonella typhimurium on fresh produce using phage-based magnetoelastic biosensors. Biosens Bioelectron 2010; 26:1313-9. [DOI: 10.1016/j.bios.2010.07.029] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/06/2010] [Accepted: 07/09/2010] [Indexed: 11/22/2022]
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50
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Hua Y, Dagan S, Wickramasekara S, Boday DJ, Wysocki VH. Analysis of deprotonated acids with silicon nanoparticle-assisted laser desorption/ ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1394-1401. [PMID: 21038364 DOI: 10.1002/jms.1852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Chemically modified silicon nanoparticles were applied for the laser desorption/negative ionization of small acids. A series of substituted sulfonic acids and fatty acids was studied. Compared to desorption ionization on porous silicon (DIOS) and other matrix-less laser desorption/ionization techniques, silicon nanoparticle-assisted laser desorption/ionization (SPALDI) mass spectrometry allows for the analysis of acids in the negative ion mode without the observation of multimers or cation adducts. Using SPALDI, detection limits of many acids reached levels down to 50 pmol/µl. SPALDI of fatty acids with unmodified silicon nanoparticles was compared to SPALDI using the fluoroalkyl silylated silicon powder, with the unmodified particles showing better sensitivity for fatty acids, but with more low-mass background due to impurities and surfactants in the untreated silicon powder. The fatty acids exhibited a size-dependent response in both SPALDI and unmodified SPALDI, showing a signal intensity increase with the chain length of the fatty acids (C12-C18), leveling off at chain lengths of C18-C22. The size effect may be due to the crystallization of long chain fatty acids on the silicon. This hypothesis was further explored and supported by SPALDI of several, similar sized, unsaturated fatty acids with various crystallinities. Fatty acids in milk lipids and tick nymph samples were directly detected and their concentration ratios were determined by SPALDI mass spectrometry without complicated and time-consuming purification and esterification required in the traditional analysis of fatty acids by gas chromatography (GC). These results suggest that SPALDI mass spectrometry has the potential application in fast screening for small acids in crude samples with minimal sample preparation.
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Affiliation(s)
- Yimin Hua
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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