1
|
Bradley R, Simon D, Spiga L, Xiang Y, Takats Z, Williams H. Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa. mSystems 2024; 9:e0116523. [PMID: 38530056 PMCID: PMC11019781 DOI: 10.1128/msystems.01165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors. IMPORTANCE This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the identification of specific oxidative stress biomarkers, and demonstrated that hypochlorous acid, an oxidant specifically produced by human neutrophils during infection, affects quorum sensing and reduces production of the virulence factors pyocyanin and elastase. No pyocyanin was detectable and elastase levels were reduced by more than 75% in bacteria grown in the presence of hypochlorous acid. This approach has the potential to be widely applicable to the characterization of the stress responses of bacteria.
Collapse
Affiliation(s)
- Rob Bradley
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Daniel Simon
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
- The Rosalind Franklin Institute, Didcot, United Kingdom
| | - Livia Spiga
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Huw Williams
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Du Y, May RC, Cooper HJ. Native ambient mass spectrometry of intact protein assemblies directly from Escherichia coli colonies. Chem Commun (Camb) 2022; 58:6857-6860. [PMID: 35617055 PMCID: PMC9196203 DOI: 10.1039/d2cc02085h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we demonstrate that by combining electroporation with native ambient mass spectrometry, it is possible to detect intact non-covalent protein complexes directly from bacterial colonies growing on agar. Homodimers HdeA and HdeB were identified, together with the 50 kDa Mn-bound superoxide dismutase homodimer, in addition to some previously undetected monomeric proteins.
Collapse
Affiliation(s)
- Yuying Du
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| |
Collapse
|
4
|
Ding X, Liu K, Shi Z. LASER DESORPTION/ABLATION POSTIONIZATION MASS SPECTROMETRY: RECENT PROGRESS IN BIOANALYTICAL APPLICATIONS. MASS SPECTROMETRY REVIEWS 2021; 40:566-605. [PMID: 32770707 DOI: 10.1002/mas.21649] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/07/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Lasers have long been used in the field of mass spectrometric analysis for characterization of condensed matter. However, emission of neutrals upon laser irradiation surpasses the number of ions. Typically, only one in about one million analytes ejected by laser desorption/ablation is ionized, which has fueled the quest for postionization methods enabling ionization of desorbed neutrals to enhance mass spectrometric detection schemes. The development of postionization techniques can be an endeavor that integrates multiple disciplines involving photon energy transfer, electrochemistry, gas discharge, etc. The combination of lasers of different parameters and diverse ion sources has made laser desorption/ablation postionization (LD/API) a growing and lively research community, including two-step laser mass spectrometry, laser ablation atmospheric pressure photoionization mass spectrometry, and those coupled to ambient mass spectrometry. These hyphenated techniques have shown potentials in bioanalytical applications, with major inroads to be made in simultaneous location and quantification of pharmaceuticals, toxins, and metabolites in complex biomatrixes. This review is intended to provide a timely comprehensive view of the broadening bioanalytical applications of disparate LD/API techniques. We also have attempted to discuss these applications according to the classifications based on the postionization methods and to encapsulate the latest achievements in the field of LD/API by highlighting some of the very best reports in the 21st century. © 2020 John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Xuelu Ding
- Department of Pharmaceutical Analysis, School of Pharmacy, Qingdao University, Qingdao, 266021, China
| | - Kun Liu
- Department of Pharmaceutical Analysis, School of Pharmacy, Qingdao University, Qingdao, 266021, China
| | - Zhenyan Shi
- Department of Pharmaceutical Analysis, School of Pharmacy, Qingdao University, Qingdao, 266021, China
| |
Collapse
|
5
|
Zheng Y, Liu Z, Xing J, Zheng Z, Pi Z, Song F, Liu S. In situ analysis of single cell and biological samples with rGO-Cu functional probe ESI-MS spectrometry. Talanta 2020; 211:120751. [DOI: 10.1016/j.talanta.2020.120751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/17/2023]
|
6
|
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]
|
7
|
Aszyk J, Byliński H, Namieśnik J, Kot-Wasik A. Main strategies, analytical trends and challenges in LC-MS and ambient mass spectrometry–based metabolomics. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
8
|
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]
|
9
|
Okrent RA, Trippe KM, Manning VA, Walsh CM. Detection of 4-formylaminooxyvinylglycine in culture filtrates of Pseudomonas fluorescens WH6 and Pantoea ananatis BRT175 by laser ablation electrospray ionization-mass spectrometry. PLoS One 2018; 13:e0200481. [PMID: 29990341 PMCID: PMC6039020 DOI: 10.1371/journal.pone.0200481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/27/2018] [Indexed: 01/29/2023] Open
Abstract
The oxyvinylglycine 4-formylaminooxyvinylglycine (FVG) arrests the germination of weedy grasses and inhibits the growth of the bacterial plant pathogen Erwinia amylovora. Both biological and analytical methods have previously been used to detect the presence of FVG in crude and extracted culture filtrates of several Pseudomonas fluorescens strains. Although a combination of these techniques is adequate to detect FVG, none is amenable to high-throughput analysis. Likewise, filtrates often contain complex metabolite mixtures that prevent the detection of FVG using established chromatographic techniques. Here, we report the development of a new method that directly detects FVG in crude filtrates using laser ablation electrospray ionization-mass spectrometry (LAESI-MS). This approach overcomes limitations with our existing methodology and allows for the rapid analysis of complex crude culture filtrates. To validate the utility of the LAESI-MS method, we examined crude filtrates from Pantoea ananatis BRT175 and found that this strain also produces FVG. These findings are consistent with the antimicrobial activity of P. ananatis BRT175 and indicate that the spectrum of bacteria that produce FVG stretches beyond rhizosphere-associated Pseudomonas fluorescens.
Collapse
Affiliation(s)
- Rachel A. Okrent
- USDA-ARS Forage Seed Production Research Unit, Corvallis, Oregon, United States of America
| | - Kristin M. Trippe
- USDA-ARS Forage Seed Production Research Unit, Corvallis, Oregon, United States of America
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Viola A. Manning
- USDA-ARS Forage Seed Production Research Unit, Corvallis, Oregon, United States of America
| | - Callee M. Walsh
- Protea Biosciences, Inc., Morgantown, West Virginia, United States of America
| |
Collapse
|
10
|
Bianchi F, Riboni N, Termopoli V, Mendez L, Medina I, Ilag L, Cappiello A, Careri M. MS-Based Analytical Techniques: Advances in Spray-Based Methods and EI-LC-MS Applications. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:1308167. [PMID: 29850370 PMCID: PMC5937452 DOI: 10.1155/2018/1308167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/26/2018] [Indexed: 05/15/2023]
Abstract
Mass spectrometry is the most powerful technique for the detection and identification of organic compounds. It can provide molecular weight information and a wealth of structural details that give a unique fingerprint for each analyte. Due to these characteristics, mass spectrometry-based analytical methods are showing an increasing interest in the scientific community, especially in food safety, environmental, and forensic investigation areas where the simultaneous detection of targeted and nontargeted compounds represents a key factor. In addition, safety risks can be identified at the early stage through online and real-time analytical methodologies. In this context, several efforts have been made to achieve analytical instrumentation able to perform real-time analysis in the native environment of samples and to generate highly informative spectra. This review article provides a survey of some instrumental innovations and their applications with particular attention to spray-based MS methods and food analysis issues. The survey will attempt to cover the state of the art from 2012 up to 2017.
Collapse
Affiliation(s)
- Federica Bianchi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Nicolò Riboni
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Veronica Termopoli
- Department of Pure and Applied Sciences, LC-MS Laboratory, Piazza Rinascimento 6, 61029 Urbino, Italy
| | - Lucia Mendez
- Instituto de Investigaciones Marinas, Spanish National Research Council (IIM-CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Isabel Medina
- Instituto de Investigaciones Marinas, Spanish National Research Council (IIM-CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Leopold Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Achille Cappiello
- Department of Pure and Applied Sciences, LC-MS Laboratory, Piazza Rinascimento 6, 61029 Urbino, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| |
Collapse
|
11
|
Yang Y, Huang Y, Wu J, Liu N, Deng J, Luan T. Single-cell analysis by ambient mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
12
|
Stopka SA, Shrestha B, Maréchal É, Falconet D, Vertes A. Metabolic transformation of microalgae due to light acclimation and genetic modifications followed by laser ablation electrospray ionization mass spectrometry with ion mobility separation. Analyst 2015; 139:5945-53. [PMID: 25254963 DOI: 10.1039/c4an01368a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolic profiling of various microalga species and their genetic variants, grown under varied environmental conditions, has become critical to accelerate the exploration of phytoplankton biodiversity and biology. The accumulation of valuable metabolites, such as glycerolipids, is also sought in microalgae for biotechnological applications ranging from food, feed, medicine, cosmetics to bioenergy and green chemistry. In this report we describe the direct analysis of metabolites and lipids in small cell populations of the green alga Chlamydomonas reinhardtii, using laser ablation electrospray ionization (LAESI) mass spectrometry (MS) coupled with ion mobility separation (IMS). These microorganisms are capable of redirecting energy storage pathways from starch to neutral lipids depending on environmental conditions and nutrient availability. Metabolite and lipid productions were monitored in wild type (WT), and genetically modified C. reinhardtii strains with an impaired starch pathway. Lipids, such as triacylglycerols (TAG) and diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), were monitored over time under altered light conditions. More than 200 ions related to metabolites, e.g., arginine, cysteine, serine, palmitate, chlorophyll a, chlorophyll b, etc., were detected. The lipid profiles at different light intensities for strains with impaired starch pathway (Sta1 and Sta6) contained 26 glycerolipids, such as DGTS, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), as well as 33 TAG species. Results were obtained over a 72 hour time period under high and low light conditions for the WT species and the two mutants. Our results indicate that LAESI-IMS-MS can be utilized for the rapid analysis of increased TAG production at elevated light intensities. Compared to WT, the Sta6 strain showed 2.5 times higher lipid production at 72 hours under high light conditions. The results demonstrate our ability to rapidly observe numerous changes in metabolite and lipid levels in microalgal population. These capabilities are expected to facilitate the exploration of genetically altered microalgal strains for biofuel production.
Collapse
Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, DC 20052, USA.
| | | | | | | | | |
Collapse
|
13
|
Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
Collapse
Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | | |
Collapse
|
14
|
O'Brien JT, Williams ER, Holman HYN. Ambient infrared laser ablation mass spectrometry (AIRLAB-MS) of live plant tissue with plume capture by continuous flow solvent probe. Anal Chem 2015; 87:2631-8. [PMID: 25622206 DOI: 10.1021/ac503383p] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new experimental setup for spatially resolved ambient infrared laser ablation-mass spectrometry (AIRLAB-MS) that uses an infrared microscope with an infinity-corrected reflective objective and a continuous flow solvent probe coupled to a Fourier transform ion cyclotron resonance mass spectrometer is described. The efficiency of material transfer from the sample to the electrospray ionization emitter was determined using glycerol/methanol droplets containing 1 mM nicotine and is ∼50%. This transfer efficiency is significantly higher than values reported for similar techniques. Laser desorption does not induce fragmentation of biomolecules in droplets containing bradykinin, leucine enkephalin and myoglobin, but loss of the heme group from myoglobin occurs as a result of the denaturing solution used. An application of AIRLAB-MS to biological materials is demonstrated for tobacco leaves. Chemical components are identified from the spatially resolved mass spectra of the ablated plant material, including nicotine and uridine. The reproducibility of measurements made using AIRLAB-MS on plant material was demonstrated by the ablation of six closely spaced areas (within 2 × 2 mm) on a young tobacco leaf, and the results indicate a standard deviation of <10% in the uridine signal obtained for each area. The spatial distribution of nicotine was measured for selected leaf areas and variation in the relative nicotine levels (15-100%) was observed. Comparative analysis of the nicotine distribution was demonstrated for two tobacco plant varieties, a genetically modified plant and its corresponding wild-type, indicating generally higher nicotine levels in the mutant.
Collapse
Affiliation(s)
- Jeremy T O'Brien
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-0001, United States
| | | | | |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | - Sylvie Morin
- Department of Chemistry
- York University
- Toronto
- Canada
| | | |
Collapse
|
16
|
Bartels B, Svatoš A. Spatially resolved in vivo plant metabolomics by laser ablation-based mass spectrometry imaging (MSI) techniques: LDI-MSI and LAESI. FRONTIERS IN PLANT SCIENCE 2015; 6:471. [PMID: 26217345 PMCID: PMC4498035 DOI: 10.3389/fpls.2015.00471] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This short review aims to summarize the current developments and applications of mass spectrometry-based methods for in situ profiling and imaging of plants with minimal or no sample pre-treatment or manipulation. Infrared-laser ablation electrospray ionization and UV-laser desorption/ionization methods are reviewed. The underlying mechanisms of the ionization techniques-namely, laser ablation of biological samples and electrospray ionization-as well as variations of the LAESI ion source for specific targets of interest are described.
Collapse
Affiliation(s)
| | - Aleš Svatoš
- *Correspondence: Aleš Svatoš,Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Hans-Knöll-Straße 8, Jena D-07745, Germany,
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Ahmed M Hamid
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University , West Lafayette, Indiana 47907, United States
| | | | | | | | | | | | | |
Collapse
|
18
|
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
| |
Collapse
|
19
|
GC constituents and relative codon expressed amino acid composition in cyanobacterial phycobiliproteins. Gene 2014; 546:162-71. [PMID: 24933001 DOI: 10.1016/j.gene.2014.06.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/17/2014] [Accepted: 06/12/2014] [Indexed: 02/01/2023]
Abstract
The genomic as well as structural relationship of phycobiliproteins (PBPs) in different cyanobacterial species are determined by nucleotides as well as amino acid composition. The genomic GC constituents influence the amino acid variability and codon usage of particular subunit of PBPs. We have analyzed 11 cyanobacterial species to explore the variation of amino acids and causal relationship between GC constituents and codon usage. The study at the first, second and third levels of GC content showed relatively more amino acid variability on the levels of G3+C3 position in comparison to the first and second positions. The amino acid encoded GC rich level including G rich and C rich or both correlate the codon variability and amino acid availability. The fluctuation in amino acids such as Arg, Ala, His, Asp, Gly, Leu and Glu in α and β subunits was observed at G1C1 position; however, fluctuation in other amino acids such as Ser, Thr, Cys and Trp was observed at G2C2 position. The coding selection pressure of amino acids such as Ala, Thr, Tyr, Asp, Gly, Ile, Leu, Asn, and Ser in α and β subunits of PBPs was more elaborated at G3C3 position. In this study, we observed that each subunit of PBPs is codon specific for particular amino acid. These results suggest that genomic constraint linked with GC constituents selects the codon for particular amino acids and furthermore, the codon level study may be a novel approach to explore many problems associated with genomics and proteomics of cyanobacteria.
Collapse
|
20
|
Bouslimani A, Sanchez LM, Garg N, Dorrestein PC. Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 2014; 31:718-29. [PMID: 24801551 PMCID: PMC4161218 DOI: 10.1039/c4np00044g] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this Highlight, we feature emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade.
Collapse
Affiliation(s)
- Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | | | | | | |
Collapse
|
21
|
Kiss A, Smith DF, Reschke BR, Powell MJ, Heeren RMA. Top-down mass spectrometry imaging of intact proteins by laser ablation ESI FT-ICR MS. Proteomics 2014; 14:1283-9. [PMID: 24375984 DOI: 10.1002/pmic.201300306] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/02/2013] [Indexed: 11/06/2022]
Abstract
Laser ablation ESI (LAESI) is a recent development in MS imaging. It has been shown that lipids and small metabolites can be imaged in various samples such as plant material, tissue sections or bacterial colonies without any sample pretreatment. Further, LAESI has been shown to produce multiply charged protein ions from liquids or solid surfaces. This presents a means to address one of the biggest challenges in MS imaging; the identification of proteins directly from biological tissue surfaces. Such identification is hindered by the lack of multiply charged proteins in common MALDI ion sources and the difficulty of performing tandem MS on such large, singly charged ions. We present here top-down identification of intact proteins from tissue with a LAESI ion source combined with a hybrid ion-trap FT-ICR mass spectrometer. The performance of the system was first tested with a standard protein with electron capture dissociation and infrared multiphoton dissociation fragmentation to prove the viability of LAESI FT-ICR for top-down proteomics. Finally, the imaging of a tissue section was performed, where a number of intact proteins were measured and the hemoglobin α chain was identified directly from tissue using CID and infrared multiphoton dissociation fragmentation.
Collapse
Affiliation(s)
- András Kiss
- FOM Institute AMOLF, Amsterdam, The Netherlands
| | | | | | | | | |
Collapse
|
22
|
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
|
23
|
Flanigan P, Levis R. Ambient femtosecond laser vaporization and nanosecond laser desorption electrospray ionization mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:229-256. [PMID: 25014343 DOI: 10.1146/annurev-anchem-071213-020343] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent investigations of ambient laser-based transfer of molecules into the gas phase for subsequent mass spectral analysis have undergone a renaissance resulting from the separation of vaporization and ionization events. Here, we seek to provide a snapshot of recent femtosecond (fs) duration laser vaporization and nanosecond (ns) duration laser desorption electrospray ionization mass spectrometry experiments. The former employs pulse durations of <100 fs to enable matrix-free laser vaporization with little or no fragmentation. When coupled to electrospray ionization, femtosecond laser vaporization provides a universal, rapid mass spectral analysis method requiring no sample workup. Remarkably, laser pulses with intensities exceeding 10(13) W cm(-2) desorb intact macromolecules, such as proteins, and even preserve the condensed phase of folded or unfolded protein structures according to the mass spectral charge state distribution, as demonstrated for cytochrome c and lysozyme. Because of the ability to vaporize and ionize multiple components from complex mixtures for subsequent analysis, near perfect classification of explosive formulations, plant tissue phenotypes, and even the identity of the manufacturer of smokeless powders can be determined by multivariate statistics. We also review the more mature field of nanosecond laser desorption for ambient mass spectrometry, covering the wide range of systems analyzed, the need for resonant absorption, and the spatial imaging of complex systems like tissue samples.
Collapse
Affiliation(s)
- Paul Flanigan
- Center for Advanced Photonics Research, Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122; ,
| | | |
Collapse
|
24
|
Relative quantitation in single-cell metabolomics by laser ablation electrospray mass spectrometry. Methods Mol Biol 2014; 1083:31-9. [PMID: 24218208 DOI: 10.1007/978-1-62703-661-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-cell analysis of metabolites by mass spectrometry (MS) is challenging due to the very limited volume and inherent molecular complexity of the sample. Quantitative metabolomic analysis of individual cells provides information on the metabolic heterogeneity of cells unattainable by aggregate analysis of multiple cells. Depending on the ionization method, MS can offer quantitative analysis for a broad class of metabolites exhibiting both high sensitivity and selectivity. Laser ablation electrospray ionization (LAESI) has been successfully exploited to analyze metabolites from broad range of biological samples, including single cells and small cell populations. In this work, we describe a protocol for the relative quantitation of metabolites in single cells by LAESI-mass spectrometry.
Collapse
|
25
|
Heath BS, Marshall MJ, Laskin J. The characterization of living bacterial colonies using nanospray desorption electrospray ionization mass spectrometry. Methods Mol Biol 2014; 1151:199-208. [PMID: 24838888 DOI: 10.1007/978-1-4939-0554-6_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanospray desorption electrospray ionization (nano-DESI) coupled with high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) enable detailed molecular characterization of living bacterial colonies directly from nutrient agar. The ability to detect molecular signatures of living microbial communities is important for investigating metabolic exchange between species without affecting the viability of the colonies. We describe the protocol for bacterial growth, sample preparation, ambient profiling, and data analysis of microbial communities using nano-DESI MS.
Collapse
Affiliation(s)
- Brandi S Heath
- Physical Sciences Division, Pacific Northwest National Laboratory, 999, MSIN K8-88, Richland, WA, 99352, USA
| | | | | |
Collapse
|
26
|
Lanekoff I, Geydebrekht O, Pinchuk GE, Konopka AE, Laskin J. Spatially resolved analysis of glycolipids and metabolites in living Synechococcus sp. PCC 7002 using nanospray desorption electrospray ionization. Analyst 2013; 138:1971-8. [PMID: 23392077 DOI: 10.1039/c3an36716a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms release a diversity of organic compounds that couple interspecies metabolism, enable communication, or provide benefits to other microbes. Increased knowledge of microbial metabolite production will contribute to understanding of the dynamic microbial world and can potentially lead to new developments in drug discovery, biofuel production, and clinical research. Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables detailed chemical characterization of molecules from a specific location on a surface without special sample pretreatment. Due to its ambient nature, living bacterial colonies growing on agar plates can be rapidly analyzed without affecting the viability of the colony. In this study we demonstrate for the first time the utility of nano-DESI for spatial profiling of chemical gradients generated by microbial communities on agar plates. We found that despite the high salt content of the agar used in this study (~350 mM), nano-DESI analysis enables detailed characterization of metabolites produced by the Synechococcus sp. PCC 7002 colonies. High resolution mass spectrometry and MS/MS analysis of the living Synechococcus sp. PCC 7002 colonies allowed us to detect metabolites and lipids on the colony and on the surrounding agar, and confirm their identities. High sensitivity of nano-DESI enabled identification of several glycolipids that have not been previously reported by extracting the cells using conventional methods. Spatial profiling demonstrated that a majority of lipids and metabolites were localized on the colony while sucrose and glucosylglycerol, an osmoprotective compound produced by cyanobacteria, were secreted onto agar. Furthermore, we demonstrated that the chemical gradients of sucrose and glucosylglycerol on agar depend on the age of the colony. The methodology presented in this study will facilitate future studies focused on molecular-level characterization of interactions between bacterial colonies.
Collapse
Affiliation(s)
- Ingela Lanekoff
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, PO Box 999, K8-88 Richland, WA 99352, USA.
| | | | | | | | | |
Collapse
|
27
|
Monge ME, Harris GA, Dwivedi P, Fernández FM. Mass Spectrometry: Recent Advances in Direct Open Air Surface Sampling/Ionization. Chem Rev 2013; 113:2269-308. [DOI: 10.1021/cr300309q] [Citation(s) in RCA: 404] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- María Eugenia Monge
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Glenn A. Harris
- Department
of Biochemistry and
the Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prabha Dwivedi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| |
Collapse
|
28
|
Vertes A, Hitchins V, Phillips KS. Analytical Challenges of Microbial Biofilms on Medical Devices. Anal Chem 2012; 84:3858-66. [DOI: 10.1021/ac2029997] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Akos Vertes
- The George Washington University, Department of Chemistry
| | | | | |
Collapse
|