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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:1-24. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
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Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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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.
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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
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Cai G, Hu X, Zhang R, Wang J, Fang X, Pang X, Bai J, Zhang T, Zhang T, Lv H, You X, He W, Yu L. Subplenones A-J: Dimeric Xanthones with Antibacterial Activity from the Endophytic Fungus Subplenodomus sp. CPCC 401465. JOURNAL OF NATURAL PRODUCTS 2023; 86:2474-2486. [PMID: 37862150 DOI: 10.1021/acs.jnatprod.3c00628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Subplenones A-J (1-10), 10 new xanthone dimers, have been isolated and characterized from the endophytic fungus Subplenodomus sp. CPCC 401465, which resides within the Chinese medicinal plant Gentiana straminea. The isolation process was guided by antibacterial assays and molecular-networking-based analyses. The chemical structures of these compounds were elucidated through the interpretation of nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry (HRESIMS) data. Furthermore, the relative configuration of the compounds was determined using NMR and single-crystal X-ray diffraction analyses, and the absolute configuration was established using electronic circular dichroism calculations. All of the isolated compounds exhibited significant inhibitory activity against Gram-positive bacteria. Notably, compounds 1, 5, and 7 displayed remarkable inhibitory activity against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 700698, with a minimum inhibitory concentration (MIC) of 0.25 μg/mL, and against vancomycin-resistant Enterococcus faecium (VRE) ATCC 700221, with MIC values ranging from 0.5 to 1.0 μg/mL.
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Affiliation(s)
- Guowei Cai
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xinxin Hu
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
| | - Ran Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - JuXian Wang
- Department of Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xiaomei Fang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
| | - Xu Pang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jinglin Bai
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
| | - Hui Lv
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xuefu You
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
| | - Wenni He
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, People's Republic of China
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Ahearne A, Phillips KE, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism. Front Microbiol 2023; 14:1227206. [PMID: 37601375 PMCID: PMC10435759 DOI: 10.3389/fmicb.2023.1227206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Methods In this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Results Nine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Discussion Continued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Kayleigh E. Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, United States
| | - David Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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Ahearne A, Phillips K, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species: Archangium lansinium sp. nov., Myxococcus landrumus sp. nov., Nannocystis bainbridgea sp. nov., Nannocystis poenicansa sp. nov., Nannocystis radixulma sp. nov., Polyangium mundeleinium sp. nov., Pyxidicoccus parkwaysis sp. nov., Sorangium aterium sp. nov., Stigmatella ashevillena sp. nov. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531766. [PMID: 36945379 PMCID: PMC10028903 DOI: 10.1101/2023.03.08.531766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Continued discovery and sequencing of novel myxobacteria from the environment provides BGCs for the genome mining pipeline. Herein, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates where determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions are provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Utilizing complete or near complete genome sequences we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Kayleigh Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
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Wang C, Xiao Y, Wang Y, Liu Y, Yao Q, Zhu H. Comparative genomics and transcriptomics insight into myxobacterial metabolism potentials and multiple predatory strategies. Front Microbiol 2023; 14:1146523. [PMID: 37213496 PMCID: PMC10196010 DOI: 10.3389/fmicb.2023.1146523] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023] Open
Abstract
Myxobacteria are part of the phylum Myxococcota, encompassing four orders. Most of them display complex lifestyles and broad predation profiles. However, metabolic potential and predation mechanisms of different myxobacteria remains poorly understood. Herein, we used comparative genomics and transcriptomics to analyze metabolic potentials and differentially expressed gene (DEG) profiles of Myxococcus xanthus monoculture (Mx) compared to coculture with Escherichia coli (MxE) and Micrococcus luteus (MxM) prey. The results showed that myxobacteria had conspicuous metabolic deficiencies, various protein secretion systems (PSSs) and the common type II secretion system (T2SS). RNA-seq data demonstrated that M. xanthus overexpressed the potential predation DEGs, particularly those encoding T2SS, the tight adherence (Tad) pilus, different secondary metabolites (myxochelin A/B, myxoprincomide, myxovirescin A1, geosmin and myxalamide), glycosyl transferases and peptidase during predation. Furthermore, the myxalamide biosynthesis gene clusters, two hypothetical gene clusters and one arginine biosynthesis clusters were highly differential expressed in MxE versus MxM. Additionally, homologue proteins of the Tad (kil) system and five secondary metabolites were in different obligate or facultative predators. Finally, we provided a working model for exhibiting multiple predatory strategies when M. xanthus prey on M. luteus and E. coli. These results might spur application-oriented research on the development of novel antibacterial strategies.
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Affiliation(s)
- Chunling Wang
- College of Life Science, Huizhou University, Huizhou, Guangdong, China
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yi Xiao
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yong Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yumin Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou, Guangdong, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- *Correspondence: Honghui Zhu,
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Pérez J, Contreras-Moreno FJ, Muñoz-Dorado J, Moraleda-Muñoz A. Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus. Front Microbiol 2022; 13:1004476. [PMID: 36225384 PMCID: PMC9548883 DOI: 10.3389/fmicb.2022.1004476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus is a multicellular bacterium with a complex lifecycle. It is a soil-dwelling predator that preys on a wide variety of microorganisms by using a group and collaborative epibiotic strategy. In the absence of nutrients this myxobacterium enters in a unique developmental program by using sophisticated and complex regulatory systems where more than 1,400 genes are transcriptional regulated to guide the community to aggregate into macroscopic fruiting bodies filled of environmentally resistant myxospores. Herein, we analyze the predatosome of M. xanthus, that is, the transcriptomic changes that the predator undergoes when encounters a prey. This study has been carried out using as a prey Sinorhizobium meliloti, a nitrogen fixing bacteria very important for the fertility of soils. The transcriptional changes include upregulation of genes that help the cells to detect, kill, lyse, and consume the prey, but also downregulation of genes not required for the predatory process. Our results have shown that, as expected, many genes encoding hydrolytic enzymes and enzymes involved in biosynthesis of secondary metabolites increase their expression levels. Moreover, it has been found that the predator modifies its lipid composition and overproduces siderophores to take up iron. Comparison with developmental transcriptome reveals that M. xanthus downregulates the expression of a significant number of genes coding for regulatory elements, many of which have been demonstrated to be key elements during development. This study shows for the first time a global view of the M. xanthus lifecycle from a transcriptome perspective.
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Paglia G, Smith AJ, Astarita G. Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics. MASS SPECTROMETRY REVIEWS 2022; 41:722-765. [PMID: 33522625 DOI: 10.1002/mas.21686] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.
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Affiliation(s)
- Giuseppe Paglia
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Andrew J Smith
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
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11
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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12
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McCann A, Kune C, La Rocca R, Oetjen J, Arias AA, Ongena M, Far J, Eppe G, Quinton L, De Pauw E. Rapid visualization of lipopeptides and potential bioactive groups of compounds by combining ion mobility and MALDI imaging mass spectrometry. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:81-88. [PMID: 34906328 DOI: 10.1016/j.ddtec.2021.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 11/27/2022]
Abstract
Mass spectrometry imaging (MSI) has become a powerful method for mapping metabolite distribution in a tissue. Applied to bacterial colonies, MSI has a bright future, both for the discovery of new bioactive compounds and for a better understanding of bacterial antibiotic resistance mechanisms. Coupled with separation techniques such as ion mobility mass spectrometry (IM-MS), the identification of metabolites directly on the image is now possible and does not require additional analysis such as HPLC-MS/MS. In this article, we propose to apply a semi-targeted workflow for rapid IM-MSI data analysis focused on the search for bioactive compounds. First, chemically-related compounds showing a repetitive mass unit (i.e. lipids and lipopeptides) were targeted based on the Kendrick mass defect analysis. The detected groups of potentially bioactive compounds were then confirmed by fitting their measured ion moibilites to their measured m/z values. Using both their m/z and ion mobility values, the selected groups of compounds were identified using the available databases and finally their distribution was observed on the image. Using this workflow on a co-culture of bacteria, we were able to detect and localize bioactive compounds involved in the microbial interaction.
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Affiliation(s)
- Andréa McCann
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Raphael La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Janina Oetjen
- Bruker Daltonik GmbH, Fahrenheitsstr. 4, 28359 Bremen, Germany
| | | | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Loic Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
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Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies. Proc Natl Acad Sci U S A 2021; 118:2109633118. [PMID: 34857637 DOI: 10.1073/pnas.2109633118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Reading and writing DNA were once the rate-limiting step in synthetic biology workflows. This has been replaced by the search for the optimal target sequences to produce systems with desired properties. Directed evolution and screening mutant libraries are proven technologies for isolating strains with enhanced performance whenever specialized assays are available for rapidly detecting a phenotype of interest. Armed with technologies such as CRISPR-Cas9, these experiments are capable of generating libraries of up to 1010 genetic variants. At a rate of 102 samples per day, standard analytical methods for assessing metabolic phenotypes represent a major bottleneck to modern synthetic biology workflows. To address this issue, we have developed a desorption electrospray ionization-imaging mass spectrometry screening assay that directly samples microorganisms. This technology increases the throughput of metabolic measurements by reducing sample preparation and analyzing organisms in a multiplexed fashion. To further accelerate synthetic biology workflows, we utilized untargeted acquisitions and unsupervised analytics to assess multiple targets for future engineering strategies within a single acquisition. We demonstrate the utility of the developed method using Escherichia coli strains engineered to overproduce free fatty acids. We determined discrete metabolic phenotypes associated with each strain, which include the primary fatty acid product, secondary products, and additional metabolites outside the engineered product pathway. Furthermore, we measured changes in amino acid levels and membrane lipid composition, which affect cell viability. In sum, we present an analytical method to accelerate synthetic biology workflows through rapid, untargeted, and multiplexed metabolomic analyses.
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14
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Akbar S, Phillips KE, Misra SK, Sharp JS, Stevens DC. Differential response to prey quorum signals indicates predatory specialization of myxobacteria and ability to predate Pseudomonas aeruginosa. Environ Microbiol 2021; 24:1263-1278. [PMID: 34674390 PMCID: PMC9257966 DOI: 10.1111/1462-2920.15812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/20/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022]
Abstract
Multiomic analysis of transcriptional and metabolic responses from the predatory myxobacteria Myxococcus xanthus and Cystobacter ferrugineus exposed to prey signalling molecules of the acylhomoserine lactone and quinolone quorum signalling classes provided insight into predatory specialization. Acylhomoserine lactone quorum signals elicited a general response from both myxobacteria. We suggest that this is likely due to the generalist predator lifestyles of myxobacteria and ubiquity of acylhomoserine lactone signals. We also provide data that indicates the core homoserine lactone moiety included in all acylhomoserine lactone scaffolds to be sufficient to induce this general response. Comparing both myxobacteria, unique transcriptional and metabolic responses were observed from Cystobacter ferrugineus exposed to the quinolone signal 2‐heptylquinolin‐4(1H)‐one (HHQ) natively produced by Pseudomonas aeruginosa. We suggest that this unique response and ability to metabolize quinolone signals contribute to the superior predation of P. aeruginosa observed from C. ferrugineus. These results further demonstrate myxobacterial eavesdropping on prey signalling molecules and provide insight into how responses to exogenous signals might correlate with prey range of myxobacteria.
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Affiliation(s)
- Shukria Akbar
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA
| | - Kayleigh E Phillips
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Department of Chemistry and Biochemistry, University of Mississippi, University, University, MS, USA
| | - D Cole Stevens
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA
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15
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Akbar S, Stevens DC. Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator. Sci Rep 2021; 11:16445. [PMID: 34385565 PMCID: PMC8360965 DOI: 10.1038/s41598-021-96046-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Predation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Predator-prey experiments utilizing myxobacteria have provided details into predatory mechanisms and features that facilitate consumption of prey. However, prey resistance to myxobacterial predation remains underexplored, and prey resistances have been observed exclusively from predator-prey experiments that included the model myxobacterium Myxococcus xanthus. Utilizing a predator-prey pairing that instead included the myxobacterium, Cystobacter ferrugineus, with Pseudomonas putida as prey, we observed surviving phenotypes capable of eluding predation. Comparative transcriptomics between P. putida unexposed to C. ferrugineus and the survivor phenotype suggested that increased expression of efflux pumps, genes associated with mucoid conversion, and various membrane features contribute to predator avoidance. Unique features observed from the survivor phenotype when compared to the parent P. putida include small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion. These results demonstrate the utility of myxobacterial predator-prey models and provide insight into prey resistances in response to predatory stress that might contribute to the phenotypic diversity and structure of bacterial communities.
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Affiliation(s)
- Shukria Akbar
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA
| | - D Cole Stevens
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.
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16
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Taylor AL, Davis DE, Codreanu SG, Harrison FE, Sherrod SD, McLean JA. Targeted and Untargeted Mass Spectrometry Reveals the Impact of High-Fat Diet on Peripheral Amino Acid Regulation in a Mouse Model of Alzheimer's Disease. J Proteome Res 2021; 20:4405-4414. [PMID: 34382806 DOI: 10.1021/acs.jproteome.1c00344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent research regarding amino acid metabolism has shown that there may be a link between obesity and Alzheimer's disease (AD). This work reports a metabolomics study using targeted and untargeted mass spectrometry-based metabolomic strategies to investigate this link. Targeted hydrophilic interaction liquid chromatography-triple quadrupole mass spectrometry and untargeted reversed-phase liquid chromatography-high resolution tandem mass spectrometry assays were developed to analyze the metabolic changes that occur in AD and obesity. APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type littermate controls were fed either a high-fat diet (HFD, 60% kcal from lard) or a low-fat diet (LFD, 10% kcal from lard) from 2 months of age or a reversal diet (HFD, followed by LFD from 9.5 months). For targeted analyses, we applied the guidelines outlined in the Clinical and Laboratory Standards Institute (CLSI) LC-MS C62-A document and the U.S. Food and Drug Administration (FDA) bioanalytical method validation guidance for industry to evaluate the figures of merit of the assays. Our targeted and untargeted metabolomics results suggest that numerous peripheral pathways, specifically amino acid metabolism and fatty acid metabolism, were significantly affected by AD and diet. Multiple amino acids (including alanine, glutamic acid, leucine, isoleucine, and phenylalanine), carnitines, and members of the fatty acid oxidation pathway were significantly increased in APP/PSEN1 mice on HFD compared to those on LFD. More substantial effects and changes were observed in the APP/PSEN1 mice than in the WT mice, suggesting that they were more sensitive to an HFD. These dysregulated peripheral pathways include numerous amino acid pathways and fatty acid beta oxidation and suggest that obesity combined with AD further enhances cognitive impairment, possibly through aggravated mitochondrial dysfunction. Furthermore, partial reversibility of many altered pathways was observed, which highlights that diet change can mitigate the metabolic effects of AD. The same trends in individual amino acids were observed in both strategies, highlighting the biological validity of the results.
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Affiliation(s)
- Amelia L Taylor
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Don E Davis
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Fiona E Harrison
- Vanderbilt University Medical Center, Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| | - Stacy D Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
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17
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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18
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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19
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Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
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Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
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Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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