The Experts below are selected from a list of 21081 Experts worldwide ranked by ideXlab platform
Richard M Caprioli - One of the best experts on this subject based on the ideXlab platform.
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multimodal Imaging Mass Spectrometry of murine gastrointestinal tract with retained luminal content shows molecular localization patterns
bioRxiv, 2021Co-Authors: Emma R Guiberson, Jeffrey M Spraggins, Aaron G Wexler, Christopher J Good, Eric P Skaar, Richard M CaprioliAbstract:Digestive diseases impact 62 million people a year in the United States. Despite the central role of the gut to human health, past Imaging Mass Spectrometry (IMS) investigations into the gastrointestinal tract are incomplete. The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing Imaging approaches remove luminal content, and images focus on small regions of tissue. Here, we demonstrate the use of a workflow to collect multimodal Imaging data for both intestinal tissue and luminal content. This workflow for matrix-assisted laser desorption/ionization Imaging Mass Spectrometry retains luminal content and expands the amount of tissue imaged on one slide. Results comparing tissue and luminal content show unique molecular distributions using multimodal Imaging modalities including protein, lipid, and elemental Imaging. Leveraging this method to investigate intestinal tissue infected with Clostridioides difficile compared to control tissue shows clear differences in lipid abundance of various lipid classes in luminal content during infection. These data highlight the potential for this approach to detect unique biological and markers of infection in the gut.
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dynamic range expansion by gas phase ion fractionation and enrichment for Imaging Mass Spectrometry
Analytical Chemistry, 2020Co-Authors: Boone M Prentice, Richard M Caprioli, Daniel J Ryan, Kerri J Grove, Shannon D Cornett, Jeffrey M SpragginsAbstract:In the analysis of biological tissue by Imaging Mass Spectrometry (IMS), the limit of detection and dynamic range are of paramount importance in obtaining experimental results that provide insight into underlying biological processes. Many important biomolecules are present in the tissue milieu in low concentrations and in complex mixtures with other compounds of widely ranging abundances, challenging the limits of analytical technologies. In many IMS experiments, the ion signal can be dominated by a few highly abundant ion species. On trap-based instrument platforms that accumulate ions prior to Mass analysis, these high abundance ions can diminish the detection and dynamic range of lower abundance ions. Herein, we describe two strategies for combating these challenges during IMS experiments on a hybrid QhFT-ICR MS. In one iteration, the Mass resolving capabilities of a quadrupole Mass filter are used to selectively enrich ions of interest via a technique previously termed continuous accumulation of selected ions. Second, we have introduced a supplemental dipolar AC waveform to the quadrupole Mass filter of a commercial QhFT-ICR Mass spectrometer to perform selected ion ejection prior to the ion accumulation region. This setup allows the selective ejection of the most abundant ion species prior to ion accumulation, thereby greatly improving the molecular depth with which IMS can probe tissue samples. The gain in sensitivity of both of these approaches roughly scales with the number of accumulated laser shots up to the charge capacity of the ion accumulation cell. The efficiencies of these two strategies are described here by performing lipid Imaging Mass Spectrometry analyses of a rat brain.
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resolving the complexity of spatial lipidomics using maldi tims Imaging Mass Spectrometry
ChemRxiv, 2020Co-Authors: Katerina V Djambazova, Richard M Caprioli, Raf Van De Plas, Dustin R Klein, Lukasz G Migas, Elizabeth K Neumann, Emilio S Rivera, Jeffrey M SpragginsAbstract:Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS) allows for direct map-ping of biomolecules in tissue. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) Mass spectrometer with trapped ion mobility Spectrometry (TIMS) enables approximately a ~270% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn-backbone isomers, acyl chain isomers, as well as double bond positional and geometric isomers are demonstrated. As a proof-of-concept, in situ separation and Imaging of lipid isomers with distinct spatial distributions was performed using tissue sections from a whole-body mouse pup.
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resolving the complexity of spatial lipidomics using maldi tims Imaging Mass Spectrometry
Analytical Chemistry, 2020Co-Authors: Katerina V Djambazova, Richard M Caprioli, Raf Van De Plas, Dustin R Klein, Lukasz G Migas, Elizabeth K Neumann, Emilio S Rivera, Jeffrey M SpragginsAbstract:Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) Mass spectrometer with trapped ion mobility Spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and Imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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unsupervised machine learning for exploratory data analysis in Imaging Mass Spectrometry
Mass Spectrometry Reviews, 2020Co-Authors: Richard M Caprioli, Raf Van De Plas, Nico VerbeeckAbstract:Imaging Mass Spectrometry (IMS) is a rapidly advancing molecular Imaging modality that can map the spatial distribution of molecules with high chemical specificity. IMS does not require prior tagging of molecular targets and is able to measure a large number of ions concurrently in a single experiment. While this makes it particularly suited for exploratory analysis, the large amount and high-dimensional nature of data generated by IMS techniques make automated computational analysis indispensable. Research into computational methods for IMS data has touched upon different aspects, including spectral preprocessing, data formats, dimensionality reduction, spatial registration, sample classification, differential analysis between IMS experiments, and data-driven fusion methods to extract patterns corroborated by both IMS and other Imaging modalities. In this work, we review unsupervised machine learning methods for exploratory analysis of IMS data, with particular focus on (a) factorization, (b) clustering, and (c) manifold learning. To provide a view across the various IMS modalities, we have attempted to include examples from a range of approaches including matrix assisted laser desorption/ionization, desorption electrospray ionization, and secondary ion Mass Spectrometry-based IMS. This review aims to be an entry point for both (i) analytical chemists and Mass Spectrometry experts who want to explore computational techniques; and (ii) computer scientists and data mining specialists who want to enter the IMS field. © 2019 The Authors. Mass Spectrometry Reviews published by Wiley Periodicals, Inc. Mass SpecRev 00:1-47, 2019.
Pieter C Dorrestein - One of the best experts on this subject based on the ideXlab platform.
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metabolic profiling directly from the petri dish using nanospray desorption electrospray ionization Imaging Mass Spectrometry
Analytical Chemistry, 2013Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C Dorrestein, Patrick J Roach, Brandi S Heath, Julia LaskinAbstract:Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) Imaging Mass Spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofi...
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Interkingdom metabolic transformations captured by microbial Imaging Mass Spectrometry
Proceedings of the National Academy of Sciences, 2012Co-Authors: Wilna J. Moree, V. V. Phelan, D. Shannon. Cornett, Nuno Bandeira, Brendan M. Duggan, C.h. Wu, Pieter C DorresteinAbstract:In polymicrobial infections, microbes can interact with both the host immune system and one another through direct contact or the secretion of metabolites, affecting disease progression and treatment options. The thick mucus in the lungs of patients with cystic fibrosis is highly susceptible to polymicrobial infections by opportunistic pathogens, including the bacterium Pseudomonas aeruginosa and the fungus Aspergillus fumigatus. Unravelling the hidden molecular interactions within such polymicrobial communities and their metabolic exchange processes will require effective enabling technologies applied to model systems. In the present study, MALDI-TOF and MALDI-FT-ICR Imaging Mass Spectrometry (MALDI-IMS) combined with MS/MS networking were used to provide insight into the interkingdom interaction between P. aeruginosa and A. fumigatus at the molecular level. The combination of these technologies enabled the visualization and identification of metabolites secreted by these microorganisms grown on agar. A complex molecular interplay was revealed involving suppression, increased production, and biotransformation of a range of metabolites. Of particular interest is the observation that P. aeruginosa phenazine metabolites were converted by A. fumigatus into other chemical entities with alternative properties, including enhanced toxicities and the ability to induce fungal siderophores. This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations.
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Imaging Mass Spectrometry in microbiology
Nature Reviews Microbiology, 2011Co-Authors: Jeramie D. Watrous, Pieter C DorresteinAbstract:Imaging Mass Spectrometry (IMS) allows a visualization of the distribution of trace metals, metabolites, lipids, peptides and proteins in biological samples. Here, Watrous and Dorrestein describe the use of various IMS approaches in the analysis of microbial samples, from single cells to complex communities.
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the evolving field of Imaging Mass Spectrometry and its impact on future biological research
Journal of Mass Spectrometry, 2011Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C DorresteinAbstract:Within the past decade, Imaging Mass Spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-Mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution andcurrent state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research. Copyright c � 2011 John Wiley & Sons, Ltd.
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capturing bacterial metabolic exchange using thin film desorption electrospray ionization Imaging Mass Spectrometry
Analytical Chemistry, 2010Co-Authors: Jeramie D. Watrous, Nathan G Hendricks, Michael J Meehan, Pieter C DorresteinAbstract:Over 60% of current pharmaceutical drugs have origins in natural products. To expand on current methods allowing one to characterize natural products directly from bacterial culture, herein we describe the use of desorption electrospray ionization (DESI) Imaging Mass Spectrometry in monitoring the exchange of secondary metabolites between Bacillus subtilis and Streptomyces coelicolor using a simple imprinting technique.
Jeffrey M Spraggins - One of the best experts on this subject based on the ideXlab platform.
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multimodal Imaging Mass Spectrometry of murine gastrointestinal tract with retained luminal content shows molecular localization patterns
bioRxiv, 2021Co-Authors: Emma R Guiberson, Jeffrey M Spraggins, Aaron G Wexler, Christopher J Good, Eric P Skaar, Richard M CaprioliAbstract:Digestive diseases impact 62 million people a year in the United States. Despite the central role of the gut to human health, past Imaging Mass Spectrometry (IMS) investigations into the gastrointestinal tract are incomplete. The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing Imaging approaches remove luminal content, and images focus on small regions of tissue. Here, we demonstrate the use of a workflow to collect multimodal Imaging data for both intestinal tissue and luminal content. This workflow for matrix-assisted laser desorption/ionization Imaging Mass Spectrometry retains luminal content and expands the amount of tissue imaged on one slide. Results comparing tissue and luminal content show unique molecular distributions using multimodal Imaging modalities including protein, lipid, and elemental Imaging. Leveraging this method to investigate intestinal tissue infected with Clostridioides difficile compared to control tissue shows clear differences in lipid abundance of various lipid classes in luminal content during infection. These data highlight the potential for this approach to detect unique biological and markers of infection in the gut.
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dynamic range expansion by gas phase ion fractionation and enrichment for Imaging Mass Spectrometry
Analytical Chemistry, 2020Co-Authors: Boone M Prentice, Richard M Caprioli, Daniel J Ryan, Kerri J Grove, Shannon D Cornett, Jeffrey M SpragginsAbstract:In the analysis of biological tissue by Imaging Mass Spectrometry (IMS), the limit of detection and dynamic range are of paramount importance in obtaining experimental results that provide insight into underlying biological processes. Many important biomolecules are present in the tissue milieu in low concentrations and in complex mixtures with other compounds of widely ranging abundances, challenging the limits of analytical technologies. In many IMS experiments, the ion signal can be dominated by a few highly abundant ion species. On trap-based instrument platforms that accumulate ions prior to Mass analysis, these high abundance ions can diminish the detection and dynamic range of lower abundance ions. Herein, we describe two strategies for combating these challenges during IMS experiments on a hybrid QhFT-ICR MS. In one iteration, the Mass resolving capabilities of a quadrupole Mass filter are used to selectively enrich ions of interest via a technique previously termed continuous accumulation of selected ions. Second, we have introduced a supplemental dipolar AC waveform to the quadrupole Mass filter of a commercial QhFT-ICR Mass spectrometer to perform selected ion ejection prior to the ion accumulation region. This setup allows the selective ejection of the most abundant ion species prior to ion accumulation, thereby greatly improving the molecular depth with which IMS can probe tissue samples. The gain in sensitivity of both of these approaches roughly scales with the number of accumulated laser shots up to the charge capacity of the ion accumulation cell. The efficiencies of these two strategies are described here by performing lipid Imaging Mass Spectrometry analyses of a rat brain.
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resolving the complexity of spatial lipidomics using maldi tims Imaging Mass Spectrometry
Analytical Chemistry, 2020Co-Authors: Katerina V Djambazova, Richard M Caprioli, Raf Van De Plas, Dustin R Klein, Lukasz G Migas, Elizabeth K Neumann, Emilio S Rivera, Jeffrey M SpragginsAbstract:Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) Mass spectrometer with trapped ion mobility Spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and Imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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resolving the complexity of spatial lipidomics using maldi tims Imaging Mass Spectrometry
ChemRxiv, 2020Co-Authors: Katerina V Djambazova, Richard M Caprioli, Raf Van De Plas, Dustin R Klein, Lukasz G Migas, Elizabeth K Neumann, Emilio S Rivera, Jeffrey M SpragginsAbstract:Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS) allows for direct map-ping of biomolecules in tissue. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) Mass spectrometer with trapped ion mobility Spectrometry (TIMS) enables approximately a ~270% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn-backbone isomers, acyl chain isomers, as well as double bond positional and geometric isomers are demonstrated. As a proof-of-concept, in situ separation and Imaging of lipid isomers with distinct spatial distributions was performed using tissue sections from a whole-body mouse pup.
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protein identification strategies in maldi Imaging Mass Spectrometry a brief review
Current Opinion in Chemical Biology, 2019Co-Authors: Daniel J Ryan, Jeffrey M Spraggins, Richard M CaprioliAbstract:Matrix assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS) is a powerful technology used to investigate the spatial distributions of thousands of molecules throughout a tissue section from a single experiment. As proteins represent an important group of functional molecules in tissue and cells, the Imaging of proteins has been an important point of focus in the development of IMS technologies and methods. Protein identification is crucial for the biological contextualization of molecular Imaging data. However, gas-phase fragmentation efficiency of MALDI generated proteins presents significant challenges, making protein identification directly from tissue difficult. This review highlights methods and technologies specifically related to protein identification that have been developed to overcome these challenges in MALDI IMS experiments.
Jeramie D. Watrous - One of the best experts on this subject based on the ideXlab platform.
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benchmark datasets for 3d maldi and desi Imaging Mass Spectrometry
GigaScience, 2015Co-Authors: Janina Oetjen, Jeramie D. Watrous, Jan Hendrik Kobarg, Michael Becker, Kirill Veselkov, James S Mckenzie, Lena Hauberglotte, Nicole Strittmatter, Anna Mroz, Franziska HoffmannAbstract:Background Three-dimensional (3D) Imaging Mass Spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-Imaging MS has unique advantages over existing 3D Imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D Imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms.
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metabolic profiling directly from the petri dish using nanospray desorption electrospray ionization Imaging Mass Spectrometry
Analytical Chemistry, 2013Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C Dorrestein, Patrick J Roach, Brandi S Heath, Julia LaskinAbstract:Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) Imaging Mass Spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofi...
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Primer on Agar-Based Microbial Imaging Mass Spectrometry
Journal of Bacteriology, 2012Co-Authors: Jane Y Yang, Jeramie D. Watrous, V. V. Phelan, Rachelle M. Trial, Roland Wenter, Tinya C. Fleming, Susan S. Golden, Ryan Simkovsky, Bradley S. Moore, Kit PoglianoAbstract:Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Imaging Mass Spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to investigate metabolic exchange factors of intraspecies, interspecies, and polymicrobial interactions. Based on our experience of the thousands of images we have generated in the laboratory, we present five steps of microbial IMS: culturing, matrix application, dehydration of the sample, data acquisition, and data analysis/interpretation. We also address the common challenges encountered during sample preparation, matrix selection and application, and sample adherence to the MALDI target plate. With the practical guidelines described herein, microbial IMS use can be extended to bio-based agricultural, biofuel, diagnostic, and therapeutic discovery applications.
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Imaging Mass Spectrometry in microbiology
Nature Reviews Microbiology, 2011Co-Authors: Jeramie D. Watrous, Pieter C DorresteinAbstract:Imaging Mass Spectrometry (IMS) allows a visualization of the distribution of trace metals, metabolites, lipids, peptides and proteins in biological samples. Here, Watrous and Dorrestein describe the use of various IMS approaches in the analysis of microbial samples, from single cells to complex communities.
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the evolving field of Imaging Mass Spectrometry and its impact on future biological research
Journal of Mass Spectrometry, 2011Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C DorresteinAbstract:Within the past decade, Imaging Mass Spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-Mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution andcurrent state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research. Copyright c � 2011 John Wiley & Sons, Ltd.
Theodore Alexandrov - One of the best experts on this subject based on the ideXlab platform.
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Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE
'MDPI AG', 2021Co-Authors: Don D. Nguyen, Vitaly Kovalev, Veronika Saharuka, Lachlan Stuart, Massimo Del Prete, Kinga Lubowiecka, René De Mot, Vittorio Venturi, Theodore AlexandrovAbstract:Metabolite annotation from Imaging Mass Spectrometry (Imaging MS) data is a difficult undertaking that is extremely resource intensive. Here, we adapted METASPACE, cloud software for Imaging MS metabolite annotation and data interpretation, to quickly annotate microbial specialized metabolites from high-resolution and high-Mass accuracy Imaging MS data. Compared with manual ion image and MS1 annotation, METASPACE is faster and, with the appropriate database, more accurate. We applied it to data from microbial colonies grown on agar containing 10 diverse bacterial species and showed that METASPACE was able to annotate 53 ions corresponding to 32 different microbial metabolites. This demonstrates METASPACE to be a useful tool to annotate the chemistry and metabolic exchange factors found in microbial interactions, thereby elucidating the functions of these molecules
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metabolic profiling directly from the petri dish using nanospray desorption electrospray ionization Imaging Mass Spectrometry
Analytical Chemistry, 2013Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C Dorrestein, Patrick J Roach, Brandi S Heath, Julia LaskinAbstract:Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) Imaging Mass Spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofi...
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MALDI Imaging Mass Spectrometry: statistical data analysis and current computational challenges.
BMC bioinformatics, 2012Co-Authors: Theodore AlexandrovAbstract:Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) Imaging Mass Spectrometry, also called MALDI-Imaging, is a label-free bioanalytical technique used for spatially-resolved chemical analysis of a sample. Usually, MALDI-Imaging is exploited for analysis of a specially prepared tissue section thaw mounted onto glass slide. A tremendous development of the MALDI-Imaging technique has been observed during the last decade. Currently, it is one of the most promising innovative measurement techniques in biochemistry and a powerful and versatile tool for spatially-resolved chemical analysis of diverse sample types ranging from biological and plant tissues to bio and polymer thin films. In this paper, we outline computational methods for analyzing MALDI-Imaging data with the emphasis on multivariate statistical methods, discuss their pros and cons, and give recommendations on their application. The methods of unsupervised data mining as well as supervised classification methods for biomarker discovery are elucidated. We also present a high-throughput computational pipeline for interpretation of MALDI-Imaging data using spatial segmentation. Finally, we discuss current challenges associated with the statistical analysis of MALDI-Imaging data.
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On the importance of mathematical methods for analysis of MALDI-Imaging Mass Spectrometry data.
Journal of integrative bioinformatics, 2012Co-Authors: Dennis Trede, Janina Oetjen, Jan Hendrik Kobarg, Peter Maass, Herbert Thiele, Theodore AlexandrovAbstract:In the last decade, matrix-assisted laser desorption/ionization (MALDI) Imaging Mass Spectrometry (IMS), also called as MALDI-Imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-Imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-Imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-Imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.
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the evolving field of Imaging Mass Spectrometry and its impact on future biological research
Journal of Mass Spectrometry, 2011Co-Authors: Jeramie D. Watrous, Theodore Alexandrov, Pieter C DorresteinAbstract:Within the past decade, Imaging Mass Spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-Mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution andcurrent state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research. Copyright c � 2011 John Wiley & Sons, Ltd.
