Ronald Moore - Academia.edu (original) (raw)

Papers by Ronald Moore

Research paper thumbnail of Plasma Proteome Response to Severe Burn Injury Revealed by 18 O-Labeled “Universal” Reference-Based Quantitative Proteomics

J Proteome Res, 2010

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Research paper thumbnail of Making Broad Proteome Protein Measurements in 1--5 mm Using High-Speed RPLC Separations and High-Accuracy Mass Measurements

Analytical Chemistry, 2005

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Research paper thumbnail of Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags

Pnas, 2002

Understanding biological systems and the roles of their constituents is facilitated by the abilit... more Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.

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Research paper thumbnail of Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry

The Analyst, Jan 6, 2016

Understanding how biological molecules are generated, metabolized and eliminated in living system... more Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Mass spectrometry (MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids' biological roles is challenging due to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are often unresolvable using present approaches. Here we show that combining liquid chromatography (LC) and structurally-based ion mobility spectrometry (IMS...

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Research paper thumbnail of SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities

Endocrinology, Jan 8, 2016

Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious ... more Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious approach to achieve in-depth protein coverage and quantitative reproducibility. Biological samples are often severely mass-limited and can preclude the application of more robust bulk sample processing workflows. In this study, we present a system that minimizes sample handling by using online immobilized trypsin digestion and solid phase extraction to create a simple, sensitive, robust, and reproducible platform for the analysis of nanogram-size proteomic samples. To demonstrate the effectiveness of our Simplified Nano-Proteomics Platform (SNaPP), we utilized the system to analyze preimplantation blastocysts collected on day 4 of pregnancy by flushing the uterine horns with saline. For each of our 3 sample groups, blastocysts were pooled from 3 mice resulting in 22, 22, and 25 blastocysts, respectively. The resulting proteomic data provides novel insight into mouse blastocyst protein ex...

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Research paper thumbnail of Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

J Proteome Res, 2005

Most current methods for purification and identification of protein complexes use endogenous expr... more Most current methods for purification and identification of protein complexes use endogenous expression of affinity-tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, and gel separation and in-gel digestion prior to mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pull-down assay with denaturing elution, trypsin digestion in organic solvent, and LC-ESI MS/MS protein identification using SEQUEST analysis. Our method is simple and easy to scale-up and automate, making it suitable for high-throughput mapping of protein interaction networks and functional proteomics.

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Research paper thumbnail of Proteome analyses of diazotrophic cyanobacteria Cyanothece ATCC 51142 and PCC 7822 under culture conditions of enhanced H2-production

Applied and Environmental Microbiology, Nov 30, 2012

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Research paper thumbnail of Application of Pressurized Solvents for Ultrafast Trypsin Hydrolysis in Proteomics: Proteomics on the Fly

Journal of Proteome Research, Aug 1, 2008

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Research paper thumbnail of Method and Apparatus for Continuous Fluid Leak Monitoring and Detection in Analytical Instruments and Instrument Systems

ABSTRACT A method and device are disclosed that provide for detection of fluid leaks in analytica... more ABSTRACT A method and device are disclosed that provide for detection of fluid leaks in analytical instruments and instrument systems. The leak detection device includes a collection tube, a fluid absorbing material, and a circuit that electrically couples to an indicator device. When assembled, the leak detection device detects and monitors for fluid leaks, providing a preselected response in conjunction with the indicator device when contacted by a fluid.

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Research paper thumbnail of Automated 20 kpsi RPLC-MS and MS/MS with Chromatographic Peak Capacities of 1000−1500 and Capabilities in Proteomics and Metabolomics

Analytical Chemistry, Jun 1, 2005

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Research paper thumbnail of Preparation of 20-�m-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis

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Research paper thumbnail of Analysis by Multidimensional Separation Coupled With Mass Spectrometry*□ S

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Research paper thumbnail of Site-specific S-nitrosylation in Mouse Muscle Profiled by Cys-Enrichment Coupled with LC-MS/MS

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Research paper thumbnail of Extensive Oxidative Protein Modifications Observed in Human Plasma and Candidate Biomarkers of Systemic Chronic Inflammatory and Oxidative Stress

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Research paper thumbnail of NIH Public Access

PROTEOMICS

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Research paper thumbnail of Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

PLOS ONE, 2015

Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive ... more Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive energy from specialized fungus gardens they cultivate using prodigious amounts of foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary food source of ant colonies. Gongylidia also contain plant biomass-degrading enzymes that become concentrated in ant digestive tracts and are deposited within fecal droplets onto fresh foliar material as ants incorporate it into the fungus garden. Although the enzymes concentrated by L. gongylophorus within gongylidia are thought to be critical to the initial degradation of plant biomass, only a few enzymes present in these hyphal swellings have been identified. Here we use proteomic methods to identify proteins present in the gongylidia of three Atta cephalotes colonies. Our results demonstrate that a diverse but consistent set of enzymes is present in gongylidia, including numerous plant biomass-degrading enzymes likely involved in the degradation of polysaccharides, plant toxins, and proteins. Overall, gongylidia contained over three quarters of all biomass-degrading enzymes identified in the L. gongylophorus genome, demonstrating that the majority of the enzymes produced by this fungus for biomass breakdown are ingested by the ants. We also identify a set of 40 of these enzymes enriched in gongylidia compared to whole fungus garden samples, suggesting that certain enzymes may be particularly important in the initial degradation of foliar material. Our work sheds light on the complex interplay between leaf-cutter ants and their fungal symbiont that allows for the host insects to occupy an herbivorous niche by indirectly deriving energy from plant biomass.

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Research paper thumbnail of An Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry

Analytical chemistry, Jan 24, 2015

The electrodynamic ion funnel facilitates efficient focusing and transfer of charged particles in... more The electrodynamic ion funnel facilitates efficient focusing and transfer of charged particles in the higher pressure regions (e.g. ion source interfaces) of mass spectrometers, and thus provides increased sensitivity. An "off-axis" ion funnel design has been developed to reduce the source contamination and interferences from, e.g. ESI droplet residue and other poorly focused neutral or charged particles with very high mass-to charge ratios. In this study a dual ion funnel interface consisting of an orthogonal higher pressure electrodynamic ion funnel (HPIF) and an ion funnel trap combined with a triple quadrupole mass spectrometer was developed and characterized. An orthogonal ion injection inlet and a repeller plate electrode was used to direct ions to an ion funnel HPIF at 9-10 Torr pressure. Key factors for the HPIF performance characterized included the effects of RF amplitude, the DC gradient, and operating pressure. Compared to the triple quadrupole standard interfa...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

Proteomics, Jan 5, 2015

Proteomic measurements with greater throughput, sensitivity and structural information are essent... more Proteomic measurements with greater throughput, sensitivity and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements. This article is protected by copyri...

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Research paper thumbnail of Top-down Characterization of Core Histones using an Online 2D Nanocapillary LC System

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Research paper thumbnail of Membrane Proteome Quantification Using Membrane-Impermeable Chemical Probe and Stable Isotopic Labeling

In this study, we have developed a large scale membrane proteome quantification strategy by combi... more In this study, we have developed a large scale membrane proteome quantification strategy by combining membrane protein enrichment using a membrane-impermeable chemical probe and quantifications using high-performance mass spectrometry and stable isotopic labeling. Membrane-impermeable chemical probe has been applied for the enrichment of membrane proteins expressed by Shewanella oneidensis MR-1, a gram-negative bacterium with known metal-reduction capability via extracellular electron transfer between outer membrane proteins and environmental electron receptors. LC/MS/MS analysis resulted in identifying 2,780 unique peptides from 321 membrane proteins which corresponded to 87% and 79% of all the identified unique peptides and proteins in the experiment, respectively. To demonstrate that the proposed strategy was specific and sensitive to protein abundance change in cell membranes, quantifications of enriched membrane proteins by stable isotopic labeling were further carried out for ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Plasma Proteome Response to Severe Burn Injury Revealed by 18 O-Labeled “Universal” Reference-Based Quantitative Proteomics

J Proteome Res, 2010

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Making Broad Proteome Protein Measurements in 1--5 mm Using High-Speed RPLC Separations and High-Accuracy Mass Measurements

Analytical Chemistry, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags

Pnas, 2002

Understanding biological systems and the roles of their constituents is facilitated by the abilit... more Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry

The Analyst, Jan 6, 2016

Understanding how biological molecules are generated, metabolized and eliminated in living system... more Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Mass spectrometry (MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids' biological roles is challenging due to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are often unresolvable using present approaches. Here we show that combining liquid chromatography (LC) and structurally-based ion mobility spectrometry (IMS...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities

Endocrinology, Jan 8, 2016

Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious ... more Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious approach to achieve in-depth protein coverage and quantitative reproducibility. Biological samples are often severely mass-limited and can preclude the application of more robust bulk sample processing workflows. In this study, we present a system that minimizes sample handling by using online immobilized trypsin digestion and solid phase extraction to create a simple, sensitive, robust, and reproducible platform for the analysis of nanogram-size proteomic samples. To demonstrate the effectiveness of our Simplified Nano-Proteomics Platform (SNaPP), we utilized the system to analyze preimplantation blastocysts collected on day 4 of pregnancy by flushing the uterine horns with saline. For each of our 3 sample groups, blastocysts were pooled from 3 mice resulting in 22, 22, and 25 blastocysts, respectively. The resulting proteomic data provides novel insight into mouse blastocyst protein ex...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

J Proteome Res, 2005

Most current methods for purification and identification of protein complexes use endogenous expr... more Most current methods for purification and identification of protein complexes use endogenous expression of affinity-tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, and gel separation and in-gel digestion prior to mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pull-down assay with denaturing elution, trypsin digestion in organic solvent, and LC-ESI MS/MS protein identification using SEQUEST analysis. Our method is simple and easy to scale-up and automate, making it suitable for high-throughput mapping of protein interaction networks and functional proteomics.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Proteome analyses of diazotrophic cyanobacteria Cyanothece ATCC 51142 and PCC 7822 under culture conditions of enhanced H2-production

Applied and Environmental Microbiology, Nov 30, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Application of Pressurized Solvents for Ultrafast Trypsin Hydrolysis in Proteomics: Proteomics on the Fly

Journal of Proteome Research, Aug 1, 2008

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Method and Apparatus for Continuous Fluid Leak Monitoring and Detection in Analytical Instruments and Instrument Systems

ABSTRACT A method and device are disclosed that provide for detection of fluid leaks in analytica... more ABSTRACT A method and device are disclosed that provide for detection of fluid leaks in analytical instruments and instrument systems. The leak detection device includes a collection tube, a fluid absorbing material, and a circuit that electrically couples to an indicator device. When assembled, the leak detection device detects and monitors for fluid leaks, providing a preselected response in conjunction with the indicator device when contacted by a fluid.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Automated 20 kpsi RPLC-MS and MS/MS with Chromatographic Peak Capacities of 1000−1500 and Capabilities in Proteomics and Metabolomics

Analytical Chemistry, Jun 1, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Preparation of 20-�m-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Analysis by Multidimensional Separation Coupled With Mass Spectrometry*□ S

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Site-specific S-nitrosylation in Mouse Muscle Profiled by Cys-Enrichment Coupled with LC-MS/MS

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Extensive Oxidative Protein Modifications Observed in Human Plasma and Candidate Biomarkers of Systemic Chronic Inflammatory and Oxidative Stress

Bookmarks Related papers MentionsView impact

Research paper thumbnail of NIH Public Access

PROTEOMICS

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

PLOS ONE, 2015

Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive ... more Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive energy from specialized fungus gardens they cultivate using prodigious amounts of foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary food source of ant colonies. Gongylidia also contain plant biomass-degrading enzymes that become concentrated in ant digestive tracts and are deposited within fecal droplets onto fresh foliar material as ants incorporate it into the fungus garden. Although the enzymes concentrated by L. gongylophorus within gongylidia are thought to be critical to the initial degradation of plant biomass, only a few enzymes present in these hyphal swellings have been identified. Here we use proteomic methods to identify proteins present in the gongylidia of three Atta cephalotes colonies. Our results demonstrate that a diverse but consistent set of enzymes is present in gongylidia, including numerous plant biomass-degrading enzymes likely involved in the degradation of polysaccharides, plant toxins, and proteins. Overall, gongylidia contained over three quarters of all biomass-degrading enzymes identified in the L. gongylophorus genome, demonstrating that the majority of the enzymes produced by this fungus for biomass breakdown are ingested by the ants. We also identify a set of 40 of these enzymes enriched in gongylidia compared to whole fungus garden samples, suggesting that certain enzymes may be particularly important in the initial degradation of foliar material. Our work sheds light on the complex interplay between leaf-cutter ants and their fungal symbiont that allows for the host insects to occupy an herbivorous niche by indirectly deriving energy from plant biomass.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of An Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry

Analytical chemistry, Jan 24, 2015

The electrodynamic ion funnel facilitates efficient focusing and transfer of charged particles in... more The electrodynamic ion funnel facilitates efficient focusing and transfer of charged particles in the higher pressure regions (e.g. ion source interfaces) of mass spectrometers, and thus provides increased sensitivity. An "off-axis" ion funnel design has been developed to reduce the source contamination and interferences from, e.g. ESI droplet residue and other poorly focused neutral or charged particles with very high mass-to charge ratios. In this study a dual ion funnel interface consisting of an orthogonal higher pressure electrodynamic ion funnel (HPIF) and an ion funnel trap combined with a triple quadrupole mass spectrometer was developed and characterized. An orthogonal ion injection inlet and a repeller plate electrode was used to direct ions to an ion funnel HPIF at 9-10 Torr pressure. Key factors for the HPIF performance characterized included the effects of RF amplitude, the DC gradient, and operating pressure. Compared to the triple quadrupole standard interfa...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

Proteomics, Jan 5, 2015

Proteomic measurements with greater throughput, sensitivity and structural information are essent... more Proteomic measurements with greater throughput, sensitivity and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements. This article is protected by copyri...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Top-down Characterization of Core Histones using an Online 2D Nanocapillary LC System

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Membrane Proteome Quantification Using Membrane-Impermeable Chemical Probe and Stable Isotopic Labeling

In this study, we have developed a large scale membrane proteome quantification strategy by combi... more In this study, we have developed a large scale membrane proteome quantification strategy by combining membrane protein enrichment using a membrane-impermeable chemical probe and quantifications using high-performance mass spectrometry and stable isotopic labeling. Membrane-impermeable chemical probe has been applied for the enrichment of membrane proteins expressed by Shewanella oneidensis MR-1, a gram-negative bacterium with known metal-reduction capability via extracellular electron transfer between outer membrane proteins and environmental electron receptors. LC/MS/MS analysis resulted in identifying 2,780 unique peptides from 321 membrane proteins which corresponded to 87% and 79% of all the identified unique peptides and proteins in the experiment, respectively. To demonstrate that the proposed strategy was specific and sensitive to protein abundance change in cell membranes, quantifications of enriched membrane proteins by stable isotopic labeling were further carried out for ...

Bookmarks Related papers MentionsView impact